Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008334.1 Hibiscus syriacus cultivar Beakdansim tig00111047_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: 195962
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2614 original size:14 final size:16
Alignment explanation
Indices: 2593--2630 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
2583 TCTTACTTAC
2593 ATATAAAAACA-AATG
1 ATATAAAAACATAATG
2608 A-AT-AAAACATAATG
1 ATATAAAAACATAATG
2622 ATATAAAAA
1 ATATAAAAA
2631 TGATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.30
14 7 0.35
15 3 0.15
16 4 0.20
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (16 bp):
ATATAAAAACATAATG
Found at i:14181 original size:16 final size:16
Alignment explanation
Indices: 14160--14190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14150 TTTATTTATA
14160 TACACTTATATACATG
1 TACACTTATATACATG
*
14176 TACACTTGTATACAT
1 TACACTTATATACAT
14191 AAACTGTTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
TACACTTATATACATG
Found at i:17870 original size:16 final size:16
Alignment explanation
Indices: 17849--17881 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17839 TTATAAATGC
*
17849 ACTTGTAATTTTGGAA
1 ACTTGTAATTTTAGAA
17865 ACTTGTAATTTTAGAA
1 ACTTGTAATTTTAGAA
17881 A
1 A
17882 AGCATCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (16 bp):
ACTTGTAATTTTAGAA
Found at i:19012 original size:2 final size:2
Alignment explanation
Indices: 19005--19038 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18995 TTTCCTATTA
19005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19039 TGGGAGGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24854 original size:64 final size:64
Alignment explanation
Indices: 24785--25005 Score: 234
Period size: 64 Copynumber: 3.5 Consensus size: 64
24775 TTGAAGGTGT
* **
24785 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
24848 C
64 C
* * **
24849 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATTAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
** * * ** *
24913 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
24977 ACCGATGCATCA-GTAGTGCACCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
25006 ACCTTCATTA
Statistics
Matches: 133, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 126 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:25325 original size:12 final size:12
Alignment explanation
Indices: 25307--25342 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
25297 TATATATGTT
25307 CATGTGATATGA
1 CATGTGATATGA
*
25319 TATGTGATATGA
1 CATGTGATATGA
25331 CATGTGATATGA
1 CATGTGATATGA
25343 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:25364 original size:23 final size:26
Alignment explanation
Indices: 25307--25375 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
25297 TATATATGTT
**
25307 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
25331 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
25356 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
25376 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:31754 original size:64 final size:64
Alignment explanation
Indices: 31685--31905 Score: 225
Period size: 64 Copynumber: 3.5 Consensus size: 64
31675 TTGAAGGTGT
* **
31685 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
31748 C
64 C
* * * **
31749 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAATATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
** * * ** *
31813 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
31877 ACCGATGCATCA-GTAGTACATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
31906 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
63 1 0.01
64 124 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:32232 original size:12 final size:12
Alignment explanation
Indices: 32214--32249 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
32204 TATATATGTT
32214 CATGTGATATGA
1 CATGTGATATGA
*
32226 TATGTGATATGA
1 CATGTGATATGA
32238 CATGTGATATGA
1 CATGTGATATGA
32250 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:32271 original size:23 final size:26
Alignment explanation
Indices: 32214--32282 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
32204 TATATATGTT
**
32214 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
32238 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
32263 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
32283 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:34767 original size:30 final size:30
Alignment explanation
Indices: 34732--34801 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
34722 TTGAGTGATA
34732 GAATGGAAAAATTTTAAAATTAGATAACAT
1 GAATGGAAAAATTTTAAAATTAGATAACAT
34762 GAATGGAAAAATTTTAAAATTAGATAACAT
1 GAATGGAAAAATTTTAAAATTAGATAACAT
*
34792 GAATAGAAAA
1 GAATGGAAAA
34802 TTGATAGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (30 bp):
GAATGGAAAAATTTTAAAATTAGATAACAT
Found at i:38817 original size:26 final size:27
Alignment explanation
Indices: 38761--38817 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
38751 TTGAGTTAAT
* *
38761 TTTTATTTACGTTTGTTTGATTTTAAA
1 TTTTATTTACGTTTGTTCGATTATAAA
**
38788 -TTTATTTGTGTTTGTTCG-TTATAAA
1 TTTTATTTACGTTTGTTCGATTATAAA
38813 TTTTA
1 TTTTA
38818 AAAAATTGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.21, C:0.04, G:0.12, T:0.63
Consensus pattern (27 bp):
TTTTATTTACGTTTGTTCGATTATAAA
Found at i:40570 original size:20 final size:20
Alignment explanation
Indices: 40542--40586 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40532 CTCTTTTAAT
* *
40542 ATTTTATTTTAAAAATAAAA
1 ATTTAATTTCAAAAATAAAA
* *
40562 ATTTAATTTCATAGATAAAA
1 ATTTAATTTCAAAAATAAAA
40582 ATTTA
1 ATTTA
40587 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTAATTTCAAAAATAAAA
Found at i:43685 original size:22 final size:22
Alignment explanation
Indices: 43660--43705 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
43650 AGTTTAAAAT
*
43660 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
43682 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
43704 AG
1 AG
43706 TACTGCTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:43713 original size:11 final size:11
Alignment explanation
Indices: 43697--43722 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43687 ACCGATTCCC
43697 CTGCTACAGTA
1 CTGCTACAGTA
43708 CTGCTACAGTA
1 CTGCTACAGTA
43719 CTGC
1 CTGC
43723 CGTAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:44268 original size:21 final size:21
Alignment explanation
Indices: 44219--44282 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
44209 CATATGAAAT
* *
44219 TTGTCCCGAAGAACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
* *
44240 TATGTCCCGAAGGACTTATGAG
1 T-TGTCCCGAAGGACCTATGAA
44262 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
44283 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:50606 original size:22 final size:22
Alignment explanation
Indices: 50581--50626 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
50571 GTTTACAAAT
*
50581 AGGGAATCGATTCCCCTGCCAC
1 AGGGAACCGATTCCCCTGCCAC
*
50603 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCCAC
50625 AG
1 AG
50627 TACTGCTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCCAC
Found at i:50634 original size:11 final size:11
Alignment explanation
Indices: 50618--50643 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
50608 ACCGATTCCC
50618 CTGCTACAGTA
1 CTGCTACAGTA
50629 CTGCTACAGTA
1 CTGCTACAGTA
50640 CTGC
1 CTGC
50644 CGTAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:51189 original size:21 final size:21
Alignment explanation
Indices: 51140--51203 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
51130 CATATGAAAT
* *
51140 TTGTCTCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
51161 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
51183 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
51204 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:53526 original size:407 final size:406
Alignment explanation
Indices: 52772--53581 Score: 1341
Period size: 407 Copynumber: 2.0 Consensus size: 406
52762 TCCAAAACAA
* * *
52772 AGTTAATTGGTTTTGCATATATAATATTTATGTCAGATCCTCATAATGGTAAATCATAGATTGGA
1 AGTTAATTGGTTTTGCATATACAATATTTACGTCAGATCCTCATAATGGTAAATCATAGACTGGA
* * * * *
52837 TATTTTTTATATATGGTGGTACAATAATCTCTTGGCGCTTCATGAAGCAAACGCTTGCATCAACT
66 TATTTTTTACATATGGTGGTACAACAATCTCTTGGCGCTCCATGAAGCAAACGATTGCAGCAACT
*
52902 TCTTCTAATCATGCAAAAATCTTAGCAATCCATGAAGCTAGTCGTGAATGTGTATGGCTAAAATC
131 TCTTCTAATCATGCAAAAATCTTAGCAATCCATGAAGCTAGTCGTGAATGTGTATGACTAAAATC
* * * *
52967 TATGATTCAGTATATACGGAATAATTATGGTTTATCATCTAGAAAAGAAGTTCCTACTGTCTTTT
196 TATGATTCAGCATATACGGAATAATTATGGTTTATCATATAGAAAAGAAGTTCCTAATGTCTTGT
* *
53032 TTTAAGACAATATAGCATGCATTGAACAACTCAAGAGTGGGCACATCAAAGGTAATGGAACAAAA
261 TTGAAGACAATATAGCATGCATTGAACAACTCAAGAGTGGGCACATCAAAGGTAATAGAACAAAA
*
53097 CACATTGTACCTAAATTCTTCTTCACTCATGACCTTCAGAAGCTTAAAGAGATAAAAGTTAACCA
326 CACATTGTACCTAAATTCTTCTTCACTCATGACCTTCAGAAGATTAAAGAGATAAAAGTTAACCA
53162 GATCAGTTCAAGTAAG
391 GATCAGTTCAAGTAAG
* * *
53178 AGTTAATTGGTTTTGCATATGCAATATTTACGTCATATCCTTATAATGGTAAATCATAGACTGGA
1 AGTTAATTGGTTTTGCATATACAATATTTACGTCAGATCCTCATAATGGTAAATCATAGACTGGA
* *
53243 TATGTTTTTACATATGGTGGTACAACAATCTCTTGGTGCTCCATGAAGCAAACGATTGTAGCAAC
66 TAT-TTTTTACATATGGTGGTACAACAATCTCTTGGCGCTCCATGAAGCAAACGATTGCAGCAAC
*
53308 TTCTTCTAATCATGCAAAAATCTTAGCAATCCATGAAGCTAGTCGTGAATGTGTATGACTAAGAT
130 TTCTTCTAATCATGCAAAAATCTTAGCAATCCATGAAGCTAGTCGTGAATGTGTATGACTAAAAT
* **
53373 CTATGATTCAGCATATACGGAATAATTATGGTTTATCATATGGAAAAGAAGTTTTTAATGTCTTG
195 CTATGATTCAGCATATACGGAATAATTATGGTTTATCATATAGAAAAGAAGTTCCTAATGTCTTG
* * *
53438 TTTGAAGATAATATAGCATGCATTGAACAACTCAATAGTGGGCATATCAAAGGTAATAGAACAAA
260 TTTGAAGACAATATAGCATGCATTGAACAACTCAAGAGTGGGCACATCAAAGGTAATAGAACAAA
* *
53503 ACACATTGTACCTAAATTCTTCTTCACTTATGACCTTCAGAAGATTAAAGAGATAAAAGTTAATC
325 ACACATTGTACCTAAATTCTTCTTCACTCATGACCTTCAGAAGATTAAAGAGATAAAAGTTAACC
53568 AGATCAGTTCAAGT
390 AGATCAGTTCAAGT
53582 GAGAATTTGA
Statistics
Matches: 373, Mismatches: 30, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
406 62 0.17
407 311 0.83
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (406 bp):
AGTTAATTGGTTTTGCATATACAATATTTACGTCAGATCCTCATAATGGTAAATCATAGACTGGA
TATTTTTTACATATGGTGGTACAACAATCTCTTGGCGCTCCATGAAGCAAACGATTGCAGCAACT
TCTTCTAATCATGCAAAAATCTTAGCAATCCATGAAGCTAGTCGTGAATGTGTATGACTAAAATC
TATGATTCAGCATATACGGAATAATTATGGTTTATCATATAGAAAAGAAGTTCCTAATGTCTTGT
TTGAAGACAATATAGCATGCATTGAACAACTCAAGAGTGGGCACATCAAAGGTAATAGAACAAAA
CACATTGTACCTAAATTCTTCTTCACTCATGACCTTCAGAAGATTAAAGAGATAAAAGTTAACCA
GATCAGTTCAAGTAAG
Found at i:54041 original size:2 final size:2
Alignment explanation
Indices: 54036--54070 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54026 TCCTCATCCT
54036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54071 GGGGTTCATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55199 original size:6 final size:6
Alignment explanation
Indices: 55188--55221 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
55178 AATCATGTGC
* *
55188 TTCTTT TTCTTT TTCTTT TTCTTC TTCTTC TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
55222 CATTAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTCTTT
Found at i:56649 original size:3 final size:3
Alignment explanation
Indices: 56641--56725 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
56631 GACTTTTGAT
56641 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
56689 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
56726 TTTGAATTTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:76724 original size:21 final size:20
Alignment explanation
Indices: 76688--76726 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
76678 TTTGGTGTAG
*
76688 AGGGAATCGATCCCCCCATA
1 AGGGAACCGATCCCCCCATA
76708 AGGGAACCGATTCCCCCCA
1 AGGGAACCGA-TCCCCCCA
76727 CAGGGGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.38, G:0.21, T:0.13
Consensus pattern (20 bp):
AGGGAACCGATCCCCCCATA
Found at i:76744 original size:21 final size:20
Alignment explanation
Indices: 76688--76745 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
76678 TTTGGTGTAG
*
76688 AGGGAATCGATCCCCCCATA
1 AGGGAATCGATCCCCCCACA
*
76708 AGGGAACCGATTCCCCCCACA
1 AGGGAATCGA-TCCCCCCACA
* *
76729 GGGGAATTGATACCCCC
1 AGGGAATCGAT-CCCCC
76746 TTGGGGTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.28, C:0.36, G:0.22, T:0.14
Consensus pattern (20 bp):
AGGGAATCGATCCCCCCACA
Found at i:77450 original size:21 final size:21
Alignment explanation
Indices: 77426--77465 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
77416 ACCGTCAACC
*
77426 AAATCCACCTCCAAATCCTCA
1 AAATCCAACTCCAAATCCTCA
*
77447 AAATCCAACTCCTAATCCT
1 AAATCCAACTCCAAATCCT
77466 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATCCAACTCCAAATCCTCA
Found at i:85431 original size:13 final size:13
Alignment explanation
Indices: 85413--85454 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
85403 CAAAAAAATC
85413 CGGAATCGTTAAT
1 CGGAATCGTTAAT
*
85426 CGGAATCGTTAAC
1 CGGAATCGTTAAT
* *
85439 CGTAACCGTTAAT
1 CGGAATCGTTAAT
85452 CGG
1 CGG
85455 TATAACCGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (13 bp):
CGGAATCGTTAAT
Found at i:86616 original size:29 final size:29
Alignment explanation
Indices: 86572--86630 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
86562 ATTTTCACCT
86572 AACTAAATTGACGTAAGCAATGACATCAA
1 AACTAAATTGACGTAAGCAATGACATCAA
*
86601 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGACGTAAGCAATGACATCAA
86630 A
1 A
86631 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AACTAAATTGACGTAAGCAATGACATCAA
Found at i:94706 original size:20 final size:20
Alignment explanation
Indices: 94683--94725 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
94673 AATCCACCAC
*
94683 ATGCAACTATAT-GCTCCTAA
1 ATGCAACTAAATGGC-CCTAA
*
94703 ATGCATCTAAATGGCCCTAA
1 ATGCAACTAAATGGCCCTAA
94723 ATG
1 ATG
94726 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (20 bp):
ATGCAACTAAATGGCCCTAA
Found at i:98245 original size:20 final size:21
Alignment explanation
Indices: 98192--98253 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
98182 TTCCCCTGTG
98192 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
98216 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
98236 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
98254 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:102028 original size:22 final size:21
Alignment explanation
Indices: 101986--102025 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
101976 GAGTTTGTTT
*
101986 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
102007 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
102026 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:107263 original size:29 final size:29
Alignment explanation
Indices: 107219--107277 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
107209 ATTTTCACCT
*
107219 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGACGTAAGCAATGACATCAA
107248 AACTAAATTGACGTAAGCAATGACATCAA
1 AACTAAATTGACGTAAGCAATGACATCAA
107277 A
1 A
107278 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AACTAAATTGACGTAAGCAATGACATCAA
Found at i:122428 original size:31 final size:31
Alignment explanation
Indices: 122390--122545 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
122380 CCCGAAGGAC
* *
122390 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
122421 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
**
122452 CAGTCTGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
122483 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
122514 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
122545 C
1 C
122546 CCTCGACCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:123040 original size:16 final size:18
Alignment explanation
Indices: 123019--123059 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
123009 GCATGTTAAC
123019 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
123035 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
123053 TCATATA
1 ACATATA
123060 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:123443 original size:21 final size:21
Alignment explanation
Indices: 123413--123457 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
123403 ATTCTGTCGT
* *
123413 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
123434 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
123455 TTG
1 TTG
123458 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:126534 original size:31 final size:31
Alignment explanation
Indices: 126496--126651 Score: 226
Period size: 31 Copynumber: 5.0 Consensus size: 31
126486 CCCGAAGGAC
* *
126496 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
126527 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
126558 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
126589 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
126620 CAGTCCATATG-TCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
126651 C
1 C
126652 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 3 0.03
31 111 0.97
32 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:127147 original size:16 final size:18
Alignment explanation
Indices: 127126--127166 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
127116 GCATGTTAAC
127126 ACATATAA-TCATG-CAT
1 ACATATAATTCATGTCAT
127142 ACATATAATTCATGTCAT
1 ACATATAATTCATGTCAT
*
127160 TCATATA
1 ACATATA
127167 CGTATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 9 0.41
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (18 bp):
ACATATAATTCATGTCAT
Found at i:127548 original size:21 final size:21
Alignment explanation
Indices: 127518--127562 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
127508 ATTCTGTCGT
* *
127518 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
127539 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
127560 TTG
1 TTG
127563 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:133118 original size:4 final size:4
Alignment explanation
Indices: 133109--133135 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
133099 AAATGCGTGT
133109 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
133136 CATAGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:133212 original size:14 final size:14
Alignment explanation
Indices: 133193--133225 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
133183 TGGGGAGTAA
*
133193 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
133207 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
133221 TCCCT
1 TCCCT
133226 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:138051 original size:2 final size:2
Alignment explanation
Indices: 138038--138089 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
138028 GAGAAAAGGA
*
138038 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
138080 AG AG AG AG AG
1 AG AG AG AG AG
138090 TTGAGTAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:138617 original size:23 final size:23
Alignment explanation
Indices: 138559--138617 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
138549 AGTCTATATA
138559 TATGACACGTTTTTATTTGTCTT
1 TATGACACGTTTTTATTTGTCTT
* ** *
138582 TGTGGTACGTTTTCT-TCTGTC-T
1 TATGACACGTTTT-TATTTGTCTT
138604 TATGACACGTTTTT
1 TATGACACGTTTTT
138618 TGCCTTTTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.39
23 15 0.54
24 1 0.04
ACGTcount: A:0.14, C:0.15, G:0.17, T:0.54
Consensus pattern (23 bp):
TATGACACGTTTTTATTTGTCTT
Found at i:139750 original size:2 final size:2
Alignment explanation
Indices: 139743--139768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
139733 CAACGAGAAA
139743 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
139769 GATTATTAAT
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):
AT
Found at i:146070 original size:22 final size:21
Alignment explanation
Indices: 146040--146152 Score: 80
Period size: 21 Copynumber: 5.6 Consensus size: 21
146030 GAAGATATAT
*
146040 AGAAA-AAAAAACACACAAAAG
1 AGAAAGAAAAAA-ACAAAAAAG
*
146061 -GAAAGTAAAAAAAGAAAAAAG
1 AGAAAG-AAAAAAACAAAAAAG
146082 AGAAAGAAAAAAGA-AAAAAA-
1 AGAAAGAAAAAA-ACAAAAAAG
* *
146102 AGAAAG-AGAAAAC--AGAAG
1 AGAAAGAAAAAAACAAAAAAG
* *
146120 AAAAAGAAAAAAAGAAAAAA-
1 AGAAAGAAAAAAACAAAAAAG
*
146140 AGAAAGAAGAAAA
1 AGAAAGAAAAAAA
146153 TAGACAGATC
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
17 3 0.04
18 6 0.08
19 9 0.12
20 21 0.29
21 22 0.30
22 12 0.16
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.01
Consensus pattern (21 bp):
AGAAAGAAAAAAACAAAAAAG
Found at i:146074 original size:9 final size:8
Alignment explanation
Indices: 146062--146144 Score: 80
Period size: 8 Copynumber: 9.9 Consensus size: 8
146052 ACACAAAAGG
146062 AAAGTAAAA
1 AAAG-AAAA
146071 AAAGAAAA
1 AAAGAAAA
146079 AAGAGAAAGA
1 AA-AGAAA-A
146089 AAA-AAGAA
1 AAAGAA-AA
*
146097 AAA-AAAG
1 AAAGAAAA
146104 AAAGAGAAA
1 AAAGA-AAA
*
146113 ACAGAAGAA
1 AAAGAA-AA
146122 AAAGAAAA
1 AAAGAAAA
146130 AAAGAAAA
1 AAAGAAAA
146138 AAAGAAA
1 AAAGAAA
146145 GAAGAAAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
7 4 0.06
8 33 0.52
9 24 0.38
10 3 0.05
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (8 bp):
AAAGAAAA
Found at i:146080 original size:7 final size:7
Alignment explanation
Indices: 146068--146152 Score: 75
Period size: 7 Copynumber: 11.6 Consensus size: 7
146058 AAGGAAAGTA
146068 AAAAAAG
1 AAAAAAG
146075 AAAAAAG
1 AAAAAAG
*
146082 -AGAAAG
1 AAAAAAG
146088 AAAAAAG
1 AAAAAAG
146095 AAAAAA-
1 AAAAAAG
146101 AAGAAAGAG
1 AA-AAA-AG
*
146110 AAAACAG
1 AAAAAAG
146117 AAGAAAAAG
1 -A-AAAAAG
146126 AAAAAAAG
1 -AAAAAAG
146134 AAAAAAAG
1 -AAAAAAG
*
146142 AAAGAAG
1 AAAAAAG
146149 AAAA
1 AAAA
146153 TAGACAGATC
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
6 7 0.11
7 32 0.48
8 18 0.27
9 9 0.14
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:146086 original size:42 final size:41
Alignment explanation
Indices: 146019--146147 Score: 111
Period size: 42 Copynumber: 3.0 Consensus size: 41
146009 TTAACAACAC
* * *
146019 AGAGAGAAAAAGAAGATATATAGAAAAAAAAACACACAAAAGGAA
1 AGAGA-AAAAAGAAGA-A-AAAGAAAAAAAAACA-AAAAAAAGAA
*
146064 AGTA-AAAAAAGAA-AAAAGAGAAAGAAAAAAGAAAAAAAAGAA
1 AG-AGAAAAAAGAAGAAAA-AGAAA-AAAAAACAAAAAAAAGAA
*
146106 AGAGAAAACAGAAGAAAAAGAAAAAAAGAA-AAAAAGAAAGAA
1 AGAGAAAAAAGAAGAAAAAGAAAAAAA-AACAAAAA-AAAGAA
146148 GAAAATAGAC
Statistics
Matches: 72, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
41 11 0.15
42 37 0.51
43 12 0.17
44 8 0.11
45 3 0.04
46 1 0.01
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (41 bp):
AGAGAAAAAAGAAGAAAAAGAAAAAAAAACAAAAAAAAGAA
Found at i:146090 original size:26 final size:25
Alignment explanation
Indices: 146061--146152 Score: 84
Period size: 26 Copynumber: 3.7 Consensus size: 25
146051 CACACAAAAG
146061 GAAAGTAAAAAAAGAAAAAAGAGAAA
1 GAAAG-AAAAAAAGAAAAAAGAGAAA
*
146087 GAAA-AAAGAAAAAAAAGAAAGAGAAA
1 GAAAGAAA-AAAAGAAA-AAAGAGAAA
*
146113 -ACAGAAGAAAAAGAAAAAA-AGAAA
1 GAAAGAA-AAAAAGAAAAAAGAGAAA
* *
146137 AAAAG-AAAGAAGAAAA
1 GAAAGAAAAAAAGAAAA
146153 TAGACAGATC
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
23 9 0.16
24 9 0.16
25 15 0.27
26 22 0.39
27 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (25 bp):
GAAAGAAAAAAAGAAAAAAGAGAAA
Found at i:146138 original size:38 final size:39
Alignment explanation
Indices: 146079--146152 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
146069 AAAAAGAAAA
*
146079 AAGAGAAAGAAAAAAGAAAAAAAAGAAAG-AGAAAACAG
1 AAGAAAAAGAAAAAAGAAAAAAAAGAAAGAAGAAAACAG
146117 AAGAAAAAGAAAAAA-AGAAAAAAAGAAAGAAGAAAA
1 AAGAAAAAGAAAAAAGA-AAAAAAAGAAAGAAGAAAA
146153 TAGACAGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 1 0.03
38 26 0.79
39 6 0.18
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (39 bp):
AAGAAAAAGAAAAAAGAAAAAAAAGAAAGAAGAAAACAG
Found at i:146147 original size:20 final size:20
Alignment explanation
Indices: 146056--146152 Score: 94
Period size: 20 Copynumber: 4.8 Consensus size: 20
146046 AAAAACACAC
*
146056 AAAAGGAAAGTAAAAAAAGAA
1 AAAAAGAAAG-AAAAAAAGAA
146077 AAAAGAGAAAG-AAAAAAGAAA
1 AAAA-AGAAAGAAAAAAAG-AA
*
146098 AAAAAGAAAGAGAAAACAG--
1 AAAAAGAAAGA-AAAAAAGAA
*
146117 AAGAA-AAAGAAAAAAAGAA
1 AAAAAGAAAGAAAAAAAGAA
146136 AAAAAGAAAGAAGAAAA
1 AAAAAGAAAGAA-AAAA
146153 TAGACAGATC
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
17 6 0.10
18 5 0.08
19 8 0.13
20 19 0.30
21 14 0.22
22 11 0.17
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAGAAAAAAAGAA
Found at i:146869 original size:28 final size:29
Alignment explanation
Indices: 146804--146875 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 29
146794 GCCAACCCGG
* * *
146804 AACACATTGCC-TCCCCAAATTGACCTAA
1 AACACATTACCTTCCCCAAACTAACCTAA
* *
146832 AACGCATTA-CTTCCCCAAACTAACCTGA
1 AACACATTACCTTCCCCAAACTAACCTAA
*
146860 AACACGTTACCTTCCC
1 AACACATTACCTTCCC
146876 AAGGAATCCT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 1 0.03
28 28 0.80
29 6 0.17
ACGTcount: A:0.33, C:0.38, G:0.07, T:0.22
Consensus pattern (29 bp):
AACACATTACCTTCCCCAAACTAACCTAA
Found at i:153778 original size:23 final size:23
Alignment explanation
Indices: 153736--153797 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
153726 ATAGGGCAGA
* * *
153736 GGGAATCGATACCCCC-TTGACG
1 GGGAACCGATTCCCCCTTTGAAG
*
153758 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
153781 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
153798 AGGGAAATCG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:156431 original size:19 final size:19
Alignment explanation
Indices: 156407--156454 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
156397 CTGAGGGAAC
156407 CGATTCCCCCCAGGGGTAT
1 CGATTCCCCCCAGGGGTAT
156426 CGATTCCCCCCAGGGGTAT
1 CGATTCCCCCCAGGGGTAT
156445 CGATTCCCCC
1 CGATTCCCCC
156455 TACTGTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.15, C:0.42, G:0.23, T:0.21
Consensus pattern (19 bp):
CGATTCCCCCCAGGGGTAT
Found at i:157710 original size:55 final size:53
Alignment explanation
Indices: 157651--157952 Score: 284
Period size: 55 Copynumber: 5.6 Consensus size: 53
157641 TGTTTTTTTT
* * * * *
157651 AAACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAG
1 AAACTAAGCCTAATTTTCAGGAGTTTCTTGA-TATTTTCAAATGA-ATTTTAAAG
* * * * *
157706 AAACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAAT-AACCTTTCAAAT
1 AAACTAAGCCTAATTTTCAGGAGTTTCTTGAT-ATTTTCAAATGAA--TTTTAAAG
* * * * * *
157761 AAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAACTGAATTTGAAAG
1 AAACTAAGCCTAATTTTCAGGAGTTTCTTGATATTTTCAAATGAATTTTAAAG
* * * * *
157814 AAGCTAGGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAG
1 AAACTAAGCCTAATTTTCAGGAGTTTCTTGATATTTTCAAATGAATTTT-AAAG
* * * * *
157868 AAATTAAGCCTAATTTTCAGGGGTTTCATGTTATTTTCAAATGCATTTTTAAAG
1 AAACTAAGCCTAATTTTCAGGAGTTTCTTGATATTTTCAAATG-AATTTTAAAG
*
157922 AAACTAAACCTAATTTT-AGGAGTTTCTTGAT
1 AAACTAAGCCTAATTTTCAGGAGTTTCTTGAT
157953 GATAACTGAA
Statistics
Matches: 207, Mismatches: 34, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
53 59 0.29
54 67 0.32
55 81 0.39
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (53 bp):
AAACTAAGCCTAATTTTCAGGAGTTTCTTGATATTTTCAAATGAATTTTAAAG
Found at i:157892 original size:54 final size:54
Alignment explanation
Indices: 157651--157953 Score: 290
Period size: 54 Copynumber: 5.6 Consensus size: 54
157641 TGTTTTTTTT
* * ** ** *
157651 AAACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTT-AAAG
1 AAACTAAGCCTAATTTTCAGGGGTTTCTTGA-TGTTTTCAAATGA-ATTTTCAAAG
* ** * * *
157706 AAACTAAGTCTAATTTTCAGAAGTTTCTTGATGATTTTTAAAT-AACCTTTCAAAT
1 AAACTAAGCCTAATTTTCAGGGGTTTCTTGATG-TTTTCAAATGAA-TTTTCAAAG
* * * *
157761 AAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAACTGAA-TTTGAAAG
1 AAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAG
* * *
157814 AAGCTAGGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAG
1 AAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAG
* * * * * *
157868 AAATTAAGCCTAATTTTCAGGGGTTTCATGTTATTTTCAAATGCATTTTTAAAG
1 AAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAG
* *
157922 AAACTAAACCTAATTTT-AGGAGTTTCTTGATG
1 AAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
157954 ATAACTGAAA
Statistics
Matches: 207, Mismatches: 36, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
53 56 0.27
54 78 0.38
55 73 0.35
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (54 bp):
AAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTCAAAG
Found at i:157905 original size:107 final size:108
Alignment explanation
Indices: 157651--157955 Score: 294
Period size: 107 Copynumber: 2.8 Consensus size: 108
157641 TGTTTTTTTT
* * ** * * * * **
157651 AAACTAAGTCTGATTTTCAGAAGTTTCTTGACAATTTTCAAATG-AGCTTTTAAAGAAACTAAGT
1 AAACTAAGCCTAATTTTCAGGGGTTTCATGA-TATTTTCAAATGCA-ATTTGAAAGAAACTAAAC
* * *
157715 CTAATTTTCAGAAGTTTCTTGATGATTTTTAAATAACCTTTCAAAT
64 CTAATTTT-AGGAGTTTCTTGATGATTTTCAAATAACCTTTCAAAG
* * * * * * **
157761 AAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAACTG-AATTTGAAAGAAGCTAGGCCT
1 AAACTAAGCCTAATTTTCAGGGGTTTCATGATATTTTCAAATGCAATTTGAAAGAAACTAAACCT
* *
157825 AATTTTTAGGGGTTTCTTGATG-TTTTCAAATGAA-TTTTCAAAG
66 AA-TTTTAGGAGTTTCTTGATGATTTTCAAAT-AACCTTTCAAAG
* * * *
157868 AAATTAAGCCTAATTTTCAGGGGTTTCATGTTATTTTCAAATGCATTTTTAAAGAAACTAAACCT
1 AAACTAAGCCTAATTTTCAGGGGTTTCATGATATTTTCAAATGCAATTTGAAAGAAACTAAACCT
157933 AATTTTAGGAGTTTCTTGATGAT
66 AATTTTAGGAGTTTCTTGATGAT
157956 AACTGAAAAA
Statistics
Matches: 163, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
107 69 0.42
108 51 0.31
109 14 0.09
110 29 0.18
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (108 bp):
AAACTAAGCCTAATTTTCAGGGGTTTCATGATATTTTCAAATGCAATTTGAAAGAAACTAAACCT
AATTTTAGGAGTTTCTTGATGATTTTCAAATAACCTTTCAAAG
Found at i:158469 original size:274 final size:274
Alignment explanation
Indices: 157980--158517 Score: 742
Period size: 274 Copynumber: 2.0 Consensus size: 274
157970 ATATTTTAAG
* *
157980 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCTGGGGCATTAGTAAGTCTTTC
1 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCTGGGACATCAGTAAGTCTTTC
*
158045 GAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCATTCGAGCAAGATGATAAGTCCTTCGA
66 GAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCATTCGAGCAAGATGATAAGTCATTCGA
* * * * * * * *
158110 GCCATCCATATGGCCTTTGGGCAGGATGTTTTCAAATAAGTTTTTAGGAATTAAGCTTGATTTTC
131 GCCATCCATAAGACCTTCGGGCACGATGTTTTCAAATAAGTTTTTAGAAACTAAGCCTAATTTTC
* * * **
158175 AGGGGTTTCTTGATGATTATCTCCAAAGAGTTTTTAAAAAGAATTTAAACCTAATTTTTA-GGGT
196 AAGGGTTTCTTGACGATTATCTCCAAAGAATTTTT-AAAAGAAGCTAAACCTAATTTTTAGGGGT
158239 TCCTTAACAACTAAA
260 TCCTTAACAACTAAA
* *
158254 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCATTCT-GGATATCAGTAAGTCTTT
1 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTC-TTCTGGGACATCAGTAAGTCTTT
* * * * * *
158318 TGAG-AGTGGTGCTTAAATCTTTTGGGTCATCTATAAGTCTTTTGAGCAAGATGATAAGTCATTC
65 CGAGCA-TGATGCTTAAATCCTTCGGGTCATCTATAAGTCATTCGAGCAAGATGATAAGTCATTC
* *
158382 G-GACCATCTATAAGACCTTCGGGCACGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATT
129 GAG-CCATCCATAAGACCTTCGGGCACGATGTTTTCAAATAAGTTTTTAGAAACTAAGCCTAATT
* * * *
158446 TTCAAGGGTTTCTTGACGATTATCTCCAAATAATTTTTAAAGGAAGCTAAGCCTACTTTTTAGGG
193 TTCAAGGGTTTCTTGACGATTATCTCCAAAGAATTTTTAAAAGAAGCTAAACCTAATTTTTAGGG
158511 GTTCCTT
258 GTTCCTT
158518 GACGACAACT
Statistics
Matches: 230, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
273 21 0.09
274 205 0.89
275 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (274 bp):
AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCTGGGACATCAGTAAGTCTTTC
GAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCATTCGAGCAAGATGATAAGTCATTCGA
GCCATCCATAAGACCTTCGGGCACGATGTTTTCAAATAAGTTTTTAGAAACTAAGCCTAATTTTC
AAGGGTTTCTTGACGATTATCTCCAAAGAATTTTTAAAAGAAGCTAAACCTAATTTTTAGGGGTT
CCTTAACAACTAAA
Found at i:159327 original size:138 final size:139
Alignment explanation
Indices: 159043--159575 Score: 775
Period size: 139 Copynumber: 3.8 Consensus size: 139
159033 GAACCAATAC
* * *
159043 ACATTTCAAATGGAGAGTTCATAATTAGAAGAACTCA-TCTGATGAAGGAGAAGAAGTTTATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTC-GATGAAGGAGAAGAAGTTCATAAT
* * *
159107 GAGAAGAGCTTGTTCGACCTTAGCTCGATTCATCGTATATGGAGTTGAATCAGCAACACCTCACT
65 GAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACT
*
159172 CGAGGTATCA
130 CGAGGGATCA
159182 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAAGGAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAAGGAGAAGAAGTTCATAATG
* * * *
159247 AGAAGAGC-TATTCGACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTA
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
159311 GAGGGATCA
131 GAGGGATCA
*
159320 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATG
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAAGGAGAAGAAGTTCATAATG
* * ** * * *
159385 AGAAGAACTTGTTTAACCTTAGCTCTATTGGTCTCATATGGAGTTGAATCAGTAATACCTCACTC
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
159450 GAGGGATCA
131 GAGGGATCA
* * * *
159459 TCATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATTTGAT-AAGGGAGACGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAA-GGAGAAGAAGTTCATAAT
* * * *
159523 GAGAAGAACTTGTTCAACCTTAGCTTGTTTCTATCGCATAAGGAGTTGGATCA
65 GAGAAGAACTTGTTCAACCTTAGCTCGATTC-ATCGCATATGGAGTTGAATCA
159576 ACATCATCGT
Statistics
Matches: 357, Mismatches: 33, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
138 134 0.38
139 204 0.57
140 19 0.05
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (139 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAAGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCAACACCTCACTC
GAGGGATCA
Found at i:159426 original size:277 final size:279
Alignment explanation
Indices: 159043--159575 Score: 804
Period size: 277 Copynumber: 1.9 Consensus size: 279
159033 GAACCAATAC
* * *
159043 ACATTTCAAATGGAGAGTTCATAATTAGAAGAACTCATCTGATGAAGGAGAAGAAGTTTATAATG
1 ACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATG
* *
159108 AGAAGAGCTTGTTCGACCTTAGCTCGATTCATCGTATATGGAGTTGAATCAGCAACACCTCACTC
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGTATATGGAGTTGAATCAGCAACACCTCACTC
*
159173 GAGGTATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGAA-GGAGAAGAA
131 GAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGAT-AAGGGAGAAGAA
* * *
159237 GTTCATAATGAGAAGAGC-TATTCGACCTTAGCTCGATTC-ATCGCATATGGAGTTGAATCAGCA
195 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCTATCGCATAAGGAGTTGAATCAGCA
159300 ACACCTCACTAGAGGGATCA
260 ACACCTCACTAGAGGGATCA
*
159320 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATG
1 ACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATG
* * ** * *
159385 AGAAGAACTTGTTTAACCTTAGCTCTATTGGTC-TCATATGGAGTTGAATCAGTAATACCTCACT
66 AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGT-ATATGGAGTTGAATCAGCAACACCTCACT
* * * *
159449 CGAGGGATCATCATTTCCATTGGAGAGTTCATAATGAGAAGAACTCATTTGATAAGGGAGACGAA
130 CGAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAAGGGAGAAGAA
* * * *
159514 GTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCTATCGCATAAGGAGTTGGATCA
195 GTTCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCTATCGCATAAGGAGTTGAATCA
159576 ACATCATCGT
Statistics
Matches: 228, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
276 3 0.01
277 189 0.83
278 17 0.07
279 19 0.08
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (279 bp):
ACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTAGCTCGATTCATCGTATATGGAGTTGAATCAGCAACACCTCACTC
GAGGGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAAGGGAGAAGAAG
TTCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCTATCGCATAAGGAGTTGAATCAGCAA
CACCTCACTAGAGGGATCA
Found at i:160932 original size:28 final size:28
Alignment explanation
Indices: 160901--160987 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 28
160891 TGCGTATTAA
* *
160901 TTTTATTATTTTTTTAATTTAGTCACT-T
1 TTTTA-TATTTATTCAATTTAGTCACTGT
* *
160929 TTTTATGTTTATTCATTTTAGTCACTGT
1 TTTTATATTTATTCAATTTAGTCACTGT
* *
160957 TTTTAATGTTTATTCATTTTAGTCACTGT
1 TTTT-ATATTTATTCAATTTAGTCACTGT
160986 TT
1 TT
160988 GGATTTTGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 17 0.32
28 10 0.19
29 26 0.49
ACGTcount: A:0.20, C:0.09, G:0.08, T:0.63
Consensus pattern (28 bp):
TTTTATATTTATTCAATTTAGTCACTGT
Found at i:160969 original size:29 final size:28
Alignment explanation
Indices: 160918--160987 Score: 124
Period size: 29 Copynumber: 2.5 Consensus size: 28
160908 ATTTTTTTAA
160918 TTTAGTCACT-TTTTTATGTTTATTCAT
1 TTTAGTCACTGTTTTTATGTTTATTCAT
160945 TTTAGTCACTGTTTTTAATGTTTATTCAT
1 TTTAGTCACTGTTTTT-ATGTTTATTCAT
160974 TTTAGTCACTGTTT
1 TTTAGTCACTGTTT
160988 GGATTTTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 10 0.24
28 5 0.12
29 26 0.63
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTAGTCACTGTTTTTATGTTTATTCAT
Found at i:165140 original size:9 final size:9
Alignment explanation
Indices: 165128--165163 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
165118 ACAAAATTGG
165128 CGGTTTTTC
1 CGGTTTTTC
165137 CGGTTTTTTC
1 CGG-TTTTTC
165147 CGGTTTTTC
1 CGGTTTTTC
*
165156 CGATTTTT
1 CGGTTTTT
165164 AGTCAGTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.03, C:0.19, G:0.19, T:0.58
Consensus pattern (9 bp):
CGGTTTTTC
Found at i:165146 original size:10 final size:10
Alignment explanation
Indices: 165131--165163 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
165121 AAATTGGCGG
165131 TTTTTCCGGT
1 TTTTTCCGGT
165141 TTTTTCCGG-
1 TTTTTCCGGT
*
165150 TTTTTCCGAT
1 TTTTTCCGGT
165160 TTTT
1 TTTT
165164 AGTCAGTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.03, C:0.18, G:0.15, T:0.64
Consensus pattern (10 bp):
TTTTTCCGGT
Found at i:168813 original size:16 final size:16
Alignment explanation
Indices: 168792--168825 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
168782 TACTATTCAC
*
168792 GTGAATAATGAATTTT
1 GTGAATAATAAATTTT
*
168808 GTGAATAGTAAATTTT
1 GTGAATAATAAATTTT
168824 GT
1 GT
168826 TGGCGATAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (16 bp):
GTGAATAATAAATTTT
Found at i:172485 original size:21 final size:21
Alignment explanation
Indices: 172456--172557 Score: 125
Period size: 21 Copynumber: 4.8 Consensus size: 21
172446 AGGATGTCAA
*
172456 AGTGAATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
172477 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
* *
172498 AGTGCATCCATGTACCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
172519 AGTGCATTCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
*
172541 TAGTGCATCGATGCACC
1 -AGTGCATCCATGCACC
172558 ATGTAGTGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
21 53 0.76
22 1 0.01
23 16 0.23
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:172621 original size:20 final size:20
Alignment explanation
Indices: 172596--172688 Score: 132
Period size: 20 Copynumber: 4.7 Consensus size: 20
172586 AATGCAATTA
172596 GTGCATCGATGCATCCTACT
1 GTGCATCGATGCATCCTACT
*
172616 GTGCATCGATGCATCCTAAT
1 GTGCATCGATGCATCCTACT
*
172636 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTACT
* *
172656 GTACATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTACT
* *
172676 ATGCATCCATGCA
1 GTGCATCGATGCA
172689 CCAAGGCTGC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTACT
Found at i:181147 original size:14 final size:14
Alignment explanation
Indices: 181128--181158 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
181118 ATTAAAATCG
*
181128 AAATAAAAAAGAGT
1 AAATAAAAAAGAAT
181142 AAATAAAAAAGAAT
1 AAATAAAAAAGAAT
181156 AAA
1 AAA
181159 GGAAAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAATAAAAAAGAAT
Found at i:181926 original size:23 final size:24
Alignment explanation
Indices: 181898--181950 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
181888 ATACTATTTC
181898 GAAAAT-AAT-AATAAAAAACTATT
1 GAAAATAAATAAAT-AAAAACTATT
181921 GAAAATAAATAAATAAAAACTATT
1 GAAAATAAATAAATAAAAACTATT
*
181945 AAAAAT
1 GAAAAT
181951 TCAAAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 18 0.67
25 3 0.11
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
GAAAATAAATAAATAAAAACTATT
Found at i:182217 original size:20 final size:20
Alignment explanation
Indices: 182189--182233 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
182179 ATTGTGAGTA
*
182189 GAGGGAGACAAGGACTAGTG
1 GAGGCAGACAAGGACTAGTG
182209 GAGGCAGACAAGGACTAGTG
1 GAGGCAGACAAGGACTAGTG
182229 GAGGC
1 GAGGC
182234 TTGGTGGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.44, T:0.09
Consensus pattern (20 bp):
GAGGCAGACAAGGACTAGTG
Found at i:183044 original size:170 final size:170
Alignment explanation
Indices: 182856--183275 Score: 786
Period size: 170 Copynumber: 2.5 Consensus size: 170
182846 TGCTGGTGGA
* *
182856 CACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
*
182921 GTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
182986 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
*
183026 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTTGAGTCCAATATCCTTCGTCGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
183091 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
183156 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
*
183196 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTTGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
*
183261 GTTGAAATTGACTCT
66 GTTGAAATTGGCTCT
183276 AGCTAGAACC
Statistics
Matches: 243, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
170 243 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (170 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
Found at i:183050 original size:46 final size:44
Alignment explanation
Indices: 182983--183098 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 44
182973 CTTTGAATTG
* *
182983 GATATCCTTCG-CTGTAAAGTTGAAATCCAAT-GTTGTTTGTGAG-CAC
1 GATATCCTTCGTC-GTGAAGTTGAAAT-C-ATGGATGTTT-TGAGTC-C
*
183029 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTTGAGTCC
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGTTTTGAGTCC
*
183073 AATATCCTTCGTCGTGAAGTTGAAAT
1 GATATCCTTCGTCGTGAAGTTGAAAT
183099 TGGCTCTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
44 31 0.49
45 8 0.13
46 23 0.37
47 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (44 bp):
GATATCCTTCGTCGTGAAGTTGAAATCATGGATGTTTTGAGTCC
Found at i:190867 original size:39 final size:39
Alignment explanation
Indices: 190813--190892 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
190803 TTAACAGTAG
*
190813 ATGCAACTTTCCCTTTGGTAGAGGATGAGTCAC-CGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTC-CTCGGGTA
*
190852 ATGCAACTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
190891 AT
1 AT
190893 ACTCCGGGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (39 bp):
ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
Found at i:195381 original size:23 final size:24
Alignment explanation
Indices: 195342--195388 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
195332 TACTATTTCG
*
195342 AAATAATAAAAAAACTATTGAAAT
1 AAATAATAAAAAAACTATTAAAAT
*
195366 AAATAA-ATAAAAACTATTAAAAT
1 AAATAATAAAAAAACTATTAAAAT
195389 TCAAAACAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATAATAAAAAAACTATTAAAAT
Found at i:195649 original size:20 final size:20
Alignment explanation
Indices: 195621--195665 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
195611 ATTGTGAGTA
*
195621 GAGGGAGACAAGGACTAGTG
1 GAGGCAGACAAGGACTAGTG
195641 GAGGCAGACAAGGACTAGTG
1 GAGGCAGACAAGGACTAGTG
195661 GAGGC
1 GAGGC
195666 TTGTGGCCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.44, T:0.09
Consensus pattern (20 bp):
GAGGCAGACAAGGACTAGTG
Done.