Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000945.1 Hibiscus syriacus cultivar Beakdansim tig00001887_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: 93576
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2222 original size:17 final size:16
Alignment explanation
Indices: 2196--2229 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2186 ATATAATAAG
*
2196 AAAGAGAACAAGAGTTT
1 AAAGAAAACAAGA-TTT
2213 AAAGAAAACAAGATTT
1 AAAGAAAACAAGATTT
2229 A
1 A
2230 GAAGTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (16 bp):
AAAGAAAACAAGATTT
Found at i:4760 original size:12 final size:12
Alignment explanation
Indices: 4743--4768 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4733 TTCACTAGTT
4743 TTTTTCTAATAG
1 TTTTTCTAATAG
4755 TTTTTCTAATAG
1 TTTTTCTAATAG
4767 TT
1 TT
4769 ATAGATGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTTTCTAATAG
Found at i:7430 original size:29 final size:29
Alignment explanation
Indices: 7388--7444 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
7378 AATAAAAAAT
7388 TATTTACTAACTCTTGAAACTTTAATAAC
1 TATTTACTAACTCTTGAAACTTTAATAAC
*
7417 TATTTTCTAACTCTTGAAACTTTAATAA
1 TATTTACTAACTCTTGAAACTTTAATAA
7445 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.44
Consensus pattern (29 bp):
TATTTACTAACTCTTGAAACTTTAATAAC
Found at i:10997 original size:20 final size:20
Alignment explanation
Indices: 10972--11016 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
10962 CAATAGTTAA
**
10972 AGTCAACGATTTAAGTCAAT
1 AGTCAACGATCAAAGTCAAT
10992 AGTCAACGATCAAAGTCAAT
1 AGTCAACGATCAAAGTCAAT
*
11012 TGTCA
1 AGTCA
11017 GGTCAATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
AGTCAACGATCAAAGTCAAT
Found at i:16418 original size:24 final size:24
Alignment explanation
Indices: 16383--16444 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
16373 TTGATATTAT
16383 AATAT-TTATAAATATATACTT-TCA
1 AATATGTT-TAAATATATACTTGT-A
* *
16407 AATATGTTTAAATATATAGTTGTG
1 AATATGTTTAAATATATACTTGTA
16431 AATATGTTTAAATA
1 AATATGTTTAAATA
16445 ATTAAATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (24 bp):
AATATGTTTAAATATATACTTGTA
Found at i:16454 original size:24 final size:24
Alignment explanation
Indices: 16407--16454 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
16397 TATACTTTCA
**
16407 AATATGTTTAAATATATAGTTGTG
1 AATATGTTTAAATATATAAATGTG
16431 AATATGTTTAAATA-ATTAAATGTG
1 AATATGTTTAAATATA-TAAATGTG
16455 TATTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (24 bp):
AATATGTTTAAATATATAAATGTG
Found at i:19429 original size:21 final size:20
Alignment explanation
Indices: 19344--19500 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
19334 AATGACCAAT
** *
19344 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
19363 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
19383 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
19403 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
19424 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
19445 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
19466 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
19486 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
19501 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:19529 original size:20 final size:20
Alignment explanation
Indices: 19467--19660 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
19457 CGATTTTCCA
* ** *
19467 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
19487 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
19507 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
19527 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
19547 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
19567 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
19587 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
19607 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
19627 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
19648 AAATCGCAACGCG
1 AAATCGCAACGCG
19661 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:19551 original size:60 final size:60
Alignment explanation
Indices: 19467--19660 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
19457 CGATTTTCCA
* ** * *
19467 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
19527 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
19587 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
19648 AAATCGCAACGCG
1 AAATCGCAACGCG
19661 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:20082 original size:33 final size:33
Alignment explanation
Indices: 20043--20113 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
20033 TTCACTTAGA
*
20043 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
20076 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
20109 TTTCA
1 TTTCA
20114 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:20237 original size:20 final size:20
Alignment explanation
Indices: 20195--20302 Score: 104
Period size: 21 Copynumber: 5.7 Consensus size: 20
20185 CAGAAGAGTT
*
20195 GCAACGAGATAAATGAAAATC
1 GCAACGAGA-GAATGAAAATC
***
20216 GCAACGAGAGAATGACTGTC
1 GCAACGAGAGAATGAAAATC
20236 GCAACGAGAGAAATGAAAATC
1 GCAACGAGAG-AATGAAAATC
20257 GCAAC--GAG-A-G--AATC
1 GCAACGAGAGAATGAAAATC
*
20271 GCAACGCGA-AATGAAAATC
1 GCAACGAGAGAATGAAAATC
20290 GCAACGAGAGAAT
1 GCAACGAGAGAAT
20303 CACAACGCGA
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 2 0.03
19 15 0.21
20 20 0.28
21 21 0.30
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
GCAACGAGAGAATGAAAATC
Found at i:20252 original size:41 final size:37
Alignment explanation
Indices: 20195--20302 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 37
20185 CAGAAGAGTT
*
20195 GCAACGAGATAAATGAAAATCGCAACGAGAGAATGACTGTC
1 GCAACGAGAGAAATGAAAATCGCAACGAGAGAAT-A---TC
20236 GCAACGAGAGAAATGAAAATCGCAACGAGAG-A-ATC
1 GCAACGAGAGAAATGAAAATCGCAACGAGAGAATATC
*
20271 GCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 GCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
20303 CACAACGCGA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
33 23 0.37
34 1 0.02
35 7 0.11
38 1 0.02
40 1 0.02
41 30 0.48
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (37 bp):
GCAACGAGAGAAATGAAAATCGCAACGAGAGAATATC
Found at i:20272 original size:14 final size:14
Alignment explanation
Indices: 20253--20309 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
20243 GAGAAATGAA
20253 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
20267 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
20286 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
20300 AATCACAACG
1 AATCGCAACG
20310 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:20285 original size:33 final size:33
Alignment explanation
Indices: 20245--20325 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
20235 CGCAACGAGA
*
20245 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
20278 GAAATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGAGAGAATCACAACGC
**
20311 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
20326 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAACGC
Found at i:20343 original size:19 final size:19
Alignment explanation
Indices: 20321--20448 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
20311 GAAACCAAAA
*
20321 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
20340 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
20354 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
20373 TCGCGTTGC-A-ATTC---
1 TCGCGTTGCGATTTTCATT
*
20387 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
20407 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
20427 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
20447 TC
1 TC
20449 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
14 18 0.21
15 1 0.01
16 6 0.07
17 6 0.07
18 1 0.01
19 20 0.24
20 19 0.22
21 14 0.16
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:20362 original size:14 final size:14
Alignment explanation
Indices: 20343--20399 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
20333 TTTCATTTCG
20343 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
20357 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
20376 CGTTGCAATTCTCT
1 CGTTGCGATTCTCT
20390 CGTTGCGATT
1 CGTTGCGATT
20400 TTCATTTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:20368 original size:33 final size:33
Alignment explanation
Indices: 20326--20448 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
20316 CAAAATCGCA
20326 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
20359 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
20392 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
20433 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
20449 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 44 0.56
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 2 0.03
40 2 0.03
41 21 0.27
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:20410 original size:21 final size:21
Alignment explanation
Indices: 20384--20448 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
20374 CGCGTTGCAA
20384 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
20405 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
20425 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
20446 TTC
1 TTC
20449 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:22305 original size:93 final size:92
Alignment explanation
Indices: 22146--22335 Score: 371
Period size: 93 Copynumber: 2.1 Consensus size: 92
22136 TAGATTGCTT
22146 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
22211 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
22239 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
22304 TTTGTCTTTGTTTTGTCTTTTGGTTGA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGA
22331 AGTAA
1 AGTAA
22336 TGCAATCCAT
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 6 0.06
93 91 0.94
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:22423 original size:19 final size:20
Alignment explanation
Indices: 22383--22429 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
22373 TAGTTTACTT
* *
22383 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTGAAAA
22403 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTGAAAA
22422 TCGCAACG
1 TCGCAACG
22430 ACAGAATCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAACTGAAAA
Found at i:22458 original size:19 final size:19
Alignment explanation
Indices: 22383--22459 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 19
22373 TAGTTTACTT
* *
22383 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
22403 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
22422 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
22436 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
22455 TCGCA
1 TCGCA
22460 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 19 0.41
20 12 0.26
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:22477 original size:19 final size:19
Alignment explanation
Indices: 22455--22608 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
22445 GAAACCAAAA
*
22455 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
22474 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
22490 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
22507 TCACATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
22523 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
22540 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
22559 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
22578 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
22598 TCGTGTTGCGA
1 TCGCGTTGCGA
22609 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
14 15 0.14
16 11 0.10
17 11 0.10
19 60 0.55
20 12 0.11
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:22496 original size:14 final size:14
Alignment explanation
Indices: 22477--22533 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
22467 TTTCATTTCG
22477 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
22491 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
22508 CACATTGCGATTCTGT
1 --CGTTGCGATTCTTT
22524 CGTTGCGATT
1 CGTTGCGATT
22534 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:22502 original size:33 final size:33
Alignment explanation
Indices: 22460--22590 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
22450 CAAAATCGCA
22460 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* * *
22493 TTGCGATTTTCATTTCACATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
22526 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TT--CTT-TCG
*
22564 TTGCGATTATCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
22591 TTAAGTTTCG
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
33 53 0.62
35 2 0.02
36 2 0.02
37 1 0.01
38 27 0.32
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:24550 original size:14 final size:14
Alignment explanation
Indices: 24531--24566 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
24521 ATTGTTTAAT
24531 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
24545 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
24559 TGATTTGT
1 TGATTTGT
24567 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:24727 original size:20 final size:19
Alignment explanation
Indices: 24673--24737 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
24663 AAAAATGATT
24673 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
24692 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
24711 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
24731 ATCGCAA
1 ATCGCAA
24738 CGAGAGAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 29 0.64
20 16 0.36
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:24774 original size:19 final size:19
Alignment explanation
Indices: 24746--24896 Score: 143
Period size: 19 Copynumber: 8.7 Consensus size: 19
24736 AACGAGAGAA
* *
24746 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
24765 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
24781 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
24798 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
24817 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
24833 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
24850 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
24868 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
24884 TCGCATTGCGATT
1 TCGCATTGCGATT
24897 CTCTCGTTGC
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
14 23 0.21
16 16 0.15
17 12 0.11
18 3 0.03
19 42 0.39
20 12 0.11
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:24809 original size:52 final size:52
Alignment explanation
Indices: 24746--24865 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
24736 AACGAGAGAA
*
24746 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
24798 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
24850 TCCGCATTGCGATTTT
1 T-CGCATTGCGATTTT
24866 CATGTTGGGA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 51 0.78
53 14 0.22
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:24918 original size:33 final size:33
Alignment explanation
Indices: 24803--24910 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
24793 TCATTTCGCA
24803 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
24836 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
24870 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
24903 TTGCGATT
1 TTGCGATT
24911 GTAATTTCCG
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:27210 original size:12 final size:12
Alignment explanation
Indices: 27193--27217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27183 TCTTCGGGGA
27193 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27205 CTTTTTCTTCTT
1 CTTTTTCTTCTT
27217 C
1 C
27218 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:28148 original size:20 final size:20
Alignment explanation
Indices: 28120--28349 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
28110 AAATTTCAGT
* * *
28120 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28140 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
28160 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
28180 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
28200 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
28220 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
28240 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
28260 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
28280 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
28300 GTTGTGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
28320 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
28340 GTTGCGATTT
1 GTTGCGATTT
28350 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:28366 original size:21 final size:21
Alignment explanation
Indices: 28336--28418 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
28326 ATTTTCATAT
*
28336 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
28357 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
28378 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
28399 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
28419 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:28409 original size:42 final size:43
Alignment explanation
Indices: 28316--28414 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
28306 ATTTATGTGT
*
28316 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
28357 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
28399 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
28415 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:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:32419 original size:2 final size:2
Alignment explanation
Indices: 32412--32464 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
32402 ATGATAAGTG
32412 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32454 TA TA TA TA TA T
1 TA TA TA TA TA T
32465 TAAACTTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32836 original size:2 final size:2
Alignment explanation
Indices: 32831--32862 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
32821 TTAATCAATG
32831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32863 GTTCTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34890 original size:2 final size:2
Alignment explanation
Indices: 34883--34948 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
34873 CTCCAGTGCA
* * * *
34883 TC TC TC TC TC TC CC TC TC CC TC TC CC TC TC CC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
34925 TG TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
34949 CGTTTCTCTG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.55, G:0.02, T:0.44
Consensus pattern (2 bp):
TC
Found at i:34956 original size:12 final size:12
Alignment explanation
Indices: 34883--34957 Score: 66
Period size: 12 Copynumber: 6.4 Consensus size: 12
34873 CTCCAGTGCA
34883 TCTCTCT-C-TC
1 TCTCTCTCCGTC
* *
34893 TCCCTCTCCCTC
1 TCTCTCTCCGTC
* *
34905 TCCCTCTCCCTC
1 TCTCTCTCCGTC
*
34917 TCTCTCTCTGTC
1 TCTCTCTCCGTC
34929 TCTCTCTCTC-TC
1 TCTCTCTC-CGTC
*
34941 TCTCTCTCCGTT
1 TCTCTCTCCGTC
34953 TCTCT
1 TCTCT
34958 GCATATCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
10 6 0.11
11 2 0.04
12 47 0.85
ACGTcount: A:0.00, C:0.52, G:0.03, T:0.45
Consensus pattern (12 bp):
TCTCTCTCCGTC
Found at i:38587 original size:22 final size:21
Alignment explanation
Indices: 38553--38596 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
38543 GGGAGAGAGG
*
38553 GAAAAATATATAATAATAATA
1 GAAAAATAAATAATAATAATA
*
38574 GAAAAATTAAATAATAATTATA
1 GAAAAA-TAAATAATAATAATA
38596 G
1 G
38597 CGTATAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
GAAAAATAAATAATAATAATA
Found at i:38588 original size:19 final size:21
Alignment explanation
Indices: 38553--38591 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
38543 GGGAGAGAGG
38553 GAAAAATATATAATAATAATA
1 GAAAAATATATAATAATAATA
38574 GAAAAAT-TA-AATAATAAT
1 GAAAAATATATAATAATAAT
38592 TATAGCGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
GAAAAATATATAATAATAATA
Found at i:38598 original size:123 final size:125
Alignment explanation
Indices: 38470--38717 Score: 324
Period size: 129 Copynumber: 2.0 Consensus size: 125
38460 ATGTAAAATA
* *
38470 ATAGCGTATAAGGTAAAAT-T-AA-TAAAAAAACATATAATAATATTAATTCCATATATATATAA
1 ATAGCGTATAAAGTAAAATATAAAGTAAAAAAACATATAATAATATTAATACCATATATATATAA
* * ** *
38532 TAGCTAAATATGGGAGAGAGGGAAAAA-TATATAATAATAATAGAAAAATTAAATAATAATT
66 TAACTAAATATGAGAG-GA-AAAAAAACTATATAATAATAATAGAAAAACTAAATAATAATT
*
38593 ATAGCGTATAAAGTAAAATAAATAAAGTTAATAAAACATATAATAATATTAATACCATATATATA
1 ATAGCGTATAAAGTAAAAT--ATAAAG-TAAAAAAACATATAATAATATTAATACCATATATATA
* *
38658 TAATAACTAAATATGAGAGGAAAAAAAATCTATATAATAGTAATGGAAAAACTAAATAAT
63 TAATAACTAAATATGAGAGGAAAAAAAA-CTATATAATAATAATAGAAAAACTAAATAAT
38718 GAAGATAAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
123 18 0.17
126 1 0.01
127 7 0.07
128 2 0.02
129 79 0.74
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (125 bp):
ATAGCGTATAAAGTAAAATATAAAGTAAAAAAACATATAATAATATTAATACCATATATATATAA
TAACTAAATATGAGAGGAAAAAAAACTATATAATAATAATAGAAAAACTAAATAATAATT
Found at i:41939 original size:143 final size:145
Alignment explanation
Indices: 41679--41966 Score: 562
Period size: 143 Copynumber: 2.0 Consensus size: 145
41669 AAGTATAGTT
41679 TTTCCCAGCTGTTTGTCTCATGGGGAGAAAAACAAGTTACGTAATGGTGGGGTTTTGGGAAGTTA
1 TTTCCCAGCTGTTTGTCTCATGGGGAGAAAAACAAGTTACGTAATGGTGGGGTTTTGGGAAGTTA
41744 GGTTTTTTCTTATTAGGTTAAAGCCACAGTAATGAGCTTGGACAATGATCTCCTGCTACAAACTT
66 GGTTTTTTCTTATTAGGTTAAAGCCACAGTAATGAGCTTGGACAATGATCTCCTGCTACAAACTT
41809 TATTATTATTAATGA
131 TATTATTATTAATGA
41824 TTTCCCAGCTGTTTGTCTCATGGGGAGAAAAACAAGTTACGTAAT-G-GGGGTTTTGGGAAGTTA
1 TTTCCCAGCTGTTTGTCTCATGGGGAGAAAAACAAGTTACGTAATGGTGGGGTTTTGGGAAGTTA
41887 GGTTTTTTCTTATTAGGTTAAAGCCACAGTAATGAGCTTGGACAATGATCTCCTGCTACAAACTT
66 GGTTTTTTCTTATTAGGTTAAAGCCACAGTAATGAGCTTGGACAATGATCTCCTGCTACAAACTT
41952 TATTATTATTAATGA
131 TATTATTATTAATGA
41967 AGAAAGTGAA
Statistics
Matches: 143, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
143 97 0.68
144 1 0.01
145 45 0.31
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (145 bp):
TTTCCCAGCTGTTTGTCTCATGGGGAGAAAAACAAGTTACGTAATGGTGGGGTTTTGGGAAGTTA
GGTTTTTTCTTATTAGGTTAAAGCCACAGTAATGAGCTTGGACAATGATCTCCTGCTACAAACTT
TATTATTATTAATGA
Found at i:49554 original size:23 final size:25
Alignment explanation
Indices: 49525--49571 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
49515 CATGAAGGAG
*
49525 ACAAAAACATG-T-TAAAAGAAGAT
1 ACAAAAACACGTTATAAAAGAAGAT
49548 ACAAAAACACGTTATAAAAGAAGA
1 ACAAAAACACGTTATAAAAGAAGA
49572 CAAAATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 1 0.05
25 10 0.48
ACGTcount: A:0.62, C:0.11, G:0.13, T:0.15
Consensus pattern (25 bp):
ACAAAAACACGTTATAAAAGAAGAT
Found at i:49574 original size:23 final size:21
Alignment explanation
Indices: 49523--49576 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
49513 ATCATGAAGG
*
49523 AGACAAAAACATGTTAAAAGA
1 AGACAAAAACACGTTAAAAGA
49544 AGATACAAAAACACGTTATAAAAGA
1 AG--ACAAAAACACG-T-TAAAAGA
49569 AGACAAAA
1 AGACAAAA
49577 TTATCCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
23 16 0.57
24 1 0.04
25 9 0.32
ACGTcount: A:0.63, C:0.11, G:0.13, T:0.13
Consensus pattern (21 bp):
AGACAAAAACACGTTAAAAGA
Found at i:60158 original size:15 final size:15
Alignment explanation
Indices: 60132--60178 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
60122 TTAGTTTCTC
* *
60132 TTCGAAATATTTGTA
1 TTCGACATATTTGAA
*
60147 TTTGACATATTTGAA
1 TTCGACATATTTGAA
60162 TTCGACATATTTTGAA
1 TTCGACATA-TTTGAA
60178 T
1 T
60179 ATGGATAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.47
Consensus pattern (15 bp):
TTCGACATATTTGAA
Found at i:64697 original size:20 final size:20
Alignment explanation
Indices: 64672--64735 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
64662 TACACATTTA
64672 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** *
64692 TGCGATAGTTGAAATTCGCGT
1 TGCGAT-TTTCCATTTCGCGT
*
64713 TGCGATTTTTCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
64733 TGC
1 TGC
64736 AATAGTCTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.42
Consensus pattern (20 bp):
TGCGATTTTCCATTTCGCGT
Found at i:64757 original size:42 final size:41
Alignment explanation
Indices: 64672--64766 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
64662 TACACATTTA
* *
64672 TGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGT
1 TGCGATTTTCCATTTCGCGTTGCAATAGTTGAAACTCGCGT
* *
64713 TGCGATTTTTCATTTCGCGTTGCAATAGTCT-ACAGCT-GTCGT
1 TGCGATTTTCCATTTCGCGTTGCAATAGT-TGA-AACTCG-CGT
64755 TGCGATTTTCCA
1 TGCGATTTTCCA
64767 AATTCGTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 29 0.63
42 17 0.37
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (41 bp):
TGCGATTTTCCATTTCGCGTTGCAATAGTTGAAACTCGCGT
Found at i:65303 original size:6 final size:6
Alignment explanation
Indices: 65294--65331 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
65284 CCGTCTCGTC
65294 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
65332 ATACGTGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.18, G:0.47, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:77776 original size:299 final size:295
Alignment explanation
Indices: 77105--77870 Score: 1112
Period size: 299 Copynumber: 2.6 Consensus size: 295
77095 GTGTGCGCAC
* * * * *
77105 ACAGATTTTCAATGATATTCTAAAATTCTTTTCAGCAAATATTCACTGTTTAAACGTTGGAAGCT
1 ACAGATTTGCAATGATATTCTAAAA-TCCTTTCATCAAATATGCACTGTTTAAACTTTGGAAGCT
*
77170 CAGAAGCCAAGCGTAACAA-CTACATTTCA-ATGAAGAATCCAACAAATAGATCCTTCTTACATG
65 CAGAAGCCAAGCGTAACAAGC-AAATTTCACA-GAAGAATCCAACAAATAGATCCTTCTTACATG
* * * *
77233 TTATTGCTTCATCACTGCAACACAAATCTTCCAA-AAAAAAT-AATTTTGGATATGGACGGAAAC
128 TTATTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAAC
* * *
77296 CACACCTCTAGACAAATTAAAAAGGGACATAATACAAGAGCAAGCATGACATAAGCTAGCTACAG
193 CACACCTCTAGAAAAATTAAAAAGGGACATAAAACAAGAACAAGCATGACATAAGCTAGCTACAG
* *
77361 TAACTTTAGAGGGGAAATTCCACATGCACACACATAGT
258 TAACGTTAGAGGGGAAATTCCACATGCACACACATAAT
* * *
77399 ACAGATTTGCAATGATATTCTAAAATCCGTTTCATCAAATATGTATTGTTTAAACTATGGAAGCT
1 ACAGATTTGCAATGATATTCTAAAATCC-TTTCATCAAATATGCACTGTTTAAACTTTGGAAGCT
*
77464 CAGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTTCATGTT
65 CAGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTACATGTT
*
77529 ATTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAATCA
130 ATTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAACCA
* *
77594 CACTTCTAGAAAAAATTAAAAAAGGGACATAAAACAAGAACTAGCATGACATAAGCTAGCTACA-
195 CACCTCTAG-AAAAATT-AAAAAGGGACATAAAACAAGAACAAGCATGACATAAGCTAGCTACAG
77658 TAAACGTTAGAGGGGAAATTTCCACATGCACACACATAAT
258 T-AACGTTAGAGGGGAAA-TTCCACATGCACACACATAAT
* * * *
77698 GCAGATTTGCAATGATATTCTACAATCCTTCTCATCGAATATGCACTATTTAAACTTTGGAAGCT
1 ACAGATTTGCAATGATATTCTAAAATCCTT-TCATCAAATATGCACTGTTTAAACTTTGGAAGCT
* * * * *
77763 CAGAAGCCAAGCGTAACAAGTATATTTCACATAAGAATCCAACAAATGGATCCTTCTTGCATGTT
65 CAGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTACATGTT
*
77828 ATTGCTTCATCACTGCAAGACACAA-CTTCCAAGAAAAAATAAA
130 ATTGCTTCATCACTGCAACACA-AATCTTCCAAGAAAAAATAAA
77871 TTTTAATATG
Statistics
Matches: 426, Mismatches: 35, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
293 2 0.00
294 145 0.34
295 9 0.02
296 27 0.06
297 7 0.02
298 60 0.14
299 174 0.41
300 2 0.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (295 bp):
ACAGATTTGCAATGATATTCTAAAATCCTTTCATCAAATATGCACTGTTTAAACTTTGGAAGCTC
AGAAGCCAAGCGTAACAAGCAAATTTCACAGAAGAATCCAACAAATAGATCCTTCTTACATGTTA
TTGCTTCATCACTGCAACACAAATCTTCCAAGAAAAAATAAAATTTGGATAAGCACGCAAACCAC
ACCTCTAGAAAAATTAAAAAGGGACATAAAACAAGAACAAGCATGACATAAGCTAGCTACAGTAA
CGTTAGAGGGGAAATTCCACATGCACACACATAAT
Done.