Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 151 of 230
Found at i:44528152 original size:6 final size:6
Alignment explanation
Indices: 44528141--44528174 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
44528131 AAAAAATAAT
*
44528141 TTTAAA TTTAAA TTTAAT TTTAAA TTTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTT
44528175 TTTATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:44528160 original size:18 final size:19
Alignment explanation
Indices: 44528137--44528174 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
44528127 CCAAAAAAAA
44528137 TAATTTTAAA-TTTAAATT
1 TAATTTTAAATTTTAAATT
44528155 TAATTTTAAATTTTAAATT
1 TAATTTTAAATTTTAAATT
44528174 T
1 T
44528175 TTTATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAATTTTAAATTTTAAATT
Found at i:44528188 original size:7 final size:7
Alignment explanation
Indices: 44528138--44528175 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
44528128 CAAAAAAAAT
44528138 AATTTTA
1 AATTTTA
44528145 AA-TTTA
1 AATTTTA
44528151 AA-TTT-
1 AATTTTA
44528156 AATTTTA
1 AATTTTA
44528163 AATTTTA
1 AATTTTA
44528170 AATTTT
1 AATTTT
44528176 TTATTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 12 0.41
7 15 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:44531727 original size:29 final size:30
Alignment explanation
Indices: 44531654--44531728 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
44531644 AAACTACACC
* * * *
44531654 ATTGGTCACACAACTATGGATTTTCTTTTA
1 ATTGGTCACTCAACTATGAATTTTCATTAA
* *
44531684 TTTGGCCACTCAACTATGAATTTT-ATTAA
1 ATTGGTCACTCAACTATGAATTTTCATTAA
44531713 ATTGGTCACTCAACTA
1 ATTGGTCACTCAACTA
44531729 ATTGGATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (30 bp):
ATTGGTCACTCAACTATGAATTTTCATTAA
Found at i:44535127 original size:43 final size:43
Alignment explanation
Indices: 44535080--44535160 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
44535070 ATTCTAGAAA
* * *
44535080 AAAAAAGAATTTAAAAA-AGGAGAAGATAATCTTGGGTTGTTG
1 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTTGTTG
44535122 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTT
1 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTT
44535161 ATTGGATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 17 0.49
43 18 0.51
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.22
Consensus pattern (43 bp):
AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTTGTTG
Found at i:44539977 original size:6 final size:6
Alignment explanation
Indices: 44539962--44540044 Score: 50
Period size: 6 Copynumber: 14.5 Consensus size: 6
44539952 TATAATTCTG
* * ** * *
44539962 AAAAAT -AAAAT -AAAA- ACAAAT AACAAT AAAAAT AAATGT ACAACT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
44540007 AAAAAT AAAAAG AAAAAT --AAAT AAAACAT AAAACT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAA
44540045 TAGACTCAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
4 4 0.07
5 12 0.21
6 36 0.62
7 6 0.10
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:44539991 original size:16 final size:15
Alignment explanation
Indices: 44539964--44539998 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
44539954 TAATTCTGAA
44539964 AAATAAAATAAAAAC
1 AAATAAAATAAAAAC
*
44539979 AAATAACAATAAAAAT
1 AAATAA-AATAAAAAC
44539995 AAAT
1 AAAT
44539999 GTACAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:44540013 original size:24 final size:22
Alignment explanation
Indices: 44539962--44540044 Score: 78
Period size: 24 Copynumber: 3.7 Consensus size: 22
44539952 TATAATTCTG
44539962 AAAAAT-AAAATAAAAACAAAT
1 AAAAATAAAAATAAAAACAAAT
* * *
44539983 AACAATAAAAATAAATGTACAACT
1 AAAAATAAAAATAAA--AACAAAT
* *
44540007 AAAAATAAAAAGAAAAATAAAT
1 AAAAATAAAAATAAAAACAAAT
*
44540029 AAAACATAAAACTAAA
1 AAAA-ATAAAAATAAA
44540045 TAGACTCAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.10
22 16 0.33
23 9 0.19
24 18 0.38
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAATAAAAACAAAT
Found at i:44540030 original size:16 final size:17
Alignment explanation
Indices: 44540009--44540046 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
44539999 GTACAACTAA
44540009 AAATAAAA-AGAAAAAT
1 AAATAAAACAGAAAAAT
* *
44540025 AAATAAAACATAAAACT
1 AAATAAAACAGAAAAAT
44540042 AAATA
1 AAATA
44540047 GACTCAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAAAACAGAAAAAT
Found at i:44547972 original size:72 final size:72
Alignment explanation
Indices: 44547890--44548033 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
44547880 AAGGAAATTT
* * *
44547890 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTATCAAATTGTTCATCCATGTGGTCTTTCTTCA
1 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
44547955 ACTTTGC
66 ACTTTGC
*
44547962 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCGTCCATGCGATCTTTCTTCA
1 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
44548027 ACTTTGC
66 ACTTTGC
44548034 CGGATATGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (72 bp):
AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
ACTTTGC
Found at i:44548137 original size:27 final size:26
Alignment explanation
Indices: 44548080--44548142 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
44548070 TGTTGTTTGA
44548080 ATTTTCTCATTTTTTGCCACCTCATC
1 ATTTTCTCATTTTTTGCCACCTCATC
44548106 ATTTTCTCATTTTTTGCCACCTCATC
1 ATTTTCTCATTTTTTGCCACCTCATC
44548132 ATTTTTCTCAT
1 A-TTTTCTCAT
44548143 CAGTTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.75
27 9 0.25
ACGTcount: A:0.16, C:0.29, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTTTCTCATTTTTTGCCACCTCATC
Found at i:44554286 original size:22 final size:24
Alignment explanation
Indices: 44554260--44554306 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
44554250 TAGACATAAA
*
44554260 TTTGAAA-AA-AATATTTTTGAGG
1 TTTGAAAGAAGAAAATTTTTGAGG
44554282 TTTGAAAGAAGTAAAATTTTTGAGG
1 TTTGAAAGAAG-AAAATTTTTGAGG
44554307 GAAAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 2 0.10
25 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGAAAGAAGAAAATTTTTGAGG
Found at i:44554315 original size:20 final size:20
Alignment explanation
Indices: 44554290--44554338 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
44554280 GGTTTGAAAG
*
44554290 AAGTAAAA-TTTTTGAGGGAA
1 AAGTAAAAGTTTTAGA-GGAA
*
44554310 AAGTAAACGTTTTAGAGGAA
1 AAGTAAAAGTTTTAGAGGAA
44554330 AAGTAAAAG
1 AAGTAAAAG
44554339 AAAAAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (20 bp):
AAGTAAAAGTTTTAGAGGAA
Found at i:44555107 original size:18 final size:20
Alignment explanation
Indices: 44555060--44555107 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
44555050 CTCTAACTTA
44555060 ATTTAAATT-TAATTAAATT
1 ATTTAAATTATAATTAAATT
*
44555079 ACTTAAA--ATAATT-AATT
1 ATTTAAATTATAATTAAATT
44555096 -TTTAAATTATAA
1 ATTTAAATTATAA
44555108 ACAAATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.21
17 4 0.17
18 9 0.38
19 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAATTATAATTAAATT
Found at i:44555294 original size:21 final size:20
Alignment explanation
Indices: 44555268--44555307 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
44555258 ATTTTATCAT
44555268 GAACCTCAAACCTAGAACCCC
1 GAACCTCAAA-CTAGAACCCC
* *
44555289 GAACCTTAAACTCGAACCC
1 GAACCTCAAACTAGAACCC
44555308 TGAATCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (20 bp):
GAACCTCAAACTAGAACCCC
Found at i:44555307 original size:20 final size:21
Alignment explanation
Indices: 44555268--44555318 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
44555258 ATTTTATCAT
*
44555268 GAACCTCAAACCTAGAACCCC
1 GAACCTTAAACCTAGAACCCC
* *
44555289 GAACCTTAAA-CTCGAACCCT
1 GAACCTTAAACCTAGAACCCC
*
44555309 GAATCTTAAA
1 GAACCTTAAA
44555319 TCTTAAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (21 bp):
GAACCTTAAACCTAGAACCCC
Found at i:44555464 original size:35 final size:35
Alignment explanation
Indices: 44555361--44555465 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 35
44555351 GAGTTCGGAA
* *
44555361 TTTAAGGTTTAAGGTTCAA--GTTTGGGTTTTGGG
1 TTTAGGGTTTAAGGTTCAAGGGTTTGGGTTTTGAG
* * *
44555394 TTTAGGGTTCAA-GTTCAAGGGTTCGGGATTATGAG
1 TTTAGGGTTTAAGGTTCAAGGGTTTGGG-TTTTGAG
*
44555429 TTT-GGGTTTAAGGTTTAAGGGTTTGGAGTTTTGAG
1 TTTAGGGTTTAAGGTTCAAGGGTTTGG-GTTTTGAG
44555464 TT
1 TT
44555466 ATGAGTTTGG
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
32 6 0.10
33 10 0.17
34 13 0.22
35 28 0.48
36 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.34, T:0.43
Consensus pattern (35 bp):
TTTAGGGTTTAAGGTTCAAGGGTTTGGGTTTTGAG
Found at i:44563791 original size:15 final size:15
Alignment explanation
Indices: 44563767--44563799 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44563757 AACTTAATCT
44563767 ATATAAGTTATAATA
1 ATATAAGTTATAATA
*
44563782 ATATATGTTATAATA
1 ATATAAGTTATAATA
44563797 ATA
1 ATA
44563800 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
ATATAAGTTATAATA
Found at i:44564629 original size:16 final size:16
Alignment explanation
Indices: 44564566--44564631 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
44564556 GATTGATATT
*
44564566 GAAATGGAAAAGATGA
1 GAAATGGAAAATATGA
44564582 GAAAT-G--AATATGA
1 GAAATGGAAAATATGA
*
44564595 G--ATGAGAAAAATAT-T
1 GAAATG-G-AAAATATGA
44564610 GAAATGGAAAATATGA
1 GAAATGGAAAATATGA
44564626 GAAATG
1 GAAATG
44564632 ATATATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
11 2 0.05
13 8 0.21
15 9 0.23
16 17 0.44
17 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.20
Consensus pattern (16 bp):
GAAATGGAAAATATGA
Found at i:44565889 original size:49 final size:48
Alignment explanation
Indices: 44565808--44565903 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 48
44565798 TCTAAAAGGG
* *
44565808 ATAAATAGTGATAAGATGTAGACAATGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGATGTAGACAATGGAAGACGAAGTTTAGAAATGT
*
44565856 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACGAAGTTTAGAAATG
1 ATAAATAGTGATAAGA-TGTAGACAATGGAAGACGAAGTTTAGAAATG
44565904 CATAGCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 16 0.36
49 28 0.64
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (48 bp):
ATAAATAGTGATAAGATGTAGACAATGGAAGACGAAGTTTAGAAATGT
Found at i:44571234 original size:15 final size:16
Alignment explanation
Indices: 44571168--44571231 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 16
44571158 ATGATATGTG
44571168 TATATG-TATAATATA
1 TATATGTTATAATATA
44571183 TATTATGTTAGCTTAATATA
1 TA-TATGTTA---TAATATA
*
44571203 TATAAGTTATAATA-A
1 TATATGTTATAATATA
44571218 TATATGTTATAATA
1 TATATGTTATAATA
44571232 ATAAAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 16 0.38
16 9 0.21
17 2 0.05
19 6 0.14
20 9 0.21
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (16 bp):
TATATGTTATAATATA
Found at i:44572044 original size:43 final size:43
Alignment explanation
Indices: 44571994--44572079 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
44571984 TATGTGATTG
*
44571994 ATATTGAAATGGCAAAGATGAGAAATGAATATGTGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
* *
44572037 ATATTGAAATGGCAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
44572080 TGAGATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (43 bp):
ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:44574186 original size:20 final size:20
Alignment explanation
Indices: 44574161--44574199 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44574151 TGGAGCAGGA
*
44574161 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
44574181 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
44574200 AATTATTGAT
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:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:44576198 original size:23 final size:23
Alignment explanation
Indices: 44576172--44576226 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
44576162 GACTAAGCGC
44576172 GCAAGTGATAATGGCACTATAGT
1 GCAAGTGATAATGGCACTATAGT
* * *
44576195 GCAAGTGTTAGTGGCACTTTAGT
1 GCAAGTGATAATGGCACTATAGT
44576218 GCAAAGTGA
1 GC-AAGTGA
44576227 CATCCACATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (23 bp):
GCAAGTGATAATGGCACTATAGT
Found at i:44576263 original size:24 final size:24
Alignment explanation
Indices: 44576216--44576267 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44576206 TGGCACTTTA
*
44576216 GTGCAAAGTGACATCCACATGTCT
1 GTGCAAAGTGACATCCACAAGTCT
***
44576240 GTGCAAAGTGACATTTGCAAGTCT
1 GTGCAAAGTGACATCCACAAGTCT
44576264 GTGC
1 GTGC
44576268 GAAGAATAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (24 bp):
GTGCAAAGTGACATCCACAAGTCT
Found at i:44579245 original size:16 final size:16
Alignment explanation
Indices: 44579209--44579241 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
44579199 GTCAGATCCC
44579209 TATTTATTCAATTTTA
1 TATTTATTCAATTTTA
44579225 TATTTATT--ATTTTA
1 TATTTATTCAATTTTA
44579239 TAT
1 TAT
44579242 ATTTGAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATTCAATTTTA
Found at i:44581621 original size:21 final size:21
Alignment explanation
Indices: 44581579--44581622 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
44581569 CTCCTGTTGG
* *
44581579 TTAGGGTTTTGGGATTTTGTT
1 TTAGGGTTTAGGGATTTGGTT
44581600 TTAGGGTTTAGGG-TTATGGTT
1 TTAGGGTTTAGGGATT-TGGTT
44581621 TT
1 TT
44581623 GTGGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.11, C:0.00, G:0.34, T:0.55
Consensus pattern (21 bp):
TTAGGGTTTAGGGATTTGGTT
Found at i:44582071 original size:125 final size:126
Alignment explanation
Indices: 44581841--44582257 Score: 622
Period size: 126 Copynumber: 3.3 Consensus size: 126
44581831 TAATTTAAAA
* * * * *
44581841 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTTGAGAAGACATTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTT
* *
44581906 TTGAGCAAATAGTGTAAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAG
* * *
44581967 AAGCTTCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAA-AATTTCAAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTT
*
44582031 CTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTTAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAG
* * * * * *
44582092 AAGCTCCCACGTGTATGCACTTTTGCTATAATAGCTCCTGAAAAAATAATTTCGAGCAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTT
* * *
44582157 CTGAGAAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGAT-AGCAAAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTG-TCAGCAAAAGTACTGAAAG
*
44582218 AAGCTCCCACGAGGACGCGCTTTTGCTACAGTAGCTCCTG
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
44582258 TTTGGTCTGA
Statistics
Matches: 262, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
125 112 0.43
126 149 0.57
127 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTT
CTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAG
Found at i:44585469 original size:116 final size:116
Alignment explanation
Indices: 44585259--44585469 Score: 287
Period size: 116 Copynumber: 1.8 Consensus size: 116
44585249 GTATTATTTA
* * * *
44585259 TATTTTTTTAAATCAAATAATATGGAAATATTTAGAATATTGACTTATTTAAAAGAAAATCTATT
1 TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATCTATT
* * *
44585324 TTATTAAAAATATTAAAGTGAATTACAATTACTTTATTCAAAACAATGTTT
66 ATATTAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAACAATGTTT
* ** ** *
44585375 TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTGTTATTTAAAAGAATTTTTATT
1 TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATCTATT
* *
44585440 ATATTAAAAATGTAAAAGTAAATTTCAATT
66 ATATTAAAAATATAAAAGTAAATTACAATT
44585470 TTATTACATG
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
116 80 1.00
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (116 bp):
TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATCTATT
ATATTAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAACAATGTTT
Found at i:44585672 original size:21 final size:21
Alignment explanation
Indices: 44585648--44585688 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
44585638 CCAACTTTCG
* *
44585648 GCGGGGGTTGTGGTTGCTCCA
1 GCGGGGATTGTGGTTCCTCCA
*
44585669 GCGGGGATTTTGGTTCCTCC
1 GCGGGGATTGTGGTTCCTCC
44585689 GGTAGGGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.22, G:0.41, T:0.32
Consensus pattern (21 bp):
GCGGGGATTGTGGTTCCTCCA
Found at i:44585971 original size:18 final size:18
Alignment explanation
Indices: 44585945--44585987 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
44585935 GATTAGAAAA
* * *
44585945 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
44585963 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
44585981 AGGATAC
1 AGGATAC
44585988 GTGCTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:44586611 original size:7 final size:7
Alignment explanation
Indices: 44586599--44586623 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44586589 TATTAGTTAT
44586599 ATACATA
1 ATACATA
44586606 ATACATA
1 ATACATA
44586613 ATACATA
1 ATACATA
44586620 ATAC
1 ATAC
44586624 TAAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:44586629 original size:7 final size:7
Alignment explanation
Indices: 44586619--44586644 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44586609 CATAATACAT
44586619 AATACTA
1 AATACTA
44586626 AATACTA
1 AATACTA
44586633 AATACTA
1 AATACTA
44586640 AATAC
1 AATAC
44586645 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:44586629 original size:14 final size:14
Alignment explanation
Indices: 44586599--44586644 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
44586589 TATTAGTTAT
44586599 ATACATAATAC-ATA
1 ATACATAATACTA-A
44586613 ATACATAATACTAA
1 ATACATAATACTAA
44586627 ATAC-TAAATACTAA
1 ATACAT-AATACTAA
44586641 ATAC
1 ATAC
44586645 CAATCGACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.03
14 28 0.93
15 1 0.03
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (14 bp):
ATACATAATACTAA
Found at i:44587864 original size:11 final size:11
Alignment explanation
Indices: 44587850--44587886 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
44587840 AGCTTTTTTA
44587850 AGAGGAATTTG
1 AGAGGAATTTG
*
44587861 AGAGGAAATTG
1 AGAGGAATTTG
*
44587872 AAAGGAATTTG
1 AGAGGAATTTG
44587883 AGAG
1 AGAG
44587887 AATATTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:44587877 original size:22 final size:24
Alignment explanation
Indices: 44587852--44587908 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
44587842 CTTTTTTAAG
44587852 AGGAATTTGAGAGGAA-ATT-GAA
1 AGGAATTTGAGAGGAATATTGGAA
44587874 AGGAATTTGAGA-GAATATTGGAA
1 AGGAATTTGAGAGGAATATTGGAA
*
44587897 A-GAAATTGAGAG
1 AGGAATTTGAGAG
44587909 AAAGGATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 3 0.10
22 24 0.77
23 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.23
Consensus pattern (24 bp):
AGGAATTTGAGAGGAATATTGGAA
Found at i:44589120 original size:12 final size:12
Alignment explanation
Indices: 44589099--44589132 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
44589089 TATATATTTT
*
44589099 AAAATTATATAA
1 AAAATAATATAA
44589111 AAAATAATATAA
1 AAAATAATATAA
*
44589123 AAATTAATAT
1 AAAATAATAT
44589133 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:44593287 original size:30 final size:29
Alignment explanation
Indices: 44593252--44593309 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
44593242 CCAAATTCTC
44593252 CCCCAAACGTTTT-TTCCCCCTCTGCTGGTT
1 CCCCAAA--TTTTCTTCCCCCTCTGCTGGTT
*
44593282 CCCCAAATTTTCTTTCCCCTCTGCTGGT
1 CCCCAAATTTTCTTCCCCCTCTGCTGGT
44593310 GAAATTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 15 0.58
30 7 0.27
ACGTcount: A:0.10, C:0.40, G:0.12, T:0.38
Consensus pattern (29 bp):
CCCCAAATTTTCTTCCCCCTCTGCTGGTT
Found at i:44594728 original size:50 final size:50
Alignment explanation
Indices: 44594653--44594948 Score: 332
Period size: 50 Copynumber: 5.9 Consensus size: 50
44594643 TTTATACACG
* *
44594653 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
* * *
44594703 TAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-A
* * *
44594754 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
* * * *
44594804 TAGGTCACATGTGTAGTACTATGTGTAGGCTACTATGCGTACTGG-ATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-A
* * * * *
44594855 TCGATCAC--GTGTAGTACTATGTGCAGGCTACTACGTGTATCAG-ATGAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATG-A
* *
44594903 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
44594949 GTATCATTTA
Statistics
Matches: 203, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.00
49 42 0.21
50 80 0.39
51 76 0.37
52 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
Found at i:44594834 original size:101 final size:101
Alignment explanation
Indices: 44594657--44594940 Score: 457
Period size: 101 Copynumber: 2.8 Consensus size: 101
44594647 TACACGTAGG
*
44594657 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCACATGTGTAGTAC
44594722 TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
*
44594758 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGGTCACATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCACATGTGTAGTAC
* * *
44594823 TATGTGTAGGCTACTATGCGTACTGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
* * *
44594859 TCAC--GTGTAGTACTATGTGCAGGCTACTACGTGTATCAG-ATGAAAATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA-GGTCACATGTGTAGT
44594921 ACTATGTGCAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
44594941 TGAACCGGGT
Statistics
Matches: 171, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
98 3 0.02
99 34 0.20
100 34 0.20
101 100 0.58
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
Found at i:44602370 original size:23 final size:20
Alignment explanation
Indices: 44602344--44602382 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44602334 GAAAGACCAA
44602344 AAAAACAATTTATTAAAAACC
1 AAAAA-AATTTATTAAAAACC
*
44602365 ATAAAAATTTATTAAAAA
1 AAAAAAATTTATTAAAAA
44602383 TAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAATTTATTAAAAACC
Found at i:44602391 original size:22 final size:21
Alignment explanation
Indices: 44602350--44602406 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
44602340 CCAAAAAAAC
**
44602350 AATTTATTAAAAA-CCATAAA
1 AATTTATTAAAAATAAATAAA
44602370 AATTTATTAAAAATAAATTAAA
1 AATTTATTAAAAATAAA-TAAA
*
44602392 TATTT-TATAAAAATA
1 AATTTAT-TAAAAATA
44602407 TTTTTCTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
22 16 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTTATTAAAAATAAATAAA
Found at i:44602630 original size:13 final size:13
Alignment explanation
Indices: 44602612--44602636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44602602 AAATATTTAA
44602612 TTTTTTTATAAAT
1 TTTTTTTATAAAT
44602625 TTTTTTTATAAA
1 TTTTTTTATAAA
44602637 AATGAACCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTTATAAAT
Found at i:44603306 original size:20 final size:20
Alignment explanation
Indices: 44603273--44603310 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
44603263 AATGTGAATA
44603273 ATTTTTTTCAAAATATTTATG
1 ATTTTTTTCAAAAT-TTTATG
*
44603294 ATTTTTTT-GAAATTTTA
1 ATTTTTTTCAAAATTTTA
44603311 GTAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 4 0.25
21 8 0.50
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTTTTCAAAATTTTATG
Found at i:44603339 original size:29 final size:30
Alignment explanation
Indices: 44603283--44603337 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
44603273 ATTTTTTTCA
44603283 AAATATTTATGATTTTTTTGAAATTTTAGT
1 AAATATTTATGATTTTTTTGAAATTTTAGT
44603313 AAAT-TTTATG-TATTTTTT-AAATTTT
1 AAATATTTATGAT-TTTTTTGAAATTTT
44603338 TATGAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 8 0.33
29 12 0.50
30 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (30 bp):
AAATATTTATGATTTTTTTGAAATTTTAGT
Found at i:44608344 original size:11 final size:11
Alignment explanation
Indices: 44608313--44608344 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
44608303 CGGGTATTTG
44608313 ACTAAAATAAT
1 ACTAAAATAAT
44608324 AC-AAAA-AAT
1 ACTAAAATAAT
44608333 ACTAAAATAAT
1 ACTAAAATAAT
44608344 A
1 A
44608345 TACAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 5 0.26
10 8 0.42
11 6 0.32
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (11 bp):
ACTAAAATAAT
Found at i:44609856 original size:16 final size:18
Alignment explanation
Indices: 44609825--44609865 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
44609815 TATTATTATT
44609825 ATTTTATAACATACATAC
1 ATTTTATAACATACATAC
* * *
44609843 ATTTTATAATACATATAC
1 ATTTTATAACATACATAC
44609861 ATTTT
1 ATTTT
44609866 TTTTCATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTATAACATACATAC
Found at i:44611334 original size:158 final size:151
Alignment explanation
Indices: 44611020--44611543 Score: 718
Period size: 152 Copynumber: 3.4 Consensus size: 151
44611010 GGTTTCGACA
* *
44611020 AATAAAATTAGAAAATAGTATATTTTTTT-AAAGTAATAAAATCCGGGAAAAAAATACGAACAAA
1 AATAAAA-TAGAAAATAATATATTTTTTTAAAAGTAATAAAATCC-GAAAAAAAATACGAACAAA
* * *
44611084 TGACCGAAATAATG-GTTTTTTTAAATTTATTTAAAAAACACAGTAAATTAAAACATTTCAAACA
64 TGGCCGAAATAA-GAGTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACA
*
44611148 TAATTTACTAAAATAATGTAAAAT
128 TAATGTACTAAAATAATGTAAAAT
* *
44611172 AATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGAAAAAAAATACGAACAA
1 AATAAAATA-GAAAATAATATATTTTT-TTAAAAGTAATAAAATCC-GAAAAAAAATACGAACAA
** *
44611237 ATGGCCGAAATAAGAGTTTTTTTAAAAAAATTTAAATAAAAAACACACTAAATGAATACATTTCA
63 ATGGCCGAAATAAGAGTTTTTTT----AAATTTATTTAAAAAACACACTAAATTAATACATTTCA
44611302 AACATAATGTACTAAAATAATGTAAAAT
124 AACATAATGTACTAAAATAATGTAAAAT
* *
44611330 AATAAAATTAGAAAATAGTATA-TTTTTTAAAAGTAATAAAATCCGAGGAAAAAATACGAACAAA
1 AATAAAA-TAGAAAATAATATATTTTTTTAAAAGTAATAAAATCCGA-AAAAAAATACGAACAAA
* * *
44611394 GGGCTGAAATAA-AGATTTTTTTTAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACA
64 TGGCCGAAATAAGAG-TTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACA
*
44611458 CAATGTACTAAAATAATGTAAAAT
128 TAATGTACTAAAATAATGTAAAAT
* *
44611482 AATAAATTAGAAAAT-A-GTATTTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAT
1 AATAAAATAGAAAATAATATATTTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAT
44611544 AGTTGAAATA
Statistics
Matches: 334, Mismatches: 26, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
149 18 0.05
150 24 0.07
151 10 0.03
152 89 0.27
153 3 0.01
154 53 0.16
155 4 0.01
156 50 0.15
157 4 0.01
158 77 0.23
159 2 0.01
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (151 bp):
AATAAAATAGAAAATAATATATTTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAATG
GCCGAAATAAGAGTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAA
TGTACTAAAATAATGTAAAAT
Found at i:44611701 original size:18 final size:19
Alignment explanation
Indices: 44611670--44611708 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
44611660 CTTTTTTGTA
*
44611670 TATTATTTTGGTATTTTTT
1 TATTATTTTGGTATTATTT
*
44611689 TATT-TTTTTGTATTATTT
1 TATTATTTTGGTATTATTT
44611707 TA
1 TA
44611709 GTAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (19 bp):
TATTATTTTGGTATTATTT
Found at i:44612014 original size:10 final size:10
Alignment explanation
Indices: 44611985--44612094 Score: 64
Period size: 10 Copynumber: 11.2 Consensus size: 10
44611975 TTCATTCTAG
44611985 AATTATTAAA
1 AATTATTAAA
* *
44611995 AA-AATAAAA
1 AATTATTAAA
44612004 AATTATTAAA
1 AATTATTAAA
*
44612014 AATCATTAAA
1 AATTATTAAA
** *
44612024 GTTTACTAAA
1 AATTATTAAA
*
44612034 ATTTA-TAAA
1 AATTATTAAA
* *
44612043 ATTTATTAGA
1 AATTATTAAA
*
44612053 AATTATTCCAA
1 AATTATT-AAA
*
44612064 AATCA-TAAA
1 AATTATTAAA
* *
44612073 ATTTATAAAA
1 AATTATTAAA
*
44612083 AAATATTAAA
1 AATTATTAAA
44612093 AA
1 AA
44612095 CCATAAAAAT
Statistics
Matches: 74, Mismatches: 22, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
9 21 0.28
10 48 0.65
11 5 0.07
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (10 bp):
AATTATTAAA
Found at i:44612407 original size:19 final size:20
Alignment explanation
Indices: 44612354--44612407 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
44612344 ATTTTACAAA
*
44612354 TTTTATAAAATTTTATGATT
1 TTTTATAAAATTTAATGATT
* **
44612374 TTTAATTAATTTTTAAT-ATT
1 TTTTA-TAAAATTTAATGATT
44612394 TTTTATAAAATTTA
1 TTTTATAAAATTTA
44612408 TTTTTATTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
19 7 0.27
20 11 0.42
21 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTATAAAATTTAATGATT
Found at i:44612415 original size:22 final size:21
Alignment explanation
Indices: 44612354--44612446 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 21
44612344 ATTTTACAAA
* *
44612354 TTTTATAA-AATTTTATGA-T
1 TTTTATAATAATTTTTTTATT
* *
44612373 TTTTA-ATTAATTTTTAATATT
1 TTTTATAATAATTTTT-TTATT
44612394 TTTTATAA-AATTTATTTTTATT
1 TTTTATAATAA-TT-TTTTTATT
*
44612416 TAGTTT-TAATGATTTTTTTATT
1 T--TTTATAATAATTTTTTTATT
44612438 TTTTATAAT
1 TTTTATAAT
44612447 TCCATAATGT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
18 1 0.02
19 11 0.19
20 4 0.07
21 12 0.21
22 17 0.30
23 8 0.14
24 4 0.07
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTTATAATAATTTTTTTATT
Found at i:44612919 original size:86 final size:84
Alignment explanation
Indices: 44612770--44612962 Score: 235
Period size: 86 Copynumber: 2.2 Consensus size: 84
44612760 CTTTAAGAAA
* * *
44612770 AAAAAACAATTAAGCACCTCT-TTTTTCTTTACACTTAATTGAGCACTTGAACTTTTAAAATGCA
1 AAAAAACAATTAAGC-CC-CTAATTTT-TTT--ACTCAATTGAGCACTTGAACTTTCAAAATGCA
* *** *
44612834 TTAAAAGGGCCCTCAAACTTTTTC
61 TCAAAAACACCCTCAAAATTTTTC
*
44612858 AAAAAAAGCAATTAAGCCCCTAATTTTTTTACTCAATTGGGCACTTGAACTTTCAAAATGCATCA
1 -AAAAAA-CAATTAAGCCCCTAATTTTTTTACTCAATTGAGCACTTGAACTTTCAAAATGCATCA
44612923 AAAACACCCTCAAAATTTTTC
64 AAAACACCCTCAAAATTTTTC
44612944 AAAAAACAATTAAGCCCCT
1 AAAAAACAATTAAGCCCCT
44612963 GTTCTTATTA
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
84 13 0.14
85 6 0.06
86 48 0.52
88 5 0.05
89 12 0.13
90 9 0.10
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (84 bp):
AAAAAACAATTAAGCCCCTAATTTTTTTACTCAATTGAGCACTTGAACTTTCAAAATGCATCAAA
AACACCCTCAAAATTTTTC
Found at i:44616771 original size:10 final size:10
Alignment explanation
Indices: 44616756--44616783 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
44616746 TTTTTTTTTA
44616756 AATTAGTATT
1 AATTAGTATT
44616766 AATTAGTATT
1 AATTAGTATT
44616776 AATTAGTA
1 AATTAGTA
44616784 GGGTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (10 bp):
AATTAGTATT
Found at i:44618808 original size:29 final size:27
Alignment explanation
Indices: 44618769--44618823 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
44618759 AATTTTTAAA
44618769 AATTCTCATTAAACATTTTCAAAATTTTC
1 AATTCTCATTAAAC-TTTT-AAAATTTTC
*
44618798 AATTTTCATTAAACTTTTAAAATTTT
1 AATTCTCATTAAACTTTTAAAATTTT
44618824 TGAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.32
28 4 0.16
29 13 0.52
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTCTCATTAAACTTTTAAAATTTTC
Found at i:44619144 original size:13 final size:12
Alignment explanation
Indices: 44619126--44619175 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
44619116 TCTTCATTGC
44619126 TTTTGAAAAGTGA
1 TTTTGAAAAGT-A
44619139 TTTTGAAAAGTA
1 TTTTGAAAAGTA
* *
44619151 TTGTAGAAAAATA
1 TT-TTGAAAAGTA
44619164 CTTTTGAAAAGT
1 -TTTTGAAAAGT
44619176 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 3 0.10
13 26 0.84
14 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (12 bp):
TTTTGAAAAGTA
Found at i:44624601 original size:3 final size:3
Alignment explanation
Indices: 44624593--44624617 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44624583 TCAATTGGCA
44624593 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
44624618 AAGAACTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:44627320 original size:34 final size:34
Alignment explanation
Indices: 44627269--44627338 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
44627259 CAGCTTGATG
*
44627269 TGTTTAGGTAGTCGAATGACTTGTTTAGTTAGCT
1 TGTTTAGATAGTCGAATGACTTGTTTAGTTAGCT
*
44627303 TGTTTAGATAGTTGAATGACTTGTTTAGTTAGCT
1 TGTTTAGATAGTCGAATGACTTGTTTAGTTAGCT
44627337 TG
1 TG
44627339 CTGACAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.46
Consensus pattern (34 bp):
TGTTTAGATAGTCGAATGACTTGTTTAGTTAGCT
Found at i:44630722 original size:22 final size:22
Alignment explanation
Indices: 44630694--44630741 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
44630684 ATCGGATCCA
*
44630694 ACTCCACCTCCACCGA-TTCACG
1 ACTCCACCTCCA-CGACTCCACG
*
44630716 ACTCCACGTCCACGACTCCACG
1 ACTCCACCTCCACGACTCCACG
44630738 ACTC
1 ACTC
44630742 TACGGTGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.23, C:0.50, G:0.10, T:0.17
Consensus pattern (22 bp):
ACTCCACCTCCACGACTCCACG
Found at i:44631816 original size:13 final size:13
Alignment explanation
Indices: 44631793--44631884 Score: 123
Period size: 13 Copynumber: 7.0 Consensus size: 13
44631783 TGAGTTCGGT
44631793 TATATTGTTTTAA
1 TATATTGTTTTAA
44631806 TATACTT-TTTTAA
1 TATA-TTGTTTTAA
44631819 TATATTGTTTTAA
1 TATATTGTTTTAA
*
44631832 TATATTGTTATAA
1 TATATTGTTTTAA
* *
44631845 TATACTGTTATAA
1 TATATTGTTTTAA
44631858 TTATATTGTTTTAA
1 -TATATTGTTTTAA
*
44631872 TATAATGTTTTAA
1 TATATTGTTTTAA
44631885 CTTTTAAATT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
12 2 0.03
13 56 0.79
14 13 0.18
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.58
Consensus pattern (13 bp):
TATATTGTTTTAA
Found at i:44631925 original size:66 final size:66
Alignment explanation
Indices: 44631792--44631925 Score: 150
Period size: 66 Copynumber: 2.0 Consensus size: 66
44631782 ATGAGTTCGG
* * * *
44631792 TTATATTGTTTTAATATACTTTTTTAATATATTGTTTTAATATATTGTTATAATATACTGTTATA
1 TTATATTGTTTTAATATAATGTTTTAATATATTATTTTAATATATTGTTATAATATACTATTATA
44631857 A
66 A
* *
44631858 TTATATTGTTTTAATATAATGTTTTAACT-T-TTAAATTTTAGTATGTTGTTATAAATATAC-AT
1 TTATATTGTTTTAATATAATGTTTTAA-TATATT--ATTTTAATATATTGTTAT-AATATACTAT
44631920 T-TAA
62 TATAA
44631924 TT
1 TT
44631926 TGTAACACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
65 2 0.03
66 31 0.53
67 18 0.31
68 7 0.12
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.57
Consensus pattern (66 bp):
TTATATTGTTTTAATATAATGTTTTAATATATTATTTTAATATATTGTTATAATATACTATTATA
A
Found at i:44631940 original size:15 final size:15
Alignment explanation
Indices: 44631920--44631953 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
44631910 AAATATACAT
*
44631920 TTAATTTGTAACACA
1 TTAATTTCTAACACA
44631935 TTAATTTCTAACACA
1 TTAATTTCTAACACA
44631950 TTAA
1 TTAA
44631954 AAAAAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAATTTCTAACACA
Found at i:44634557 original size:26 final size:26
Alignment explanation
Indices: 44634528--44634584 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
44634518 AACAGGTATC
*
44634528 AGGATAATGATGATGATGGAAAACAT
1 AGGACAATGATGATGATGGAAAACAT
44634554 AGGACAATGATGATGATGGAAAACAT
1 AGGACAATGATGATGATGGAAAACAT
44634580 AGGAC
1 AGGAC
44634585 TACTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.19
Consensus pattern (26 bp):
AGGACAATGATGATGATGGAAAACAT
Found at i:44634918 original size:5 final size:5
Alignment explanation
Indices: 44634908--44634935 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
44634898 AGAATGAAAG
44634908 AAAAC AAAAC AAAAC AAAAC AAAAC AAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAA
44634936 CATAATGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:44636269 original size:4 final size:4
Alignment explanation
Indices: 44636255--44636297 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
44636245 AAAAAATGGG
*
44636255 GAAA AAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
44636298 GGAAGGAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:44637936 original size:52 final size:52
Alignment explanation
Indices: 44637876--44637974 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
44637866 ACAAATCCTA
* *
44637876 TCTCAA-TTTCATTCCAAAACCCTCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTTC-TTCCAAAACCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
*
44637928 TCTCAATTTTCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
1 TCTCAATTTTCTTCCAAAACCCTCTCAATTTCATTCCAAAAATCTCT
44637975 CAAATCCATA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 39 0.91
53 4 0.09
ACGTcount: A:0.30, C:0.31, G:0.00, T:0.38
Consensus pattern (52 bp):
TCTCAATTTTCTTCCAAAACCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
Found at i:44637952 original size:22 final size:22
Alignment explanation
Indices: 44637927--44637977 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
44637917 TTCTCTTAAA
44637927 CTCTCAATTTTC-TTCC-AAAAT
1 CTCTCAA-TTTCATTCCAAAAAT
44637948 CCTCTCAATTTCATTCCAAAAAT
1 -CTCTCAATTTCATTCCAAAAAT
44637971 CTCTCAA
1 CTCTCAA
44637978 ATCCATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCAATTTCATTCCAAAAAT
Found at i:44638049 original size:31 final size:33
Alignment explanation
Indices: 44638011--44638079 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 33
44638001 CCTCAATTTC
*
44638011 ATTTTTTTAAAATAA-TTTCAAA-TTTTTTTAT
1 ATTTTTTTAAAATAATTTTAAAATTTTTTTTAT
44638042 ATTTTTTTAAAATAATTTTAAAATTTTTTTTAT
1 ATTTTTTTAAAATAATTTTAAAATTTTTTTTAT
44638075 ATTTT
1 ATTTT
44638080 CATCAATGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 15 0.43
32 6 0.17
33 14 0.40
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (33 bp):
ATTTTTTTAAAATAATTTTAAAATTTTTTTTAT
Found at i:44638079 original size:11 final size:11
Alignment explanation
Indices: 44638011--44638071 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
44638001 CCTCAATTTC
44638011 ATTTTTTTAAA
1 ATTTTTTTAAA
** *
44638022 A-TAATTTCAA
1 ATTTTTTTAAA
*
44638032 ATTTTTTT-AT
1 ATTTTTTTAAA
44638042 ATTTTTTTAAA
1 ATTTTTTTAAA
**
44638053 ATAATTTTAAA
1 ATTTTTTTAAA
44638064 ATTTTTTT
1 ATTTTTTT
44638072 TATATTTTCA
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
10 16 0.43
11 21 0.57
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTTTAAA
Found at i:44638981 original size:21 final size:19
Alignment explanation
Indices: 44638953--44638991 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
44638943 TAACGAGGAA
44638953 AATTTTATATTACATTTTGG
1 AATTTTATA-TACATTTTGG
*
44638973 AATTGTTATATAGATTTTG
1 AATT-TTATATACATTTTG
44638992 TAAGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (19 bp):
AATTTTATATACATTTTGG
Found at i:44640599 original size:115 final size:115
Alignment explanation
Indices: 44640409--44641223 Score: 1067
Period size: 115 Copynumber: 7.1 Consensus size: 115
44640399 TTTATTTCAT
44640409 ACCCTAACCCTAACCTAATTTAATTTAAAACCCTAAACC-TAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCCTAACCTAATTTAA-TTAAAACCCT-AACCTTAACCTAATTTAATTAAAAACCCTA
* *
44640473 ACCCTAACCTAATTTATTTAAAAACCCTAACCCTACCCTAATTTAATTAAAA
64 ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
* *
44640525 ACCATAACCCTAACCTAATTTAATTAAAACCTTAACCTTAACCTAATTTAATTAAAAACCCTAAC
1 ACCCTAACCCTAACCTAATTTAATTAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAC
* *
44640590 CGTACCCTAATTTAATT--AAA----AACCCTAACCTAATTTAATT-AAA
66 CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
* * *
44640633 ACCTTAACCCTAAACCTAACTTAATTAAAACCCTAACCCTAACCTAATTTAATT-AAAACCCTAA
1 ACCCTAACCCT-AACCTAATTTAATTAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
* *
44640697 CCCTAAACCTAATTTAATTAAAAACCCTAACCTTAACATAATTTAATTAAAA
65 CCCT-AACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
*
44640749 ACCCTAACCCTAATCTAATTTAATTAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAC
1 ACCCTAACCCTAACCTAATTTAATTAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAC
* *
44640814 CATACCCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
66 CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
*
44640864 ACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAACCCTAACCCTAAC
1 ACCCTAACCCTAACCTAATTTAATT-AAAACCCTAACCTTAACCTAATTTAA---T-----TAA-
* * *
44640929 CCTAACCCTAACCCTAACCTAATTTAATT-AAAACCCGAACCTTAACCTAATTTAATTAAAA
56 --AAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
* *
44640990 ACCCTAA-CCTAAAACCTAATTTATTTAAAAACCCTAACCTTAA-C--A--TAATT--TAACCCT
1 ACCCTAACCCT--AACCTAATTTAATT-AAAACCCTAACCTTAACCTAATTTAATTAAAAACCCT
*
44641047 AACCCTAACCTAATTTAATT-AAAACCCTAACCTTAACCTAATTTAATTAAAA
63 AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
* * *
44641099 ACCCTAA-CCTAAACTTAATTTATTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCCT-AACCTAATTTAATT-AAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTA
* *
44641163 ACCTTAACCTAATTTAATTAAAAACCCTAACCCTACCCTAATTTAATTAAAA
64 ACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
44641215 ACCCTAACC
1 ACCCTAACC
44641224 TAATTTATTT
Statistics
Matches: 627, Mismatches: 38, Indels: 67
0.86 0.05 0.09
Matches are distributed among these distances:
108 56 0.09
109 140 0.22
111 4 0.01
113 8 0.01
114 5 0.01
115 199 0.32
116 111 0.18
117 1 0.00
119 2 0.00
122 3 0.00
124 4 0.01
125 2 0.00
126 38 0.06
127 54 0.09
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (115 bp):
ACCCTAACCCTAACCTAATTTAATTAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAC
CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAA
Found at i:44640906 original size:6 final size:6
Alignment explanation
Indices: 44640892--44640947 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
44640882 TTTAATTAAA
* **
44640892 AACCCT AACCTT AA-CCT AA-TTT AACCCT AACCCT AACCCT AACCCT
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT
44640938 AACCCT AACC
1 AACCCT AACC
44640948 TAATTTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
5 7 0.16
6 36 0.84
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (6 bp):
AACCCT
Found at i:44640964 original size:40 final size:40
Alignment explanation
Indices: 44640892--44640975 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
44640882 TTTAATTAAA
* ** *
44640892 AACCCTAACCTTAACCTAATTTAACCCTAACCCTAACCCT
1 AACCCTAACCCTAACCTAATTTAACCAAAACCCGAACCCT
** *
44640932 AACCCTAACCCTAACCTAATTTAATTAAAACCCGAACCTT
1 AACCCTAACCCTAACCTAATTTAACCAAAACCCGAACCCT
44640972 AACC
1 AACC
44640976 TAATTTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.38, C:0.37, G:0.01, T:0.24
Consensus pattern (40 bp):
AACCCTAACCCTAACCTAATTTAACCAAAACCCGAACCCT
Found at i:44641101 original size:23 final size:23
Alignment explanation
Indices: 44640938--44641275 Score: 120
Period size: 29 Copynumber: 12.7 Consensus size: 23
44640928 CCCTAACCCT
*
44640938 AACCCTAACCTAATTTAATTAAAA
1 AACCTTAACCTAATTTAATT-AAA
44640962 CCCGAACCTTAACCTAATTTAATTAAA
1 ----AACCTTAACCTAATTTAATTAAA
*
44640989 AACCCTAACCTAAAACCTAATTTATTTAAA
1 AA-CCT----T--AACCTAATTTAATTAAA
* ** *
44641019 AACCCTAACCTTAACATAATTTAACCCT
1 AACCTTAACC-TAATTTAA-TTAA---A
*
44641047 AACCCTAACCTAATTTAATTAAAA
1 AACCTTAACCTAATTTAATT-AAA
44641071 CCCTAACCTTAACCTAATTTAATTAAA
1 ----AACCTTAACCTAATTTAATTAAA
* *
44641098 AACCCTAACCTAAACTTAATTTATTTAAA
1 AA-CCT----T-AACCTAATTTAATTAAA
44641127 AACCCTAACCCTAACCTAATTTAATTAAAAA
1 AA-CCT-----TAACCTAATTTAATT--AAA
44641158 CCCTAACCTTAACCTAATTTAATTAAA
1 ----AACCTTAACCTAATTTAATTAAA
*
44641185 AACCCTAACCCTACCCTAATTTAATTAAA
1 AA-CCT-----TAACCTAATTTAATTAAA
* *
44641214 AACCCTAACCTAATTTATTTAAA
1 AACCTTAACCTAATTTAATTAAA
* *
44641237 AACCCTAACCTAATTTATTTAAA
1 AACCTTAACCTAATTTAATTAAA
44641260 AATCC-TAACCTAATTT
1 AA-CCTTAACCTAATTT
44641276 TACCTAATTT
Statistics
Matches: 253, Mismatches: 20, Indels: 79
0.72 0.06 0.22
Matches are distributed among these distances:
23 62 0.25
24 16 0.06
25 5 0.02
26 2 0.01
27 17 0.07
28 52 0.21
29 69 0.27
30 22 0.09
31 3 0.01
34 3 0.01
35 2 0.01
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (23 bp):
AACCTTAACCTAATTTAATTAAA
Found at i:44641269 original size:29 final size:29
Alignment explanation
Indices: 44640409--44641223 Score: 1053
Period size: 29 Copynumber: 28.3 Consensus size: 29
44640399 TTTATTTCAT
*
44640409 ACCCTAACCCTAACCTAATTTAATTTAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640438 ACCCTAAACCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640467 ACCCTAACCCTAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640496 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640525 ACCATAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
44640553 ACCTTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
44640582 ACCCTAACCGTACCCTAATTTAATT--AA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
44640609 A----AACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
44640633 ACCTTAACCCTAAACCTAACTTAATT-AAA
1 ACCCTAACCCT-AACCTAATTTAATTAAAA
44640662 ACCCTAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
44640690 ACCCTAACCCTAAACCTAATTTAATTAAAA
1 ACCCTAACCCT-AACCTAATTTAATTAAAA
* *
44640720 ACCCTAACCTTAACATAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640749 ACCCTAACCCTAATCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640777 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
44640806 ACCCTAACCATACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
44640835 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640864 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* * *
44640893 ACCCTAACCTTAACCTAATTTAACCCTAACCCTA
1 ACCCTAACCCTAACCTAATTTAA--TTAA---AA
44640927 ACCCTAACCCTAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAA-CC-----TAATTTAATTAAAA
* *
44640961 ACCCGAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44640990 ACCCTAA-CCTAAAACCTAATTTATTTAAAA
1 ACCCTAACCCT--AACCTAATTTAATTAAAA
* *
44641020 ACCCTAACCTTAA-C--A--TAATT--TA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
44641042 ACCCTAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44641070 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
44641099 ACCCTAA-CCTAAACTTAATTTATTTAAAA
1 ACCCTAACCCT-AACCTAATTTAATTAAAA
44641128 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44641157 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
44641186 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
44641215 ACCCTAACC
1 ACCCTAACC
44641224 TAATTTATTT
Statistics
Matches: 698, Mismatches: 54, Indels: 68
0.85 0.07 0.08
Matches are distributed among these distances:
22 13 0.02
23 19 0.03
24 7 0.01
25 1 0.00
26 1 0.00
27 8 0.01
28 125 0.18
29 440 0.63
30 40 0.06
31 5 0.01
33 2 0.00
34 25 0.04
35 2 0.00
37 1 0.00
38 1 0.00
40 8 0.01
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (29 bp):
ACCCTAACCCTAACCTAATTTAATTAAAA
Found at i:44641330 original size:56 final size:56
Alignment explanation
Indices: 44641270--44641393 Score: 178
Period size: 56 Copynumber: 2.2 Consensus size: 56
44641260 AATCCTAACC
* * ** *
44641270 TAATTTTACCTAATTTGAT-AATCTTACTAACCATTAACACACTTTTTTGAGCTTAA
1 TAATTTTACATAATTTGATAAAT-TTACTAACCATTAACAAAAGTTATTGAGCTTAA
*
44641326 TAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTAA
1 TAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGAGCTTAA
44641382 TAATTTTACATA
1 TAATTTTACATA
44641394 GCTTTACATA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 58 0.95
57 3 0.05
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (56 bp):
TAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGAGCTTAA
Found at i:44649588 original size:24 final size:24
Alignment explanation
Indices: 44649504--44649590 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 24
44649494 TTCGGGAATA
*
44649504 CTCATACGAG-CACTTAAACGGGAAG
1 CTCATACGAGCCA-TT-AACGGAAAG
* **
44649529 CTTATGTGAGCCATGTAACGGAAAG
1 CTCATACGAGCCAT-TAACGGAAAG
**
44649554 CTCCGGA-GAGCCATTAACGGAAAG
1 CT-CATACGAGCCATTAACGGAAAG
44649578 CTCATACGAGCCA
1 CTCATACGAGCCA
44649591 ATATCGGGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
23 2 0.04
24 18 0.38
25 25 0.52
26 3 0.06
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.17
Consensus pattern (24 bp):
CTCATACGAGCCATTAACGGAAAG
Found at i:44649655 original size:26 final size:26
Alignment explanation
Indices: 44649610--44649692 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
44649600 AGGTTCAAGT
* *
44649610 GAGCCAA-T-ATCAGGAAGCTCTGGA
1 GAGCCAATTAATCGGGAAGCTCTGAA
44649634 GAGCCAATTAATCGGGAAGCTCATGAAA
1 GAGCCAATTAATCGGGAAGCTC-TG-AA
** *
44649662 GAG-CTTTTAATCGAGAAGCTCTGAA
1 GAGCCAATTAATCGGGAAGCTCTGAA
44649687 GAGCCA
1 GAGCCA
44649693 TATATCGGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 7 0.15
25 6 0.12
26 14 0.29
27 17 0.35
28 4 0.08
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (26 bp):
GAGCCAATTAATCGGGAAGCTCTGAA
Found at i:44659594 original size:35 final size:34
Alignment explanation
Indices: 44659532--44659601 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 34
44659522 ATTTTATTTG
*
44659532 TTTAATTATATAATTAATGATATTTAAA-TATAA
1 TTTAATTATATAATTAATGATAATTAAATTATAA
*
44659565 TTTACATTATATGAATTTATGATAATTAAATTATAA
1 TTTA-ATTATAT-AATTAATGATAATTAAATTATAA
44659601 T
1 T
44659602 GATATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 4 0.12
34 7 0.22
35 15 0.47
36 6 0.19
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (34 bp):
TTTAATTATATAATTAATGATAATTAAATTATAA
Found at i:44659603 original size:25 final size:23
Alignment explanation
Indices: 44659559--44659619 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
44659549 TGATATTTAA
*
44659559 ATATAATTTACATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
44659583 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
44659608 ATATTATTAAAT
1 ATATAATTAAAT
44659620 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:44659609 original size:35 final size:34
Alignment explanation
Indices: 44659536--44659617 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
44659526 TATTTGTTTA
* *
44659536 ATTATATAATTAATGATATTTAAATATAATTTAC
1 ATTATATAATTAATGATAATTAAATATAATTGAC
* *
44659570 ATTATATGAATTTATGATAATTAAATTATAA-TGAT
1 ATTATAT-AATTAATGATAATTAAA-TATAATTGAC
*
44659605 ATTATATTATTAA
1 ATTATATAATTAA
44659618 ATAAATCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 11 0.28
35 24 0.60
36 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (34 bp):
ATTATATAATTAATGATAATTAAATATAATTGAC
Found at i:44660934 original size:3 final size:3
Alignment explanation
Indices: 44660920--44660975 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
44660910 GTGAGGTAAG
* * * * *
44660920 TAT TAA TAT TAT TAT TAG TAA TAG TAT TAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44660968 TAT TAT TA
1 TAT TAT TA
44660976 AGATGAGTGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:44661163 original size:24 final size:27
Alignment explanation
Indices: 44661126--44661189 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
44661116 AATTGCGGAT
*
44661126 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
44661150 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
44661176 TTGTGATTGAATTG
1 TAATGATTGAATTG
44661190 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:44680541 original size:14 final size:14
Alignment explanation
Indices: 44680520--44680553 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
44680510 CGGTATGGGT
44680520 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
44680533 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
44680547 TTATAGG
1 TTATAGG
44680554 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:44692758 original size:35 final size:34
Alignment explanation
Indices: 44692677--44692758 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 34
44692667 TAATAAACAC
44692677 AAAA-AAATATTTTAAAAATAAAAAATAAAAATA
1 AAAATAAATATTTTAAAAATAAAAAATAAAAATA
**** *
44692710 TTTTTAAAGTATTTTAAAATTAAAAAATAAAAATAA
1 AAAATAAA-TATTTTAAAAATAAAAAATAAAAAT-A
*
44692746 AAAATATATATTT
1 AAAATAAATATTT
44692759 ATTATATTCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
34 3 0.08
35 29 0.81
36 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (34 bp):
AAAATAAATATTTTAAAAATAAAAAATAAAAATA
Found at i:44696256 original size:9 final size:9
Alignment explanation
Indices: 44696242--44696308 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
44696232 TTTGGTTAAA
44696242 AATTAACCG
1 AATTAACCG
*
44696251 AATTAACCA
1 AATTAACCG
*
44696260 AATTACCCG
1 AATTAACCG
44696269 AATTAACCG
1 AATTAACCG
* *
44696278 GATTACCCG
1 AATTAACCG
*
44696287 AATTACCCG
1 AATTAACCG
44696296 AATTAACCG
1 AATTAACCG
44696305 AATT
1 AATT
44696309 GAATCACTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:44696282 original size:27 final size:27
Alignment explanation
Indices: 44696242--44696308 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
44696232 TTTGGTTAAA
44696242 AATTAACCGAATTAACCAAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
* * *
44696269 AATTAACCGGATTACCCGAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
44696296 AATTAACCGAATT
1 AATTAACCGAATT
44696309 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.24
Consensus pattern (27 bp):
AATTAACCGAATTAACCAAATTACCCG
Found at i:44696345 original size:8 final size:7
Alignment explanation
Indices: 44696332--44696389 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 7
44696322 ATTAAATTAT
44696332 TTTTAGA
1 TTTTAGA
44696339 CTTTTAGA
1 -TTTTAGA
44696347 TTTTAG-
1 TTTTAGA
44696353 TTTTAG-
1 TTTTAGA
44696359 TTTTAG-
1 TTTTAGA
44696365 TTTTAG-
1 TTTTAGA
44696371 TTTTAG-
1 TTTTAGA
44696377 TTTTAGAA
1 TTTTAG-A
44696385 TTTTA
1 TTTTA
44696390 TTTTATTTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
6 30 0.62
7 6 0.12
8 12 0.25
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.62
Consensus pattern (7 bp):
TTTTAGA
Found at i:44696358 original size:6 final size:6
Alignment explanation
Indices: 44696340--44696382 Score: 77
Period size: 6 Copynumber: 7.0 Consensus size: 6
44696330 ATTTTTAGAC
44696340 TTTTAG ATTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
1 TTTTAG -TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
44696383 AATTTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (6 bp):
TTTTAG
Found at i:44696370 original size:18 final size:19
Alignment explanation
Indices: 44696340--44696394 Score: 87
Period size: 18 Copynumber: 2.9 Consensus size: 19
44696330 ATTTTTAGAC
44696340 TTTTAGATTTTAGTTTTAG
1 TTTTAGATTTTAGTTTTAG
44696359 TTTTAG-TTTTAGTTTTAG
1 TTTTAGATTTTAGTTTTAG
44696377 TTTTAGAATTTTA-TTTTA
1 TTTTAG-ATTTTAGTTTTA
44696395 TTTATTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.53
19 11 0.32
20 5 0.15
ACGTcount: A:0.22, C:0.00, G:0.13, T:0.65
Consensus pattern (19 bp):
TTTTAGATTTTAGTTTTAG
Found at i:44696449 original size:13 final size:13
Alignment explanation
Indices: 44696431--44696464 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
44696421 GATTGGGTTG
44696431 GGTTGGGTAATTA
1 GGTTGGGTAATTA
*
44696444 GGTTGGGTAATTG
1 GGTTGGGTAATTA
44696457 GGTTGGGT
1 GGTTGGGT
44696465 TGAATACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (13 bp):
GGTTGGGTAATTA
Found at i:44697961 original size:6 final size:6
Alignment explanation
Indices: 44697950--44697974 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44697940 CCCTCCCTAA
44697950 TTTCAC TTTCAC TTTCAC TTTCAC T
1 TTTCAC TTTCAC TTTCAC TTTCAC T
44697975 CACAATCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAC
Found at i:44699062 original size:37 final size:37
Alignment explanation
Indices: 44698953--44699064 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
44698943 ATTTTAATTC
* *
44698953 AAGACTTATGTAATGTTTTTAGTTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
44698990 AAGACTTATGTAATATTTTTAATTATGCAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
44699027 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
44699064 A
1 A
44699065 TTTGGATAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.46
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
Found at i:44699304 original size:12 final size:12
Alignment explanation
Indices: 44699287--44699311 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44699277 AACAAGTTCG
44699287 GGTCGGTTAACC
1 GGTCGGTTAACC
44699299 GGTCGGTTAACC
1 GGTCGGTTAACC
44699311 G
1 G
44699312 ACTGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:44700838 original size:18 final size:18
Alignment explanation
Indices: 44700815--44700857 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
44700805 TGGCAGGTGC
* *
44700815 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
44700833 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
44700851 GTTTCCT
1 GTATCCT
44700858 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:44701144 original size:21 final size:21
Alignment explanation
Indices: 44701120--44701159 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44701110 CTACCGGATG
*
44701120 AACCAAAATCCACGCCGGAGC
1 AACCAAAACCCACGCCGGAGC
* *
44701141 AACCACAACCCTCGCCGGA
1 AACCAAAACCCACGCCGGA
44701160 AGCTGGACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.42, G:0.17, T:0.05
Consensus pattern (21 bp):
AACCAAAACCCACGCCGGAGC
Found at i:44701335 original size:49 final size:49
Alignment explanation
Indices: 44701281--44701584 Score: 509
Period size: 49 Copynumber: 6.2 Consensus size: 49
44701271 TATATTAATG
* * *
44701281 TAATAAAAGACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATA
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
* *
44701330 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTAATG
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
*
44701379 TAATAAAATACAAAATAGTTTATTTTGAATTTTTTGATATTATTTCATT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
* * *
44701428 TAATAAAATATAAAATAGTTTATTTTGAATATTTTGATATTATTTGATG
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
*
44701477 TAATAAAATACAAAATAGTTTATTTTGAATTTTTTGATATTATTTCATT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
*
44701526 TAATAAAATATAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
44701575 TAATAAAATA
1 TAATAAAATA
44701585 ATGAATATTT
Statistics
Matches: 239, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 239 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (49 bp):
TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
Found at i:44704801 original size:125 final size:124
Alignment explanation
Indices: 44704538--44704949 Score: 691
Period size: 125 Copynumber: 3.3 Consensus size: 124
44704528 CCCAAACATG
* *
44704538 CTACTGTAGCAAAAATGCGTCCATGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
44704603 TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
*
44704662 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
44704727 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACT-AGAAATTATTTTTTCAGGAC
66 TTGAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTCA-AAATTATTTTTTCAGGAC
* * * * *
44704787 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGACAAAACATCCTAC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
*
44704852 TTGAAGCTTTTTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* *
44704912 CTACTATAGCAAAAACGCGTCCACGTGGGAGTGATTTC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTC
44704950 CTTAATAAAT
Statistics
Matches: 272, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
124 70 0.26
125 201 0.74
126 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (124 bp):
CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:44722061 original size:12 final size:13
Alignment explanation
Indices: 44722035--44722062 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
44722025 ACTTTTCCAC
44722035 AATACTTTTTAAA
1 AATACTTTTTAAA
44722048 AATACTTTTTAAA
1 AATACTTTTTAAA
44722061 AA
1 AA
44722063 CAATGCTAAA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
AATACTTTTTAAA
Found at i:44732691 original size:42 final size:42
Alignment explanation
Indices: 44732625--44732958 Score: 524
Period size: 42 Copynumber: 7.9 Consensus size: 42
44732615 AGCGTTTACA
*
44732625 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* * *
44732667 AAAAAAGCGCCTCTAAATACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* * *
44732709 AAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
44732751 AAAAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
44732793 AAAAAAAAAAGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 --AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
44732837 AAAAAAAACGCCGCTAAAGACCATATTCTTTAGTGGCGCTTAG
1 -AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
44732880 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
44732922 AAAAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
44732959 TTTTTATACA
Statistics
Matches: 267, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
42 187 0.70
43 40 0.15
44 40 0.15
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
Found at i:44732908 original size:171 final size:170
Alignment explanation
Indices: 44732624--44732958 Score: 544
Period size: 171 Copynumber: 2.0 Consensus size: 170
44732614 CAGCGTTTAC
* * * *
44732624 AAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAGCGCCTCTAAATACCA
1 AAAAAAAAAGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCA
*
44732689 TGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAAA
66 TATTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAAA
*
44732754 AAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGA
131 AAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA
*
44732794 AAAAAAAAAGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGACC
1 AAAAAAAAAGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGACC
* * * *
44732859 ATATTCTTTAGTGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
65 ATATTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAA
* *
44732924 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCG
130 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
44732959 TTTTTATACA
Statistics
Matches: 151, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
170 41 0.27
171 110 0.73
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (170 bp):
AAAAAAAAAGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCA
TATTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAAA
AAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA
Found at i:44733333 original size:27 final size:27
Alignment explanation
Indices: 44733282--44733333 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
44733272 GGCCTGCTCT
* *
44733282 GCTTCTCTCGCTGCAGCTTCCGCTTCC
1 GCTTCCCTCGCTGCAGCCTCCGCTTCC
* *
44733309 GCTTCCCTCGCTGCCGCCTCTGCTT
1 GCTTCCCTCGCTGCAGCCTCCGCTT
44733334 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.02, C:0.46, G:0.19, T:0.33
Consensus pattern (27 bp):
GCTTCCCTCGCTGCAGCCTCCGCTTCC
Found at i:44738863 original size:9 final size:9
Alignment explanation
Indices: 44738845--44739069 Score: 179
Period size: 9 Copynumber: 24.8 Consensus size: 9
44738835 TGATATATTT
44738845 TTATGTAAG
1 TTATGTAAG
*
44738854 TTATGCAAG
1 TTATGTAAG
44738863 TTTATGTAAG
1 -TTATGTAAG
*
44738873 TTACT-TAAT
1 TTA-TGTAAG
44738882 TTATGTAAG
1 TTATGTAAG
44738891 TTATAG-AAG
1 TTAT-GTAAG
* *
44738900 TTATTTAAT
1 TTATGTAAG
*
44738909 TTATGTAGG
1 TTATGTAAG
44738918 TTATGTAAG
1 TTATGTAAG
* *
44738927 TTATTTAAT
1 TTATGTAAG
*
44738936 TTATGCAAG
1 TTATGTAAG
* *
44738945 TTTATGCATG
1 -TTATGTAAG
*
44738955 TTATGTAGG
1 TTATGTAAG
*
44738964 TTACT-TAAT
1 TTA-TGTAAG
44738973 TTATGTAAG
1 TTATGTAAG
44738982 TTATGTAAG
1 TTATGTAAG
* *
44738991 TTATTTAAT
1 TTATGTAAG
*
44739000 TTATGTAGG
1 TTATGTAAG
44739009 TTATGTAAG
1 TTATGTAAG
*
44739018 TTATGTAAC
1 TTATGTAAG
* *
44739027 TTATTTAAT
1 TTATGTAAG
44739036 TTAT-TCAAG
1 TTATGT-AAG
44739045 TTATGTAAG
1 TTATGTAAG
* * *
44739054 TAATTTAAT
1 TTATGTAAG
44739063 TTATGTA
1 TTATGTA
44739070 TAAGCTTGTA
Statistics
Matches: 170, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
8 3 0.02
9 147 0.86
10 20 0.12
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:44741621 original size:21 final size:21
Alignment explanation
Indices: 44741597--44741644 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
44741587 CCCATTTTGA
*
44741597 TATATTTTTAAAATATTAATT
1 TATATTTATAAAATATTAATT
* * *
44741618 TATATTTATATAATTTTCATT
1 TATATTTATAAAATATTAATT
44741639 TATATT
1 TATATT
44741645 AATCTAGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTTATAAAATATTAATT
Found at i:44742845 original size:115 final size:114
Alignment explanation
Indices: 44742722--44742937 Score: 342
Period size: 115 Copynumber: 1.9 Consensus size: 114
44742712 TTTTCCCTAG
*** * * *
44742722 CGCCGCTAATAATGTGCTTTAGCGGCGTTTTTATAGAAACGCCACCAATTCTACTATACCTCAAT
1 CGCCGCTAATAATCCACTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCAACTATACCTCAAT
*
44742787 CTTGTACGTTGCGTTTTGTTTAACATTTTTTTGCGGCGCTTACAAACAAA
66 CTTGTACGCTGCGTTTTGTTTAACA-TTTTTTGCGGCGCTTACAAACAAA
* *
44742837 CGCCGCTAATGATCCACTTCAGCGGCGTTTTTATAGAAACGTCACAAATTCAACTATACCTCAAT
1 CGCCGCTAATAATCCACTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCAACTATACCTCAAT
44742902 CTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGC
66 CTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGC
44742938 ATTTTTACAG
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
114 11 0.12
115 81 0.88
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (114 bp):
CGCCGCTAATAATCCACTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCAACTATACCTCAAT
CTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAA
Found at i:44742981 original size:75 final size:75
Alignment explanation
Indices: 44742858--44743012 Score: 256
Period size: 75 Copynumber: 2.1 Consensus size: 75
44742848 ATCCACTTCA
* * *
44742858 GCGGCGTTTTTATAGAAACGTCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCATTTTTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
44742923 AACATTTTTT
66 AACATTTTTT
** *
44742933 GCGGCATTTTTACAGAAACGCCATTAATTCCACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCATTTTTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
44742998 AACATTTTTT
66 AACATTTTTT
44743008 GCGGC
1 GCGGC
44743013 GCTTACAAGC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (75 bp):
GCGGCATTTTTACAGAAACGCCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
AACATTTTTT
Found at i:44743084 original size:189 final size:190
Alignment explanation
Indices: 44742743--44743126 Score: 617
Period size: 189 Copynumber: 2.0 Consensus size: 190
44742733 ATGTGCTTTA
* * * *
44742743 GCGGCGTTTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGTTGCGTTTTGTTT
1 GCGGCATTTTTACAGAAACGCCACCAATTCCACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* *
44742808 AACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTTATAG
66 AACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAG
* *
44742873 AAACGTCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTT
131 AAACGCCACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTT
**
44742933 GCGGCATTTTTACAGAAACGCCATTAATTCCACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCATTTTTACAGAAACGCCACCAATTCCACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * *
44742998 AACA-TTTTTTGCGGCGCTTACAAGCAAATGCTGCTAATGATCCACTTCAGCGGCGTTTTGACAG
66 AACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAG
* *
44743062 AAACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTT
131 AAACGCCACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTT
*
44743122 ACGGC
1 GCGGC
44743127 GCTTACAAAC
Statistics
Matches: 178, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
189 115 0.65
190 63 0.35
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (190 bp):
GCGGCATTTTTACAGAAACGCCACCAATTCCACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
AACATTTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAG
AAACGCCACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTT
Found at i:44743133 original size:114 final size:114
Alignment explanation
Indices: 44742933--44743489 Score: 898
Period size: 114 Copynumber: 4.9 Consensus size: 114
44742923 AACATTTTTT
* ** *
44742933 GCGGCATTTTTACAGAAACGCCATTAATTCCACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * *
44742998 AACATTTTTTGCGGCGCTTACAAGCAAATGCTGCTAATGATCCACTTCA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
* *
44743047 GCGGCGTTTTGACAGAAACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * * *
44743112 AACATTTTTTACGGCGCTTACAAACAAATGTCGCTAATGATACACTTCA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
* * *
44743161 GTGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGTTGCATTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* *
44743226 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTATTTATCCACTTCA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
44743275 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* *
44743340 AACATTTTTTACGGCGCTTACAAACAAACGCCGCTAATGATCCACTCCA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
* * *
44743389 GCGGCATTTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTACGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
*
44743454 AACATTGTTTGCGGCGCTTACAAACAAACGCCGCTA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTA
44743490 CTGCCACTAT
Statistics
Matches: 409, Mismatches: 34, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 409 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (114 bp):
GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCA
Found at i:44746907 original size:43 final size:45
Alignment explanation
Indices: 44746781--44746907 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 45
44746771 AAAGATTGCT
44746781 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTGACAACTTAAA
1 TATGTAAGCTATATTTAAATTTTATTAATAAT--ATT-ACAACTTAAA
* * * * **
44746829 TAAGTATTA-CTATATTTTTAATATTA-TACAT-ATATT-C-ATTTACG
1 TATGTA--AGCTATA-TTTAAATTTTATTA-ATAATATTACAACTTAAA
44746873 TATGTAAGCTATATTTAAATTTTATTAATAATATT
1 TATGTAAGCTATATTTAAATTTTATTAATAATATT
44746908 TAAACATATT
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
42 12 0.19
43 12 0.19
44 9 0.14
45 1 0.02
47 3 0.05
48 5 0.08
49 9 0.14
50 12 0.19
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (45 bp):
TATGTAAGCTATATTTAAATTTTATTAATAATATTACAACTTAAA
Found at i:44751278 original size:21 final size:21
Alignment explanation
Indices: 44751252--44751298 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
44751242 CTACAACTTA
* *
44751252 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAACGAGGG
44751273 AAGCAGAGGCCGCAACGAGGG
1 AAGCAGAGGCCGCAACGAGGG
44751294 AAGCA
1 AAGCA
44751299 AAGCAGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.45, T:0.00
Consensus pattern (21 bp):
AAGCAGAGGCCGCAACGAGGG
Found at i:44751880 original size:41 final size:42
Alignment explanation
Indices: 44751707--44751909 Score: 318
Period size: 42 Copynumber: 4.8 Consensus size: 42
44751697 TAAGAATAAA
44751707 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTCTAAG
* *
44751750 CGCCGCTAACGAACATAGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * * *
44751792 CGCTGCTAAAGAACATGGTCTTTAGAGGCCTTTTTTTCAAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
**
44751834 CGCCGCTAAAGAACATGGTCTTTAAAGGCGTTTTTTT-TAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
44751875 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
44751910 GTTTGTAAAC
Statistics
Matches: 146, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 36 0.25
42 82 0.56
43 28 0.19
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:44752873 original size:16 final size:16
Alignment explanation
Indices: 44752854--44752890 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
44752844 AAAAAATAAA
44752854 AAAAAATAAAAAATTT
1 AAAAAATAAAAAATTT
* *
44752870 AAAAAATACATAATTT
1 AAAAAATAAAAAATTT
44752886 AAAAA
1 AAAAA
44752891 GATTGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATAAAAAATTT
Found at i:44754538 original size:31 final size:31
Alignment explanation
Indices: 44754500--44754563 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
44754490 CTCAAAAGTT
44754500 TTCATTTAAATCTATCAGATTGTTAAAATTG
1 TTCATTTAAATCTATCAGATTGTTAAAATTG
44754531 TTCATTTAAATCTATCAGATTGTTAAAATTG
1 TTCATTTAAATCTATCAGATTGTTAAAATTG
44754562 TT
1 TT
44754564 GTTGTATGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (31 bp):
TTCATTTAAATCTATCAGATTGTTAAAATTG
Found at i:44767949 original size:24 final size:24
Alignment explanation
Indices: 44767890--44767952 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
44767880 CTCCATCGTG
*
44767890 GTCTTTTTCTTCATCTTCATCTCT
1 GTCTTTGTCTTCATCTTCATCTCT
* * *
44767914 -ACTCTTGGCTTCATCTTCATCTTT
1 GTCT-TTGTCTTCATCTTCATCTCT
44767938 GTCTTTGTCTTCATC
1 GTCTTTGTCTTCATC
44767953 GTCTTTCTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
23 2 0.06
24 27 0.87
25 2 0.06
ACGTcount: A:0.10, C:0.29, G:0.08, T:0.54
Consensus pattern (24 bp):
GTCTTTGTCTTCATCTTCATCTCT
Found at i:44770072 original size:11 final size:9
Alignment explanation
Indices: 44770042--44770080 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
44770032 AATTTAAAAC
44770042 AGAACTTGAG
1 AGAA-TTGAG
44770052 AGAATTGAG
1 AGAATTGAG
*
44770061 AGAATTAAG
1 AGAATTGAG
*
44770070 AGAGTTGAG
1 AGAATTGAG
44770079 AG
1 AG
44770081 TTTAGAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.44, C:0.03, G:0.33, T:0.21
Consensus pattern (9 bp):
AGAATTGAG
Found at i:44772036 original size:46 final size:44
Alignment explanation
Indices: 44771962--44772086 Score: 146
Period size: 44 Copynumber: 2.8 Consensus size: 44
44771952 CCACTAAATA
*
44771962 TTTAATTAAATTACATAGTATCTATTATAAATTATTAAAAACGAAT
1 TTTAATTAAATTACATAGTATTTATTAT-AATTATT-AAAACGAAT
* * * * *
44772008 TTTAACTAAATTACATAGTATTTGTTATAATTATTCATACTAAT
1 TTTAATTAAATTACATAGTATTTATTATAATTATTAAAACGAAT
* *
44772052 TTTAATTAAATTATATAGTATTCATTAT--TTATTAA
1 TTTAATTAAATTACATAGTATTTATTATAATTATTAA
44772087 GACTTAGCTA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 6 0.09
44 30 0.44
45 7 0.10
46 25 0.37
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (44 bp):
TTTAATTAAATTACATAGTATTTATTATAATTATTAAAACGAAT
Found at i:44778838 original size:4 final size:4
Alignment explanation
Indices: 44778829--44778857 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
44778819 ACGGTAAATT
44778829 TAAC TAAC TAAC TAAC TAAC TAAC TAAC T
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC T
44778858 TAGCATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAC
Found at i:44782324 original size:32 final size:32
Alignment explanation
Indices: 44782288--44782373 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
44782278 ACTTTTTCGA
* *
44782288 AAAATATTTTCAGGAAATC-TGCCAAACAGCAG
1 AAAATATTTTCAGCAAATCAT-CCAAACACCAG
*
44782320 AAAATATTTTACA-CAGATTCATCCAAACACCAG
1 AAAATATTTT-CAGCA-AATCATCCAAACACCAG
*
44782353 AAAATATTTTCAGTAAATCAT
1 AAAATATTTTCAGCAAATCAT
44782374 TTTCTAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
32 18 0.40
33 26 0.58
34 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (32 bp):
AAAATATTTTCAGCAAATCATCCAAACACCAG
Found at i:44782389 original size:20 final size:20
Alignment explanation
Indices: 44782364--44782403 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
44782354 AAATATTTTC
* *
44782364 AGTAAATCATTTTCTAGAAA
1 AGTAAATCACTTTCCAGAAA
44782384 AGTAAATCACTTTCCAGAAA
1 AGTAAATCACTTTCCAGAAA
44782404 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCACTTTCCAGAAA
Found at i:44785710 original size:69 final size:66
Alignment explanation
Indices: 44785613--44785743 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 66
44785603 TTCAAATAAG
** *
44785613 AAAAGACAAAACTACATCGTTTTGATAAATGTTCACCTTTTCTAAATTAAAAGTCAAAATCATTA
1 AAAAGACAAAACTACATCGTTTTGATAAA-GTTCA-CTCAT-TAAATTAAAAGGCAAAATCATTA
44785678 AGTT
63 AGTT
* *
44785682 AAAAGACAAAACTACGA-CGTTTTGATAAAGTTTACTCATTAAGTTAAAAGGCAAAATCATTA
1 AAAAGACAAAACTAC-ATCGTTTTGATAAAGTTCACTCATTAAATTAAAAGGCAAAATCATTA
44785744 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
66 21 0.38
67 3 0.05
68 4 0.07
69 27 0.48
70 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (66 bp):
AAAAGACAAAACTACATCGTTTTGATAAAGTTCACTCATTAAATTAAAAGGCAAAATCATTAAGT
T
Done.