Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006891.1 Hibiscus syriacus cultivar Beakdansim tig00017584_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: 158581
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7990 original size:15 final size:15
Alignment explanation
Indices: 7970--8001 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
7960 CTTACTCACC
7970 TTGCTTGAGGATTTA
1 TTGCTTGAGGATTTA
7985 TTGCTTGAGGATTTA
1 TTGCTTGAGGATTTA
8000 TT
1 TT
8002 TGTGCTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (15 bp):
TTGCTTGAGGATTTA
Found at i:9808 original size:27 final size:27
Alignment explanation
Indices: 9771--9822 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9761 AAATAGTATA
*
9771 AATAATACTCGAATCGGATCTAAAATT
1 AATAATACTCGAATCAGATCTAAAATT
* *
9798 AATAATTCTCGAATCAGATTTAAAA
1 AATAATACTCGAATCAGATCTAAAA
9823 GTAACATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (27 bp):
AATAATACTCGAATCAGATCTAAAATT
Found at i:11927 original size:60 final size:60
Alignment explanation
Indices: 11859--11976 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
11849 CAAATGATCC
* * *
11859 CGACTATAGGGTGCT-ATTTTATTAAGTCCCTCGACTATTAAAACTTATAAAATGGTCATT
1 CGACTATAGAGTGCTGA-TTTATTAAGTCCCTCAACTATTAAAACTTACAAAATGGTCATT
* * * * *
11919 CGACTATAGAGTGTTGATTTGTTGAGTCCGTCAACTATTAAAAGTTACAAAATGGTCA
1 CGACTATAGAGTGCTGATTTATTAAGTCCCTCAACTATTAAAACTTACAAAATGGTCA
11977 CATTACTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 48 0.98
61 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (60 bp):
CGACTATAGAGTGCTGATTTATTAAGTCCCTCAACTATTAAAACTTACAAAATGGTCATT
Found at i:12577 original size:18 final size:18
Alignment explanation
Indices: 12554--12592 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12544 TTTTTAAAAA
12554 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
* * *
12572 TTTAAATTTTTTATGTAT
1 TTTAAAATTATTATATAT
12590 TTT
1 TTT
12593 TAATTGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:15363 original size:21 final size:21
Alignment explanation
Indices: 15334--15377 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
15324 CCCTAACTTA
* *
15334 AAACCATAAATTATAAACCCT
1 AAACAATAAACTATAAACCCT
* *
15355 AAACAATAACCTCTAAACCCT
1 AAACAATAAACTATAAACCCT
15376 AA
1 AA
15378 CTTATAGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACAATAAACTATAAACCCT
Found at i:29513 original size:2 final size:2
Alignment explanation
Indices: 29506--29556 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
29496 TTGTAAGAGG
29506 AT AT AT AT 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 AT AT AT AT
29548 AT AT AT AT A
1 AT AT AT AT A
29557 AAAGCAAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30553 original size:250 final size:252
Alignment explanation
Indices: 30056--30570 Score: 953
Period size: 252 Copynumber: 2.0 Consensus size: 252
30046 ATGCAAGGAA
* *
30056 AAATACGAAAATTCAAATGAGGAAAAAGGAAAGAAATGGAGAAAATATAAACAAATAAATAAAAA
1 AAATACGAAAATTCAAATGAAGAAAAAGGAAAGAAATGGAAAAAATATAAACAAATAAAT-AAAA
30121 AATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATATATATATAA
65 AATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATATATATATAA
*
30186 TAAAATAACATATAAATAAAGGAAAATAGGTGATGTATGTATATATATATATATAAACATAAGAA
130 TAAAATAACATATAAATAAAGGAAAATAGGTAATGTA-GTATATATATATATATAAACATAAGAA
30251 TATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
194 TATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
*
30310 AAATACGAAAATTCAAATGAAGAAAAAGGAAAGGAATGGAAAAAATATAAACAAATAAAT-AAAA
1 AAATACGAAAATTCAAATGAAGAAAAAGGAAAGAAATGGAAAAAATATAAACAAATAAATAAAAA
30374 ATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATATATATATAAT
66 ATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATATATATATAAT
*
30439 AAAATAACATGTAAATAAAGGAAAATAGGTAATGTA-TATATATATATATATAAACATAAGAATA
131 AAAATAACATATAAATAAAGGAAAATAGGTAATGTAGTATATATATATATATAAACATAAGAATA
30503 TAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
196 TAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
30560 AAATACGAAAA
1 AAATACGAAAA
30571 ATAATAAAAA
Statistics
Matches: 256, Mismatches: 5, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
250 96 0.38
252 103 0.40
254 57 0.22
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (252 bp):
AAATACGAAAATTCAAATGAAGAAAAAGGAAAGAAATGGAAAAAATATAAACAAATAAATAAAAA
ATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATATATATATAAT
AAAATAACATATAAATAAAGGAAAATAGGTAATGTAGTATATATATATATATAAACATAAGAATA
TAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
Found at i:30757 original size:200 final size:201
Alignment explanation
Indices: 30362--30987 Score: 1071
Period size: 200 Copynumber: 3.1 Consensus size: 201
30352 AAATATAAAC
30362 AAATAAATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTA
1 AAAT-AATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAG--
30427 TATATATATAATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATATAA
63 TATATATAT-ATAAAATAACATGTAAATAAAGGAAAATAGGTAATG--TATATATATATATATAA
30492 ACATAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAAT
125 ACATAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAAT
30557 AGTAAATACGAA
190 AGTAAATACGAA
30569 AAATAATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTAT
1 AAATAATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTAT
30634 ATATATATAAAATAACATGTAAATAAAGG-AAATAGGTAATGTATATATATATATATAAACATAA
66 ATATATATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATAAACATAA
30698 GAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGTAAA
131 GAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGTAAA
30763 TACGAA
196 TACGAA
* *
30769 AAATAATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAAGATATGAGTAGTAT
1 AAATAATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTAT
*
30834 ATATA-ATAAAATAACATATAAATAAAGGAAAATAGGTAATG--TATATATATATATAAACATAA
66 ATATATATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATAAACATAA
* * *
30896 GAATATAATACAATATAGCATAAACAAATAAAAATTCAAATATATATATATATATAAATAAATAG
131 GAATATAATACAATATAGCGTAAACAAATAAAAATTC--A-A-ATATATATATGTAAGTAAATAG
30961 TAAATACGAA
192 TAAATACGAA
*
30971 ATATAATAAAAATATAT
1 AAATAATAAAAATATAT
30988 ATAAGTATAA
Statistics
Matches: 407, Mismatches: 7, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
198 57 0.14
199 22 0.05
200 175 0.43
201 1 0.00
202 58 0.14
203 23 0.06
204 9 0.02
206 58 0.14
207 4 0.01
ACGTcount: A:0.59, C:0.04, G:0.11, T:0.27
Consensus pattern (201 bp):
AAATAATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTAT
ATATATATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATAAACATAA
GAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGTAAA
TACGAA
Found at i:32621 original size:105 final size:105
Alignment explanation
Indices: 32478--33252 Score: 1487
Period size: 105 Copynumber: 7.4 Consensus size: 105
32468 GTATTGTTCC
* * * *
32478 GAGTCCAATGTTCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
32543 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
32583 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
32648 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
32688 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
32753 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
32793 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
32858 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
32898 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
32963 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
33003 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
33068 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
33108 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
33173 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
33213 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTG
33253 GGTAAAACCT
Statistics
Matches: 661, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 661 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:45099 original size:204 final size:204
Alignment explanation
Indices: 44626--45216 Score: 1016
Period size: 206 Copynumber: 2.9 Consensus size: 204
44616 ATAAACAAAT
*
44626 AAAT-AAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATAT
1 AAATAAAAAAAATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATAT
44690 ATATATAATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATATATATA
66 ATATATAATAAAATAACATGTAAATAAAGGAAAATAGGTAATG------TATATATATATATATA
44755 TAAACATAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTA
125 TAAACATAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTA
44820 AATAGTAAATACGAA
190 AATAGTAAATACGAA
44835 AAATAATAAAAATATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTAT
1 AAATAA-AAAAA-ATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTAT
44900 ATATATATAATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATATAAA
64 ATATATATAATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATATAAA
44965 CATAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATA
129 CATAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATA
45030 GTAAATACGAA
194 GTAAATACGAA
* *
45041 AAATAAAAAAAATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAAGATATGAGTAG----T
1 AAATAAAAAAAATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATAT
*
45102 ATATATAATAAAATAACATATAAATAAAGGAAAATAGGTAATG--TATATATATATATATAAACA
66 ATATATAATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATATAAACA
*
45165 TAAGAATATAATACAATATAGCATAAACAAATAAAAATTCAAATATATATAT
131 TAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATAT
45217 ATATATATAT
Statistics
Matches: 374, Mismatches: 5, Indels: 17
0.94 0.01 0.04
Matches are distributed among these distances:
198 71 0.19
200 43 0.11
204 47 0.13
205 5 0.01
206 102 0.27
209 4 0.01
210 1 0.00
211 4 0.01
212 97 0.26
ACGTcount: A:0.58, C:0.04, G:0.11, T:0.27
Consensus pattern (204 bp):
AAATAAAAAAAATATGTGAAAAAATGTAAAAACAAAGAAGATGAAGAAATACATGAGTAGTATAT
ATATATAATAAAATAACATGTAAATAAAGGAAAATAGGTAATGTATATATATATATATATAAACA
TAAGAATATAATACAATATAGCGTAAACAAATAAAAATTCAAATATATATATGTAAGTAAATAGT
AAATACGAA
Found at i:46265 original size:18 final size:18
Alignment explanation
Indices: 46240--46287 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
46230 AGTTTACTAA
*
46240 AACA-ATAATATTTATAC
1 AACATATAATATATATAC
* *
46257 AATATATAATATATATAT
1 AACATATAATATATATAC
46275 AACATATAA-ATAT
1 AACATATAATATAT
46288 GTGTGATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AACATATAATATATATAC
Found at i:52467 original size:20 final size:20
Alignment explanation
Indices: 52442--52482 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
52432 ATTTGAACAT
52442 TAAATACAAGCTCAAATTAA
1 TAAATACAAGCTCAAATTAA
52462 TAAATACAAGCTCAAATTAA
1 TAAATACAAGCTCAAATTAA
52482 T
1 T
52483 TAACTATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAATACAAGCTCAAATTAA
Found at i:57645 original size:17 final size:17
Alignment explanation
Indices: 57599--57651 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
57589 TAAATTTATT
*
57599 AATTTATATTTATATTAA
1 AATTTATATAT-TATTAA
*
57617 AATATATAATATTATTAA
1 AATTTAT-ATATTATTAA
* *
57635 ATTTTATATATGATTAA
1 AATTTATATATTATTAA
57652 GAAAATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 9 0.31
18 17 0.59
19 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATTTATATATTATTAA
Found at i:69520 original size:21 final size:21
Alignment explanation
Indices: 69494--69538 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
69484 GATTTATGGG
* *
69494 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
69515 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
69536 CAA
1 CAA
69539 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:71243 original size:13 final size:13
Alignment explanation
Indices: 71225--71287 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
71215 TTATATGGCA
71225 CTACGGTGCAATT
1 CTACGGTGCAATT
71238 CTACGG-GC-A--
1 CTACGGTGCAATT
*
71247 CTTCGGTGCAATT
1 CTACGGTGCAATT
71260 CTACGG-GC-A--
1 CTACGGTGCAATT
*
71269 CTTCGGTGCAATT
1 CTACGGTGCAATT
71282 CTACGG
1 CTACGG
71288 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:71253 original size:22 final size:22
Alignment explanation
Indices: 71221--71301 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
71211 ATCATTATAT
*
71221 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
71243 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
71265 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
71288 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
71302 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:76585 original size:2 final size:2
Alignment explanation
Indices: 76580--76614 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
76570 AAAAAAAAAA
76580 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76615 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76619 original size:2 final size:2
Alignment explanation
Indices: 76614--76644 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76604 ATATATATAT
76614 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
76645 ATTAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:83986 original size:42 final size:43
Alignment explanation
Indices: 83906--83993 Score: 124
Period size: 42 Copynumber: 2.0 Consensus size: 43
83896 CCATACAGAA
**
83906 CTATGTGAAGAAATCCACCAAAATTTCAATATTTTTTTTCATGTC
1 CTATGTGAAGAAAT-C-CCAAAATTTCAATATAGTTTTTCATGTC
*
83951 CTATGTGAAGAAAT-CCAAAATTTTAATATAGTTTTTCATGTC
1 CTATGTGAAGAAATCCCAAAATTTCAATATAGTTTTTCATGTC
83993 C
1 C
83994 ATGCAGAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 26 0.65
45 14 0.35
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (43 bp):
CTATGTGAAGAAATCCCAAAATTTCAATATAGTTTTTCATGTC
Found at i:85354 original size:23 final size:23
Alignment explanation
Indices: 85322--85370 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
85312 AAACTATCAT
* *
85322 AAAGATAGAGATAAATGTGACAC
1 AAAGACAGAGATAAACGTGACAC
*
85345 AAAGACAGAGATAAACGTGTCAC
1 AAAGACAGAGATAAACGTGACAC
85368 AAA
1 AAA
85371 AATATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.14
Consensus pattern (23 bp):
AAAGACAGAGATAAACGTGACAC
Found at i:87189 original size:19 final size:18
Alignment explanation
Indices: 87145--87180 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
87135 CATATAATAT
87145 TTTTAAATTACGATTCTTA
1 TTTTAAATTAC-ATTCTTA
87164 TTTTAAATTA-ATTCTTA
1 TTTTAAATTACATTCTTA
87181 AATTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTTAAATTACATTCTTA
Found at i:88618 original size:2 final size:2
Alignment explanation
Indices: 88598--88637 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
88588 GCCTGGTACG
* * *
88598 TA TA TA CA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88638 GGCGAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:93835 original size:2 final size:2
Alignment explanation
Indices: 93828--93867 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
93818 AATAAAAAGA
93828 AT AT AT 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 AT AT AT
93868 TGAAAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107484 original size:7 final size:7
Alignment explanation
Indices: 107472--107509 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
107462 TCTTAACTTA
107472 AAACCCT
1 AAACCCT
107479 AAACCCT
1 AAACCCT
107486 AAACCCT
1 AAACCCT
107493 AAACCCT
1 AAACCCT
107500 AAACCCT
1 AAACCCT
107507 AAA
1 AAA
107510 TAATAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.47, C:0.39, G:0.00, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:118050 original size:6 final size:6
Alignment explanation
Indices: 118034--118096 Score: 119
Period size: 6 Copynumber: 10.7 Consensus size: 6
118024 CTTTTATGCT
118034 CATAA- CATAAG CATAAG CATAAG CATAAG CATAAG CATAAG CATAAG
1 CATAAG CATAAG CATAAG CATAAG CATAAG CATAAG CATAAG CATAAG
118081 CATAAG CATAAG CATA
1 CATAAG CATAAG CATA
118097 GAAAAGATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.09
6 52 0.91
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (6 bp):
CATAAG
Found at i:118736 original size:6 final size:6
Alignment explanation
Indices: 118435--118733 Score: 571
Period size: 6 Copynumber: 49.8 Consensus size: 6
118425 TATACATATA
118435 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
*
118483 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACA
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
*
118531 TACACG TACACG TACACG TACACA TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
118579 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
118627 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
118675 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
*
118723 TACACA TACAC
1 TACACG TACAC
118734 ATATACATAT
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 288 1.00
ACGTcount: A:0.34, C:0.33, G:0.15, T:0.17
Consensus pattern (6 bp):
TACACG
Found at i:118741 original size:6 final size:6
Alignment explanation
Indices: 118726--118768 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
118716 GTACACGTAC
*
118726 ACATAC ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
118769 TATGCAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (6 bp):
ACATAT
Found at i:120786 original size:15 final size:15
Alignment explanation
Indices: 120766--120885 Score: 91
Period size: 15 Copynumber: 7.5 Consensus size: 15
120756 TAATAAGGTT
120766 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
120781 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
120796 ATTTATTATAAAATATGGATTA
1 ATTTATT-T-TAA-A---A-TA
120818 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
120833 AATTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
120847 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
120865 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
120879 ATTTATT
1 ATTTATT
120886 AGTATGGATT
Statistics
Matches: 86, Mismatches: 8, Indels: 23
0.74 0.07 0.20
Matches are distributed among these distances:
14 21 0.24
15 33 0.38
16 4 0.05
17 3 0.03
18 11 0.13
19 1 0.01
20 2 0.02
21 2 0.02
22 9 0.10
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:120875 original size:32 final size:32
Alignment explanation
Indices: 120835--120995 Score: 241
Period size: 32 Copynumber: 5.3 Consensus size: 32
120825 TTAAAATAAA
*
120835 TTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
120867 TTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
*
120899 TTATTTT---TAA---A--A-TATGAATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
120922 TTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
120954 TTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
120986 TTATTTTAAA
1 TTATTTTAAA
120996 ATATGGATTG
Statistics
Matches: 117, Mismatches: 3, Indels: 18
0.85 0.02 0.13
Matches are distributed among these distances:
23 17 0.15
24 1 0.01
26 4 0.03
29 4 0.03
31 1 0.01
32 90 0.77
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:120926 original size:55 final size:55
Alignment explanation
Indices: 120856--120960 Score: 210
Period size: 55 Copynumber: 1.9 Consensus size: 55
120846 AATTTATTAG
120856 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAA
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAA
120911 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
120961 AAATAATTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (55 bp):
TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAA
Found at i:120934 original size:87 final size:86
Alignment explanation
Indices: 120835--121027 Score: 359
Period size: 87 Copynumber: 2.2 Consensus size: 86
120825 TTAAAATAAA
120835 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
1 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
120900 TATTTTTAAAATATGAATTGAT
66 TA-TTTTAAAATATGAATTGAT
*
120922 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
1 TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
*
120987 TATTTTAAAATATGGATTGAT
66 TATTTTAAAATATGAATTGAT
121008 TTATTTTAAATAATTTATTA
1 TTATTTTAAATAATTTATTA
121028 TTGTAGTTGT
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 38 0.37
87 66 0.63
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.53
Consensus pattern (86 bp):
TTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
TATTTTAAAATATGAATTGAT
Found at i:121000 original size:22 final size:22
Alignment explanation
Indices: 120975--121017 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
120965 AATTTATTAG
120975 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
120997 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
121018 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:121099 original size:31 final size:31
Alignment explanation
Indices: 121042--121100 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
121032 AGTTGTATGG
**
121042 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
121073 ATTATTTAAATCTT-AGTATTACAAAACT
1 ATTATTTAAAT-TTCAGTATTACAAAACT
121101 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:133477 original size:17 final size:17
Alignment explanation
Indices: 133455--133487 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
133445 AACCTTTAAT
133455 ATATAATATT-TAAATAC
1 ATATAAT-TTCTAAATAC
133472 ATATAATTTCTAAATA
1 ATATAATTTCTAAATA
133488 TTTAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATAATTTCTAAATAC
Found at i:135083 original size:14 final size:15
Alignment explanation
Indices: 135058--135127 Score: 60
Period size: 14 Copynumber: 4.8 Consensus size: 15
135048 TAATAAGGTT
* *
135058 ATTTATTTTAAATTA
1 ATTTATTATAAATAA
135073 A-TTATTATAAA-AA
1 ATTTATTATAAATAA
135086 ATTTATTATAAA-ATA
1 ATTTATTATAAATA-A
135101 ATTTACTT-TAAAATAA
1 ATTTA-TTAT-AAATAA
135117 A-TTATTATAAA
1 ATTTATTATAAA
135128 ATATGGATTG
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 2 0.04
14 25 0.53
15 12 0.26
16 7 0.15
17 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATTATAAATAA
Found at i:135105 original size:15 final size:15
Alignment explanation
Indices: 135058--135130 Score: 89
Period size: 15 Copynumber: 5.0 Consensus size: 15
135048 TAATAAGGTT
* *
135058 ATTTATTTTAAATTA
1 ATTTATTATAAAATA
135073 A-TTATTATAAAA-A
1 ATTTATTATAAAATA
135086 ATTTATTATAAAATA
1 ATTTATTATAAAATA
135101 ATTTACTT-TAAAATA
1 ATTTA-TTATAAAATA
*
135116 AATTATTATAAAATA
1 ATTTATTATAAAATA
135131 TGGATTGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
13 2 0.04
14 22 0.43
15 25 0.49
16 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:135166 original size:13 final size:14
Alignment explanation
Indices: 135058--135172 Score: 74
Period size: 15 Copynumber: 7.5 Consensus size: 14
135048 TAATAAGGTT
*
135058 ATTTATTTTAAATTA
1 ATTTA-TTTAAAATA
135073 A-TTATTATAAAA-A
1 ATTTATT-TAAAATA
135086 ATTTATTATAAAATA
1 ATTTATT-TAAAATA
135101 ATTTACTTTAAAATA
1 ATTTA-TTTAAAATA
*
135116 AATTATTATAAAATATGGA
1 ATTTATT-T-AAA-AT--A
135135 TTGATTTATTTTAAAATA
1 ---ATTTA-TTTAAAATA
135153 ATTTATTT-AAATA
1 ATTTATTTAAAATA
135166 ATTTATT
1 ATTTATT
135173 AGTATGAATT
Statistics
Matches: 84, Mismatches: 3, Indels: 28
0.73 0.03 0.24
Matches are distributed among these distances:
13 16 0.19
14 23 0.27
15 24 0.29
16 5 0.06
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 3 0.04
22 5 0.06
23 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTTATTTAAAATA
Found at i:135191 original size:22 final size:22
Alignment explanation
Indices: 135176--135217 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
135166 ATTTATTAGT
135176 ATGAATTGATTTATTTTAAAGA
1 ATGAATTGATTTATTTTAAAGA
*
135198 ATGGATTGATTTATTTTAAA
1 ATGAATTGATTTATTTTAAA
135218 TAATTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGAATTGATTTATTTTAAAGA
Found at i:135243 original size:18 final size:18
Alignment explanation
Indices: 135220--135267 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
135210 ATTTTAAATA
*
135220 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
135238 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
135260 ATTTATTA
1 ATTTATTA
135268 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:135318 original size:32 final size:31
Alignment explanation
Indices: 135276--135468 Score: 188
Period size: 32 Copynumber: 6.7 Consensus size: 31
135266 TATTGTAGTT
135276 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAA-TTATTA
*
135308 GTATGGATTGATTTATTTTAAATAATTATTA
1 GTATGAATTGATTTATTTTAAATAATTATTA
*
135339 GTATGTATTGATTTATTTT--A-AA--A-TA
1 GTATGAATTGATTTATTTTAAATAATTATTA
135364 -T-TG-ATTGATTTATTTTAAA-A--TA-T-
1 GTATGAATTGATTTATTTTAAATAATTATTA
135387 G---G-ATTGATTTATTTTAAATAATTTATTA
1 GTATGAATTGATTTATTTTAAATAA-TTATTA
* *
135415 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGAATTGATTTATTTTAAATAA-TTATTA
*
135447 GTATGGATTGATTTATTTTAAA
1 GTATGAATTGATTTATTTTAAA
135469 ATATGGATTG
Statistics
Matches: 144, Mismatches: 3, Indels: 28
0.82 0.02 0.16
Matches are distributed among these distances:
22 30 0.21
23 3 0.02
24 5 0.03
25 2 0.01
26 3 0.02
27 1 0.01
28 3 0.02
29 1 0.01
31 25 0.17
32 71 0.49
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (31 bp):
GTATGAATTGATTTATTTTAAATAATTATTA
Found at i:135373 original size:22 final size:22
Alignment explanation
Indices: 135340--135404 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
135330 TAATTATTAG
*
135340 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
135362 TATTGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
135384 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
135405 TAATTTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:135473 original size:22 final size:22
Alignment explanation
Indices: 135448--135643 Score: 104
Period size: 22 Copynumber: 8.0 Consensus size: 22
135438 AATTTATTTG
135448 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
135470 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
**
135496 TATGGATTGATTTATTTATATATT
1 TATGGATTGATTTATTT-TA-AAA
* * *
135520 TATTAGTATGGATTGATTTATTTAAAA
1 TA-T-GGATTGATT--TAT-TTTAAAA
135547 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* *
135571 TTTATTAGTATTGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
*
135601 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
135623 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
135644 TAATTTATTA
Statistics
Matches: 135, Mismatches: 20, Indels: 38
0.70 0.10 0.20
Matches are distributed among these distances:
22 43 0.32
23 5 0.04
24 11 0.08
25 13 0.10
26 33 0.24
27 5 0.04
28 15 0.11
29 4 0.03
30 2 0.01
31 2 0.01
32 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:135587 original size:131 final size:129
Alignment explanation
Indices: 135340--135677 Score: 400
Period size: 131 Copynumber: 2.6 Consensus size: 129
135330 TAATTATTAG
* * * * *
135340 TATGTATTGATTTATTTTAAAATATTGATTGATTTATTTTAAAATATGGATTGATTTATTTTA-A
1 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATAGA
* * * *
135404 ATAATTTA-TT--AGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTT
61 TTGATTTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
135466 AAAA
126 AAAA
* *** * *
135470 TATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTA-TTTATAT-ATTTATTAGTATGGAT
1 TATGAATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGAT
*
135533 TGATTTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTA
62 TGATTTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA
135598 AAA
127 AAA
135601 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
*
135666 TTATTTTAAATA
66 TTATTTAAAATA
135678 ATTTATTTGT
Statistics
Matches: 176, Mismatches: 22, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
127 19 0.11
128 19 0.11
129 34 0.19
130 14 0.08
131 67 0.38
132 5 0.03
133 5 0.03
134 13 0.07
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (129 bp):
TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
TTATTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:135628 original size:239 final size:241
Alignment explanation
Indices: 135309--135899 Score: 912
Period size: 239 Copynumber: 2.4 Consensus size: 241
135299 AATTTATTAG
135309 TATGGATTGATTTATTTTAAATAA-TTATTAGTA-TGTATTGATTTATTTTAAAATATTGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTG-ATTGATTTATTTTAAAATA-TGATTGA
*
135372 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
64 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
*
135437 TAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGA
129 TAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGA
* *
135502 TTGATTTA-TTTATAT-ATTTATTAGTATGGATTGATTTA-TTTAAAA
194 TTGATTTATTTTAAATAATTTATTAGAATGGATTGATTTATTTTAAAA
135547 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATG-ATTGAT
135612 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAT
65 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAT
135677 AATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGAT
130 AATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGAT
135742 TGATTTATTTTAAATAATTTATTAGAATGGATTGATTTATTTTAAAA
195 TGATTTATTTTAAATAATTTATTAGAATGGATTGATTTATTTTAAAA
* * * * * * *
135789 TATGGATTGATTTAGTATT--GTAGTTGTA-T-GAATTGATTTATTTTAAATAATTAATTAGTAT
1 TATGGATTGATTTA-TTTTAAATAATT-TATTAGTATTGATTGA-TTT--AT-TTTAA--AATAT
135850 GGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
58 -GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
135900 TTGTAGTTGT
Statistics
Matches: 327, Mismatches: 11, Indels: 22
0.91 0.03 0.06
Matches are distributed among these distances:
238 26 0.08
239 169 0.52
240 17 0.05
241 30 0.09
242 23 0.07
243 5 0.02
244 4 0.01
246 52 0.16
247 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (241 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGATTGATT
TATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATA
ATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATT
GATTTATTTTAAATAATTTATTAGAATGGATTGATTTATTTTAAAA
Found at i:135665 original size:32 final size:32
Alignment explanation
Indices: 135627--135707 Score: 153
Period size: 32 Copynumber: 2.5 Consensus size: 32
135617 TTAAAATATG
135627 GATTGATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
*
135659 GATTGATTTATTTTAAATAATTTATTTGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
135691 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
135708 ATATGGATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:135669 original size:18 final size:17
Alignment explanation
Indices: 135646--135702 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
135636 ATTTTAAATA
135646 ATTTATTAGTATAGATTG
1 ATTTATT-GTATAGATTG
* *
135664 ATTTATT-T-TA-AATA
1 ATTTATTGTATAGATTG
135678 ATTTATTTGTATAGATTG
1 ATTTA-TTGTATAGATTG
135696 ATTTATT
1 ATTTATT
135703 TTAAAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 2 0.06
17 4 0.13
18 14 0.45
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (17 bp):
ATTTATTGTATAGATTG
Found at i:135703 original size:18 final size:16
Alignment explanation
Indices: 135627--135706 Score: 69
Period size: 14 Copynumber: 5.0 Consensus size: 16
135617 TTAAAATATG
135627 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
* *
135643 -A-TAATTTATTAGTATA
1 GATTGATTTATT-TTA-A
135659 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
*
135675 -A-TAATTTATTTGTATA
1 GATTGATTTATTT-TA-A
135691 GATTGATTTATTTTAA
1 GATTGATTTATTTTAA
135707 AATATGGATT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
14 17 0.34
15 6 0.12
16 4 0.08
17 6 0.12
18 17 0.34
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
GATTGATTTATTTTAA
Found at i:135777 original size:112 final size:108
Alignment explanation
Indices: 135548--135787 Score: 372
Period size: 108 Copynumber: 2.2 Consensus size: 108
135538 TATTTAAAAT
*
135548 ATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGAATTGATT
1 ATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTGATT
*
135613 TATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGT
66 TATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGA
* * *
135656 ATAGATTGATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTGATT
1 ATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTGATT
***
135721 TATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGA
66 TA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGA
135768 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
135788 ATATGGATTG
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
108 63 0.53
109 1 0.01
110 2 0.02
111 2 0.02
112 51 0.43
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (108 bp):
ATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTGATT
TATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGA
Found at i:135792 original size:80 final size:82
Alignment explanation
Indices: 135366--135884 Score: 632
Period size: 80 Copynumber: 6.4 Consensus size: 82
135356 TTAAAATATT
*
135366 GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
1 GATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGATTTAT
*
135431 TTTAAATAATTTATTTGTATG
62 TTTAAATAATTTATTAGTATG
135452 GATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTA-TTT
1 GATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTATTTT
*
135513 ATAT-ATTTATTAGTATG
65 AAATAATTTATTAGTATG
* *
135530 GATTGATTTA-TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTAT
1 GATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGATTTAT
135594 TTT-AA-AA--TA-T-G-A--
62 TTTAAATAATTTATTAGTATG
* *
135606 -ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTAT
1 GATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGATTTAT
* *
135670 TTTAAATAATTTATTTGTATA
62 TTTAAATAATTTATTAGTATG
135691 GATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTATTTT
1 GATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTATTTT
*
135753 AAATAATTTATTAGAATG
65 AAATAATTTATTAGTATG
* *
135771 GATTGATTTATTTTAAAATATGGATTGATTTAGT-AT-TGTAGTT-GTATGAATTGATTTATTTT
1 GATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTATTTT
*
135833 AAATAATTAATTAGTATG
65 AAATAATTTATTAGTATG
135851 GATTGATTTATTTTAAAATATGGATTGATTTATT
1 GATTGATTTATTTTAAAATATGGATTGATTTATT
135885 TTAAATAATT
Statistics
Matches: 394, Mismatches: 17, Indels: 50
0.85 0.04 0.11
Matches are distributed among these distances:
75 9 0.02
76 56 0.14
77 23 0.06
78 25 0.06
79 9 0.02
80 166 0.42
81 9 0.02
82 7 0.02
83 20 0.05
84 7 0.02
86 63 0.16
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (82 bp):
GATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTATTAGTATGGATTGATTTATTTTA
AATAATTTATTAGTATG
Found at i:135872 original size:22 final size:22
Alignment explanation
Indices: 135847--135889 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
135837 AATTAATTAG
135847 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
135869 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
135890 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:142214 original size:31 final size:31
Alignment explanation
Indices: 142179--142292 Score: 201
Period size: 31 Copynumber: 3.7 Consensus size: 31
142169 TCAGACCATT
*
142179 GCATATGCATTGAACAGAACAATTTAGCGTG
1 GCATATGCATTGAACAGAACAATTTAACGTG
*
142210 GCATATGCATTGAACAAAACAATTTAACGTG
1 GCATATGCATTGAACAGAACAATTTAACGTG
*
142241 GTATATGCATTGAACAGAACAATTTAACGTG
1 GCATATGCATTGAACAGAACAATTTAACGTG
142272 GCATATGCATTGAACAGAACA
1 GCATATGCATTGAACAGAACA
142293 GATTACAGAA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (31 bp):
GCATATGCATTGAACAGAACAATTTAACGTG
Found at i:145142 original size:21 final size:21
Alignment explanation
Indices: 145118--145162 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
145108 TTACGTCAAT
145118 ACCGTGAACCGTCATGTCAGC
1 ACCGTGAACCGTCATGTCAGC
* *
145139 ACCGTGAACTGTCATGTTAGC
1 ACCGTGAACCGTCATGTCAGC
145160 ACC
1 ACC
145163 ATAACAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (21 bp):
ACCGTGAACCGTCATGTCAGC
Found at i:145629 original size:6 final size:6
Alignment explanation
Indices: 145618--145646 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
145608 TGGAGGTGCA
145618 GGGCAG GGGCAG GGGCAG GGGCAG GGGCA
1 GGGCAG GGGCAG GGGCAG GGGCAG GGGCA
145647 TAGATTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.66, T:0.00
Consensus pattern (6 bp):
GGGCAG
Found at i:145994 original size:2 final size:2
Alignment explanation
Indices: 145987--146034 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
145977 TGCTAAAACC
145987 AT AT AT AT 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 AT AT AT AT
146029 AT AT AT
1 AT AT AT
146035 TTGTTATGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.