Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 3 of 202
Found at i:817422 original size:23 final size:23
Alignment explanation
Indices: 817390--817435 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
817380 CAAATATAAT
*
817390 AAATA-TTTTTATTTTTTATTTTA
1 AAATACTTTTT-TTATTTATTTTA
*
817413 AAATACTTTTTTTATTTTTTTTA
1 AAATACTTTTTTTATTTATTTTA
817436 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
AAATACTTTTTTTATTTATTTTA
Found at i:817433 original size:9 final size:9
Alignment explanation
Indices: 817419--817471 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
817409 TTTAAAATAC
817419 TTTTTTTAT
1 TTTTTTTAT
817428 TTTTTTTAT
1 TTTTTTTAT
***
817437 TTTTAAAAT
1 TTTTTTTAT
817446 ATTTTTTTAT
1 -TTTTTTTAT
* *
817456 TTTTTTAAA
1 TTTTTTTAT
817465 TTTTTTT
1 TTTTTTT
817472 GGTGTTTATT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
9 28 0.82
10 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:817450 original size:28 final size:28
Alignment explanation
Indices: 817401--817461 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
817391 AATATTTTTA
817401 TTTTTTATTTTAAAATACTTTTTTTATT
1 TTTTTTATTTTAAAATACTTTTTTTATT
817429 TTTTTTATTTTTAAAATA-TTTTTTTATT
1 TTTTTTA-TTTTAAAATACTTTTTTTATT
817457 TTTTT
1 TTTTT
817462 AAATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTTTATTTTAAAATACTTTTTTTATT
Found at i:817467 original size:29 final size:29
Alignment explanation
Indices: 817395--817469 Score: 104
Period size: 28 Copynumber: 2.7 Consensus size: 29
817385 ATAATAAATA
817395 TTTTTA-TTTTTT-A-TTTTAAAATACTT
1 TTTTTATTTTTTTAATTTTTAAAATACTT
*
817421 TTTTTATTTTTTTTATTTTTAAAATA-TT
1 TTTTTATTTTTTTAATTTTTAAAATACTT
817449 TTTTTATTTTTTTAAATTTTT
1 TTTTTATTTTTTT-AATTTTT
817470 TTGGTGTTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 6 0.14
27 6 0.14
28 16 0.36
29 16 0.36
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTTTATTTTTTTAATTTTTAAAATACTT
Found at i:817469 original size:19 final size:18
Alignment explanation
Indices: 817426--817471 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
817416 TACTTTTTTT
817426 ATTTTTTTTATTTTTAAA
1 ATTTTTTTTATTTTTAAA
*
817444 ATATTTTTTTATTTTTTTAA
1 AT-TTTTTTTA-TTTTTAAA
817464 ATTTTTTT
1 ATTTTTTT
817472 GGTGTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTTTTATTTTTAAA
Found at i:818454 original size:28 final size:29
Alignment explanation
Indices: 818423--818477 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
818413 TTGAATGAAA
*
818423 ATTTAACT-TTTAAGAT-ATAAAAATAAAT
1 ATTTAA-TATTTAAAATAATAAAAATAAAT
*
818451 ATTTTATATTTAAAATAATAAAAATAA
1 ATTTAATATTTAAAATAATAAAAATAA
818478 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.04
28 12 0.52
29 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
ATTTAATATTTAAAATAATAAAAATAAAT
Found at i:824955 original size:17 final size:17
Alignment explanation
Indices: 824933--824973 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
824923 CCGGTTCTCG
824933 ATTCGACTAGTTTAACT
1 ATTCGACTAGTTTAACT
824950 ATTCGACTAGTTTAACT
1 ATTCGACTAGTTTAACT
824967 AGTTCGA
1 A-TTCGA
824974 TAGCCAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (17 bp):
ATTCGACTAGTTTAACT
Found at i:826741 original size:1 final size:1
Alignment explanation
Indices: 826703--826727 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
826693 ACTTTCAAGG
826703 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
826728 GGTATTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:828196 original size:19 final size:20
Alignment explanation
Indices: 828169--828210 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
828159 TTGCTATTTG
* *
828169 AAAATTTTTATTAAGCTCCA
1 AAAATTTTAATTAAGCCCCA
828189 AAAATTTTAATTAAGCCCCA
1 AAAATTTTAATTAAGCCCCA
828209 AA
1 AA
828211 TGTTTTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATTTTAATTAAGCCCCA
Found at i:828226 original size:30 final size:30
Alignment explanation
Indices: 828189--828261 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
828179 TTAAGCTCCA
828189 AAAATTTTAATTAAGCC-CCA-AATGTTTTTG
1 AAAATTTTAATTAAGCCTCCAGAA--TTTTTG
* * *
828219 GAAATTTTCATTAAGCCTCTAGAATTTTTG
1 AAAATTTTAATTAAGCCTCCAGAATTTTTG
828249 AAAATTTTAATTA
1 AAAATTTTAATTA
828262 CCCCCTCCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 32 0.89
31 2 0.06
32 2 0.06
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (30 bp):
AAAATTTTAATTAAGCCTCCAGAATTTTTG
Found at i:830128 original size:20 final size:20
Alignment explanation
Indices: 830061--830147 Score: 54
Period size: 20 Copynumber: 4.3 Consensus size: 20
830051 TAAGTCTTTG
* *
830061 AATTTTATTTTTATTTATTA
1 AATTTTAGTTTTAGTTATTA
*
830081 AATTATTTG-TTTAGACTT-TTA
1 AATT-TTAGTTTTAG--TTATTA
* *
830102 GACTTTAGTTTTAGTT-TTA
1 AATTTTAGTTTTAGTTATTA
* *
830121 GAATTTTATTTTTATTTATTA
1 -AATTTTAGTTTTAGTTATTA
830142 AATTTT
1 AATTTT
830148 TTATGATTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
19 5 0.10
20 29 0.57
21 15 0.29
22 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (20 bp):
AATTTTAGTTTTAGTTATTA
Found at i:833906 original size:22 final size:22
Alignment explanation
Indices: 833878--833922 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
833868 TGGGAATATA
*
833878 CAATTAGTCACTCAATTATTAG
1 CAATTAGCCACTCAATTATTAG
833900 CAATTAGCCACTCAATTATTAG
1 CAATTAGCCACTCAATTATTAG
833922 C
1 C
833923 GCGCTCATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (22 bp):
CAATTAGCCACTCAATTATTAG
Found at i:835523 original size:16 final size:17
Alignment explanation
Indices: 835502--835539 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
835492 CGTATAATTC
835502 AAAAAT-AA-AAATATTT
1 AAAAATAAACAAAT-TTT
835518 AAAAATAAACAAATTTT
1 AAAAATAAACAAATTTT
835535 AAAAA
1 AAAAA
835540 AAGTTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATAAACAAATTTT
Found at i:835535 original size:17 final size:16
Alignment explanation
Indices: 835502--835539 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
835492 CGTATAATTC
835502 AAAAATAAAAATATTT
1 AAAAATAAAAATATTT
835518 AAAAATAAACAA-ATTTT
1 AAAAATAAA-AATA-TTT
835535 AAAAA
1 AAAAA
835540 AAGTTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAAATATTT
Found at i:842496 original size:3 final size:3
Alignment explanation
Indices: 842490--842518 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
842480 ATGATGATGA
842490 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
842519 TTTGTTGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:847733 original size:24 final size:24
Alignment explanation
Indices: 847701--847747 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
847691 TTTGAGTACT
*
847701 TCTGATCAGTAACCAGTGACAAGA
1 TCTGATCAGTAACAAGTGACAAGA
*
847725 TCTGATCAGTGACAAGTGACAAG
1 TCTGATCAGTAACAAGTGACAAG
847748 TGATAAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (24 bp):
TCTGATCAGTAACAAGTGACAAGA
Found at i:850154 original size:24 final size:24
Alignment explanation
Indices: 850127--850175 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
850117 TATATATATG
850127 AAACTTTAATTTTGATTCAATTGT
1 AAACTTTAATTTTGATTCAATTGT
* *
850151 AAACTTTGATTTTGATTTAATTGT
1 AAACTTTAATTTTGATTCAATTGT
850175 A
1 A
850176 TACATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (24 bp):
AAACTTTAATTTTGATTCAATTGT
Found at i:854303 original size:24 final size:23
Alignment explanation
Indices: 854277--854320 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
854267 AAATGAAAAA
*
854277 AAAAAT-TACATTTTAACTTTCAT
1 AAAAATATACAATTTAA-TTTCAT
854300 AAAAATATACAATTTAATTTC
1 AAAAATATACAATTTAATTTC
854321 GACTCTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAATATACAATTTAATTTCAT
Found at i:856742 original size:19 final size:21
Alignment explanation
Indices: 856718--856756 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
856708 ATAATTATTT
856718 TTATTT-TGGAT-TAATATAA
1 TTATTTGTGGATGTAATATAA
*
856737 TTATTTGTGTATGTAATATA
1 TTATTTGTGGATGTAATATA
856757 TTAACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (21 bp):
TTATTTGTGGATGTAATATAA
Found at i:859393 original size:30 final size:30
Alignment explanation
Indices: 859358--859421 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
859348 ATATACCCGA
859358 TCCTCCACCCCTTAGCTCCTTTGTTAGTTC
1 TCCTCCACCCCTTAGCTCCTTTGTTAGTTC
*
859388 TCCTCCACTCCTTAGCTCCTTTGTTAGTTC
1 TCCTCCACCCCTTAGCTCCTTTGTTAGTTC
859418 TCCT
1 TCCT
859422 TAGATCATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.09, C:0.39, G:0.09, T:0.42
Consensus pattern (30 bp):
TCCTCCACCCCTTAGCTCCTTTGTTAGTTC
Found at i:859822 original size:5 final size:5
Alignment explanation
Indices: 859812--859837 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
859802 TTAACTAAGA
859812 TGGGT TGGGT TGGGT TGGGT TGGGT T
1 TGGGT TGGGT TGGGT TGGGT TGGGT T
859838 CTATTGGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.58, T:0.42
Consensus pattern (5 bp):
TGGGT
Found at i:860290 original size:18 final size:19
Alignment explanation
Indices: 860249--860292 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
860239 ATTATTTGGA
*
860249 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTAT
860268 TATTGT-TAA-TTTTGCTAT
1 TATTGTATAACTTTTG-TAT
860286 TATTGTA
1 TATTGTA
860293 GAGACAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 11 0.50
19 6 0.27
ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61
Consensus pattern (19 bp):
TATTGTATAACTTTTGTAT
Found at i:860354 original size:5 final size:5
Alignment explanation
Indices: 860344--860375 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
860334 TAAGTATAAC
860344 TAATT TAATT TAATT TAATT TAATT TCAATT T
1 TAATT TAATT TAATT TAATT TAATT T-AATT T
860376 GTTGGGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
TAATT
Found at i:862698 original size:23 final size:21
Alignment explanation
Indices: 862652--862700 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
862642 CTCTCTGAAT
*
862652 AAAAATTAAATAAATCCCCAA
1 AAAAATTAAATAAATACCCAA
*
862673 AAAAATTAAAAATAAA-ACCCAG
1 AAAAATT--AAATAAATACCCAA
862695 AAAAAT
1 AAAAAT
862701 AGTAGCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAAATTAAATAAATACCCAA
Found at i:863710 original size:215 final size:215
Alignment explanation
Indices: 863329--863831 Score: 720
Period size: 215 Copynumber: 2.3 Consensus size: 215
863319 CGAACATAGG
* * * * *
863329 TACTACAAGTAAAATGAAGAGTCTGAGCATCATAGCTTAGCATGAACTAAAACTAGGTAATGGCA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
* * * *
863394 GTGATAAAATCTTGATCTCTTAGTTGGAATTTTACTTAGCACCTATGTTGCTCCGATTTGGGTGT
66 GTGATAAAATCATGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCCGATTTGGGTGT
* * * * * *
863459 AGTTGTCCAATACTGGTAGTGTCTGATATGAGTTTAGAGGTTGTATCTCTGTATTTG-TGTGTCG
131 AGTTGTCCAATAATAGTAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTA-TTGCAGTGTCG
863523 GACATGAGGGTCAGACACAGA
195 GACATGAGGGTCAGACACAGA
*
863544 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACCAAAACTAGGTAATGGTA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
* * * * *
863609 GTGATAAAATCATGTTTTCTTATTTGGAAATTTACTTAGCACCTGTATTACTCGGATTTGGGTGT
66 GTGATAAAATCATGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCCGATTTGGGTGT
** *
863674 AGTTGTCTGATAATAGTAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTATTGCAGTGTTGG
131 AGTTGTCCAATAATAGTAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTATTGCAGTGTCGG
* *
863739 ACATGAGTGTCAGGCACAGA
196 ACATGAGGGTCAGACACAGA
* * * *
863759 TACTTCAAGAAAAATGAAGAGTTCGAGCATCATAGCTTAGGACAAACTAAAACTATGTAATGGTA
1 TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
863824 GTGATAAA
66 GTGATAAA
863832 GTCTTGGAAC
Statistics
Matches: 256, Mismatches: 31, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
214 3 0.01
215 253 0.99
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (215 bp):
TACTTCAAGAAAAATGAAGAGTCCGAGCATCATAGCTTAGCACGAACTAAAACTAGGTAATGGTA
GTGATAAAATCATGATCTCTTAGTTGGAAATTTACTTAGCACCTATATTACTCCGATTTGGGTGT
AGTTGTCCAATAATAGTAGTGTCGGACACGAGTTTAGAGGTTGTATCTCTGTATTGCAGTGTCGG
ACATGAGGGTCAGACACAGA
Found at i:868097 original size:12 final size:12
Alignment explanation
Indices: 868080--868104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
868070 AAACAGGGAT
868080 TCATCATCTTCA
1 TCATCATCTTCA
868092 TCATCATCTTCA
1 TCATCATCTTCA
868104 T
1 T
868105 TCGGTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCATCATCTTCA
Found at i:870346 original size:31 final size:31
Alignment explanation
Indices: 870277--870346 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
870267 ATTAACAGTC
* *
870277 CAGTGGCTTAAATAAAAATTTTCAAATAGTT
1 CAGTGACTTAAATAAAAATTTTCAAATAATT
* *
870308 CAATGACTTAAATGAAAATTTTCAAATAATT
1 CAGTGACTTAAATAAAAATTTTCAAATAATT
*
870339 TAGTGACT
1 CAGTGACT
870347 ATTTTGTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAATTTTCAAATAATT
Found at i:872638 original size:2 final size:2
Alignment explanation
Indices: 872631--872690 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
872621 AATGAGTGAG
872631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
872673 AT AT AT AT AA AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A
872691 AGAATTTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:877654 original size:29 final size:27
Alignment explanation
Indices: 877608--877661 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
877598 TTTCTAAATC
877608 TAAAAAAAAAATCGAGGACTAAATTAT
1 TAAAAAAAAAATCGAGGACTAAATTAT
*
877635 TAAAAATAAAAATAGGAGGACTAAATT
1 TAAAAA-AAAAAT-CGAGGACTAAATT
877662 CCAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 6 0.25
29 12 0.50
ACGTcount: A:0.59, C:0.06, G:0.13, T:0.22
Consensus pattern (27 bp):
TAAAAAAAAAATCGAGGACTAAATTAT
Found at i:878745 original size:31 final size:31
Alignment explanation
Indices: 878683--878746 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
878673 AAAATAGCAG
* * * *
878683 TTCGACTTTTTTTGAAAGGTTGATGATCAAA
1 TTCGACTCTTTTTAAAAGATTGATGACCAAA
878714 TTCGACTCTTTTTAAAAGATTGA-GAGCCAAA
1 TTCGACTCTTTTTAAAAGATTGATGA-CCAAA
878745 TT
1 TT
878747 TAGCTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (31 bp):
TTCGACTCTTTTTAAAAGATTGATGACCAAA
Found at i:879387 original size:2 final size:2
Alignment explanation
Indices: 879380--879406 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
879370 TTTACAATGG
879380 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
879407 AAGGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:879749 original size:17 final size:17
Alignment explanation
Indices: 879727--879759 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
879717 AAGCAAATAA
879727 TAATAAA-AGAAGTAAAC
1 TAATAAATAGAA-TAAAC
879744 TAATAAATAGAATAAA
1 TAATAAATAGAATAAA
879760 GGGTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (17 bp):
TAATAAATAGAATAAAC
Found at i:883887 original size:41 final size:40
Alignment explanation
Indices: 883792--883889 Score: 144
Period size: 40 Copynumber: 2.4 Consensus size: 40
883782 ATGCATGCAT
* *
883792 GCATACATGCATACATATTAAGACAAATGTAAAAAGAATG
1 GCATGCATGCATACATATTAAGAAAAATGTAAAAAGAATG
*
883832 GCATGCATGCATACATATTAAGAAAAAAATGTAAAAA-AGTG
1 GCATGCATGCATACATATTAAG--AAAAATGTAAAAAGAATG
883873 GCATGCATGCATACATA
1 GCATGCATGCATACATA
883890 CATATATACA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 21 0.40
41 20 0.38
42 12 0.23
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.22
Consensus pattern (40 bp):
GCATGCATGCATACATATTAAGAAAAATGTAAAAAGAATG
Found at i:896239 original size:49 final size:48
Alignment explanation
Indices: 896160--896257 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 48
896150 GATTCAATTG
*
896160 GTTCTGTCAGTTTTTTCGATTTACTTGATCTTTGGTTTATGGTTATTA
1 GTTCTGTCAGTTTTTTCGATTTACTCGATCTTTGGTTTATGGTTATTA
896208 GTTCTGTCAGTTTTTTTCGATTTACTCGATCTTTGGTTTATGGTTATTA
1 GTTCTGTCAG-TTTTTTCGATTTACTCGATCTTTGGTTTATGGTTATTA
896257 G
1 G
896258 GTTAAGTTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 10 0.21
49 38 0.79
ACGTcount: A:0.14, C:0.11, G:0.19, T:0.55
Consensus pattern (48 bp):
GTTCTGTCAGTTTTTTCGATTTACTCGATCTTTGGTTTATGGTTATTA
Found at i:897257 original size:40 final size:40
Alignment explanation
Indices: 897197--897280 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
897187 TATGAATCAG
897197 ATTGCATTTTACCTTCTATACTAAAAAAAAGAAGAAATAA
1 ATTGCATTTTACCTTCTATACTAAAAAAAAGAAGAAATAA
*
897237 ATTGTATTTTACCTTCTATACTAAAAAAAAGAAGAAATAA
1 ATTGCATTTTACCTTCTATACTAAAAAAAAGAAGAAATAA
897277 ATTG
1 ATTG
897281 GTTATTCCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (40 bp):
ATTGCATTTTACCTTCTATACTAAAAAAAAGAAGAAATAA
Found at i:897791 original size:31 final size:30
Alignment explanation
Indices: 897751--897810 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
897741 GTAAAAATTA
* *
897751 AAATTATACATAAATTTTGATTCAATATAC
1 AAATTATACATAAACTTTCATTCAATATAC
* *
897781 AAATTGATACATGAACTTTCATTTAATATA
1 AAATT-ATACATAAACTTTCATTCAATATA
897811 ATTATATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATTATACATAAACTTTCATTCAATATAC
Found at i:898340 original size:30 final size:33
Alignment explanation
Indices: 898270--898346 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 33
898260 TTATATTATG
*
898270 GTCACTGAACTATTTGAAAGTTTTCAGTTATAA
1 GTCACTGAACTATTTGAAAATTTTCAGTTATAA
* *
898303 CTCACTGAACTATTT-AAAATTTTTA-TT-TAA
1 GTCACTGAACTATTTGAAAATTTTCAGTTATAA
898333 GTCACTGAACTATT
1 GTCACTGAACTATT
898347 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.40
31 2 0.05
32 8 0.20
33 14 0.35
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (33 bp):
GTCACTGAACTATTTGAAAATTTTCAGTTATAA
Found at i:899078 original size:18 final size:19
Alignment explanation
Indices: 899055--899095 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
899045 TCACTTAATT
899055 TTTTTAAATATTTTTTA-A
1 TTTTTAAATATTTTTTAGA
**
899073 TTTTTATGTATTTTTTAGA
1 TTTTTAAATATTTTTTAGA
899092 TTTT
1 TTTT
899096 ATATAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTAAATATTTTTTAGA
Found at i:901895 original size:24 final size:24
Alignment explanation
Indices: 901863--901912 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
901853 ATACAATTAC
*
901863 ATATTAGACTAAAATTAATGTATA
1 ATATTAGACCAAAATTAATGTATA
*
901887 ATATTAGACCAGAATTAATGTATA
1 ATATTAGACCAAAATTAATGTATA
901911 AT
1 AT
901913 TTATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (24 bp):
ATATTAGACCAAAATTAATGTATA
Found at i:902736 original size:22 final size:21
Alignment explanation
Indices: 902707--902748 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
902697 CTTGATGTGA
*
902707 ATTAAAAATAATTATTTATTC
1 ATTAAAAAAAATTATTTATTC
902728 ATTATAAAAAAATTATTTATT
1 ATTA-AAAAAAATTATTTATT
902749 TAGATGTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAAAAAAAATTATTTATTC
Found at i:903566 original size:15 final size:15
Alignment explanation
Indices: 903519--903559 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
903509 TTGGTTGGTC
* *
903519 AGAAAAGGATGGAAA
1 AGAAAAGAAAGGAAA
903534 AGAAAAGAAAGGAAA
1 AGAAAAGAAAGGAAA
903549 AGAAAAGAAAG
1 AGAAAAGAAAG
903560 TGGAAGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02
Consensus pattern (15 bp):
AGAAAAGAAAGGAAA
Found at i:921356 original size:12 final size:12
Alignment explanation
Indices: 921325--921357 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
921315 ATTGCAGATA
*
921325 AATTAAAATTTT
1 AATTATAATTTT
921337 AATT-TAATTTT
1 AATTATAATTTT
921348 AATTATAATT
1 AATTATAATT
921358 ATTTAGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATTATAATTTT
Found at i:924137 original size:2 final size:2
Alignment explanation
Indices: 924130--924166 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
924120 ATTTGTATGC
924130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
924167 AACAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:926011 original size:31 final size:32
Alignment explanation
Indices: 925958--926028 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
925948 CTTAACAACC
*
925958 CAATGACTTAAATAAAAAAACTTTTAAATAATT
1 CAATGACTTAAAT-AAAAAACTTTCAAATAATT
* *
925991 CAATGATTTAAAT-AAAAACTTTCAAATAGTT
1 CAATGACTTAAATAAAAAACTTTCAAATAATT
*
926022 CGATGAC
1 CAATGAC
926029 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 21 0.64
33 12 0.36
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.32
Consensus pattern (32 bp):
CAATGACTTAAATAAAAAACTTTCAAATAATT
Found at i:927356 original size:32 final size:31
Alignment explanation
Indices: 927320--927382 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
927310 CTTAACAGTC
*
927320 CAATGACTTAAAACAAAAACTTTCAAATAGTT
1 CAATGACCT-AAACAAAAACTTTCAAATAGTT
** *
927352 CAATGACCTAAATGAAAACTTTCGAATAGTT
1 CAATGACCTAAACAAAAACTTTCAAATAGTT
927383 TAGTGATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
CAATGACCTAAACAAAAACTTTCAAATAGTT
Found at i:929638 original size:4 final size:4
Alignment explanation
Indices: 929631--929691 Score: 56
Period size: 4 Copynumber: 15.0 Consensus size: 4
929621 TTTCTCCTTC
*
929631 CTTT CTTT CCTT -TTT CTTTT CTTT CTTT CTTT C-TT -TTT CTTT CTGTTT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT C--TTT
929679 CGTTT CTTT CTTT
1 C-TTT CTTT CTTT
929692 TTATTTATTC
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
3 6 0.12
4 30 0.61
5 9 0.18
6 4 0.08
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:929659 original size:24 final size:24
Alignment explanation
Indices: 929620--929693 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 24
929610 AAAACCGTGG
*
929620 CTTTCTCCTTCCTTTCTTTCCTTTTT
1 CTTTCT-CTTTCTTTCTTT-CTTTTT
929646 CTTT-TCTTTCTTTCTTTCTTTTT
1 CTTTCTCTTTCTTTCTTTCTTTTT
*
929669 CTTTCTGTTTCGTTTCTTTCTTTTT
1 CTTTCTCTTTC-TTTCTTTCTTTTT
929694 ATTTATTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 10 0.23
24 16 0.36
25 14 0.32
26 4 0.09
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.72
Consensus pattern (24 bp):
CTTTCTCTTTCTTTCTTTCTTTTT
Found at i:932577 original size:12 final size:12
Alignment explanation
Indices: 932562--932593 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
932552 AAAAAAAAAT
932562 TGAAAATTTTAA
1 TGAAAATTTTAA
932574 TGAAAATTTTAA
1 TGAAAATTTTAA
932586 --AAAATTTT
1 TGAAAATTTT
932594 GGAGGATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (12 bp):
TGAAAATTTTAA
Found at i:932611 original size:31 final size:30
Alignment explanation
Indices: 932571--932682 Score: 97
Period size: 31 Copynumber: 3.7 Consensus size: 30
932561 TTGAAAATTT
*
932571 TAATGAAAATTTTAAAAAATTTTGGAGGATC
1 TAATTAAAATTTT-AAAAATTTTGGAGGATC
** * *
932602 TAATTAAAA-TTTAAACCTTTTGAAAGGCTC
1 TAATTAAAATTTTAAAAATTTTG-GAGGATC
* *
932632 -AATTAGAATTTCTAAAAATTTT-GAGGGGTC
1 TAATTAAAATTT-TAAAAATTTTGGA-GGATC
932662 TAATTAAAATTTT-AAAATTTT
1 TAATTAAAATTTTAAAAATTTT
932683 CTAAAGCTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
29 24 0.37
30 15 0.23
31 26 0.40
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (30 bp):
TAATTAAAATTTTAAAAATTTTGGAGGATC
Found at i:938405 original size:3 final size:3
Alignment explanation
Indices: 938397--938446 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
938387 ATGTCTTTAA
938397 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
938445 AT
1 AT
938447 CAATTAAGTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:940884 original size:16 final size:16
Alignment explanation
Indices: 940859--940889 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
940849 TTTTATCATT
940859 TATTAATATAAAAAGC
1 TATTAATATAAAAAGC
*
940875 TATTATTATAAAAAG
1 TATTAATATAAAAAG
940890 TAAAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
TATTAATATAAAAAGC
Found at i:949574 original size:2 final size:2
Alignment explanation
Indices: 949567--949608 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
949557 CTTTTATCTC
*
949567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
949609 CCCTTGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:953303 original size:123 final size:122
Alignment explanation
Indices: 953009--953370 Score: 399
Period size: 124 Copynumber: 2.9 Consensus size: 122
952999 CATATATATG
* * * ** *
953009 TAGTATTTACAGCATTTAGGTGCAAGCAATCTCATATTCTATCAATTGAAAGGCAAATCATACAT
1 TAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAAT
* * * *
953074 AAGCAACTATGGGACAACTAATTATTCATTGACATAACTGCAGTGTATACATATACGTC
66 AAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCA--ATATACATATACGTC
* * *
953133 TAGTATTTACAGCATGTAGATGCAAGAAACCTCATATTTTATCAATTCTAAGGCAAATCATAAAT
1 TAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAAT
* * * * *
953198 CAGCAACTA-GGGTCAACTTGTCATTCATTGGCATAACAGCAACATACATACATACAGAT-
66 AAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCAATATACAT--ATAC-G-TC
* * * * * *
953257 T-GTATTTGCAGCATTTAGATGCAATAAAACTCAAATTCTATTAATTCTGAGGCAAATAATAAAT
1 TAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAAT
* *
953321 AAGCATCTATGGGTCAA-TTAATCATTCAGTGACATAACTGCAATATACAT
66 AAGCAACTATGGGTCAACTT-ATCATTCATTGACATAACTGCAATATACAT
953371 GTACAATCAT
Statistics
Matches: 199, Mismatches: 33, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
121 6 0.03
123 93 0.47
124 99 0.50
125 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (122 bp):
TAGTATTTACAGCATTTAGATGCAAGAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAAT
AAGCAACTATGGGTCAACTTATCATTCATTGACATAACTGCAATATACATATACGTC
Found at i:953547 original size:8 final size:8
Alignment explanation
Indices: 953536--953564 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
953526 TATACATGCA
953536 TACATATC
1 TACATATC
953544 TACATATC
1 TACATATC
953552 TACATATC
1 TACATATC
953560 TACAT
1 TACAT
953565 CCATACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (8 bp):
TACATATC
Found at i:953547 original size:16 final size:16
Alignment explanation
Indices: 953528--953574 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
953518 CATATACATA
*
953528 TACATGCATACATATC
1 TACATCCATACATATC
*
953544 TACATATC-TACATATC
1 TACAT-CCATACATATC
953560 TACATCCATACATAT
1 TACATCCATACATAT
953575 AGTATTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (16 bp):
TACATCCATACATATC
Found at i:953683 original size:168 final size:165
Alignment explanation
Indices: 953405--953715 Score: 460
Period size: 168 Copynumber: 1.9 Consensus size: 165
953395 ATACATATAA
* * *
953405 ATAGTATTTACAGCATTTAGATACAAGAAAACTCGTATTCTATCAATTCTAAGGCAAATTATAGA
1 ATAGTATTTACAGCATTTAGATACAAGAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAA
* * *
953470 AAACCAACTATGGGTCAACTAACCATTCATTGACATAGCTGCAATATACATATACATATACATGC
66 AAACCAACTATGGGTCAACTAACCATTCATTAACATAACTGCAATATACATATAC-TACACATGC
953535 ATACATATCTACATATCTACATATCTACATCCATACAT
130 ATACATA-C-ACATATCTACATATCTACATCCATACAT
* * * * * *
953573 ATAGTATTTACAGCATTTATATGCGAGAGAACTCATATTCTGTCAGTTCTAAGGCAAATCATAAA
1 ATAGTATTTACAGCATTTAGATACAAGAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAA
** *
953638 AAACCAACTATGGGTCAACTAGTCATTCATTAACATAATTGCAATATACATATACTACACATGCA
66 AAACCAACTATGGGTCAACTAACCATTCATTAACATAACTGCAATATACATATACTACACATGCA
953703 TACATACACATAT
131 TACATACACATAT
953716 ATAGTATTTA
Statistics
Matches: 128, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
165 6 0.05
166 1 0.01
167 15 0.12
168 106 0.83
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (165 bp):
ATAGTATTTACAGCATTTAGATACAAGAAAACTCATATTCTATCAATTCTAAGGCAAATCATAAA
AAACCAACTATGGGTCAACTAACCATTCATTAACATAACTGCAATATACATATACTACACATGCA
TACATACACATATCTACATATCTACATCCATACAT
Found at i:953820 original size:4 final size:4
Alignment explanation
Indices: 953813--953857 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
953803 TAATTGATTG
953813 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
953858 TACAGTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:953857 original size:143 final size:141
Alignment explanation
Indices: 953696--953968 Score: 340
Period size: 143 Copynumber: 1.9 Consensus size: 141
953686 CATATACTAC
*
953696 ACATGCATACATAC--ACATATATAGTATTTACAGCATTTAGATGCAAGAAATCTCATATTCTAT
1 ACATACATACATACATACATATATAGTATTTACAGCATTTAGATGCAAGAAA-CTCATATTCTAT
* *
953759 CAATTCTAAGGCATATATAAAGAAACCAACTATGGGTCAACTAATAATTGATTGACAT-ACATAC
65 CAATTCTAAGGCATATATAAA-AAACCAACTATGGGTCAACTAATCATTAATTGACATAAC-TAC
953823 ATACATACATACAT
128 ATACATACATACAT
* * * * * *
953837 ACATACATACATACATACATATACAGTATTCAAAGTATTTAGATGCAATAAAACTCGTATTCTAT
1 ACATACATACATACATACATATATAGTATTTACAGCATTTAGATGCAA-GAAACTCATATTCTAT
* * *
953902 CAATTCTAAGGC-TAATTATTGAAAAACCAACTAT-GGTCAAGTAATCATCAATTGACATAACTA
65 CAATTCTAAGGCAT-A-TA-TAAAAAACCAACTATGGGTCAACTAATCATTAATTGACATAACTA
953965 CATA
127 CATA
953969 TATAGAGAAT
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
141 13 0.12
142 1 0.01
143 78 0.69
144 18 0.16
145 3 0.03
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.30
Consensus pattern (141 bp):
ACATACATACATACATACATATATAGTATTTACAGCATTTAGATGCAAGAAACTCATATTCTATC
AATTCTAAGGCATATATAAAAAACCAACTATGGGTCAACTAATCATTAATTGACATAACTACATA
CATACATACAT
Found at i:955059 original size:18 final size:20
Alignment explanation
Indices: 955023--955059 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
955013 TAAAAATTTA
*
955023 TATATTATATACATTTATTG
1 TATATTATATACATATATTG
955043 TATATTATA-A-ATATATT
1 TATATTATATACATATATT
955060 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.38
19 1 0.06
20 9 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TATATTATATACATATATTG
Found at i:959162 original size:14 final size:15
Alignment explanation
Indices: 959119--959162 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
959109 TTAATTATTT
*
959119 TATATATGTTTTATAA
1 TATATATATTTTA-AA
*
959135 TATATTTATTTTAAA
1 TATATATATTTTAAA
959150 TATATAT-TTTTAA
1 TATATATATTTTAA
959163 TAAGTCGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 6 0.24
15 8 0.32
16 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TATATATATTTTAAA
Found at i:959617 original size:68 final size:67
Alignment explanation
Indices: 959512--959750 Score: 178
Period size: 68 Copynumber: 3.4 Consensus size: 67
959502 TTCTTCTATC
* *
959512 AATCT-ACCAATTAGTTTATACGAGCTAAATGGTAGTTTAGATACGATATGAAACATATTTTAAA
1 AATCTAACC-ATTAATTTATACGAGTTAAAT-GTAGTTTAGATA-GATATGAAACATATTTTAAA
*
959576 ATAT-
63 ACATA
* * * * ** * *
959580 GATTTAACCATTAATTTATACGAGTTAAATATCAGTTTAAAATAGATAAAAAAAAACATATCTAA
1 AATCTAACCATTAATTTATACGAGTTAAATGT-AGTTT-AGATAGAT---ATGAAACATATTTTA
959645 AACACATA
61 AA-ACATA
* * * *
959653 AATCTAACCATTAATTTAGACGAGTTAAATGTAAGATTAGATATGAAATGAAGCATATTTTAAAA
1 AATCTAACCATTAATTTATACGAGTTAAATGT-AGTTTAGATA-GATATGAAACATATTTTAAAA
*
959718 CA-C
64 CATA
* * * *
959721 AGTCTAACCATTAGTTTGTACGAGCTAAAT
1 AATCTAACCATTAATTTATACGAGTTAAAT
959751 ACCAATTCTT
Statistics
Matches: 132, Mismatches: 30, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
67 1 0.01
68 55 0.42
69 10 0.08
70 12 0.09
71 13 0.10
72 7 0.05
73 34 0.26
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (67 bp):
AATCTAACCATTAATTTATACGAGTTAAATGTAGTTTAGATAGATATGAAACATATTTTAAAACA
TA
Found at i:960473 original size:21 final size:25
Alignment explanation
Indices: 960430--960475 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
960420 CTTTTTTCAG
960430 AAAAAAGCAAGAAAAACGCAAAAAA
1 AAAAAAGCAAGAAAAACGCAAAAAA
960455 AAAAAAG-AA-AAAAA-G-AAAAAA
1 AAAAAAGCAAGAAAAACGCAAAAAA
960476 GATAGAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 5 0.24
24 2 0.10
25 7 0.33
ACGTcount: A:0.83, C:0.07, G:0.11, T:0.00
Consensus pattern (25 bp):
AAAAAAGCAAGAAAAACGCAAAAAA
Found at i:962497 original size:20 final size:22
Alignment explanation
Indices: 962472--962512 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
962462 CAATTGAACC
962472 GAAATTTTAA-AATTT-TTTAG
1 GAAATTTTAATAATTTATTTAG
962492 GAAATTTTAATAATTTATTTA
1 GAAATTTTAATAATTTATTTA
962513 ATCGAGCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
GAAATTTTAATAATTTATTTAG
Found at i:964991 original size:20 final size:20
Alignment explanation
Indices: 964966--965006 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
964956 GTTTTTTAAA
964966 TTTTC-TAGTATTTTATTTCT
1 TTTTCTTAGTATTTT-TTTCT
964986 TTTTCTTAGTATTTTTTTCT
1 TTTTCTTAGTATTTTTTTCT
965006 T
1 T
965007 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.73
Consensus pattern (20 bp):
TTTTCTTAGTATTTTTTTCT
Found at i:968256 original size:49 final size:49
Alignment explanation
Indices: 968201--968300 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
968191 TCATTAAATT
968201 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
1 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
*
968250 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCTATAAGTCTTTATAC
1 TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
968299 TT
1 TT
968301 CATAAATTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (49 bp):
TTTAGGTTATGTTTCTATTAAGGTTAAAATACCCAATAAGTCTTTATAC
Found at i:973885 original size:32 final size:33
Alignment explanation
Indices: 973817--973885 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
973807 TTACGGTTAG
** * *
973817 TGTAAAAATAATGATGATAATAAAATTAAATAC
1 TGTAAAAATAACAATGACAATAAAATAAAATAC
973850 TGTAAAAATAACAATGACAATAAAA-AAAATAC
1 TGTAAAAATAACAATGACAATAAAATAAAATAC
973882 TGTA
1 TGTA
973886 TCGTACCGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (33 bp):
TGTAAAAATAACAATGACAATAAAATAAAATAC
Found at i:974903 original size:21 final size:21
Alignment explanation
Indices: 974879--974920 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
974869 AAATCACTTA
974879 AACAAGTCTTTGCATAGCAAT
1 AACAAGTCTTTGCATAGCAAT
974900 AACAAGTCTTTGCATAGCAAT
1 AACAAGTCTTTGCATAGCAAT
974921 GTGAAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (21 bp):
AACAAGTCTTTGCATAGCAAT
Found at i:979315 original size:16 final size:16
Alignment explanation
Indices: 979296--979344 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
979286 GCTTAAAACA
979296 ACTCAAACTCAAAATG
1 ACTCAAACTCAAAATG
* *
979312 ACTCGAACTTAAAATG
1 ACTCAAACTCAAAATG
*
979328 AC-CAAAATCCAAAATG
1 ACTCAAACT-CAAAATG
979344 A
1 A
979345 TCATAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.51, C:0.22, G:0.08, T:0.18
Consensus pattern (16 bp):
ACTCAAACTCAAAATG
Found at i:982815 original size:19 final size:19
Alignment explanation
Indices: 982791--982830 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
982781 TATATTGTTA
982791 TTTTAATACATTATATAAT
1 TTTTAATACATTATATAAT
*
982810 TTTTAATATATTATATAAT
1 TTTTAATACATTATATAAT
982829 TT
1 TT
982831 ATAACACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAATACATTATATAAT
Found at i:983745 original size:84 final size:84
Alignment explanation
Indices: 983591--983786 Score: 230
Period size: 84 Copynumber: 2.3 Consensus size: 84
983581 AATTAGCTGT
* * * * * * * *
983591 CTTTAAGATGTTTGATAAAATGTTTGTGTTGGGCCAAATCGACTTGTAGAAGAAATATTAGTGAC
1 CTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAACTTGTAGAAGAAAAATTAATGAA
*
983656 CCAAAGTCAAATAAGTTGC
66 CCAAAGACAAATAAGTTGC
* * * *
983675 CTTTCAGATGTTTGATAATATGTTTGTGTTAGACTAATTCAAGTTTTAGAAGAAAAATTAATGAA
1 CTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAACTTGTAGAAGAAAAATTAATGAA
* * *
983740 GCAAAGACAAATTAGTTGT
66 CCAAAGACAAATAAGTTGC
* *
983759 CTTTCAGATGTTTGAGAATATATTTGTG
1 CTTTCAGATGTTTGATAATATGTTTGTG
983787 AAGTGTGGTC
Statistics
Matches: 94, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 94 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (84 bp):
CTTTCAGATGTTTGATAATATGTTTGTGTTAGACCAAATCAACTTGTAGAAGAAAAATTAATGAA
CCAAAGACAAATAAGTTGC
Found at i:994240 original size:8 final size:8
Alignment explanation
Indices: 994223--994255 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
994213 GTTCTTATTC
*
994223 TTATTTTT
1 TTATTGTT
994231 TTATTGTT
1 TTATTGTT
994239 TTATTGTT
1 TTATTGTT
994247 TTATT-TT
1 TTATTGTT
994254 TT
1 TT
994256 CACAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (8 bp):
TTATTGTT
Found at i:995107 original size:2 final size:2
Alignment explanation
Indices: 995100--995126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
995090 AAGTAGGATA
995100 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
995127 AGGTCAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:997907 original size:2 final size:2
Alignment explanation
Indices: 997900--997941 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
997890 ATCTGTGCAA
997900 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
997942 GTCTTTCGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:998274 original size:2 final size:2
Alignment explanation
Indices: 998267--998291 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
998257 TGGCTAACCA
998267 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
998292 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1002932 original size:3 final size:3
Alignment explanation
Indices: 1002924--1002954 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1002914 TTTCTTGTTT
1002924 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1002955 CAAGACAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1022084 original size:49 final size:48
Alignment explanation
Indices: 1022025--1022204 Score: 213
Period size: 49 Copynumber: 3.7 Consensus size: 48
1022015 GGCAGTGAGT
1022025 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGACAGACCGATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGACAGA-CGATGA
* *
1022074 GTGCTGGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-ACAGAC-GATGA
* * * * * *
1022124 GAG-TCAGTGTAATACCATGTTTGAGACATGACATCGG-CTCGA-GATGA
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGAC-AGACGATGA
*
1022171 GTGCCAGTGTAAGACCATGTCTGGGACATGGCAT
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCAT
1022205 TGGCACCGAC
Statistics
Matches: 110, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
47 31 0.28
48 1 0.01
49 40 0.36
50 38 0.35
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (48 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGACAGACGATGA
Found at i:1022141 original size:50 final size:49
Alignment explanation
Indices: 1022025--1022215 Score: 219
Period size: 50 Copynumber: 3.9 Consensus size: 49
1022015 GGCAGTGAGT
*
1022025 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-ACAGACCGATGA
1 GTGC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGATGA
* *
1022074 GTGCTGGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGAGGA
1 GTGC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGATGA
* * * * * *
1022124 GAGTCAGTGTAATACCATGTTTGAGACATGACATCGGCTC-G--AGATGA
1 GTG-CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGATGA
* *
1022171 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCACCGACA
1 GTG-CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACA
1022216 TGTGATCCCA
Statistics
Matches: 118, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
47 37 0.31
48 1 0.01
49 37 0.31
50 42 0.36
51 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21
Consensus pattern (49 bp):
GTGCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACAGATGA
Found at i:1023833 original size:15 final size:15
Alignment explanation
Indices: 1023813--1023843 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1023803 GTCCAGTTTA
*
1023813 ATTAAATGATTCAAT
1 ATTAAATGAATCAAT
1023828 ATTAAATGAATCAAT
1 ATTAAATGAATCAAT
1023843 A
1 A
1023844 AAATTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
ATTAAATGAATCAAT
Found at i:1025038 original size:27 final size:29
Alignment explanation
Indices: 1024977--1025039 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
1024967 TATATTTTTT
1024977 AATTTTTAATTTTTCAATATTTTAAAATA
1 AATTTTTAATTTTTCAATATTTTAAAATA
** * *
1025006 CTTTTTTTATTTTT-TAT-TTTTAAAATA
1 AATTTTTAATTTTTCAATATTTTAAAATA
1025033 AATTTTT
1 AATTTTT
1025040 GGTGTTTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 15 0.54
28 2 0.07
29 11 0.39
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (29 bp):
AATTTTTAATTTTTCAATATTTTAAAATA
Found at i:1037593 original size:7 final size:7
Alignment explanation
Indices: 1037581--1037610 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1037571 GAATTCAAAA
1037581 AAAAATT
1 AAAAATT
1037588 AAAAATT
1 AAAAATT
1037595 AAAAATT
1 AAAAATT
1037602 AAAAATT
1 AAAAATT
1037609 AA
1 AA
1037611 TTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:1037618 original size:19 final size:18
Alignment explanation
Indices: 1037591--1037626 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1037581 AAAAATTAAA
1037591 AATTAAAAATTAAAAATT
1 AATTAAAAATTAAAAATT
*
1037609 AATTATAAAATTATAAAT
1 AATTA-AAAATTAAAAAT
1037627 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAAAATTAAAAATT
Found at i:1042731 original size:18 final size:19
Alignment explanation
Indices: 1042694--1042732 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1042684 ATACAAAAAT
*
1042694 AATTAAAAATAATTTTTAA
1 AATTAAAAATAATTTATAA
*
1042713 AATTCAAAAT-ATTTATAA
1 AATTAAAAATAATTTATAA
1042731 AA
1 AA
1042733 ATGTTAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAAATAATTTATAA
Found at i:1044383 original size:91 final size:91
Alignment explanation
Indices: 1044228--1044410 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
1044218 GTAGACTAGC
* * *
1044228 AAGAGTTTATAAGGAATTCAAAATGTGTCTTATGAAGTGTGTACTATTCTAGAAGACACCCATGA
1 AAGAGTGTACAAGGAATTCAAAATGTGTCTTATGAAGTGTGGACTATTCTAGAAGACACCCATGA
1044293 AGGAACTTATACAGTCAAGCTATCAA
66 AGGAACTTATACAGTCAAGCTATCAA
* * *
1044319 AAGAGTGTACAAGGAATTCAAAATGTGTCTTATGAATTGTGGACTATTCTATAAGCCACCCATGA
1 AAGAGTGTACAAGGAATTCAAAATGTGTCTTATGAAGTGTGGACTATTCTAGAAGACACCCATGA
* *
1044384 AGTAACTTATACGGTCAAGCTATCAA
66 AGGAACTTATACAGTCAAGCTATCAA
1044410 A
1 A
1044411 GCTCCACATG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (91 bp):
AAGAGTGTACAAGGAATTCAAAATGTGTCTTATGAAGTGTGGACTATTCTAGAAGACACCCATGA
AGGAACTTATACAGTCAAGCTATCAA
Found at i:1049633 original size:39 final size:39
Alignment explanation
Indices: 1049566--1049645 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 39
1049556 TGCAATTATA
* * * * *
1049566 AAGCGTAGAATTAAACTATTATAGCACAAATGGATTAAG
1 AAGCGTAGAATCAAACAATTACAACACAAATAGATTAAG
*
1049605 AAGCGTAGCATCAAACAATTACAACACAAATAGATTAAG
1 AAGCGTAGAATCAAACAATTACAACACAAATAGATTAAG
1049644 AA
1 AA
1049646 TCAGAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.21
Consensus pattern (39 bp):
AAGCGTAGAATCAAACAATTACAACACAAATAGATTAAG
Found at i:1052714 original size:29 final size:29
Alignment explanation
Indices: 1052656--1052716 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1052646 ATAAATTAAT
*
1052656 AAATGATTAAATTATTTTTAGTCCTCTTA
1 AAATGATTAAATTATTTTTAATCCTCTTA
*
1052685 AAATGA-TAAATTTTTAATTTAATCCT-TTA
1 AAATGATTAAATTATT--TTTAATCCTCTTA
1052714 AAA
1 AAA
1052717 ATTATAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.29
29 12 0.43
30 8 0.29
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (29 bp):
AAATGATTAAATTATTTTTAATCCTCTTA
Found at i:1059785 original size:22 final size:22
Alignment explanation
Indices: 1059760--1059802 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1059750 TATTCAAATA
1059760 ATAACAATAAAAT-AGTAGTAAC
1 ATAACAATAAAATGA-TAGTAAC
*
1059782 ATAACAATGAAATGATAGTAA
1 ATAACAATAAAATGATAGTAA
1059803 AACAGTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATGATAGTAAC
Found at i:1059837 original size:22 final size:22
Alignment explanation
Indices: 1059812--1059856 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1059802 AAACAGTGAG
1059812 AAAACAACAAAAAAAATAGCAAA
1 AAAACAA-AAAAAAAATAGCAAA
* *
1059835 AAAACAAAAAGAAAATATCAAA
1 AAAACAAAAAAAAAATAGCAAA
1059857 TTTCTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.78, C:0.11, G:0.04, T:0.07
Consensus pattern (22 bp):
AAAACAAAAAAAAAATAGCAAA
Found at i:1060962 original size:23 final size:24
Alignment explanation
Indices: 1060924--1060969 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1060914 ATACTCTAGT
*
1060924 AAAAAAATATAAGTACTAAATTAA
1 AAAAAAATATAAGTACCAAATTAA
*
1060948 AAAAAAAT-TAGGTACCAAATTA
1 AAAAAAATATAAGTACCAAATTA
1060970 TATATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (24 bp):
AAAAAAATATAAGTACCAAATTAA
Found at i:1064796 original size:17 final size:20
Alignment explanation
Indices: 1064755--1064797 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1064745 TTGCTACTAC
1064755 TTTGTTGTTATTGTATAACT
1 TTTGTTGTTATTGTATAACT
*
1064775 CTTGTT-TTATTGT-TAA-T
1 TTTGTTGTTATTGTATAACT
1064792 TTTGTT
1 TTTGTT
1064798 ACTACTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 3 0.14
19 7 0.33
20 5 0.24
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.65
Consensus pattern (20 bp):
TTTGTTGTTATTGTATAACT
Found at i:1068796 original size:24 final size:25
Alignment explanation
Indices: 1068769--1068824 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
1068759 TAAATTGTGT
*
1068769 ATTTTTATTA-TATATAATTTTATA
1 ATTTTTAATAGTATATAATTTTATA
* *
1068793 A-TTTTAATAGTTTATATTTTTATA
1 ATTTTTAATAGTATATAATTTTATA
1068817 ATTTTTAA
1 ATTTTTAA
1068825 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTTTTAATAGTATATAATTTTATA
Found at i:1070179 original size:28 final size:28
Alignment explanation
Indices: 1070142--1070209 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 28
1070132 TATTTTAAAT
*
1070142 ATTTTAAAAATATTTTAAAATTAAAAAA
1 ATTTAAAAAATATTTTAAAATTAAAAAA
1070170 ATTTAAAAAAAGTATTTTAAAATTAAAAAA
1 ATTT-AAAAAA-TATTTTAAAATTAAAAAA
1070200 A--TAAAAAATA
1 ATTTAAAAAATA
1070210 AAAATATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 2 0.05
27 6 0.16
28 5 0.14
29 5 0.14
30 19 0.51
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
ATTTAAAAAATATTTTAAAATTAAAAAA
Found at i:1073298 original size:28 final size:27
Alignment explanation
Indices: 1073258--1073331 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 27
1073248 CACGACCTAC
* *
1073258 CACATGGCCGTGTGGTCATCGTGTGGAT
1 CACATGGCCGTGTGGTC-CCATGTGGAT
1073286 CACATGGCCGTGTGGTTGCCCATGTGGAT
1 CACATGGCCGTGTGG-T-CCCATGTGGAT
*
1073315 CACACGGCCGTGTGGTC
1 CACATGGCCGTGTGGTC
1073332 GCCCGTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 1 0.02
28 16 0.39
29 23 0.56
30 1 0.02
ACGTcount: A:0.14, C:0.26, G:0.35, T:0.26
Consensus pattern (27 bp):
CACATGGCCGTGTGGTCCCATGTGGAT
Found at i:1073323 original size:29 final size:29
Alignment explanation
Indices: 1073279--1073341 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
1073269 GTGGTCATCG
* *
1073279 TGTGGATCACATGGCCGTGTGGTTGCCCA
1 TGTGGATCACACGGCCGTGTGGTCGCCCA
*
1073308 TGTGGATCACACGGCCGTGTGGTCGCCCG
1 TGTGGATCACACGGCCGTGTGGTCGCCCA
1073337 TGTGG
1 TGTGG
1073342 CTCCTATGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.11, C:0.25, G:0.38, T:0.25
Consensus pattern (29 bp):
TGTGGATCACACGGCCGTGTGGTCGCCCA
Found at i:1087396 original size:14 final size:14
Alignment explanation
Indices: 1087377--1087408 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1087367 AGGTCATTTA
1087377 GCCCAACCAAACTG
1 GCCCAACCAAACTG
1087391 GCCCAACCAAACTG
1 GCCCAACCAAACTG
1087405 GCCC
1 GCCC
1087409 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:1088100 original size:20 final size:20
Alignment explanation
Indices: 1088045--1088100 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1088035 TATGTTGAAC
1088045 ATCATAGAAAATTA-TTAAAA
1 ATCATA-AAAATTATTTAAAA
**
1088065 ATCATATTAATTATTTAAAA
1 ATCATAAAAATTATTTAAAA
*
1088085 CTCATAAAAATTATTT
1 ATCATAAAAATTATTT
1088101 TTTTGGCATC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (20 bp):
ATCATAAAAATTATTTAAAA
Found at i:1088189 original size:20 final size:21
Alignment explanation
Indices: 1088164--1088213 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1088154 GTTTCCAATA
1088164 AAAATTTGAGTTTTT-A-TTAG
1 AAAA-TTGAGTTTTTCATTTAG
*
1088184 AAAATTGTGTTTTTCATTTAG
1 AAAATTGAGTTTTTCATTTAG
1088205 -AAATTGAGT
1 AAAATTGAGT
1088214 AAATAGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 13 0.50
21 4 0.15
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (21 bp):
AAAATTGAGTTTTTCATTTAG
Found at i:1088204 original size:21 final size:20
Alignment explanation
Indices: 1088164--1088207 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
1088154 GTTTCCAATA
1088164 AAAATTTGAGTTTTTATTAG
1 AAAATTTGAGTTTTTATTAG
*
1088184 AAAA-TTGTGTTTTTCATTTAG
1 AAAATTTGAGTTTTT-A-TTAG
1088205 AAA
1 AAA
1088208 TTGAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 5 0.24
21 7 0.33
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (20 bp):
AAAATTTGAGTTTTTATTAG
Found at i:1095927 original size:41 final size:41
Alignment explanation
Indices: 1095845--1095940 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
1095835 CATCGGCACG
* **
1095845 AAGCCTGCTAGGCATAAAGCCTGATCTAATACACCAACATA
1 AAGCCTGCTAGGCATAAAGCCCGATAAAATACACCAACATA
** **
1095886 AAGCCTGCTAGGCATAAAGCCCGATAAAATTTACCGGCATA
1 AAGCCTGCTAGGCATAAAGCCCGATAAAATACACCAACATA
1095927 AAGCCTGCTAGGCA
1 AAGCCTGCTAGGCA
1095941 CAGAGCCTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (41 bp):
AAGCCTGCTAGGCATAAAGCCCGATAAAATACACCAACATA
Found at i:1106081 original size:18 final size:18
Alignment explanation
Indices: 1106058--1106093 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1106048 TGAATTTTAG
*
1106058 ACCTTCATACATATCAAT
1 ACCTTCACACATATCAAT
*
1106076 ACCTTCACATATATCAAT
1 ACCTTCACACATATCAAT
1106094 TACTTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.28, G:0.00, T:0.33
Consensus pattern (18 bp):
ACCTTCACACATATCAAT
Found at i:1107444 original size:2 final size:2
Alignment explanation
Indices: 1107439--1107482 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1107429 GTTCTCTCTT
1107439 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1107481 TA
1 TA
1107483 ATTAGGTACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1107553 original size:21 final size:23
Alignment explanation
Indices: 1107528--1107571 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1107518 AAAATAACTT
*
1107528 TTTTTTAT-CATTAAATATATGA
1 TTTTCTATCCATTAAATATATGA
* *
1107550 TTTTCTCTCCATTATATATATG
1 TTTTCTATCCATTAAATATATG
1107572 GTTACAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTCTATCCATTAAATATATGA
Found at i:1116343 original size:16 final size:17
Alignment explanation
Indices: 1116322--1116353 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1116312 TTATAAACAA
1116322 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
1116338 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
1116354 GCTCAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:1120692 original size:50 final size:50
Alignment explanation
Indices: 1120617--1120720 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
1120607 CCATAAAAAG
1120617 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
*
1120667 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
1120717 ATCA
1 ATCA
1120721 GTTTGGTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.36
Consensus pattern (50 bp):
ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGAA
Found at i:1122596 original size:162 final size:162
Alignment explanation
Indices: 1122309--1122633 Score: 510
Period size: 162 Copynumber: 2.0 Consensus size: 162
1122299 GTAAACCACA
* * *
1122309 CAGTTGGTCACTCAACTTTTATATGTATTCATTTTGGGCACCAAATTTAAAAGTTTACAATTTAG
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTTACAATTTAG
* * *
1122374 GTACTGTCGTTATATACTTTTATCATTTTAGTCACTATCATTACATACTTTTTTTATCATTTTAG
66 GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCATTACATACTTTTTATATCATTTTAG
* *
1122439 TCACCCATCGTTAATTTGT-CATTAAATATACT
131 TCACCCACCATTAATTT-TCCATTAAATATACT
* *
1122471 CAGTTGGCCACTTAACTTTTATAAGTATTCATTTTGGACACCAAAATTTAAAAGTTTGCAATTTA
1 CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACC-AAATTTAAAAGTTTACAATTTA
* *
1122536 GGTACTGTTATTATATACTTTTATCATTTTAGCCACTATCGTTACATAC-TTTTATATCATTTTA
65 GGTACTGTCATTATATACTTTTATCATTTTAGCCACTATCATTACATACTTTTTATATCATTTTA
1122600 GTCACCCACCATTAATTTTCCATTAAATATACT
130 GTCACCCACCATTAATTTTCCATTAAATATACT
1122633 C
1 C
1122634 TTTTTTAATC
Statistics
Matches: 149, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
161 1 0.01
162 82 0.55
163 66 0.44
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.44
Consensus pattern (162 bp):
CAGTTGGCCACTCAACTTTTATAAGTATTCATTTTGGACACCAAATTTAAAAGTTTACAATTTAG
GTACTGTCATTATATACTTTTATCATTTTAGCCACTATCATTACATACTTTTTATATCATTTTAG
TCACCCACCATTAATTTTCCATTAAATATACT
Found at i:1122760 original size:23 final size:23
Alignment explanation
Indices: 1122734--1122779 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1122724 TCTAAAAAGA
*
1122734 TAAATTAGTTTTTC-AGTAAAAAC
1 TAAAGTAGTTTTTCTA-TAAAAAC
*
1122757 TAAAGTATTTTTTCTATAAAAAC
1 TAAAGTAGTTTTTCTATAAAAAC
1122780 CTAGGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (23 bp):
TAAAGTAGTTTTTCTATAAAAAC
Found at i:1124204 original size:14 final size:13
Alignment explanation
Indices: 1124185--1124218 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1124175 TTTAGAAATA
1124185 AAAAAAATAGATTC
1 AAAAAAA-AGATTC
1124199 -AAAAAAAGATTC
1 AAAAAAAAGATTC
1124211 AAAAAAAA
1 AAAAAAAA
1124219 CTAAATGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAAAAAAGATTC
Found at i:1124208 original size:12 final size:12
Alignment explanation
Indices: 1124186--1124217 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
1124176 TTAGAAATAA
1124186 AAAAAATAGATTC
1 AAAAAA-AGATTC
1124199 AAAAAAAGATTC
1 AAAAAAAGATTC
1124211 AAAAAAA
1 AAAAAAA
1124218 ACTAAATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAAAAAGATTC
Found at i:1125033 original size:3 final size:3
Alignment explanation
Indices: 1125020--1125067 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
1125010 AGATTTCTAC
* * * *
1125020 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAC TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1125068 ATTTATCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1126345 original size:19 final size:19
Alignment explanation
Indices: 1126321--1126359 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1126311 TCACATATAG
*
1126321 TTATATGTCTCATCAATAA
1 TTATATGTCACATCAATAA
1126340 TTATATGTCACATCAATAA
1 TTATATGTCACATCAATAA
1126359 T
1 T
1126360 ACAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATATGTCACATCAATAA
Found at i:1128333 original size:15 final size:15
Alignment explanation
Indices: 1128319--1128371 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1128309 GTTATTTTTT
1128319 CTTCTTTTTTCTTTTC
1 CTTCTTTTTTC-TTTC
*
1128335 ATTCTCTTTTTCTTCTC
1 CTTCT-TTTTTCTT-TC
* *
1128352 CCTCTATTTTCTTTC
1 CTTCTTTTTTCTTTC
1128367 CTTCT
1 CTTCT
1128372 CCATTTCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 6 0.20
16 13 0.43
17 11 0.37
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTCTTTTTTCTTTC
Found at i:1134127 original size:169 final size:169
Alignment explanation
Indices: 1133810--1134127 Score: 381
Period size: 169 Copynumber: 1.9 Consensus size: 169
1133800 ATAATTATAG
* * * * * *
1133810 GTAAACATAAGTAGGAATGTGATGAGTTATATAAACTTCTAATGGAGTTGCTTTAGGACTCATTA
1 GTAAACAAAAGCAGGAAGGCGAGGAGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
*** * ** * *
1133875 ATTTGACTGCTTCAGACATATCGACTGGATTGTTTGATGGAGTTTCAAACTCGAACCAATGCAGC
66 ATCCAACTCCTTCAGACATATCGACTGGATTGCCTGATGGAGTTTCAAACTCAAACCAATGCAAC
**
1133940 AAATTACCCAGGGTAAGCTCTAATGGAGTTAGTGGAATT
131 AAATTACCCAACGTAAGCTCTAATGGAGTTAGTGGAATT
* *
1133979 GTAAACAAAAGCAGGAAGGCGAGGAGTTATATGAACTTCTAATGGAGTTGCTTTAGAACTC-TTT
1 GTAAACAAAAGCAGGAAGGCGAGGAGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
* * *
1134043 ATCCCAAGTCCTTCACG-CATATCGACT-GCTATGCCTGATGGGGTTTCAAACTCAAACCAATGC
66 AT-CCAACTCCTTCA-GACATATCGACTGGAT-TGCCTGATGGAGTTTCAAACTCAAACCAATGC
* *
1134106 AACACATTAGCCAACGTAAGCT
128 AACAAATTACCCAACGTAAGCT
1134128 GTAAAACTTG
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
168 6 0.05
169 116 0.94
170 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (169 bp):
GTAAACAAAAGCAGGAAGGCGAGGAGTTATATAAACTTCTAATGGAGTTGCTTTAGAACTCATTA
ATCCAACTCCTTCAGACATATCGACTGGATTGCCTGATGGAGTTTCAAACTCAAACCAATGCAAC
AAATTACCCAACGTAAGCTCTAATGGAGTTAGTGGAATT
Found at i:1135923 original size:19 final size:18
Alignment explanation
Indices: 1135900--1135944 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1135890 AAAAAAAAAG
*
1135900 ATTTTTGAAAAAAGATTT-
1 ATTTTTTAAAAAA-ATTTA
1135918 ATTTTTATAAAAAAATTTA
1 ATTTTT-TAAAAAAATTTA
1135937 ATTTTTTA
1 ATTTTTTA
1135945 TGGTGTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
ATTTTTTAAAAAAATTTA
Found at i:1137075 original size:17 final size:17
Alignment explanation
Indices: 1137029--1137081 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
1137019 TTATTTTCAA
1137029 AATTTATTATTAAAATAA-
1 AATTTA-TATT-AAATAAT
1137047 AATTAATATATTAAATAAT
1 AATT--TATATTAAATAAT
1137066 AATTTATATT-AATAAT
1 AATTTATATTAAATAAT
1137082 TTATTATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 10 0.31
19 8 0.25
20 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTATATTAAATAAT
Found at i:1139291 original size:50 final size:50
Alignment explanation
Indices: 1139232--1139335 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
1139222 CTATAAAAAG
*
1139232 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGTTATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
1139282 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
1 ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
1139332 ATCA
1 ATCA
1139336 GTTTGGTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (50 bp):
ATCAACAATGAATTAATAGCATTTCCAACTTCTGTATGATATTAATGGCA
Found at i:1140921 original size:31 final size:32
Alignment explanation
Indices: 1140886--1140947 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
1140876 TTAGGTACTG
*
1140886 TCGTTATATAC-TTTTATCATTTTAGTCACTA
1 TCGTTACATACTTTTTATCATTTTAGTCACTA
1140917 TCGTTACATACTTTTTTATCATTTTAGTCAC
1 TCGTTACATAC-TTTTTATCATTTTAGTCAC
1140948 CCACTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 10 0.36
33 18 0.64
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (32 bp):
TCGTTACATACTTTTTATCATTTTAGTCACTA
Found at i:1141726 original size:21 final size:22
Alignment explanation
Indices: 1141684--1141733 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1141674 CACATGCGTG
*
1141684 GGATTTTTCTTGAAATTATCTT
1 GGATTTTTCTGGAAATTATCTT
* *
1141706 GGATTTTTC-GGATATTTTCTT
1 GGATTTTTCTGGAAATTATCTT
1141727 GG-TTTTT
1 GGATTTTT
1141734 ATTGAGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.20
21 11 0.44
22 9 0.36
ACGTcount: A:0.16, C:0.08, G:0.18, T:0.58
Consensus pattern (22 bp):
GGATTTTTCTGGAAATTATCTT
Found at i:1141778 original size:15 final size:16
Alignment explanation
Indices: 1141750--1141782 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1141740 TTAATTTTGA
1141750 TTATAATTAATTAAAT
1 TTATAATTAATTAAAT
*
1141766 TTAT-ATTATTTAAAT
1 TTATAATTAATTAAAT
1141781 TT
1 TT
1141783 CTGATCAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATAATTAATTAAAT
Found at i:1142322 original size:19 final size:19
Alignment explanation
Indices: 1142298--1142336 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1142288 TAACAGATAG
*
1142298 TTATATTTCTCATCAATAA
1 TTATATCTCTCATCAATAA
1142317 TTATATCTCTCATCAATAA
1 TTATATCTCTCATCAATAA
1142336 T
1 T
1142337 ACAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATATCTCTCATCAATAA
Found at i:1143617 original size:46 final size:45
Alignment explanation
Indices: 1143546--1143675 Score: 172
Period size: 46 Copynumber: 2.8 Consensus size: 45
1143536 ACAATGCTAT
*
1143546 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTT-ACTGAAATACCATACCTACGTTTCAC
* *
1143592 GACTCAGTACGGTTTTCTTAGCTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTA-CTGAAATACCATACCTACGTTTCAC
* * *
1143638 AACTCAATATGGTTTACTTTACTGAAATA-CTTACCTAC
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTAC
1143676 ATTCCACACT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
45 9 0.12
46 62 0.84
47 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTACTGAAATACCATACCTACGTTTCAC
Found at i:1159852 original size:17 final size:17
Alignment explanation
Indices: 1159803--1159859 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
1159793 TTGAAAATGA
*
1159803 TTTTCAAAAAAATTGAT
1 TTTTCAAAAAAATTTAT
* *
1159820 TTTTGAAAAATGATTTAT
1 TTTTCAAAAA-AATTTAT
*
1159838 TTTTCTAAAAAATTTAAT
1 TTTTCAAAAAAATTT-AT
1159856 TTTT
1 TTTT
1159860 TATGGTGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTTCAAAAAAATTTAT
Done.