Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013952.1 Corchorus olitorius cultivar O-4 contig13985, 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: 28732
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:731 original size:14 final size:14
Alignment explanation
Indices: 714--743 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
704 TTATAATAGG
*
714 TATTATATATATAT
1 TATTATATAAATAT
728 TATTATATAAATAT
1 TATTATATAAATAT
742 TA
1 TA
744 ATAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATATAAATAT
Found at i:971 original size:105 final size:102
Alignment explanation
Indices: 853--1044 Score: 276
Period size: 105 Copynumber: 1.9 Consensus size: 102
843 TTACTTAAAT
* * * ** *
853 TTTTATAATTTTACTTAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATTTTTATAAGTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTTAT-A-CA
*
918 CTATTTTATTTTTGCCATTTTACTATCTTAATTAAAATAC
64 -TATTTTATTTTTACCATTTTACTATCTTAATTAAAATAC
*
958 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTTATACATA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTTATACATA
*
1023 TTTTATTTTTATCATTTTACTA
66 TTTTATTTTTACCATTTTACTA
1045 ATTTAAAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 22 0.28
103 1 0.01
104 1 0.01
105 54 0.69
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.52
Consensus pattern (102 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCCTTATACATA
TTTTATTTTTACCATTTTACTATCTTAATTAAAATAC
Found at i:1959 original size:22 final size:22
Alignment explanation
Indices: 1934--1975 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1924 AATTACAGTA
*
1934 TTCTTGGATCATCCGGGTTAAC
1 TTCTCGGATCATCCGGGTTAAC
* *
1956 TTCTCGGGTCATTCGGGTTA
1 TTCTCGGATCATCCGGGTTA
1976 CAGGTTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.38
Consensus pattern (22 bp):
TTCTCGGATCATCCGGGTTAAC
Found at i:2078 original size:11 final size:11
Alignment explanation
Indices: 2062--2092 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2052 CAATTATTTA
2062 TTTTAATTTTC
1 TTTTAATTTTC
2073 TTTTAATTTTC
1 TTTTAATTTTC
2084 TTTTAATTT
1 TTTTAATTT
2093 AAATACGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTAATTTTC
Found at i:3740 original size:18 final size:19
Alignment explanation
Indices: 3717--3754 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3707 AAGGAAAGAA
3717 GGAGGGG-GGGGGTGGGGG
1 GGAGGGGAGGGGGTGGGGG
3735 GGAGGGGAGGGGGTGGGGG
1 GGAGGGGAGGGGGTGGGGG
3754 G
1 G
3755 AGGAAAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.08, C:0.00, G:0.87, T:0.05
Consensus pattern (19 bp):
GGAGGGGAGGGGGTGGGGG
Found at i:4012 original size:25 final size:25
Alignment explanation
Indices: 3984--4051 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
3974 TTTTAAAACT
* *
3984 TGGGTTGCTA-TTTTTTTTTTTGAAA
1 TGGGCTGCTACTTTTTTTTATT-AAA
4009 TGGGCTGCTACTTTTTTTTATTAAA
1 TGGGCTGCTACTTTTTTTTATTAAA
* *
4034 TGGGCTGCCACTCTTTTT
1 TGGGCTGCTACTTTTTTT
4052 CTTTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 28 0.74
26 10 0.26
ACGTcount: A:0.15, C:0.13, G:0.19, T:0.53
Consensus pattern (25 bp):
TGGGCTGCTACTTTTTTTTATTAAA
Found at i:4095 original size:29 final size:28
Alignment explanation
Indices: 3994--4117 Score: 119
Period size: 29 Copynumber: 4.4 Consensus size: 28
3984 TGGGTTGCTA
3994 TTTTTTTTTTTGAAATGGGCTGCTAC--
1 TTTTTTTTTTTGAAATGGGCTGCTACTT
* *
4020 TTTTTTTTATT-AAATGGGCTGCCACTCTTT
1 TTTTTTTTTTTGAAATGGGCTGCTA--C-TT
* *
4050 TTCTTTTTTTTTTAAATGGACTGCTACTT
1 TT-TTTTTTTTTGAAATGGGCTGCTACTT
* *
4079 TTTTTTTTTTTGGAAATGGGCTACTACTC
1 TTTTTTTTTTT-GAAATGGGCTGCTACTT
*
4108 TTTTTCTTTT
1 TTTTTTTTTT
4118 GTGTGTGTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 13
0.78 0.10 0.13
Matches are distributed among these distances:
25 12 0.15
26 10 0.12
27 1 0.01
28 9 0.11
29 26 0.32
30 3 0.04
31 8 0.10
32 11 0.14
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.57
Consensus pattern (28 bp):
TTTTTTTTTTTGAAATGGGCTGCTACTT
Found at i:4096 original size:61 final size:58
Alignment explanation
Indices: 3995--4117 Score: 167
Period size: 61 Copynumber: 2.1 Consensus size: 58
3985 GGGTTGCTAT
* *
3995 TTTTTTTTTTGAAATGGGCTGCTACTTTTTTTTATTAAATGGGCTGCCACTCTTTTTC
1 TTTTTTTTTTGAAATGGACTGCTACTTTTTTTTATTAAATGGGCTACCACTCTTTTTC
* *
4053 TTTTTTTTTT-AAATGGACTGCTACTTTTTTTTTTTTTGGAAATGGGCTACTACTCTTTTTC
1 TTTTTTTTTTGAAATGGACTGCTAC--TTTTTTTTATT--AAATGGGCTACCACTCTTTTTC
4114 TTTT
1 TTTT
4118 GTGTGTGTGT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
57 13 0.23
58 10 0.18
59 10 0.18
61 24 0.42
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.57
Consensus pattern (58 bp):
TTTTTTTTTTGAAATGGACTGCTACTTTTTTTTATTAAATGGGCTACCACTCTTTTTC
Found at i:5908 original size:23 final size:24
Alignment explanation
Indices: 5858--5911 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5848 TTTTTATCCG
* *
5858 CTTTTT-TTTCTTTTTTAAGCAAT
1 CTTTTTATTTCTTTTTCAAACAAT
5881 CTTTTTATTTCTTTTTCAAACAA-
1 CTTTTTATTTCTTTTTCAAACAAT
*
5904 GTTTTTAT
1 CTTTTTAT
5912 GTTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.20, C:0.13, G:0.04, T:0.63
Consensus pattern (24 bp):
CTTTTTATTTCTTTTTCAAACAAT
Found at i:6158 original size:20 final size:20
Alignment explanation
Indices: 6135--6177 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6125 GCCACCCGCA
6135 CTCCGCCGCACTTCCTCTTC
1 CTCCGCCGCACTTCCTCTTC
* **
6155 CTCCGCCTCGTTTCCTCTTC
1 CTCCGCCGCACTTCCTCTTC
6175 CTC
1 CTC
6178 TCTCCTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.53, G:0.09, T:0.35
Consensus pattern (20 bp):
CTCCGCCGCACTTCCTCTTC
Found at i:9299 original size:25 final size:25
Alignment explanation
Indices: 9271--9320 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
9261 GCAAGTTATA
9271 TTATATTAAATTTATACTCAAAACT
1 TTATATTAAATTTATACTCAAAACT
*
9296 TTATATTAGATTTATACTCAAAACT
1 TTATATTAAATTTATACTCAAAACT
9321 CAAAAGTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (25 bp):
TTATATTAAATTTATACTCAAAACT
Found at i:16971 original size:70 final size:70
Alignment explanation
Indices: 16877--17060 Score: 208
Period size: 70 Copynumber: 2.6 Consensus size: 70
16867 TAAGGAGTGG
* * * * * *
16877 CATTGGACTTTCACTTGTGAGTTTTTGGAATTTACAAATTGTCGC-GGATCCAATTTGGGATTTA
1 CATTGGACTTTTACCTGTGGGTTTTTGGAATTTACAAATTG-CCCTCGACCCAATTTGGGATTTA
*
16941 TGAACT
65 TGAACC
* *
16947 CATTGGATTTTTACCTGTGGGTTTTTGGAATTTACAATTTGCCCTCGACCCAATTTGGGATTTAT
1 CATTGGACTTTTACCTGTGGGTTTTTGGAATTTACAAATTGCCCTCGACCCAATTTGGGATTTAT
*
17012 GGACC
66 GAACC
* * * * * *
17017 CATTGGACTTTTACCTGCGGGCTTTCGAAATTTACGAATCGCCC
1 CATTGGACTTTTACCTGTGGGTTTTTGGAATTTACAAATTGCCC
17061 ACCCGATGGG
Statistics
Matches: 95, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
69 2 0.02
70 93 0.98
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (70 bp):
CATTGGACTTTTACCTGTGGGTTTTTGGAATTTACAAATTGCCCTCGACCCAATTTGGGATTTAT
GAACC
Found at i:17505 original size:43 final size:44
Alignment explanation
Indices: 17457--17556 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 44
17447 ATTCGCATAT
*
17457 ATAAAGCAAATAATTCTA-AGCCATCTCTAGATAATTCATCAAA
1 ATAAAGCTAATAATTCTACAGCCATCTCTAGATAATTCATCAAA
**
17500 ATAAAGCTAAT-ATTCTACTCCTCCATCTCTAGATAATTCATCAAA
1 ATAAAGCTAATAATTCTA--CAGCCATCTCTAGATAATTCATCAAA
17545 ATAAAGCTAATA
1 ATAAAGCTAATA
17557 TTAATTGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 6 0.12
43 10 0.20
45 34 0.68
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (44 bp):
ATAAAGCTAATAATTCTACAGCCATCTCTAGATAATTCATCAAA
Found at i:18308 original size:22 final size:23
Alignment explanation
Indices: 18283--18328 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
18273 TAATATCTAC
18283 ACACAATTAAT-ATATAAT-TAAA
1 ACACAATTAATCATA-AATATAAA
*
18305 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
18328 A
1 A
18329 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:19391 original size:16 final size:16
Alignment explanation
Indices: 19372--19404 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19362 AATGACGTGT
19372 CATGTTCATGTTGTGC
1 CATGTTCATGTTGTGC
19388 CATGTTCATGTTGTGC
1 CATGTTCATGTTGTGC
19404 C
1 C
19405 CTAGTAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.42
Consensus pattern (16 bp):
CATGTTCATGTTGTGC
Found at i:19917 original size:22 final size:23
Alignment explanation
Indices: 19890--19971 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 23
19880 AAATCTTTTA
19890 TATG-AATTGTT-AGTAATCACAC
1 TATGAAATTGTTGA-TAATCACAC
*
19912 TTTGAAATT-TTGATAATCACAC
1 TATGAAATTGTTGATAATCACAC
* *
19934 TATGAAATTG-TGATAA-CTTCGC
1 TATGAAATTGTTGATAATC-ACAC
19956 TATGAAATT-TTGATAA
1 TATGAAATTGTTGATAA
19972 ACCTTCCTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
21 1 0.02
22 45 0.88
23 5 0.10
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
TATGAAATTGTTGATAATCACAC
Found at i:20097 original size:86 final size:83
Alignment explanation
Indices: 19983--20145 Score: 265
Period size: 86 Copynumber: 1.9 Consensus size: 83
19973 CCTTCCTATA
19983 AAATTTTGATAAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTATTAATTATCTCC
1 AAATTTTGATAAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTATT-A--ATCTCC
20048 CTATGAAATCTTTGATAACTAC
63 CTATGAAAT-TTTGATAACTAC
* *
20070 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACCTCATTATGGAATTTTGTTAATCTCCCTA
1 AAATTTTGATAAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTATTAATCTCCCTA
20134 TGAAATTTTGAT
66 TGAAATTTTGAT
20146 CTACATACTA
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
82 6 0.08
83 15 0.20
85 1 0.01
86 42 0.57
87 10 0.14
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.44
Consensus pattern (83 bp):
AAATTTTGATAAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTTATTAATCTCCCTA
TGAAATTTTGATAACTAC
Found at i:20239 original size:22 final size:22
Alignment explanation
Indices: 19914--20253 Score: 161
Period size: 22 Copynumber: 15.5 Consensus size: 22
19904 AATCACACTT
* *
19914 TGAAATTTTGATAATC-ACACTA
1 TGAAATTTTGATAACCTTCA-TA
* *
19936 TGAAATTGTGATAA-CTTCGCTA
1 TGAAATTTTGATAACCTTC-ATA
*
19958 TGAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AACCTTCATA
* * *
19981 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTTCATA
**
20004 TGATTTTTTGATAACC-TCATTA
1 TGAAATTTTGATAACCTTCA-TA
* * *
20026 TGAAATTTT-ATTAATTATCTCCCTA
1 TGAAATTTTGA-T-A--ACCTTCATA
20051 TGAAATCTTTGATAA----C-TA
1 TGAAAT-TTTGATAACCTTCATA
* * *
20069 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTTCATA
**
20090 TGATTTTTTGATAACC-TCATTA
1 TGAAATTTTGATAACCTTCA-TA
* * * * *
20112 TGGAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCTTCATA
* * *
20134 TGAAATTTTGATCTACATAC-TA
1 TGAAATTTTGAT-AACCTTCATA
* *
20156 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAACCTTCATA
* **
20178 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCTTCA-TA
20200 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCATA
* *
20222 TGAAATTTTGATATCCTTC--C
1 TGAAATTTTGATAACCTTCATA
20242 TGAAATTTTGAT
1 TGAAATTTTGAT
20254 TACTCCATAA
Statistics
Matches: 245, Mismatches: 49, Indels: 50
0.71 0.14 0.15
Matches are distributed among these distances:
16 8 0.03
17 4 0.02
18 2 0.01
19 1 0.00
20 13 0.05
21 12 0.05
22 138 0.56
23 46 0.19
24 4 0.02
25 11 0.04
26 5 0.02
27 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCATA
Found at i:20282 original size:42 final size:42
Alignment explanation
Indices: 20200--20284 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 42
20190 AACTAAACTA
* * * * *
20200 TGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTTCC
1 TGAAATTTTGATAACCTCCATATAAAAGTTTAATAACCTTCC
*
20242 TGAAATTTTGATTA-CTCCATAATAAAAGTTTAATAACCTTCC
1 TGAAATTTTGATAACCTCCAT-ATAAAAGTTTAATAACCTTCC
20284 T
1 T
20285 AATTTGGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (42 bp):
TGAAATTTTGATAACCTCCATATAAAAGTTTAATAACCTTCC
Found at i:20391 original size:22 final size:22
Alignment explanation
Indices: 20366--20482 Score: 112
Period size: 22 Copynumber: 5.3 Consensus size: 22
20356 TTTTGAAAAG
20366 TTGATAACCTCTTTATGAAATT
1 TTGATAACCTCTTTATGAAATT
* *
20388 TTGATAACCTCTCTATAAAATT
1 TTGATAACCTCTTTATGAAATT
* * *
20410 TTGTTGACC-CTTCTATTAAATT
1 TTGATAACCTCTT-TATGAAATT
* * * *
20432 TTGATAATCACATTATGTAATT
1 TTGATAACCTCTTTATGAAATT
*
20454 TTGATAACCTCGCTT-TGAAATT
1 TTGATAACCTC-TTTATGAAATT
20476 TTGATAA
1 TTGATAA
20483 TAACACTATG
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.03
22 70 0.92
23 4 0.05
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (22 bp):
TTGATAACCTCTTTATGAAATT
Found at i:20494 original size:22 final size:22
Alignment explanation
Indices: 20332--20505 Score: 98
Period size: 22 Copynumber: 7.9 Consensus size: 22
20322 CCAGAAATAC
* *
20332 CACTATGGAATTTTGGTAATCA
1 CACTATGAAATTTTGATAATCA
* * ** * *
20354 CATTTTGAAAAGTTGATAACCT
1 CACTATGAAATTTTGATAATCA
** * *
20376 CTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
* * * * *
20398 CTCTATAAAATTTTGTTGA-CC
1 CACTATGAAATTTTGATAATCA
* *
20419 CTTCTATTAAATTTTGATAATCA
1 C-ACTATGAAATTTTGATAATCA
* * * *
20442 CATTATGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
* * *
20464 CGCTTTGAAATTTTGATAATAA
1 CACTATGAAATTTTGATAATCA
20486 CACTATGAAATTTTGATAAT
1 CACTATGAAATTTTGATAAT
20506 TTCTTATAAA
Statistics
Matches: 114, Mismatches: 36, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
21 2 0.02
22 110 0.96
23 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
CACTATGAAATTTTGATAATCA
Found at i:20497 original size:88 final size:88
Alignment explanation
Indices: 20340--20500 Score: 207
Period size: 88 Copynumber: 1.8 Consensus size: 88
20330 ACCACTATGG
* * * ** *
20340 AATTTTGGTAATCACATTTTGAAAAGTTGATAACCTCTTTATGAAATTTTGATAACCTCTCTATA
1 AATTTTGATAATCACATTATGAAAAGTTGATAACCTCCTTATGAAATTTTGATAACAACACTATA
20405 AAATTTTGTTGACCCTTCTATTA
66 AAATTTTGTTGACCCTTCTATTA
* ** *
20428 AATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAATAACACTAT
1 AATTTTGATAATCACATTATGAAAAGTTGATAACCTC-CTTATGAAATTTTGATAACAACACTAT
*
20492 GAAATTTTG
65 AAAATTTTG
20501 ATAATTTCTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
88 59 0.97
89 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (88 bp):
AATTTTGATAATCACATTATGAAAAGTTGATAACCTCCTTATGAAATTTTGATAACAACACTATA
AAATTTTGTTGACCCTTCTATTA
Found at i:20639 original size:22 final size:21
Alignment explanation
Indices: 20622--20769 Score: 86
Period size: 22 Copynumber: 6.8 Consensus size: 21
20612 TTATAACCTT
20622 CATATGAAATTTTGATAACCA
1 CATATGAAATTTTGATAACCA
*
20643 CACTA-AAACATTTTGATAACCA
1 CA-TATGAA-ATTTTGATAACCA
* *
20665 CACCATGAAATTTTGATAACCTC
1 CA-TATGAAATTTTGATAACC-A
** * *
20688 CCCATGAAATATT-AGTAACCTC
1 CATATGAAATTTTGA-TAACC-A
* *
20710 CTTATGAAATTTTGTTAACCA
1 CATATGAAATTTTGATAACCA
*
20731 CACTATGAAATTCTT-ATAACCT
1 CA-TATGAAATT-TTGATAACCA
* *
20753 CGCTATGACATTTTGAT
1 C-ATATGAAATTTTGAT
20770 TATATCTTTG
Statistics
Matches: 101, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
21 8 0.08
22 88 0.87
23 5 0.05
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
CATATGAAATTTTGATAACCA
Found at i:20695 original size:66 final size:66
Alignment explanation
Indices: 20625--20769 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
20615 TAACCTTCAT
* *
20625 ATGAAATTTTGATAACCACACTA-AAACATTTTGATAACCACACCATGAAATTTTGATAACCTCC
1 ATGAAATTTTGATAACCACACTATGAA-ATTTTGATAACCACACTATGAAATTTTGATAACCTCC
20689 CC
65 CC
* * *
20691 ATGAAATATT-AGTAACCTC-CTTATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCT
1 ATGAAATTTTGA-TAACCACAC-TATGAAATTTTGATAACCACACTATGAAATT-TTGATAACCT
* *
20753 CGCT
63 CCCC
*
20757 ATGACATTTTGAT
1 ATGAAATTTTGAT
20770 TATATCTTTG
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
65 2 0.03
66 58 0.89
67 5 0.08
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (66 bp):
ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCC
C
Found at i:20739 original size:44 final size:44
Alignment explanation
Indices: 20624--20769 Score: 129
Period size: 44 Copynumber: 3.3 Consensus size: 44
20614 ATAACCTTCA
* * * *
20624 TATGAAATTTTGATAACCACACTA-AAACATT-TTGATAACCACAC
1 TATGAAATTTTGATAACCACACCATGAA-ATTATT-ATAACCTCGC
* * *
20668 CATGAAATTTTGATAACCTCCCCATGAAA-TATTAGTAACCTC-C
1 TATGAAATTTTGATAACCACACCATGAAATTATTA-TAACCTCGC
* * *
20711 TTATGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTCGC
1 -TATGAAATTTTGATAACCACACCATGAAATTATTATAACCTCGC
*
20756 TATGACATTTTGAT
1 TATGAAATTTTGAT
20770 TATATCTTTG
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
43 3 0.04
44 72 0.88
45 7 0.09
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACCATGAAATTATTATAACCTCGC
Found at i:20819 original size:22 final size:22
Alignment explanation
Indices: 20794--21011 Score: 140
Period size: 22 Copynumber: 9.8 Consensus size: 22
20784 CCTTTATATA
*
20794 AAATTGTGATAACCACACTATG
1 AAATTTTGATAACCACACTATG
** *** *
20816 AAATTTCAATAACCTTTCTAAG
1 AAATTTTGATAACCACACTATG
* *
20838 AAATTTTAATAATCTA-ATCCTATG
1 AAATTTTGATAA-CCACA--CTATG
*
20862 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACACTATG
* *
20884 AAATTTTGATAACCTTC-CCATG
1 AAATTTTGATAACC-ACACTATG
**
20906 AAATTTTGATAACTTTCA-TATG
1 AAATTTTGATAAC-CACACTATG
*
20928 AAATTTTGGTAACCACACTATG
1 AAATTTTGATAACCACACTATG
* *
20950 GAATTTTGATAACCTC-CTCATG
1 AAATTTTGATAACCACACT-ATG
* * * *
20972 AACTTATAATAACCATC-TTATG
1 AAATTTTGATAACCA-CACTATG
*
20994 AAATTCTGATAACCACAC
1 AAATTTTGATAACCACAC
21012 AGAGACAAGA
Statistics
Matches: 149, Mismatches: 36, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
21 5 0.03
22 123 0.83
23 6 0.04
24 15 0.10
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:20928 original size:44 final size:45
Alignment explanation
Indices: 20776--21007 Score: 158
Period size: 44 Copynumber: 5.2 Consensus size: 45
20766 TGATTATATC
* * *
20776 TTTGATAACCTTT-ATATAAAATTGTGATAACC-ACACTATGAAAT
1 TTTGATAACCTTTCATATGAAATTTTGATAACCTTC-CTATGAAAT
** * * *
20820 TTCAATAACCTTTC-TAAGAAATTTTAATAATCTAATCCTATGAAAT
1 TTTGATAACCTTTCATATGAAATTTTGATAACCT--TCCTATGAAAT
* * *
20866 TTTGGTAACC--ACACTATGAAATTTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTTTCA-TATGAAATTTTGATAACCTTCCTATGAAAT
* * *
20910 TTTGATAA-CTTTCATATGAAATTTTGGTAACC-ACACTATGGAAT
1 TTTGATAACCTTTCATATGAAATTTTGATAACCTTC-CTATGAAAT
* * * * * *
20954 TTTGATAACC--TCCTCATGAACTTATAATAACCATCTTATGAAAT
1 TTTGATAACCTTTCAT-ATGAAATTTTGATAACCTTCCTATGAAAT
*
20998 TCTGATAACC
1 TTTGATAACC
21008 ACACAGAGAC
Statistics
Matches: 145, Mismatches: 31, Indels: 24
0.73 0.16 0.12
Matches are distributed among these distances:
43 5 0.03
44 103 0.71
45 4 0.03
46 32 0.22
47 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (45 bp):
TTTGATAACCTTTCATATGAAATTTTGATAACCTTCCTATGAAAT
Found at i:20957 original size:66 final size:67
Alignment explanation
Indices: 20780--21011 Score: 247
Period size: 66 Copynumber: 3.5 Consensus size: 67
20770 TATATCTTTG
* * * ** * * *
20780 ATAACCT-TTATATAAAATTGTGATAACCACACTATGAAATTTCAATAACCTTTCTAAGAAATTT
1 ATAACCTATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTT
20844 TA
66 TA
* * *
20846 ATAATCTAATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT-ATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
*
20911 TTG
65 TTA
* * * *
20914 ATAA-CTTTCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGAACTT
1 ATAACCTATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATT
*
20977 ATA
65 TTA
* *
20980 ATAACC-ATCTTATGAAATTCTGATAACCACAC
1 ATAACCTATCATATGAAATTTTGATAACCACAC
21012 AGAGACAAGA
Statistics
Matches: 140, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
65 3 0.02
66 82 0.59
67 3 0.02
68 52 0.37
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (67 bp):
ATAACCTATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTT
TA
Found at i:21593 original size:6 final size:6
Alignment explanation
Indices: 21576--21607 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
21566 GTACTTTTAT
21576 ATATAG -TATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATA
21608 GATTTGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:22299 original size:22 final size:20
Alignment explanation
Indices: 22235--22306 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 20
22225 AAATTTTTTA
*
22235 AAAAATTTGATAATCACTAT
1 AAAATTTTGATAATCACTAT
*
22255 AAAATTTGGATAACCTC-CATAT
1 AAAATTTTGATAA--TCAC-TAT
22277 AAAATTTTGATAATTACACTAT
1 AAAATTTTGATAA-T-CACTAT
*
22299 AAAGTTTT
1 AAAATTTT
22307 TATGACGATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 11 0.26
21 2 0.05
22 28 0.67
23 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (20 bp):
AAAATTTTGATAATCACTAT
Found at i:22431 original size:22 final size:22
Alignment explanation
Indices: 22323--22900 Score: 245
Period size: 22 Copynumber: 26.3 Consensus size: 22
22313 GATATCATAG
* * *
22323 AATTTCGAGAACCTCCATATGA
1 AATTTTGATAACCTCCCTATGA
* * *
22345 AATTTTGTTAACTTCCCTATAA
1 AATTTTGATAACCTCCCTATGA
* *
22367 AATTTTG-TCACACTCCCTATAA
1 AATTTTGATAAC-CTCCCTATGA
* * *
22389 AATTTTAATAA-TTACCTAATGA
1 AATTTTGATAACCTCCCT-ATGA
*
22411 AATTTTGATAACCTCCCAATGA
1 AATTTTGATAACCTCCCTATGA
* * * **
22433 AATGTTGGTAAGCGCACATTATGA
1 AATTTTGATAA-C-CTCCCTATGA
* * *
22457 AATTTTGATAACCTTCCGATAA
1 AATTTTGATAACCTCCCTATGA
* * * * **
22479 AATATCGATAATCACATTATGA
1 AATTTTGATAACCTCCCTATGA
* * *
22501 GATTTTGATAAACATTCC-ATGA
1 AATTTTGAT-AACCTCCCTATGA
* *
22523 AATTGTGAT-ACCTCACTATGAA
1 AATTTTGATAACCTCCCTATG-A
*
22545 AATTTT-ATAAACCTCCCTATAA
1 AATTTTGAT-AACCTCCCTATGA
* *
22567 AATTTTGATAACCTCCATTTGA
1 AATTTTGATAACCTCCCTATGA
22589 AATTTTGATAACCT--C-ATGA
1 AATTTTGATAACCTCCCTATGA
* *
22608 AATTTTGAAAACC-ACCTCATGA
1 AATTTTGATAACCTCCCT-ATGA
*
22630 AATTTTGATAACCAT-CTTATGA
1 AATTTTGATAACC-TCCCTATGA
* *
22652 AATTTTGATAACATCCCTATAA
1 AATTTTGATAACCTCCCTATGA
** *
22674 ACATTTT-ATAACCTCTTTATAA
1 A-ATTTTGATAACCTCCCTATGA
* * *
22696 AATTTTGTTAACCT-CCTACGG
1 AATTTTGATAACCTCCCTATGA
* *** * *
22717 ATTTTTGATAAGAACACTATTA
1 AATTTTGATAACCTCCCTATGA
* *
22739 AAGTTTGATAACC-CCCAATGA
1 AATTTTGATAACCTCCCTATGA
* *
22760 AATTTTGATAATTAACTACACC-ATAA
1 AATTTTGAT-A--ACCT-C-CCTATGA
*** * *
22786 AATTACAATAACTTGCCTATGA
1 AATTTTGATAACCTCCCTATGA
* * *
22808 AATTTTGTTAATCTCCCTATAA
1 AATTTTGATAACCTCCCTATGA
* * *
22830 AATTTTGAAAACCAT-TCTATCA
1 AATTTTGATAACC-TCCCTATGA
* *
22852 AATTTTGTTAATCTCACC-AT-A
1 AATTTTGATAACCTC-CCTATGA
* **
22873 AATTTTGATAAACTCATTATGA
1 AATTTTGATAACCTCCCTATGA
22895 AATTTT
1 AATTTT
22901 AGTTACCACA
Statistics
Matches: 398, Mismatches: 124, Indels: 68
0.67 0.21 0.12
Matches are distributed among these distances:
19 15 0.04
20 5 0.01
21 61 0.15
22 256 0.64
23 31 0.08
24 17 0.04
25 1 0.00
26 10 0.03
27 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.37
Consensus pattern (22 bp):
AATTTTGATAACCTCCCTATGA
Found at i:22639 original size:107 final size:107
Alignment explanation
Indices: 22518--22710 Score: 252
Period size: 107 Copynumber: 1.8 Consensus size: 107
22508 ATAAACATTC
*
22518 CATGAAATTGTGAT-ACC-TCACTATGAAAATTTT-ATAAACCTCCCTATAAA-ATTTTGATAAC
1 CATGAAATTGTGATAACCATC-CTATG-AAATTTTGAT-AACATCCCTATAAACATTTT-ATAAC
*
22579 CTCCATT-TGAAATTTTGATAACCTCATGAAATTTTGAAAACCACCT
62 CT-CATTATAAAATTTTGATAACCTCATGAAATTTTGAAAACCACCT
* * *
22625 CATGAAATTTTGATAACCATCTTATGAAATTTTGATAACATCCCTATAAACATTTTATAACCTCT
1 CATGAAATTGTGATAACCATCCTATGAAATTTTGATAACATCCCTATAAACATTTTATAACCTCA
*
22690 TTATAAAATTTTGTTAACCTC
66 TTATAAAATTTTGATAACCTC
22711 CTACGGATTT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
106 3 0.04
107 56 0.75
108 14 0.19
109 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (107 bp):
CATGAAATTGTGATAACCATCCTATGAAATTTTGATAACATCCCTATAAACATTTTATAACCTCA
TTATAAAATTTTGATAACCTCATGAAATTTTGAAAACCACCT
Found at i:22980 original size:22 final size:22
Alignment explanation
Indices: 22955--23095 Score: 108
Period size: 22 Copynumber: 6.5 Consensus size: 22
22945 CCATATTATA
22955 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATG
* * * *
22977 AAATTTTGATAATCTCCCTCTG
1 AAATTTTGATAACCACACTATG
* * * *
22999 AAATTTCGATAACCTCCCCATG
1 AAATTTTGATAACCACACTATG
* **
23021 AAATTTTGTTAA-C-CTTTATG
1 AAATTTTGATAACCACACTATG
* * **
23041 AAATTGTGATTATTACACTATG
1 AAATTTTGATAACCACACTATG
* *
23063 AAATTTTGGTAACGACACT-TG
1 AAATTTTGATAACCACACTATG
23084 AAATTTTGATAA
1 AAATTTTGATAA
23096 GCTCACTCTA
Statistics
Matches: 92, Mismatches: 25, Indels: 5
0.75 0.20 0.04
Matches are distributed among these distances:
20 13 0.14
21 14 0.15
22 65 0.71
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATG
Found at i:23022 original size:44 final size:43
Alignment explanation
Indices: 22335--23457 Score: 371
Period size: 44 Copynumber: 25.5 Consensus size: 43
22325 TTTCGAGAAC
* * * *
22335 CTCCATATGAAATTTTGTTAACTTCCCTATAAAATTTTG-TCACA
1 CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-A-A
* * * *
22379 CTCCCTATAAAATTTTAATAA-TTACCTAATGAAATTTTGATAA
1 CTCCCTATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAA
* * * * **
22422 CCTCCCAATGAAATGTTGGTAAGCGCACATTATGAAATTTTGATAA
1 -CTCCCTATGAAATTTTGATAA-C-CTCCCTATGAAATTTTGATAA
* * * * * * * ** *
22468 CCTTCCGATAAAATATCGATAATCACATTATGAGATTTTGATAAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AA
* * *
22513 CATTCC-ATGAAATTGTGAT-ACCTCACTATGAAAATTTT-ATAAA
1 C-TCCCTATGAAATTTTGATAACCTCCCTATG-AAATTTTGAT-AA
* * *
22556 CCTCCCTATAAAATTTTGATAACCTCCATTTGAAATTTTGATAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
* * *
22600 C-CTC-ATGAAATTTTGAAAACC-ACCTCATGAAATTTTGATAA
1 CTCCCTATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAA
* * *
22641 C-CATCTTATGAAATTTTGATAACATCCCTATAAACATTTT-ATAA
1 CTC--CCTATGAAATTTTGATAACCTCCCTATGAA-ATTTTGATAA
** * * * * *
22685 CCTCTTTATAAAATTTTGTTAACCT-CCTACGGATTTTTGATAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
** * * * *
22728 GAACACTATTAAAGTTTGATAACC-CCCAATGAAATTTTGATAATTAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTG---A-TAA
* *** * * *
22775 CTACACC-ATAAAATTACAATAACTTGCCTATGAAATTTTGTTAA
1 CT-C-CCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
* * * * *
22819 TCTCCCTATAAAATTTTGAAAACCAT-TCTATCAAATTTTGTTAA
1 -CTCCCTATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAA
* ** * *
22863 TCTCACC-AT-AAATTTTGATAAACTCATTATGAAATTTTAGTTAC
1 -CTC-CCTATGAAATTTTGATAACCTCCCTATGAAATTTT-GATAA
* *** * * * ***
22907 CACAAAATTAAAATTTGATAACCTCTTCCTGTGAAA-TACCAT-A
1 CTCCCTATGAAATTTTGATAACCTC--CCTATGAAATTTTGATAA
* * *
22950 -T---TATAAAATTTTGATAACCACACTATGAAATTTTGATAA
1 CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
* * * *
22989 TCTCCCTCTGAAATTTCGATAACCTCCCCATGAAATTTTGTTAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
** * * * * *
23033 C-CTTTATGAAATTGTGATTA-TTACACTATGAAATTTTGGTAA
1 CTCCCTATGAAATTTTGATAACCT-CCCTATGAAATTTTGATAA
* * * *
23075 CGACACT-TGAAATTTTGATAAGCTCACTCTATCTCACTATGCAATTTTTATAA
1 C-TCCCTATGAAATTTTGAT-A----AC-C--TC-C-CTATGAAATTTTGATAA
* * * *
23128 GCACACTATGAAATTTTGATAATCTTCCTATGAAATTTTGATAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
* * * * * *
23172 CCTCCATATAAAATTTCGATAATCGCCCTATGAAATTTTGTTAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
****
23216 CCTCCCTATGAAATTTTGATAACCAGAGTATGAAATTTT-AGTAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGA-TAA
* ** *
23260 TCTCCCTGTGAAATTCCGATAACCTTCCC-ATG-AATTTCGATAA
1 -CTCCCTATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAA
* * * *
23303 CCTCCTTAGGAAATTTTAATAACCTCCATATGAAATTTTGATAA
1 -CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
* * *
23347 CAT-CCTCATGAAATTTTGATAACATCCC-ATGAACTTGTGATAA
1 C-TCCCT-ATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
* * * * * * * * *
23390 TTACACTATAAAATTTTAATATCCTACCTATTAAAGTTTGGTAA
1 CT-CCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
* *
23434 CCTCACTATAAAATTTTGATAACC
1 -CTCCCTATGAAATTTTGATAACC
23458 ACACAATAAA
Statistics
Matches: 799, Mismatches: 206, Indels: 148
0.69 0.18 0.13
Matches are distributed among these distances:
37 7 0.01
38 3 0.00
39 17 0.02
40 2 0.00
41 33 0.04
42 41 0.05
43 158 0.20
44 396 0.50
45 34 0.04
46 40 0.05
47 16 0.02
48 16 0.02
49 1 0.00
51 1 0.00
52 1 0.00
53 20 0.03
54 13 0.02
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (43 bp):
CTCCCTATGAAATTTTGATAACCTCCCTATGAAATTTTGATAA
Found at i:23034 original size:66 final size:66
Alignment explanation
Indices: 22335--23455 Score: 359
Period size: 66 Copynumber: 17.0 Consensus size: 66
22325 TTTCGAGAAC
* * * * * * * * * *
22335 CTCCATATGAAATTTTGTTAACTTCCCTATAAAATTTTG-TCACACTCCCTATAAAATTTTAATA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAAC-CACACTATGAAATTTTGATA
22399 AT
65 AT
* * * * *
22401 -TACCTAATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCACATTATGAAATTTTGA
1 CTCCCT-ATGAAATTTTGATAACCTCCCCATGAAATTTTGATAA-C-CACACTATGAAATTTTGA
*
22465 TAAC
63 TAAT
* * * * * * * *** * * ** * *
22469 CTTCCGATAAAATATCGATAATCACATTATGAGATTTTGATAAACATTCCATGAAATTGTGAT-A
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGATAA
*
22533 C
66 T
* * * * *
22534 CTCACTATGAAAATTTT-ATAAACCTCCCTATAAAATTTTGATAACCTC-CATTTGAAATTTTGA
1 CTCCCTATG-AAATTTTGAT-AACCTCCCCATGAAATTTTGATAACCACAC-TATGAAATTTTGA
22597 TAA-
63 TAAT
* * * * *
22600 C-CTC-ATGAAATTTTGAAAACCACCTCATGAAATTTTGATAACCATC-TTATGAAATTTTGATA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCA-CACTATGAAATTTTGATA
22662 A-
65 AT
* *** * * * * * *
22663 CATCCCTATAAACATTTT-ATAACCTCTTTATAAAATTTTGTTAACCTC-CTACGGATTTTTGAT
1 C-TCCCTATGAA-ATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGAT
*
22726 AAG
64 AAT
** * * * * * * * ***
22729 AACACTATTAAAGTTTGATAACC-CCCAATGAAATTTTGATAATTAACTACACCATAAAATTACA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTG---A-TAACCACACTATGAAATTTTG
22793 ATAA-
62 ATAAT
* * * * * * ** * *
22797 CTTGCCTATGAAATTTTGTTAATCTCCCTATAAAATTTTGAAAACCATTCTATCAAATTTTGTTA
1 C-TCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGATA
22862 AT
65 AT
* *** * ** * *
22864 CTCACC-AT-AAATTTTGATAAACTCATTATGAAATTTT-AGTTACCACAAAATTAAAATTTGAT
1 CTC-CCTATGAAATTTTGATAACCTCCCCATGAAATTTTGA-TAACCACACTATGAAATTTTGAT
22926 AACCT
64 AA--T
* * *** * *
22931 CTTCCTGTGAAA-TACCAT-A--T---TATAAAATTTTGATAACCACACTATGAAATTTTGATAA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGATAA
22989 T
66 T
* * * ** * *
22990 CTCCCTCTGAAATTTCGATAACCTCCCCATGAAATTTTGTTAA-C-CTTTATGAAATTGTGATTA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGATAA
23053 T
66 T
* * ** * * *
23054 -TACACTATGAAATTTTGGTAA-CGACACTTGAAATTTTGATAAGCTCACTCTATCTCACTATGC
1 CT-CCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGAT-A----AC-C-A---CACTATGA
* *
23117 AATTTTTATAAG
55 AATTTTGATAAT
* * * * * * * *
23129 CACACTATGAAATTTTGATAATCTTCCTATGAAATTTTGATAACCTC-CATATAAAATTTCGATA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACAC-TATGAAATTTTGATA
23193 AT
65 AT
* * * * *
23195 CGCCCTATGAAATTTTGTTAACCTCCCTATGAAATTTTGATAACCAGAGTATGAAATTTT-AGTA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGA-TA
23259 AT
65 AT
* ** * * * * *
23261 CTCCCTGTGAAATTCCGATAACCTTCCCATG-AATTTCGATAACCTC-CTTAGGAAATTTTAATA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACAC-TATGAAATTTTGATA
*
23324 AC
65 AT
* * * * * *
23326 CTCCATATGAAATTTTGATAACATCCTCATGAAATTTTGATAA-CATC-CCATGAACTTGTGATA
1 CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCA-CACTATGAAATTTTGATA
23389 AT
65 AT
* * * * * * * * * * *
23391 -TACACTATAAAATTTTAATATCCTACCTATTAAAGTTTGGTAACCTCACTATAAAATTTTGATA
1 CT-CCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGATA
23455 A
65 A
23456 CCACACAATA
Statistics
Matches: 757, Mismatches: 235, Indels: 126
0.68 0.21 0.11
Matches are distributed among these distances:
59 11 0.01
60 4 0.01
61 31 0.04
62 1 0.00
63 61 0.08
64 55 0.07
65 178 0.24
66 255 0.34
67 19 0.03
68 52 0.07
69 27 0.04
70 15 0.02
71 2 0.00
75 32 0.04
76 14 0.02
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (66 bp):
CTCCCTATGAAATTTTGATAACCTCCCCATGAAATTTTGATAACCACACTATGAAATTTTGATAA
T
Found at i:23457 original size:22 final size:22
Alignment explanation
Indices: 23107--23524 Score: 225
Period size: 22 Copynumber: 19.1 Consensus size: 22
23097 CTCACTCTAT
* * *
23107 CTCACTATGCAATTTTTATAAG
1 CTCACTATGAAATTTTGATAAC
*
23129 CACACTATGAAATTTTGATAATC
1 CTCACTATGAAATTTTGATAA-C
*
23152 TTC-CTATGAAATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
* * *
23173 CTC-CATATAAAATTTCGATAAT
1 CTCAC-TATGAAATTTTGATAAC
* * *
23195 CGCCCTATGAAATTTTGTTAAC
1 CTCACTATGAAATTTTGATAAC
*
23217 CTCCCTATGAAATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
** * *
23239 CAGAGTATGAAATTTT-AGTAAT
1 CTCACTATGAAATTTTGA-TAAC
* * **
23261 CTCCCTGTGAAATTCCGATAAC
1 CTCACTATGAAATTTTGATAAC
* *
23283 CTTC-CCATG-AATTTCGATAAC
1 C-TCACTATGAAATTTTGATAAC
* *
23304 CTC-CTTAGGAAATTTTAATAAC
1 CTCAC-TATGAAATTTTGATAAC
23326 CTC-CATATGAAATTTTGATAAC
1 CTCAC-TATGAAATTTTGATAAC
*
23348 ATC-CTCATGAAATTTTGATAAC
1 CTCACT-ATGAAATTTTGATAAC
* * * *
23370 ATC-CCATGAACTTGTGATAA-
1 CTCACTATGAAATTTTGATAAC
* * * *
23390 TTACACTATAAAATTTTAATATC
1 CT-CACTATGAAATTTTGATAAC
* * *
23413 CT-ACCTATTAAAGTTTGGTAAC
1 CTCA-CTATGAAATTTTGATAAC
*
23435 CTCACTATAAAATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
* * * *
23457 CACACAATAAAATTTTGAGAA-
1 CTCACTATGAAATTTTGATAAC
* * *
23478 CTACATTGTAAAATTTT-AGTAAC
1 CT-CACTATGAAATTTTGA-TAAC
* *
23501 CACACAATG-AATTTTGATAAC
1 CTCACTATGAAATTTTGATAAC
23522 CTC
1 CTC
23525 CAAAATTAAA
Statistics
Matches: 304, Mismatches: 74, Indels: 37
0.73 0.18 0.09
Matches are distributed among these distances:
20 4 0.01
21 49 0.16
22 243 0.80
23 8 0.03
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (22 bp):
CTCACTATGAAATTTTGATAAC
Found at i:24622 original size:27 final size:27
Alignment explanation
Indices: 24572--24628 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
24562 ATTTCCATTA
24572 TTTTAATAATGGAATAATTAAAATA-AT
1 TTTTAATAATGGAAT-ATTAAAATATAT
24599 TTTTAATAATGGCAAT-TTAGAAATATAT
1 TTTTAATAATGG-AATATTA-AAATATAT
24627 TT
1 TT
24629 GAAAAAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 3 0.11
27 17 0.63
28 7 0.26
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.44
Consensus pattern (27 bp):
TTTTAATAATGGAATATTAAAATATAT
Found at i:24686 original size:2 final size:2
Alignment explanation
Indices: 24679--24722 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
24669 TTCGTACTTT
24679 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24722 T
1 T
24723 TCAATTTCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Done.