Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000899.1 Hibiscus syriacus cultivar Beakdansim tig00001766_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: 86665
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1264 original size:19 final size:20
Alignment explanation
Indices: 1240--1287 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1230 AACGATTTTC
*
1240 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1259 TTTTGAAACCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1279 TTTTGAAAA
1 TTTTGAAAA
1288 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:2020 original size:34 final size:33
Alignment explanation
Indices: 1981--2051 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
1971 TTTTGTAAAG
* * *
1981 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAACCCGTG-AAAAACTA
*
2015 GGGAAAGGTTATAGTTTAACCCGTGAAAAACTA
1 GGGAAAGGTTATAGCTTAACCCGTGAAAAACTA
2048 GGGA
1 GGGA
2052 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTATAGCTTAACCCGTGAAAAACTA
Found at i:2346 original size:21 final size:21
Alignment explanation
Indices: 2290--2373 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 21
2280 CCCAACAGTC
2290 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCGAACTTG
*
2311 GATATGTAAATCGCAATGCGAACTTG
1 G--A-CT--ATCGCAATGCGAACTTG
* * *
2337 GACTATCGCAACGCAAACTTC
1 GACTATCGCAATGCGAACTTG
*
2358 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
2374 TTTACATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
21 28 0.56
23 2 0.04
24 2 0.04
26 18 0.36
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
GACTATCGCAATGCGAACTTG
Found at i:2408 original size:21 final size:21
Alignment explanation
Indices: 2382--2559 Score: 229
Period size: 21 Copynumber: 8.6 Consensus size: 21
2372 GATTTACATA
2382 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2403 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
*
2423 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
2444 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2465 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
2485 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
2506 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2527 TTTGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
2548 TTCGCGTTGCGA
1 TTCGCATTGCGA
2560 ATCTGGAAAC
Statistics
Matches: 135, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
20 33 0.24
21 102 0.76
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:2408 original size:41 final size:42
Alignment explanation
Indices: 2363--2559 Score: 219
Period size: 41 Copynumber: 4.8 Consensus size: 42
2353 ACTTCGACTA
*
2363 TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCCAAGT
* *
2404 TCGCATTGCGAT-TTACATA-TTCGCATTGTGATAGTCCAAGT
1 TCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCCAAGT
* * * *
2445 TCGCGTTGCGATAGTCCAAGTTCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCA-AGT
*
2486 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGT
* *
2528 TTGCATTGCGATAGT-CGAAGTTCGCGTTGCGA
1 TCGCATTGCGATAGTAC-AAGTTCGCATTGCGA
2560 ATCTGGAAAC
Statistics
Matches: 138, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
41 90 0.65
42 48 0.35
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (42 bp):
TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGT
Found at i:2448 original size:62 final size:62
Alignment explanation
Indices: 2382--2539 Score: 289
Period size: 62 Copynumber: 2.5 Consensus size: 62
2372 GATTTACATA
*
2382 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
*
2444 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
*
2506 TTCGCATTGCGATAGTCCAAGTTTGCATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGAT
2540 AGTCGAAGTT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 92 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
Found at i:5052 original size:60 final size:60
Alignment explanation
Indices: 4971--5085 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
4961 ACGATCTCTC
* * * *
4971 GACTATAGGACATTACTTTGTTAAG-TCTCTTGATTATTAAAAGTTATAAAATGGTTCTTT
1 GACTATAAGACATTACTTTGTTAAGTTC-CTCGACTATTAAAAGTTAGAAAATGGTTCTTT
* * * *
5031 GACTATAAGACGTTGCTTTGTTGAGTTCCTCGACTATTAAAAGTTAGAAGATGGT
1 GACTATAAGACATTACTTTGTTAAGTTCCTCGACTATTAAAAGTTAGAAAATGGT
5086 CACCCAACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 44 0.96
61 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (60 bp):
GACTATAAGACATTACTTTGTTAAGTTCCTCGACTATTAAAAGTTAGAAAATGGTTCTTT
Found at i:13225 original size:40 final size:39
Alignment explanation
Indices: 13179--13280 Score: 134
Period size: 38 Copynumber: 2.6 Consensus size: 39
13169 ATTTATCTTT
13179 TTAATTTTGTAAAAAAAATATATATATAAATTTTATGAA-A
1 TTAATTTT-T-AAAAAAATATATATATAAATTTTATGAATA
*** *
13219 TTAATTTTTTTTAAAATATATATATAAATTTTATGAATT
1 TTAATTTTTAAAAAAATATATATATAAATTTTATGAATA
13258 TTAATTTTTTAAAAAAATATATA
1 TTAA-TTTTTAAAAAAATATATA
13281 AATTAATTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 25 0.47
39 5 0.09
40 23 0.43
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (39 bp):
TTAATTTTTAAAAAAATATATATATAAATTTTATGAATA
Found at i:14105 original size:21 final size:21
Alignment explanation
Indices: 14081--14144 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
14071 TAAAGCAAGT
14081 CATAATATATATATTAAAAAC
1 CATAATATATATATTAAAAAC
* **
14102 CATAA-A-ATA-A--AGCAAGT
1 CATAATATATATATTA-AAAAC
14119 CATAATATATATATTAAAAAC
1 CATAATATATATATTAAAAAC
14140 CATAA
1 CATAA
14145 AATCAAGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
16 1 0.03
17 7 0.23
18 2 0.06
19 6 0.19
20 2 0.06
21 12 0.39
22 1 0.03
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (21 bp):
CATAATATATATATTAAAAAC
Found at i:14113 original size:38 final size:38
Alignment explanation
Indices: 14071--14147 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
14061 AAGTCATATT
14071 TAAAGCAAGTCATAATATATATATTAAAAACCATAAAA
1 TAAAGCAAGTCATAATATATATATTAAAAACCATAAAA
14109 TAAAGCAAGTCATAATATATATATTAAAAACCATAAAA
1 TAAAGCAAGTCATAATATATATATTAAAAACCATAAAA
14147 T
1 T
14148 CAAGTGAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.27
Consensus pattern (38 bp):
TAAAGCAAGTCATAATATATATATTAAAAACCATAAAA
Found at i:15657 original size:11 final size:11
Alignment explanation
Indices: 15633--15688 Score: 52
Period size: 9 Copynumber: 5.5 Consensus size: 11
15623 GTAGTTCAAA
15633 CCGGTTTT--G
1 CCGGTTTTCAG
15642 CCGGTTTTCAG
1 CCGGTTTTCAG
*
15653 CCGG--TTCACC
1 CCGGTTTTCA-G
15663 CCGGTTTTC--
1 CCGGTTTTCAG
15672 CCGGTTTTCAG
1 CCGGTTTTCAG
15683 CCGGTT
1 CCGGTT
15689 CTTCCGGTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 21 0.54
10 4 0.10
11 11 0.28
12 3 0.08
ACGTcount: A:0.05, C:0.32, G:0.27, T:0.36
Consensus pattern (11 bp):
CCGGTTTTCAG
Found at i:15660 original size:30 final size:30
Alignment explanation
Indices: 15626--15689 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
15616 TGAACCGGTA
*
15626 GTTCAAACCGGTTTTGCCGGTTTTCAGCCG
1 GTTCAAACCGGTTTTCCCGGTTTTCAGCCG
**
15656 GTTCACCCCGGTTTTCCCGGTTTTCAGCCG
1 GTTCAAACCGGTTTTCCCGGTTTTCAGCCG
15686 GTTC
1 GTTC
15690 TTCCGGTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.09, C:0.31, G:0.25, T:0.34
Consensus pattern (30 bp):
GTTCAAACCGGTTTTCCCGGTTTTCAGCCG
Found at i:17385 original size:2 final size:2
Alignment explanation
Indices: 17378--17403 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17368 AGATTATGAT
17378 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
17404 ATAGAGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17571 original size:44 final size:44
Alignment explanation
Indices: 17523--17611 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
17513 ATTATGACCC
17523 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
1 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
17567 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
1 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
17611 T
1 T
17612 CCCCAAACTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (44 bp):
TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
Found at i:27784 original size:21 final size:20
Alignment explanation
Indices: 27758--27855 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
27748 ATCAGTTTCC
27758 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
27779 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
27798 ACAAATTCGCATTGCGATTTTCA
1 A-AAA-TCGCAACGCGATTTT-G
* *
27821 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
27841 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
27856 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 38 0.61
22 3 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:27884 original size:20 final size:20
Alignment explanation
Indices: 27822--28051 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
27812 CGATTTTCAA
* ** *
27822 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
27842 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
27862 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27882 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
27902 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
27922 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27942 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
27962 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
27982 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
28002 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
28022 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
28042 AAATCACAAC
1 AAATCGCAAC
28052 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:28971 original size:12 final size:12
Alignment explanation
Indices: 28954--28978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28944 ATATAATCCT
28954 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28966 GAAGAAGAAAAA
1 GAAGAAGAAAAA
28978 G
1 G
28979 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:31292 original size:33 final size:34
Alignment explanation
Indices: 31255--31438 Score: 144
Period size: 33 Copynumber: 5.2 Consensus size: 34
31245 GCAACGAGAG
31255 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* * *
31288 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCCCAACAATGAA
*
31322 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
* * * * *
31360 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAATGAA
*
31393 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
31431 AATCGCAA
1 AATCGCAA
31439 CGAGAGAATC
Statistics
Matches: 123, Mismatches: 12, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
31 1 0.01
32 6 0.05
33 47 0.38
34 29 0.24
35 2 0.02
37 1 0.01
38 30 0.24
39 6 0.05
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCCCAACAATGAA
Found at i:31309 original size:34 final size:33
Alignment explanation
Indices: 31241--31344 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 33
31231 CGGAAATTAC
* *
31241 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
31274 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
31308 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
31341 AATC
1 AATC
31345 GCAATGCGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
32 1 0.02
33 33 0.52
34 29 0.45
35 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:31346 original size:19 final size:19
Alignment explanation
Indices: 31255--31438 Score: 227
Period size: 19 Copynumber: 10.4 Consensus size: 19
31245 GCAACGAGAG
31255 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31274 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
31288 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
31308 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
31322 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31341 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31360 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
31374 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31393 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31412 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31431 AATCGCAA
1 AATCGCAA
31439 CGAGAGAATC
Statistics
Matches: 143, Mismatches: 6, Indels: 32
0.79 0.03 0.18
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 4 0.03
18 3 0.02
19 84 0.59
20 13 0.09
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:31368 original size:52 final size:52
Alignment explanation
Indices: 31283--31419 Score: 265
Period size: 52 Copynumber: 2.6 Consensus size: 52
31273 AAATCCCAAC
31283 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
31336 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
31388 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
31420 TGCGAAATGA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 68 0.81
53 16 0.19
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:31449 original size:52 final size:52
Alignment explanation
Indices: 31285--31460 Score: 232
Period size: 52 Copynumber: 3.4 Consensus size: 52
31275 ATCCCAACAT
* *
31285 GAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
* *
31338 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
* * *
31390 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAAC
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-AAATGCGAAAC
31440 GAGAGAATCGCAATGCGAAAT
1 GA-A-AATCGCAATGCGAAAT
31461 TATAAACGCA
Statistics
Matches: 115, Mismatches: 5, Indels: 7
0.91 0.04 0.06
Matches are distributed among these distances:
50 7 0.06
51 7 0.06
52 87 0.76
53 14 0.12
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAAC
Found at i:31454 original size:33 final size:33
Alignment explanation
Indices: 31341--31460 Score: 186
Period size: 33 Copynumber: 3.5 Consensus size: 33
31331 GCGAAATGAA
31341 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
31374 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
31412 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
31445 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
31461 TATAAACGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
33 45 0.56
34 1 0.01
35 2 0.03
36 2 0.03
37 1 0.01
38 29 0.36
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:31476 original size:71 final size:71
Alignment explanation
Indices: 31322--31460 Score: 278
Period size: 71 Copynumber: 2.0 Consensus size: 71
31312 GCAACGAGAG
31322 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
31387 AATGAA
66 AATGAA
31393 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
31458 AAT
66 AAT
31461 TATAAACGCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:31571 original size:19 final size:19
Alignment explanation
Indices: 31485--31563 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
31475 GATTCTCTCG
31485 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
31505 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
31524 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
31538 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
31557 TTGCGAT
1 TTGCGAT
31564 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 17 0.33
20 15 0.29
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31689 original size:14 final size:14
Alignment explanation
Indices: 31670--31706 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
31660 CATCAATTAC
31670 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
31684 ACAAATCATCTTTT
1 ACAAATCAACTTTT
31698 ACAAATCAA
1 ACAAATCAA
31707 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:33707 original size:14 final size:14
Alignment explanation
Indices: 33688--33744 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
33678 GTGAAATGAA
*
33688 AATCGCAACGACAG
1 AATCGCAACGAAAG
33702 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
33719 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
33735 AATCGCAACG
1 AATCGCAACG
33745 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:33717 original size:33 final size:33
Alignment explanation
Indices: 33669--33761 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
33659 GCGAAACCAA
* *
33669 AATCGCAACGTGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
33702 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
33735 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
33762 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:33726 original size:19 final size:19
Alignment explanation
Indices: 33632--33766 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
33622 TAGTTTACTT
* *
33632 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
33652 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
33671 TCGCAACGTGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
33690 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
33704 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
33723 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
33737 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
33756 TCGCAATGCGA
1 TCGCAACGCGA
33767 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 10 0.11
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:33784 original size:19 final size:18
Alignment explanation
Indices: 33762--33890 Score: 112
Period size: 19 Copynumber: 7.3 Consensus size: 18
33752 AAAATCGCAA
33762 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
33781 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
33795 TGCGATTTTTGTTTCGCGT
1 TGCGA-TTTTGTTTCGCGT
*
33814 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
33828 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
33847 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
33866 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
33886 TGCGA
1 TGCGA
33891 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 4 0.04
16 2 0.02
17 2 0.02
18 5 0.06
19 45 0.50
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:33809 original size:33 final size:33
Alignment explanation
Indices: 33762--33853 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
33752 AAAATCGCAA
*
33762 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTCGTTTCGCGTTGCGATTC-TGTCGT
*
33795 TGCGATTTTTGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCGTTTCGCGTTGCGATTCTGTCGT
*
33828 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCGTTTCGCGTTGCGATT
33854 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCGTTTCGCGTTGCGATTCTGTCGT
Found at i:34054 original size:93 final size:93
Alignment explanation
Indices: 33938--34406 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
33928 ATGGATTGCA
33938 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
34002 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
34030 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
34095 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
34123 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
34188 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
34216 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
34281 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
34309 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTGAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
34374 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
34402 TTACT
1 TTACT
34407 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 370 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:36129 original size:14 final size:14
Alignment explanation
Indices: 36110--36199 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
36100 TTGAAATGAA
36110 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
36124 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
36143 AATCGCAACGAGAG
1 AATCGCAACGAGAG
36157 AATCGCAACGCGAAATGAG
1 AATCGCAA--CG--A-GAG
36176 AATCGCAACGAGAG
1 AATCGCAACGAGAG
36190 AATCGCAACG
1 AATCGCAACG
36200 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 31 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 21 0.33
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:36147 original size:33 final size:33
Alignment explanation
Indices: 36102--36216 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
36092 TCTTTTGGTT
36102 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
36135 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
36168 GAAATGAGAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
36201 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
36217 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:36148 original size:19 final size:19
Alignment explanation
Indices: 36121--36221 Score: 105
Period size: 19 Copynumber: 5.8 Consensus size: 19
36111 ATCGCAACGA
36121 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
*
36140 GACAATCGCAA--CG--A-
1 GAGAATCGCAACGCGAAAT
36154 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
36173 GAGAATCGCAA--CG--A-
1 GAGAATCGCAACGCGAAAT
36187 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
* *
36206 GAAAATCGCAATGCGA
1 GAGAATCGCAACGCGA
36222 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
14 21 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 35 0.51
ACGTcount: A:0.43, C:0.22, G:0.26, T:0.10
Consensus pattern (19 bp):
GAGAATCGCAACGCGAAAT
Found at i:36252 original size:14 final size:14
Alignment explanation
Indices: 36233--36287 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
36223 TTTGGTTTCG
36233 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36247 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
36266 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36280 CGTTGCGA
1 CGTTGCGA
36288 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36265 original size:33 final size:33
Alignment explanation
Indices: 36217--36287 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
36207 AAAATCGCAA
**
36217 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
36250 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
36283 TGCGA
1 TGCGA
36288 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:36295 original size:33 final size:33
Alignment explanation
Indices: 36228--36309 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
36218 GCGATTTTGG
***
36228 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
36261 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
36294 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
36310 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:36314 original size:20 final size:20
Alignment explanation
Indices: 36240--36328 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
36230 TCGCGTTGCG
36240 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
36260 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
36273 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
36293 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
36313 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
36329 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:36450 original size:33 final size:33
Alignment explanation
Indices: 36408--36478 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
36398 AATACTAACT
*
36408 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
36441 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
36474 TGAAA
1 TGAAA
36479 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:36711 original size:22 final size:22
Alignment explanation
Indices: 36659--36713 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
36649 TGGTTGTGAG
**
36659 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
36681 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
36703 GGATTTCTTCG
1 GGATTTCTTCG
36714 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:36885 original size:20 final size:20
Alignment explanation
Indices: 36860--37053 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
36850 CTTTAAATAT
36860 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
36880 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
36902 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
36921 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
36941 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
36961 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
36981 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37001 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
37021 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
37041 CGCGTTGCGATTT
1 CGCGTTGCGATTT
37054 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:37047 original size:60 final size:60
Alignment explanation
Indices: 36860--37053 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
36850 CTTTAAATAT
**
36860 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
36921 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
36981 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
37041 CGCGTTGCGATTT
1 CGCGTTGCGATTT
37054 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:37054 original size:20 final size:20
Alignment explanation
Indices: 37020--37117 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
37010 ATTTATGTGT
*
37020 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAA
* *
37040 TCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTT-CATAA
** *
37061 TCGCAATGCGAATTTTTACT-A
1 TCGCGTTGCG-ATTTTCA-TAA
* *
37082 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTC-ATAA
37103 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
37118 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 20 0.32
21 37 0.60
22 5 0.08
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAA
Found at i:37113 original size:42 final size:41
Alignment explanation
Indices: 37020--37117 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
37010 ATTTATGTGT
* *
37020 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTCATATTCGCATTGCGATTTTGCAAAA
** *
37061 TCGCAATGCGAATTTTTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCG-ATTTTCA-TATTCGCATTGCGATTTTGCAA-AA
37103 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
37118 GGAAACTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
41 15 0.32
42 30 0.64
43 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCATATTCGCATTGCGATTTTGCAAAA
Found at i:37911 original size:2 final size:2
Alignment explanation
Indices: 37904--37930 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37894 TTACAGTTAT
37904 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 T
37931 TAATACCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37983 original size:18 final size:18
Alignment explanation
Indices: 37960--37994 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
37950 AATGATATGC
37960 GCATAAATAAAATTTTAT
1 GCATAAATAAAATTTTAT
37978 GCATAAATAAAATTTTA
1 GCATAAATAAAATTTTA
37995 GGGCATGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (18 bp):
GCATAAATAAAATTTTAT
Found at i:38358 original size:2 final size:2
Alignment explanation
Indices: 38353--38377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38343 TAATTTAAAT
38353 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 T
38378 TAATACCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44099 original size:22 final size:22
Alignment explanation
Indices: 44071--44118 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
44061 TTATTGGTTC
44071 AATCGG-TCTGATCGGTCAAAAG
1 AATCGGTTC-GATCGGTCAAAAG
* *
44093 AATCGGTTCGATCGGTTAGAAG
1 AATCGGTTCGATCGGTCAAAAG
44115 AATC
1 AATC
44119 AGACAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (22 bp):
AATCGGTTCGATCGGTCAAAAG
Found at i:45160 original size:42 final size:40
Alignment explanation
Indices: 45101--45190 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
45091 TAACAATTAT
45101 TTATTTATTAATAAATAATAAAAATAATAAGTTAAGTAAT-ATA
1 TTATTT-TTAATAAATAAT-AAAAT-ATAA-TTAAGTAATAATA
* *
45144 TTATTTTTAATAAATAATAAAATATTATTAATTAATAATA
1 TTATTTTTAATAAATAATAAAATATAATTAAGTAATAATA
45184 TTATTTT
1 TTATTTT
45191 AATGCAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
39 8 0.18
40 13 0.30
41 5 0.11
42 12 0.27
43 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (40 bp):
TTATTTTTAATAAATAATAAAATATAATTAAGTAATAATA
Found at i:45161 original size:21 final size:21
Alignment explanation
Indices: 45105--45184 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
45095 AATTATTTAT
45105 TTATTAATAAATAATA-AA-A
1 TTATTAATAAATAATATAATA
* * * *
45124 ATAATAAGTTAAGTAATATATTA
1 TTATTAA--TAAATAATATAATA
* *
45147 TTTTTAATAAATAATAAAATA
1 TTATTAATAAATAATATAATA
*
45168 TTATTAATTAATAATAT
1 TTATTAATAAATAATAT
45185 TATTTTAATG
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
19 5 0.11
21 33 0.75
22 1 0.02
23 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TTATTAATAAATAATATAATA
Found at i:45192 original size:18 final size:18
Alignment explanation
Indices: 45132--45193 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 18
45122 AAATAATAAG
*
45132 TTAAGTAAT-ATATTATTT
1 TTAATTAATAATATTA-TT
* *
45150 TTAATAAATAATAAAATATT
1 TTAATTAATAAT--ATTATT
45170 ATTAATTAATAATATTATT
1 -TTAATTAATAATATTATT
45189 TTAAT
1 TTAAT
45194 GCAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 12 0.34
19 7 0.20
20 2 0.06
21 14 0.40
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAATTAATAATATTATT
Found at i:53761 original size:19 final size:18
Alignment explanation
Indices: 53729--53778 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
53719 AGAATCTTAA
* *
53729 AAAAATTTGATATCCATT
1 AAAATTTTGGTATCCATT
53747 AAAATTTTAGGTATCCATT
1 AAAATTTT-GGTATCCATT
*
53766 AGAATTTTGGTAT
1 AAAATTTTGGTAT
53779 TACATCATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (18 bp):
AAAATTTTGGTATCCATT
Found at i:54598 original size:19 final size:18
Alignment explanation
Indices: 54553--54597 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
54543 TATAAAGTTC
54553 TTTATTTTCTTTTCAAGT
1 TTTATTTTCTTTTCAAGT
54571 TTTCATTTTCATTTT-AAGT
1 TTT-ATTTTC-TTTTCAAGT
54590 TTTATTTT
1 TTTATTTT
54598 TAAACATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 13 0.52
20 4 0.16
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTATTTTCTTTTCAAGT
Found at i:55921 original size:49 final size:45
Alignment explanation
Indices: 55852--55994 Score: 198
Period size: 44 Copynumber: 3.1 Consensus size: 45
55842 AATAAATTTT
* *
55852 CCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAACATACTTA
1 CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
*
55897 TCATTTATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
1 -C---CATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
* *
55946 CCA-TTATTCCATAAGCTCGTAAGCTTATTTTACTAATATACTTT
1 CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
55990 CCATT
1 CCATT
55995 AACCTCATTT
Statistics
Matches: 87, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
44 42 0.48
45 2 0.02
46 1 0.01
48 1 0.01
49 41 0.47
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.41
Consensus pattern (45 bp):
CCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
Found at i:56148 original size:59 final size:58
Alignment explanation
Indices: 56085--56558 Score: 327
Period size: 59 Copynumber: 8.1 Consensus size: 58
56075 TAGTACTCTC
* * * * *
56085 AGTGCTCTATCTGGAAAATCATACACTTAGTATGCTTCCCTTTTCATTTTAGCACACGA
1 AGTGCTCTATCTGG-AAATCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTA
* * ** * ** *
56144 AGTGCCCTATTTAAAAATTCATAC-CATTAGTATGATTTTGTTACCATTTTAGCACA-TGA
1 AGTGCTCTATCTGGAAA-TCATACAC-TCAGTATGATTTCCTTATCATTTTAGCACACT-A
* * * * * * *
56203 AATGCCCTATGTGAAAATCCATAC-CATTAGTATGATTTCCTTATC-TTTGTAGCACCCTT
1 AGTGCTCTATCTGGAAAT-CATACAC-TCAGTATGATTTCCTTATCATTT-TAGCACACTA
* * * * *
56262 AGTGTTTTATCTGGAAATCCATACACTCAGTATGATTCCCTTACCTTTTTAGCACA-TAA
1 AGTGCTCTATCTGGAAAT-CATACACTCAGTATGATTTCCTTATCATTTTAGCACACT-A
* * *** * * * *
56321 AATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTGTCA-TTTAGCACGCTC
1 AGTGCTCTATCTGGAAAT-CATACACTCAGTATGATTTCCTTATCATTTTAGCACACTA
* * * *
56379 AGTACTCCATATGGAAATCTATACACTCAGTATGATTTCCTTATCA-TTTAGCACACTC
1 AGTGCTCTATCTGGAAATC-ATACACTCAGTATGATTTCCTTATCATTTTAGCACACTA
* * * * *
56437 AGTGCTCCATATTGAAATCTATACACTCAATATGATTTCCTTATCA-TTTAGCACACTC
1 AGTGCTCTATCTGGAAATC-ATACACTCAGTATGATTTCCTTATCATTTTAGCACACTA
* * * * *
56495 AGTGCTCCATAC-GAAAATCTATACACTCAGTATGGTTTCCCTATCATTTTAGCACACAA
1 AGTGCTCTAT-CTGGAAATC-ATACACTCAGTATGATTTCCTTATCATTTTAGCACACTA
56554 AGTGC
1 AGTGC
56559 CATTCGGTAA
Statistics
Matches: 336, Mismatches: 66, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
57 1 0.00
58 156 0.46
59 174 0.52
60 5 0.01
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (58 bp):
AGTGCTCTATCTGGAAATCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTA
Found at i:56312 original size:118 final size:117
Alignment explanation
Indices: 56184--56559 Score: 368
Period size: 116 Copynumber: 3.2 Consensus size: 117
56174 TATGATTTTG
* * *
56184 TTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATT-AGTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATA-CATTCAATATGATTTCCTTATC
* * ** ** *
56248 TTTGTAGCACCCTTAGTGTTTTATCTGGAAATCCATACACTCAGTATGATTCCC
65 ATT-TAGCACCCTCAGTACTCCATATGGAAATCCATACACTCAGTATGATTCCC
* * ** *
56302 TTACCTTTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTGTCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATACATTCAATATGATTTCCTTATCA
* * *
56367 TTTAGCACGCTCAGTACTCCATATGGAAATCTATACACTCAGTATGATTTCC
66 TTTAGCACCCTCAGTACTCCATATGGAAATCCATACACTCAGTATGATTCCC
* * * * *
56419 TTATCA-TTTAGCACACT-CAGTGCTCCATAT-TG-AAATCTATACACTCAATATGATTTCCTTA
1 TTACCATTTTAGCACA-TAAAATGC-CC-TATCTGAAAATCCATACATTCAATATGATTTCCTTA
* * * * * *
56480 TCATTTAGCACACTCAGTGCTCCATACGAAAATCTATACACTCAGTATGGTTTCCC
63 TCATTTAGCACCCTCAGTACTCCATATGGAAATCCATACACTCAGTAT-GATTCCC
* * *
56536 -TATCATTTTAGCACACAAAGTGCC
1 TTACCATTTTAGCACATAAAATGCC
56560 ATTCGGTAAT
Statistics
Matches: 216, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
116 87 0.40
117 71 0.33
118 58 0.27
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (117 bp):
TTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATACATTCAATATGATTTCCTTATCA
TTTAGCACCCTCAGTACTCCATATGGAAATCCATACACTCAGTATGATTCCC
Found at i:56413 original size:58 final size:58
Alignment explanation
Indices: 56231--56551 Score: 331
Period size: 58 Copynumber: 5.5 Consensus size: 58
56221 CCATACCATT
* * * * ** * *
56231 AGTATGATTTCCTTATCTTTGTAGCACCCTTAGTGTTTTATCTGGAAATCCATACACTC
1 AGTATGATTTCCTTATCATT-TAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
* * * * * * * ***
56290 AGTATGATTCCCTTACCTTTTTAGCACA-TAAAATGC-CCTATCTGGAAATCCATATTTTC
1 AGTATGATTTCCTTATC-ATTTAGCACACT-CAGTGCTCC-ATATGGAAATCTATACACTC
* * * *
56349 AATATGATTTCCTTGTCATTTAGCACGCTCAGTACTCCATATGGAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
*
56407 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATTGAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
* * *
56465 AATATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATACGAAAATCTATACACTC
1 AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
* *
56523 AGTATGGTTTCCCTATCATTTTAGCACAC
1 AGTATGATTTCCTTATCA-TTTAGCACAC
56552 AAAGTGCCAT
Statistics
Matches: 219, Mismatches: 37, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
58 149 0.68
59 67 0.31
60 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.36
Consensus pattern (58 bp):
AGTATGATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTC
Found at i:56437 original size:30 final size:30
Alignment explanation
Indices: 56401--56497 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 30
56391 GGAAATCTAT
56401 ACACTCAGTATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
* * * * *
56431 ACACTCAG--TG--CTCCATATTGAAATCTA-T
1 ACACTCAGTATGATTTCCTTA-T--CATTTAGC
*
56459 ACACTCAATATGATTTCCTTATCATTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTAGC
56489 ACACTCAGT
1 ACACTCAGT
56498 GCTCCATACG
Statistics
Matches: 47, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
26 5 0.11
27 1 0.02
28 9 0.19
29 8 0.17
30 18 0.38
31 1 0.02
32 5 0.11
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (30 bp):
ACACTCAGTATGATTTCCTTATCATTTAGC
Found at i:57017 original size:24 final size:24
Alignment explanation
Indices: 56989--57039 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
56979 GCAGTTCAGC
*
56989 CACGTGTGATTAAAAATCAGCAGT
1 CACGTGTGATTAAAAAGCAGCAGT
57013 CACGTGTGATTAAAAAGCAGCAGT
1 CACGTGTGATTAAAAAGCAGCAGT
57037 CAC
1 CAC
57040 AACCTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (24 bp):
CACGTGTGATTAAAAAGCAGCAGT
Found at i:61081 original size:16 final size:16
Alignment explanation
Indices: 61060--61093 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
61050 TAAGATGAAC
61060 ATAATTATT-AAAATAA
1 ATAATTATTCAAAA-AA
61076 ATAATTATTCAAAAAA
1 ATAATTATTCAAAAAA
61092 AT
1 AT
61094 TTATGATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAATTATTCAAAAAA
Found at i:63464 original size:9 final size:10
Alignment explanation
Indices: 63445--63495 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
63435 TAATTAAAAT
63445 AACAAAT-AA
1 AACAAATAAA
63454 AA-AAATAAA
1 AACAAATAAA
*
63463 AAC-AGTAAA
1 AACAAATAAA
63472 AACAACATAAA
1 AACAA-ATAAA
63483 TAACAAATAAA
1 -AACAAATAAA
63494 AA
1 AA
63496 TAAAATAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 4 0.11
9 14 0.40
10 3 0.09
11 9 0.26
12 5 0.14
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (10 bp):
AACAAATAAA
Found at i:64263 original size:34 final size:34
Alignment explanation
Indices: 64204--64271 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
64194 GTGGAACAAG
* *
64204 GAAACATGGAATGGTGGAAGGTTGGTAGAGGCAT
1 GAAACATGGAATAGTGGAAGCTTGGTAGAGGCAT
* * *
64238 GAAACATGGGATAGTGGGAGCTTGGTGGAGGCAT
1 GAAACATGGAATAGTGGAAGCTTGGTAGAGGCAT
64272 TGTAGTGGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.43, T:0.21
Consensus pattern (34 bp):
GAAACATGGAATAGTGGAAGCTTGGTAGAGGCAT
Found at i:64855 original size:42 final size:40
Alignment explanation
Indices: 64742--64855 Score: 93
Period size: 42 Copynumber: 2.7 Consensus size: 40
64732 GCCCGAAGGT
* * *
64742 CTTATGGATGGCCTGAAGGTCTTACCATCTTGCTCGAAAGA
1 CTTATAGATGGCCT-AAGGACTTACCATCATGCTCGAAAGA
* * * * * *
64783 CTTACAAATGGCCCGAAAGACTCACGCATCATGTTCGAAAGA
1 CTTATAGATGG-CCTAAGGACTTAC-CATCATGCTCGAAAGA
*
64825 CTTATTGATGGCCATAAGGACTTACTCATCA
1 CTTATAGATGGCC-TAAGGACTTAC-CATCA
64856 AGAAATCCTT
Statistics
Matches: 54, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
41 17 0.31
42 37 0.69
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (40 bp):
CTTATAGATGGCCTAAGGACTTACCATCATGCTCGAAAGA
Found at i:64942 original size:39 final size:39
Alignment explanation
Indices: 64888--65443 Score: 878
Period size: 39 Copynumber: 14.2 Consensus size: 39
64878 TAGTTTCTTT
** * *
64888 AAATCTTTTGTTTCGATCGAAACTATCTTAAGTGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
64927 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
64966 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGACA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
65005 AAATCTTCTGTTTCGAGGGAAATTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
65044 AAATATTTTGTTTCGAGGGAAACTACCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* *
65083 AAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGACA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
65122 AAATATTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
65161 AAATCTTATGTTTTGAGGGAAACTATCTCAAGTGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
65200 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
65239 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
65278 AAATCTTTTTGTTTCTAGGGAAACTATCTCAGGCGAGACA
1 AAATC-TTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
65318 AAATCTTATGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
* * *
65357 AAATCTTTTGTTTCGAGGAAAACTATCTTAAGCGAGACA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
*
65396 AAATCTTTTGTTTAGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
65435 AAATCTTTT
1 AAATCTTTT
65444 TTAAAAACAA
Statistics
Matches: 471, Mismatches: 45, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
39 436 0.93
40 35 0.07
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (39 bp):
AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAGATA
Found at i:65541 original size:76 final size:76
Alignment explanation
Indices: 65415--65623 Score: 243
Period size: 76 Copynumber: 2.8 Consensus size: 76
65405 GTTTAGAGGG
* *
65415 AAACTATCTCAAGCGAGATAAAATCTT-TTTT---AAAAACAATCTTGAGTGAAATGAAATGTCT
1 AAACTATCTCAAGCGAGA-CAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAAT-AAATCT-T
65476 TCT-TTT-GAGTAA
63 TCTATTTCGAGTAA
* * *
65488 AAACCATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAATAATCTTGAGTGAAATAAATCTTTTT
1 AAACTATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTTCT
65553 ATTTCGAGTAA
66 ATTTCGAGTAA
* * ** *
65564 AAACTGTCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATC
1 AAACTATCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAATC
65624 CTCTGTATTA
Statistics
Matches: 117, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
72 7 0.06
73 21 0.18
74 3 0.03
75 8 0.07
76 76 0.65
77 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (76 bp):
AAACTATCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATAAATCTTTCT
ATTTCGAGTAA
Found at i:65610 original size:36 final size:35
Alignment explanation
Indices: 65486--65623 Score: 107
Period size: 36 Copynumber: 3.7 Consensus size: 35
65476 TCTTTTGAGT
* *
65486 AAAAACCATCTCAAGCGAGACAAATCTTGTTTTAAG
1 AAAAACAATCTCAAGTGAGACAAATC-TGTTTTAAG
* ** * *
65522 AAAAATAATCTTGAGTGAAATAAATCT-TTTTATTTCGAG
1 AAAAACAATCTCAAGTGAGACAAATCTGTTTTA-----AG
**
65561 TAAAAACTGTCTCAAGTGAGACAAAGTCTGTTTTAAG
1 -AAAAACAATCTCAAGTGAGACAAA-TCTGTTTTAAG
*
65598 AAAAACAATCTCAAGTGAGATAAATC
1 AAAAACAATCTCAAGTGAGACAAATC
65624 CTCTGTATTA
Statistics
Matches: 77, Mismatches: 17, Indels: 17
0.69 0.15 0.15
Matches are distributed among these distances:
34 5 0.06
35 3 0.04
36 40 0.52
37 2 0.03
39 2 0.03
40 17 0.22
41 3 0.04
42 5 0.06
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (35 bp):
AAAAACAATCTCAAGTGAGACAAATCTGTTTTAAG
Found at i:67296 original size:20 final size:21
Alignment explanation
Indices: 67258--67299 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
67248 TTGCTTCAGG
*
67258 GGTATCGATACCTCTGCTACA
1 GGTACCGATACCTCTGCTACA
67279 GGTACCGATACC-CTGCTACA
1 GGTACCGATACCTCTGCTACA
67299 G
1 G
67300 TACTTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (21 bp):
GGTACCGATACCTCTGCTACA
Found at i:68528 original size:15 final size:16
Alignment explanation
Indices: 68493--68530 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
68483 TATCATATAA
68493 CATAT-ATCACATATTG
1 CATATAATCACATA-TG
68509 CATATAATCACATA-G
1 CATATAATCACATATG
68524 CATATAA
1 CATATAA
68531 ACTTATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 5 0.24
17 8 0.38
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (16 bp):
CATATAATCACATATG
Found at i:74197 original size:23 final size:23
Alignment explanation
Indices: 74154--74218 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
74144 ATGCATGGCA
*
74154 GAGTGCATCGATGCA-CATTCAAG
1 GAGTGCATCGGTGCATC-TTCAAG
*
74177 GAGTGCATCGGTGCATCTTC-AT
1 GAGTGCATCGGTGCATCTTCAAG
*
74199 GA-TGTATCGGTGCATCTTCA
1 GAGTGCATCGGTGCATCTTCA
74219 TGATGTATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 16 0.43
22 3 0.08
23 17 0.46
24 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
GAGTGCATCGGTGCATCTTCAAG
Found at i:74209 original size:21 final size:21
Alignment explanation
Indices: 74183--74226 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
74173 CAAGGAGTGC
74183 ATCGGTGCATCTTCATGATGT
1 ATCGGTGCATCTTCATGATGT
74204 ATCGGTGCATCTTCATGATGT
1 ATCGGTGCATCTTCATGATGT
74225 AT
1 AT
74227 TGATGCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (21 bp):
ATCGGTGCATCTTCATGATGT
Found at i:74239 original size:21 final size:21
Alignment explanation
Indices: 74183--74233 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
74173 CAAGGAGTGC
*
74183 ATCGGTGCATCTTCATGATGT
1 ATCGATGCATCTTCATGATGT
*
74204 ATCGGTGCATCTTCATGATGT
1 ATCGATGCATCTTCATGATGT
*
74225 ATTGATGCA
1 ATCGATGCA
74234 CATTCAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (21 bp):
ATCGATGCATCTTCATGATGT
Found at i:82531 original size:17 final size:17
Alignment explanation
Indices: 82501--82534 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
82491 TAAACTTGAT
82501 TTAAATATTAATCTAAA
1 TTAAATATTAATCTAAA
82518 TTAAA-ATTACATCTAAA
1 TTAAATATTA-ATCTAAA
82535 AAATAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATATTAATCTAAA
Found at i:83347 original size:33 final size:33
Alignment explanation
Indices: 83305--83369 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
83295 ATTGTTGTGG
* *
83305 GTGGAAGAAGGAAACATAGAATGGTGGAAGGTA
1 GTGGAAGAAGAAAACATAGAATGGTGCAAGGTA
*
83338 GTGGAAGAAGAAAACATGGAATGGTGCAAGGT
1 GTGGAAGAAGAAAACATAGAATGGTGCAAGGT
83370 TGGTAGAGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.38, T:0.15
Consensus pattern (33 bp):
GTGGAAGAAGAAAACATAGAATGGTGCAAGGTA
Found at i:85636 original size:15 final size:15
Alignment explanation
Indices: 85616--85653 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
85606 AGTTGTGAAA
85616 TATCTTGCTAAACAT
1 TATCTTGCTAAACAT
85631 TATCTTGCTAAACAT
1 TATCTTGCTAAACAT
*
85646 AATCTTGC
1 TATCTTGC
85654 ATTTCGAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (15 bp):
TATCTTGCTAAACAT
Done.