Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008990.1 Hibiscus syriacus cultivar Beakdansim tig00112357_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: 317955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:207128 original size:14 final size:14
Alignment explanation
Indices: 207109--207165 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
207099 TTTCATTTCG
207109 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
207123 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
207140 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
207156 CGTTGCGATT
1 CGTTGCGATT
207166 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:207134 original size:33 final size:33
Alignment explanation
Indices: 207092--207184 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
207082 CAAAATCGCA
*
207092 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
207125 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
207158 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
207185 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:209309 original size:19 final size:19
Alignment explanation
Indices: 209285--209383 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
209275 AAAATTGACT
209285 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
209304 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
209322 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
209336 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
209355 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
209375 ATCGCAATG
1 ATCGCAATG
209384 GGAGAATCGC
Statistics
Matches: 71, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
16 4 0.06
18 10 0.14
19 29 0.41
20 18 0.25
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:209361 original size:51 final size:53
Alignment explanation
Indices: 209285--209400 Score: 200
Period size: 51 Copynumber: 2.2 Consensus size: 53
209275 AAAATTGACT
209285 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
209336 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
209389 ATCGCAATGCGA
1 ATCGCAATGCGA
209401 TTTTAATTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 29 0.48
52 6 0.10
53 26 0.43
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:209418 original size:19 final size:19
Alignment explanation
Indices: 209390--209538 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
209380 AATGGGAGAA
* *
209390 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
209409 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
209425 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
209442 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
209458 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
209475 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
209494 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
209510 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
209527 TCCGCATTGCGA
1 T-CGCATTGCGA
209539 AATGTAATGG
Statistics
Matches: 106, Mismatches: 8, Indels: 31
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 18 0.17
18 2 0.02
19 41 0.39
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:209433 original size:14 final size:14
Alignment explanation
Indices: 209414--209468 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
209404 TAATTTCGCA
209414 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
209428 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
209445 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
209461 TTGCGATT
1 TTGCGATT
209469 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:209433 original size:33 final size:33
Alignment explanation
Indices: 209396--209487 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
209386 AGAATCGCAA
*
209396 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
209429 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
209462 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
209488 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:209453 original size:52 final size:52
Alignment explanation
Indices: 209428--209538 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 52
209418 GATTCTCTCG
** *
209428 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTAATTGCGATTTGCATTTCGCA
** *
209480 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTAATTGCGATTTGCATTT-CGCA
209533 TTGCGA
1 TTGCGA
209539 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 48 0.83
53 10 0.17
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTAATTGCGATTTGCATTTCGCA
Found at i:209621 original size:19 final size:19
Alignment explanation
Indices: 209597--209694 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
209587 AAAATTGACT
209597 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
209616 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
209635 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
209649 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
209668 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
209688 ATCGCAA
1 ATCGCAA
209695 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:209726 original size:53 final size:53
Alignment explanation
Indices: 209597--209713 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
209587 AAAATTGACT
209597 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
209649 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
209702 ATCGCAATGCGA
1 ATCGCAATGCGA
209714 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:212045 original size:12 final size:12
Alignment explanation
Indices: 212028--212052 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
212018 TCTTCGGGGA
212028 CTTTTTCTTCTT
1 CTTTTTCTTCTT
212040 CTTTTTCTTCTT
1 CTTTTTCTTCTT
212052 C
1 C
212053 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:212261 original size:24 final size:24
Alignment explanation
Indices: 212227--212273 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
212217 CTGAAACATC
212227 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
212251 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
212274 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:213205 original size:20 final size:20
Alignment explanation
Indices: 212955--213204 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
212945 AAAATTCAGT
* * *
212955 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
212975 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
212995 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
213015 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
213035 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
213055 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
213075 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
213095 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
213115 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
213135 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
213155 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
213175 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
213195 GTTGCGATTT
1 GTTGCGATTT
213205 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:213221 original size:21 final size:21
Alignment explanation
Indices: 213191--213273 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
213181 ATTTTCATAT
*
213191 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
213212 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
213233 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
213254 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
213274 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:213264 original size:42 final size:43
Alignment explanation
Indices: 213171--213269 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
213161 ATTTATGTGT
* *
213171 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
213212 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
213254 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
213270 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:215473 original size:21 final size:21
Alignment explanation
Indices: 215448--215489 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
215438 TTCCCCTTCC
* * *
215448 TCCTCTTCCTTTCCTCCCTTT
1 TCCTCTCCCTTCCCACCCTTT
215469 TCCTCTCCCTTCCCACCCTTT
1 TCCTCTCCCTTCCCACCCTTT
215490 CCTTATCCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.45
Consensus pattern (21 bp):
TCCTCTCCCTTCCCACCCTTT
Found at i:216270 original size:2 final size:2
Alignment explanation
Indices: 216263--216291 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
216253 GGTTTTTAGC
216263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
216292 GTTACTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:218811 original size:41 final size:41
Alignment explanation
Indices: 218754--218882 Score: 213
Period size: 41 Copynumber: 3.1 Consensus size: 41
218744 GAGCATCCAA
*
218754 GGTTCTGTACTCGAAAAACTAGTCGATATTCGAGTTGGTTT
1 GGTTCTATACTCGAAAAACTAGTCGATATTCGAGTTGGTTT
** *
218795 GGTTCTATACTCGAAAAACTAGTCGACGTTCGAGTCGGTTT
1 GGTTCTATACTCGAAAAACTAGTCGATATTCGAGTTGGTTT
218836 GGTTCTATACTCGAAAAACTAGTCGATATTCGAGTTGGTTT
1 GGTTCTATACTCGAAAAACTAGTCGATATTCGAGTTGGTTT
*
218877 GATTCT
1 GGTTCT
218883 TTGTTTACTG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (41 bp):
GGTTCTATACTCGAAAAACTAGTCGATATTCGAGTTGGTTT
Found at i:220803 original size:4 final size:4
Alignment explanation
Indices: 220794--220824 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
220784 TACGAAAAAT
220794 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
220825 AAAAGAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:226343 original size:21 final size:22
Alignment explanation
Indices: 226310--226360 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
226300 TAATTAGTTC
226310 ATTAAAAACTAATGAAA-AATTA
1 ATTAAAAACTAAT-AAACAATTA
*
226332 ATTAAAAA-TAATAAACAATTG
1 ATTAAAAACTAATAAACAATTA
*
226353 TTTAAAAA
1 ATTAAAAA
226361 ACAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 15 0.58
22 8 0.31
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (22 bp):
ATTAAAAACTAATAAACAATTA
Found at i:232883 original size:24 final size:24
Alignment explanation
Indices: 232852--232903 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
232842 TGCATCTTCT
*
232852 TTTCGGATTTATCGGTCACATAGC
1 TTTCGGATTTATCGCTCACATAGC
* *
232876 TTTCGGATTTATCGCTCACTTAGG
1 TTTCGGATTTATCGCTCACATAGC
232900 TTTC
1 TTTC
232904 AAAATTACAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (24 bp):
TTTCGGATTTATCGCTCACATAGC
Found at i:245348 original size:23 final size:21
Alignment explanation
Indices: 245321--245363 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
245311 TTTTAGTGTT
245321 TAGGGTTTAGGGTTTAGAGGTTA
1 TAGGG-TTAGGGTTTA-AGGTTA
*
245344 TAGGGTTATGGTTTAAGGTT
1 TAGGGTTAGGGTTTAAGGTT
245364 TAAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (21 bp):
TAGGGTTAGGGTTTAAGGTTA
Found at i:245350 original size:8 final size:7
Alignment explanation
Indices: 245312--245365 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
245302 TAAGCTATGT
*
245312 TTTAGTG
1 TTTAGGG
245319 TTTAGGG
1 TTTAGGG
245326 TTTAGGG
1 TTTAGGG
245333 TTTAGAGG
1 TTTAG-GG
245341 TTATAGGG
1 TT-TAGGG
*
245349 -TTATGG
1 TTTAGGG
*
245355 TTTAAGG
1 TTTAGGG
245362 TTTA
1 TTTA
245366 AAATTTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
6 4 0.10
7 28 0.68
8 6 0.15
9 3 0.07
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:245828 original size:3 final size:3
Alignment explanation
Indices: 245820--245852 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
245810 GAATTGGGTT
245820 TTG TTG TTG TTG TTG TTG TTG TTG TTG TATG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T-TG TT
245853 AGTTAGGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.00, G:0.30, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:248092 original size:21 final size:21
Alignment explanation
Indices: 248068--248121 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
248058 AAGTTTATCA
* *
248068 AAATATTATAAAATGGTCTTT
1 AAATATTATAAAATGATCATT
248089 AAATA-TATCAAAATGATCATT
1 AAATATTAT-AAAATGATCATT
*
248110 ACTATATTATAA
1 A-AATATTATAA
248122 CATGCATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (21 bp):
AAATATTATAAAATGATCATT
Found at i:248194 original size:29 final size:31
Alignment explanation
Indices: 248133--248194 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
248123 ATGCATGGAT
* *
248133 CATTTTATAATAATTTGATAAGTTTAATGAC
1 CATTTTATAATAATTTGAAAAGTTTAATAAC
*
248164 CATTTTATAAT-ATTT-AAAAGTTTATTAAC
1 CATTTTATAATAATTTGAAAAGTTTAATAAC
248193 CA
1 CA
248195 AAAAAGCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.46
30 4 0.14
31 11 0.39
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (31 bp):
CATTTTATAATAATTTGAAAAGTTTAATAAC
Found at i:248390 original size:29 final size:29
Alignment explanation
Indices: 248335--248391 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
248325 TTTATTATTC
* *
248335 AAGTTAAATTGACCATTCATATAAAAAGA
1 AAGTTAAATTGACCACTCAAATAAAAAGA
*
248364 AAGTTAAATTGATCACTCAAATGAAAAA
1 AAGTTAAATTGACCACTCAAAT-AAAAA
248392 TTAAATTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (29 bp):
AAGTTAAATTGACCACTCAAATAAAAAGA
Found at i:252587 original size:12 final size:12
Alignment explanation
Indices: 252572--252604 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
252562 ATATATATAT
252572 ATATAATTGTTG
1 ATATAATTGTTG
252584 ATATAATTGTTG
1 ATATAATTGTTG
252596 ATATAATTG
1 ATATAATTG
252605 ATTATTGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (12 bp):
ATATAATTGTTG
Found at i:252887 original size:4 final size:4
Alignment explanation
Indices: 252878--252909 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
252868 TCCATATTCC
252878 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
252910 GAATACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:254693 original size:34 final size:34
Alignment explanation
Indices: 254627--254694 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
254617 TTTTCACCCT
254627 AAACCCGAACCCGACCCGAATATCACACTTAAAA
1 AAACCCGAACCCGACCCGAATATCACACTTAAAA
*
254661 AAACCCG-ACCCGACCCGAATATCACACTTTAAA
1 AAACCCGAACCCGACCCGAATATCACACTTAAAA
254694 A
1 A
254695 TCCCGTCCCG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.43, C:0.35, G:0.09, T:0.13
Consensus pattern (34 bp):
AAACCCGAACCCGACCCGAATATCACACTTAAAA
Found at i:256009 original size:15 final size:14
Alignment explanation
Indices: 255976--256040 Score: 51
Period size: 15 Copynumber: 4.5 Consensus size: 14
255966 GGGTTTTTAG
*
255976 AAATATTTTTAGTT
1 AAATATTTTTAATT
255990 AAATATTTTTTAATT
1 AAATA-TTTTTAATT
* **
256005 TAATAAATTTAATT
1 AAATATTTTTAATT
256019 -AATATCATTTTAATT
1 AAATAT--TTTTAATT
*
256034 ATATATT
1 AAATATT
256041 AATAAAATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
13 4 0.10
14 13 0.32
15 19 0.47
16 4 0.10
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
AAATATTTTTAATT
Found at i:258685 original size:60 final size:58
Alignment explanation
Indices: 258611--258752 Score: 153
Period size: 59 Copynumber: 2.4 Consensus size: 58
258601 TAATTAATAA
* * *
258611 TCGGGTGACCATTTTGTAACTTTAAATAGTCAAGAGATTCAATAAAACAACATCATATAG
1 TCGGG-GACCATTTTGTAACTTTAAATAGTC-AGAGAATCAACAAAACAACACCATATAG
* * * * *
258671 TCGGAGGACCATTTTGTAACATTT-AATAGTCGGGGAATCAACAAAGCAATACCCTATAG
1 TCGG-GGACCATTTTGTAAC-TTTAAATAGTCAGAGAATCAACAAAACAACACCATATAG
258730 TCGGGGACCATTTGTGT-ACTTTA
1 TCGGGGACCATTT-TGTAACTTTA
258753 TTTTAAATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
57 3 0.04
58 11 0.16
59 27 0.39
60 25 0.36
61 4 0.06
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (58 bp):
TCGGGGACCATTTTGTAACTTTAAATAGTCAGAGAATCAACAAAACAACACCATATAG
Found at i:261002 original size:31 final size:31
Alignment explanation
Indices: 260909--261002 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
260899 CATCGTTATA
* * *
260909 GAGTAAAATAGGAAAGAGTGTAAAGTTTAAT
1 GAGTAAAATAAGAAAGAGTGTAAAGTTCAGT
* * * * * *
260940 GAGCAGAAT-AGAAACACTG-AAAGTACGGT
1 GAGTAAAATAAGAAAGAGTGTAAAGTTCAGT
260969 GAGTAAAATAAGAAAGAGTGTAAAGTTCAGT
1 GAGTAAAATAAGAAAGAGTGTAAAGTTCAGT
261000 GAG
1 GAG
261003 GAAATATGTA
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
29 13 0.28
30 15 0.33
31 18 0.39
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.20
Consensus pattern (31 bp):
GAGTAAAATAAGAAAGAGTGTAAAGTTCAGT
Found at i:261008 original size:30 final size:30
Alignment explanation
Indices: 260913--261008 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
260903 GTTATAGAGT
* * *
260913 AAAATAGGAAAGAGTGTAAAGTTTAATGAG
1 AAAATAAGAAAGAGTGTAAAGTTCAGTGAG
* * * * *
260943 CAGAAT-AGAAACACTG-AAAGTACGGTGAG
1 -AAAATAAGAAAGAGTGTAAAGTTCAGTGAG
260972 TAAAATAAGAAAGAGTGTAAAGTTCAGTGAG
1 -AAAATAAGAAAGAGTGTAAAGTTCAGTGAG
*
261003 GAAATA
1 AAAATA
261009 TGTAATTTAC
Statistics
Matches: 48, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
29 13 0.27
30 20 0.42
31 15 0.31
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.20
Consensus pattern (30 bp):
AAAATAAGAAAGAGTGTAAAGTTCAGTGAG
Found at i:269078 original size:22 final size:23
Alignment explanation
Indices: 269041--269087 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
269031 AACCCTAAAC
269041 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
269064 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
269086 AA
1 AA
269088 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:272977 original size:9 final size:9
Alignment explanation
Indices: 272965--272990 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
272955 TGATTAACTA
272965 AATTAACCG
1 AATTAACCG
272974 AATTAACCG
1 AATTAACCG
272983 AATTAACC
1 AATTAACC
272991 AAAAATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:274585 original size:7 final size:7
Alignment explanation
Indices: 274575--274601 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
274565 ACTAAAAAGA
274575 AAAATAT
1 AAAATAT
274582 AAAATAT
1 AAAATAT
274589 AAAATAT
1 AAAATAT
274596 AAAATA
1 AAAATA
274602 GTTATATGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATAT
Found at i:278504 original size:2 final size:2
Alignment explanation
Indices: 278497--278523 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
278487 TTTTAAATTC
278497 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
278524 ATTTTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:279898 original size:2 final size:2
Alignment explanation
Indices: 279891--279948 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
279881 ATGGTGTTGC
279891 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
279933 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
279949 CTTTTAGCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:280140 original size:2 final size:2
Alignment explanation
Indices: 280133--280165 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
280123 ATATCATCTT
280133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
280166 CATTTGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:283213 original size:14 final size:16
Alignment explanation
Indices: 283175--283215 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
283165 TTGTGTAATT
283175 TATTTATTTATTTATAA
1 TATTTATTT-TTTATAA
283192 TATTTATTTTTTA-AA
1 TATTTATTTTTTATAA
283207 T-TTTATTTT
1 TATTTATTTT
283216 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 4 0.17
17 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTATTTTTTATAA
Found at i:284663 original size:44 final size:44
Alignment explanation
Indices: 284530--284672 Score: 132
Period size: 44 Copynumber: 3.3 Consensus size: 44
284520 ATATCGAAAA
* * * *
284530 TTTAA-AATAATTAAAATAATATATTTTTTAATAATTTATTATATT
1 TTTAATAATAATTTAAAT-AT-TAATTTTTAAAAATTTATAATATT
* * * ** * *
284575 GTTAATAAT-TTTTAAATATTAATTGTT--AGTTTTATGATACT
1 TTTAATAATAATTTAAATATTAATTTTTAAAAATTTATAATATT
*
284616 TTTAATAATAATTTAAATATTAATTTTTAAAAATTTAAAATATT
1 TTTAATAATAATTTAAATATTAATTTTTAAAAATTTATAATATT
284660 TTTAATAATAATT
1 TTTAATAATAATT
284673 CCGTCCTGAT
Statistics
Matches: 76, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
41 17 0.22
42 16 0.21
43 6 0.08
44 24 0.32
45 10 0.13
46 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (44 bp):
TTTAATAATAATTTAAATATTAATTTTTAAAAATTTATAATATT
Found at i:284672 original size:22 final size:25
Alignment explanation
Indices: 284615--284672 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 25
284605 TTTATGATAC
284615 TTTTAATAATAATTTAAATATTAAT
1 TTTTAATAATAATTTAAATATTAAT
284640 TTTT-A-AA-AATTTAAA-A-T-AT
1 TTTTAATAATAATTTAAATATTAAT
284659 TTTTAATAATAATT
1 TTTTAATAATAATT
284673 CCGTCCTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
19 6 0.20
20 2 0.07
21 3 0.10
22 12 0.40
23 2 0.07
24 1 0.03
25 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAATAATAATTTAAATATTAAT
Found at i:287847 original size:21 final size:20
Alignment explanation
Indices: 287799--287839 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
287789 TGAGCCGTGA
287799 GATGAACCCGGAAACGAAGG
1 GATGAACCCGGAAACGAAGG
287819 GATGAACCCGGAAACGAAGG
1 GATGAACCCGGAAACGAAGG
287839 G
1 G
287840 CGTGAACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.37, T:0.05
Consensus pattern (20 bp):
GATGAACCCGGAAACGAAGG
Found at i:289485 original size:62 final size:62
Alignment explanation
Indices: 289407--289532 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
289397 TATCCATCCC
289407 TACTTGTCAAAGGTTATAGTTTAGAGATTAATTTAGAATGATGATAGTTTAGAAATCAAATA
1 TACTTGTCAAAGGTTATAGTTTAGAGATTAATTTAGAATGATGATAGTTTAGAAATCAAATA
**
289469 TACTTGTCTGAGGTTATAGTTTAGAGATTAATTTAGAATGATGATAGTTTAGAAATCAAATA
1 TACTTGTCAAAGGTTATAGTTTAGAGATTAATTTAGAATGATGATAGTTTAGAAATCAAATA
289531 TA
1 TA
289533 ATATATAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (62 bp):
TACTTGTCAAAGGTTATAGTTTAGAGATTAATTTAGAATGATGATAGTTTAGAAATCAAATA
Found at i:295698 original size:13 final size:13
Alignment explanation
Indices: 295680--295705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295670 AAAGTGCCAC
295680 ATTGAATTTATTT
1 ATTGAATTTATTT
295693 ATTGAATTTATTT
1 ATTGAATTTATTT
295706 TTTAAGTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTGAATTTATTT
Found at i:297195 original size:60 final size:59
Alignment explanation
Indices: 297050--297212 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 59
297040 ACAATTTCAC
* * * *
297050 CCTCAAACTATGACTTTAATTTTAAATTAGTCCTTAAACTTTTAATAGTCCAATTCAAT
1 CCTCAAACTATGAATCTAATTCTAAATTAGTCCTTAAACTTTTAACAGTCCAATTCAAT
* * * * * **
297109 TCTCAAACTACGAATCTAATTCTAAATTAGTCCTTAAACTTTTGAACATTCGAGTTTTAT
1 CCTCAAACTATGAATCTAATTCTAAATTAGTCCTTAAACTTTT-AACAGTCCAATTCAAT
* * *
297169 CCTTAAACTATGAATCTCATTCTAAATT-GATCCCTAAACTTTTA
1 CCTCAAACTATGAATCTAATTCTAAATTAG-TCCTTAAACTTTTA
297213 CATCTTTTAA
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 40 0.47
60 46 0.53
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (59 bp):
CCTCAAACTATGAATCTAATTCTAAATTAGTCCTTAAACTTTTAACAGTCCAATTCAAT
Found at i:298579 original size:60 final size:61
Alignment explanation
Indices: 298420--298584 Score: 187
Period size: 60 Copynumber: 2.7 Consensus size: 61
298410 TTATGACTTT
* * *
298420 CATTTTAAATTAGTCCTTAAACTTTTAAATAGTTT-AATTTTATCCTCAAACTATGACTCTA
1 CATTCTAAATTAGTCCTTAAACTTTTAAAT-CTTTCAATTTTATCCTCAAACTATGAATCTA
* * *
298481 -ATTCTAAATTAATCCTTAAACTTTTGAA-CATTCAAATTTTATTCCT-AAACTATGAATC-A
1 CATTCTAAATTAGTCCTTAAACTTTTAAATCTTTC-AATTTTA-TCCTCAAACTATGAATCTA
* * *
298540 CATTCTAAATTGGTCCCTAAACTTTTAAATCTTTCAATTTCATCC
1 CATTCTAAATTAGTCCTTAAACTTTTAAATCTTTCAATTTTATCC
298585 AAATATGCAA
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.02
59 4 0.05
60 73 0.84
61 8 0.09
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (61 bp):
CATTCTAAATTAGTCCTTAAACTTTTAAATCTTTCAATTTTATCCTCAAACTATGAATCTA
Found at i:298703 original size:62 final size:62
Alignment explanation
Indices: 298606--298732 Score: 200
Period size: 62 Copynumber: 2.0 Consensus size: 62
298596 CCATTTCAAT
* * * **
298606 TAAAATTATGATTGTAGGGTTACTATATCTATTATATATAAAATTATTGATTGGGTTTAATA
1 TAAAATTATGATCGTAGGGTTACTATATCTATTATATATAAAACTATTGATCGACTTTAATA
*
298668 TAAAATTATGATCGTATGGTTACTATATCTATTATATATAAAACTATTGATCGACTTTAATA
1 TAAAATTATGATCGTAGGGTTACTATATCTATTATATATAAAACTATTGATCGACTTTAATA
298730 TAA
1 TAA
298733 CGAATCGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (62 bp):
TAAAATTATGATCGTAGGGTTACTATATCTATTATATATAAAACTATTGATCGACTTTAATA
Found at i:299059 original size:2 final size:2
Alignment explanation
Indices: 299052--299088 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
299042 TTTTTGCCGT
299052 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
299089 TCTTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:300763 original size:5 final size:5
Alignment explanation
Indices: 300753--300777 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
300743 CTAAACGAGT
300753 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
300778 CTAGGGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:309250 original size:180 final size:181
Alignment explanation
Indices: 308945--309295 Score: 508
Period size: 180 Copynumber: 1.9 Consensus size: 181
308935 GTCTTCCCTC
*
308945 AAAATCGTAACCTTCTCTATTCCAACATTGTTGTTCCTCACCACCTTCAACTTATCGTTGGAGCT
1 AAAATCGTAACCTTCTCTATCCCAACA-T-TTGTTCCTCACCACCTTCAACTTATCGTTGGAGCT
* *
309010 AGATCTCTTCGAGACGGCATGATCCGAACCGATCCGCTTCATCTGAACGGGCTTCTTGTTAAATC
64 AGATCTCTTCGAAACGGCATGATCCGAACCGACCCGCTTCATCTGAACGGGCTTCTTGTTAAATC
* *
309075 TACCGT-TCCCATGATAACTAGGGCTAAATCCGCCGTTTCCGCAGCCTCGCCTA
129 TACCGTGT-CCATGATAACCAGGGCTAAATCCACCGTTTCCGCAGCCTCGCCTA
* *
309128 AAAATCGTAACCTTCTCTATCCCAACA-TTGTTCCTCACCACCTTCAGCTTGTCGTTGGAGCTAG
1 AAAATCGTAACCTTCTCTATCCCAACATTTGTTCCTCACCACCTTCAACTTATCGTTGGAGCTAG
* * * * * * *
309192 ATCTTTTCGAAACTGCTTGATCCGACCCGACCCGCTTCTTCTGAATGGGCTTCTTGTTAAATCTC
66 ATCTCTTCGAAACGGCATGATCCGAACCGACCCGCTTCATCTGAACGGGCTTCTTGTTAAATCTA
* * *
309257 CCGTGTCCGTGATAACCAGGGTTGAATCCACCGTTTCCG
131 CCGTGTCCATGATAACCAGGGCTAAATCCACCGTTTCCG
309296 TATCTCCGGC
Statistics
Matches: 150, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
180 123 0.82
181 1 0.01
183 26 0.17
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (181 bp):
AAAATCGTAACCTTCTCTATCCCAACATTTGTTCCTCACCACCTTCAACTTATCGTTGGAGCTAG
ATCTCTTCGAAACGGCATGATCCGAACCGACCCGCTTCATCTGAACGGGCTTCTTGTTAAATCTA
CCGTGTCCATGATAACCAGGGCTAAATCCACCGTTTCCGCAGCCTCGCCTA
Found at i:310415 original size:35 final size:35
Alignment explanation
Indices: 310346--310418 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
310336 CAGAGCCAGA
* * **
310346 GATAATTCCGGCAGCTCCGGATCTTCCTGGATATC
1 GATAATTCCGGCAGCTCCGGAACTTACTCAATATC
*
310381 GATAATTCCGGCTGCTCCGGAACTTACTCAATATC
1 GATAATTCCGGCAGCTCCGGAACTTACTCAATATC
310416 GAT
1 GAT
310419 TTCGATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (35 bp):
GATAATTCCGGCAGCTCCGGAACTTACTCAATATC
Done.