Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014759.1 Corchorus olitorius cultivar O-4 contig14792, 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: 36034
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3258 original size:15 final size:15
Alignment explanation
Indices: 3224--3274 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
3214 GAGACGTTTT
*
3224 TTTTTCAAGAAAA-T
1 TTTTTCAAGAAAAGG
3238 TGTTTTCAAGAAAAGG
1 T-TTTTCAAGAAAAGG
3254 TTTTT-AA-AAAAGG
1 TTTTTCAAGAAAAGG
*
3267 GTTTTCAA
1 TTTTTCAA
3275 AAGGTTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 10 0.31
14 5 0.16
15 16 0.50
16 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (15 bp):
TTTTTCAAGAAAAGG
Found at i:3269 original size:14 final size:13
Alignment explanation
Indices: 3225--3276 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
3215 AGACGTTTTT
*
3225 TTTTCAAGAAAATTG
1 TTTTCAA-AAAA-GG
3240 TTTTCAAGAAAAGG
1 TTTTCAA-AAAAGG
*
3254 TTTTTAAAAAAGGG
1 TTTTCAAAAAA-GG
3268 TTTTCAAAA
1 TTTTCAAAA
3277 GGTTTTGGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.12
14 17 0.52
15 12 0.36
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:3583 original size:12 final size:12
Alignment explanation
Indices: 3568--3592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3558 TCATCAAGTG
3568 ATTCAAATCAAA
1 ATTCAAATCAAA
3580 ATTCAAATCAAA
1 ATTCAAATCAAA
3592 A
1 A
3593 GTGAATCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTCAAATCAAA
Found at i:4300 original size:11 final size:11
Alignment explanation
Indices: 4284--4308 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4274 TAATGATTAA
4284 AAATTGTTTTG
1 AAATTGTTTTG
4295 AAATTGTTTTG
1 AAATTGTTTTG
4306 AAA
1 AAA
4309 GTAAATTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (11 bp):
AAATTGTTTTG
Found at i:5194 original size:35 final size:35
Alignment explanation
Indices: 5148--5524 Score: 437
Period size: 35 Copynumber: 10.8 Consensus size: 35
5138 CATTACCATC
5148 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
5183 TTCAGATGACTCGGTGTAGCATCTTCGAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* *
5218 TCCAGATGACTCGGTGTAGCATCTTCAAAGTTGAGC
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGA-A
*
5254 TT-AGATGACTCGGTGCAGCATCTTCTAAA-TTGAA
1 TTCAGATGACTCGGTGTAGCATCTTC-AAAGTTGAA
* * *
5288 CTCAGATGACTCGGTATAGCATCTTCGAAGTTGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* * *
5323 TCCAGATGACTCGGTGTAGCATCTCCAAAGATGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* * * *
5358 CTCGGATGACTCGGTGTAGTATCTTCAAAGATGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
* * *
5393 CTCGGATGACTCGGTGTAGCATCTTCAAAGATGAA
1 TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
*
5428 TTCAGATGACTCGGTGTAGCATCTTCATAA--TGGA
1 TTCAGATGACTCGGTGTAGCATCTTCA-AAGTTGAA
* * * *
5462 CTCAG-TGGGCTCGGTGCAGCAAATCTTCAAA-TAG-A
1 TTCAGAT-GACTCGGTGTAGC--ATCTTCAAAGTTGAA
5497 TT-AGGATGACTCGGTGTAGCATCTTCAA
1 TTCA-GATGACTCGGTGTAGCATCTTCAA
5525 TATGAACTCG
Statistics
Matches: 298, Mismatches: 33, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
33 9 0.03
34 22 0.07
35 252 0.85
36 15 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (35 bp):
TTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA
Found at i:5333 original size:105 final size:105
Alignment explanation
Indices: 5149--5522 Score: 481
Period size: 105 Copynumber: 3.6 Consensus size: 105
5139 ATTACCATCT
*
5149 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCGAAGT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAACTCAGATGACTCGGTGTAGCATCTTCGAAGT
* *
5214 TGAATCCAGATGACTCGGTGTAGCATCTTCAAAGTTGAGC
66 TGAATCCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC
* * *
5254 TTAGATGACTCGGTGCAGCATCTTCTAAA-TTGAACTCAGATGACTCGGTATAGCATCTTCGAAG
1 TCAGATGACTCGGTGTAGCATCTTC-AAAGTTGAACTCAGATGACTCGGTGTAGCATCTTCGAAG
*
5318 TTGAATCCAGATGACTCGGTGTAGCATCTCCAAAGATGAAC
65 TTGAATCCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC
* * * * * *
5359 TCGGATGACTCGGTGTAGTATCTTCAAAGATGAACTCGGATGACTCGGTGTAGCATCTTCAAAGA
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAACTCAGATGACTCGGTGTAGCATCTTCGAAGT
* * *
5424 TGAATTCAGATGACTCGGTGTAGCATCTTCATA-ATGGAC
66 TGAATCCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC
* * * *
5463 TCAG-TGGGCTCGGTGCAGCAAATCTTCAAA-TAG-A-TTAGGATGACTCGGTGTAGCATCTTC
1 TCAGAT-GACTCGGTGTAGC--ATCTTCAAAGTTGAACTCA-GATGACTCGGTGTAGCATCTTC
5523 AATATGAACT
Statistics
Matches: 235, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
103 2 0.01
104 44 0.19
105 177 0.75
106 12 0.05
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (105 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAACTCAGATGACTCGGTGTAGCATCTTCGAAGT
TGAATCCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC
Found at i:5792 original size:27 final size:27
Alignment explanation
Indices: 5762--5887 Score: 132
Period size: 26 Copynumber: 4.7 Consensus size: 27
5752 AGGGTCATCC
*
5762 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTTCACACTA
* * *
5789 A-GGGCATTTTGGTCATTTGCATA-TCC
1 AGGGGCATTTTGGTCATTTTCACACT-A
*
5815 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTTCACACTA
* * * *
5842 A-GGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTTCACACTA
*
5868 AGGGGCATGTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
5888 AAGTCCACCC
Statistics
Matches: 80, Mismatches: 15, Indels: 8
0.78 0.15 0.08
Matches are distributed among these distances:
25 1 0.01
26 41 0.51
27 37 0.46
28 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACACTA
Found at i:5793 original size:26 final size:26
Alignment explanation
Indices: 5764--5859 Score: 138
Period size: 26 Copynumber: 3.7 Consensus size: 26
5754 GGTCATCCAG
5764 GGGCATTTTGGTCATTTTTACACTAA
1 GGGCATTTTGGTCATTTTTACACTAA
** * * *
5790 GGGCATTTTGGTCATTTGCATATCCAG
1 GGGCATTTTGGTCATTTTTACA-CTAA
5817 GGGCATTTTGGTCATTTTTACACTAA
1 GGGCATTTTGGTCATTTTTACACTAA
5843 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
5860 GCATATTCAG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 38 0.64
27 21 0.36
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.42
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTTTACACTAA
Found at i:5823 original size:53 final size:53
Alignment explanation
Indices: 5758--5887 Score: 242
Period size: 53 Copynumber: 2.5 Consensus size: 53
5748 CTTTAGGGTC
5758 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
1 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
5811 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
1 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
* *
5864 ATTCAGGGGCATGTTGGTCATTTT
1 ATCCAGGGGCATTTTGGTCATTTT
5888 AAGTCCACCC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (53 bp):
ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
Found at i:28801 original size:25 final size:24
Alignment explanation
Indices: 28773--28824 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
28763 GTGGATTGTA
*
28773 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
28798 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
28822 AAA
1 AAA
28825 AAAACTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:28836 original size:25 final size:25
Alignment explanation
Indices: 28771--28836 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
28761 TAGTGGATTG
* *
28771 TAAAATAAATTGAATAATTAAGACAT
1 TAAAA-AAATTCAAGAATTAAGACAT
* *
28797 TAAATAAATTTAAGAATTAA-ACAT
1 TAAAAAAATTCAAGAATTAAGACAT
28821 TAAAAAAACTTCAAGA
1 TAAAAAAA-TTCAAGA
28837 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 11 0.32
25 19 0.56
26 4 0.12
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (25 bp):
TAAAAAAATTCAAGAATTAAGACAT
Found at i:30194 original size:213 final size:214
Alignment explanation
Indices: 29961--30384 Score: 805
Period size: 213 Copynumber: 2.0 Consensus size: 214
29951 ACCTTTCCCA
29961 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACCCTTTAAATGTTGAGGCCT
1 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACCCTTTAAATGTTGAGGCCT
30026 CCAAATCTCGACACGTGTCTCTAATCAATTCTAATATTCATTATATTGATATATTGATTAG-AAA
66 CCAAATCTCGACACGTGTCTCTAATCAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
30090 AAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTA
131 AAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTA
30155 AAAAATAAAGAAATCATAT
196 AAAAATAAAGAAATCATAT
*
30174 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACTCTTTAAATGTTGAGGCCT
1 ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACCCTTTAAATGTTGAGGCCT
*
30239 CCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
66 CCAAATCTCGACACGTGTCTCTAATCAATTCTAATATTCATTATATTGATATATTGATTAG--AA
30304 AAAAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAAT
129 AAAAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAAT
30369 TAAAAAATAAAGAAAT
194 TAAAAAATAAAGAAAT
30385 TAATAATGAA
Statistics
Matches: 206, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
213 124 0.60
216 82 0.40
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (214 bp):
ATCATATATATATAATGATAACAATGTACACTACAAATATGGAAACCCTTTAAATGTTGAGGCCT
CCAAATCTCGACACGTGTCTCTAATCAATTCTAATATTCATTATATTGATATATTGATTAGAAAA
AAAGCCTTTGGTATATTTTAAGAAAGAACAATAATTTCTCTTACAAATTTTTAAGATTTTAATTA
AAAAATAAAGAAATCATAT
Found at i:31727 original size:12 final size:13
Alignment explanation
Indices: 31704--31732 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31694 TAAGTTTGGT
31704 TTCTCTCTTCTTC
1 TTCTCTCTTCTTC
31717 TTCTC-CTTCTTC
1 TTCTCTCTTCTTC
31729 TTCT
1 TTCT
31733 TTCGTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTCTCTTCTTC
Found at i:34787 original size:202 final size:200
Alignment explanation
Indices: 34185--35912 Score: 2471
Period size: 202 Copynumber: 8.6 Consensus size: 200
34175 ATAAGTTTAT
*
34185 TATAAGAAAAATTACACTACAATACATC-GTCAGTGGAGTTTAGCAGACTTCACGTGCGGGGTTT
1 TATAAGAAAAATT--A-TACAATACA-CAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTT
* * *
34249 AAGGGTTGACATATGTCCCCTTAGGAAATATGTATTAATATTAAATATTTAATTAGTTATGAAAT
62 AAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAAT
* * *
34314 GGGGTATGTGTCAACTTCTTAATCTGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTAT
127 GGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTAT
*
34379 AATAGT-CC
192 AATAATCCC
* *
34387 TATAAGAAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCGAGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* *
34452 GTTGACATGTGT-CCCTAAGGGAATATGTATTAATATTAAATATTTAATTTATTATGAAATGGGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
* * *
34516 TATGTGTCAACTTCTTAACCTGCTTATGGAGTCCAAAATTTACACCGACAGTGTATTGCATAATA
131 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
34581 ATCCC
196 ATCCC
34586 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
34651 GTTGACATGTGTCCCCTTAGGGAATACT-TATTAATATTAAATGTATTTAATTAATTATGAAATG
66 GTTGACATGTGTCCCCTTAGGGAATA-TGTATTAATATTAAA--TATTTAATTAATTATGAAATG
* *
34715 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACAGTGACAGTGTATTGTACA
128 GGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
*
34780 TTAATCCC
193 ATAATCCC
* * * *
34788 TATAAGAAAAATTACACAATACACAGTTAGTGGAGTTTAGCAGATTGCACGTGCGAGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* * *
34853 GTTGACATGTGTCCCATTAGGGAATATGTATCAATATTAAATATATATAATTTATTATGAAATGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATAT-T-TAATTAATTATGAAATGG
* * ** * * *
34918 GGTATGTGTCGATTTCTTAACCAACTTATGTAGTCCAAATTTTACACTGACAATGTATTGTATAA
129 GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
34983 TAATCCC
194 TAATCCC
* * * *
34990 TATAAGAAAAATTATACAATACACCA-TTATTGGAGTTTAGCAGAATGCACGTGTGGGGTTTAAG
1 TATAAGAAAAATTATACAATACA-CAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAG
* *
35054 GGTTGACATGTGTCCCATTAGGGAATATGTATTAATATTAAATATTGAATTAATTATGAAAT--G
65 GGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGG
35117 G---GTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAAT
130 GTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAAT
**
35179 -ATTAC
195 AATCCC
* *
35184 TATAAGAAAAATTATACGATACACAGTCAGTGGAGTTTAGCAGACTGCATGTGCGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* * *
35249 TTTAACATGTGTCCCCTTAGGGAATATGTATTGATATTAAATATATTTAATTAATTATGAAATGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATT-AA-ATATTTAATTAATTATGAAATGG
* * *
35314 GGTATGTGGCAACTT-TCTAACCCGCTTATAGAGTCCAAAATTTACACCGACAGTGTATTGTATA
129 GGTATGTGTCAACTTCT-TAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
35378 ATAATCCC
193 ATAATCCC
* * * * *
35386 TATAAGAAAAATTATACAATACACCGTTAGTGGA-TCTTAGCAGACTGCACGTGTGGGTTTTATG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGT-TTAGCAGACTGCACGTGCGGGGTTTAAG
*
35450 GGTTGACATGTGTCCCCTTAGGGAATATGCCTTAATTAATATTAAATATTTAATTTATTATGAAA
65 GGTTGACATGTGTCCCCTTAGGGAATATG---T-ATTAATATTAAATATTTAATTAATTATGAAA
* *
35515 T-GGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGCA
126 TGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTA
35579 TAATAATCCC
191 TAATAATCCC
* * *
35589 TATAAGAAAAATTATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* * * * *
35654 GTTGGCATATGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATTGAG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
* * *
35719 TATGTGTCAACCTT-TTAACCCGTTTATGGAGTCCAAAATTTACACTTACAATGTATTGTATAAT
131 TATGTGTCAA-CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAAT
*
35783 AAT-CA
195 AATCCC
* * * * ** *
35788 TATAAGAAAAATTATAGAATACACCGTCAGTAGAGTTTAGCAGACTGCACGGGCGATGTGTAAGG
1 TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
* * *
35853 GTTGACATGTGTCGCCTTAGGGAATATGTGTTAATATTTAATATTTAATTAATTATGAAA
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAA
35913 AAGCTCAGTT
Statistics
Matches: 1382, Mismatches: 115, Indels: 61
0.89 0.07 0.04
Matches are distributed among these distances:
193 2 0.00
194 93 0.07
195 56 0.04
196 20 0.01
198 115 0.08
199 280 0.20
200 106 0.08
201 63 0.05
202 462 0.33
203 152 0.11
204 22 0.02
205 3 0.00
206 8 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (200 bp):
TATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGG
GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
ATCCC
Found at i:35337 original size:598 final size:593
Alignment explanation
Indices: 34185--35912 Score: 2472
Period size: 598 Copynumber: 2.9 Consensus size: 593
34175 ATAAGTTTAT
*
34185 TATAAGAAAAATTACACTACAATACATCGTCAGTGGAGTTTAGCAGACTT-CACGTGCGGGGTTT
1 TATAAGAAAAATT--AC-ACAATACA-CGTTAGTGGAGTTTAGCAGA-TTGCACGTGC-GGGTTT
* *
34249 AAGGGTTGACATATGTCCCCTTAGGAAATATGTATTAATATTAAATATTTAA-TTAGTTATGAAA
60 AAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTTA-TTATGAAA
* * *
34313 TGGGGTATGTGTCAACTTCTTAATCTGCTTATGGAGTTCAAAATTTACACTGACAGTGTATTGTA
124 TGGGGTATGTGTCAACTTCTTAACCAGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTA
* * *
34378 TAATAGT-CCTATAAGAAAAATTATACAATACACTGTCAGTGGAGTTTAGCAGACTGCACGTGCG
189 TAATAATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTG
* * *
34442 AGGTTTAAGGGTTGACATGTGTCCCTAAGGGAATATGTATTAATATTAAATATTTAATTTATTAT
254 GGGTTTAAGGGTTGACATGTGTCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTAT
* *
34507 GAAATGGGGTATGTGTCAACTTCTTAACCTGCTTATGGAGTCCAAAATTTACACCGACAGTGTAT
319 GAAAT--GG--TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTAT
* * *
34572 TGCATAATAATCCCTATAAGAAAAATTATACAATACACAGTCAGTGGAGTTTAGCAGACTGCACG
380 TGTATAAT-AT-TCTATAAGAAAAATTATACGATACACAGTCAGTGGAGTTTAGCAGACTGCACG
*
34637 TGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATACT-TATTAATATTAAATGTATTTAA
443 TGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA-TGTATTAATATTAAATATATTTAA
* * **
34701 TTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACAGTGA
507 TTAATTATGAAATGGGGTATGTGGCAACTTCTTAACCCGCTTATAGAGTCCAAAATTTACACCGA
*
34766 CAGTGTATTGTACATTAATCCC
572 CAGTGTATTGTACAATAATCCC
34788 TATAAGAAAAATTACACAATACACAGTTAGTGGAGTTTAGCAGATTGCACGTGCGAGGTTTAAGG
1 TATAAGAAAAATTACACAATACAC-GTTAGTGGAGTTTAGCAGATTGCACGTGCG-GGTTTAAGG
* *
34853 GTTGACATGTGTCCCATTAGGGAATATGTATCAATATTAAATATATATAATTTATTATGAAATGG
64 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATAT-T-TAATTTATTATGAAATGG
* * * * * *
34918 GGTATGTGTCGATTTCTTAACCAACTTATGTAGTCCAAATTTTACACTGACAATGTATTGTATAA
127 GGTATGTGTCAACTTCTTAACCAGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAA
* * * *
34983 TAATCCCTATAAGAAAAATTATACAATACACCATTATTGGAGTTTAGCAGAATGCACGTGTGGGG
192 TAATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGG
*
35048 TTTAAGGGTTGACATGTGTCCCATTAGGGAATATGTATTAATATTAAATATTGAATTAATTATGA
257 TTTAAGGGTTGACATGTGTCCC-TTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGA
35113 AATGG-GTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
321 AATGGTGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATA
*
35177 ATATTACTATAAGAAAAATTATACGATACACAGTCAGTGGAGTTTAGCAGACTGCATGTGCGGGG
386 ATATT-CTATAAGAAAAATTATACGATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGG
* * *
35242 TTTAAGGTTTAACATGTGTCCCCTTAGGGAATATGTATTGATATTAAATATATTTAATTAATTAT
450 TTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTAATTAATTAT
35307 GAAATGGGGTATGTGGCAACTT-TCTAACCCGCTTATAGAGTCCAAAATTTACACCGACAGTGTA
515 GAAATGGGGTATGTGGCAACTTCT-TAACCCGCTTATAGAGTCCAAAATTTACACCGACAGTGTA
*
35371 TTGTATAATAATCCC
579 TTGTACAATAATCCC
* * * *
35386 TATAAGAAAAATTATACAATACACCGTTAGTGGA-TCTTAGCAGACTGCACGTGTGGGTTTTATG
1 TATAAGAAAAATTACACAATACA-CGTTAGTGGAGT-TTAGCAGATTGCACGTGCGGG-TTTAAG
35450 GGTTGACATGTGTCCCCTTAGGGAATATGCCTTAATTAATATTAAATATTTAATTTATTATGAAA
63 GGTTGACATGTGTCCCCTTAGGGAATATG---T-ATTAATATTAAATATTTAATTTATTATGAAA
* * *
35515 T-GGGTATGTGTCAACCTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGCA
124 TGGGGTATGTGTCAACTTCTTAACCAGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTA
*
35579 TAATAATCCCTATAAGAAAAATTATATAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTG
189 TAATAATCCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTG
* *
35644 GGGTTTAAGGGTTGGCATATGTCTCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTA
254 GGGTTTAAGGGTTGACATGTGTC-CCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTA
* * *
35709 TGAAATTGAGTATGTGTCAACCTT-TTAACCCGTTTATGGAGTCCAAAATTTACACTTACAATGT
318 TGAAA-TG-G--TGTGTCAA-CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGT
* * *
35773 ATTGTATAATAATCATATAAGAAAAATTATA-GAATACACCGTCAGTAGAGTTTAGCAGACTGCA
378 ATTGTATAATATTC-TATAAGAAAAATTATACG-ATACACAGTCAGTGGAGTTTAGCAGACTGCA
* ** * * * *
35837 CGGGCGATGTGTAAGGGTTGACATGTGTCGCCTTAGGGAATATGTGTTAATATT-TA-ATATTTA
441 CGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTA
35900 ATTAATTATGAAA
506 ATTAATTATGAAA
35913 AAGCTCAGTT
Statistics
Matches: 1017, Mismatches: 81, Indels: 55
0.88 0.07 0.05
Matches are distributed among these distances:
597 5 0.00
598 270 0.27
599 241 0.24
600 102 0.10
601 6 0.01
602 109 0.11
603 94 0.09
604 187 0.18
605 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (593 bp):
TATAAGAAAAATTACACAATACACGTTAGTGGAGTTTAGCAGATTGCACGTGCGGGTTTAAGGGT
TGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTTATTATGAAATGGGGTA
TGTGTCAACTTCTTAACCAGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAAT
CCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTGTGGGGTTTA
AGGGTTGACATGTGTCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGG
TGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATATT
CTATAAGAAAAATTATACGATACACAGTCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAG
GGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATATTTAATTAATTATGAAATG
GGGTATGTGGCAACTTCTTAACCCGCTTATAGAGTCCAAAATTTACACCGACAGTGTATTGTACA
ATAATCCC
Found at i:35942 original size:16 final size:16
Alignment explanation
Indices: 35921--35951 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35911 AAAAGCTCAG
*
35921 TTAATAAGGTTACTAA
1 TTAATAAGATTACTAA
35937 TTAATAAGATTACTA
1 TTAATAAGATTACTA
35952 TACAACTTGA
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:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (16 bp):
TTAATAAGATTACTAA
Done.