Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008079.1 Corchorus capsularis cultivar CVL-1 contig08100, 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: 160631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:637 original size:29 final size:30
Alignment explanation
Indices: 604--680 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
594 ACTTGTAGTG
*
604 TTTGGACGTTTTGT-CCCATGAACTTCAAT
1 TTTGGACGTTTTGTCCCCATCAACTTCAAT
*
633 TTTGGACATTTT-TCCCCATCAACTTCAAT
1 TTTGGACGTTTTGTCCCCATCAACTTCAAT
*
662 TTTGGGACGTTTTGCCCCC
1 TTT-GGACGTTTTGTCCCC
681 TTAGACTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.02
29 28 0.68
30 8 0.20
31 4 0.10
ACGTcount: A:0.18, C:0.26, G:0.16, T:0.40
Consensus pattern (30 bp):
TTTGGACGTTTTGTCCCCATCAACTTCAAT
Found at i:909 original size:30 final size:30
Alignment explanation
Indices: 872--944 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
862 GACGGAGTGA
*
872 GGGGCAAAACGTCGCAAA-ATTGAAGTTCAT
1 GGGGCAAAACGTC-CAAAGATTGAAATTCAT
* *
902 TGGGCAAAATGT-CAAAGATTGAAATTCAT
1 GGGGCAAAACGTCCAAAGATTGAAATTCAT
931 GGGGCAAAACGTCC
1 GGGGCAAAACGTCC
945 GAACACTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.11
29 21 0.58
30 11 0.31
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (30 bp):
GGGGCAAAACGTCCAAAGATTGAAATTCAT
Found at i:5246 original size:2 final size:2
Alignment explanation
Indices: 5241--5265 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5231 TTTTTGGTAC
5241 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5266 GTTTGGCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15151 original size:21 final size:21
Alignment explanation
Indices: 15127--15190 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
15117 ACTGCTCTAA
*
15127 TAATTTCATCTGTAGAGTACC
1 TAATTTCATCTGTACAGTACC
* *
15148 TAATTTGATCTGTATAGTA--
1 TAATTTCATCTGTACAGTACC
**
15167 TAATCACATCTGTACAGTACC
1 TAATTTCATCTGTACAGTACC
15188 TAA
1 TAA
15191 ACAGTGTCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 15 0.43
21 20 0.57
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
TAATTTCATCTGTACAGTACC
Found at i:22211 original size:22 final size:21
Alignment explanation
Indices: 22167--22211 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
22157 TCATCAACAC
* * *
22167 TTTTATATAACTTTTAAATTT
1 TTTTAAATAACTTTGAAAATT
22188 TTTTAAATAAACTTTGAAAATT
1 TTTTAAAT-AACTTTGAAAATT
22210 TT
1 TT
22212 AAAACTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTAAATAACTTTGAAAATT
Found at i:22270 original size:12 final size:12
Alignment explanation
Indices: 22253--22282 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
22243 AAATTTTAAC
22253 TTCATATAATTT
1 TTCATATAATTT
22265 TTCATATAATTT
1 TTCATATAATTT
22277 TTCATA
1 TTCATA
22283 AATAATGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCATATAATTT
Found at i:22870 original size:11 final size:11
Alignment explanation
Indices: 22856--22893 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22846 ATTCATAACA
22856 AATTTATAATT
1 AATTTATAATT
22867 AATTTATAATT
1 AATTTATAATT
22878 -ATTTGATAATT
1 AATTT-ATAATT
*
22889 TATTT
1 AATTT
22894 TATATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:30153 original size:19 final size:19
Alignment explanation
Indices: 30125--30170 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30115 AAAAGTTTAA
* *
30125 AATTTGTTAATGGGTTTTTT
1 AATTT-TTAATGGCTTTGTT
30145 AATTTTTAATGGCTTTGTT
1 AATTTTTAATGGCTTTGTT
*
30164 AGTTTTT
1 AATTTTT
30171 TTACTAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.20, C:0.02, G:0.17, T:0.61
Consensus pattern (19 bp):
AATTTTTAATGGCTTTGTT
Found at i:62184 original size:33 final size:33
Alignment explanation
Indices: 62140--62236 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
62130 TCACTAGGAC
*
62140 GGCTCAGCCACGGCGGAGCCTCCCCAGTGGGGA
1 GGCTCAACCACGGCGGAGCCTCCCCAGTGGGGA
* * *
62173 GGCTCAACCACGGCGGAACCTCCCAAGTGGTGA
1 GGCTCAACCACGGCGGAGCCTCCCCAGTGGGGA
*
62206 GGCTCAACCACGGCGGAGCCTCCCCACTGGG
1 GGCTCAACCACGGCGGAGCCTCCCCAGTGGG
62237 CGGCTTCGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.19, C:0.37, G:0.34, T:0.10
Consensus pattern (33 bp):
GGCTCAACCACGGCGGAGCCTCCCCAGTGGGGA
Found at i:62701 original size:29 final size:28
Alignment explanation
Indices: 62643--62702 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
62633 TATAAAAAAT
*
62643 AAAAAAACAGAAAAACGAAAACAATAAC
1 AAAAAAACAGAAAAACGAAAACAAGAAC
62671 AAAAAAACAGAAAAACGAAAACAAGATAC
1 AAAAAAACAGAAAAACGAAAACAAGA-AC
62700 AAA
1 AAA
62703 CGACCGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.75, C:0.13, G:0.08, T:0.03
Consensus pattern (28 bp):
AAAAAAACAGAAAAACGAAAACAAGAAC
Found at i:62703 original size:17 final size:16
Alignment explanation
Indices: 62646--62705 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 16
62636 AAAAAATAAA
62646 AAAAC-AGAA-AAACG
1 AAAACAAGAACAAACG
*
62660 AAAACAATAACAAA--
1 AAAACAAGAACAAACG
62674 AAAAC-AGAA-AAACG
1 AAAACAAGAACAAACG
62688 AAAACAAGATACAAACG
1 AAAACAAGA-ACAAACG
62705 A
1 A
62706 CCGAGTTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 15 0.41
15 6 0.16
16 4 0.11
17 6 0.16
ACGTcount: A:0.72, C:0.15, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAACAAGAACAAACG
Found at i:78343 original size:17 final size:17
Alignment explanation
Indices: 78299--78351 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
78289 AACCCATATA
*
78299 ATCTTTGATCACCGGTG
1 ATCTTTGATCACTGGTG
78316 ATC-TTGCATCACTGGTG
1 ATCTTTG-ATCACTGGTG
*
78333 ATCTTTGATCACTAGTG
1 ATCTTTGATCACTGGTG
78350 AT
1 AT
78352 TTGGGGGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 3 0.09
17 26 0.81
18 3 0.09
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (17 bp):
ATCTTTGATCACTGGTG
Found at i:79193 original size:14 final size:14
Alignment explanation
Indices: 79174--79204 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
79164 AATTTTGCTG
*
79174 CAGGCCACCCCCAC
1 CAGGCCACCACCAC
79188 CAGGCCACCACCAC
1 CAGGCCACCACCAC
79202 CAG
1 CAG
79205 CACTACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.58, G:0.16, T:0.00
Consensus pattern (14 bp):
CAGGCCACCACCAC
Found at i:79252 original size:6 final size:6
Alignment explanation
Indices: 79241--79267 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
79231 TTAGCTCCCA
79241 CCATTT CCATTT CCATTT CCATTT CCA
1 CCATTT CCATTT CCATTT CCATTT CCA
79268 ATTTTTGTTT
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:0.19, C:0.37, G:0.00, T:0.44
Consensus pattern (6 bp):
CCATTT
Found at i:82128 original size:20 final size:20
Alignment explanation
Indices: 82103--82145 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
82093 GACTTGCAAG
82103 TCATTAAGAACCATCAATTT
1 TCATTAAGAACCATCAATTT
* *
82123 TCATTAAGAACCTTGAATTT
1 TCATTAAGAACCATCAATTT
82143 TCA
1 TCA
82146 CACTAGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (20 bp):
TCATTAAGAACCATCAATTT
Found at i:86970 original size:1 final size:1
Alignment explanation
Indices: 86964--87005 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
86954 CCTCGAATGG
**
86964 AAAAAAAAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
87006 CCTCATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.95, C:0.00, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:87419 original size:31 final size:31
Alignment explanation
Indices: 87381--87440 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
87371 ATTAAAATCC
87381 TTTAGAAAGTGGTCCTTTCTAAGGACTTTTT
1 TTTAGAAAGTGGTCCTTTCTAAGGACTTTTT
*
87412 TTTAGAAAGTGGTCCTTTGTAAGGACTTT
1 TTTAGAAAGTGGTCCTTTCTAAGGACTTT
87441 ATTGTCTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (31 bp):
TTTAGAAAGTGGTCCTTTCTAAGGACTTTTT
Found at i:88412 original size:21 final size:21
Alignment explanation
Indices: 88381--88444 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
88371 GCTGCTCTAA
88381 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
* * *
88402 TAATTTGATCTGTACAATA--
1 TAATCTCATCTGTACAGTACC
*
88421 TAATCTCATCTGCACAGTACC
1 TAATCTCATCTGTACAGTACC
88442 TAA
1 TAA
88445 ACAGTGTCAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.34
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTACC
Found at i:96771 original size:3 final size:3
Alignment explanation
Indices: 96763--96801 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
96753 ATATCCTGAA
* * *
96763 GAT GAT GAT GAG GAT GAC GAT GAT GAC GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
96802 AGTGGTGACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:112135 original size:13 final size:13
Alignment explanation
Indices: 112117--112141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
112107 TTAAGAAGTA
112117 AAAAAAAAAAGAT
1 AAAAAAAAAAGAT
112130 AAAAAAAAAAGA
1 AAAAAAAAAAGA
112142 AGGTGAAAGC
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:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAGAT
Found at i:115787 original size:2 final size:2
Alignment explanation
Indices: 115780--115808 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
115770 TTAGGCAAGT
115780 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115809 GTTTTCACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:115801 original size:13 final size:13
Alignment explanation
Indices: 115783--115808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
115773 GGCAAGTTAT
115783 ATATATATATATA
1 ATATATATATATA
115796 ATATATATATATA
1 ATATATATATATA
115809 GTTTTCACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:120684 original size:34 final size:35
Alignment explanation
Indices: 120640--120708 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
120630 GCAGAGATTA
*
120640 ATATTGATACCAACTAAT-ATTAAT-ATTAAAAAAT
1 ATATTAATACCAACTAATAATT-ATCATTAAAAAAT
*
120674 ATATTAATACCAACTAGTAATTATCATTAAAAAAT
1 ATATTAATACCAACTAATAATTATCATTAAAAAAT
120709 TACTATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (35 bp):
ATATTAATACCAACTAATAATTATCATTAAAAAAT
Found at i:121600 original size:2 final size:2
Alignment explanation
Indices: 121585--121617 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
121575 ACCACTTCAA
121585 TC TC -C TC T- TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
121618 ATCTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:130489 original size:18 final size:19
Alignment explanation
Indices: 130450--130491 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
130440 CTTTTGTTAA
130450 TTTTGCTTTAATCTGACTT
1 TTTTGCTTTAATCTGACTT
*
130469 TTTTGCTTTAATCTGTCTT
1 TTTTGCTTTAATCTGACTT
130488 TTTT
1 TTTT
130492 CCCTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.14, G:0.10, T:0.64
Consensus pattern (19 bp):
TTTTGCTTTAATCTGACTT
Found at i:136911 original size:15 final size:15
Alignment explanation
Indices: 136891--136921 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
136881 ACAATAAGGT
*
136891 TTTTTTTTTCTTTTC
1 TTTTTTTTTCCTTTC
136906 TTTTTTTTTCCTTTC
1 TTTTTTTTTCCTTTC
136921 T
1 T
136922 GATATACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTCCTTTC
Found at i:138012 original size:2 final size:2
Alignment explanation
Indices: 138007--138038 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
137997 TGTTTTTTAA
138007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
138039 GTCAATCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:143993 original size:20 final size:20
Alignment explanation
Indices: 143968--144007 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
143958 CTATCGTTAT
143968 TTTTTTTTTTCACCAAATTA
1 TTTTTTTTTTCACCAAATTA
143988 TTTTTTTTTTCACCAAATTA
1 TTTTTTTTTTCACCAAATTA
144008 ACTCTCTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTTTTTTCACCAAATTA
Found at i:148758 original size:42 final size:42
Alignment explanation
Indices: 148662--148758 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
148652 CCAGAAATTG
* * * **
148662 CAGCAGCAAAACCTGATCTTCCTACCATAAAACCTGAAAGGG
1 CAGCAGCAAAACCAGATCTCCCTACCACAAAACCTGAAAGCA
* * * *
148704 CATCAGCTAAACCAGATCTCCCTACCACAAGACCTGTAAGCA
1 CAGCAGCAAAACCAGATCTCCCTACCACAAAACCTGAAAGCA
*
148746 CAGCACCAAAACC
1 CAGCAGCAAAACC
148759 CGATTACTTC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.34, G:0.13, T:0.14
Consensus pattern (42 bp):
CAGCAGCAAAACCAGATCTCCCTACCACAAAACCTGAAAGCA
Found at i:152065 original size:20 final size:21
Alignment explanation
Indices: 152028--152070 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
152018 AACACGTTAA
*
152028 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
152049 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
152069 TT
1 TT
152071 GACACGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:152128 original size:42 final size:43
Alignment explanation
Indices: 152058--152140 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
152048 CTTAAACGTG
152058 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
*
152101 TTAATCGTGTC-TGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTTGACACGATTAC-GACACGAAACACGATAA
152141 GCCAAACACG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 1 0.03
42 26 0.68
43 11 0.29
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (43 bp):
TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
Found at i:154354 original size:2 final size:2
Alignment explanation
Indices: 154347--154379 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
154337 ATCAAATTAC
154347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
154380 CATCATTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:156670 original size:25 final size:24
Alignment explanation
Indices: 156629--156677 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
156619 ATAAGTATTC
*
156629 TTTTTAGTCATTTAACTTATTTAT
1 TTTTTAGTCATTCAACTTATTTAT
* *
156653 TTTTTAGATGATTCAACTTTTTTAT
1 TTTTTAG-TCATTCAACTTATTTAT
156678 AAATTATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTTTAGTCATTCAACTTATTTAT
Found at i:157721 original size:331 final size:330
Alignment explanation
Indices: 157052--160631 Score: 3294
Period size: 332 Copynumber: 10.8 Consensus size: 330
157042 GCCAAGGAAA
** * * *
157052 AAAAGCGTGAAAAGCCCTCGTC-AT-TTTTACGTTGAATTATATA-TTTTTATGAGTATTTTAGT
1 AAAAGCGTGAAAAGCCCT--TCAATCTTTTTGGTTTAAATATATATTTTTTATGAGTATTTTAGC
* * * * *
157114 CAAAAATTGAGGAGAAAACA-TTCGTGTTAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAT
64 CAAAAATTGAGGA-AATATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-----T
* * *
157178 AACTAACCATCACGGTTTTTTCGC-AAAAAACGCGTTCT-GGGGACCCGCCAT-AGTTTTGCATT
123 AA-TAACCATCACGG-TTTTTGGCTAAAAAA-GCGTTCTCGGGG-CCCGGC-TCAGTTTTGCATG
* ** ** * * * * *
157240 ATTGTTAACTTCGAGACTACTTGAATTATCTATATTCATCTAATCAAATCTCAGCTACATTGGAT
183 ATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCAT
* * *
157305 TTAAGGATTT-TTTTTATGAG-AGTCTGAATCTTGTTTCAATTTAATTAGAAACTAATTC-GAAA
248 TTAAGGATTTGTTTTTACGAGCA-TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AA
*
157367 AAAATAGGGAAAACGATATT
311 AAAATAGGAAAAACGATATT
*
157387 AAAA-CGTCAAAAGCCCTTCAATCTTTTTGGCTTTGAAATATATATTTTTTATGAGTATTTTAGC
1 AAAAGCGTGAAAAGCCCTTCAATCTTTTTGG-TTT-AAATATATATTTTTTATGAGTATTTTAGC
* *** * *
157451 CAAAAATTGAGGAAATATCTTTCAAATAAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAAC
64 CAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAAC
** * * *
157516 CATCACAATTTTTGGCTAAAAAAGCGTTTTGGGGGCCCAGCTCAGTTTTGCATGATTTTTGGCGC
129 CATCACGGTTTTTGGCTAAAAAAGCGTTCTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGC
* * * * * * * *
157581 CAAGACTCCATGAGATATCCATATTCATATAATCAAATCTCAGCTACATTGGATTTTAGAATTTG
194 CAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTG
*
157646 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAA
259 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAA
157711 CGATATT
324 CGATATT
* * * * * * *
157718 AAAAGCATGAAAAGTCCTCCAATCTTTTTGGAGTTAAATTATTTATATTTTATGAGTATTTTATC
1 AAAAGCGTGAAAAGCCCTTCAATCTTTTTGG-TTTAAA-TATATATTTTTTATGAGTATTTTAGC
* * * *
157783 CAATAATTGAGGAGAAT-T-TTTCGGGT-AATTTTTTGCAAAATTTTAGACAAAATCGTGTACTA
64 CAAAAATTGAGGA-AATATATTTCGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCGTGTAATA
* * * *
157845 ACCATCACGGTTTTTGGCT-AAAAA-CGTGTGTCGGGGCCTCAGCTAAGTTTTGCATGAGTTTTG
127 ACCATCACGGTTTTTGGCTAAAAAAGCGT-TCTCGGGGCC-CGGCTCAGTTTTGCATGATTTTTG
* * * * * * *
157908 GCACCGAGACTCCTTGAAATATTTATATTCATGTAATAAAATCTTAGCCACATTGCATTTAAGAA
190 GCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGA
* * *
157973 TTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTCATTCAG-AAAAGTAGGA
255 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGA
158037 AAAACGATATT
320 AAAACGATATT
* * * * *
158048 AGAATCGTAAAAAACCC-T---TC--------------A-ATATTTTTTATGATTATTTTAGCCA
1 AAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTTTAAATATATATTTTTTATGAGTATTTTAGCCA
** * * *
158094 AAAATTGAGGAAATATATTTCCAGTCAATTTTTGCAAAATGTCAGCCGAAATCGTGTAATAATCA
66 AAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCA
* * * * * * * * *
158159 TAACGGTTTTTTGCTAAAAATGCGTTCT-AGGACCCGGCTTAGTTTTACATGATTTTTGCCGCAA
131 TCACGGTTTTTGGCTAAAAAAGCGTTCTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCA
* * ***
158223 AGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAAGCCACATTGCATTTAAGGATTTGTT
196 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTT
* * * * * * *
158288 TTTACGAGAAACAGAATCTTGTTTGGATTGGATTTAATAAAAATATTAATTCAGAAAAAATATGA
261 TTTACGAGCATCTGAATCTTG--T---TTCGATTTAATTAGAA-ATTAATTCAGAAAAAATAGGA
*
158353 AAAACGATATG
320 AAAACGATATT
* * * * * * *
158364 AAAAGCGTGAAAAGTCCTCCAA-CTTTTTTGTGTTAAATTATATATATTTCAGGATTATTTTAGC
1 AAAAGCGTGAAAAGCCCTTCAATCTTTTTGGT-TTAAA-TATATATTTTTTATGAGTATTTTAGC
* * * * *
158428 CAAAAATTGAGGAAAAATATTTCGGGTCATTCTTTTGCAAAATTTTAGTCGAAAGCGTGTATTAA
64 CAAAAATTGAGGAAATATATTTCGGGTCAAT-TTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* * *
158493 CCATCACGGTTATTTGG-TAAAAACGCGTT-TCGGGGCTACGGCTCAATTTTGCATGATTTTTGG
128 CCATCACGGTT-TTTGGCTAAAAAAGCGTTCTCGGGGC-CCGGCTCAGTTTTGCATGATTTTTGG
* * *
158556 CGCCGAGAATCCTTGAAATATCTATATTCATCTAATCAAATCTCCGCCACATTGCATTTAAGGAT
191 CGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGAT
* * *
158621 TTGTTTTCACGAGCATCTGAATCTTGTATCGATTTAATTAGAAATTAATTCGGAAAAAA-AGGAA
256 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGG-A
158685 AAAACGAT-TT
320 AAAACGATATT
* *
158695 AGAAA-CGTCAAAAGCCCTTCAATCCTTTTGGTGTTGAAATATATA-TTTTTATGAGTATTTTAG
1 A-AAAGCGTGAAAAGCCCTTCAATCTTTTTGGT-TT-AAATATATATTTTTTATGAGTATTTTAG
* * * * * * *
158758 CCAAAAATTGAGGAAATATCTATCGGATAAATTCTTACAAAATTTTA-CCGAAATCGTGAAATAA
63 CCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* ** *
158822 CCATAACAATTTTTGGCTAAAAAAGCGTT-TTGGGGCCCAGG-TCAGTTTTGCATGATTTTTGGC
128 CCATCACGGTTTTTGGCTAAAAAAGCGTTCTCGGGGCCC-GGCTCAGTTTTGCATGATTTTTGGC
* * * ***
158885 TCCAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAATAACATTGCATTTAAGGATT
192 GCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATT
* * * *
158950 TGTTTTCACGAGCATCTGAATCTTGTATCGATTTCATTAGAAATTAATTCAGAAAAAATATGAAA
257 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAA
159015 AACGATATT
322 AACGATATT
* * * *
159024 AAAAGCATGAAAAGTCCC-CCAATCTTTTTGGTTTTAAAT-TATTTTTAATTTATGAGTGTTTTA
1 AAAAGCGTGAAAAG-CCCTTCAATCTTTTTGG-TTTAAATATATATTT--TTTATGAGTATTTTA
* * * * * *
159087 TCCAAAAATTGAGGAAA-ATTTTTTCGGGTCATTTTTTGCAAAATTTTAGACAAAATCGTGTACT
62 GCCAAAAATTGAGGAAATA-TATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT
* * * * *
159151 AACCATCACAGTTTTTGGCTAAAAAAGTG-TGTCAGGGCCTCGACTCAGTTTTGCATGATTTTTG
126 AACCATCACGGTTTTTGGCTAAAAAAGCGTTCTCGGGGCC-CGGCTCAGTTTTGCATGATTTTTG
* * * * * * * *
159215 GCACCGAGACTTCTTGAAATATTTATATTCATGTAATAAAATCTTAGCCACATTGCATTTAAGAA
190 GCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGA
* * * * *
159280 TTTGTTTCTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATTCATTCAGAAAAAGTAAGA
255 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGA
*
159345 AAAGCGATATT
320 AAAACGATATT
* * * * * * * * * *
159356 AGAATCCTAAAAAACCCATCAATATTTTTTGGATTTTAATCTAATATTTTTTACGAGTATTTTAG
1 AAAAGCGTGAAAAGCCCTTCAAT-CTTTTTGG-TTTAAATAT-ATATTTTTTATGAGTATTTTAG
* ** * *
159421 CCAAAAATTGAGGAGATATATTTCCAGTCAATTTTTGCAAAATGTCAGCCGAAATCGTGTAATAA
63 CCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* * * * ** * *
159486 TCATAACGGTTTTTTGCTAAAAATA-CGTTCTAGGACCCCGGCTTAGTTTTGCATGATTTTTGAC
128 CCATCACGGTTTTTGGCTAAAAA-AGCGTTCTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGC
* * * ***
159550 GCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAAGCCACATTGCATTTAAGGATT
192 GCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATT
* * * * * *
159615 TGTTTTTACGAGAAACCGAATCTTGTTTGGATTGGATTTAATAAAAAAATTAATTCAGAAAAAAT
257 TGTTTTTACGAGCATCTGAATCTTG--T---TTCGATTTAAT-TAGAAATTAATTCAGAAAAAAT
* *
159680 ATGAAAAACGATATG
316 AGGAAAAACGATATT
* * * * *
159695 AAAAGCGTGAAAAGTCCTCCAA-CTTTTTTGGTATTAAATTATATATATTTCATGATTATTTTAG
1 AAAAGCGTGAAAAGCCCTTCAATC-TTTTTGGT-TTAAA-TATATATTTTTTATGAGTATTTTAG
* * *
159759 CCAAAAATTGAGGAAAAATATTTCGGGTC-ATTCTGTTGCAAAATTTTAGCCGAAATTGTGTATT
63 CCAAAAATTGAGGAAATATATTTCGGGTCAATT-T-TTGCAAAATTTTAGCCGAAATCGTGTAAT
* * * * * *
159823 AACCATCACGGTTATTTGG-TGAAAACGCGTT-TTGGGGCTCCGACTCAAG-TTTGCATTATTCT
126 AACCATCACGGTT-TTTGGCTAAAAAAGCGTTCTCGGGGC-CCGGCTC-AGTTTTGCATGATTTT
* * * * *
159885 TGGCACCGAGAATCCTTGAAATATCTAAATTCATCTAATCAAATCTCATCCACATTGCATTTAAG
188 TGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAG
* * * *
159950 GATTTGTTTTCACGAGCATCTGATTCTTGTTTCGATTTCATTAGAAATTAATTCAGAAAAAATAC
253 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAG
160015 GAAAAACGATATT
318 GAAAAACGATATT
* * * * *
160028 AAAAGTGTGAAAAGTCC-TCGAGTCTTTTTGGTGTTAAAT-TATTTTTATCTTATGAGTTTTTTA
1 AAAAGCGTGAAAAGCCCTTC-AATCTTTTTGGT-TTAAATATATATTT-T-TTATGAGTATTTTA
** * * * * * *
160091 TTCAAAAATTGAGGAAA-ATTTTTTCGGGTCATTTTTTGTAAAATTTTAGACAAAATCGTGTACT
62 GCCAAAAATTGAGGAAATA-TATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT
* * * *
160155 AACCATCATGGTTTTTGGCT--AAAACCGTGTGTCGGGGCCTCGGCTCAGTTTTGCATGATTTTA
126 AACCATCACGGTTTTTGGCTAAAAAAGCGT-TCTCGGGGCC-CGGCTCAGTTTTGCATGATTTTT
* * * * * * *
160218 GGC-ACATCGACTCCTTTAAATATTTATATTCATGTAATAAAATCTTAGCCACATTGCATTTAAG
189 GGCGCCA-AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAG
* * * * * * *
160282 AATTTGTTTCTACGAGCATATGAATCTTGTTTCAATTTAATTAGAAATTCATTTAGAAAAAGTAG
253 GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAG
160347 GAAAAACGATATT
318 GAAAAACGATATT
* * * * * * * * * * *
160360 AGAATCGTAAAAAACCCATGAATAATTTTTGGATTTTAATCTAATATTTTTTACGATTATTTTAG
1 AAAAGCGTGAAAAGCCCTTCAAT-CTTTTTGG-TTTAAATAT-ATATTTTTTATGAGTATTTTAG
* ** * * * *
160425 CCAAAAATTGAGAAAATATATTTCCAGTCAATTTTTGCAAACTGTCAGCCAAAATCGTGTAATAA
63 CCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* * * * ** * *
160490 TCATAAC-GTTTTTTGCTAAAAATTA-CGTTCTAGGACCCCGGCTTAGTTTTACATGATTTTTGG
128 CCATCACGGTTTTTGGCTAAAAA--AGCGTTCTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGG
* * * *** *
160553 CGCAAAGACTCCTTGAGATATTCCATATTCATCTAATCAAATGAAAGCCACATTACATTTAAGGA
191 CGCCAAGACTCCTTGAAATA-TCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGA
160618 TTTGTTTTTACGAG
255 TTTGTTTTTACGAG
Statistics
Matches: 2635, Mismatches: 490, Indels: 241
0.78 0.15 0.07
Matches are distributed among these distances:
308 3 0.00
309 127 0.05
310 55 0.02
311 9 0.00
312 3 0.00
314 13 0.00
315 9 0.00
316 30 0.01
319 1 0.00
326 2 0.00
327 3 0.00
328 157 0.06
329 70 0.03
330 209 0.08
331 388 0.15
332 466 0.18
333 428 0.16
334 99 0.04
335 21 0.01
336 61 0.02
337 119 0.05
338 172 0.07
339 184 0.07
340 6 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (330 bp):
AAAAGCGTGAAAAGCCCTTCAATCTTTTTGGTTTAAATATATATTTTTTATGAGTATTTTAGCCA
AAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCA
TCACGGTTTTTGGCTAAAAAAGCGTTCTCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCA
AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTT
TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACG
ATATT
Found at i:159315 original size:332 final size:329
Alignment explanation
Indices: 158069--160631 Score: 2350
Period size: 333 Copynumber: 7.7 Consensus size: 329
158059 AAACCCTTCA
* ** *
158069 ATATTT-TTTATGATTATTTTAGCCAAAAATTGAGG-AAATATATTTCCAGTCAATTTTTGCAAA
1 ATATTTATTTATGAGTATTTTAGCCAAAAATTGAGGAAAAT-TATTTCGGGTCATTTTTTGCAAA
* * * * * * *
158132 ATGTCAGCCGAAATCGTGTAATAATCATAACGGTTTTTTGCTAAAAATGCGTTCTAGGACC-CGG
65 ATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAAAGCGTTC-AGGGCCTCGG
* * * * * * * **
158196 CTTAGTTTTACATGATTTTTGCCGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGG
129 CTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
* * * *
158261 AAGCCACATTGCATTTAAGGATTTGTTTTTACGAG-AAACAGAATCTTGTTTGGATTGGATTTAA
194 CAGCCACATTGCATTTAAGGATTTG-TTTTACGAGCATA-TGAATCTTG--T---TTCGATTTAA
* * * *
158325 TAAAAATATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAA-CTT
252 TTAGAA-ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCCCCAATCTT
* *
158389 TTTTGTGTTAAATT
316 TTTGGTTTTAAATT
* * * *
158403 ATATATATTTCAGGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCATTCTTTTGCAA
1 ATATTTATTT-ATGAGTATTTTAGCCAAAAATTGAGGAAAATTATTTCGGGTCATT-TTTTGCAA
* * * * *
158468 AATTTTAGTCGAAAGCGTGTATTAACCATCACGGTTATTTGG-TAAAAACGCGTTTC-GGGGCTA
64 AATTTTAGCCGAAATCGTGTAATAACCATCACGGTT-TTTGGCTAAAAAAGCG-TTCAGGGCCT-
* * * *
158531 CGGCTCAATTTTGCATGATTTTTGGCGCCGAGAATCCTTGAAATATCTATATTCATCTAATCAAA
126 CGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
* * *
158596 TCTCCGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTGTATCGATTTAATTA
191 TCTCAGCCACATTGCATTTAAGGATTTGTTTT-ACGAGCATATGAATCTTGTTTCGATTTAATTA
* * * * *
158661 GAAATTAATTCGGAAAAAA-AGGAAAAAACGAT-TTAGAAA-CGTCAAAAG-CCCTTCAATCCTT
255 GAAATTAATTCAGAAAAAATATG-AAAAACGATATTA-AAAGCGTGAAAAGTCCC-CCAATCTTT
*
158722 TTGGTGTTGAAA-T
317 TTGGT-TTTAAATT
* * * * *
158735 ATATATT-TTTATGAGTATTTTAGCCAAAAATTGAGG-AAA-TATCTATCGGATAAATTCTTACA
1 ATAT-TTATTTATGAGTATTTTAGCCAAAAATTGAGGAAAATTAT-T-TCGGGTCATTTTTTGCA
* * ** **
158797 AAATTTTA-CCGAAATCGTGAAATAACCATAACAATTTTTGGCTAAAAAAGCGTTTTGGGGCC-C
63 AAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAAAGCG-TTCAGGGCCTC
* * *
158860 AGG-TCAGTTTTGCATGATTTTTGGCTCCAAGACTCCTTGAGATATCCATATTCATCTAATCAAA
127 -GGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
*** * * *
158924 TCTCAATAACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTGTATCGATTTCATTA
191 TCTCAGCCACATTGCATTTAAGGATTTGTTTT-ACGAGCATATGAATCTTGTTTCGATTTAATTA
*
158989 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCCCCAATCTTTTTG
255 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCCCCAATCTTTTTG
159054 GTTTTAAATT
320 GTTTTAAATT
* * * *
159064 ATTTTTAATTTATGAGTGTTTTATCCAAAAATTGAGGAAAATTTTTTCGGGTCATTTTTTGCAAA
1 ATATTT-ATTTATGAGTATTTTAGCCAAAAATTGAGGAAAATTATTTCGGGTCATTTTTTGCAAA
* * * * * *
159129 ATTTTAGACAAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAAGTGTGTCAGGGCCTCGA
65 ATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAAAGCGT-TCAGGGCCTCGG
* * * * *
159194 CTCAGTTTTGCATGATTTTTGGCACCGAGACTTCTTGAAATATTTATATTCATGTAATAAAATCT
129 CTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
* *
159259 TAGCCACATTGCATTTAAGAATTTGTTTCTACGAGCATATGAATCTTGTTTCGATTTAATTAGAA
194 CAGCCACATTGCATTTAAGGATTTGTTT-TACGAGCATATGAATCTTGTTTCGATTTAATTAGAA
* * * * * * * ** * *
159324 ATTCATTCAGAAAAAGTAAGAAAAGCGATATTAGAATCCT-AAAAAACCCATCAATATTTTTTGG
258 ATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCC-CCAAT-CTTTTTGG
159388 ATTTT-AATCT
321 -TTTTAAAT-T
* * ** *
159398 AATATTT-TTTACGAGTATTTTAGCCAAAAATTGAGG-AGATATATTTCCAGTCAATTTTTGCAA
1 -ATATTTATTTATGAGTATTTTAGCCAAAAATTGAGGAAAAT-TATTTCGGGTCATTTTTTGCAA
* * * * * * *
159461 AATGTCAGCCGAAATCGTGTAATAATCATAACGGTTTTTTGCTAAAAATA-CGTTCTAGGACCCC
64 AATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAA-AGCGTTC-AGGGCCTC
* * * * * *
159525 GGCTTAGTTTTGCATGATTTTTGACGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAAT
127 GGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAAT
*** * * *
159590 GGAAGCCACATTGCATTTAAGGATTTGTTTTTACGAG-AAACCGAATCTTGTTTGGATTGGATTT
192 CTCAGCCACATTGCATTTAAGGATTTG-TTTTACGAGCATA-TGAATCTTG--T---TTCGATTT
* * * *
159654 AATAAAAAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAA-C
250 AAT-TAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCCCCAATC
*
159718 TTTTTTGGTATTAAATT
314 -TTTTTGGTTTTAAATT
* * * *
159735 ATATATATTTCATGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCATTCTGTTGCAA
1 ATATTTATTT-ATGAGTATTTTAGCCAAAAATTGAGGAAAATTATTTCGGGTCATT-TTTTGCAA
* * * * ** *
159800 AATTTTAGCCGAAATTGTGTATTAACCATCACGGTTATTTGG-TGAAAACGCGTTTTGGGGCTCC
64 AATTTTAGCCGAAATCGTGTAATAACCATCACGGTT-TTTGGCTAAAAAAGCGTTCAGGGCCT-C
* * * * * *
159864 GACTCAAG-TTTGCATTATTCTTGGCACCGAGAATCCTTGAAATATCTAAATTCATCTAATCAAA
127 GGCTC-AGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
* * * *
159928 TCTCATCCACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGATTCTTGTTTCGATTTCATTA
191 TCTCAGCCACATTGCATTTAAGGATTTGTTTT-ACGAGCATATGAATCTTGTTTCGATTTAATTA
* * * * *
159993 GAAATTAATTCAGAAAAAATACGAAAAACGATATTAAAAGTGTGAAAAGTCCTCGAGTCTTTTTG
255 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCCCCAATCTTTTTG
*
160058 GTGTTAAATT
320 GTTTTAAATT
* * ** * *
160068 ATTTTTATCTTATGAGTTTTTTATTCAAAAATTGAGGAAAATTTTTTCGGGTCATTTTTTGTAAA
1 ATATTTAT-TTATGAGTATTTTAGCCAAAAATTGAGGAAAATTATTTCGGGTCATTTTTTGCAAA
* * * * ** * *
160133 ATTTTAGACAAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAACCGTGTGTCGGGGCCTCGG
65 ATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAAAGCGT-TCAGGGCCTCGG
* * * * * *
160198 CTCAGTTTTGCATGATTTTAGGCA-CATCGACTCCTTTAAATATTTATATTCATGTAATAAAATC
129 CTCAGTTTTGCATGATTTTTGGCACCA-AGACTCCTTGAAATATCTATATTCATCTAATCAAATC
* * *
160262 TTAGCCACATTGCATTTAAGAATTTGTTTCTACGAGCATATGAATCTTGTTTCAATTTAATTAGA
193 TCAGCCACATTGCATTTAAGGATTTGTTT-TACGAGCATATGAATCTTGTTTCGATTTAATTAGA
* * * * * * ** ** *
160327 AATTCATTTAGAAAAAGTAGGAAAAACGATATTAGAATCGT-AAAAAACCCATGAATAATTTTTG
257 AATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCC-CCAAT-CTTTTTG
160391 GATTTT-AATCT
320 G-TTTTAAAT-T
* * ** *
160402 AATATTT-TTTACGATTATTTTAGCCAAAAATTGA-GAAAATATATTTCCAGTCAATTTTTGCAA
1 -ATATTTATTTATGAGTATTTTAGCCAAAAATTGAGGAAAAT-TATTTCGGGTCATTTTTTGCAA
* * * * * * * * *
160465 ACTGTCAGCCAAAATCGTGTAATAATCATAAC-GTTTTTTGCTAAAAATTA-CGTTCTAGGACCC
64 AATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAA--AGCGTTC-AGGGCCT
* * * * * *
160528 CGGCTTAGTTTTACATGATTTTTGGCGCAAAGACTCCTTGAGATATTCCATATTCATCTAATCAA
126 CGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATA-TCTATATTCATCTAATCAA
*** *
160593 ATGAAAGCCACATTACATTTAAGGATTTGTTTTTACGAG
190 ATCTCAGCCACATTGCATTTAAGGATTTG-TTTTACGAG
Statistics
Matches: 1811, Mismatches: 335, Indels: 166
0.78 0.14 0.07
Matches are distributed among these distances:
328 158 0.09
329 66 0.04
330 74 0.04
331 115 0.06
332 409 0.23
333 441 0.24
334 77 0.04
335 17 0.01
336 45 0.02
337 61 0.03
338 162 0.09
339 173 0.10
340 13 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (329 bp):
ATATTTATTTATGAGTATTTTAGCCAAAAATTGAGGAAAATTATTTCGGGTCATTTTTTGCAAAA
TTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAAAGCGTTCAGGGCCTCGGCT
CAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
GCCACATTGCATTTAAGGATTTGTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGAAATT
AATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCCCCAATCTTTTTGGTTTTA
AATT
Found at i:160207 original size:671 final size:666
Alignment explanation
Indices: 158072--160297 Score: 2686
Period size: 671 Copynumber: 3.3 Consensus size: 666
158062 CCCTTCAATA
* ** * *
158072 TTTTTTATGATTATTTTAGCCAAAAATTGAGGAAATATATTTCCAGTCAATTTTTGCAAAATGTC
1 TTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTT
* * * * *
158137 AGCCGAAATCGTGTAATAATCATAACGGTTTTTTGCTAAAAATGCGT-TCTAGGACCCGGCTTAG
66 AGCCGAAATCGTGTAATAACCATAACGGTTTTTGGCTAAAAA--CGTGTCTGGGGCCCGGCTCAG
* *
158201 TTTTACATGATTTTTGCCGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAAGCC
129 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAAGCC
158266 ACATTGCATTTAAGGATTTGTTTTTACGAGAAACAGAATCTTGTTTGGATTGGATTTAATAAAAA
194 ACATTGCATTTAAGGATTTGTTTTTACGAGAAACAGAATCTTGTTTGGATTGGATTTAATAAAAA
*
158331 TATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACTTTTTT-GT
259 AATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACTTTTTTGGT
* *
158395 GTTAAATTATATATATTTCAGGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCATTC
324 ATTAAATTATATATATTTCATGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCATTC
* *
158460 TTTTGCAAAATTTTAGTCGAAAGCGTGTATTAACCATCACGGTTATTTGGTAAAAACGCGTTTCG
389 TTTTGCAAAATTTTAGACGAAATCGTGTATTAACCATCACGGTTATTTGGTAAAAACGCGTTTCG
* * * *
158525 GGGCTACGGCTCAATTTTGCATGATTTTTGGCGCCGAGAATCCTTGAAATATCTATATTCATCTA
454 GGGCTCCGACTCAAGTTTGCATGATTTTTGGCACCGAGAATCCTTGAAATATCTATATTCATCTA
* *
158590 ATCAAATCTCCGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTGTATCGATT
519 ATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTGTTTCGATT
* * * * *
158655 TAATTAGAAATTAATTCGGAAAAAA-AGGAAAAAACGAT-TTAGAAACGTCAAAAGCCCTTCAAT
584 TAATTAGAAATTAATTCAGAAAAAATAAG-AAAAACGATATTA-AAATGTAAAAAGCCCATCAAT
*
158718 CCTTTTGGTGTTGAAA-TATAT
647 CTTTTTGGTGTT-AAATTAT-T
* * * * * * *
158739 ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTATCGGATAAATTCTTACAAAATTTT
1 TTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTT
* ** *
158804 A-CCGAAATCGTGAAATAACCATAACAATTTTTGGCTAAAAAAGCGT-TTTGGGGCCCAGG-TCA
66 AGCCGAAATCGTGTAATAACCATAACGGTTTTTGGCT-AAAAA-CGTGTCTGGGGCCC-GGCTCA
* * **
158866 GTTTTGCATGATTTTTGGCTCCAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAA-
128 GTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAAT-GGAAG
** * * * * * * *
158930 TAACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTG--T--A-TCGATTTCAT-TA
192 CCACATTGCATTTAAGGATTTGTTTTTACGAGAAACAGAATCTTGTTTGGATTGGATTTAATAAA
* * * *
158989 GAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCCCCAA-TCTTTTT
257 AAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACT-TTTTT
* * * * * * * *
159053 GGTTTTAAATTATTTTTAATTT-ATGAGTGTTTTATCCAAAAATTGAGGAAAATTTTTTCGGGTC
321 GGTATTAAATTATATAT-ATTTCATGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTC
* * * * *
159117 ATT-TTTTGCAAAATTTTAGACAAAATCGTGTACTAACCATCACAGTT-TTTGGCTAAAAAAGTG
385 ATTCTTTTGCAAAATTTTAGACGAAATCGTGTATTAACCATCACGGTTATTTGG-TAAAAACGCG
* * * * *
159180 TGTCAGGGC-CTCGACTC-AGTTTTGCATGATTTTTGGCACCGAGACTTCTTGAAATATTTATAT
449 TTTCGGGGCTC-CGACTCAAG-TTTGCATGATTTTTGGCACCGAGAATCCTTGAAATATCTATAT
* * * * *
159243 TCATGTAATAAAATCTTAGCCACATTGCATTTAAGAATTTG-TTTCTACGAGCATATGAATCTTG
512 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTC-ACGAGCATCTGAATCTTG
* * * * * *
159307 TTTCGATTTAATTAGAAATTCATTCAGAAAAAGTAAGAAAAGCGATATTAGAATCCTAAAAAACC
576 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAT-GTAAAAAGCC
* * *
159372 CATCAATATTTTTTGGAT-TTTAATCTAATA
640 CATCAAT-CTTTTTGG-TGTTAAAT-T-ATT
* * ** * *
159402 TTTTTTACGAGTATTTTAGCCAAAAATTGAGGAGATATATTTCCAGTCAATTTTTGCAAAATGTC
1 TTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTT
* * ** *
159467 AGCCGAAATCGTGTAATAATCATAACGGTTTTTTGCTAAAAATACGT-TCTAGGACCCCGGCTTA
66 AGCCGAAATCGTGTAATAACCATAACGGTTTTTGGCT-AAAA-ACGTGTCT-GGGGCCCGGCTCA
*
159531 GTTTTGCATGATTTTTGACGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAAGC
128 GTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAAGC
*
159596 CACATTGCATTTAAGGATTTGTTTTTACGAGAAACCGAATCTTGTTTGGATTGGATTTAATAAAA
193 CACATTGCATTTAAGGATTTGTTTTTACGAGAAACAGAATCTTGTTTGGATTGGATTTAATAAAA
159661 AAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACTTTTTTGG
258 AAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACTTTTTTGG
159726 TATTAAATTATATATATTTCATGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCATT
323 TATTAAATTATATATATTTCATGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCATT
* * * * *
159791 CTGTTGCAAAATTTTAGCCGAAATTGTGTATTAACCATCACGGTTATTTGGTGAAAACGCGTTTT
388 CTTTTGCAAAATTTTAGACGAAATCGTGTATTAACCATCACGGTTATTTGGTAAAAACGCGTTTC
* * *
159856 GGGGCTCCGACTCAAGTTTGCATTATTCTTGGCACCGAGAATCCTTGAAATATCTAAATTCATCT
453 GGGGCTCCGACTCAAGTTTGCATGATTTTTGGCACCGAGAATCCTTGAAATATCTATATTCATCT
* *
159921 AATCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGATTCTTGTTTCGAT
518 AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTGTTTCGAT
* * * * *
159986 TTCATTAGAAATTAATTCAGAAAAAATACGAAAAACGATATTAAAAGTGTGAAAAGTCC-TCGAG
583 TTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAA-TGTAAAAAGCCCATC-AA
160050 TCTTTTTGGTGTTAAATTATT
646 TCTTTTTGGTGTTAAATTATT
* ** * * *
160071 TTTATCTTATGAGTTTTTTATTCAAAAATTGAGGAAA-ATTTTTTCGGGTCATTTTTTGTAAAAT
1 TTT-T-TTATGAGTATTTTAGCCAAAAATTGAGGAAATA-TATTTCGGGTCAATTTTTGCAAAAT
* * * * * * *
160135 TTTAGACAAAATCGTGTACTAACCATCATGGTTTTTGGCTAAAACCGTGTGTCGGGGCCTCGGCT
63 TTTAGCCGAAATCGTGTAATAACCATAACGGTTTTTGGCTAAAAACGTGTCT-GGGGCC-CGGCT
* * ** * * ** * * ***
160200 CAGTTTTGCATGATTTTAGGCACATCGACTCCTTTAAATATTTATATTCATGTAATAAAATCTTA
126 CAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAA
* *
160265 GCCACATTGCATTTAAGAATTTGTTTCTACGAG
191 GCCACATTGCATTTAAGGATTTGTTTTTACGAG
160298 CATATGAATC
Statistics
Matches: 1299, Mismatches: 216, Indels: 84
0.81 0.14 0.05
Matches are distributed among these distances:
659 11 0.01
660 248 0.19
661 80 0.06
662 13 0.01
663 55 0.04
664 47 0.04
665 103 0.08
666 137 0.11
667 64 0.05
669 9 0.01
670 26 0.02
671 290 0.22
672 203 0.16
673 13 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (666 bp):
TTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATATTTCGGGTCAATTTTTGCAAAATTTT
AGCCGAAATCGTGTAATAACCATAACGGTTTTTGGCTAAAAACGTGTCTGGGGCCCGGCTCAGTT
TTGCATGATTTTTGGCGCAAAGACTCCTTGAGATATCCATATTCATCTAATCAAATGGAAGCCAC
ATTGCATTTAAGGATTTGTTTTTACGAGAAACAGAATCTTGTTTGGATTGGATTTAATAAAAAAA
TTAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAAGTCCTCCAACTTTTTTGGTAT
TAAATTATATATATTTCATGATTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTCATTCTT
TTGCAAAATTTTAGACGAAATCGTGTATTAACCATCACGGTTATTTGGTAAAAACGCGTTTCGGG
GCTCCGACTCAAGTTTGCATGATTTTTGGCACCGAGAATCCTTGAAATATCTATATTCATCTAAT
CAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTCACGAGCATCTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAATGTAAAAAGCCCATCAATCTTT
TTGGTGTTAAATTATT
Done.