Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006156.1 Hibiscus syriacus cultivar Beakdansim tig00014627_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: 67794
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2960 original size:19 final size:19
Alignment explanation
Indices: 2936--2986 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2926 TGAAATATTC
2936 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2955 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2974 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2987 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3008 original size:64 final size:63
Alignment explanation
Indices: 2830--3036 Score: 215
Period size: 64 Copynumber: 3.3 Consensus size: 63
2820 GTGCACCAAG
* * * * *
2830 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCTG-GTGCATCGATGCAT-GAC
1 TGTGCATCGGTGCATGAAATGCATTCGATGTTTCAAATAT-TCAGAGTGCATCGATGCATGGAC
* * * *
2892 TTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAATATTCAGAGTGCATCGATGCATGGAG
1 -TGTGCATCGGTGCATGAAATGCATTCGATG-TTTCAAATATTCAGAGTGCATCGATGCATGGAC
* * *
2957 AGTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGA-TGCATCGATGCATGGA
1 TGTGCATCGGTGCATGAAATGCATTCGATGTTTCAAAT-ATTCA--GAGTGCATCGATGCATGGA
3020 C
63 C
*
3021 TGAGCATCGGTGCATG
1 TGTGCATCGGTGCATG
3037 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
62 5 0.04
63 36 0.29
64 79 0.64
65 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (63 bp):
TGTGCATCGGTGCATGAAATGCATTCGATGTTTCAAATATTCAGAGTGCATCGATGCATGGAC
Found at i:3396 original size:31 final size:31
Alignment explanation
Indices: 3358--3437 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
3348 ATCGATTTTG
3358 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
*
3389 AAAAACTTACTCCCCATTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
3420 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
3438 TTGTTAATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:8373 original size:22 final size:21
Alignment explanation
Indices: 8331--8370 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8321 GAGTTTGTTT
*
8331 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
8352 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
8371 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:10343 original size:64 final size:64
Alignment explanation
Indices: 10275--10452 Score: 196
Period size: 64 Copynumber: 2.8 Consensus size: 64
10265 GAACACTTGA
* ** *
10275 TGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-G
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAG
** ** * **
10339 TGCATCGATGCATGACTTGTATATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAG
* * * *
10404 TGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
10453 CAATTAATTC
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
64 49 0.53
65 43 0.47
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAG
Found at i:10424 original size:19 final size:19
Alignment explanation
Indices: 10400--10450 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
10390 GAAAATATTC
10400 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
10419 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
10438 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
10451 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:10435 original size:65 final size:65
Alignment explanation
Indices: 10293--10452 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
10283 TGCACCAAGT
* **
10293 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGACTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGACGA
** * **
10357 GTATATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGA-
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCAT-GAC
10420 GA
64 GA
* *
10422 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
10453 CAATTAATTC
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 34 0.43
65 44 0.55
66 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGACGA
Found at i:10913 original size:2 final size:2
Alignment explanation
Indices: 10906--10951 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
10896 AATTAAAAAT
10906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10948 TA TA
1 TA TA
10952 AATAAAGCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11357 original size:18 final size:18
Alignment explanation
Indices: 11334--11414 Score: 74
Period size: 18 Copynumber: 4.5 Consensus size: 18
11324 CTCGATTAGG
* *
11334 GTTTAGGTTTGAGTTTTA
1 GTTTAGGTTTGGGTTTGA
*
11352 GTTTAGATTTGGGTTTGA
1 GTTTAGGTTTGGGTTTGA
*
11370 GTTTGGGTTTGGGTTTG-
1 GTTTAGGTTTGGGTTTGA
** *
11387 GATTCGGGTTTGGGTTTGT
1 G-TTTAGGTTTGGGTTTGA
*
11406 GTTTGGGTT
1 GTTTAGGTT
11415 CAGGTTTGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
17 1 0.02
18 52 0.96
19 1 0.02
ACGTcount: A:0.09, C:0.01, G:0.38, T:0.52
Consensus pattern (18 bp):
GTTTAGGTTTGGGTTTGA
Found at i:11374 original size:12 final size:12
Alignment explanation
Indices: 11334--11414 Score: 74
Period size: 12 Copynumber: 6.8 Consensus size: 12
11324 CTCGATTAGG
*
11334 GTTTAGGTTTGA
1 GTTTGGGTTTGA
**
11346 GTTTTAGTTT-A
1 GTTTGGGTTTGA
11357 GATTTGGGTTTGA
1 G-TTTGGGTTTGA
*
11370 GTTTGGGTTTGG
1 GTTTGGGTTTGA
* * *
11382 GTTTGGATTCGG
1 GTTTGGGTTTGA
*
11394 GTTTGGGTTTGT
1 GTTTGGGTTTGA
11406 GTTTGGGTT
1 GTTTGGGTT
11415 CAGGTTTGGG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
11 2 0.04
12 53 0.93
13 2 0.04
ACGTcount: A:0.09, C:0.01, G:0.38, T:0.52
Consensus pattern (12 bp):
GTTTGGGTTTGA
Found at i:11387 original size:6 final size:6
Alignment explanation
Indices: 11359--11426 Score: 82
Period size: 6 Copynumber: 11.3 Consensus size: 6
11349 TTAGTTTAGA
* * * *
11359 TTTGGG TTTGAG TTTGGG TTTGGG TTTGGA TTCGGG TTTGGG TTTGTG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
**
11407 TTTGGG TTCAGG TTTGGG TT
1 TTTGGG TTTGGG TTTGGG TT
11427 GAAGAAGATG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.04, C:0.03, G:0.43, T:0.50
Consensus pattern (6 bp):
TTTGGG
Found at i:11801 original size:109 final size:109
Alignment explanation
Indices: 11606--11812 Score: 294
Period size: 109 Copynumber: 1.9 Consensus size: 109
11596 ACAGTTTAAT
**
11606 TTTTGGGTGTTTGATAAAAAACAGGAATAGGTTTAGGTTTTGGTGTTTGTGAAGATCAAAAAATT
1 TTTTGGGTGTTTGATAAAAAACAGGAATAGGTTTAGGTTTTGGTGTTTGTGAAGATCAAAAAAGG
*
11671 GTTTAGGGAAGAACTGGGATGAACACGGATGAACAAGGGTTGAAA
66 GTTTAGGGAAGAAAT-GGATGAACACGGATGAACAAGGGTTGAAA
* *
11716 TTTTGGGTGTTTGATAAAAAA-AGGAA-ATGGTTTGGGTTTTGGTGTTTGTGAAGATCAAAGAAG
1 TTTTGGGTGTTTGATAAAAAACAGGAATA-GGTTTAGGTTTTGGTGTTTGTGAAGATCAAAAAAG
* *
11779 GGTTTTTGGGATGCAAAT-GATGAACACGGATGAA
65 GG-TTTAGGGAAG-AAATGGATGAACACGGATGAA
11813 TTTCTAGAGA
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
108 1 0.01
109 54 0.62
110 29 0.33
111 3 0.03
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (109 bp):
TTTTGGGTGTTTGATAAAAAACAGGAATAGGTTTAGGTTTTGGTGTTTGTGAAGATCAAAAAAGG
GTTTAGGGAAGAAATGGATGAACACGGATGAACAAGGGTTGAAA
Found at i:12061 original size:34 final size:34
Alignment explanation
Indices: 12017--12109 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 34
12007 TCCAATTTAG
12017 TCCAAATTTAATGATGCAATGTATTAATTTAAAC
1 TCCAAATTTAATGATGCAATGTATTAATTTAAAC
* * * * *
12051 TCCATATTTAA-AAT---TTGT-TCAATTT--AG
1 TCCAAATTTAATGATGCAATGTATTAATTTAAAC
*
12078 TCCAAATTTAATGTTGCAATGTATTAATTTAA
1 TCCAAATTTAATGATGCAATGTATTAATTTAA
12110 GCTTCATATT
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
27 11 0.26
28 1 0.02
29 6 0.14
30 3 0.07
31 3 0.07
32 6 0.14
33 2 0.05
34 10 0.24
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (34 bp):
TCCAAATTTAATGATGCAATGTATTAATTTAAAC
Found at i:12074 original size:61 final size:61
Alignment explanation
Indices: 12001--12136 Score: 236
Period size: 61 Copynumber: 2.2 Consensus size: 61
11991 CCTAGTTTTT
*
12001 AATTTGTCCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTCCATATTTAA
1 AATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTCCATATTTAA
* * *
12062 AATTTGTTCAATTTAGTCCAAATTTAATGTTGCAATGTATTAATTTAAGCTTCATATTTAA
1 AATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTCCATATTTAA
12123 AATTTGTTCAATTT
1 AATTTGTTCAATTT
12137 GATCCTTATA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (61 bp):
AATTTGTTCAATTTAGTCCAAATTTAATGATGCAATGTATTAATTTAAACTCCATATTTAA
Found at i:12231 original size:33 final size:33
Alignment explanation
Indices: 12194--12279 Score: 163
Period size: 33 Copynumber: 2.6 Consensus size: 33
12184 TTAATAAATT
*
12194 AATATATAGTTTATATATACTAATGAAGTATAA
1 AATATATAGTTTATATATACTAATGAACTATAA
12227 AATATATAGTTTATATATACTAATGAACTATAA
1 AATATATAGTTTATATATACTAATGAACTATAA
12260 AATATATAGTTTATATATAC
1 AATATATAGTTTATATATAC
12280 CATATAGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (33 bp):
AATATATAGTTTATATATACTAATGAACTATAA
Found at i:12298 original size:33 final size:32
Alignment explanation
Indices: 12194--12311 Score: 123
Period size: 33 Copynumber: 3.6 Consensus size: 32
12184 TTAATAAATT
12194 AATATATAGTTTATATATACTAATGAAGTATA-A
1 AATATATAGTTTATATATACTAAT--AGTATATA
*
12227 AATATATAGTTTATATATACTAAT-GAACTATAA
1 AATATATAGTTTATATATACTAATAGTA-TAT-A
* *
12260 AATATATAGTTTATATATACCATATAGTTTATA
1 AATATATAGTTTATATATACTA-ATAGTATATA
* * *
12293 TATATATAATTTTTATATA
1 AATATATAGTTTATATATA
12312 TAGTTCACAT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
30 2 0.03
31 2 0.03
33 63 0.86
34 5 0.07
35 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (32 bp):
AATATATAGTTTATATATACTAATAGTATATA
Found at i:12309 original size:15 final size:15
Alignment explanation
Indices: 12261--12313 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
12251 GAACTATAAA
*
12261 ATATATAGTTTATAT
1 ATATATAATTTATAT
*
12276 ATACCATATAGTTTATAT
1 AT---ATATAATTTATAT
*
12294 ATATATAATTTTTAT
1 ATATATAATTTATAT
12309 ATATA
1 ATATA
12314 GTTCACATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 18 0.55
18 15 0.45
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATATAATTTATAT
Found at i:12344 original size:18 final size:20
Alignment explanation
Indices: 12323--12362 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
12313 AGTTCACATG
12323 TAAACTATATA-GTA-TATA
1 TAAACTATATATGTAGTATA
*
12341 TAAACTATGTATGTAGTATA
1 TAAACTATATATGTAGTATA
12361 TA
1 TA
12363 CTATATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
TAAACTATATATGTAGTATA
Found at i:12448 original size:15 final size:14
Alignment explanation
Indices: 12419--12467 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
12409 ATACATATAA
* *
12419 TATATACTTTGAATT
1 TATATACTAT-AAAT
12434 TATATACTATAAAT
1 TATATACTATAAAT
*
12448 TATATAAATATAAAT
1 TATAT-ACTATAAAT
12463 TATAT
1 TATAT
12468 TATATAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (14 bp):
TATATACTATAAAT
Found at i:12493 original size:27 final size:27
Alignment explanation
Indices: 12448--12573 Score: 117
Period size: 27 Copynumber: 5.0 Consensus size: 27
12438 TACTATAAAT
* * *
12448 TATATAAATATAAATTATATTATATAG
1 TATATAAATATTAACTATAGTATATAG
*
12475 TATATAAATATCTAA-TATAGTACATAG
1 TATATAAATAT-TAACTATAGTATATAG
*
12502 T-T-T--ATA-T-A-TATAATATATAG
1 TATATAAATATTAACTATAGTATATAG
*
12522 TATATAAATATCAACTATAGTATATAG
1 TATATAAATATTAACTATAGTATATAG
*
12549 TATATAAATA-TAACTATAGTTTATA
1 TATATAAATATTAACTATAGTATATA
12574 AATATATAGT
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
20 12 0.15
21 2 0.02
22 1 0.01
23 3 0.04
24 3 0.04
25 1 0.01
26 15 0.18
27 43 0.52
28 2 0.02
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (27 bp):
TATATAAATATTAACTATAGTATATAG
Found at i:12527 original size:47 final size:47
Alignment explanation
Indices: 12455--12578 Score: 162
Period size: 47 Copynumber: 2.6 Consensus size: 47
12445 AATTATATAA
*
12455 ATATAAATTATATTATATAGTATATAAATATCTAA-TATAGTACATAGT
1 ATATAAA-TATAATATATAGTATATAAATATC-AACTATAGTACATAGT
* * *
12503 TTATATATATAATATATAGTATATAAATATCAACTATAGTATATAGT
1 ATATAAATATAATATATAGTATATAAATATCAACTATAGTACATAGT
* *
12550 ATATAAATATAA-CTATAGTTTATAAATAT
1 ATATAAATATAATATATAGTATATAAATAT
12579 ATAGTTTATA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 17 0.25
47 45 0.67
48 5 0.07
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (47 bp):
ATATAAATATAATATATAGTATATAAATATCAACTATAGTACATAGT
Found at i:12532 original size:74 final size:78
Alignment explanation
Indices: 12434--12609 Score: 207
Period size: 74 Copynumber: 2.3 Consensus size: 78
12424 ACTTTGAATT
* * * * * *
12434 TATATACTATAAATTATATAAATATAAATTATATTATATAGTATATAAATAT-CTA-A-TAT-AG
1 TATATAATATATACTATATAAATATAAACTATAGTATATAGTATATAAATATACTATATTATAAA
12495 TACATAGTTTATA
66 TACATAGTTTATA
* *
12508 TATATAATATATAGTATATAAATATCAACTATAGTATATAGTATATAAATATAACTATAGTTTAT
1 TATATAATATATACTATATAAATATAAACTATAGTATATAGTATATAAATAT-ACTATA--TTAT
*
12573 AAATATATAGTTTATA
63 AAATACATAGTTTATA
*
12589 TATATAGTATATACTATATAA
1 TATATAATATATACTATATAA
12610 TTAATTTATA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
74 46 0.54
76 3 0.04
77 1 0.01
80 3 0.04
81 32 0.38
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (78 bp):
TATATAATATATACTATATAAATATAAACTATAGTATATAGTATATAAATATACTATATTATAAA
TACATAGTTTATA
Found at i:12549 original size:7 final size:7
Alignment explanation
Indices: 12537--12608 Score: 53
Period size: 7 Copynumber: 10.6 Consensus size: 7
12527 AAATATCAAC
12537 TATAGTA
1 TATAGTA
12544 TATAGTA
1 TATAGTA
*
12551 TATA-AA
1 TATAGTA
12557 TATA--A
1 TATAGTA
*
12562 CTATAGTT
1 -TATAGTA
*
12570 TATAAATA
1 TAT-AGTA
*
12578 TATAGTT
1 TATAGTA
12585 TATA-TA
1 TATAGTA
12591 TATAGTA
1 TATAGTA
*
12598 TATACTA
1 TATAGTA
12605 TATA
1 TATA
12609 ATTAATTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
5 1 0.02
6 14 0.27
7 32 0.62
8 5 0.10
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (7 bp):
TATAGTA
Found at i:12554 original size:81 final size:78
Alignment explanation
Indices: 12463--12723 Score: 212
Period size: 81 Copynumber: 3.3 Consensus size: 78
12453 AAATATAAAT
*
12463 TATATTATATAGTATATAAATA-TCTAATATAGTACATAGTTTATATATATAATATATAGTATAT
1 TATAGTATATA-TATATAAATAGT-TAATA-AGTA-ATAGTTTATATATATAATATATAGTATAT
12527 AAATATCAACTATAGTA
62 AAATATCAACTATAGTA
* * * * *
12544 TATAGTATATAAATATAACTATAGTTTATAAATATATAGTTTATATATATAGTATATACTATATA
1 TATAGTATATATATATAA--ATAGTTAATAAGTA-ATAGTTTATATATATAATATATAGTATATA
* **
12609 ATTAATTTA-TATAGT-
63 AAT-ATCAACTATAGTA
* * * ** *
12624 TCAT--TAATACACTATATATATAGTTCATAAGTAATAATGTAAACTATATATATTATATAGTAT
1 T-ATAGT-ATATA-TATATAAATAGTTAATAAGTAAT-A-GTTTA-TATATATAATATATAGTAT
12687 ATAAATATCAACTATAGTA
60 ATAAATATCAACTATAGTA
12706 TATAGT-T-TATATATAAAT
1 TATAGTATATATATATAAAT
12724 TATAGTTTAT
Statistics
Matches: 142, Mismatches: 24, Indels: 30
0.72 0.12 0.15
Matches are distributed among these distances:
78 2 0.01
79 22 0.15
80 18 0.13
81 87 0.61
82 11 0.08
83 2 0.01
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (78 bp):
TATAGTATATATATATAAATAGTTAATAAGTAATAGTTTATATATATAATATATAGTATATAAAT
ATCAACTATAGTA
Found at i:12583 original size:15 final size:15
Alignment explanation
Indices: 12563--12594 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12553 TAAATATAAC
12563 TATAGTTTATAAATA
1 TATAGTTTATAAATA
*
12578 TATAGTTTATATATA
1 TATAGTTTATAAATA
12593 TA
1 TA
12595 GTATATACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TATAGTTTATAAATA
Found at i:12606 original size:27 final size:27
Alignment explanation
Indices: 12463--12749 Score: 106
Period size: 27 Copynumber: 10.7 Consensus size: 27
12453 AAATATAAAT
* * *
12463 TATATTATATAGTATATAAATAT-CTAA
1 TATAGTATATAGTATATATATATAGT-A
* * *
12490 TATAGTACATAGTTTATATATATAATA
1 TATAGTATATAGTATATATATATAGTA
*
12517 TATAGTATATA-AATATCA-ACTATAGTA
1 TATAGTATATAGTATAT-ATA-TATAGTA
* *
12544 TATAGTATATA-AATATA-ACTATAGTT
1 TATAGTATATAGTATATATA-TATAGTA
* *
12570 TATAAATATATAGTTTATATATATAGTA
1 TAT-AGTATATAGTATATATATATAGTA
* * *
12598 TATACTATATAAT-TAATTTATATAGT-
1 TATAGTATATAGTAT-ATATATATAGTA
*
12624 TCAT--TA-ATA-CACTATATATATAGT-
1 T-ATAGTATATAGTA-TATATATATAGTA
* *
12648 TCATAAGTA-ATAATGTAAACTATATATATTA
1 T-AT-AGTATAT-A-GTATA-TATATATAGTA
*
12679 TATAGTATATA-AATATCA-ACTATAGTA
1 TATAGTATATAGTATAT-ATA-TATAGTA
* *
12706 TATAGTTTATA-TATAAAT-TATAGTTTA
1 TATAGTATATAGTATATATATATAG--TA
*
12733 TATAGTTTATA-TATATA
1 TATAGTATATAGTATATA
12750 GAGAAAATCG
Statistics
Matches: 207, Mismatches: 29, Indels: 48
0.73 0.10 0.17
Matches are distributed among these distances:
24 17 0.08
25 8 0.04
26 21 0.10
27 124 0.60
28 15 0.07
29 7 0.03
30 14 0.07
31 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (27 bp):
TATAGTATATAGTATATATATATAGTA
Found at i:12608 original size:9 final size:8
Alignment explanation
Indices: 12434--12608 Score: 67
Period size: 9 Copynumber: 21.0 Consensus size: 8
12424 ACTTTGAATT
12434 TATATACTA
1 TATATA-TA
*
12443 TAAAT-TA
1 TATATATA
*
12450 TATAAATA
1 TATATATA
*
12458 TAAAT-TA
1 TATATATA
12465 TAT-TATA
1 TATATATA
12472 TAGTATATA
1 TA-TATATA
* *
12481 AATATCTA
1 TATATATA
12489 -ATATAGTA
1 TATATA-TA
* *
12497 CATAGTTTA
1 TATA-TATA
12506 TATATATA
1 TATATATA
12514 -ATATATA
1 TATATATA
*
12521 GTATATAAA
1 -TATATATA
12530 TATCA-ACTA
1 TAT-ATA-TA
12539 TAGTATATA
1 TA-TATATA
*
12548 GTATATAAA
1 -TATATATA
12557 TATA-ACTA
1 TATATA-TA
*
12565 TAGTTTATA
1 TA-TATATA
*
12574 AATATATA
1 TATATATA
*
12582 GTTTATATA
1 -TATATATA
12591 TATAGTATA
1 TATA-TATA
12600 TACTATATA
1 TA-TATATA
12609 ATTAATTTAT
Statistics
Matches: 124, Mismatches: 22, Indels: 40
0.67 0.12 0.22
Matches are distributed among these distances:
6 1 0.01
7 25 0.20
8 35 0.28
9 55 0.44
10 8 0.06
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (8 bp):
TATATATA
Found at i:12736 original size:9 final size:9
Alignment explanation
Indices: 12704--12745 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
12694 TCAACTATAG
12704 TATATAGTT
1 TATATAGTT
*
12713 TATATA-TA
1 TATATAGTT
*
12721 AATTATAGTT
1 TA-TATAGTT
12731 TATATAGTT
1 TATATAGTT
12740 TATATA
1 TATATA
12746 TATAGAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 23 0.85
10 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:12958 original size:20 final size:20
Alignment explanation
Indices: 12933--13226 Score: 152
Period size: 20 Copynumber: 14.7 Consensus size: 20
12923 GATTTTCCAG
*
12933 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* * *
12953 AATCGCAACGCGAACA-TAT
1 AATCGCAACGCGAATACGAA
* *
12972 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * * *
12992 TATCACAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
13013 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
13033 AATCGAAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* *
13054 AATCGCAACGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
* *
13074 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* ** *
13094 AATCGCAACGCGTATTTGTA
1 AATCGCAACGCGAATACGAA
* * *
13114 AGTCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
13134 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
13154 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
13175 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
13195 AATCGCAATGCG-AT-CGATA
1 AATCGCAACGCGAATACGA-A
*
13214 ATTCGCAACGCGA
1 AATCGCAACGCGA
13227 TCTCCGGTAT
Statistics
Matches: 208, Mismatches: 52, Indels: 28
0.72 0.18 0.10
Matches are distributed among these distances:
18 3 0.01
19 27 0.13
20 129 0.62
21 49 0.24
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:13065 original size:121 final size:117
Alignment explanation
Indices: 12933--13227 Score: 328
Period size: 121 Copynumber: 2.4 Consensus size: 117
12923 GATTTTCCAG
12933 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAATCGCAACGCGATTCTG-ACTA-TC
1 AATCGCAACGCG-ATATGAAAATCGCAACGCGAACATA-AATCGCAACGCGATT-TGTA--AGTC
* *
12996 ACAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGAAACGACAATACGTAA
61 ACAACGAGAATACGT-AAATCGCAACGCGTATCCGTAAATCGAAACGACAATACGTAA
* * *
13054 AATCGCAACGCG-TATCCATAAATCGCAACGAGAATACGTAAATCGCAACGCGTATTTGTAAGTC
1 AATCGCAACGCGATAT-GA-AAATCGCAACGCG-A-ACATAAATCGCAACGCG-ATTTGTAAGTC
* * *
13118 GCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAA
61 ACAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGAAACGACAATACGTAA
* * * *
13175 AATCGCAACGCG-TATCCGTAAATCGCAATGCGATCGATAATTCGCAACGCGAT
1 AATCGCAACGCGATAT--GAAAATCGCAACGCGAAC-ATAAATCGCAACGCGAT
13228 CTCCGGTATC
Statistics
Matches: 150, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
119 6 0.04
120 15 0.10
121 91 0.61
122 30 0.20
123 8 0.05
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (117 bp):
AATCGCAACGCGATATGAAAATCGCAACGCGAACATAAATCGCAACGCGATTTGTAAGTCACAAC
GAGAATACGTAAATCGCAACGCGTATCCGTAAATCGAAACGACAATACGTAA
Found at i:13108 original size:40 final size:41
Alignment explanation
Indices: 12997--13202 Score: 308
Period size: 41 Copynumber: 5.1 Consensus size: 41
12987 CTGACTATCA
* *
12997 CAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
* * *
13038 AAACGACAATACGTAAAATCGCAACGCGTATCCATAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
** *
13079 CAACGAGAATACGT-AAATCGCAACGCGTATTTGTAAGTCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
13119 CAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
*
13159 CAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCG
1 CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
13200 CAA
1 CAA
13203 TGCGATCGAT
Statistics
Matches: 147, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 71 0.48
41 76 0.52
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
CAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCG
Found at i:13305 original size:21 final size:21
Alignment explanation
Indices: 13276--13330 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
13266 ATTATGACTA
13276 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
13297 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
13318 TCGCAATGCGATT
1 TCGCATTGCGATT
13331 ACGTAAATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:13347 original size:20 final size:20
Alignment explanation
Indices: 13322--13360 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13312 CCTAATTCGC
*
13322 AATGCGATTACGTAAATCGT
1 AATGCGAATACGTAAATCGT
13342 AATGCGAATACGTAAATCG
1 AATGCGAATACGTAAATCG
13361 CAACGAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (20 bp):
AATGCGAATACGTAAATCGT
Found at i:16733 original size:20 final size:21
Alignment explanation
Indices: 16708--16796 Score: 114
Period size: 20 Copynumber: 4.4 Consensus size: 21
16698 CAATGCGGAA
*
16708 ATCGCAATGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
* *
16728 ATCGCAACAC-GAAAATGACT
1 ATCGCAACGCGGAATATGACT
*
16748 ATCGCAATGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
16768 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
16788 ATCGCAACG
1 ATCGCAACG
16797 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:16767 original size:40 final size:40
Alignment explanation
Indices: 16708--16794 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
16698 CAATGCGGAA
16708 ATCGCAATGCGAATATGACTATCGCAACACGAAAATGACT
1 ATCGCAATGCGAATATGACTATCGCAACACGAAAATGACT
* *
16748 ATCGCAATGCGGAAT-TGACTATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAATATGACTATCGCAACACGAAAATGACT
16788 ATCGCAA
1 ATCGCAA
16795 CGAGAGAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (40 bp):
ATCGCAATGCGAATATGACTATCGCAACACGAAAATGACT
Found at i:16830 original size:19 final size:19
Alignment explanation
Indices: 16805--16940 Score: 174
Period size: 19 Copynumber: 7.4 Consensus size: 19
16795 CGAGAGAATC
16805 GCAATGCGAAATGAAAATT
1 GCAATGCGAAATGAAAATT
*
16824 ACAATGCGAAATGAAAATT
1 GCAATGCGAAATGAAAATT
*
16843 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATT
*
16862 GCAA--CG-AGTG--AATT
1 GCAATGCGAAATGAAAATT
* *
16876 GCAATGTGAAAATGAAAATA
1 GCAATGCG-AAATGAAAATT
16896 GCAATGCGAAATGAAAATT
1 GCAATGCGAAATGAAAATT
*
16915 GCAATGTGAAATGAAAATT
1 GCAATGCGAAATGAAAATT
16934 GCAATGC
1 GCAATGC
16941 AGAATTCACT
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
14 7 0.07
16 4 0.04
17 2 0.02
18 3 0.03
19 73 0.74
20 10 0.10
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATT
Found at i:16910 original size:72 final size:71
Alignment explanation
Indices: 16779--16937 Score: 230
Period size: 72 Copynumber: 2.2 Consensus size: 71
16769 TCGCAACGCG
**
16779 GAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTACAATGCGAAATGAAAATTG
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTACAATGCGAAATGAAAATTG
16844 CAATGC
66 CAATGC
* * *
16850 GAAATGAAAATCGCAACGAGTGAATTGCAATGTGAAAATGAAAA-TAGCAATGCGAAATGAAAAT
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGCG-AAATGAAAATTA-CAATGCGAAATGAAAAT
*
16914 TGCAATGT
64 TGCAATGC
*
16922 GAAATGAAAATTGCAA
1 GAAATGAAAATCGCAA
16938 TGCAGAATTC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 31 0.39
72 48 0.61
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.19
Consensus pattern (71 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATTACAATGCGAAATGAAAATTG
CAATGC
Found at i:16991 original size:33 final size:34
Alignment explanation
Indices: 16944--17012 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
16934 GCAATGCAGA
**
16944 ATTCACTCGTTGCGATTTTCATTT-CGCATTGCG
1 ATTCACTCGTTGCGATAGTCATTTCCGCATTGCG
* *
16977 ATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCG
1 ATTCACTCGTTGCGATAGTCATTTCCGCATTGCG
17011 AT
1 AT
17013 AGCCTGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 21 0.68
34 10 0.32
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (34 bp):
ATTCACTCGTTGCGATAGTCATTTCCGCATTGCG
Found at i:17133 original size:14 final size:14
Alignment explanation
Indices: 17114--17150 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17104 CATCAATTAA
17114 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
17128 ACAAATCATCTTTT
1 ACAAATCAACATTT
17142 ACAAATCAA
1 ACAAATCAA
17151 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:18571 original size:21 final size:18
Alignment explanation
Indices: 18547--18591 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
18537 AAACGGTGGG
18547 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
18568 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
18586 AGGGGA
1 AGGGGA
18592 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:19112 original size:20 final size:20
Alignment explanation
Indices: 19089--19175 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
19079 GAAACTTAAA
*
19089 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
19109 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
19129 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
19149 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
19169 ATCGCAA
1 ATCGCAA
19176 CGAGAGAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:19235 original size:19 final size:19
Alignment explanation
Indices: 19211--19292 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
19201 AAATCGCAAC
*
19211 GCGATTATAGTTTTGCGTT
1 GCGATTATAGTTTCGCGTT
* *
19230 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
*
19249 GCGATTTTCA-TTTCGCGTT
1 GCGATTAT-AGTTTCGCGTT
* * *
19268 GCAATTTTCA-TTTCTCGTT
1 GCGATTAT-AGTTTCGCGTT
19287 GCGATT
1 GCGATT
19293 CTCTCATTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 55 1.00
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:19563 original size:94 final size:93
Alignment explanation
Indices: 19393--19767 Score: 635
Period size: 94 Copynumber: 4.0 Consensus size: 93
19383 ACGGATTGCA
* *
19393 TTACTTCAA-CAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
19457 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
19485 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
19550 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
19579 TTACTTTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
19644 TTAACAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
19673 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
19738 TTAGCAGTATTGGCAGCAATCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
19767 T
1 T
19768 ACTAAGCAAT
Statistics
Matches: 270, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
92 4 0.01
93 24 0.09
94 242 0.90
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.21
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:19643 original size:17 final size:17
Alignment explanation
Indices: 19621--19653 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19611 ATACTAACTT
19621 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
19638 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
19654 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:21417 original size:25 final size:25
Alignment explanation
Indices: 21367--21417 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
21357 TATACCAAAA
* * *
21367 ATATACCAAAAACTACACTGTGAAG
1 ATATACCAAAAACTAAACTATAAAG
21392 ATATACCAAAAACATAAAC-ATAAAG
1 ATATACCAAAAAC-TAAACTATAAAG
21417 A
1 A
21418 GTAGTAGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.57, C:0.18, G:0.08, T:0.18
Consensus pattern (25 bp):
ATATACCAAAAACTAAACTATAAAG
Found at i:21503 original size:20 final size:20
Alignment explanation
Indices: 21480--21535 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
21470 TGAAATGAAA
21480 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
21500 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
21520 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
21536 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:21557 original size:19 final size:19
Alignment explanation
Indices: 21471--21597 Score: 85
Period size: 20 Copynumber: 7.1 Consensus size: 19
21461 TCTTTTGGTT
*
21471 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
21490 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
21510 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
21528 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
21544 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
21561 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
21577 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
21596 GA
1 GA
21598 TTTTGGTTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 18 0.21
15 2 0.02
16 4 0.05
17 3 0.04
18 3 0.04
19 25 0.29
20 28 0.33
21 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:21557 original size:33 final size:33
Alignment explanation
Indices: 21471--21592 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
21461 TCTTTTGGTT
21471 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
**
21510 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
21544 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
21577 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
21593 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 45 0.59
34 10 0.13
36 2 0.03
37 1 0.01
38 3 0.04
40 15 0.20
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:21664 original size:20 final size:20
Alignment explanation
Indices: 21604--21681 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
21594 GCGATTTTGG
*
21604 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
**
21624 TTCTC-TCGTTGCGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
*
21645 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
21665 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
21682 AAGTTTAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.53
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:22261 original size:20 final size:20
Alignment explanation
Indices: 22236--22452 Score: 190
Period size: 20 Copynumber: 10.7 Consensus size: 20
22226 CTTTAAAAAT
22236 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22256 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
22276 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
22297 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * *
22317 CTCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
22337 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22357 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
22377 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
22398 CGCGTTGCAATTTTACTGACA
1 CGCGTTGCGA-TTTACGGATA
* *
22419 CTCGTTGCGATAGTTA-GAAT-
1 CGCGTTGCGAT--TTACGGATA
22439 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
22453 TATGTTCGCG
Statistics
Matches: 161, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.02
20 105 0.65
21 50 0.31
22 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:22386 original size:41 final size:41
Alignment explanation
Indices: 22236--22413 Score: 175
Period size: 41 Copynumber: 4.4 Consensus size: 41
22226 CTTTAAAAAT
* * * * *
22236 CGCGTTGCGA-TTTACGGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTTACGTATTCTCATTGCGA-TTTACGGATA
* * * * * *
22276 TGTCGTTGCGA-TTTACGGATACGCATTGCGATTTACGTATT
1 CG-CGTTGCGATTTTACGTATTCTCATTGCGATTTACGGATA
* *
22317 CTCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCATTGCGATTTACGGATA
*
22357 CGCGTTGCGATTTTACGTATTGTCATTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCATTGCGATTTACGGATA
*
22398 CGCGTTGCAATTTTAC
1 CGCGTTGCGATTTTAC
22414 TGACACTCGT
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
40 51 0.42
41 70 0.58
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCATTGCGATTTACGGATA
Found at i:22427 original size:41 final size:41
Alignment explanation
Indices: 22301--22429 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 41
22291 CGGATACGCA
* * * * **
22301 TTGCGATTTACGTATTCTCGTTGCGA-TTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCAATTTTACGTACACTCG
* *** *
22341 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCA
1 TTGCGATTTACGGATACGCGTTGCAATTTTACGTACACTCG
22382 TTGCGATTTACGGATACGCGTTGCAATTTTAC-TGACACTCG
1 TTGCGATTTACGGATACGCGTTGCAATTTTACGT-ACACTCG
22423 TTGCGAT
1 TTGCGAT
22430 AGTTAGAATC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
40 24 0.31
41 53 0.69
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (41 bp):
TTGCGATTTACGGATACGCGTTGCAATTTTACGTACACTCG
Found at i:22461 original size:20 final size:20
Alignment explanation
Indices: 22438--22490 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
22428 ATAGTTAGAA
22438 TCGCGTTGCGATTT-ATATGT
1 TCGCGTTGCGATTTCATAT-T
*
22458 TCGCGTTGCAATTTTCATATT
1 TCGCGTTGCGA-TTTCATATT
22479 T-GCGTTGCGATT
1 TCGCGTTGCGATT
22491 CTGGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 18 0.62
21 5 0.17
22 4 0.14
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTCATATT
Found at i:22589 original size:20 final size:19
Alignment explanation
Indices: 22540--22593 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
22530 ATTCTACATA
22540 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
22559 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
22580 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
22594 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:22736 original size:24 final size:24
Alignment explanation
Indices: 22696--22758 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
22686 TATGGTATAC
* *
22696 TATATAAA-TAGTTTATATAGTTCA
1 TATATAAACTA-TATATATAATTCA
22720 T-TAATAAACTATATATATAATTCA
1 TAT-ATAAACTATATATATAATTCA
*
22744 TATGTAAACTATATA
1 TATATAAACTATATA
22759 GTTTATATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 1 0.03
24 29 0.88
25 3 0.09
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (24 bp):
TATATAAACTATATATATAATTCA
Found at i:22766 original size:20 final size:20
Alignment explanation
Indices: 22733--22807 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
22723 ATAAACTATA
* *
22733 TATATAATTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
*
22753 TATATAGTTTATATAGTTTATAC
1 TATATAGTTTATAT-G--TAAAC
*
22776 -ATGTAGTTTATATGTAAAC
1 TATATAGTTTATATGTAAAC
22795 TATATAGTTTATA
1 TATATAGTTTATA
22808 CATATAGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.09
20 23 0.51
21 2 0.04
22 12 0.27
23 4 0.09
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (20 bp):
TATATAGTTTATATGTAAAC
Found at i:22766 original size:33 final size:33
Alignment explanation
Indices: 22729--22833 Score: 102
Period size: 42 Copynumber: 2.9 Consensus size: 33
22719 ATTAATAAAC
22729 TATATATATAATTCATATGTAAACTATATAGTT
1 TATATATATAATTCATATGTAAACTATATAGTT
*
22762 TATATAGTTTATACATGTAGTTTATATGTAAACTATATAGTT
1 TATATA---TAT--A---A-TTCATATGTAAACTATATAGTT
* *
22804 TATACATATAGTTCATATGTAAACTATATA
1 TATATATATAATTCATATGTAAACTATATA
22834 TATAATTTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
33 24 0.41
36 3 0.05
37 1 0.02
38 1 0.02
39 3 0.05
41 1 0.02
42 26 0.44
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.45
Consensus pattern (33 bp):
TATATATATAATTCATATGTAAACTATATAGTT
Found at i:23049 original size:20 final size:20
Alignment explanation
Indices: 23033--23320 Score: 172
Period size: 20 Copynumber: 14.4 Consensus size: 20
23023 TTGTATAGTT
*
23033 TATATATAATTTATATATAA
1 TATATATAGTTTATATATAA
*
23053 -ACTATATAATTTATAT-TAA
1 TA-TATATAGTTTATATATAA
* **
23072 TAAACTATATAGTTTATACATGC
1 T--A-TATATAGTTTATATATAA
23095 TATATATAGTTTATATATAA
1 TATATATAGTTTATATATAA
* *
23115 TATGTATATAGTATATATATAG
1 TA--TATATAGTTTATATATAA
* * *
23137 TATATACTAATATAAATATAA
1 TATATA-TAGTTTATATATAA
* *
23158 -ACTATATGGTTTATACATAA
1 TA-TATATAGTTTATATATAA
*
23178 TATATATA-TATATATAT-A
1 TATATATAGTTTATATATAA
*
23196 TATATATAGTATATAATATAA
1 TATATATAGTTTAT-ATATAA
** *
23217 -ATATA-A-ACTATAGT-TCA
1 TATATATAGTTTATA-TATAA
*
23234 TATATATA-TATA-ATATAA
1 TATATATAGTTTATATATAA
23252 -ATATATAGTTATATATATATA
1 TATATATAGTT-TATATATA-A
*
23273 TATATATA-TATATATATATA
1 TATATATAGTTTATATATA-A
*
23293 TATATATA-TATATATATATA
1 TATATATAGTTTATATATA-A
23313 TATATATA
1 TATATATA
23321 TATATTATAA
Statistics
Matches: 218, Mismatches: 28, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
17 11 0.05
18 22 0.10
19 22 0.10
20 102 0.47
21 20 0.09
22 39 0.18
23 2 0.01
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATATAGTTTATATATAA
Found at i:23058 original size:22 final size:21
Alignment explanation
Indices: 23033--23325 Score: 165
Period size: 22 Copynumber: 13.9 Consensus size: 21
23023 TTGTATAGTT
*
23033 TATATATAATTTATATATAAA
1 TATATATAATATATATATAAA
* *
23054 -CTATATAATTTATATTAATAAA
1 TATATATAATATATA-T-ATAAA
* * * * **
23076 -CTATATAGTTTATACAT-GC
1 TATATATAATATATATATAAA
* *
23095 TATATATAGTTTATATATAATA
1 TATATATAATATATATATAA-A
* * *
23117 TGTATATAGTATATATAT-AG
1 TATATATAATATATATATAAA
*
23137 TATATACTAATATAAATATAAA
1 TATATA-TAATATATATATAAA
* ** * *
23159 -CTATATGGTTTATACATAATA
1 TATATATAATATATATATAA-A
*
23180 TATATATATATATATATATATA
1 TATATATA-ATATATATATAAA
*
23202 TAGTATATAATATAAATATAAA
1 TA-TATATAATATATATATAAA
* *
23224 CTATAGT-TCATATATATATATA
1 -TATA-TATAATATATATATAAA
*
23246 -ATATA-AATATATAGT-TATA
1 TATATATAATATATA-TATAAA
*
23265 TATATAT-ATATATATATATA
1 TATATATAATATATATATAAA
*
23285 TATATATATATATATATATATA
1 TATATATA-ATATATATATAAA
23307 TATATATATATATATATAT
1 TATATATA-ATATATATAT
23326 TATAATTGTT
Statistics
Matches: 218, Mismatches: 34, Indels: 39
0.75 0.12 0.13
Matches are distributed among these distances:
19 13 0.06
20 71 0.33
21 17 0.08
22 100 0.46
23 17 0.08
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (21 bp):
TATATATAATATATATATAAA
Found at i:23100 original size:2 final size:2
Alignment explanation
Indices: 23095--23329 Score: 225
Period size: 2 Copynumber: 116.0 Consensus size: 2
23085 TTATACATGC
* *
23095 TA TA TA TA GTT TA TA TA TA -A TA TG TA TA TA GTA TA TA TA TA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* * * * *
23139 TA TA CTA -A TA TA AA TA TA AA CTA TA TGG TT TA TA CA TA -A TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA
*
23180 TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA -A TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* *
23222 AA CTA TA GT- TCA TA TA TA TA TA TA -A TA TA AA TA TA TA GT- TA
1 TA -TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
23263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23305 TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
23330 ATTGTTTTAA
Statistics
Matches: 195, Mismatches: 19, Indels: 38
0.77 0.08 0.15
Matches are distributed among these distances:
1 8 0.04
2 172 0.88
3 15 0.08
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:25597 original size:2 final size:2
Alignment explanation
Indices: 25590--25620 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
25580 ATAATTAATA
25590 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25621 TAAAATGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:26552 original size:42 final size:42
Alignment explanation
Indices: 26505--26613 Score: 146
Period size: 42 Copynumber: 2.6 Consensus size: 42
26495 AAGCTGTTGG
* * ** *
26505 AGAAGCATCAAAGAGAGATTTTGATGTTGTTGGTGATATGGA
1 AGAAGCATCAAAGAGAGATCTTCATACTATTGGTGATATGGA
*
26547 AGAAGCTTCAAAGAGAGATCTTCATACTATTGGTGATATGGA
1 AGAAGCATCAAAGAGAGATCTTCATACTATTGGTGATATGGA
* *
26589 AGAAGCATCAAAGAAAGAACTTCAT
1 AGAAGCATCAAAGAGAGATCTTCAT
26614 GCTGCAACCA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.27
Consensus pattern (42 bp):
AGAAGCATCAAAGAGAGATCTTCATACTATTGGTGATATGGA
Found at i:44222 original size:3 final size:3
Alignment explanation
Indices: 44214--44254 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
44204 GTGACACTTC
44214 CTT CTT CTT CTT CTT CTT CTT C-T CATT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CT
44255 CGCTTCACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:44907 original size:28 final size:28
Alignment explanation
Indices: 44860--44925 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
44850 TTGTGAAGAA
*
44860 GAAGAAGAAGTTATAAGTTTAAGCTCTT
1 GAAGAAGAAGCTATAAGTTTAAGCTCTT
** *
44888 GAAGAAGAAGCTATGGGTTTTAGCTCTT
1 GAAGAAGAAGCTATAAGTTTAAGCTCTT
44916 GAAGAAGAAG
1 GAAGAAGAAG
44926 AAAAAGAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (28 bp):
GAAGAAGAAGCTATAAGTTTAAGCTCTT
Found at i:44933 original size:37 final size:37
Alignment explanation
Indices: 44892--44964 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
44882 GCTCTTGAAG
* * *
44892 AAGAAGCTATGGGTTTTAGCTCTTGAAGAAGAAGAAA
1 AAGAAGCTATGGGCTTAAGCTCTTAAAGAAGAAGAAA
44929 AAGAAGCTATGGGCTTAAGCTCTTAAAGAAGAAGAA
1 AAGAAGCTATGGGCTTAAGCTCTTAAAGAAGAAGAA
44965 TGAGGAGGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (37 bp):
AAGAAGCTATGGGCTTAAGCTCTTAAAGAAGAAGAAA
Found at i:48418 original size:37 final size:37
Alignment explanation
Indices: 48368--48441 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
48358 CTACTATTTT
48368 GTTTCTTTCTTCTTGCTTGCACTTGTAACTTTTAAAC
1 GTTTCTTTCTTCTTGCTTGCACTTGTAACTTTTAAAC
48405 GTTTCTTTCTTCTTGCTTGCACTTGTAACTTTTAAAC
1 GTTTCTTTCTTCTTGCTTGCACTTGTAACTTTTAAAC
48442 ATGTAAAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.11, T:0.51
Consensus pattern (37 bp):
GTTTCTTTCTTCTTGCTTGCACTTGTAACTTTTAAAC
Found at i:61907 original size:2 final size:2
Alignment explanation
Indices: 61900--61930 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61890 TCATTACTGC
61900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61931 GGATAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.