Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000877.1 Hibiscus syriacus cultivar Beakdansim tig00001707_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: 81994
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:131 original size:12 final size:12
Alignment explanation
Indices: 87--131 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
77 ATTGGCAAGG
*
87 AGAAAGAGGAGGA
1 AGAAA-AGGAAGA
*
100 AGAAGAGGAAGA
1 AGAAAAGGAAGA
112 AGAAAAGGAAGA
1 AGAAAAGGAAGA
*
124 AGAGAAGG
1 AGAAAAGG
132 TATAATAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAAAAGGAAGA
Found at i:4246 original size:12 final size:12
Alignment explanation
Indices: 4223--4249 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4213 GAGGAAGAAG
4223 AGGAAGAAGAGA
1 AGGAAGAAGAGA
4235 AGGAAGAAGAGA
1 AGGAAGAAGAGA
4247 AGG
1 AGG
4250 TATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (12 bp):
AGGAAGAAGAGA
Found at i:10590 original size:200 final size:198
Alignment explanation
Indices: 10083--10696 Score: 806
Period size: 200 Copynumber: 3.1 Consensus size: 198
10073 ACCTAGTACT
* * *
10083 TATAAGTATCGATACTTGTATTCCAATATTCATCACAAATAATTTGCACGCA-AAACGTAATGAT
1 TATAAGTATCGATACTTATATTCCAATATACATCACAAACAATTTGCACGCACAAA-GT-ATGAT
** * *
10147 ACACATATCACAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAATTAATAGGTAAATT
64 ACATGTATCACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATT
* * * ** *
10212 TACGATATAGATGGT-AAAATCTA-TCGGTTTAATGATAATAGATGTAAACATAAAGTAGCGATA
129 TACAATGTAAATGGTAAAAATCTACT-GGTTTAATGATAATAGGCGTAAACATAAAGTATCGATA
*
10275 CGATTTG
193 C-TTTTG
* * * * *** * *
10282 TATAGGTATTGATACTTTTAGTCCAATATGTTTCTC-AACAACTTGCACGCACAAAGTATTGATA
1 TATAAGTATCGATACTTATATTCCAATATACATCACAAACAATTTGCACGCACAAAGTA-TGATA
10346 CATGTATCACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTT
65 CATGTATCACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTT
*
10411 ACAATGTAAATGGTAAAAATCTACTGGTTTAATGA-AATTAGGCGTAAACATAAAGTATCGATGC
130 ACAATGTAAATGGTAAAAATCTACTGGTTTAATGATAA-TAGGCGTAAACATAAAGTATCGATAC
10475 TTGTTG
194 TT-TTG
*
10481 TATAAGTATCGATACTTATATTCCAATATACATCACAAACAATTTGCACGTACAAAGTATCGATA
1 TATAAGTATCGATACTTATATTCCAATATACATCACAAACAATTTGCACGCACAAAGTAT-GATA
* * **
10546 CATGTATCACAAATATTGATACTTATAATTTCAAAATATATTACTTTAAAGTAATAGGTAAATTT
65 CATGTATCACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTT
* * * *
10611 ACAGTGTAATTGGTAAAAATCTACTAGTTTAATGATAATAGGCGTAAACATAAAGTATCTATACT
130 ACAATGTAAATGGTAAAAATCTACTGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACT
*
10676 TTGG
195 TTTG
*
10680 TATAGGTATCGATACTT
1 TATAAGTATCGATACTT
10697 TCGATCTAAA
Statistics
Matches: 363, Mismatches: 43, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
197 1 0.00
198 95 0.26
199 121 0.33
200 144 0.40
201 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (198 bp):
TATAAGTATCGATACTTATATTCCAATATACATCACAAACAATTTGCACGCACAAAGTATGATAC
ATGTATCACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTA
CAATGTAAATGGTAAAAATCTACTGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTT
TTG
Found at i:11215 original size:18 final size:18
Alignment explanation
Indices: 11192--11237 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
11182 TCCGAGACAG
11192 TTCTTCTCAACCAAAACC
1 TTCTTCTCAACCAAAACC
***
11210 TTCTTCTCAACCAAGGTC
1 TTCTTCTCAACCAAAACC
11228 TTCTTCTCAA
1 TTCTTCTCAA
11238 GTGATGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (18 bp):
TTCTTCTCAACCAAAACC
Found at i:15008 original size:90 final size:92
Alignment explanation
Indices: 14886--15065 Score: 283
Period size: 90 Copynumber: 2.0 Consensus size: 92
14876 TAATCCTGAA
* * * * *
14886 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-A-AAATCCTTAATATG
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAATAAAACCCTAATATA
*
14949 ATTAGGGTAACTTGTATATAAAAGGAT
66 ATTAGGGTAACTTGGATATAAAAGGAT
14976 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAATAAAACCCTAATATA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAATAAAACCCTAATATA
*
15041 ATTAGGGTAACTTGGCTATAAAAGG
66 ATTAGGGTAACTTGGATATAAAAGG
15066 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
90 46 0.57
91 1 0.01
92 34 0.42
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (92 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAATAAAACCCTAATATA
ATTAGGGTAACTTGGATATAAAAGGAT
Found at i:24028 original size:15 final size:16
Alignment explanation
Indices: 24008--24037 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23998 CCCTTTCACC
24008 TAGAGTG-TGGGATGG
1 TAGAGTGATGGGATGG
24023 TAGAGTGATGGGATG
1 TAGAGTGATGGGATG
24038 ACTCCCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.50, T:0.27
Consensus pattern (16 bp):
TAGAGTGATGGGATGG
Found at i:29520 original size:227 final size:227
Alignment explanation
Indices: 29139--29565 Score: 635
Period size: 227 Copynumber: 1.9 Consensus size: 227
29129 CAATATTTAT
* *** * *
29139 AATTTAGAAACCTATTACTTTAAAGTTATAGGTAAATTTACAACGTAAATGGTAAAAGTCTATCG
1 AATTTAGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAACGTAAACAATAAAAGTCTACCA
* *
29204 GTTTAATGATAATAGGTGTAAACATAAAGTATCTATACTTTTTGTATAGGTATTGATACTTTTAG
66 ATTTAATGATAATAGGCGTAAACATAAAGTATCTATACTTTTTGTATAGGTATTGATACTTTTAG
* *
29269 TCCAATATGCTTCTAATAAATTTGCAAGCACAAAGTTTCGATATACAAATATAAAGTATCGATAC
131 TCCAATATGCTTCTAATAAATTTGCAAGCACAAAGTGTCGATACACAAATATAAAGTATCGATAC
29334 GCGGATTTCTTAAAAAAAGTATCGATACGCGG
196 GCGGATTTCTTAAAAAAAGTATCGATACGCGG
* * * *
29366 AATTTCGAAACCGATTACTTTAAAGTTATAGGTAATTTTACAATGTCAACAATAAAAGTCTACCA
1 AATTTAGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAACGTAAACAATAAAAGTCTACCA
29431 ATTTAATGATAATAGGCGTAAACATAAAGTAT-TGATA-TTTTTGGTATAGGTATTGATACTTTT
66 ATTTAATGATAATAGGCGTAAACATAAAGTATCT-ATACTTTTT-GTATAGGTATTGATACTTTT
* * * **
29494 AGTCCAGTATGCTTCTCAA-CAATTTGCACGCACAAAGTGTCGATACACATGTATAAAGTATCGA
129 AGTCCAATATGCTTCT-AATAAATTTGCAAGCACAAAGTGTCGATACACAAATATAAAGTATCGA
29558 TACGCGGA
193 TACGCGGA
29566 ATTTTGAAAT
Statistics
Matches: 178, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
226 6 0.03
227 170 0.96
228 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (227 bp):
AATTTAGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAACGTAAACAATAAAAGTCTACCA
ATTTAATGATAATAGGCGTAAACATAAAGTATCTATACTTTTTGTATAGGTATTGATACTTTTAG
TCCAATATGCTTCTAATAAATTTGCAAGCACAAAGTGTCGATACACAAATATAAAGTATCGATAC
GCGGATTTCTTAAAAAAAGTATCGATACGCGG
Found at i:29695 original size:199 final size:199
Alignment explanation
Indices: 29349--30681 Score: 1461
Period size: 199 Copynumber: 6.6 Consensus size: 199
29339 TTTCTTAAAA
* *
29349 AAAGTATCGATACGCGGAATTTCGAAACCGATTACTTTAAAGTTATAGGTAATTTTACAATGTCA
1 AAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
** * ** * *
29414 ACAATAAAAGTCTACCAATTTAATGATAATAGGCGTAAACATAAAGTATTGATATTTTTGGTATA
66 ACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTTGTATA
* * *
29479 GGTATTGATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCACAAAGTGTCGATACACAT
131 GGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACAT
29544 GTAT
196 GTAT
*
29548 AAAGTATCGATACGCGGAATTTTGAAATCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
1 AAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
* *
29613 ACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAATATAAAGTATCAATATTTTTTGTATA
66 ACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTTGTATA
* * * * * * *
29678 TGTATCGATAATTTTAGTCTAGTATGTTTCTCAACAATTTGCACACACAAAGTATTGATACACAT
131 GGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACAT
29743 GTAT
196 GTAT
* * * *
29747 AAAGTATCGATGCGCGGAATTTTGAAACCAATTATTTTAAAATTATAGGTAAATTTACAATGTCA
1 AAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
* * * * *
29812 ACAGTAAAAGTCTATCAGTTTAATGATAATAGGGGTAAAGATAAAGTATCGATA-CTTTTGTATA
66 ACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTTGTATA
* * *
29876 GGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCATGTACAAAGTATCTATACACAT
131 GGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACAT
29941 GTAT
196 GTAT
* * ** * * * *
29945 AAAATATCGTTACGTAGAATTTTGAAACCTATTACTTTTAAGTTATAGGTAAATTTATAATGTAA
1 AAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
*
30010 ACGGTAAAAGTCTA-CTGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTGTAT
66 ACGGTAAAAGTCTATC-GGTTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTTGTAT
* * * * * * *
30074 AGGTATCGATTCTTTTAGTCTAGTATGCTTTTCAACAATTTGTAGGTACAAAGTATCGATACACA
130 AGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACA
30139 TGTAT
195 TGTAT
* * * * * * *
30144 AAAGTTTTGATACGCGGAATGTAGAAACTGATTACTTTAAATTTATAGGTAAATTTGCAATGTCA
1 AAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
* * * *
30209 ACGATAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAGTTTTTGTGTA
66 ACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTTGTATA
* * * *
30274 GGTATCGATAGTTTTTGTGTAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGAAT
131 GGTATCGATA---CTT-T-TA-G--TC----C----AAT---A--TGCTTCTCAACAATTTGCAC
**
30339 GCACAAAGTATCGATATGCATGTAT
175 GCACAAAGTATCGATACACATGTAT
* * *
30364 AAAGTATCGATACGCGGAATTTCGAAACCGGTTACTTTAAAGTTATAGGTAAA-TTAAAATGTCA
1 AAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
* * * * * * * * * *
30428 ACGGTAAAAGTTTATAGGTATATTGATAATAGGCGTAAATATCAAGTATTGATATTGTCTATATA
66 ACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTTGTATA
* * *
30493 GGTATCGATACTTTTATTCCAATATGCTTTTCAAACAATTTGCACG-AGAAATGTATCGATACAC
131 GGTATCGATACTTTTAGTCCAATATGCTTCTC-AACAATTTGCACGCACAAA-GTATCGATACAC
*
30557 ATATAT
194 ATGTAT
**** ** * * * * * *
30563 AAAGTATC-AGTACTTATAATTTCAAAAACCTATTACTGTAAGGTAATAGGTTAATTTACAATGA
1 AAAGTATCGA-TACGCGGAATTT-TGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGT
* * * * * * * *
30627 AAATGGTAAAAGTTTACCGATATAATGATAATAGGTGTAAACATCAAGTATCGAT
64 CAACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGAT
30682 GCACATGTAT
Statistics
Matches: 958, Mismatches: 147, Indels: 56
0.83 0.13 0.05
Matches are distributed among these distances:
197 1 0.00
198 182 0.19
199 520 0.54
200 25 0.03
201 53 0.06
202 2 0.00
203 3 0.00
204 2 0.00
205 1 0.00
207 3 0.00
211 2 0.00
214 2 0.00
215 4 0.00
216 2 0.00
218 1 0.00
219 70 0.07
220 85 0.09
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (199 bp):
AAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCA
ACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTTGTATA
GGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACAT
GTAT
Found at i:30083 original size:397 final size:396
Alignment explanation
Indices: 29349--30681 Score: 1519
Period size: 397 Copynumber: 3.3 Consensus size: 396
29339 TTTCTTAAAA
* * *
29349 AAAGTATCGATACGCGGAATTTCGAAACCGATTACTTTAAAGTTATAGGTAATTTTACAATGTCA
1 AAAGTATCGATACGCGGAATTTAGAAACCGATTACTTTAAAATTATAGGTAAATTTACAATGTCA
* * * * *
29414 ACAATAAAAGTCTACCAATTTAATGATAATAGGCGTAAACATAAAGTATTGATATTTTTGGTATA
66 ACAGTAAAAGTCTACCAGTTTAATGATAATAGGGGTAAAGATAAAGTATCGATATTTTT-GTATA
* * * *
29479 GGTATTGATACTTTTAGTCCAGTATGCTTCTCAACAATTTGCACGCACAAAGTGTCGATACACAT
130 GGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCATGCACAAAGTATCGATACACAT
* *
29544 GTATAAAGTATCGATACGCGGAATTTTGAAATCGATTACTTTAAAGTTATAGGTAAATTTACAAT
195 GTATAAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTAAAAT
* *
29609 GTCAACGGTAAAAGTCTATCGGTTTAATGATAATAGGCGTAAATATAAAGTATCAATATTTTTTG
260 GTCAACGGTAAAAGTCTATAGGTTTAATGATAATAGGCGTAAATATAAAGTATCGATA-TTTTTG
* * *
29674 TATATGTATCGATAATTTTAGTCTAGTATG-TTTCTCAACAATTTGCACACACAAAGTATTGATA
324 TATAGGTATCGATACTTTTAGTCTAGTATGCTTT-TCAACAATTTGCACACACAAAGTATCGATA
29738 CACATGTAT
388 CACATGTAT
* * * *
29747 AAAGTATCGATGCGCGGAATTTTGAAACCAATTATTTTAAAATTATAGGTAAATTTACAATGTCA
1 AAAGTATCGATACGCGGAATTTAGAAACCGATTACTTTAAAATTATAGGTAAATTTACAATGTCA
* *
29812 ACAGTAAAAGTCTATCAGTTTAATGATAATAGGGGTAAAGATAAAGTATCGATACTTTTGTATAG
66 ACAGTAAAAGTCTACCAGTTTAATGATAATAGGGGTAAAGATAAAGTATCGATATTTTTGTATAG
* *
29877 GTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCATGTACAAAGTATCTATACACATG
131 GTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCATGCACAAAGTATCGATACACATG
* * ** * * *
29942 TATAAAATATCGTTACGTAGAATTTTGAAACCTATTACTTTTAAGTTATAGGTAAATTTATAATG
196 TATAAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTAAAATG
* *
30007 TAAACGGTAAAAGTCTACT-GGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTTG
261 TCAACGGTAAAAGTCTA-TAGGTTTAATGATAATAGGCGTAAATATAAAGTATCGATA-TTTTTG
* * ***
30071 TATAGGTATCGATTCTTTTAGTCTAGTATGCTTTTCAACAATTTGTAGGTACAAAGTATCGATAC
324 TATAGGTATCGATACTTTTAGTCTAGTATGCTTTTCAACAATTTGCACACACAAAGTATCGATAC
30136 ACATGTAT
389 ACATGTAT
* * * * * *
30144 AAAGTTTTGATACGCGGAATGTAGAAACTGATTACTTTAAATTTATAGGTAAATTTGCAATGTCA
1 AAAGTATCGATACGCGGAATTTAGAAACCGATTACTTTAAAATTATAGGTAAATTTACAATGTCA
* *
30209 AC-GATAAAAGTCTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAGTTTTTGTGT
66 ACAG-TAAAAGTCTACCAGTTTAATGATAATAGG-G-----GTAAAG-AT--A-A----------
* *
30273 AGGTATCGATAGTTTTTGTGTAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGAA
110 A-GTATCGATA-TTTTTGTATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCA
** * *
30338 TGCACAAAGTATCGATATGCATGTATAAAGTATCGATACGCGGAATTTCGAAACCGGTTACTTTA
173 TGCACAAAGTATCGATACACATGTATAAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTA
* * *
30403 AAGTTATAGGTAAA-TTAAAATGTCAACGGTAAAAGTTTATAGGTATATTGATAATAGGCGTAAA
238 AAGTTATAGGTAAATTTAAAATGTCAACGGTAAAAGTCTATAGGTTTAATGATAATAGGCGTAAA
* * * * * * *
30467 TATCAAGTATTGATATTGTCTATATAGGTATCGATACTTTTATTCCAATATGCTTTTCAAACAAT
303 TATAAAGTATCGATATT-TTTGTATAGGTATCGATACTTTTAGTCTAGTATGCTTTTC-AACAAT
* * *
30532 TTGCACGAGA-AATGTATCGATACACATATAT
366 TTGCAC-ACACAAAGTATCGATACACATGTAT
**** * * * ** * * *
30563 AAAGTATC-AGTACTTATAATTTCAAAAACCTATTACTGTAAGGTAATAGGTTAATTTACAATGA
1 AAAGTATCGA-TACGCGGAATTT-AGAAACCGATTACTTTAAAATTATAGGTAAATTTACAATGT
* ** * * * * *
30627 AAATGGTAAAAGTTTACC-GATATAATGATAATAGGTGTAAACATCAAGTATCGAT
64 CAACAGTAAAAGTCTACCAG-TTTAATGATAATAGGGGTAAAGATAAAGTATCGAT
30682 GCACATGTAT
Statistics
Matches: 790, Mismatches: 112, Indels: 65
0.82 0.12 0.07
Matches are distributed among these distances:
396 1 0.00
397 325 0.41
398 116 0.15
399 8 0.01
400 1 0.00
403 5 0.01
404 2 0.00
406 1 0.00
407 1 0.00
410 1 0.00
413 2 0.00
414 4 0.01
417 4 0.01
418 99 0.13
419 160 0.20
420 59 0.07
421 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (396 bp):
AAAGTATCGATACGCGGAATTTAGAAACCGATTACTTTAAAATTATAGGTAAATTTACAATGTCA
ACAGTAAAAGTCTACCAGTTTAATGATAATAGGGGTAAAGATAAAGTATCGATATTTTTGTATAG
GTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGCATGCACAAAGTATCGATACACATG
TATAAAGTATCGATACGCGGAATTTTGAAACCGATTACTTTAAAGTTATAGGTAAATTTAAAATG
TCAACGGTAAAAGTCTATAGGTTTAATGATAATAGGCGTAAATATAAAGTATCGATATTTTTGTA
TAGGTATCGATACTTTTAGTCTAGTATGCTTTTCAACAATTTGCACACACAAAGTATCGATACAC
ATGTAT
Found at i:30099 original size:20 final size:20
Alignment explanation
Indices: 30054--30099 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
30044 GTAAACATAA
*
30054 AGTATCGATACTTTTTGTAT
1 AGTATCGATACTTTTAGTAT
* *
30074 AGGTATCGATTCTTTTAGTCT
1 A-GTATCGATACTTTTAGTAT
30095 AGTAT
1 AGTAT
30100 GCTTTTCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (20 bp):
AGTATCGATACTTTTAGTAT
Found at i:30158 original size:596 final size:605
Alignment explanation
Indices: 29365--30681 Score: 1633
Period size: 596 Copynumber: 2.2 Consensus size: 605
29355 TCGATACGCG
* * * * * **
29365 GAATTTCGAAACCGATTACTTTAAAGTTATAGGTAATTTTACAATGTCAACAATAAAAGTCTACC
1 GAATTTAGAAACCTATTACTTTTAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACC
* * *
29430 AATTTAATGATAATAGGCGTAAACATAAAGTATTGATATTTTTGGTATAGGTATTGATACTTTTA
66 GATTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTGGTATAGGTATCGATACTTTTA
*
29495 GTCCAGTATGCTTCTCAACAATTTGCACGCACAAAGTGTCGATACACATGTATAAAGTATCGATA
131 GTCCAGTATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCGATA
* * *
29560 CGCGGAATTTTGAAA-TCGATTACTTTAAAGTTATAGGTAAATTTACAATGTCAACGGTAAAAGT
196 CGCGGAATGTAGAAACT-GATTACTTTAAAGTTATAGGTAAATTTACAATGTCAACGATAAAAGT
* *
29624 CTATCGGTTTAATGATAATAGGCGTAAATATAAAGTATCAATA-TTTT-T-T-G-T-ATA-T-GT
260 CTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCAATAGTTTTGTGTAGATCATATTAGT
* * * * *
29681 ATCGATAATTTTAGTCTAGTATGTTTCTCAACAATTTGCACACACAAAGTATTGATACACATGTA
325 ATCGATAATTTTAGTCCAATATGCTTCTCAACAATTTGAACACACAAAGTATCGATACACATGTA
* * * *
29746 TAAAGTATCGATGCGCGGAATTTTGAAACCAATTATTTTAAAATTATAGGTAAATTTACAATGTC
390 TAAAGTATCGATACGCGGAATTTCGAAACCAATTACTTTAAAATTATAGGTAAA-TTAAAATGTC
* * *
29811 AACAGTAAAAGTCTATCA-GTTTAATGATAATAGGGGTAAAGATAAAGTATCGATACTT-T-TGT
454 AACAGTAAAAGTCTAT-AGGTATAATGATAATAGGCGTAAAGATAAAGTATCGATA-TTGTCTAT
* *
29873 ATAGGTATCGATACTTTTAGTCCAATATGCTTCTC-AACAATTTGCATGTACAAA-GTATCTATA
517 ATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAAACAATTTGCACG-ACAAATGTATCGATA
*
29936 CACATGTATAAAATATC-GTTACGTA
581 CACATATATAAAATATCAG-TACGTA
* * *
29961 GAATTTTGAAACCTATTACTTTTAAGTTATAGGTAAATTTATAATGTAAACGGTAAAAGTCTACT
1 GAATTTAGAAACCTATTACTTTTAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACC
* *
30026 GGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTT-GTATAGGTATCGATTCTTTT
66 GATTTAATGATAATAGGCGTAAACATAAAGTATCGATA-TTTTTGGTATAGGTATCGATACTTTT
* * * * * * *
30090 AGTCTAGTATGCTTTTCAACAATTTGTAGGTACAAAGTATCGATACACATGTATAAAGTTTTGAT
130 AGTCCAGTATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCGAT
* *
30155 ACGCGGAATGTAGAAACTGATTACTTTAAATTTATAGGTAAATTTGCAATGTCAACGATAAAAGT
195 ACGCGGAATGTAGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTCAACGATAAAAGT
*
30220 CTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAGTTTTTGTGTAGGTATCGATAG
260 CTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCAATAG-TTTTGTGTA-G-ATC-ATA-
* **
30285 TTTTTGTGTAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGAATGCACAAAGTAT
320 ------T-TA-GTATCGATAATTTTAGTCCAATATGCTTCTCAACAATTTGAACACACAAAGTAT
** ** *
30350 CGATATGCATGTATAAAGTATCGATACGCGGAATTTCGAAACCGGTTACTTTAAAGTTATAGGTA
377 CGATACACATGTATAAAGTATCGATACGCGGAATTTCGAAACCAATTACTTTAAAATTATAGGTA
* * * * * *
30415 AATTAAAATGTCAACGGTAAAAGTTTATAGGTATATTGATAATAGGCGTAAATATCAAGTATTGA
442 AATTAAAATGTCAACAGTAAAAGTCTATAGGTATAATGATAATAGGCGTAAAGATAAAGTATCGA
* * *
30480 TATTGTCTATATAGGTATCGATACTTTTATTCCAATATGCTTTTCAAACAATTTGCACGAGAAAT
507 TATTGTCTATATAGGTATCGATACTTTTAGTCCAATATGCTTCTCAAACAATTTGCACGACAAAT
* *
30545 GTATCGATACACATATATAAAGTATCAGTACTTA
572 GTATCGATACACATATATAAAATATCAGTACGTA
* * * * * * * *
30579 TAATTTCAAAAACCTATTAC-TGTAAGGTAATAGGTTAATTTACAATGAAAATGGTAAAAGTTTA
1 GAATTT-AGAAACCTATTACTTTTAA-GTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTA
* * *
30643 CCGATATAATGATAATAGGTGTAAACATCAAGTATCGAT
64 CCGATTTAATGATAATAGGCGTAAACATAAAGTATCGAT
30682 GCACATGTAT
Statistics
Matches: 611, Mismatches: 79, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
596 264 0.43
597 6 0.01
598 4 0.01
599 1 0.00
600 1 0.00
602 1 0.00
604 1 0.00
606 3 0.00
615 4 0.01
616 55 0.09
617 144 0.24
618 49 0.08
619 78 0.13
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (605 bp):
GAATTTAGAAACCTATTACTTTTAAGTTATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACC
GATTTAATGATAATAGGCGTAAACATAAAGTATCGATATTTTTGGTATAGGTATCGATACTTTTA
GTCCAGTATGCTTCTCAACAATTTGCACGCACAAAGTATCGATACACATGTATAAAGTATCGATA
CGCGGAATGTAGAAACTGATTACTTTAAAGTTATAGGTAAATTTACAATGTCAACGATAAAAGTC
TACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCAATAGTTTTGTGTAGATCATATTAGTA
TCGATAATTTTAGTCCAATATGCTTCTCAACAATTTGAACACACAAAGTATCGATACACATGTAT
AAAGTATCGATACGCGGAATTTCGAAACCAATTACTTTAAAATTATAGGTAAATTAAAATGTCAA
CAGTAAAAGTCTATAGGTATAATGATAATAGGCGTAAAGATAAAGTATCGATATTGTCTATATAG
GTATCGATACTTTTAGTCCAATATGCTTCTCAAACAATTTGCACGACAAATGTATCGATACACAT
ATATAAAATATCAGTACGTA
Found at i:30278 original size:21 final size:21
Alignment explanation
Indices: 30254--30309 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
30244 TAAACATAAA
30254 GTATCGATAGTTTTTGTGTAG
1 GTATCGATAGTTTTTGTGTAG
30275 GTATCGATAGTTTTTGTGTAG
1 GTATCGATAGTTTTTGTGTAG
*
30296 GTATCGATACTTTT
1 GTATCGATAGTTTT
30310 AGTCCAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.48
Consensus pattern (21 bp):
GTATCGATAGTTTTTGTGTAG
Found at i:30676 original size:201 final size:198
Alignment explanation
Indices: 30293--30677 Score: 450
Period size: 201 Copynumber: 1.9 Consensus size: 198
30283 AGTTTTTGTG
* **
30293 TAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGAATGCACAAAGTATCGATATGC
1 TAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGAACGCACAAAGTATCGATACAC
* * * * * *
30358 ATGTATAAAGTATCGATACGCGGAATTTCGAAACCGGTTACTTTAAAGTTATAGGTAAATTAAAA
66 ATATATAAAGTATCGATACGCAGAATTTCAAAACCGATTACTGTAAAGTAATAGGTAAATTAAAA
** * * * *
30423 TGTCAACGGTAAAAGTTTATAGGTATATTGATAATAGGCGTAAATATCAAGTATTGATATTGTCT
131 TGAAAACGGTAAAAGTTTACAGATATAATGATAATAGGCGTAAACATCAAGTATTGATATTGTCT
30488 ATA
196 ATA
* * * *
30491 TAGGTATCGATACTTTTATTCCAATATGCTTTTCAAACAATTTGCACG-AGAAATGTATCGATAC
1 TAGGTATCGATACTTTTAGTCCAATATGCTTCTC-AACAATTTGAACGCACAAA-GTATCGATAC
** * * * *
30555 ACATATATAAAGTATC-AGTACTTATAATTTCAAAAACCTATTACTGTAAGGTAATAGGTTAATT
64 ACATATATAAAGTATCGA-TACGCAGAATTTC-AAAACCGATTACTGTAAAGTAATAGG-TAAAT
* * * *
30619 TACAATGAAAATGGTAAAAGTTTACCGATATAATGATAATAGGTGTAAACATCAAGTAT
126 TAAAATGAAAACGGTAAAAGTTTACAGATATAATGATAATAGGCGTAAACATCAAGTAT
30678 CGATGCACAT
Statistics
Matches: 153, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
198 37 0.24
199 43 0.28
200 20 0.13
201 53 0.35
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (198 bp):
TAGGTATCGATACTTTTAGTCCAATATGCTTCTCAACAATTTGAACGCACAAAGTATCGATACAC
ATATATAAAGTATCGATACGCAGAATTTCAAAACCGATTACTGTAAAGTAATAGGTAAATTAAAA
TGAAAACGGTAAAAGTTTACAGATATAATGATAATAGGCGTAAACATCAAGTATTGATATTGTCT
ATA
Found at i:31881 original size:13 final size:13
Alignment explanation
Indices: 31856--31898 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
31846 AGTTTTGTGT
31856 TTTTAATATAATAA
1 TTTTAA-ATAATAA
31870 TTTTAAATAATAA
1 TTTTAAATAATAA
31883 TTTT-AATAAATAA
1 TTTTAAAT-AATAA
31896 TTT
1 TTT
31899 GTGTTAGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.11
13 19 0.68
14 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTTAAATAATAA
Found at i:35571 original size:14 final size:14
Alignment explanation
Indices: 35552--35579 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35542 TATCGGGTAC
35552 GAAAACATCAATTT
1 GAAAACATCAATTT
35566 GAAAACATCAATTT
1 GAAAACATCAATTT
35580 AGGAGAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
GAAAACATCAATTT
Found at i:39490 original size:25 final size:24
Alignment explanation
Indices: 39436--39490 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
39426 CTTAGGGTTT
39436 TTAAA-GTTATTTCGAATTAATAAA
1 TTAAATGTTATTTC-AATTAATAAA
*
39460 TAAAATGTTATTT-AATTAATTCAAA
1 TTAAATGTTATTTCAATTAA-T-AAA
39485 TTAAAT
1 TTAAAT
39491 ATACATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.23
24 5 0.19
25 15 0.58
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (24 bp):
TTAAATGTTATTTCAATTAATAAA
Found at i:44245 original size:16 final size:16
Alignment explanation
Indices: 44220--44250 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44210 CTGGGCGGGC
*
44220 GGATGTGGGGCGGGTT
1 GGATGCGGGGCGGGTT
44236 GGATGCGGGGCGGGT
1 GGATGCGGGGCGGGT
44251 AATGTCTCAA
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:0.06, C:0.10, G:0.65, T:0.19
Consensus pattern (16 bp):
GGATGCGGGGCGGGTT
Found at i:54936 original size:6 final size:6
Alignment explanation
Indices: 54920--55109 Score: 362
Period size: 6 Copynumber: 31.7 Consensus size: 6
54910 TTATATGAAT
* *
54920 ATGAGT ATGAGT ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
1 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
54968 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
1 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
55016 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
1 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC
55064 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGA
1 ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGAGC ATGA
55110 ATATGAATAT
Statistics
Matches: 183, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 183 1.00
ACGTcount: A:0.34, C:0.15, G:0.33, T:0.18
Consensus pattern (6 bp):
ATGAGC
Found at i:55115 original size:6 final size:6
Alignment explanation
Indices: 55106--55249 Score: 288
Period size: 6 Copynumber: 24.0 Consensus size: 6
55096 GAGCATGAGC
55106 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
1 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
55154 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
1 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
55202 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
1 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
55250 TCTCAAATAT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 138 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATGAAT
Found at i:59873 original size:34 final size:34
Alignment explanation
Indices: 59814--59880 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
59804 TTCTTGAGAG
*
59814 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAACTTGTTA
59848 TTGTTTTCTCCTTGTTAGATC-GAGAGAACTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAACTTGT
59881 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAACTTGTTA
Found at i:61736 original size:3 final size:3
Alignment explanation
Indices: 61728--61806 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
61718 CTTGGTCCTT
61728 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
61776 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
61807 ATTTACAATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:63491 original size:30 final size:29
Alignment explanation
Indices: 63444--63652 Score: 136
Period size: 30 Copynumber: 7.1 Consensus size: 29
63434 ACCATTTCAA
** *
63444 TCCTTTAAACTTCTATTTTTTTCTTTTTAA
1 TCCTTTAAGTTTCTA-TTTTTTCTTTTTAG
* * *
63474 TCCTTTAAGTTTTTATTTGTGCTATTTTAG
1 TCCTTTAAGTTTCTATTTTTTCT-TTTTAG
* * *
63504 TCCATTGAGTTTCTATTTTTT-ATTTTAG
1 TCCTTTAAGTTTCTATTTTTTCTTTTTAG
* *
63532 TCCATTAACTTTCTATTTTTTCTATTTTAG
1 TCCTTTAAGTTTCTATTTTTTCT-TTTTAG
* * *
63562 TCCTTTAACTTT-TGTTTTTATTTTTTTAG
1 TCCTTTAAGTTTCTATTTTT-TCTTTTTAG
* * *
63591 TCATTTAAGTTTTTGTTTTTGT-TGTTTTAG
1 TCCTTTAAGTTTCTATTTTT-TCT-TTTTAG
* * * * * *
63621 TCCTGTAAATTTCTGTTATTACTATTTAG
1 TCCTTTAAGTTTCTATTTTTTCTTTTTAG
63650 TCC
1 TCC
63653 CTTATTTTAT
Statistics
Matches: 144, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
28 25 0.17
29 37 0.26
30 82 0.57
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (29 bp):
TCCTTTAAGTTTCTATTTTTTCTTTTTAG
Found at i:63610 original size:58 final size:55
Alignment explanation
Indices: 63444--63624 Score: 130
Period size: 58 Copynumber: 3.1 Consensus size: 55
63434 ACCATTTCAA
* * * *
63444 TCCTTTAAACTTCTATTTTTTTCTTTTTAATCCTTTAAGTTTTTATTTGTGCTATTTTAG
1 TCCTTT-AACTT-T-TTTTTTTTTTTTTAGTCATTTAAGTTTTT-TTT-TTCTATTTTAG
* * * * * *
63504 TCCATTGAGTTTCTATTTTTTATTTTAGTCCA-TTAACTTTCTATTTTTTCTATTTTAG
1 TCCTTTAACTTT-TTTTTTTTTTTTTAGT-CATTTAAGTTT-T-TTTTTTCTATTTTAG
* *
63562 TCCTTTAACTTTTGTTTTTATTTTTTTAGTCATTTAAGTTTTTGTTTTTGTTGTTTTAG
1 TCCTTTAACTTTT-TTTTT-TTTTTTTAGTCATTTAAGTTTTT-TTTTT-CTATTTTAG
63621 TCCT
1 TCCT
63625 GTAAATTTCT
Statistics
Matches: 94, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
57 2 0.02
58 51 0.54
59 35 0.37
60 6 0.06
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.63
Consensus pattern (55 bp):
TCCTTTAACTTTTTTTTTTTTTTTTAGTCATTTAAGTTTTTTTTTTCTATTTTAG
Found at i:63949 original size:10 final size:10
Alignment explanation
Indices: 63936--63964 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
63926 TACTTTTCAT
63936 TTTTATTTTG
1 TTTTATTTTG
63946 TTTTATTTTG
1 TTTTATTTTG
63956 TTTTATTTT
1 TTTTATTTT
63965 ATCTTTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTTATTTTG
Found at i:69412 original size:64 final size:63
Alignment explanation
Indices: 69221--69442 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 63
69211 GAAGATTATC
* *
69221 AATATCATTTAAG-TTGTTTCACTTGAAACAAATTTTGTCTCTCA-AGACAGTTTCTTTT-A-AA
1 AATAT-ATTTGAGTTTGTTTC-TTTGAAACAAATTTTGTCTCT-AGAGACAGTTTCTTTTGAGAA
69282 A
63 A
* * * * * * *
69283 AA-ATCTTTGAGTTTATTTCTCTGGAAACAATTTTTTGTCTCTCTTGAGACAATTTATTTTGAGA
1 AATATATTTGAGTTTGTTTCT-TTGAAACAA-ATTTTG--TCTCTAGAGACAGTTTCTTTTGAGA
69347 AA
62 AA
*
69349 AATATATTTGAGTTTGTTTCCTTTGAAACAAACTTTGTCTCTAGAGACAGTTTCTTTTGAGAAA
1 AATATATTTGAGTTTGTTT-CTTTGAAACAAATTTTGTCTCTAGAGACAGTTTCTTTTGAGAAA
* * *
69413 CAT-T-CTTGAGTCTGTTTCTTTGGAAACAAA
1 AATATATTTGAGTTTGTTTCTTT-GAAACAAA
69443 ATTTACCATC
Statistics
Matches: 129, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
60 5 0.04
61 20 0.16
62 26 0.20
63 1 0.01
64 43 0.33
65 1 0.01
66 9 0.07
67 22 0.17
68 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (63 bp):
AATATATTTGAGTTTGTTTCTTTGAAACAAATTTTGTCTCTAGAGACAGTTTCTTTTGAGAAA
Found at i:69458 original size:128 final size:128
Alignment explanation
Indices: 69221--69458 Score: 281
Period size: 128 Copynumber: 1.9 Consensus size: 128
69211 GAAGATTATC
*
69221 AATATCATTTAAGTTGTTTCACTTGAAACAAATTTTGTCTCTCAAGACAGTTTCTTTTAAAAAAA
1 AATATCATTTAAGTTGTTTCACTTGAAACAAACTTTGTCTCTCAAGACAGTTTCTTTTAAAAAAA
* ** **
69286 TCTTTGAGTTTATTTCTCTGGAAACAATTTTTTGTCTCTCTTGAGACAATTTATTTTGAGAAA
66 TCTTTGAGTCTATTTCTCTGGAAACAATAATTTACCTCTCTTGAGACAATTTATTTTGAGAAA
* *
69349 AATAT-ATTTGAGTTTGTTTC-CTTTGAAACAAACTTTGTCTCT-AGAGACAGTTTCTTTTGAGA
1 AATATCATTTAAG-TTGTTTCAC-TTGAAACAAACTTTGTCTCTCA-AGACAGTTTCTTTT-AAA
* * *
69411 AACAT-TCTTGAGTCTGTTTCTTTGGAAACAA-AATTTACCATCT-TTGAG
62 AAAATCT-TTGAGTCTATTTCTCTGGAAACAATAATTTACC-TCTCTTGAG
69459 TCTGTTTCCC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
127 8 0.09
128 55 0.59
129 30 0.32
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (128 bp):
AATATCATTTAAGTTGTTTCACTTGAAACAAACTTTGTCTCTCAAGACAGTTTCTTTTAAAAAAA
TCTTTGAGTCTATTTCTCTGGAAACAATAATTTACCTCTCTTGAGACAATTTATTTTGAGAAA
Found at i:69534 original size:133 final size:130
Alignment explanation
Indices: 69355--69598 Score: 289
Period size: 133 Copynumber: 1.8 Consensus size: 130
69345 GAAAAATATA
* * * * * * * *
69355 TTTGAGTTTGTTTCCTTTGAAACAAACTTTGTCTCTAGAGACAGTTTCTTTTGAGAA-AC-ATTC
1 TTTGAGATCGTTTCCATTCAAACAAACTTTCTCCCTAGAGACAGTTTCTTTGGA-AACACAAATC
69418 -TTGAGTCTGTTTCT-TTGGAAACAAAATTTACCATCTTTGAGTCTGTTTCCCTTTAAACAAAAC
65 TTTGAGTCTGTTTCTATT-GAAAC-AAA---ACCATCTTTGAGTC-GTTTCCCTTTAAACAAAAC
69481 AAACATC
124 AAACATC
* * *
69488 TTTGAGATCGTTTCCATTCAAACAAATTTTCTCCCTTGAGGCAGTTTCTTTGGAAACACAAAATC
1 TTTGAGATCGTTTCCATTCAAACAAACTTTCTCCCTAGAGACAGTTTCTTTGGAAACAC-AAATC
69553 TTTGAGTCTGTTTCTATTGAAACAAAACCATCTTTGAGTCGTTTCC
65 TTTGAGTCTGTTTCTATTGAAACAAAACCATCTTTGAGTCGTTTCC
69599 TTGAAACGAA
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
131 6 0.06
132 16 0.17
133 46 0.48
135 6 0.06
136 19 0.20
137 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (130 bp):
TTTGAGATCGTTTCCATTCAAACAAACTTTCTCCCTAGAGACAGTTTCTTTGGAAACACAAATCT
TTGAGTCTGTTTCTATTGAAACAAAACCATCTTTGAGTCGTTTCCCTTTAAACAAAACAAACATC
Found at i:69545 original size:105 final size:95
Alignment explanation
Indices: 69417--69612 Score: 230
Period size: 100 Copynumber: 2.0 Consensus size: 95
69407 GAGAAACATT
* * * *
69417 CTTGAGTCTGTTTCTTTGGAAACAAAATTTACCATCTTTGAGTCTGTTTCCCTTTAAACAAAACA
1 CTTGAGGCAGTTTCTTTGGAAACAAAA---A--ATCTTTGAGTCTGTTTCCATTGAAACAAAAC-
69482 AACATCTTTGAGATCGTTTCCATTCAAACAAATTTTCTCC
60 --CATCTTTGAG-TCGTTTCC-TTCAAACAAATTTTCTCC
* *
69522 CTTGAGGCAGTTTCTTTGGAAACACAAAATCTTTGAGTCTGTTTCTATTGAAACAAAACCATCTT
1 CTTGAGGCAGTTTCTTTGGAAACAAAAAATCTTTGAGTCTGTTTCCATTGAAACAAAACCATCTT
* *
69587 TGAGTCGTTTCCTTGAAACGAATTTT
66 TGAGTCGTTTCCTTCAAACAAATTTT
69613 GTCTCTATTG
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
95 12 0.14
96 8 0.10
97 10 0.12
100 28 0.34
102 1 0.01
105 24 0.29
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (95 bp):
CTTGAGGCAGTTTCTTTGGAAACAAAAAATCTTTGAGTCTGTTTCCATTGAAACAAAACCATCTT
TGAGTCGTTTCCTTCAAACAAATTTTCTCC
Found at i:69566 original size:31 final size:29
Alignment explanation
Indices: 69531--69605 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 29
69521 CCTTGAGGCA
69531 GTTTCTTTGGAAACACAAA-ATCTTTGAGTC
1 GTTTCTTT-GAAACA-AAACATCTTTGAGTC
69561 TGTTTCTATTGAAACAAAACCATCTTTGAGTC
1 -GTTTCT-TTGAAACAAAA-CATCTTTGAGTC
*
69593 GTTTCCTTGAAAC
1 GTTTCTTTGAAAC
69606 GAATTTTGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 10 0.25
31 17 0.43
32 13 0.32
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (29 bp):
GTTTCTTTGAAACAAAACATCTTTGAGTC
Found at i:71190 original size:7 final size:7
Alignment explanation
Indices: 71172--71226 Score: 101
Period size: 7 Copynumber: 7.7 Consensus size: 7
71162 GAATTATGAT
71172 TCTCTCCC
1 TCTCT-CC
71180 TCTCTCC
1 TCTCTCC
71187 TCTCTCC
1 TCTCTCC
71194 TCTCTCC
1 TCTCTCC
71201 TCTCTCC
1 TCTCTCC
71208 TCTCTCC
1 TCTCTCC
71215 TCTCTCC
1 TCTCTCC
71222 TCTCT
1 TCTCT
71227 TATTTTGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
7 42 0.89
8 5 0.11
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (7 bp):
TCTCTCC
Found at i:71855 original size:30 final size:30
Alignment explanation
Indices: 71801--71952 Score: 130
Period size: 30 Copynumber: 5.1 Consensus size: 30
71791 TCCATTAAAC
* *
71801 TTCTATTTTT-TTCTTTTTAATCCTTTAAGT
1 TTCTATTTTTGTT-ATTTTAGTCCTTTAAGT
* * * * *
71831 TTTTGTTTGTGCTATTTTAGTCCTTTGAGT
1 TTCTATTTTTGTTATTTTAGTCCTTTAAGT
* *
71861 TTCTA-TTTT-TTATTTTAGTTCTTTAACT
1 TTCTATTTTTGTTATTTTAGTCCTTTAAGT
* * *
71889 TTCTATTTTTATTTTTTTAGTCATTTAAGT
1 TTCTATTTTTGTTATTTTAGTCCTTTAAGT
* * * *
71919 TTCTGTTTTTGTTGTTTTAGTCCTGTAAAT
1 TTCTATTTTTGTTATTTTAGTCCTTTAAGT
71949 TTCT
1 TTCT
71953 GTTATTACTA
Statistics
Matches: 95, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
28 20 0.21
29 7 0.07
30 67 0.71
31 1 0.01
ACGTcount: A:0.15, C:0.11, G:0.10, T:0.64
Consensus pattern (30 bp):
TTCTATTTTTGTTATTTTAGTCCTTTAAGT
Found at i:71884 original size:28 final size:27
Alignment explanation
Indices: 71843--71903 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
71833 TTGTTTGTGC
* *
71843 TATTTTAGTCCTTTGAGTTTCTATTTTT
1 TATTTTAGTCCTTTAACTTTCTA-TTTT
*
71871 TATTTTAGTTCTTTAACTTTCTATTTT
1 TATTTTAGTCCTTTAACTTTCTATTTT
71898 TATTTT
1 TATTTT
71904 TTTAGTCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.16, C:0.10, G:0.07, T:0.67
Consensus pattern (27 bp):
TATTTTAGTCCTTTAACTTTCTATTTT
Found at i:75083 original size:58 final size:58
Alignment explanation
Indices: 75017--75202 Score: 309
Period size: 58 Copynumber: 3.2 Consensus size: 58
75007 CTACCCAAAG
*
75017 TAGATTTTTTATTATTAATAAACGTAAAAGAAAATAGATTTTTCATTTCTAATTAAAT
1 TAGATTTTTTATTATTAATAAACATAAAAGAAAATAGATTTTTCATTTCTAATTAAAT
* *
75075 TAGATTTTTTATTATTAATAAACATAAAAGAAAATAGATTTTTCATTTTTAATTAAAG
1 TAGATTTTTTATTATTAATAAACATAAAAGAAAATAGATTTTTCATTTCTAATTAAAT
* * *
75133 TAGATTTTTAATTATTAATGAACATAAAAGAAAATAGAATTTTCATTTCTAATTAAAT
1 TAGATTTTTTATTATTAATAAACATAAAAGAAAATAGATTTTTCATTTCTAATTAAAT
*
75191 TAGATTCTTTAT
1 TAGATTTTTTAT
75203 CTTCTATAAT
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 118 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (58 bp):
TAGATTTTTTATTATTAATAAACATAAAAGAAAATAGATTTTTCATTTCTAATTAAAT
Found at i:75127 original size:34 final size:33
Alignment explanation
Indices: 75075--75179 Score: 93
Period size: 34 Copynumber: 3.4 Consensus size: 33
75065 CTAATTAAAT
*
75075 TAGATTTTTTATTATTAATAAACATAAAAGAAAA
1 TAGATTTTTCATTATTAAT-AACATAAAAGAAAA
*
75109 TAGATTTTTCATT-TT--T-A-ATTAAAG----
1 TAGATTTTTCATTATTAATAACATAAAAGAAAA
*
75133 TAGATTTTTAATTATTAATGAACATAAAAGAAAA
1 TAGATTTTTCATTATTAAT-AACATAAAAGAAAA
*
75167 TAGAATTTTCATT
1 TAGATTTTTCATT
75180 TCTAATTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
24 12 0.22
25 2 0.04
27 1 0.02
28 6 0.11
29 2 0.04
30 6 0.11
31 1 0.02
33 2 0.04
34 23 0.42
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (33 bp):
TAGATTTTTCATTATTAATAACATAAAAGAAAA
Found at i:75308 original size:30 final size:30
Alignment explanation
Indices: 75274--75333 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
75264 AAATTATAAC
75274 ATCTAATATTAAAAATATACAAATGGTTAT
1 ATCTAATATTAAAAATATACAAATGGTTAT
75304 ATCTAATATTAAAAATATACAAATGGTTAT
1 ATCTAATATTAAAAATATACAAATGGTTAT
75334 GTTAAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (30 bp):
ATCTAATATTAAAAATATACAAATGGTTAT
Found at i:77127 original size:23 final size:23
Alignment explanation
Indices: 77097--77142 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
77087 TAAACTTAGC
77097 TTCTTTGTATATTACAATTATTG
1 TTCTTTGTATATTACAATTATTG
77120 TTCTTTGTATATTACAATTATTG
1 TTCTTTGTATATTACAATTATTG
77143 AAGTCCCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (23 bp):
TTCTTTGTATATTACAATTATTG
Found at i:78061 original size:30 final size:30
Alignment explanation
Indices: 78006--78150 Score: 116
Period size: 30 Copynumber: 4.8 Consensus size: 30
77996 CTTTAAGTAT
**
78006 TAAAATAGCAAAAATGGACAA-TTAAAAGAC
1 TAAAATAGCAAAAACAGA-AATTTAAAAGAC
*
78036 TAAAATAGCACAAACAGAAATTTAAAA-AGC
1 TAAAATAGCAAAAACAGAAATTTAAAAGA-C
* ** * **
78066 TAGAATAATAAAAATAGAAATTTTGAAGAC
1 TAAAATAGCAAAAACAGAAATTTAAAAGAC
* * * *
78096 -CAAATATCACAAACTGAAATTTAAAAGAC
1 TAAAATAGCAAAAACAGAAATTTAAAAGAC
*
78125 TAAAATGGCAAAAACAGAAACTTTAA
1 TAAAATAGCAAAAACAGAAA-TTTAA
78151 GTCCTAAAAT
Statistics
Matches: 86, Mismatches: 24, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
29 23 0.27
30 57 0.66
31 6 0.07
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (30 bp):
TAAAATAGCAAAAACAGAAATTTAAAAGAC
Done.