Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012790.1 Kokia drynarioides strain JFW-HI SEQ_127803, 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: 173816
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 239 characters in sequence are not A, C, G, or T
Found at i:2526 original size:12 final size:12
Alignment explanation
Indices: 2509--2533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2499 TGTAACTTAG
2509 ACAAAATATCAT
1 ACAAAATATCAT
2521 ACAAAATATCAT
1 ACAAAATATCAT
2533 A
1 A
2534 TTTAGTAACT
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ACAAAATATCAT
Found at i:3224 original size:6 final size:6
Alignment explanation
Indices: 3213--3247 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3203 CTCAAAGCTC
3213 CACCAG CACCAG CACCAG CACCAG CACCAG CACCA
1 CACCAG CACCAG CACCAG CACCAG CACCAG CACCA
3248 CCCTCATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.51, G:0.14, T:0.00
Consensus pattern (6 bp):
CACCAG
Found at i:10968 original size:2 final size:2
Alignment explanation
Indices: 10961--10985 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10951 TACGAATACA
10961 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 A
10986 GTTTTGATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13412 original size:20 final size:21
Alignment explanation
Indices: 13376--13414 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
13366 TCAAAATATT
*
13376 AATAATATTTTATTAAATAAA
1 AATAATATTTTAATAAATAAA
13397 AATAATA-TTTAATAAATA
1 AATAATATTTTAATAAATA
13415 GAATTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATAATATTTTAATAAATAAA
Found at i:17184 original size:18 final size:16
Alignment explanation
Indices: 17159--17198 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
17149 TTTAAACAAA
17159 TTTTTTTAAACTTATGT
1 TTTTTTTAAACTT-TGT
17176 TTTTATTTAAACTTT-T
1 TTTT-TTTAAACTTTGT
17192 TTTTTTT
1 TTTTTTT
17199 TTAAATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 5 0.23
18 9 0.41
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTTTAAACTTTGT
Found at i:17904 original size:23 final size:24
Alignment explanation
Indices: 17853--17904 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
17843 ATTTTTTTTT
* *
17853 TCGAA-TTTCGAGTTCGAATTAAG
1 TCGAATTTTCGAATTCGAATTAAA
*
17876 TTGAATTTTCGAATTCGAA-TAAA
1 TCGAATTTTCGAATTCGAATTAAA
17899 TCGAAT
1 TCGAAT
17905 AAAATTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (24 bp):
TCGAATTTTCGAATTCGAATTAAA
Found at i:20187 original size:27 final size:27
Alignment explanation
Indices: 20149--20202 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
20139 ACAGGATTCT
20149 GTTGGATATTTTAAGTTTACAATTATC
1 GTTGGATATTTTAAGTTTACAATTATC
20176 GTTGGATATTTTAAGTTTACAATTATC
1 GTTGGATATTTTAAGTTTACAATTATC
20203 CCCATAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (27 bp):
GTTGGATATTTTAAGTTTACAATTATC
Found at i:21761 original size:87 final size:87
Alignment explanation
Indices: 21327--21745 Score: 610
Period size: 87 Copynumber: 4.8 Consensus size: 87
21317 TTTGAGGTGA
* *
21327 ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAAATT-CAGCTTTGTCCACATCC
1 ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCA-CTTTGTCCACATTC
* *
21391 GTTTCCTGCTGAACCAGATTCTT
65 ATTTCCTGCTGAACCGGATTCTT
* * * * **
21414 ATGTTCATTTGCCGTAGATGATTCTTGCTTCTTACCTTTTTCAGATTCCGTTTTGTCCACATTCA
1 ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCACTTTGTCCACATTCA
*
21479 TTTCCTGTTGAACCGGATTCTT
66 TTTCCTGCTGAACCGGATTCTT
* *
21501 ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCACTTTGTCCATATTCC
1 ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCACTTTGTCCACATTCA
21566 TTTCCTGCTGAACCGGATTCTT
66 TTTCCTGCTGAACCGGATTCTT
*
21588 ATATTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATT-CAGCTTTGTCCACA-TC
1 ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCA-CTTTGTCCACATTC
*
21651 TGTTTCCTGCTGAACCGGATTCTT
65 -ATTTCCTGCTGAACCGGATTCTT
* ** * *
21675 ATGTTTATTTGCCGTAGATGATTCTTGCTTCTTCCCTTTCTCACCTTCCATTTTGTCCACTTTCA
1 ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCACTTTGTCCACATTCA
21740 TTTCCT
66 TTTCCT
21746 TCTGCAGCAG
Statistics
Matches: 297, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
86 4 0.01
87 288 0.97
88 5 0.02
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.45
Consensus pattern (87 bp):
ATGTTTATTTGCCATAGATGATTCTTGCTTCTTCCCTTTCTCAGATTCCACTTTGTCCACATTCA
TTTCCTGCTGAACCGGATTCTT
Found at i:23765 original size:17 final size:17
Alignment explanation
Indices: 23743--23776 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23733 TCAGGTAAGT
*
23743 AGAAAAGAAAATAGAGG
1 AGAAAAGAAAAAAGAGG
23760 AGAAAAGAAAAAAGAGG
1 AGAAAAGAAAAAAGAGG
23777 TATTTTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (17 bp):
AGAAAAGAAAAAAGAGG
Found at i:33569 original size:18 final size:18
Alignment explanation
Indices: 33546--33581 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
33536 TTTTCGTTTA
33546 AGAGTAAATGATTTAATG
1 AGAGTAAATGATTTAATG
33564 AGAGTAAATGATTTAATG
1 AGAGTAAATGATTTAATG
33582 TTAAGAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (18 bp):
AGAGTAAATGATTTAATG
Found at i:34543 original size:21 final size:21
Alignment explanation
Indices: 34514--34600 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 21
34504 AGTACTATGT
*
34514 AACACTCGATTTAAACATATA
1 AACAATCGATTTAAACATATA
* *
34535 AACAATCGA-TTCAA-A-AGA
1 AACAATCGATTTAAACATATA
* *
34553 AACAAT--ATTT-TAC-CAT-
1 AACAATCGATTTAAACATATA
*
34569 GACAATCGATTTAAACATATA
1 AACAATCGATTTAAACATATA
*
34590 AAAAATCGATT
1 AACAATCGATT
34601 CAAAATAAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
16 7 0.15
17 3 0.06
18 12 0.25
19 3 0.06
20 6 0.12
21 17 0.35
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (21 bp):
AACAATCGATTTAAACATATA
Found at i:35981 original size:2 final size:2
Alignment explanation
Indices: 35974--36009 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
35964 TTCTTTTCTT
35974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36010 TACATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36016 original size:14 final size:14
Alignment explanation
Indices: 35983--36025 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
35973 TTATATATAT
*
35983 ATATATATATATATAT
1 ATATATA-ATAT-TAC
35999 ATATATAATATTAC
1 ATATATAATATTAC
*
36013 ATATAAAATATTA
1 ATATATAATATTA
36026 TTATGTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 14 0.56
15 4 0.16
16 7 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATAATATTAC
Found at i:38459 original size:16 final size:16
Alignment explanation
Indices: 38438--38488 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
38428 AATCAGTTAT
38438 TTAATTAATTTAATTA
1 TTAATTAATTTAATTA
38454 TTAATTCAATTTTAATGATA
1 TTAATT-AA-TTTAAT--TA
38474 TT-A-TAATTTAATTA
1 TTAATTAATTTAATTA
38488 T
1 T
38489 CAAATCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.10
16 12 0.39
17 4 0.13
18 7 0.23
19 1 0.03
20 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTAATTAATTTAATTA
Found at i:63960 original size:22 final size:22
Alignment explanation
Indices: 63921--63980 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
63911 CGATCTAAGA
*
63921 AAAAATAAAAG--AACAGAATT
1 AAAAATAAAAGAAAATAGAATT
63941 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
63963 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
63981 GGAAATCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:63971 original size:15 final size:16
Alignment explanation
Indices: 63946--63975 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
63936 GAATTAAAAA
63946 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
63962 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
63976 AATAGGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:64816 original size:19 final size:19
Alignment explanation
Indices: 64792--64834 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
64782 AAACATAAAT
64792 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
64811 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
64830 TAAAT
1 TAAAT
64835 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:80840 original size:72 final size:71
Alignment explanation
Indices: 80763--80922 Score: 162
Period size: 71 Copynumber: 2.2 Consensus size: 71
80753 TATCGAAACC
* * * *
80763 CAATAAATTGAACTAAAATAGTCTTTTTAAAAACACATAATCG-AATAGACGGTTTTACTTATTA
1 CAATAAATTGAACTAAAATAATC-TTCTAAAAACACATAA-CGAAATAAACGGTTTTACTTAATA
*
80827 TC-AAATT
64 TCAAAAAT
** * *** *
80834 CTAATAAATCAAACTAAATTAATCTTCTAAAAATGTATAACGAAATAAACGTTTTTACTTAATAT
1 C-AATAAATTGAACTAAAATAATCTTCTAAAAACACATAACGAAATAAACGGTTTTACTTAATAT
80899 CAAAAAT
65 CAAAAAT
*
80906 CAATAAACTGAACTAAA
1 CAATAAATTGAACTAAA
80923 TTAACTTTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
70 2 0.03
71 46 0.65
72 23 0.32
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (71 bp):
CAATAAATTGAACTAAAATAATCTTCTAAAAACACATAACGAAATAAACGGTTTTACTTAATATC
AAAAAT
Found at i:80893 original size:71 final size:71
Alignment explanation
Indices: 80799--82096 Score: 685
Period size: 71 Copynumber: 18.1 Consensus size: 71
80789 TTAAAAACAC
* * * * * *
80799 ATAATCGAATAGACGGTTTTACTTATTATCAAATTCTAATAAATCAAACTAAATTAATCTTCTAA
1 ATAATTGAATAAACGATTTTACTTAATATCAAATTCTAATAAATCAAACTAAATTAACCTTTTAA
80864 AAATGT
66 AAATGT
* * * *
80870 ATAA-CGAAATAAACGTTTTTACTTAATATCAAAAATC-AATAAA-CTGAACTAAATTAACTTTT
1 ATAATTG-AATAAACGATTTTACTTAATATC-AAATTCTAATAAATC-AAACTAAATTAAC----
* ** * *
80932 TTTTTTTAAACGC
59 CTTTTAAAAATGT
* ** * * * * * * *
80945 ATAATTAAACGAACAATTTTACTTATTATC-AATGTTTAACAAATCAAACTAAATTAGCCTTCTG
1 ATAATTGAATAAACGATTTTACTTAATATCAAAT-TCTAATAAATCAAACTAAATTAACCTTTTA
81009 AAAATGT
65 AAAATGT
* * * ** * *
81016 ATAACAT-AATAAACGGTTATACTTAATATCATAA--CATAATAAATTTGAATTAAATTAAGCTT
1 ATAA-TTGAATAAACGATTTTACTTAATATCA-AATTC-TAATAAA-TCAAACTAAATTAACCTT
*
81078 TTAAAAAATGC
62 TT-AAAAATGT
** * * * * * *
81089 ATAATTGAACCAACGGTTTTACTTACTATAAAATT-TCAATAAATTAAACTAAATTAGCCTTCTA
1 ATAATTGAATAAACGATTTTACTTAATATCAAATTCT-AATAAATCAAACTAAATTAACCTTTTA
*
81153 GAAATGT
65 AAAATGT
* * * * *
81160 ACAATAGAATAAACAATTTTACTTAATATCAAAATTC-AATATATCAAACTAAATT-AGCTTTAT
1 ATAATTGAATAAACGATTTTACTTAATATC-AAATTCTAATAAATCAAACTAAATTAACCTTT-T
** *
81223 GGAAATGA
64 AAAAATGT
** * * * * **
81231 ATAACAGAATAAA-AAGTTTTACTTAATACCAAA-ACTCAATAAATCAAATTAAATTAAGTTTTT
1 ATAATTGAATAAACGA-TTTTACTTAATATCAAATTCT-AATAAATCAAACTAAATTAA-CCTTT
* ***
81294 TTAAAACAC
63 TAAAAATGT
* ** * * * * * *
81303 ACAATTGAGCAAATGATCTTACTTAATATCAAAATTC-AACAAATCAAACTAAATTTACCTTCTG
1 ATAATTGAATAAACGATTTTACTTAATATC-AAATTCTAATAAATCAAACTAAATTAACCTTTTA
81367 AAAATGT
65 AAAATGT
* * * * ** *
81374 ATAATTGAATAAACGGTTCTACTTACTATCAAA-ACTTAATAAATTGAACTAAATTAACTTTTTT
1 ATAATTGAATAAACGATTTTACTTAATATCAAATTC-TAATAAATCAAACTAAATTAAC-CTTTT
*
81438 AAAAATGC
64 AAAAATGT
* * * * *
81446 ACAATTGAACAAACGAGTTTACTTAATATCAAACTTC-AAT-AATCAAACTAAATTAGCCTTTTG
1 ATAATTGAATAAACGATTTTACTTAATATCAAA-TTCTAATAAATCAAACTAAATTAACCTTTTA
81509 AAAATGT
65 AAAATGT
* * * * * *
81516 ATAACTGAATAAA-TAGTTCTACTTAATATCGAAACTC-AATAAATCGAACTAAATTAACCTTCT
1 ATAATTGAATAAACGA-TTTTACTTAATATC-AAATTCTAATAAATCAAACTAAATTAACCTTTT
81579 AAAAATGT
64 AAAAATGT
* * * *
81587 ATAATTGAATAAACGGTTTTACTTAATATCAAA-ACTCAATAAATTAAACAAAATTAACCTTTTT
1 ATAATTGAATAAACGATTTTACTTAATATCAAATTCT-AATAAATCAAACTAAATTAACC-TTTT
* ***
81651 AAGAACAC
64 AAAAATGT
* * * *
81659 ATAATTGAACAAACGGTTTTACTTAATATCAAATT-TCAATAAATCATACTAAATT-AGCTTTAT
1 ATAATTGAATAAACGATTTTACTTAATATCAAATTCT-AATAAATCAAACTAAATTAACCTTT-T
*
81722 GAAAATGT
64 AAAAATGT
* * * * * * * *
81730 ATAAATGAATAAACGATTCTACTCAGTATCAAAATT-TAATAAATTAGATTAAATTAACCTTTTT
1 ATAATTGAATAAACGATTTTACTTAATATC-AAATTCTAATAAATCAAACTAAATTAACCTTTTA
*
81794 AAAATGC
65 AAAATGT
* * *
81801 ATAATTGAACAAACGATTTTACTTAATATC-AATTTTCAATAAATCAAACTAAATTAATCC-TCT
1 ATAATTGAATAAACGATTTTACTTAATATCAAATTCT-AATAAATCAAACTAAATTAA-CCTTTT
*
81864 GAAAATGT
64 AAAAATGT
** * * * **
81872 ATAACCGAATAAACGATTCTACTTAATATCAAAAGT-TAATAGATTGAACTAAATT-A--TTTAA
1 ATAATTGAATAAACGATTTTACTTAATATC-AAATTCTAATAAATCAAACTAAATTAACCTTT--
* ***
81933 AAAAAAACACAC
63 --TAAAA-ATGT
* * * * * * * *
81945 ATGATTGAATAAACAATTTTATTTAATATCAAAATTCGAAAAAATCGAATTAAATT-AGCTTTCT
1 ATAATTGAATAAACGATTTTACTTAATATC-AAATTCTAATAAATCAAACTAAATTAACCTTT-T
*
82009 GAAAATGT
64 AAAAATGT
* * * * * * * * *
82017 GTAACTGAATTAACGGTTCTGCTTAATATCAAA-ACTCAATAAATCGAATTAAATTAACCTTTTT
1 ATAATTGAATAAACGATTTTACTTAATATCAAATTCT-AATAAATCAAACTAAATTAACC--TTT
*
82081 TAAAAACGT
63 TAAAAATGT
82090 ATAATTG
1 ATAATTG
82097 GACAAATTAA
Statistics
Matches: 917, Mismatches: 244, Indels: 130
0.71 0.19 0.10
Matches are distributed among these distances:
68 1 0.00
69 8 0.01
70 60 0.07
71 462 0.50
72 222 0.24
73 94 0.10
74 21 0.02
75 45 0.05
76 4 0.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (71 bp):
ATAATTGAATAAACGATTTTACTTAATATCAAATTCTAATAAATCAAACTAAATTAACCTTTTAA
AAATGT
Found at i:80995 original size:146 final size:148
Alignment explanation
Indices: 80815--81220 Score: 379
Period size: 144 Copynumber: 2.8 Consensus size: 148
80805 GAATAGACGG
* *
80815 TTTTACTTATTATCAAATTCTAATAAATCAAACTAAATTAATCTTCTAAAAATGTATAACGA-AA
1 TTTTACTTATTATCAAATTCTAACAAATCAAACTAAATTAACCTTCTAAAAATGTATAAC-ATAA
* *
80879 TAAACGTTTTTACTTAATATCA-AAAATCAATAAA-CTGAACTAAATTAA-CTTTTTTTTTTTAA
65 TAAACGGTTATACTTAATATCATAAAAT-AATAAATCTGAACTAAATTAAGCTTTTTTTTTTTAA
80941 ACGCATAATTAAACGAACAA
129 ACGCATAATTAAACGAACAA
* * *
80961 TTTTACTTATTATC-AATGTTTAACAAATCAAACTAAATTAGCCTTCTGAAAATGTATAACATAA
1 TTTTACTTATTATCAAAT-TCTAACAAATCAAACTAAATTAACCTTCTAAAAATGTATAACATAA
* * * ***
81025 TAAACGGTTATACTTAATATCATAACATAATAAATTTGAATTAAATTAAGC----TTTTAAAAAA
65 TAAACGGTTATACTTAATATCATAAAATAATAAATCTGAACTAAATTAAGCTTTTTTTTTTTAAA
* * * **
81086 TGCATAATTGAACCAACGG
130 CGCATAATTAAACGAACAA
* * * * * * * * *
81105 TTTTACTTACTATAAAATT-TCAATAAATTAAACTAAATTAGCCTTCTAGAAATGTACAATAGAA
1 TTTTACTTATTATCAAATTCT-AACAAATCAAACTAAATTAACCTTCTAAAAATGTATAACATAA
** * * * *
81169 TAAACAATTTTACTTAATATCA-AAATTCAATATATC-AAACTAAATT-AGCTTT
65 TAAACGGTTATACTTAATATCATAAAAT-AATAAATCTGAACTAAATTAAGCTTT
81221 ATGGAAATGA
Statistics
Matches: 213, Mismatches: 36, Indels: 23
0.78 0.13 0.08
Matches are distributed among these distances:
142 3 0.01
143 12 0.06
144 95 0.45
145 7 0.03
146 79 0.37
147 16 0.08
148 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (148 bp):
TTTTACTTATTATCAAATTCTAACAAATCAAACTAAATTAACCTTCTAAAAATGTATAACATAAT
AAACGGTTATACTTAATATCATAAAATAATAAATCTGAACTAAATTAAGCTTTTTTTTTTTAAAC
GCATAATTAAACGAACAA
Found at i:81551 original size:142 final size:141
Alignment explanation
Indices: 81124--81927 Score: 600
Period size: 143 Copynumber: 5.6 Consensus size: 141
81114 CTATAAAATT
* * * * * * * *
81124 TCAATAAATTAAACTAAATTAGCCTTCTAGAAATGTACAATAGAATAAACAATTTTACTTAATAT
1 TCAATAAATCAAACTAAATTAACCTTCTAAAAATGCACAATTGAACAAACGAGTTTACTTAATAT
* * * *
81189 CAAAATTCAATATATCAAACTAAATTAG-CTTTATGGAAATGAATAACAGAATAAAAAGTTTTAC
66 CAAAATTCAATA-ATCAAACTAAATTAGCCTTT-TGAAAATGTATAACTGAATAAAAAGTTCTAC
*
81253 TTAATACCAAAAC
129 TTAATATCAAAAC
* ** * * ** * *
81266 TCAATAAATCAAATTAAATTAAGTTTTTTTAAAACACACAATTGAGCAAATGA-TCTTACTTAAT
1 TCAATAAATCAAACTAAATTAA-CCTTCTAAAAATGCACAATTGAACAAACGAGT-TTACTTAAT
* * * **
81330 ATCAAAATTCAACAAATCAAACTAAATTTA-CCTTCTGAAAATGTATAATTGAATAAACGGTTCT
64 ATCAAAATTCAA-TAATCAAACTAAA-TTAGCCTTTTGAAAATGTATAACTGAATAAAAAGTTCT
*
81394 ACTTACTATCAAAAC
127 ACTTAATATCAAAAC
* ** * *
81409 TTAATAAATTGAACTAAATTAACTTTTTTAAAAATGCACAATTGAACAAACGAGTTTACTTAATA
1 TCAATAAATCAAACTAAATTAAC-CTTCTAAAAATGCACAATTGAACAAACGAGTTTACTTAATA
* *
81474 TCAAACTTCAATAATCAAACTAAATTAGCCTTTTGAAAATGTATAACTGAATAAATAGTTCTACT
65 TCAAAATTCAATAATCAAACTAAATTAGCCTTTTGAAAATGTATAACTGAATAAAAAGTTCTACT
*
81539 TAATATCGAAAC
130 TAATATCAAAAC
* * * *
81551 TCAATAAATCGAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACG-GTTTTACTTAATA
1 TCAATAAATCAAACTAAATTAACCTTCTAAAAATGCACAATTGAACAAACGAG-TTTACTTAATA
* * * * * *** * * ** *
81615 TCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAGAACACATAATTGAACAAACGGTTTTA
65 TCAAAATTCAAT-AATCAAACTAAATTAGCCTTTTGAA-AATGTATAACTGAATAAAAAGTTCTA
**
81680 CTTAATATCAAATT
128 CTTAATATCAAAAC
* * * * * * * * * * *
81694 TCAATAAATCATACTAAATTAGCTTTATGAAAATGTATAAATGAATAAACGA-TTCTACTCAGTA
1 TCAATAAATCAAACTAAATTAACCTTCTAAAAATGCACAATTGAACAAACGAGTT-TACTTAATA
* * * * * * * * * * *
81758 TCAAAATTTAATAAATTAGATTAAATTAACCTTTTTAAAATGCATAATTGAA-CAAACGATTTTA
65 TCAAAATTCAAT-AATCAAACTAAATTAGCCTTTTGAAAATGTATAACTGAATAAAAAG-TTCTA
***
81822 CTTAATATCAATTT
128 CTTAATATCAAAAC
* * * ** *
81836 TCAATAAATCAAACTAAATTAATCC-TCTGAAAATGTATAACCGAATAAACGA-TTCTACTTAAT
1 TCAATAAATCAAACTAAATTAA-CCTTCTAAAAATGCACAATTGAACAAACGAGTT-TACTTAAT
**
81899 ATCAAAAGTT-AATAGATTGAACTAAATTA
64 ATCAAAA-TTCAATA-ATCAAACTAAATTA
81928 TTTAAAAAAA
Statistics
Matches: 545, Mismatches: 100, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
140 1 0.00
141 51 0.09
142 223 0.41
143 262 0.48
144 8 0.01
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (141 bp):
TCAATAAATCAAACTAAATTAACCTTCTAAAAATGCACAATTGAACAAACGAGTTTACTTAATAT
CAAAATTCAATAATCAAACTAAATTAGCCTTTTGAAAATGTATAACTGAATAAAAAGTTCTACTT
AATATCAAAAC
Found at i:81592 original size:213 final size:214
Alignment explanation
Indices: 80678--81857 Score: 739
Period size: 214 Copynumber: 5.5 Consensus size: 214
80668 ATGGTTTTAT
* ** * * ** * * *
80678 TTAATACCAAAATTCAATAAATCAAACTAAACCAACATTCTGAAAACATATTATTGAATAAGCAG
1 TTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACGG
* * * * ** * *
80743 CTTTA-TTAAATATCGAAACCCAATAAATTGAACTAAAA-TAGTCTTTTTAAAAACACATAATCG
66 TTTTACTT-AATATCAAAACTCAATAAATTAAAC-AAAATTAACCTTTTTAAAAACACACAATTG
* * * *
80806 AATAGACGGTTTTACTTATTATCAAA-TTCTAATAAATCAAACTAAATTAATCTTCTA--AAAAT
129 AACAAACGGTTTTACTTAATATCAAACTTC-AATAAATCAAACTAAATT-AGCTT-TATGAAAAT
* * * *
80868 GTAT-AACGAAATAAACGTTTTTAC
191 GTATAAATG-AATAAAAGATTCTAC
* * * * ** * * * **
80892 TTAATATCAAAAATCAATAAA-CTGAACTAAATTAACTTTTTTTTTTTAAACGCATAATTAAACG
1 TTAATATCAAAATTCAATAAATC-AAACTAAATTAAC----CTTCTAAAAATGTATAATTGAATA
** * *** * * * * * * * *
80956 AACAATTTTACTTATTATCAATGTTTAACAAATCAAACTAAATTAGCCTTCTGAAAATGTATA-A
61 AACGGTTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAAA---ACACA
* * * ** *
81020 C-A-T-AATAAACGGTTATACTTAATATCATAACAT-AATAAATTTGAATTAAATTAAGCTTT-T
123 CAATTGAACAAACGGTTTTACTTAATATCA-AACTTCAATAAA-TCAAACTAAATT-AGCTTTAT
* * * ** * * *
81080 AAAAAATGCATAATTGAACCAACGGTTTTAC
185 -GAAAATGTATAAATGAATAAAAGATTCTAC
* * * * * * *
81111 TTACTAT-AAAATTTCAATAAATTAAACTAAATTAGCCTTCTAGAAATGTACAATAGAATAAACA
1 TTAATATCAAAA-TTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACG
* * * * * * ** ** * **
81175 ATTTTACTTAATATCAAAATTCAATATATCAAACTAAATT-AGCTTTATGGAAATGA-ATAACAG
65 GTTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTT-TTAAAAACACACAATTG
* ** * * * * * **
81238 AATAAAAAGTTTTACTTAATACCAAAAC-TCAATAAATCAAATTAAATTAAGTTTTTTTAAAACA
129 AACAAACGGTTTTACTTAATATC-AAACTTCAATAAATCAAACTAAATT-AGCTTTATGAAAATG
* * * ** *
81302 CACAATTGAGCAAATGA-TCTTAC
192 TATAAATGAATAAAAGATTC-TAC
* * *
81325 TTAATATCAAAATTCAACAAATCAAACTAAATTTACCTTCTGAAAATGTATAATTGAATAAACGG
1 TTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACGG
* * * * * * **
81390 TTCTACTTACTATCAAAACTTAATAAATTGAACTAAATTAACTTTTTTAAAAATGCACAATTGAA
66 TTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAAAACACACAATTGAA
81455 CAAACGAG-TTTACTTAATATCAAACTTCAAT-AATCAAACTAAATTAGCCTTT-TGAAAATGTA
131 CAAACG-GTTTTACTTAATATCAAACTTCAATAAATCAAACTAAATTAG-CTTTATGAAAATGTA
*
81517 TAACTGAATAAATAG-TTCTAC
194 TAAATGAATAAA-AGATTCTAC
* * *
81538 TTAATATCGAAACTCAATAAATCGAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACGG
1 TTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACGG
* *
81603 TTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAGAACACATAATTGAA
66 TTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAAAACACACAATTGAA
* *
81668 CAAACGGTTTTACTTAATATCAAATTTCAATAAATCATACTAAATTAGCTTTATGAAAATGTATA
131 CAAACGGTTTTACTTAATATCAAACTTCAATAAATCAAACTAAATTAGCTTTATGAAAATGTATA
*
81733 AATGAATAAACGATTCTAC
196 AATGAATAAAAGATTCTAC
* * * * * * * * * * *
81752 TCAGTATCAAAATTTAATAAATTAGATTAAATTAACCTTTTTAAAATGCATAATTGAACAAACGA
1 TTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACGG
*** * *
81817 TTTTACTTAATATCAATTTTCAATAAATCAAACTAAATTAA
66 TTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAA
81858 TCCTCTGAAA
Statistics
Matches: 750, Mismatches: 177, Indels: 78
0.75 0.18 0.08
Matches are distributed among these distances:
212 3 0.00
213 169 0.23
214 305 0.41
215 119 0.16
216 2 0.00
217 31 0.04
218 67 0.09
219 49 0.07
220 3 0.00
221 2 0.00
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (214 bp):
TTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAACGG
TTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAAAACACACAATTGAA
CAAACGGTTTTACTTAATATCAAACTTCAATAAATCAAACTAAATTAGCTTTATGAAAATGTATA
AATGAATAAAAGATTCTAC
Found at i:81622 original size:356 final size:353
Alignment explanation
Indices: 80818--81927 Score: 1245
Period size: 356 Copynumber: 3.1 Consensus size: 353
80808 TAGACGGTTT
* * *
80818 TACTTATTATC-AAATTCTAATAAATCAAACTAAATTAATCTTCTAAAAATGTATAACGAAATAA
1 TACTTAATATCAAAATTC-AATAAATCAAACTAAATTAACCTTCTAAAAATGTATAAAG-AATAA
* * * * *
80882 ACGTTTTTACTTAATATCAAAAATCAATAAA-CTGAACTAAATTAACTTTTTTTTTTTAAACGCA
64 ACGGTTTTACTTAATATCAAAACTCAATAAATC-AAACTAAATTAA----TTTTTTTAAAACACA
* * * * ** *
80946 TAATTAAACGAACAATTTTACTTATTATCAATGTTTAACAAATCAAACTAAATTAGCCTTCTGAA
124 TAATTGAACAAACGATTTTACTTAATATCAAAATTCAACAAATCAAACTAAATTAGCCTTCTGAA
* * *
81011 AATGTATAACAT-AATAAACGGTTATACTTAATATCATAACATAATAAATTTGAATTAAATTAAG
189 AATGTATAA-ATGAATAAACGGTTCTACTTAATATCAAAACTTAATAAA-TTGAATTAAATTAA-
* * * * *
81075 CTTTTAAAAAATGCATAATTGAACCAACG-GTTTTACTTACTATAAAATTTCAATAAATTAAACT
251 CTTTTTAAAAATGCATAATTGAACAAACGAG-TTTACTTAATATCAAATTTCAATAAATCAAACT
* * *
81139 AAATTAGCCTTCT-AGAAATGTACAA-TAGAATAAACAATTT
315 AAATTAGCCTTCTGA-AAATGTATAACT-GAATAAA-AGTTC
* * * * ** *
81179 TACTTAATATCAAAATTCAATATATCAAACTAAATTAGCTTTATGGAAATGAATAACAGAATAAA
1 TACTTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAA-AGAATAAA
** * * *
81244 AAGTTTTACTTAATACCAAAACTCAATAAATCAAATTAAATTAAGTTTTTTTAAAACACACAATT
65 CGGTTTTACTTAATATCAAAACTCAATAAATCAAACTAAATTAA-TTTTTTTAAAACACATAATT
* * *
81309 GAGCAAATGATCTTACTTAATATCAAAATTCAACAAATCAAACTAAATTTA-CCTTCTGAAAATG
129 GAACAAACGATTTTACTTAATATCAAAATTCAACAAATCAAACTAAA-TTAGCCTTCTGAAAATG
* * *
81373 TATAATTGAATAAACGGTTCTACTTACTATCAAAACTTAATAAATTGAACTAAATTAACTTTTTT
193 TATAAATGAATAAACGGTTCTACTTAATATCAAAACTTAATAAATTGAATTAAATTAAC-TTTTT
* *
81438 AAAAATGCACAATTGAACAAACGAGTTTACTTAATATCAAACTTCAAT-AATCAAACTAAATTAG
257 AAAAATGCATAATTGAACAAACGAGTTTACTTAATATCAAATTTCAATAAATCAAACTAAATTAG
*
81502 CCTTTTGAAAATGTATAACTGAATAAATAGTTC
322 CCTTCTGAAAATGTATAACTGAATAAA-AGTTC
* * * *
81535 TACTTAATATCGAAACTCAATAAATCGAACTAAATTAACCTTCTAAAAATGTATAATTGAATAAA
1 TACTTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAA-AGAATAAA
* * **
81600 CGGTTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAGAACACATAATT
65 CGGTTTTACTTAATATCAAAACTCAATAAATCAAACTAAATTAATTTTTTTAA-AACACATAATT
* * * * * *
81665 GAACAAACGGTTTTACTTAATATCAAATTTCAATAAATCATACTAAATTAGCTTTATGAAAATGT
129 GAACAAACGATTTTACTTAATATCAAAATTCAACAAATCAAACTAAATTAGCCTTCTGAAAATGT
* * * *
81730 ATAAATGAATAAACGATTCTACTCAGTATCAAAATTTAATAAATT-AGATTAAATTAACCTTTTT
194 ATAAATGAATAAACGGTTCTACTTAATATCAAAACTTAATAAATTGA-ATTAAATTAA-CTTTTT
* *
81794 -AAAATGCATAATTGAACAAACGATTTTACTTAATATCAATTTTCAATAAATCAAACTAAATTAA
257 AAAAATGCATAATTGAACAAACGAGTTTACTTAATATCAAATTTCAATAAATCAAACTAAATT-A
* * *
81858 TCC-TCTGAAAATGTATAACCGAATAAACGATTC
321 GCCTTCTGAAAATGTATAACTGAATAAAAG-TTC
* **
81891 TACTTAATATCAAAAGTT-AATAGATTGAACTAAATTA
1 TACTTAATATCAAAA-TTCAATAAATCAAACTAAATTA
81928 TTTAAAAAAA
Statistics
Matches: 635, Mismatches: 97, Indels: 39
0.82 0.13 0.05
Matches are distributed among these distances:
355 55 0.09
356 317 0.50
357 66 0.10
358 105 0.17
359 3 0.00
361 81 0.13
362 8 0.01
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (353 bp):
TACTTAATATCAAAATTCAATAAATCAAACTAAATTAACCTTCTAAAAATGTATAAAGAATAAAC
GGTTTTACTTAATATCAAAACTCAATAAATCAAACTAAATTAATTTTTTTAAAACACATAATTGA
ACAAACGATTTTACTTAATATCAAAATTCAACAAATCAAACTAAATTAGCCTTCTGAAAATGTAT
AAATGAATAAACGGTTCTACTTAATATCAAAACTTAATAAATTGAATTAAATTAACTTTTTAAAA
ATGCATAATTGAACAAACGAGTTTACTTAATATCAAATTTCAATAAATCAAACTAAATTAGCCTT
CTGAAAATGTATAACTGAATAAAAGTTC
Found at i:81665 original size:285 final size:282
Alignment explanation
Indices: 80671--81927 Score: 937
Period size: 285 Copynumber: 4.4 Consensus size: 282
80661 TAAAACAATG
* * * ** * ** *
80671 GTTTTATTTAATACCAAAATTCAATAAATCAAACTAAACCAA-CATTCTGAAAACATATTATTGA
1 GTTTTACTTAATATC-AAACTCAATAAATCAAACTAAATTAAGCCTTCTGAAAATGTATAATTGA
* * * * * * * * **
80735 ATAAGC-AGCTTTA-TTAAATATCGAAACCCAATAAATTGAACTAAAATAGTCTTTTTAAAAACA
65 ATAAACGA-TTTTACTT-AATATCAAAACTCAATAAATTAAACTAAATTA-ACCTTTTAAAAATG
* * * * * *
80798 CATAATCGAATAGACGGTTTTACTTATTATC-AAA-TTCTAATAAATCAAACTAAATTA-ATCTT
127 CATAATTGAACAAACGGTTTTACTTACTATCAAAATTTC-AATAAATTAAACTAAATTAGCT-TT
* * * * * * *
80860 CTAAAAATGTATAA-CGAAATAAACGTTTTTACTTAATATCAAAAATCAATAAACTGAACTAAAT
190 ATAAAAATGTACAATTG-AATAAACG-ATTTACTTAATATCAAAATTCAATAATC-AAACTAAAT
* * ** * * * * *
80924 TAACTTTTTTTTTTTAAACGCATAATTAAACGAACAA
252 TAGC----CTTTTGAAAATGAATAACTGAA-TAA-AA
* ** * * *
80961 -TTTTACTTATTATCAATGTTTAACAAATCAAACTAAATT-AGCCTTCTGAAAATGTATAACAT-
1 GTTTTACTTAATATCAA-ACTCAATAAATCAAACTAAATTAAGCCTTCTGAAAATGTATAA-TTG
* * * * * *
81023 AATAAACGGTTATACTTAATATCATAACAT-AATAAATTTGAATTAAATTAAGCTTTTAAAAAAT
64 AATAAACGATTTTACTTAATATCAAAAC-TCAATAAA-TTAAACTAAATTAACCTTTT-AAAAAT
* * *
81087 GCATAATTGAACCAACGGTTTTACTTACTAT-AAAATTTCAATAAATTAAACTAAATTAGCCTTC
126 GCATAATTGAACAAACGGTTTTACTTACTATCAAAATTTCAATAAATTAAACTAAATTAGCTTTA
* * *
81151 TAGAAATGTACAATAGAATAAACAATTTTACTTAATATCAAAATTCAATATATCAAACTAAATTA
191 TAAAAATGTACAATTGAATAAACGA-TTTACTTAATATCAAAATTCAATA-ATCAAACTAAATTA
* *
81216 G-CTTTATGGAAATGAATAACAGAATAAAAA
254 GCCTTT-TGAAAATGAATAACTGAAT-AAAA
* * ** * * *** *
81246 GTTTTACTTAATACCAAAACTCAATAAATCAAATTAAATTAAGTTTTTTTAAAACACACAATTGA
1 GTTTTACTTAATATC-AAACTCAATAAATCAAACTAAATTAAGCCTTCTGAAAATGTATAATTGA
** * * * * * * * * *
81311 GCAAATGATCTTACTTAATATCAAAATTCAACAAATCAAACTAAATTTACCTTCTGAAAATGTAT
65 ATAAACGATTTTACTTAATATCAAAACTCAATAAATTAAACTAAATTAACCTTTTAAAAATGCAT
* * * * * *
81376 AATTGAATAAACGGTTCTACTTACTATCAAAACTT-AATAAATTGAACTAAATTAACTTTTTTAA
130 AATTGAACAAACGGTTTTACTTACTATCAAAATTTCAATAAATTAAACTAAATTAGC-TTTATAA
* * *
81440 AAATGCACAATTGAACAAACGAGTTTACTTAATATCAAACTTCAATAATCAAACTAAATTAGCCT
194 AAATGTACAATTGAATAAACGA-TTTACTTAATATCAAAATTCAATAATCAAACTAAATTAGCCT
*
81505 TTTGAAAATGTATAACTGAATAAATA
258 TTTGAAAATGAATAACTGAATAAA-A
* * *
81531 GTTCTACTTAATATCGAAACTCAATAAATCGAACTAAATTAA-CCTTCTAAAAATGTATAATTGA
1 GTTTTACTTAATATC-AAACTCAATAAATCAAACTAAATTAAGCCTTCTGAAAATGTATAATTGA
* * * **
81595 ATAAACGGTTTTACTTAATATCAAAACTCAATAAATTAAACAAAATTAACCTTTTTAAGAACACA
65 ATAAACGATTTTACTTAATATCAAAACTCAATAAATTAAACTAAATTAACC-TTTTAAAAATGCA
* * * *
81660 TAATTGAACAAACGGTTTTACTTAATATC-AAATTTCAATAAATCATACTAAATTAGCTTTATGA
129 TAATTGAACAAACGGTTTTACTTACTATCAAAATTTCAATAAATTAAACTAAATTAGCTTTATAA
* * * * * * * * *
81724 AAATGTATAAATGAATAAACGATTCTACTCAGTATCAAAATTTAATAAATTAGATTAAATTAACC
194 AAATGTACAATTGAATAAACGATT-TACTTAATATCAAAATTCAAT-AATCAAACTAAATTAGCC
* * * * *
81789 TTTTTAAAATGCATAATTGAACAAAC
257 TTTTGAAAATGAATAACTGAATAAAA
** * **
81815 GATTTTACTTAATATCAATTTTCAATAAATCAAACTAAATTAATCC-TCTGAAAATGTATAACCG
1 G-TTTTACTTAATATCAA-ACTCAATAAATCAAACTAAATTAAGCCTTCTGAAAATGTATAATTG
* * * * *
81879 AATAAACGATTCTACTTAATATCAAAAGTTAATAGATTGAACTAAATTA
64 AATAAACGATTTTACTTAATATCAAAACTCAATAAATTAAACTAAATTA
81928 TTTAAAAAAA
Statistics
Matches: 761, Mismatches: 174, Indels: 69
0.76 0.17 0.07
Matches are distributed among these distances:
283 2 0.00
284 106 0.14
285 301 0.40
286 115 0.15
287 39 0.05
288 3 0.00
289 70 0.09
290 119 0.16
291 6 0.01
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (282 bp):
GTTTTACTTAATATCAAACTCAATAAATCAAACTAAATTAAGCCTTCTGAAAATGTATAATTGAA
TAAACGATTTTACTTAATATCAAAACTCAATAAATTAAACTAAATTAACCTTTTAAAAATGCATA
ATTGAACAAACGGTTTTACTTACTATCAAAATTTCAATAAATTAAACTAAATTAGCTTTATAAAA
ATGTACAATTGAATAAACGATTTACTTAATATCAAAATTCAATAATCAAACTAAATTAGCCTTTT
GAAAATGAATAACTGAATAAAA
Found at i:82070 original size:145 final size:144
Alignment explanation
Indices: 81804--82072 Score: 333
Period size: 145 Copynumber: 1.9 Consensus size: 144
81794 AAAATGCATA
* ** *
81804 ATTGAACAAACGATTTTACTTAATATCAATTTTCAATAAATCAAACTAAATTAATCCTCTGAAAA
1 ATTGAACAAACAATTTTACTTAATATCAAAATTCAAAAAATCAAACTAAATTAATCCTCTGAAAA
* * * *
81869 TGTATAACCGAATAAACGATTCTACTTAATATCAAAAGTTAATAGATTGAACTAAATTATTTAAA
66 TGTATAACCGAATAAACGATTCTACTTAATATCAAAACTCAATAAATCGAACTAAATTATTTAAA
81934 AAAAAACACACATG
131 AAAAAACACACATG
* * * * * *
81948 ATTGAATAAACAATTTTATTTAATATCAAAATTCGAAAAAATCGAATTAAATT-AGCTTTCTGAA
1 ATTGAACAAACAATTTTACTTAATATCAAAATTC-AAAAAATCAAACTAAATTAATC-CTCTGAA
* * * * * *
82012 AATGTGTAACTGAATTAACGGTTCTGCTTAATATCAAAACTCAATAAATCGAATTAAATTA
64 AATGTATAACCGAATAAACGATTCTACTTAATATCAAAACTCAATAAATCGAACTAAATTA
82073 ACCTTTTTTA
Statistics
Matches: 103, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
144 31 0.30
145 72 0.70
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (144 bp):
ATTGAACAAACAATTTTACTTAATATCAAAATTCAAAAAATCAAACTAAATTAATCCTCTGAAAA
TGTATAACCGAATAAACGATTCTACTTAATATCAAAACTCAATAAATCGAACTAAATTATTTAAA
AAAAAACACACATG
Found at i:82180 original size:71 final size:70
Alignment explanation
Indices: 82100--82239 Score: 165
Period size: 71 Copynumber: 2.0 Consensus size: 70
82090 ATAATTGGAC
* * ***
82100 AAATTAAATTGACCTTTTGAAAGTGTGTAACTAAATAAACGATTATACTTAATATCAAAA-CTCA
1 AAATTAAATTAACCTTTTGAAAATACATAACTAAATAAACGATTATACTTAATA--AAAATCTCA
82164 ATAAATT
64 ATAAATT
* * * * *
82171 AAATTAAATTAACTTTTTTAAAATACATAATTAAATAAACGGTTTTACTTAATAAAAATCTCAAT
1 AAATTAAATTAACCTTTTGAAAATACATAACTAAATAAACGATTATACTTAATAAAAATCTCAAT
82236 AAAT
66 AAAT
82240 CGAACTAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
69 4 0.07
70 10 0.17
71 44 0.76
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36
Consensus pattern (70 bp):
AAATTAAATTAACCTTTTGAAAATACATAACTAAATAAACGATTATACTTAATAAAAATCTCAAT
AAATT
Found at i:82182 original size:109 final size:108
Alignment explanation
Indices: 81992--82193 Score: 298
Period size: 109 Copynumber: 1.9 Consensus size: 108
81982 GAAAAAATCG
* * * * * *
81992 AATTAAATTAGCTTTCTGAAAATGTGTAACTGAATTAACGGTTCTGCTTAATATCAAAACTCAAT
1 AATTAAATTACCTTTCTGAAAATGTGTAACTAAATAAACGATTATACTTAATATCAAAACTCAAT
*
82057 AAATCGAATTAAATTAACCTTTTTTAAAAACGTATAATTGGACA
66 AAATCAAATTAAATTAA-CTTTTTTAAAAACGTATAATTGGACA
*
82101 AATTAAATTGACCTTT-TGAAAGTGTGTAACTAAATAAACGATTATACTTAATATCAAAACTCAA
1 AATTAAATT-ACCTTTCTGAAAATGTGTAACTAAATAAACGATTATACTTAATATCAAAACTCAA
*
82165 TAAATTAAATTAAATTAACTTTTTTAAAA
65 TAAATCAAATTAAATTAACTTTTTTAAAA
82194 TACATAATTA
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
108 11 0.13
109 67 0.81
110 5 0.06
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (108 bp):
AATTAAATTACCTTTCTGAAAATGTGTAACTAAATAAACGATTATACTTAATATCAAAACTCAAT
AAATCAAATTAAATTAACTTTTTTAAAAACGTATAATTGGACA
Found at i:85615 original size:18 final size:17
Alignment explanation
Indices: 85574--85607 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
85564 TTTTTTGGAG
85574 AAGAAAAAAAAAGTAAC
1 AAGAAAAAAAAAGTAAC
*
85591 AAAAAAAAAAATAGTAA
1 AAGAAAAAAAA-AGTAA
85608 TATGAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAGAAAAAAAAAGTAAC
Found at i:90703 original size:19 final size:19
Alignment explanation
Indices: 90679--90735 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
90669 CAGAATTATT
*
90679 ATTTTATGAAATTTTTAA-A
1 ATTTTA-GAATTTTTTAATA
90698 ATTTTA-AATTTTTTATATA
1 ATTTTAGAATTTTTTA-ATA
90717 ATTTTAGAATTTTTTAATA
1 ATTTTAGAATTTTTTAATA
90736 TAACTTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 8 0.24
18 1 0.03
19 16 0.47
20 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTTAGAATTTTTTAATA
Found at i:90736 original size:21 final size:20
Alignment explanation
Indices: 90697--90809 Score: 83
Period size: 20 Copynumber: 5.7 Consensus size: 20
90687 AAATTTTTAA
*
90697 AATTTTAAATTTTTT-ATAT
1 AATTTTGAATTTTTTAATAT
90716 AATTTTAGAATTTTTTAATAT
1 AATTTT-GAATTTTTTAATAT
*
90737 AACTTTTGAAATTTTATAA-AT
1 AA-TTTTG-AATTTTTTAATAT
* * *
90758 -ATTTT-AA-ATTTAAAGAT
1 AATTTTGAATTTTTTAATAT
* *
90775 CATTTTGAATTTTTTAAAAT
1 AATTTTGAATTTTTTAATAT
*
90795 TATTTTGTAATTTTT
1 AATTTTG-AATTTTT
90810 GTTGAGGAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.05
17 4 0.05
18 5 0.07
19 12 0.16
20 22 0.29
21 16 0.21
22 13 0.17
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTGAATTTTTTAATAT
Found at i:90758 original size:23 final size:21
Alignment explanation
Indices: 90697--90759 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
90687 AAATTTTTAA
*
90697 AATTTTA-AATTTTT-TATAT
1 AATTTTAGAATTTTTAAATAT
*
90716 AATTTTAGAATTTTTTAATAT
1 AATTTTAGAATTTTTAAATAT
90737 AACTTTT-GAAATTTTATAAATAT
1 AA-TTTTAG-AATTTT-TAAATAT
90760 TTTAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 7 0.19
20 7 0.19
21 7 0.19
22 10 0.27
23 6 0.16
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (21 bp):
AATTTTAGAATTTTTAAATAT
Found at i:90785 original size:58 final size:57
Alignment explanation
Indices: 90685--90809 Score: 146
Period size: 58 Copynumber: 2.2 Consensus size: 57
90675 TATTATTTTA
** * *
90685 TGAAATTTTTAAAATTTTAAATTTTTTATATAATTTTAGAATTTTTTAATATAACTTT
1 TGAAATTTTTAAAATTTTAAATTTTAAAGATAATTTTAGAATTTTTTAAAATAA-TTT
* *
90743 TGAAATTTTATAAATATTTTAAA-TTTAAAGATCATTTT-GAATTTTTTAAAATTATTT
1 TGAAATTTT-TAAA-ATTTTAAATTTTAAAGATAATTTTAGAATTTTTTAAAATAATTT
*
90800 TGTAATTTTT
1 TGAAATTTTT
90810 GTTGAGGAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 1 0.02
57 11 0.19
58 23 0.40
59 15 0.26
60 8 0.14
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (57 bp):
TGAAATTTTTAAAATTTTAAATTTTAAAGATAATTTTAGAATTTTTTAAAATAATTT
Found at i:90801 original size:20 final size:20
Alignment explanation
Indices: 90697--90809 Score: 76
Period size: 21 Copynumber: 5.7 Consensus size: 20
90687 AAATTTTTAA
* *
90697 AATTTTAAATTTTTT-ATAT
1 AATTTTGAATTTTTTAAAAT
*
90716 AATTTTAGAATTTTTTAATAT
1 AATTTT-GAATTTTTTAAAAT
*
90737 AACTTTTGAA-ATTTTATAAAT
1 AA-TTTTGAATTTTTTA-AAAT
*
90758 -ATTTT-AA--ATTTAAAGAT
1 AATTTTGAATTTTTTAAA-AT
*
90775 CATTTTGAATTTTTTAAAAT
1 AATTTTGAATTTTTTAAAAT
*
90795 TATTTTGTAATTTTT
1 AATTTTG-AATTTTT
90810 GTTGAGGAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.03
17 6 0.08
18 7 0.09
19 12 0.15
20 22 0.28
21 25 0.32
22 4 0.05
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTGAATTTTTTAAAAT
Found at i:91844 original size:5 final size:5
Alignment explanation
Indices: 91834--91858 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
91824 CTAATAAAAA
91834 TCCCC TCCCC TCCCC TCCCC TCCCC
1 TCCCC TCCCC TCCCC TCCCC TCCCC
91859 CGTTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
TCCCC
Found at i:96903 original size:22 final size:22
Alignment explanation
Indices: 96864--96905 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
96854 AAATAAAGTA
*
96864 TAAATATTTAATAATTTGATTT
1 TAAATAATTAATAATTTGATTT
* *
96886 TAAATAATTATTATTTTGAT
1 TAAATAATTAATAATTTGAT
96906 AACCATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TAAATAATTAATAATTTGATTT
Found at i:117969 original size:41 final size:41
Alignment explanation
Indices: 117918--117998 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
117908 TTTTTATTGT
*
117918 ATTTTCAATTTGTTTATTATTTTACGAATTGTTTTAATATC
1 ATTTTCAATTTGTTTATTATTTTAAGAATTGTTTTAATATC
* * * * *
117959 ATTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATAT
1 ATTTTCAATTTGTTTATTATTTTAAGAATTGTTTTAATAT
117999 TTTTAAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.63
Consensus pattern (41 bp):
ATTTTCAATTTGTTTATTATTTTAAGAATTGTTTTAATATC
Found at i:117992 original size:12 final size:12
Alignment explanation
Indices: 117975--118000 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
117965 AATTTGTTTG
117975 TTGTTTTAATAT
1 TTGTTTTAATAT
117987 TTGTTTTAATAT
1 TTGTTTTAATAT
117999 TT
1 TT
118001 TTAAATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:127574 original size:18 final size:17
Alignment explanation
Indices: 127548--127582 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
127538 TCACTTCTTC
127548 TTTTTTTTTCTTTTTCA
1 TTTTTTTTTCTTTTTCA
127565 TTTTTGTTTTCTTTTTCA
1 TTTTT-TTTTCTTTTTCA
127583 ATATTCTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTTTTTCTTTTTCA
Found at i:128611 original size:5 final size:5
Alignment explanation
Indices: 128596--128627 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
128586 TTCAAAGAGC
128596 TTTGAG TTTGG TTTGG TTTGG TTTGG TTTGG T
1 TTTG-G TTTGG TTTGG TTTGG TTTGG TTTGG T
128628 GTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.03, C:0.00, G:0.38, T:0.59
Consensus pattern (5 bp):
TTTGG
Found at i:128826 original size:3 final size:3
Alignment explanation
Indices: 128779--128843 Score: 53
Period size: 3 Copynumber: 21.0 Consensus size: 3
128769 ATATATGATG
* * *
128779 TTC TTC TCTC TTC CTC TTCC TT- TTC TTA TTC -TC GTGTC GTC TTC TTC
1 TTC TTC T-TC TTC TTC TT-C TTC TTC TTC TTC TTC -T-TC TTC TTC TTC
128826 TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC
128844 ACCTTCACCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
2 4 0.08
3 38 0.76
4 6 0.12
5 2 0.04
ACGTcount: A:0.02, C:0.34, G:0.05, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:128849 original size:6 final size:6
Alignment explanation
Indices: 128840--128881 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
128830 TCTTCTTCTT
128840 CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC
1 CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC
128882 TTCCATTCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CTTCAC
Found at i:134941 original size:22 final size:21
Alignment explanation
Indices: 134911--134963 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 21
134901 ATGCATTGTC
*
134911 AAAAGATTAAAAAAATATAAAT
1 AAAAAATTAAAAAAATAT-AAT
* ** *
134933 AAAAAATTACACTAATATATT
1 AAAAAATTAAAAAAATATAAT
134954 AAAAAATTAA
1 AAAAAATTAA
134964 TTAAATATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAAAAAATATAAT
Found at i:134970 original size:21 final size:23
Alignment explanation
Indices: 134923--134971 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
134913 AAGATTAAAA
134923 AAATATAAATAAAAAATTACACT
1 AAATATAAATAAAAAATTACACT
* *
134946 -AATAT-ATTAAAAAATTA-ATT
1 AAATATAAATAAAAAATTACACT
134966 AAATAT
1 AAATAT
134972 CAATTCAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 16 0.70
22 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAAATAAAAAATTACACT
Found at i:136564 original size:15 final size:15
Alignment explanation
Indices: 136546--136585 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
136536 TAACAATTAA
136546 AGCAACAACAAA-AAT
1 AGCAACAA-AAATAAT
136561 AGCAACAAAAATAAT
1 AGCAACAAAAATAAT
*
136576 AGCATCAAAA
1 AGCAACAAAA
136586 CAGTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.65, C:0.17, G:0.07, T:0.10
Consensus pattern (15 bp):
AGCAACAAAAATAAT
Found at i:136651 original size:21 final size:22
Alignment explanation
Indices: 136627--136671 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
136617 ACACTAAAAC
*
136627 AATAAAAAAAAACAA-TATCAA
1 AATAAAAAAAAACAACAATCAA
**
136648 AATAGCAAAAAACAACAATCAA
1 AATAAAAAAAAACAACAATCAA
136670 AA
1 AA
136672 CAGCAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.73, C:0.13, G:0.02, T:0.11
Consensus pattern (22 bp):
AATAAAAAAAAACAACAATCAA
Found at i:136657 original size:24 final size:22
Alignment explanation
Indices: 136612--136681 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
136602 CGAAAACAAT
* **
136612 AAAAAACACT-AAAACAATAAA
1 AAAAAACAATCAAAACAGCAAA
*
136633 AAAAAACAATATCAAAATAGCAAA
1 AAAAAAC-A-ATCAAAACAGCAAA
*
136657 AAACAACAATCAAAACAGCAAA
1 AAAAAACAATCAAAACAGCAAA
136679 AAA
1 AAA
136682 TAGCACCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 7 0.17
22 17 0.43
23 2 0.05
24 14 0.35
ACGTcount: A:0.73, C:0.16, G:0.03, T:0.09
Consensus pattern (22 bp):
AAAAAACAATCAAAACAGCAAA
Found at i:136679 original size:21 final size:21
Alignment explanation
Indices: 136633--136681 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
136623 AAACAATAAA
* *
136633 AAAAAACAATATCAAAATAGC
1 AAAAAACAAAATCAAAACAGC
136654 AAAAAACAACAATCAAAACAGC
1 AAAAAACAA-AATCAAAACAGC
136676 AAAAAA
1 AAAAAA
136682 TAGCACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.71, C:0.16, G:0.04, T:0.08
Consensus pattern (21 bp):
AAAAAACAAAATCAAAACAGC
Found at i:152154 original size:4 final size:4
Alignment explanation
Indices: 152147--152181 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
152137 AAAAAAAAAG
152147 AGAA AGAA AGAA AGAA AGAA AGAA AG-A AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
152182 GGGGAAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:152595 original size:20 final size:21
Alignment explanation
Indices: 152554--152596 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
152544 TAATTTACTT
152554 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
152575 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
152595 TA
1 TA
152597 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:153120 original size:16 final size:16
Alignment explanation
Indices: 153074--153122 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
153064 TAAACCTAGC
*
153074 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
153090 T-A-TAA-TATAAAAA
1 TAATTAATTATCAAAA
153103 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
153119 TAAT
1 TAAT
153123 ATCCTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:153189 original size:30 final size:30
Alignment explanation
Indices: 153155--153249 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
153145 AAATGATACA
*
153155 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
** * * * * *
153185 AAAT-AAT-GGTGTGTGGATACTATTTTGGT
1 AAATAAATATATATTTTG-TACCATTTTAGT
*
153214 ATATAAATATATATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTAGT
153244 AAATAA
1 AAATAA
153250 CACATTTTGG
Statistics
Matches: 46, Mismatches: 16, Indels: 6
0.68 0.24 0.09
Matches are distributed among these distances:
28 4 0.09
29 16 0.35
30 22 0.48
31 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTAGT
Found at i:155144 original size:45 final size:45
Alignment explanation
Indices: 155071--155207 Score: 168
Period size: 45 Copynumber: 3.0 Consensus size: 45
155061 GCATAGCTCA
* * *
155071 TCAAGCCAAGGATATCAGTCTCAGTTTGATGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
*
155116 TCAAGCCAATGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
** * * * *
155161 TCAAGGGAAGGATATCAAG-TTGAGTTTGACGAGCCACCGCGATAC
1 TCAAGCCAAGGATATC-AGCCTCAATTTGACGAGCCACCGCAATAC
155206 TC
1 TC
155208 TATTCCTCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 78 0.98
46 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
Found at i:155242 original size:21 final size:21
Alignment explanation
Indices: 155202--155244 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
155192 AGCCACCGCG
* *
155202 ATACTCTATTCCTCCCGGGCA
1 ATACTCTACTCCTCACGGGCA
*
155223 ATACTCTACTCCTCAGGGGCA
1 ATACTCTACTCCTCACGGGCA
155244 A
1 A
155245 ATGAACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.16, T:0.26
Consensus pattern (21 bp):
ATACTCTACTCCTCACGGGCA
Found at i:155505 original size:14 final size:13
Alignment explanation
Indices: 155487--155540 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
155477 ACCAAAATTA
155487 TAAACCCTAAACT
1 TAAACCCTAAACT
*
155500 TAAAACCCTAAATCG
1 T-AAACCCTAAA-CT
*
155515 TAAACACTAAACT
1 TAAACCCTAAACT
*
155528 TGAAACTCTAAAC
1 T-AAACCCTAAAC
155541 CGTAAACACT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.09
14 29 0.85
15 2 0.06
ACGTcount: A:0.48, C:0.26, G:0.04, T:0.22
Consensus pattern (13 bp):
TAAACCCTAAACT
Found at i:155512 original size:28 final size:28
Alignment explanation
Indices: 155473--155551 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
155463 CATTAAACCC
* * *
155473 TAAAA-CCAAAATTATAAACCCTAAACT
1 TAAAACCCTAAATCATAAACACTAAACT
*
155500 TAAAACCCTAAATCGTAAACACTAAACT
1 TAAAACCCTAAATCATAAACACTAAACT
* * * *
155528 TGAAACTCTAAACCGTAAACACTA
1 TAAAACCCTAAATCATAAACACTA
155552 GATTGATTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 5 0.11
28 39 0.89
ACGTcount: A:0.51, C:0.24, G:0.04, T:0.22
Consensus pattern (28 bp):
TAAAACCCTAAATCATAAACACTAAACT
Found at i:159371 original size:4 final size:4
Alignment explanation
Indices: 159339--159397 Score: 55
Period size: 4 Copynumber: 14.2 Consensus size: 4
159329 AACACATTAC
* * * * *
159339 CTTT CTTT CCTCT CCTT CTTC CTTC CTTT CTTT CTTT CTTT ATTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT
159389 CTTT CTTT C
1 CTTT CTTT C
159398 CCGTTTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
4 39 0.87
5 6 0.13
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:160084 original size:17 final size:17
Alignment explanation
Indices: 160044--160101 Score: 66
Period size: 16 Copynumber: 3.4 Consensus size: 17
160034 TTAAATATTC
160044 AAAATAATA-TATAAAAATT
1 AAAA-AATATTAT-AAAA-T
160063 AAAAAATATTATAAAAT
1 AAAAAATATTATAAAAT
*
160080 AAAAAATATT-TAAATT
1 AAAAAATATTATAAAAT
160096 AAAAAA
1 AAAAAA
160102 ATTGCAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 11 0.30
17 11 0.30
18 8 0.22
19 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATATTATAAAAT
Found at i:160103 original size:17 final size:17
Alignment explanation
Indices: 160044--160101 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
160034 TTAAATATTC
*
160044 AAAATAATATATAAAAATT
1 AAAA-AATAT-TATAAATT
*
160063 AAAAAATATTATAAAAT
1 AAAAAATATTATAAATT
160080 AAAAAATATT-TAAATT
1 AAAAAATATTATAAATT
160096 AAAAAA
1 AAAAAA
160102 ATTGCAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.31
17 16 0.44
18 5 0.14
19 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATATTATAAATT
Found at i:170173 original size:29 final size:26
Alignment explanation
Indices: 170120--170173 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
170110 CATTTGTTTA
**
170120 TAATTTAAAAAATTAATTATTTTAAG
1 TAATTTAAAAAATTAATTAAGTTAAG
170146 TAATTTAATTAAAATTAAATTAAGTTAA
1 TAATTTAA--AAAATT-AATTAAGTTAA
170174 AAAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
28 6 0.26
29 9 0.39
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
TAATTTAAAAAATTAATTAAGTTAAG
Done.