Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008929.1 Hibiscus syriacus cultivar Beakdansim tig00112234_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: 268382
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:213244 original size:20 final size:20
Alignment explanation
Indices: 213219--213268 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
213209 TTGAAGATGA
213219 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
213239 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
213259 TTGCGATTTT
1 TTGCGATTTT
213269 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:214158 original size:24 final size:24
Alignment explanation
Indices: 214131--214184 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
214121 GTGTTCGAAA
*
214131 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
214155 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
214179 TTTGAT
1 TTTGAT
214185 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:214376 original size:12 final size:12
Alignment explanation
Indices: 214359--214395 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
214349 ATATAATCCT
214359 GAAGAAGAAAAA
1 GAAGAAGAAAAA
214371 GAAGAAGAAAAA
1 GAAGAAGAAAAA
214383 GAAGAAGAAAAA
1 GAAGAAGAAAAA
214395 G
1 G
214396 TCCTCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:216711 original size:19 final size:19
Alignment explanation
Indices: 216689--216786 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
216679 GGAAATTACT
216689 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
216708 ATCGCAA----AGA-GAGA
1 ATCGCAATGCGAAATGAAA
216722 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
216741 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
216755 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
216774 ATCGCAACGCGAA
1 ATCGCAATGCGAA
216787 TTTAATTTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 19 0.32
15 3 0.05
16 2 0.03
17 2 0.03
18 3 0.05
19 31 0.52
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:216781 original size:33 final size:33
Alignment explanation
Indices: 216689--216782 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
216679 GGAAATTACT
*
216689 ATCGCAATGCGAAATGAAAATCGCAAAGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
216722 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
216755 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
216783 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:216836 original size:19 final size:19
Alignment explanation
Indices: 216812--216857 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
216802 CGATTCTCTT
216812 GTTGCGATTTTCATTTCGC
1 GTTGCGATTTTCATTTCGC
216831 GTTGCGATTTTCATTTCGC
1 GTTGCGATTTTCATTTCGC
*
216850 ATTGCGAT
1 GTTGCGAT
216858 AGTACTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
GTTGCGATTTTCATTTCGC
Found at i:216983 original size:14 final size:14
Alignment explanation
Indices: 216964--217000 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
216954 CATCAATTAA
216964 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
216978 ACAAATCACCTTTT
1 ACAAATCAACTTTT
216992 ACAAATCAA
1 ACAAATCAA
217001 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:218423 original size:21 final size:21
Alignment explanation
Indices: 218357--218423 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
218347 GTGAATCAGG
*
218357 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
218377 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
218399 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
218420 CTCT
1 CTCT
218424 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:218442 original size:42 final size:41
Alignment explanation
Indices: 218357--218479 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
218347 GTGAATCAGG
* * * *
218357 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
218399 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
218441 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
218480 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:220498 original size:20 final size:19
Alignment explanation
Indices: 220467--220588 Score: 84
Period size: 20 Copynumber: 6.8 Consensus size: 19
220457 TCTTTTGGTT
220467 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
220486 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
220507 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
220526 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
220540 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
220559 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
220573 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
220589 TGCAATTTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 4 0.05
19 21 0.26
20 29 0.36
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:220535 original size:14 final size:14
Alignment explanation
Indices: 220516--220571 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
220506 GGAAATGACT
220516 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
220530 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
220547 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
220563 ATCGCAACG
1 ATCGCAACG
220572 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:220549 original size:33 final size:33
Alignment explanation
Indices: 220492--220588 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
220482 ACGAGATAAT
220492 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
220526 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
220559 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
220589 TGCAATTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:220647 original size:20 final size:19
Alignment explanation
Indices: 220600--220652 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
220590 GCAATTTTGG
**
220600 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATAGTTA
220619 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
220638 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
220653 TTTCATTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:221227 original size:20 final size:20
Alignment explanation
Indices: 221175--221246 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
221165 GCTATGTAAA
* *
221175 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
221195 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
221215 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
221236 TCGCATTGCGA
1 TCGCATTGCGA
221247 ATTATGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 3 0.07
20 30 0.65
21 13 0.28
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:221260 original size:21 final size:21
Alignment explanation
Indices: 221236--221308 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
221226 TTTTCCTAAT
* *
221236 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
221257 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
221277 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
221298 TTGCATTGCGA
1 TCGCAATGCGA
221309 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:221366 original size:20 final size:21
Alignment explanation
Indices: 221318--221366 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
221308 ATAGTCAGTA
*
221318 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
221339 TTGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
221359 TCGCATTG
1 TCGCATTG
221367 TGAATTGGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:223580 original size:2 final size:2
Alignment explanation
Indices: 223573--223607 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
223563 AATCGAAATG
223573 AT AT AT AT 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 AT AT AT AT A
223608 AGTATGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:224408 original size:25 final size:25
Alignment explanation
Indices: 224375--224431 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
224365 CTGTAGTGAC
224375 AGCATATGTATATACTCAATGTACT
1 AGCATATGTATATACTCAATGTACT
224400 AGCATATGTATATACTCAATGTACT
1 AGCATATGTATATACTCAATGTACT
*
224425 CGCATAT
1 AGCATAT
224432 CTTTAGTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (25 bp):
AGCATATGTATATACTCAATGTACT
Found at i:225299 original size:30 final size:30
Alignment explanation
Indices: 225251--225307 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
225241 AATATAAATT
*
225251 TTAAATTTATTTTAATAAATAT-TAAATATA
1 TTAAATATATTTTAATAAA-ATCTAAATATA
* *
225281 TTAAATATCTTTTTATAAAATCTAAAT
1 TTAAATATATTTTAATAAAATCTAAAT
225308 CTAAACTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAAATATATTTTAATAAAATCTAAATATA
Found at i:226628 original size:19 final size:19
Alignment explanation
Indices: 226606--226645 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
226596 GTGTCTAGCT
*
226606 TTGAATAGAGACAATGAGA
1 TTGAATAGAAACAATGAGA
*
226625 TTGAATAGAAACTATGAGA
1 TTGAATAGAAACAATGAGA
226644 TT
1 TT
226646 ATTGATAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28
Consensus pattern (19 bp):
TTGAATAGAAACAATGAGA
Found at i:226989 original size:34 final size:37
Alignment explanation
Indices: 226946--227022 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 37
226936 AATCATTCTA
*
226946 AAAATTATATAATATATGAG-TTTT-TAAA-TA-TTTTG
1 AAAA-TATATAATATAT-AGCTTTTGAAAATTAGTTTTG
226981 AAAATATATAATATATAGCTTTTGAAAATTAGTTTTG
1 AAAATATATAATATATAGCTTTTGAAAATTAGTTTTG
227018 AAAAT
1 AAAAT
227023 TAGTTTTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 2 0.05
34 16 0.43
35 7 0.19
36 2 0.05
37 10 0.27
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.44
Consensus pattern (37 bp):
AAAATATATAATATATAGCTTTTGAAAATTAGTTTTG
Found at i:227065 original size:13 final size:13
Alignment explanation
Indices: 227000--227108 Score: 79
Period size: 13 Copynumber: 8.7 Consensus size: 13
226990 AATATATAGC
*
227000 TTTTGAAAATTAG
1 TTTTTAAAATTAG
*
227013 TTTTGAAAATTAG
1 TTTTTAAAATTAG
*
227026 TTTTTAAAAATA-
1 TTTTTAAAATTAG
* *
227038 TATGTT-ATA-TAG
1 T-TTTTAAAATTAG
227050 TTTTTAAAATTAG
1 TTTTTAAAATTAG
227063 TTTTT-AAATATA-
1 TTTTTAAAAT-TAG
* *
227075 TATATT-ATA-TAG
1 T-TTTTAAAATTAG
227087 TTTTTAAAATTAG
1 TTTTTAAAATTAG
227100 TTTTTAAAA
1 TTTTTAAAA
227109 GTATATATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
11 10 0.13
12 14 0.18
13 53 0.69
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.51
Consensus pattern (13 bp):
TTTTTAAAATTAG
Found at i:227153 original size:38 final size:37
Alignment explanation
Indices: 227010--227210 Score: 233
Period size: 37 Copynumber: 5.3 Consensus size: 37
227000 TTTTGAAAAT
* *
227010 TAGTTTTGAAAATTAGTTTTTAAAAATATATGTTATA
1 TAGTTTTAAAAATTAGTTTTTAAAAATATATATTATA
* *
227047 TAGTTTTTAAAATTAGTTTTTAAATATATATATTATA
1 TAGTTTTAAAAATTAGTTTTTAAAAATATATATTATA
* *
227084 TAGTTTTTAAAATTAGTTTTTAAAAGTATATATATTATC
1 TAGTTTTAAAAATTAGTTTTTAAAA--ATATATATTATA
* *
227123 TAGTTTTAAAAATTATTCTTTTAAAAATATATAATATA
1 TAGTTTTAAAAATTAGT-TTTTAAAAATATATATTATA
* * * * *
227161 T-GATTTTGAAAATTATTTTTTTTAAAACATATATTGTA
1 TAG-TTTTAAAAATTA-GTTTTTAAAAATATATATTATA
227199 TAGTTTTAAAAA
1 TAGTTTTAAAAA
227211 AATGTTTTTC
Statistics
Matches: 143, Mismatches: 15, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
37 59 0.41
38 47 0.33
39 29 0.20
40 8 0.06
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.50
Consensus pattern (37 bp):
TAGTTTTAAAAATTAGTTTTTAAAAATATATATTATA
Found at i:227241 original size:4 final size:4
Alignment explanation
Indices: 227221--227286 Score: 62
Period size: 4 Copynumber: 15.8 Consensus size: 4
227211 AATGTTTTTC
* *
227221 ATTT ACTT ATAT ATTT ATTT ATTTT ATTT -TATT ATTT ATTT ATCTT ATTT
1 ATTT ATTT ATTT ATTT ATTT A-TTT ATTT AT-TT ATTT ATTT AT-TT ATTT
*
227271 ATTAT TTTT ATTT ATT
1 ATT-T ATTT ATTT ATT
227287 ATTAATTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 1 0.02
4 38 0.75
5 12 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:227255 original size:17 final size:17
Alignment explanation
Indices: 227235--227294 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
227225 ACTTATATAT
227235 TTATTTATTTTATTTTA
1 TTATTTATTTTATTTTA
*
227252 TTATTTA-TTTATCTTA
1 TTATTTATTTTATTTTA
227268 TT-TATTATTTT-TATTTA
1 TTAT-TTATTTTAT-TTTA
*
227285 TTATTAATTT
1 TTATTTATTT
227295 CTTTTTCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 1 0.03
16 14 0.39
17 20 0.56
18 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTATTTTATTTTA
Found at i:227289 original size:13 final size:12
Alignment explanation
Indices: 227227--227286 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
227217 TTTCATTTAC
* *
227227 TTATATATTTAT
1 TTATTTATTTTT
*
227239 TTATTTTATTTTA
1 TTA-TTTATTTTT
*
227252 TTATTTATTTATC
1 TTATTTATTT-TT
227265 TTATTTATTATTT
1 TTATTTATT-TTT
227278 TTATTTATT
1 TTATTTATT
227287 ATTAATTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.25
13 29 0.73
14 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:233688 original size:49 final size:49
Alignment explanation
Indices: 233616--233720 Score: 201
Period size: 49 Copynumber: 2.1 Consensus size: 49
233606 AGATTAGTGT
233616 TGAGGGGGATAGAGGCACGTCTAGAAACACACGATTACATGTGAAATAC
1 TGAGGGGGATAGAGGCACGTCTAGAAACACACGATTACATGTGAAATAC
*
233665 TGAGGGGGATAGAGGCACGTCTAGCAACACACGATTACATGTGAAATAC
1 TGAGGGGGATAGAGGCACGTCTAGAAACACACGATTACATGTGAAATAC
233714 TGAGGGG
1 TGAGGGG
233721 AAAATACAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.18
Consensus pattern (49 bp):
TGAGGGGGATAGAGGCACGTCTAGAAACACACGATTACATGTGAAATAC
Found at i:237563 original size:7 final size:7
Alignment explanation
Indices: 237547--237594 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
237537 AATCAAGAAC
237547 AAAAAGAG
1 AAAAA-AG
237555 AAAAAAG
1 AAAAAAG
237562 AAAAAAG
1 AAAAAAG
*
237569 AAAAGAG
1 AAAAAAG
*
237576 AAAATA-
1 AAAAAAG
*
237582 AAAAGAG
1 AAAAAAG
237589 AAAAAA
1 AAAAAA
237595 CAAAGGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 5 0.14
7 25 0.71
8 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:237570 original size:14 final size:14
Alignment explanation
Indices: 237547--237594 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
237537 AATCAAGAAC
*
237547 AAAAAGAGAAAAAAG
1 AAAAA-AGAAAAGAG
237562 AAAAAAGAAAAGAG
1 AAAAAAGAAAAGAG
*
237576 AAAATA-AAAAGAG
1 AAAAAAGAAAAGAG
237589 AAAAAA
1 AAAAAA
237595 CAAAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 12 0.40
14 13 0.43
15 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAGAG
Found at i:237579 original size:13 final size:12
Alignment explanation
Indices: 237555--237604 Score: 59
Period size: 13 Copynumber: 4.1 Consensus size: 12
237545 ACAAAAAGAG
237555 AAAAAAGA-AAA
1 AAAAAAGAGAAA
237566 AAGAAAAGAGAAA
1 AA-AAAAGAGAAA
237579 ATAAAAAGAGAAA
1 A-AAAAAGAGAAA
237592 AAACAAAG-GAAA
1 AAA-AAAGAGAAA
237604 A
1 A
237605 TTGAAGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.06
12 13 0.37
13 19 0.54
14 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:237584 original size:25 final size:25
Alignment explanation
Indices: 237555--237605 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
237545 ACAAAAAGAG
*
237555 AAAAA-AGAAAAAAGAAAAGAGAAAAT
1 AAAAAGAGAAAAAA-CAAAG-GAAAAT
237581 AAAAAGAGAAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAACAAAGGAAAAT
237606 TGAAGAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 9 0.39
27 8 0.35
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (25 bp):
AAAAAGAGAAAAAACAAAGGAAAAT
Found at i:240159 original size:36 final size:36
Alignment explanation
Indices: 240058--240219 Score: 234
Period size: 36 Copynumber: 4.5 Consensus size: 36
240048 CTTTGAGATT
* * *
240058 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
** * *
240094 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
**
240131 GTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
240167 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
240203 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
240220 ATCTTTGAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 82 0.73
37 30 0.27
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:240162 original size:21 final size:21
Alignment explanation
Indices: 240136--240198 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
240126 AGACAGTTTA
240136 TCTTGAAACAAATTTTGTCTC
1 TCTTGAAACAAATTTTGTCTC
* *
240157 TCTTGAGAC--A-GTT-TC-C
1 TCTTGAAACAAATTTTGTCTC
240173 -CTTGAAACAAATTTTGTCTC
1 TCTTGAAACAAATTTTGTCTC
240193 TCTTGA
1 TCTTGA
240199 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 7 0.22
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 13 0.41
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (21 bp):
TCTTGAAACAAATTTTGTCTC
Found at i:240169 original size:73 final size:72
Alignment explanation
Indices: 240058--240392 Score: 346
Period size: 73 Copynumber: 4.7 Consensus size: 72
240048 CTTTGAGATT
* ** * *
240058 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTACCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
240123 TTGAGACA
65 TTGAGACA
* * *
240131 GTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
1 GTTTACCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
240196 TGAGACA
66 TGAGACA
* * * * *
240203 GTTTCCCTTGAAACAAA----ATCT---TTGA-ATATGTTTTCCTTGAAACAAATTTCGTCTCTC
1 GTTTACCTTGAAACAAATTTCGTCTCCCTTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCTC
240260 TTGAGACA
65 TTGAGACA
* * * * * * *
240268 GTTT-CTTTTGGAAATAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTTTCTCT
1 GTTTAC-CTT-GAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCT
240332 CTTGAGACA
64 CTTGAGACA
* * * *
240341 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 GTTTACCTTGAAACAAA-TTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACA
240393 CAAAAAAACC
Statistics
Matches: 223, Mismatches: 26, Indels: 26
0.81 0.09 0.09
Matches are distributed among these distances:
64 3 0.01
65 44 0.20
66 7 0.03
68 3 0.01
70 3 0.01
72 43 0.19
73 117 0.52
74 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (72 bp):
GTTTACCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCT
TGAGACA
Found at i:240325 original size:36 final size:36
Alignment explanation
Indices: 240234--240392 Score: 239
Period size: 37 Copynumber: 4.4 Consensus size: 36
240224 TTGAATATGT
*
240234 TTTC-CTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
240269 TTTCTTTTGGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTT-GAAACAAATTTTGTCTCTCTTGAGACAG
* *
240306 TTTCTCTTGAAATAAATTTTTTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
240342 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
240379 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
240393 CAAAAAAACC
Statistics
Matches: 112, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
35 4 0.04
36 43 0.38
37 65 0.58
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:240347 original size:174 final size:175
Alignment explanation
Indices: 240048--240392 Score: 604
Period size: 174 Copynumber: 2.0 Consensus size: 175
240038 TATCAATCGC
* *
240048 CTTTGAGATTGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGT
1 CTTTGAGATTGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAATAAAT
240113 TTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
66 TTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
240178 AACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
131 AACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
*
240222 CTTTGA-ATATGTTTTCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTTTTGGAAATAAA
1 CTTTGAGAT-TGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAATAAA
* * *
240286 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTTTCTCTCTTGAGACAGTTTCCCTTG
65 TTTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
240351 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
130 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
240393 CAAAAAAACC
Statistics
Matches: 162, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
173 2 0.01
174 127 0.78
175 33 0.20
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (175 bp):
CTTTGAGATTGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAAATAAAT
TTTGTCTCTCTTGAGACAGTTTATCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGA
AACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
Found at i:240437 original size:33 final size:32
Alignment explanation
Indices: 240378--240492 Score: 157
Period size: 33 Copynumber: 3.6 Consensus size: 32
240368 TCTTGAGACA
240378 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAT
1 GTTTCTCTTGAAACAC-AAAAAACCTTTGAAAT
240411 CGTTTCTCTTGAAACACAAAAAACCTTTGAAATT
1 -GTTTCTCTTGAAACACAAAAAACCTTTGAAA-T
240445 GTTTCTCTTG--A-A-AAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTG-AAAT
*
240474 GTTTCTCTTGAAACGCAAA
1 GTTTCTCTTGAAACACAAA
240493 GACCGTCGAG
Statistics
Matches: 74, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
29 23 0.31
30 4 0.05
31 2 0.03
33 28 0.38
34 17 0.23
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (32 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAAT
Found at i:240462 original size:29 final size:29
Alignment explanation
Indices: 240394--240486 Score: 132
Period size: 29 Copynumber: 3.1 Consensus size: 29
240384 CTTGAAACAC
*
240394 AAAAAAACCTTTGAAATCGTTTCTCTTGAAA
1 AAAAAAACCTTTGAAATTGTTTCTCTTG--A
240425 CACAAAAAACCTTTGAAATTGTTTCTCTTGA
1 -A-AAAAAACCTTTGAAATTGTTTCTCTTGA
*
240456 AAAAAAACCTTTGAAAATGTTTCTCTTGA
1 AAAAAAACCTTTGAAATTGTTTCTCTTGA
240485 AA
1 AA
240487 CGCAAAGACC
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
29 29 0.50
30 1 0.02
31 1 0.02
32 1 0.02
33 26 0.45
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (29 bp):
AAAAAAACCTTTGAAATTGTTTCTCTTGA
Found at i:240959 original size:34 final size:36
Alignment explanation
Indices: 240891--240980 Score: 139
Period size: 34 Copynumber: 2.5 Consensus size: 36
240881 GAAATCATAC
*
240891 TGAAAATTATAAAATATATGGGGTTTTTTTAAATATTT
1 TGAAAA-TATATAATATATGGGG-TTTTTTAAATATTT
240929 TGAAAATATATAATATAT-GGG-TTTTTAAATATTT
1 TGAAAATATATAATATATGGGGTTTTTTAAATATTT
240963 TGAAAATATATAATATAT
1 TGAAAATATATAATATAT
240981 AGCTTTTGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
34 31 0.61
36 3 0.06
37 11 0.22
38 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (36 bp):
TGAAAATATATAATATATGGGGTTTTTTAAATATTT
Found at i:241002 original size:13 final size:13
Alignment explanation
Indices: 240984--241008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
240974 AATATATAGC
240984 TTTTGAAAACATT
1 TTTTGAAAACATT
240997 TTTTGAAAACAT
1 TTTTGAAAACAT
241009 ATATTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:241124 original size:13 final size:13
Alignment explanation
Indices: 241103--241162 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
241093 TATTATATAA
*
241103 TTTTGAAAATTAG
1 TTTTTAAAATTAG
*
241116 TTTTTAAAAATA-
1 TTTTTAAAATTAG
* * *
241128 TATAT-ATATATAG
1 TTTTTAAAAT-TAG
241141 TTTTTAAAATTAG
1 TTTTTAAAATTAG
241154 TTTTTAAAA
1 TTTTTAAAA
241163 GTATATATAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
11 2 0.06
12 5 0.14
13 25 0.71
14 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTTTAAAATTAG
Found at i:241138 original size:38 final size:38
Alignment explanation
Indices: 241047--241262 Score: 228
Period size: 38 Copynumber: 5.7 Consensus size: 38
241037 AAAAATATAT
* *
241047 AAATATATA-ATATATAGTTTTTAAAAATA-TTTTTGAA
1 AAATATATATATATATAGTTTTGAAAATTAGTTTTT-AA
* *
241084 AAACATATATATTATATAATTTTGAAAATTAGTTTTTAA
1 AAATATATATA-TATATAGTTTTGAAAATTAGTTTTTAA
*
241123 AAATATATATATATATAGTTTTTAAAATTAGTTTTTAA
1 AAATATATATATATATAGTTTTGAAAATTAGTTTTTAA
* * *
241161 AAGTATATATATTATCTAGTTTTGAAAATTATTCTTTTAA
1 AAATATATATA-TATATAGTTTTGAAAATTAGT-TTTTAA
* *
241201 AAATATATA-CTATAT-GATTTTGAAAATTA-TTTTTTA
1 AAATATATATATATATAG-TTTTGAAAATTAGTTTTTAA
* * *
241237 AAACATATAT-TGTATAGTTTTAAAAA
1 AAATATATATATATATAGTTTTGAAAA
241263 AATGTTTTTC
Statistics
Matches: 153, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
36 25 0.16
37 11 0.07
38 52 0.34
39 46 0.30
40 19 0.12
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.47
Consensus pattern (38 bp):
AAATATATATATATATAGTTTTGAAAATTAGTTTTTAA
Found at i:241169 original size:77 final size:76
Alignment explanation
Indices: 241047--241246 Score: 269
Period size: 77 Copynumber: 2.6 Consensus size: 76
241037 AAAAATATAT
*
241047 AAATATATAATATATAGTTTTTAAAAATATTTTTGAAAAACATATATATTATATAATTTTGAAAA
1 AAATATATAATATATAGTTTTTAAAATTATTTTT-AAAAACATATATATTATATAATTTTGAAAA
241112 TTAGT-TTTTAA
65 TTAGTCTTTTAA
** * *
241123 AAATATATATATATATAGTTTTTAAAATTAGTTTTTAAAAGTATATATATTATCTAGTTTTGAAA
1 AAATATATA-ATATATAGTTTTTAAAATTA-TTTTTAAAAACATATATATTATATAATTTTGAAA
*
241188 ATTATTCTTTTAA
64 ATTAGTCTTTTAA
* * *
241201 AAATATATACTATAT-GATTTTGAAAATTATTTTTTAAAACATATAT
1 AAATATATAATATATAG-TTTTTAAAATTATTTTTAAAAACATATAT
241247 TGTATAGTTT
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
76 24 0.22
77 65 0.60
78 20 0.18
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (76 bp):
AAATATATAATATATAGTTTTTAAAATTATTTTTAAAAACATATATATTATATAATTTTGAAAAT
TAGTCTTTTAA
Found at i:241293 original size:4 final size:4
Alignment explanation
Indices: 241273--241330 Score: 55
Period size: 4 Copynumber: 13.8 Consensus size: 4
241263 AATGTTTTTC
* *
241273 ATTT ACTT ATCT ATTT ATTT ATTTT ATTTT ATTT -TATT ATTT ATTT ATCTT
1 ATTT ATTT ATTT ATTT ATTT A-TTT A-TTT ATTT AT-TT ATTT ATTT AT-TT
241324 ATTT ATT
1 ATTT ATT
241331 ATTAATTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 1 0.02
4 31 0.67
5 14 0.30
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:242808 original size:13 final size:13
Alignment explanation
Indices: 242792--242834 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
242782 TCCCATCTTT
242792 TTTATTTGATTT-G
1 TTTATTT-ATTTAG
*
242805 TTTATTTATTTAT
1 TTTATTTATTTAG
*
242818 TTTATTTATTTAT
1 TTTATTTATTTAG
242831 TTTA
1 TTTA
242835 CTTTTTCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTATTTATTTAG
Found at i:242814 original size:4 final size:4
Alignment explanation
Indices: 242792--242832 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
242782 TCCCATCTTT
*
242792 TTTA TTTGA TTTG TTTA TTTA TTTA TTTTA TTTA TTTA TTT
1 TTTA TTT-A TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTT
242833 TACTTTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 25 0.76
5 8 0.24
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:242814 original size:17 final size:17
Alignment explanation
Indices: 242792--242832 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
242782 TCCCATCTTT
*
242792 TTTATTTGA-TTTGTTTA
1 TTTATTT-ATTTTATTTA
242809 TTTATTTATTTTATTTA
1 TTTATTTATTTTATTTA
242826 TTTATTT
1 TTTATTT
242833 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTATTTATTTTATTTA
Found at i:245015 original size:30 final size:30
Alignment explanation
Indices: 244981--245045 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
244971 TAGTTAAACA
244981 GTTAGCAAGATTAGTTA-AG-GAGTTGAAGTT
1 GTTAGCAAGATT-GTTAGAGTGAGTTG-AGTT
* *
245011 GTTAGCAATATTGTTAGAGTTAGTTGAGTT
1 GTTAGCAAGATTGTTAGAGTGAGTTGAGTT
245041 GTTAG
1 GTTAG
245046 ACTTGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.13
30 22 0.71
31 5 0.16
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.38
Consensus pattern (30 bp):
GTTAGCAAGATTGTTAGAGTGAGTTGAGTT
Found at i:246667 original size:36 final size:36
Alignment explanation
Indices: 246625--246903 Score: 443
Period size: 36 Copynumber: 7.8 Consensus size: 36
246615 TTTCATCTAT
* *
246625 ACTTCCGATTCAAGTCGAACGGATGGAGGCATCGGC
1 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
246661 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
1 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
246697 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
1 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
**
246733 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGGT
1 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
* *
246769 ACTTCCGATTCAAGTCGAACAGAATGAGGCATCGAC
1 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
* *
246805 ACTTCCGATTCAAGTCGAACGGAAGGAAGCA-CTGGC
1 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATC-GAC
* *
246841 ACTTCCGATTCAAGTCGAACGAAAGGAAGCATCGAC
1 ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
*
246877 ACTTCCGATTCAAGTCTAACGGAAGGA
1 ACTTCCGATTCAAGTCGAACGGAAGGA
246904 TGTAGTGCAC
Statistics
Matches: 225, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
35 1 0.00
36 223 0.99
37 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (36 bp):
ACTTCCGATTCAAGTCGAACGGAAGGAGGCATCGAC
Found at i:247115 original size:30 final size:30
Alignment explanation
Indices: 247081--247145 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
247071 TAGTTAAACA
247081 GTTAGCAAGATTAGTTA-AG-GAGTTGAAGTT
1 GTTAGCAAGATT-GTTATAGTGAGTTG-AGTT
* *
247111 GTTAGCAATATTGTTATAGTTAGTTGAGTT
1 GTTAGCAAGATTGTTATAGTGAGTTGAGTT
247141 GTTAG
1 GTTAG
247146 ACTTGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.13
30 22 0.71
31 5 0.16
ACGTcount: A:0.29, C:0.03, G:0.28, T:0.40
Consensus pattern (30 bp):
GTTAGCAAGATTGTTATAGTGAGTTGAGTT
Found at i:255828 original size:111 final size:103
Alignment explanation
Indices: 255622--255828 Score: 261
Period size: 111 Copynumber: 1.9 Consensus size: 103
255612 GTTGATGAAT
* * * *
255622 ATGATTAAATGATCATTGAAAAGTTGGTGAAATGGTGCATTATTTAGCCTATGCATGTTTTTTTG
1 ATGATTAAATGACCACTGAAAAGTTGGTGAAATGCTGCATTATTTAGCCTATGCATGTTTTTCTG
* *
255687 ATATGCACTGTTAATGCACCACTGAAAAGTTGTTGCAG
66 ATATGAACTGATAATGCACCACTGAAAAGTTGTTGCAG
* *
255725 ATGATTAAATGACCACTGCAAAAGTTGGTGAAATGCTGCATTATTTGGCCTATGTGAAATATACG
1 ATGATTAAATGACCACTG-AAAAGTTGGTGAAATGCTGCATTATTTAGCCTA--TG---CAT--G
*
255790 TTTTTCTGATATGAAGTGATAATGCACCACTGAAAAGTT
58 TTTTTCTGATATGAACTGATAATGCACCACTGAAAAGTT
255829 TTCTAAAATG
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
103 16 0.18
104 31 0.36
106 2 0.02
109 2 0.02
111 36 0.41
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (103 bp):
ATGATTAAATGACCACTGAAAAGTTGGTGAAATGCTGCATTATTTAGCCTATGCATGTTTTTCTG
ATATGAACTGATAATGCACCACTGAAAAGTTGTTGCAG
Found at i:255987 original size:134 final size:133
Alignment explanation
Indices: 255723--255967 Score: 373
Period size: 134 Copynumber: 1.8 Consensus size: 133
255713 AAGTTGTTGC
* * * *
255723 AGATGATTAAATGACCACTGCAAAAGTTGGTGAAATGCTGCATTATTTGGCCTATGTGAAATATA
1 AGATGACTAAATGACAACTGCAAAAGTTGGTGAAATGCTGCATTATTTAGCCTATGTGAAATACA
*
255788 CGTTTTTCTGATATGAAGTGATAATGCACCACTGAAAAGTTTTCTAAAATGAGTTGATATATCAC
66 CGTTTTTCTGATATGAAGTGATAATGCACCACTAAAAAGTTTTCTAAAATGAGTTGATATATCAC
255853 TAA
131 TAA
* * *
255856 AGATGACTAAATGACAACTGCAAAAAGTTGGTGAGATGGTGTATTATTTAGCCTATGTGAAATAC
1 AGATGACTAAATGACAACTGC-AAAAGTTGGTGAAATGCTGCATTATTTAGCCTATGTGAAATAC
* * *
255921 ACATTTTTTCTGATATGAAGTGTTAATGCACCATTAAAAAGTTTTCT
65 AC-GTTTTTCTGATATGAAGTGATAATGCACCACTAAAAAGTTTTCT
255968 TATTTAGTTG
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
133 19 0.19
134 40 0.40
135 40 0.40
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (133 bp):
AGATGACTAAATGACAACTGCAAAAGTTGGTGAAATGCTGCATTATTTAGCCTATGTGAAATACA
CGTTTTTCTGATATGAAGTGATAATGCACCACTAAAAAGTTTTCTAAAATGAGTTGATATATCAC
TAA
Done.