Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 61 of 126
Found at i:12286024 original size:45 final size:45
Alignment explanation
Indices: 12285929--12286025 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
12285919 ATATATTAAC
* * * * * *
12285929 AAATAAATAAATAAATAATAATAAATATATATTAATAAATAGTAA
1 AAATAAATAAATAAATAAAAATAAATAGATATCAAAAAAAAATAA
* *
12285974 TAATAAATAAATAAATAAAAATACATAAGATA-CAAAAAAAAATAA
1 AAATAAATAAATAAATAAAAATAAAT-AGATATCAAAAAAAAATAA
12286019 AAATAAA
1 AAATAAA
12286026 AATGAAAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
45 38 0.90
46 4 0.10
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (45 bp):
AAATAAATAAATAAATAAAAATAAATAGATATCAAAAAAAAATAA
Found at i:12286034 original size:39 final size:41
Alignment explanation
Indices: 12285972--12286059 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 41
12285962 AATAAATAGT
12285972 AATAATAAATAAATAAATAAAAATACAT-AAGATAC-AAA-AAAA
1 AATAA-AAATAAATAAATAAAAAT--ATGAA-ATACAAAATAAAA
*
12286014 AATAAAAAT-AA-AAATGAAAATATGAAATACAAAATAAAA
1 AATAAAAATAAATAAATAAAAATATGAAATACAAAATAAAA
12286053 AATAAAA
1 AATAAAA
12286060 TGGGCTTACC
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
37 6 0.14
38 5 0.12
39 20 0.48
40 2 0.05
41 4 0.10
42 5 0.12
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.18
Consensus pattern (41 bp):
AATAAAAATAAATAAATAAAAATATGAAATACAAAATAAAA
Found at i:12286055 original size:14 final size:13
Alignment explanation
Indices: 12285972--12286059 Score: 72
Period size: 12 Copynumber: 6.5 Consensus size: 13
12285962 AATAAATAGT
12285972 AATAATAAATAAATA
1 AATAA-AAATAAA-A
12285987 AATAAAAATACATAA
1 AATAAAAATA-A-AA
* *
12286002 GATACAAA-AAAA
1 AATAAAAATAAAA
12286014 AATAAAAAT-AAA
1 AATAAAAATAAAA
* **
12286026 AATGAAAATATGA
1 AATAAAAATAAAA
12286039 AATACAAAATAAAA
1 AATA-AAAATAAAA
12286053 AATAAAA
1 AATAAAA
12286060 TGGGCTTACC
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
12 19 0.33
13 8 0.14
14 17 0.29
15 13 0.22
16 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.18
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:12286416 original size:43 final size:43
Alignment explanation
Indices: 12286234--12286573 Score: 363
Period size: 42 Copynumber: 8.0 Consensus size: 43
12286224 AAAATTTGAT
* * *
12286234 CAAAACTCCTCTAAGCAGAGGCTTAACGACTTTGAAAAACATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAA-ATAAA
** * *
12286279 CAAAGCTCCTCTAATGAGTGGTTCAACGACTTT-AAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * *
12286321 TAAAGCTCTTCTAAGCAGAGGCTCAACGACTTTG-AAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * *
12286363 TAAAGCTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * *
12286406 TAAAGCTCCTCTAAATAGAGGCTCAACCACTTTG-AAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * *
12286448 CAAAGCTCCTCTAAGCAGAGGCTCTATGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
* * *
12286491 CAAAGCTCCTCTAAACAGAGGCTCAACCAATTTTG-AAAGT-AA
1 CAAAGCTCCTCTAAACAGAGGCTCAA-CGACTTTGAAAAATAAA
** *
12286533 -AGTGCTCCTCTAAACAGAGGCATC-ACAACTTTG-AAAATAAA
1 CAAAGCTCCTCTAAACAGAGGC-TCAACGACTTTGAAAAATAAA
12286574 AGGTTCCTAT
Statistics
Matches: 255, Mismatches: 34, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
40 11 0.04
41 22 0.09
42 110 0.43
43 80 0.31
44 5 0.02
45 27 0.11
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (43 bp):
CAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAA
Found at i:12286427 original size:85 final size:85
Alignment explanation
Indices: 12286239--12286517 Score: 382
Period size: 85 Copynumber: 3.3 Consensus size: 85
12286229 TTGATCAAAA
* * * *
12286239 CTCCTCTAAGCAGAGGCTTAACGACTTTGAAAAACATAAACAAAGCTCCTCT-AATGAGTGGTTC
1 CTCCTCTAAACAGAGGCTCAACGACTTTG--AAA-ATAAACAAAGCTCCTCTAAAT-AGAGGCTC
*
12286303 AACGACTTT-AAAAATAAATAAAG
62 AATGACTTTGAAAAATAAATAAAG
* * *
12286326 CTCTTCTAAGCAGAGGCTCAACGACTTTGAAAATAAATAAAGCTCCTCTAAATAGAGGCTCAATG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAATAAACAAAGCTCCTCTAAATAGAGGCTCAATG
12286391 ACTTTGAAAAATAAATAAAG
66 ACTTTGAAAAATAAATAAAG
* * ** *
12286411 CTCCTCTAAATAGAGGCTCAACCACTTTGAAAATAAACAAAGCTCCTCTAAGCAGAGGCTCTATG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGAAAATAAACAAAGCTCCTCTAAATAGAGGCTCAATG
*
12286476 ACTTTGAAAAATAAACAAAG
66 ACTTTGAAAAATAAATAAAG
12286496 CTCCTCTAAACAGAGGCTCAAC
1 CTCCTCTAAACAGAGGCTCAAC
12286518 CAATTTTGAA
Statistics
Matches: 174, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
84 30 0.17
85 117 0.67
87 27 0.16
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (85 bp):
CTCCTCTAAACAGAGGCTCAACGACTTTGAAAATAAACAAAGCTCCTCTAAATAGAGGCTCAATG
ACTTTGAAAAATAAATAAAG
Found at i:12287646 original size:11 final size:11
Alignment explanation
Indices: 12287621--12287651 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12287611 TTTCTTTTCA
*
12287621 TTTTCTTTTAT
1 TTTTATTTTAT
12287632 TTTTATTTTAT
1 TTTTATTTTAT
12287643 TTTTATTTT
1 TTTTATTTT
12287652 TTCATTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:12298235 original size:61 final size:62
Alignment explanation
Indices: 12298097--12298379 Score: 355
Period size: 58 Copynumber: 4.5 Consensus size: 62
12298087 AATTTCGAGA
*
12298097 AAAATTGATACTTTCAATTTTTCCTCGAAAAGAAAAACTCTTTTTTTATAAAAAAATTTATTTTC
1 AAAATTGATACTTTCAACTTTTCCTCG---A-AAAAACT-TTTTTTT-T-AAAAAATTTATTTTC
12298162 AAGG
59 AAGG
12298166 AAAATTGATACTTTCAACTTTTCCTCGAAAAAACTTTTTTTTTAAAAAATTTATTTTCAA-G
1 AAAATTGATACTTTCAACTTTTCCTCGAAAAAACTTTTTTTTTAAAAAATTTATTTTCAAGG
** *
12298227 AAAATTGATACTTTCAACTTTTCCTC-AAAAAACCTTTTTTTAGGAAAAAACTTTATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCGAAAAAA-CTTTTTTT-TTAAAAAA-TTTATTTTCAAGG
* * *
12298291 AAAATTGATACTTTCAACTTTTCCTCG--AAAA--TATTTTTTAGAAAACTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCTCGAAAAAACTTTTTTTTTAAAAAATTTATTTTCAAGG
*
12298349 AAAATTGATACTTTCAACTTTTTCTC-AAAAA
1 AAAATTGATACTTTCAACTTTTCCTCGAAAAA
12298380 TAATTTTTGG
Statistics
Matches: 196, Mismatches: 11, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
58 36 0.18
59 8 0.04
60 11 0.06
61 35 0.18
62 23 0.12
63 16 0.08
64 33 0.17
65 7 0.04
66 1 0.01
69 26 0.13
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (62 bp):
AAAATTGATACTTTCAACTTTTCCTCGAAAAAACTTTTTTTTTAAAAAATTTATTTTCAAGG
Found at i:12298275 original size:125 final size:122
Alignment explanation
Indices: 12298039--12298379 Score: 404
Period size: 125 Copynumber: 2.7 Consensus size: 122
12298029 TTTTGTGCAG
* * * * * * * *
12298039 GAAAAATTGATATTTTCAACTTCTCC-CCAAAATA-TTTTT-AGAAGCTTTAATTTCGAGAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAAAAAAC-TTATTTTCAAGGAAAA
* *
12298101 TTGATACTTTCAATTTTTCCTCGAAAAGAAAAACTCTTTTTTTATAAAAAAATTTATTTTCAA
65 TTGATACTTTCAACTTTTCCTC----A-AAAAACTCTTTTTTTAGAAAAAAATTTATTTTCAA
* * *
12298164 GGAAAATTGATACTTTCAACTTTTCCTCGAAAAAACTTTTTTTTTAAAAAATTTATTTTCAA-GA
1 GAAAAATTGATACTTTCAACTTTTCCTCG--AAAA--TATTTTTTAAAAAACTTATTTTCAAGGA
*
12298228 AAATTGATACTTTCAACTTTTCCTCAAAAAAC-CTTTTTTTAGGAAAAAACTTTATTTTCAA
62 AAATTGATACTTTCAACTTTTCCTCAAAAAACTCTTTTTTTA-GAAAAAAATTTATTTTCAA
*
12298289 GAAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAGAAAACTTATTTTCAAGGAAAAT
1 GAAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAAAAAACTTATTTTCAAGGAAAAT
*
12298354 TGATACTTTCAACTTTTTCTCAAAAA
66 TGATACTTTCAACTTTTCCTCAAAAA
12298380 TAATTTTTGG
Statistics
Matches: 188, Mismatches: 19, Indels: 21
0.82 0.08 0.09
Matches are distributed among these distances:
121 22 0.12
122 31 0.16
123 4 0.02
124 9 0.05
125 74 0.39
126 2 0.01
128 4 0.02
130 26 0.14
131 13 0.07
132 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (122 bp):
GAAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAAAAAACTTATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAAACTCTTTTTTTAGAAAAAAATTTATTTTCAA
Found at i:12298292 original size:19 final size:18
Alignment explanation
Indices: 12298253--12298294 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12298243 ACTTTTCCTC
*
12298253 AAAAAACCTTTTTTTAGG
1 AAAAAACCTTTTTTTAAG
12298271 AAAAAA-CTTTATTTTCAAG
1 AAAAAACCTTT-TTTT-AAG
12298290 AAAAA
1 AAAAA
12298295 TTGATACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 10 0.48
19 7 0.33
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAAAACCTTTTTTTAAG
Found at i:12298417 original size:6 final size:6
Alignment explanation
Indices: 12298406--12298471 Score: 70
Period size: 6 Copynumber: 11.7 Consensus size: 6
12298396 ATTTAAAGAG
* *
12298406 AATAAA AAT-AA AAT-AA AATAAA AATAAA AATAAA GATAAA AAT-AG
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
12298451 AAT-AA AAT-AA AATAAGA AATA
1 AATAAA AATAAA AATAA-A AATA
12298472 CTAAATGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
5 23 0.43
6 25 0.47
7 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:12298418 original size:5 final size:5
Alignment explanation
Indices: 12298410--12298465 Score: 67
Period size: 5 Copynumber: 10.4 Consensus size: 5
12298400 AAAGAGAATA
*
12298410 AAAAT AAAAT AAAAT AAAAAT AAAAAT AAAGAT AAAAAT AGAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT -AAAAT AAA-AT -AAAAT AAAAT AAAAT
12298459 AAAAT AA
1 AAAAT AA
12298466 GAAATACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
5 28 0.61
6 15 0.33
7 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:12298445 original size:34 final size:34
Alignment explanation
Indices: 12298407--12298471 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
12298397 TTTAAAGAGA
12298407 ATAAAAATAAAATAAAATAAAAATAA-AAATAAAG
1 ATAAAAATAAAATAAAAT-AAAATAAGAAATAAAG
*
12298441 ATAAAAATAGAATAAAATAAAATAAGAAATA
1 ATAAAAATAAAATAAAATAAAATAAGAAATA
12298472 CTAAATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (34 bp):
ATAAAAATAAAATAAAATAAAATAAGAAATAAAG
Found at i:12298507 original size:3 final size:3
Alignment explanation
Indices: 12298488--12298528 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
12298478 GATTCTAATC
*
12298488 TAA TCAA TAA GTAA TAA TAA CAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12298529 ATAAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:12298544 original size:16 final size:15
Alignment explanation
Indices: 12298509--12298553 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
12298499 TAATAATAAC
12298509 AATAAT-AAT-AAT-
1 AATAATAAATAAATA
12298521 AATAATAAATAAATA
1 AATAATAAATAAATA
*
12298536 AATATATAAATATATA
1 AATA-ATAAATAAATA
12298552 AA
1 AA
12298554 AAAAATCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 3 0.11
14 3 0.11
15 4 0.14
16 12 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:12299371 original size:17 final size:16
Alignment explanation
Indices: 12299345--12299461 Score: 62
Period size: 17 Copynumber: 7.0 Consensus size: 16
12299335 TAATTAAAAG
12299345 AAAATAATTAGATAAATA
1 AAAAT-ATTA-ATAAATA
*
12299363 AAAATATTAATAGATA
1 AAAATATTAATAAATA
*
12299379 AATAATAATAAT-AATA
1 AA-AATATTAATAAATA
*
12299395 GATAAATAATAATAAATA
1 -A-AAATATTAATAAATA
* * **
12299413 TATATTAACATATAAATA
1 -AAAATATTA-ATAAATA
12299431 AAAA-A-TAAT-AATA
1 AAAATATTAATAAATA
12299444 AATATATATTAATAAATA
1 AA-A-ATATTAATAAATA
12299462 GTAATAATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
13 6 0.08
14 3 0.04
15 2 0.03
16 13 0.16
17 33 0.42
18 22 0.28
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAATATTAATAAATA
Found at i:12299378 original size:20 final size:20
Alignment explanation
Indices: 12299328--12299409 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
12299318 TAAAAAATGG
* *
12299328 TAATAGATAATTAAAAGAAAA
1 TAATAGATAAATAAAA-ATAA
*
12299349 TAATTAGATAAATAAAAATAT
1 TAA-TAGATAAATAAAAATAA
*
12299370 TAATAGATAAATAATAATAA
1 TAATAGATAAATAAAAATAA
*
12299390 TAATAGATAAATAATAATAA
1 TAATAGATAAATAAAAATAA
12299410 ATATATATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 35 0.64
21 8 0.15
22 12 0.22
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (20 bp):
TAATAGATAAATAAAAATAA
Found at i:12299383 original size:4 final size:4
Alignment explanation
Indices: 12299346--12299494 Score: 52
Period size: 4 Copynumber: 38.5 Consensus size: 4
12299336 AATTAAAAGA
* * * *
12299346 AAAT AATT AGAT AAAT AAA- AATAT TAAT AGAT AAAT -AAT -AAT -AAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
12299391 -AAT AGAT AAAT -AAT -AAT AAAT ATATAT TAAC ATAT AAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT AAAT
* *
12299437 -AAT -AAT AAAT ATATAT TAAT AAAT AGTAAT -AAT AAAT AAAT ACAT
1 AAAT AAAT AAAT A-A-AT AAAT AAAT A--AAT AAAT AAAT AAAT AAAT
*
12299482 -AAT AAAT ACAT AA
1 AAAT AAAT AAAT AA
12299495 GATACAAAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 28
0.69 0.14 0.18
Matches are distributed among these distances:
3 34 0.31
4 63 0.58
5 5 0.05
6 7 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:12299387 original size:3 final size:3
Alignment explanation
Indices: 12299359--12299486 Score: 62
Period size: 3 Copynumber: 38.7 Consensus size: 3
12299349 TAATTAGATA
* *
12299359 AAT AAA AAT ATT AAT AGAT AAAT AAT AAT AAT AAT AGAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT A-AT -AAT AAT AAT
* * *
12299408 AAAT ATAT ATT AAC ATAT AAAT AA- AA- AAT AAT AAT AAAT ATAT ATT
1 -AAT A-AT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT -AAT A-AT AAT
*
12299454 AAT AAAT AGT AAT AAT AAAT AAAT ACAT AAT AA
1 AAT -AAT AAT AAT AAT -AAT -AAT A-AT AAT AA
12299487 ATACATAAGA
Statistics
Matches: 99, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
2 4 0.04
3 56 0.57
4 36 0.36
5 3 0.03
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12299387 original size:14 final size:13
Alignment explanation
Indices: 12299359--12299494 Score: 95
Period size: 14 Copynumber: 10.2 Consensus size: 13
12299349 TAATTAGATA
*
12299359 AATAA-AAATATT
1 AATAATAAATAAT
12299371 AATAGATAAATAAT
1 AATA-ATAAATAAT
12299385 AATAAT-AATAGAT
1 AATAATAAATA-AT
12299398 AAATAAT-AATAAAT
1 -AATAATAAAT-AAT
*
12299412 ATATATTAACAT-AT
1 A-ATAATAA-ATAAT
*
12299426 -A-AATAAAAAAT
1 AATAATAAATAAT
12299437 AATAATAAATATAT
1 AATAATAAATA-AT
* *
12299451 ATTAATAAATAGT
1 AATAATAAATAAT
12299464 AATAATAAATAAAT
1 AATAATAAAT-AAT
12299478 ACATAATAAATACAT
1 A-ATAATAAATA-AT
12299493 AA
1 AA
12299495 GATACAAAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
10 1 0.01
11 6 0.06
12 10 0.10
13 23 0.23
14 44 0.44
15 14 0.14
16 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:12299436 original size:25 final size:23
Alignment explanation
Indices: 12299356--12299474 Score: 75
Period size: 25 Copynumber: 5.0 Consensus size: 23
12299346 AAATAATTAG
* *
12299356 ATAAAT-AAAAATATTAAT--AG
1 ATAAATAAAAAATAATAATAAAT
* *
12299376 ATAAAT-AATAATAATAATAGAT
1 ATAAATAAAAAATAATAATAAAT
* * *
12299398 AAATAATAATAAATATATATTAACAT
1 ATA-AATAAAAAATA-ATAATAA-AT
12299424 ATAAATAAAAAATAATAATAAAT
1 ATAAATAAAAAATAATAATAAAT
*
12299447 ATATATTAATAAATAGTAATAATAAAT
1 ATA-AATAA-AAA-A-TAATAATAAAT
12299474 A
1 A
12299475 AATACATAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
20 16 0.21
22 3 0.04
23 8 0.10
24 15 0.19
25 18 0.23
26 5 0.06
27 12 0.16
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.32
Consensus pattern (23 bp):
ATAAATAAAAAATAATAATAAAT
Found at i:12299493 original size:69 final size:65
Alignment explanation
Indices: 12299356--12299515 Score: 166
Period size: 66 Copynumber: 2.4 Consensus size: 65
12299346 AAATAATTAG
* *
12299356 ATAAATAAAAATATTAATAGATAAATAATAATAATAATAGATAAATAATAATAAATATATATTAA
1 ATAAATAAAAA-A-TAATA-ATAAATAATAATAATAATAGATAAATAATAATAAATACATATAAA
12299421 CAT
63 CAT
*
12299424 ATAAATAAAAAATAATAATAAATATATATTAATAAATAG-T-AATAATAAATAAATACATAATAA
1 ATAAATAAAAAATAATAATAAATA-ATAATAAT-AATAGATAAATAAT-AATAAATACAT-ATAA
* *
12299487 ATAC
62 ACAT
12299491 ATAAGATACAAAAA-AATAA-AAATAA
1 ATAA-ATA-AAAAATAATAATAAATAA
12299516 AAATGAAAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
65 13 0.16
66 24 0.30
67 20 0.25
68 19 0.23
69 5 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (65 bp):
ATAAATAAAAAATAATAATAAATAATAATAATAATAGATAAATAATAATAAATACATATAAACAT
Found at i:12299517 original size:5 final size:6
Alignment explanation
Indices: 12299502--12299550 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
12299492 TAAGATACAA
* *
12299502 AAAAAT AAAAAT AAAAAT GAAAAT ATGAAAT ACAAAAT AAAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAAT A-AAAAT -AAAAAT AAAA
12299551 TGGGCTTACC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 21 0.58
7 14 0.39
8 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:12299551 original size:19 final size:19
Alignment explanation
Indices: 12299464--12299551 Score: 60
Period size: 19 Copynumber: 4.8 Consensus size: 19
12299454 AATAAATAGT
* *
12299464 AATAATAAAT-AAATACAT
1 AATAAAAAATAAAATACAA
* *
12299482 AATAAATACATAAGATAC-A
1 AATAAA-AAATAAAATACAA
*
12299501 AA-AAAATA-AAAATA-AA
1 AATAAAAAATAAAATACAA
* *
12299517 AATGAAAATATGAAATACAA
1 AAT-AAAAAATAAAATACAA
12299537 AATAAAAAATAAAAT
1 AATAAAAAATAAAAT
12299552 GGGCTTACCC
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
16 8 0.15
17 2 0.04
18 14 0.26
19 20 0.37
20 10 0.19
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (19 bp):
AATAAAAAATAAAATACAA
Found at i:12314414 original size:48 final size:48
Alignment explanation
Indices: 12314343--12314438 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
12314333 TCGTAAGAAT
* * * *
12314343 CACTAAGTGCTACATGATGGTTTGGTGTGCTCTTAGTCTTGTGATTAG
1 CACTAAGTACTACATGATAGTTTGGTGTGATCTTAATCTTGTGATTAG
* *
12314391 CACTAAGTACTACATGGTAGTTTGGTGTGATTTTAATCTTGTGATTAG
1 CACTAAGTACTACATGATAGTTTGGTGTGATCTTAATCTTGTGATTAG
12314439 ATTCAGCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (48 bp):
CACTAAGTACTACATGATAGTTTGGTGTGATCTTAATCTTGTGATTAG
Found at i:12324306 original size:33 final size:33
Alignment explanation
Indices: 12324257--12324349 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
12324247 ATGATTATTG
* *
12324257 CTAACTATTATAACCCGTTAGCCAGGGCTTACA
1 CTAACTACTATTACCCGTTAGCCAGGGCTTACA
12324290 CTAACTACTATTACCCGTTAGCCAGGGCTTACA
1 CTAACTACTATTACCCGTTAGCCAGGGCTTACA
12324323 CTAACTACTATTACCCGTTAGCCAGGG
1 CTAACTACTATTACCCGTTAGCCAGGG
12324350 TCATACGATA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (33 bp):
CTAACTACTATTACCCGTTAGCCAGGGCTTACA
Found at i:12336949 original size:35 final size:35
Alignment explanation
Indices: 12336895--12336962 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
12336885 GGTACTATCG
* *
12336895 TGGAATAATTCTTGATGATTTAATCTCGAATTTAA
1 TGGAATAAATCTTGATGATTCAATCTCGAATTTAA
*
12336930 TGGAATAAATCTT-AGTGATTCAATCTCGGATTT
1 TGGAATAAATCTTGA-TGATTCAATCTCGAATTT
12336963 GTTAGGCGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (35 bp):
TGGAATAAATCTTGATGATTCAATCTCGAATTTAA
Found at i:12341756 original size:27 final size:28
Alignment explanation
Indices: 12341708--12341788 Score: 110
Period size: 27 Copynumber: 2.9 Consensus size: 28
12341698 ATAAAATCAT
* *
12341708 CACTTGTAAGATTTCAACCAATCTTTTG
1 CACTTGTAAGATTTCAAACAATCATTTG
* *
12341736 CCCTTGTAA-AATTCAAACAATCATTTG
1 CACTTGTAAGATTTCAAACAATCATTTG
*
12341763 CACTTGTAAGATTTCAAACGATCATT
1 CACTTGTAAGATTTCAAACAATCATT
12341789 CTTAACCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 23 0.51
28 22 0.49
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (28 bp):
CACTTGTAAGATTTCAAACAATCATTTG
Found at i:12343731 original size:48 final size:47
Alignment explanation
Indices: 12343660--12343751 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
12343650 GTAATCAAGC
* * * *
12343660 CAAATCATGGGTCAATCATTAAAAATCATCATAAATTATCTTTATATA
1 CAAATCATAGATCAATCATT-AAAATCATCATAAATCATCATTATATA
*
12343708 CAAATCATAGATCAATCTTTAAAATCATCATAAATCATCATTAT
1 CAAATCATAGATCAATCATTAAAATCATCATAAATCATCATTAT
12343752 CATTAGTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 22 0.56
48 17 0.44
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (47 bp):
CAAATCATAGATCAATCATTAAAATCATCATAAATCATCATTATATA
Found at i:12346354 original size:5 final size:5
Alignment explanation
Indices: 12346344--12346370 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12346334 CAAGTTTTCC
12346344 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
12346371 TAACCCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:12346465 original size:15 final size:15
Alignment explanation
Indices: 12346447--12346493 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
12346437 TTCTGCCACT
12346447 AATATTTTTGAAAAA
1 AATATTTTTGAAAAA
* *
12346462 AATATATTTAAAAAA
1 AATATTTTTGAAAAA
*
12346477 AATCTTTTTGAAAAA
1 AATATTTTTGAAAAA
12346492 AA
1 AA
12346494 GAAAAAATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (15 bp):
AATATTTTTGAAAAA
Found at i:12351071 original size:20 final size:20
Alignment explanation
Indices: 12351046--12351083 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12351036 ATTATATTAT
12351046 TTTTAATGA-ATTTTTACTTA
1 TTTTAAT-ATATTTTTACTTA
12351066 TTTTAATATATTTTTACT
1 TTTTAATATATTTTTACT
12351084 GTGTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTAATATATTTTTACTTA
Found at i:12351283 original size:20 final size:21
Alignment explanation
Indices: 12351258--12351297 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12351248 AGACTTTTTG
12351258 TTATAT-TAAAAGAAAATATT
1 TTATATCTAAAAGAAAATATT
12351278 TTATATGCTAAAAGAAAATA
1 TTATAT-CTAAAAGAAAATA
12351298 CTTCCAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (21 bp):
TTATATCTAAAAGAAAATATT
Found at i:12353231 original size:20 final size:19
Alignment explanation
Indices: 12353212--12353323 Score: 59
Period size: 19 Copynumber: 5.7 Consensus size: 19
12353202 AGTTCACAAT
12353212 TAAATTCAAAGATTTTCAA
1 TAAATTCAAAGATTTTCAA
* * ** *
12353231 TTTGAATTTAAAGACCTGCAA
1 --TAAATTCAAAGATTTTCAA
*
12353252 -AACATTCAAAG-TTCTCTAA
1 TAA-ATTCAAAGATTTTC-AA
* *
12353271 AAAATTCAAAGATTTGCAAA
1 TAAATTCAAAGATTTTC-AA
12353291 TAAATTCAAA-ATTTTGCAA
1 TAAATTCAAAGATTTT-CAA
* *
12353310 GAAAATCAAAGATT
1 TAAATTCAAAGATT
12353324 CGCAAGGATT
Statistics
Matches: 67, Mismatches: 18, Indels: 13
0.68 0.18 0.13
Matches are distributed among these distances:
18 2 0.03
19 31 0.46
20 20 0.30
21 14 0.21
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (19 bp):
TAAATTCAAAGATTTTCAA
Found at i:12353328 original size:19 final size:20
Alignment explanation
Indices: 12353271--12353329 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
12353261 AGTTCTCTAA
12353271 AAAATTCAAAGATTTGCAA-
1 AAAATTCAAAGATTTGCAAG
12353290 ATAAATTCAAA-ATTTTGCAAG
1 A-AAATTCAAAGA-TTTGCAAG
*
12353311 AAAA-TCAAAGATTCGCAAG
1 AAAATTCAAAGATTTGCAAG
12353330 GATTTAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 14 0.40
20 20 0.57
21 1 0.03
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (20 bp):
AAAATTCAAAGATTTGCAAG
Found at i:12353441 original size:73 final size:73
Alignment explanation
Indices: 12353362--12353510 Score: 237
Period size: 73 Copynumber: 2.0 Consensus size: 73
12353352 AAAATTCATA
* *
12353362 AAAGATTCAAAGGTTTC-CAAAAAATTTCAAGATTTGCAAAGGTTCCCAGATTCATAAAGATTAT
1 AAAGATTCAAA-GATTCGCAAAAAATTTCAAGATTTGCAAAGGTTCCAAGATTCATAAAGATTAT
12353426 AAATTTCAC
65 AAATTTCAC
* * *
12353435 AAAGATTCTAAGATTCGTAAAAGATTTCAAGATTTGCAAAGGTTCCAAGATTCATAAAGATTATA
1 AAAGATTCAAAGATTCGCAAAAAATTTCAAGATTTGCAAAGGTTCCAAGATTCATAAAGATTATA
12353500 AATTTCAC
66 AATTTCAC
12353508 AAA
1 AAA
12353511 TAAATTTCAC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 4 0.06
73 66 0.94
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (73 bp):
AAAGATTCAAAGATTCGCAAAAAATTTCAAGATTTGCAAAGGTTCCAAGATTCATAAAGATTATA
AATTTCAC
Found at i:12353493 original size:18 final size:18
Alignment explanation
Indices: 12353399--12353496 Score: 63
Period size: 18 Copynumber: 5.4 Consensus size: 18
12353389 CAAGATTTGC
* *
12353399 AAAGGTTCCCAGATTCAT
1 AAAGATTCCAAGATTCAT
** *
12353417 AAAGATTATAA-ATTTCAC
1 AAAGATTCCAAGA-TTCAT
* *
12353435 AAAGATTCTAAGATTCGT
1 AAAGATTCCAAGATTCAT
* ***
12353453 AAAAGATTTCAAGATTTGC
1 -AAAGATTCCAAGATTCAT
*
12353472 AAAGGTTCCAAGATTCAT
1 AAAGATTCCAAGATTCAT
12353490 AAAGATT
1 AAAGATT
12353497 ATAAATTTCA
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
17 1 0.02
18 43 0.73
19 15 0.25
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (18 bp):
AAAGATTCCAAGATTCAT
Found at i:12353515 original size:13 final size:13
Alignment explanation
Indices: 12353497--12353523 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12353487 CATAAAGATT
12353497 ATAAATTTCACAA
1 ATAAATTTCACAA
12353510 ATAAATTTCACAA
1 ATAAATTTCACAA
12353523 A
1 A
12353524 GATTCTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAATTTCACAA
Found at i:12353700 original size:54 final size:54
Alignment explanation
Indices: 12353618--12353738 Score: 145
Period size: 54 Copynumber: 2.2 Consensus size: 54
12353608 CGCAAAGATC
* * * * *
12353618 AAAGATCCACAAAAATTCTAAGATTTGCAAAGAATTTCAAAGTTT-AGCAATCGT
1 AAAGATTCATAAAGATTCCAAGATTTGCAAAGAATTTCAAAGTTTCA-CAATCAT
* * * *
12353672 AAAGATTCGTAAAGATTCCAAGATTTGCAAAGAGTTTTAAAGTTTCACAATTAT
1 AAAGATTCATAAAGATTCCAAGATTTGCAAAGAATTTCAAAGTTTCACAATCAT
12353726 AAAGATTCATAAA
1 AAAGATTCATAAA
12353739 TAATTTCAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 55 0.98
55 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (54 bp):
AAAGATTCATAAAGATTCCAAGATTTGCAAAGAATTTCAAAGTTTCACAATCAT
Found at i:12353871 original size:21 final size:21
Alignment explanation
Indices: 12353842--12353910 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
12353832 AAAAAACTTA
12353842 AAAGATTCAAATCTAAGATTC
1 AAAGATTCAAATCTAAGATTC
* * * * *
12353863 AAAGGTTCATATTCAAAAATCTT
1 AAAGATTCA-AATCTAAGAT-TC
* *
12353886 AGAGATTCACATCTAAGATTC
1 AAAGATTCAAATCTAAGATTC
12353907 AAAG
1 AAAG
12353911 GTTTGCATTA
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
21 12 0.36
22 13 0.39
23 8 0.24
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAGATTCAAATCTAAGATTC
Found at i:12353925 original size:44 final size:45
Alignment explanation
Indices: 12353818--12353925 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 45
12353808 CCAAAATTTT
*
12353818 AAAGATTTACATTAAAAAAACTTAAAAGATTCAAATCTAAGATTC
1 AAAGGTTTACATTAAAAAAACTTAAAAGATTCAAATCTAAGATTC
* * * * * *
12353863 AAAGGTTCATATTCAAAAATCTT-AGAGATTCACATCTAAGATTC
1 AAAGGTTTACATTAAAAAAACTTAAAAGATTCAAATCTAAGATTC
*
12353907 AAAGGTTTGCATTAAAAAA
1 AAAGGTTTACATTAAAAAA
12353926 CATTTATTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
44 34 0.65
45 18 0.35
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (45 bp):
AAAGGTTTACATTAAAAAAACTTAAAAGATTCAAATCTAAGATTC
Found at i:12354039 original size:4 final size:4
Alignment explanation
Indices: 12354030--12354101 Score: 65
Period size: 4 Copynumber: 17.8 Consensus size: 4
12354020 AAAAATATTT
* * * *
12354030 ATAA ATAA ATAA ATAC ATAT AT-A GTCAA ATAA ATAAA ATAA ACAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA AT-AA ATAA ATAA ATAA
* *
12354079 ACAA ATAA ACAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATA
12354102 GACAATTATG
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
3 1 0.02
4 47 0.87
5 6 0.11
ACGTcount: A:0.69, C:0.07, G:0.01, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:12360462 original size:27 final size:28
Alignment explanation
Indices: 12360432--12360484 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
12360422 TGAATAACAC
*
12360432 CATATTTTGTA-A-TGATTTATGAATTAA
1 CATATTTTG-ACATTGATTTATAAATTAA
12360459 CATATTTTGACATTGATTTATAAATT
1 CATATTTTGACATTGATTTATAAATT
12360485 TATGATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 10 0.43
28 12 0.52
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (28 bp):
CATATTTTGACATTGATTTATAAATTAA
Found at i:12367573 original size:29 final size:30
Alignment explanation
Indices: 12367508--12367573 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
12367498 GAATGACTCT
*
12367508 TAAATTTTAATGAAATGTTTAATATAATGTC
1 TAAATTTTAA-GAAATGTTTAATATAATATC
* * **
12367539 TGAATTTTAA-AAATTTTTAATATGGTATC
1 TAAATTTTAAGAAATGTTTAATATAATATC
12367568 TAAATT
1 TAAATT
12367574 ATGAATCTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 20 0.69
31 9 0.31
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (30 bp):
TAAATTTTAAGAAATGTTTAATATAATATC
Found at i:12369541 original size:19 final size:19
Alignment explanation
Indices: 12369517--12369553 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
12369507 GGTTTGCCTC
12369517 GTTAAATTTATG-TTTTTGG
1 GTTAAATTT-TGATTTTTGG
12369536 GTTAAATTTTGATTTTTG
1 GTTAAATTTTGATTTTTG
12369554 AAAATTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (19 bp):
GTTAAATTTTGATTTTTGG
Found at i:12371399 original size:86 final size:87
Alignment explanation
Indices: 12371292--12371466 Score: 271
Period size: 86 Copynumber: 2.0 Consensus size: 87
12371282 TTGACTTTTC
* * *
12371292 CTACTTAAGTTGAGTTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCGACTAGAATTATGAAA
1 CTACTTAAGTTGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAA
* * *
12371357 GTTTAATTATCGTTTTATATTT
66 GTGTAATGATCATTTTATATTT
* *
12371379 CTAC-TAAGTTGAATTATAGTGTTTGTCCTTAAGCAAGTTGATTGAGTCAACTAGAATTATAAAA
1 CTACTTAAGTTGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAA
12371443 GTGTAATGATCATTTTATATTT
66 GTGTAATGATCATTTTATATTT
12371465 CT
1 CT
12371467 GTTATACCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 76 0.95
87 4 0.05
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (87 bp):
CTACTTAAGTTGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAA
GTGTAATGATCATTTTATATTT
Found at i:12374739 original size:18 final size:19
Alignment explanation
Indices: 12374693--12374741 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
12374683 ATGTAGCTAT
12374693 CATAAAATCATTCTTTAAA
1 CATAAAATCATTCTTTAAA
12374712 CATAAAATCATTCTTTAAA
1 CATAAAATCATTCTTTAAA
12374731 CAT-AAATCATT
1 CATAAAATCATT
12374742 TTCTCATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
CATAAAATCATTCTTTAAA
Found at i:12384659 original size:189 final size:189
Alignment explanation
Indices: 12384334--12384696 Score: 450
Period size: 189 Copynumber: 1.9 Consensus size: 189
12384324 AATGTTGCAT
** * *
12384334 AGTGGGAACGACCTCTAAAATCTCAATGTCTAGTATGATTCTGTGATTTGTGTGTGATTTGTGTT
1 AGTGGGAACGACCTCTAAAATCTCAACATCTAGTATGATTCTGTGATCTGTGTGTGATTTGTGTC
* * * *
12384399 AGGCTTGCCCAATGCTTGATATGATTTGATAGATCTATGTGCTTTATGATTGACTTGACAGGAAT
66 AGGCTTGCCCAACGCTTGATATGATTCGATAGATCTATGTACTTTATGATTGACTTGACAGGAAC
*
12384464 GTCAAGTTTTAACGA-AGAGAGTTTATAACGCTCCAATCTCACATTGTGATTGACTTGAC
131 GTCAAGTTTTAA-GATAGAGAGTTTATAACGCTCCAATCCCACATTGTGATTGACTTGAC
* * * *
12384523 AGTGGGAATGACCTTTAAAATCTCAACATCTTA-TGTGA-TCTTGTGATCTGTGTGTGCTTTGTG
1 AGTGGGAACGACCTCTAAAATCTCAACATC-TAGTATGATTC-TGTGATCTGTGTGTGATTTGTG
* * *
12384586 TCAGGCTTGCCCAACGCTT-AGTGTGATTCGATGGATCTATGTACTTTGTG-TTGGACTTGAC-G
64 TCAGGCTTGCCCAACGCTTGA-TATGATTCGATAGATCTATGTACTTTATGATT-GACTTGACAG
* * * *
12384648 AGAACGTCAAGTTTTAATATGGAGAGTTTGTAATGCTCCAATCCCACAT
127 -GAACGTCAAGTTTTAAGATAGAGAGTTTATAACGCTCCAATCCCACAT
12384697 CAAGATATTC
Statistics
Matches: 148, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
188 7 0.05
189 139 0.94
190 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (189 bp):
AGTGGGAACGACCTCTAAAATCTCAACATCTAGTATGATTCTGTGATCTGTGTGTGATTTGTGTC
AGGCTTGCCCAACGCTTGATATGATTCGATAGATCTATGTACTTTATGATTGACTTGACAGGAAC
GTCAAGTTTTAAGATAGAGAGTTTATAACGCTCCAATCCCACATTGTGATTGACTTGAC
Found at i:12385880 original size:97 final size:97
Alignment explanation
Indices: 12385694--12385873 Score: 270
Period size: 97 Copynumber: 1.9 Consensus size: 97
12385684 TGAAATTGAC
*
12385694 CCATAAATTATCAACATTTCCCTAATTAAAACCTAGTAACCTATAATGACTTTACCAAACATATG
1 CCATAAATTATAAACATTTCCCTAATTAAAACCTAGTAACCTATAATGACTTTACCAAACATATG
* * **
12385759 AAATATGGAGACTTGCACTCAACCTATGAGAT
66 AAATATGAAAACTCACACTCAACCTATGAGAT
* * * *
12385791 CCATAAATTCTAAACATTTCCTTAATTAAAACCTAGTAACCTATCATGACTTTACCAAACATATT
1 CCATAAATTATAAACATTTCCCTAATTAAAACCTAGTAACCTATAATGACTTTACCAAACATATG
*
12385856 AAATGTGAAAACTCACAC
66 AAATATGAAAACTCACAC
12385874 ATAACCTGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 73 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (97 bp):
CCATAAATTATAAACATTTCCCTAATTAAAACCTAGTAACCTATAATGACTTTACCAAACATATG
AAATATGAAAACTCACACTCAACCTATGAGAT
Found at i:12386088 original size:26 final size:26
Alignment explanation
Indices: 12386059--12386112 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
12386049 ATCACAGGAT
*
12386059 TACACCAGA-TATTGGGATTCTAAAGA
1 TACACCAGACT-TTGAGATTCTAAAGA
*
12386085 TACACCAGACTTTGAGATTTTAAAGA
1 TACACCAGACTTTGAGATTCTAAAGA
12386111 TA
1 TA
12386113 GCTACCACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (26 bp):
TACACCAGACTTTGAGATTCTAAAGA
Found at i:12386967 original size:44 final size:44
Alignment explanation
Indices: 12386885--12386968 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
12386875 TCAAACTCGT
* * ** *
12386885 TAGGATTCTAGAGGTGGCTCTCATCGTATGACATTTAGCTCCCA
1 TAGGATTCTAGAGATGACTCTCATCGTACAACAGTTAGCTCCCA
* *
12386929 TAGGATTCTAGAGATGATTCTCATCGTGCAACAGTTAGCT
1 TAGGATTCTAGAGATGACTCTCATCGTACAACAGTTAGCT
12386969 TTCACAGGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (44 bp):
TAGGATTCTAGAGATGACTCTCATCGTACAACAGTTAGCTCCCA
Found at i:12388743 original size:18 final size:18
Alignment explanation
Indices: 12388722--12388804 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 18
12388712 TATACTTTTT
12388722 AATATAAATATAAAATT-
1 AATATAAATATAAAATTA
12388739 AA-ATAAATATATAAA-TA
1 AATATAAATATA-AAATTA
* *
12388756 TATATAAATAAAAAATTA
1 AATATAAATATAAAATTA
* *
12388774 AATAATTAAT-TAAAAATA
1 AAT-ATAAATATAAAATTA
*
12388792 AATTATATATATA
1 AA-TATAAATATA
12388805 TTGTCAGATC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.20
17 9 0.18
18 24 0.47
19 8 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAAATATAAAATTA
Found at i:12390026 original size:29 final size:29
Alignment explanation
Indices: 12389955--12390026 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
12389945 AATTATTTTT
*
12389955 AATTATAATAAAATATTTAATATAATACTTA
1 AATTAT-AT-AAATATGTAATATAATACTTA
* *
12389986 AATTTTAAAAATATGTAATATAATA-TCTA
1 AATTATATAAATATGTAATATAATACT-TA
12390015 AATTATATAAAT
1 AATTATATAAAT
12390027 CTATTAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.03
29 28 0.80
30 1 0.03
31 5 0.14
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (29 bp):
AATTATATAAATATGTAATATAATACTTA
Found at i:12392065 original size:111 final size:111
Alignment explanation
Indices: 12391947--12392264 Score: 338
Period size: 111 Copynumber: 2.9 Consensus size: 111
12391937 GTTTGGAACC
* **
12391947 AAAAAAAATGAGTTCACACCAAAG-AATCAGGTCCAGGTAAATGCAAAATGCTGCAGACCCACTT
1 AAAAAAAATGAGTTCACACCAAAGAAATCAGGTCAAGGTAAATGC-AAATGCAACAGACCCACTT
*
12392011 -TTTTATTTTCCA-TGTCATTATCTAGTTAGATTCC-CCCACCAAAAAAA
65 CTTTGA--TTCCATTGTCATTATCTAGTTAGATTCCTCCC-CCAAAAAAA
**
12392058 AAAAAAAATGAGTTCACACCAAAGAAATCAGGTCAAGGTAAATGCAAATGCAACAGACTTACTTC
1 AAAAAAAATGAGTTCACACCAAAGAAATCAGGTCAAGGTAAATGCAAATGCAACAGACCCACTTC
12392123 TTTGATTCCATTGTCATTATCTAGTTAGATTCCTCCCCC-------
66 TTTGATTCCATTGTCATTATCTAGTTAGATTCCTCCCCCAAAAAAA
* * * *
12392162 -AAAAAAATGACTTCACACCAAAAAAATCAGTTCAACGTAAACGCATGCAAATGCAACAGACCCA
1 AAAAAAAATGAGTTCACACCAAAGAAATCAGGTCAAGGT-AA---ATGCAAATGCAACAGACCCA
* *
12392226 CTTCTTT-ATTTTTCCATTGTCATTATCTGGTCAGATTCC
62 CTTCTTTGA---TTCCATTGTCATTATCTAGTTAGATTCC
12392265 ACCATTCTCT
Statistics
Matches: 182, Mismatches: 14, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
103 34 0.19
104 2 0.01
106 1 0.01
107 25 0.14
109 26 0.14
110 5 0.03
111 63 0.35
112 26 0.14
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.27
Consensus pattern (111 bp):
AAAAAAAATGAGTTCACACCAAAGAAATCAGGTCAAGGTAAATGCAAATGCAACAGACCCACTTC
TTTGATTCCATTGTCATTATCTAGTTAGATTCCTCCCCCAAAAAAA
Found at i:12392177 original size:103 final size:105
Alignment explanation
Indices: 12392059--12392264 Score: 274
Period size: 103 Copynumber: 1.9 Consensus size: 105
12392049 CCAAAAAAAA
* * * **
12392059 AAAAAAATGAGTTCACACCAAAGAAATCAGGTCAAGGT-AA-ATGCAAATGCAACAGACTTACTT
1 AAAAAAATGACTTCACACCAAAAAAATCAGGTCAACGTAAACATGCAAATGCAACAGACCCACTT
*
12392122 CTTTGA-TTCCATTGTCATTATCTAGTTAGATTCCTCCCCC
66 CTTT-ATTTCCATTGTCATTATCTAGTCAGATTCCTCCCCC
*
12392162 AAAAAAATGACTTCACACCAAAAAAATCAGTTCAACGTAAACGCATGCAAATGCAACAGACCCAC
1 AAAAAAATGACTTCACACCAAAAAAATCAGGTCAACGTAAA--CATGCAAATGCAACAGACCCAC
*
12392227 TTCTTTATTTTTCCATTGTCATTATCTGGTCAGATTCC
64 TTCTTTA--TTTCCATTGTCATTATCTAGTCAGATTCC
12392265 ACCATTCTCT
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
103 34 0.39
104 2 0.02
106 1 0.01
107 25 0.28
109 26 0.30
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (105 bp):
AAAAAAATGACTTCACACCAAAAAAATCAGGTCAACGTAAACATGCAAATGCAACAGACCCACTT
CTTTATTTCCATTGTCATTATCTAGTCAGATTCCTCCCCC
Found at i:12398424 original size:28 final size:28
Alignment explanation
Indices: 12398357--12398425 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
12398347 TAAATTTTAG
* * *
12398357 TAAAA-TGTTTAATGTGATGTTTGAATTT
1 TAAAACTG-TTAATGTGATATTTAAATTA
* *
12398385 TAAAAGTTTTAATGTGATATTTAAATTA
1 TAAAACTGTTAATGTGATATTTAAATTA
*
12398413 TAAATCTGTTAAT
1 TAAAACTGTTAAT
12398426 TAATATAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (28 bp):
TAAAACTGTTAATGTGATATTTAAATTA
Found at i:12402557 original size:19 final size:20
Alignment explanation
Indices: 12402520--12402560 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
12402510 AAGCTTGATT
*
12402520 TTTAAAAAATATATTAAAATA
1 TTTAAAAAATACA-TAAAATA
12402541 TTTAAAAAATACA-AAAATA
1 TTTAAAAAATACATAAAATA
12402560 T
1 T
12402561 GAATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTAAAAAATACATAAAATA
Found at i:12407261 original size:32 final size:32
Alignment explanation
Indices: 12407225--12407286 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
12407215 CATTGAGAGA
*
12407225 TCTTATAAATTTAGACCTTTCTAGAAACAAGG
1 TCTTACAAATTTAGACCTTTCTAGAAACAAGG
12407257 TCTTACAAATTTAGACCTTTCTAGAAACAA
1 TCTTACAAATTTAGACCTTTCTAGAAACAA
12407287 TCTCATTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (32 bp):
TCTTACAAATTTAGACCTTTCTAGAAACAAGG
Found at i:12412051 original size:311 final size:311
Alignment explanation
Indices: 12411488--12412109 Score: 1019
Period size: 311 Copynumber: 2.0 Consensus size: 311
12411478 ACTGAAGCAG
* * * *
12411488 AGTTTATTGCTGCAACAGCTGCTGTTAATCAAGCTTTGTGGCTAAGGAAGATTTTAATCGATCTT
1 AGTTTATTACTACAACAGCTGCTGTTAATCAAGCTTTGTAGCTAAGAAAGATTTTAATCGATCTT
12411553 AACTTAGAGCAGGAGAAAAGCACAAAGATTCTTGTTAACAACCAAGCTGCCATTGCTATCTCTCA
66 AACTTAGAGCAGGAGAAAAGCACAAAGATTCTTGTTAACAACCAAGCTGCCATTGCTATCTCTCA
* * **
12411618 AAATCCTGTGTTTCACAGGAAAACTAAACATTTTAATATCAAATTATTCTTCTTAAGGGAAGTAC
131 AAATCCTATGTTTCACAAGAAAACTAAACATTTTAATATCAAATTATTCTTCTTAAGAAAAGTAC
* * * *
12411683 AGAAAGATGAAGCTGTTGTTTTTGTCTACTGCAAAATAGAAGATCAGGTTGCAGATGTTTTCACC
196 AAAAAGATGAAGCTGTTGTTCTTGTCTACTGCAAAACAAAAGATCAGGTTGCAGATGTTTTCACC
* * * *
12411748 AAGCCACTGCCAGTTAGCAAGTTTGAATTTTTGAGGATAAAACTTGGTGTT
261 AAGCCACTACCAGTTAGCAAGTTTGAATTTCTGAAGACAAAACTTGGTGTT
12411799 AGTTTATTACTACAACAGCTGCTGTTAATCAAGCTTTGTAGCTAAGAAAGATTTTAATCGATCTT
1 AGTTTATTACTACAACAGCTGCTGTTAATCAAGCTTTGTAGCTAAGAAAGATTTTAATCGATCTT
* ** * *
12411864 AACTTAGAGCAGGAGGAAAGCATGAAGATTCTTGTTGACAACCAAGTTGCCATTGCTATCTCTCA
66 AACTTAGAGCAGGAGAAAAGCACAAAGATTCTTGTTAACAACCAAGCTGCCATTGCTATCTCTCA
* * *
12411929 AAATCTTATGTTTCACAAGAAAACTAAACATTTTAATATTAAATTATTCTTCTTAAGAAAAGTAT
131 AAATCCTATGTTTCACAAGAAAACTAAACATTTTAATATCAAATTATTCTTCTTAAGAAAAGTAC
*
12411994 AAAAAGATGGAGCTGTTGTTCTTGTCTACTGCAAAACAAAAGATCAGGTTGCAGATGTTTTCACC
196 AAAAAGATGAAGCTGTTGTTCTTGTCTACTGCAAAACAAAAGATCAGGTTGCAGATGTTTTCACC
12412059 AAGCCACTACCAGTTAGCAAGTTTGAATTTCTGAAGACAAAACTTGGTGTT
261 AAGCCACTACCAGTTAGCAAGTTTGAATTTCTGAAGACAAAACTTGGTGTT
12412110 TGCAGCTCCT
Statistics
Matches: 286, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
311 286 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (311 bp):
AGTTTATTACTACAACAGCTGCTGTTAATCAAGCTTTGTAGCTAAGAAAGATTTTAATCGATCTT
AACTTAGAGCAGGAGAAAAGCACAAAGATTCTTGTTAACAACCAAGCTGCCATTGCTATCTCTCA
AAATCCTATGTTTCACAAGAAAACTAAACATTTTAATATCAAATTATTCTTCTTAAGAAAAGTAC
AAAAAGATGAAGCTGTTGTTCTTGTCTACTGCAAAACAAAAGATCAGGTTGCAGATGTTTTCACC
AAGCCACTACCAGTTAGCAAGTTTGAATTTCTGAAGACAAAACTTGGTGTT
Found at i:12418328 original size:10 final size:10
Alignment explanation
Indices: 12418313--12418342 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
12418303 TAAAGGGAAG
12418313 AAGGAAAAGA
1 AAGGAAAAGA
12418323 AAGGAAAAGA
1 AAGGAAAAGA
12418333 AAGGAAAAGA
1 AAGGAAAAGA
12418343 GGAAAGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAGGAAAAGA
Found at i:12426847 original size:28 final size:28
Alignment explanation
Indices: 12426775--12426854 Score: 110
Period size: 27 Copynumber: 2.9 Consensus size: 28
12426765 CACAAATCAT
*
12426775 CACTTGTAAGATTTCAACCAATC-TTTA
1 CACTTGTAAGATTTCAAACAATCATTTA
* * *
12426802 CCCTTGTAA-AATTCAAACAATCATTTG
1 CACTTGTAAGATTTCAAACAATCATTTA
12426829 CACTTGTAAGATTTCAAACAATCATT
1 CACTTGTAAGATTTCAAACAATCATT
12426855 CTTAACCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.24
27 19 0.42
28 15 0.33
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.35
Consensus pattern (28 bp):
CACTTGTAAGATTTCAAACAATCATTTA
Found at i:12427681 original size:26 final size:27
Alignment explanation
Indices: 12427632--12427713 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
12427622 ATCAACAAAA
*
12427632 TAACTACACCAAGAATTCATTGAATCAT
1 TAACTACTCCAA-AATTCATTGAATCAT
* * * *
12427660 TAATTCCT-CAAAATTCATTGAAACTT
1 TAACTACTCCAAAATTCATTGAATCAT
*
12427686 TAACTACTCCAAAATTCATCGAATCAT
1 TAACTACTCCAAAATTCATTGAATCAT
12427713 T
1 T
12427714 TACTTGTACT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
26 19 0.44
27 19 0.44
28 5 0.12
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (27 bp):
TAACTACTCCAAAATTCATTGAATCAT
Found at i:12428739 original size:16 final size:16
Alignment explanation
Indices: 12428718--12428756 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12428708 ATCATTAAAA
*
12428718 ATCATCGTAAATCATC
1 ATCATCATAAATCATC
12428734 ATCATCATAAATCATC
1 ATCATCATAAATCATC
*
12428750 ATTATCA
1 ATCATCA
12428757 ATGGTTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (16 bp):
ATCATCATAAATCATC
Found at i:12438923 original size:30 final size:31
Alignment explanation
Indices: 12438882--12438958 Score: 129
Period size: 30 Copynumber: 2.5 Consensus size: 31
12438872 TAAGATAACT
12438882 CTTTATTTGGGTTTGATCAATTT-ATTGGGC
1 CTTTATTTGGGTTTGATCAATTTCATTGGGC
* *
12438912 CTTTCTTTGGGTTTGATCAATTTCTTTGGGC
1 CTTTATTTGGGTTTGATCAATTTCATTGGGC
12438943 CTTTATTTGGGTTTGA
1 CTTTATTTGGGTTTGA
12438959 ATTATAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 22 0.51
31 21 0.49
ACGTcount: A:0.13, C:0.12, G:0.23, T:0.52
Consensus pattern (31 bp):
CTTTATTTGGGTTTGATCAATTTCATTGGGC
Found at i:12446862 original size:357 final size:356
Alignment explanation
Indices: 12446142--12447751 Score: 1971
Period size: 357 Copynumber: 4.5 Consensus size: 356
12446132 TATAATAAAT
* * * ** ** *
12446142 TATTAAAGGTGTTTTATAATAAAAGACATCTTTAATAAT-TTAAAAAATTTTTTTGGA-AAATTA
1 TATTGAAGGTGTGTCATAATAAAAGACGCCTTTAATAATCCGAAAAAATTTTTTTAGAGAAATTA
** * * * *
12446205 TTGAAGGCATTGTTATCTGCAATCACCTTTAATAATTATATACAAACTTTGATAGGAATTATTAA
66 TTGAAGGTGTTGTTATCTGCAATCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAA
* *
12446270 AGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGGCAGTATATAGAAG
131 AGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAATATATA-AAG
* * * *
12446335 GTATTTTATAATAAAAGACGCCTTTAATAATTCTTAAAATATTTAGTGAAAAAATTTTGAAGGCG
195 GTATTTTACAGTAGAAGACGCCTTTAATAATTCTTAAAATTTTTAGTGAAAAAATTTTGAAGGCG
*** * *
12446400 TCTGTTATTAACAAACGTTTTTAGTAATAGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTT
260 TCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTT
* *
12446465 TTTAATAAACGTCTTCCATTACCATTGTAGTA
325 TTTAATAAACGCCTTCCATTACCATCGTAGTA
* * *
12446497 TTTTGAAGGTGTTTCATAATAAAAGACGCTTTTAATAATCCGAAAAAATTTTTTTAGAGAAATTA
1 TATTGAAGGTGTGTCATAATAAAAGACGCCTTTAATAATCCGAAAAAATTTTTTTAGAGAAATTA
* * * * * * *
12446562 TTAAAAGCGTTGTTATCTGCAA-CTGCCTTTAGTAATTATTTATAAACTATGATAAGAATTATTA
66 TTGAAGGTGTTGTTATCTGCAATC-GCCTTCAGTAATTATATACAAACTATGATAGGAATTATTA
* * * * ***
12446626 AAGGCATCTTTCTTAGATATAGGCTTTCAATAATAGTGTTAGAATTTGTGTGATGGTATATAACA
130 AAGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAATATATAA-A
* *
12446691 GGCATTTTACAGTAGAAGACGCTTTTAATAATTCTTAAAATTTTTAGTGAAAAAATTTTGAAGGC
194 GGTATTTTACAGTAGAAGACGCCTTTAATAATTCTTAAAATTTTTAGTGAAAAAATTTTGAAGGC
* ** *
12446756 GTCTGTTATTAACAAACACCTTCAGTAATGGATTACGAAGTTTAAAGGTATATTGAAAACATCTT
259 GTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCACCTT
*
12446821 TTTTAATAAACGCCTTCCATTACCATCGTGGTA
324 TTTTAATAAACGCCTTCCATTACCATCGTAGTA
* * * **
12446854 TATTGAAGGTGTGTCATAATAAAAGACACCTTTAACAATCTGAAAAAAACTTTTTAGAGAAATTA
1 TATTGAAGGTGTGTCATAATAAAAGACGCCTTTAATAATCCGAAAAAATTTTTTTAGAGAAATTA
* * * * *
12446919 TTGAAGGTGTTGTTACCTACAATCGCCTTCAGTAATTATCTAAAAACTGTGATAGGAATTATTAA
66 TTGAAGGTGTTGTTATCTGCAATCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAA
* * * * *
12446984 AAGTATCTTTCTTGGATATACACCTTCAATAACACTATTAGAATTTGTGTGACAATATATAAAAG
131 AGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAATATAT-AAAG
* * *
12447049 GTATTTTACAGTAGAAGATGCCTTTAATAATTTTTAAAATTTTTAGTGAAAAAATTTTGAAAGCG
195 GTATTTTACAGTAGAAGACGCCTTTAATAATTCTTAAAATTTTTAGTGAAAAAATTTTGAAGGCG
** * ***
12447114 TCTGTTATTAACAAATGCCTTTA--AATGGATTACTAAGTTTAAAGGTATATTGAAGGTGTC-TT
260 TCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTT
* * *
12447176 TTTAATAAACGCCTTCCATTACAATCATGGTA
325 TTTAATAAACGCCTTCCATTACCATCGTAGTA
* * * * *
12447208 TATTGAAGATGAGTCATAATAAAAGACGCCTTTAATAATTC--AAAAATTTTTTTAAAAAAAAAT
1 TATTGAAGGTGTGTCATAATAAAAGACGCCTTTAATAATCCGAAAAAATTTTTTT--AGAGAAAT
* * * * * **
12447271 TATTGAAGGTTTTGTTACCTGCAATCGCATTCGGTAATTATCTACAAACTATGATAAAAATTATT
64 TATTGAAGGTGTTGTTATCTGCAATCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATT
** * * ** *
12447336 AAAGGTGTCTTTCTTGGATATACACCTTCAATAATAGTGTTAGAATTTGTGTGATGATTTATAAA
129 AAAGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAATATATAAA
* * *
12447401 TGGTATTTTATAGTAGAAGAAGCCTTTAATAATTCTCAAAATTTTTAGTGAAAAAATTTTGAAGG
194 -GGTATTTTACAGTAGAAGACGCCTTTAATAATTCTTAAAATTTTTAGTGAAAAAATTTTGAAGG
* * * **
12447466 CGTCTGTTATTAATAAATACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAATGTGCCT
258 CGTCTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCACCT
** * *
12447531 TTTCGAATAAACGCCTTCTATAACCATCGTAGTA
323 TTTTTAATAAACGCCTTCCATTACCATCGTAGTA
* * * *
12447565 TATTAAAGGCGTGTCATAATAAAAGACGCCTTTAATAATCCAAAAAAAGTTTTTTAG-GAAAATT
1 TATTGAAGGTGTGTCATAATAAAAGACGCCTTTAATAATCCGAAAAAATTTTTTTAGAG-AAATT
* * * * *
12447629 ATTAAAGGTGTTGTTTTCTGCAACCGCCTTCA-CAATTATATACAAACTGTGATAGGAATTATTA
65 ATTGAAGGTGTTGTTATCTGCAATCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTA
* * * * *
12447693 AAGGCATCTTTTTTGGATATACGCCTTCAATAACCGTGTTAAAATTTATGTGACGATAT
130 AAGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAATAT
12447752 GTTCAAAGTG
Statistics
Matches: 1079, Mismatches: 161, Indels: 29
0.85 0.13 0.02
Matches are distributed among these distances:
352 10 0.01
353 3 0.00
354 265 0.25
355 65 0.06
356 128 0.12
357 594 0.55
358 3 0.00
359 11 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (356 bp):
TATTGAAGGTGTGTCATAATAAAAGACGCCTTTAATAATCCGAAAAAATTTTTTTAGAGAAATTA
TTGAAGGTGTTGTTATCTGCAATCGCCTTCAGTAATTATATACAAACTATGATAGGAATTATTAA
AGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGACAATATATAAAGG
TATTTTACAGTAGAAGACGCCTTTAATAATTCTTAAAATTTTTAGTGAAAAAATTTTGAAGGCGT
CTGTTATTAACAAACACCTTCAGTAATGGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTTT
TTAATAAACGCCTTCCATTACCATCGTAGTA
Found at i:12447568 original size:711 final size:711
Alignment explanation
Indices: 12446142--12447726 Score: 2135
Period size: 711 Copynumber: 2.2 Consensus size: 711
12446132 TATAATAAAT
* * * * * *
12446142 TATTAAAGGTGTTTTATAATAAAAGACATCTTTAATAAT-TTAAAAAATTTTTTTGGA-AAATTA
1 TATTAAAGGTGTGTCATAATAAAAGACACCTTTAATAATCTCAAAAAAATTTTTTAGAGAAATTA
** * * *
12446205 TTGAAGGCATTGTTATCTGCAATCACCTTTAATAATTATATACAAACTTTGATAGGAATTATTAA
66 TTGAAGGTGTTGTTATCTGCAATCGCC-TTCATAATTATATACAAACTGTGATAGGAATTATTAA
* * * * *
12446270 AGGCATCTTTCTTGGATATACGCCTTCAATAACAGTGTTAGAATTTGTGTGGCAGTATATAGAAG
130 AGGCATCTTTCTTGGATATACGCCTTCAATAACACTATTAGAATTTGTGTGACAATATATAAAAG
* *
12446335 GTATTTTATAATAAAAGACGCCTTTAATAATTCTTAAAATATTTAGTGAAAAAATTTTGAAGGCG
195 GTATTTTACAATAAAAGACGCCTTTAATAATTCTTAAAATATTTAGTGAAAAAATTTTGAAAGCG
**
12446400 TCTGTTATTAACAAACGTTTTTAGTAATAGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTT
260 TCTGTTATTAACAAACGCCTTTAG-AATAGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTT
* * ** * * ** *
12446465 TTTAATAAACGTCTTCCATTACCATTGTAGTATTTTGAAGGTGTTTCATAATAAAAGACGCTTTT
324 TTTAATAAACGCCTTCCATTACAATCATAGTATATTGAAGATGAGTCATAATAAAAGACGCCTTT
* * * * *
12446530 AATAATCCGAAAAAATTTTTTTAGAGAAATTATTAAAAGCGTTGTTATCTGCAACTGCCTTTAGT
389 AATAATCC-AAAAAATTTTTTTAAAAAAATTATTAAAAGCGTTGTTACCTGCAACTGCATTCAGT
* * * ** *
12446595 AATTATTTATAAACTATGATAAGAATTATTAAAGGCATCTTTCTTAGATATAGGCTTTCAATAAT
453 AATTATCTACAAACTATGATAAAAATTATTAAAGGCATCTTTCTTAGATATACACCTTCAATAAT
* * *
12446660 AGTGTTAGAATTTGTGTGATGGTATATAACAGGCATTTTACAGTAGAAGACGCTTTTAATAATTC
518 AGTGTTAGAATTTGTGTGATGATATATAACAGGCATTTTACAGTAGAAGAAGCCTTTAATAATTC
*
12446725 TTAAAATTTTTAGTGAAAAAATTTTGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATT
583 TCAAAATTTTTAGTGAAAAAATTTTGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATT
* ** * *
12446790 ACGAAGTTTAAAGGTATATTGAAAACATCTTTTTTAATAAACGCCTTCCATTACCATCGTGGTA
648 ACGAAGTTTAAAGGTATATTGAAAACACCTTTTCGAATAAACGCCTTCCATAACCATCGTAGTA
* * * *
12446854 TATTGAAGGTGTGTCATAATAAAAGACACCTTTAACAATCTGAAAAAAACTTTTTAGAGAAATTA
1 TATTAAAGGTGTGTCATAATAAAAGACACCTTTAATAATCTCAAAAAAATTTTTTAGAGAAATTA
* * * *
12446919 TTGAAGGTGTTGTTACCTACAATCGCCTTCAGTAATTATCTAAAAACTGTGATAGGAATTATTAA
66 TTGAAGGTGTTGTTATCTGCAATCGCCTTCA-TAATTATATACAAACTGTGATAGGAATTATTAA
* * *
12446984 AAGTATCTTTCTTGGATATACACCTTCAATAACACTATTAGAATTTGTGTGACAATATATAAAAG
130 AGGCATCTTTCTTGGATATACGCCTTCAATAACACTATTAGAATTTGTGTGACAATATATAAAAG
* * * * *
12447049 GTATTTTACAGTAGAAGATGCCTTTAATAATTTTTAAAATTTTTAGTGAAAAAATTTTGAAAGCG
195 GTATTTTACAATAAAAGACGCCTTTAATAATTCTTAAAATATTTAGTGAAAAAATTTTGAAAGCG
* * ***
12447114 TCTGTTATTAACAAATGCCTTTA-AATGGATTACTAAGTTTAAAGGTATATTGAAGGTGTC-TTT
260 TCTGTTATTAACAAACGCCTTTAGAATAGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTTT
*
12447177 TTAATAAACGCCTTCCATTACAATCATGGTATATTGAAGATGAGTCATAATAAAAGACGCCTTTA
325 TTAATAAACGCCTTCCATTACAATCATAGTATATTGAAGATGAGTCATAATAAAAGACGCCTTTA
* * * ** *
12447242 ATAATTC-AAAAATTTTTTTAAAAAAAAATTATTGAAGGTTTTGTTACCTGCAA-TCGCATTCGG
390 ATAATCCAAAAAATTTTTTT--AAAAAAATTATTAAAAGCGTTGTTACCTGCAACT-GCATTCAG
** *
12447305 TAATTATCTACAAACTATGATAAAAATTATTAAAGGTGTCTTTCTTGGATATACACCTTCAATAA
452 TAATTATCTACAAACTATGATAAAAATTATTAAAGGCATCTTTCTTAGATATACACCTTCAATAA
* * *
12447370 TAGTGTTAGAATTTGTGTGATGATTTATAA-ATGGTATTTTATAGTAGAAGAAGCCTTTAATAAT
517 TAGTGTTAGAATTTGTGTGATGATATATAACA-GGCATTTTACAGTAGAAGAAGCCTTTAATAAT
* *
12447434 TCTCAAAATTTTTAGTGAAAAAATTTTGAAGGCGTCTGTTATTAATAAATACCTTCAGTAATGGA
581 TCTCAAAATTTTTAGTGAAAAAATTTTGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGA
* **** *
12447499 TTACTAAGTTTAAAGGTATATTGAATGTGCCTTTTCGAATAAACGCCTTCTATAACCATCGTAGT
646 TTACGAAGTTTAAAGGTATATTGAAAACACCTTTTCGAATAAACGCCTTCCATAACCATCGTAGT
12447564 A
711 A
* *
12447565 TATTAAAGGCGTGTCATAATAAAAGACGCCTTTAATAATC-CAAAAAAAGTTTTTTAG-GAAAAT
1 TATTAAAGGTGTGTCATAATAAAAGACACCTTTAATAATCTCAAAAAAA-TTTTTTAGAG-AAAT
* * * *
12447628 TATTAAAGGTGTTGTTTTCTGCAACCGCCTTCACAATTATATACAAACTGTGATAGGAATTATTA
64 TATTGAAGGTGTTGTTATCTGCAATCGCCTTCATAATTATATACAAACTGTGATAGGAATTATTA
*
12447693 AAGGCATCTTTTTTGGATATACGCCTTCAATAAC
129 AAGGCATCTTTCTTGGATATACGCCTTCAATAAC
12447727 CGTGTTAAAA
Statistics
Matches: 756, Mismatches: 108, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
709 12 0.02
710 69 0.09
711 398 0.53
712 67 0.09
713 17 0.02
714 193 0.26
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (711 bp):
TATTAAAGGTGTGTCATAATAAAAGACACCTTTAATAATCTCAAAAAAATTTTTTAGAGAAATTA
TTGAAGGTGTTGTTATCTGCAATCGCCTTCATAATTATATACAAACTGTGATAGGAATTATTAAA
GGCATCTTTCTTGGATATACGCCTTCAATAACACTATTAGAATTTGTGTGACAATATATAAAAGG
TATTTTACAATAAAAGACGCCTTTAATAATTCTTAAAATATTTAGTGAAAAAATTTTGAAAGCGT
CTGTTATTAACAAACGCCTTTAGAATAGATTACTAAGTTTAAAGGTATATTGAAGGCACCTTTTT
TAATAAACGCCTTCCATTACAATCATAGTATATTGAAGATGAGTCATAATAAAAGACGCCTTTAA
TAATCCAAAAAATTTTTTTAAAAAAATTATTAAAAGCGTTGTTACCTGCAACTGCATTCAGTAAT
TATCTACAAACTATGATAAAAATTATTAAAGGCATCTTTCTTAGATATACACCTTCAATAATAGT
GTTAGAATTTGTGTGATGATATATAACAGGCATTTTACAGTAGAAGAAGCCTTTAATAATTCTCA
AAATTTTTAGTGAAAAAATTTTGAAGGCGTCTGTTATTAACAAACACCTTCAGTAATGGATTACG
AAGTTTAAAGGTATATTGAAAACACCTTTTCGAATAAACGCCTTCCATAACCATCGTAGTA
Found at i:12467521 original size:35 final size:35
Alignment explanation
Indices: 12467457--12467523 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
12467447 GATGTATGGG
* *
12467457 TGCATATGGGTATGCGTTTGGTTATGTTGAAAGGA
1 TGCACATGGGTATGCGTTTGGTTAGGTTGAAAGGA
* * *
12467492 TGCACATGGGTATGTGTTTGTTTGGGTTGAAA
1 TGCACATGGGTATGCGTTTGGTTAGGTTGAAA
12467524 ATACTCTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.21, C:0.06, G:0.34, T:0.39
Consensus pattern (35 bp):
TGCACATGGGTATGCGTTTGGTTAGGTTGAAAGGA
Found at i:12472145 original size:124 final size:124
Alignment explanation
Indices: 12471951--12472257 Score: 293
Period size: 125 Copynumber: 2.5 Consensus size: 124
12471941 TTTTTTGAAA
* * * * ** *
12471951 AAAAAAATGCCATCAATAATTCCTTCCAATTTTTTTGAGGAGAGTATTTG-AGGCGTTTTTT-TG
1 AAAAAAATGCCTTTAATAATTCCTTCTAA-TTTTAT-AAAAGATTA-TTGAAGGCGTTTTTTAT-
* * ** *
12472014 ACAAAAATGCTTTCAATAATCCCCTTTAA-TTTTTTAAAAGGGATTATTAAAGGTATTTTCT-G
62 A-GAAAATGCCTTCAATAATCCCCTCCAATTTTTTTAAAAGGGATTATTAAAGGCATTTTCTAG
* * * *
12472076 CAAAAAATGCTTTTAAT-ATTGCCCTTC-ATTTTATATGAAAAGATTATTGAATGCGTTTTTTAT
1 AAAAAAATGCCTTTAATAATT--CCTTCTAATTT-TAT-AAAAGATTATTGAAGGCGTTTTTTAT
* * * * *
12472139 AGAAAATGCCTTCAATAATCCTCTCCAATTTTTTTAGAGGGGATTATTGAAGGCATTTTCTAT
62 AGAAAATGCCTTCAATAATCCCCTCCAATTTTTTTAAAAGGGATTATTAAAGGCATTTTCTAG
*
12472202 AAAAAAATGCCTTTAATAATTCCTTCTAATTTTATAAGAGATTATTGAAGGCGTTT
1 AAAAAAATGCCTTTAATAATTCCTTCTAATTTTATAAAAGATTATTGAAGGCGTTT
12472258 CAGGTAAAAA
Statistics
Matches: 148, Mismatches: 25, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
124 50 0.34
125 70 0.47
126 25 0.17
127 3 0.02
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (124 bp):
AAAAAAATGCCTTTAATAATTCCTTCTAATTTTATAAAAGATTATTGAAGGCGTTTTTTATAGAA
AATGCCTTCAATAATCCCCTCCAATTTTTTTAAAAGGGATTATTAAAGGCATTTTCTAG
Found at i:12472282 original size:124 final size:124
Alignment explanation
Indices: 12472016--12472270 Score: 275
Period size: 124 Copynumber: 2.1 Consensus size: 124
12472006 TTTTTTTGAC
* * ** * *
12472016 AAAAATGCTTTCAATAATCCCCTTTAA-TTTTTTAAAAGGGATTATTAAAGGTATTTTCTGCAAA
1 AAAAATGCCTTCAATAATCCTCTCCAATTTTTTTAAAAGGGATTATTAAAGGCATTTTCTGAAAA
* * * ***
12472080 AAATGCTTTTAATATTGCCCTTCATTTTATATGAAAAGATTATTGAATGCGTTTTTTATA
66 AAATGCCTTTAATATT-CCCTTCAATTTATATGAAAAGATTATTGAAGGCGTTTCAGATA
* * * * *
12472140 GAAAATGCCTTCAATAATCCTCTCCAATTTTTTTAGAGGGGATTATTGAAGGCATTTTCTATAAA
1 AAAAATGCCTTCAATAATCCTCTCCAATTTTTTTAAAAGGGATTATTAAAGGCATTTTCT-GAAA
* *
12472205 AAAATGCCTTTAATAATT-CCTTCTAATTT-TAT-AAGAGATTATTGAAGGCGTTTCAGGTA
65 AAAATGCCTTTAAT-ATTCCCTTC-AATTTATATGAAAAGATTATTGAAGGCGTTTCAGATA
12472264 AAAAATG
1 AAAAATG
12472271 TCTTAACTAA
Statistics
Matches: 107, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
124 49 0.46
125 36 0.34
126 19 0.18
127 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (124 bp):
AAAAATGCCTTCAATAATCCTCTCCAATTTTTTTAAAAGGGATTATTAAAGGCATTTTCTGAAAA
AAATGCCTTTAATATTCCCTTCAATTTATATGAAAAGATTATTGAAGGCGTTTCAGATA
Found at i:12479141 original size:21 final size:21
Alignment explanation
Indices: 12479115--12479160 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
12479105 TATGGTTTAC
12479115 AAGTTTAAAAAACAATTGTCT
1 AAGTTTAAAAAACAATTGTCT
*
12479136 AAGTTTAAAAAATAATTGTCT
1 AAGTTTAAAAAACAATTGTCT
12479157 AAGT
1 AAGT
12479161 CCTTTGACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (21 bp):
AAGTTTAAAAAACAATTGTCT
Found at i:12486052 original size:2 final size:2
Alignment explanation
Indices: 12486045--12486072 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12486035 TAATGGCCAA
12486045 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12486073 TCAACCATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12494316 original size:23 final size:23
Alignment explanation
Indices: 12494290--12494337 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
12494280 TGCAGCTTCT
12494290 CTTTATTGTTTGTATTTTAATTG
1 CTTTATTGTTTGTATTTTAATTG
12494313 CTTTATTGTTTGTATTTTAATTG
1 CTTTATTGTTTGTATTTTAATTG
12494336 CT
1 CT
12494338 CTTTTGATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.06, G:0.12, T:0.65
Consensus pattern (23 bp):
CTTTATTGTTTGTATTTTAATTG
Found at i:12495008 original size:31 final size:32
Alignment explanation
Indices: 12494951--12495017 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
12494941 ACGAAATTAT
12494951 TAGTATAAAGTTTTTTCTATGTGTTGAAAATGA
1 TAGTATAAAGTTTTTTC-ATGTGTTGAAAATGA
*
12494984 TAGTATAAAGTTTTTTC-TGTGTTGAAATTGA
1 TAGTATAAAGTTTTTTCATGTGTTGAAAATGA
12495015 TAG
1 TAG
12495018 GTGAGTTTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 16 0.48
33 17 0.52
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.46
Consensus pattern (32 bp):
TAGTATAAAGTTTTTTCATGTGTTGAAAATGA
Found at i:12499754 original size:16 final size:16
Alignment explanation
Indices: 12499733--12499765 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12499723 ATTAAAAATC
*
12499733 ATCATAAATGATCATT
1 ATCATAAATCATCATT
12499749 ATCATAAATCATCATT
1 ATCATAAATCATCATT
12499765 A
1 A
12499766 ACATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (16 bp):
ATCATAAATCATCATT
Found at i:12503458 original size:20 final size:20
Alignment explanation
Indices: 12503421--12503458 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12503411 TTTTAATTTA
*
12503421 AAATAAGAAATAATAAAAGC
1 AAATAAGAAATAACAAAAGC
12503441 AAATAA-AAATAAACAAAA
1 AAATAAGAAAT-AACAAAA
12503459 TAAGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (20 bp):
AAATAAGAAATAACAAAAGC
Found at i:12505409 original size:86 final size:86
Alignment explanation
Indices: 12505295--12505461 Score: 237
Period size: 86 Copynumber: 1.9 Consensus size: 86
12505285 AACTTCGTAG
* * ** * *
12505295 AGGTTATAGATTCACAAAGGCTCCAGGTTTGCAAGGACTTTTAAATTCACAAGAAAGAAAGATTT
1 AGGTTATAGATTCACAAAGGATCAAGGTTCACAAGGACTTTCAAATTCACAAGAAAGAAAGATTC
12505360 ACAAGATTTCAAGTTTTGTAA
66 ACAAGATTTCAAGTTTTGTAA
* *
12505381 AGGTTCTAGATTCACAAA-GATGCAAGGTTCATAAGGACTTTCAAATTCACAAGAAAGAAAGATT
1 AGGTTATAGATTCACAAAGGAT-CAAGGTTCACAAGGACTTTCAAATTCACAAGAAAGAAAGATT
*
12505445 CGCAAGATTTCAAGTTT
65 CACAAGATTTCAAGTTT
12505462 CACAAAGGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 2 0.03
86 69 0.97
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (86 bp):
AGGTTATAGATTCACAAAGGATCAAGGTTCACAAGGACTTTCAAATTCACAAGAAAGAAAGATTC
ACAAGATTTCAAGTTTTGTAA
Found at i:12505591 original size:17 final size:17
Alignment explanation
Indices: 12505569--12505605 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12505559 TCAAGTTCAC
12505569 AAGATACAAGATTCGCA
1 AAGATACAAGATTCGCA
* *
12505586 AAGATATAAGATTTGCA
1 AAGATACAAGATTCGCA
12505603 AAG
1 AAG
12505606 GTGCAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (17 bp):
AAGATACAAGATTCGCA
Found at i:12505629 original size:68 final size:69
Alignment explanation
Indices: 12505395--12505684 Score: 324
Period size: 69 Copynumber: 4.2 Consensus size: 69
12505385 TCTAGATTCA
* *
12505395 CAAAGATGCAAGGTTCATAAGGACTTTCAA-ATTCACAAGAAAGAAAGATTCGCAAGATTTCAAG
1 CAAAGGTGCAAGGTTCACAAGGACTTTCAAGATTCACAAGAAA-AAAGATTCGCAAGATTTCAAG
*
12505459 TTTCA
65 TTTCG
* * *
12505464 CAAAGGTGCAAGGTTCACAAGGACTTT-TAGATTCGCAAGACAAAAAGATTTGCAAGACTTT-AA
1 CAAAGGTGCAAGGTTCACAAGGACTTTCAAGATTCACAAGA-AAAAAGATTCGCAAGA-TTTCAA
*
12505527 GTTTTG
64 GTTTCG
* ** * * * *
12505533 TAAATATGCAAGGTTCACAAGGATTTTCAAG-TTCACAAGATACAAGATTCGCAAAGATAT-AAG
1 CAAAGGTGCAAGGTTCACAAGGACTTTCAAGATTCACAAGAAAAAAGATTCGC-AAGATTTCAAG
12505596 ATTT-G
65 -TTTCG
* * * *
12505601 CAAAGGTGCAAGGTTCACAAAGACTTTC-AGATTCACGAGAAAAAATATTCGTAAGATTTCAAGT
1 CAAAGGTGCAAGGTTCACAAGGACTTTCAAGATTCACAAGAAAAAAGATTCGCAAGATTTCAAGT
12505665 TTCG
66 TTCG
12505669 CAAAGGTGCAAGGTTC
1 CAAAGGTGCAAGGTTC
12505685 GCAAAGATGC
Statistics
Matches: 184, Mismatches: 28, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
67 11 0.06
68 75 0.41
69 91 0.49
70 7 0.04
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (69 bp):
CAAAGGTGCAAGGTTCACAAGGACTTTCAAGATTCACAAGAAAAAAGATTCGCAAGATTTCAAGT
TTCG
Found at i:12505680 original size:17 final size:17
Alignment explanation
Indices: 12505660--12505697 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12505650 CGTAAGATTT
* *
12505660 CAAGTTTCGCAAAGGTG
1 CAAGGTTCGCAAAGATG
12505677 CAAGGTTCGCAAAGATG
1 CAAGGTTCGCAAAGATG
12505694 CAAG
1 CAAG
12505698 ATTCATAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.18
Consensus pattern (17 bp):
CAAGGTTCGCAAAGATG
Found at i:12505862 original size:86 final size:86
Alignment explanation
Indices: 12505594--12505863 Score: 260
Period size: 86 Copynumber: 3.2 Consensus size: 86
12505584 CAAAGATATA
* * * * * * * *
12505594 AGATTTGCAAAGGTGCAAGGTTCACAA-AGACTTTCAGATTCACGAGAAA-AAATATTCGTAAGA
1 AGATTCGCAAAGATGCAAGATTCACAAGA-ATTTTCAGGTTCACAAGAAAGAAAAATTCATAAGA
* * * *
12505657 TTTCAAGTTTCGCAAAGGTGCA
65 CTCCAAGTTTCGCAAAGGTTCT
* * *
12505679 AGGTTCGCAAAGATGCAAGATTCATAAGAATTTTCGGGTTCACAAGAAAGAAAAATTCATAAGAC
1 AGATTCGCAAAGATGCAAGATTCACAAGAATTTTCAGGTTCACAAGAAAGAAAAATTCATAAGAC
* *
12505744 TCCAAGTTTTGCAGAGGTTCT
66 TCCAAGTTTCGCAAAGGTTCT
* * * * **
12505765 AAATTTGCAAAGATGCAAGATTCACAAGGATTTTTAGGTTTGCAAGAAAGAAAAATTAGCA-AA-
1 AGATTCGCAAAGATGCAAGATTCACAAGAATTTTCAGGTTCACAAGAAAGAAAAATT--CATAAG
*
12505828 ACTCCAAGTTTCGCAAAGGTTTT
64 ACTCCAAGTTTCGCAAAGGTTCT
*
12505851 AGATTCACAAAGA
1 AGATTCGCAAAGA
12505864 CTTTCAGATT
Statistics
Matches: 149, Mismatches: 32, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
85 38 0.26
86 107 0.72
87 2 0.01
88 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (86 bp):
AGATTCGCAAAGATGCAAGATTCACAAGAATTTTCAGGTTCACAAGAAAGAAAAATTCATAAGAC
TCCAAGTTTCGCAAAGGTTCT
Found at i:12506830 original size:7 final size:7
Alignment explanation
Indices: 12506818--12506885 Score: 59
Period size: 7 Copynumber: 9.7 Consensus size: 7
12506808 TGTCATCATT
12506818 TTTTTTA
1 TTTTTTA
12506825 TTTTTTTA
1 -TTTTTTA
*
12506833 TTTTTTG
1 TTTTTTA
* *
12506840 CTTTTTC
1 TTTTTTA
12506847 TTGTTTT-
1 TT-TTTTA
*
12506854 TTTATT-
1 TTTTTTA
12506860 TTTTTTA
1 TTTTTTA
*
12506867 TGTTTTA
1 TTTTTTA
12506874 TTTTTTA
1 TTTTTTA
12506881 TTTTT
1 TTTTT
12506886 GCTTTTTCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
6 8 0.16
7 31 0.62
8 11 0.22
ACGTcount: A:0.09, C:0.03, G:0.04, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:12506830 original size:8 final size:8
Alignment explanation
Indices: 12506817--12506885 Score: 70
Period size: 8 Copynumber: 8.6 Consensus size: 8
12506807 TTGTCATCAT
12506817 TTTTTTTA
1 TTTTTTTA
12506825 TTTTTTTA
1 TTTTTTTA
**
12506833 TTTTTTGC
1 TTTTTTTA
*
12506841 TTTTTCTTG
1 TTTTT-TTA
12506850 TTTTTTTA
1 TTTTTTTA
12506858 TTTTTTT-
1 TTTTTTTA
*
12506865 TATGTTTTA
1 T-TTTTTTA
12506874 -TTTTTTA
1 TTTTTTTA
12506881 TTTTT
1 TTTTT
12506886 GCTTTTTCTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
7 7 0.14
8 37 0.74
9 6 0.12
ACGTcount: A:0.09, C:0.03, G:0.04, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:12506909 original size:47 final size:49
Alignment explanation
Indices: 12506820--12506911 Score: 136
Period size: 47 Copynumber: 1.9 Consensus size: 49
12506810 TCATCATTTT
* *
12506820 TTTTATTTTTTTATTTTTTGCTTTTTCTTGTTTTTTTATTTTTTTTATG
1 TTTTATTTTTTTATTTTTTGCTTTTTCTTCTTTCTTTATTTTTTTTATG
12506869 TTTTA-TTTTTTA-TTTTTGCTTTTTCTTCTTCTCTTT-TTTTTTT
1 TTTTATTTTTTTATTTTTTGCTTTTTCTTCTT-TCTTTATTTTTTT
12506912 CACTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 24 0.60
48 11 0.28
49 5 0.12
ACGTcount: A:0.07, C:0.08, G:0.04, T:0.82
Consensus pattern (49 bp):
TTTTATTTTTTTATTTTTTGCTTTTTCTTCTTTCTTTATTTTTTTTATG
Found at i:12509686 original size:16 final size:16
Alignment explanation
Indices: 12509665--12509698 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12509655 ACGCATAAGA
12509665 ATGAATGCAATG-ATGC
1 ATGAATGC-ATGCATGC
12509681 ATGAATGCATGCATGC
1 ATGAATGCATGCATGC
12509697 AT
1 AT
12509699 AAAAAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (16 bp):
ATGAATGCATGCATGC
Found at i:12511156 original size:20 final size:20
Alignment explanation
Indices: 12511119--12511156 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12511109 TTTTAATTGA
*
12511119 AAATAAGAAATAATAAAAGT
1 AAATAAGAAATAACAAAAGT
12511139 AAATAA-AAATAAACAAAA
1 AAATAAGAAAT-AACAAAA
12511157 TAAGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAAGAAATAACAAAAGT
Found at i:12511165 original size:19 final size:19
Alignment explanation
Indices: 12511143--12511183 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
12511133 AAAAGTAAAT
12511143 AAAAATA-AA-CAAAATAAG
1 AAAAATAGAATCAAAAT-AG
12511161 AAAAATAGAATCAAAATAG
1 AAAAATAGAATCAAAATAG
12511180 AAAA
1 AAAA
12511184 TGGAGTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAATAGAATCAAAATAG
Found at i:12512028 original size:23 final size:23
Alignment explanation
Indices: 12511992--12512039 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12511982 CCTTGGATAG
*
12511992 AAAGTTTTTCTTTT-ATTTTATT
1 AAAGTTTTTCTTTTCAATTTATT
*
12512014 AAAGATTTTTTTTTTCAATTTATT
1 AAAG-TTTTTCTTTTCAATTTATT
12512038 AA
1 AA
12512040 GGAGAGTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (23 bp):
AAAGTTTTTCTTTTCAATTTATT
Found at i:12519742 original size:150 final size:154
Alignment explanation
Indices: 12519442--12519750 Score: 493
Period size: 150 Copynumber: 2.0 Consensus size: 154
12519432 AAAAAAAAAA
* *
12519442 AAAAAGAGAGGGGATCATGATTGAGGAGAGAACATGATTATAACTCTGTTAAACACAAATGACTT
1 AAAAAGAGAGGGGATCATGATTAAGGAGAGAACATGATTATAACTCTGTAAAACACAAA-GAC-T
* *
12519507 AATAGTTAATATTAATTAGTAATTAATAATCTAGAAGATACACGTACATAAAACTTAATATTTTA
64 AATACTTAATACTAATTAGTAATTAATAATCTAGAAGATACACGTACATAAAACTTAATATTTTA
* *
12519572 CATTCTGTGGTTCTTATATTTCAGAC
129 CATTCTATGGTTCTTATATTTCAAAC
12519598 AAAAAGAAGAGGGGATCATGATTAAGGAGAGAACATGATTATAACTCTGTAAAACAC-AA-A-T-
1 AAAAAG-AGAGGGGATCATGATTAAGGAGAGAACATGATTATAACTCTGTAAAACACAAAGACTA
12519659 A-ACTTAATACTAATTAGTAATTAATAATCTAGAAGATACACGTACATAAAACTTAATATTTTAC
65 ATACTTAATACTAATTAGTAATTAATAATCTAGAAGATACACGTACATAAAACTTAATATTTTAC
*
12519723 ATTCTATGGTTCTTGTATTTCAAAC
130 ATTCTATGGTTCTTATATTTCAAAC
12519748 AAA
1 AAA
12519751 TTATCGAATA
Statistics
Matches: 145, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
150 86 0.59
151 1 0.01
152 1 0.01
154 1 0.01
156 8 0.06
157 48 0.33
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (154 bp):
AAAAAGAGAGGGGATCATGATTAAGGAGAGAACATGATTATAACTCTGTAAAACACAAAGACTAA
TACTTAATACTAATTAGTAATTAATAATCTAGAAGATACACGTACATAAAACTTAATATTTTACA
TTCTATGGTTCTTATATTTCAAAC
Found at i:12522891 original size:42 final size:42
Alignment explanation
Indices: 12522868--12523100 Score: 335
Period size: 42 Copynumber: 5.5 Consensus size: 42
12522858 GAGGTGAAAC
* * * * *
12522868 AACTTTGAAAAAATAAATAGCTCCCCTGAATAAAGGCAATAA
1 AACTTTGAAAAAATAAATGGCTCCTCTGAATAGAGGCAACAG
*
12522910 AACTTTGAAAACATAAATGGCTCCTCTGAATAGAGGCAACAG
1 AACTTTGAAAAAATAAATGGCTCCTCTGAATAGAGGCAACAG
* * *
12522952 AACTTTGAAAAAAATAAATGGCTCTTCTGAATAAAGGCAATAG
1 AACTTTG-AAAAAATAAATGGCTCCTCTGAATAGAGGCAACAG
* *
12522995 AACTTTGAAAAAATAAATGGCTCATCTGAATACAGGCAACAG
1 AACTTTGAAAAAATAAATGGCTCCTCTGAATAGAGGCAACAG
12523037 AACTTTG-AAAAATAAATGGCTCCTCTGAATAGAGGCAACACG
1 AACTTTGAAAAAATAAATGGCTCCTCTGAATAGAGGCAACA-G
12523079 -ACTTTGAAAAAATAAATGGCTC
1 AACTTTGAAAAAATAAATGGCTC
12523101 ATTGATAATC
Statistics
Matches: 173, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
41 37 0.21
42 98 0.57
43 38 0.22
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (42 bp):
AACTTTGAAAAAATAAATGGCTCCTCTGAATAGAGGCAACAG
Found at i:12522992 original size:85 final size:84
Alignment explanation
Indices: 12522868--12523102 Score: 355
Period size: 85 Copynumber: 2.8 Consensus size: 84
12522858 GAGGTGAAAC
* * *
12522868 AACTTTGAAAAAATAAATAGCTCCCCTGAATAAAGGCAATAAAACTTTGAAAACATAAATGGCTC
1 AACTTTGAAAAAATAAATGGCTCCTCTGAATAAAGGCAATAAAACTTTGAAAAAATAAATGGCTC
* *
12522933 CTCTGAATAGAGGCAACAG
66 ATCTGAATACAGGCAACAG
* *
12522952 AACTTTGAAAAAAATAAATGGCTCTTCTGAATAAAGGCAATAGAACTTTGAAAAAATAAATGGCT
1 AACTTTG-AAAAAATAAATGGCTCCTCTGAATAAAGGCAATAAAACTTTGAAAAAATAAATGGCT
12523017 CATCTGAATACAGGCAACAG
65 CATCTGAATACAGGCAACAG
* * **
12523037 AACTTTG-AAAAATAAATGGCTCCTCTGAATAGAGGCAACACGACTTTGAAAAAATAAATGGCTC
1 AACTTTGAAAAAATAAATGGCTCCTCTGAATAAAGGCAATAAAACTTTGAAAAAATAAATGGCTC
12523101 AT
66 AT
12523103 TGATAATCAT
Statistics
Matches: 138, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
83 54 0.39
84 7 0.05
85 77 0.56
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (84 bp):
AACTTTGAAAAAATAAATGGCTCCTCTGAATAAAGGCAATAAAACTTTGAAAAAATAAATGGCTC
ATCTGAATACAGGCAACAG
Found at i:12523651 original size:21 final size:21
Alignment explanation
Indices: 12523575--12523652 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
12523565 ATTTCACACC
*
12523575 TCAAAGATTCTT-ATTTTGAAAC
1 TCAAAGATT-TTCA-TTTGAAAT
*
12523597 TCAAAGATTTTCTTTTGAAAT
1 TCAAAGATTTTCATTTGAAAT
* * *
12523618 TTAAAGACTTTCATTCGAAAT
1 TCAAAGATTTTCATTTGAAAT
12523639 TCAAAGATTTTCAT
1 TCAAAGATTTTCAT
12523653 CAAAAAGTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 38 0.81
22 9 0.19
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
TCAAAGATTTTCATTTGAAAT
Found at i:12524099 original size:63 final size:63
Alignment explanation
Indices: 12523998--12524233 Score: 285
Period size: 63 Copynumber: 3.7 Consensus size: 63
12523988 GCTTCTTAGT
* * * * ** *
12523998 ACAAATTTCTTCCTCCATCACTTGATCATTGTTCATGGGCTTCTCAGTACTAGCTATTTCAGA
1 ACAAATTTCATCATCTATCACTTGGTCATCATTCATGGGCTTCTCAGTACTAGCCATTTCAGA
* * * *
12524061 ATAAATTTCATCATCTGTCACTTGGTCATCA-TCTATGGGCTTTTTAGTACTAGCCATTTCAGA
1 ACAAATTTCATCATCTATCACTTGGTCATCATTC-ATGGGCTTCTCAGTACTAGCCATTTCAGA
* * *
12524124 ACAAATTTCATCCTCTATCACTTGGTCATCGTTCATAGGCTTCTCAGTACTAGCCATTTCAGA
1 ACAAATTTCATCATCTATCACTTGGTCATCATTCATGGGCTTCTCAGTACTAGCCATTTCAGA
* * * * *
12524187 ACAAATTTCATCTTTTATCACTTGGTCATCGTTCATGAGCTTTTCAG
1 ACAAATTTCATCATCTATCACTTGGTCATCATTCATGGGCTTCTCAG
12524234 CACCAGTTTC
Statistics
Matches: 148, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
62 2 0.01
63 144 0.97
64 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.39
Consensus pattern (63 bp):
ACAAATTTCATCATCTATCACTTGGTCATCATTCATGGGCTTCTCAGTACTAGCCATTTCAGA
Found at i:12524229 original size:126 final size:126
Alignment explanation
Indices: 12523998--12524230 Score: 342
Period size: 126 Copynumber: 1.8 Consensus size: 126
12523988 GCTTCTTAGT
* * * * *
12523998 ACAAATTTCTTCCTCCATCACTTGATCATTGTTCATGGGCTTCTCAGTACTAGCTATTTCAGAAT
1 ACAAATTTCATCCTCCATCACTTGATCATCGTTCATAGGCTTCTCAGTACTAGCCATTTCAGAAC
* *
12524063 AAATTTCATCATCTGTCACTTGGTCATCATCTATGGGCTTTTTAGTACTAGCCATTTCAGA
66 AAATTTCATCATCTATCACTTGGTCATCATCTATGAGCTTTTTAGTACTAGCCATTTCAGA
* *
12524124 ACAAATTTCATCCTCTATCACTTGGTCATCGTTCATAGGCTTCTCAGTACTAGCCATTTCAGAAC
1 ACAAATTTCATCCTCCATCACTTGATCATCGTTCATAGGCTTCTCAGTACTAGCCATTTCAGAAC
* * *
12524189 AAATTTCATCTTTTATCACTTGGTCATCGT-TCATGAGCTTTT
66 AAATTTCATCATCTATCACTTGGTCATCATCT-ATGAGCTTTT
12524231 CAGCACCAGT
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
125 1 0.01
126 93 0.99
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (126 bp):
ACAAATTTCATCCTCCATCACTTGATCATCGTTCATAGGCTTCTCAGTACTAGCCATTTCAGAAC
AAATTTCATCATCTATCACTTGGTCATCATCTATGAGCTTTTTAGTACTAGCCATTTCAGA
Found at i:12524709 original size:15 final size:16
Alignment explanation
Indices: 12524683--12524716 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12524673 CATTGGGATG
12524683 AATGAGATATTCAAAC
1 AATGAGATATTCAAAC
*
12524699 AATGA-ATATTCAAGC
1 AATGAGATATTCAAAC
12524714 AAT
1 AAT
12524717 TCTAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (16 bp):
AATGAGATATTCAAAC
Found at i:12529632 original size:193 final size:195
Alignment explanation
Indices: 12529243--12529637 Score: 474
Period size: 193 Copynumber: 2.1 Consensus size: 195
12529233 CAACCAAAAA
*
12529243 TTTTTTGTTTCGAAAAAGAATACAATTACTTTTATTGAAATTTTCATCTAAATTATTTCACCATT
1 TTTTTTGTTTCGAAAAAGAATACAATTACTTTTATTGAAACTTTCATCTAAATTATTTCACCATT
* * * ** *
12529308 TGAGATAAATTTAGAGAAAATTTCTCACTTAGAGATTTCTTAGGAATTTACTATTTGAAATTTTT
66 TGAGATAAATTTAGAGAAAATTTCTCACCTAAAAATTTCTTAAAAATTTACCATTTGAAATTTTT
** *
12529373 AAAAATCTCATCATAAGGTAATTTGTATTTAATTCACACAATTTTTATATTTTTTTCATTTTTAT
131 AAAAATCTCATCATAAGGTAATTAATATTTAATTCACAAAATTTTTATATTTTTTTCATTTTTAT
*
12529438 TTTTTTGTTT-GAAAATA-AATATTAATTA-TTGTTATTGAAACTTT-ATCTAAATTATTTCACC
1 TTTTTTGTTTCGAAAA-AGAATA-CAATTACTT-TTATTGAAACTTTCATCTAAATTATTTCACC
* *
12529499 ATTT-AGGTCAAATTTAGA-CAAATTTCTCACCTAAAAATTT-TATAAAAATTTACCATTTGAAA
63 ATTTGAGAT-AAATTTAGAGAAAATTTCTCACCTAAAAATTTCT-TAAAAATTTACCATTTGAAA
* * * * *
12529561 TTTTTATAAAT-TCCTCAT-TGGATAATTAATATTT-ATTCCCAAAATTTTTAT-TTTTATT-AT
126 TTTTTAAAAATCTCATCATAAGG-TAATTAATATTTAATTCACAAAATTTTTATATTTTTTTCAT
12529621 TTTTAT
190 TTTTAT
12529627 TTATTTT-TTTC
1 TT-TTTTGTTTC
12529638 ATGAAAAAAT
Statistics
Matches: 174, Mismatches: 18, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
189 13 0.07
190 10 0.06
191 17 0.10
192 17 0.10
193 48 0.28
194 41 0.24
195 28 0.16
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (195 bp):
TTTTTTGTTTCGAAAAAGAATACAATTACTTTTATTGAAACTTTCATCTAAATTATTTCACCATT
TGAGATAAATTTAGAGAAAATTTCTCACCTAAAAATTTCTTAAAAATTTACCATTTGAAATTTTT
AAAAATCTCATCATAAGGTAATTAATATTTAATTCACAAAATTTTTATATTTTTTTCATTTTTAT
Found at i:12538665 original size:5 final size:5
Alignment explanation
Indices: 12538655--12538687 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
12538645 AATAAGAGGA
12538655 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
12538688 AGATTGAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:12546229 original size:41 final size:41
Alignment explanation
Indices: 12546167--12546358 Score: 215
Period size: 41 Copynumber: 4.4 Consensus size: 41
12546157 ATGATTGTCA
12546167 AGGAGCAATTTA-TTTTCCAAAGTCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTCATGGTGCCTCTGTTTAG
12546208 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAA------GT-CA----TGGTGCCTCTGTTTAG
* * *
12546260 AGGAACAATTTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAA-TTTACTTTTCAAAGTCATGGTGCCTCTGTTTAG
* *
12546302 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAG
12546343 AGGAGCAATTTACTTT
1 AGGAGCAATTTACTTT
12546359 CCCATTTAGA
Statistics
Matches: 132, Mismatches: 6, Indels: 26
0.80 0.04 0.16
Matches are distributed among these distances:
41 63 0.48
42 27 0.20
46 1 0.01
47 4 0.03
48 2 0.02
52 23 0.17
53 12 0.09
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAG
Found at i:12546270 original size:52 final size:53
Alignment explanation
Indices: 12546187--12546291 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 53
12546177 TATTTTCCAA
*
12546187 AGTCATGGTGCCTCTGTTTAGAGGAGCAA-TTTACTTTTCAAAGTCGTGGTGC
1 AGTCATGGTGCCTCTGTTTAGAGGAACAATTTTACTTTTCAAAGTCGTGGTGC
* *
12546239 AGTCGTGGTGCCTCTGTTTAGAGGAACAATTTTATTTTTCAAAGTCGTGGTGC
1 AGTCATGGTGCCTCTGTTTAGAGGAACAATTTTACTTTTCAAAGTCGTGGTGC
12546292 CTCTGTTTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 27 0.55
53 22 0.45
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (53 bp):
AGTCATGGTGCCTCTGTTTAGAGGAACAATTTTACTTTTCAAAGTCGTGGTGC
Found at i:12546366 original size:25 final size:25
Alignment explanation
Indices: 12546338--12546385 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12546328 GGTGCCTCTG
12546338 TTTAGAGGAGCAATTTACTTTCCCA
1 TTTAGAGGAGCAATTTACTTTCCCA
12546363 TTTAGAGGAGCAATTTACTTTCC
1 TTTAGAGGAGCAATTTACTTTCC
12546386 AAAAGTCGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (25 bp):
TTTAGAGGAGCAATTTACTTTCCCA
Found at i:12546412 original size:67 final size:66
Alignment explanation
Indices: 12546297--12546427 Score: 253
Period size: 67 Copynumber: 2.0 Consensus size: 66
12546287 GGTGCCTCTG
12546297 TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCC
1 TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCC
12546362 A
66 A
12546363 TTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC
1 TTTAGAGGAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC
12546428 AAAGTCGTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
66 23 0.36
67 41 0.64
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (66 bp):
TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCC
A
Found at i:12546422 original size:42 final size:41
Alignment explanation
Indices: 12546363--12546591 Score: 201
Period size: 42 Copynumber: 5.3 Consensus size: 41
12546353 TACTTTCCCA
12546363 TTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTG
1 TTTAGAGGAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTG
*
12546405 TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTACCTCTG
1 TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTG
12546446 TTTAGAGGAACAATTTAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTG
1 TTT--A-G--------AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTG
* * * * *
12546498 TTTAGAGGAGTAATTTATTTTTCCAAAGTTGTTGAGCCTCTG
1 TTTAGAGGAGCAATTTA-CTTTCCAAAGTCGTGGTGCCTCTG
* * * * * *
12546540 ATTAGAGGAGCCATTTATTTTTTTCAAAGT--TTGAGCCTCTG
1 TTTAGAGGAGCAATTTA--CTTTCCAAAGTCGTGGTGCCTCTG
12546581 TTTAGAGGAGC
1 TTTAGAGGAGC
12546592 TTTGGTTAAA
Statistics
Matches: 162, Mismatches: 12, Indels: 27
0.81 0.06 0.13
Matches are distributed among these distances:
41 52 0.32
42 57 0.35
43 12 0.07
44 1 0.01
49 1 0.01
50 1 0.01
52 38 0.23
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (41 bp):
TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTG
Found at i:12546444 original size:108 final size:101
Alignment explanation
Indices: 12546255--12546556 Score: 352
Period size: 108 Copynumber: 3.0 Consensus size: 101
12546245 GGTGCCTCTG
* * *
12546255 TTTAGAGGAACAATTTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC
1 TTTAGAGGAGCAA-TTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC
* *
12546320 AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCCA
65 AAAGTCGTGGTACCTCTGTTTAGAGGAGC-ATTTA-----CAA
12546363 TTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC
1 TTTAGAGGAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC
12546428 AAAGTCGTGGTACCTCTGTTTAGA-G-G-A---ACAA
65 AAAGTCGTGGTACCTCTGTTTAGAGGAGCATTTACAA
* *
12546459 TTT--AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGTAATTTATTTTTCC
1 TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTCC
* * *
12546522 AAAGTTGTTG-AGCCTCTGATTAGAGGAGCCATTTA
65 AAAGTCGTGGTA-CCTCTGTTTAGAGGAG-CATTTA
12546557 TTTTTTTCAA
Statistics
Matches: 174, Mismatches: 10, Indels: 27
0.82 0.05 0.13
Matches are distributed among these distances:
93 35 0.20
94 42 0.24
95 1 0.01
96 6 0.03
98 1 0.01
101 2 0.01
104 1 0.01
106 1 0.01
107 9 0.05
108 76 0.44
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (101 bp):
TTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCA
AAGTCGTGGTACCTCTGTTTAGAGGAGCATTTACAA
Found at i:12546556 original size:94 final size:94
Alignment explanation
Indices: 12546368--12546548 Score: 285
Period size: 94 Copynumber: 1.9 Consensus size: 94
12546358 TCCCATTTAG
12546368 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
1 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
*
12546433 CGTGGTACCTCTGTTTAGAGGAACAATTT
66 CGTGGTACCTCTGATTAGAGGAACAATTT
* *
12546462 AGGAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGTAATTTATTTTTCCAAAG
1 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-CTTTCCAAAG
* *
12546526 TTGTTG-AGCCTCTGATTAGAGGA
65 TCGTGGTA-CCTCTGATTAGAGGA
12546549 GCCATTTATT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
93 35 0.44
94 45 0.56
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (94 bp):
AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
CGTGGTACCTCTGATTAGAGGAACAATTT
Found at i:12546622 original size:10 final size:9
Alignment explanation
Indices: 12546599--12546658 Score: 61
Period size: 10 Copynumber: 6.4 Consensus size: 9
12546589 AGCTTTGGTT
12546599 AAAAA-AAA
1 AAAAACAAA
12546607 AAAAACAAA
1 AAAAACAAA
12546616 AACAAACAAA
1 AA-AAACAAA
12546626 AAAAATCAAA
1 AAAAA-CAAA
12546636 AGTAAAA-AAA
1 A--AAAACAAA
*
12546646 AAAATCAAA
1 AAAAACAAA
12546655 AAAA
1 AAAA
12546659 TGAAAATGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
8 8 0.18
9 15 0.33
10 18 0.40
12 4 0.09
ACGTcount: A:0.85, C:0.08, G:0.02, T:0.05
Consensus pattern (9 bp):
AAAAACAAA
Found at i:12546628 original size:20 final size:19
Alignment explanation
Indices: 12546600--12546656 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
12546590 GCTTTGGTTA
*
12546600 AAAAAAAAAAAACAAAAAC
1 AAAAAAAAAAATCAAAAAC
**
12546619 AAACAAAAAAAATCAAAAGT
1 AAA-AAAAAAAATCAAAAAC
12546639 AAAAAAAAAAATCAAAAA
1 AAAAAAAAAAATCAAAAA
12546657 AATGAAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAATCAAAAAC
Found at i:12546850 original size:23 final size:23
Alignment explanation
Indices: 12546807--12546851 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12546797 TAAGTCCAAT
* *
12546807 TTTATTTTTGTTATTTTTTTTAC
1 TTTATTTTTCTTATTTATTTTAC
12546830 TTTATTTTTCTT-TTATATTTTA
1 TTTATTTTTCTTATT-TATTTTA
12546852 TGTACATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTATTTTTCTTATTTATTTTAC
Found at i:12546894 original size:4 final size:4
Alignment explanation
Indices: 12546885--12546975 Score: 64
Period size: 4 Copynumber: 22.0 Consensus size: 4
12546875 TATGTATCTA
*
12546885 TTAT TTAT TTA- TTAT TACTAT TTAT TTAT ATATAT TTAT TTTT ATTAT
1 TTAT TTAT TTAT TTAT T--TAT TTAT TTAT -T-TAT TTAT TTAT -TTAT
* *
12546933 TT-T ATATT TTAT TTAT TT-T TGTAT TT-T TTAT TTAT TTAA TTAT
1 TTAT TTA-T TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT
12546976 ATATCTGTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 22
0.71 0.06 0.22
Matches are distributed among these distances:
3 10 0.14
4 43 0.61
5 10 0.14
6 7 0.10
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:12546910 original size:24 final size:24
Alignment explanation
Indices: 12546883--12546975 Score: 73
Period size: 27 Copynumber: 3.7 Consensus size: 24
12546873 TCTATGTATC
12546883 TATTATTTATTTATTATTACTATT
1 TATTATTTATTTATTATTACTATT
* *
12546907 TATTTATATATATTTATTTTTATTATT
1 TA-TTAT-T-TATTTATTATTACTATT
**
12546934 T-TATATTTTATTTATT-TTTGTATT
1 TAT-TA-TTTATTTATTATTACTATT
*
12546958 TTTTATTTATTTAATTAT
1 TATTATTTATTT-ATTAT
12546976 ATATCTGTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
23 7 0.12
24 14 0.25
25 15 0.26
26 4 0.07
27 17 0.30
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (24 bp):
TATTATTTATTTATTATTACTATT
Found at i:12546936 original size:14 final size:14
Alignment explanation
Indices: 12546883--12546951 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 14
12546873 TCTATGTATC
12546883 TATTA-TTTATTTAT
1 TATTATTTTATTT-T
*
12546897 TATTACTATTTATTTA
1 TATTA-T-TTTATTTT
12546913 TA-TATATTTATTTT
1 TATTAT-TTTATTTT
12546927 TATTATTTTATATTT
1 TATTATTTTAT-TTT
12546942 TATTTATTTT
1 TA-TTATTTT
12546952 TGTATTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
14 21 0.45
15 10 0.21
16 9 0.19
17 7 0.15
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTTATTTT
Found at i:12546947 original size:19 final size:19
Alignment explanation
Indices: 12546903--12546969 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
12546893 TTATTATTAC
* *
12546903 TATTTATTTATATATATTT
1 TATTTATTTTTGTATATTT
*
12546922 ATTTTTATTATTT-TATATTT
1 -TATTTATT-TTTGTATATTT
*
12546942 TATTTATTTTTGTATTTTT
1 TATTTATTTTTGTATATTT
12546961 TATTTATTT
1 TATTTATTT
12546970 AATTATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 3 0.07
19 22 0.54
20 14 0.34
21 2 0.05
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.75
Consensus pattern (19 bp):
TATTTATTTTTGTATATTT
Found at i:12547548 original size:20 final size:21
Alignment explanation
Indices: 12547519--12547566 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
12547509 AACTTTCTGG
* *
12547519 TGAA-ATTTTCCAGATTTCGA
1 TGAACATTTTCCAGAATCCGA
12547539 TG-ACATTTTCCAGAATCCGA
1 TGAACATTTTCCAGAATCCGA
12547559 TGAACATT
1 TGAACATT
12547567 CCACCGGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (21 bp):
TGAACATTTTCCAGAATCCGA
Found at i:12547917 original size:15 final size:15
Alignment explanation
Indices: 12547860--12547927 Score: 66
Period size: 15 Copynumber: 4.3 Consensus size: 15
12547850 TTATTTAATA
12547860 TTTTTTATCTTTATCT
1 TTTTTTATCTTTAT-T
* *
12547876 TATTTTTATTTTTGTT
1 T-TTTTTATCTTTATT
*
12547892 TTACTTT-TCTTTATT
1 TT-TTTTATCTTTATT
12547907 TTTTTTATCTTTATT
1 TTTTTTATCTTTATT
12547922 TATTTT
1 T-TTTT
12547928 CACATTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.07
15 18 0.43
16 10 0.24
17 11 0.26
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTTTATCTTTATT
Found at i:12548182 original size:57 final size:56
Alignment explanation
Indices: 12547965--12548649 Score: 886
Period size: 57 Copynumber: 11.7 Consensus size: 56
12547955 ATAAAAATCA
**
12547965 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACCAATTTTC
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* ** *
12548022 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTC
1 -AAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* *
12548081 AAAAAAAACATATTTTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTAGAAATAAATTTTC
1 ---AAAAA-ATA-TTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
12548143 GAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
1 AAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* ** *
12548200 AAAAAAGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTC
1 AAAAAA-TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
* *
12548259 AAAAAAATATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 --AAAAA-ATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
12548319 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
*
12548375 TAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTC
1 -AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTC
* *
12548435 GAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAGATTTTC
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* *
12548492 AAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCC
1 AAAAAA--TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
* * *
12548551 AAAAAATATTTTTGGGGAAAGGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTCC
1 AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
12548608 AAAAAACTATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAA-TATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCC
12548650 CTACACAAGA
Statistics
Matches: 565, Mismatches: 38, Indels: 48
0.87 0.06 0.07
Matches are distributed among these distances:
56 5 0.01
57 209 0.37
58 120 0.21
59 120 0.21
60 10 0.02
61 52 0.09
62 10 0.02
63 39 0.07
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (56 bp):
AAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC
Found at i:12548507 original size:175 final size:174
Alignment explanation
Indices: 12547965--12548649 Score: 988
Period size: 175 Copynumber: 3.9 Consensus size: 174
12547955 ATAAAAATCA
* * *
12547965 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAACCAATTTTCAAAAAAAG
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAA-TAAATTTCTAAAAAAG
*
12548030 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAAAAAACATATT
65 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC--AAAAAA-ATATT
*
12548095 TTTTGAGGAAAAGTTGAAAGCATCAATTTTCCTTAGAAATAAATTTTC
127 TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* *
12548143 GAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT-TCAAAAAAG
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCT-AAAAAA-
*
12548207 GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTTTCAAAAAAATATATT
64 GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAATAT-TT
*
12548272 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
128 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
*
12548319 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCTAAAAAATA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCTAAAAAAGA
* * *
12548384 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTC-GAAAAATATTTTT
66 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAAGTTTCAAAAAAATATTTTT
* * *
12548448 AG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAGATTTTC
130 TGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* * *
12548492 AAAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAA
1 AAAAAA--TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCTAAAAAA
* * * * * *
12548557 TATTTTTGGGGAAAGGTTGAAAGTATCAATTTTTCTTAAAAAT-AAA-TTTCCAAAAAACTA-TT
64 GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTT-CAAAAAAATATTT
12548619 TTTG-GGAAAAAGTTGAAAGTATCAATTTTCC
128 TTTGAGG-AAAAGTTGAAAGTATCAATTTTCC
12548650 CTACACAAGA
Statistics
Matches: 470, Mismatches: 27, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
172 3 0.01
173 56 0.12
174 35 0.07
175 147 0.31
176 119 0.25
177 12 0.03
178 98 0.21
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (174 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCTAAAAAAGA
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCAAAAAAATATTTTTT
GAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
Found at i:12549396 original size:62 final size:62
Alignment explanation
Indices: 12549163--12549403 Score: 189
Period size: 62 Copynumber: 3.9 Consensus size: 62
12549153 CAAAAAAATT
* ** * * * *
12549163 ACCTTGAATAATTTCTTA-AAAAAATTGGAAAGGG-TTATTGAAGGCATTTTTTCCAAAATAC
1 ACCTTCAATAATTTCTTATAAAAAATT-TCAGGGGATTATTAAAGGTATTTTTTGCAAAATAC
* * * * *
12549224 ACCTTCAATAATTTATTATAAAAAATTTCAGGGGATTATTAAAAGTATTTTTTGGAAAAAAAAT
1 ACCTTCAATAATTTCTTATAAAAAATTTCAGGGGATTATTAAAGGTATTTTTT-G-CAAAATAC
* ** ** ** * * *
12549288 ACTTTCAATAATCCCTTAATAAAAAATTGGAGGAAATTATTAAAGGTATTTTCTGCACAATAG
1 ACCTTCAATAATTTCTT-ATAAAAAATTTCAGGGGATTATTAAAGGTATTTTTTGCAAAATAC
* * * * *
12549351 GCCTTCAATAATTTCTTTTAAAAAATTTTAGGGGATTATTGAAGGTGTTTTTT
1 ACCTTCAATAATTTCTTATAAAAAATTTCAGGGGATTATTAAAGGTATTTTTT
12549404 TTATTAAAAT
Statistics
Matches: 137, Mismatches: 38, Indels: 9
0.74 0.21 0.05
Matches are distributed among these distances:
61 20 0.15
62 51 0.37
63 17 0.12
64 19 0.14
65 30 0.22
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (62 bp):
ACCTTCAATAATTTCTTATAAAAAATTTCAGGGGATTATTAAAGGTATTTTTTGCAAAATAC
Found at i:12549466 original size:126 final size:127
Alignment explanation
Indices: 12549197--12549445 Score: 295
Period size: 127 Copynumber: 2.0 Consensus size: 127
12549187 TTGGAAAGGG
* * * * **
12549197 TTATTGAAGGCATTTTTTCCAAAATACACCTTCAATAATTTATTATAAAAAATTTCAGGGGATTA
1 TTATTAAAGGCATTTTCTGCACAATAGGCCTTCAATAATTTATTATAAAAAATTTCAGGGGATTA
*
12549262 TTAAAAGTATTTTTTGGAAAAAAAATACTTTCAATAATCCCTTAATAAAAAATTGGAGGAAA
66 TTAAAAGTATTTTTTGGAAAAAAAATACCTTCAATAATCCCTTAATAAAAAATTGGAGGAAA
* * * *
12549324 TTATTAAAGGTATTTTCTGCACAATAGGCCTTCAATAATTTCTTTTAAAAAATTTTAGGGGATTA
1 TTATTAAAGGCATTTTCTGCACAATAGGCCTTCAATAATTTATTATAAAAAATTTCAGGGGATTA
* * * ** ** * *
12549389 TTGAAGGTGTTTTTT-TTATTAAAATGCCTTCAATAATCCAC-TGATAAAAAATTGGAG
66 TTAAAAGTATTTTTTGGAAAAAAAATACCTTCAATAATCC-CTTAATAAAAAATTGGAG
12549446 TGGATTATTA
Statistics
Matches: 101, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
126 33 0.33
127 68 0.67
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (127 bp):
TTATTAAAGGCATTTTCTGCACAATAGGCCTTCAATAATTTATTATAAAAAATTTCAGGGGATTA
TTAAAAGTATTTTTTGGAAAAAAAATACCTTCAATAATCCCTTAATAAAAAATTGGAGGAAA
Found at i:12549484 original size:127 final size:127
Alignment explanation
Indices: 12549225--12549485 Score: 276
Period size: 127 Copynumber: 2.1 Consensus size: 127
12549215 CCAAAATACA
12549225 CCTTCAATAATTTATTATAAAAAATTTCAGGGGATTATTAAAAGTATTTTTTGGAAAAAAAATAC
1 CCTTCAATAATTTATTATAAAAAATTTCAGGGGATTATTAAAAGTATTTTTTGGAAAAAAAATAC
* * * * * *
12549290 TTTCAATAATCCCTTAATAAAAAATTGGAGGAAATTATTAAAGGTATTTTCTGCACAATAGG
66 CTTCAATAATCCCTTAATAAAAAATTGGAGGAAATTATTAAAGGCATTTTCCGAAAAAAAGG
* * * * * * ** ** *
12549352 CCTTCAATAATTTCTTTTAAAAAATTTTAGGGGATTATTGAAGGTGTTTTTT-TTATTAAAATGC
1 CCTTCAATAATTTATTATAAAAAATTTCAGGGGATTATTAAAAGTATTTTTTGGAAAAAAAATAC
* * * * *
12549416 CTTCAATAATCCAC-TGATAAAAAATTGGAGTG-GATTATTAGAGGCGTTTTCCGTAAAAAAATG
66 CTTCAATAATCC-CTTAATAAAAAATTGGAG-GAAATTATTAAAGGCATTTTCCG-AAAAAAAGG
12549479 CCTTCAA
1 CCTTCAA
12549486 AAATCTCTCA
Statistics
Matches: 109, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
126 49 0.45
127 60 0.55
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (127 bp):
CCTTCAATAATTTATTATAAAAAATTTCAGGGGATTATTAAAAGTATTTTTTGGAAAAAAAATAC
CTTCAATAATCCCTTAATAAAAAATTGGAGGAAATTATTAAAGGCATTTTCCGAAAAAAAGG
Found at i:12549538 original size:63 final size:62
Alignment explanation
Indices: 12549409--12549584 Score: 156
Period size: 62 Copynumber: 2.8 Consensus size: 62
12549399 TTTTTTTATT
* * * * * * * *
12549409 AAAATGCCTTCAATAATCCACTGATAAAAAATTGGAGTGGATTATTAGAGGCGTTTTCCGTAAA
1 AAAATGCCTTCAATAAT-CTCTCATACAAAATTGAAGGGGATTATTAAAGGCATTTTCAGT-AA
* * * *
12549473 AAAATGCCTTCAAAAATCTCTCATCCAAAATTGAAGGGGATTATTAAAGGCATTTTTAGTCA
1 AAAATGCCTTCAATAATCTCTCATACAAAATTGAAGGGGATTATTAAAGGCATTTTCAGTAA
* * * * * *
12549535 AAAACGCTTTTAATAATCTC-CTTGTCAAAATTTAAGGGGATTATTAAAGG
1 AAAATGCCTTCAATAATCTCTCAT-ACAAAATTGAAGGGGATTATTAAAGG
12549585 TGTTTTATGC
Statistics
Matches: 92, Mismatches: 19, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
61 2 0.02
62 41 0.45
63 33 0.36
64 16 0.17
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (62 bp):
AAAATGCCTTCAATAATCTCTCATACAAAATTGAAGGGGATTATTAAAGGCATTTTCAGTAA
Found at i:12549612 original size:62 final size:61
Alignment explanation
Indices: 12549498--12549614 Score: 137
Period size: 62 Copynumber: 1.9 Consensus size: 61
12549488 ATCTCTCATC
* * * *
12549498 CAAAATTGAAGGGGATTATTAAAGGCATTTTTAGTCAAAAACGCTTTTAATAATCTCCTTGT
1 CAAAATTGAAGGGGATTATTAAAGG-ATTTTTAGCCAAAAACACCTTCAATAATCTCCTTGT
* **
12549560 CAAAATTTAAGGGGATTATTAAAGG-TGTTTTATGCCTGAAACACCTTCAATAATC
1 CAAAATTGAAGGGGATTATTAAAGGAT-TTTTA-GCCAAAAACACCTTCAATAATC
12549615 CCCTAAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 1 0.02
61 5 0.11
62 40 0.87
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (61 bp):
CAAAATTGAAGGGGATTATTAAAGGATTTTTAGCCAAAAACACCTTCAATAATCTCCTTGT
Found at i:12550096 original size:17 final size:17
Alignment explanation
Indices: 12550074--12550106 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12550064 GTATAAAAAT
12550074 TTTCTCCAAA-ACCCATC
1 TTTCT-CAAATACCCATC
12550091 TTTCTCAAATACCCAT
1 TTTCTCAAATACCCAT
12550107 TGGAACCCAT
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:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTCTCAAATACCCATC
Found at i:12551482 original size:56 final size:56
Alignment explanation
Indices: 12551396--12551507 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
12551386 CAAAACTACA
**
12551396 GATTCTATGAGGTAGAATTGTGATAAGTGGACGGATGATGGATCAATGAGGCATCC
1 GATTCTATGAGGTAGAATCATGATAAGTGGACGGATGATGGATCAATGAGGCATCC
*
12551452 GATTCTATGAGGTAGCATCATGATAAGTGGACGGATGATGGATCAATGAGGCATCC
1 GATTCTATGAGGTAGAATCATGATAAGTGGACGGATGATGGATCAATGAGGCATCC
12551508 AATAGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.30, C:0.12, G:0.31, T:0.26
Consensus pattern (56 bp):
GATTCTATGAGGTAGAATCATGATAAGTGGACGGATGATGGATCAATGAGGCATCC
Done.