Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008343.1 Hibiscus syriacus cultivar Beakdansim tig00111070_pilon, 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: 738381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:636765 original size:84 final size:84
Alignment explanation
Indices: 636664--637446 Score: 710
Period size: 84 Copynumber: 9.5 Consensus size: 84
636654 TCGGGGGTCT
* * * *
636664 TTGGCAGATAGCCCTTCTCGACTTAAGTTGTGCTACAAATGATATG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
*
636728 TCAAACTCGAAGGTCTTTGG
66 TCGAACTCGAAGGTCTTT-G
* * * * * * *
636748 TTGGCAGACAACCCTTCTCGACTTCAGGTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
*
636813 TCGAACTCG-GGGATC--T-
66 TCGAACTCGAAGG-TCTTTG
* * * * * * * * *
636829 TTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGGAAATGATGTGTCGTT-GAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
* *
636893 TCGAACTCAAAGGACTTTTG
66 TCGAACTCGAAGGTC-TTTG
* ** *** * * * * * * *
636913 GTCACAGATAACCCTTCTATCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGTTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
**
636978 TCGAACTCGGGGGTC--T-
66 TCGAACTCGAAGGTCTTTG
* * *
636994 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
*
637058 TCGAACTCAAAGGTCTTTTG
66 TCGAACTCGAAGGTC-TTTG
* * * * * *
637078 TTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCCTCGAAGCTGAGTGT-G
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
**
637142 ATCGAACTCGGGGGTC--T-
66 -TCGAACTCGAAGGTCTTTG
* *
637159 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
*
637223 TCGAACTCAAAGGTC-TT-
66 TCGAACTCGAAGGTCTTTG
* * * * * * * * *
637240 TTGGTCATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAACTGAGTG
1 TTGG-C--AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCG
* * *
637305 TAATCGAACTCG-GGGTC---C
63 TAGTCGAACTCGAAGGTCTTTG
* *
637323 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
*
637387 TCGAACTCAAAGGTCTTTGG
66 TCGAACTCGAAGGTCTTT-G
637407 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
637447 AGTTTGTTTA
Statistics
Matches: 554, Mismatches: 119, Indels: 52
0.76 0.16 0.07
Matches are distributed among these distances:
79 21 0.04
80 107 0.19
81 124 0.22
82 4 0.01
83 7 0.01
84 201 0.36
85 90 0.16
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGGAGCTGAGCGTAG
TCGAACTCGAAGGTCTTTG
Found at i:636822 original size:165 final size:165
Alignment explanation
Indices: 636619--637446 Score: 1196
Period size: 165 Copynumber: 5.0 Consensus size: 165
636609 GCTATGTTGT
* * * *
636619 AAATGATATGACCTCGAAGTTGAATGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* * * * * *
636684 ACTTAAGTTGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* * * * *
636749 TGGCAGACAACCCTTCTCGACTTCAGGTATGCTGC
131 TCGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * *
636784 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGATCTTTGACAGATAGCCCTTCTTG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* * * * *
636849 CCTTGAGCTATGCTGGAAATGATGTGTCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGACTTTTG
66 ACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTG
* ** * *
636913 G-TCACAGATAACCCTTCTATCCTTGAGTTATGCTGT
129 GTTCGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
*
636949 AAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
* *
637014 ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* * *
637079 TAGCAGATAACCCTTCTTGACTTAAGTTATACTGC
131 TCGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
*
637114 AAATGATGTGCCCTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
637179 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGG
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGG
** * * *
637244 -TCATAGATAACCCTTCTAGCCTTGAGTTATGCTGT
130 TTCGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * *
637279 AAATGATATGCCCTCGAAACTGAGTGTAATCGAACTC-GGGGTCCTTGGCAGATAGCCCTTCTCG
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
637343 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
66 ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
* *
637408 TGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
131 TCGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
637443 AAAT
1 AAAT
637447 AGTTTGTTTA
Statistics
Matches: 588, Mismatches: 69, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
163 5 0.01
164 124 0.21
165 447 0.76
166 12 0.02
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (165 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT
TCGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:637201 original size:330 final size:330
Alignment explanation
Indices: 636594--637446 Score: 1370
Period size: 330 Copynumber: 2.6 Consensus size: 330
636584 TGACAAATAG
* * * *
636594 CCCTTCT-TGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAATGTAATCGAACTCGG
1 CCCTTCTAT-CCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCGG
* * * *
636658 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTGTGCTACAAATGATATGCCTTGGAGCTGAG
65 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
* * * * *
636723 CGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTCAGGTATGCTGCAAAT
130 CGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
* *
636788 GATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGATCTTTGACAGATAGCCCTTCTTGCCTT
195 GATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGATCTTTGACAGATAGCCCTTCTCGACTT
* * *
636853 GAGCTATGCTGGAAATGATGTGTCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGGTCA
260 AAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGGTCA
636917 CAGATAA
324 CAGATAA
*
636924 CCCTTCTATCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
1 CCCTTCTATCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
*
636989 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * * *
637054 GTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATG
131 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
* * *
637119 ATGTGCCCTCGAAGCTGAGTGTGATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTA
196 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGATCTTTGACAGATAGCCCTTCTCGACTTA
* *
637184 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCATA
261 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGGTCACA
637249 GATAA
326 GATAA
* **
637254 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAACTGAGTGTAATCGAACTC-GG
1 CCCTTCTATCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
*
637318 GGTCCTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
637383 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
131 GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
637447 AGTTTGTTTA
Statistics
Matches: 482, Mismatches: 39, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
329 128 0.27
330 353 0.73
331 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (330 bp):
CCCTTCTATCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCGGG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGATCTTTGACAGATAGCCCTTCTCGACTTA
AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGACTTTTGGTCACA
GATAA
Found at i:640797 original size:18 final size:19
Alignment explanation
Indices: 640753--640797 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
640743 AGTTAATGTG
640753 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
* *
640772 AATCCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
640790 AATGCAAA
1 AATGCAAA
640798 ATGTCTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:642638 original size:30 final size:30
Alignment explanation
Indices: 642602--642661 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
642592 ATAAAAGAAT
*
642602 AAAATAACAAATT-AAAAAAAATGAAAAATA
1 AAAATAA-AAATTGAAAAAAAAGGAAAAATA
* *
642632 AAAATAAAAGTTGCAAAAAAAGGAAAAATA
1 AAAATAAAAATTGAAAAAAAAGGAAAAATA
642662 TGGTACATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (30 bp):
AAAATAAAAATTGAAAAAAAAGGAAAAATA
Found at i:642802 original size:17 final size:19
Alignment explanation
Indices: 642775--642822 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
642765 TAGAAGCAAT
*
642775 AAAATAAAATAAT-ACGAG
1 AAAACAAAATAATGACGAG
*
642793 AAAA-AAAATAATGACGAT
1 AAAACAAAATAATGACGAG
642811 AAAACAAAATAA
1 AAAACAAAATAA
642823 AATAAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.30
18 12 0.44
19 7 0.26
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (19 bp):
AAAACAAAATAATGACGAG
Found at i:644220 original size:29 final size:31
Alignment explanation
Indices: 644161--644221 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
644151 AAAATTATAT
* **
644161 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
644192 ATTATATA-ATATTT-AAATGTTTTAAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
644221 A
1 A
644222 ATTCAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 14 0.52
30 5 0.19
31 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTAAAAAA
Found at i:644293 original size:75 final size:75
Alignment explanation
Indices: 644148--644351 Score: 193
Period size: 75 Copynumber: 2.8 Consensus size: 75
644138 CAGAAACGGT
** * * * * *
644148 TTAAAAATTATATATTATATATA-TTTT-TAAAATGTTTTTCAAAAATTATATAATATTTAAATG
1 TTAAAAACAATATATTATATA-AGTTTTCAAAAATGATTTT-AAAAACTATATAATATATAAATC
*
644211 TTTTAAAAAAAA
64 TTCTAAAAAAAA
* * *
644223 TTCAAAACAATATATTATATAAGTTTTCAAAAATGATTTTAAAAACTATATATTATATATATCTT
1 TTAAAAACAATATATTATATAAGTTTTCAAAAATGATTTTAAAAACTATATAATATATAAATCTT
****
644288 CTAAAATGTT
66 CTAAAAAAAA
* * *
644298 TTAAAAACTATATACTATAT-AGTTTTCAAAAAT-ATTTT-AAAACTATATTATATA
1 TTAAAAACAATATATTATATAAGTTTTCAAAAATGATTTTAAAAACTATATAATATA
644352 CATTTTCAAA
Statistics
Matches: 107, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
72 14 0.13
73 5 0.05
74 14 0.13
75 64 0.60
76 10 0.09
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (75 bp):
TTAAAAACAATATATTATATAAGTTTTCAAAAATGATTTTAAAAACTATATAATATATAAATCTT
CTAAAAAAAA
Found at i:644309 original size:37 final size:36
Alignment explanation
Indices: 644023--644388 Score: 211
Period size: 37 Copynumber: 10.1 Consensus size: 36
644013 ATAATAATAC
* * * * *
644023 TATATATATATATAAATAT-TTTCAAAAA-TATGTAA
1 TATATATATTTCTAAA-ATGTTTTAAAAACTATATAT
* *
644058 TATATAAATTTCCAAAATGATTTTAAAAACTATATAT
1 TATATATATTTCTAAAATG-TTTTAAAAACTATATAT
* * *
644095 TATACATGTTT-TAAAAACGTTTTAAAAACT-T-TA-
1 TATATATATTTCT-AAAATGTTTTAAAAACTATATAT
* * *
644128 TA-ATATATTTC-AGAAACGGTTTAAAAATTATATAT
1 TATATATATTTCTA-AAATGTTTTAAAAACTATATAT
* * *
644163 TATATATATTTTTAAAATGTTTTTCAAAAATTATATAA
1 TATATATATTTCTAAAATG-TTTT-AAAAACTATATAT
* * * **** * *
644201 TATTTAAATGTTTTAAAAAAAATTCAAAACAATATAT
1 TATATATAT-TTCTAAAATGTTTTAAAAACTATATAT
*
644238 TATATA-AGTTTTCAAAAATGATTTTAAAAACTATATAT
1 TATATATA--TTTCTAAAATG-TTTTAAAAACTATATAT
*
644276 TATATATATCTTCTAAAATGTTTTAAAAACTATATAC
1 TATATATAT-TTCTAAAATGTTTTAAAAACTATATAT
* *
644313 TATATAGT-TTTCAAAAATATTTT-AAAAC--TATAT
1 TATATA-TATTTCTAAAATGTTTTAAAAACTATATAT
* *
644346 TATATACATTT-TCAAAATGTTTTCAAAAATTATGTATAT
1 TATATATATTTCT-AAAATGTTTT-AAAAACTA--TATAT
644385 TATA
1 TATA
644389 AGTATTTTCA
Statistics
Matches: 255, Mismatches: 48, Indels: 52
0.72 0.14 0.15
Matches are distributed among these distances:
31 1 0.00
32 20 0.08
33 25 0.10
34 6 0.02
35 24 0.09
36 44 0.17
37 66 0.26
38 51 0.20
39 18 0.07
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (36 bp):
TATATATATTTCTAAAATGTTTTAAAAACTATATAT
Found at i:645527 original size:191 final size:184
Alignment explanation
Indices: 645084--645602 Score: 562
Period size: 191 Copynumber: 2.7 Consensus size: 184
645074 ACATTCCAGA
645084 AAAGACACAGGGTCAG-CCGTGCATAAAATTAACATTCATCATTTTTCTATTATCTGGGATCCTA
1 AAAGACACAGGGTCAGTCC-TGCATAAAATTAACATTCATCATTTTTCT-TT-TCTGGGATCCTA
** * * *
645148 GGTGCTTACTAGGACTCGTATGCAAGTGTTGTGACATAAGTGT-AACACGATAATTCAACAAAAA
63 GGTGCTTACTAGGACTCGTATGCAAGTGTTGCAACATAAGTTTCAACAAGATAATTCAAAAAAAA
* * * *
645212 TGAAGAAACGAAACATGGATTGGAATCTAAGTTATGCATTTTAACAAGAATCTTGCATACCTAAG
128 TGAAGAAACCAAAC--------GAATCGAAGTTATGCATTTTAACAAGAAGCCTGCATACCTAAG
* * **
645277 AAAGACACAGGGTCAATCCTGCATAAAATTAACATTCATCGTTTTTCTCGTCTGGGATCCTAGGT
1 AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTTCTTTTCTGGGATCCTAGGT
* * * *
645342 GCTTACTTGGATTCGTATGCAAGTGTTGCAACATAAGTTTCAAACATGATAGTTCAAAAAAAAAA
66 GCTTACTAGGACTCGTATGCAAGTGTTGCAACATAAGTTTC-AACAAGATAATTC---AAAAAAA
* *
645407 ATTTGAAGAAACCAAAC-AATCGAAGTTATGCATTTTGACAA-ACAGCCTGCATACTTAAG
127 A--TGAAGAAACCAAACGAATCGAAGTTATGCATTTTAACAAGA-AGCCTGCATACCTAAG
* * * *
645466 AATGAGACGGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTTACGTTTTCGGGGATCCTAG
1 AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTT-C-TTTTCTGGGATCCTAG
* * * *
645531 GTGTTTACTCA-GACTCGTACGCAAGTGTTGCAACATAAGTTTCGAACAAGATAATTCTATAAAA
64 GTGCTTACT-AGGACTCGTATGCAAGTGTTGCAACATAAGTTTC-AACAAGATAATTCAAAAAAA
645595 ATGAAGAA
127 ATGAAGAA
645603 TCGAAACAAC
Statistics
Matches: 279, Mismatches: 35, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
186 7 0.03
188 7 0.03
189 76 0.27
190 1 0.00
191 112 0.40
193 54 0.19
194 2 0.01
196 7 0.03
198 13 0.05
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (184 bp):
AAAGACACAGGGTCAGTCCTGCATAAAATTAACATTCATCATTTTTCTTTTCTGGGATCCTAGGT
GCTTACTAGGACTCGTATGCAAGTGTTGCAACATAAGTTTCAACAAGATAATTCAAAAAAAATGA
AGAAACCAAACGAATCGAAGTTATGCATTTTAACAAGAAGCCTGCATACCTAAG
Found at i:652519 original size:2 final size:2
Alignment explanation
Indices: 652512--652573 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
652502 CAGTTAAGTC
652512 AT AT AT AT AT 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 AT AT AT AT AT
652554 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
652574 TAAGGTTGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:655842 original size:36 final size:36
Alignment explanation
Indices: 655798--655898 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
655788 CAAATTGTAA
655798 AATA-TTATATATTTTCTTTAAAAAATTAAATTCAT
1 AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
655833 AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
1 AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
* *
655869 AATATTTATATAATTT-TTTACAAAATTAAA
1 AATATTTATATATTTTCTTTAAAAAATTAAA
655899 AATATAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 17 0.27
36 46 0.73
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATTAAATTCAT
Found at i:657452 original size:25 final size:25
Alignment explanation
Indices: 657424--657472 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
657414 AATTCGAGTC
*
657424 AGATTAGATATTCAAACGAGATTAA
1 AGATTAGATATTCAAACAAGATTAA
657449 AGATTAGATATTCAAACAAGATTA
1 AGATTAGATATTCAAACAAGATTA
657473 GAATCCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (25 bp):
AGATTAGATATTCAAACAAGATTAA
Found at i:668459 original size:20 final size:20
Alignment explanation
Indices: 668434--668472 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
668424 GACAATCTAT
668434 GGTGACATATTAACATGACG
1 GGTGACATATTAACATGACG
668454 GGTGACATATTAACATGAC
1 GGTGACATATTAACATGAC
668473 AGATGACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (20 bp):
GGTGACATATTAACATGACG
Found at i:668479 original size:20 final size:20
Alignment explanation
Indices: 668436--668481 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
668426 CAATCTATGG
* *
668436 TGACATATTAACATGACGGG
1 TGACATATTAACATGACAGA
668456 TGACATATTAACATGACAGA
1 TGACATATTAACATGACAGA
668476 TGACAT
1 TGACAT
668482 GACAGATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (20 bp):
TGACATATTAACATGACAGA
Found at i:671240 original size:20 final size:20
Alignment explanation
Indices: 671193--671246 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
671183 AGTAGGCTTT
* *
671193 AGAGTTTC-AAAATTTTACA
1 AGAGTTTCGAAACTTTGACA
* *
671212 AAAGCTTCGAAACTTTGACA
1 AGAGTTTCGAAACTTTGACA
671232 AGAGTTTCGAAACTT
1 AGAGTTTCGAAACTT
671247 ACCTTGCAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AGAGTTTCGAAACTTTGACA
Found at i:671492 original size:11 final size:11
Alignment explanation
Indices: 671476--671538 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
671466 AAAATTACAT
671476 TATTAAAAATA
1 TATTAAAAATA
671487 TATTAAAAATA
1 TATTAAAAATA
* * ***
671498 CACTATTGATA
1 TATTAAAAATA
671509 -ATTATAAAAT-
1 TATTA-AAAATA
671519 T-TTAAAAATA
1 TATTAAAAATA
671529 TATTAAAAAT
1 TATTAAAAAT
671539 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:671625 original size:14 final size:14
Alignment explanation
Indices: 671583--671640 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
671573 GTCCTTGCAA
*
671583 TAAACTCTAAACCC
1 TAAACTCTAAATCC
*
671597 TAAACAAAACTAAATCC
1 TAAAC---TCTAAATCC
*
671614 TAAACTCTAAATCA
1 TAAACTCTAAATCC
*
671628 TAAACCCTAAATC
1 TAAACTCTAAATC
671641 ATACTTATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 24 0.67
17 12 0.33
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACTCTAAATCC
Found at i:671641 original size:14 final size:14
Alignment explanation
Indices: 671590--671643 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
671580 CAATAAACTC
671590 TAAACCCTAAA-CA
1 TAAACCCTAAATCA
*
671603 -AAA--CTAAATCC
1 TAAACCCTAAATCA
*
671614 TAAACTCTAAATCA
1 TAAACCCTAAATCA
671628 TAAACCCTAAATCA
1 TAAACCCTAAATCA
671642 TA
1 TA
671644 CTTATCTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 5 0.15
11 1 0.03
12 6 0.18
14 22 0.65
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:673090 original size:11 final size:11
Alignment explanation
Indices: 673074--673155 Score: 65
Period size: 11 Copynumber: 7.3 Consensus size: 11
673064 AACAATCCTC
673074 GAGCTTGAATT
1 GAGCTTGAATT
673085 GAGCTTGAATT
1 GAGCTTGAATT
* * *
673096 GAGTTTGTATC
1 GAGCTTGAATT
*
673107 GAGCTTCAATT
1 GAGCTTGAATT
* * *
673118 CAGTTTTAATT
1 GAGCTTGAATT
*
673129 GAGTTTGAAATTT
1 GAGCTTG-AA-TT
*
673142 GAGCTTTAATT
1 GAGCTTGAATT
673153 GAG
1 GAG
673156 TTTTTGAATT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
11 44 0.80
12 4 0.07
13 7 0.13
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (11 bp):
GAGCTTGAATT
Found at i:673129 original size:33 final size:33
Alignment explanation
Indices: 673072--673135 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
673062 AAAACAATCC
* *
673072 TCGAGCTTGAATTGAGCTTGAATTGAGTTTGTA
1 TCGAGCTTCAATTCAGCTTGAATTGAGTTTGTA
* *
673105 TCGAGCTTCAATTCAGTTTTAATTGAGTTTG
1 TCGAGCTTCAATTCAGCTTGAATTGAGTTTG
673136 AAATTTGAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.42
Consensus pattern (33 bp):
TCGAGCTTCAATTCAGCTTGAATTGAGTTTGTA
Found at i:673278 original size:15 final size:16
Alignment explanation
Indices: 673251--673280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
673241 CTTGAATTTA
673251 TTTTTGAGTTTGAGTC
1 TTTTTGAGTTTGAGTC
673267 TTTTTGAG-TTGAGT
1 TTTTTGAGTTTGAGT
673281 TTCAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.03, G:0.27, T:0.57
Consensus pattern (16 bp):
TTTTTGAGTTTGAGTC
Found at i:675095 original size:3 final size:3
Alignment explanation
Indices: 675087--675181 Score: 154
Period size: 3 Copynumber: 31.7 Consensus size: 3
675077 ATATTATAAA
* * *
675087 TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT TAC TAT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
675135 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
675182 AATAGATTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:676480 original size:14 final size:15
Alignment explanation
Indices: 676461--676494 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
676451 CTAGTTGTAT
676461 TTTTA-TTGTTTTAA
1 TTTTATTTGTTTTAA
*
676475 TTTTATTTGTTTTAT
1 TTTTATTTGTTTTAA
676490 TTTTA
1 TTTTA
676495 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTATTTGTTTTAA
Found at i:678115 original size:2 final size:2
Alignment explanation
Indices: 678108--678154 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
678098 GTAGGAAACG
* *
678108 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
678150 TA TA T
1 TA TA T
678155 TGTTGTCCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:687505 original size:15 final size:14
Alignment explanation
Indices: 687485--687523 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
687475 CCAGCCTCTA
687485 AATTACTAACATACT
1 AATTACTAAC-TACT
*
687500 AATTACTAACTCCT
1 AATTACTAACTACT
687514 AACTTACTAA
1 AA-TTACTAA
687524 TTTTTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTACTAACTACT
Found at i:687811 original size:28 final size:29
Alignment explanation
Indices: 687752--687822 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 29
687742 TATTCTTTAA
* *
687752 TTTT-TGTCATTTATATTTATGCACTTTAT
1 TTTTCTGTTATTTACATTTATGCAC-TTAT
* *
687781 TTTTCTGTTGTTTACATTTATGCAC-TCT
1 TTTTCTGTTATTTACATTTATGCACTTAT
687809 TTTTCTGTTATTTA
1 TTTTCTGTTATTTA
687823 TACTTCTGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.42
29 4 0.11
30 17 0.47
ACGTcount: A:0.17, C:0.13, G:0.08, T:0.62
Consensus pattern (29 bp):
TTTTCTGTTATTTACATTTATGCACTTAT
Found at i:690094 original size:3 final size:3
Alignment explanation
Indices: 690086--690110 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
690076 TATTTGAAGC
690086 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
690111 CTACTACGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:691255 original size:3 final size:3
Alignment explanation
Indices: 691247--691313 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
691237 CATCCTCTAA
* * * * *
691247 CTC CTC CTC CTC AAT- CTC CTC TTC TTC TTC CTC CTC CTC CTC TTC
1 CTC CTC CTC CTC -CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* *
691292 CTC CTC CTC CTC TTC TTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC C
691314 AAATCACCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.96
4 1 0.02
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (3 bp):
CTC
Found at i:691265 original size:15 final size:15
Alignment explanation
Indices: 691247--691313 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
691237 CATCCTCTAA
*
691247 CTCCTCCTCCTCAAT-
1 CTCCTCCTCCTC-TTC
* *
691262 CTCCTCTTCTTCTTC
1 CTCCTCCTCCTCTTC
691277 CTCCTCCTCCTCTTC
1 CTCCTCCTCCTCTTC
691292 CTCCTCCTCCTCTTC
1 CTCCTCCTCCTCTTC
*
691307 TTCCTCC
1 CTCCTCC
691314 AAATCACCCC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 1 0.02
15 44 0.98
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (15 bp):
CTCCTCCTCCTCTTC
Found at i:691310 original size:18 final size:18
Alignment explanation
Indices: 691262--691313 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
691252 CCTCCTCAAT
*
691262 CTCCTCTTCTTCTTCCTC
1 CTCCTCTTCTTCCTCCTC
*
691280 CTCCTCCTCTTCCTCCTC
1 CTCCTCTTCTTCCTCCTC
691298 CTCCTCTTCTTCCTCC
1 CTCCTCTTCTTCCTCC
691314 AAATCACCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (18 bp):
CTCCTCTTCTTCCTCCTC
Found at i:698095 original size:47 final size:47
Alignment explanation
Indices: 697991--698472 Score: 239
Period size: 47 Copynumber: 10.5 Consensus size: 47
697981 ATCAGTTGTC
* * * *
697991 ATGTATATGATAATCAATGATAT-AATATCTAAATCGGTCG-GGAGTTA
1 ATGTACATGATAATCAATAATATCAA-ATCTAAACCGGTCGATG-GTTA
* * * *
698038 ATATATATGATAATCAATAATATCAAATCCAAACCGGTCGATGGTTT
1 ATGTACATGATAATCAATAATATCAAATCTAAACCGGTCGATGGTTA
** * ** * * *
698085 ATGTACATGATAAAT-TGTGATATCGGATTTGAACCGGT-TAGTGGTTA
1 ATGTACATGAT-AATCAATAATATCAAATCTAAACCGGTCGA-TGGTTA
* * * * * **
698132 ATGTACATGATAATCAGTAGTATCAGAT-AAGAATCGGTAAATGGTTA
1 ATGTACATGATAATCAATAATATCAAATCTA-AACCGGTCGATGGTTA
* * **
698179 ATGTACATG-------ATAAT-T---A-GTGAACCGGTCGAGAGTTA
1 ATGTACATGATAATCAATAATATCAAATCTAAACCGGTCGATGGTTA
* * *
698214 ATGTACATGATAATCAATAATATCAAATCCAAACCGATCAATGGTTA
1 ATGTACATGATAATCAATAATATCAAATCTAAACCGGTCGATGGTTA
* * * * ** *** *
698261 ATGAACATGATAATTAGTGATATCGTATCTAAACTAATATG-TGGTTA
1 ATGTACATGATAATCAATAATATCAAATCTAAACCGGT-CGATGGTTA
* * * ** *
698308 ATATCCATGATAATCAATGATATCCGATCTAAACCGGTCGGTGGTTA
1 ATGTACATGATAATCAATAATATCAAATCTAAACCGGTCGATGGTTA
* * * **
698355 ATGTACATGATAATTAGTGATATCAAATCTAAACCGGTC-AGTAATTA
1 ATGTACATGATAATCAATAATATCAAATCTAAACCGGTCGA-TGGTTA
* * **
698402 ATGTACATGATAATCAGAT-ATATCGAATCTGAACCTATCGATGGTTA
1 ATGTACATGATAATCA-ATAATATCAAATCTAAACCGGTCGATGGTTA
* *
698449 ATGTACATGATAATTAGTAATATC
1 ATGTACATGATAATCAATAATATC
698473 GGATCCAAAC
Statistics
Matches: 326, Mismatches: 83, Indels: 52
0.71 0.18 0.11
Matches are distributed among these distances:
35 20 0.06
36 1 0.00
39 1 0.00
40 3 0.01
42 5 0.02
43 1 0.00
46 7 0.02
47 279 0.86
48 9 0.03
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (47 bp):
ATGTACATGATAATCAATAATATCAAATCTAAACCGGTCGATGGTTA
Found at i:698106 original size:94 final size:92
Alignment explanation
Indices: 697991--698471 Score: 335
Period size: 94 Copynumber: 5.2 Consensus size: 92
697981 ATCAGTTGTC
* * * * *
697991 ATGTATATGATAATCAATGATATAATATCTAAATCGGTCGGGAGTTAATATATATGATAATCAAT
1 ATGTACATGATAATTAGTGATATAA-ATCTAAA-CGGTCGGGAGTTAATGTACATGATAATCAAT
*
698056 AATATCAAATCCAAACCGGTCGATGGTTT
64 AATATCAAATCCAAACCGGTCGATGGTTA
** * * * *
698085 ATGTACATGATAAATT-GTGATATCGGATTTGAACCGGTTAGTG-GTTAATGTACATGATAATCA
1 ATGTACATGAT-AATTAGTGATAT-AAATCT-AAACGG-TCGGGAGTTAATGTACATGATAATCA
* * * * * **
698148 GTAGTATCAGAT-AAGAATCGGTAAATGGTTA
62 ATAATATCAAATCCA-AACCGGTCGATGGTTA
*
698179 ATGTACATGATAATTAGTG-----AA-C----CGGTCGAGAGTTAATGTACATGATAATCAATAA
1 ATGTACATGATAATTAGTGATATAAATCTAAACGGTCGGGAGTTAATGTACATGATAATCAATAA
* *
698234 TATCAAATCCAAACCGATCAATGGTTA
66 TATCAAATCCAAACCGGTCGATGGTTA
* ** ** * * * *
698261 ATGAACATGATAATTAGTGATATCGTATCTAAACTAATATGTG-GTTAATATCCATGATAATCAA
1 ATGTACATGATAATTAGTGATAT-AAATCTAAAC-GGT-CGGGAGTTAATGTACATGATAATCAA
* ** * *
698325 TGATATCCGATCTAAACCGGTCGGTGGTTA
63 TAATATCAAATCCAAACCGGTCGATGGTTA
* * *
698355 ATGTACATGATAATTAGTGATATCAAATCTAAACCGGTCAGTAATTAATGTACATGATAATCAGA
1 ATGTACATGATAATTAGTGATAT-AAATCTAAA-CGGTCGGGAGTTAATGTACATGATAATCA-A
* ** **
698420 T-ATATCGAATCTGAACCTATCGATGGTTA
63 TAATATCAAATCCAAACCGGTCGATGGTTA
*
698449 ATGTACATGATAATTAGTAATAT
1 ATGTACATGATAATTAGTGATAT
698472 CGGATCCAAA
Statistics
Matches: 299, Mismatches: 64, Indels: 48
0.73 0.16 0.12
Matches are distributed among these distances:
81 3 0.01
82 63 0.21
83 1 0.00
88 2 0.01
89 1 0.00
93 6 0.02
94 210 0.70
95 13 0.04
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (92 bp):
ATGTACATGATAATTAGTGATATAAATCTAAACGGTCGGGAGTTAATGTACATGATAATCAATAA
TATCAAATCCAAACCGGTCGATGGTTA
Found at i:698257 original size:82 final size:82
Alignment explanation
Indices: 698128--698280 Score: 218
Period size: 82 Copynumber: 1.9 Consensus size: 82
698118 CCGGTTAGTG
* * * * * *
698128 GTTAATGTACATGATAATCAGTAGTATCAGATAAGAATCGGTAAATGGTTAATGTACATGATAAT
1 GTTAATGTACATGATAATCAATAATATCAAATAAGAACCGATAAATGGTTAATGAACATGATAAT
698193 TAGTGAACCGGTCGAGA
66 TAGTGAACCGGTCGAGA
* *
698210 GTTAATGTACATGATAATCAATAATATCAAATCCA-AACCGATCAATGGTTAATGAACATGATAA
1 GTTAATGTACATGATAATCAATAATATCAAAT-AAGAACCGATAAATGGTTAATGAACATGATAA
698274 TTAGTGA
65 TTAGTGA
698281 TATCGTATCT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 61 0.98
83 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (82 bp):
GTTAATGTACATGATAATCAATAATATCAAATAAGAACCGATAAATGGTTAATGAACATGATAAT
TAGTGAACCGGTCGAGA
Found at i:698355 original size:176 final size:176
Alignment explanation
Indices: 698025--698374 Score: 438
Period size: 176 Copynumber: 2.0 Consensus size: 176
698015 ATATCTAAAT
* * * * * *
698025 CGGTCGGGAGTTAATATATATGATAATCAATAATATCAAATCCAAACCGGTCGATGGTTTATGTA
1 CGGTCGAGAGTTAATATACATGATAATCAATAATATCAAATCCAAACCGATCAATGGTTAATGAA
* * ** * *
698090 CATGATAAATTGTGATATCGGATTTGAACCGGTTAGTGGTTAATGTACATGATAATCAGTAGTAT
66 CATGATAAATTGTGATATCGGATCTAAACCAATTAGTGGTTAATATACATGATAATCAATAGTAT
*
698155 CAGATAAGAATCGGTAAATGGTTAATGTACATGATAATTAGTGAAC
131 CAGATAAGAACCGGTAAATGGTTAATGTACATGATAATTAGTGAAC
*
698201 CGGTCGAGAGTTAATGTACATGATAATCAATAATATCAAATCCAAACCGATCAATGGTTAATGAA
1 CGGTCGAGAGTTAATATACATGATAATCAATAATATCAAATCCAAACCGATCAATGGTTAATGAA
* * *
698266 CATGAT-AATTAGTGATATCGTATCTAAACTAA-TATGTGGTTAATATCCATGATAATCAAT-GA
66 CATGATAAATT-GTGATATCGGATCTAAACCAATTA-GTGGTTAATATACATGATAATCAATAG-
* * ***
698328 TATCCGATCTA-AACCGGTCGGTGGTTAATGTACATGATAATTAGTGA
128 TATCAGAT-AAGAACCGGTAAATGGTTAATGTACATGATAATTAGTGA
698375 TATCAAATCT
Statistics
Matches: 148, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
175 7 0.05
176 140 0.95
177 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (176 bp):
CGGTCGAGAGTTAATATACATGATAATCAATAATATCAAATCCAAACCGATCAATGGTTAATGAA
CATGATAAATTGTGATATCGGATCTAAACCAATTAGTGGTTAATATACATGATAATCAATAGTAT
CAGATAAGAACCGGTAAATGGTTAATGTACATGATAATTAGTGAAC
Found at i:698472 original size:141 final size:141
Alignment explanation
Indices: 698210--698482 Score: 318
Period size: 141 Copynumber: 1.9 Consensus size: 141
698200 CCGGTCGAGA
**
698210 GTTAATGTACATGATAATCAATAATATCAAATCCAAACCGATCAATGGTTAATGAACATGATAAT
1 GTTAATGTACATGATAATCAATAATATCAAATCCAAACCGATCAATAATTAATGAACATGATAAT
* * * * * *
698275 TAGTGATATCGTATCTAAACTAATATGTGGTTAATATCCATGATAATCAATGATATCCGATCTAA
66 CAGTGATATCGAATCTAAACTAATACGTGGTTAATATACATGATAATCAATAATATCCGATCCAA
698340 ACCGGTCGGTG
131 ACCGGTCGGTG
* * * * * * *
698351 GTTAATGTACATGATAATTAGTGATATCAAATCTAAACCGGTCAGTAATTAATGTACATGATAAT
1 GTTAATGTACATGATAATCAATAATATCAAATCCAAACCGATCAATAATTAATGAACATGATAAT
* * * * *
698416 CAGAT-ATATCGAATCTGAACCT-AT-CGATGGTTAATGTACATGATAATTAGTAATATCGGATC
66 CAG-TGATATCGAATCT-AAACTAATACG-TGGTTAATATACATGATAATCAATAATATCCGATC
698478 CAAAC
128 CAAAC
698483 TGCCAGGTCC
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
140 1 0.01
141 103 0.94
142 5 0.05
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (141 bp):
GTTAATGTACATGATAATCAATAATATCAAATCCAAACCGATCAATAATTAATGAACATGATAAT
CAGTGATATCGAATCTAAACTAATACGTGGTTAATATACATGATAATCAATAATATCCGATCCAA
ACCGGTCGGTG
Found at i:701571 original size:37 final size:35
Alignment explanation
Indices: 701528--701967 Score: 288
Period size: 37 Copynumber: 12.3 Consensus size: 35
701518 TATATATATT
*
701528 TATATATTATATAGTTTGTAAATA-ATTTTTGAAAGTATA
1 TATATAATATATAGTTT-TAAA-ACATTTTTG-AA--ATA
* * * *
701567 TATATAATATATGAATTTGAAAATATATTTGAAAATA
1 TATATAATATAT-AGTTTTAAAACATTTTTG-AAATA
* *
701604 TTTATATATTATATAATTTTTAAAACA-TTTTGAAAATA
1 --TATATAATATAT-AGTTTTAAAACATTTTTG-AAATA
* *
701642 AATATAATATATAGTTTTTAAAATATTTTTGAATATA
1 TATATAATATATAG-TTTTAAAACATTTTTGAA-ATA
*
701679 TATATATTATATAGTTTTTAAAACA-TTTTGAAGATA
1 TATATAATATATAG-TTTTAAAACATTTTTGAA-ATA
* * * *
701715 AATATAATATATAGTTTTAAAAATATTTTTTAAAAA
1 TATATAATATATAGTTTT-AAAACATTTTTGAAATA
*
701751 TTATATAATATATAGTTTTGAAAACATTTTTGAAAAAA
1 -TATATAATATATAGTTTT-AAAACATTTTTG-AAATA
* *
701789 TATATAATATATAATTTTGAAAACATTTTTGAAAAA
1 TATATAATATATAGTTTT-AAAACATTTTTGAAATA
701825 TTATATAATATATAGTTTTAAAAACATTTTTTTTGAAA-A
1 -TATATAATATATAGTTTT-AAAACA---TTTTTGAAATA
701864 CT-TAT-ATA-ATA-TTTTCAAAACA-TTTTG-AA-A
1 -TATATAATATATAGTTTT-AAAACATTTTTGAAATA
** *
701894 GCTAT-ATATATAGTTTTGAAAACTTTTTTG----A
1 TATATAATATATAGTTTT-AAAACATTTTTGAAATA
**
701925 -ATATAATATATAG-TTT-AAATTTTTTTGAAATA
1 TATATAATATATAGTTTTAAAACATTTTTGAAATA
*
701957 TATATTATATA
1 TATATAATATA
701968 ATTTATATCA
Statistics
Matches: 338, Mismatches: 38, Indels: 56
0.78 0.09 0.13
Matches are distributed among these distances:
28 10 0.03
30 15 0.04
31 17 0.05
32 10 0.03
33 14 0.04
35 15 0.04
36 58 0.17
37 122 0.36
38 19 0.06
39 45 0.13
40 13 0.04
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (35 bp):
TATATAATATATAGTTTTAAAACATTTTTGAAATA
Found at i:701612 original size:73 final size:73
Alignment explanation
Indices: 701527--701855 Score: 336
Period size: 73 Copynumber: 4.4 Consensus size: 73
701517 TTATATATAT
*
701527 TTATAT-ATTATATAGTTTGTAAATA-ATTTTTGAAAGTATATATATAATATAT-GAATTTGAAA
1 TTATATAATTATATAGTTT-TAAA-ACATTTTTGAAA--ATAAATATAATATATAG-ATTTGAAA
*
701589 ATATATTTGAAAA
61 ATATTTTTGAAAA
* * * *
701602 TATTTATATATTATATAATTTTTAAAACA-TTTTGAAAATAAATATAATATATAGTTTTTAAAAT
1 T-TATATA-ATTATAT-AGTTTTAAAACATTTTTGAAAATAAATATAATATATAGATTTGAAAAT
*
701666 ATTTTTGAATA
63 ATTTTTGAAAA
* * *
701677 -TATATATATTATATAGTTTTTAAAACA-TTTTGAAGATAAATATAATATATAGTTTTAAAAATA
1 TTATATA-ATTATATAG-TTTTAAAACATTTTTGAAAATAAATATAATATATAGATTTGAAAATA
*
701740 TTTTTTAAAAA
64 -TTTTTGAAAA
*
701751 TTATATAA-TATATAGTTTTGAAAACATTTTTGAAAA-AATATATAATATATA-ATTTTGAAAAC
1 TTATATAATTATATAGTTTT-AAAACATTTTTGAAAATAA-ATATAATATATAGA-TTTGAAAAT
701813 ATTTTTGAAAAA
63 ATTTTTG-AAAA
701825 TTATATAA-TATATAGTTTTAAAAACATTTTT
1 TTATATAATTATATAGTTTT-AAAACATTTTT
701856 TTTGAAAACT
Statistics
Matches: 221, Mismatches: 19, Indels: 29
0.82 0.07 0.11
Matches are distributed among these distances:
72 5 0.02
73 77 0.35
74 71 0.32
75 38 0.17
76 5 0.02
77 9 0.04
78 12 0.05
79 4 0.02
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (73 bp):
TTATATAATTATATAGTTTTAAAACATTTTTGAAAATAAATATAATATATAGATTTGAAAATATT
TTTGAAAA
Found at i:701904 original size:74 final size:74
Alignment explanation
Indices: 701527--701936 Score: 332
Period size: 73 Copynumber: 5.6 Consensus size: 74
701517 TTATATATAT
* * * *
701527 TTATATATTATATAGTTTGTAAATA-ATTTTTGAAAGTATATATATAATATATGAA-TTTGAAAA
1 TTATATAATATATAGTTT-TAAAAACATTTTTGAAA--AAATATATAATATAT-AATTTTCAAAA
* *
701590 TATATTTGAAAATA
62 CATTTTTGAAAA-A
* * * * * *
701604 TTTATATATTATATAATTTTTAAAACA-TTTTGAAAATAA-ATATAATATATAGTTTTTAAAATA
1 -TTATATAATATATAGTTTTAAAAACATTTTTGAAAA-AATATATAATATATAATTTTCAAAACA
*
701667 TTTTTG-AATA
64 TTTTTGAAAAA
* * * * * *
701677 TATATATATTATATAGTTTTTAAAACA-TTTTGAAGATAA-ATATAATATATAGTTTTAAAAATA
1 T-TATATAATATATAGTTTTAAAAACATTTTTGAA-AAAATATATAATATATAATTTTCAAAACA
*
701740 TTTTTTAAAAA
64 TTTTTGAAAAA
* *
701751 TTATATAATATATAGTTTTGAAAACATTTTTGAAAAAATATATAATATATAATTTTGAAAACATT
1 TTATATAATATATAGTTTTAAAAACATTTTTGAAAAAATATATAATATATAATTTTCAAAACATT
701816 TTTGAAAAA
66 TTTGAAAAA
*
701825 TTATATAATATATAGTTTTAAAAACATTTTTTTTG-AAAACT-TAT-ATA-AT-ATTTTCAAAAC
1 TTATATAATATATAGTTTTAAAAACA---TTTTTGAAAAAATATATAATATATAATTTTCAAAAC
701885 A-TTTTG--AAA
63 ATTTTTGAAAAA
** * * *
701894 -GCTAT-ATATATAGTTTTGAAAACTTTTTTGAATATAATATATA
1 TTATATAATATATAGTTTTAAAAACATTTTTGAA-AAAATATATA
701937 GTTTAAATTT
Statistics
Matches: 288, Mismatches: 29, Indels: 40
0.81 0.08 0.11
Matches are distributed among these distances:
64 6 0.02
65 1 0.00
66 3 0.01
67 20 0.07
68 3 0.01
69 3 0.01
71 5 0.02
72 12 0.04
73 90 0.31
74 74 0.26
75 29 0.10
76 6 0.02
77 18 0.06
78 18 0.06
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (74 bp):
TTATATAATATATAGTTTTAAAAACATTTTTGAAAAAATATATAATATATAATTTTCAAAACATT
TTTGAAAAA
Found at i:701949 original size:29 final size:30
Alignment explanation
Indices: 701886--701972 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
701876 TTTCAAAACA
**
701886 TTTTGAAAGCTATATATATAGTTTTGAAAACTT
1 TTTTGAAATATATATATATAG-TTT--AAACTT
*
701919 TTTTG-AATATA-ATATATAGTTTAAATTT
1 TTTTGAAATATATATATATAGTTTAAACTT
*
701947 TTTTGAAATATATATTATATAATTTA
1 TTTTGAAATATATA-TATATAGTTTA
701973 TATCATATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
28 10 0.21
29 6 0.13
30 4 0.09
31 18 0.38
32 4 0.09
33 5 0.11
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTTGAAATATATATATATAGTTTAAACTT
Found at i:703359 original size:9 final size:9
Alignment explanation
Indices: 703329--703388 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
703319 TTATATTTTG
703329 TTTTTTT-C
1 TTTTTTTAC
* *
703337 TTCTCTTTAA
1 TT-TTTTTAC
703347 TTTTTTTAC
1 TTTTTTTAC
*
703356 TTTTTTTTTCC
1 --TTTTTTTAC
703367 TTTTTTTAC
1 TTTTTTTAC
*
703376 TTTTTTTCC
1 TTTTTTTAC
703385 TTTT
1 TTTT
703389 GATTTATTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
8 2 0.05
9 29 0.71
10 2 0.05
11 8 0.20
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:703361 original size:29 final size:29
Alignment explanation
Indices: 703329--703388 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
703319 TTATATTTTG
703329 TTTTTTT-CTTCTCTTTAATTTTTTTACTT
1 TTTTTTTCCTT-TCTTTAATTTTTTTACTT
* * *
703358 TTTTTTTCCTTTTTTTACTTTTTTTCCTT
1 TTTTTTTCCTTTCTTTAATTTTTTTACTT
703387 TT
1 TT
703389 GATTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTTTTCCTTTCTTTAATTTTTTTACTT
Found at i:703370 original size:18 final size:17
Alignment explanation
Indices: 703349--703418 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 17
703339 CTCTTTAATT
703349 TTTTTACTTTTTTTTTCC
1 TTTTTA-TTTTTTTTTCC
703367 TTTTT-TTACTTTTTTTCC
1 TTTTTATT--TTTTTTTCC
* *
703385 TTTTGATTTATTATTT-C
1 TTTTTATTT-TTTTTTCC
*
703402 TTTTT-TCTTTTTTTCC
1 TTTTTATTTTTTTTTCC
703418 T
1 T
703419 CTTTGATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
15 5 0.12
16 6 0.14
17 6 0.14
18 23 0.55
19 2 0.05
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.77
Consensus pattern (17 bp):
TTTTTATTTTTTTTTCC
Found at i:709779 original size:21 final size:21
Alignment explanation
Indices: 709753--709792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
709743 TTTATTATGT
*
709753 TAATTACAAGAGTTACAAAAG
1 TAATTACAACAGTTACAAAAG
*
709774 TAATTACAACCGTTACAAA
1 TAATTACAACAGTTACAAA
709793 CTCCTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (21 bp):
TAATTACAACAGTTACAAAAG
Done.