Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007445.1 Hibiscus syriacus cultivar Beakdansim tig00020346_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: 100381
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1986 original size:31 final size:31
Alignment explanation
Indices: 1950--2008 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1940 AACTTAAAAG
*
1950 AGTTTTGCAATACTAAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
* *
1981 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
2009 ACATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:2060 original size:22 final size:22
Alignment explanation
Indices: 2032--2075 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2022 ATAATAATTT
2032 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2054 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
2076 CTGAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:2307 original size:22 final size:22
Alignment explanation
Indices: 2258--2306 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2248 ATAAATTTTT
* **
2258 TAAAATAAATCAATTTATATTT
1 TAAAATAAATCAATTCATATAA
2280 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATTCATA-TAA
2303 TAAA
1 TAAA
2307 TTATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:2469 original size:219 final size:222
Alignment explanation
Indices: 1886--2499 Score: 941
Period size: 223 Copynumber: 2.8 Consensus size: 222
1876 TGTTTATTTT
* * *
1886 TTAATGTCTGCAGACTGCTAAAATAAACTGAAATATGAATAAACTAATTTTTTAAACTTAAAAGA
1 TTAATGTCTGCAAACTGCTAAAATAAACTGAAATATAAATAAACTGATTTTTTAAACTTAAAAGA
*
1951 GTTTTGCAATACTAAAATTTAAATAATTTTAGTTTTATAATACTGAAATTTAAATAATACATACA
66 GTTTTGCAATACTAAAATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAAT-CATACA
*
2016 ACTACAATAATAATTTTTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTGAA
130 ACTACAATAATAATTTTTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATTCATACTGAA
2081 TAAATTATTTAATAAATAACTTTATTAAA
195 TAAATTATTTAATAAAT-ACTTTATTAAA
*
2110 TTAATGTCTGCAAACTGCTAAAATAAACTAAAATATAAATAAACTGA-TTTTTAAACTTAAAAGA
1 TTAATGTCTGCAAACTGCTAAAATAAACTGAAATATAAATAAACTGATTTTTTAAACTTAAAAGA
* * * * * *
2174 GTTTTGTAATACTGAGATTTAAATCATTTTAGTTTTACAATACTGAAATTTAAATAAACCATATA
66 GTTTTGCAATACTAAAATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAAT-AATCATACA
* **
2239 ACTACAATAATAAATTTTTTAAAATAAATCAATTTATATTTTAAAATAAATCAATTCATACT-AA
130 ACTACAATAATAATTTTTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATTCATACTGAA
2303 TAAATTATTTAAT-AAT-C-TTATTAAA
195 TAAATTATTTAATAAATACTTTATTAAA
* * * *
2328 TTAACGTCTGCATATTGTTAAAATAAACTGAAATATAAATAAACTGATTTTTTAAACTTAAAAGA
1 TTAATGTCTGCAAACTGCTAAAATAAACTGAAATATAAATAAACTGATTTTTTAAACTTAAAAGA
* * * *
2393 ATTTTACAATACAAAAATTTAAATAATTTTAGTTTTACAATACTAAAATTTAAATAATCTATACA
66 GTTTTGCAATACTAAAATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATC-ATACA
*
2458 ACTATAATAATAATTTTTTTAAAATAAATCAATCAATATTTT
130 ACTACAATAATAATTTTTTTAAAATAAATCAATCAATATTTT
2500 TTTAATGTTC
Statistics
Matches: 354, Mismatches: 33, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
218 53 0.15
219 107 0.30
221 3 0.01
222 15 0.04
223 131 0.37
224 45 0.13
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (222 bp):
TTAATGTCTGCAAACTGCTAAAATAAACTGAAATATAAATAAACTGATTTTTTAAACTTAAAAGA
GTTTTGCAATACTAAAATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATCATACAA
CTACAATAATAATTTTTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATTCATACTGAAT
AAATTATTTAATAAATACTTTATTAAA
Found at i:2757 original size:21 final size:23
Alignment explanation
Indices: 2728--2770 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2718 AATGATACTG
2728 AGAAAATTAAA-TA-AAAATTTA
1 AGAAAATTAAATTACAAAATTTA
*
2749 AGAACATTAAATTACAAAATTT
1 AGAAAATTAAATTACAAAATTT
2771 TATAAACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (23 bp):
AGAAAATTAAATTACAAAATTTA
Found at i:3251 original size:28 final size:26
Alignment explanation
Indices: 3213--3268 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
3203 ATAATTTAAA
* * *
3213 AAAATATATATAATATATAGTTTTTG
1 AAAATGTATATATTATATAGATTTTG
3239 AAAATGTATATATTATATAGATTTTG
1 AAAATGTATATATTATATAGATTTTG
3265 AAAA
1 AAAA
3269 ACATTTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (26 bp):
AAAATGTATATATTATATAGATTTTG
Found at i:3282 original size:66 final size:63
Alignment explanation
Indices: 3172--3307 Score: 179
Period size: 66 Copynumber: 2.1 Consensus size: 63
3162 TAAAAATTGA
3172 TTTTTAAAA--TATATAATATATAGTTTTGAAAATAATTTAAAAAAATATATATAATATATAG
1 TTTTTAAAATGTATATAATATATAGTTTTGAAAATAATTTAAAAAAATATATATAATATATAG
* ** *
3233 TTTTTGAAAATGTATATATTATATAGATTTTGAAAA-ACATTTTTGAAAAATATATATAATTTAT
1 TTTTT-AAAATGTATATAATATATAG-TTTTGAAAATA-A-TTTAAAAAAATATATATAATATAT
3297 AG
62 AG
3299 TTTTTAAAA
1 TTTTTAAAA
3308 CATTTTGAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
61 5 0.08
62 4 0.06
64 14 0.22
65 14 0.22
66 28 0.43
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.45
Consensus pattern (63 bp):
TTTTTAAAATGTATATAATATATAGTTTTGAAAATAATTTAAAAAAATATATATAATATATAG
Found at i:3308 original size:38 final size:39
Alignment explanation
Indices: 3233--3406 Score: 144
Period size: 38 Copynumber: 4.5 Consensus size: 39
3223 TAATATATAG
* *
3233 TTTTTG-AAAATGTATAT-ATTATATAGATTTTGAAAAACA
1 TTTTTGAAAAATATATATAATT-TATAGATTTT-TAAAACA
3272 TTTTTGAAAAATATATATAATTTATAG-TTTTTAAAACA
1 TTTTTGAAAAATATATATAATTTATAGATTTTTAAAACA
* * * *
3310 -TTTTGAAAACATCTATATAATATATAG-TTTTTGAAATA
1 TTTTTGAAAA-ATATATATAATTTATAGATTTTTAAAACA
* * *
3348 TTTTTG-AATATATATATTATATTATTAGATTTTGAAAACA
1 TTTTTGAAAAATATATATAAT-TTA-TAGATTTTTAAAACA
*** *
3388 AAATTCAAAAATATATATA
1 TTTTTGAAAAATATATATA
3407 TTATATATAG
Statistics
Matches: 108, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
37 18 0.17
38 34 0.31
39 18 0.17
40 25 0.23
41 13 0.12
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (39 bp):
TTTTTGAAAAATATATATAATTTATAGATTTTTAAAACA
Found at i:3327 original size:78 final size:78
Alignment explanation
Indices: 3239--3413 Score: 187
Period size: 78 Copynumber: 2.2 Consensus size: 78
3229 ATAGTTTTTG
*
3239 AAAATGTATATATTATATAGATTTTGAAAAACATTTTTGAAAAATATATATAAT-TTA-TAG-TT
1 AAAATATATATATTATATAGATTTTG--AAACATTTTTG-AAAATATATATAATATTATTAGATT
* ** *
3301 TTTAAAAC-ATTTTGA
63 TTGAAAACAAAATTCA
* * * * * *
3316 AAACATCTATATAATATATAGTTTTTGAAATATTTTTGAATATATATATTATATTATTAGATTTT
1 AAA-ATATATATATTATATAGATTTTGAAACATTTTTGAAAATATATATAATATTATTAGATTTT
3381 GAAAACAAAATTCA
65 GAAAACAAAATTCA
3395 AAAATATATATATTATATA
1 AAAATATATATATTATATA
3414 TAGGGATGGC
Statistics
Matches: 81, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
75 12 0.15
76 13 0.16
77 6 0.07
78 43 0.53
79 7 0.09
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (78 bp):
AAAATATATATATTATATAGATTTTGAAACATTTTTGAAAATATATATAATATTATTAGATTTTG
AAAACAAAATTCA
Found at i:5198 original size:24 final size:24
Alignment explanation
Indices: 5159--5216 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
5149 TTAATATTTA
**
5159 TTTTTT-TTTAACATTTTTCAT-T
1 TTTTTTATTTAACATTTAGCATGT
*
5181 TTTTTTATTTCAATATTTAGCATGT
1 TTTTTTATTT-AACATTTAGCATGT
5206 TTTATTTATTT
1 TTT-TTTATTT
5217 TATTTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 6 0.21
23 3 0.10
24 9 0.31
25 4 0.14
26 7 0.24
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (24 bp):
TTTTTTATTTAACATTTAGCATGT
Found at i:5280 original size:27 final size:26
Alignment explanation
Indices: 5206--5283 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 26
5196 TTTAGCATGT
*
5206 TTTATTTATTTTATTTTGTTTTATTTCA
1 TTTATTTATTTT-CTTT-TTTTATTTCA
* * *
5234 TTT-TTTA-TTTCGGTTGTTTATCTTTA
1 TTTATTTATTTTC-TTTTTTTAT-TTCA
5260 TTTATTTATTTTCTTTTTTTATTT
1 TTTATTTATTTTCTTTTTTTATTT
5284 ATCTCTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
25 5 0.12
26 13 0.32
27 15 0.38
28 7 0.17
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (26 bp):
TTTATTTATTTTCTTTTTTTATTTCA
Found at i:5285 original size:31 final size:32
Alignment explanation
Indices: 5250--5314 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
5240 ATTTCGGTTG
* ** *
5250 TTTATCTTTATTTATTTATTTTCTTT-TTTTA
1 TTTATCTCTATTTATCCATTTTATTTATTTTA
5281 TTTATCTCTATTTATCCATTTTATTTATTTTA
1 TTTATCTCTATTTATCCATTTTATTTATTTTA
5313 TT
1 TT
5315 ATTATTATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.72
Consensus pattern (32 bp):
TTTATCTCTATTTATCCATTTTATTTATTTTA
Found at i:13347 original size:23 final size:23
Alignment explanation
Indices: 13319--13369 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
13309 GTGTTATATT
*
13319 ATATTTTAAAAATATTAATTAGA
1 ATATTTTAAAAATATTAATTAAA
* * *
13342 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
13365 ATATT
1 ATATT
13370 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:13468 original size:18 final size:18
Alignment explanation
Indices: 13388--13495 Score: 60
Period size: 18 Copynumber: 6.0 Consensus size: 18
13378 ATTATATTAA
*
13388 TATTAATATATAAATAATAT
1 TATTAATA-ATATA-AATAT
* *
13408 TATTCATTAATA-AAATAA
1 TATT-AATAATATAAATAT
* ** *
13426 TATTATTTCTATGAA-AT
1 TATTAATAATATAAATAT
* *
13443 TATAAATAATATAAATTT
1 TATTAATAATATAAATAT
* *
13461 TATTAATAATTTATATAT
1 TATTAATAATATAAATAT
*
13479 TATTAA-AATAAAAATAT
1 TATTAATAATATAAATAT
13496 AATATCTATA
Statistics
Matches: 66, Mismatches: 19, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
17 24 0.36
18 31 0.47
19 1 0.02
20 7 0.11
21 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (18 bp):
TATTAATAATATAAATAT
Found at i:16222 original size:24 final size:24
Alignment explanation
Indices: 16195--16282 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
16185 GATATCAGAA
*
16195 ATCAAAACAGAATTCAGAACATAT
1 ATCAAAACAGAATTCAGATCATAT
* * * * *
16219 ATCATAATAGAATCCAGATCAGAA
1 ATCAAAACAGAATTCAGATCATAT
* *
16243 ATCAAAACAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAGATCATAT
* *
16267 ATCATAACATAATTCA
1 ATCAAAACAGAATTCA
16283 AGTCGGAAAT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCATAT
Found at i:16292 original size:48 final size:48
Alignment explanation
Indices: 16188--16292 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
16178 AAACGGAGAT
* *
16188 ATCAGAAATCAAAACAGAATTCAGAACATATATCATAATAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGAACATATATCATAACAGAATCAAG
** * *
16236 ATCAGAAATCAAAACAGAATTCAGGTCATGTATCATAACATAATTCAAG
1 ATCAGAAATCAAAACAGAATTCAGAACATATATCATAACAGAA-TCAAG
*
16285 -TCGGAAAT
1 ATCAGAAAT
16293 AAGATAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
48 45 0.92
49 4 0.08
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGAACATATATCATAACAGAATCAAG
Found at i:17411 original size:18 final size:18
Alignment explanation
Indices: 17388--17426 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17378 CTTTCGTTCG
17388 ATCTTACTATTAAATTCA
1 ATCTTACTATTAAATTCA
* * *
17406 ATCTTATTATTTATTTCA
1 ATCTTACTATTAAATTCA
17424 ATC
1 ATC
17427 ATTTCGAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (18 bp):
ATCTTACTATTAAATTCA
Found at i:19753 original size:30 final size:30
Alignment explanation
Indices: 19719--19785 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
19709 AACACTAGAC
19719 TGAACCACCTGAACCTAAAATTAATGATGT
1 TGAACCACCTGAACCTAAAATTAATGATGT
*
19749 TGAACCACCTGAACCTTAAATTAATGATGT
1 TGAACCACCTGAACCTAAAATTAATGATGT
19779 TGAACCA
1 TGAACCA
19786 TTTGAGGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (30 bp):
TGAACCACCTGAACCTAAAATTAATGATGT
Found at i:27639 original size:16 final size:16
Alignment explanation
Indices: 27599--27639 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
27589 ATTAAATCAA
27599 TGGTGCTCATCGTTAG
1 TGGTGCTCATCGTTAG
**
27615 TGGAACTCATCGTTAG
1 TGGTGCTCATCGTTAG
27631 TGGTGCTCA
1 TGGTGCTCA
27640 GCAGTGTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (16 bp):
TGGTGCTCATCGTTAG
Found at i:28238 original size:20 final size:19
Alignment explanation
Indices: 28208--28253 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
28198 TATAAAAATA
28208 TATTTTTAAAAGTATAAAC
1 TATTTTTAAAAGTATAAAC
*
28227 TATTTATTAAAATTATAAA-
1 TATTT-TTAAAAGTATAAAC
28246 T-TTTTTAA
1 TATTTTTAA
28254 TTCATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 4 0.16
18 3 0.12
19 6 0.24
20 12 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTTTTAAAAGTATAAAC
Found at i:29461 original size:16 final size:16
Alignment explanation
Indices: 29440--29543 Score: 81
Period size: 16 Copynumber: 6.6 Consensus size: 16
29430 TAGTTGGAGC
29440 GAAAGCAACCTAAACA
1 GAAAGCAACCTAAACA
* *
29456 GAAAGCAACCTGAACT
1 GAAAGCAACCTAAACA
** *
29472 GAAA--AAATTCAAACC
1 GAAAGCAACCT-AAACA
29487 GAAAGCAACCTAAACA
1 GAAAGCAACCTAAACA
* *
29503 GAAAGCAACCTGAACT
1 GAAAGCAACCTAAACA
* *
29519 GAAA--AAACTCAAACC
1 GAAAGCAACCT-AAACA
29534 GAAAGCAACC
1 GAAAGCAACC
29544 CATAATTAGT
Statistics
Matches: 67, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
14 7 0.10
15 14 0.21
16 40 0.60
17 6 0.09
ACGTcount: A:0.53, C:0.25, G:0.13, T:0.09
Consensus pattern (16 bp):
GAAAGCAACCTAAACA
Found at i:29500 original size:47 final size:47
Alignment explanation
Indices: 29439--29543 Score: 201
Period size: 47 Copynumber: 2.2 Consensus size: 47
29429 TTAGTTGGAG
*
29439 CGAAAGCAACCTAAACAGAAAGCAACCTGAACTGAAAAAATTCAAAC
1 CGAAAGCAACCTAAACAGAAAGCAACCTGAACTGAAAAAACTCAAAC
29486 CGAAAGCAACCTAAACAGAAAGCAACCTGAACTGAAAAAACTCAAAC
1 CGAAAGCAACCTAAACAGAAAGCAACCTGAACTGAAAAAACTCAAAC
29533 CGAAAGCAACC
1 CGAAAGCAACC
29544 CATAATTAGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.52, C:0.26, G:0.13, T:0.09
Consensus pattern (47 bp):
CGAAAGCAACCTAAACAGAAAGCAACCTGAACTGAAAAAACTCAAAC
Found at i:29595 original size:3 final size:3
Alignment explanation
Indices: 29587--29619 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
29577 AATGAATAAT
29587 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
29620 TTAACATTGA
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:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31174 original size:17 final size:17
Alignment explanation
Indices: 31152--31185 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31142 ATGCACGAAA
31152 TTAAACTTTCATTCAAC
1 TTAAACTTTCATTCAAC
31169 TTAAACTTTCATTCAAC
1 TTAAACTTTCATTCAAC
31186 ATGCTTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAACTTTCATTCAAC
Found at i:43292 original size:2 final size:2
Alignment explanation
Indices: 43281--43352 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
43271 CTGACAATAC
43281 TA TA -A 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
43322 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 T
43353 TCGACGACGT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45022 original size:21 final size:21
Alignment explanation
Indices: 44997--45051 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
44987 AGTCGAAGGT
*
44997 TATATGAGGTCCTTTGGGACA
1 TATATGAGGTCCTTTGAGACA
45018 TATATGAGGTCCTTTGAGACA
1 TATATGAGGTCCTTTGAGACA
*
45039 TATATGACGTCCT
1 TATATGAGGTCCT
45052 ATGGTACAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TATATGAGGTCCTTTGAGACA
Found at i:47376 original size:17 final size:17
Alignment explanation
Indices: 47354--47386 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
47344 ACTATTAACC
47354 GTTGA-CATGCGTTGACT
1 GTTGACCAT-CGTTGACT
47371 GTTGACCATCGTTGAC
1 GTTGACCATCGTTGAC
47387 CAGAACTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (17 bp):
GTTGACCATCGTTGACT
Found at i:49801 original size:24 final size:24
Alignment explanation
Indices: 49774--49866 Score: 107
Period size: 24 Copynumber: 3.9 Consensus size: 24
49764 CCGATTTGAT
* *
49774 TTCTGTTATGATACCTGACCTGGA
1 TTCTGATATGATACTTGACCTGGA
* *
49798 TTCTGATATGAT-TTTGACATGGA
1 TTCTGATATGATACTTGACCTGGA
* * *
49821 TTCTGATCTAATACATGACCTGGA
1 TTCTGATATGATACTTGACCTGGA
*
49845 TTATGATATGATACTTGACCTG
1 TTCTGATATGATACTTGACCTG
49867 ATATATGTTT
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
23 18 0.33
24 37 0.67
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
TTCTGATATGATACTTGACCTGGA
Found at i:50048 original size:2 final size:2
Alignment explanation
Indices: 50041--50069 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
50031 CGAATGGGTG
50041 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
50070 GTTTTAAAAG
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:54503 original size:24 final size:24
Alignment explanation
Indices: 54476--54559 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
54466 TGAATTTTTT
* *
54476 TATGATACCTGACCTGGATTCTGA
1 TATGATACTTGACATGGATTCTGA
*
54500 TATGATA-TTGACATGTATTCTGA
1 TATGATACTTGACATGGATTCTGA
* *
54523 TATGATACATGATATGGATTCTGA
1 TATGATACTTGACATGGATTCTGA
*
54547 TCTGATACTTGAC
1 TATGATACTTGAC
54560 CTGATTTATG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.40
24 30 0.60
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (24 bp):
TATGATACTTGACATGGATTCTGA
Found at i:54547 original size:12 final size:12
Alignment explanation
Indices: 54490--54547 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
54480 ATACCTGACC
54490 TGGATTCTGATA
1 TGGATTCTGATA
*
54502 T-GATAT-TGACA
1 TGGAT-TCTGATA
*
54513 TGTATTCTGATA
1 TGGATTCTGATA
*
54525 T-GATACATGATA
1 TGGATTC-TGATA
54537 TGGATTCTGAT
1 TGGATTCTGAT
54548 CTGATACTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
11 12 0.34
12 19 0.54
13 4 0.11
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (12 bp):
TGGATTCTGATA
Found at i:58303 original size:571 final size:570
Alignment explanation
Indices: 57207--58346 Score: 2154
Period size: 571 Copynumber: 2.0 Consensus size: 570
57197 TTTGATGATA
*
57207 GCTTTATTTTGACTAGGTTGATGAGGAAAGATGTGGCATTTTCTTGGACTCTTGAGTGTCAAGAA
1 GCTTTATTTTGACTAGGTTGATGAGGAAAGATGTGGCATTTGCTTGGACTCTTGAGTGTCAAGAA
57272 AGTTTTGATATGTTAAAGAAAATTTGACAAAAACTTTAGTCTTGGTTTAACCTGAGTCTGGTAAG
66 AGTTTTGATATGTTAAAGAAAATTTGACAAAAACTTTAGTCTTGGTTTAACCTGAGTCTGGTAAG
57337 AACTACATGGTTTATAGTGACGCGTCCCATATCGGCTTGGGATGTGTATTGATGCAAGAAGGCAA
131 AACTACATGGTTTATAGTGACGCGTCCCATATCGGCTTGGGATGTGTATTGATGCAAGAAGGCAA
57402 AGTGGTGGCCTATGCGTCTAGACAATTGAAACCACATGAAAAGAACTATCCAACGCATGACTTGG
196 AGTGGTGGCCTATGCGTCTAGACAATTGAAACCACATGAAAAGAACTATCCAACGCATGACTTGG
*
57467 AGTTAGTTGCAGTAGTGTTCGCTCTTAGGATTTGGCCTCACTACTTATATGGTGAATGTTGTTAC
261 AGTTAGTTGCAGTAGTGTTCGCTCTTAAGATTTGGCCTCACTACTTATATGGTGAATGTTGTTAC
*
57532 TTATATACAGATCATAAGAGCTTGAAATATCTGATGACCCAAAAACAGTTGAATTTAAGGCATAG
326 TTATATACAGATCATAAGAGCTTGAAATATCTGATGACCCAAAAACAGTTGAATTTAAGGCAGAG
57597 AAGATGGGTAGAATTTCTAAAGGATTATGATGTGGTAATCGAATTTCATCCTGGAAAAGTAAACG
391 AAGATGGGTAGAATTTCTAAAGGATTATGATGTGGTAATCGAATTTCATCCTGGAAAAGTAAACG
*
57662 TGGTAGTATATGCCTTAAGCCGAAAAATATTTACAGCCTTACGAGCTCTAGATGCTAGATTGTCA
456 TGGTAGTATATGCCTTAAGCCGAAAAACATTTACAGCCTTACGAGCTCTAGATGCTAGATTGTCA
*
57727 TTGGATGGATATGGAGTAATATGTGAAGAATTGAAGCTTAAGCCAACATT
521 TTGGATGGAGATGGAGTAATATGTGAAGAATTGAAGCTTAAGCCAACATT
57777 GCTTTATCTTTGACTAGGTTGATGAGGAAAGATGTGGCATTTGCTTGGACTCTTGAGTGTCAAGA
1 GCTTTAT-TTTGACTAGGTTGATGAGGAAAGATGTGGCATTTGCTTGGACTCTTGAGTGTCAAGA
* *
57842 AAGTTTTGATATGTTAAAGAAAATTTGACAGAAACTTTAGTCTTGGTTTAACCTGAGTTTGGTAA
65 AAGTTTTGATATGTTAAAGAAAATTTGACAAAAACTTTAGTCTTGGTTTAACCTGAGTCTGGTAA
*
57907 GAACTACGTGGTTTATAGTGACGCGTCCCATATCGGCTTGGGATGTGTATTGATGCAAGAAGGCA
130 GAACTACATGGTTTATAGTGACGCGTCCCATATCGGCTTGGGATGTGTATTGATGCAAGAAGGCA
57972 AAGTGGTGGCCTATGCGTCTAGACAATTGAAACCACATGAAAAGAACTATCCAACGCATGACTTG
195 AAGTGGTGGCCTATGCGTCTAGACAATTGAAACCACATGAAAAGAACTATCCAACGCATGACTTG
58037 GAGTTAGTTGCAGTAGTGTTCGCTCTTAAGATTTGGCCTCACTACTTATATGGTGAATGTTGTTA
260 GAGTTAGTTGCAGTAGTGTTCGCTCTTAAGATTTGGCCTCACTACTTATATGGTGAATGTTGTTA
* *
58102 CTTATATACAGATCATAAGAGCTTGAAATATCTGATGATCTAAAAACAGTTGAATTTAAGGCAGA
325 CTTATATACAGATCATAAGAGCTTGAAATATCTGATGACCCAAAAACAGTTGAATTTAAGGCAGA
*
58167 GAAGATGGGTGGAATTTCTAAAGGATTATGATGTGGTAATCGAATTTCATCCTGGAAAAGTAAAC
390 GAAGATGGGTAGAATTTCTAAAGGATTATGATGTGGTAATCGAATTTCATCCTGGAAAAGTAAAC
*
58232 GTGGTAGTATATGCCTTAAGCCGAAAAACATTTACAGCCTTACGAGCTCTAGATGCTAGATTGTT
455 GTGGTAGTATATGCCTTAAGCCGAAAAACATTTACAGCCTTACGAGCTCTAGATGCTAGATTGTC
*
58297 ATTGGATGGAGATGGAGTAATATGTGCAGAATTGAAGCTTAAGCCAACAT
520 ATTGGATGGAGATGGAGTAATATGTGAAGAATTGAAGCTTAAGCCAACAT
58347 GGTTGGATCG
Statistics
Matches: 556, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
570 7 0.01
571 549 0.99
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (570 bp):
GCTTTATTTTGACTAGGTTGATGAGGAAAGATGTGGCATTTGCTTGGACTCTTGAGTGTCAAGAA
AGTTTTGATATGTTAAAGAAAATTTGACAAAAACTTTAGTCTTGGTTTAACCTGAGTCTGGTAAG
AACTACATGGTTTATAGTGACGCGTCCCATATCGGCTTGGGATGTGTATTGATGCAAGAAGGCAA
AGTGGTGGCCTATGCGTCTAGACAATTGAAACCACATGAAAAGAACTATCCAACGCATGACTTGG
AGTTAGTTGCAGTAGTGTTCGCTCTTAAGATTTGGCCTCACTACTTATATGGTGAATGTTGTTAC
TTATATACAGATCATAAGAGCTTGAAATATCTGATGACCCAAAAACAGTTGAATTTAAGGCAGAG
AAGATGGGTAGAATTTCTAAAGGATTATGATGTGGTAATCGAATTTCATCCTGGAAAAGTAAACG
TGGTAGTATATGCCTTAAGCCGAAAAACATTTACAGCCTTACGAGCTCTAGATGCTAGATTGTCA
TTGGATGGAGATGGAGTAATATGTGAAGAATTGAAGCTTAAGCCAACATT
Found at i:62767 original size:23 final size:21
Alignment explanation
Indices: 62716--62796 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
62706 CCAGAACCCC
* * **
62716 AGGGGGTATCGATTCCCCTGT
1 AGGGGGAATCGGTTCCCCTCA
62737 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCC-TC-A
62760 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGAATCGGTTCCCCTCA
* *
62780 AGGGGGGATCGATTCCC
1 AGGGGGAATCGGTTCCC
62797 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 13 0.25
21 20 0.39
22 4 0.08
23 14 0.27
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCCTCA
Found at i:62784 original size:20 final size:21
Alignment explanation
Indices: 62737--62798 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 21
62727 ATTCCCCTGT
62737 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTT-CCC-TCAA
62760 AGGGGGAATCGGTTCCCTC-A
1 AGGGGGAATCGGTTCCCTCAA
* *
62780 AGGGGGGATCGATTCCCTC
1 AGGGGGAATCGGTTCCCTC
62799 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.49
21 2 0.05
22 3 0.08
23 14 0.38
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
AGGGGGAATCGGTTCCCTCAA
Found at i:71056 original size:21 final size:21
Alignment explanation
Indices: 71027--71081 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
71017 AGTCGAGGGT
71027 TATATGAGGTCCTTCGGGACA
1 TATATGAGGTCCTTCGGGACA
* * *
71048 TATACGAGGTCATTCGGGATA
1 TATATGAGGTCCTTCGGGACA
*
71069 TACATGAGGTCCT
1 TATATGAGGTCCT
71082 CTGAGATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (21 bp):
TATATGAGGTCCTTCGGGACA
Found at i:71661 original size:3 final size:3
Alignment explanation
Indices: 71646--71686 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
71636 CAAAAGCTCT
* *
71646 TTC TTC TTA TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
71687 TCACGTGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:72942 original size:44 final size:44
Alignment explanation
Indices: 72856--73106 Score: 270
Period size: 45 Copynumber: 5.6 Consensus size: 44
72846 TGAAAATAAT
* *** * * *
72856 AATGCATATGGGTTCATTATTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATAT-GGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* * *
72901 AATGCATATGGTGTATTATCAACATAAATGTATGCTATAGTTAA
1 AATGCATATGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* * *
72945 AATGCATATGGGTGTATTATCAACAGAAAAGTATACTATAGTTGA
1 AATGCATAT-GGTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
72990 AATGCATATGAGTGCATTATCAACAAAAAAGTATGTTATAGTTGA
1 AATGCATATG-GTGCATTATCAACATAAAAGTATGCTATAGTTGA
* *
73035 AAT-CATATGGGTGCATTATCAACATAAAAGTATGATATAGTGGAAA
1 AATGCATAT-GGTGCATTATCAACATAAAAGTATGCTATAGTTG--A
*
73081 AATGCATAATGGTGCATTATAAACAT
1 AATGCAT-ATGGTGCATTATCAACAT
73107 GAGTGGAGGT
Statistics
Matches: 177, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
44 70 0.40
45 83 0.47
46 4 0.02
47 18 0.10
48 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (44 bp):
AATGCATATGGTGCATTATCAACATAAAAGTATGCTATAGTTGA
Found at i:73042 original size:89 final size:89
Alignment explanation
Indices: 72893--73105 Score: 286
Period size: 89 Copynumber: 2.4 Consensus size: 89
72883 AAAGGATGCC
* * *
72893 ATAGTTGAAATGCATATGGTGTATTATCAACATAAATGTATGCTATAGTTAAAATGCATATGGGT
1 ATAGTTGAAATGCATATGGTGCATTATCAACAAAAAAGTATGCTATAGTTAAAATGCATATGGGT
*
72958 GTATTATCAACAGAAAAGTAT-ACT
66 GCATTATCAACAGAAAAGTATGA-T
* *
72982 ATAGTTGAAATGCATATGAGTGCATTATCAACAAAAAAGTATGTTATAGTTGAAAT-CATATGGG
1 ATAGTTGAAATGCATATG-GTGCATTATCAACAAAAAAGTATGCTATAGTTAAAATGCATATGGG
*
73046 TGCATTATCAACATAAAAGTATGAT
65 TGCATTATCAACAGAAAAGTATGAT
* *
73071 ATAGTGGAAAAATGCATAATGGTGCATTATAAACA
1 ATAGTTG--AAATGCAT-ATGGTGCATTATCAACA
73106 TGAGTGGAGG
Statistics
Matches: 110, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
89 53 0.48
90 33 0.30
91 21 0.19
92 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.31
Consensus pattern (89 bp):
ATAGTTGAAATGCATATGGTGCATTATCAACAAAAAAGTATGCTATAGTTAAAATGCATATGGGT
GCATTATCAACAGAAAAGTATGAT
Found at i:74560 original size:32 final size:32
Alignment explanation
Indices: 74514--74579 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
74504 CTTGGATTTG
*
74514 GGAATTTTGTTGTGATGTTGCACCTGCTGCTA
1 GGAATTTTGCTGTGATGTTGCACCTGCTGCTA
* *
74546 GGAATTTTGCTGTGATGTTGCGCCTGCTGTTA
1 GGAATTTTGCTGTGATGTTGCACCTGCTGCTA
74578 GG
1 GG
74580 TATAACTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.14, C:0.15, G:0.32, T:0.39
Consensus pattern (32 bp):
GGAATTTTGCTGTGATGTTGCACCTGCTGCTA
Found at i:82270 original size:30 final size:32
Alignment explanation
Indices: 82211--82276 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 32
82201 TACGGGTTGA
82211 CATACGAGCCATACGAGCCAATTGTTCTCCCCATG
1 CATACGAGCCATACGAGCC-A--GTTCTCCCCATG
82246 CATACGAGCCATACGAG-C-GTTCTCCCCATG
1 CATACGAGCCATACGAGCCAGTTCTCCCCATG
82276 C
1 C
82277 GAGGTGGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 13 0.42
34 1 0.03
35 17 0.55
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.21
Consensus pattern (32 bp):
CATACGAGCCATACGAGCCAGTTCTCCCCATG
Found at i:82295 original size:13 final size:13
Alignment explanation
Indices: 82279--82326 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
82269 CCCCATGCGA
*
82279 GGTGGCCATACGG
1 GGTGGACATACGG
82292 GGT-GACATAC-G
1 GGTGGACATACGG
*
82303 GGTTGACATACGG
1 GGTGGACATACGG
82316 GGT-GACATACG
1 GGTGGACATACG
82327 AGCCATACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 4 0.12
12 21 0.66
13 7 0.22
ACGTcount: A:0.23, C:0.19, G:0.40, T:0.19
Consensus pattern (13 bp):
GGTGGACATACGG
Found at i:82302 original size:12 final size:12
Alignment explanation
Indices: 82285--82326 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
82275 GCGAGGTGGC
82285 CATACGGGGTGA
1 CATACGGGGTGA
*
82297 CATACGGGTTGA
1 CATACGGGGTGA
82309 CATACGGGGTGA
1 CATACGGGGTGA
82321 CATACG
1 CATACG
82327 AGCCATACGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (12 bp):
CATACGGGGTGA
Found at i:82361 original size:35 final size:35
Alignment explanation
Indices: 82321--82407 Score: 165
Period size: 35 Copynumber: 2.5 Consensus size: 35
82311 TACGGGGTGA
82321 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
82356 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
*
82391 CATAGGAGCCATACGAG
1 CATACGAGCCATACGAG
82408 TGTTCTCCCC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (35 bp):
CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
Found at i:82425 original size:26 final size:26
Alignment explanation
Indices: 82396--82450 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
82386 CCATGCATAG
*
82396 GAGCCATACGAGTGTTCTCCCCATGC
1 GAGCCATACGAGCGTTCTCCCCATGC
82422 GAGCCATACGAGCGTTCTCCCCATGC
1 GAGCCATACGAGCGTTCTCCCCATGC
82448 GAG
1 GAG
82451 GTGGCCATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (26 bp):
GAGCCATACGAGCGTTCTCCCCATGC
Found at i:82523 original size:29 final size:29
Alignment explanation
Indices: 82473--82610 Score: 224
Period size: 29 Copynumber: 4.8 Consensus size: 29
82463 TGGAATAGAG
* *
82473 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
*
82502 AGGTCGCCATGTGGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
82531 AGGTCGCCATGTGGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
82560 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
82589 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
82611 CCATTCCCAT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
29 102 0.98
30 2 0.02
ACGTcount: A:0.13, C:0.31, G:0.33, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:82629 original size:13 final size:13
Alignment explanation
Indices: 82611--82642 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
82601 AGTCCCGGCG
82611 CCATTCCCATCAT
1 CCATTCCCATCAT
82624 CCATTCCCATCAT
1 CCATTCCCATCAT
82637 CCATTC
1 CCATTC
82643 ACATGCAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.47, G:0.00, T:0.31
Consensus pattern (13 bp):
CCATTCCCATCAT
Found at i:82843 original size:25 final size:25
Alignment explanation
Indices: 82814--82865 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
82804 TGTACAATTA
82814 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
82839 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
82864 TT
1 TT
82866 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:82906 original size:23 final size:23
Alignment explanation
Indices: 82878--82923 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
82868 AAAAGAAAGA
82878 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
82901 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
82924 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:82936 original size:4 final size:4
Alignment explanation
Indices: 82927--83009 Score: 62
Period size: 4 Copynumber: 20.5 Consensus size: 4
82917 ATTGCAGCCG
** **
82927 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGGG AGAA AGGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA AGAA
** *
82977 AGAA AGGG AGAA AGGAA AGTA AG-A AG-A AGAA AG
1 AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG
83010 GGAGATAAGG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
3 6 0.10
4 44 0.71
5 12 0.19
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (4 bp):
AGAA
Found at i:82938 original size:25 final size:23
Alignment explanation
Indices: 82878--82938 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
82868 AAAAGAAAGA
**
82878 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
82901 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
82924 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
82939 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:82952 original size:21 final size:21
Alignment explanation
Indices: 82928--83001 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
82918 TTGCAGCCGA
82928 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
82949 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
82970 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
82991 GAAAGTAAGAA
1 GAAAGAAAGAA
83002 GAAGAAAGGG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.01
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:82994 original size:13 final size:13
Alignment explanation
Indices: 82930--83001 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 13
82920 GCAGCCGAGA
82930 AAGAAA-GAAAGG
1 AAGAAAGGAAAGG
* *
82942 GAGAAAGGAAAGA
1 AAGAAAGGAAAGG
82955 AAGAAAGGGAGAAAGG
1 AAGAAA--G-GAAAGG
82971 AAAGAAA-GAAAGG
1 -AAGAAAGGAAAGG
* *
82984 GAGAAAGGAAAGT
1 AAGAAAGGAAAGG
82997 AAGAA
1 AAGAA
83002 GAAGAAAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 10 0.21
13 25 0.53
15 1 0.02
16 5 0.11
17 6 0.13
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.01
Consensus pattern (13 bp):
AAGAAAGGAAAGG
Found at i:83371 original size:32 final size:33
Alignment explanation
Indices: 83335--83411 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
83325 TTAGTTAGTA
83335 AGTTTATTAGTAG-TATA-TTATA-ATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTATATA-G-AAAAAT
*
83367 AGTTTATTAGTTAGTTTTAGTTATATAGAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAGAAAAAT
*
83401 ATTTTATTAGT
1 AGTTTATTAGT
83412 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 4 0.10
34 18 0.46
35 6 0.15
36 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAGAAAAAT
Found at i:83489 original size:16 final size:16
Alignment explanation
Indices: 83457--83503 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
83447 TTTAAAAAGT
*
83457 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
83473 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
83489 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
83504 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:83498 original size:15 final size:14
Alignment explanation
Indices: 83478--83508 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
83468 GTTTATTAGT
83478 TTATTATATTATAAG
1 TTATTATATTA-AAG
83493 TTATTATATTAAAG
1 TTATTATATTAAAG
83507 TT
1 TT
83509 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:85680 original size:17 final size:17
Alignment explanation
Indices: 85658--85690 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
85648 CAATGATTTT
*
85658 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
85675 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
85691 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:85707 original size:24 final size:22
Alignment explanation
Indices: 85675--85743 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
85665 AAATCATTAC
85675 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
85697 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
85722 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
85744 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:85929 original size:12 final size:13
Alignment explanation
Indices: 85892--86311 Score: 195
Period size: 12 Copynumber: 31.8 Consensus size: 13
85882 AAATAATAAC
*
85892 TAAATAATTATTA
1 TAAATCATTATTA
85905 TAAAATCATTATTA
1 T-AAATCATTATTA
*
85919 T-AATGATTATTA
1 TAAATCATTATTA
85931 TCAAATCATTACTAAATCA
1 T-AAATCATTA-T---T-A
*
85950 TCAAATCATTAAATATT
1 T-AAATCATT--AT-TA
85967 TAAATCATTA-T-
1 TAAATCATTATTA
*
85978 TAAATCATTTTTA
1 TAAATCATTATTA
*
85991 T-AATTATTATTA
1 TAAATCATTATTA
86003 CTAAATCATTATTA
1 -TAAATCATTATTA
*
86017 T-AATGATTATTA
1 TAAATCATTATTA
*
86029 TCAAATCATTACTA
1 T-AAATCATTATTA
*
86043 T-AATGATTA-TA
1 TAAATCATTATTA
86054 TCAAATCATTACTAAATCA
1 T-AAATCATTA-T---T-A
86073 TCAAATCATTAAAAATT-
1 T-AAATCATT----ATTA
86090 TAAATCATTA-T-
1 TAAATCATTATTA
*
86101 TAAATCATTTTTA
1 TAAATCATTATTA
*
86114 T-AATGATTATTA
1 TAAATCATTATTA
86126 CTAAATCATTATTA
1 -TAAATCATTATTA
*
86140 T-AATGATTATTA
1 TAAATCATTATTA
*
86152 TCAAATCATTACTA
1 T-AAATCATTATTA
*
86166 T-AATGATTATTA
1 TAAATCATTATTA
*
86178 TCAAATCATTA--C
1 T-AAATCATTATTA
* *
86190 TAAATCATCAATCA
1 TAAATCAT-TATTA
*
86204 TTAA--A-TATT-
1 TAAATCATTATTA
86213 TAAATCATTA-T-
1 TAAATCATTATTA
*
86224 TAAATCATTTTTA
1 TAAATCATTATTA
*
86237 T-AATGATTATTA
1 TAAATCATTATTA
86249 CTAAATCATTATTA
1 -TAAATCATTATTA
*
86263 T-AATGATTATTA
1 TAAATCATTATTA
*
86275 TCAAATCATTACTA
1 T-AAATCATTATTA
*
86289 T-AATGATTATTA
1 TAAATCATTATTA
86301 TCAAATCATTA
1 T-AAATCATTA
86312 CTAAATCATC
Statistics
Matches: 317, Mismatches: 40, Indels: 99
0.70 0.09 0.22
Matches are distributed among these distances:
9 3 0.01
10 2 0.01
11 40 0.13
12 108 0.34
13 17 0.05
14 97 0.31
15 1 0.00
16 16 0.05
17 2 0.01
18 4 0.01
19 23 0.07
20 1 0.00
21 1 0.00
22 1 0.00
23 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (13 bp):
TAAATCATTATTA
Found at i:85936 original size:26 final size:26
Alignment explanation
Indices: 85898--86311 Score: 327
Period size: 26 Copynumber: 16.7 Consensus size: 26
85888 TAACTAAATA
*
85898 ATTATTATAAAATCATTATTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
85924 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * *
85949 ATCA-AATC-ATTAAATATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * * *
85970 ATCATTATTAAATCATTTTTATAATT
1 ATTATTATCAAATCATTATTATAATG
85996 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
86022 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
86048 ATTA-TATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * * **
86072 ATCA-AATC-ATTAAAAATT-TAA--
1 ATTATTATCAAATCATTATTATAATG
* * *
86093 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
86119 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
86145 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
* *
86171 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATCAAATCATTATTATAATG
* * * *
86196 ATCAATCATTAAAT-A-T-TTA-AATC
1 AT-TATTATCAAATCATTATTATAATG
*
86219 ATTA-T-T-AAATCATTTTTATAATG
1 ATTATTATCAAATCATTATTATAATG
86242 ATTATTA-CTAAATCATTATTATAATG
1 ATTATTATC-AAATCATTATTATAATG
*
86268 ATTATTATCAAATCATTACTATAATG
1 ATTATTATCAAATCATTATTATAATG
86294 ATTATTATCAAATCATTA
1 ATTATTATCAAATCATTA
86312 CTAAATCATC
Statistics
Matches: 313, Mismatches: 49, Indels: 52
0.76 0.12 0.13
Matches are distributed among these distances:
19 4 0.01
20 2 0.01
21 9 0.03
22 8 0.03
23 41 0.13
24 20 0.06
25 28 0.09
26 198 0.63
27 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTATCAAATCATTATTATAATG
Found at i:86074 original size:123 final size:124
Alignment explanation
Indices: 85898--86369 Score: 894
Period size: 123 Copynumber: 3.8 Consensus size: 124
85888 TAACTAAATA
* *
85898 ATTATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
*
85963 TATTTAAATCATTATTAAATCATTTTTATAATTATTATTACTAAATCATTATTATAATG
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
86022 ATTATTATCAAATCATTACTATAATGATTA-TATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
*
86086 AATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
86145 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATC-AATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
86209 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
86268 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
1 ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
86333 TATTTAAATCATTATTAAATCATTTTTATAATGATTA
66 TATTTAAATCATTATTAAATCATTTTTATAATGATTA
86370 ATAAATACAT
Statistics
Matches: 341, Mismatches: 5, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
123 243 0.71
124 98 0.29
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (124 bp):
ATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAA
TATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATG
Found at i:86077 original size:19 final size:18
Alignment explanation
Indices: 86053--86108 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
86043 TAATGATTAT
86053 ATCAAATCATTACTAAATC
1 ATCAAATCATTA-TAAATC
*
86072 ATCAAATCATTAAAAAT-
1 ATCAAATCATTATAAATC
*
86089 -TTAAATCATTATTAAATC
1 ATCAAATCATTA-TAAATC
86107 AT
1 AT
86109 TTTTATAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
18 4 0.13
19 13 0.42
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (18 bp):
ATCAAATCATTATAAATC
Found at i:86254 original size:149 final size:144
Alignment explanation
Indices: 85973--86314 Score: 399
Period size: 149 Copynumber: 2.3 Consensus size: 144
85963 TATTTAAATC
* * *
85973 ATTATTAAATCATTTTTATAATTATTATTA-CTAAATCATTATTATAATGATTATTATCAAATCA
1 ATTA-TAAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCA
* *
86037 TTACTATAATGATTATATCAAATCATTACTAAATCATCAAATCATTAAAAATTTAAATCATTATT
64 TTACTATAATCATAATATCAAATCATTA-TAAATCAT---ATCATTAAAAATTTAAATCATTATT
*
86102 AAATCATTTTTATAATGATT
125 AAATCATTATTATAATGATT
86122 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTA-TAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCAT
* * *
86187 TACTA-AATCATCAATCATTAAAT-ATT-TAAATCAT-T-ATTAAATCATTTTTATAATGATTAT
65 TACTATAATCAT-AAT-ATCAAATCATTATAAATCATATCATTAAA--A-ATTTA-AATCATTA-
86247 TACTAAATCATTATTATAATGATT
123 T--TAAATCATTATTATAATGATT
*
86271 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTA
1 ATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTA
86315 AATCATCAAA
Statistics
Matches: 171, Mismatches: 11, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
142 6 0.04
143 1 0.01
144 1 0.01
145 4 0.02
146 7 0.04
147 9 0.05
148 6 0.04
149 130 0.76
150 7 0.04
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (144 bp):
ATTATAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATT
ACTATAATCATAATATCAAATCATTATAAATCATATCATTAAAAATTTAAATCATTATTAAATCA
TTATTATAATGATT
Found at i:86326 original size:97 final size:95
Alignment explanation
Indices: 86128--86330 Score: 259
Period size: 97 Copynumber: 2.1 Consensus size: 95
86118 GATTATTACT
86128 AAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAA
1 AAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAA
* *
86193 ATCATCAATCATTAAATATTTAAATCATTATT
66 ATCATCAATCATCAAATATTTAAATC--TATC
* *
86225 AAATCATTTTTATAATGATTATTA-CTAAATCATTATTATAATGATTATTATCAAATCATTACTA
1 AAATCATTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCATTACTA
* * *
86289 TAATGAT-TATTATCAAATCATTACTAAATC-ATC
65 -AATCATCAATCATCAAAT-ATT--TAAATCTATC
86322 AAATCATTA
1 AAATCATTA
86331 AATATTTAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
96 1 0.01
97 78 0.84
98 8 0.09
100 6 0.06
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.42
Consensus pattern (95 bp):
AAATCATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAA
ATCATCAATCATCAAATATTTAAATCTATC
Found at i:89252 original size:26 final size:24
Alignment explanation
Indices: 89194--89252 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
89184 CTAATAAACC
*
89194 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
89218 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
89246 TAATAAT
1 TAATAAT
89253 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:90032 original size:49 final size:50
Alignment explanation
Indices: 89985--90081 Score: 116
Period size: 49 Copynumber: 2.0 Consensus size: 50
89975 AGACACTAAC
*
89985 AAATTAATTAATATTTTT-TAT-AT-T-TAATAACTTAAACTAAGAAACT-
1 AAATTAACTAAT-TTTTTATATAATATATAATAACTTAAACTAAGAAACTA
*
90031 -AATTAACTAATTTTTTATATAATATAATAATAACTTAAACTAATAAACTA
1 AAATTAACTAATTTTTTATATAATAT-ATAATAACTTAAACTAAGAAACTA
90081 A
1 A
90082 TATAATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
44 5 0.12
45 13 0.31
46 2 0.05
47 1 0.02
49 21 0.50
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (50 bp):
AAATTAACTAATTTTTTATATAATATATAATAACTTAAACTAAGAAACTA
Found at i:90097 original size:28 final size:29
Alignment explanation
Indices: 90050--90111 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
90040 ATTTTTTATA
*
90050 TAATATAATAATAACTTAAACTAATAAAC
1 TAATATAATAATAACTTAAACTAACAAAC
90079 TAATATAAT-ATAACTTAAACTAACAAAC
1 TAATATAATAATAACTTAAACTAACAAAC
90107 TAATA
1 TAATA
90112 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 23 0.72
29 9 0.28
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (29 bp):
TAATATAATAATAACTTAAACTAACAAAC
Found at i:90121 original size:21 final size:21
Alignment explanation
Indices: 90088--90136 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
90078 CTAATATAAT
90088 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
90109 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
90130 ATTAACT
1 A-TAACT
90137 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:90714 original size:15 final size:15
Alignment explanation
Indices: 90694--90757 Score: 74
Period size: 15 Copynumber: 4.1 Consensus size: 15
90684 CCATCCCCTC
90694 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
*
90709 CCCCATGCATTCTCA
1 CCCCATGCATTCCCA
* *
90724 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
90742 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
90757 C
1 C
90758 GTCCCATGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 16 0.40
16 12 0.30
17 11 0.28
18 1 0.03
ACGTcount: A:0.17, C:0.53, G:0.08, T:0.22
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:90732 original size:17 final size:16
Alignment explanation
Indices: 90695--90765 Score: 81
Period size: 17 Copynumber: 4.4 Consensus size: 16
90685 CATCCCCTCC
90695 CCCATGCATTCCCAC-
1 CCCATGCATTCCCACT
*
90710 CCCATGCATTCTCACGT
1 CCCATGCATTCCCAC-T
* * *
90727 CCCATGCATCCCCTCC
1 CCCATGCATTCCCACT
90743 CCCATGCATTCCCACGT
1 CCCATGCATTCCCAC-T
90760 CCCATG
1 CCCATG
90766 TTGATTGCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.31
16 13 0.29
17 18 0.40
ACGTcount: A:0.17, C:0.51, G:0.10, T:0.23
Consensus pattern (16 bp):
CCCATGCATTCCCACT
Found at i:90748 original size:16 final size:16
Alignment explanation
Indices: 90685--90751 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
90675 TCCAATGCAC
90685 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
* *
90701 CATTCCC-ACCCCATG
1 CATCCCCTCCCCCATG
* * * *
90716 CATTCTCACGTCCCATG
1 CATCCCCTC-CCCCATG
90733 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
90749 CAT
1 CAT
90752 TCCCACGTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 13 0.32
16 15 0.38
17 12 0.30
ACGTcount: A:0.16, C:0.54, G:0.07, T:0.22
Consensus pattern (16 bp):
CATCCCCTCCCCCATG
Found at i:90750 original size:33 final size:32
Alignment explanation
Indices: 90695--90765 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 32
90685 CATCCCCTCC
* *
90695 CCCATGCATTCCCACCCCATGCATTCTCACGT
1 CCCATGCATCCCCACCCCATGCATTCCCACGT
*
90727 CCCATGCATCCCCTCCCCCATGCATTCCCACGT
1 CCCATGCATCCCC-ACCCCATGCATTCCCACGT
90760 CCCATG
1 CCCATG
90766 TTGATTGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.17, C:0.51, G:0.10, T:0.23
Consensus pattern (32 bp):
CCCATGCATCCCCACCCCATGCATTCCCACGT
Found at i:90847 original size:29 final size:29
Alignment explanation
Indices: 90805--90864 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
90795 AAATACACAC
90805 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
90834 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
90863 AG
1 AG
90865 ACCACTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.37, G:0.32, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:91059 original size:21 final size:21
Alignment explanation
Indices: 91033--91073 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
91023 TGTTATAAAA
*
91033 ATATAATATTTTCGGTTGAGC
1 ATATAACATTTTCGGTTGAGC
91054 ATATAACATTTTCGGTTGAG
1 ATATAACATTTTCGGTTGAG
91074 ATCAACCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (21 bp):
ATATAACATTTTCGGTTGAGC
Found at i:91373 original size:3 final size:3
Alignment explanation
Indices: 91365--91414 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
91355 AAAATATTTT
91365 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
91412 TTA
1 TTA
91415 CATTATTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:92749 original size:30 final size:30
Alignment explanation
Indices: 92714--92816 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
92704 GTAATTACTA
*
92714 TTTAGTCTTTTAAGTTTCTATTTTTGCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
* *
92744 TTTAGTCCTTTAAATTTCTATTTTTTCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
* *
92774 TTTAGTCCTTTAAGTTTATGTTTTTGCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
*
92804 TTTGGTCCTTTAA
1 TTTAGTCCTTTAA
92817 ATCAAATATG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (30 bp):
TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
Found at i:98824 original size:31 final size:31
Alignment explanation
Indices: 98779--98850 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
98769 CTAATGTCTC
*
98779 AGTGACTAAATCTTAATAAAACGATAACATA
1 AGTGACCAAATCTTAATAAAACGATAACATA
* **
98810 AGTGGCCAAATCTTAATAAAACGATAATGTA
1 AGTGACCAAATCTTAATAAAACGATAACATA
98841 AGTGACCAAA
1 AGTGACCAAA
98851 ACTTGTCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (31 bp):
AGTGACCAAATCTTAATAAAACGATAACATA
Done.