Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 2 of 22
Found at i:565935 original size:30 final size:30
Alignment explanation
Indices: 565736--566427 Score: 122
Period size: 30 Copynumber: 22.5 Consensus size: 30
565726 CCAACCTAAC
* * *
565736 TAGACTTAAACATCTTGGATACTAGCTA-AAT
1 TAGACTTAAACATCTTTG-TGCTA-ATATAAT
* * * *
565767 TAGGCTTAAACATCTTTGTGCCAATCTAAC
1 TAGACTTAAACATCTTTGTGCTAATATAAT
* * *
565797 TGGACTTAAACATCTTGGATGCTAGCTA-AATTT
1 TAGACTTAAACATCTTTG-TGCTA-ATATAA--T
* *
565830 TAG-CTTAAATC-TCTTTGTGCTAACATAGT
1 TAGACTTAAA-CATCTTTGTGCTAATATAAT
* *
565859 TAGACTTAAACATCTTAGATGCTAGT-TAAAT
1 TAGACTTAAACATCTTTG-TGCTAATAT-AAT
* * * * *
565890 TGGGCTTAAATATCTTTGTGCCAATATAAC
1 TAGACTTAAACATCTTTGTGCTAATATAAT
* *
565920 TAGACTTAAACATCTTGGATGCTAGCTA-AATT
1 TAGACTTAAACATCTTTG-TGCTA-ATATAA-T
* ** * * * ***
565952 TGGGTTTAAATC-TCTTTATGCCAACATTGC
1 TAGACTTAAA-CATCTTTGTGCTAATATAAT
* *
565982 TAGACTTAAACATCTTAGATGCTAGCTA-AAT
1 TAGACTTAAACATCTTTG-TGCTA-ATATAAT
* ** * * *
566013 TAGGCTTAAATGTCTTTATGTTAATATATT
1 TAGACTTAAACATCTTTGTGCTAATATAAT
* * ***
566043 TAGTCTTAAACATCTTGGATGCCGGCTA-AAT
1 TAGACTTAAACATCTTTG-TG-CTAATATAAT
* * * * * **
566074 TTGTGCTTAAATC-TCTTTATGCCAACATAGC
1 TAG-ACTTAAA-CATCTTTGTGCTAATATAAT
* * *
566105 TAGACTTAAACATCTTGGATGCCAGCTA-AAT
1 TAGACTTAAACATCTTTG-TGCTA-ATATAAT
* * * ** *
566136 TGGGCTTAAATATCTTTGTGCCCATATAAC
1 TAGACTTAAACATCTTTGTGCTAATATAAT
* *
566166 TAGACTTAAACATCTTAGATCCTAACTA-AATT
1 TAGACTTAAACATCTTTG-TGCTAA-TATAA-T
* * * **
566198 TGGGCTTAAATC-TCTTTGTGCCAATATAGC
1 TAGACTTAAA-CATCTTTGTGCTAATATAAT
* *
566228 TAGACTTAAACATCTTGGATGCTAGCTA-AAT
1 TAGACTTAAACATCTTTG-TGCTA-ATATAAT
* ** * * *
566259 TGGGTTTAAACATTTTTGTGCCAATATAAC
1 TAGACTTAAACATCTTTGTGCTAATATAAT
* * * * *
566289 TAGACTTAAATATCTTGGGTGCCAGCTA-AGTT
1 TAGACTTAAACATCTT-TGTGCTA-ATATA-AT
* * * * **
566321 TAGGCTTAAATC-TCTTTGTACCAACATAGC
1 TAGACTTAAA-CATCTTTGTGCTAATATAAT
* * *
566351 TAGACTTAAACATCTTGGATACTAGCTA-AAT
1 TAGACTTAAACATCTTTG-TGCTA-ATATAAT
* * * *
566382 TGGGCTTAAATATCTTTGTGCCAATATAAT
1 TAGACTTAAACATCTTTGTGCTAATATAAT
* *
566412 TGGGCTTAAACATCTT
1 TAGACTTAAACATCTT
566428 GGATGCCAAT
Statistics
Matches: 449, Mismatches: 164, Indels: 97
0.63 0.23 0.14
Matches are distributed among these distances:
29 18 0.04
30 185 0.41
31 168 0.37
32 72 0.16
33 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (30 bp):
TAGACTTAAACATCTTTGTGCTAATATAAT
Found at i:567792 original size:11 final size:11
Alignment explanation
Indices: 567778--567816 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
567768 TGTTCTCTCT
567778 TTTTTTTATCC
1 TTTTTTTATCC
567789 TTTTTTTATCTC
1 TTTTTTTATC-C
567801 TTTTTTT-T-C
1 TTTTTTTATCC
567810 TTTTTTT
1 TTTTTTT
567817 CATTGATCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.30
11 11 0.41
12 8 0.30
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTATCC
Found at i:567793 original size:12 final size:13
Alignment explanation
Indices: 567773--567808 Score: 58
Period size: 11 Copynumber: 2.9 Consensus size: 13
567763 TTCTTTGTTC
567773 TCTCTTTTTTTTA
1 TCTCTTTTTTTTA
567786 TC-C-TTTTTTTA
1 TCTCTTTTTTTTA
567797 TCTCTTTTTTTT
1 TCTCTTTTTTTT
567809 CTTTTTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
12 2 0.10
13 9 0.43
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTCTTTTTTTTA
Found at i:569261 original size:22 final size:24
Alignment explanation
Indices: 569231--569275 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
569221 CACTTGGTTA
*
569231 AGGCATTGAGAGTGTTTA-AAGAT
1 AGGCATTGAGAATGTTTATAAGAT
569254 AGGC-TTGAGAATGTTTATAAGA
1 AGGCATTGAGAATGTTTATAAGA
569276 ATGAGTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (24 bp):
AGGCATTGAGAATGTTTATAAGAT
Found at i:573201 original size:31 final size:30
Alignment explanation
Indices: 573165--573303 Score: 98
Period size: 29 Copynumber: 4.9 Consensus size: 30
573155 TGTAATAAAT
573165 TTTTTTTCAACATGACATGTAATAACAATA
1 TTTTTTTCAACATGACATGTAATAACAATA
* * * * *
573195 TTTTTTT-AATATGGCATGTAACAATAA-C
1 TTTTTTTCAACATGACATGTAATAACAATA
* * *
573223 TTATTTTCAATAT-AGC--GT-GTAA-AATA
1 TTTTTTTCAACATGA-CATGTAATAACAATA
* * *
573249 TTTTTGT--ACATGACGTGTAATAATAATA
1 TTTTTTTCAACATGACATGTAATAACAATA
573277 TTTTTTTTCAACATGACATGTAATAAC
1 -TTTTTTTCAACATGACATGTAATAAC
573304 CTTTTTTAAT
Statistics
Matches: 81, Mismatches: 17, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
24 4 0.05
25 3 0.04
26 9 0.11
27 5 0.06
28 10 0.12
29 28 0.35
30 7 0.09
31 15 0.19
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (30 bp):
TTTTTTTCAACATGACATGTAATAACAATA
Found at i:573336 original size:81 final size:81
Alignment explanation
Indices: 573174--573370 Score: 215
Period size: 81 Copynumber: 2.4 Consensus size: 81
573164 TTTTTTTTCA
* * *
573174 ACATGACATGTAATAACAATATTTTTTT-AATATGGCATGTAACAATAACTTATTTTCAATATAG
1 ACATGACATGTAATAATAATATTTTTTTCAACATGACATGT-A-AATAACTTATTTTCAATATAG
*
573238 CGTGTAAAATATTTTTGT
64 CGTGTAAAATACTTTTGT
* *
573256 ACATGACGTGTAATAATAATATTTTTTTTCAACATGACATGT-AATAACCTT-TTTT-AATCATT
1 ACATGACATGTAATAATAATA-TTTTTTTCAACATGACATGTAAATAA-CTTATTTTCAAT-ATA
*
573318 GCGTGTAACATACTTTTGT
63 GCGTGTAAAATACTTTTGT
* * * *
573337 ACATAACATATAATGATAACA-TTTTTTCAACATG
1 ACATGACATGTAATAATAATATTTTTTTCAACATG
573371 GCGTATAATA
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
79 13 0.13
80 3 0.03
81 44 0.44
82 22 0.22
83 7 0.07
84 10 0.10
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (81 bp):
ACATGACATGTAATAATAATATTTTTTTCAACATGACATGTAAATAACTTATTTTCAATATAGCG
TGTAAAATACTTTTGT
Found at i:574943 original size:22 final size:22
Alignment explanation
Indices: 574916--574964 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
574906 ACTAACGTTG
*
574916 GCATTACGAGACTAGTTTTTAA
1 GCATTACAAGACTAGTTTTTAA
574938 GCATTACAAGACTAGTTTTTAA
1 GCATTACAAGACTAGTTTTTAA
574960 GCATT
1 GCATT
574965 GCATTACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
GCATTACAAGACTAGTTTTTAA
Found at i:575067 original size:22 final size:23
Alignment explanation
Indices: 575042--575103 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 23
575032 GGGTATTGTA
575042 TGACTAGTTTTTAAGTATTAC-G
1 TGACTAGTTTTTAAGTATTACGG
* * *
575064 TGACT--TTTTTAGGTACTGCGG
1 TGACTAGTTTTTAAGTATTACGG
575085 TGACTAGTTTTTAAGTATT
1 TGACTAGTTTTTAAGTATT
575104 GCATAACTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.34
21 6 0.19
22 5 0.16
23 10 0.31
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.47
Consensus pattern (23 bp):
TGACTAGTTTTTAAGTATTACGG
Found at i:575133 original size:23 final size:22
Alignment explanation
Indices: 575099--575160 Score: 88
Period size: 23 Copynumber: 2.8 Consensus size: 22
575089 TAGTTTTTAA
*
575099 GTATTGCATAACTGGTTGATATG
1 GTATTGCATAACTAGTTGATA-G
*
575122 GTATTGCGTAACTAGTTGATAG
1 GTATTGCATAACTAGTTGATAG
*
575144 GCATTGCATAACTAGTT
1 GTATTGCATAACTAGTT
575161 AGAAAATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (22 bp):
GTATTGCATAACTAGTTGATAG
Found at i:575180 original size:23 final size:23
Alignment explanation
Indices: 575154--575202 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
575144 GCATTGCATA
*
575154 ACTAGTTAG-AAAATCATTGTGTG
1 ACTAGTTAGTAAAA-CATTGTGCG
*
575177 ACTAGTTAGTAAGACATTGTGCG
1 ACTAGTTAGTAAAACATTGTGCG
575200 ACT
1 ACT
575203 TAGGTTGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (23 bp):
ACTAGTTAGTAAAACATTGTGCG
Found at i:575267 original size:20 final size:21
Alignment explanation
Indices: 575244--575285 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
575234 TAAAAACTAG
*
575244 TCACGTAATG-CCAAAACCAA
1 TCACATAATGTCCAAAACCAA
*
575264 TCACATAATGTCTAAAACCAA
1 TCACATAATGTCCAAAACCAA
575285 T
1 T
575286 TACGCAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.21
Consensus pattern (21 bp):
TCACATAATGTCCAAAACCAA
Found at i:579257 original size:11 final size:11
Alignment explanation
Indices: 579226--579257 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
579216 TTTTGTTCTC
579226 TCTTTTTTTTA
1 TCTTTTTTTTA
*
579237 TCCTTTTTTTA
1 TCTTTTTTTTA
579248 TCTTTTTTTT
1 TCTTTTTTTT
579258 TTCATTGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTTTTTA
Found at i:582281 original size:280 final size:280
Alignment explanation
Indices: 581768--582469 Score: 983
Period size: 280 Copynumber: 2.5 Consensus size: 280
581758 GAACGAGAAT
* * *
581768 CAACAACTGGCCCAGCAACTCTTTGGGCCTAAACCACGTGGTCCTTAAAAGCTTAAGCTCAAGTT
1 CAACCACTGACCCAGCAACTCTTTGGGCCTAAACCACGTGATCCTTAAAAGCTTAAGCTCAAGTT
581833 GTTAGTAGTAGTAGACTTGGATTGTTATATAGGTCTTAACAATCACATTCACATCAGATGTGGGA
66 GTTAGTAGTAGTAGACTTGGATTGTTATATAGGTCTTAACAATCACATTCACATCAGATGTGGGA
* *
581898 TGTTGGGTATCACAATCCCACCCATTCAAATCCTTGATGTCCTCATTAAGCCCACACACCACATC
131 TGTTGGGTATCACAATCCCACCCACTCAAATCCTTGATGTCCTCATCAAGCCCACACACCACATC
* * * * *
581963 CATAGGACCAAGATCTCACCATAGCAATGTAAAAGCTCACATCAGACTAACGCAGGCTCTGATAC
196 CACAAGACCAAGATCTCACCAGAACAATGTAAAAGCTCACATCAGACTAACGCAGGCTCTAATAC
* *
582028 CATTTGTAACGATCCAAGTC
261 AATTTGTAACGACCCAAGTC
* * ** *
582048 TAACCACTGACTCAGCAACTCTTTATGCCTAAACCACGTGA-CTCTCAAAAGCTTAAGCTCAAGT
1 CAACCACTGACCCAGCAACTCTTTGGGCCTAAACCACGTGATC-CTTAAAAGCTTAAGCTCAAGT
** * ** * * * * * *
582112 TACTAGTAGTAGTATACTTACATTTTTATATAAGTCTTAACAATCATATTTACATAAGATGTGAG
65 TGTTAGTAGTAGTAGACTTGGATTGTTATATAGGTCTTAACAATCACATTCACATCAGATGTGGG
** ** ** *
582177 ATGTTGGGTATCACAATTTCACCCACTCAAATCCTTGATGTCCTCATCAAGGTCACGTATCACAT
130 ATGTTGGGTATCACAATCCCACCCACTCAAATCCTTGATGTCCTCATCAAGCCCACACACCACAT
* * * * * *
582242 CCACAAGACCAAGATTTTACCAGAATAATGTGAAAGCTCACATCGGACTGACGCAGGCTCTAATA
195 CCACAAGACCAAGATCTCACCAGAACAATGTAAAAGCTCACATCAGACTAACGCAGGCTCTAATA
582307 CAATTTGTAACGACCCAAGTC
260 CAATTTGTAACGACCCAAGTC
* * *
582328 CAACCATTGACCCAGCAACTCTTTGGGCCTAAACCACTTGATCCTTAAAAGCTTAAGCTCAAATT
1 CAACCACTGACCCAGCAACTCTTTGGGCCTAAACCACGTGATCCTTAAAAGCTTAAGCTCAAGTT
*
582393 GTTAGTAGTGGTAGACTTGGATTGTTATATAGGTCTTAACAATCACATTCACATCAGATGTGGGA
66 GTTAGTAGTAGTAGACTTGGATTGTTATATAGGTCTTAACAATCACATTCACATCAGATGTGGGA
582458 TGTTGGGTATCA
131 TGTTGGGTATCA
582470 TAATGAGTAT
Statistics
Matches: 359, Mismatches: 61, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
279 1 0.00
280 357 0.99
281 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (280 bp):
CAACCACTGACCCAGCAACTCTTTGGGCCTAAACCACGTGATCCTTAAAAGCTTAAGCTCAAGTT
GTTAGTAGTAGTAGACTTGGATTGTTATATAGGTCTTAACAATCACATTCACATCAGATGTGGGA
TGTTGGGTATCACAATCCCACCCACTCAAATCCTTGATGTCCTCATCAAGCCCACACACCACATC
CACAAGACCAAGATCTCACCAGAACAATGTAAAAGCTCACATCAGACTAACGCAGGCTCTAATAC
AATTTGTAACGACCCAAGTC
Found at i:585368 original size:29 final size:30
Alignment explanation
Indices: 585288--585385 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 30
585278 GACAACAACA
585288 TTTTAAACATTAA-AGTGTAAC-A-AAT-TTT
1 TTTTAAACA-TAACA-TGTAACAACAATATTT
*
585316 TTTTAAACATAACATGTAATAACAATATTT
1 TTTTAAACATAACATGTAACAACAATATTT
** *
585346 TTTT-AACATGGCATTTAACAACAATATTT
1 TTTTAAACATAACATGTAACAACAATATTT
*
585375 TTTTCAACATA
1 TTTTAAACATA
585386 GCGTATAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
27 8 0.14
28 11 0.19
29 28 0.47
30 12 0.20
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTTAAACATAACATGTAACAACAATATTT
Found at i:594170 original size:21 final size:22
Alignment explanation
Indices: 594129--594213 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
594119 GTGACTTAAT
* *
594129 CATTGCGTAATTGGTTTTTAGA
1 CATTACGTGATTGGTTTTTAGA
* *
594151 CATTATGTGATTGG-TTTTAGG
1 CATTACGTGATTGGTTTTTAGA
* *
594172 CATTACGTGACTAGTTTTTA-A
1 CATTACGTGATTGGTTTTTAGA
* *
594193 GCATTGCGTGATTGCTTTTTA
1 -CATTACGTGATTGGTTTTTA
594214 AGCAATACCT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
21 17 0.35
22 32 0.65
ACGTcount: A:0.21, C:0.11, G:0.22, T:0.46
Consensus pattern (22 bp):
CATTACGTGATTGGTTTTTAGA
Found at i:594251 original size:23 final size:23
Alignment explanation
Indices: 594225--594273 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
594215 GCAATACCTA
*
594225 AGTCGCACAATG-TCTTACTAACT
1 AGTCACACAATGAT-TTACTAACT
*
594248 AGTCACACAATGATTTTCTAACT
1 AGTCACACAATGATTTACTAACT
594271 AGT
1 AGT
594274 TATGCAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (23 bp):
AGTCACACAATGATTTACTAACT
Found at i:594295 original size:22 final size:23
Alignment explanation
Indices: 594267--594328 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
594257 ATGATTTTCT
*
594267 AACTAGTTATGCAATGCC-TATC
1 AACTAGTTATGCAATACCATATC
*
594289 AACTAGTTACGCAATACCATATC
1 AACTAGTTATGCAATACCATATC
*
594312 AACCAGTTATGCAATAC
1 AACTAGTTATGCAATAC
594329 TTAAAAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.27
Consensus pattern (23 bp):
AACTAGTTATGCAATACCATATC
Found at i:594385 original size:22 final size:22
Alignment explanation
Indices: 594322--594394 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
594312 AACCAGTTAT
594322 GCAATACTTAAAAACTAGTCAC
1 GCAATACTTAAAAACTAGTCAC
* *
594344 GCAGTACCTAAAAA-TGAGTCAC
1 GCAATACTTAAAAACT-AGTCAC
* * *
594366 GTAATGCTTAAAAACTAGTCAT
1 GCAATACTTAAAAACTAGTCAC
594388 GCAATAC
1 GCAATAC
594395 CCAAAGTCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (22 bp):
GCAATACTTAAAAACTAGTCAC
Found at i:594490 original size:22 final size:22
Alignment explanation
Indices: 594447--594513 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
594437 TCACACAATA
* ** *
594447 CTTAAAAATTAGTAATGCAATG
1 CTTAAAAACTAGTCTTGTAATG
594469 CTTAAAAACTAGTCTTGTAATG
1 CTTAAAAACTAGTCTTGTAATG
*
594491 CTTAAAAACTAGTCTCGTAATG
1 CTTAAAAACTAGTCTTGTAATG
594513 C
1 C
594514 CAACGTTAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (22 bp):
CTTAAAAACTAGTCTTGTAATG
Found at i:597515 original size:15 final size:17
Alignment explanation
Indices: 597497--597530 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
597487 TTCTTCCTCA
597497 TTTTCTT-TGTTT-TTT
1 TTTTCTTCTGTTTCTTT
597512 TTTTCTTCTGTTTCTTT
1 TTTTCTTCTGTTTCTTT
597529 TT
1 TT
597531 ATTTTCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTCTTCTGTTTCTTT
Found at i:597529 original size:16 final size:15
Alignment explanation
Indices: 597497--597530 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
597487 TTCTTCCTCA
*
597497 TTTTCTTTGTTTTTT
1 TTTTCTTTGTTTCTT
597512 TTTTCTTCTGTTTCTT
1 TTTTCTT-TGTTTCTT
597528 TTT
1 TTT
597531 ATTTTCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTCTTTGTTTCTT
Found at i:608261 original size:27 final size:29
Alignment explanation
Indices: 608231--608285 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
608221 TTTTTCCAAA
* *
608231 ATAATGTATAGCAA-AAT-TTTTTTAAAT
1 ATAACGTATAACAATAATATTTTTTAAAT
608258 ATAACGTATAACAATAATATTTTTTAAA
1 ATAACGTATAACAATAATATTTTTTAAA
608286 CATGGCGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 3 0.12
29 9 0.38
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (29 bp):
ATAACGTATAACAATAATATTTTTTAAAT
Found at i:608280 original size:29 final size:27
Alignment explanation
Indices: 608214--608285 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
608204 TCTGCATGTG
* * *
608214 ACAACATTTTTTCCAAA-ATAATGTATA
1 ACAAAATTTTTT-TAAATATAACGTATA
*
608241 GCAAAATTTTTTTAAATATAACGTATA
1 ACAAAATTTTTTTAAATATAACGTATA
608268 ACAATAATATTTTTTAAA
1 ACAA-AAT-TTTTTTAAA
608286 CATGGCGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 3 0.08
27 22 0.59
28 3 0.08
29 9 0.24
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (27 bp):
ACAAAATTTTTTTAAATATAACGTATA
Found at i:608425 original size:29 final size:30
Alignment explanation
Indices: 608370--608428 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
608360 TTTTCAACTG
* **
608370 TAACAATATTTTTTTAAACATTGTATGTAA
1 TAACAACATTTTTTTAAACATAATATGTAA
608400 TAACAACA-TTTTTTAAACATAATATGTAA
1 TAACAACATTTTTTTAAACATAATATGTAA
608429 CTTGGTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (30 bp):
TAACAACATTTTTTTAAACATAATATGTAA
Found at i:612474 original size:21 final size:21
Alignment explanation
Indices: 612446--612485 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
612436 CAAGGTAAGA
612446 ATTTAGCTCAT-TATTGAAAG
1 ATTTAGCTCATATATTGAAAG
612466 ATTTGAGCTCATATATTGAA
1 ATTT-AGCTCATATATTGAA
612486 TTGAGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (21 bp):
ATTTAGCTCATATATTGAAAG
Found at i:627182 original size:20 final size:20
Alignment explanation
Indices: 627150--627194 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
627140 TATAATTAAA
* *
627150 AATA-ATAATTTTTTAAAAT
1 AATATATAACTTTTAAAAAT
627169 AATATATAACTTTTAAAAAT
1 AATATATAACTTTTAAAAAT
627189 -ATATAT
1 AATATAT
627195 TATACCGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATATAACTTTTAAAAAT
Found at i:627191 original size:17 final size:18
Alignment explanation
Indices: 627145--627193 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
627135 TTAATTATAA
*
627145 TTAAAAATA-ATAATTTT
1 TTAAAAATATATAATCTT
627162 TTAAAATAATATATAA-CTT
1 TT-AAA-AATATATAATCTT
627181 TTAAAAATATATA
1 TTAAAAATATATA
627194 TTATACCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 10 0.36
18 6 0.21
19 8 0.29
20 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAAATATATAATCTT
Found at i:628029 original size:116 final size:116
Alignment explanation
Indices: 627823--628037 Score: 263
Period size: 116 Copynumber: 1.9 Consensus size: 116
627813 ATTAACTTTG
* * * * * ** * *
627823 AAAATAGAGATTTAAATAAGTTTATAAATCATGGGTTCATATTTGTGACCTAAAAAACATGCTTG
1 AAAATAAAAATTTAAATAAGCTTATAAATCATGAGTTCACATTTGCAACCTAAAAAACATACTTA
* * *
627888 ATAAGTGGTGAAAGATCCATATTTATATATTCAAAATAGTTTTAAACTCTA
66 ATAAATAGTGAAAGATCCATATTTATATACTCAAAATAGTTTTAAACTCTA
*
627939 AAAATAAAAATTTAAATAAGCTTATAAATCATGAGTTCACATTTGCAATCC-AAAAGACATACTT
1 AAAATAAAAATTTAAATAAGCTTATAAATCATGAGTTCACATTTGCAA-CCTAAAAAACATACTT
* *
628003 AATAAATAGTGAAAGA-CTTATGTTTATATACTCAA
65 AATAAATAGTGAAAGATC-CATATTTATATACTCAA
628038 GGCTCACTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
115 1 0.01
116 79 0.96
117 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (116 bp):
AAAATAAAAATTTAAATAAGCTTATAAATCATGAGTTCACATTTGCAACCTAAAAAACATACTTA
ATAAATAGTGAAAGATCCATATTTATATACTCAAAATAGTTTTAAACTCTA
Found at i:630102 original size:18 final size:18
Alignment explanation
Indices: 630081--630174 Score: 73
Period size: 18 Copynumber: 5.2 Consensus size: 18
630071 ATATACACAT
630081 TTAAACATGATAACACGA
1 TTAAACATGATAACACGA
* * * *
630099 TTAAACACGTTTATAC-A
1 TTAAACATGATAACACGA
* *
630116 TCTGAACACGATAACACGA
1 T-TAAACATGATAACACGA
* * * *
630135 TTAAACATGTTTAGACGT
1 TTAAACATGATAACACGA
*
630153 TTAAACATGATAACATGA
1 TTAAACATGATAACACGA
630171 TTAA
1 TTAA
630175 CACGATTAAT
Statistics
Matches: 55, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
17 2 0.04
18 51 0.93
19 2 0.04
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.29
Consensus pattern (18 bp):
TTAAACATGATAACACGA
Found at i:630130 original size:36 final size:36
Alignment explanation
Indices: 630077--630178 Score: 125
Period size: 36 Copynumber: 2.9 Consensus size: 36
630067 TCATATATAC
* *
630077 ACATTTAAACATGATAACACGATTAAACACGTTTAT
1 ACATCTAAACATGATAACACGATTAAACACGTTTAG
* * *
630113 ACATCTGAACACGATAACACGATTAAACATGTTTAG
1 ACATCTAAACATGATAACACGATTAAACACGTTTAG
* * *
630149 ACGTTTAAACATGATAACATGATT-AACACG
1 ACATCTAAACATGATAACACGATTAAACACG
630179 ATTAATTAAG
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
35 5 0.09
36 50 0.91
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (36 bp):
ACATCTAAACATGATAACACGATTAAACACGTTTAG
Found at i:630899 original size:34 final size:34
Alignment explanation
Indices: 630837--630933 Score: 88
Period size: 34 Copynumber: 2.9 Consensus size: 34
630827 CTACAGTAAA
* * * *
630837 AAATGTTACACGCC-AAGATCAAAACTTTAACACT
1 AAATGTTATACGCCAAAG-CCAAAGCTTTAACACC
*
630871 AAATGTTATACGCCAAAGCCAAAGCTTTAATACC
1 AAATGTTATACGCCAAAGCCAAAGCTTTAACACC
* * * * *
630905 AGATGTTATATGTCAATGCCCAAGCTTTA
1 AAATGTTATACGCCAAAGCCAAAGCTTTA
630934 GTATCAAGTA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 49 0.94
35 3 0.06
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (34 bp):
AAATGTTATACGCCAAAGCCAAAGCTTTAACACC
Found at i:631523 original size:17 final size:17
Alignment explanation
Indices: 631494--631526 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
631484 TTTTGTCATT
631494 AAATTATAATTGATAGA
1 AAATTATAATTGATAGA
631511 AAATT-TAATTTGATAG
1 AAATTATAA-TTGATAG
631527 TAATTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
AAATTATAATTGATAGA
Found at i:632167 original size:15 final size:16
Alignment explanation
Indices: 632139--632180 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
632129 AAATATTACC
*
632139 TCAATAAAAA-CCTTA
1 TCAAAAAAAACCCTTA
632154 T-AAAAAAAACCCTTA
1 TCAAAAAAAACCCTTA
*
632169 TCAAGAAAAACC
1 TCAAAAAAAACC
632181 TAGTATGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
16 9 0.39
ACGTcount: A:0.57, C:0.21, G:0.02, T:0.19
Consensus pattern (16 bp):
TCAAAAAAAACCCTTA
Found at i:635601 original size:43 final size:45
Alignment explanation
Indices: 635538--635623 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 45
635528 ATTTGCTTCT
* *
635538 ATATTTTTCTCTCTTTTAGCATTCAGTAATGTTTGATAAAGTTTA
1 ATATTTTTCTCTCTTTTAGCATTCAATAATATTTGATAAAGTTTA
* *
635583 ATATTTTT-T-TCTTTTAGCATTTAATGATATTTGATAAAGTT
1 ATATTTTTCTCTCTTTTAGCATTCAATAATATTTGATAAAGTT
635624 CAACAAGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 28 0.76
44 1 0.03
45 8 0.22
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (45 bp):
ATATTTTTCTCTCTTTTAGCATTCAATAATATTTGATAAAGTTTA
Found at i:635784 original size:28 final size:28
Alignment explanation
Indices: 635752--635806 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
635742 TCTTCACTAT
635752 TCATCCACTTT-TAGTAGATTAAAAATAC
1 TCATCCA-TTTCTAGTAGATTAAAAATAC
635780 TCATCCATTTCTAGTAGATTAAAAATA
1 TCATCCATTTCTAGTAGATTAAAAATA
635807 TTTACCCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (28 bp):
TCATCCATTTCTAGTAGATTAAAAATAC
Found at i:635819 original size:28 final size:28
Alignment explanation
Indices: 635756--635819 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
635746 CACTATTCAT
* *
635756 CCACTTTTAGTAGATTAAAAATACTCAT
1 CCACTTCTAGTAGATTAAAAATACTCAC
* * *
635784 CCATTTCTAGTAGATTAAAAATATTTAC
1 CCACTTCTAGTAGATTAAAAATACTCAC
635812 CCACTTCT
1 CCACTTCT
635820 GTGTGGGTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (28 bp):
CCACTTCTAGTAGATTAAAAATACTCAC
Found at i:635853 original size:29 final size:28
Alignment explanation
Indices: 635798--635876 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 28
635788 TTCTAGTAGA
* * * * *
635798 TTAAAAATATTTACCCACTTCTGTGTGGG
1 TTAAAAGTATATATCCACTTTTATGT-GG
635827 TTAAAAGTATATATCCACTTTTATGTGG
1 TTAAAAGTATATATCCACTTTTATGTGG
* *
635855 AT-AGAGTTATATATCCACTTTT
1 TTAAAAG-TATATATCCACTTTT
635877 GGTGGATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.07
28 18 0.43
29 21 0.50
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (28 bp):
TTAAAAGTATATATCCACTTTTATGTGG
Found at i:635889 original size:27 final size:28
Alignment explanation
Indices: 635830--635891 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
635820 GTGTGGGTTA
*
635830 AAAG-TATATATCCACTTTTATGTGGAT
1 AAAGTTATATATCCACTTTTAGGTGGAT
*
635857 AGAGTTATATATCCACTTTT-GGTGGAT
1 AAAGTTATATATCCACTTTTAGGTGGAT
635884 AAAGTTAT
1 AAAGTTAT
635892 TGTTATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (28 bp):
AAAGTTATATATCCACTTTTAGGTGGAT
Found at i:636276 original size:64 final size:64
Alignment explanation
Indices: 636165--636290 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 64
636155 ATTGAAATCT
* * *
636165 TTTTGAAGCTTGGAGAGGATGAAAACAAAATAATGCCAACACCTACCTAATTTACTAAAACTCC
1 TTTTGAAGCTTGGAGAAGATGAAAACAAAATAATACCAACACCTACCTAATTGACTAAAACTCC
* * ** *
636229 TTTTGAAGCTTGGAGAAGATGAAAATAAAATAATACGAACATTTACCTAATTGGCTAAAACT
1 TTTTGAAGCTTGGAGAAGATGAAAACAAAATAATACCAACACCTACCTAATTGACTAAAACT
636291 AGAAATCAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (64 bp):
TTTTGAAGCTTGGAGAAGATGAAAACAAAATAATACCAACACCTACCTAATTGACTAAAACTCC
Found at i:637010 original size:2 final size:2
Alignment explanation
Indices: 637005--637031 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
636995 ACACACGCAC
637005 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
637032 ATAAAGTCAA
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:640314 original size:16 final size:17
Alignment explanation
Indices: 640282--640314 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
640272 AATCAGAATG
640282 GCAGAAACAGAGGAAGA
1 GCAGAAACAGAGGAAGA
*
640299 GCAGAACCAG-GGAAGA
1 GCAGAAACAGAGGAAGA
640315 AAATGAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.15, G:0.36, T:0.00
Consensus pattern (17 bp):
GCAGAAACAGAGGAAGA
Found at i:663043 original size:29 final size:29
Alignment explanation
Indices: 663011--663095 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
663001 AAGGCACAAG
663011 AGAAGAAAGTGTACGTGAATAGGTATAAA
1 AGAAGAAAGTGTACGTGAATAGGTATAAA
* * * *
663040 AGAAG-AAGCTGCACGTAAATAGGTACAAG
1 AGAAGAAAG-TGTACGTGAATAGGTATAAA
*
663069 AGAA-AAAGGTGTATGTGAATAGGTATA
1 AGAAGAAA-GTGTACGTGAATAGGTATA
663096 CTAGAATAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.07
29 41 0.91
30 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.28, T:0.20
Consensus pattern (29 bp):
AGAAGAAAGTGTACGTGAATAGGTATAAA
Found at i:664643 original size:2 final size:2
Alignment explanation
Indices: 664636--664661 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
664626 TAAGTAGTGT
664636 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
664662 ATTGTTTAAA
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):
TA
Found at i:666884 original size:62 final size:62
Alignment explanation
Indices: 666809--666935 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 62
666799 ATCTATTCTC
* *
666809 TAAAGTAAATGTAACAATACTTAATTTAATAATTATGGTCATTAATGTAAAAGAAGTCGTCA
1 TAAAGTAAATGTAACAATACATAATTTAATAATTATGGTCATTAATGTAAAAAAAGTCGTCA
* * *
666871 TAAAGTGAATGTAACAATACATAATTTAATAATTATGGTCATTGATGTAAAAAAAGTTGTCA
1 TAAAGTAAATGTAACAATACATAATTTAATAATTATGGTCATTAATGTAAAAAAAGTCGTCA
666933 TAA
1 TAA
666936 TAATTACAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (62 bp):
TAAAGTAAATGTAACAATACATAATTTAATAATTATGGTCATTAATGTAAAAAAAGTCGTCA
Found at i:667195 original size:32 final size:32
Alignment explanation
Indices: 667154--667218 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
667144 CGGCTGTGCT
667154 CCTCAAGGGAGGGGAGCATTAGAAAGGGAGCA
1 CCTCAAGGGAGGGGAGCATTAGAAAGGGAGCA
667186 CCTCAAGGGAGGGGAGCATTAGAAAGGGAGCA
1 CCTCAAGGGAGGGGAGCATTAGAAAGGGAGCA
667218 C
1 C
667219 TTTTGGGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.40, T:0.09
Consensus pattern (32 bp):
CCTCAAGGGAGGGGAGCATTAGAAAGGGAGCA
Found at i:671088 original size:26 final size:24
Alignment explanation
Indices: 671027--671088 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
671017 TTTTAAAAAA
671027 TTTAAATAAATTTTTTTTTATTAT
1 TTTAAATAAATTTTTTTTTATTAT
* * *
671051 GTTCAATTAAATTTTTTTATTTTTAT
1 -TTTAAATAAATTTTTTT-TTATTAT
671077 TTTAAATCAAAT
1 TTTAAAT-AAAT
671089 AAATCATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTAAATAAATTTTTTTTTATTAT
Found at i:675032 original size:29 final size:29
Alignment explanation
Indices: 674995--675060 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
674985 AAAGTGTATG
* *
674995 AATTATTTA-AAAATTTTAATTAAGTTTTT
1 AATTTTTTATAAAA-TTAAATTAAGTTTTT
* *
675024 AATTTTTTATTACATTAAATTAAGTTTTT
1 AATTTTTTATAAAATTAAATTAAGTTTTT
675053 ATATTTTT
1 A-ATTTTT
675061 ATTTTAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AATTTTTTATAAAATTAAATTAAGTTTTT
Found at i:677150 original size:31 final size:29
Alignment explanation
Indices: 677111--677174 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
677101 AATCAAGTTA
* *
677111 TTATATTTTCACTTTGAATCAAATAATTTT
1 TTATATTTT-ACTTTAAATCAAATAAATTT
*
677141 TTATAATTTTATTTTAAATCAAATAAATTT
1 TTAT-ATTTTACTTTAAATCAAATAAATTT
677171 TTAT
1 TTAT
677175 GAATAATGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (29 bp):
TTATATTTTACTTTAAATCAAATAAATTT
Found at i:678918 original size:29 final size:29
Alignment explanation
Indices: 678871--678964 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
678861 TCTACTTTTT
*
678871 CCTTATTCTCTTATACTTGTTCACGTACAA
1 CCTT-TTCTCTTGTACTTGTTCACGTACAA
*
678901 CCTTTTCTCTTGTACTTGTTCATGTAC-A
1 CCTTTTCTCTTGTACTTGTTCACGTACAA
* * *
678929 GCTTTCTCTCTTGTACCTGTTCACATACAA
1 CCTTT-TCTCTTGTACTTGTTCACGTACAA
*
678959 CTTTTT
1 CCTTTT
678965 TTTATTAGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 5 0.09
29 41 0.76
30 8 0.15
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.47
Consensus pattern (29 bp):
CCTTTTCTCTTGTACTTGTTCACGTACAA
Found at i:688684 original size:14 final size:14
Alignment explanation
Indices: 688667--688770 Score: 66
Period size: 14 Copynumber: 7.3 Consensus size: 14
688657 CCCCACCCAC
688667 TTTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
688681 TTTT-TATTCAAAG
1 TTTTCCCTCCAAAG
* *
688694 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
688709 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
688723 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
688737 TATTCCCCCCCAAAAG
1 T-TTTCCCTCC-AAAG
*
688753 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
688767 TTTT
1 TTTT
688771 GGAAGGTTCT
Statistics
Matches: 62, Mismatches: 24, Indels: 8
0.66 0.26 0.09
Matches are distributed among these distances:
13 9 0.15
14 27 0.44
15 22 0.35
16 4 0.06
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.35
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:688714 original size:15 final size:15
Alignment explanation
Indices: 688696--688765 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
688686 ATTCAAAGTA
*
688696 TTCCCCCCAAAAGAT
1 TTCCCTCCAAAAGAT
*
688711 TTCCCTCC-AAAGTT
1 TTCCCTCCAAAAGAT
** *
688725 TTCAATTC-AAAGTAT
1 TTCCCTCCAAAAG-AT
* *
688740 TCCCCCCCAAAAGAT
1 TTCCCTCCAAAAGAT
688755 TTCCCTCCAAA
1 TTCCCTCCAAA
688766 GTTTTGGAAG
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
14 14 0.35
15 22 0.55
16 4 0.10
ACGTcount: A:0.31, C:0.36, G:0.06, T:0.27
Consensus pattern (15 bp):
TTCCCTCCAAAAGAT
Found at i:688734 original size:43 final size:43
Alignment explanation
Indices: 688668--688770 Score: 181
Period size: 44 Copynumber: 2.4 Consensus size: 43
688658 CCCACCCACT
*
688668 TTTCCCTCCAAAGTTTTTATTCAAAGTATT-CCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTAATTCAAAGTATTCCCCCCCAAAAGA
688710 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTT-AATTCAAAGTATTCCCCCCCAAAAGA
688754 TTTCCCTCCAAAGTTTT
1 TTTCCCTCCAAAGTTTT
688771 GGAAGGTTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
42 17 0.29
43 12 0.21
44 29 0.50
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (43 bp):
TTTCCCTCCAAAGTTTTAATTCAAAGTATTCCCCCCCAAAAGA
Found at i:693903 original size:14 final size:14
Alignment explanation
Indices: 693886--693990 Score: 59
Period size: 14 Copynumber: 7.3 Consensus size: 14
693876 CCCCACCCAC
693886 TTTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
693900 TTTT-TATTCAAAG
1 TTTTCCCTCCAAAG
* *
693913 TATTCCCCCCAAAAG
1 TTTTCCCTCC-AAAG
*
693928 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
** *
693942 TTTTCAATTCAAAG
1 TTTTCCCTCCAAAG
* *
693956 TATTCCCCCCCCAAAAG
1 T-TT-TCCCTCC-AAAG
*
693973 ATTTCCCTCCAAAG
1 TTTTCCCTCCAAAG
693987 TTTT
1 TTTT
693991 GGAAGGTTCT
Statistics
Matches: 62, Mismatches: 24, Indels: 10
0.65 0.25 0.10
Matches are distributed among these distances:
13 9 0.15
14 27 0.44
15 18 0.29
16 4 0.06
17 4 0.06
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.34
Consensus pattern (14 bp):
TTTTCCCTCCAAAG
Found at i:693981 original size:45 final size:42
Alignment explanation
Indices: 693887--693990 Score: 172
Period size: 45 Copynumber: 2.4 Consensus size: 42
693877 CCCACCCACT
*
693887 TTTCCCTCCAAAGTTTTTATTCAAAGTATTCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTTAATTCAAAGTATTCCCCCCAAAAGA
693929 TTTCCCTCCAAAGTTTTCAATTCAAAGTATTCCCCCCCCAAAAGA
1 TTTCCCTCCAAAGTTTT-AATTCAAAGTATT--CCCCCCAAAAGA
693974 TTTCCCTCCAAAGTTTT
1 TTTCCCTCCAAAGTTTT
693991 GGAAGGTTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
42 17 0.29
43 12 0.21
45 29 0.50
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.34
Consensus pattern (42 bp):
TTTCCCTCCAAAGTTTTAATTCAAAGTATTCCCCCCAAAAGA
Found at i:696292 original size:29 final size:28
Alignment explanation
Indices: 696248--696308 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
696238 ATAGGCTTAT
* * *
696248 TTGACAAAATATAAATATAAGAGTTTGA
1 TTGACAAAATAAAAATATAAAAATTTGA
696276 TTGACAATAATAAAAATATAAAAATTTGA
1 TTGACAA-AATAAAAATATAAAAATTTGA
696305 TTGA
1 TTGA
696309 ACGCAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.33
Consensus pattern (28 bp):
TTGACAAAATAAAAATATAAAAATTTGA
Found at i:696420 original size:88 final size:88
Alignment explanation
Indices: 696271--696447 Score: 345
Period size: 88 Copynumber: 2.0 Consensus size: 88
696261 AATATAAGAG
696271 TTTGATTGACAATAATAAAAATATAAAAATTTGATTGAACGCAATAAAAGTGTAAGTTTATTTAA
1 TTTGATTGACAATAATAAAAATATAAAAATTTGATTGAACGCAATAAAAGTGTAAGTTTATTTAA
696336 ATTTTCTTGAATAATTACAGATT
66 ATTTTCTTGAATAATTACAGATT
*
696359 TTTGATTGACAATAATAAAAATATAAACATTTGATTGAACGCAATAAAAGTGTAAGTTTATTTAA
1 TTTGATTGACAATAATAAAAATATAAAAATTTGATTGAACGCAATAAAAGTGTAAGTTTATTTAA
696424 ATTTTCTTGAATAATTACAGATT
66 ATTTTCTTGAATAATTACAGATT
696447 T
1 T
696448 ATTTGAGTAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (88 bp):
TTTGATTGACAATAATAAAAATATAAAAATTTGATTGAACGCAATAAAAGTGTAAGTTTATTTAA
ATTTTCTTGAATAATTACAGATT
Found at i:703561 original size:23 final size:23
Alignment explanation
Indices: 703531--703588 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
703521 GTAATGCCTA
703531 AGTCACACAATACCTTACTAACT
1 AGTCACACAATACCTTACTAACT
* * ** *
703554 AGTTACACTATGGCTTATTAACT
1 AGTCACACAATACCTTACTAACT
*
703577 AGTCACGCAATA
1 AGTCACACAATA
703589 GTGTACTAAC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (23 bp):
AGTCACACAATACCTTACTAACT
Found at i:703613 original size:46 final size:46
Alignment explanation
Indices: 703563--703679 Score: 148
Period size: 46 Copynumber: 2.6 Consensus size: 46
703553 TAGTTACACT
*
703563 ATGGCTTATTAACTAGTCACGCAATAG-TGTACTAACAAATCATGCA
1 ATGGCTTACTAACTAGTCACGCAATAGCT-TACTAACAAATCATGCA
* * * *
703609 ATGGCTTACTAACAAGTCATGCAATGGCTTACTAACAAGTCATGCA
1 ATGGCTTACTAACTAGTCACGCAATAGCTTACTAACAAATCATGCA
* *
703655 AT-GCTTACCAACTAGTCACGTAATA
1 ATGGCTTACTAACTAGTCACGCAATA
703680 CCTAAAAATA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
45 18 0.30
46 41 0.68
47 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (46 bp):
ATGGCTTACTAACTAGTCACGCAATAGCTTACTAACAAATCATGCA
Found at i:703671 original size:22 final size:23
Alignment explanation
Indices: 703563--703672 Score: 134
Period size: 23 Copynumber: 4.8 Consensus size: 23
703553 TAGTTACACT
* * *
703563 ATGGCTTATTAACTAGTCACGCA
1 ATGGCTTACTAACAAGTCATGCA
* *
703586 ATAG-TGTACTAACAAATCATGCA
1 ATGGCT-TACTAACAAGTCATGCA
703609 ATGGCTTACTAACAAGTCATGCA
1 ATGGCTTACTAACAAGTCATGCA
703632 ATGGCTTACTAACAAGTCATGCA
1 ATGGCTTACTAACAAGTCATGCA
* *
703655 AT-GCTTACCAACTAGTCA
1 ATGGCTTACTAACAAGTCA
703673 CGTAATACCT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
22 15 0.20
23 60 0.79
24 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.27
Consensus pattern (23 bp):
ATGGCTTACTAACAAGTCATGCA
Found at i:703728 original size:21 final size:21
Alignment explanation
Indices: 703704--703743 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
703694 ACACAGTGCC
*
703704 CAAAGTCAGTCACGCAATGTA
1 CAAAGTAAGTCACGCAATGTA
703725 CAAAGTAAGTCACGCAATG
1 CAAAGTAAGTCACGCAATG
703744 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (21 bp):
CAAAGTAAGTCACGCAATGTA
Found at i:703760 original size:22 final size:22
Alignment explanation
Indices: 703645--703766 Score: 65
Period size: 21 Copynumber: 5.6 Consensus size: 22
703635 GCTTACTAAC
* * *
703645 AAGTCATGCAATGCTTACCAACT
1 AAGTCACGCAATGC-TACAAAAT
* *
703668 -AGTCACGTAATACCTA-AAAAT
1 AAGTCACGCAAT-GCTACAAAAT
* * * *
703689 AAGTCACACAGTGC-CCAAAGT
1 AAGTCACGCAATGCTACAAAAT
* *
703710 CAGTCACGCAATG-TACAAAGT
1 AAGTCACGCAATGCTACAAAAT
703731 AAGTCACGCAATGCTTA-AAAAT
1 AAGTCACGCAATGC-TACAAAAT
* *
703753 TAGTCACGTAATGC
1 AAGTCACGCAATGC
703767 CCAAAAATCA
Statistics
Matches: 74, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
21 36 0.49
22 35 0.47
23 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (22 bp):
AAGTCACGCAATGCTACAAAAT
Found at i:703772 original size:22 final size:22
Alignment explanation
Indices: 703667--703774 Score: 67
Period size: 21 Copynumber: 5.0 Consensus size: 22
703657 GCTTACCAAC
* * *
703667 TAGTCACGTAATACCTAAAAAT
1 TAGTCACGCAATGCCCAAAAAT
* * * *
703689 AAGTCACACAGTGCCC-AAAGT
1 TAGTCACGCAATGCCCAAAAAT
* ** *
703710 CAGTCACGCAATGTAC-AAAGT
1 TAGTCACGCAATGCCCAAAAAT
* **
703731 AAGTCACGCAATGCTTAAAAAT
1 TAGTCACGCAATGCCCAAAAAT
*
703753 TAGTCACGTAATGCCCAAAAAT
1 TAGTCACGCAATGCCCAAAAAT
703775 CACCAAAATT
Statistics
Matches: 64, Mismatches: 21, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
21 32 0.50
22 32 0.50
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (22 bp):
TAGTCACGCAATGCCCAAAAAT
Found at i:703988 original size:60 final size:60
Alignment explanation
Indices: 703880--703992 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
703870 ACAAAGAATG
* * * * *
703880 CTCAAAATGTTCAAAGTTTTTGTTCATATATCAAAAATCATTTCAAAATGCTTAAAAATA
1 CTCAAAACGCTCAAAGGTTTTCTTCATATATCAAAAATCATCTCAAAATGCTTAAAAATA
*
703940 CTCAAAACGCTCAAAGGTTTTCTTCGTATATCAAAAA-C-TACTCTAAAATGCTT
1 CTCAAAACGCTCAAAGGTTTTCTTCATATATCAAAAATCAT-CTC-AAAATGCTT
703993 TAATGTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.02
59 3 0.07
60 41 0.91
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.35
Consensus pattern (60 bp):
CTCAAAACGCTCAAAGGTTTTCTTCATATATCAAAAATCATCTCAAAATGCTTAAAAATA
Found at i:713205 original size:38 final size:38
Alignment explanation
Indices: 713135--713207 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
713125 AACCTAACCC
* * * *
713135 CACTAACTTATACGTGATAATAAAATTGACTTTAAACG
1 CACTAACTTAAACATGATAATAAAACTAACTTTAAACG
713173 CACTAACTTAAACATGATAA-ATAAACTAACTTTAA
1 CACTAACTTAAACATGATAATA-AAACTAACTTTAA
713208 TTAAACTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.03
38 29 0.97
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (38 bp):
CACTAACTTAAACATGATAATAAAACTAACTTTAAACG
Found at i:729149 original size:38 final size:38
Alignment explanation
Indices: 729107--729181 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
729097 AGAAGTTTAA
729107 TTAAAGTCAG-TTTATTTATCACGTTTAAGTTAGTGGGG
1 TTAAAGTCAGTTTTA-TTATCACGTTTAAGTTAGTGGGG
*
729145 TTAAAGTCAGTTTTATTATCACGTTTAATTTAGTGGG
1 TTAAAGTCAGTTTTATTATCACGTTTAAGTTAGTGGG
729182 ATTAGGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 31 0.89
39 4 0.11
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (38 bp):
TTAAAGTCAGTTTTATTATCACGTTTAAGTTAGTGGGG
Found at i:746973 original size:2 final size:2
Alignment explanation
Indices: 746966--747014 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
746956 TACCATTTAG
746966 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
747008 TC TC TC T
1 TC TC TC T
747015 TATATTATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:747025 original size:2 final size:2
Alignment explanation
Indices: 747015--747058 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
747005 CTCTCTCTCT
*
747015 TA TA T- TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
747054 TA TA T
1 TA TA T
747059 GCAATGTTCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:747041 original size:22 final size:22
Alignment explanation
Indices: 747016--747058 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
747006 TCTCTCTCTT
*
747016 ATATTATATATATATATATATA
1 ATATTATATATACATATATATA
747038 ATATTATATATACATATATAT
1 ATATTATATATACATATATAT
747059 GCAATGTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTATATATACATATATATA
Found at i:747588 original size:24 final size:24
Alignment explanation
Indices: 747544--747589 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
747534 TCTCTTTCCT
* *
747544 TCTCTTCGTCCCTAATTCTCTCCA
1 TCTCTTCGTCCCAAATACTCTCCA
747568 TCTCTTC-TCCCAAAATACTCTC
1 TCTCTTCGTCCC-AAATACTCTC
747590 TAATTCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.17, C:0.41, G:0.02, T:0.39
Consensus pattern (24 bp):
TCTCTTCGTCCCAAATACTCTCCA
Found at i:747849 original size:18 final size:18
Alignment explanation
Indices: 747816--747850 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
747806 ATCTTTATGA
* *
747816 TTATTAGTTAATATACTG
1 TTATTAGTGAAAATACTG
747834 TTATTAGTGAAAATACT
1 TTATTAGTGAAAATACT
747851 AATCCTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (18 bp):
TTATTAGTGAAAATACTG
Found at i:752184 original size:21 final size:20
Alignment explanation
Indices: 752160--752208 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
752150 TTTAGAACAG
*
752160 GGAAAAGATTCAGACCAGAGA
1 GGAAAAGATT-AGACCAGAAA
* * *
752181 GGAAAAAATTGGAGCAGAAA
1 GGAAAAGATTAGACCAGAAA
752201 GGAAAAGA
1 GGAAAAGA
752209 GATTGAAGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.53, C:0.08, G:0.31, T:0.08
Consensus pattern (20 bp):
GGAAAAGATTAGACCAGAAA
Found at i:758286 original size:6 final size:6
Alignment explanation
Indices: 758247--758283 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
758237 ACATGGTTTG
* *
758247 CCGGCT CCGGCT CCGGCT CCGGCT CCAGCT CTGGCT C
1 CCGGCT CCGGCT CCGGCT CCGGCT CCGGCT CCGGCT C
758284 TGGTGGGGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.49, G:0.30, T:0.19
Consensus pattern (6 bp):
CCGGCT
Found at i:762602 original size:17 final size:16
Alignment explanation
Indices: 762580--762620 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
762570 TCAAGTATCT
762580 TTTGCTGTTTTAATT-G
1 TTTGCTGTTTT-ATTAG
762596 CTTTGCT-TTTTATTAG
1 -TTTGCTGTTTTATTAG
762612 TTTGCTGTT
1 TTTGCTGTT
762621 AAAAAGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.63
Consensus pattern (16 bp):
TTTGCTGTTTTATTAG
Found at i:763697 original size:59 final size:59
Alignment explanation
Indices: 763604--763719 Score: 223
Period size: 59 Copynumber: 2.0 Consensus size: 59
763594 GATATTTTAG
*
763604 ATCTTTATATTAATTCGTTTTGCTTGTTTGGAGTAGTCTTGAAGTCCCTACGTTAATCC
1 ATCTTTATATTAATTCGTTTTGCTTGTTTAGAGTAGTCTTGAAGTCCCTACGTTAATCC
763663 ATCTTTATATTAATTCGTTTTGCTTGTTTAGAGTAGTCTTGAAGTCCCTACGTTAAT
1 ATCTTTATATTAATTCGTTTTGCTTGTTTAGAGTAGTCTTGAAGTCCCTACGTTAAT
763720 TTCGATTAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (59 bp):
ATCTTTATATTAATTCGTTTTGCTTGTTTAGAGTAGTCTTGAAGTCCCTACGTTAATCC
Found at i:775407 original size:342 final size:343
Alignment explanation
Indices: 774774--775449 Score: 1056
Period size: 342 Copynumber: 2.0 Consensus size: 343
774764 TAAAGTTTAA
* *
774774 TTTAGAGAAAAATAATTGATAATAATGGAACTTTTTTTCTTGTATTCTACAAGAATGCTTTTTAG
1 TTTAGAGAAAAATAATTGATAATAATGAAACTTTTTTTCTTGTACTCTACAAGAATGCTTTTTAG
* *
774839 AGTAATTATGCTACTATTAACTCATTATGATTTAGAGCGGCACAAAATGGATGTTAAGATTGTCT
66 AGTAATTATGCTACTAATAACTCATTATGATTTAGAGCGCCACAAAATGGATGTTAAGATTGTCT
* * *
774904 TCCTGAATGTGAATCTTGTTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTATGGTT
131 TCCTGAATGAGAATCTTGTTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTATAGCT
*
774969 AAGATCAACTTTTGTGTAGACTCAAAGAGTATTTATGAGTTCAAACAAGCTTCTCGTCAGTAGTA
196 AAAATCAACTTTTGTGTAGACTCAAAGAGTATTTATGAGTTCAAACAAGCTTCTCGTCAGTAGTA
* * *
775034 TCTTAAATTTGATGAATTGATAGTCTCTTTTGATTTTCTTAAAAACGAAGTAGACTGATGCATAT
261 TCTTAAATTTGATGAATTGATAATCTCTTTTGATTTTCTTAAAAACAAAGTAAACTGATGCATAT
*
775099 TTCTAAAGACTATGGAAC
326 TTCCAAAGACTATGGAAC
775117 TTTAGAGAAAAATAATTGATAATAATGAAACTTTTTTT-TCTGTACTCTACAA-AATGCTTTTTA
1 TTTAGAGAAAAATAATTGATAATAATGAAACTTTTTTTCT-TGTACTCTACAAGAATGCTTTTTA
* *
775180 GAGTAATTATGGC-ATTAATAGCTCATTATGATTTA-AG-GCCATACAAAATGGATGTTAAGATT
65 GAGTAATTAT-GCTACTAATAACTCATTATGATTTAGAGCGCC--ACAAAATGGATGTTAAGATT
* *
775242 GTCTTCTTGAATGAGAATCTTGTTAGAGAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTAT
127 GTCTTCCTGAATGAGAATCTTGTTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTAT
** * * *
775307 AGCTAAAATCATTTTTTGTGTAGACTCAAAGTGTATTTATGAGTTCAAATAAGCTTTTCGTCAGT
192 AGCTAAAATCAACTTTTGTGTAGACTCAAAGAGTATTTATGAGTTCAAACAAGCTTCTCGTCAGT
* * * *
775372 AGTATCTTAAATTTGATGAATTGATAATTTCTTTTGATTTTGTTAAGAACAAAGTAAACTGTTGC
257 AGTATCTTAAATTTGATGAATTGATAATCTCTTTTGATTTTCTTAAAAACAAAGTAAACTGATGC
775437 ATATTTCCAAAGA
322 ATATTTCCAAAGA
775450 TTGTGGAAGC
Statistics
Matches: 304, Mismatches: 25, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
340 2 0.01
341 2 0.01
342 250 0.82
343 50 0.16
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (343 bp):
TTTAGAGAAAAATAATTGATAATAATGAAACTTTTTTTCTTGTACTCTACAAGAATGCTTTTTAG
AGTAATTATGCTACTAATAACTCATTATGATTTAGAGCGCCACAAAATGGATGTTAAGATTGTCT
TCCTGAATGAGAATCTTGTTAGAAAGGTCTATATGTTGTAACTTAAGTATTTAAAGAGTATAGCT
AAAATCAACTTTTGTGTAGACTCAAAGAGTATTTATGAGTTCAAACAAGCTTCTCGTCAGTAGTA
TCTTAAATTTGATGAATTGATAATCTCTTTTGATTTTCTTAAAAACAAAGTAAACTGATGCATAT
TTCCAAAGACTATGGAAC
Found at i:779971 original size:57 final size:56
Alignment explanation
Indices: 779910--780129 Score: 178
Period size: 57 Copynumber: 3.8 Consensus size: 56
779900 TGAAAATTTT
* *
779910 AATATGTTTGTCTTAATTTAGATAAGAAAACATATTATGTCTTAATTTAGAAAAAAA
1 AATATGTTTGTCTTAATTTAGACAAGAAAA-ATATTTTGTCTTAATTTAGAAAAAAA
* * * *
779967 AATATAG-TTGTCTTAATTTAGA-TA-AAATATCATGTTTGGGCTTAATTTA-AACAAAA
1 AATAT-GTTTGTCTTAATTTAGACAAGAAAAAT-AT-TTT-GTCTTAATTTAGAAAAAAA
* ** * * * *
780023 AATGTGTTTGTCTTAATCGAAGACAAGAAAAATTTTTTTTGTCTTAATCTAGACAAGAA
1 AATATGTTTGTCTTAAT-TTAGACAAGAAAAA--TATTTTGTCTTAATTTAGAAAAAAA
* * *
780082 AACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTGTCTTAATT
1 AATATGTTTGTCTTAATTTAGACAAGA-AAAATA-TTTTGTCTTAATT
780130 AAACACAAGA
Statistics
Matches: 126, Mismatches: 24, Indels: 25
0.72 0.14 0.14
Matches are distributed among these distances:
54 2 0.02
55 6 0.05
56 23 0.18
57 34 0.27
58 31 0.25
59 28 0.22
60 1 0.01
61 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (56 bp):
AATATGTTTGTCTTAATTTAGACAAGAAAAATATTTTGTCTTAATTTAGAAAAAAA
Found at i:779979 original size:28 final size:28
Alignment explanation
Indices: 779917--779993 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 28
779907 TTTAATATGT
* *
779917 TTGTCTTAATTTAGATAAGAAAACATAT
1 TTGTCTTAATTTAGATAAAAAAACATAG
* *
779945 TATGTCTTAATTTAGAAAAAAAAATATAG
1 T-TGTCTTAATTTAGATAAAAAAACATAG
779974 TTGTCTTAATTTAGATAAAA
1 TTGTCTTAATTTAGATAAAA
779994 TATCATGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 19 0.44
29 24 0.56
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.39
Consensus pattern (28 bp):
TTGTCTTAATTTAGATAAAAAAACATAG
Found at i:780103 original size:28 final size:28
Alignment explanation
Indices: 779916--780129 Score: 148
Period size: 28 Copynumber: 7.4 Consensus size: 28
779906 TTTTAATATG
*
779916 TTTGTCTTAATTTAGATAAGAAAACATA
1 TTTGTCTTAATTTAGACAAGAAAACATA
* * *
779944 TTATGTCTTAATTTAGAAAAAAAAATATA
1 TT-TGTCTTAATTTAGACAAGAAAACATA
* * * *
779973 GTTGTCTTAATTTAGATAA-AATATCATG
1 TTTGTCTTAATTTAGACAAGAA-AACATA
* * ** *
780001 TTTGGGCTTAATTTAAACAA-AAAATGTG
1 TTT-GTCTTAATTTAGACAAGAAAACATA
** *
780029 TTTGTCTTAATCGAAGACAAGAAAA-ATTTTT
1 TTTGTCTTAAT-TTAGACAAGAAAACA---TA
*
780060 TTTGTCTTAATCTAGACAAGAAAACATA
1 TTTGTCTTAATTTAGACAAGAAAACATA
*
780088 TTTGTCTCAATTTAGACAAGATAAA-ATA
1 TTTGTCTTAATTTAGACAAGA-AAACATA
780116 TTTTTGTCTTAATT
1 --TTTGTCTTAATT
780130 AAACACAAGA
Statistics
Matches: 147, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
27 9 0.06
28 57 0.39
29 46 0.31
30 22 0.15
31 13 0.09
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAGAAAACATA
Found at i:788159 original size:22 final size:22
Alignment explanation
Indices: 788107--788163 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
788097 AGAAAGAAAA
788107 TAGGTTG-ACAGATTAGGTTGAT
1 TAGGTTGAACA-ATTAGGTTGAT
* * * *
788129 CATGCTGAACAATTAGGTTGCT
1 TAGGTTGAACAATTAGGTTGAT
788151 TAGGTTGAACAAT
1 TAGGTTGAACAAT
788164 GGTTATATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (22 bp):
TAGGTTGAACAATTAGGTTGAT
Found at i:789258 original size:31 final size:31
Alignment explanation
Indices: 789220--789281 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
789210 TCTATCTATT
789220 TGACTTTAAATATCAGAAGATAAAATAACGA
1 TGACTTTAAATATCAGAAGATAAAATAACGA
*
789251 TGACTTTAATTATCAGAAGATAAAATAACGA
1 TGACTTTAAATATCAGAAGATAAAATAACGA
789282 CTAGAAAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (31 bp):
TGACTTTAAATATCAGAAGATAAAATAACGA
Found at i:794562 original size:74 final size:74
Alignment explanation
Indices: 794475--794631 Score: 233
Period size: 74 Copynumber: 2.1 Consensus size: 74
794465 AAACATATAT
* *
794475 TTATAAATATGTATTCATTAAATAACAATTATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
794540 TTAAACCAA
66 TTAAACCAA
* * **
794549 TTATAAATGTGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
** *
794614 TTATTCCAT
66 TTAAACCAA
794623 TTATAAATA
1 TTATAAATA
794632 AAAAATTTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
TTAAACCAA
Found at i:794741 original size:35 final size:35
Alignment explanation
Indices: 794700--794787 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 35
794690 GTTGTATAAT
794700 TTAAATATTAATATTTTAAATTATT-TATTTTAAA
1 TTAAATATTAATATTTTAAATTATTATATTTTAAA
** *
794734 GTTAAATATTAATATTTTTTATTTTTTTAATATTTTAAA
1 -TTAAATATTAATA--TTTTAAATTATT-ATATTTTAAA
794773 TTAAATATTAATATT
1 TTAAATATTAATATT
794788 AATCAAACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
35 13 0.28
36 2 0.04
37 9 0.20
38 13 0.28
39 9 0.20
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
TTAAATATTAATATTTTAAATTATTATATTTTAAA
Found at i:795163 original size:28 final size:28
Alignment explanation
Indices: 795124--795223 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
795114 TTCAATGAGC
*
795124 TCACCATAAACCCATGGTTTTAACAAGT
1 TCACCACAAACCCATGGTTTTAACAAGT
* * * **
795152 TTACCACAAACCCACGATTTTAATGAGT
1 TCACCACAAACCCATGGTTTTAACAAGT
* *
795180 TCACCACAAACTCATGGTTTTTAA-AAGGA
1 TCACCACAAACCCATGG-TTTTAACAA-GT
*
795209 TCACTACAAACCCAT
1 TCACCACAAACCCAT
795224 ACACTAACTT
Statistics
Matches: 56, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
28 36 0.64
29 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.27
Consensus pattern (28 bp):
TCACCACAAACCCATGGTTTTAACAAGT
Found at i:804524 original size:66 final size:67
Alignment explanation
Indices: 804277--804658 Score: 479
Period size: 67 Copynumber: 5.8 Consensus size: 67
804267 ATACCATAAT
* * * *
804277 CATATCAACCATAATATAAAAAAATTCAATGGTTGATAACTAT--A-CAT-CATAATCATATCAA
1 CATATCAACCTTAATACAAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAA
804338 GC
66 GC
* * * *
804340 CATAACAACCTTAATACAAAAAAATTCAAAGGTCGATAACTAAACACCATACATAATCATATCAA
1 CATATCAACCTTAATACAAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAA
804405 GC
66 GC
* ** * * *
804407 CATATCAACCTTCATACAAAAAAATTCAAAAATTGATAATTATACACCATATATGATTATATCAA
1 CATATCAACCTTAATACAAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAA
804472 GC
66 GC
* * **
804474 CATATCAACTTTAATA-AAAAAAATTCAAAAGTTGATAACTATATGCCATATATAATCATATCAA
1 CATATCAACCTTAATACAAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAA
804538 GC
66 GC
* * * *
804540 CATATTAACCTTAATACAAAAAAAATTCAAATGTTGATAATTATAAACCATATATAATCATATCA
1 CATATCAACCTTAATAC-AAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCA
804605 AGC
65 AGC
* * *
804608 CATATCAACATTAACAC-AAAAAATTGCAAAGGTTGATAACTAGACACCATA
1 CATATCAACCTTAATACAAAAAAATT-CAAAGGTTGATAACTATACACCATA
804659 ACCATATCAA
Statistics
Matches: 275, Mismatches: 37, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
63 37 0.13
65 1 0.00
66 69 0.25
67 108 0.39
68 60 0.22
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (67 bp):
CATATCAACCTTAATACAAAAAAATTCAAAGGTTGATAACTATACACCATATATAATCATATCAA
GC
Found at i:806250 original size:22 final size:21
Alignment explanation
Indices: 806201--806253 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
806191 TTTGTTAAAC
*
806201 CTTTTTCTTTTCTCTCTACAG
1 CTTTTTTTTTTCTCTCTACAG
806222 -TTGTTTTTTTTCCTCTCT-CAG
1 CTT-TTTTTTTT-CTCTCTACAG
806243 ACTTTTTTTTT
1 -CTTTTTTTTT
806254 CAACTATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 2 0.07
21 10 0.37
22 13 0.48
23 2 0.07
ACGTcount: A:0.08, C:0.23, G:0.06, T:0.64
Consensus pattern (21 bp):
CTTTTTTTTTTCTCTCTACAG
Found at i:806882 original size:13 final size:13
Alignment explanation
Indices: 806835--806883 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
806825 TTTATAAATA
*
806835 ATATAAATACTATT
1 ATATATATACT-TT
806849 ATATATATACTTT
1 ATATATATACTTT
806862 CAGTATATATACTTT
1 -A-TATATATACTTT
*
806877 AAATATA
1 ATATATA
806884 AACATATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
15 12 0.39
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (13 bp):
ATATATATACTTT
Found at i:806883 original size:15 final size:15
Alignment explanation
Indices: 806849--806883 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
806839 AAATACTATT
*
806849 ATATATATACTTTCA
1 ATATATATACTTTAA
*
806864 GTATATATACTTTAA
1 ATATATATACTTTAA
806879 ATATA
1 ATATA
806884 AACATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:807735 original size:14 final size:14
Alignment explanation
Indices: 807694--807740 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
807684 GTAAAGAGAA
*
807694 ATAATGTATAAAAT
1 ATAATATATAAAAT
*
807708 ATAA-ATAATTAAAT
1 ATAATAT-ATAAAAT
807722 ATAATATATAAAAT
1 ATAATATATAAAAT
807736 -TAATA
1 ATAATA
807741 ATTTTCTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 6 0.21
14 20 0.71
15 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
ATAATATATAAAAT
Found at i:815055 original size:7 final size:8
Alignment explanation
Indices: 815026--815054 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
815016 CTCCTCAATG
815026 TTCTTTGT
1 TTCTTTGT
815034 TTCTTTGT
1 TTCTTTGT
815042 TTCTTT-T
1 TTCTTTGT
815049 TTCTTT
1 TTCTTT
815055 TCTCACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (8 bp):
TTCTTTGT
Found at i:850390 original size:4 final size:4
Alignment explanation
Indices: 850381--850415 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
850371 TTTATTTTAT
850381 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
850416 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:850704 original size:24 final size:25
Alignment explanation
Indices: 850677--850725 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
850667 TAAATAAACA
850677 TATTATTTT-ATTATTATTA-GTTTT
1 TATT-TTTTGATTATTATTATGTTTT
850701 TATTTTTTGATTATTATTATGTTTT
1 TATTTTTTGATTATTATTATGTTTT
850726 AAAATGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (25 bp):
TATTTTTTGATTATTATTATGTTTT
Found at i:851272 original size:2 final size:2
Alignment explanation
Indices: 851267--851297 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
851257 TATATATATA
851267 TG TG 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 TG TG T
851298 CTTCATCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:857529 original size:16 final size:17
Alignment explanation
Indices: 857508--857542 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
857498 TAGTAGCTCT
857508 TTAATCGATTAAA-TTG
1 TTAATCGATTAAACTTG
857524 TTAATCGATTAAACTTG
1 TTAATCGATTAAACTTG
857541 TT
1 TT
857543 CCTACAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (17 bp):
TTAATCGATTAAACTTG
Found at i:858652 original size:17 final size:17
Alignment explanation
Indices: 858630--858672 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
858620 CTTTTTTGGC
*
858630 CTATTAGGCTATCTAGG
1 CTATTAGGCTAACTAGG
*
858647 CTATTAGCCTAACTAGG
1 CTATTAGGCTAACTAGG
*
858664 TTATT-GGCT
1 CTATTAGGCT
858673 TGCCTAAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (17 bp):
CTATTAGGCTAACTAGG
Found at i:862246 original size:29 final size:25
Alignment explanation
Indices: 862195--862270 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
862185 CAAAAGCATA
* *
862195 AAAATAAATAAATAACAACTAAACT
1 AAAATAAATAAATAAAAACTAAAAT
862220 AAAATAAATAAATATAAAAATCATAAAAT
1 AAAATAAAT-AA-ATAAAAA-C-TAAAAT
* *
862249 AAAATAACTTAATAAAAA-TAAA
1 AAAATAAATAAATAAAAACTAAA
862271 CTAATTAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
24 4 0.09
25 9 0.21
26 2 0.05
27 13 0.30
28 2 0.05
29 13 0.30
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAATAAATAAATAAAAACTAAAAT
Found at i:862275 original size:14 final size:13
Alignment explanation
Indices: 862192--862275 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 13
862182 TTACAAAAGC
862192 ATAAAAATAAATAA
1 ATAAAAATAAAT-A
*
862206 ATAACAACTAAACTA
1 ATAA-AAATAAA-TA
862221 A-AATAAATAAAT-
1 ATAA-AAATAAATA
862233 ATAAAAATCATAA-A
1 ATAAAAAT-A-AATA
*
862247 AT-AAAATAACTTA
1 ATAAAAATAA-ATA
862260 ATAAAAATAAACTA
1 ATAAAAATAAA-TA
862274 AT
1 AT
862276 TAGAAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
11 1 0.02
12 6 0.11
13 12 0.22
14 27 0.49
15 8 0.15
16 1 0.02
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAAAAATAAATA
Found at i:867036 original size:45 final size:45
Alignment explanation
Indices: 866972--867061 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
866962 CTTCTAAATG
*
866972 ACCTTCGAAACCCTTTTATGCTAAAGTCTCCATGAATGGATTAAC
1 ACCTTCGAAACCATTTTATGCTAAAGTCTCCATGAATGGATTAAC
* *
867017 ACCTTCGAAGCCATTTTATGCTAAAGTCTTCATGAATGGATTAAC
1 ACCTTCGAAACCATTTTATGCTAAAGTCTCCATGAATGGATTAAC
867062 GAGGTTCTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (45 bp):
ACCTTCGAAACCATTTTATGCTAAAGTCTCCATGAATGGATTAAC
Found at i:886046 original size:192 final size:192
Alignment explanation
Indices: 885714--886093 Score: 645
Period size: 192 Copynumber: 2.0 Consensus size: 192
885704 ACGAGCTTGA
*
885714 CAAAATCAATTTGGATAATATTTTAATAAATACCATTTAATCTTTCTTTTTGTTTAGTTCTGATT
1 CAAAATCAATTTCGATAATATTTTAATAAATACCATTTAATCTTTCTTTTTGTTTAGTTCTGATT
* * *
885779 TCTTAATTTACTTTAATAATTGTTTAGCTTTATTTTTGCTCTTTTTGTTTATGCATTTGTAAATT
66 TCTTAATTTACTTTAATAATTGTTTACCATTACTTTTGCTCTTTTTGTTTATGCATTTGTAAATT
*
885844 TTTTAAGAATTGCATTAAAGCCAGCAATTGATTAGGAGAAAGGTGTATTTCTCATTTGCAAC
131 TTTCAAGAATTGCATTAAAGCCAGCAATTGATTAGGAGAAAGGTGTATTTCTCATTTGCAAC
* * *
885906 CAAAATCAATTTCGATAATGTTTTAATAAATAGCATTTAATCTTTCTTTTTGTTTGGTTCTGATT
1 CAAAATCAATTTCGATAATATTTTAATAAATACCATTTAATCTTTCTTTTTGTTTAGTTCTGATT
* *
885971 TCTTAATTTACTTTAATATTTTTTTACCATTACTTTTGCGT-TTTTTGTTTATGCATTTGTAAAT
66 TCTTAATTTACTTTAATAATTGTTTACCATTACTTTTGC-TCTTTTTGTTTATGCATTTGTAAAT
*
886035 TTTTCAAGAATTGCATTAAAGCCAGCAATTGTTTAGGAGAAAGGTGTATTTCTCATTTG
130 TTTTCAAGAATTGCATTAAAGCCAGCAATTGATTAGGAGAAAGGTGTATTTCTCATTTG
886094 TTTAGCTATA
Statistics
Matches: 176, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
192 175 0.99
193 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.48
Consensus pattern (192 bp):
CAAAATCAATTTCGATAATATTTTAATAAATACCATTTAATCTTTCTTTTTGTTTAGTTCTGATT
TCTTAATTTACTTTAATAATTGTTTACCATTACTTTTGCTCTTTTTGTTTATGCATTTGTAAATT
TTTCAAGAATTGCATTAAAGCCAGCAATTGATTAGGAGAAAGGTGTATTTCTCATTTGCAAC
Found at i:891495 original size:2 final size:2
Alignment explanation
Indices: 891488--891516 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
891478 AGTTTGATTT
891488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
891517 GTTTAGCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:895417 original size:20 final size:18
Alignment explanation
Indices: 895389--895431 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
895379 TTTTAATATT
895389 TATAATTTTATATTATATCA
1 TATAATTTTATATT-TAT-A
*
895409 TATATTTTTATATTTATA
1 TATAATTTTATATTTATA
895427 TATAA
1 TATAA
895432 CTAGATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 13 0.62
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TATAATTTTATATTTATA
Found at i:902394 original size:622 final size:622
Alignment explanation
Indices: 901192--902398 Score: 1655
Period size: 622 Copynumber: 1.9 Consensus size: 622
901182 GGATACCACC
* * *
901192 AACTTTCTTTTTCAATTCCTTGAAATTTAAAAATACCCTTATATCCTCAAAAGTGAGAGTGTCTC
1 AACTTTCTTCTTCAATTCCTTAAAATTTAAAAATACCCTTACATCCTCAAAAGTGAGAGTGTCTC
*
901257 GACCATATAACATAGTATCCACAAAGTTTTCATACGATAGAGGCAAAGAACATAAAATAATTAAG
66 GACCATATAACATAGTATCCACAAAGTTTTCATACGATAGAGGCAAAGAACATAAAAGAATTAAG
* ** * *
901322 ACTAGGTTTTCATCCTCAATTTTAATATCGATATTCTTTAAATTAAGAATAACTCTATTAAATTC
131 ACTAAGTCGTCATCCTCAATTTTAACATCGATATTCTTTAAATCAAGAATAACTCTATTAAATTC
* * * * *
901387 ATCAATGTTGGTATTAACGGACGTACTTTCACTCATCTTGAGAGTATACAATCGTTGCTTCATAT
196 ATCAATGTCGGTATTAACGGACGTACCTTCACTCATCTTGAGAGAATAAAATCATTGCTTCATAT
* * * *
901452 AAAGTCAATTTGTTAGGGATTTGGTCATATAAATACTCTCGAGTTTAAACCACACTGCAGTAGTA
261 AAAGCCAATTCGTTAGGGATTTGGTCATATAAATACTCTCGAGTTTAAACCACACTGCAGCAATA
* * * * * *
901517 GATTCTACATCCATGACTTGTTTTAGCACCTCATCAGACAAAGCTAGGAGAATAGCATTATTTTC
326 GATTCTACATCCATGACTTCTTTTAGCACCTCATCAAACAAAACGAGGAGAATAGCATTATATGC
* * * * * *
901582 TTTTTTCATAAGGTCATCTTTCTTACCATTAGATATATTTAAGGGAAGATGGTCTTTTCCCTTCA
391 TTTCTCCATAAGGTCATCTTTCTCACCATCAGATAAATTTAAGGGAAGATGCTCTTTTCCCTTCA
* *** *
901647 ATGCCTTCAACAGTCCTTGTTGCACTAGCAATACGTGCATCTTAACATGCCACAAGATGAAATTG
456 ATGCCTTCAACAGTCCTTGTTGCACTAACAATACACCCATCTTAACATGCCACAAGATAAAATTG
* *
901712 TTTCTTCCATTAAACTTTTCAATCTCATACTTAGTTGACAAAATTGCCATAGCGAGATTCAGATT
521 TTTCTCCCATTAAACTTTTCAATCTCATACTTAGTTGACAAAATTGCCATAGCAAGATTCAGATT
901777 GACTCAAGAGTTGCCCAAAATCTTACTCAATCCATTA
586 GACTCAAGAGTTGCCCAAAATCTTACTCAATCCATTA
* * * * *
901814 AACTTTCTTCTTCAATTCCTTAAAATTTAAAGATGCCTTTACATCCTCTAAAGTGAGAGTGTCTT
1 AACTTTCTTCTTCAATTCCTTAAAATTTAAAAATACCCTTACATCCTCAAAAGTGAGAGTGTCTC
* * ** * * *
901879 GGCCATATAACATAGTATTCATGAAGTTTTCATATGATGGAGGCAAAGAACATAGAAGAATTAAG
66 GACCATATAACATAGTATCCACAAAGTTTTCATACGATAGAGGCAAAGAACATAAAAGAATTAAG
* *
901944 GCTAAGTCGTCATCCTCAATTTTAACATCGATATTCTTTAAATCAAGAATAACTTTATTAAATTC
131 ACTAAGTCGTCATCCTCAATTTTAACATCGATATTCTTTAAATCAAGAATAACTCTATTAAATTC
* *
902009 ATCAATG-CGGATATTAACGGACGTACCTTCTCTCATCTTGAGAGAATAAAATCATT-CTTTTAT
196 ATCAATGTCGG-TATTAACGGACGTACCTTCACTCATCTTGAGAGAATAAAATCATTGC-TTCAT
* * * * *
902072 ATAAAGCCGATTCGTTAGGGATTTGGTCATATAAATACTTTTGAGTTTAAGCTACACTGCAGCAA
259 ATAAAGCCAATTCGTTAGGGATTTGGTCATATAAATACTCTCGAGTTTAAACCACACTGCAGCAA
** * * *
902137 TAGATTCTTTATTCATGACTTCTTTTAGTACCTCATCAAATAAAACGAGGAGAATAGCATTATAT
324 TAGATTCTACATCCATGACTTCTTTTAGCACCTCATCAAACAAAACGAGGAGAATAGCATTATAT
* * *
902202 GCTTTCTCCATAAGGTCTTCTTTCTCACCATCAGATAAATTTCAA-GGAAGATGCTCTTTTTCTT
389 GCTTTCTCCATAAGGTCATCTTTCTCACCATCAGATAAATTT-AAGGGAAGATGCTCTTTTCCCT
*** * * * *
902266 TTGGTGCCTTCAACAGTCCTTGTTGCACTAATAATGCACCCATTTTAACATGCCACAAGCTAAAA
453 TCAATGCCTTCAACAGTCCTTGTTGCACTAACAATACACCCATCTTAACATGCCACAAGATAAAA
* * * * * *
902331 TTGTTTCTCCCATTAAACTTTTCAATCTCATATTTGGTTGTCAAAGTTGTCATAGTAAGATTCAG
518 TTGTTTCTCCCATTAAACTTTTCAATCTCATACTTAGTTGACAAAATTGCCATAGCAAGATTCAG
902396 ATT
583 ATT
902399 ACCCTAAGAC
Statistics
Matches: 503, Mismatches: 79, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
621 3 0.01
622 498 0.99
623 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (622 bp):
AACTTTCTTCTTCAATTCCTTAAAATTTAAAAATACCCTTACATCCTCAAAAGTGAGAGTGTCTC
GACCATATAACATAGTATCCACAAAGTTTTCATACGATAGAGGCAAAGAACATAAAAGAATTAAG
ACTAAGTCGTCATCCTCAATTTTAACATCGATATTCTTTAAATCAAGAATAACTCTATTAAATTC
ATCAATGTCGGTATTAACGGACGTACCTTCACTCATCTTGAGAGAATAAAATCATTGCTTCATAT
AAAGCCAATTCGTTAGGGATTTGGTCATATAAATACTCTCGAGTTTAAACCACACTGCAGCAATA
GATTCTACATCCATGACTTCTTTTAGCACCTCATCAAACAAAACGAGGAGAATAGCATTATATGC
TTTCTCCATAAGGTCATCTTTCTCACCATCAGATAAATTTAAGGGAAGATGCTCTTTTCCCTTCA
ATGCCTTCAACAGTCCTTGTTGCACTAACAATACACCCATCTTAACATGCCACAAGATAAAATTG
TTTCTCCCATTAAACTTTTCAATCTCATACTTAGTTGACAAAATTGCCATAGCAAGATTCAGATT
GACTCAAGAGTTGCCCAAAATCTTACTCAATCCATTA
Found at i:905437 original size:18 final size:19
Alignment explanation
Indices: 905391--905453 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
905381 AAGTTTTTTC
*
905391 TTATATCTTCTTCT-TTTAAT
1 TTATAT-TTATTCTATTT-AT
*
905411 TTATATTTATT-TATTTTT
1 TTATATTTATTCTATTTAT
*
905429 TTATTTTTATTCTATTTAT
1 TTATATTTATTCTATTTAT
905448 TTATAT
1 TTATAT
905454 ATTTTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 12 0.33
19 18 0.50
20 6 0.17
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATATTTATTCTATTTAT
Found at i:905444 original size:23 final size:22
Alignment explanation
Indices: 905404--905458 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
905394 TATCTTCTTC
* *
905404 TTTTAATTTATATTTATTTATT
1 TTTTTATTTTTATTTATTTATT
905426 TTTTTATTTTTATTCTATTTATT
1 TTTTTATTTTTATT-TATTTATT
* *
905449 TATATATTTT
1 TTTTTATTTT
905459 AAATTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTATTTTTATTTATTTATT
Found at i:905603 original size:15 final size:17
Alignment explanation
Indices: 905580--905612 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
905570 CTTTTTTCTA
905580 TTGTAGATTTT-ATTTT
1 TTGTAGATTTTAATTTT
905596 TTGT-GATTTTAATTTT
1 TTGTAGATTTTAATTTT
905612 T
1 T
905613 AAAAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (17 bp):
TTGTAGATTTTAATTTT
Found at i:905783 original size:28 final size:27
Alignment explanation
Indices: 905728--905793 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
905718 GAGTAAATTA
* *
905728 TTAATCTTATATATTATATTTAACTAT
1 TTAATATTATACATTATATTTAACTAT
* *
905755 TTACATTTTATACATTATAGTTTTA-TAT
1 TTA-ATATTATACATTATA-TTTAACTAT
905783 TTAATATTATA
1 TTAATATTATA
905794 AGTTTAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.30
28 19 0.58
29 4 0.12
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAATATTATACATTATATTTAACTAT
Found at i:908078 original size:39 final size:39
Alignment explanation
Indices: 908019--908114 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
908009 TCACGGGCCA
*
908019 CAGTCCAAACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
1 CAGTCCAGACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
*
908058 CAGTCCAGACCCACCTGGAGGCCCAAGAGGGTGCCAGCC
1 CAGTCCAGACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
* *
908097 CAGTCCAGTCACACCAGG
1 CAGTCCAGACCCACCAGG
908115 GGGGCCAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.26, C:0.39, G:0.28, T:0.07
Consensus pattern (39 bp):
CAGTCCAGACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
Found at i:909767 original size:60 final size:60
Alignment explanation
Indices: 909669--909785 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
909659 GAGATAGCCA
* *
909669 GTCCAAGGATAGTGGCGAGGGCAAGCCACACCCCAGGTGGAGAGGTAGTTCCACATCGAG
1 GTCCAAGGATAGTGGCGAGGGCAAGCCACACCCAAGGTGGAGAGATAGTTCCACATCGAG
* * ** *
909729 GTCCAGGGATGGTGGCGAGGGCAAGCCACATTCAAGGTGGGGAGATAGTTCCACATC
1 GTCCAAGGATAGTGGCGAGGGCAAGCCACACCCAAGGTGGAGAGATAGTTCCACATC
909786 AAAGTGGAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.26, C:0.23, G:0.36, T:0.15
Consensus pattern (60 bp):
GTCCAAGGATAGTGGCGAGGGCAAGCCACACCCAAGGTGGAGAGATAGTTCCACATCGAG
Found at i:910822 original size:39 final size:39
Alignment explanation
Indices: 910737--910832 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
910727 TCACGGGCCA
*
910737 CAGTCCAAACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
1 CAGTCCAGACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
*
910776 CAGTCCAGACCCACCTGGAGGCCCAAGAGGGTGCCAGCC
1 CAGTCCAGACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
* *
910815 CAGTCCAGTCACACCAGG
1 CAGTCCAGACCCACCAGG
910833 GGGGCCCAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.26, C:0.39, G:0.28, T:0.07
Consensus pattern (39 bp):
CAGTCCAGACCCACCAGGAGGCCCAAGAGGGTGCCAGCC
Found at i:910978 original size:14 final size:14
Alignment explanation
Indices: 910917--911022 Score: 59
Period size: 14 Copynumber: 7.3 Consensus size: 14
910907 AGAACCTTCC
910917 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
* *
910931 AAATCTTTTGGGGGGGG
1 AAAAC-TTT--GGAGGG
* * **
910948 AATACTTTGAATTG
1 AAAACTTTGGAGGG
910962 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
* *
910976 AAATCTTTTGGGGGG
1 AAAAC-TTTGGAGGG
* * ***
910991 AATACTTTGAATTA
1 AAAACTTTGGAGGG
911005 AAAACTTTGGAGGG
1 AAAACTTTGGAGGG
911019 AAAA
1 AAAA
911023 GTGGGTGGGG
Statistics
Matches: 62, Mismatches: 26, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
14 37 0.60
15 14 0.23
16 3 0.05
17 8 0.13
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.29
Consensus pattern (14 bp):
AAAACTTTGGAGGG
Found at i:911003 original size:43 final size:44
Alignment explanation
Indices: 910917--911021 Score: 185
Period size: 43 Copynumber: 2.4 Consensus size: 44
910907 AGAACCTTCC
*
910917 AAAACTTTGGAGGGAAATCTTTTGGGGGGGGAATACTTTGAATTG
1 AAAACTTTGGAGGGAAATCTTTT-GGGGGGGAATACTTTGAATTA
910962 AAAACTTTGGAGGGAAATCTTTT-GGGGGGAATACTTTGAATTA
1 AAAACTTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTA
911005 AAAACTTTGGAGGGAAA
1 AAAACTTTGGAGGGAAA
911022 AGTGGGTGGG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
43 36 0.61
45 23 0.39
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (44 bp):
AAAACTTTGGAGGGAAATCTTTTGGGGGGGAATACTTTGAATTA
Found at i:914947 original size:2 final size:2
Alignment explanation
Indices: 914940--914965 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
914930 TGAGACTTTA
914940 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
914966 CAATTGTTAT
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:926224 original size:15 final size:15
Alignment explanation
Indices: 926204--926232 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
926194 ACAAAATGGA
926204 CTAATAATAATAATT
1 CTAATAATAATAATT
926219 CTAATAATAATAAT
1 CTAATAATAATAAT
926233 AATAGGCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
CTAATAATAATAATT
Found at i:929902 original size:3 final size:3
Alignment explanation
Indices: 929894--929926 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
929884 CCCGAATGAA
929894 TTC TTC TTC TTC TTC TTC TTC TTC GTT- TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
929927 GAGTTTCGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:943658 original size:7 final size:7
Alignment explanation
Indices: 943646--943672 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
943636 GAGAATGAAG
943646 CAAAGAT
1 CAAAGAT
943653 CAAAGAT
1 CAAAGAT
943660 CAAAGAT
1 CAAAGAT
943667 CAAAGA
1 CAAAGA
943673 ATTTAAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (7 bp):
CAAAGAT
Found at i:949486 original size:5 final size:5
Alignment explanation
Indices: 949469--949513 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
949459 CACCAAATTG
* *
949469 AAATA ATAATA AAATA AAATA AAATA AAAAA TAAATA AATTA AAA
1 AAATA A-AATA AAATA AAATA AAATA AAATA -AAATA AAATA AAA
949514 AATTAAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 25 0.74
6 9 0.26
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:949498 original size:16 final size:16
Alignment explanation
Indices: 949469--949516 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
949459 CACCAAATTG
*
949469 AAATAATAATAAAATA-
1 AAATAA-AATAAAAAAT
949485 AAATAAAATAAAAAAT
1 AAATAAAATAAAAAAT
*
949501 AAATAAATTAAAAAAT
1 AAATAAAATAAAAAAT
949517 TAAAATTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAAAATAAAAAAT
Found at i:953652 original size:8 final size:8
Alignment explanation
Indices: 953639--953684 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
953629 CAAGATAGTA
953639 CTATATAT
1 CTATATAT
953647 CTATATAT
1 CTATATAT
953655 CTATATAT
1 CTATATAT
*
953663 CTATCTAT
1 CTATATAT
*
953671 ATATATAT
1 CTATATAT
*
953679 ATATAT
1 CTATAT
953685 TAACCATACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (8 bp):
CTATATAT
Found at i:953653 original size:2 final size:2
Alignment explanation
Indices: 953640--953684 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
953630 AAGATAGTAC
* * * *
953640 TA TA TA TC TA TA TA TC TA TA TA TC TA TC 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
953682 TA T
1 TA T
953685 TAACCATACA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:953669 original size:20 final size:20
Alignment explanation
Indices: 953644--953682 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
953634 TAGTACTATA
*
953644 TATCTATATATCTATATATC
1 TATCTATATATATATATATC
953664 TATCTATATATATATATAT
1 TATCTATATATATATATAT
953683 ATTAACCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
TATCTATATATATATATATC
Found at i:957495 original size:18 final size:18
Alignment explanation
Indices: 957452--957495 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
957442 TTTTCTCATC
957452 TTTTTTTTAAAAACACAT
1 TTTTTTTTAAAAACACAT
* *
957470 CTTTTTTTAAAAAGA-AT
1 TTTTTTTTAAAAACACAT
957487 TTTTCTTTT
1 TTTT-TTTT
957496 TGTTTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTTTTTAAAAACACAT
Done.