Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 154 of 163
Found at i:42853099 original size:15 final size:16
Alignment explanation
Indices: 42853072--42853102 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42853062 GGAGGAGGAG
42853072 AGGGATATTAGAAATT
1 AGGGATATTAGAAATT
42853088 AGGGAT-TTAGAAATT
1 AGGGATATTAGAAATT
42853103 GGTTTTCGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (16 bp):
AGGGATATTAGAAATT
Found at i:42853542 original size:111 final size:113
Alignment explanation
Indices: 42853416--42853618 Score: 313
Period size: 113 Copynumber: 1.8 Consensus size: 113
42853406 AATTCAATTA
* * *
42853416 TGAAATTATTAAAATAT-TTTTCATATATAAATTAAGTTATAT-TTTTATGAGGGA-GTTTTTAT
1 TGAAATTATTAAAATATATTTTCATATACAAATTAAATTATATCTTTTATGA-GAATGTTTTTAT
* *
42853478 TTTTTTCTATAATAAATCAATAAAAAATTTATCTCAAGAGATTTGAAAT
65 TCTTTTATATAATAAATCAATAAAAAATTTATCTCAAGAGATTTGAAAT
* *
42853527 TGAAATTATTAAAATATATTTTTATATACAAATTAAATTATATCTTTTATGAGAATGTTTTTGTT
1 TGAAATTATTAAAATATATTTTCATATACAAATTAAATTATATCTTTTATGAGAATGTTTTTATT
42853592 CTTTTATATAATAAATCAATAAAAAAT
66 CTTTTATATAATAAATCAATAAAAAAT
42853619 AATTATAATG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
111 17 0.21
112 24 0.29
113 41 0.50
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (113 bp):
TGAAATTATTAAAATATATTTTCATATACAAATTAAATTATATCTTTTATGAGAATGTTTTTATT
CTTTTATATAATAAATCAATAAAAAATTTATCTCAAGAGATTTGAAAT
Found at i:42859066 original size:22 final size:23
Alignment explanation
Indices: 42859027--42859071 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
42859017 TTTTAAATAT
* * *
42859027 ATATTTAATTATTTTATT-TTTA
1 ATATTTAATAAATATATTCTTTA
42859049 ATATTTAATAAATATATTCTTTA
1 ATATTTAATAAATATATTCTTTA
42859072 TTACATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTTAATAAATATATTCTTTA
Found at i:42859729 original size:20 final size:20
Alignment explanation
Indices: 42859692--42859729 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42859682 CTCTAGTGAG
*
42859692 ACTTTTATCCGTAGAACTCC
1 ACTTTTATCCGTACAACTCC
42859712 ACTTTTAT-CGATACAACT
1 ACTTTTATCCG-TACAACT
42859730 ACAGTTCTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (20 bp):
ACTTTTATCCGTACAACTCC
Found at i:42862980 original size:21 final size:24
Alignment explanation
Indices: 42862954--42863002 Score: 77
Period size: 21 Copynumber: 2.2 Consensus size: 24
42862944 AAAAGCTATC
42862954 TACAAAATCA-ATC-TCT-AAGAT
1 TACAAAATCATATCTTCTAAAGAT
42862975 TACAAAATCATATCTTCTAAAGAT
1 TACAAAATCATATCTTCTAAAGAT
42862999 TACA
1 TACA
42863003 TATCAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.40
22 3 0.12
23 3 0.12
24 9 0.36
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (24 bp):
TACAAAATCATATCTTCTAAAGAT
Found at i:42863967 original size:11 final size:11
Alignment explanation
Indices: 42863947--42863988 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
42863937 CCTAACTTGG
42863947 ATTTTAAATTA
1 ATTTTAAATTA
*
42863958 ATTTTGAATTA
1 ATTTTAAATTA
*
42863969 ATTTTAAATTT
1 ATTTTAAATTA
42863980 A-TTTAAATT
1 ATTTTAAATT
42863989 TAAATTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:42863988 original size:17 final size:17
Alignment explanation
Indices: 42863949--42864010 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
42863939 TAACTTGGAT
*
42863949 TTTAAA-TTAATTTTGA
1 TTTAAATTTAAATTTGA
* *
42863965 ATTAATTTTAAATTT-A
1 TTTAAATTTAAATTTGA
*
42863981 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATTTGA
42863998 TTTAAATTTAAAT
1 TTTAAATTTAAAT
42864011 ACACATAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTTGA
Found at i:42863994 original size:27 final size:27
Alignment explanation
Indices: 42863955--42864007 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
42863945 GGATTTTAAA
* *
42863955 TTAATTTTGAATTAATTTTAAATTTAT
1 TTAAATTTAAATTAATTTTAAATTTAT
**
42863982 TTAAATTTAAATTTGTTTTAAATTTA
1 TTAAATTTAAATTAATTTTAAATTTA
42864008 AATACACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
TTAAATTTAAATTAATTTTAAATTTAT
Found at i:42866024 original size:29 final size:30
Alignment explanation
Indices: 42865988--42866088 Score: 124
Period size: 29 Copynumber: 3.5 Consensus size: 30
42865978 CCCAAGCTTT
*
42865988 CCAAAATT-CCATTTTGACCCTAATTTCAC
1 CCAAAATTACCATTTTGACCCCAATTTCAC
42866017 CCAAAATTACCATTTT-ACCCCCAAGCTTT---
1 CCAAAATTACCATTTTGA-CCCCAA--TTTCAC
42866046 CCAAAATT-CCATTTTGACCCCAATTTCAC
1 CCAAAATTACCATTTTGACCCCAATTTCAC
42866075 CCAAAATTACCATT
1 CCAAAATTACCATT
42866089 CTTTGGACTT
Statistics
Matches: 62, Mismatches: 1, Indels: 17
0.77 0.01 0.21
Matches are distributed among these distances:
26 3 0.05
28 13 0.21
29 26 0.42
30 17 0.27
32 3 0.05
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.32
Consensus pattern (30 bp):
CCAAAATTACCATTTTGACCCCAATTTCAC
Found at i:42866071 original size:58 final size:58
Alignment explanation
Indices: 42865977--42866088 Score: 215
Period size: 58 Copynumber: 1.9 Consensus size: 58
42865967 GCTCTCTAGT
*
42865977 CCCCAAGCTTTCCAAAATTCCATTTTGACCCTAATTTCACCCAAAATTACCATTTTAC
1 CCCCAAGCTTTCCAAAATTCCATTTTGACCCCAATTTCACCCAAAATTACCATTTTAC
42866035 CCCCAAGCTTTCCAAAATTCCATTTTGACCCCAATTTCACCCAAAATTACCATT
1 CCCCAAGCTTTCCAAAATTCCATTTTGACCCCAATTTCACCCAAAATTACCATT
42866089 CTTTGGACTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.31, C:0.34, G:0.04, T:0.31
Consensus pattern (58 bp):
CCCCAAGCTTTCCAAAATTCCATTTTGACCCCAATTTCACCCAAAATTACCATTTTAC
Found at i:42879282 original size:29 final size:30
Alignment explanation
Indices: 42879240--42879298 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
42879230 GAGTCGGATC
* * *
42879240 AAATCTAAATTTCATGTATAAAATTGCACA
1 AAATCTAAAGTTCATATATAAAATTACACA
*
42879270 AAATC-AAAGTTCATATATATAATTACACA
1 AAATCTAAAGTTCATATATAAAATTACACA
42879299 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCTAAAGTTCATATATAAAATTACACA
Found at i:42883127 original size:21 final size:21
Alignment explanation
Indices: 42883089--42883128 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42883079 AGCAGCAGCA
*
42883089 TCGCCTCCACCGCCGCCTCAG
1 TCGCCTCCACCGCAGCCTCAG
*
42883110 TCGCCTCCACCTCAGCCTC
1 TCGCCTCCACCGCAGCCTC
42883129 CTAAGGCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.57, G:0.15, T:0.17
Consensus pattern (21 bp):
TCGCCTCCACCGCAGCCTCAG
Found at i:42883296 original size:6 final size:6
Alignment explanation
Indices: 42883281--42883324 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
42883271 ACCAGCTTCA
* * * *
42883281 CCACCC CCACCT CCACCA CCGCCT CCACCT CCACCT CCTCCT CC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CC
42883325 GCCGCCAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.14, C:0.70, G:0.02, T:0.14
Consensus pattern (6 bp):
CCACCT
Found at i:42884829 original size:20 final size:20
Alignment explanation
Indices: 42884792--42884830 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
42884782 TTTTTATATA
*
42884792 TATTTTTTAGATTCTTTTAC
1 TATTTTTTAAATTCTTTTAC
42884812 TATTTTTTATAATT-TTTTA
1 TATTTTTTA-AATTCTTTTA
42884831 AAAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (20 bp):
TATTTTTTAAATTCTTTTAC
Found at i:42884894 original size:20 final size:20
Alignment explanation
Indices: 42884847--42884917 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 20
42884837 ATAAAAATTG
*
42884847 AAATTTTTATAAAC-ATTTT
1 AAATTTTTAAAAACTATTTT
* *
42884866 GAA-TTTTAAAAACTATCTT
1 AAATTTTTAAAAACTATTTT
*
42884885 AAATTTTTAAAAATTATTTTT
1 AAATTTTTAAAAACTA-TTTT
*
42884906 AAAATTTTAAAA
1 AAATTTTTAAAA
42884918 TTTTATGGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 9 0.21
19 8 0.19
20 11 0.26
21 14 0.33
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (20 bp):
AAATTTTTAAAAACTATTTT
Found at i:42887478 original size:14 final size:15
Alignment explanation
Indices: 42887426--42887480 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
42887416 AAATATGCAT
42887426 TAAAAA-TAATATATAA
1 TAAAAATTAA-ATAT-A
*
42887442 TAAATAATGAAATATA
1 TAAA-AATTAAATATA
42887458 TATAAAATTAAA-ATA
1 TA-AAAATTAAATATA
42887473 TAAAAATT
1 TAAAAATT
42887481 CATTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 13 0.38
17 8 0.24
18 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAAAATTAAATATA
Found at i:42894254 original size:18 final size:18
Alignment explanation
Indices: 42894228--42894262 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42894218 TAAATAATAA
* *
42894228 AATATTATTATTTATTAT
1 AATAATATTATTAATTAT
42894246 AATAATATTATTAATTA
1 AATAATATTATTAATTA
42894263 ATATATCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAATATTATTAATTAT
Found at i:42894254 original size:21 final size:20
Alignment explanation
Indices: 42894224--42894267 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
42894214 AATATAAATA
* *
42894224 ATAAAATATTATTATTTATT
1 ATAAAATATTATTAATTAAT
42894244 ATAATAATATTATTAATTAAT
1 ATAA-AATATTATTAATTAAT
42894265 ATA
1 ATA
42894268 TCATTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATATTATTAATTAAT
Found at i:42894832 original size:26 final size:25
Alignment explanation
Indices: 42894777--42894832 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
42894767 AACGATAAAT
*
42894777 TAATTATTTAATTCAATGTTTATGA
1 TAATTATTTAATTCAATGTTGATGA
* *
42894802 AAATTATTTTAATTTTAATGTTGAT-A
1 TAATTA-TTTAA-TTCAATGTTGATGA
42894828 TAATT
1 TAATT
42894833 GTAACTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 5 0.20
26 10 0.40
27 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (25 bp):
TAATTATTTAATTCAATGTTGATGA
Found at i:42897062 original size:185 final size:190
Alignment explanation
Indices: 42896684--42897079 Score: 500
Period size: 185 Copynumber: 2.1 Consensus size: 190
42896674 TAACAAAATA
* * * *
42896684 TTTTTTCTCATTTTGTTTTATATTCTTTCTTCTTCTCGCTTTCTCTTTTCCCTCCTCCAAATTTT
1 TTTTTTCTCATTTTGTTTCATATTCTTTCTTCTTCCCGCATTCTCTCTT--CTCCTCCAAATTTT
* **
42896749 TCTCTCATTTTCTCTCATGTCAAACACCATTTTGCTTCTTCAAAACTCAGAATTTAACACAATAA
64 TCTCTCATTTTCTCTCATGCCAAACACCATTTTGCTTCTTCAAAACTC---A-CCAACACAATAA
42896814 ATCGTTAAAAATGGGTTGAGTCAGAAAAAAAAATCCCAAATCATCTCAAAACCTAATTTAATACA
125 ATCGTTAAAAATGGGTTGAGTCAG-AAAAAAAATCCCAAATCATCTCAAAACCTAATTTAATACA
42896879 AT
189 AT
* * * * *
42896881 TTTTTTTTCATTTTGTTTCATCTTCTTTTTTCTTCCCTCATTCTCTCTT-TCC-CCAATTTTTTC
1 TTTTTTCTCATTTTGTTTCATATTCTTTCTTCTTCCCGCATTCTCTCTTCTCCTCCAAATTTTTC
* * *
42896944 TCTCATTTTCTCTCTTGCCAAACACCATTTT-CTTCTTCAAAACTTC-CCCACA-AATTAA-CGT
66 TCTCATTTTCTCTCATGCCAAACACCATTTTGCTTCTTCAAAAC-TCACCAACACAATAAATCGT
**
42897005 TAAAAATGGGTTGATGTTTG-AAAAAAATCCCAAATCATCTCAAAACCTAATTTAATACAAT
130 TAAAAATGGGTTGA-GTCAGAAAAAAAATCCCAAATCATCTCAAAACCTAATTTAATACAAT
*
42897066 TTTTTTCTCCTTTT
1 TTTTTTCTCATTTT
42897080 CTCTATTGCC
Statistics
Matches: 178, Mismatches: 19, Indels: 16
0.84 0.09 0.08
Matches are distributed among these distances:
185 53 0.30
186 17 0.10
187 8 0.04
188 3 0.02
192 12 0.07
193 41 0.23
194 3 0.02
197 41 0.23
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (190 bp):
TTTTTTCTCATTTTGTTTCATATTCTTTCTTCTTCCCGCATTCTCTCTTCTCCTCCAAATTTTTC
TCTCATTTTCTCTCATGCCAAACACCATTTTGCTTCTTCAAAACTCACCAACACAATAAATCGTT
AAAAATGGGTTGAGTCAGAAAAAAAATCCCAAATCATCTCAAAACCTAATTTAATACAAT
Found at i:42919993 original size:28 final size:28
Alignment explanation
Indices: 42919940--42920005 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
42919930 AGGTCATAAG
42919940 AGCAT-ACTCTGTATTTTGGCTCGTAAA
1 AGCATAACTCTGTATTTTGGCTCGTAAA
* *
42919967 AGCATAACTCTGTATTCTT-GCTTGTAAG
1 AGCATAACTCTGTATT-TTGGCTCGTAAA
42919995 AGCATAACTCT
1 AGCATAACTCT
42920006 AGCTCATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 5 0.14
28 28 0.80
29 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (28 bp):
AGCATAACTCTGTATTTTGGCTCGTAAA
Found at i:42923923 original size:22 final size:22
Alignment explanation
Indices: 42923895--42923950 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
42923885 CTGCTGGGGA
*
42923895 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAATGCTG
*
42923917 AACAGAAGCATACACAATGCTG
1 AACAGAAGCACACACAATGCTG
42923939 AACAGTAAGCAC
1 AACAG-AAGCAC
42923951 GCTAACGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.45, C:0.25, G:0.20, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAATGCTG
Found at i:42960062 original size:17 final size:18
Alignment explanation
Indices: 42960022--42960062 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
42960012 TTGTCTCTAG
42960022 GTGATTATTTGCATGTAT
1 GTGATTATTTGCATGTAT
*
42960040 GT-ATTATTT-CATTTAT
1 GTGATTATTTGCATGTAT
*
42960056 TTGATTA
1 GTGATTA
42960063 GCATGAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 11 0.55
18 2 0.10
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.56
Consensus pattern (18 bp):
GTGATTATTTGCATGTAT
Found at i:42965253 original size:118 final size:118
Alignment explanation
Indices: 42965044--42965277 Score: 423
Period size: 118 Copynumber: 2.0 Consensus size: 118
42965034 AAAAAAAGAT
42965044 CAATGTCTGCTTTAGGCAATTAATGCATCAATTAGTTTGAGTTCGAGGCTCTGCTTATAGGCATA
1 CAATGTCTGCTTTAGGCAATTAATGCATCAATTAGTTTGAGTTCGAGGCTCTGCTTATAGGCATA
42965109 AAGACAAGCATGGCTAGTTACATAAGTATGATTGCTCCCTCCCCACAAAAAAC
66 AAGACAAGCATGGCTAGTTACATAAGTATGATTGCTCCCTCCCCACAAAAAAC
* *
42965162 CAATGTCTGCTTTGGGCAATTAATGCATCAATTAGTTTGAGTTCTAGGCTCTGCTTATAGGCATA
1 CAATGTCTGCTTTAGGCAATTAATGCATCAATTAGTTTGAGTTCGAGGCTCTGCTTATAGGCATA
** *
42965227 AAGACAAGCATGGCTAGTTATGTAAGTATGATTGCTCCCTCTCCACAAAAA
66 AAGACAAGCATGGCTAGTTACATAAGTATGATTGCTCCCTCCCCACAAAAA
42965278 TCAAGAAGAA
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 111 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (118 bp):
CAATGTCTGCTTTAGGCAATTAATGCATCAATTAGTTTGAGTTCGAGGCTCTGCTTATAGGCATA
AAGACAAGCATGGCTAGTTACATAAGTATGATTGCTCCCTCCCCACAAAAAAC
Found at i:42985171 original size:20 final size:20
Alignment explanation
Indices: 42985143--42985181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42985133 TTAAAGATAT
* *
42985143 TATTTTTATAAAATAAATTA
1 TATTATTATAAAAAAAATTA
42985163 TATTATTATAAAAAAAATT
1 TATTATTATAAAAAAAATT
42985182 TGTCCTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTATTATAAAAAAAATTA
Found at i:42989389 original size:15 final size:15
Alignment explanation
Indices: 42989365--42989399 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42989355 TCTTTTTTTT
*
42989365 GAGG-GGGGGGGGGG
1 GAGGAGGGGGGAGGG
42989379 GAGGAGGGGGGAGGG
1 GAGGAGGGGGGAGGG
42989394 GAGGAG
1 GAGGAG
42989400 CCTAATAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (15 bp):
GAGGAGGGGGGAGGG
Found at i:42989394 original size:18 final size:17
Alignment explanation
Indices: 42989365--42989399 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
42989355 TCTTTTTTTT
*
42989365 GAGGGGGGGGGGGGGAG
1 GAGGGGGGGGGGAGGAG
42989382 GAGGGGGGAGGGGAGGAG
1 GAGGGGGG-GGGGAGGAG
42989400 CCTAATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (17 bp):
GAGGGGGGGGGGAGGAG
Found at i:42993019 original size:10 final size:10
Alignment explanation
Indices: 42993004--42993046 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
42992994 CAAAATTTAT
42993004 ATTTTAAAAA
1 ATTTTAAAAA
42993014 ATTTT-AAAA
1 ATTTTAAAAA
42993023 ATTTTAAAAA
1 ATTTTAAAAA
*
42993033 ATATATAAAAA
1 AT-TTTAAAAA
42993044 ATT
1 ATT
42993047 AAAATTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.30
10 12 0.40
11 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:42993038 original size:33 final size:35
Alignment explanation
Indices: 42992969--42993038 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 35
42992959 TAATTTTCCA
* **
42992969 ATTTTCAAAATATTTATAAAAATTTCAAAATTTAT
1 ATTTTCAAAAAATTTATAAAAATTTCAAAAAATAT
*
42993004 ATTTT-AAAAAATTT-TAAAAATTTTAAAAAATAT
1 ATTTTCAAAAAATTTATAAAAATTTCAAAAAATAT
42993037 AT
1 AT
42993039 AAAAAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 18 0.58
34 8 0.26
35 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (35 bp):
ATTTTCAAAAAATTTATAAAAATTTCAAAAAATAT
Found at i:42993042 original size:19 final size:19
Alignment explanation
Indices: 42993004--42993043 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42992994 CAAAATTTAT
*
42993004 ATTTTAAAAAATTTTAAAA
1 ATTTTAAAAAATTATAAAA
42993023 ATTTTAAAAAATATATAAAA
1 ATTTTAAAAAAT-TATAAAA
42993043 A
1 A
42993044 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTTAAAAAATTATAAAA
Found at i:42993048 original size:19 final size:19
Alignment explanation
Indices: 42993007--42993050 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
42992997 AATTTATATT
* *
42993007 TTAAAAAATTTTAAAAATT
1 TTAAAAAATTATAAAAATA
42993026 TTAAAAAATATATAAAAA-A
1 TTAAAAAAT-TATAAAAATA
42993045 TTAAAA
1 TTAAAA
42993051 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAAAATTATAAAAATA
Found at i:42993399 original size:67 final size:68
Alignment explanation
Indices: 42993273--42993401 Score: 197
Period size: 67 Copynumber: 1.9 Consensus size: 68
42993263 AACGAAAAAA
* * **
42993273 TTTCAAATTGAAATTAGGATGATAAAACAGGATTCGTGAATTCGACTAACTTACTATTTTTTCAC
1 TTTCAAATTGAAATTAGGATGATAAAACAGGATTCGTGAATTAGACTAACTCAAAATTTTTTCAC
42993338 TCG
66 TCG
* *
42993341 TTTCAAATTG-AATTAGGATGATAAAATAGGATTTGTGAATTAGACTAACTCAAAATTTTTT
1 TTTCAAATTGAAATTAGGATGATAAAACAGGATTCGTGAATTAGACTAACTCAAAATTTTTT
42993402 TATTCGATTC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
67 45 0.82
68 10 0.18
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (68 bp):
TTTCAAATTGAAATTAGGATGATAAAACAGGATTCGTGAATTAGACTAACTCAAAATTTTTTCAC
TCG
Found at i:43005539 original size:12 final size:12
Alignment explanation
Indices: 43005522--43005605 Score: 59
Period size: 12 Copynumber: 7.3 Consensus size: 12
43005512 ATAACATCCA
* *
43005522 AACAACTAAAAT
1 AACAACAAAAAC
*
43005534 AACAACCAAAAC
1 AACAACAAAAAC
* * *
43005546 AGCAGCAAAAAT
1 AACAACAAAAAC
43005558 AACAAC-AAAAC
1 AACAACAAAAAC
*
43005569 AATAAC--AAA-
1 AACAACAAAAAC
*
43005578 AACAACAAAAAT
1 AACAACAAAAAC
*
43005590 AGCAACAAAAAC
1 AACAACAAAAAC
43005602 AACA
1 AACA
43005606 GCATCAAAAT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
9 5 0.09
10 3 0.05
11 12 0.22
12 35 0.64
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:43005557 original size:44 final size:44
Alignment explanation
Indices: 43005508--43005605 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
43005498 AAAAACGCAT
* * * * *
43005508 AAAAATAACATCCAAACAACTAA-AATAACAACCAAAACAGCAGC
1 AAAAATAACAACAAAACAA-TAACAAAAACAACAAAAACAGCAAC
*
43005552 AAAAATAACAACAAAACAATAACAAAAACAACAAAAATAGCAAC
1 AAAAATAACAACAAAACAATAACAAAAACAACAAAAACAGCAAC
*
43005596 AAAAACAACA
1 AAAAATAACA
43005606 GCATCAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.68, C:0.21, G:0.03, T:0.07
Consensus pattern (44 bp):
AAAAATAACAACAAAACAATAACAAAAACAACAAAAACAGCAAC
Found at i:43005579 original size:24 final size:24
Alignment explanation
Indices: 43005522--43005585 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
43005512 ATAACATCCA
*
43005522 AACAACTAAAATAACAACCAAAAC
1 AACAACAAAAATAACAACCAAAAC
* *
43005546 AGCAGCAAAAATAACAA-CAAAAC
1 AACAACAAAAATAACAACCAAAAC
* *
43005569 AATAACAAAAACAACAA
1 AACAACAAAAATAACAA
43005586 AAATAGCAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 19 0.58
24 14 0.42
ACGTcount: A:0.69, C:0.22, G:0.03, T:0.06
Consensus pattern (24 bp):
AACAACAAAAATAACAACCAAAAC
Found at i:43005668 original size:19 final size:17
Alignment explanation
Indices: 43005644--43005683 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
43005634 AACAGTAACT
43005644 AAAACAATAGGAAAAAACC
1 AAAACAATA--AAAAAACC
*
43005663 AAAACAGTAAAAAAACC
1 AAAACAATAAAAAAACC
43005680 AAAA
1 AAAA
43005684 TAGCAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.72, C:0.15, G:0.07, T:0.05
Consensus pattern (17 bp):
AAAACAATAAAAAAACC
Found at i:43005694 original size:18 final size:17
Alignment explanation
Indices: 43005655--43005696 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
43005645 AAACAATAGG
*
43005655 AAAAAACCAAAACAGTA
1 AAAAAACCAAAACAGCA
*
43005672 AAAAAACCAAAATAGCA
1 AAAAAACCAAAACAGCA
43005689 ATAAAAAC
1 A-AAAAAC
43005697 AGTAAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (17 bp):
AAAAAACCAAAACAGCA
Found at i:43031331 original size:31 final size:32
Alignment explanation
Indices: 43031271--43031331 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
43031261 AATCTTTTCT
43031271 TTTTTCTCTCAAAAACAATTTGTTTAGAAATA
1 TTTTTCTCTCAAAAACAATTTGTTTAGAAATA
* * *
43031303 TTTTTGTCTCAAAAA-TATTTTTTTAGAAA
1 TTTTTCTCTCAAAAACAATTTGTTTAGAAA
43031332 CGATACAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (32 bp):
TTTTTCTCTCAAAAACAATTTGTTTAGAAATA
Found at i:43044731 original size:21 final size:21
Alignment explanation
Indices: 43044707--43044746 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43044697 ACTAATTGAA
*
43044707 TATAAACTATTTATTTTATAT
1 TATAAACTATTAATTTTATAT
* *
43044728 TATAATCTCTTAATTTTAT
1 TATAAACTATTAATTTTAT
43044747 TAAAAATACA
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:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TATAAACTATTAATTTTATAT
Found at i:43044991 original size:6 final size:6
Alignment explanation
Indices: 43044976--43045009 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
43044966 ATTTTATTTT
*
43044976 ATTTGA ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTGG ATTT
43045010 CTCTCTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (6 bp):
ATTTGG
Found at i:43049540 original size:17 final size:17
Alignment explanation
Indices: 43049514--43049547 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43049504 TGGACCAATA
*
43049514 ATTTATTGAATAAAATC
1 ATTTAGTGAATAAAATC
43049531 ATTTAGTGAATAAAATC
1 ATTTAGTGAATAAAATC
43049548 TCGTGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (17 bp):
ATTTAGTGAATAAAATC
Found at i:43050823 original size:51 final size:51
Alignment explanation
Indices: 43050713--43050896 Score: 280
Period size: 51 Copynumber: 3.6 Consensus size: 51
43050703 TTTCATTTAA
* * * *
43050713 TACTCACGATGACATATTA-TCATCGAACCATTTAATTCGTCATGGATTCATT
1 TACTCACGATGACA-CTTAGTCATCGGACC-TTTAATTCGTAAAGGATTCATT
*
43050765 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
*
43050816 TAATCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
*
43050867 TACTGACGATGACACTTAGTCATCGGACCT
1 TACTCACGATGACACTTAGTCATCGGACCT
43050897 ATCGTTTATA
Statistics
Matches: 122, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
51 99 0.81
52 23 0.19
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
Found at i:43057210 original size:70 final size:69
Alignment explanation
Indices: 43057122--43057266 Score: 227
Period size: 70 Copynumber: 2.1 Consensus size: 69
43057112 ATAAAATCTA
* * *
43057122 ATTTTTAATAAAATTCGTGATTCCAAATATATTATTATTCTTTATATTTTTTAATAAAAAATTTA
1 ATTTTCAATAAAACTCGTGATTCCAAATATATTATTATTCTCTATATTTTTTAATAAAAAATTTA
43057187 TTGT
66 TTGT
* * *
43057191 AGTTTTCAATAAAACTCGTGATTCTAAATATATTATTATTCTCTATATTTTTTAGTAAAAATTTT
1 A-TTTTCAATAAAACTCGTGATTCCAAATATATTATTATTCTCTATATTTTTTAATAAAAAATTT
43057256 ATTGT
65 ATTGT
43057261 ATTTTC
1 ATTTTC
43057267 TCATGCACTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
69 6 0.09
70 63 0.91
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (69 bp):
ATTTTCAATAAAACTCGTGATTCCAAATATATTATTATTCTCTATATTTTTTAATAAAAAATTTA
TTGT
Found at i:43059893 original size:16 final size:17
Alignment explanation
Indices: 43059872--43059905 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
43059862 TTATGATAGA
43059872 AGATTTAATTG-AAGTG
1 AGATTTAATTGAAAGTG
43059888 AGATTTAATTGAAAGTG
1 AGATTTAATTGAAAGTG
43059905 A
1 A
43059906 TATGTTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (17 bp):
AGATTTAATTGAAAGTG
Found at i:43060082 original size:23 final size:24
Alignment explanation
Indices: 43060056--43060100 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
43060046 TACTATAAAA
43060056 AAATAG-ATCATTTACGTAATTTT
1 AAATAGAATCATTTACGTAATTTT
* * *
43060079 AAATTGAATTATTTTCGTAATT
1 AAATAGAATCATTTACGTAATT
43060101 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (24 bp):
AAATAGAATCATTTACGTAATTTT
Found at i:43069499 original size:20 final size:20
Alignment explanation
Indices: 43069474--43069520 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
43069464 TACATATTAT
43069474 TATTGTTCATGATTTGATCC
1 TATTGTTCATGATTTGATCC
43069494 TATTGTTCATGATTTGATCC
1 TATTGTTCATGATTTGATCC
43069514 TATTGTT
1 TATTGTT
43069521 TATAGGACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.13, G:0.15, T:0.53
Consensus pattern (20 bp):
TATTGTTCATGATTTGATCC
Found at i:43087570 original size:30 final size:30
Alignment explanation
Indices: 43087531--43087588 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
43087521 CTTAATAACC
* *
43087531 CAATTACTTAAATAAAAACTTTCGAATAGT
1 CAATGACTTAAATAAAAACTTTCAAATAGT
*
43087561 CAATGACTTAAATGAAAACTTTCAAATA
1 CAATGACTTAAATAAAAACTTTCAAATA
43087589 ATTTAGTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (30 bp):
CAATGACTTAAATAAAAACTTTCAAATAGT
Found at i:43094401 original size:97 final size:97
Alignment explanation
Indices: 43094235--43094428 Score: 273
Period size: 97 Copynumber: 2.0 Consensus size: 97
43094225 AACCTTAAAA
* * * *
43094235 AAGGGGATTTGATTATCCCAGTTTAAAGAAAAGTCGCGCCTAGTAAGTTCAGGCACAAATTTTCA
1 AAGGGGATTCGATTATCCCAGTTTAAAGAAAAATCGCGCCTAGTAAGTTAAGGAACAAATTTTCA
*
43094300 AAACCCA-AAATAAAAGAATATCACCTTGATTT
66 AAA-CCAGAAATAAAAGAATATCACCTCGATTT
* * * *
43094332 AAGGGTATTCGATTATCTCAGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGAACGAATTTTCA
1 AAGGGGATTCGATTATCCCAGTTTAAAGAAAAATCGCGCCTAGTAAGTTAAGGAACAAATTTTCA
* *
43094397 AAACCAGAAATAAAGGAATATTACCTCGATTT
66 AAACCAGAAATAAAAGAATATCACCTCGATTT
43094429 TAAATATTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 3 0.04
97 82 0.96
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (97 bp):
AAGGGGATTCGATTATCCCAGTTTAAAGAAAAATCGCGCCTAGTAAGTTAAGGAACAAATTTTCA
AAACCAGAAATAAAAGAATATCACCTCGATTT
Found at i:43094768 original size:29 final size:29
Alignment explanation
Indices: 43094736--43094876 Score: 149
Period size: 29 Copynumber: 4.8 Consensus size: 29
43094726 GAAAGTTTTA
*
43094736 AGGGCAAAAATGTCATTTTTGGAAAATTC
1 AGGGCAAAAATGTGATTTTTGGAAAATTC
* * *
43094765 AGGGTAAAAATGTGATTTTTGGAAATTTG
1 AGGGCAAAAATGTGATTTTTGGAAAATTC
*
43094794 AGGGCAAAAATGTGATTTTT-GAAAGTTC
1 AGGGCAAAAATGTGATTTTTGGAAAATTC
* ** * *
43094822 GGGGGCAAAAAATGCAATTTTTGGAAGATTG
1 -AGGGC-AAAAATGTGATTTTTGGAAAATTC
* *
43094853 AGGGTAGAAATGTGATTTTTGGAA
1 AGGGCAAAAATGTGATTTTTGGAA
43094877 GTTCGAGGGG
Statistics
Matches: 91, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
28 6 0.07
29 64 0.70
30 16 0.18
31 5 0.05
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
AGGGCAAAAATGTGATTTTTGGAAAATTC
Found at i:43094804 original size:88 final size:88
Alignment explanation
Indices: 43094712--43095024 Score: 271
Period size: 88 Copynumber: 3.6 Consensus size: 88
43094702 GTTTGGGGTT
** **
43094712 AAAATGTAATTTAGGAAAGTTTTAAGGGCAAAAATGTCATTTTTGGAAAATTCAGGGTAAAAATG
1 AAAATGTAATTTTTGAAAG-TTTGGGGGCAAAAATGTCATTTTTGGAAAATTCAGGGTAAAAATG
*
43094777 TGATTTTTGGAAATTTGA-GGGCA
65 TGATTTTTGGAAATTCGAGGGGCA
* * * * *
43094800 AAAATGTGATTTTTGAAAGTTCGGGGGCAAAAAATG-CAATTTTTGGAAGATTGAGGGTAGAAAT
1 AAAATGTAATTTTTGAAAGTTTGGGGGC-AAAAATGTC-ATTTTTGGAAAATTCAGGGTAAAAAT
* **
43094864 GTGATTTTTGGAAGTTCGAGGGGTG
64 GTGATTTTTGGAAATTCGAGGGGCA
* ** ** **
43094889 AAAATGTAATTTTTGAGAAGTTTGGGGGCAAAAATGTAATTTTAAG-AAGGTC-GGGGCAAAATG
1 AAAATGTAATTTTTGA-AAGTTTGGGGGCAAAAATGTCATTTTTGGAAAATTCAGGGTAAAAATG
* * * *
43094952 TAATTTTTGCGAAGTTTGA-GGGTA
65 TGATTTTTG-GAAATTCGAGGGGCA
* * *
43094976 AAAATATAATTTTTGAGAAGTTTGGGGGTC-GAAATGT-AATTTTGGAAAA
1 AAAATGTAATTTTTGA-AAGTTTGGGGG-CAAAAATGTCATTTTTGGAAAA
43095025 GTATAGGGGT
Statistics
Matches: 183, Mismatches: 34, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
86 5 0.03
87 62 0.34
88 74 0.40
89 31 0.17
90 11 0.06
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (88 bp):
AAAATGTAATTTTTGAAAGTTTGGGGGCAAAAATGTCATTTTTGGAAAATTCAGGGTAAAAATGT
GATTTTTGGAAATTCGAGGGGCA
Found at i:43094864 original size:59 final size:60
Alignment explanation
Indices: 43094736--43095018 Score: 246
Period size: 59 Copynumber: 4.8 Consensus size: 60
43094726 GAAAGTTTTA
* * * * *
43094736 AGGGCAAAAATGTCATTTTTG-GAAAATTC-AGGGTAAAAATGTGATTTTTG-GAA-ATTTG
1 AGGGCAAAAATGTGATTTTTGAG-AAGTTCGGGGGCAAAAATGTAATTTTTGAGAAGA-TTG
*
43094794 AGGGCAAAAATGTGATTTTTGA-AAGTTCGGGGGCAAAAAATGCAATTTTTG-GAAGATTG
1 AGGGCAAAAATGTGATTTTTGAGAAGTTCGGGGGC-AAAAATGTAATTTTTGAGAAGATTG
* * ** *
43094853 AGGGTAGAAATGTGATTTTTG-GAAGTTCGAGGGGTGAAAATGTAATTTTTGAGAAGTTTG
1 AGGGCAAAAATGTGATTTTTGAGAAGTTCG-GGGGCAAAAATGTAATTTTTGAGAAGATTG
* * * * * *
43094913 GGGGCAAAAATGT-AATTTTAAGAAGGTC-GGGGC-AAAATGTAATTTTTGCGAAGTTTG
1 AGGGCAAAAATGTGATTTTTGAGAAGTTCGGGGGCAAAAATGTAATTTTTGAGAAGATTG
* * * * *
43094970 AGGGTAAAAATATAATTTTTGAGAAGTTTGGGGGTC-GAAATGTAATTTT
1 AGGGCAAAAATGTGATTTTTGAGAAGTTCGGGGG-CAAAAATGTAATTTT
43095019 GGAAAAGTAT
Statistics
Matches: 186, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
57 38 0.20
58 38 0.20
59 69 0.37
60 41 0.22
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (60 bp):
AGGGCAAAAATGTGATTTTTGAGAAGTTCGGGGGCAAAAATGTAATTTTTGAGAAGATTG
Found at i:43094877 original size:29 final size:29
Alignment explanation
Indices: 43094684--43095022 Score: 210
Period size: 30 Copynumber: 11.6 Consensus size: 29
43094674 ATCGGGATCG
* * *
43094684 AAAATG-AAGTTTTGGAGAGTTTG-GGGTT
1 AAAATGTAATTTTTGGA-AGATTGAGGGTA
* * * *
43094712 AAAATGTAA-TTTAGGAAAGTTTTAAGGGCA
1 AAAATGTAATTTTTGG-AAG-ATTGAGGGTA
* * *
43094742 AAAATGTCATTTTTGGAAAATTCAGGGTA
1 AAAATGTAATTTTTGGAAGATTGAGGGTA
* *
43094771 AAAATGTGATTTTTGGAA-ATTTGAGGGCA
1 AAAATGTAATTTTTGGAAGA-TTGAGGGTA
* * * *
43094800 AAAATGTGATTTTTGAAAG-TTCGGGGGCAA
1 AAAATGTAATTTTTGGAAGATT-GAGGG-TA
*
43094830 AAAATGCAATTTTTGGAAGATTGAGGGTA
1 AAAATGTAATTTTTGGAAGATTGAGGGTA
* * *
43094859 GAAATGTGATTTTTGGAAG-TTCGAGGGGTG
1 AAAATGTAATTTTTGGAAGATT-GA-GGGTA
* * *
43094889 AAAATGTAATTTTTGAGAAGTTTGGGGGCA
1 AAAATGTAATTTTTG-GAAGATTGAGGGTA
** * * *
43094919 AAAATGTAATTTTAAGAAGGTCG-GGG-C
1 AAAATGTAATTTTTGGAAGATTGAGGGTA
*
43094946 AAAATGTAATTTTTGCGAAGTTTGAGGGTA
1 AAAATGTAATTTTTG-GAAGATTGAGGGTA
* * * *
43094976 AAAATATAATTTTTGAGAAGTTTGGGGGTC
1 AAAATGTAATTTTTG-GAAGATTGAGGGTA
*
43095006 GAAATGTAA-TTTTGGAA
1 AAAATGTAATTTTTGGAA
43095023 AAGTATAGGG
Statistics
Matches: 248, Mismatches: 46, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
27 13 0.05
28 30 0.12
29 91 0.37
30 100 0.40
31 12 0.05
32 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGATTGAGGGTA
Found at i:43095034 original size:30 final size:30
Alignment explanation
Indices: 43094971--43095047 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
43094961 CGAAGTTTGA
* * * * *
43094971 GGGTAAAAATATAATTTTTGAGAAGTTTGG
1 GGGTCAAAATATAATTTTGGAAAAGTATAG
* *
43095001 GGGTCGAAATGTAATTTTGGAAAAGTATAG
1 GGGTCAAAATATAATTTTGGAAAAGTATAG
*
43095031 GGGTCAAAATATGATTT
1 GGGTCAAAATATAATTT
43095048 CTAGACAGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTGGAAAAGTATAG
Found at i:43096171 original size:4 final size:4
Alignment explanation
Indices: 43096162--43096215 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
43096152 CTTTCAACTA
* * *
43096162 TTAT TTAT TTAT TTAT TTAT TAAT ATTAT TTAAT ATAT TTAT TAAT TATAT
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TT-AT TTAT TTAT TTAT T-TAT
43096213 TTA
1 TTA
43096216 ATATACAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 32 0.78
5 9 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (4 bp):
TTAT
Found at i:43096200 original size:22 final size:21
Alignment explanation
Indices: 43096160--43096220 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
43096150 TCCTTTCAAC
*
43096160 TATT-ATTTATTT-ATTTATT
1 TATTAATTTATTTAATATATT
43096179 TATTAATATTATTTAATATATT
1 TATTAAT-TTATTTAATATATT
43096201 TATTAATTATATTTAATATA
1 TATTAATT-TATTTAATATA
43096221 CAATAAATGC
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 4 0.11
20 2 0.05
21 7 0.19
22 24 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTAATTTATTTAATATATT
Found at i:43096203 original size:13 final size:13
Alignment explanation
Indices: 43096162--43096215 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
43096152 CTTTCAACTA
*
43096162 TTATTT-ATTTAT
1 TTATTTAATATAT
*
43096174 TTATTTATTA-AT
1 TTATTTAATATAT
43096186 ATTATTTAATATAT
1 -TTATTTAATATAT
43096200 TTA-TTAATTATAT
1 TTATTTAA-TATAT
43096213 TTA
1 TTA
43096216 ATATACAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 12 0.34
13 21 0.60
14 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTTAATATAT
Found at i:43096841 original size:6 final size:6
Alignment explanation
Indices: 43096830--43096940 Score: 81
Period size: 6 Copynumber: 19.3 Consensus size: 6
43096820 GGATATTATT
* ** *
43096830 AATTTA AATTTA GAA--TA ATTTTA AATTTA AAAATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
43096877 AA-TTA AATTTA AATTTA AA-ATA AATTTA AACTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
** *
43096922 ACCTTA AA-ATA AATTTA AA
1 AATTTA AATTTA AATTTA AA
43096941 AAGAAATAGG
Statistics
Matches: 81, Mismatches: 17, Indels: 14
0.72 0.15 0.12
Matches are distributed among these distances:
4 1 0.01
5 19 0.23
6 59 0.73
7 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:43096854 original size:17 final size:17
Alignment explanation
Indices: 43096830--43096940 Score: 150
Period size: 17 Copynumber: 6.5 Consensus size: 17
43096820 GGATATTATT
*
43096830 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
43096847 ATTTTAAATTTAAAAATA
1 AATTTAAATTT-AAAATA
* *
43096865 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
43096882 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
43096899 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
**
43096916 AATTTAACCTTAAAATA
1 AATTTAAATTTAAAATA
43096933 AATTTAAA
1 AATTTAAA
43096941 AAGAAATAGG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
17 69 0.83
18 14 0.17
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:43102124 original size:13 final size:13
Alignment explanation
Indices: 43102106--43102138 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
43102096 CACTTTGGTC
43102106 CACATTTTTTTTT
1 CACATTTTTTTTT
43102119 CACA-TTTTTTTT
1 CACATTTTTTTTT
43102131 CACATTTT
1 CACATTTT
43102139 AGCCCAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (13 bp):
CACATTTTTTTTT
Found at i:43102315 original size:22 final size:23
Alignment explanation
Indices: 43102229--43102308 Score: 144
Period size: 23 Copynumber: 3.5 Consensus size: 23
43102219 GCTGGGGAAA
*
43102229 CAGTAAGCACACACAGTGCAATC
1 CAGTAGGCACACACAGTGCAATC
43102252 CAGTAGGCACACACAGTGCAATC
1 CAGTAGGCACACACAGTGCAATC
43102275 CAGTAGGCACACACAGTGCAAT-
1 CAGTAGGCACACACAGTGCAATC
43102297 CAGTAGGCACAC
1 CAGTAGGCACAC
43102309 GAGGTGCGAA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 12 0.21
23 44 0.79
ACGTcount: A:0.36, C:0.30, G:0.21, T:0.12
Consensus pattern (23 bp):
CAGTAGGCACACACAGTGCAATC
Found at i:43102330 original size:45 final size:46
Alignment explanation
Indices: 43102225--43102332 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 46
43102215 AAGTGCTGGG
43102225 GAAACAGTAAGCACACACAGTGCAATCCAGTAGGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGCAATCCAGTAGGCACACACAGTGC
* * *
43102271 -AATCCAGTAGGCACACACAGTGCAAT-CAGTAGGCACACGA-GGTGC
1 GAA-ACAGTAAGCACACACAGTGCAATCCAGTAGGCACAC-ACAGTGC
*
43102316 GAAACAATAAGCACACA
1 GAAACAGTAAGCACACA
43102333 AAATGCGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 29 0.55
46 24 0.45
ACGTcount: A:0.40, C:0.27, G:0.22, T:0.11
Consensus pattern (46 bp):
GAAACAGTAAGCACACACAGTGCAATCCAGTAGGCACACACAGTGC
Found at i:43109478 original size:22 final size:23
Alignment explanation
Indices: 43109444--43109499 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
43109434 GCTGGGGAAA
* **
43109444 CAGTAAGCACACACAGTGC-AAT
1 CAGTAGGCACACACAGCACAAAT
* *
43109466 CAGTAGGCGCACATAGCACAAAT
1 CAGTAGGCACACACAGCACAAAT
43109489 CAGTAGGCACA
1 CAGTAGGCACA
43109500 TGAGGTGCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.12
Consensus pattern (23 bp):
CAGTAGGCACACACAGCACAAAT
Found at i:43110467 original size:33 final size:36
Alignment explanation
Indices: 43110407--43110472 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
43110397 CTCTTTTACC
* *
43110407 CCTTGCTCTATTCTTTTCCTTTGTCTTCAATTTGAT
1 CCTTGCTCTATTCTTCTCCTTTCTCTTCAATTTGAT
43110443 CCTTG-TCT-TTCTTCT-CTTTCTCTTCAATTT
1 CCTTGCTCTATTCTTCTCCTTTCTCTTCAATTT
43110473 CACATAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 14 0.50
34 6 0.21
35 3 0.11
36 5 0.18
ACGTcount: A:0.09, C:0.27, G:0.06, T:0.58
Consensus pattern (36 bp):
CCTTGCTCTATTCTTCTCCTTTCTCTTCAATTTGAT
Found at i:43110536 original size:48 final size:48
Alignment explanation
Indices: 43110474--43110575 Score: 195
Period size: 48 Copynumber: 2.1 Consensus size: 48
43110464 CTTCAATTTC
43110474 ACATAAACACATATAAGCTATAAGCTATAATTTAATAATTTTCATGCT
1 ACATAAACACATATAAGCTATAAGCTATAATTTAATAATTTTCATGCT
43110522 ACATAAACACATATAAGCTATAAGCTATAATTTAATAATTTTCATGCT
1 ACATAAACACATATAAGCTATAAGCTATAATTTAATAATTTTCATGCT
*
43110570 AAATAA
1 ACATAA
43110576 CAGTAAAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (48 bp):
ACATAAACACATATAAGCTATAAGCTATAATTTAATAATTTTCATGCT
Found at i:43115687 original size:14 final size:14
Alignment explanation
Indices: 43115668--43115694 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43115658 CAAATTTATA
43115668 GTATGCATTGGATC
1 GTATGCATTGGATC
43115682 GTATGCATTGGAT
1 GTATGCATTGGAT
43115695 ATAGCAAAAT
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:0.22, C:0.11, G:0.30, T:0.37
Consensus pattern (14 bp):
GTATGCATTGGATC
Found at i:43119211 original size:17 final size:17
Alignment explanation
Indices: 43119189--43119227 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
43119179 AGGTGGAGAA
* *
43119189 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
43119206 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
43119223 CTTGT
1 CTTGT
43119228 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:43123966 original size:15 final size:14
Alignment explanation
Indices: 43123941--43123971 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
43123931 TTTAAAACAT
43123941 AATTTAAAATTTAA
1 AATTTAAAATTTAA
43123955 AATTTAAAAATTTAA
1 AATTT-AAAATTTAA
43123970 AA
1 AA
43123972 AGTTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTAAAATTTAA
Found at i:43123987 original size:8 final size:7
Alignment explanation
Indices: 43123941--43123971 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
43123931 TTTAAAACAT
43123941 AATTTAA
1 AATTTAA
43123948 AATTTAA
1 AATTTAA
43123955 AATTTAAA
1 AATTT-AA
43123963 AATTTAA
1 AATTTAA
43123970 AA
1 AA
43123972 AGTTATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AATTTAA
Found at i:43124415 original size:13 final size:13
Alignment explanation
Indices: 43124397--43124421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43124387 TAATGATTTT
43124397 TAATTTTTATAAA
1 TAATTTTTATAAA
43124410 TAATTTTTATAA
1 TAATTTTTATAA
43124422 TGTTTTTGAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTTTTATAAA
Found at i:43135908 original size:17 final size:18
Alignment explanation
Indices: 43135888--43135922 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
43135878 AACAGATCAT
*
43135888 TATTACAAA-AAAAATAA
1 TATTAAAAATAAAAATAA
43135905 TATTAAAAATAAAAATAA
1 TATTAAAAATAAAAATAA
43135923 AATCATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TATTAAAAATAAAAATAA
Found at i:43136343 original size:23 final size:21
Alignment explanation
Indices: 43136317--43136369 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
43136307 GAAAATTTAA
43136317 AAATGTTAATTTTGTTAAATAAT
1 AAAT-TTAATTTT-TTAAATAAT
*
43136340 AAA-TTATATTTTTTAAATAGT
1 AAATTTA-ATTTTTTAAATAAT
43136361 AAATATTAA
1 AAAT-TTAA
43136370 GTTTATTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 14 0.54
22 6 0.23
23 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (21 bp):
AAATTTAATTTTTTAAATAAT
Found at i:43138342 original size:31 final size:30
Alignment explanation
Indices: 43138275--43138350 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 30
43138265 TATCTTTTAA
43138275 AAAATATTTCAAAATATTTTTTATAATTAATAT
1 AAAAT-TTT-AAAATATTTTTTATAATT-ATAT
*
43138308 AAAATTTTAAAATAGTTTTTTTATAATT-TTT
1 AAAATTTTAAAATA--TTTTTTATAATTATAT
*
43138339 AAAATTTAAAAA
1 AAAATTTTAAAA
43138351 AATTAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 19 0.49
32 3 0.08
33 17 0.44
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
AAAATTTTAAAATATTTTTTATAATTATAT
Found at i:43140448 original size:20 final size:18
Alignment explanation
Indices: 43140420--43140467 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
43140410 TCACGTCAAT
*
43140420 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
43140440 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
43140460 AAATTATT
1 AAATTATT
43140468 AAATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 13 0.52
21 2 0.08
22 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:43140461 original size:29 final size:31
Alignment explanation
Indices: 43140429--43140501 Score: 123
Period size: 29 Copynumber: 2.4 Consensus size: 31
43140419 TAAATAATTT
43140429 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
*
43140458 TAAAATTATTAAATTTATTTTTTTAAAATAA
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
43140489 TAAAATTATTAAA
1 TAAAATTATTAAA
43140502 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 16 0.39
30 11 0.27
31 14 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAA
Found at i:43141524 original size:26 final size:24
Alignment explanation
Indices: 43141479--43141526 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
43141469 GGTTATTAGA
**
43141479 AAAATGTAAGAAAATCTGAAAATT
1 AAAATGTAAGAAAAGATGAAAATT
43141503 AAAATGATAAAGAAAAGATGAAAA
1 AAAATG-T-AAGAAAAGATGAAAA
43141527 GATGAAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 1 0.05
26 13 0.65
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.19
Consensus pattern (24 bp):
AAAATGTAAGAAAAGATGAAAATT
Found at i:43141586 original size:27 final size:27
Alignment explanation
Indices: 43141556--43141632 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 27
43141546 AAATTGGAAA
*
43141556 TTAAAATTA-TTTAATAATTTTATTATT
1 TTAAAATAATTTTAATAATTTTA-TATT
43141583 TTAAAAAATAATTTTAATAATTTTATATT
1 TT--AAAATAATTTTAATAATTTTATATT
43141612 TTAAAAAATAATTTTAA-AATT
1 TT--AAAATAATTTTAATAATT
43141633 ATTTGTTGAC
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 2 0.04
28 4 0.09
29 27 0.59
30 13 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAAAATAATTTTAATAATTTTATATT
Found at i:43141596 original size:13 final size:13
Alignment explanation
Indices: 43141580--43141630 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
43141570 TAATTTTATT
43141580 ATTTTAAAAAATA
1 ATTTTAAAAAATA
**
43141593 ATTTTAATAATTTTA
1 ATTTTAA-AA-AATA
43141608 TATTTTAAAAAATA
1 -ATTTTAAAAAATA
43141622 ATTTTAAAA
1 ATTTTAAAA
43141631 TTATTTGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 16 0.52
14 4 0.13
15 4 0.13
16 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTTTAAAAAATA
Found at i:43141596 original size:29 final size:28
Alignment explanation
Indices: 43141558--43141625 Score: 109
Period size: 29 Copynumber: 2.4 Consensus size: 28
43141548 ATTGGAAATT
*
43141558 AAAATTATTTAATAATTTTATTATTTTAA
1 AAAATAATTTAATAATTTTA-TATTTTAA
43141587 AAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAA-TTTAATAATTTTATATTTTAA
43141616 AAAATAATTT
1 AAAATAATTT
43141626 TAAAATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 3 0.08
29 21 0.57
30 13 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AAAATAATTTAATAATTTTATATTTTAA
Found at i:43141626 original size:29 final size:30
Alignment explanation
Indices: 43141565--43141632 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
43141555 ATTAAAATTA
43141565 TTTAATAATTTTATTATTTTAAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAATAAT
43141595 TTTAATAATTTTA-TATTTTAAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAATAAT
43141624 TTTAA-AATT
1 TTTAATAATT
43141633 ATTTGTTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 4 0.11
29 21 0.55
30 13 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTAATAATTTTATTATTTTAAAAAATAAT
Found at i:43144548 original size:2 final size:2
Alignment explanation
Indices: 43144541--43144584 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
43144531 GAAAGGAAAG
43144541 CT CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT CT
43144583 CT
1 CT
43144585 TTCAATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:43148412 original size:38 final size:38
Alignment explanation
Indices: 43148361--43148436 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
43148351 CCTCCTGGTA
43148361 ACATGGTTGCTTCAAGAAGTTGACCCCTCTTCAATTCT
1 ACATGGTTGCTTCAAGAAGTTGACCCCTCTTCAATTCT
43148399 ACATGGTTGCTTCAAGAAGTTGACCCCTCTTCAATTCT
1 ACATGGTTGCTTCAAGAAGTTGACCCCTCTTCAATTCT
43148437 TTCTTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (38 bp):
ACATGGTTGCTTCAAGAAGTTGACCCCTCTTCAATTCT
Found at i:43150847 original size:3 final size:3
Alignment explanation
Indices: 43150839--43150868 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
43150829 AATCAAAATG
43150839 GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
43150869 CATGCGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43151497 original size:15 final size:14
Alignment explanation
Indices: 43151483--43151518 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
43151473 GAGTAATTTA
43151483 ATTTTTTTTCTTTT
1 ATTTTTTTTCTTTT
*
43151497 ATGTTCTTTTCTTTT
1 AT-TTTTTTTCTTTT
43151512 ATTTTTT
1 ATTTTTT
43151519 ATTTTCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTCTTTT
Found at i:43153029 original size:26 final size:25
Alignment explanation
Indices: 43152996--43153044 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
43152986 TAAAATTTTT
43152996 TATATAAAAAAATTAAAATATATAA
1 TATATAAAAAAATTAAAATATATAA
*
43153021 TATATTAAAAATATTAAAATATAT
1 TATA-TAAAAAAATTAAAATATAT
43153045 GTTTCTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TATATAAAAAAATTAAAATATATAA
Found at i:43171390 original size:27 final size:27
Alignment explanation
Indices: 43171360--43171415 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
43171350 TGGTTGTAAT
43171360 TGTTGTTG-AGCATGTTGCTGTAGCTGC
1 TGTTGTTGCAGCA-GTTGCTGTAGCTGC
* *
43171387 TGTTGTTGCAGTAGTTGCTGTTGCTGC
1 TGTTGTTGCAGCAGTTGCTGTAGCTGC
43171414 TG
1 TG
43171416 CTGATGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.09, C:0.14, G:0.34, T:0.43
Consensus pattern (27 bp):
TGTTGTTGCAGCAGTTGCTGTAGCTGC
Found at i:43171395 original size:18 final size:18
Alignment explanation
Indices: 43171372--43171415 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43171362 TTGTTGAGCA
43171372 TGTTGCTGTAGCTGCTGT
1 TGTTGCTGTAGCTGCTGT
* *
43171390 TGTTGCAGTAGTTGCTGT
1 TGTTGCTGTAGCTGCTGT
*
43171408 TGCTGCTG
1 TGTTGCTG
43171416 CTGATGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.34, T:0.43
Consensus pattern (18 bp):
TGTTGCTGTAGCTGCTGT
Found at i:43176057 original size:13 final size:13
Alignment explanation
Indices: 43176008--43176057 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
43175998 TTAAATCAAG
* *
43176008 CTTTTTAAAAATA
1 CTTTTCAAAAGTA
*
43176021 CTTTTCAAAATTA
1 CTTTTCAAAAGTA
*
43176034 CTTTTCCAAAGTA
1 CTTTTCAAAAGTA
*
43176047 CTTCTCAAAAG
1 CTTTTCAAAAG
43176058 CAATGCTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (13 bp):
CTTTTCAAAAGTA
Found at i:43181231 original size:23 final size:23
Alignment explanation
Indices: 43181205--43181315 Score: 127
Period size: 23 Copynumber: 4.8 Consensus size: 23
43181195 TTACTGTTCA
*
43181205 GCACTATGTGTGCTTACTGATTC
1 GCACTATGTGTGCTTACTGATTT
*
43181228 GCACTATATGTGCTTACTGATTT
1 GCACTATGTGTGCTTACTGATTT
* * *
43181251 GCACTGTGTGTACTTACTGTTTT
1 GCACTATGTGTGCTTACTGATTT
*
43181274 GCACTTCATGTGT-C-TATTGATTT
1 GCAC-T-ATGTGTGCTTACTGATTT
*
43181297 GCACTGTGTGTGCTTACTG
1 GCACTATGTGTGCTTACTG
43181316 TTTTCCCAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.07
22 2 0.03
23 59 0.81
24 2 0.03
25 5 0.07
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (23 bp):
GCACTATGTGTGCTTACTGATTT
Found at i:43181316 original size:46 final size:46
Alignment explanation
Indices: 43181205--43181319 Score: 153
Period size: 46 Copynumber: 2.5 Consensus size: 46
43181195 TTACTGTTCA
* * *
43181205 GCACTATGTGTGCTTACTGATTCGCACTATATGTGCTTACTGATTT
1 GCACTGTGTGTGCTTACTGTTTTGCACTATATGTGCTTACTGATTT
* *
43181251 GCACTGTGTGTACTTACTGTTTTGCACT-TCATGTG-TCTATTGATTT
1 GCACTGTGTGTGCTTACTGTTTTGCACTAT-ATGTGCT-TACTGATTT
43181297 GCACTGTGTGTGCTTACTGTTTT
1 GCACTGTGTGTGCTTACTGTTTT
43181320 CCCAGCACTT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 2 0.03
46 59 0.97
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (46 bp):
GCACTGTGTGTGCTTACTGTTTTGCACTATATGTGCTTACTGATTT
Found at i:43182186 original size:13 final size:14
Alignment explanation
Indices: 43182158--43182204 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
43182148 TATTTAGAAA
*
43182158 TTTAATATTGTATT
1 TTTAATATTTTATT
*
43182172 TTTTAT-TTTTA-T
1 TTTAATATTTTATT
43182184 TTTAATATTTTATT
1 TTTAATATTTTATT
*
43182198 TTAAATA
1 TTTAATA
43182205 AACCTAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 12 0.44
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (14 bp):
TTTAATATTTTATT
Found at i:43182204 original size:14 final size:13
Alignment explanation
Indices: 43182158--43182201 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
43182148 TATTTAGAAA
*
43182158 TTTAATATTGTAT
1 TTTAATATTTTAT
*
43182171 TTT-TTATTTTTAT
1 TTTAATA-TTTTAT
43182184 TTTAATATTTTAT
1 TTTAATATTTTAT
43182197 TTTAA
1 TTTAA
43182202 ATAAACCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTAATATTTTAT
Found at i:43183234 original size:36 final size:37
Alignment explanation
Indices: 43183194--43183265 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
43183184 TCCATCCCCT
*
43183194 ATTAATTCC-T-AGTTGAATCCAATCTAAATTCTAAAC
1 ATTAATTCCTTAAGTTG-ATCCAATCTAAACTCTAAAC
* *
43183230 ATTAATTCCTTAATTTGATCCAATTTAAACTCTAAA
1 ATTAATTCCTTAAGTTGATCCAATCTAAACTCTAAA
43183266 AGATAAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 9 0.29
37 18 0.58
38 4 0.13
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.39
Consensus pattern (37 bp):
ATTAATTCCTTAAGTTGATCCAATCTAAACTCTAAAC
Found at i:43183318 original size:19 final size:19
Alignment explanation
Indices: 43183294--43183350 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
43183284 AAACATAAAT
43183294 TAAATACAAATTTAAATAA
1 TAAATACAAATTTAAATAA
* *
43183313 TAAATA-ATATCTTAAATAT
1 TAAATACAAAT-TTAAATAA
* * *
43183332 TAAATCCTAATTAAAATAA
1 TAAATACAAATTTAAATAA
43183351 AGTAAAACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 3 0.10
19 24 0.83
20 2 0.07
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATACAAATTTAAATAA
Found at i:43184090 original size:107 final size:106
Alignment explanation
Indices: 43183895--43184093 Score: 240
Period size: 107 Copynumber: 1.9 Consensus size: 106
43183885 ATATATTGGA
* * * * * *
43183895 CTTTTTGACGCGAAATGAAATGATACCCAAGCACTCCATCCCGGTTACTCAACCTAACATACTCC
1 CTTTTTGACGCGAAATGAAATAACAACCAAACACTCCATCCCGATTACTCAACCTAACACACTCC
* *
43183960 CAATCATTTTTTTCCTTTTTCTTTTTTCTAGAACGTGTCAGT
66 CAAT-ATTTTTTTCATTTCTCTTTTTTCTAGAACGTGTCAGT
* **
43184002 CTTTTTGACGCGAAATGAAATAACAACCAAACACTCCATCTCGATTACTCAGTCTAACACACT-C
1 CTTTTTGACGCGAAATGAAATAACAACCAAACACTCCATCCCGATTACTCAACCTAACACACTCC
*
43184066 CAAT-TTTACTTATTTATTTCTCTTTTTT
66 CAATATTT--TT-TTCATTTCTCTTTTTT
43184094 TTACCCGATT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
104 3 0.04
106 7 0.09
107 67 0.87
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (106 bp):
CTTTTTGACGCGAAATGAAATAACAACCAAACACTCCATCCCGATTACTCAACCTAACACACTCC
CAATATTTTTTTCATTTCTCTTTTTTCTAGAACGTGTCAGT
Found at i:43190894 original size:21 final size:21
Alignment explanation
Indices: 43190809--43190882 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
43190799 CCTCAATTTT
*
43190809 CTTTTGAAAATCTATAGTTTG
1 CTTTTGAAAATCTACAGTTTG
*
43190830 CTTTTGAAAATCTGCAGTTTG
1 CTTTTGAAAATCTACAGTTTG
*
43190851 CTTTTGAAAATCTGCAGTTTG
1 CTTTTGAAAATCTACAGTTTG
43190872 CTTTTGAAAAT
1 CTTTTGAAAAT
43190883 TTATAGATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (21 bp):
CTTTTGAAAATCTACAGTTTG
Found at i:43190894 original size:42 final size:42
Alignment explanation
Indices: 43190809--43190894 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
43190799 CCTCAATTTT
* * *
43190809 CTTTTGAAAATCTATAGTTTGCTTTTGAAAATCTGCAGTTTG
1 CTTTTGAAAATCTACAGTTTGCTTTTGAAAATCTACAGATTG
* * *
43190851 CTTTTGAAAATCTGCAGTTTGCTTTTGAAAATTTATAGATTG
1 CTTTTGAAAATCTACAGTTTGCTTTTGAAAATCTACAGATTG
43190893 CT
1 CT
43190895 ACTGAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (42 bp):
CTTTTGAAAATCTACAGTTTGCTTTTGAAAATCTACAGATTG
Found at i:43192937 original size:31 final size:31
Alignment explanation
Indices: 43192902--43192970 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
43192892 CTCTAAAAGA
43192902 TAAATACAAAAAAATAAATATAAAATAAAT-T
1 TAAAT-CAAAAAAATAAATATAAAATAAATAT
** * *
43192933 TAAATTTAAATAATAAATAATAAATTAAATAT
1 TAAATCAAAAAAATAAAT-ATAAAATAAATAT
43192965 TAAATC
1 TAAATC
43192971 CTAATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 10 0.32
31 15 0.48
32 6 0.19
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (31 bp):
TAAATCAAAAAAATAAATATAAAATAAATAT
Found at i:43194846 original size:6 final size:6
Alignment explanation
Indices: 43194837--43194863 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43194827 AACACAACAC
43194837 AACAAA AACAAA AACAAA AACAAA AAC
1 AACAAA AACAAA AACAAA AACAAA AAC
43194864 TCAATCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:43196871 original size:16 final size:16
Alignment explanation
Indices: 43196852--43196882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43196842 AAATTTATTT
*
43196852 TTATATAAAAATAATA
1 TTATAAAAAAATAATA
43196868 TTATAAAAAAATAAT
1 TTATAAAAAAATAAT
43196883 GTTGGCGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTATAAAAAAATAATA
Found at i:43206186 original size:19 final size:19
Alignment explanation
Indices: 43206162--43206198 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
43206152 TATAAAAAAA
43206162 ATAAATTGTGAAAGAGAAG
1 ATAAATTGTGAAAGAGAAG
43206181 ATAAATTGTGAAAGAGAA
1 ATAAATTGTGAAAGAGAA
43206199 AGAGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (19 bp):
ATAAATTGTGAAAGAGAAG
Found at i:43206306 original size:21 final size:22
Alignment explanation
Indices: 43206273--43206314 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
43206263 TAATAATTCG
*
43206273 ATAATTTAAAATAATTTTTTTAA
1 ATAATTT-AAATAATTATTTTAA
43206296 ATAATTT-AATAATTATTTT
1 ATAATTTAAATAATTATTTT
43206315 GAAACGAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATAATTTAAATAATTATTTTAA
Found at i:43217716 original size:16 final size:15
Alignment explanation
Indices: 43217695--43217749 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
43217685 ATTTAAAATC
43217695 ATTAAAAATAGTAAAA
1 ATTAAAAATA-TAAAA
*
43217711 ATT-AAATTATAAAA
1 ATTAAAAATATAAAA
*
43217725 AATAAAAATATTAAAA
1 ATTAAAAATA-TAAAA
43217741 ATTACAAAA
1 ATTA-AAAA
43217750 GAATGTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 7 0.22
15 10 0.31
16 11 0.34
17 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
ATTAAAAATATAAAA
Found at i:43217797 original size:29 final size:29
Alignment explanation
Indices: 43217726--43217828 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 29
43217716 ATTATAAAAA
* *
43217726 ATAAAAATATTA-AAAATTACAAAAGAATGT
1 ATAAAATTATTATAAAATGACAAAA-AAT-T
* *
43217756 GTAAAAATA-TATAAAAGTGA-AAAAAATT
1 ATAAAATTATTATAAAA-TGACAAAAAATT
43217784 ATAAAATTATTAT-AAATGACTAAAAAATT
1 ATAAAATTATTATAAAATGAC-AAAAAATT
43217813 ATAAAAATTATTATAA
1 AT-AAAATTATTATAA
43217829 TTATCATAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 13
0.78 0.05 0.16
Matches are distributed among these distances:
27 3 0.05
28 11 0.18
29 18 0.29
30 27 0.44
31 3 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (29 bp):
ATAAAATTATTATAAAATGACAAAAAATT
Found at i:43217818 original size:8 final size:9
Alignment explanation
Indices: 43217714--43217823 Score: 57
Period size: 9 Copynumber: 11.8 Consensus size: 9
43217704 AGTAAAAATT
43217714 AAATTATAA
1 AAATTATAA
43217723 AAA--ATAA
1 AAATTATAA
43217730 AAA-TATTAA
1 AAATTA-TAA
*
43217739 AAATTACAAA
1 AAATTA-TAA
*
43217749 AGAATGTGTAA
1 A-AAT-TATAA
43217760 AAATATATAA
1 AAAT-TATAA
* * *
43217770 AAGTGAAAA
1 AAATTATAA
43217779 AAATTAT-A
1 AAATTATAA
*
43217787 AAATTATTAT
1 AAATTA-TAA
*
43217797 AAATGACTAAA
1 AAATTA-T-AA
43217808 AAATTATAA
1 AAATTATAA
43217817 AAATTAT
1 AAATTAT
43217824 TATAATTATC
Statistics
Matches: 76, Mismatches: 17, Indels: 16
0.70 0.16 0.15
Matches are distributed among these distances:
7 7 0.09
8 8 0.11
9 26 0.34
10 22 0.29
11 12 0.16
12 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (9 bp):
AAATTATAA
Found at i:43217844 original size:29 final size:30
Alignment explanation
Indices: 43217776--43217849 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
43217766 ATAAAAGTGA
* *
43217776 AAAAAAT-TATAAAATTATTATAAATGACT
1 AAAAAATATAGAAAATTATTATAAATCACT
43217805 AAAAAATTATA-AAAATTATTATAATTATCA-T
1 AAAAAA-TATAGAAAATTATTATAA--ATCACT
43217836 -AAAAATATAGAAAA
1 AAAAAATATAGAAAA
43217850 GTGCAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
29 10 0.26
30 23 0.59
31 3 0.08
32 3 0.08
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAAAATATAGAAAATTATTATAAATCACT
Found at i:43218157 original size:2 final size:2
Alignment explanation
Indices: 43218150--43218187 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
43218140 TTTTAACATT
*
43218150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43218188 GTCTTTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:43218233 original size:19 final size:20
Alignment explanation
Indices: 43218200--43218237 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
43218190 CTTTAATATT
*
43218200 TATAATATTTTATAATTTTC
1 TATAATATTTAATAATTTTC
43218220 TATAAT-TTTAATAATTTT
1 TATAATATTTAATAATTTT
43218238 AATTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATAATATTTAATAATTTTC
Found at i:43218239 original size:9 final size:9
Alignment explanation
Indices: 43218191--43218240 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
43218181 ATTTATAGTC
43218191 TTTAAT-AT
1 TTTAATAAT
43218199 TTATAAT-AT
1 TT-TAATAAT
43218208 TTT-ATAAT
1 TTTAATAAT
*
43218216 TTTCTATAAT
1 TTT-AATAAT
43218226 TTTAATAAT
1 TTTAATAAT
43218235 TTTAAT
1 TTTAAT
43218241 TATAAAACAC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
7 2 0.05
8 8 0.22
9 19 0.51
10 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTAATAAT
Found at i:43222326 original size:27 final size:27
Alignment explanation
Indices: 43222271--43222330 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
43222261 TATTAAAAAA
*
43222271 ATTT-TAAATTATAAAATATTTTGTAT
1 ATTTATAAATTATAAAATATTTTATAT
43222297 ATTTATAAATTTATAAAA-A-TTTATATT
1 ATTTATAAA-TTATAAAATATTTTATA-T
43222324 ATTTATA
1 ATTTATA
43222331 TCCTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 9 0.30
27 13 0.43
28 8 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTATAAATTATAAAATATTTTATAT
Found at i:43225753 original size:2 final size:2
Alignment explanation
Indices: 43225746--43225772 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43225736 TCTTATTATT
43225746 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
43225773 CTTTTTATAT
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:43232256 original size:24 final size:23
Alignment explanation
Indices: 43232221--43232269 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
43232211 GTATTTATGT
43232221 TTATATTATAAA-AAGTAAAATTAA
1 TTATATTATAAATAAG-AAAA-TAA
43232245 TTATA-TATTAAATAAGAAAATAA
1 TTATATTA-TAAATAAGAAAATAA
43232268 TT
1 TT
43232270 TGATTCGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.30
24 13 0.57
25 3 0.13
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
TTATATTATAAATAAGAAAATAA
Found at i:43243326 original size:3 final size:3
Alignment explanation
Indices: 43243318--43243352 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
43243308 TTAATAGCAG
*
43243318 AAT AAT AAT GAT AAT AAT AAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
43243353 TTGGAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43243342 original size:16 final size:16
Alignment explanation
Indices: 43243321--43243352 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43243311 ATAGCAGAAT
*
43243321 AATAATGATAATAATA
1 AATAATAATAATAATA
43243337 AATAATAATAATAATA
1 AATAATAATAATAATA
43243353 TTGGAAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:43244714 original size:15 final size:15
Alignment explanation
Indices: 43244691--43244728 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
43244681 TGGTTCTTTC
*
43244691 TTTTCTTCTTTTTTT
1 TTTTTTTCTTTTTTT
43244706 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTTTT
43244721 TTTCTTTT
1 TTT-TTTT
43244729 TTGAAAGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTCTTTTTTT
Found at i:43244714 original size:18 final size:18
Alignment explanation
Indices: 43244691--43244730 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
43244681 TGGTTCTTTC
43244691 TTTTCTTCTTTTTTTT-TT
1 TTTTCTT-TTTTTTTTCTT
43244709 TTTTCTTTTTTTTTTCTT
1 TTTTCTTTTTTTTTTCTT
43244727 TTTT
1 TTTT
43244731 GAAAGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (18 bp):
TTTTCTTTTTTTTTTCTT
Found at i:43244717 original size:11 final size:11
Alignment explanation
Indices: 43244687--43244730 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
43244677 GGGTTGGTTC
43244687 TTTCTTTTCTTCT
1 TTTCTTTT-TT-T
43244700 TTT-TTTTTTT
1 TTTCTTTTTTT
43244710 TTTCTTTTTTT
1 TTTCTTTTTTT
43244721 TTTCTTTTTT
1 TTTCTTTTTT
43244731 GAAAGGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.13
11 19 0.63
12 4 0.13
13 3 0.10
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:43246100 original size:18 final size:18
Alignment explanation
Indices: 43246077--43246116 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
43246067 TAAATTTTCG
43246077 AACCTAAATGATTAACCC
1 AACCTAAATGATTAACCC
43246095 AACCTAAATGATTAACCC
1 AACCTAAATGATTAACCC
43246113 AACC
1 AACC
43246117 ATGATCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (18 bp):
AACCTAAATGATTAACCC
Found at i:43247198 original size:19 final size:20
Alignment explanation
Indices: 43247171--43247210 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43247161 GTTTTTACAG
* *
43247171 AAAATTAATTTAT-TTTTAA
1 AAAACTAATCTATCTTTTAA
43247190 AAAACTAATCTATCTTTTAA
1 AAAACTAATCTATCTTTTAA
43247210 A
1 A
43247211 CTTGTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAACTAATCTATCTTTTAA
Found at i:43250827 original size:18 final size:18
Alignment explanation
Indices: 43250804--43250858 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
43250794 TCAGAGTGAA
43250804 TTTAAAACTTTACACATT
1 TTTAAAACTTTACACATT
** **
43250822 TTTAAAAAAATTA-ACAAA
1 TTT-AAAACTTTACACATT
43250840 TTTAAAACTTTACACATT
1 TTTAAAACTTTACACATT
43250858 T
1 T
43250859 GGTTGGTTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
17 7 0.26
18 13 0.48
19 7 0.26
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAACTTTACACATT
Found at i:43251343 original size:19 final size:18
Alignment explanation
Indices: 43251319--43251356 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
43251309 ATATTCATTT
43251319 ATTTTTAAATATTTTTATA
1 ATTTTTAAATA-TTTTATA
*
43251338 ATTTTTATATATTTTATA
1 ATTTTTAAATATTTTATA
43251356 A
1 A
43251357 AATCATATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTAAATATTTTATA
Done.