Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 231 of 250
Found at i:71301856 original size:41 final size:41
Alignment explanation
Indices: 71301780--71301857 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
71301770 AGGATAATAC
* * *
71301780 GCTTCATCACAATTTAACCCATATATTCCTGTATTGAAAAT
1 GCTTCAGCACAATCTAACCCATATATTCCTATATTGAAAAT
* * *
71301821 GCTTCAGCACAGTCTAACCCATATCTTCTTATATTGA
1 GCTTCAGCACAATCTAACCCATATATTCCTATATTGA
71301858 CATTTGACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (41 bp):
GCTTCAGCACAATCTAACCCATATATTCCTATATTGAAAAT
Found at i:71313416 original size:25 final size:26
Alignment explanation
Indices: 71313387--71313444 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 26
71313377 AAATTAATGA
71313387 AATATTTAAAATATATTTTT-TAATT
1 AATATTTAAAATATATTTTTATAATT
*
71313412 AATATTT--TATATATTTTTATAATT
1 AATATTTAAAATATATTTTTATAATT
71313436 AA-ATTTAAA
1 AATATTTAAA
71313445 TAATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 14 0.50
24 7 0.25
25 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATATTTAAAATATATTTTTATAATT
Found at i:71331611 original size:20 final size:20
Alignment explanation
Indices: 71331586--71331635 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
71331576 TGGCTTAAAA
71331586 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
71331606 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
71331623 GTGGTAGTGGATT
1 TTGGTAGTGGATT
71331636 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:71336250 original size:20 final size:20
Alignment explanation
Indices: 71336225--71336274 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
71336215 TGGCTTAAAA
71336225 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
71336245 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
71336262 GTGGTAGTGGATT
1 TTGGTAGTGGATT
71336275 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:71338170 original size:27 final size:25
Alignment explanation
Indices: 71338109--71338182 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 25
71338099 CCTTTAAAAA
* *
71338109 AAAAAGTCAAGCTTAATTTTTTTTAT
1 AAAAAGTCAAACTTAA-TTTTTTGAT
71338135 AAAAAGTCAAACTTAATTTTTTGAT
1 AAAAAGTCAAACTTAATTTTTTGAT
* *
71338160 ACAGAAGGTCAAACTTAGTTTTT
1 A-A-AAAGTCAAACTTAATTTTT
71338183 GATTCTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
25 9 0.21
26 16 0.38
27 17 0.40
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (25 bp):
AAAAAGTCAAACTTAATTTTTTGAT
Found at i:71343512 original size:21 final size:22
Alignment explanation
Indices: 71343486--71343540 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
71343476 AACTGCGGTG
71343486 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTGTA
71343507 GCGGTGAGATT-GGATACTGTA
1 GCGGTGAGATTAGGATACTGTA
71343528 GCGGTGAGATTAG
1 GCGGTGAGATTAG
71343541 AAACAGCGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTGTA
Found at i:71343677 original size:19 final size:18
Alignment explanation
Indices: 71343653--71343699 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
71343643 AGAAGTTTTT
*
71343653 AAAATTATTTAACAATTA
1 AAAATTATTAAACAATTA
* *
71343671 CAAAATTAATAAATAATTA
1 -AAAATTATTAAACAATTA
71343690 AAAATTATTA
1 AAAATTATTA
71343700 CAATTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAACAATTA
Found at i:71343802 original size:36 final size:34
Alignment explanation
Indices: 71343761--71343871 Score: 120
Period size: 36 Copynumber: 3.6 Consensus size: 34
71343751 GAAAAATTCA
71343761 AAAATATCAAAATATTTTACAGATTATATTCATAAT
1 AAAATATCAAAATATTTTA-A-ATTATATTCATAAT
71343797 AAAATATCAAAATATTTTAAA-TATA--C--AAT
1 AAAATATCAAAATATTTTAAATTATATTCATAAT
71343826 -AAA-AT----AT-TTTTAAATTATATTCATAAT
1 AAAATATCAAAATATTTTAAATTATATTCATAAT
71343853 AAAATATCAAAATATTTTA
1 AAAATATCAAAATATTTTA
71343872 CAGATTAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 26
0.71 0.00 0.29
Matches are distributed among these distances:
22 7 0.11
23 6 0.10
25 1 0.02
27 5 0.08
28 6 0.10
29 5 0.08
31 1 0.02
33 6 0.10
34 6 0.10
35 1 0.02
36 19 0.30
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (34 bp):
AAAATATCAAAATATTTTAAATTATATTCATAAT
Found at i:71345907 original size:13 final size:13
Alignment explanation
Indices: 71345889--71345913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71345879 CCTTCTTTTA
71345889 TTTTTAATTAATG
1 TTTTTAATTAATG
71345902 TTTTTAATTAAT
1 TTTTTAATTAAT
71345914 AAATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:71348726 original size:25 final size:25
Alignment explanation
Indices: 71348697--71348746 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
71348687 AAAAGTAGAA
*
71348697 AAGGAATTATTTAGGTTTTTTTTAC
1 AAGGAATTATTTAGGCTTTTTTTAC
71348722 AAGGAATTATTTAGGCTTTTTTTAC
1 AAGGAATTATTTAGGCTTTTTTTAC
71348747 TTAAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (25 bp):
AAGGAATTATTTAGGCTTTTTTTAC
Found at i:71353306 original size:28 final size:30
Alignment explanation
Indices: 71353264--71353321 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
71353254 GAATTGGATC
71353264 AAATCAAAATTTTATGTAT-GAATTACACA
1 AAATCAAAATTTTATGTATAGAATTACACA
*
71353293 AAATCAAAA-TTTATGTATATAATTACACA
1 AAATCAAAATTTTATGTATAGAATTACACA
71353322 TTCATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTTTATGTATAGAATTACACA
Found at i:71354001 original size:18 final size:17
Alignment explanation
Indices: 71353980--71354013 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
71353970 AAAGATTAAA
71353980 ATATA-TTTTAATTTTT
1 ATATATTTTTAATTTTT
*
71353996 ATATATTTTTTATTTTT
1 ATATATTTTTAATTTTT
71354013 A
1 A
71354014 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATATATTTTTAATTTTT
Found at i:71354409 original size:37 final size:38
Alignment explanation
Indices: 71354319--71354417 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 38
71354309 GATATCGAAG
*
71354319 GTCGCAATTTTAAATCAAGCGAACCATAAAAAATAACA
1 GTCGCAATATTAAATCAAGCGAACCATAAAAAATAACA
** ** * * *
71354357 GTCGTGATACCAAATCAAGCGAATCAT-AAAAATGATA
1 GTCGCAATATTAAATCAAGCGAACCATAAAAAATAACA
* *
71354394 GTCGCAATGTTAAATCAAGTGAAC
1 GTCGCAATATTAAATCAAGCGAAC
71354418 TGGTGAAATG
Statistics
Matches: 46, Mismatches: 15, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
37 25 0.54
38 21 0.46
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.22
Consensus pattern (38 bp):
GTCGCAATATTAAATCAAGCGAACCATAAAAAATAACA
Found at i:71354467 original size:40 final size:37
Alignment explanation
Indices: 71354319--71354468 Score: 88
Period size: 37 Copynumber: 3.9 Consensus size: 37
71354309 GATATCGAAG
* * ***
71354319 GTCGCAATTTTAAATCAAGCGAACCATAAAAAATAACA
1 GTCGCAATCTTAAATCAAGTGAACCAT-AAAAATGTTA
** * * * *
71354357 GTCGTGATAC-CAAATCAAGCGAATCATAAAAATGATA
1 GTCGCAAT-CTTAAATCAAGTGAACCATAAAAATGTTA
* ** *
71354394 GTCGCAATGTTAAATCAAGTGAACTGGT-GAAATGTTGAA
1 GTCGCAATCTTAAATCAAGTGAAC-CATAAAAATGTT--A
*
71354433 GATCGCGATCTTAAATCAAGTGAACCATAAAAATGT
1 G-TCGCAATCTTAAATCAAGTGAACCATAAAAATGT
71354469 CATTTATGAT
Statistics
Matches: 83, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
37 31 0.37
38 22 0.27
39 3 0.04
40 27 0.33
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (37 bp):
GTCGCAATCTTAAATCAAGTGAACCATAAAAATGTTA
Found at i:71354598 original size:37 final size:36
Alignment explanation
Indices: 71354475--71354609 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 36
71354465 ATGTCATTTA
* *
71354475 TGATGTTAAATCAAGCGAACTATTAAAAGATCAAATGTCG
1 TGATGTTAAATCAAGCGAATTA-TAAAA-ATAAAAT-T-G
* * * * * * *
71354515 TAATCTTAAATCAAGTGAATTGTAAAAATGACAAGTA
1 TGATGTTAAATCAAGCGAATTATAAAAAT-AAAATTG
* *
71354552 CGATATTAAATCAAGCGAATTATAAAAATAAAAATTG
1 TGATGTTAAATCAAGCGAATTATAAAAAT-AAAATTG
71354589 TGATGTTAAATCAAGCGAATT
1 TGATGTTAAATCAAGCGAATT
71354610 GTCAGAATAT
Statistics
Matches: 74, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
37 47 0.64
38 3 0.04
39 7 0.09
40 17 0.23
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.29
Consensus pattern (36 bp):
TGATGTTAAATCAAGCGAATTATAAAAATAAAATTG
Found at i:71355827 original size:17 final size:17
Alignment explanation
Indices: 71355779--71355829 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
71355769 GAAATATTTA
*
71355779 TTTTAATATTTTTATTAT
1 TTTTAATTTTTTTA-TAT
* * *
71355797 TTTTGA-TGTATTATAT
1 TTTTAATTTTTTTATAT
71355813 TTTTAATTTTTTTATAT
1 TTTTAATTTTTTTATAT
71355830 AAAAAAACAA
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 5 0.20
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTTTTATAT
Found at i:71358417 original size:2 final size:2
Alignment explanation
Indices: 71358410--71358435 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71358400 CACTCGACAG
71358410 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
71358436 TATATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:71366075 original size:12 final size:11
Alignment explanation
Indices: 71366051--71366080 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
71366041 CATTTTGTTA
71366051 TTTAGTTTCTTT
1 TTTA-TTTCTTT
71366063 TTTATTTCTTT
1 TTTATTTCTTT
71366074 TTTATTT
1 TTTATTT
71366081 TTGTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTATTTCTTT
Found at i:71369799 original size:2 final size:2
Alignment explanation
Indices: 71369786--71369826 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
71369776 GGGATGTATT
* *
71369786 TG TG TG TT TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
71369827 AACAACCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.02, C:0.00, G:0.44, T:0.54
Consensus pattern (2 bp):
TG
Found at i:71374555 original size:35 final size:35
Alignment explanation
Indices: 71374504--71374636 Score: 144
Period size: 35 Copynumber: 3.8 Consensus size: 35
71374494 GGGTGTTACA
*
71374504 TATGGTATTATCCATACTGAGTTATGACACGTAGG
1 TATGGTATTATCCATACTGAGTTATGAAACGTAGG
* * * *
71374539 TATGGTATTATTCATACGGAGCTAT-AATACTTAGG
1 TATGGTATTATCCATACTGAGTTATGAA-ACGTAGG
* *
71374574 TATGGTATT-TCCCATACCGAGTTGTGAAACGTAGG
1 TATGGTATTAT-CCATACTGAGTTATGAAACGTAGG
** *
71374609 TATGGTATTAAACATACTGAGTTGTGAA
1 TATGGTATTATCCATACTGAGTTATGAA
71374637 TCGTGGCACT
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
34 2 0.02
35 77 0.95
36 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (35 bp):
TATGGTATTATCCATACTGAGTTATGAAACGTAGG
Found at i:71385209 original size:16 final size:16
Alignment explanation
Indices: 71385188--71385239 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
71385178 ATGGCCAGTC
*
71385188 TAATGGAATAGGGTTG
1 TAATGGAATAGAGTTG
**
71385204 TAATGGAATAGAACTG
1 TAATGGAATAGAGTTG
71385220 TAATGGAATAGAGTTG
1 TAATGGAATAGAGTTG
71385236 TAAT
1 TAAT
71385240 AGAAGAGAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGTTG
Found at i:71385224 original size:32 final size:32
Alignment explanation
Indices: 71385188--71385255 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
71385178 ATGGCCAGTC
* * *
71385188 TAATGGAATAGGGTTGTAATGGAATAGAACTG
1 TAATGGAATAGAGTTGTAATAGAAGAGAACTG
71385220 TAATGGAATAGAGTTGTAATAGAAGAGAACTG
1 TAATGGAATAGAGTTGTAATAGAAGAGAACTG
71385252 TAAT
1 TAAT
71385256 AGTAATTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (32 bp):
TAATGGAATAGAGTTGTAATAGAAGAGAACTG
Found at i:71385253 original size:16 final size:16
Alignment explanation
Indices: 71385202--71385257 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
71385192 GGAATAGGGT
*
71385202 TGTAATGGAATAGAAC
1 TGTAATAGAATAGAAC
* **
71385218 TGTAATGGAATAGAGT
1 TGTAATAGAATAGAAC
*
71385234 TGTAATAGAAGAGAAC
1 TGTAATAGAATAGAAC
71385250 TGTAATAG
1 TGTAATAG
71385258 TAATTCAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.43, C:0.04, G:0.27, T:0.27
Consensus pattern (16 bp):
TGTAATAGAATAGAAC
Found at i:71385528 original size:21 final size:20
Alignment explanation
Indices: 71385500--71385539 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
71385490 AATTTATTAT
71385500 TAATTATAATTTAACAATAA
1 TAATTATAATTTAACAATAA
*
71385520 TAATATATAATTTAATAATA
1 TAAT-TATAATTTAACAATA
71385540 TTCTTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATTATAATTTAACAATAA
Found at i:71385600 original size:22 final size:21
Alignment explanation
Indices: 71385563--71385608 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 21
71385553 AATTACTAAA
71385563 ATATAAATTAATAAAAATAAT
1 ATATAAATTAATAAAAATAAT
71385584 ATATAATATTACA-AAAAATAAT
1 ATATAA-ATTA-ATAAAAATAAT
71385606 ATA
1 ATA
71385609 CAACCTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.26
22 16 0.70
23 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAAATTAATAAAAATAAT
Found at i:71386533 original size:15 final size:15
Alignment explanation
Indices: 71386507--71386546 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
71386497 GATACAAATC
71386507 AAAA-AAAA-AAAAA
1 AAAAGAAAAGAAAAA
71386520 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
71386535 AAAAGAAAAGAA
1 AAAAGAAAAGAA
71386547 CATATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 4 0.16
14 4 0.16
15 17 0.68
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAA
Found at i:71389524 original size:17 final size:17
Alignment explanation
Indices: 71389498--71389569 Score: 53
Period size: 17 Copynumber: 4.1 Consensus size: 17
71389488 AAATGATCAG
71389498 ATTAATAAAATATATAAAT
1 ATTAA-AAAA-ATATAAAT
71389517 ATT--AAAAAT-TAAATTT
1 ATTAAAAAAATATAAA--T
71389533 ATTTAAAAAAATACTAAAT
1 A-TTAAAAAAATA-TAAAT
*
71389552 -TTAAAAAAATATATAT
1 ATTAAAAAAATATAAAT
71389568 AT
1 AT
71389570 ATATATATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 18
0.70 0.02 0.29
Matches are distributed among these distances:
14 4 0.09
15 2 0.05
16 10 0.23
17 14 0.32
19 10 0.23
21 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAAAAAATATAAAT
Found at i:71394475 original size:17 final size:18
Alignment explanation
Indices: 71394453--71394488 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
71394443 TAAATGAGTT
71394453 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
71394470 AATTAGGATATAAATTGG
1 AATTAGGATATAAATTGG
71394488 A
1 A
71394489 TAGAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:71395153 original size:41 final size:40
Alignment explanation
Indices: 71395105--71395204 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 40
71395095 TCGACCTCAA
* *
71395105 GTCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** * *
71395145 ATTCGATGAGGTACT-AG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
71395183 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
71395205 ACTTTGCTTC
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
37 10 0.23
38 17 0.39
39 4 0.09
40 2 0.05
41 11 0.25
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:71395209 original size:38 final size:39
Alignment explanation
Indices: 71395107--71395215 Score: 96
Period size: 38 Copynumber: 2.8 Consensus size: 39
71395097 GACCTCAAGT
* **
71395107 CGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCGGATAGAGC
** * * * *
71395148 CGATGAGGTACTAGGT-ACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
*
71395185 CGATGAGACACTGGGTGTCAACTTTGCTTCG
1 CGATGAGACACTGGGTGTCAACTTTACTTCG
71395216 AACTATCCGA
Statistics
Matches: 52, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
37 13 0.25
38 25 0.48
40 1 0.02
41 13 0.25
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGGATAGAGC
Found at i:71396475 original size:18 final size:18
Alignment explanation
Indices: 71396452--71396487 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
71396442 CTTTTGAGAA
71396452 AAAAAAAAGATGATGGTT
1 AAAAAAAAGATGATGGTT
71396470 AAAAAAAAGATGATGGTT
1 AAAAAAAAGATGATGGTT
71396488 GTGATATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAAAAAAGATGATGGTT
Found at i:71401774 original size:22 final size:21
Alignment explanation
Indices: 71401749--71401794 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
71401739 CTCATATTTA
* *
71401749 ATTTTAATTTTAATTATAACTT
1 ATTTAAATTATAATTATAA-TT
71401771 ATTTAAATTATAATTATAATT
1 ATTTAAATTATAATTATAATT
71401792 ATT
1 ATT
71401795 AAGATATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAAATTATAATTATAATT
Found at i:71414886 original size:3 final size:3
Alignment explanation
Indices: 71414880--71414917 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
71414870 AGGAGGAGAG
71414880 GAA GAA GAA GGAA -AA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
71414918 CAGAGAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:71423656 original size:88 final size:87
Alignment explanation
Indices: 71423499--71423717 Score: 278
Period size: 88 Copynumber: 2.5 Consensus size: 87
71423489 ATAAGACTTT
* * * * *
71423499 TTTTCATTATTAATAGCACTACT-AAAAAGAGGTAAAGTAAAGTAGTTTTATTTAATACCTAAAA
1 TTTT-ATTATTAATA-CACTACTAAAAAAAAAGTGAAGTAACGTAGTTTTATTTAATAACTAAAA
* *
71423563 GGTTTTTTTATGTTTGGAAACGTA
64 AGTTTTGTTATGTTTGGAAACGTA
71423587 TTTTATTATTAATGACACTACTAAAAAAAAAGTGAAGTAACGTAGTTTTATTTAATAACTAAAAA
1 TTTTATTATTAAT-ACACTACTAAAAAAAAAGTGAAGTAACGTAGTTTTATTTAATAACTAAAAA
*
71423652 GTTTTGTTATGTTTGGAAATGTA
65 GTTTTGTTATGTTTGGAAACGTA
* * *
71423675 TTTCATTATTAATTATACTATTTAAAAAAAAAAGTGAAGTAAC
1 TTTTATTATTAA-TACACTA-CT-AAAAAAAAAGTGAAGTAAC
71423718 ATAAAAAGTT
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
87 16 0.14
88 78 0.68
89 2 0.02
90 19 0.17
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (87 bp):
TTTTATTATTAATACACTACTAAAAAAAAAGTGAAGTAACGTAGTTTTATTTAATAACTAAAAAG
TTTTGTTATGTTTGGAAACGTA
Found at i:71423777 original size:73 final size:72
Alignment explanation
Indices: 71423642--71423790 Score: 203
Period size: 73 Copynumber: 2.1 Consensus size: 72
71423632 TTTTATTTAA
* * *
71423642 TAACTAAAAAGTTTTGTTATGTTTGGAAATGTATTTCATTATTAATTATACTATTTAAAAAAAAA
1 TAACTAAAAAGTTTTGTTATGTTTGGAAATGTATTTCATTATTAATGACACTAGTTAAAAAAAAA
71423707 AGTGAAG
66 AGTGAAG
*
71423714 TAACATAAAAAGTTTTTTTATGTTTGGAAATGTA-TTCTATTATTAATGACACT-GTTAAGAAAA
1 TAAC-TAAAAAGTTTTGTTATGTTTGGAAATGTATTTC-ATTATTAATGACACTAGTTAA-AAAA
* *
71423777 AAAGGTTAAG
63 AAAAGTGAAG
71423787 TAAC
1 TAAC
71423791 GTAATTTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
72 11 0.16
73 57 0.84
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (72 bp):
TAACTAAAAAGTTTTGTTATGTTTGGAAATGTATTTCATTATTAATGACACTAGTTAAAAAAAAA
AGTGAAG
Found at i:71423899 original size:96 final size:92
Alignment explanation
Indices: 71423726--71424122 Score: 401
Period size: 86 Copynumber: 4.4 Consensus size: 92
71423716 ACATAAAAAG
* * *
71423726 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTGTTAAGAAAAAAAGGTTAAGTAAC
1 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACAC---TAATAAAAAATGGTGAAGTAAC
71423791 GTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
63 GTAATTTTATTTAATACCTAAAAA----TTTTTT
* * *
71423825 TTTTTTTATGTTTTGAAATGTATTCTATTATTAATCACACTAATAAAAAATGGTGGAGTAACGTA
1 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTAATAAAAAATGGTGAAGTAACGTA
71423890 ATTTTATTTAATACCT-AAAATGTTTTT
66 ATTTTATTTAATACCTAAAAAT-TTTTT
* * * * *
71423917 TTTTTTTATGTTTGGAAATGTATTTTTTTTATTAATGAGACTATTAAAAAAAT-GTAAAGTAACG
1 TTTTTTTATGTTTGGAAATGTA-TTCTATTATTAATGACACTAAT-AAAAAATGGTGAAGTAACG
* * * * *
71423981 T-AGTTT-TTT-AT--TTAATAA--CTAT
64 TAATTTTATTTAATACCTAAAAATTTTTT
* *
71424003 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAA-AGTGAAGTAACGTA
1 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTAATAAAAAATGGTGAAGTAACGTA
*
71424067 GTTTTATTTAATACCT---AA--TTTT
66 ATTTTATTTAATACCTAAAAATTTTTT
* * *
71424089 TTTTTTAATCTTTGGAAATGTATTCCATTATTAA
1 TTTTTTTATGTTTGGAAATGTATTCTATTATTAA
71424123 AAAAGTGAAG
Statistics
Matches: 257, Mismatches: 31, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
84 17 0.07
85 22 0.09
86 62 0.24
87 2 0.01
88 1 0.00
89 4 0.02
90 2 0.01
91 4 0.02
92 30 0.12
93 27 0.11
94 7 0.03
95 4 0.02
96 37 0.14
99 38 0.15
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (92 bp):
TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTAATAAAAAATGGTGAAGTAACGTA
ATTTTATTTAATACCTAAAAATTTTTT
Found at i:71423919 original size:99 final size:97
Alignment explanation
Indices: 71423726--71424084 Score: 342
Period size: 99 Copynumber: 3.9 Consensus size: 97
71423716 ACATAAAAAG
* *
71423726 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTGTTAAGAAAAAAAGGTTAAGTAAC
1 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATCACAC--TTAAGAAAAAAAGGTGAAGTAAC
71423791 GTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
64 GTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
* * * *
71423825 TTTTTTTATGTTTTGAAATGTATTCTATTATTAATCACAC-TAATAAAAAATGGTGGAGTAACGT
1 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATCACACTTAAGAAAAAAAGGTGAAGTAACGT
*
71423889 AATTTTATTTAATACCT-AAAA---TGTTTTT
66 AATTTTATTTAATACCTAAAAAGTTTTTTTTT
* * * * ** * *
71423917 TTTTTTTATGTTTGGAAATGTATTTTTTTTATTAATGAGAC-TATTAAAAAAATGTAAAGTAACG
1 TTTTTTTATGTTTGGAAATGTA-TTCTATTATTAATCACACTTAAGAAAAAAAGGTGAAGTAACG
* * * * *
71423981 T-AGTTT-TTT-AT--TTAATAA------CTAT
65 TAATTTTATTTAATACCTAAAAAGTTTTTTTTT
* **
71424003 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACAC-TATTAAAAAAA-GTGAAGTAACGT
1 TTTTTTTATGTTTGGAAATGTATTCTATTATTAATCACACTTAAGAAAAAAAGGTGAAGTAACGT
*
71424066 AGTTTTATTTAATACCTAA
66 AATTTTATTTAATACCTAA
71424085 TTTTTTTTTT
Statistics
Matches: 224, Mismatches: 29, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
84 11 0.05
85 29 0.13
86 27 0.12
87 2 0.01
88 1 0.00
89 6 0.03
90 2 0.01
91 3 0.01
92 31 0.14
93 33 0.15
95 4 0.02
96 37 0.17
99 38 0.17
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (97 bp):
TTTTTTTATGTTTGGAAATGTATTCTATTATTAATCACACTTAAGAAAAAAAGGTGAAGTAACGT
AATTTTATTTAATACCTAAAAAGTTTTTTTTT
Found at i:71425995 original size:3 final size:3
Alignment explanation
Indices: 71425987--71426037 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
71425977 AACCTTCACA
* * * *
71425987 TAT TAT TAT TAT TGT TAT TAT TAT TAT TTT TAC TAT CTAA TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
71426032 TAT TAT
1 TAT TAT
71426038 ATTTATTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:71426142 original size:18 final size:17
Alignment explanation
Indices: 71426095--71426148 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
71426085 TTATTGTACG
*
71426095 TATATA-TATACTTTTA
1 TATATAGTATATTTTTA
71426111 TATATAGTATTATTTTTA
1 TATATAGTA-TATTTTTA
*
71426129 TATATCATTATATTTATTA
1 TATAT-AGTATATTT-TTA
71426148 T
1 T
71426149 TATGCTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 17 0.53
19 7 0.22
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TATATAGTATATTTTTA
Found at i:71426764 original size:17 final size:17
Alignment explanation
Indices: 71426744--71426796 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
71426734 TCGGATCCCA
71426744 AAAATTTTCGTGTTTTC
1 AAAATTTTCGTGTTTTC
*
71426761 AAAATTTTCGTGTTTTAA
1 AAAATTTTCGTGTTTT-C
*
71426779 AAAATTCTCGT-TTTTC
1 AAAATTTTCGTGTTTTC
71426795 AA
1 AA
71426797 TCGGATCACG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.06
17 20 0.62
18 10 0.31
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (17 bp):
AAAATTTTCGTGTTTTC
Found at i:71427712 original size:35 final size:35
Alignment explanation
Indices: 71427666--71427826 Score: 170
Period size: 35 Copynumber: 4.7 Consensus size: 35
71427656 ACGAGATTTT
**
71427666 TTTTTGAAAACACGAAAATTTTCAAAACACCG-AAA
1 TTTTTGAAAACACGAAAATTTTTGAAACA-CGAAAA
* ** * *
71427701 TTTTTGAAAACAAGAGGATTTTTGAAATATGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
*
71427736 ATTTTGAAAACACGAAAATTTTTGAAACACGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
71427771 TTTTTG-AAA-ACGAAAATTTTTGAAACAC--AAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
* * *
71427802 TTTTTAGAAGACACTAAAAATTTTG
1 TTTTT-GAAAACACGAAAATTTTTG
71427827 GAAAATGGAT
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
31 8 0.08
32 1 0.01
33 21 0.20
34 15 0.14
35 60 0.57
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGAAAA
Found at i:71427806 original size:16 final size:17
Alignment explanation
Indices: 71427666--71427826 Score: 150
Period size: 17 Copynumber: 9.4 Consensus size: 17
71427656 ACGAGATTTT
71427666 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
**
71427684 TTTTCAAAACACCG-AAA
1 TTTTTGAAACA-CGAAAA
* **
71427701 TTTTTGAAAACAAGAGGA
1 TTTTTG-AAACACGAAAA
* *
71427719 TTTTTGAAATATGAAAA
1 TTTTTGAAACACGAAAA
*
71427736 ATTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
71427754 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
71427771 TTTTTGAAA-ACGAAAA
1 TTTTTGAAACACGAAAA
71427787 TTTTTGAAACAC--AAA
1 TTTTTGAAACACGAAAA
*
71427802 TTTTTAGAAGACACTAAAA
1 TTTTT-GAA-ACACGAAAA
*
71427821 ATTTTG
1 TTTTTG
71427827 GAAAATGGAT
Statistics
Matches: 118, Mismatches: 16, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
15 8 0.07
16 19 0.16
17 51 0.43
18 33 0.28
19 7 0.06
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:71428028 original size:19 final size:17
Alignment explanation
Indices: 71428004--71428048 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
71427994 AATATATTTT
71428004 TTTTGAAACACGAGAAAAA
1 TTTTGAAACAC--GAAAAA
*
71428023 TTTTGAAGGCACGAAAAA
1 TTTTGAA-ACACGAAAAA
71428041 TTTTGAAA
1 TTTTGAAA
71428049 AATAGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 13 0.57
19 7 0.30
20 3 0.13
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.27
Consensus pattern (17 bp):
TTTTGAAACACGAAAAA
Found at i:71428417 original size:8 final size:8
Alignment explanation
Indices: 71428404--71428501 Score: 103
Period size: 8 Copynumber: 12.2 Consensus size: 8
71428394 GAATTGAAAC
71428404 TCTTTTTT
1 TCTTTTTT
71428412 TCTTTTTT
1 TCTTTTTT
71428420 TCTTCTTTTT
1 TC-T-TTTTT
71428430 TCCTTTTTT
1 T-CTTTTTT
*
71428439 CCTTTTTT
1 TCTTTTTT
*
71428447 TC-TCTTT
1 TCTTTTTT
71428454 TCTTTTTT
1 TCTTTTTT
*
71428462 TC-TTCTT
1 TCTTTTTT
71428469 TCTTTTTT
1 TCTTTTTT
71428477 TC-TTTTT
1 TCTTTTTT
* *
71428484 TCTTTCTC
1 TCTTTTTT
71428492 TCTTTTTT
1 TCTTTTTT
71428500 TC
1 TC
71428502 CTGGCCTGCT
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
7 19 0.26
8 41 0.55
9 6 0.08
10 7 0.09
11 1 0.01
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:71428458 original size:15 final size:15
Alignment explanation
Indices: 71428404--71428499 Score: 111
Period size: 15 Copynumber: 6.1 Consensus size: 15
71428394 GAATTGAAAC
71428404 TCTTTTTTTCTTTTTT
1 TCTTTTTTTC-TTTTT
71428420 TCTTCTTTTTTCCTTTTT
1 TC-T-TTTTTT-CTTTTT
*
71428438 TCCTTTTTTTCTCTTT
1 T-CTTTTTTTCTTTTT
*
71428454 TCTTTTTTTCTTCTT
1 TCTTTTTTTCTTTTT
71428469 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
* *
71428484 TCTTTCTCTCTTTTT
1 TCTTTTTTTCTTTTT
71428499 T
1 T
71428500 TCCTGGCCTG
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
15 40 0.57
16 8 0.11
17 7 0.10
18 13 0.19
19 2 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTTTTCTTTTT
Found at i:71428490 original size:23 final size:22
Alignment explanation
Indices: 71428404--71428488 Score: 66
Period size: 26 Copynumber: 3.6 Consensus size: 22
71428394 GAATTGAAAC
71428404 TCTTTTTTTCTTTTTTTCTTCTTTTT
1 TCTTTTTTTCTTTTTTT-TTC---TT
* *
71428430 TCCTTTTTTCCTTTTTTTCTCTTT
1 TCTTTTTTTCTTTTTTTT-TC-TT
71428454 TCTTTTTTTCTTCTTTCTTTT-TT
1 TCTTTTTTTCTT-TTT-TTTTCTT
71428477 TC-TTTTTTCTTT
1 TCTTTTTTTCTTT
71428489 CTCTCTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.02
22 9 0.17
23 4 0.08
24 13 0.25
25 5 0.10
26 20 0.38
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TCTTTTTTTCTTTTTTTTTCTT
Found at i:71428495 original size:23 final size:22
Alignment explanation
Indices: 71428403--71428501 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 22
71428393 CGAATTGAAA
71428403 CTCTTTTTTTC--TTTTTTTCT
1 CTCTTTTTTTCTTTTTTTTTCT
* *
71428423 -TCTTTTTTCCTTTTTTCCTTTTT
1 CTCTTTTTTTCTTTTTT--TTTCT
* *
71428446 TTC-TCTTTTCTTTTTTTCTTCT
1 CTCTTTTTTTCTTTTTTT-TTCT
*
71428468 TTCTTTTTTTCTTTTTTCTTTCT
1 CTCTTTTTTTCTTTTTT-TTTCT
71428491 CTCTTTTTTTC
1 CTCTTTTTTTC
71428502 CTGGCCTGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
19 9 0.14
21 5 0.08
22 6 0.09
23 41 0.64
24 3 0.05
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
CTCTTTTTTTCTTTTTTTTTCT
Found at i:71428655 original size:15 final size:14
Alignment explanation
Indices: 71428616--71428654 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
71428606 TGTTTTTTGT
71428616 TTTTTTTTTGGGCC
1 TTTTTTTTTGGGCC
71428630 TTTTCTTTTTGGGCTGC
1 TTTT-TTTTTGGGC--C
71428647 TTTTTTTT
1 TTTTTTTT
71428655 GCTTTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 4 0.18
17 5 0.23
ACGTcount: A:0.00, C:0.13, G:0.18, T:0.69
Consensus pattern (14 bp):
TTTTTTTTTGGGCC
Found at i:71428821 original size:3 final size:3
Alignment explanation
Indices: 71428815--71428852 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
71428805 TTTTTTTTCT
71428815 TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC T
71428853 CCTCCTACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:71428949 original size:20 final size:20
Alignment explanation
Indices: 71428924--71428971 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
71428914 GTACTCTTTC
71428924 TTTTCTTCTCCTCTTTC-TC-T
1 TTTTCTTCT-CT-TTTCTTCTT
71428944 TTTTCTTCTCTTTTCTTCTT
1 TTTTCTTCTCTTTTCTTCTT
71428964 TTTTCTTC
1 TTTTCTTC
71428972 GAAAAATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 18 0.69
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTTCTCTTTTCTTCTT
Found at i:71428954 original size:11 final size:11
Alignment explanation
Indices: 71428938--71428971 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
71428928 CTTCTCCTCT
71428938 TTCTCTTTTTC
1 TTCTCTTTTTC
71428949 TTCTC-TTTTC
1 TTCTCTTTTTC
71428959 TTCT-TTTTTC
1 TTCTCTTTTTC
71428969 TTC
1 TTC
71428972 GAAAAATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTCTTTTTC
Found at i:71428969 original size:17 final size:17
Alignment explanation
Indices: 71428917--71428971 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
71428907 GACGCCGGTA
*
71428917 CTCTTTCT-TTTCTTCTC
1 CTCTTTCTCTTT-TTCTT
71428934 CTCTTTCTCTTTTTCTT
1 CTCTTTCTCTTTTTCTT
71428951 CTCTTTTCTTCTTTTTTCTT
1 CTC-TTTC-TC-TTTTTCTT
71428971 C
1 C
71428972 GAAAAATCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 15 0.45
18 7 0.21
19 2 0.06
20 9 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CTCTTTCTCTTTTTCTT
Found at i:71429270 original size:30 final size:30
Alignment explanation
Indices: 71429230--71429331 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
71429220 ATTTAGGATT
*
71429230 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
71429260 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
71429290 AAAATAAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
71429320 AAAATGCAATTT
1 AAAATGAAATTT
71429332 TTTTTTTTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 2 0.03
30 58 0.97
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:71429348 original size:13 final size:13
Alignment explanation
Indices: 71429330--71429359 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
71429320 AAAATGCAAT
*
71429330 TTTTTTTTTTAAA
1 TTTTTTTTTGAAA
71429343 TTTTTTTTTGAAA
1 TTTTTTTTTGAAA
71429356 TTTT
1 TTTT
71429360 GAAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTGAAA
Found at i:71429780 original size:54 final size:55
Alignment explanation
Indices: 71429599--71429815 Score: 315
Period size: 54 Copynumber: 4.1 Consensus size: 55
71429589 CACGTGAGCC
* *
71429599 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
71429654 AAGGCTCAACTCACCTCTCGCAATATG-GTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
71429704 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
71429758 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
71429813 AAG
1 AAG
71429816 TAGAAATTGA
Statistics
Matches: 148, Mismatches: 6, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
50 43 0.29
51 4 0.03
52 1 0.01
54 57 0.39
55 37 0.25
56 6 0.04
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:71429790 original size:105 final size:103
Alignment explanation
Indices: 71429599--71429807 Score: 330
Period size: 104 Copynumber: 2.0 Consensus size: 103
71429589 CACGTGAGCC
* *
71429599 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT-CAAAAGGCTCAAC
*
71429664 TCACCTCTCGCAATATGGTTGATTTTTTGAAAAATAGAAA
65 TCACCTCTCGCAATATGGTTGA-TTTTTGAAAAACAGAAA
* *
71429704 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTCAAAAGGCTCAAC
71429768 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA
65 TCACCTCTCGCAATATG-GTTGATTTTTGAAAAACAGAAA
71429808 TTGAAAAGTA
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
104 45 0.46
105 42 0.43
106 10 0.10
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (103 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTCAAAAGGCTCAACT
CACCTCTCGCAATATGGTTGATTTTTGAAAAACAGAAA
Found at i:71429813 original size:14 final size:14
Alignment explanation
Indices: 71429794--71429828 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
71429784 GAGTTGATTT
71429794 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
71429808 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
71429822 TTGAAAA
1 TTGAAAA
71429829 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:71429922 original size:12 final size:14
Alignment explanation
Indices: 71429886--71429920 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
71429876 ATTTTTTTTG
*
71429886 AAACACAAATTAAA
1 AAACAGAAATTAAA
71429900 AAACAGAAATT-AA
1 AAACAGAAATTAAA
71429913 AAACAGAA
1 AAACAGAA
71429921 TTTGAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.11
Consensus pattern (14 bp):
AAACAGAAATTAAA
Found at i:71433065 original size:17 final size:18
Alignment explanation
Indices: 71433038--71433071 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
71433028 AAAAATATTT
71433038 TTTATATTTTTAAAAATC
1 TTTATATTTTTAAAAATC
71433056 TTTA-ATTTTTAAAAAT
1 TTTATATTTTTAAAAAT
71433072 AGTTTCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATATTTTTAAAAATC
Found at i:71433229 original size:9 final size:9
Alignment explanation
Indices: 71433215--71433265 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
71433205 ATAAATAAAC
71433215 AAAAATTAA
1 AAAAATTAA
71433224 AAAAATT-A
1 AAAAATTAA
*
71433232 AAAAA-GAA
1 AAAAATTAA
71433240 AAAAATTAA
1 AAAAATTAA
*
71433249 ATCAAAATTTA
1 A--AAAATTAA
71433260 AAAAAT
1 AAAAAT
71433266 ATTTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
8 12 0.34
9 15 0.43
11 8 0.23
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (9 bp):
AAAAATTAA
Found at i:71437592 original size:17 final size:17
Alignment explanation
Indices: 71437570--71437603 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
71437560 ATCCACTAAT
*
71437570 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
71437587 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
71437604 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:71442226 original size:17 final size:17
Alignment explanation
Indices: 71442204--71442237 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
71442194 ATCCACTAAT
*
71442204 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
71442221 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
71442238 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:71453809 original size:24 final size:24
Alignment explanation
Indices: 71453782--71453828 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
71453772 TTAGTATCAT
*
71453782 AATT-TAAATTAATACGAAGTAAAA
1 AATTATAAATT-ATACAAAGTAAAA
*
71453806 AATTATATATTATACAAAGTAAA
1 AATTATAAATTATACAAAGTAAA
71453829 GGAAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
AATTATAAATTATACAAAGTAAAA
Found at i:71460974 original size:17 final size:17
Alignment explanation
Indices: 71460934--71460967 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
71460924 AATATTAAAA
* *
71460934 TTATTATTATTATGGTT
1 TTATAATTATTATGATT
71460951 TTATAATTATTATGATT
1 TTATAATTATTATGATT
71460968 ATTTAATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
TTATAATTATTATGATT
Found at i:71462343 original size:41 final size:42
Alignment explanation
Indices: 71462298--71462397 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 42
71462288 CGACCTCAAG
* *
71462298 TCGATGAGACACTGGGTGTCACTAAATTT-CTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
** * * *
71462339 TCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
71462378 T-GATGAGACACTGGGTGTCA
1 TCGATGAGACACTGGGTGTCA
71462398 ACTATTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
38 16 0.35
39 14 0.30
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
Found at i:71462406 original size:39 final size:40
Alignment explanation
Indices: 71462298--71462409 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 40
71462288 CGACCTCAAG
* *
71462298 TCGATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCAACT--ATTACTTCGGATAGAC
** ** * *
71462339 TCGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
71462378 T-GATGAGACACTGGGTGTCAACTATTACTTCG
1 TCGATGAGACACTGGGTGTCAACTATTACTTCG
71462410 AACTATCCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 18 0.32
39 20 0.35
41 16 0.28
42 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
Found at i:71462558 original size:18 final size:18
Alignment explanation
Indices: 71462537--71462576 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
71462527 AAAAAAAAAG
71462537 GAAATT-GAATTATGAATA
1 GAAATTGGAATTATG-ATA
*
71462555 GAAATTGGAATTGTGATA
1 GAAATTGGAATTATGATA
71462573 GAAA
1 GAAA
71462577 GAGAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAATTGGAATTATGATA
Found at i:71463087 original size:20 final size:20
Alignment explanation
Indices: 71463064--71463101 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
71463054 GTTATTAAGT
71463064 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
71463084 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
71463102 ATGTGAAACA
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:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:71473336 original size:27 final size:25
Alignment explanation
Indices: 71473306--71473374 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
71473296 TAATAAGAGT
71473306 AATAATAATTAAAATAATAAGAAAAT-A
1 AATAA-AA-TAAAATAATAA-AAAATAA
*
71473333 AATAAAAACAAAAATAATAAAAAATAA
1 AAT-AAAA-TAAAATAATAAAAAATAA
71473360 AATAAAATAAAATAA
1 AATAAAATAAAATAA
71473375 AATGAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 7 0.19
26 9 0.24
27 19 0.51
28 2 0.05
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (25 bp):
AATAAAATAAAATAATAAAAAATAA
Found at i:71473361 original size:5 final size:5
Alignment explanation
Indices: 71473315--71473377 Score: 58
Period size: 5 Copynumber: 12.2 Consensus size: 5
71473305 TAATAATAAT
* *
71473315 TAAAA TAATAA GAAAA T-AAA TAAAAA CAAAAA TAATAA -AAAA TAAAA
1 TAAAA TAA-AA TAAAA TAAAA T-AAAA -TAAAA TAA-AA TAAAA TAAAA
71473362 TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA T
71473378 GAAAGAATAG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 6 0.12
5 29 0.60
6 13 0.27
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:71475138 original size:46 final size:46
Alignment explanation
Indices: 71475078--71475351 Score: 433
Period size: 46 Copynumber: 6.0 Consensus size: 46
71475068 TTTGACATGA
* * * * * *
71475078 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
71475124 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
71475170 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
71475216 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
71475262 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
71475308 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
71475352 AGAGCACACT
Statistics
Matches: 214, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 4 0.02
46 210 0.98
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:71479450 original size:16 final size:17
Alignment explanation
Indices: 71479419--71479452 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
71479409 GATAAAAAAT
*
71479419 GAATACTACGATATAAA
1 GAATAATACGATATAAA
71479436 GAATAATAC-ATATAAA
1 GAATAATACGATATAAA
71479452 G
1 G
71479453 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.24
Consensus pattern (17 bp):
GAATAATACGATATAAA
Found at i:71480153 original size:44 final size:43
Alignment explanation
Indices: 71480105--71480264 Score: 124
Period size: 44 Copynumber: 3.8 Consensus size: 43
71480095 ATGAAGTAAC
*
71480105 AATATATATAAGTAATTAATAAATATAATATATGAAAATATAAT
1 AATATATATAAGTAATTAATAAATATAATATAAGAAAA-ATAAT
*
71480149 AATATATATAAG-AGATGT-A-AAATAATAATTTAAGAAAAATAAT
1 AATATATATAAGTA-AT-TAATAAAT-ATAATATAAGAAAAATAAT
*
71480192 -ATATA-ATAAGTAA-TAATAATATATAAT-TAA-AAATAATACT
1 AATATATATAAGTAATTAATAA-ATATAATATAAGAAA-AATAAT
* * *
71480232 TATA-ATA-AAATAATTTTATAATATATAATATAA
1 AATATATATAAGTAA-TTAATAA-ATATAATATAA
71480265 AAGTAAAATT
Statistics
Matches: 98, Mismatches: 5, Indels: 27
0.75 0.04 0.21
Matches are distributed among these distances:
39 4 0.04
40 15 0.15
41 17 0.17
42 21 0.21
43 13 0.13
44 27 0.28
45 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (43 bp):
AATATATATAAGTAATTAATAAATATAATATAAGAAAAATAAT
Found at i:71480159 original size:27 final size:26
Alignment explanation
Indices: 71480121--71480177 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
71480111 TATAAGTAAT
* *
71480121 TAATAAATATAATATATGAAAATATAA
1 TAATAAATATAAGAGATGAAAA-ATAA
* *
71480148 TAATATATATAAGAGATGTAAAATAA
1 TAATAAATATAAGAGATGAAAAATAA
71480174 TAAT
1 TAAT
71480178 TTAAGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (26 bp):
TAATAAATATAAGAGATGAAAAATAA
Found at i:71480192 original size:3 final size:3
Alignment explanation
Indices: 71480186--71480245 Score: 50
Period size: 3 Copynumber: 19.0 Consensus size: 3
71480176 ATTTAAGAAA
* * *
71480186 AAT AAT ATAT AAT AAGT AAT AAT AAT ATAT AATT AAA AAT AAT ACT TAT
1 AAT AAT A-AT AAT AA-T AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
71480235 AAT AA- AAT AAT
1 AAT AAT AAT AAT
71480246 TTTATAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 2 0.04
3 32 0.70
4 12 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:71480209 original size:20 final size:20
Alignment explanation
Indices: 71480145--71480239 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
71480135 TATGAAAATA
*
71480145 TAATAAT-ATATATAAGAGATG
1 TAATAATAATATATAATA-A-G
*
71480166 TAA-AATAATA-AT-TTAAG
1 TAATAATAATATATAATAAG
*
71480183 -AAAAATAATATATAATAAG
1 TAATAATAATATATAATAAG
71480202 TAATAATAATATATAATTAA-
1 TAATAATAATATATAA-TAAG
* *
71480222 AAATAATACT-TATAATAA
1 TAATAATAATATATAATAA
71480240 AATAATTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
16 2 0.03
17 8 0.13
18 6 0.10
19 10 0.16
20 27 0.44
21 9 0.15
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (20 bp):
TAATAATAATATATAATAAG
Found at i:71480217 original size:17 final size:16
Alignment explanation
Indices: 71480108--71480261 Score: 59
Period size: 17 Copynumber: 9.0 Consensus size: 16
71480098 AAGTAACAAT
71480108 ATATATAAGTAATTAATA
1 ATATATAA-TAA-TAATA
71480126 A-ATATAATATATGAA-A
1 ATATATAATA-AT-AATA
71480142 ATATAATAAT-ATATATAA
1 ATAT-ATAATAATA-AT-A
* *
71480160 GAGATGTAA-AATAATA
1 -ATATATAATAATAATA
* * *
71480176 ATTTAAGAAAAATAAT-
1 ATAT-ATAATAATAATA
71480192 ATATAATAAGTAATAATA
1 ATAT-ATAA-TAATAATA
*
71480210 ATATATAATTAAAAATA
1 ATATATAA-TAATAATA
71480227 ATACTTATAATAA-AATA
1 ATA--TATAATAATAATA
*
71480244 ATTTTATAATATATAATA
1 A-TATATAATA-ATAATA
71480262 TAAAAGTAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 36
0.69 0.08 0.23
Matches are distributed among these distances:
15 3 0.03
16 25 0.24
17 45 0.42
18 25 0.24
19 8 0.08
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.36
Consensus pattern (16 bp):
ATATATAATAATAATA
Found at i:71480224 original size:37 final size:41
Alignment explanation
Indices: 71480183--71480266 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
71480173 ATAATTTAAG
*
71480183 AAAAATAATA-TATAAT-AAGTAA-TAATAATATATAAT-T
1 AAAAATAATACTATAATAAAATAATTAATAATATATAATAT
*
71480220 AAAAATAATACTTATAATAAAATAATTTTATAATATATAATAT
1 AAAAATAATAC-TATAATAAAATAA-TTAATAATATATAATAT
71480263 AAAA
1 AAAA
71480267 GTAAAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 10 0.26
39 6 0.15
40 5 0.13
42 13 0.33
43 5 0.13
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (41 bp):
AAAAATAATACTATAATAAAATAATTAATAATATATAATAT
Found at i:71480242 original size:54 final size:52
Alignment explanation
Indices: 71480167--71480324 Score: 135
Period size: 54 Copynumber: 2.9 Consensus size: 52
71480157 TAAGAGATGT
* *
71480167 AAAATAATAATT-TAAGAAAAATAATATATAATAAGTAATAATAATATATAATTA
1 AAAATAATACTTATAA-TAAAATAATATATAATAA-TAATAATAA-ATATAATTA
* *
71480221 AAAATAATACTTATAATAAAATAATTTTATAATATATAAT-ATAAAAGTAAAATTA
1 AAAATAATACTTATAATAAAATAA-TATATAATA-ATAATAAT-AAA-TATAATTA
* **
71480276 GAAATAA-ACGAATAATAAAATATATATATGGAATAAT-ATAATAAATATA
1 AAAATAATACTTATAATAAAATA-ATATAT--AATAATAATAATAAATATA
71480325 GGACTAAATT
Statistics
Matches: 86, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
53 3 0.03
54 43 0.50
55 35 0.41
56 5 0.06
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (52 bp):
AAAATAATACTTATAATAAAATAATATATAATAATAATAATAAATATAATTA
Found at i:71480252 original size:16 final size:17
Alignment explanation
Indices: 71480166--71480254 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
71480156 ATAAGAGATG
*
71480166 TAAAATAATAATT-TAA
1 TAAAATAATACTTATAA
*
71480182 GAAAAATAATA--TATAA
1 -TAAAATAATACTTATAA
*
71480198 TAAGTAATAATAATATATAA
1 TAA--AATAATACT-TATAA
71480218 TTAAAAATAATACTTATAA
1 -T-AAAATAATACTTATAA
*
71480237 TAAAATAAT-TTTATAA
1 TAAAATAATACTTATAA
71480253 TA
1 TA
71480255 TATAATATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.05
16 11 0.18
17 24 0.40
18 1 0.02
19 5 0.08
20 13 0.22
21 1 0.02
22 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (17 bp):
TAAAATAATACTTATAA
Found at i:71480311 original size:21 final size:21
Alignment explanation
Indices: 71480285--71480324 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
71480275 AGAAATAAAC
*
71480285 GAATAATAAAATATATATATG
1 GAATAATAAAATAAATATATG
*
71480306 GAATAATATAATAAATATA
1 GAATAATAAAATAAATATA
71480325 GGACTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
GAATAATAAAATAAATATATG
Found at i:71485310 original size:6 final size:6
Alignment explanation
Indices: 71485299--71485323 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
71485289 CTAAAAAAAT
71485299 ATTTTA ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA ATTTTA A
71485324 ATTGTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:71493008 original size:20 final size:20
Alignment explanation
Indices: 71492959--71493008 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
71492949 ATAAAAATAA
*
71492959 TTATATTAATTATATATGTT
1 TTATATTTATTATATATGTT
** * *
71492979 AAATAATTATTATATATTTT
1 TTATATTTATTATATATGTT
71492999 TTATATTTAT
1 TTATATTTAT
71493009 ATTAAATTAC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATATTTATTATATATGTT
Found at i:71509859 original size:21 final size:21
Alignment explanation
Indices: 71509835--71509878 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
71509825 AAGGAAAGTT
71509835 AAAA-TAATATAAAATGAAAAA
1 AAAAGTAAT-TAAAATGAAAAA
*
71509856 AAAAGTACTTAAAATGAAAAA
1 AAAAGTAATTAAAATGAAAAA
71509877 AA
1 AA
71509879 TATAGGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (21 bp):
AAAAGTAATTAAAATGAAAAA
Found at i:71510461 original size:20 final size:21
Alignment explanation
Indices: 71510436--71510475 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
71510426 ATTATAAGCA
71510436 TTTAACAAT-TCATCCTGTAC
1 TTTAACAATCTCATCCTGTAC
*
71510456 TTTAACAATCTCATCGTGTA
1 TTTAACAATCTCATCCTGTA
71510476 TAAATTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTAACAATCTCATCCTGTAC
Found at i:71518089 original size:25 final size:24
Alignment explanation
Indices: 71518061--71518113 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
71518051 AAATTCAAGT
71518061 TTAATTATTAATAATATTATTTTTA
1 TTAATTATTAATAATA-TATTTTTA
** *
71518086 TTAATTATTTTTATTATATTTTTA
1 TTAATTATTAATAATATATTTTTA
71518110 TTAA
1 TTAA
71518114 ATGAGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTAATTATTAATAATATATTTTTA
Found at i:71518094 original size:13 final size:13
Alignment explanation
Indices: 71518076--71518113 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
71518066 TATTAATAAT
71518076 ATTATTTTTATTA
1 ATTATTTTTATTA
71518089 ATTATTTTTATT-
1 ATTATTTTTATTA
71518101 A-TATTTTTATTA
1 ATTATTTTTATTA
71518113 A
1 A
71518114 ATGAGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 10 0.42
12 2 0.08
13 12 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTATTTTTATTA
Found at i:71518110 original size:24 final size:24
Alignment explanation
Indices: 71518078--71518131 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
71518068 TTAATAATAT
* *
71518078 TATTTTTATT-AATTATTTTTATTA
1 TATTTTTATTAAATGAGTTTT-TTA
71518102 TATTTTTATTAAATGAGTTTTTTA
1 TATTTTTATTAAATGAGTTTTTTA
71518126 TATTTT
1 TATTTT
71518132 AAATATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
TATTTTTATTAAATGAGTTTTTTA
Found at i:71526655 original size:11 final size:11
Alignment explanation
Indices: 71526641--71526678 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
71526631 TTTTCTCTCC
71526641 ATTTTACTACT
1 ATTTTACTACT
*
71526652 ATTTTACTATT
1 ATTTTACTACT
*
71526663 ATATTACTACT
1 ATTTTACTACT
71526674 ATTTT
1 ATTTT
71526679 GTTGTTATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTACTACT
Found at i:71526861 original size:21 final size:21
Alignment explanation
Indices: 71526837--71526886 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
71526827 TTTGTTGAAA
*
71526837 AATATTTATTTTGATAT-TTTT
1 AATATTTATTTT-ATATATTAT
71526858 AATATTT-TTTTATATATTAT
1 AATATTTATTTTATATATTAT
71526878 ACATATTTA
1 A-ATATTTA
71526887 AAAAACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
AATATTTATTTTATATATTAT
Found at i:71529706 original size:16 final size:16
Alignment explanation
Indices: 71529682--71529714 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
71529672 TCTTGAAAAG
71529682 AAAAAAGAAT-TCTTT
1 AAAAAAGAATGTCTTT
71529697 AAAAATAGAATGTCTTT
1 AAAAA-AGAATGTCTTT
71529714 A
1 A
71529715 CAGTTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAAAAGAATGTCTTT
Found at i:71541848 original size:19 final size:21
Alignment explanation
Indices: 71541807--71541855 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
71541797 CTCAATGAAT
71541807 ATAAACAATTTATTATTTCAA
1 ATAAACAATTTATTATTTCAA
71541828 ATAAACTAATTTA-TA-TT-AA
1 ATAAAC-AATTTATTATTTCAA
71541847 ATAAA-AATT
1 ATAAACAATT
71541856 AAGGACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.15
19 7 0.26
20 2 0.07
21 8 0.30
22 6 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAACAATTTATTATTTCAA
Found at i:71542281 original size:6 final size:6
Alignment explanation
Indices: 71542270--71542296 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
71542260 TTCAAAGCAG
71542270 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
71542297 TGCAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:71548622 original size:18 final size:20
Alignment explanation
Indices: 71548576--71548624 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
71548566 AAATGGAAAT
* *
71548576 TTTTATTTGAAATATATAGA
1 TTTTATTTAAAAAATATAGA
*
71548596 TTTTGTTTAAAAAATA-AG-
1 TTTTATTTAAAAAATATAGA
71548614 TTTTATTTAAA
1 TTTTATTTAAA
71548625 TACATTATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTATTTAAAAAATATAGA
Found at i:71554378 original size:22 final size:22
Alignment explanation
Indices: 71554351--71554421 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
71554341 TATTTATTAG
71554351 GTAGATAAAATAATTTAATTGT
1 GTAGATAAAATAATTTAATTGT
* * *
71554373 GTAGATTAACTTATTT-ATTAG-
1 GTAGATAAAATAATTTAATT-GT
71554394 GTAGATAAAATAATTTAATTGT
1 GTAGATAAAATAATTTAATTGT
71554416 GTAGAT
1 GTAGAT
71554422 TAACTAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 17 0.43
22 23 0.57
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.42
Consensus pattern (22 bp):
GTAGATAAAATAATTTAATTGT
Found at i:71554384 original size:43 final size:43
Alignment explanation
Indices: 71554336--71554426 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
71554326 TGCGAGAAGA
71554336 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
1 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
71554379 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
1 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
71554422 TAACT
1 TAACT
71554427 AAACTTATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (43 bp):
TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
Found at i:71565047 original size:17 final size:16
Alignment explanation
Indices: 71565025--71565075 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 16
71565015 ATATTTTACT
71565025 ATAAAAATAATTAAAAA
1 ATAAAAA-AATTAAAAA
71565042 ATAAAAAAAATTATAAAA
1 AT-AAAAAAATTA-AAAA
71565060 ATAGAAAAAA-TAAAAA
1 ATA-AAAAAATTAAAAA
71565076 TATTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.13
17 10 0.32
18 17 0.55
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (16 bp):
ATAAAAAAATTAAAAA
Found at i:71565049 original size:9 final size:9
Alignment explanation
Indices: 71565027--71565075 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
71565017 ATTTTACTAT
71565027 AAAAATAATTA
1 AAAAATAA--A
71565038 AAAAATAAA
1 AAAAATAAA
* *
71565047 AAAAATTAT
1 AAAAATAAA
*
71565056 AAAAATAGA
1 AAAAATAAA
71565065 AAAAATAAA
1 AAAAATAAA
71565074 AA
1 AA
71565076 TATTAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 24 0.75
11 8 0.25
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (9 bp):
AAAAATAAA
Found at i:71565059 original size:18 final size:17
Alignment explanation
Indices: 71565025--71565075 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
71565015 ATATTTTACT
*
71565025 ATAAAAATAATTAAAAA
1 ATAAAAAAAATTAAAAA
71565042 ATAAAAAAAATTATAAAA
1 ATAAAAAAAATTA-AAAA
*
71565060 ATAGAAAAAA-TAAAAA
1 ATAAAAAAAATTAAAAA
71565076 TATTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 4 0.13
17 14 0.45
18 13 0.42
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
ATAAAAAAAATTAAAAA
Found at i:71565153 original size:10 final size:9
Alignment explanation
Indices: 71565033--71565162 Score: 83
Period size: 9 Copynumber: 14.7 Consensus size: 9
71565023 CTATAAAAAT
71565033 AATTA-AAA
1 AATTATAAA
* *
71565041 AATAAAAAA
1 AATTATAAA
71565050 AATTATAAA
1 AATTATAAA
*
71565059 AA-TAGAAA
1 AATTATAAA
71565067 AA--ATAAA
1 AATTATAAA
71565074 AA-TATTAAA
1 AATTA-TAAA
** *
71565083 TTTTATTAA
1 AATTATAAA
71565092 AATTATAAA
1 AATTATAAA
* *
71565101 AACTTGTCAA
1 AA-TTATAAA
*
71565111 TATTATAAA
1 AATTATAAA
71565120 AA-TATAAA
1 AATTATAAA
*
71565128 AATTCTAATA
1 AATTATAA-A
71565138 AATTATAAA
1 AATTATAAA
71565147 AATTTATAAA
1 AA-TTATAAA
*
71565157 ACTTAT
1 AATTAT
71565163 TTAAAATATT
Statistics
Matches: 94, Mismatches: 20, Indels: 15
0.73 0.16 0.12
Matches are distributed among these distances:
7 6 0.06
8 20 0.21
9 44 0.47
10 24 0.26
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:71565162 original size:19 final size:18
Alignment explanation
Indices: 71565113--71565162 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
71565103 CTTGTCAATA
*
71565113 TTATAAAAATATAAAAAT
1 TTATAAAATTATAAAAAT
71565131 TCTA-ATAAATTATAAAAAT
1 T-TATA-AAATTATAAAAAT
71565150 TTATAAAACTTAT
1 TTATAAAA-TTAT
71565163 TTAAAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
TTATAAAATTATAAAAAT
Found at i:71565201 original size:10 final size:10
Alignment explanation
Indices: 71565181--71565214 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
71565171 TTTTAGATTA
71565181 AAAATTTTTT
1 AAAATTTTTT
* *
71565191 AGAATTCTTT
1 AAAATTTTTT
71565201 AAAATTTTTT
1 AAAATTTTTT
71565211 AAAA
1 AAAA
71565215 ATTGTACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:71565685 original size:19 final size:19
Alignment explanation
Indices: 71565661--71565718 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
71565651 CATTCCAATT
*
71565661 TAAGTTTTTATTATTTTTA
1 TAAGTTTTTATAATTTTTA
*
71565680 TAAGTTTATATCAA-TTTTA
1 TAAGTTTTTAT-AATTTTTA
* *
71565699 -ATGCTTTTATAATTTTTA
1 TAAGTTTTTATAATTTTTA
71565717 TA
1 TA
71565719 GAATTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 16 0.52
20 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
TAAGTTTTTATAATTTTTA
Found at i:71565706 original size:28 final size:28
Alignment explanation
Indices: 71565675--71565728 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
71565665 TTTTTATTAT
71565675 TTTTATAAGTTTATAT-CAATTTTAATGC
1 TTTTATAA-TTTATATACAATTTTAATGC
* *
71565703 TTTTATAATTTTTATAGAATTTTAAT
1 TTTTATAATTTATATACAATTTTAAT
71565729 ACGTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTTATAATTTATATACAATTTTAATGC
Found at i:71572459 original size:131 final size:131
Alignment explanation
Indices: 71572206--71572538 Score: 408
Period size: 131 Copynumber: 2.6 Consensus size: 131
71572196 AAAAAACCGA
* * * * * *
71572206 AACCCAGCAC-AGTAGGGCACGATTCCTCAAATTTCTAAACATCGAGCATTGCC-TCATTTT-AG
1 AACCCAGCACGA-TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAG
* * * * * * *
71572268 AA--TTTAGAGAACATTAGTGAAATTCTAGAGGGATATTCGATTATTTTGAATAAACGGGAAATT
65 AATTTTTAAAGAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATC
71572331 GC
130 GC
*
71572333 AACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTGAAG
1 AACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTT-AAG
* * *
71572398 AATTTTTAAAG-ACGTGAGTGAAATTCCAAAGGAATATTCGATTGTTTTGAAAAAAGGGGAAATC
65 AATTTTTAAAGAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATC
71572462 GC
130 GC
* * * *
71572464 AATCCAACACGATGGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTTGTTTTTAAG
1 AACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCG-TTTTAAG
71572529 AATTTTTAAA
65 AATTTTTAAA
71572539 TGAATAATTA
Statistics
Matches: 177, Mismatches: 22, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
127 45 0.25
128 7 0.04
130 4 0.02
131 111 0.63
132 10 0.06
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (131 bp):
AACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAGA
ATTTTTAAAGAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATCG
C
Found at i:71576605 original size:21 final size:21
Alignment explanation
Indices: 71576579--71576629 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
71576569 CTGTTTCTAC
*
71576579 TCTCACCGCTACAGTATCCAA
1 TCTCACCGCTACAGTAACCAA
* *
71576600 TCTCACCGCTATAGTAACTAA
1 TCTCACCGCTACAGTAACCAA
71576621 TCTCACCGC
1 TCTCACCGC
71576630 CACCGCTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.25
Consensus pattern (21 bp):
TCTCACCGCTACAGTAACCAA
Found at i:71581768 original size:20 final size:21
Alignment explanation
Indices: 71581739--71581780 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
71581729 TAATTAAAAT
*
71581739 AATACCAAACATATATT-TAA
1 AATACCAAACACATATTCTAA
*
71581759 AATACTAAACACATATTCTAA
1 AATACCAAACACATATTCTAA
71581780 A
1 A
71581781 GAAAATAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (21 bp):
AATACCAAACACATATTCTAA
Found at i:71596753 original size:23 final size:21
Alignment explanation
Indices: 71596710--71596754 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
71596700 TTCAAATATA
* *
71596710 ACACTTAATAAATACATAATT
1 ACACTTAATAAATAAAAAATT
71596731 ACACTTATATATAATAAAAAATT
1 ACACTTA-ATA-AATAAAAAATT
71596754 A
1 A
71596755 ACCTTATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (21 bp):
ACACTTAATAAATAAAAAATT
Found at i:71600528 original size:39 final size:38
Alignment explanation
Indices: 71600480--71600617 Score: 181
Period size: 39 Copynumber: 3.6 Consensus size: 38
71600470 ATAAAGTATG
*
71600480 GTTTTAATTAATAATAAAACAAAATAGTATGTGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATG-GGAAGTA
*
71600519 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAACAATAAAACAAAATAGTAT-GGGAAGTA
* *
71600558 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAGT-
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
* *
71600595 GTTTTTGATT-ATAATAAAACAAA
1 G-TTTTAATTAACAATAAAACAAA
71600618 GTAACATGGG
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
37 13 0.14
38 12 0.13
39 64 0.71
40 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (38 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
Found at i:71601441 original size:17 final size:17
Alignment explanation
Indices: 71601419--71601451 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
71601409 ATATTTCTAA
*
71601419 TACTATTATGTTATTAC
1 TACTATTATATTATTAC
71601436 TACTATTATATTATTA
1 TACTATTATATTATTA
71601452 TTATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (17 bp):
TACTATTATATTATTAC
Found at i:71603777 original size:27 final size:27
Alignment explanation
Indices: 71603723--71603773 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
71603713 TGTCTTTCTT
*
71603723 CTCCTCTTCCTATCCCACGCTTTCACC
1 CTCCTCCTCCTATCCCACGCTTTCACC
* *
71603750 CTCCTCCTCCT-TCCCTCTCTTTCA
1 CTCCTCCTCCTATCCCACGCTTTCA
71603774 ACCCCACTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.08, C:0.53, G:0.02, T:0.37
Consensus pattern (27 bp):
CTCCTCCTCCTATCCCACGCTTTCACC
Found at i:71610674 original size:39 final size:37
Alignment explanation
Indices: 71610607--71610699 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
71610597 ACCAGAATGG
* *
71610607 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
71610646 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
71610683 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
71610700 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:71610896 original size:23 final size:24
Alignment explanation
Indices: 71610875--71610919 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
71610865 CACTTTCAAT
* *
71610875 TCAATCATT-TTTC-CACATTCAA
1 TCAATAATTATTTCACAAATTCAA
71610897 TCAATAATTATTTCACAAATTCA
1 TCAATAATTATTTCACAAATTCA
71610920 CACATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (24 bp):
TCAATAATTATTTCACAAATTCAA
Found at i:71610913 original size:22 final size:23
Alignment explanation
Indices: 71610869--71610919 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
71610859 TTCTCACACT
*
71610869 TTCAATTCAATCATTTTTCCACA
1 TTCAATTCAATAATTTTTCCACA
*
71610892 TTCAA-TCAATAATTATTTCACAAA
1 TTCAATTCAATAATT-TTTC-CACA
71610916 TTCA
1 TTCA
71610920 CACATTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.33
23 9 0.38
24 7 0.29
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCAATTCAATAATTTTTCCACA
Found at i:71611814 original size:17 final size:16
Alignment explanation
Indices: 71611782--71611815 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
71611772 TTGGCTATTC
*
71611782 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
71611798 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
71611815 T
1 T
71611816 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:71611863 original size:14 final size:14
Alignment explanation
Indices: 71611804--71611854 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
71611794 CTTTTGTTTC
*
71611804 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
71611817 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
71611832 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
71611846 TTTTATTTC
1 TTTTATTTC
71611855 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:71612023 original size:14 final size:17
Alignment explanation
Indices: 71612004--71612040 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
71611994 ATTTATTTCT
71612004 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
71612018 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
71612035 TAATAT
1 TAATAT
71612041 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:71624839 original size:29 final size:29
Alignment explanation
Indices: 71624767--71624839 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
71624757 AACTTTTAAA
*
71624767 TTAATAAA-TATAAAATTACACTTTAACAC
1 TTAA-AAATTATAAAATTACAATTTAACAC
* * *
71624796 TTAAAAATGACAAAATT-CAATTTAATCAT
1 TTAAAAATTATAAAATTACAATTTAA-CAC
71624825 TTAAAAATTATAAAA
1 TTAAAAATTATAAAA
71624840 ATATAAACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 10 0.28
29 26 0.72
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (29 bp):
TTAAAAATTATAAAATTACAATTTAACAC
Found at i:71632843 original size:2 final size:2
Alignment explanation
Indices: 71632836--71632861 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71632826 TTCATCTTTA
71632836 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
71632862 GGAAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71643993 original size:7 final size:7
Alignment explanation
Indices: 71643981--71644020 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
71643971 ATTTTAATAA
71643981 TATTTAC
1 TATTTAC
71643988 TATTTAC
1 TATTTAC
71643995 TATTTAC
1 TATTTAC
71644002 TATTTAC
1 TATTTAC
71644009 TATTTAC
1 TATTTAC
71644016 TATTT
1 TATTT
71644021 CAATCCTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTTAC
Done.