Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007724.1 Hibiscus syriacus cultivar Beakdansim tig00109971_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: 1221931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:202355 original size:36 final size:36
Alignment explanation
Indices: 202304--202419 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
202294 GGAAACTGTC
*
202304 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
* *
202340 TCAAGGGAAATTGTCTTAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
* *
202376 TCAAGAGAAACTGTCTCAAGGGAGCCAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
202412 TCAAGGGA
1 TCAAGGGA
202420 GATAAAGTGT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 72 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
Found at i:202455 original size:72 final size:68
Alignment explanation
Indices: 202285--202455 Score: 163
Period size: 72 Copynumber: 2.4 Consensus size: 68
202275 AAGCTAAGGT
*
202285 TGTTTCAAGGGAAACTGTCTCAAG-G-GAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
*
202348 AAT
66 AAG
* * *
202351 TGTCTT-AAGGGAGACAAAATTTGTTTC-A-AGAGAAACTGTCTCAAGGGAGCCAAAATTTGTTT
1 TGT-TTCAA-GG-G---AAA-CTGTCTCAAGAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTT
202413 CAAGGGAGATAAAG
59 CAA-GG-G--AAAG
202427 TGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGA
202456 CAAAACTTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
66 5 0.06
67 4 0.05
68 1 0.01
70 5 0.06
71 9 0.11
72 42 0.51
73 2 0.02
74 2 0.02
75 4 0.05
76 8 0.10
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (68 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
AAG
Found at i:202495 original size:128 final size:127
Alignment explanation
Indices: 202304--202547 Score: 416
Period size: 128 Copynumber: 1.9 Consensus size: 127
202294 GGAAACTGTC
* * * *
202304 TCAAGGGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTTAAGGGAGACAAA
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAA
*
202369 ATTTGTTTCAAGAGAAACTGTCTCAAGGGAGCCAAAATTTGTTTCAAGGGAGATAAAGTGTT
66 ATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAGATAAAGTGTT
*
202431 TCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGGGTGACAA
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAA
*
202496 AATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
65 AATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
202548 AATTATCTCA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
127 28 0.26
128 81 0.74
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (127 bp):
TCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAA
ATTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAGATAAAGTGTT
Found at i:202509 original size:36 final size:36
Alignment explanation
Indices: 202427--202693 Score: 273
Period size: 36 Copynumber: 7.4 Consensus size: 36
202417 GGAGATAAAG
*
202427 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA-TT
*
202464 TGTTTCAAGGGAAACTGTCTCAAGGGTGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
202500 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
202536 TGTTTCAAGGGAAATTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * *
202572 TGGTTCAAGGGAAACTGTAAACTGTCTCAAAGGAGACAAAATA
1 TGTTTCAA-GG-----G-AAACTGTCTCAAGGGAGACAAAATT
**
202615 TGTTTCAAGGGAAA------CAA---ATTCAAAGATGT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAA-AT-T
* * *
202644 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
202680 TGTTTCAAGGGAAA
1 TGTTTCAAGGGAAA
202694 TAAATTCAAA
Statistics
Matches: 193, Mismatches: 19, Indels: 37
0.78 0.08 0.15
Matches are distributed among these distances:
27 5 0.03
28 2 0.01
29 13 0.07
30 3 0.02
35 3 0.02
36 95 0.49
37 37 0.19
38 4 0.02
42 3 0.02
43 28 0.15
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
Found at i:202570 original size:72 final size:68
Alignment explanation
Indices: 202427--202816 Score: 286
Period size: 65 Copynumber: 5.6 Consensus size: 68
202417 GGAGATAAAG
* * *
202427 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGGGTG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAATTAT-TCAA---AG
202492 ACAAAATT
61 ACAAAATT
*
202500 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTATCTCAAGGGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATTAT-TCAA---AGA
202565 CAAAATT
62 CAAAATT
* *
202572 TGGTTCAAGGGAAACTGTAAACTGTCTCAA-AGGAGACAAAATATGTTTCAAGGG-AA--A--CA
1 TGTTTCAA-GG-----G-AAACTGTCTCAAGA-GAGACAAAATTTGTTTCAAGGGAAATTATTCA
**
202631 AATTCAAAGATGT
58 AAGACAAA-AT-T
* * *
202644 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAATAAATTCAAAG----
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAT-TATTCAAAGACAA
*
202705 ATTT
65 AATT
* * * * *
202709 TGTTTCAAGAGAAAATGTCTCAAGAGAGAAAAAATTTGTTTCAATGGAAACATAATT-AAAG---
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GGGAA-ATTATTCAAAGACA
**
202770 ATTTT
64 AAATT
* *
202775 GTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAACTTTGTTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
202817 TGAGAGGAAA
Statistics
Matches: 272, Mismatches: 24, Indels: 48
0.79 0.07 0.14
Matches are distributed among these distances:
65 79 0.29
66 16 0.06
67 39 0.14
69 1 0.00
70 5 0.02
71 7 0.03
72 50 0.18
73 38 0.14
76 1 0.00
78 3 0.01
79 33 0.12
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.28
Consensus pattern (68 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATTATTCAAAGACAAA
ATT
Found at i:202799 original size:67 final size:65
Alignment explanation
Indices: 202590--202816 Score: 314
Period size: 65 Copynumber: 3.5 Consensus size: 65
202580 GGGAAACTGT
* *
202590 AAACTGTCTCAA-AGGAGACAAAATATGTTTCAAGGGAAACAAATTCAAAGATGTTGTTTCAAGA
1 AAACTGTCTCAAGA-GAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGA
202654 G
65 G
* *
202655 AAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGAG
* * *
202720 AAAATGTCTCAAGAGAGAAAAAATTTGTTTCAATGGAAACATAATT-AAAGATTTTGTGTTTCAA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACA-AATTCAAAGA-TTT-TGTTTCAA
*
202784 GGG
63 GAG
* *
202787 AAACTGTCTCAAGGGAGACAAACTTTGTTT
1 AAACTGTCTCAAGAGAGACAAAATTTGTTT
202817 TGAGAGGAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
65 101 0.70
66 8 0.06
67 36 0.25
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (65 bp):
AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGAG
Found at i:202902 original size:36 final size:35
Alignment explanation
Indices: 202850--202964 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 35
202840 GACAAAATTC
* *
202850 ATTTT-TTTTAGAGAAAACAATCTCAAGTGAGATTA
1 ATTTTGTTTTAG-GAAAACTATCTCAAGTGAGATAA
* * * * * *
202885 ATTTTGTTTTAAGGAAAATTGTCTCCAGCGTGACAA
1 ATTTTGTTTT-AGGAAAACTATCTCAAGTGAGATAA
* * *
202921 AATTTGTTCTTAGGAAAACTATCTCATGTGAGATCA
1 ATTTTGTT-TTAGGAAAACTATCTCAAGTGAGATAA
202957 ATTTTGTT
1 ATTTTGTT
202965 CTATATATTT
Statistics
Matches: 59, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
35 5 0.08
36 50 0.85
37 4 0.07
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (35 bp):
ATTTTGTTTTAGGAAAACTATCTCAAGTGAGATAA
Found at i:203156 original size:37 final size:37
Alignment explanation
Indices: 203062--203319 Score: 258
Period size: 37 Copynumber: 7.2 Consensus size: 37
203052 AACAACTTGG
* *
203062 AATTTGTGTTCAGAAGGAAAATGTCTCAAGTGAGACGA
1 AATTTGTTTTAAG-AGGAAAATGTCTCAAGTGAGACGA
203100 AATTTG-TTTAAGAGGAAAATGTCTCAAGTGAGACGA
1 AATTTGTTTTAAGAGGAAAATGTCTCAAGTGAGACGA
* *
203136 AATTTGTTTTAAGAGGAAAATGTATCAAGTGAGACAA
1 AATTTGTTTTAAGAGGAAAATGTCTCAAGTGAGACGA
*
203173 AATTTGTTTTAAGA-GACAAATGTCTCAAGTGA-ACAA
1 AATTTGTTTTAAGAGGA-AAATGTCTCAAGTGAGACGA
* * **
203209 AATTTGTTTTTA-A-GAAAA-----CAACT---TTGA
1 AATTTGTTTTAAGAGGAAAATGTCTCAAGTGAGACGA
203236 AATTT-TTTTCCAA-AGGAAAATGTCTCAAGTGAGACGA
1 AATTTGTTTT--AAGAGGAAAATGTCTCAAGTGAGACGA
* * *
203273 AATTTGTTTTAAGAGAAAAATGGCTCAAGTGAGACAA
1 AATTTGTTTTAAGAGGAAAATGTCTCAAGTGAGACGA
203310 AATTTTGTTT
1 AA-TTTGTTT
203320 CGAGAGAAAC
Statistics
Matches: 187, Mismatches: 17, Indels: 32
0.79 0.07 0.14
Matches are distributed among these distances:
26 4 0.02
27 6 0.03
28 2 0.01
29 9 0.05
34 7 0.04
35 3 0.02
36 49 0.26
37 90 0.48
38 17 0.09
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (37 bp):
AATTTGTTTTAAGAGGAAAATGTCTCAAGTGAGACGA
Found at i:203450 original size:42 final size:41
Alignment explanation
Indices: 203395--203480 Score: 163
Period size: 42 Copynumber: 2.1 Consensus size: 41
203385 AGAAGATCTT
203395 ATTGTTCCTTCAATATGTTGAATATTCAATGATGCCTCAAC
1 ATTGTTCCTTCAATATGTTGAATATTCAATGATGCCTCAAC
203436 ATTGTTCACTTCAATATGTTGAATATTCAATGATGCCTCAAC
1 ATTGTTC-CTTCAATATGTTGAATATTCAATGATGCCTCAAC
203478 ATT
1 ATT
203481 CAGCATTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 7 0.16
42 37 0.84
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (41 bp):
ATTGTTCCTTCAATATGTTGAATATTCAATGATGCCTCAAC
Found at i:204553 original size:14 final size:15
Alignment explanation
Indices: 204524--204574 Score: 70
Period size: 14 Copynumber: 3.4 Consensus size: 15
204514 TTTATTTTTT
204524 TCTTGTTTTTCTTTGC
1 TCTT-TTTTTCTTTGC
204540 TCTTTTTTTC-TTGC
1 TCTTTTTTTCTTTGC
204554 TC-TTTTTTCTTTGC
1 TCTTTTTTTCTTTGC
204568 TCATTTT
1 TC-TTTT
204575 CATGTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.22
14 12 0.38
15 6 0.19
16 7 0.22
ACGTcount: A:0.02, C:0.20, G:0.08, T:0.71
Consensus pattern (15 bp):
TCTTTTTTTCTTTGC
Found at i:208015 original size:56 final size:57
Alignment explanation
Indices: 207949--208057 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 57
207939 TGTGCATCGA
* * * *
207949 TGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGCGTGCATCGATGCATGGCTTG
1 TGCATCAAATGCATTCGATGTTTTAAAAATAGCCAGAGTGCATCGATGCATGGCTTG
**
208005 TGCATCAAATGCATTCGATGTTTTAAAAATATTCAGAGTGCATCGATGCATGG
1 TGCATCAAATGCATTCGATGTTTTAAAAATAGCCAGAGTGCATCGATGCATGG
208058 AGAATGCATC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 19 0.41
57 27 0.59
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (57 bp):
TGCATCAAATGCATTCGATGTTTTAAAAATAGCCAGAGTGCATCGATGCATGGCTTG
Found at i:208081 original size:17 final size:19
Alignment explanation
Indices: 208043--208089 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
208033 ATATTCAGAG
208043 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
208062 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
208079 TGCATTCGATG
1 TGCA-TCGATG
208090 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:216318 original size:19 final size:19
Alignment explanation
Indices: 216294--216362 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
216284 GAACACTTGA
216294 TGCATCGGTGCACCAAGTG
1 TGCATCGGTGCACCAAGTG
216313 TGCATCGGTGCACCAAGTG
1 TGCATCGGTGCACCAAGTG
216332 TGCATCGGTGCACCAAGTG
1 TGCATCGGTGCACCAAGTG
*
216351 TGCATCGATGCA
1 TGCATCGGTGCA
216363 TGAAATGCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (19 bp):
TGCATCGGTGCACCAAGTG
Found at i:216418 original size:64 final size:63
Alignment explanation
Indices: 216347--216510 Score: 206
Period size: 65 Copynumber: 2.6 Consensus size: 63
216337 CGGTGCACCA
*
216347 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCTT-GCGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATA--TTAGAGTGCATCGATGCATGG
** *
216411 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATT-AGAGTGCATCGATGCATGG
** *
216476 AGAATGCATC-AGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGA-TGCATGAAATGCATTCGATGTTT
216511 CAATTAATTC
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
63 2 0.02
64 33 0.38
65 51 0.59
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (63 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATTAGAGTGCATCGATGCATGG
Found at i:216485 original size:19 final size:17
Alignment explanation
Indices: 216461--216507 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
216451 ATATTCAGAG
216461 TGCATCGATGCATGGAGAA
1 TGCATCGATGCAT-G-GAA
216480 TGCATC-AGTGCATGGAA
1 TGCATCGA-TGCATGGAA
216497 TGCATTCGATG
1 TGCA-TCGATG
216508 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:217428 original size:15 final size:15
Alignment explanation
Indices: 217408--217450 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
217398 CTTTTTTGGT
217408 AAAATATTACCTATA
1 AAAATATTACCTATA
** *
217423 AAAATATTTTCGATA
1 AAAATATTACCTATA
*
217438 AAAAAATTACCTA
1 AAAATATTACCTA
217451 AAACATTATT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAATATTACCTATA
Found at i:217486 original size:21 final size:21
Alignment explanation
Indices: 217444--217487 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
217434 GATAAAAAAA
*
217444 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATTAATATTT
*
217465 TTACCTAAAACATTAATGTTT
1 TTACCTAAAACATTAATATTT
217486 TT
1 TT
217488 TAACATTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (21 bp):
TTACCTAAAACATTAATATTT
Found at i:219241 original size:14 final size:13
Alignment explanation
Indices: 219222--219265 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
219212 AATTTTTATC
219222 TTAAAAATGATTTT
1 TTAAAAAT-ATTTT
219236 TTAAAAA-ATTGTT
1 TTAAAAATATT-TT
219249 TTAAAATATATTTT
1 TTAAAA-ATATTTT
219263 TTA
1 TTA
219266 GGTGTTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.11
13 8 0.30
14 13 0.48
15 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (13 bp):
TTAAAAATATTTT
Found at i:219244 original size:15 final size:14
Alignment explanation
Indices: 219224--219265 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
219214 TTTTTATCTT
219224 AAAAATGATTTTTTA
1 AAAAAT-ATTTTTTA
*
219239 AAAAAT-TGTTTTA
1 AAAAATATTTTTTA
*
219252 AAATATATTTTTTA
1 AAAAATATTTTTTA
219266 GGTGTTCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.48
14 6 0.26
15 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (14 bp):
AAAAATATTTTTTA
Found at i:219825 original size:171 final size:173
Alignment explanation
Indices: 219528--219875 Score: 542
Period size: 173 Copynumber: 2.0 Consensus size: 173
219518 TGATAGAAAA
* *
219528 AGAAAACTAAAAATGTACCACAACGACAACAGATGTAAAGTTATTCTTATTAAAAAAAAAGAGAA
1 AGAAAACGAAAAACGTACCACAACGACAACAGATGTAAAGTTATTCTTATTAAAAAAAAAGAGAA
*
219593 TCAATGAACAATTAACATCAAAACTGATGTCCCTATTAGTTAAACAAAACTAAAGAAAAAATGAT
66 TCAATGAACAATTAACATCAAAACTGACGTCCCTATTAGTTAAACAAAACTAAAGAAAAAATGAT
*
219658 ATGATCT-TTAAAAA-AATACAAACTCTAAAAAAAACAAATAG
131 ATGATCTATAAAAAACAATACAAACTCTAAAAAAAACAAATAG
* *
219699 AGAAAACGAAAAACGTACCACAACGACAACAGATGTAAAGTTATTCTTATTTAAAAAAGAGATAG
1 AGAAAACGAAAAACGTACCACAACGACAACAGATGTAAAGTTATTCTTA-TTAAAAAA-AAAGAG
* * ** *
219764 GATCAATGAACAATTAACATCAAAACTGGCGTTGCTGTTAGTTAAACAAAACT-AA-AAAAAATG
64 AATCAATGAACAATTAACATCAAAACTGACGTCCCTATTAGTTAAACAAAACTAAAGAAAAAATG
*
219827 ATATGGTCTATAAAAAACAATACAAACTCTAAAAAAAACAAATAG
129 ATATGATCTATAAAAAACAATACAAACTCTAAAAAAAACAAATAG
219872 AGAA
1 AGAA
219876 CCACACAAAC
Statistics
Matches: 161, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
171 63 0.39
172 16 0.10
173 82 0.51
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (173 bp):
AGAAAACGAAAAACGTACCACAACGACAACAGATGTAAAGTTATTCTTATTAAAAAAAAAGAGAA
TCAATGAACAATTAACATCAAAACTGACGTCCCTATTAGTTAAACAAAACTAAAGAAAAAATGAT
ATGATCTATAAAAAACAATACAAACTCTAAAAAAAACAAATAG
Found at i:232929 original size:33 final size:33
Alignment explanation
Indices: 232891--232977 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
232881 GTTTTCTTTG
* **
232891 TTTAATAGGTAGTGAGTTTTTAGT-AGGTTTTTA
1 TTTAATAGGTAGTGAGTTTTTAGTGA-ATGATTA
* *
232924 TTTAATGGGTATTGAGTTTTTAGTGAATGATTA
1 TTTAATAGGTAGTGAGTTTTTAGTGAATGATTA
*
232957 TTTAATAGGTAGTGGGTTTTT
1 TTTAATAGGTAGTGAGTTTTT
232978 TAGATTAAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
33 44 0.98
34 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (33 bp):
TTTAATAGGTAGTGAGTTTTTAGTGAATGATTA
Found at i:233008 original size:3 final size:3
Alignment explanation
Indices: 232989--233037 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
232979 AGATTAAGTG
*
232989 ATA ATTA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
233035 ATA
1 ATA
233038 TTTAATAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:233603 original size:20 final size:21
Alignment explanation
Indices: 233578--233629 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
233568 TTTTCCCAAT
*
233578 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
233598 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
233619 TCGCAATGCGA
1 TCGCAATGCGA
233630 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:233643 original size:20 final size:20
Alignment explanation
Indices: 233618--233711 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
233608 AATTGGGAAA
*
233618 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
233638 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
233659 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
233679 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
233699 TTCGCAACGCGAT
1 ATCGCAACGCGAT
233712 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:233952 original size:27 final size:27
Alignment explanation
Indices: 233922--233977 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
233912 ATCGCCGGCG
233922 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCACAGTCAA
233949 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCACAGTCAA
233976 AA
1 AA
233978 CAGTCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.36, G:0.04, T:0.18
Consensus pattern (27 bp):
AAATCCCTCACAACCATTCACAGTCAA
Found at i:234274 original size:14 final size:14
Alignment explanation
Indices: 234255--234290 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
234245 ATTGTTTAAT
234255 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
234269 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
234283 TGATTTGT
1 TGATTTGT
234291 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:234516 original size:19 final size:19
Alignment explanation
Indices: 234492--234584 Score: 80
Period size: 19 Copynumber: 5.4 Consensus size: 19
234482 TCCGCTTGCG
234492 ATTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
* *
234511 ATTGCGA-----AATTAGC
1 ATTGCGATTTTCATTTCGC
*
234525 GTTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
*
234544 ATTGCGA--TTC-TCTCG-
1 ATTGCGATTTTCATTTCGC
234559 -TTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
234577 ATTGCGAT
1 ATTGCGAT
234585 AGTAATTTCC
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
14 17 0.30
16 7 0.12
17 7 0.12
19 25 0.45
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (19 bp):
ATTGCGATTTTCATTTCGC
Found at i:234535 original size:33 final size:34
Alignment explanation
Indices: 234493--234583 Score: 141
Period size: 33 Copynumber: 2.7 Consensus size: 34
234483 CCGCTTGCGA
234493 TTGCGATTTTCATTTCGCATTGCGAAAT-TAGCG
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
* **
234526 TTGCGATTTTCATTTCGCATTGCG-ATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
234559 TTGCGATTTTCATTTCGCATTGCGA
1 TTGCGATTTTCATTTCGCATTGCGA
234584 TAGTAATTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 51 0.96
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCATTGCGAAATCTAGCG
Found at i:237110 original size:24 final size:24
Alignment explanation
Indices: 237076--237129 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
237066 CTGAAACATC
* *
237076 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
237100 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
237124 ATCAAA
1 ATCAAA
237130 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:237704 original size:22 final size:21
Alignment explanation
Indices: 237675--237715 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
237665 TTCCGGATGG
*
237675 GGAAGGATGTCGTTGGAGATA
1 GGAAGGATGTCGTCGGAGATA
237696 GGAACGGATGTCGTCGGAGA
1 GGAA-GGATGTCGTCGGAGA
237716 GAGTGATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.27, C:0.10, G:0.44, T:0.20
Consensus pattern (21 bp):
GGAAGGATGTCGTCGGAGATA
Found at i:239709 original size:19 final size:20
Alignment explanation
Indices: 239685--239727 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
239675 GAAACTTAAA
239685 ATCGCAACGC-GAAATGACT
1 ATCGCAACGCGGAAATGACT
*
239704 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
239724 ATCG
1 ATCG
239728 AATGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:240235 original size:18 final size:18
Alignment explanation
Indices: 240209--240253 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
240199 GTCGATCAGA
*
240209 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
240227 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
240245 TGATGGCTC
1 TGATGGCTC
240254 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:241589 original size:20 final size:20
Alignment explanation
Indices: 241564--241606 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
241554 AATAGTTTCT
241564 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
241584 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
241604 GAA
1 GAA
241607 TTCGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:241912 original size:22 final size:22
Alignment explanation
Indices: 241884--241927 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
241874 GATGGAGATA
*
241884 GACGGATTT-TTCTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
241906 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
241928 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.18, C:0.11, G:0.43, T:0.27
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:242141 original size:20 final size:20
Alignment explanation
Indices: 242116--242167 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
242106 ATTATGTATT
*
242116 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTAAGA
*
242136 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGA
*
242156 ATCTCGTTGCGA
1 ATCGCGTTGCGA
242168 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGA
Found at i:242229 original size:21 final size:21
Alignment explanation
Indices: 242203--242273 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
242193 CAGTACCGCA
242203 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
242224 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
*
242244 TTGCAATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
242265 TTGCGATTT
1 TTGCGATTT
242274 ACTTACTCGC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:242242 original size:20 final size:20
Alignment explanation
Indices: 242217--242290 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
242207 GATTTTCCCA
*
242217 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* * **
242237 ATTCGCATTGCAATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
242258 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
*
242278 ACTCGCATTGCGA
1 ATTCGCATTGCGA
242291 ATTGGGAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:242273 original size:41 final size:41
Alignment explanation
Indices: 242199--242293 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
242189 TAGTCAGTAC
* *
242199 CGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATT
1 CGCATTGCAATTTTCCCAATTCGCGTTGCGATTTACTTACT
242240 CGCATTGCAATTTTCCCAATTCGCGTTGCGATTTACTTACT
1 CGCATTGCAATTTTCCCAATTCGCGTTGCGATTTACTTACT
242281 CGCATTGCGAATT
1 CGCATTGC-AATT
242294 GGGAAAATCG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 47 0.92
42 4 0.08
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (41 bp):
CGCATTGCAATTTTCCCAATTCGCGTTGCGATTTACTTACT
Found at i:249582 original size:16 final size:16
Alignment explanation
Indices: 249557--249603 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
249547 ATTCATATAG
* *
249557 AGCATCTGAATCATTT
1 AGCATTTGAATCATTC
249573 AGCATTTGAATCATTC
1 AGCATTTGAATCATTC
*
249589 AGCA-TTAAATCATTC
1 AGCATTTGAATCATTC
249604 TGAAGTAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (16 bp):
AGCATTTGAATCATTC
Found at i:249972 original size:20 final size:20
Alignment explanation
Indices: 249896--249986 Score: 112
Period size: 20 Copynumber: 4.5 Consensus size: 20
249886 GCGATTTTTC
249896 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
**
249916 GAAAATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
249936 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGAATAT
* *
249956 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGAATAT
249976 GACTATCGCAA
1 GACTATCGCAA
249987 CACGATTCTG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.02
20 62 0.97
21 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:249992 original size:20 final size:20
Alignment explanation
Indices: 249949--250009 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
249939 AATCGCAATG
* **
249949 CGATTATGACTATCGCAATG
1 CGATTCTGACTATCGCAACA
249969 CGATTCTGACTATCGCAACA
1 CGATTCTGACTATCGCAACA
* *
249989 CGATTCTGACTGTCACAACA
1 CGATTCTGACTATCGCAACA
250009 C
1 C
250010 TGAATTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (20 bp):
CGATTCTGACTATCGCAACA
Found at i:250879 original size:24 final size:24
Alignment explanation
Indices: 250821--250867 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
250811 AGTCGGTATT
* *
250821 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTCGTCAATACC
250845 CGAACTTTGATCTTCGTCAATAC
1 CGAACTTTGATCTTCGTCAATAC
250868 TCGGGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTCGTCAATACC
Found at i:256745 original size:19 final size:19
Alignment explanation
Indices: 256721--256764 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
256711 TCATACTTTA
256721 CCAAATTTGCAATTTGGTC
1 CCAAATTTGCAATTTGGTC
256740 CCAAATTTGCAATTTGGTC
1 CCAAATTTGCAATTTGGTC
256759 CCAAAT
1 CCAAAT
256765 CAATATTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (19 bp):
CCAAATTTGCAATTTGGTC
Found at i:263583 original size:43 final size:44
Alignment explanation
Indices: 263492--263600 Score: 175
Period size: 43 Copynumber: 2.5 Consensus size: 44
263482 TCATTTACTA
* *
263492 TGTGCAAGGGTAAGACCTTACCATTTATGAAGGCTCCTTTGCTC
1 TGTGCAAGGGTAAGACCTTACCATTTATGAAGGCTCCTCTGATC
* *
263536 TGTGCAAGGGTAAAACCTTACCATTT-TGAAGGCTCCTCTGATG
1 TGTGCAAGGGTAAGACCTTACCATTTATGAAGGCTCCTCTGATC
263579 TGTGCAAGGGTAAGACCTTACC
1 TGTGCAAGGGTAAGACCTTACC
263601 GCTTTCCATA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
43 35 0.58
44 25 0.42
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (44 bp):
TGTGCAAGGGTAAGACCTTACCATTTATGAAGGCTCCTCTGATC
Found at i:265266 original size:38 final size:39
Alignment explanation
Indices: 265204--265314 Score: 170
Period size: 38 Copynumber: 2.9 Consensus size: 39
265194 TCTAATGATT
* *
265204 TATTTCCTTTTACAAAACATGAAAATAAATCCAACAATC
1 TATTTCCTTTTACAAAATAGGAAAATAAATCCAACAATC
* *
265243 TATTT-CTTTTACAAAATAGGAAAATAAATCCAACGATT
1 TATTTCCTTTTACAAAATAGGAAAATAAATCCAACAATC
*
265281 TATTTCCTTTTATAAAATAGGAAAATAAATCCAA
1 TATTTCCTTTTACAAAATAGGAAAATAAATCCAA
265315 TGATTTGTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 34 0.52
39 32 0.48
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (39 bp):
TATTTCCTTTTACAAAATAGGAAAATAAATCCAACAATC
Found at i:265332 original size:39 final size:39
Alignment explanation
Indices: 265186--265325 Score: 183
Period size: 39 Copynumber: 3.6 Consensus size: 39
265176 GATTTCCAAA
* * * * *
265186 AAAATATATCTAATGATTTATTTCCTTTTACAAAACATG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
* *
265225 AAAATAAATCCAACAATCTATTT-CTTTTACAAAATAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
*
265263 AAAATAAATCCAACGATTTATTTCCTTTTATAAAATAGG
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
* *
265302 AAAATAAATCCAATGATTTGTTTC
1 AAAATAAATCCAACGATTTATTTC
265326 AGTTTATTTC
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 34 0.39
39 54 0.61
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (39 bp):
AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAGG
Found at i:265440 original size:58 final size:58
Alignment explanation
Indices: 265339--265583 Score: 305
Period size: 58 Copynumber: 4.2 Consensus size: 58
265329 TTATTTCTTT
* *
265339 TTACAAA-ATAGAATCATTCAAGATTCTCATGGAAAATAAATTCAACAATTTATTTTCC
1 TTACAAAGTTAGAATCATTCAAGATTCTCAAGG-AAATAAATTCAACAATTTATTTTCC
* *
265397 TTACAAAGTTATAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTCAT-C
1 TTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATT-TTCC
* * * * * *
265455 TTACAAGGTTAGAGTCATTTAAGATTCTGAAGGAAATAAATTTAACTATTTATTTTCC
1 TTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCC
* * * * * * *
265513 TTACAAAGTTAGAATCATTTAAGTTTTTCAAGTAAATAAATTGAACTATTTATTTTCT
1 TTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCC
265571 TTACAAAGTTAGA
1 TTACAAAGTTAGA
265584 TCAACGTAAG
Statistics
Matches: 164, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
57 1 0.01
58 140 0.85
59 23 0.14
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (58 bp):
TTACAAAGTTAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTCC
Found at i:265920 original size:45 final size:46
Alignment explanation
Indices: 265871--265964 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 46
265861 GGATTTTTAA
* * * *
265871 TTTTGGCAACTCAATGATCAAAA-GAACTAATCGTTTGATTTTATT
1 TTTTGGCAACACAATAATCAAAATGAACTAATCCTTTGATTTTACT
265916 TTTTGGCAACACAATAATCAAAATGAACTAATCCTTTGATTTTACT
1 TTTTGGCAACACAATAATCAAAATGAACTAATCCTTTGATTTTACT
265962 TTT
1 TTT
265965 GATAACCCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 21 0.48
46 23 0.52
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (46 bp):
TTTTGGCAACACAATAATCAAAATGAACTAATCCTTTGATTTTACT
Found at i:265965 original size:45 final size:44
Alignment explanation
Indices: 265734--265984 Score: 149
Period size: 45 Copynumber: 5.7 Consensus size: 44
265724 GGAACAATCC
* * * * *
265734 TTTAATTTTAGCAGCCCAATAATCACAAGGAA-TTATCCTTTGAT
1 TTTAATTTTGGCAACACAATAATCA-AAAGAACTAATCCTTTGAT
* * *
265778 TTTAGTTTTCGCAATC-CAATAATCGAAAAGGAACTAGTCCTTTGAT
1 TTTAATTTTGGCAA-CACAATAATC-AAAA-GAACTAATCCTTTGAT
*** * * *
265824 TTTAATTTCAACAA-ATTAATTAATCAAAAAGAATTAA-----GGATT
1 TTTAATTTTGGCAACA-CAA-TAATC-AAAAGAACTAATCCTTTGA-T
* * *
265866 TTTAATTTTGGCAACTCAATGATCAAAAGAACTAATCGTTTGAT
1 TTTAATTTTGGCAACACAATAATCAAAAGAACTAATCCTTTGAT
*
265910 TTTATTTTTTGGCAACACAATAATCAAAATGAACTAATCCTTTGAT
1 TTTA-ATTTTGGCAACACAATAATCAAAA-GAACTAATCCTTTGAT
* ** * *
265956 TTTACTTTTGATAACCCAATATTCAAAAG
1 TTTAATTTTGGCAACACAATAATCAAAAG
265985 CCTTAGATTG
Statistics
Matches: 159, Mismatches: 32, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
40 10 0.06
41 6 0.04
42 14 0.09
44 27 0.17
45 47 0.30
46 46 0.29
47 9 0.06
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (44 bp):
TTTAATTTTGGCAACACAATAATCAAAAGAACTAATCCTTTGAT
Found at i:276575 original size:20 final size:21
Alignment explanation
Indices: 276550--276595 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
276540 GACCAAGAAA
276550 AAAGAT-GAAAAATGTGTCAC
1 AAAGATAGAAAAATGTGTCAC
276570 AAAGATAGAAAAATGTGTCAC
1 AAAGATAGAAAAATGTGTCAC
276591 AAAGA
1 AAAGA
276596 CAATTATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (21 bp):
AAAGATAGAAAAATGTGTCAC
Found at i:278782 original size:22 final size:24
Alignment explanation
Indices: 278757--278808 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
278747 CTTCACTGTA
*
278757 TAAAATATT-TTATTATTCATT-T
1 TAAAATATTATTATTAATCATTGT
*
278779 T-AAATTTTATTATTAATCATTGT
1 TAAAATATTATTATTAATCATTGT
*
278802 TACAATA
1 TAAAATA
278809 ATGATTATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 2 0.09
24 3 0.13
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
TAAAATATTATTATTAATCATTGT
Found at i:280558 original size:20 final size:21
Alignment explanation
Indices: 280530--280568 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
280520 AAAGGCTTTA
*
280530 TAGTCTCGAGACC-ATGGTCC
1 TAGTATCGAGACCGATGGTCC
280550 TAGTATCGAGACCGATGGT
1 TAGTATCGAGACCGATGGT
280569 TGAGTATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (21 bp):
TAGTATCGAGACCGATGGTCC
Found at i:285979 original size:20 final size:20
Alignment explanation
Indices: 285954--286000 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
285944 CTCGGTCTCG
285954 ATACCAATATCCTGGTATCA
1 ATACCAATATCCTGGTATCA
285974 ATACCAATATCCTGGTATCA
1 ATACCAATATCCTGGTATCA
285994 ATACCAA
1 ATACCAA
286001 ATGTGTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.28
Consensus pattern (20 bp):
ATACCAATATCCTGGTATCA
Found at i:287643 original size:19 final size:18
Alignment explanation
Indices: 287610--287645 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
287600 AAAACATAAA
287610 TTTATAAAATAATATTAT
1 TTTATAAAATAATATTAT
*
287628 TTTATAAATTTAATATTA
1 TTTATAAA-ATAATATTA
287646 ATATGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTATAAAATAATATTAT
Found at i:287725 original size:23 final size:23
Alignment explanation
Indices: 287673--287727 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
287663 CATTTTAATA
*
287673 AAAATATTAATTATTAACATATTT
1 AAAATA-TATTTATTAACATATTT
*
287697 AAAATATATTTATTAATAT-TTT
1 AAAATATATTTATTAACATATTT
287719 AATAATATA
1 AA-AATATA
287728 ATATATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 5 0.18
23 17 0.61
24 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATATTTATTAACATATTT
Found at i:287736 original size:23 final size:22
Alignment explanation
Indices: 287684--287739 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
287674 AAATATTAAT
* *
287684 TATTAACATATTTAAAATATATT
1 TATTAATAT-TTTAAAATATATA
287707 TATTAATATTTTAATAATATA-A
1 TATTAATATTTTAA-AATATATA
287729 TATATAATATT
1 TAT-TAATATT
287740 ATTATTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTAATATTTTAAAATATATA
Found at i:287754 original size:23 final size:23
Alignment explanation
Indices: 287728--287785 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 23
287718 TAATAATATA
287728 ATATATAATATTATTATTACAAT
1 ATATATAATATTATTATTACAAT
* *
287751 ATAT-TCA-ATTA-TATTATAAT
1 ATATATAATATTATTATTACAAT
*
287771 ATATGATACTATTAT
1 ATAT-ATAATATTAT
287786 ATTCTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
20 12 0.44
21 4 0.15
22 3 0.11
23 8 0.30
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATATAATATTATTATTACAAT
Found at i:287765 original size:49 final size:49
Alignment explanation
Indices: 287699--287794 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 49
287689 ACATATTTAA
* *
287699 AATATATTTATTAATATTTTAATAATATAATA-TATAATATTATTATTAC
1 AATATATTAATTAATATTATAAT-ATATAATACTATAATATTATTATTAC
* * *
287748 AATATATTCAATT-ATATTATAATATATGATACTATTATATTCTTATT
1 AATATATT-AATTAATATTATAATATATAATACTATAATATTATTATT
287795 TAATAGTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 7 0.17
49 30 0.75
50 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (49 bp):
AATATATTAATTAATATTATAATATATAATACTATAATATTATTATTAC
Found at i:287948 original size:23 final size:21
Alignment explanation
Indices: 287921--287975 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
287911 TAGCCTAATA
287921 ATATTATAAAAATTCCTTAAAAT
1 ATATTATAAAAATT--TTAAAAT
*
287944 ATATTTATTAATAATTTTAAAAT
1 ATA-TTA-TAAAAATTTTAAAAT
*
287967 ATAATATAA
1 ATATTATAA
287976 TATTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
23 13 0.46
24 3 0.11
25 7 0.25
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTATAAAAATTTTAAAAT
Found at i:287976 original size:21 final size:23
Alignment explanation
Indices: 287937--287983 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
287927 TAAAAATTCC
*
287937 TTAAAATATATTTATTAATAATT
1 TTAAAATATATATATTAATAATT
*
287960 TTAAAATATA-ATA-TAATATTT
1 TTAAAATATATATATTAATAATT
287981 TTA
1 TTA
287984 TTTTTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAATATATATATTAATAATT
Found at i:288142 original size:17 final size:18
Alignment explanation
Indices: 288120--288162 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
288110 TAAATTATTC
288120 TAATATT-GTTTATATAA
1 TAATATTAGTTTATATAA
*
288137 TAATATTAAGTTTTTATAA
1 TAATATT-AGTTTATATAA
288156 TAA-ATTA
1 TAATATTA
288163 TAATATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 3 0.13
19 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TAATATTAGTTTATATAA
Found at i:289254 original size:14 final size:13
Alignment explanation
Indices: 289235--289269 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
289225 AATAACAACA
*
289235 AAAAATATTAAGAG
1 AAAAATAATAA-AG
289249 AAAAATAATAAAG
1 AAAAATAATAAAG
289262 AAAAATAA
1 AAAAATAA
289270 AGAAAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (13 bp):
AAAAATAATAAAG
Found at i:289423 original size:30 final size:30
Alignment explanation
Indices: 289382--289438 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
289372 AAAGATAAAT
289382 AAATAAAAATTTAAAGGATCAAATTGAAAC
1 AAATAAAAATTTAAAGGATCAAATTGAAAC
* * *
289412 AAATCAAAATTTTATGGATCAAATTGA
1 AAATAAAAATTTAAAGGATCAAATTGA
289439 TGCTAAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (30 bp):
AAATAAAAATTTAAAGGATCAAATTGAAAC
Found at i:290777 original size:38 final size:37
Alignment explanation
Indices: 290718--290816 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 37
290708 AAAAAATACA
*
290718 TTTTCAAAAACTATATTATATATACGTCTTCAAAAATG
1 TTTTC-AAAACTATATAATATATACGTCTTCAAAAATG
* *
290756 TTTTTCAAAACTATATAATATATATGTTTTCAAAAATG
1 -TTTTCAAAACTATATAATATATACGTCTTCAAAAATG
* * *
290794 TTTTCAAAATTACATATTATATA
1 TTTTCAAAACTATATAATATATA
290817 TATATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
37 20 0.37
38 29 0.54
39 5 0.09
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTCAAAACTATATAATATATACGTCTTCAAAAATG
Found at i:290815 original size:37 final size:38
Alignment explanation
Indices: 290718--290818 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 38
290708 AAAAAATACA
290718 TTTTCAAAA-ACTATATTATATATACGTCTTCAAAAATGT
1 TTTTCAAAATAC-ATATTATATATA-GTCTTCAAAAATGT
* * *
290757 TTTTCAAAACTATATAATATATAT-GTTTTCAAAAATG-
1 TTTTCAAAA-TACATATTATATATAGTCTTCAAAAATGT
290794 TTTTCAAAATTACATATTATATATA
1 TTTTCAAAA-TACATATTATATATA
290819 TATATATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
37 21 0.40
38 12 0.23
39 9 0.17
40 10 0.19
41 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (38 bp):
TTTTCAAAATACATATTATATATAGTCTTCAAAAATGT
Found at i:290818 original size:2 final size:2
Alignment explanation
Indices: 290807--290865 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
290797 TCAAAATTAC
* *
290807 AT AT -T AT AT AT AT AT AT AT AT AT AT TT TT AT AT AT -T AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
290846 A- AT AT A- AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
290866 TTATTAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
1 5 0.10
2 44 0.90
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:290869 original size:25 final size:25
Alignment explanation
Indices: 290835--290892 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
290825 TATATATTTT
* *
290835 TATATA-TTATTAATA-TAACATATA
1 TATATATTTATTAAAATTAAAAT-TA
290859 TATATATTTATTAAAATTAAAATTA
1 TATATATTTATTAAAATTAAAATTA
290884 TATATATTT
1 TATATATTT
290893 TATTTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 6 0.20
25 19 0.63
26 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TATATATTTATTAAAATTAAAATTA
Found at i:298535 original size:16 final size:17
Alignment explanation
Indices: 298516--298561 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
298506 AAAACATATT
298516 AAAATTAAAAAAA-ATA
1 AAAATTAAAAAAAGATA
298532 AAAATATAAAAAAAGATA
1 AAAAT-TAAAAAAAGATA
*
298550 AATAAATAAAAA
1 AA-AATTAAAAA
298562 TTTAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 11 0.42
19 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAATTAAAAAAAGATA
Found at i:299673 original size:16 final size:16
Alignment explanation
Indices: 299647--299703 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
299637 AAAATAAAAA
299647 AATATTAATAACAT-TAT
1 AATA-TAATAA-ATATAT
299664 AATATAATAAATATAT
1 AATATAATAAATATAT
*
299680 ACTA-AATAATATATAT
1 AATATAATAA-ATATAT
299696 AA-ATAATA
1 AATATAATA
299704 TGTATACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
15 8 0.23
16 23 0.66
17 4 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAATAAATATAT
Found at i:299700 original size:13 final size:12
Alignment explanation
Indices: 299662--299704 Score: 61
Period size: 11 Copynumber: 3.6 Consensus size: 12
299652 TAATAACATT
299662 ATAATATAATAA
1 ATAATATAATAA
*
299674 AT-ATATACTAA
1 ATAATATAATAA
299685 ATAATATATATAA
1 ATAATATA-ATAA
299698 ATAATAT
1 ATAATAT
299705 GTATACTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 10 0.37
12 7 0.26
13 10 0.37
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATATAATAA
Found at i:299709 original size:13 final size:13
Alignment explanation
Indices: 299662--299709 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
299652 TAATAACATT
299662 ATAATATA-ATAA
1 ATAATATATATAA
*
299674 AT-ATATA-CTAA
1 ATAATATATATAA
299685 ATAATATATATAA
1 ATAATATATATAA
*
299698 ATAATATGTATA
1 ATAATATATATA
299710 CTAAATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.32
12 7 0.23
13 14 0.45
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (13 bp):
ATAATATATATAA
Found at i:299714 original size:16 final size:14
Alignment explanation
Indices: 299673--299715 Score: 61
Period size: 13 Copynumber: 3.0 Consensus size: 14
299663 TAATATAATA
299673 AATATATACTAAAT
1 AATATATACTAAAT
299687 AATATATA-TAAAT
1 AATATATACTAAAT
299700 AATATGTATACTAAAT
1 AATA--TATACTAAAT
299716 TTATTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.35
14 8 0.31
15 4 0.15
16 5 0.19
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (14 bp):
AATATATACTAAAT
Found at i:299723 original size:29 final size:28
Alignment explanation
Indices: 299659--299724 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 28
299649 TATTAATAAC
299659 ATTATAATATAATAAATATATACTAAATA
1 ATTAT-ATATAATAAATATATACTAAATA
* *
299688 A-TATATATAAATAATATGTATACTAAATTT
1 ATTATATAT-AATAA-ATATATACTAAA-TA
299718 ATTATAT
1 ATTATAT
299725 TTTCAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 4 0.13
28 8 0.26
29 12 0.39
30 2 0.06
31 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (28 bp):
ATTATATATAATAAATATATACTAAATA
Found at i:299791 original size:33 final size:34
Alignment explanation
Indices: 299736--300008 Score: 174
Period size: 34 Copynumber: 7.7 Consensus size: 34
299726 TTCAAAAACC
*
299736 ATTTTAAAAACTATATACTATATGTTTTCAAAAT
1 ATTTTAAAAACTATATATTATATGTTTTCAAAAT
* * *
299770 A-TTTAAAATCTATTTATTATATGTTTTTAAAAAAT
1 ATTTTAAAAACTATATATTATATG-TTTT-CAAAAT
* *
299805 ACGTTTTCAAAAACT-TAATTATATATACGTTTCTTAAAAT
1 A--TTTT-AAAAACTAT-A-TAT-TATATGTTT-TCAAAAT
* *
299845 ATTTT-AAAATTATATATTATATGTTTTCAAAAAA
1 ATTTTAAAAACTATATATTATATGTTTTC-AAAAT
*** *
299879 AAAATCAAAACTATATAATATATATGTTTTCAAAAGT
1 ATTTTAAAAACTATAT-AT-TATATGTTTTCAAAA-T
* * * * *
299916 GTTTTCAAAATTACATATTATATATATTTCAAAAAT
1 ATTTTAAAAACTATATATTATATGT-TTTC-AAAAT
* * * * * *
299952 GTTTTTAAAACCATATATTATATTTTTTTAAAAC
1 ATTTTAAAAACTATATATTATATGTTTTCAAAAT
*
299986 ATTTTTAAAACTATATATTATAT
1 ATTTTAAAAACTATATATTATAT
300009 ATATTTTCGA
Statistics
Matches: 188, Mismatches: 33, Indels: 36
0.73 0.13 0.14
Matches are distributed among these distances:
33 20 0.11
34 44 0.23
35 27 0.14
36 39 0.21
37 26 0.14
38 8 0.04
39 6 0.03
40 12 0.06
41 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (34 bp):
ATTTTAAAAACTATATATTATATGTTTTCAAAAT
Found at i:299955 original size:36 final size:36
Alignment explanation
Indices: 299720--300048 Score: 196
Period size: 36 Copynumber: 9.1 Consensus size: 36
299710 CTAAATTTAT
** * *
299720 TATAT-TTTCAAAAACCATTTTAAAAACTATATACTA
1 TATATATTTCAAAAA-TGTTTTCAAAACTATATATTA
* * *
299756 TATGT-TTTC-AAAAT-ATTT-AAAATCTATTTATTA
1 TATATATTTCAAAAATGTTTTCAAAA-CTATATATTA
* * *
299789 TATGTTTTTAAAAAATACGTTTTCAAAAACT-TA-ATTA
1 TATATATTTCAAAAAT--GTTTTC-AAAACTATATATTA
* * *
299826 TATATACGTTTCTTAAAATATTTT-AAAATTATATATTA
1 TATATA--TTTC-AAAAATGTTTTCAAAACTATATATTA
* ***** *
299864 TATGT-TTTCAAAAAAAAAATCAAAACTATATAATA
1 TATATATTTCAAAAATGTTTTCAAAACTATATATTA
* * * *
299899 TATATGTTTTCAAAAGTGTTTTCAAAATTACATATTA
1 TATAT-ATTTCAAAAATGTTTTCAAAACTATATATTA
* *
299936 TATATATTTCAAAAATGTTTTTAAAACCATATATTA
1 TATATATTTCAAAAATGTTTTCAAAACTATATATTA
* *
299972 TAT-TTTTTTAAAACAT-TTTT-AAAACTATATATTA
1 TATATATTTCAAAA-ATGTTTTCAAAACTATATATTA
* *
300006 TATATATTTTCGAAAAATGTTCTCAAAATTATATATTA
1 TATATA-TTTC-AAAAATGTTTTCAAAACTATATATTA
300044 TATAT
1 TATAT
300049 GTTATATGTA
Statistics
Matches: 226, Mismatches: 45, Indels: 42
0.72 0.14 0.13
Matches are distributed among these distances:
32 4 0.02
33 16 0.07
34 25 0.11
35 42 0.19
36 48 0.21
37 43 0.19
38 34 0.15
39 5 0.02
40 9 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
TATATATTTCAAAAATGTTTTCAAAACTATATATTA
Found at i:307381 original size:27 final size:30
Alignment explanation
Indices: 307321--307379 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
307311 AAGAGTTGCA
307321 TTTAGAGGACTAAATTGAATAAATATAAAG
1 TTTAGAGGACTAAATTGAATAAATATAAAG
307351 TTTAGAGG-CTAAATTG-A-AAATA-AAAG
1 TTTAGAGGACTAAATTGAATAAATATAAAG
307377 TTT
1 TTT
307380 TATTATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 7 0.24
27 5 0.17
28 1 0.03
29 8 0.28
30 8 0.28
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.32
Consensus pattern (30 bp):
TTTAGAGGACTAAATTGAATAAATATAAAG
Found at i:308341 original size:30 final size:31
Alignment explanation
Indices: 308301--308359 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
308291 AAATTAAATA
*
308301 TTTAGAAAATATAACGATAGACTCCTAAAAG
1 TTTAGAAAATATAACGATAGACACCTAAAAG
* *
308332 TTTA-AAAATATAATGGTAGACACCTAAA
1 TTTAGAAAATATAACGATAGACACCTAAA
308360 GTGTAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (31 bp):
TTTAGAAAATATAACGATAGACACCTAAAAG
Found at i:310287 original size:20 final size:18
Alignment explanation
Indices: 310264--310320 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
310254 AAAATTATTA
*
310264 TTATTATATTATTTATAC
1 TTATTATATTATTTATAT
310282 TT-TTATTATTATATTATAT
1 TTATTA-TATTAT-TTATAT
*
310301 TTATTATAATTATTTTTAT
1 TTATTAT-ATTATTTATAT
310320 T
1 T
310321 ATTTTTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 3 0.09
18 8 0.24
19 14 0.42
20 8 0.24
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATATTATTTATAT
Found at i:310356 original size:3 final size:3
Alignment explanation
Indices: 310240--310336 Score: 87
Period size: 3 Copynumber: 33.0 Consensus size: 3
310230 TATCCATTTG
**
310240 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA -TA TTA TT- TATA CTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA
* * *
310284 TTA TTA TTA -TA TTA -TA TTTA TTA TAA TTA TTT TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
310328 TTA TTA TTA
1 TTA TTA TTA
310337 ATAAAAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
2 9 0.12
3 63 0.83
4 3 0.04
5 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:310405 original size:19 final size:19
Alignment explanation
Indices: 310379--310428 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
310369 AAACAGAACG
*
310379 ACCC-AAACCCAACAAGAA
1 ACCCTAAACCCAACAAAAA
310397 ACCCTAAACCCAACAAAAA
1 ACCCTAAACCCAACAAAAA
*
310416 ACCTTAAACCCAA
1 ACCCTAAACCCAA
310429 TTAAGGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.54, C:0.38, G:0.02, T:0.06
Consensus pattern (19 bp):
ACCCTAAACCCAACAAAAA
Found at i:315853 original size:15 final size:15
Alignment explanation
Indices: 315833--315864 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
315823 GATCAATACC
315833 TTTTGCATACATTCA
1 TTTTGCATACATTCA
315848 TTTTGCATACATTCA
1 TTTTGCATACATTCA
315863 TT
1 TT
315865 ATTCATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:321229 original size:18 final size:18
Alignment explanation
Indices: 321186--321223 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
321176 GTGAAGTATG
321186 AATGGTGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
321204 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
321222 AA
1 AA
321224 GTGTGTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.37, T:0.34
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:327679 original size:18 final size:18
Alignment explanation
Indices: 327636--327673 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
327626 GTGAAGTATG
*
327636 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
327654 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
327672 AA
1 AA
327674 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:327804 original size:12 final size:12
Alignment explanation
Indices: 327782--327810 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
327772 GTGACCCACT
327782 AGCTA-TATATG
1 AGCTAGTATATG
327793 AGCTAGTATATG
1 AGCTAGTATATG
327805 AGCTAG
1 AGCTAG
327811 GAACTAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (12 bp):
AGCTAGTATATG
Found at i:331065 original size:12 final size:11
Alignment explanation
Indices: 331048--331102 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
331038 ATGCTTGAAG
331048 AAGAAAAAAATA
1 AAGAAAAAAA-A
331060 AAGAAAATAAAA
1 AAGAAAA-AAAA
331072 AAGAAAGAAAAA
1 AAGAAA-AAAAA
* *
331084 CAGGAAAAAAA
1 AAGAAAAAAAA
*
331095 AGGAAAAA
1 AAGAAAAA
331103 TATAAAAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 10 0.28
12 22 0.61
13 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.04
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:331073 original size:16 final size:16
Alignment explanation
Indices: 331052--331082 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
331042 TTGAAGAAGA
*
331052 AAAAAATAAAGAAAAT
1 AAAAAAGAAAGAAAAT
331068 AAAAAAGAAAGAAAA
1 AAAAAAGAAAGAAAA
331083 ACAGGAAAAA
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:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAAGAAAGAAAAT
Found at i:332415 original size:20 final size:22
Alignment explanation
Indices: 332366--332423 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
332356 CATATCTACA
332366 TCTCTCTTCAAAGATGATAGAT
1 TCTCTCTTCAAAGATGATAGAT
332388 TCTCTCTTCAAAGATGATAGAT
1 TCTCTCTTCAAAGATGATAGAT
* *
332410 TCTCTTTTTAAAGA
1 TCTCTCTTCAAAGA
332424 AGAAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (22 bp):
TCTCTCTTCAAAGATGATAGAT
Found at i:332775 original size:112 final size:112
Alignment explanation
Indices: 332615--333064 Score: 480
Period size: 112 Copynumber: 3.8 Consensus size: 112
332605 TCCATCACTC
* *
332615 GATGGATCAACATTT-CAGGTAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 GATGGATCAACATTTCCAGG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
* * *
332679 TTCATAATGAGAAGAACTTGTTTAACCTTTTGTTGAAT-TCATCAC-TC
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTGTTGACTCT-ATCACATA
* * *
332726 GATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
1 GATGGATCAACATTTCCAGG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAG
* *
332791 TTCATAATGAGAAGAATTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATA
65 TTCATAATGAGAAGAACTTGTTCAACCTTTTG-TTGACTCTATCAC--------ATA
* *
332848 GATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA-AAGGAAGAAGA
1 GAT--GGATCAACATTTCCAG-GAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGA
*
332912 AGTTCATAATAAGAAGAACTTGTTCAACCTTTTGTATGACTCTATCACATAAAGA
63 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGT-TGACTCTATCACAT----A
332967 GATAGATTAGTATCAACATTTCCA-GAAATGTTCATAATGAGAAGAACTTATCTGAAGAAGG-AG
1 GAT-G----G-ATCAACATTTCCAGGAAA-GTTCATAATGAGAAGAACTTATCTGAAGAAGGAAG
* *
333030 AAGAAGTTCATAATGAGAAGAATTTATTCAACCTT
59 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
333065 GCCTTAATTC
Statistics
Matches: 289, Mismatches: 23, Indels: 43
0.81 0.06 0.12
Matches are distributed among these distances:
111 13 0.04
112 76 0.26
113 9 0.03
114 1 0.00
115 2 0.01
118 2 0.01
119 4 0.01
121 4 0.01
122 65 0.22
123 71 0.25
124 41 0.14
125 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (112 bp):
GATGGATCAACATTTCCAGGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACCTTTTGTTGACTCTATCACATA
Found at i:333062 original size:122 final size:124
Alignment explanation
Indices: 332749--333064 Score: 521
Period size: 123 Copynumber: 2.6 Consensus size: 124
332739 TGCCAGGTAG
332749 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
332814 AACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAA
66 AACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAGCATCAACATTTCCAGAGAA
* *
332873 AGTTCATAATGAGAAGAACTTATCTGAA-AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * *
332937 AACCTTTTGTATGACTCTATCACATAAAGAGATAGATTAGTATCAACATTTCCAGA-AA
66 AACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAGCATCAACATTTCCAGAGAA
* *
332995 TGTTCATAATGAGAAGAACTTATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
333059 AACCTT
66 AACCTT
333065 GCCTTAATTC
Statistics
Matches: 179, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
122 63 0.35
123 88 0.49
124 28 0.16
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (124 bp):
AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAGCATCAACATTTCCAGAGAA
Found at i:333512 original size:3 final size:3
Alignment explanation
Indices: 333431--333495 Score: 75
Period size: 3 Copynumber: 22.0 Consensus size: 3
333421 TATCCATTTG
333431 TTA TTA TTA TTA TTA TTA -TA TTA TT- TATA CTT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA
333475 -TA TTTA TTA TTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA
333496 AAAAAATATT
Statistics
Matches: 55, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
2 7 0.13
3 44 0.80
4 3 0.05
5 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:335339 original size:2 final size:2
Alignment explanation
Indices: 335332--335374 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
335322 TCATATTAAC
335332 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
335373 AT
1 AT
335375 TTATTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:335522 original size:34 final size:32
Alignment explanation
Indices: 335459--335533 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 32
335449 ATAAATATCA
*
335459 TATTTTTATAAATTATATATTAACTTATTTTAAT
1 TATTTTTATAAAATATATATTAAC-TA-TTTAAT
* *
335493 TATTTTTATAGAAATATTTTATTAA-TATTTATT
1 TATTTTTATA-AAATA-TATATTAACTATTTAAT
335526 TATTTTTA
1 TATTTTTA
335534 AATATTAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 13 0.36
34 12 0.33
35 4 0.11
36 7 0.19
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (32 bp):
TATTTTTATAAAATATATATTAACTATTTAAT
Found at i:339846 original size:17 final size:15
Alignment explanation
Indices: 339822--339863 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
339812 TATCATCGTG
339822 TTTAGATTATTTTAGT
1 TTTAGATT-TTTTAGT
339838 TTTAGGATTTTTTAG-
1 TTTA-GATTTTTTAGT
339853 TTTA-ATTTTTT
1 TTTAGATTTTTT
339864 CAACTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
15 4 0.16
16 10 0.40
17 4 0.16
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (15 bp):
TTTAGATTTTTTAGT
Found at i:341112 original size:2 final size:2
Alignment explanation
Indices: 341105--341145 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
341095 TAGTTTTCTC
341105 AT AT AT AT AT 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 AT AT AT AT AT A
341146 AAAGAATGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:343145 original size:33 final size:33
Alignment explanation
Indices: 343108--343175 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
343098 TAATTAAGGA
343108 ATTGATGTTATCCTTTAAGCTTACGAGTTTGAT
1 ATTGATGTTATCCTTTAAGCTTACGAGTTTGAT
343141 ATTGATGTTATCCTTTAAGCTTACGAGTTTGAT
1 ATTGATGTTATCCTTTAAGCTTACGAGTTTGAT
343174 AT
1 AT
343176 GTAGGTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTGATGTTATCCTTTAAGCTTACGAGTTTGAT
Found at i:343683 original size:20 final size:20
Alignment explanation
Indices: 343660--343701 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
343650 TATAGTACAT
*
343660 GTATGTATAAACCATGTATA
1 GTATGTATAAACCATATATA
*
343680 GTATGTATAAACTATATATA
1 GTATGTATAAACCATATATA
343700 GT
1 GT
343702 GTGTGTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
GTATGTATAAACCATATATA
Found at i:343744 original size:13 final size:15
Alignment explanation
Indices: 343713--343746 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
343703 TGTGTGTGTA
343713 TATATATATATAACG
1 TATATATATATAACG
343728 TATATATATA-AAC-
1 TATATATATATAACG
343741 TATATA
1 TATATA
343747 AAGTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 3 0.16
15 10 0.53
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAACG
Found at i:343893 original size:14 final size:14
Alignment explanation
Indices: 343822--343893 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
343812 AGTTTTATAG
*
343822 AAACCCTAAACCCT
1 AAACCATAAACCCT
** *
343836 AATTCATAACCCCT
1 AAACCATAAACCCT
**
343850 AAATCC-TAAACTTT
1 AAA-CCATAAACCCT
* *
343864 AAACCATACACACT
1 AAACCATAAACCCT
343878 AAACCATAAACCCT
1 AAACCATAAACCCT
343892 AA
1 AA
343894 TATAAATGAA
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
13 2 0.05
14 39 0.93
15 1 0.02
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:344306 original size:2 final size:2
Alignment explanation
Indices: 344262--344297 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
344252 ATAAACCATG
344262 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
344298 AACTATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:344390 original size:7 final size:7
Alignment explanation
Indices: 344380--344440 Score: 86
Period size: 7 Copynumber: 8.7 Consensus size: 7
344370 TAGTTTATAG
344380 AAACCCT
1 AAACCCT
344387 AAACCCT
1 AAACCCT
344394 AAACCCT
1 AAACCCT
344401 AAACCCT
1 AAACCCT
**
344408 AAAATCT
1 AAACCCT
**
344415 AAACTTT
1 AAACCCT
344422 AAACCCT
1 AAACCCT
344429 AAACCCT
1 AAACCCT
344436 AAACC
1 AAACC
344441 ATAATATATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:344466 original size:17 final size:16
Alignment explanation
Indices: 344444--344483 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
344434 CTAAACCATA
344444 ATATATGTATTACATGC
1 ATATATGTA-TACATGC
*
344461 ATATATGTATATATGC
1 ATATATGTATACATGC
344477 ATA-ATGT
1 ATATATGT
344484 GTGTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 9 0.41
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (16 bp):
ATATATGTATACATGC
Found at i:344714 original size:15 final size:16
Alignment explanation
Indices: 344673--344730 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 16
344663 AAATATATTA
* *
344673 ATGTGTGTATGATACAT
1 ATGTATGTATG-TATAT
*
344690 ATGT-TATATGTATAT
1 ATGTATGTATGTATAT
344705 AT-TATGTATGTATAT
1 ATGTATGTATGTATAT
344720 ATGTATGTATG
1 ATGTATGTATG
344731 ATGCATGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 1 0.03
15 18 0.50
16 13 0.36
17 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (16 bp):
ATGTATGTATGTATAT
Found at i:344721 original size:23 final size:23
Alignment explanation
Indices: 344689--344740 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
344679 GTATGATACA
*
344689 TATGT-TATATGTATATATTATG
1 TATGTATATATGTATATATGATG
*
344711 TATGTATATATGTATGTATGATG
1 TATGTATATATGTATATATGATG
*
344734 CATGTAT
1 TATGTAT
344741 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (23 bp):
TATGTATATATGTATATATGATG
Found at i:344722 original size:8 final size:8
Alignment explanation
Indices: 344688--344730 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
344678 TGTATGATAC
344688 ATATGT-T
1 ATATGTAT
344695 ATATGTAT
1 ATATGTAT
344703 ATAT-TAT
1 ATATGTAT
*
344710 GTATGTAT
1 ATATGTAT
344718 ATATGTAT
1 ATATGTAT
*
344726 GTATG
1 ATATG
344731 ATGCATGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 12 0.39
8 19 0.61
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (8 bp):
ATATGTAT
Found at i:345058 original size:24 final size:24
Alignment explanation
Indices: 345031--345091 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
345021 TAGTTGGCGC
345031 CAAATCACCCGCCTCTAAACTCAT
1 CAAATCACCCGCCTCTAAACTCAT
345055 CAAATCACCCGCCTCTAAACTCAT
1 CAAATCACCCGCCTCTAAACTCAT
345079 CAAATCACCCGCC
1 CAAATCACCCGCC
345092 AGTATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.33, C:0.44, G:0.05, T:0.18
Consensus pattern (24 bp):
CAAATCACCCGCCTCTAAACTCAT
Found at i:346255 original size:14 final size:16
Alignment explanation
Indices: 346228--346402 Score: 64
Period size: 14 Copynumber: 11.9 Consensus size: 16
346218 TTGGTACTTT
346228 ATATATAAAGTATAAA
1 ATATATAAAGTATAAA
346244 ATATAT-AA-TATAAA
1 ATATATAAAGTATAAA
* * ***
346258 GTA-ATAAAGTGTTTG
1 ATATATAAAGTATAAA
346273 A-ATAT-AAGTATTAAA
1 ATATATAAAGTA-TAAA
*
346288 GTATATAAA-TAT-AA
1 ATATATAAAGTATAAA
*
346302 GTAT-TAAA-TATAAA
1 ATATATAAAGTATAAA
*
346316 GTATAT-AAGTACTAAA
1 ATATATAAAGTA-TAAA
*
346332 GTATAT-AA-TATAAA
1 ATATATAAAGTATAAA
* * *
346346 TTAT-TAAACTAT-AT
1 ATATATAAAGTATAAA
*
346360 A-ATAT-AAGTAT-TA
1 ATATATAAAGTATAAA
346373 A-ATATAAAGTATTAAA
1 ATATATAAAGTA-TAAA
*
346389 GTATATAAA-TATAA
1 ATATATAAAGTATAA
346403 GTATTAGTTA
Statistics
Matches: 123, Mismatches: 19, Indels: 35
0.69 0.11 0.20
Matches are distributed among these distances:
13 22 0.18
14 45 0.37
15 20 0.16
16 27 0.22
17 9 0.07
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (16 bp):
ATATATAAAGTATAAA
Found at i:346281 original size:22 final size:22
Alignment explanation
Indices: 346230--346378 Score: 132
Period size: 22 Copynumber: 6.9 Consensus size: 22
346220 GGTACTTTAT
*
346230 ATATAAAGTA-TAAAATATAT-A
1 ATAT-AAGTATTAAAGTATATAA
* * * *
346251 ATATAAAGTAATAAAGTGTTTGA
1 ATAT-AAGTATTAAAGTATATAA
346274 ATATAAGTATTAAAGTATATAA
1 ATATAAGTATTAAAGTATATAA
346296 ATATAAGTATTAAA-TATA-AA
1 ATATAAGTATTAAAGTATATAA
*
346316 GTATATAAGTACTAAAGTATAT-A
1 --ATATAAGTATTAAAGTATATAA
* *
346339 ATATAAATTATTAAACTATAT-A
1 ATAT-AAGTATTAAAGTATATAA
346361 ATATAAGTATTAAA-TATA
1 ATATAAGTATTAAAGTATA
346379 AAGTATTAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.06
21 27 0.25
22 66 0.61
23 10 0.09
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (22 bp):
ATATAAGTATTAAAGTATATAA
Found at i:346293 original size:44 final size:43
Alignment explanation
Indices: 346230--346401 Score: 156
Period size: 44 Copynumber: 3.9 Consensus size: 43
346220 GGTACTTTAT
* * *
346230 ATATAAAGTA-TAAAATATATAATATAAAGTAATAAAGTGTTTGA
1 ATAT-AAGTATTAAAGTATATAATATAAAGTAATAAA-TATATGA
* * *
346274 ATATAAGTATTAAAGTATATAA-ATATAAGTATTAAATATAAAGT
1 ATATAAGTATTAAAGTATATAATATA-AAGTAATAAATAT-ATGA
* * *
346318 ATATAAGTACTAAAGTATATAATATAAATTATTAAACTATAT-A
1 ATATAAGTATTAAAGTATATAATATAAAGTAATAAA-TATATGA
346361 ATATAAGTATTAAA-TATA-AAGTATTAAAGTATATAAATATA
1 ATATAAGTATTAAAGTATATAA-TA-TAAAGTA-ATAAATATA
346402 AGTATTAGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
41 2 0.02
42 6 0.06
43 33 0.31
44 60 0.56
45 6 0.06
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (43 bp):
ATATAAGTATTAAAGTATATAATATAAAGTAATAAATATATGA
Found at i:346311 original size:65 final size:64
Alignment explanation
Indices: 346227--346401 Score: 207
Period size: 65 Copynumber: 2.7 Consensus size: 64
346217 TTTGGTACTT
* * *
346227 TATAT-ATA-AAGTATAAAATATATAA-TATAAAGTAATAAAGTGTTTGAATAT-AAGTATTAAA
1 TATATAATATAAGTATTAAATATA-AAGTATAAAGTAATAAAGTATAT-AATATAAAGTATTAAA
*
346288 G
64 C
* *
346289 TATATAAATATAAGTATTAAATATAAAGTATATAAGTACTAAAGTATATAATATAAATTATTAAA
1 TATAT-AATATAAGTATTAAATATAAAGTATA-AAGTAATAAAGTATATAATATAAAGTATTAAA
346354 C
64 C
346355 TATATAATATAAGTATTAAATATAAAGTATTAAAGTATATAAA-TATA
1 TATATAATATAAGTATTAAATATAAAGTA-TAAAGTA-ATAAAGTATA
346402 AGTATTAGTT
Statistics
Matches: 98, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
62 5 0.05
64 5 0.05
65 55 0.56
66 33 0.34
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (64 bp):
TATATAATATAAGTATTAAATATAAAGTATAAAGTAATAAAGTATATAATATAAAGTATTAAAC
Found at i:346404 original size:14 final size:14
Alignment explanation
Indices: 346286--346406 Score: 76
Period size: 14 Copynumber: 8.4 Consensus size: 14
346276 ATAAGTATTA
346286 AAGTATATAAATAT
1 AAGTATATAAATAT
346300 AAGTAT-TAAATAT
1 AAGTATATAAATAT
*
346313 AAAGTATATAAGTACT
1 -AAGTATATAAATA-T
346329 AAAGTATAT-AATAT
1 -AAGTATATAAATAT
*
346343 AAAT-TATTAAACTAT
1 AAGTATA-TAAA-TAT
*
346358 -A-TAATATAAGTATT
1 AAGT-ATATAAATA-T
346372 AA--ATATAAAGTATT
1 AAGTATATAAA-TA-T
346386 AAAGTATATAAATAT
1 -AAGTATATAAATAT
346401 AAGTAT
1 AAGTAT
346407 TAGTTATAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 28
0.73 0.04 0.23
Matches are distributed among these distances:
12 2 0.02
13 20 0.23
14 30 0.34
15 17 0.19
16 12 0.14
17 7 0.08
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTATATAAATAT
Found at i:347357 original size:9 final size:10
Alignment explanation
Indices: 347322--347354 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
347312 CATAAAACAT
347322 ATTTAAAAAA
1 ATTTAAAAAA
347332 ATTTAAAAAA
1 ATTTAAAAAA
347342 ATTTAAAAAA
1 ATTTAAAAAA
347352 ATT
1 ATT
347355 AAAGAGACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:349116 original size:24 final size:24
Alignment explanation
Indices: 349089--349159 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
349079 AAACGGAAAT
*
349089 ATCAAAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
349113 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
349137 TTCAGAAATC-AAACAGAACTCAG
1 ATCAGAAATCAAAACAGAATTCAG
349160 GTAGTGTATC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 10 0.26
24 28 0.74
ACGTcount: A:0.51, C:0.20, G:0.11, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:349194 original size:24 final size:24
Alignment explanation
Indices: 349089--349194 Score: 51
Period size: 24 Copynumber: 4.5 Consensus size: 24
349079 AAACGGAAAT
*
349089 ATCAAAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAAAA-AGAATTCAAG
* * *
349113 ATCAGATATCATAACAGAA-TCCAG
1 ATCAGAAATCA-AAAAGAATTCAAG
* * *
349137 TTCAGAAATCAAACAGAACTC-AG
1 ATCAGAAATCAAAAAGAATTCAAG
* **
349160 GT-AGTGTATCATAAAAGAATTCAAG
1 ATCAG-AAATCA-AAAAGAATTCAAG
349185 -TCAGAAATCA
1 ATCAGAAATCA
349195 GATAAATATT
Statistics
Matches: 63, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
22 2 0.03
23 16 0.25
24 39 0.62
25 6 0.10
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAAAGAATTCAAG
Found at i:355728 original size:20 final size:20
Alignment explanation
Indices: 355703--355740 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
355693 CCCCCTTTGA
*
355703 AGGGGAATCGATTCCCCCCT
1 AGGGGAATCGATACCCCCCT
355723 AGGGGAATCGATACCCCC
1 AGGGGAATCGATACCCCC
355741 ATGGGGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (20 bp):
AGGGGAATCGATACCCCCCT
Found at i:355746 original size:19 final size:20
Alignment explanation
Indices: 355703--355746 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
355693 CCCCCTTTGA
* *
355703 AGGGGAATCGATTCCCCCCT
1 AGGGGAATCGATACCCCCAT
355723 AGGGGAATCGATACCCCCAT
1 AGGGGAATCGATACCCCCAT
355743 -GGGG
1 AGGGG
355747 TTCTGGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.16
Consensus pattern (20 bp):
AGGGGAATCGATACCCCCAT
Found at i:360164 original size:17 final size:19
Alignment explanation
Indices: 360142--360179 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
360132 TCTTATGCAC
360142 ATCAATA-GT-TTTATCAG
1 ATCAATATGTCTTTATCAG
*
360159 ATCAATATGTCTTTTTCAG
1 ATCAATATGTCTTTATCAG
360178 AT
1 AT
360180 TTATTAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 2 0.11
19 9 0.50
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (19 bp):
ATCAATATGTCTTTATCAG
Found at i:363061 original size:18 final size:20
Alignment explanation
Indices: 363024--363061 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
363014 TTAATAATTT
*
363024 AATATTAATATGTTTTAAAA
1 AATATTAATATGTTTAAAAA
363044 AATATT-ATA-GTTTAAAAA
1 AATATTAATATGTTTAAAAA
363062 TATTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
AATATTAATATGTTTAAAAA
Found at i:364432 original size:50 final size:50
Alignment explanation
Indices: 364373--364469 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
364363 CCCACTGAAC
* * * *
364373 CGCGATATACGCTGATTTGGCGCCATGTGGGTATAACGTGCCCCCTGCCT
1 CGCGATATACGATGATATGGCGCCACGTGGGTATAACGCGCCCCCTGCCT
*
364423 CGCGATATACGATGATATGGCGCCACGTGGGTATAGCGCGCCCCCTG
1 CGCGATATACGATGATATGGCGCCACGTGGGTATAACGCGCCCCCTG
364470 ATCCGTGCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.23
Consensus pattern (50 bp):
CGCGATATACGATGATATGGCGCCACGTGGGTATAACGCGCCCCCTGCCT
Found at i:364599 original size:10 final size:10
Alignment explanation
Indices: 364584--364623 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
364574 TTTATCACAC
364584 CAAATTCTCT
1 CAAATTCTCT
364594 CAAATTCTCT
1 CAAATTCTCT
364604 -AAATTTCTCT
1 CAAA-TTCTCT
*
364614 CAAATACTCT
1 CAAATTCTCT
364624 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:364943 original size:111 final size:111
Alignment explanation
Indices: 364749--364970 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
364739 ATGAAATCAT
* * *** *
364749 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTGTTAGTAA
1 ATATCTCGACACTTTGATGATACAACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
364814 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
364860 ATATCTCGACACTTTGATGATACAACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGATGATACAACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
364925 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
364971 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGATGATACAACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Done.