Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 30 of 56
Found at i:5064847 original size:18 final size:18
Alignment explanation
Indices: 5064826--5064865 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5064816 AGTATTGATT
5064826 TAATAAAAATAATAATTA
1 TAATAAAAATAATAATTA
* *
5064844 TAATATAAATTATAATTA
1 TAATAAAAATAATAATTA
5064862 TAAT
1 TAAT
5064866 TTGATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAAAAATAATAATTA
Found at i:5064995 original size:21 final size:21
Alignment explanation
Indices: 5064975--5065020 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5064965 ATCTCATTAT
5064975 TAAT-TTTAATTTTATCGTTA
1 TAATATTTAATTTTATCGTTA
**
5064995 TAATATTTAATTTTATAATTA
1 TAATATTTAATTTTATCGTTA
5065016 TAATA
1 TAATA
5065021 ATTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TAATATTTAATTTTATCGTTA
Found at i:5067481 original size:13 final size:14
Alignment explanation
Indices: 5067463--5067493 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5067453 TTCATATTTA
5067463 AAAAATTTTAAA-T
1 AAAAATTTTAAATT
5067476 AAAAATTTTAAATT
1 AAAAATTTTAAATT
5067490 AAAA
1 AAAA
5067494 GTATAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAATTTTAAATT
Found at i:5067617 original size:19 final size:20
Alignment explanation
Indices: 5067574--5067622 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5067564 TAATATTAAT
*
5067574 TTTTTAAAAAAATTTAATTA
1 TTTTTAAAAAAAATTAATTA
5067594 TTTTTAAAAAAAATT-ATCTA
1 TTTTTAAAAAAAATTAAT-TA
5067614 -TTTTAAAAA
1 TTTTTAAAAA
5067623 TATTAACTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTTAAAAAAAATTAATTA
Found at i:5068405 original size:17 final size:17
Alignment explanation
Indices: 5068350--5068409 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
5068340 TATGTTTTAT
5068350 ATATTTTAT-TATATTA
1 ATATTTTATATATATTA
*
5068366 ATATATTTATATTATATTT
1 ATAT-TTTATA-TATATTA
5068385 ATATTTTATATA-ATATA
1 ATATTTTATATATAT-TA
5068402 ATATTTTA
1 ATATTTTA
5068410 AAAATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.16
17 16 0.42
18 6 0.16
19 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTATATATATTA
Found at i:5068419 original size:44 final size:45
Alignment explanation
Indices: 5068336--5068453 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 45
5068326 ATGTATTAAT
* * * * *
5068336 TATTTATGTTTTATATATTTTATTATATTAATATATTTATA-TTA
1 TATTTATATTTTATATAATATAATATATTAAAATATTTATAGTTA
*
5068380 TATTTATATTTTATATAATATAATATTTTAAAA-ATTTTATATGTTA
1 TATTTATATTTTATATAATATAATATATTAAAATA-TTTATA-GTTA
*
5068426 TATTTATA--TTATATAATAATAATTTATT
1 TATTTATATTTTATATAAT-ATAATATATT
5068454 CGAAATTAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
43 1 0.02
44 42 0.68
45 8 0.13
46 11 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (45 bp):
TATTTATATTTTATATAATATAATATATTAAAATATTTATAGTTA
Found at i:5070219 original size:18 final size:17
Alignment explanation
Indices: 5070192--5070229 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5070182 ATTTTTTTCC
5070192 TTTTTTTCTTTACT-TTT
1 TTTTTTTCTTT-CTCTTT
5070209 TTTTTTCTCTTTCTCTTT
1 TTTTTT-TCTTTCTCTTT
5070227 TTT
1 TTT
5070230 GTTAATTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTCTCTTT
Found at i:5070870 original size:3 final size:3
Alignment explanation
Indices: 5070864--5070890 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5070854 AATAAAAGCC
5070864 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5070891 TTTTATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5070905 original size:13 final size:13
Alignment explanation
Indices: 5070865--5070907 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5070855 ATAAAAGCCA
5070865 TTATTATTATTATT
1 TTATTATTATT-TT
5070879 ATTATTATTATTTT
1 -TTATTATTATTTT
5070893 TTATTCATT-TTTT
1 TTATT-ATTATTTT
5070906 TT
1 TT
5070908 GTTTTGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.41
14 5 0.19
15 11 0.41
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:5073649 original size:17 final size:17
Alignment explanation
Indices: 5073607--5073651 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
5073597 CCAGCAACTC
*
5073607 ATGTTAAAAAAACACTA
1 ATGTTAAAAAAACACGA
* *
5073624 ATGCATAAAAAAACACGG
1 ATG-TTAAAAAAACACGA
5073642 ATGTTAAAAA
1 ATGTTAAAAA
5073652 TCTTTGAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (17 bp):
ATGTTAAAAAAACACGA
Found at i:5074703 original size:14 final size:15
Alignment explanation
Indices: 5074672--5074706 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5074662 TAAAATAAAA
*
5074672 TTTATTTGTTAATTT
1 TTTATTTGTTAATAT
5074687 TTTATTT-TTAATAT
1 TTTATTTGTTAATAT
5074701 TTTATT
1 TTTATT
5074707 AATTTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTATTTGTTAATAT
Found at i:5075410 original size:27 final size:28
Alignment explanation
Indices: 5075364--5075418 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
5075354 TAAATTAATA
* *
5075364 AAAATATAATAAAATTTTAATTTATTTAT
1 AAAATATAATAAAATGTTAAATT-TTTAT
5075393 AAAAT-TAAT-AAATGTTAAATTTTTAT
1 AAAATATAATAAAATGTTAAATTTTTAT
5075419 GTATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 10 0.42
28 4 0.17
29 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAAATATAATAAAATGTTAAATTTTTAT
Found at i:5077032 original size:2 final size:2
Alignment explanation
Indices: 5077025--5077050 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5077015 TACCCAGTCC
5077025 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5077051 GTGCCTAGGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5079904 original size:5 final size:5
Alignment explanation
Indices: 5079894--5079926 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5079884 TTTAGTTGTG
5079894 CATAT CATAT CATAT CATAT CATAT CATAT CAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CAT
5079927 GCTTTCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:5081714 original size:17 final size:16
Alignment explanation
Indices: 5081692--5081723 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5081682 ATTTTAATTG
5081692 CTTTTTTTTTTCTTTTT
1 CTTTTTTTTTT-TTTTT
5081709 CTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTT
5081724 AAACATCCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (16 bp):
CTTTTTTTTTTTTTTT
Found at i:5085359 original size:26 final size:26
Alignment explanation
Indices: 5085322--5085383 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
5085312 TTCAATTTAT
*
5085322 TATTT-TTAAGTTAAATTTAAGTAAA
1 TATTTATTGAGTTAAATTTAAGTAAA
* *
5085347 TATTTATTGAGTTAGATTTAATTAAA
1 TATTTATTGAGTTAAATTTAAGTAAA
5085373 -ATTTTATTGAG
1 TA-TTTATTGAG
5085384 ATATAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (26 bp):
TATTTATTGAGTTAAATTTAAGTAAA
Found at i:5086580 original size:51 final size:51
Alignment explanation
Indices: 5086504--5086604 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
5086494 AAAATAAATG
* * *
5086504 ACCCAAATAAAATTTTTGCTTAGGCCATATTAGATAGGTTAAGTTTAGTGA
1 ACCCAAATAAAATTTTTACTTAGGCCATATTAGATAGGCTAAATTTAGTGA
* * *
5086555 ACCCAAATAGAGTTTTTACTTAGGCCATATTAGATGGGCTAAATTTAGTG
1 ACCCAAATAAAATTTTTACTTAGGCCATATTAGATAGGCTAAATTTAGTG
5086605 TATTTGGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (51 bp):
ACCCAAATAAAATTTTTACTTAGGCCATATTAGATAGGCTAAATTTAGTGA
Found at i:5088005 original size:18 final size:18
Alignment explanation
Indices: 5087968--5088015 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
5087958 TCTTTAAATT
**
5087968 ATTTTTAT-AATATTTTA
1 ATTTTTATAAATATTAAA
5087985 ATTTTTATAAATATTAAA
1 ATTTTTATAAATATTAAA
*
5088003 A-TTTAATAAATAT
1 ATTTTTATAAATAT
5088016 ATAATATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTTATAAATATTAAA
Found at i:5094471 original size:15 final size:15
Alignment explanation
Indices: 5094451--5094498 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5094441 AAAAATTATA
5094451 TAAATATAAAATATT
1 TAAATATAAAATATT
*
5094466 TAAATAT-AATTATT
1 TAAATATAAAATATT
*
5094480 TAACA-ATAAAATATA
1 TAA-ATATAAAATATT
5094495 TAAA
1 TAAA
5094499 CACAAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATATAAAATATT
Found at i:5094488 original size:14 final size:14
Alignment explanation
Indices: 5094444--5094482 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
5094434 ACGTATCAAA
*
5094444 AATTATATAAATAT
1 AATTATTTAAATAT
*
5094458 AAAATATTTAAATAT
1 -AATTATTTAAATAT
5094473 AATTATTTAA
1 AATTATTTAA
5094483 CAATAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTATTTAAATAT
Found at i:5095571 original size:2 final size:2
Alignment explanation
Indices: 5095564--5095590 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5095554 ATAACAATGA
5095564 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
5095591 AAGTAAGGTT
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:5097721 original size:24 final size:24
Alignment explanation
Indices: 5097694--5097739 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5097684 TGTACATACT
*
5097694 GTTACAATTATATATATATATAAA
1 GTTACAATGATATATATATATAAA
* *
5097718 GTTATAGTGATATATATATATA
1 GTTACAATGATATATATATATA
5097740 TACAATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (24 bp):
GTTACAATGATATATATATATAAA
Found at i:5097731 original size:26 final size:26
Alignment explanation
Indices: 5097702--5097756 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
5097692 CTGTTACAAT
5097702 TATATATATATATA-AAGTTATAGTGA
1 TATATATATATATACAA-TTATAGTGA
5097728 TATATATATATATACAATTATAGTGA
1 TATATATATATATACAATTATAGTGA
5097754 TAT
1 TAT
5097757 GTACATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (26 bp):
TATATATATATATACAATTATAGTGA
Found at i:5097991 original size:22 final size:21
Alignment explanation
Indices: 5097966--5098090 Score: 84
Period size: 22 Copynumber: 6.1 Consensus size: 21
5097956 ATACATTCAG
*
5097966 TTATAATCATATGTATATACTA
1 TTATAGTCATATGTATATA-TA
* *
5097988 TTATAGTGATATGTGTATATAA
1 TTATAGTCATATGTATATAT-A
* *
5098010 GTATAGTCATATATATATATA
1 TTATAGTCATATGTATATATA
5098031 -TATA-T-ATA-GT-TATATA
1 TTATAGTCATATGTATATATA
* *
5098047 GTTATAGTGATATGTACATAATA
1 -TTATAGTCATATGTATAT-ATA
* *
5098070 TTACAGT-A-ATTTATATATA
1 TTATAGTCATATGTATATATA
5098089 TT
1 TT
5098091 GTTATAATGA
Statistics
Matches: 83, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
16 6 0.07
17 1 0.01
18 7 0.08
19 7 0.08
20 13 0.16
21 5 0.06
22 41 0.49
23 3 0.04
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (21 bp):
TTATAGTCATATGTATATATA
Found at i:5098316 original size:22 final size:22
Alignment explanation
Indices: 5098254--5098326 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
5098244 GTTTGTTTAT
* *
5098254 TTATAATTATATATACATTTAA
1 TTATAGTTATATATACATATAA
* * *
5098276 TTATAGTCATGTGTACATATAA
1 TTATAGTTATATATACATATAA
5098298 TTATAGTTATATATACATA-ATA
1 TTATAGTTATATATACATATA-A
5098320 TTATAGT
1 TTATAGT
5098327 GATGTTAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 1 0.02
22 41 0.98
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (22 bp):
TTATAGTTATATATACATATAA
Found at i:5099237 original size:31 final size:31
Alignment explanation
Indices: 5099181--5099264 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
5099171 GGTTCAGAAT
*
5099181 AAAAACTACTATTTTTAT-CGGTGGCACGAC
1 AAAAACTACTATTATTATCCGGTGGCACGAC
* * *
5099211 AAAAACCACTATTATTATCCGGTGGCATGGC
1 AAAAACTACTATTATTATCCGGTGGCACGAC
5099242 AAAAACTACTATTATTATCCGGT
1 AAAAACTACTATTATTATCCGGT
5099265 TGTGTAGCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 16 0.33
31 32 0.67
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (31 bp):
AAAAACTACTATTATTATCCGGTGGCACGAC
Found at i:5099275 original size:31 final size:30
Alignment explanation
Indices: 5099181--5099295 Score: 94
Period size: 31 Copynumber: 3.8 Consensus size: 30
5099171 GGTTCAGAAT
* *
5099181 AAAAACTACTATTTTTAT-CGG-TGGCACGAC
1 AAAAACTACTATTATTATCCGGTTGGTA-G-C
* *
5099211 AAAAACCACTATTATTATCCGG-TGGCATGGC
1 AAAAACTACTATTATTATCCGGTTGG--TAGC
5099242 AAAAACTACTATTATTATCCGGTTGTGTAGC
1 AAAAACTACTATTATTATCCGGTTG-GTAGC
* *
5099273 AAAAA-TCACTATTCTTAACCGGT
1 AAAAACT-ACTATTATTATCCGGT
5099296 AGCATTGTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
30 17 0.24
31 50 0.70
32 3 0.04
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (30 bp):
AAAAACTACTATTATTATCCGGTTGGTAGC
Found at i:5099295 original size:62 final size:61
Alignment explanation
Indices: 5099181--5099300 Score: 145
Period size: 62 Copynumber: 2.0 Consensus size: 61
5099171 GGTTCAGAAT
* * *
5099181 AAAAACTACTATTTTTATCGGTGGCACGACAAAAACCACTATTATTATCCGGTGGCATGGC
1 AAAAACTACTATTATTATCGGTGGCACGACAAAAACCACTATTATTAACCGGTAGCATGGC
* * *
5099242 AAAAACTACTATTATTATCCGGTTGTGTA-G-CAAAAATCACTATTCTTAACCGGTAGCAT
1 AAAAACTACTATTATTAT-CGG-TG-GCACGACAAAAACCACTATTATTAACCGGTAGCAT
5099301 TGTTTGAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 17 0.34
62 28 0.56
63 3 0.06
64 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (61 bp):
AAAAACTACTATTATTATCGGTGGCACGACAAAAACCACTATTATTAACCGGTAGCATGGC
Found at i:5100379 original size:173 final size:174
Alignment explanation
Indices: 5100089--5100439 Score: 695
Period size: 173 Copynumber: 2.0 Consensus size: 174
5100079 TAGACACCAA
5100089 ATTTTGTCCGGGTATTTTTGGGACACCCGTTTTCAATTATTTTTTTGGGACACCAACGGTGCCCG
1 ATTTTGTCCGGGTATTTTTGGGACACCCGTTTTCAATTATTTTTTTGGGACACCAACGGTGCCCG
5100154 ACGAAAATAAACTTTTGGATTATTGGAGTTTTCTGACAAATGCAAATTTTTTCCCATTACCCTTC
66 ACGAAAATAAACTTTTGGATTATTGGAGTTTTCTGACAAATGCAAATTTTTTCCCATTACCCTTC
5100219 GTGGAGGCAAGGTGTTCGGGATGCAAAAAGTGTGGAAAAGTCAC
131 GTGGAGGCAAGGTGTTCGGGATGCAAAAAGTGTGGAAAAGTCAC
5100263 ATTTTGTCCGGGTATTTTTGGGACACCCGTTTTCAATTA-TTTTTTGGGACACCAACGGTGCCCG
1 ATTTTGTCCGGGTATTTTTGGGACACCCGTTTTCAATTATTTTTTTGGGACACCAACGGTGCCCG
5100327 ACGAAAATAAACTTTTGGATTATTGGAGTTTTCTGACAAATGCAAATTTTTTCCCATTACCCTTC
66 ACGAAAATAAACTTTTGGATTATTGGAGTTTTCTGACAAATGCAAATTTTTTCCCATTACCCTTC
5100392 GTGGAGGCAAGGTGTTCGGGATGCAAAAAGTGTGGAAAAGTCAC
131 GTGGAGGCAAGGTGTTCGGGATGCAAAAAGTGTGGAAAAGTCAC
5100436 ATTT
1 ATTT
5100440 CATACCCTGA
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 138 0.78
174 39 0.22
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (174 bp):
ATTTTGTCCGGGTATTTTTGGGACACCCGTTTTCAATTATTTTTTTGGGACACCAACGGTGCCCG
ACGAAAATAAACTTTTGGATTATTGGAGTTTTCTGACAAATGCAAATTTTTTCCCATTACCCTTC
GTGGAGGCAAGGTGTTCGGGATGCAAAAAGTGTGGAAAAGTCAC
Found at i:5100495 original size:20 final size:19
Alignment explanation
Indices: 5100449--5100525 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
5100439 TCATACCCTG
* *
5100449 ATGTATCGATGCATTTTTCA
1 ATGTATCGATACA-TTATCA
* *
5100469 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
5100489 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
5100509 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
5100526 GTCTTTTTAC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:5100516 original size:40 final size:39
Alignment explanation
Indices: 5100449--5100526 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
5100439 TCATACCCTG
* * *
5100449 ATGTATCGATGCATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
5100489 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
5100527 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:5105363 original size:22 final size:22
Alignment explanation
Indices: 5105338--5105379 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5105328 AGTTATAGTG
* * *
5105338 TTATATTGTTATGTACATATTA
1 TTATAATGATATGAACATATTA
5105360 TTATAATGATATGAACATAT
1 TTATAATGATATGAACATAT
5105380 AGGTCATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (22 bp):
TTATAATGATATGAACATATTA
Found at i:5107271 original size:31 final size:29
Alignment explanation
Indices: 5107240--5107350 Score: 102
Period size: 27 Copynumber: 3.8 Consensus size: 29
5107230 TTAATTTTTA
5107240 AATTT-TACTTAAATAAACCTTTAACCTTTT
1 AATTTATACTTAAATAAA-CTTTAACC-TTT
* * * * *
5107270 AACTTATAATTAAATAAGCCCTTAAACTTT
1 AATTTATACTTAAATAA-ACTTTAACCTTT
* *
5107300 GATTTATA-TTCAA-AAACTTTAACCTTT
1 AATTTATACTTAAATAAACTTTAACCTTT
*
5107327 AATTTATACATAAATAAACTTTAA
1 AATTTATACTTAAATAAACTTTAA
5107351 AACAAATTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 9
0.73 0.16 0.10
Matches are distributed among these distances:
27 16 0.25
28 5 0.08
29 13 0.21
30 13 0.21
31 16 0.25
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.41
Consensus pattern (29 bp):
AATTTATACTTAAATAAACTTTAACCTTT
Found at i:5107447 original size:22 final size:23
Alignment explanation
Indices: 5107367--5107448 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 23
5107357 TTTTCATTTA
** *
5107367 AAATAAAAAGTTTATTTAGATAT
1 AAATAAAAAAATTATTTAAATAT
5107390 AAATAAAAAATTAAACTTATTTAAATAT
1 AAAT--AAAA--AAA-TTATTTAAATAT
*
5107418 AAATAAAAAAATTATTTAAATCT
1 AAATAAAAAAATTATTTAAATAT
5107441 -AATAAAAA
1 AAATAAAAA
5107449 TAAAATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
22 8 0.16
23 15 0.30
24 3 0.06
25 4 0.08
26 4 0.08
27 1 0.02
28 15 0.30
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATAAAAAAATTATTTAAATAT
Found at i:5107456 original size:22 final size:23
Alignment explanation
Indices: 5107408--5107457 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
5107398 AATTAAACTT
*
5107408 ATTTAAATATAAATAAAAAAATT
1 ATTTAAATATAAATAAAAAAATA
*
5107431 ATTTAAATCT-AATAAAAATAA-A
1 ATTTAAATATAAATAAAAA-AATA
5107453 ATTTA
1 ATTTA
5107458 TTAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTTAAATATAAATAAAAAAATA
Found at i:5109523 original size:24 final size:25
Alignment explanation
Indices: 5109495--5109541 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5109485 TTGCATCCGT
*
5109495 TTTATATAAATTTAGA-TATATTCA
1 TTTATATAAATTCAGATTATATTCA
* *
5109519 TTTATTTATATTCAGATTATATT
1 TTTATATAAATTCAGATTATATT
5109542 TTTTTTCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
TTTATATAAATTCAGATTATATTCA
Found at i:5110050 original size:11 final size:11
Alignment explanation
Indices: 5110022--5110072 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
5110012 ATATAGAATA
*
5110022 ATTAAATTCAT
1 ATTATATTCAT
5110033 A-TATATTCAT
1 ATTATATTCAT
*
5110043 ATTATATTTAT
1 ATTATATTCAT
*
5110054 ATTATTTTACAT
1 ATTATATT-CAT
5110066 -TTATATT
1 ATTATATT
5110073 TTACTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 9 0.27
11 22 0.67
12 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTATATTCAT
Found at i:5110069 original size:16 final size:17
Alignment explanation
Indices: 5110034--5110072 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
5110024 TAAATTCATA
*
5110034 TATATTCATATTATATT
1 TATATTCATATTACATT
*
5110051 TATATT-ATTTTACATT
1 TATATTCATATTACATT
5110067 TATATT
1 TATATT
5110073 TTACTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTCATATTACATT
Found at i:5110891 original size:7 final size:7
Alignment explanation
Indices: 5110845--5110918 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
5110835 GTACAAACAT
5110845 AATATAA
1 AATATAA
*
5110852 AATAT-T
1 AATATAA
*
5110858 AATAAAA
1 AATATAA
5110865 AATATATTA
1 AATATA--A
5110874 TAATATAA
1 -AATATAA
*
5110882 AATTTAA
1 AATATAA
5110889 AATATAA
1 AATATAA
5110896 AATA-AA
1 AATATAA
*
5110902 TATATAA
1 AATATAA
5110909 ATATATAA
1 A-ATATAA
5110917 AA
1 AA
5110919 ATTTATATGA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 9 0.17
7 29 0.55
8 8 0.15
9 1 0.02
10 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
AATATAA
Found at i:5110894 original size:19 final size:20
Alignment explanation
Indices: 5110872--5110925 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 20
5110862 AAAAATATAT
5110872 TATAATATAAAATTTA-AAA
1 TATAATATAAAATTTATAAA
* *
5110891 TATAAAAT-AAATATATAAA
1 TATAATATAAAATTTATAAA
5110910 TAT-ATA-AAAATTTATA
1 TATAATATAAAATTTATA
5110926 TGATATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAATATAAAATTTATAAA
Found at i:5110906 original size:35 final size:38
Alignment explanation
Indices: 5110849--5110923 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 38
5110839 AAACATAATA
*
5110849 TAAAATATTAATAAAAAATATAT-TATA-ATATAAAATT
1 TAAAATATTAATAAAAAATATATAAATATATA-AAAATT
*
5110886 TAAAATA-TAA-AATAAATATATAAATATATAAAAATT
1 TAAAATATTAATAAAAAATATATAAATATATAAAAATT
5110922 TA
1 TA
5110924 TATGATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 10 0.29
36 14 0.41
37 10 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (38 bp):
TAAAATATTAATAAAAAATATATAAATATATAAAAATT
Found at i:5110958 original size:27 final size:27
Alignment explanation
Indices: 5110902--5110980 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
5110892 ATAAAATAAA
* * *
5110902 TATATAAATATATAAAAATTT--ATAT
1 TATATAAATATATAATATTTTAAATTT
*
5110927 GATATAAAT-TATTAAT-TTATTAAATTT
1 TATATAAATATA-TAATATT-TTAAATTT
5110954 TATATAAATATATAATATTTTAAATTT
1 TATATAAATATATAATATTTTAAATTT
5110981 AAATATAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
24 3 0.07
25 13 0.30
27 23 0.53
28 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
TATATAAATATATAATATTTTAAATTT
Found at i:5110965 original size:33 final size:34
Alignment explanation
Indices: 5110890--5110971 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 34
5110880 AAAATTTAAA
5110890 ATATAAA-ATAAATATATAAATATATAAAAATTT
1 ATATAAATATAAATATATAAATATATAAAAATTT
* * * * *
5110923 ATAT-GATATAAAT-TATTAATTTATTAAATTTT
1 ATATAAATATAAATATATAAATATATAAAAATTT
5110955 ATATAAATATATAATAT
1 ATATAAATATA-AATAT
5110972 TTTAAATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
32 20 0.51
33 15 0.38
34 3 0.08
35 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (34 bp):
ATATAAATATAAATATATAAATATATAAAAATTT
Found at i:5111269 original size:16 final size:18
Alignment explanation
Indices: 5111237--5111271 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
5111227 ATTTTAAATA
5111237 TTGAATTTATCATTAATT
1 TTGAATTTATCATTAATT
5111255 TTGAATTT-T-ATTAATT
1 TTGAATTTATCATTAATT
5111271 T
1 T
5111272 ATAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (18 bp):
TTGAATTTATCATTAATT
Found at i:5111609 original size:4 final size:4
Alignment explanation
Indices: 5111602--5111643 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
5111592 TATATATATA
5111602 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
5111644 GACCAATTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:5112010 original size:27 final size:26
Alignment explanation
Indices: 5111979--5112039 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
5111969 TATTAGAATA
5111979 AAAATTTTAATAATTTTAATTA-TTATT
1 AAAATTTTAA-AATTTT-ATTATTTATT
* *
5112006 TAAATAATTAAAATTTTATTATTTATT
1 AAAAT-TTTAAAATTTTATTATTTATT
5112033 AAAATTT
1 AAAATTT
5112040 AATTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
26 5 0.18
27 19 0.68
28 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AAAATTTTAAAATTTTATTATTTATT
Found at i:5112020 original size:21 final size:20
Alignment explanation
Indices: 5111982--5112054 Score: 53
Period size: 21 Copynumber: 3.7 Consensus size: 20
5111972 TAGAATAAAA
* **
5111982 ATTTTAATAATTTTAATTATT
1 ATTTAAATAATTAAAATT-TT
5112003 ATTTAAATAATTAAAATTTT
1 ATTTAAATAATTAAAATTTT
* * *
5112023 A-TT-ATTTATTAAAATTTA
1 ATTTAAATAATTAAAATTTT
5112041 ATTATAAAT-ATTAA
1 ATT-TAAATAATTAA
5112055 TAAAAAATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 13 0.31
19 3 0.07
20 9 0.21
21 17 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAATAATTAAAATTTT
Found at i:5113151 original size:2 final size:2
Alignment explanation
Indices: 5113144--5113207 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
5113134 ATAATGGGAA
* *
5113144 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5113186 AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
5113208 GAATTTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5113447 original size:2 final size:2
Alignment explanation
Indices: 5113440--5113477 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5113430 TTCGGCATTG
5113440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5113478 CAACAGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5113917 original size:28 final size:26
Alignment explanation
Indices: 5113866--5113940 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 26
5113856 AAAAATCACC
5113866 TTTTATTTGTCAAAAATAGTGATTAT
1 TTTTATTTGTCAAAAATAGTGATTAT
* * *
5113892 TTTGTGTTTGTCAAAAATGATTGATTCT
1 TTT-TATTTGTCAAAAAT-AGTGATTAT
5113920 TTTTATTTGTCAAAAATAGTG
1 TTTTATTTGTCAAAAATAGTG
5113941 GCATGTTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.14
27 26 0.62
28 10 0.24
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (26 bp):
TTTTATTTGTCAAAAATAGTGATTAT
Found at i:5118455 original size:27 final size:27
Alignment explanation
Indices: 5118423--5118495 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
5118413 AGCCACCCTT
*
5118423 TGTTTGTCAAAAATAGTGGTTGCTTTG
1 TGTTTGTAAAAAATAGTGGTTGCTTTG
* * * *
5118450 TGTTTGTAAAAAATGGTTGTTTCTTTT
1 TGTTTGTAAAAAATAGTGGTTGCTTTG
* * *
5118477 TATTTTTTAAAAATAGTGG
1 TGTTTGTAAAAAATAGTGG
5118496 CATGTTGTTT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.04, G:0.21, T:0.49
Consensus pattern (27 bp):
TGTTTGTAAAAAATAGTGGTTGCTTTG
Found at i:5119196 original size:27 final size:28
Alignment explanation
Indices: 5119144--5119201 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
5119134 TATATATAGC
*
5119144 TATATATAAAATTATAATTATCAATT-T
1 TATACATAAAATTATAATTATCAATTAT
5119171 TATACATAATAATTA-AATTAAT-AATTAT
1 TATACATAA-AATTATAATT-ATCAATTAT
5119199 TAT
1 TAT
5119202 TTTAGAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
TATACATAAAATTATAATTATCAATTAT
Found at i:5120731 original size:33 final size:33
Alignment explanation
Indices: 5120682--5120757 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
5120672 TTAAAATATT
* * *
5120682 TTAAAGATAATATTTATTTTTAATATTATT-AAA
1 TTAAA-ATAATATTTATCTGTAATATAATTAAAA
*
5120715 TTAAGAATAATTTTTATCTGTAATATAATTAAAA
1 TTAA-AATAATATTTATCTGTAATATAATTAAAA
5120749 TTAAAATAA
1 TTAAAATAA
5120758 AAAAATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 29 0.78
34 8 0.22
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (33 bp):
TTAAAATAATATTTATCTGTAATATAATTAAAA
Found at i:5121385 original size:13 final size:13
Alignment explanation
Indices: 5121367--5121394 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5121357 GCCAAGGAAA
5121367 TGTATCGATACAT
1 TGTATCGATACAT
5121380 TGTATCGATACAT
1 TGTATCGATACAT
5121393 TG
1 TG
5121395 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5127899 original size:19 final size:20
Alignment explanation
Indices: 5127849--5127899 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
5127839 TGCTGATGTC
*
5127849 GCTTTTGACTATGCTGACATG
1 GCTTTTGACTA-GATGACATG
** *
5127870 GCACTTAACTA-ATGACATG
1 GCTTTTGACTAGATGACATG
5127889 GCTTTTGACTA
1 GCTTTTGACTA
5127900 TGTTACATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 15 0.65
21 8 0.35
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (20 bp):
GCTTTTGACTAGATGACATG
Found at i:5128485 original size:14 final size:14
Alignment explanation
Indices: 5128466--5128492 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5128456 ACTATTACTA
5128466 CAAAATTGTAAGAG
1 CAAAATTGTAAGAG
5128480 CAAAATTGTAAGA
1 CAAAATTGTAAGA
5128493 AAATTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
CAAAATTGTAAGAG
Found at i:5129344 original size:2 final size:2
Alignment explanation
Indices: 5129337--5129366 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5129327 AAAATTTTGC
*
5129337 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5129367 TAATGATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5129720 original size:25 final size:25
Alignment explanation
Indices: 5129686--5129743 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
5129676 AAGATACCTT
*
5129686 TGAAGTTAGATCAGGATTCATGTTG
1 TGAAGTTAGATAAGGATTCATGTTG
5129711 TGAAGTTAGATAAGGATTCATGTTG
1 TGAAGTTAGATAAGGATTCATGTTG
*
5129736 TGATGTTA
1 TGAAGTTA
5129744 AACAAGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (25 bp):
TGAAGTTAGATAAGGATTCATGTTG
Found at i:5129750 original size:25 final size:25
Alignment explanation
Indices: 5129698--5129750 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5129688 AAGTTAGATC
* *
5129698 AGGATTCATGTTGTGAAGTTAGATA
1 AGGATTCATGTTGTGAAGTTAAACA
*
5129723 AGGATTCATGTTGTGATGTTAAACA
1 AGGATTCATGTTGTGAAGTTAAACA
5129748 AGG
1 AGG
5129751 TAGTCCACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (25 bp):
AGGATTCATGTTGTGAAGTTAAACA
Found at i:5131117 original size:34 final size:34
Alignment explanation
Indices: 5131050--5131265 Score: 222
Period size: 34 Copynumber: 6.4 Consensus size: 34
5131040 TACTCATATC
* **
5131050 TGTTGATTAAAT-AGTAATTTGGTAATTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * * *
5131083 TGTTGATTAAATGAGTGATTTGATGGTTTGCCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * *
5131117 TGTTGACTAAAT-AGGAGATTTGGTAGCTTACTAT
1 TGTTGATTAAATGA-GTGATTTGGTAGCTTACCAT
**
5131151 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * * *
5131185 TATTGATTAAATGGGTGATTTAGTGGCTTACCAT
1 TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
* * *
5131219 TGTTGACTAAATG-GTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGAGT-GATTTGGTAGCTTACCAT
5131253 TGTTGATTAAATG
1 TGTTGATTAAATG
5131266 GTGGTTTTTA
Statistics
Matches: 151, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
33 15 0.10
34 135 0.89
35 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGAGTGATTTGGTAGCTTACCAT
Found at i:5131241 original size:102 final size:102
Alignment explanation
Indices: 5131050--5131265 Score: 303
Period size: 102 Copynumber: 2.1 Consensus size: 102
5131040 TACTCATATC
* * * * *
5131050 TGTTGATTAAAT-AGTAATTTGGTAATTTACCATTGTTGATTAAATGAGTGATTTGATGGTTTGC
1 TGTTGATTAAATGAGAAATTTGGTAACTTACCATTATTGATTAAATGAGTGATTTGATGGCTTAC
*
5131114 CATTGTTGACTAAATAGGAGATTTGGTAGCTTACTAT
66 CATTGTTGACTAAATAGGAGATTTGGTAGCTTACCAT
* *
5131151 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTT-AGTGGCTTA
1 TGTTGATTAAATGAGAAATTTGGTAACTTACCATTATTGATTAAATGAGTGATTTGA-TGGCTTA
* *
5131215 CCATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
65 CCATTGTTGACTAAATAGG-AGATTTGGTAGCTTACCAT
5131253 TGTTGATTAAATG
1 TGTTGATTAAATG
5131266 GTGGTTTTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
101 15 0.15
102 87 0.85
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.41
Consensus pattern (102 bp):
TGTTGATTAAATGAGAAATTTGGTAACTTACCATTATTGATTAAATGAGTGATTTGATGGCTTAC
CATTGTTGACTAAATAGGAGATTTGGTAGCTTACCAT
Found at i:5136672 original size:34 final size:33
Alignment explanation
Indices: 5136624--5136842 Score: 244
Period size: 34 Copynumber: 6.5 Consensus size: 33
5136614 TGGTAAAAAC
5136624 CACCATTTAATCAACAATGGTAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
5136657 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
5136691 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** * *
5136725 TTCTCATTTAATCAACAATAGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * **
5136759 CTCCCATTTAGTCAACAATGACAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATG-GTAACCTACCAAAT
* *
5136793 CACCCATTTAATCAACAATGATAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
5136827 CACCATTTAATCAACA
1 CACCATTTAATCAACA
5136843 TATAGGCTTT
Statistics
Matches: 157, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 21 0.13
34 130 0.83
35 6 0.04
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:5136803 original size:102 final size:101
Alignment explanation
Indices: 5136624--5136847 Score: 331
Period size: 102 Copynumber: 2.2 Consensus size: 101
5136614 TGGTAAAAAC
* ** *
5136624 CACCATTTAATCAACAATGGTAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATAGTAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
* * *
5136689 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAAT
** * *
5136725 TTCTCATTTAATCAACAATAGTAAGCTACCAAATCTCCCATTTAGTCAACAATGACAAACCACCA
1 CAC-CATTTAATCAACAATAGTAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCA
5136790 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
5136827 CACCATTTAATCAACATATAG
1 CACCATTTAATCAACA-ATAG
5136848 GCTTTCTTGC
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
101 14 0.13
102 94 0.87
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATAGTAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:5139869 original size:14 final size:17
Alignment explanation
Indices: 5139852--5139888 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
5139842 TAATAAATAA
5139852 ATAAAAAT-A-TTTAT-
1 ATAAAAATAATTTTATC
5139866 ATAAAAATAATTTTATC
1 ATAAAAATAATTTTATC
5139883 ATAAAA
1 ATAAAA
5139889 TAAAAAGAAA
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 5 0.25
17 6 0.30
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAATAATTTTATC
Found at i:5140194 original size:25 final size:23
Alignment explanation
Indices: 5140161--5140217 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
5140151 CTACATTCAG
5140161 AAAA-GAAACAAAAAAATATGATAT
1 AAAATGAAAC-AAAAAA-ATGATAT
**
5140185 AAAATGAAACTCAAAAATGATAT
1 AAAATGAAACAAAAAAATGATAT
5140208 AAAATGAAAC
1 AAAATGAAAC
5140218 TCTTTTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 17 0.57
24 8 0.27
25 5 0.17
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAATGAAACAAAAAAATGATAT
Found at i:5140208 original size:23 final size:24
Alignment explanation
Indices: 5140173--5140219 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
5140163 AAGAAACAAA
5140173 AAAATATGATATAAAATGAAACTC
1 AAAATATGATATAAAATGAAACTC
5140197 AAAA-ATGATATAAAATGAAACTC
1 AAAATATGATATAAAATGAAACTC
5140220 TTTTAGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (24 bp):
AAAATATGATATAAAATGAAACTC
Found at i:5140964 original size:18 final size:18
Alignment explanation
Indices: 5140943--5140989 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5140933 AAAAATATAA
5140943 TTAATCTTAAAATTAT-TT
1 TTAAT-TTAAAATTATATT
*
5140961 TTAATTATTAAATTATATT
1 TTAATT-TAAAATTATATT
5140980 TTAATTTAAA
1 TTAATTTAAA
5140990 TACATACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.04
18 16 0.64
19 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTAAAATTATATT
Found at i:5142476 original size:16 final size:16
Alignment explanation
Indices: 5142431--5142479 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
5142421 CTTAAAATTT
5142431 AAAT-TTAA-ATTTATA
1 AAATATTAATATTTA-A
*
5142446 AAATA-TCATATTTTAA
1 AAATATTAATA-TTTAA
5142462 AAATATTAATATTTAA
1 AAATATTAATATTTAA
5142478 AA
1 AA
5142480 TAATTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 6 0.21
16 14 0.50
17 8 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATATTAATATTTAA
Found at i:5142774 original size:2 final size:2
Alignment explanation
Indices: 5142767--5142813 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
5142757 CAAATCTGTT
5142767 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5142808 TA TA TA
1 TA TA TA
5142814 AAGTTGTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5143275 original size:9 final size:9
Alignment explanation
Indices: 5143251--5143280 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
5143241 ATAAGTGATT
5143251 TAATTTTTA
1 TAATTTTTA
5143260 TATATTTTTA
1 TA-ATTTTTA
5143270 TAATTTTTA
1 TAATTTTTA
5143279 TA
1 TA
5143281 TAATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5143276 original size:8 final size:10
Alignment explanation
Indices: 5143253--5143296 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
5143243 AAGTGATTTA
5143253 ATTTTTATAT
1 ATTTTTATAT
5143263 ATTTTTATA-
1 ATTTTTATAT
5143272 ATTTTTATAT
1 ATTTTTATAT
* *
5143282 AATTTATATTT
1 -ATTTTTATAT
5143293 ATTT
1 ATTT
5143297 AATTTAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.30
10 13 0.43
11 8 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:5143282 original size:11 final size:11
Alignment explanation
Indices: 5143251--5143286 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5143241 ATAAGTGATT
5143251 TAATTTTTATA
1 TAATTTTTATA
5143262 T-A-TTTT-TA
1 TAATTTTTATA
5143270 TAATTTTTATA
1 TAATTTTTATA
5143281 TAATTT
1 TAATTT
5143287 ATATTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.14
9 5 0.23
10 5 0.23
11 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:5143297 original size:19 final size:19
Alignment explanation
Indices: 5143251--5143289 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5143241 ATAAGTGATT
*
5143251 TAATTTTTATATATTTTTA
1 TAATTTTTATATATATTTA
5143270 TAATTTTTATATA-ATTTA
1 TAATTTTTATATATATTTA
5143288 TA
1 TA
5143290 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTTTATATATATTTA
Found at i:5143304 original size:20 final size:20
Alignment explanation
Indices: 5143281--5143326 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
5143271 AATTTTTATA
*
5143281 TAATTTA-TATTTATTTAATT
1 TAATTTATTATTT-TTAAATT
5143301 TAA-TTATTATTTTTAAATT
1 TAATTTATTATTTTTAAATT
*
5143320 TTATTTA
1 TAATTTA
5143327 AGTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TAATTTATTATTTTTAAATT
Found at i:5143334 original size:29 final size:29
Alignment explanation
Indices: 5143290--5143350 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
5143280 ATAATTTATA
* * *
5143290 TTTATTTAATTTAATTAT-TATTTTTAAAT
1 TTTATTTAAGTAAATTATATA-TGTTAAAT
5143319 TTTATTTAAGTAAATTATATATGTTAAAT
1 TTTATTTAAGTAAATTATATATGTTAAAT
5143348 TTT
1 TTT
5143351 GAATAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (29 bp):
TTTATTTAAGTAAATTATATATGTTAAAT
Found at i:5146322 original size:26 final size:22
Alignment explanation
Indices: 5146293--5146372 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 22
5146283 GCTATACTTA
5146293 ATAATATTAAATATAATTATATAAAT
1 ATAATA-TAAATATAA-T-TA-AAAT
5146319 ATAATATAAA-A-AATTAAAAT
1 ATAATATAAATATAATTAAAAT
*
5146339 ATAATATAAATAT-TTTAAAA-
1 ATAATATAAATATAATTAAAAT
*
5146359 ATTATAT-AATATAA
1 ATAATATAAATATAA
5146373 ATTATTAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
19 5 0.10
20 20 0.42
21 9 0.19
22 1 0.02
23 2 0.04
24 1 0.02
25 4 0.08
26 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATATAAATATAATTAAAAT
Found at i:5146384 original size:20 final size:20
Alignment explanation
Indices: 5146294--5146385 Score: 64
Period size: 20 Copynumber: 4.4 Consensus size: 20
5146284 CTATACTTAA
5146294 TAATAT-TAA-ATATAATTAT
1 TAATATATAATATA-AATTAT
**
5146313 ATAA-ATATAATATAAAAAAT
1 -TAATATATAATATAAATTAT
* *
5146333 TAAAATATAATATAAATATTT
1 TAATATATAATATAAAT-TAT
5146354 TAAAAATTATATAATATAAATTAT
1 T---AA-TATATAATATAAATTAT
5146378 TAATATAT
1 TAATATAT
5146386 TAAAATTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
19 5 0.09
20 27 0.47
21 7 0.12
24 5 0.09
25 13 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATATATAATATAAATTAT
Found at i:5146387 original size:25 final size:25
Alignment explanation
Indices: 5146307--5146380 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
5146297 TATTAAATAT
5146307 AATTATATAA-ATATAATATA--AAA
1 AATTATATAATATA-AATATATTAAA
*
5146330 AATTAAAATATAATATAAATATTTTAAA
1 AATT---ATATAATATAAATATATTAAA
5146358 AATTATATAATATAAAT-TATTAA
1 AATTATATAATATAAATATATTAA
5146381 TATATTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
23 4 0.09
24 5 0.12
25 13 0.30
26 11 0.26
27 3 0.07
28 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATTATATAATATAAATATATTAAA
Found at i:5146395 original size:18 final size:18
Alignment explanation
Indices: 5146374--5146415 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5146364 ATAATATAAA
*
5146374 TTATTAATATATTAAA-AT
1 TTATTAA-ATATAAAATAT
5146392 TTATATAAATATAAAATAT
1 TTAT-TAAATATAAAATAT
5146411 TTATT
1 TTATT
5146416 TGGCTTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATTAAATATAAAATAT
Found at i:5146402 original size:20 final size:20
Alignment explanation
Indices: 5146322--5146404 Score: 58
Period size: 20 Copynumber: 4.5 Consensus size: 20
5146312 TATAAATATA
* *
5146322 ATATAAA-AAATTAAAATATA
1 ATATAAATATATTAAAAT-TT
* *
5146342 ATATAAATATTTTAAAAATT
1 ATATAAATATATTAAAATTT
5146362 ATAT--A-ATA-T-AAA-TT
1 ATATAAATATATTAAAATTT
5146376 AT-T-AATATATTAAAATTT
1 ATATAAATATATTAAAATTT
5146394 ATATAAATATA
1 ATATAAATATA
5146405 AAATATTTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 1 0.02
14 5 0.10
15 6 0.12
16 2 0.04
17 5 0.10
18 5 0.10
19 1 0.02
20 18 0.36
21 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAAATATATTAAAATTT
Found at i:5146406 original size:17 final size:17
Alignment explanation
Indices: 5146354--5146408 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5146344 ATAAATATTT
*
5146354 TAAAAATTATAT-AATA
1 TAAAATTTATATAAATA
5146370 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
5146385 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
5146403 TAAAAT
1 TAAAAT
5146409 ATTTATTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 2 0.06
17 9 0.27
18 7 0.21
19 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:5146410 original size:25 final size:26
Alignment explanation
Indices: 5146295--5146411 Score: 71
Period size: 25 Copynumber: 4.2 Consensus size: 26
5146285 TATACTTAAT
5146295 AATATTAAATATAATTATATAAATAT--
1 AATATTAAA-AT-ATTATATAAATATAA
* *
5146321 AATA-TAAAAAATTAAAATATAATATAA
1 AATATTAAAATATT-ATATA-AATATAA
*
5146348 ATATTTTAAAAATTATATAATATAAATTATTAA
1 A-ATATT-AAAA-TAT-T-ATATAAA-TA-TAA
*
5146381 TATATTAAAAT-TTATATAAATATAA
1 AATATTAAAATATTATATAAATATAA
5146406 AATATT
1 AATATT
5146412 TATTTGGCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
23 3 0.04
24 5 0.07
25 17 0.24
26 6 0.08
27 8 0.11
28 3 0.04
29 2 0.03
30 5 0.07
31 8 0.11
32 12 0.17
33 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATTAAAATATTATATAAATATAA
Found at i:5146982 original size:24 final size:24
Alignment explanation
Indices: 5146955--5147014 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
5146945 TAAATTAGTG
*
5146955 ATAAAGT-TTTAAATTTTATATTTT
1 ATAAAGTATTTAAATATTAT-TTTT
*
5146979 AT-AATTATTTAAATATTATTTTT
1 ATAAAGTATTTAAATATTATTTTT
*
5147002 ATAAA-TAATTAAA
1 ATAAAGTATTTAAA
5147015 ATAATTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATAAAGTATTTAAATATTATTTTT
Found at i:5147005 original size:23 final size:24
Alignment explanation
Indices: 5146962--5147024 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
5146952 GTGATAAAGT
* *
5146962 TTTAAATTTTATATTTTATAATTA
1 TTTAAATATTATATTTTATAAATA
5146986 TTTAAATATTAT-TTTTATAAATAA
1 TTTAAATATTATATTTTATAAAT-A
*
5147010 TTAAAATAATTATAT
1 TTTAAAT-ATTATAT
5147025 CATTAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 9 0.27
24 18 0.55
25 5 0.15
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTAAATATTATATTTTATAAATA
Found at i:5150123 original size:2 final size:2
Alignment explanation
Indices: 5150116--5150158 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5150106 ATTGGCCTCC
*
5150116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
5150158 T
1 T
5150159 GTGAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5150760 original size:21 final size:21
Alignment explanation
Indices: 5150727--5150770 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5150717 AATAAATTTA
*
5150727 TTAAAATATAATTAAATCAAT
1 TTAAAATAAAATTAAATCAAT
* *
5150748 TTAATATAAAATTAAATTAAT
1 TTAAAATAAAATTAAATCAAT
5150769 TT
1 TT
5150771 TATACATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAAATAAAATTAAATCAAT
Found at i:5152645 original size:17 final size:17
Alignment explanation
Indices: 5152623--5152655 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5152613 TCTATACTCC
5152623 ATAAAA-TATAATTAAAA
1 ATAAAATTA-AATTAAAA
5152640 ATAAAATTAAATTAAA
1 ATAAAATTAAATTAAA
5152656 CTTAAGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAATTAAATTAAAA
Found at i:5152751 original size:2 final size:2
Alignment explanation
Indices: 5152744--5152770 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5152734 ATTATTCATT
5152744 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 T
5152771 GTAACGAGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5153096 original size:3 final size:3
Alignment explanation
Indices: 5153088--5153114 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5153078 CAGTCATCTT
5153088 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5153115 ATGCATACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5153498 original size:20 final size:22
Alignment explanation
Indices: 5153459--5153500 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5153449 AACATTTAAA
5153459 TTAAATATATAAATATAATTTT
1 TTAAATATATAAATATAATTTT
5153481 TTAAATATATAAA-A-AATTTT
1 TTAAATATATAAATATAATTTT
5153501 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAATATATAAATATAATTTT
Found at i:5153502 original size:18 final size:21
Alignment explanation
Indices: 5153459--5153515 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
5153449 AACATTTAAA
5153459 TTAAATATATAAATATAATTTT
1 TTAAATATATAAATATAA-TTT
5153481 TTAAATATATAAA-A-AATTT
1 TTAAATATATAAATATAATTT
* *
5153500 TAAAAAAT-TAAATATA
1 TTAAATATATAAATATA
5153516 TTCATATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 4 0.13
19 10 0.32
20 3 0.10
21 1 0.03
22 13 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAATATATAAATATAATTT
Found at i:5154707 original size:16 final size:17
Alignment explanation
Indices: 5154676--5154718 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5154666 TTTAATATTT
*
5154676 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
5154693 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
*
5154708 TTAAAATTTAT
1 ATAAAATTTAT
5154719 TTTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:5154768 original size:43 final size:45
Alignment explanation
Indices: 5154671--5154763 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 45
5154661 CGAGTTTTAA
* *
5154671 TATTTATAAAATTTTTAATTAAATAAAATTATAATTATTAAAATT
1 TATTTATAAAATATTTAATTAAATAAAATTATAATAATTAAAATT
*
5154716 TATTT-TAAAATATTTAA-TAAAT-AAATT-TAA-AATTTAAATT
1 TATTTATAAAATATTTAATTAAATAAAATTATAATAATTAAAATT
5154756 TATTTATA
1 TATTTATA
5154764 TAAAAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
40 13 0.30
41 5 0.11
42 5 0.11
43 5 0.11
44 11 0.25
45 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (45 bp):
TATTTATAAAATATTTAATTAAATAAAATTATAATAATTAAAATT
Found at i:5155046 original size:31 final size:31
Alignment explanation
Indices: 5155005--5155066 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5154995 AACATGGTAA
*
5155005 GAATACATTAATATGTCAAAATGTAGATAAAT
1 GAATACATTAATATGTAAAAAT-TAGATAAAT
* *
5155037 GAATA-ATTAATGTGTAAAAATTATATAAAT
1 GAATACATTAATATGTAAAAATTAGATAAAT
5155067 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 8 0.30
31 14 0.52
32 5 0.19
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (31 bp):
GAATACATTAATATGTAAAAATTAGATAAAT
Found at i:5155754 original size:16 final size:16
Alignment explanation
Indices: 5155729--5155778 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
5155719 TTTTTCTCCC
5155729 ATAT-ATAAAATAAA-
1 ATATAATAAAATAAAT
5155743 ATATACATAAAAATATATAT
1 ATATA-AT-AAAATA-A-AT
5155763 ATATAATAAAATAAAT
1 ATATAATAAAATAAAT
5155779 TATTAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 4 0.13
16 4 0.13
17 7 0.23
18 7 0.23
19 3 0.10
20 5 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATAATAAAATAAAT
Found at i:5155863 original size:8 final size:8
Alignment explanation
Indices: 5155850--5155879 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
5155840 AACATATACA
5155850 TTTTTTAT
1 TTTTTTAT
5155858 TTTTTTAT
1 TTTTTTAT
5155866 TTTTTTAT
1 TTTTTTAT
5155874 TTTTTT
1 TTTTTT
5155880 CTTCTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:5155890 original size:4 final size:4
Alignment explanation
Indices: 5155877--5155919 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
5155867 TTTTTATTTT
* *
5155877 TTTC -TTC TTTC TTTC -TTC TTTC TTTC TTTT TTTC TTTT TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
5155920 CGAATGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 6 0.18
4 27 0.82
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:5155891 original size:11 final size:11
Alignment explanation
Indices: 5155877--5155904 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5155867 TTTTTATTTT
5155877 TTTCTTCTTTC
1 TTTCTTCTTTC
5155888 TTTCTTCTTTC
1 TTTCTTCTTTC
5155899 TTTCTT
1 TTTCTT
5155905 TTTTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:5155914 original size:7 final size:7
Alignment explanation
Indices: 5155874--5155916 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
5155864 ATTTTTTTAT
5155874 TTTTTTC
1 TTTTTTC
*
5155881 TTCTTTC
1 TTTTTTC
*
5155888 TTTCTTC
1 TTTTTTC
5155895 TTTCTTTC
1 TTT-TTTC
5155903 TTTTTTTC
1 -TTTTTTC
5155911 TTTTTT
1 TTTTTT
5155917 TCTCGAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
7 20 0.67
8 7 0.23
9 3 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:5155917 original size:11 final size:11
Alignment explanation
Indices: 5155857--5155917 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
5155847 ACATTTTTTA
*
5155857 TTTTTTTATTT
1 TTTTTTTCTTT
5155868 TTTTATTT-TTT
1 TTTT-TTTCTTT
*
5155879 TCTTCTTTCTTT
1 T-TTTTTTCTTT
* *
5155891 CTTCTTTCTTT
1 TTTTTTTCTTT
5155902 CTTTTTTTCTTT
1 -TTTTTTTCTTT
5155914 TTTT
1 TTTT
5155918 CTCGAATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 25 0.60
12 17 0.40
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:5157028 original size:16 final size:17
Alignment explanation
Indices: 5156999--5157039 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
5156989 ATTTGTAAAT
5156999 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
5157014 AAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
5157031 AAATTTTAT
1 AAATTTTAT
5157040 AAATATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:5157049 original size:18 final size:17
Alignment explanation
Indices: 5156999--5157050 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
5156989 ATTTGTAAAT
*
5156999 AAATTTTAT-TAATT-A
1 AAATTTTATAAAATTAA
**
5157014 AAATTTTATTTAATTAA
1 AAATTTTATAAAATTAA
5157031 AAATTTTATAAATATTAA
1 AAATTTTATAAA-ATTAA
5157049 AA
1 AA
5157051 CCTCAGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 9 0.28
16 5 0.16
17 11 0.34
18 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATTTTATAAAATTAA
Found at i:5157135 original size:18 final size:17
Alignment explanation
Indices: 5157102--5157152 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
5157092 AACTCAATAT
5157102 ATATAAAAAATAATATGCA
1 ATATAAAAAAT-ATATG-A
5157121 ATATAAAAAATATATGA
1 ATATAAAAAATATATGA
*
5157138 ATATATCAAAATATA
1 ATATA-AAAAATATA
5157153 AATAAACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.20
18 13 0.43
19 11 0.37
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (17 bp):
ATATAAAAAATATATGA
Found at i:5157353 original size:18 final size:19
Alignment explanation
Indices: 5157318--5157356 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5157308 ATTAAATTAT
* *
5157318 TAATATATAAATTTTTTTA
1 TAATATATAAAATATTTTA
5157337 TAATA-ATAAAATATTTTA
1 TAATATATAAAATATTTTA
5157355 TA
1 TA
5157357 TAAAAATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATATAAAATATTTTA
Found at i:5157353 original size:20 final size:19
Alignment explanation
Indices: 5157326--5157365 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5157316 ATTAATATAT
* *
5157326 AAATTTTTTTATAATAATA
1 AAATTTTTATATAAAAATA
5157345 AAATATTTTATATAAAAATA
1 AAAT-TTTTATATAAAAATA
5157365 A
1 A
5157366 CAAATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTTTATATAAAAATA
Found at i:5158776 original size:21 final size:20
Alignment explanation
Indices: 5158751--5158805 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
5158741 AAACAATATT
5158751 TATTTTAAAAAATTATAA-AG
1 TATTTTAAAAAATT-TAATAG
* *
5158771 TGATTTTTAAAAGTTTAATAG
1 T-ATTTTAAAAAATTTAATAG
5158792 TATATTTAAAAAAT
1 TAT-TTTAAAAAAT
5158806 AAATATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
TATTTTAAAAAATTTAATAG
Found at i:5163523 original size:16 final size:17
Alignment explanation
Indices: 5163458--5163550 Score: 58
Period size: 16 Copynumber: 5.8 Consensus size: 17
5163448 ATGTGTATAT
*
5163458 TTTTATCTTAT-TAATA
1 TTTTATATTATATAATA
*
5163474 TATTT-T-TTATATCATA
1 T-TTTATATTATATAATA
* *
5163490 -ATTATATT-TAAAATA
1 TTTTATATTATATAATA
5163505 TTTTATATTATATAA-A
1 TTTTATATTATATAATA
5163521 TTTTGATA-TAT-TAATA
1 TTTT-ATATTATATAATA
* *
5163537 ATTCATATTATATA
1 TTTTATATTATATA
5163551 GATTTTAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
14 2 0.03
15 16 0.27
16 29 0.49
17 12 0.20
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTTATATTATATAATA
Found at i:5170247 original size:22 final size:22
Alignment explanation
Indices: 5170170--5170247 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
5170160 TATATTTTTA
*
5170170 AAAAATAAAATGTACATATATAGT
1 AAAAATAATATGTAC--ATATAGT
* *
5170194 AAAAA-AATATGTATATATAAT
1 AAAAATAATATGTACATATAGT
** ** *
5170215 GGATCTGATATGTACATATAGT
1 AAAAATAATATGTACATATAGT
5170237 AAAAATAATAT
1 AAAAATAATAT
5170248 TTTTGATTAA
Statistics
Matches: 38, Mismatches: 15, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
21 7 0.18
22 19 0.50
23 7 0.18
24 5 0.13
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (22 bp):
AAAAATAATATGTACATATAGT
Found at i:5170372 original size:22 final size:23
Alignment explanation
Indices: 5170342--5170393 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
5170332 TTTAAATAAG
*
5170342 ATAACATGTACATTCAATAAAA-
1 ATAATATGTACATTCAATAAAAT
* * *
5170364 ATAATATGTATATTTAGTAAAAT
1 ATAATATGTACATTCAATAAAAT
5170387 ATAATAT
1 ATAATAT
5170394 ATATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (23 bp):
ATAATATGTACATTCAATAAAAT
Found at i:5170407 original size:19 final size:19
Alignment explanation
Indices: 5170385--5170434 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
5170375 ATTTAGTAAA
* *
5170385 ATATAATATATATATATAT
1 ATATAATAAATATATATAC
5170404 ATATAACGTAAATATATATAC
1 ATATAA--TAAATATATATAC
5170425 ATATAATAAA
1 ATATAATAAA
5170435 AATGAAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
21 17 0.63
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
ATATAATAAATATATATAC
Found at i:5172461 original size:25 final size:26
Alignment explanation
Indices: 5172440--5172493 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
5172430 GTGAATTTAA
5172440 AAATTAT-ATAA-AAT-TTAAAA-TT
1 AAATTATAATAATAATATTAAAATTT
*
5172462 AAATTATAATAATAATATTAAAA-TA
1 AAATTATAATAATAATATTAAAATTT
5172487 AAATTAT
1 AAATTAT
5172494 TTAAGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 7 0.25
23 4 0.14
24 3 0.11
25 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATTATAATAATAATATTAAAATTT
Found at i:5173317 original size:2 final size:2
Alignment explanation
Indices: 5173310--5173335 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5173300 TGGAGTAAAT
5173310 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
5173336 AGAAGTTGAA
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:5173989 original size:29 final size:29
Alignment explanation
Indices: 5173953--5174008 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
5173943 AAATCATCAA
* *
5173953 AAATAAAAATACAATGATATATTTCAATC
1 AAATAAAAATACAATAATAAATTTCAATC
*
5173982 AAATAAAAATGCAATAATAAATTTCAA
1 AAATAAAAATACAATAATAAATTTCAA
5174009 CACCATAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.29
Consensus pattern (29 bp):
AAATAAAAATACAATAATAAATTTCAATC
Found at i:5174431 original size:25 final size:25
Alignment explanation
Indices: 5174399--5174453 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
5174389 TTTATAATTT
5174399 TATAGATTTTTTTCTCAACAATTCC
1 TATAGATTTTTTTCTCAACAATTCC
*
5174424 TATAGATTTTTTTCTCAATAATTCC
1 TATAGATTTTTTTCTCAACAATTCC
5174449 TATAG
1 TATAG
5174454 TTTGAATCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (25 bp):
TATAGATTTTTTTCTCAACAATTCC
Found at i:5174865 original size:47 final size:48
Alignment explanation
Indices: 5174794--5174889 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 48
5174784 CTTTATAAAT
**
5174794 ATTTATTATTTAAAATAATAAAATATATATTGTTTGTTAATATT-AATA
1 ATTTATTATTTAAAATAATAAAATATATA-TGTTTAATAATATTCAATA
*
5174842 ATTTATTA-TTAAAAT-ATAAAAATATTTATGTTTAATAATATTCAATA
1 ATTTATTATTTAAAATAAT-AAAATATATATGTTTAATAATATTCAATA
5174889 A
1 A
5174890 ATATTTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 14 0.33
47 21 0.49
48 8 0.19
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (48 bp):
ATTTATTATTTAAAATAATAAAATATATATGTTTAATAATATTCAATA
Found at i:5174881 original size:24 final size:24
Alignment explanation
Indices: 5174790--5174896 Score: 69
Period size: 24 Copynumber: 4.4 Consensus size: 24
5174780 AATACTTTAT
*
5174790 AAATATTTATTATTTAAAATA-ATA
1 AAATATTTATTGTTTAAAATATA-A
* ** *
5174814 AAATATATATTGTTTGTTAATATTA
1 AAATATTTATTGTTT-AAAATATAA
* *
5174839 ATA-ATTTATT-ATTAAAATATAA
1 AAATATTTATTGTTTAAAATATAA
5174861 AAATATTTA-TGTTTAATAATATTCAA
1 AAATATTTATTGTTTAA-AATA-T-AA
5174887 TAAATATTTA
1 -AAATATTTA
5174897 AAATTAAATA
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
22 9 0.15
23 11 0.18
24 23 0.37
25 8 0.13
26 2 0.03
27 9 0.15
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.48
Consensus pattern (24 bp):
AAATATTTATTGTTTAAAATATAA
Found at i:5175666 original size:29 final size:29
Alignment explanation
Indices: 5175633--5175700 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
5175623 AATTAAATAA
*
5175633 AAATTTTAAA-AATAATACGAT-AAAAAATT
1 AAATTTAAAAGAATAATA--ATAAAAAAATT
*
5175662 AAATTTAAAAGAATTATAATAAAAAAATT
1 AAATTTAAAAGAATAATAATAAAAAAATT
*
5175691 AAAATTAAAA
1 AAATTTAAAA
5175701 TTTGAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 26 0.76
30 6 0.18
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (29 bp):
AAATTTAAAAGAATAATAATAAAAAAATT
Found at i:5175670 original size:14 final size:13
Alignment explanation
Indices: 5175653--5175700 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
5175643 AATAATACGA
5175653 TAAAAAATTAAATT
1 TAAAAAATTAAA-T
5175667 TAAAAGAATTATAAT
1 TAAAA-AATTA-AAT
*
5175682 AAAAAAATTAAAAT
1 TAAAAAATT-AAAT
5175696 TAAAA
1 TAAAA
5175701 TTTGAAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 16 0.55
15 11 0.38
16 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
TAAAAAATTAAAT
Found at i:5181223 original size:20 final size:19
Alignment explanation
Indices: 5181183--5181224 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5181173 TGATAAAATT
*
5181183 ATTTTAAATTAAAAATTAA
1 ATTTTAAATTAAAAATAAA
5181202 ATTTTAAAATTATAAAA-AAA
1 ATTTT-AAATTA-AAAATAAA
5181222 ATT
1 ATT
5181225 ATTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTTTAAATTAAAAATAAA
Found at i:5195680 original size:17 final size:16
Alignment explanation
Indices: 5195658--5195702 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
5195648 ATTTTTGTAT
*
5195658 TATTTATTTAGATTATA
1 TATTTATTTA-ATTAAA
5195675 TATTTAATTTAATTAAA
1 TATTT-ATTTAATTAAA
5195692 TATTTATTTAA
1 TATTTATTTAA
5195703 GACAAGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 15 0.58
18 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATTTATTTAATTAAA
Done.