Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:603755 original size:17 final size:17
Alignment explanation
Indices: 603735--603767 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
603725 AAGCAGCTTG
*
603735 AAATTATGTCATTCAAT
1 AAATTATGACATTCAAT
603752 AAATTATGACATTCAA
1 AAATTATGACATTCAA
603768 GCTCCACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATTATGACATTCAAT
Found at i:603856 original size:3 final size:3
Alignment explanation
Indices: 603848--603897 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
603838 AATTTAGGTT
603848 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
603894 TTA T
1 TTA T
603898 ATATATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:603900 original size:2 final size:2
Alignment explanation
Indices: 603888--603929 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
603878 TTATTATTAT
603888 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
603929 T
1 T
603930 TAGGGTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:606991 original size:14 final size:15
Alignment explanation
Indices: 606949--606994 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
606939 GATTGTACCA
606949 TAAATAGGTATATTC
1 TAAATAGGTATATTC
*
606964 TTAA-AGGCTCATATT-
1 TAAATAGG-T-ATATTC
606979 TAAATAGGTATATTC
1 TAAATAGGTATATTC
606994 T
1 T
606995 TGTGGTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 8 0.32
15 9 0.36
16 8 0.32
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (15 bp):
TAAATAGGTATATTC
Found at i:608452 original size:24 final size:24
Alignment explanation
Indices: 608397--608461 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
608387 CACCGAAGTG
608397 CCACATAG-ATTTGTCCCAAAGGA
1 CCACATAGAATTTGTCCCAAAGGA
*** * *
608420 CCGTGTAGAATTTGTCGCAAATGA
1 CCACATAGAATTTGTCCCAAAGGA
608444 CCACATAGAAATTTGTCC
1 CCACATAG-AATTTGTCC
608462 TGAATAACCG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 5 0.16
24 18 0.58
25 8 0.26
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCAAAGGA
Found at i:608629 original size:15 final size:15
Alignment explanation
Indices: 608609--608678 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
608599 CACATAGGGT
*
608609 ATTTTCACGTAGAAC
1 ATTTTCACATAGAAC
* * *
608624 ATTTTCACTTAGCAT
1 ATTTTCACATAGAAC
*
608639 ATTTTTACATAGAAC
1 ATTTTCACATAGAAC
*
608654 ATTTTCATATA-AAC
1 ATTTTCACATAGAAC
*
608668 ATATTCACATA
1 ATTTTCACATA
608679 CAAATAATAT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
14 12 0.27
15 32 0.73
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (15 bp):
ATTTTCACATAGAAC
Found at i:611992 original size:31 final size:31
Alignment explanation
Indices: 611957--612082 Score: 227
Period size: 31 Copynumber: 4.1 Consensus size: 31
611947 GTTATATGAG
611957 CTATGTGATAAAGGTATGGAAAATGATATGT
1 CTATGTGATAAAGGTATGGAAAATGATATGT
*
611988 CTATGTGATAAATGTATGGAAAATGATATGT
1 CTATGTGATAAAGGTATGGAAAATGATATGT
612019 CTATGTGATAAAGGTATGGAAAATGATATGT
1 CTATGTGATAAAGGTATGGAAAATGATATGT
*
612050 CTATGTGATAAAGGTAT-GAAAATAATATGT
1 CTATGTGATAAAGGTATGGAAAATGATATGT
612080 CTA
1 CTA
612083 CGAGATACAC
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 15 0.16
31 77 0.84
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (31 bp):
CTATGTGATAAAGGTATGGAAAATGATATGT
Found at i:612353 original size:48 final size:49
Alignment explanation
Indices: 612301--612395 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 49
612291 ATTTCTATGT
* *
612301 GGTCCTTATGGAC-AA-TCTTATATGGCACTTCAG-TGCAAATTTATACGC
1 GGTCCTTAGGGACAAATTC-TACATGGCACTTC-GTTGCAAATTTATACGC
*
612349 GGTCCTTCGGGACAAATTCTACATGGCACTTCGTTGCAAATTTATAC
1 GGTCCTTAGGGACAAATTCTACATGGCACTTCGTTGCAAATTTATAC
612396 AAGCTGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
48 12 0.29
49 27 0.66
50 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (49 bp):
GGTCCTTAGGGACAAATTCTACATGGCACTTCGTTGCAAATTTATACGC
Found at i:612484 original size:9 final size:9
Alignment explanation
Indices: 612470--612503 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
612460 GTATCATGGG
*
612470 CTATTGAAT
1 CTATTGAAC
612479 CTATTGAAC
1 CTATTGAAC
612488 CTATTGAAC
1 CTATTGAAC
*
612497 TTATTGA
1 CTATTGA
612504 TATGAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (9 bp):
CTATTGAAC
Found at i:613656 original size:21 final size:21
Alignment explanation
Indices: 613539--613676 Score: 66
Period size: 21 Copynumber: 6.7 Consensus size: 21
613529 ACGCGAAATA
**
613539 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
613559 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* **
613579 AAAATCGCAACGCGATTCTGG
1 AAAATCGCAACGCGATTTTCC
* * **
613600 AAAATCGCAATGCGAATTTAT
1 AAAATCGCAACGCGATTTTCC
** **
613621 ACTATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
613642 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
613662 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
613677 ACACATAAAT
Statistics
Matches: 85, Mismatches: 31, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
19 1 0.01
20 37 0.44
21 47 0.55
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:613738 original size:20 final size:20
Alignment explanation
Indices: 613644--613872 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
613634 GATTTTCCAG
* ** *
613644 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
613664 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
613684 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
613704 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
613724 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
613744 AATCACAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
613764 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
613784 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
613804 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
613824 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
613844 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
613864 AATCACAAC
1 AATCGCAAC
613873 ACTGAAATTT
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 173 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:614604 original size:24 final size:24
Alignment explanation
Indices: 614565--614611 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
614555 AAATTTGGTC
614565 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
614589 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
614612 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:614803 original size:12 final size:12
Alignment explanation
Indices: 614786--614810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
614776 ATATAATCCT
614786 GAAGAAGAAAAA
1 GAAGAAGAAAAA
614798 GAAGAAGAAAAA
1 GAAGAAGAAAAA
614810 G
1 G
614811 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:617145 original size:33 final size:34
Alignment explanation
Indices: 617094--617344 Score: 178
Period size: 33 Copynumber: 7.2 Consensus size: 34
617084 CGGAAATTAC
* *
617094 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
617127 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
617161 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
617200 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
* *
617233 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * * *
617266 AATTGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
617305 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
617338 AATCGCA
1 AATCGCA
617345 TTGCGATTCT
Statistics
Matches: 171, Mismatches: 24, Indels: 46
0.71 0.10 0.19
Matches are distributed among these distances:
32 3 0.02
33 62 0.36
34 54 0.32
35 1 0.01
36 1 0.01
37 1 0.01
38 19 0.11
39 28 0.16
40 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:617171 original size:53 final size:53
Alignment explanation
Indices: 617108--617344 Score: 424
Period size: 53 Copynumber: 4.5 Consensus size: 53
617098 GCAACGAGAG
* *
617108 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
617161 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
617214 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
617266 AATTGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
617319 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
617345 TTGCGATTCT
Statistics
Matches: 178, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
52 51 0.29
53 126 0.71
54 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:617177 original size:19 final size:19
Alignment explanation
Indices: 617108--617350 Score: 265
Period size: 19 Copynumber: 13.7 Consensus size: 19
617098 GCAACGAGAG
617108 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
617127 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
617141 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
617161 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
617180 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
617194 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
617214 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
617233 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
617247 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
617266 AATTGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
617285 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
617299 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
617319 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
617338 AATCGCATTGCGA
1 AATCGCAATGCGA
617351 TTCTCTCGTT
Statistics
Matches: 190, Mismatches: 11, Indels: 46
0.77 0.04 0.19
Matches are distributed among these distances:
14 42 0.22
15 3 0.02
16 5 0.03
17 9 0.05
18 1 0.01
19 88 0.46
20 42 0.22
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:617251 original size:86 final size:84
Alignment explanation
Indices: 617094--617273 Score: 233
Period size: 86 Copynumber: 2.1 Consensus size: 84
617084 CGGAAATTAC
617094 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
617159 AAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
617180 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
617243 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
*
617266 AATTGCAA
1 AATCGCAA
617274 TGCGAAATGA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
86 53 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:617294 original size:105 final size:106
Alignment explanation
Indices: 617108--617344 Score: 424
Period size: 105 Copynumber: 2.2 Consensus size: 106
617098 GCAACGAGAG
*
617108 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
617173 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
* *
617214 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATTGCAATGC
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
617277 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
65 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
617319 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
617345 TTGCGATTCT
Statistics
Matches: 127, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
105 86 0.68
106 40 0.31
107 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:617384 original size:53 final size:52
Alignment explanation
Indices: 617321--617436 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
617311 GAAATGAAAA
*
617321 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
617373 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
617426 TTGCATTGCGA
1 TCGCATTGCGA
617437 TTCTCTCGTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 10 0.18
53 45 0.82
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:617399 original size:19 final size:19
Alignment explanation
Indices: 617359--617479 Score: 136
Period size: 19 Copynumber: 6.8 Consensus size: 19
617349 GATTCTCTCG
617359 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
617379 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
617398 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
617412 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
*
617431 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
617445 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
617464 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
617480 AACATAATGC
Statistics
Matches: 85, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
14 12 0.14
16 13 0.15
17 13 0.15
19 32 0.38
20 15 0.18
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:617421 original size:33 final size:33
Alignment explanation
Indices: 617379--617471 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
617369 CATTTCCGCA
617379 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
617412 TTGCGATTTTCATTTTGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
617445 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
617472 TTCATTTCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:617589 original size:14 final size:14
Alignment explanation
Indices: 617570--617606 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
617560 CATCAATTAC
617570 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
617584 ACAAATCATCTTTT
1 ACAAATCAACTTTT
617598 ACAAATCAA
1 ACAAATCAA
617607 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:619571 original size:19 final size:19
Alignment explanation
Indices: 619529--619701 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
619519 TAGTTTACTT
* *
619529 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
619549 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
619568 TCGCAACGAGAAACAAAAA
1 TCGCAACGCGAAATGAAAA
**
619587 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
619606 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
619625 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
619639 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
619658 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
619672 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
619691 TCGCAATGCGA
1 TCGCAACGCGA
619702 TTTTGGTTTC
Statistics
Matches: 129, Mismatches: 14, Indels: 21
0.79 0.09 0.13
Matches are distributed among these distances:
14 16 0.12
16 11 0.09
17 11 0.09
19 79 0.61
20 12 0.09
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:619642 original size:14 final size:14
Alignment explanation
Indices: 619623--619679 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
619613 GCGAAATGAA
*
619623 AATCGCAACGACAG
1 AATCGCAACGAAAG
619637 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
619654 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
619670 AATCGCAACG
1 AATCGCAACG
619680 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:619650 original size:33 final size:33
Alignment explanation
Indices: 619604--619696 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
619594 GCGAAACCAA
*
619604 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
619637 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
619670 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
619697 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:619732 original size:14 final size:14
Alignment explanation
Indices: 619713--619739 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
619703 TTTGGTTTCG
619713 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
619727 CGTTGCGATTTTG
1 CGTTGCGATTTTG
619740 GTTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:619739 original size:33 final size:32
Alignment explanation
Indices: 619697--619790 Score: 143
Period size: 33 Copynumber: 2.9 Consensus size: 32
619687 AAAATCGCAA
619697 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTT-TCGT
*
619730 TGCGATTTTGGTTTCGCGTTGCGATTCTTTTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTTCGT
**
619763 TGCGATTTTCATTTCGCGTTGCGATTTT
1 TGCGATTTTGGTTTCGCGTTGCGATTTT
619791 AAGTTTCGTG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.50
Consensus pattern (32 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTTCGT
Found at i:619751 original size:19 final size:18
Alignment explanation
Indices: 619697--619806 Score: 92
Period size: 19 Copynumber: 6.3 Consensus size: 18
619687 AAAATCGCAA
619697 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
619716 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
619730 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
619749 TGCGATTCT-TTT---GT
1 TGCGATTTTGTTTCGCGT
*
619763 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
619782 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
619802 TGCGA
1 TGCGA
619807 AAGTAAACTA
Statistics
Matches: 75, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 4 0.05
17 4 0.05
18 1 0.01
19 31 0.41
20 12 0.16
ACGTcount: A:0.09, C:0.15, G:0.27, T:0.48
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:619987 original size:93 final size:93
Alignment explanation
Indices: 619851--620597 Score: 1455
Period size: 93 Copynumber: 8.1 Consensus size: 93
619841 ATGGATTGCA
619851 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
619915 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
619943 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620008 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
620036 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620101 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
620129 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620194 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
620222 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620287 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
620315 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620379 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
620407 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620472 TAGCAGAATTGGCAGCAACC-AAGCAAAT
66 TAGCAGAATTGGCAGCAACCGAA-CAAAT
620500 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
620565 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
620593 TTACT
1 TTACT
620598 AAGCAATCTA
Statistics
Matches: 650, Mismatches: 1, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
92 98 0.15
93 550 0.85
94 2 0.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:620539 original size:278 final size:279
Alignment explanation
Indices: 619851--620597 Score: 1455
Period size: 278 Copynumber: 2.7 Consensus size: 279
619841 ATGGATTGCA
619851 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
619915 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
619980 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
620045 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
620110 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
620129 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620194 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
620259 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
620324 ACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
196 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
620388 TGGCAGCAACCGAACAAAT
261 TGGCAGCAACCGAACAAAT
620407 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
620472 TAGCAGAATTGGCAGCAACC-AAGCAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
66 TAGCAGAATTGGCAGCAACCGAA-CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC
*
620536 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
130 TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
620598 AAGCAATCTA
Statistics
Matches: 466, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
277 2 0.00
278 264 0.57
279 200 0.43
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (279 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
TGGCAGCAACCGAACAAAT
Found at i:622324 original size:20 final size:20
Alignment explanation
Indices: 622294--622390 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
622284 TTTTGGTTGA
622294 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
**
622314 AATGACTATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
622334 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
622353 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
622368 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
622388 AAT
1 AAT
622391 CGCAACGCGA
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
14 9 0.14
16 4 0.06
17 2 0.03
19 15 0.23
20 21 0.33
21 13 0.20
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:622345 original size:21 final size:21
Alignment explanation
Indices: 622292--622356 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
622282 TCTTTTGGTT
622292 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
**
622313 G-AATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
622333 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
622354 GAA
1 GAA
622357 TCGCAACGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.49, C:0.15, G:0.25, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:622360 original size:14 final size:14
Alignment explanation
Indices: 622341--622397 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
622331 GAGAAATGAA
622341 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
622355 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
622374 AATCGCAACGAGAG
1 AATCGCAACGAGAG
622388 AATCGCAACG
1 AATCGCAACG
622398 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:622374 original size:33 final size:33
Alignment explanation
Indices: 622292--622414 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
622282 TCTTTTGGTT
*
622292 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAAC--GC
622333 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
622366 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
622399 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
622415 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 8 0.10
37 2 0.02
38 1 0.01
39 3 0.04
41 17 0.21
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:622450 original size:14 final size:14
Alignment explanation
Indices: 622431--622487 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
622421 TTTGGTTTCG
622431 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
622445 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
622464 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
622478 CGTTGCGATT
1 CGTTGCGATT
622488 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:622463 original size:33 final size:33
Alignment explanation
Indices: 622415--622495 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
622405 AAAATCGCAA
**
622415 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
622448 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
622481 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
622496 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:622628 original size:33 final size:33
Alignment explanation
Indices: 622586--622656 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
622576 AATACTAACT
622586 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
622619 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
622652 TGAAA
1 TGAAA
622657 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:623064 original size:20 final size:20
Alignment explanation
Indices: 623037--623249 Score: 216
Period size: 20 Copynumber: 10.6 Consensus size: 20
623027 CTTTAAATAT
*
623037 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
* * *
623057 CTCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
623079 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
623098 CGCGTTGCCATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
623118 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
623138 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
623158 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
623178 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* *
623198 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
623218 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
623238 CGCGTTGCGATT
1 CGCGTTGCGATT
623250 CTGGAAAATC
Statistics
Matches: 167, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 148 0.89
21 16 0.10
22 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:630575 original size:20 final size:20
Alignment explanation
Indices: 630552--630594 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
630542 AATCCACCGC
*
630552 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
630572 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
630592 ATG
1 ATG
630595 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:635520 original size:20 final size:20
Alignment explanation
Indices: 635497--635539 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
635487 AATCCACCAC
*
635497 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
635517 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
635537 ATG
1 ATG
635540 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:650375 original size:19 final size:19
Alignment explanation
Indices: 650353--650392 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
650343 TTTCAAATTC
*
650353 GTTGCGATAGTCTACAGTT
1 GTTGCGAAAGTCTACAGTT
650372 GTTGCGAAAGTCTACAGTT
1 GTTGCGAAAGTCTACAGTT
650391 GT
1 GT
650393 CGTTGCGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.35
Consensus pattern (19 bp):
GTTGCGAAAGTCTACAGTT
Found at i:650400 original size:22 final size:20
Alignment explanation
Indices: 650350--650400 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
650340 ATTTTTCAAA
*
650350 TTCGTTGCGATAGTCTACAG
1 TTCGTTGCGAAAGTCTACAG
650370 TT-GTTGCGAAAGTCTACAG
1 TTCGTTGCGAAAGTCTACAG
650389 TTGTCGTTGCGA
1 -T-TCGTTGCGA
650401 TTTTCCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 16 0.59
20 3 0.11
21 1 0.04
22 7 0.26
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
TTCGTTGCGAAAGTCTACAG
Found at i:651136 original size:19 final size:19
Alignment explanation
Indices: 651112--651175 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
651102 TAAACTATCA
651112 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
651131 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
651153 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
651172 CAAC
1 CAAC
651176 AACAACTGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 17 0.50
20 2 0.06
21 2 0.06
22 13 0.38
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:651154 original size:22 final size:22
Alignment explanation
Indices: 651127--651198 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
651117 AATTTGGAAA
651127 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
651149 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
651168 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
651190 ATCGCAACG
1 ATCGCAACG
651199 CGAACTGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:651162 original size:41 final size:41
Alignment explanation
Indices: 651105--651198 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
651095 CTTTTTTTAA
* *
651105 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACAACAACTGTAG
651146 ACTATCGCAACGAATTTGGAAAATCGCAACAACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACAACAACTGTAG
651187 ACTATCGCAACG
1 ACTATCGCAACG
651199 CGAACTGGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACAACAACTGTAG
Found at i:651218 original size:20 final size:20
Alignment explanation
Indices: 651193--651266 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
651183 GTAGACTATC
651193 GCAACGCGAACTGGAAAATT
1 GCAACGCGAACTGGAAAATT
651213 GCAACGCGAACTGGAAAATCGCGT
1 GCAACGCGAACTGGAAAAT----T
* *
651237 AGCAACGCGAACTGAAAAATC
1 -GCAACGCGAACTGGAAAATT
651258 GCAACGCGA
1 GCAACGCGA
651267 TTTTCAACTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 28 0.60
24 1 0.02
25 18 0.38
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.11
Consensus pattern (20 bp):
GCAACGCGAACTGGAAAATT
Found at i:651247 original size:25 final size:23
Alignment explanation
Indices: 651193--651259 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 23
651183 GTAGACTATC
651193 GCAACGCGAACTGGAAAAT---T
1 GCAACGCGAACTGGAAAATCGCT
651213 GCAACGCGAACTGGAAAATCGCGT
1 GCAACGCGAACTGGAAAATCGC-T
*
651237 AGCAACGCGAACTGAAAAATCGC
1 -GCAACGCGAACTGGAAAATCGC
651260 AACGCGATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 19 0.46
24 1 0.02
25 21 0.51
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (23 bp):
GCAACGCGAACTGGAAAATCGCT
Found at i:651770 original size:24 final size:24
Alignment explanation
Indices: 651689--651805 Score: 121
Period size: 24 Copynumber: 4.9 Consensus size: 24
651679 CATAATTCAC
*
651689 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAT
* * * *
651713 GTCAAGTATCAGATCATAATACAA
1 GTCAAGTATCATATCAAAATCCAT
* *
651737 GTCAAGTATCAGATCAAAATTCAT
1 GTCAAGTATCATATCAAAATCCAT
*
651761 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAAAATCCAT
*
651785 GTCATA-TATCATATCAGAATC
1 GTCA-AGTATCATATCAAAATC
651806 AAATCGAAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
23 2 0.03
24 77 0.96
26 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
GTCAAGTATCATATCAAAATCCAT
Found at i:651831 original size:72 final size:72
Alignment explanation
Indices: 651682--651834 Score: 161
Period size: 72 Copynumber: 2.1 Consensus size: 72
651672 ATCAAGTCAT
* * * *
651682 AATTCACGTCA-AGTATCATATCAAAATCCAGGTCAAGTATCAGATCATAATACAAGTCAAGTAT
1 AATTCATGTCAGA-TATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATACAAATCAAGAAT
*
651746 CAGATCAA
65 CAGATAAA
* * *
651754 AATTCATGTCAGATATCATATCAGAATCCATGTCATA-TATCATATCAGAAT-CAAATCGAA-AA
1 AATTCATGTCAGATATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATACAAATC-AAGAA
*
651816 TCAGGTAAA
64 TCAGATAAA
651825 ATATTCATGT
1 A-ATTCATGT
651835 GAGTAGGGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
71 14 0.21
72 52 0.76
73 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (72 bp):
AATTCATGTCAGATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATACAAATCAAGAATC
AGATAAA
Found at i:655526 original size:20 final size:20
Alignment explanation
Indices: 655490--655527 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
655480 ATCCTATTCC
**
655490 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
655510 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
655528 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:661800 original size:2 final size:2
Alignment explanation
Indices: 661795--661930 Score: 98
Period size: 2 Copynumber: 72.0 Consensus size: 2
661785 ATAAAAACAC
*
661795 TA TA TA TA -A TA TA -A TA TA -A TA TA -A TA TA -A TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
661832 TA TA TG T- TA TA TA CTA TG TA -A TA TA AA TA TA TA CTA TA -A TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
661873 TA TA TA TA TA TA TA T- TA TA TA -A TA TA TA TA CTA TA CTA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA
*
661915 -A AA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
661931 ATAAAAATAA
Statistics
Matches: 108, Mismatches: 10, Indels: 32
0.72 0.07 0.21
Matches are distributed among these distances:
1 12 0.11
2 88 0.81
3 8 0.07
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:661806 original size:5 final size:5
Alignment explanation
Indices: 661798--661933 Score: 85
Period size: 5 Copynumber: 28.6 Consensus size: 5
661788 AAAACACTAT
* *
661798 ATATA ATATA ATATA ATATA ATATA ATAT- ATA-A ATAT- ATGTT ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * *
661845 CTATGTA ATATA A-AT- ATATA CTATA ATAT- ATAT- ATATA TATATT
1 --ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA
* * * * *
661889 ATATA ATAT- ATATA CTATA CTAT- GTAAA ATATA TTAT- ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
661934 AAAATAAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
3 1 0.01
4 30 0.29
5 64 0.62
6 4 0.04
7 4 0.04
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:661830 original size:7 final size:7
Alignment explanation
Indices: 661803--661933 Score: 81
Period size: 7 Copynumber: 18.1 Consensus size: 7
661793 ACTATATATA
661803 ATATAAT
1 ATATAAT
661810 ATA-ATAT
1 ATATA-AT
661817 AATATAAT
1 -ATATAAT
661825 ATATAAAT
1 ATAT-AAT
**
661833 ATATGTT
1 ATATAAT
*
661840 ATATACT
1 ATATAAT
*
661847 ATGTAAT
1 ATATAAT
661854 ATA-AAT
1 ATATAAT
*
661860 ATATACT
1 ATATAAT
661867 ATA-ATAT
1 ATATA-AT
661874 ATATATAT
1 ATATA-AT
*
661882 ATATATT
1 ATATAAT
661889 ATATAAT
1 ATATAAT
661896 ATAT-AT
1 ATATAAT
661902 ACTATACTAT
1 A-TATA--AT
* *
661912 GTAAAAT
1 ATATAAT
*
661919 ATATTAT
1 ATATAAT
661926 ATATAAT
1 ATATAAT
661933 A
1 A
661934 AAAATAAAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
6 11 0.11
7 58 0.60
8 21 0.22
9 4 0.04
10 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (7 bp):
ATATAAT
Found at i:661939 original size:20 final size:21
Alignment explanation
Indices: 661778--661939 Score: 95
Period size: 20 Copynumber: 7.7 Consensus size: 21
661768 AAAATACCAA
* * *
661778 ATATATTATAAAA-ACACTAT
1 ATATAATATAAAATATATTAT
*
661798 ATATAATAT--AATATAATAT
1 ATATAATATAAAATATATTAT
661817 AATATAATATATAAATATATGT-T
1 -ATATAATATA-AAATATAT-TAT
* ** *
661840 ATATACTATGTAATATA-AAT
1 ATATAATATAAAATATATTAT
* *
661860 ATATACTATAATATATATATAT
1 ATATAATATAAAATATAT-TAT
* *
661882 ATATATTATATAATATA-TAT
1 ATATAATATAAAATATATTAT
*
661902 ACTATACTATGTAAAATATATTAT
1 A-TATA--ATATAAAATATATTAT
661926 ATATAATA-AAAATA
1 ATATAATATAAAATA
661940 AAAATTCCGA
Statistics
Matches: 110, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 42 0.38
21 12 0.11
22 24 0.22
23 20 0.18
24 5 0.05
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATAATATAAAATATATTAT
Found at i:662164 original size:3 final size:3
Alignment explanation
Indices: 662158--662243 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
662148 TTTTTATCCA
*
662158 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
662206 TAT TAT TAT TAT TAT TAT CAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
662244 AATATATTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:662770 original size:20 final size:20
Alignment explanation
Indices: 662729--662772 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
662719 ACAGAAACAG
*
662729 AAACAGAGAGAAAGAAAAAA
1 AAACAGAGAGAAAAAAAAAA
*
662749 AAACAGAGA-AAGAAAAAAA
1 AAACAGAGAGAAAAAAAAAA
662768 AAACA
1 AAACA
662773 ACAACAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (20 bp):
AAACAGAGAGAAAAAAAAAA
Found at i:662772 original size:19 final size:18
Alignment explanation
Indices: 662735--662769 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
662725 ACAGAAACAG
662735 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
662753 AGAGAAAGAAAAAAAAA
1 AGAGAAAGAAAAAAAAA
662770 ACAACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAAAAAAAC
Found at i:662775 original size:22 final size:20
Alignment explanation
Indices: 662700--662769 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
662690 CCCCATCTGC
**
662700 AAGAAAAAAAAAGGGAGAGA
1 AAGAAAAAAAAACAGAGAGA
* * *
662720 CAGAAACAGAAACAGAGAGA
1 AAGAAAAAAAAACAGAGAGA
662740 AAGAAAAAAAAAC--AGAGA
1 AAGAAAAAAAAACAGAGAGA
662758 AAGAAAAAAAAA
1 AAGAAAAAAAAA
662770 ACAACAACAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.40
20 25 0.60
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAAACAGAGAGA
Found at i:663707 original size:22 final size:21
Alignment explanation
Indices: 663668--663710 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
663658 AGAATTTTTC
**
663668 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
663689 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
663711 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:675078 original size:1 final size:1
Alignment explanation
Indices: 675072--675156 Score: 71
Period size: 1 Copynumber: 85.0 Consensus size: 1
675062 ATGCTTGAAG
* * * * * * *
675072 AAAAAAAAAGAAAAAGAAAAAGAAAAAAAGAGAAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
675137 AGAGAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAA
675157 GGAGGATCAA
Statistics
Matches: 62, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:675087 original size:6 final size:6
Alignment explanation
Indices: 675072--675157 Score: 102
Period size: 6 Copynumber: 13.8 Consensus size: 6
675062 ATGCTTGAAG
*
675072 AAAA-A AAAAGA AAAAGA AAAAGAAA AAAAGA GAAAAGA AAAAGA AAAAAA
1 AAAAGA AAAAGA AAAAGA AAAAG--A AAAAGA -AAAAGA AAAAGA AAAAGA
* *
675122 AAAAAA AAAAAA AAAAGA GAAAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAGA -AAAAGA AAAAGA AAAAG
675158 GAGGATCAAG
Statistics
Matches: 74, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
5 4 0.05
6 52 0.70
7 12 0.16
8 6 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:675099 original size:21 final size:21
Alignment explanation
Indices: 675073--675157 Score: 111
Period size: 20 Copynumber: 4.0 Consensus size: 21
675063 TGCTTGAAGA
675073 AAAAAAAAGAAAAAGAAAAAG
1 AAAAAAAAGAAAAAGAAAAAG
675094 -AAAAAAAGAGAAAAGAAAAAG
1 AAAAAAAAGA-AAAAGAAAAAG
* *
675115 AAAAAAAA-AAAAAAAAAAAA
1 AAAAAAAAGAAAAAGAAAAAG
675135 AAAGAGAAAAGAAAAAGAAAAAG
1 AAA-A-AAAAGAAAAAGAAAAAG
675158 GAGGATCAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
20 21 0.38
21 13 0.24
22 11 0.20
23 10 0.18
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAAAGAAAAAG
Found at i:675107 original size:27 final size:25
Alignment explanation
Indices: 675075--675156 Score: 112
Period size: 26 Copynumber: 3.2 Consensus size: 25
675065 CTTGAAGAAA
675075 AAAAAAGAAAAAGAAAAAGAAAAAA
1 AAAAAAGAAAAAGAAAAAGAAAAAA
675100 AGAGAAAAGAAAAAGAAAAA-AAAAAA
1 A-A-AAAAGAAAAAGAAAAAGAAAAAA
* *
675126 AAAAAAAAAAAAGAGAAAAGAAAAAG
1 AAAAAAGAAAAAGA-AAAAGAAAAAA
675152 AAAAA
1 AAAAA
675157 GGAGGATCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.22
25 6 0.12
26 18 0.35
27 16 0.31
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAAAAGAAAAAGAAAAAA
Found at i:675111 original size:37 final size:37
Alignment explanation
Indices: 675069--675156 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
675059 ATTATGCTTG
* *
675069 AAGAAAAA-AAAAGAAAAAGAAAAAGAAAAAAAGAGAA
1 AAGAAAAAGAAAA-AAAAAAAAAAAAAAAAAAAGAGAA
675106 AAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAGAA
1 AAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAGAA
675143 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
675157 GGAGGATCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 44 0.92
38 4 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (37 bp):
AAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAGAGAA
Found at i:676231 original size:84 final size:84
Alignment explanation
Indices: 676090--676724 Score: 1085
Period size: 84 Copynumber: 7.6 Consensus size: 84
676080 AACCTTTTAT
*
676090 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAAG
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
*
676155 CATTGAATTCAGAAGATGA
66 CATTGAATTTAGAAGATGA
*
676174 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAT
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
676239 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
* * *
676258 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATTAGACAGAATCAAG
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
676323 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
* *
676342 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAAG
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
676407 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
* *
676426 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAG
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
676491 CATTGAATTTAGAAGATGA
66 CATTGAATTTAGAAGATGA
* * *
676510 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAAAACCAAT
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
*
676575 CATTGAATTTGGAAGATGA
66 CATTGAATTTAGAAGATGA
* * * *
676594 ATGTGCTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGACAGAA-CAAT
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
*
676658 CATTGAATTTGGAAGATGA
66 CATTGAATTTAGAAGATGA
676677 ATGTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
676725 ATTCAGTAAG
Statistics
Matches: 525, Mismatches: 26, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
82 41 0.08
83 29 0.06
84 455 0.87
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (84 bp):
ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAAG
CATTGAATTTAGAAGATGA
Found at i:677873 original size:113 final size:112
Alignment explanation
Indices: 677466--678235 Score: 1132
Period size: 113 Copynumber: 6.8 Consensus size: 112
677456 TCATTTGAAA
*
677466 GATCATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* ** *
677531 TATTGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATG
65 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATC-AATTGATG
* *
677580 GATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* ** *
677645 TGATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATG
65 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATC-AATTGATG
* *
677694 GATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
677759 TAACGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGGTG
65 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATG
* *
677807 GATCATATTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
1 GATCATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* *
677871 ATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTG
64 ATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATG
*
677920 GATCATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
1 GATCATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
** * * *
677984 ATAATGAGAAGAATTTGTTCAACCTTTTATATGAATCCATTATTTAATG
64 ATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATG
*
678033 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
678098 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATG
65 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATG
* * *
678146 GATTATCTTTTCCGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAT
1 GATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
678211 AATAAGAAGAACTTGTTCAA-CTTTT
66 AATGAGAAGAATTTGTTCAACCTTTT
678236 GGCATAATTC
Statistics
Matches: 618, Mismatches: 34, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
111 6 0.01
112 65 0.11
113 333 0.54
114 213 0.34
115 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
GATCATCTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAATTGATG
Found at i:678563 original size:3 final size:3
Alignment explanation
Indices: 678557--678633 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
678547 TTTTTATCCA
*
678557 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
678605 TAT TAT TAT CAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
678634 AATATATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:679171 original size:21 final size:19
Alignment explanation
Indices: 679131--679167 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
679121 ACAGAAACGG
679131 AGAGAAAGAAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAAC
679150 AGAGAAAGAAAAAAAAAA
1 AGAGAAAGAAAAAAAAAA
679168 AACAACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (19 bp):
AGAGAAAGAAAAAAAAAAC
Found at i:680106 original size:22 final size:21
Alignment explanation
Indices: 680067--680109 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
680057 AGAATTTTTC
**
680067 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
680088 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
680110 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:685181 original size:10 final size:10
Alignment explanation
Indices: 685166--685190 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
685156 ACATAATTTT
685166 AAATTATTAA
1 AAATTATTAA
685176 AAATTATTAA
1 AAATTATTAA
685186 AAATT
1 AAATT
685191 CTAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTATTAA
Found at i:685726 original size:17 final size:17
Alignment explanation
Indices: 685706--685738 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
685696 ATATTTATTT
685706 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
685723 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
685739 TATGATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:686991 original size:35 final size:34
Alignment explanation
Indices: 686906--686992 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
686896 AAAATAATTT
* *
686906 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
686940 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
686978 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
686993 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:689331 original size:25 final size:23
Alignment explanation
Indices: 689298--689351 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
689288 TTTATATCTG
*
689298 TAAAAAAATTAAATAAGTAAAATAT
1 TAAAAAAATTAAAT-A-CAAAATAT
*
689323 TAAATAAATTAAATACAAAATAT
1 TAAAAAAATTAAATACAAAATAT
689346 TAAAAA
1 TAAAAA
689352 TATAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.46
24 1 0.04
25 13 0.50
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAAAAAATTAAATACAAAATAT
Found at i:689995 original size:20 final size:20
Alignment explanation
Indices: 689970--690012 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
689960 AGATTTATAT
*
689970 AAAGATTTATATCATTCTAG
1 AAAGATTTATATCAATCTAG
*
689990 AAAGATTTATTTCAATCTAG
1 AAAGATTTATATCAATCTAG
690010 AAA
1 AAA
690013 TTAAAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (20 bp):
AAAGATTTATATCAATCTAG
Found at i:701056 original size:17 final size:17
Alignment explanation
Indices: 701034--701067 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
701024 TAATGTTAAA
701034 TAAATAAAAATTATATT
1 TAAATAAAAATTATATT
* *
701051 TAAATAGATATTATATT
1 TAAATAAAAATTATATT
701068 ATGTATACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATAAAAATTATATT
Found at i:704359 original size:50 final size:50
Alignment explanation
Indices: 704266--704361 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
704256 TTGAAATTTA
* * * * *
704266 AATTTCTTTATATTAGTTGTTCATTTTACTGAAGATATTCATCCTATACG
1 AATTTATTTACATTAATTGTTAATTTTACTGAAGATATACATCCTATACG
* * *
704316 AATTTATTTACATTAATTGTTAATTTTATTGAAGGTGTACATCCTA
1 AATTTATTTACATTAATTGTTAATTTTACTGAAGATATACATCCTA
704362 AAATATTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.48
Consensus pattern (50 bp):
AATTTATTTACATTAATTGTTAATTTTACTGAAGATATACATCCTATACG
Found at i:704476 original size:2 final size:2
Alignment explanation
Indices: 704469--704496 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
704459 TACAAATCCA
704469 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
704497 TTAATGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:710724 original size:42 final size:42
Alignment explanation
Indices: 710663--710742 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
710653 TTTTTAAAAA
* *
710663 AATAAATATATAATTTGATTTGTTTGTTTTAATTTATCCTAT
1 AATAAATATATAATCTGATTTGTTCGTTTTAATTTATCCTAT
*
710705 AATAAATATTTAATCTGATTTGTTCGTTTTAATTTATC
1 AATAAATATATAATCTGATTTGTTCGTTTTAATTTATC
710743 TCAAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (42 bp):
AATAAATATATAATCTGATTTGTTCGTTTTAATTTATCCTAT
Found at i:712258 original size:7 final size:7
Alignment explanation
Indices: 712246--712325 Score: 101
Period size: 7 Copynumber: 11.7 Consensus size: 7
712236 TGGCTTTATT
712246 TGGAGGA
1 TGGAGGA
712253 TGGAGGA
1 TGGAGGA
712260 TGGAGGA
1 TGGAGGA
712267 TGGAGGA
1 TGGAGGA
712274 TGGAGGA
1 TGGAGGA
712281 TGGAGGA
1 TGGAGGA
*
712288 AGGAGGA
1 TGGAGGA
*
712295 AGGAGGA
1 TGGAGGA
*
712302 -GAAGGA
1 TGGAGGA
*
712308 AGGAGGA
1 TGGAGGA
712315 -GGAGGA
1 TGGAGGA
*
712321 AGGAG
1 TGGAG
712326 ATGAAAAGGA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
6 11 0.16
7 57 0.84
ACGTcount: A:0.35, C:0.00, G:0.57, T:0.07
Consensus pattern (7 bp):
TGGAGGA
Found at i:712808 original size:32 final size:32
Alignment explanation
Indices: 712767--712839 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
712757 AGGTTTTTGG
712767 TCCACCCGACCCGACTCGAGAACAAGGGAACC
1 TCCACCCGACCCGACTCGAGAACAAGGGAACC
712799 TCCACCCGACCCGACTCGAGAACAAGGGAACC
1 TCCACCCGACCCGACTCGAGAACAAGGGAACC
712831 TCCACCCGA
1 TCCACCCGA
712840 GACCCGACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.30, C:0.42, G:0.21, T:0.07
Consensus pattern (32 bp):
TCCACCCGACCCGACTCGAGAACAAGGGAACC
Found at i:713106 original size:33 final size:33
Alignment explanation
Indices: 713064--713134 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
713054 ACCCGAACAT
* *
713064 GACCCGAATATCACACTTAAAAAAA-TCCGACCC
1 GACCCGAATATCAAACTTAAAAAAACT-AGACCC
713097 GACCCGAATATCAAACTTAAAAAAACTAGACCC
1 GACCCGAATATCAAACTTAAAAAAACTAGACCC
713130 GACCC
1 GACCC
713135 CAAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14
Consensus pattern (33 bp):
GACCCGAATATCAAACTTAAAAAAACTAGACCC
Found at i:713149 original size:32 final size:32
Alignment explanation
Indices: 713113--713194 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
713103 AATATCAAAC
713113 TTAAAAAAACTAGACCCGACCCCAAATT-TTTT
1 TTAAAAAAACT-GACCCGACCCCAAATTCTTTT
* * **
713145 TTAAAAAATCCT-ACCCGATCCTGAATTCTTTT
1 TTAAAAAA-ACTGACCCGACCCCAAATTCTTTT
*
713177 TTTAAAAAACTGACCCGA
1 TTAAAAAAACTGACCCGA
713195 ACCGAATATC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
31 14 0.34
32 25 0.61
33 2 0.05
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.30
Consensus pattern (32 bp):
TTAAAAAAACTGACCCGACCCCAAATTCTTTT
Found at i:715441 original size:30 final size:30
Alignment explanation
Indices: 715402--715476 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
715392 CATTATTTTG
715402 AACACATGACAATATAACATAATCACTTTA
1 AACACATGACAATATAACATAATCACTTTA
* * * * *
715432 AACATATGACAATATCACGTCATCACTTTG
1 AACACATGACAATATAACATAATCACTTTA
* *
715462 GACACATGATAATAT
1 AACACATGACAATAT
715477 TATATCATTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (30 bp):
AACACATGACAATATAACATAATCACTTTA
Found at i:718854 original size:2 final size:2
Alignment explanation
Indices: 718847--718874 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
718837 TATAAATACA
718847 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
718875 GATTAATCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:720184 original size:22 final size:21
Alignment explanation
Indices: 720129--720194 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
720119 AAGAGATAGC
* *
720129 TCCTTTTCATCAAGGGATCAA
1 TCCTTTTCGTGAAGGGATCAA
*
720150 TCCTTTTGGTGAAGGGATCAA
1 TCCTTTTCGTGAAGGGATCAA
* * *
720171 TCATTTTTCTTGAA-GGATCGA
1 TC-CTTTTCGTGAAGGGATCAA
720192 TCC
1 TCC
720195 AAAACTTACT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 28 0.78
22 8 0.22
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (21 bp):
TCCTTTTCGTGAAGGGATCAA
Found at i:722044 original size:14 final size:15
Alignment explanation
Indices: 722022--722068 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
722012 TATAAGGTAA
*
722022 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
722036 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
722051 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
722067 TT
1 TT
722069 GAAAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:725573 original size:17 final size:19
Alignment explanation
Indices: 725551--725587 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
725541 CTTTAAGGTA
725551 TATTTTATTA-T-ATTTAT
1 TATTTTATTAGTAATTTAT
725568 TATTTTATTAGTAATTTAT
1 TATTTTATTAGTAATTTAT
725587 T
1 T
725588 TAGCTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 1 0.06
19 7 0.39
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TATTTTATTAGTAATTTAT
Found at i:730441 original size:52 final size:51
Alignment explanation
Indices: 730308--730485 Score: 257
Period size: 51 Copynumber: 3.5 Consensus size: 51
730298 TGATAAGTCT
* * * *
730308 GCTCCCTTTTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAACGTGTCC
* **
730359 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAT-AAACGTGTCC
* *
730411 GCTCCCTATTCCATCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAACGTGTCC
*
730462 GCTCCCTATTGCTTCAGAGAGTAT
1 GCTCCCTATTCCTTCAGAGAGTAT
730486 GGAACTCAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
51 66 0.59
52 46 0.41
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAACGTGTCC
Found at i:730522 original size:54 final size:54
Alignment explanation
Indices: 730480--730774 Score: 446
Period size: 54 Copynumber: 5.5 Consensus size: 54
730470 TTGCTTCAGA
* * * * * *
730480 GAGTATGGAACTCAAACGTCTTCTTCTTACAGGTTCACTCCCTCTTTATATAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
730534 GAGTATGGAACTCGAACATTTTCTTCTTACGGATTTGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
730588 GAGTATAGAAATCGAGCATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
730642 GAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
730696 GAGTATGGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCTTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
*
730750 GAGTATGAAACTCGAACATCTTCTT
1 GAGTATGGAACTCGAACATCTTCTT
730775 TACCACTTTC
Statistics
Matches: 217, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 217 1.00
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:731199 original size:37 final size:37
Alignment explanation
Indices: 731158--731262 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 37
731148 CTCTTCCGAG
* *
731158 AAGGCTTAAAAAGGATATGCTTCACTACTCTTCGGTA
1 AAGGCTTAAAATGGATTTGCTTCACTACTCTTCGGTA
* * *
731195 AAGGCTTAAGATGG-TTTGCTTCACTACTCTTTGGTG
1 AAGGCTTAAAATGGATTTGCTTCACTACTCTTCGGTA
* *
731231 AAGGCTCAAAATGGATTTGCTTCATTACTCTT
1 AAGGCTTAAAATGGATTTGCTTCACTACTCTT
731263 TGGTGAAGAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 31 0.53
37 28 0.47
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (37 bp):
AAGGCTTAAAATGGATTTGCTTCACTACTCTTCGGTA
Found at i:731263 original size:37 final size:37
Alignment explanation
Indices: 731157--731270 Score: 158
Period size: 37 Copynumber: 3.1 Consensus size: 37
731147 ACTCTTCCGA
* * *
731157 GAAGGCTTAAAAAGGATATGCTTCACTACTCTTCGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
* *
731194 AAAGGCTTAAGATGG-TTTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
* *
731230 GAAGGCTCAAAATGGATTTGCTTCATTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
731267 GAAG
1 GAAG
731271 ACTTGGCTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 31 0.46
37 36 0.54
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (37 bp):
GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
Found at i:732680 original size:125 final size:125
Alignment explanation
Indices: 732487--732712 Score: 362
Period size: 125 Copynumber: 1.8 Consensus size: 125
732477 TGATACGGGC
* * ** *
732487 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTCAAAGCCTTCTTGGTTTGAATCTT
1 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTAATTCTCAAAGCCTTCTTCGTCCGAATCAT
* ** *
732552 GTCATTTCATCATGATGTGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGAGT
66 GTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGAGT
*
732612 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTAATTCTCAATGCCTTCTTCGTCCGAATCAT
1 CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTAATTCTCAAAGCCTTCTTCGTCCGAATCAT
732677 GTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCA
66 GTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCA
732713 GTGTGGGTAT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
125 91 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (125 bp):
CTTCAAAATGCCCCAACACCTCAAATTGTAAGGCTAATTCTCAAAGCCTTCTTCGTCCGAATCAT
GTCATCTCAAAATGATGGGGGTTCAGTCATGCCCCAATATAATCTTTTACTGGTACGAGT
Found at i:741718 original size:149 final size:150
Alignment explanation
Indices: 741529--741844 Score: 564
Period size: 150 Copynumber: 2.1 Consensus size: 150
741519 GGGTAGAGGG
* *
741529 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
741593 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
741658 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
741678 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
741743 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
741808 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
741828 TCTAAGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
741845 TGCATTTATA
Statistics
Matches: 160, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
149 52 0.32
150 108 0.68
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:745269 original size:72 final size:72
Alignment explanation
Indices: 745152--745298 Score: 249
Period size: 72 Copynumber: 2.0 Consensus size: 72
745142 TAACAGGTTT
*
745152 TTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACTCGAAGTCTTCA
1 TTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
*
745217 TCTGTTC
66 TATGTTC
* *
745224 TTGATCATTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
1 TTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
*
745289 TATTTTC
66 TATGTTC
745296 TTG
1 TTG
745299 TGTAATAGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.37
Consensus pattern (72 bp):
TTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
TATGTTC
Found at i:746039 original size:55 final size:55
Alignment explanation
Indices: 745945--746075 Score: 163
Period size: 55 Copynumber: 2.4 Consensus size: 55
745935 AACATCTTTA
* ** * * *
745945 GGATGTCTTTCTTTGTGGATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATT
1 GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
* * *
746000 GGATGTCCTTCTTCATGAATCGTTCTTCAGTCAGGTTCAAATTTCTTCATTCGTC
1 GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
* *
746055 GAATGTTCTTCTTCATGAATC
1 GGATGTCCTTCTTCATGAATC
746076 ATCTGAACGC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (55 bp):
GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
Found at i:750024 original size:52 final size:51
Alignment explanation
Indices: 749891--750068 Score: 266
Period size: 51 Copynumber: 3.5 Consensus size: 51
749881 TGATAAGTCT
* * *
749891 GCTCCCTATTTCTTCAGAGAGTATAGGACTTGATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAACGTGTCC
* * **
749942 GCTCCCTATTCATTCAGAGAGTATAGGACTCGATCTTCAATAAAATGTGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAAT-AAACGTGTCC
*
749994 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAACGTGTCC
*
750045 GCTCCCTATTGCTTCAGAGAGTAT
1 GCTCCCTATTCCTTCAGAGAGTAT
750069 GGAACTCAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 67 0.59
52 46 0.41
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTCAATAAACGTGTCC
Found at i:750105 original size:54 final size:54
Alignment explanation
Indices: 750063--750360 Score: 515
Period size: 54 Copynumber: 5.5 Consensus size: 54
750053 TTGCTTCAGA
* * * *
750063 GAGTATGGAACTCAAACGTCTTCTTATTACGGGTTCGCTCCCTCTTTATCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
750117 GAGTATGGAACTCGAACATTTTCTTCTTACGGATTTGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
* *
750171 GAGTATAGAACTCGAGCATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
750225 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
750279 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
750333 GAGTATGGAACTCGAACATCTTCTTCTT
1 GAGTATGGAACTCGAACATCTTCTTCTT
750361 TACCACTTTC
Statistics
Matches: 230, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 230 1.00
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:750846 original size:37 final size:37
Alignment explanation
Indices: 750743--750856 Score: 158
Period size: 37 Copynumber: 3.1 Consensus size: 37
750733 ACTTTTCCGA
* * *
750743 GAAGGCTTAAAAGGGATATGCTTCACTACTCTTCGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
* *
750780 GAAGGCTTGAGATGG-TTTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
* *
750816 GAAGGCTCAAAATGGATTTGCTTCATTACTCTTTGGT
1 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
750853 GAAG
1 GAAG
750857 ACTTGGCTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 31 0.46
37 36 0.54
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (37 bp):
GAAGGCTTAAAATGGATTTGCTTCACTACTCTTTGGT
Found at i:757407 original size:21 final size:21
Alignment explanation
Indices: 757366--757407 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
757356 ATTTTTGAAA
* *
757366 TCAATTTTGAAATTACTCCCC
1 TCAATTTTGAAATAACACCCC
757387 TCAATTTTGAAATAACACCCC
1 TCAATTTTGAAATAACACCCC
757408 CTTACTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (21 bp):
TCAATTTTGAAATAACACCCC
Found at i:759242 original size:18 final size:18
Alignment explanation
Indices: 759212--759247 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
759202 AGTTTTCATG
759212 AAAACAACATAATTAAAT
1 AAAACAACATAATTAAAT
759230 AAAA-AACATTAATTAAAT
1 AAAACAACA-TAATTAAAT
759248 CACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAACAACATAATTAAAT
Found at i:759513 original size:19 final size:19
Alignment explanation
Indices: 759486--759532 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
759476 ATGTTGTTTT
*
759486 GCACGATTTAATGATAGTA
1 GCACAATTTAATGATAGTA
759505 GCACAATTTAATGATAGTA
1 GCACAATTTAATGATAGTA
759524 GCACAATTT
1 GCACAATTT
759533 GAAGATGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (19 bp):
GCACAATTTAATGATAGTA
Found at i:759749 original size:21 final size:23
Alignment explanation
Indices: 759687--759766 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
759677 AATTCGACAG
*
759687 GTGTATCGATGCACATTCATAGA
1 GTGTATCGATGCATATTCATAGA
* * *
759710 GTGCATCGGTGCATCTTCAT-GA
1 GTGTATCGATGCATATTCATAGA
* *
759732 -TGTATCGATTCATATTCAAAG-
1 GTGTATCGATGCATATTCATAGA
*
759753 GATATATCGATGCA
1 G-TGTATCGATGCA
759767 CTAGCTAGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
21 14 0.33
22 3 0.07
23 26 0.60
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (23 bp):
GTGTATCGATGCATATTCATAGA
Found at i:764100 original size:21 final size:21
Alignment explanation
Indices: 764075--764124 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
764065 AATACTTCTT
*
764075 GGATCATTTTTTAACGTTGGG
1 GGATCATTTTTTAACATTGGG
*
764096 GGATCAATTTTTAACATTGGG
1 GGATCATTTTTTAACATTGGG
764117 GGATCATT
1 GGATCATT
764125 AATGGAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (21 bp):
GGATCATTTTTTAACATTGGG
Found at i:764331 original size:65 final size:64
Alignment explanation
Indices: 764262--764435 Score: 208
Period size: 65 Copynumber: 2.7 Consensus size: 64
764252 GAAGACTTAA
*
764262 TGCATCGATACACTAGG-GGTGCATCGATGCATAAAATGCATTCGATGTTTCAA-ACAAGCCTGG
1 TGCATCGATACA-T-GGCGGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAAGCCT-G
764325 AG
63 AG
* * *
764327 TGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAATCCTGAG
1 TGCATCGATACATGG-CGGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAAGCCTGAG
* * ** * *
764392 TGCATCAATGCATGGCTATGTATCGGTGCATAAAATGCATTCGA
1 TGCATCGATACATGGCGGTGCATCGATGCATAAAATGCATTCGA
764436 AATAGAGTGT
Statistics
Matches: 98, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
63 2 0.02
64 27 0.28
65 63 0.64
66 6 0.06
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (64 bp):
TGCATCGATACATGGCGGTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAAGCCTGAG
Found at i:766449 original size:31 final size:31
Alignment explanation
Indices: 766407--766465 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
766397 AATTTAAAAG
* *
766407 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
766438 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
766466 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:766718 original size:21 final size:21
Alignment explanation
Indices: 766689--766741 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
766679 ATTCTGACTA
766689 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
766710 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
766731 TCGCAATGCGA
1 TCGCATTGCGA
766742 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:766756 original size:20 final size:20
Alignment explanation
Indices: 766731--766844 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
766721 TTTTCCTAAT
766731 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
766751 TCGCAACGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
766772 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
766792 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
766812 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
766832 TCGCAATGCGAAT
1 TCGCAATGCGAAT
766845 CTGACTATCG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 67 0.81
21 16 0.19
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:766828 original size:40 final size:40
Alignment explanation
Indices: 766731--766862 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
766721 TTTTCCTAAT
* *
766731 TCGCAATGCGAATACGTAAATCGCAACGCGAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAA-TACGAAAA
* *
766772 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
* **
766812 TCGTAATGCGAATACGTAAATCGCAATGCGAAT-CTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GAAAA
766852 TCGCAATGCGA
1 TCGCAATGCGA
766863 TTTACATAGT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 49 0.61
41 30 0.38
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACGAAAA
Found at i:767110 original size:22 final size:22
Alignment explanation
Indices: 767046--767110 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
767036 ATCCGTCCCT
*
767046 ATCTCCGACGAAATCAGTCCCC
1 ATCTCCGACGAAATCAGTCTCC
* * *
767068 ATCGCCGACGATAGCAGTCTCC
1 ATCTCCGACGAAATCAGTCTCC
* *
767090 ATCTCCGGCGAAATCATTCTC
1 ATCTCCGACGAAATCAGTCTC
767111 GGTCAGAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.22
Consensus pattern (22 bp):
ATCTCCGACGAAATCAGTCTCC
Found at i:767514 original size:20 final size:20
Alignment explanation
Indices: 767441--767530 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
767431 GCGATTCTGT
767441 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
767460 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
767480 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
767500 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
767520 TGTTGCGATTT
1 CGTTGCGATTT
767531 AAAGTTTTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
19 12 0.19
20 50 0.81
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:769463 original size:33 final size:33
Alignment explanation
Indices: 769410--769486 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
769400 TTTACTATCA
** * * *
769410 CAATGCGAAAATGACTATCGCAACGAGAGAATCG
1 CAATGCG-AAATGAAAATCGCAACAACAAAATCG
*
769444 CAATGCGAAATGAAAATCGCAACAACAAAATTG
1 CAATGCGAAATGAAAATCGCAACAACAAAATCG
769477 CAATGCGAAA
1 CAATGCGAAA
769487 ATGACTATCG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACAACAAAATCG
Found at i:769501 original size:20 final size:20
Alignment explanation
Indices: 769476--769599 Score: 185
Period size: 20 Copynumber: 6.2 Consensus size: 20
769466 CAACAAAATT
769476 GCAATGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
769496 GCAATGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
**
769516 ATAATGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
*
769536 GCAATGCGAAAATCACTATC
1 GCAATGCGAAAATGACTATC
*
769556 ACAATGCGAAAATGACTATC
1 GCAATGCGAAAATGACTATC
** *
769576 GCAATGCGAATTTGGCTATC
1 GCAATGCGAAAATGACTATC
769596 GCAA
1 GCAA
769600 CAAAAGAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
GCAATGCGAAAATGACTATC
Found at i:769723 original size:33 final size:34
Alignment explanation
Indices: 769669--769762 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
769659 ATTCGCATTA
* *
769669 CGATAGTCATTTTCGCGTTGCGATTTTGTTGATG
1 CGATAGTCATTTTCGCGTTGCGATTTTCTCGATG
** * * *
769703 CGATTTTCA-TTTCGCATTGCGATTCTCTCGTTG
1 CGATAGTCATTTTCGCGTTGCGATTTTCTCGATG
769736 CGATAGTCATTTTCGCGTTGCGATTTT
1 CGATAGTCATTTTCGCGTTGCGATTTT
769763 AAGTTTCAGA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 26 0.54
34 22 0.46
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (34 bp):
CGATAGTCATTTTCGCGTTGCGATTTTCTCGATG
Found at i:770334 original size:21 final size:20
Alignment explanation
Indices: 770243--770341 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
770233 GACTCACCTG
770243 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
770263 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGG-CCCTC
** *
770285 TCATCCCTCAAGAGTCTCCTC
1 TCATCGTTCAAGAGGC-CCTC
* * *
770306 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
770327 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
770342 TCTCTCCCAA
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
20 3 0.05
21 51 0.88
22 1 0.02
23 3 0.05
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:770340 original size:42 final size:43
Alignment explanation
Indices: 770240--770350 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 43
770230 TCCGACTCAC
* * * *
770240 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
* **
770282 CTATCATCCCTCAAGA-GTCTCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
*
770324 CTGTCATCGTTGAAGAGGTCT-CTCCCA
1 CTGTCATCGTTCAAGAGGTCTCCTCCCA
770351 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 5 0.09
42 47 0.84
43 4 0.07
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
CTGTCATCGTTCAAGAGGTCTCCTCCCACCGTTCAAGAGGCCA
Found at i:771751 original size:14 final size:14
Alignment explanation
Indices: 771732--771767 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
771722 ATTGTTTAAT
771732 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
771746 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
771760 TGATTTGT
1 TGATTTGT
771768 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:771923 original size:33 final size:33
Alignment explanation
Indices: 771873--771968 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
771863 AAAACAGACT
* **
771873 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* * *
771907 ATCGCAATGCGAAATGAAAATCACAATGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
771940 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
771969 CGAAATTAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:772040 original size:33 final size:33
Alignment explanation
Indices: 771983--772067 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
771973 ATTAGTTTCG
771983 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
772017 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
772050 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
772068 CGCGTTACGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:772078 original size:20 final size:20
Alignment explanation
Indices: 772050--772118 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
772040 GCGATTCTCT
772050 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
772070 CGTTACGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
772090 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
772110 CGTTGCGAT
1 CGTTGCGAT
772119 TTCCACGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:774581 original size:24 final size:24
Alignment explanation
Indices: 774547--774600 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
774537 CTGAAAAATC
774547 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
774571 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
774595 ATCAAA
1 ATCAAA
774601 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Done.