Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021137.1 Corchorus olitorius cultivar O-4 contig21170, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 117218
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:521 original size:69 final size:70
Alignment explanation
Indices: 406--564 Score: 270
Period size: 69 Copynumber: 2.3 Consensus size: 70
396 TACGTATCAG
* * *
406 AGGGAATCC-TCCTCCATCTCCAACTCCAACTCCTCCAACCCTACCAACTTACACTCCTCCGACA
1 AGGGAACCCTTCCTCCATCTCCAACTCCAACTCCTCCAACCCGACCAACTTACACTCCTCCAACA
470 CAATC
66 CAATC
475 AGGGAA-CCTTCCTCCATCTCCAACTCCAACTCCTCCAACCCGACCAACTTACACTCCTCCAACA
1 AGGGAACCCTTCCTCCATCTCCAACTCCAACTCCTCCAACCCGACCAACTTACACTCCTCCAACA
539 CAATC
66 CAATC
544 AGGGAACCCTT-CTCCATCTCC
1 AGGGAACCCTTCCTCCATCTCC
565 TCCAACTACT
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
68 2 0.02
69 80 0.93
70 4 0.05
ACGTcount: A:0.27, C:0.46, G:0.07, T:0.20
Consensus pattern (70 bp):
AGGGAACCCTTCCTCCATCTCCAACTCCAACTCCTCCAACCCGACCAACTTACACTCCTCCAACA
CAATC
Found at i:600 original size:93 final size:95
Alignment explanation
Indices: 480--657 Score: 229
Period size: 93 Copynumber: 1.9 Consensus size: 95
470 CAATCAGGGA
* * * *
480 ACCTTCCTCCATCTCCAACTCCAACTCC-TCCA-ACCCGACCAACTTACACTCCTCCAACACAAT
1 ACCTTCCACCATCTCC-ACTCCAACTCCAACCACA-CC-ACCAACTTACACTCCTCAAACACAAA
*
543 CAGGGAACCCTTCTCCATCTCCTCCAACTACTT
63 CAGGGAACCCTCCTCCATCTCCTCCAACTACTT
* *
576 ACCTTCCACCATCT-C-CTCCCACTCCAACCTCACCACCAACTTACACTCCTCAAACACAAACAG
1 ACCTTCCACCATCTCCACTCCAACTCCAACCACACCACCAACTTACACTCCTCAAACACAAACAG
*
639 GGAACCGTCCTCCATCTCC
66 GGAACCCTCCTCCATCTCC
658 AACTCCATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
93 53 0.74
94 4 0.06
95 2 0.03
96 13 0.18
ACGTcount: A:0.27, C:0.48, G:0.04, T:0.21
Consensus pattern (95 bp):
ACCTTCCACCATCTCCACTCCAACTCCAACCACACCACCAACTTACACTCCTCAAACACAAACAG
GGAACCCTCCTCCATCTCCTCCAACTACTT
Found at i:7126 original size:18 final size:18
Alignment explanation
Indices: 7105--7141 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
7095 AGTTGAAAAA
7105 TGATGACCCCATGAATGC
1 TGATGACCCCATGAATGC
7123 TGATGACCCCATGAATGC
1 TGATGACCCCATGAATGC
7141 T
1 T
7142 TTTTCTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (18 bp):
TGATGACCCCATGAATGC
Found at i:7336 original size:15 final size:15
Alignment explanation
Indices: 7316--7347 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7306 TAGCAATGTG
7316 TTAATGGTATCATGC
1 TTAATGGTATCATGC
7331 TTAATGGTATCATGC
1 TTAATGGTATCATGC
7346 TT
1 TT
7348 CACTTAGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (15 bp):
TTAATGGTATCATGC
Found at i:25990 original size:21 final size:21
Alignment explanation
Indices: 25966--26033 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
25956 GTACGTAACT
* *
25966 GGAGGATACGCTGAAGGTGGG
1 GGAGGATACGCAGAAGGTGGA
* *
25987 GGAGGGTATGCAGAAGGTGGA
1 GGAGGATACGCAGAAGGTGGA
* **
26008 GGAGGATATGCAGCTGGTGGA
1 GGAGGATACGCAGAAGGTGGA
26029 GGAGG
1 GGAGG
26034 GTATGTTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.25, C:0.07, G:0.53, T:0.15
Consensus pattern (21 bp):
GGAGGATACGCAGAAGGTGGA
Found at i:26038 original size:21 final size:21
Alignment explanation
Indices: 25978--26038 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
25968 AGGATACGCT
*
25978 GAAGGTGGGGGAGGGTATGCA
1 GAAGGTGGAGGAGGGTATGCA
*
25999 GAAGGTGGAGGAGGATATGCA
1 GAAGGTGGAGGAGGGTATGCA
**
26020 GCTGGTGGAGGAGGGTATG
1 GAAGGTGGAGGAGGGTATG
26039 TTGTTGGAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.05, G:0.54, T:0.16
Consensus pattern (21 bp):
GAAGGTGGAGGAGGGTATGCA
Found at i:35973 original size:24 final size:24
Alignment explanation
Indices: 35946--35995 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
35936 TTGATTTTAT
**
35946 TTTTTTTTCTAATTCGCATAGTAA
1 TTTTTTTTAAAATTCGCATAGTAA
**
35970 TTTTTTTTAAAATTTTCATAGTAA
1 TTTTTTTTAAAATTCGCATAGTAA
35994 TT
1 TT
35996 AGTATTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTTTTTTAAAATTCGCATAGTAA
Found at i:41337 original size:30 final size:30
Alignment explanation
Indices: 41301--41363 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
41291 ATAAGTTGTC
41301 ACTGCCTTTTGTATATATTCGTAATTGATT
1 ACTGCCTTTTGTATATATTCGTAATTGATT
* *
41331 ACTGCCTTTTGTATATCTTCGTAATTGGTT
1 ACTGCCTTTTGTATATATTCGTAATTGATT
41361 ACT
1 ACT
41364 TTAACCTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (30 bp):
ACTGCCTTTTGTATATATTCGTAATTGATT
Found at i:41776 original size:18 final size:18
Alignment explanation
Indices: 41749--41783 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41739 TAAATGTCCT
41749 ATATCTAAATG-AGTTAC
1 ATATCTAAATGAAGTTAC
41766 ATATCCTAAATGAAGTTA
1 ATAT-CTAAATGAAGTTA
41784 GAGTTTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
ATATCTAAATGAAGTTAC
Found at i:43160 original size:1 final size:1
Alignment explanation
Indices: 43154--43183 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
43144 CTCTCTCTTC
*
43154 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43184 AATTTTCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:43170 original size:13 final size:13
Alignment explanation
Indices: 43149--43183 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
43139 TCCCTCTCTC
*
43149 TCTTCTTTTTTTT
1 TCTTTTTTTTTTT
43162 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
43175 T-TTTTTTTT
1 TCTTTTTTTT
43184 AATTTTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:44276 original size:64 final size:65
Alignment explanation
Indices: 44125--44284 Score: 189
Period size: 67 Copynumber: 2.4 Consensus size: 65
44115 TGGCTTATAT
* * * * * *
44125 ATAATTTGCGGTCCACCGAGACTTGC-AAAGATTGTTGGTGAAATTGATGCAATGTCCCGTATGA
1 ATAATTTGCGGTCCACTGAGACTTGCAAAAGATTGGTCGTGAAATCGATACAATGTCCCGTACGA
*
44189 ATAATTATTTGCGGTCCACTGAGACTTGCAAAAG-TTGGTCGTGAAATCGATACAATGTCCCTTA
1 AT-A--ATTTGCGGTCCACTGAGACTTGCAAAAGATTGGTCGTGAAATCGATACAATGTCCCGTA
*
44253 CGG
63 CGA
* *
44256 ATAATTTGCAGTCCATTGAGACTTGCAAA
1 ATAATTTGCGGTCCACTGAGACTTGCAAA
44285 GGTTTACTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
64 26 0.32
65 1 0.01
66 1 0.01
67 50 0.61
68 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (65 bp):
ATAATTTGCGGTCCACTGAGACTTGCAAAAGATTGGTCGTGAAATCGATACAATGTCCCGTACGA
Found at i:44428 original size:162 final size:162
Alignment explanation
Indices: 44166--44560 Score: 640
Period size: 162 Copynumber: 2.5 Consensus size: 162
44156 TTGTTGGTGA
* * ** *
44166 AATTGATGCAATGTCCCGTATGAATAATTATTTGCGGTCCACTGAGACTTGCAAAAGTTGGTCG-
1 AATTGATGCAATGTCCC-TATGAAT-A--ATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGT
44230 T-GAA---AT-CGATACAATGTCCCTTACGGATAATTTGCAGTCCATTGAGACTTGCAAAGGTTT
62 TGGAATTGATGCGATACAATGTCCCTTACGGATAATTTGCAGTCCATTGAGACTTGCAAAGGTTT
*
44290 ACTGTTGGAATCGATGCAATGTCCCAAATAATTTGC
127 ACTGTTGGAATCGATGCAATATCCCAAATAATTTGC
44326 AATTGATGCAATGTCCCTATGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGA
1 AATTGATGCAATGTCCCTATGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGA
*
44391 ATTGATGCGATACAATGTCCCTTGCGGATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTACTG
66 ATTGATGCGATACAATGTCCCTTACGGATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTACTG
*
44456 TTGGAATCGATGCAATATCCCGAATAATTTGC
131 TTGGAATCGATGCAATATCCCAAATAATTTGC
44488 AATTGATGCAATGTCCCTATGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGA
1 AATTGATGCAATGTCCCTATGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGA
44553 ATTGATGC
66 ATTGATGC
44561 AACGTCCCGA
Statistics
Matches: 221, Mismatches: 8, Indels: 10
0.92 0.03 0.04
Matches are distributed among these distances:
156 30 0.14
157 1 0.00
158 4 0.02
159 7 0.03
160 17 0.08
161 2 0.01
162 160 0.72
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (162 bp):
AATTGATGCAATGTCCCTATGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGA
ATTGATGCGATACAATGTCCCTTACGGATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTACTG
TTGGAATCGATGCAATATCCCAAATAATTTGC
Found at i:44575 original size:92 final size:96
Alignment explanation
Indices: 44418--44691 Score: 324
Period size: 110 Copynumber: 2.8 Consensus size: 96
44408 TCCCTTGCGG
* * * *
44418 ATAATTTGCAGTCCATTGAGACTTGCAAAGGTTTACTGTTGGAATCGATGCAATATCCCGAATAA
1 ATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAA
44483 TTTGCA-A-TTG-ATGCAATGTCCC-TATGA
66 TTTGCAGACTTGAATGCAATGTCCCGTATGA
*
44510 ATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAACGTCCCGAATAA
1 ATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAA
44575 TTTGCAGTCCTCTAGACTTGCAAATTGATGCAATGTCCCGTATGA
66 TTT---G----C-AGACTTG---A---ATGCAATGTCCCGTATGA
*
44620 ACAATTTGCAGTCCACT-ATGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATA
1 ATAATTTGCAGTCCACTGA-GACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATA
44684 ATTTGCAG
65 ATTTGCAG
44692 TCCTCTGCAC
Statistics
Matches: 156, Mismatches: 7, Indels: 28
0.82 0.04 0.15
Matches are distributed among these distances:
92 63 0.40
95 1 0.01
99 1 0.01
100 1 0.01
101 1 0.01
102 5 0.03
103 1 0.01
107 1 0.01
109 13 0.08
110 69 0.44
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (96 bp):
ATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAATAA
TTTGCAGACTTGAATGCAATGTCCCGTATGA
Found at i:44603 original size:45 final size:47
Alignment explanation
Indices: 44552--44648 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 47
44542 TTATTGTTGG
* *
44552 AATTGATGCAACGTCCC-GAATAATTTGCAGTCCTCTA-GACTTGCA
1 AATTGATGCAACGTCCCTGAACAATTTGCAGTCCACTATGACTTGCA
*
44597 AATTGATGCAATGTCCCGTATGAACAATTTGCAGTCCACTATGACTTGCA
1 AATTGATGCAACGTCCC---TGAACAATTTGCAGTCCACTATGACTTGCA
44647 AA
1 AA
44649 GGTTTATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
45 16 0.36
49 18 0.41
50 10 0.23
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (47 bp):
AATTGATGCAACGTCCCTGAACAATTTGCAGTCCACTATGACTTGCA
Found at i:44643 original size:110 final size:110
Alignment explanation
Indices: 44484--44780 Score: 471
Period size: 110 Copynumber: 2.7 Consensus size: 110
44474 CCCGAATAAT
44484 TTGC-AATTGATGCAATGTCCC-TATGAATAATTTGCAGTCCACTGA-GACTTGCAAAGGTTTAT
1 TTGCAAATTGATGCAATGTCCCGTATGAATAATTTGCAGTCCACT-ATGACTTGCAAAGGTTTAT
44546 TGTTGGAATTGATGCAACGTCCCGAATAATTTGCAGTCCTCTAG-AC
65 TGTTGGAATTGATGCAACGTCCCGAATAATTTGCAGTCCTCT-GCAC
*
44592 TTGCAAATTGATGCAATGTCCCGTATGAACAATTTGCAGTCCACTATGACTTGCAAAGGTTTATT
1 TTGCAAATTGATGCAATGTCCCGTATGAATAATTTGCAGTCCACTATGACTTGCAAAGGTTTATT
*
44657 GTTGGAATTGATGCAATGTCCCGAATAATTTGCAGTCCTCTGCAC
66 GTTGGAATTGATGCAACGTCCCGAATAATTTGCAGTCCTCTGCAC
* * * *
44702 TTGCAAATTGATGCAATGTCCCGCATGAATAATTTGTAGTCCACTGTGACTTGCAAA-GTTTAAT
1 TTGCAAATTGATGCAATGTCCCGTATGAATAATTTGCAGTCCACTATGACTTGCAAAGGTTTATT
44766 GTT-GAAGTTGATGCA
66 GTTGGAA-TTGATGCA
44781 TGGTCGCTTA
Statistics
Matches: 177, Mismatches: 7, Indels: 9
0.92 0.04 0.05
Matches are distributed among these distances:
108 7 0.04
109 36 0.20
110 134 0.76
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (110 bp):
TTGCAAATTGATGCAATGTCCCGTATGAATAATTTGCAGTCCACTATGACTTGCAAAGGTTTATT
GTTGGAATTGATGCAACGTCCCGAATAATTTGCAGTCCTCTGCAC
Found at i:46731 original size:19 final size:19
Alignment explanation
Indices: 46684--46721 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46674 TTTGGGGAAT
46684 ATGCTCTGTTACAATTTAA
1 ATGCTCTGTTACAATTTAA
46703 ATGCTCTGTTACAATTTAA
1 ATGCTCTGTTACAATTTAA
46722 GATCTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
ATGCTCTGTTACAATTTAA
Found at i:52668 original size:67 final size:67
Alignment explanation
Indices: 52564--52723 Score: 193
Period size: 66 Copynumber: 2.4 Consensus size: 67
52554 GCTTATATAT
* * * * *
52564 AATTTGCTGTCCACCGAGACTTGC-AAAGATTGAT-G-GTGAAATTGATGCAATGTCCCGTATGA
1 AATTTGCAGTCCACTGAGACTTGCAAAAGATTGATGGTGTGAAATCGATACAATGTCCCGTAGGA
52626 ATA
66 A-A
* * *
52629 ATTATTTGCGGTCCACTGAGACTTGCAAAAG-TTGGTGGTGTGAAATCGATACAATGTCCCTTAG
1 A--ATTTGCAGTCCACTGAGACTTGCAAAAGATTGATGGTGTGAAATCGATACAATGTCCCGTAG
52693 GAAA
64 GAAA
52697 AATTTGCAGTCCACTGAGACTTGCAAA
1 AATTTGCAGTCCACTGAGACTTGCAAA
52724 TGTTTGTTGT
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
65 1 0.01
66 25 0.30
67 25 0.30
68 7 0.09
69 24 0.29
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (67 bp):
AATTTGCAGTCCACTGAGACTTGCAAAAGATTGATGGTGTGAAATCGATACAATGTCCCGTAGGA
AA
Found at i:52951 original size:22 final size:22
Alignment explanation
Indices: 52923--52969 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
52913 TTTGAGAGGC
*
52923 TCCAATTTGATGAAATATTAGT
1 TCCAATTTGATGAAATATAAGT
52945 TCCAATTTGATGAAATATAAGT
1 TCCAATTTGATGAAATATAAGT
52967 TCC
1 TCC
52970 GTTACGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TCCAATTTGATGAAATATAAGT
Found at i:54616 original size:63 final size:65
Alignment explanation
Indices: 54454--54702 Score: 217
Period size: 63 Copynumber: 3.9 Consensus size: 65
54444 TGTGGCTTAC
* * * * *
54454 GAATAATTTGCAGTCCACTGAGACTTGCAAAGATTAACGGTGAACTTGATGCAATGTCCTGTACG
1 GAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTAATGATGAAATTGATGCAATGTCCTATACG
* * ** *
54519 GATATTAATTTGCGGTCCACTGGGACTTGCAAAGGTTGTTGATGAAATTGATGTAATGTCC-ATA
1 GA-A-TAATTTGCAGTCCACTGAGACTTGCAAAGGTTAATGATGAAATTGATGCAATGTCCTATA
*
54583 -T
64 CG
* * * *
54584 GAATAATTTGCAGTCCACCGAGACTTGTAAAGGTTAATGTTGAAATGGATGCAATGTCC----C-
1 GAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTAATGATGAAATTGATGCAATGTCCTATACG
** ** ** * *
54644 GAATAATTTGTGGTCCA-TTTGACTCACAAAGATTAATGTTGAAATTGATGCAATGTCCT
1 GAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTAATGATGAAATTGATGCAATGTCCT
54703 GTTGCAAGTC
Statistics
Matches: 150, Mismatches: 30, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
59 33 0.22
60 15 0.10
63 47 0.31
64 1 0.01
65 4 0.03
66 3 0.02
67 47 0.31
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (65 bp):
GAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTAATGATGAAATTGATGCAATGTCCTATACG
Found at i:68981 original size:15 final size:16
Alignment explanation
Indices: 68956--68985 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
68946 AATAATTATT
68956 TTTAGATTATAATATA
1 TTTAGATTATAATATA
68972 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
68986 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:70026 original size:331 final size:331
Alignment explanation
Indices: 69433--70150 Score: 832
Period size: 331 Copynumber: 2.2 Consensus size: 331
69423 ATATAATATT
* * * *
69433 AAATCTTTTTGGCGTTGAATCATATA-TTTTTATGAGTATTTTAGCTAAAAATTTAGAAGAAATC
1 AAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTATCCAAAAA-TTAGAAGAAATC
* * * *
69497 CTTTGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACGAACCATCACAGTTTTTGG
65 CTTTCTATCAATTTTTACAAAATTTTAGCCAAAATCGTG-A-TAACGAACCATCACAGTTTTTGG
* * * * *
69562 CTAAAAACGCGTTCCGGGGACCCGACTCAATTTTGTATAATTTTTGGCTTCGAGACTACTTGAAA
128 CTAAAAAAGCGTTCCGGGGACCCGACTCAATTTTGCATAATTTTTAGC-TCAACACTACTTGAAA
* * * *
69627 TATTTATATTCATCTAATCGAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGTATCT
192 TATTCATATTCATCTAATCGAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCT
* * * *
69692 GAATTTTGTTTCGTTTTAATTAGAAATTAATTTGAAAAAAATAGGAAAAAACGATATTGAAAA-C
257 GAATTTTATTTCGATTTAATTAAAAATTAA-TTCAAAAAAATAGG-AAAAACGATATT-AAAAGC
*
69756 GTCTAAAA-CCCTTC
319 GT-GAAAAGCCC-TC
* *
69770 -AATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTATCCAAAAATT-GAGGAAATAT
1 AAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTATCCAAAAATTAGAAGAAAT-C
* *
69833 TTTTCTAATCAATTTTTACAAAATTTTAGCCAAAATCGTG-TAA-TAACCATCACAGTTTTTGGC
65 CTTTCT-ATCAATTTTTACAAAATTTTAGCCAAAATCGTGATAACGAACCATCACAGTTTTTGGC
* * * * * * * *
69896 TAAAAAAGTGTT-CTGGG-CCTTGGCTCAGTTTTGCATGATTTTTAAGC-CAACACTCCTTGAGA
129 TAAAAAAGCGTTCCGGGGACC-CGACTCAATTTTGCATAATTTTT-AGCTCAACACTACTTGAAA
69958 T-TTCCATATTCATCTAATC-AATTCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCAT
192 TATT-CATATTCATCTAATCGAA-TCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCAT
* *
70021 CTGAATTTTATTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCG
255 CTGAATTTTATTTCGATTTAATTAAAAATTAATTCAAAAAAATAGGAAAAACGATATTAAAAGCG
*
70086 TGAAAAGTCCTC
320 TGAAAAGCCCTC
* * * *
70098 AAATTTTTTTGGC-TATAAATTATATATATTTTATAAGTATTTTATCCAGAAAT
1 AAATTTTTTTGGCGT-TGAATTATATATTTTTTATGAGTATTTTATCCAAAAAT
70151 AGGTGAAAAG
Statistics
Matches: 329, Mismatches: 41, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
328 11 0.03
329 63 0.19
330 15 0.05
331 95 0.29
332 22 0.07
333 31 0.09
334 3 0.01
335 7 0.02
336 29 0.09
337 53 0.16
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (331 bp):
AAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTATCCAAAAATTAGAAGAAATCC
TTTCTATCAATTTTTACAAAATTTTAGCCAAAATCGTGATAACGAACCATCACAGTTTTTGGCTA
AAAAAGCGTTCCGGGGACCCGACTCAATTTTGCATAATTTTTAGCTCAACACTACTTGAAATATT
CATATTCATCTAATCGAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACAAGCATCTGAAT
TTTATTTCGATTTAATTAAAAATTAATTCAAAAAAATAGGAAAAACGATATTAAAAGCGTGAAAA
GCCCTC
Found at i:71508 original size:332 final size:330
Alignment explanation
Indices: 70387--73200 Score: 2806
Period size: 332 Copynumber: 8.5 Consensus size: 330
70377 ATCCCAACCA
* * * *
70387 TTGTTTTTACAAACATCTGAATCATGTTTC-ATTTTAATTAGAAATCAATTCGGAAAAAAATA-G
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTAATTC--AAAAAAATATG
* * * * *
70450 AAAAAACGATATTAAAAGCATGAAAAGCCCTTCAAT-TTTTTTAGCATTGAATTATATATTTTTT
63 -AAAAACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGA-CGTTGAATTATATATATTTT
* * * * * * * * *
70514 ATGAGCATTGTGGCTAAAAATTGAGAGAATATTTTTTTGGTCATTTTTTGCAAAATTTTAGGCGA
126 ATGAGTATTTTAGCTAAAAATTGAG-GAAAAATCTTTCGGTCAATTTTTGCAAAATTTTAGCCGA
* * * * * * *
70579 AATCGTGTACTAACAATCACAGTTTTTTTTTGCTAAAAGCGCGTTTCGGGGCCCCGACTCAGTTT
190 AATCGTGTACTAACCATCAC-G--GTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTT
* * * * **
70644 TGTATGA-TTTTTGACGTCGAGACTCC-TCAAA-A--TAT-TT-A--TAAT-AAATCTCAGTGAC
252 TGCATGATTTTTTG-CGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAC
* **
70699 ATTGCATTTGTGGAT
316 ATTGGATTTAAGGAT
* * * *
70714 TTGTTTTTAC-ATGCAACTGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAATATAAA
1 TTGTTTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATAT-GA
* * * * *
70778 AAAACGATATTAAAAGTGAGAAAAGTCCTCCAAT-TTTTGGA-GTTGAATTATATATATCTTATG
64 AAAACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATG
* * *
70841 AGTATTTTAGAC-AAAAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAT
129 AGTATTTTAG-CTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAA
* * * * * * * ** *
70905 TCGTGTATGTTAGTCGAAATCTCGGTTTTTGTCTAAAAACGCGTTCCGGGACCATGTTTCAGTAT
192 TCGTGTA--CTA-AC--CATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTT
* * * * * *
70970 TGCATGATTTTTTGCGCCGAGACTCCTTCAAATATCTACATTCATCCAACCAAATTTCAGCCACA
252 TGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACA
*
71035 TTGGATTTAAGAAT
317 TTGGATTTAAGGAT
*** * * * *
71049 TTG-TAAAACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC--AAAAAAATATGA
* * * * * * *
71113 AAAACGATATTAGAAGCATGAAAA-ACCTTTAATATTTTTGGCGTTGCATTATATA-ATTTTTAT
64 AAAACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATA-TTTTAT
** * * *
71176 GAGTATTGCAGATAAAAATTGAGGAAATAA-CTTTCGAGTCAATTTTTGTAAAATTCTAGCCGAA
128 GAGTATTTTAGCTAAAAATTGAGGAAA-AATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAA
* * * * * *
71240 ATCGTATAATAATCATCACGGTTTTTGGCTAAAAATTGCGTTCTGGGGCCCCGGCT-AGGTTTTG
191 ATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA-CGCGTTCCGGGGCCACGGCTCA-GTTTTG
* * * * * * **
71304 CATGATTTTTTGCGCCAAAACTCTTTGAGATATCCATATTCATTTAATCTAATCTCAGGTACATT
254 CATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
* *
71369 GGATTGAAGAAT
319 GGATTTAAGGAT
71381 TTGTTTTTACGAGCATCTGAATC-TGATTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAA
1 TTGTTTTTACGAGCATCTGAATCTTG-TTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAA
* * *
71445 AAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGACATTAAATTATATATATTTTATGA
65 AAACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGA
* *
71510 GTATTTTAG-TGAAAAATTGATGGAAAAATATTTTGTGTCAATTTTTGCAAAATTTTAGCCGAAA
130 GTATTTTAGCT-AAAAATTGA-GGAAAAATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAA
* * *
71574 TCGTGTACACTAACCATCACGGTTTTCGGTTAAAAACGCATTCCGGGGCC-CGGCTCAGTTTTGC
192 TCGTGT--ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTTTGC
* * * * *
71638 ATGATTTTTGGGGACGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACACTG
255 ATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG
* *
71703 AATTTAATGAT
320 GATTTAAGGAT
* * *
71714 TTTTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATAAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAAAAATATGAA
* * * **
71779 AAACGATATTAAAAGCGTGAAAAAGGCTTTCAATTTTTTTGGTGTTGAA-T-TATATATTTTATG
65 AAACGATATTAAAAGCGTG-AAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATG
* * *
71842 AGTATTTTCGCTAGAAATTGAGGAAAAATCTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAAT
129 AGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAAT
* * * * **** *
71907 CATGTATTAACCATCACGGTTTTCGGCTAAAACCGCGTTCCGGGG-TTTTGCTCGGTTTTGCATG
193 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTTTGCATG
* ** * * *
71971 A-TATTTGATACTAAGACTCCTTGAAATATCGATATTCATCTAACCAAATCTCAGCCACATTGGA
258 ATTTTTTG-CGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA
72035 TTTAAGGAT
322 TTTAAGGAT
* *
72044 TTGTTTTTACGAGCATCTGAATCTTGATTCGATTTAATTAGAAAATTAATTTGAAAAAAAT-TGG
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATTAA-TTCAAAAAAATAT-G
* * * * * * * *
72108 AAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATATTTTTGATGTCGAATTATATATTTTTTAT
63 AAAAACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTAT
* *
72173 GAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAA-TTTTGCAAAATTTTAGCCGAAA
128 GAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGG-TCAATTTTTGCAAAATTTTAGCCGAAA
* * ** *
72237 TCGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCAGGGCCACAACTCTGTTTTGCAT
192 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTTTGCAT
* * * * * *
72302 GA-TTTTTGACGCCGATACTCCTTGAAATATTTTTCTTCATCTAATCAAATCTCAAG-CACATTA
257 GATTTTTTG-CGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC-AGCCACATTG
72365 GATTTAAGGAT
320 GATTTAAGGAT
* * * * * *
72376 TTG-TTTTATGTGAATCTGAATGTTGTTTCGACTTAATTAGAAATT-A-T---AAAAATATGAGA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAA
* * * * *
72435 AACGGTATTAAAAACGTGAAAAGTCCTCCAATCCTTTTGACGTTGAATTATATATTTTTTATGAG
66 AACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAG
** * * *
72500 TATTTTCTCTAGAAATCGAGGAAAAATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCA
131 TATTTTAGCTAAAAATTGAGGAAAAATCTTTCGG-TCAATTTTTGCAAAATTTTAGCCGAAATCG
* * * ** *
72565 TGTACTAACCATCACGATTTTCGGCT-AAAACAGCGTTTCGGGG-TTCGGCTCAGTTTTGCTTGA
195 TGTACTAACCATCACGGTTTTTGGCTAAAAAC-GCGTTCCGGGGCCACGGCTCAGTTTTGCATGA
* * * **
72628 TTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CTAAATCTTAGCCACATTAAAT
259 TTTTTTGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGCCACATTGGAT
*
72692 TTAACGAT
323 TTAAGGAT
* ** *
72700 TT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTTATTAGAAATTAATTTGAAAAAATAGGAAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAA
* * * * * * *
72764 AACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAG
66 AACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAG
* * * * *
72829 CATTTTAGCCAAAAATTGAGGAAATATTTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCA
131 TATTTTAGCTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCG
* * ** * * *
72894 TGTACTAACTATCACGGTTTTTAGCTAAAAACGCACTCCAGGGCCACGGATCTGTTTTGCATGAT
195 TGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTTTGCATGAT
* * *
72959 TTTTGGCACCAAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCATG-CACATTGGATT
260 TTTTTGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA-GCCACATTGGATT
73023 TAAGGA-
324 TAAGGAT
* * **
73029 TT-TTTTTATGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGTAAAAATATGAAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAA
* * * * * * *
73093 AATGATGTTAAAAACGTGAAAAGTCCTCCAATCCTTTTGGCATTGAATTATATATATTTTATGAG
66 AACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAG
* *
73158 TATTTTTGCCAAAAATTGAGGAAAAATCTTTCGGGTC-ATTTTT
131 TATTTTAGCTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTT
73201 ACCATCATGG
Statistics
Matches: 2056, Mismatches: 358, Indels: 145
0.80 0.14 0.06
Matches are distributed among these distances:
323 11 0.01
324 272 0.13
325 72 0.04
326 86 0.04
327 56 0.03
328 9 0.00
329 299 0.15
330 258 0.13
331 183 0.09
332 303 0.15
333 231 0.11
334 95 0.05
335 98 0.05
336 81 0.04
337 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (330 bp):
TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAA
AACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGACGTTGAATTATATATATTTTATGAG
TATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
GTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGGCTCAGTTTTGCATGATT
TTTTGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTA
AGGAT
Found at i:72027 original size:330 final size:328
Alignment explanation
Indices: 70390--73200 Score: 2708
Period size: 329 Copynumber: 8.5 Consensus size: 328
70380 CCAACCATTG
* * * * *
70390 TTTTTACAAACATCTGAATCATGTTTC-ATTTTAATTAGAAATCAATTCGGAAAAAA-ATAGAAA
1 TTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTAATTCAGAAAAAATAT-G-AA
* * * *
70453 AAACGATATTAAAAGCATGAAAAGCCCTTCAATTTTTTTAGCATTGAATTATATATTTTTTATGA
63 AAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGA
* * * * * * * * *
70518 GCATTGTGGCTAAAAATTGAGAGAATATTTTTTTGGTCATTTTTTGCAAAATTTTAGGCGAAATC
127 GTATTTTAGCTAAAAATTGAG-GAAAAATCTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATC
* * * * * * *
70583 GTGTACTAACAATCACAGTTTTTTTTTGCTAAAAGCGCGTTTCGGGGCCCCGACTCAGTTTTGTA
191 GTGTACTAACCATCAC-G--GTTTTTGGCTAAAAACGCGTTCCGGGG-CCCGGCTCAGTTTTGCA
* * **
70648 TGATTTTTG-ACGTCGAGACTCC-TCAAA-A--TAT-TT-A--TAAT-AAATCTCAGTGACATTG
252 TGATTTTTGCAC--CAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG
* ** *
70703 CATTTGTGGATTTG
315 GATTTAAGGATTTT
* * *
70717 TTTTTAC-ATGCAACTGAATCTTGTTTCAATTTAATTAGAAATTAATTCAG-AAAAATATAAAAA
1 TTTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAT-GAAA
* * * * * *
70780 AACGATATTAAAAGTGAGAAAAGTCCTCCAA--TTTTTGGAGTTGAATTATATATATCTTATGAG
64 AACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAG
* * *
70843 TATTTTAGAC-AAAAATTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAATTC
128 TATTTTAG-CTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATC
* * * * * * * ** *
70907 GTGTATGTTAGTCGAAATCTCGGTTTTTGTCTAAAAACGCGTTCCGGGACCATGTTTCAGTATTG
191 GTGTA--CTA-AC--CATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTG
* * * * * * *
70972 CATGATTTTTTGCGCCGAGACTCCTTCAAATATCTACATTCATCCAACCAAATTTCAGCCACATT
250 CATGA-TTTTTGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT
*
71037 GGATTTAA-GAATTT
314 GGATTTAAGGATTTT
* *** * * * *
71051 GTAAAACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAA
1 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAA-AATATGAAAA
* * * * * *
71116 ACGATATTAGAAGCATGAAAA-ACCTTTAATATTTTTGGCGTTGCATTATATAATTTTTATGAGT
65 ACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTATGAGT
** * * *
71180 ATTGCAGATAAAAATTGAGGAAATAA-CTTTCGAGTCAATTTTTGTAAAATTCTAGCCGAAATCG
129 ATTTTAGCTAAAAATTGAGGAAA-AATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCG
* * * * *
71244 TATAATAATCATCACGGTTTTTGGCTAAAAATTGCGTTCTGGGGCCCCGGCT-AGGTTTTGCATG
192 TGTACTAACCATCACGGTTTTTGGCTAAAAA-CGCGTTCCGGGG-CCCGGCTCA-GTTTTGCATG
* * * * * * * **
71308 ATTTTTTGCGCCAAAACTCTTTGAGATATCCATATTCATTTAATCTAATCTCAGGTACATTGGAT
254 A-TTTTTGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGAT
* * *
71373 TGAAGAATTTG
318 TTAAGGATTTT
71384 TTTTTACGAGCATCTGAATC-TGATTTCGATTTAATTAGAAATTAATTCA-AAAAAATATGAAAA
1 TTTTTACGAGCATCTGAATCTTG-TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAA
* * * * *
71447 ACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGACATTAAATTATATATATTTTATGAGT
65 ACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGT
* *
71512 ATTTTAG-TGAAAAATTGATGGAAAAATATTTTGTGTCAATTTTTGCAAAATTTTAGCCGAAATC
129 ATTTTAGCT-AAAAATTGA-GGAAAAATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATC
* * *
71576 GTGTACACTAACCATCACGGTTTTCGGTTAAAAACGCATTCCGGGGCCCGGCTCAGTTTTGCATG
191 GTGT--ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATG
* * * *
71641 ATTTTTGGGGA-CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACACTGAA
254 ATTTTT--GCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA
*
71705 TTTAATGATTTT
317 TTTAAGGATTTT
* *
71717 TTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATAAAAAA
1 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAA
* * * *
71782 CGATATTAAAAGCGTGAAAAAGGCTTTCAATTTTTTTGGTGTTGAATTATATA-TTTTATGAGTA
66 CGATATTAAAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTA
* * * *
71846 TTTTCGCTAGAAATTGAGGAAAAATCTTTCGAGTCAATTTTTACAAAATTTTAGCCGAAATCATG
130 TTTTAGCTAAAAATTGAGGAAAAATCTTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* * * **** * *
71911 TATTAACCATCACGGTTTTCGGCTAAAACCGCGTTCCGGGGTTTTGCTCGGTTTTGCATGATATT
194 TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTT
* * * *
71976 TGATACTAAGACTCCTTGAAATATCGATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAG
259 TG-CACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAG
*
72041 GATTTG
323 GATTTT
* *
72047 TTTTTACGAGCATCTGAATCTTGATTCGATTTAATTAGAAAATTAATT-TGAAAAAA-ATTGGAA
1 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAATTAATTCAGAAAAAATA-T-GAA
* * * * ** *
72110 AAACAATATTAGAAGCGTTAAAAGCCCTTCAATATTTTTGATGTCGAATTATATATTTTTTATGA
63 AAACGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGA
* *
72175 GTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGATCAA-TTTTGCAAAATTTTAGCCGAAATC
127 GTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGG-TCAATTTTTGCAAAATTTTAGCCGAAATC
* * ** *
72239 GTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTCCAGGGCCACAACTCTGTTTTGCATGA
191 GTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTGCATGA
* * * * * * *
72304 TTTTTGACGCCGATACTCCTTGAAATATTTTTCTTCATCTAATCAAATCTCAAG-CACATTAGAT
255 TTTTTG-CACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTC-AGCCACATTGGAT
72368 TTAAGGA-TTT
318 TTAAGGATTTT
* * * * * * *
72378 GTTTTATGTGAATCTGAATGTTGTTTCGACTTAATTAGAAATT-A-T----AAAAATATGAGAAA
1 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAA
* * * * * *
72437 CGGTATTAAAAACGTGAAAAGTCCTCCAATCCTTTTGACGTTGAATTATATATTTTTTATGAGTA
66 CGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTA
** * * *
72502 TTTTCTCTAGAAATCGAGGAAAAATCTTTCGGATCAATTTTTGCAAAATTTTAGCCGAAATCATG
130 TTTTAGCTAAAAATTGAGGAAAAATCTTTCGG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* * * ** *
72567 TACTAACCATCACGATTTTCGGCT-AAAACAGCGTTTCGGGGTTCGGCTCAGTTTTGCTTGATTT
194 TACTAACCATCACGGTTTTTGGCTAAAAAC-GCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTT
** * **
72631 TTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAA-CTAAATCTTAGCCACATTAAATTTA
258 TT-GCACCAAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGCCACATTGGATTTA
*
72695 ACGA-TTT
321 AGGATTTT
* * *
72702 TTTTTACGAGCATCTGAATCTTGTTTCGATTTTATTAGAAATTAATT-TGAAAAAATAGGAAAAA
1 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAA
* * * ** * *
72766 CAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGCA
66 CGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTA
* * * *
72831 TTTTAGCCAAAAATTGAGGAAATATTTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCATG
130 TTTTAGCTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* * ** * * *
72896 TACTAACTATCACGGTTTTTAGCTAAAAACGCACTCCAGGGCCACGGATCTGTTTTGCATGATTT
194 TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTGCATGATTT
*
72961 TTGGCACCAAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCATG-CACATTGGATTTA
258 TT-GCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA-GCCACATTGGATTTA
73025 AGGA--TT
321 AGGATTTT
* * *
73031 TTTTTATGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GTAAAAATATGAAAAA
1 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAA
* * * * * * *
73095 TGATGTTAAAAACGTGAAAAGTCCTCCAATCCTTTTGGCATTGAATTATATATATTTTATGAGTA
66 CGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTA
* *
73160 TTTTTGCCAAAAATTGAGGAAAAATCTTTCGGGTC-ATTTTT
130 TTTTAGCTAAAAATTGAGGAAAAATCTTTC-GGTCAATTTTT
73201 ACCATCATGG
Statistics
Matches: 2050, Mismatches: 355, Indels: 157
0.80 0.14 0.06
Matches are distributed among these distances:
323 12 0.01
324 276 0.13
325 67 0.03
326 82 0.04
327 56 0.03
328 13 0.01
329 296 0.14
330 276 0.13
331 177 0.09
332 290 0.14
333 224 0.11
334 97 0.05
335 96 0.05
336 84 0.04
337 4 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAA
CGATATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTAT
TTTAGCTAAAAATTGAGGAAAAATCTTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
CTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTG
CACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT
TTT
Found at i:77742 original size:33 final size:33
Alignment explanation
Indices: 77705--77772 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
77695 TCCTGAATGT
*
77705 CCACCACCACC-TCATCCGCCGCCGCCGCCACCA
1 CCACCACCACCACCA-CCGCCGCCGCCGCCACCA
*
77738 CCACCACCACCACCACCTCCGCCGCCGCCACCA
1 CCACCACCACCACCACCGCCGCCGCCGCCACCA
77771 CC
1 CC
77773 GCCTCCGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.19, C:0.66, G:0.10, T:0.04
Consensus pattern (33 bp):
CCACCACCACCACCACCGCCGCCGCCGCCACCA
Found at i:97951 original size:16 final size:16
Alignment explanation
Indices: 97930--97960 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
97920 CGGGTTGATC
*
97930 GGGTTCGGGTCATTTT
1 GGGTTCGGGTAATTTT
97946 GGGTTCGGGTAATTT
1 GGGTTCGGGTAATTT
97961 CAGGTTCCGG
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:0.10, C:0.10, G:0.39, T:0.42
Consensus pattern (16 bp):
GGGTTCGGGTAATTTT
Found at i:98599 original size:46 final size:51
Alignment explanation
Indices: 98548--98663 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 51
98538 AATCCGTTAT
98548 AAATTGCATGGTAAAAGCTTTG-TTT-TTTT-TTTTTTTTT-TTTTTT-CC
1 AAATTGCATGGTAAAAGCTTTGTTTTGTTTTGTTTTTTTTTGTTTTTTGCC
98594 AAATTGCATGGTAAAAGCTTTGTTTTGTTTTGTTTTTTTTTGTTTTTTGCC
1 AAATTGCATGGTAAAAGCTTTGTTTTGTTTTGTTTTTTTTTGTTTTTTGCC
*
98645 AAATTGCATGGTAACAGCT
1 AAATTGCATGGTAAAAGCT
98664 AGTTTTAACT
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
46 22 0.34
47 3 0.05
48 4 0.06
49 9 0.14
50 6 0.09
51 20 0.31
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.55
Consensus pattern (51 bp):
AAATTGCATGGTAAAAGCTTTGTTTTGTTTTGTTTTTTTTTGTTTTTTGCC
Found at i:98630 original size:51 final size:46
Alignment explanation
Indices: 98548--98663 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 46
98538 AATCCGTTAT
* *
98548 AAATTGCATGGTAAAAGCTTTGTTTTTTTTTTTTTTTTTTTTTTCC
1 AAATTGCATGGTAAAAGCTTTGTTTTTTTTTTTTTTGTTTTTTGCC
98594 AAATTGCATGGTAAAAGCTTTGTTTTGTTTTGTTTTTTTTTGTTTTTTGCC
1 AAATTGCATGGTAAAAGCTTTG---T-TTTT-TTTTTTTTTGTTTTTTGCC
*
98645 AAATTGCATGGTAACAGCT
1 AAATTGCATGGTAAAAGCT
98664 AGTTTTAACT
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
46 22 0.35
49 1 0.02
50 4 0.06
51 35 0.56
ACGTcount: A:0.20, C:0.09, G:0.16, T:0.55
Consensus pattern (46 bp):
AAATTGCATGGTAAAAGCTTTGTTTTTTTTTTTTTTGTTTTTTGCC
Found at i:98640 original size:10 final size:10
Alignment explanation
Indices: 98612--98641 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
98602 TGGTAAAAGC
*
98612 TTTGTTTTGT
1 TTTGTTTTTT
98622 TTTGTTTTTT
1 TTTGTTTTTT
98632 TTTGTTTTTT
1 TTTGTTTTTT
98642 GCCAAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTGTTTTTT
Done.