Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold609
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: 125725
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8787 original size:13 final size:13
Alignment explanation
Indices: 8769--8793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8759 CAACATTCCT
8769 TGTATCGATACAG
1 TGTATCGATACAG
8782 TGTATCGATACA
1 TGTATCGATACA
8794 TAGATTACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:13496 original size:18 final size:18
Alignment explanation
Indices: 13473--13507 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13463 AGATAGATTG
*
13473 CTATAGCTATTCCTTCTA
1 CTATAGCTACTCCTTCTA
13491 CTATAGCTACTCCTTCT
1 CTATAGCTACTCCTTCT
13508 GCCCAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.31, G:0.06, T:0.43
Consensus pattern (18 bp):
CTATAGCTACTCCTTCTA
Found at i:18218 original size:33 final size:35
Alignment explanation
Indices: 18155--18219 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 35
18145 ACCCCAATTA
*
18155 ATAATTATTTACTCTAGCTTTTAAATATTTTATGC
1 ATAATTATTTACTCTAGCTTTTAAAGATTTTATGC
* *
18190 ATAATTATTTA-TTTA-TTTTTAAAGATTTTA
1 ATAATTATTTACTCTAGCTTTTAAAGATTTTA
18220 GATATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 13 0.48
34 3 0.11
35 11 0.41
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (35 bp):
ATAATTATTTACTCTAGCTTTTAAAGATTTTATGC
Found at i:20009 original size:15 final size:15
Alignment explanation
Indices: 19989--20018 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19979 TTGACATAAA
19989 TATTAAAATATTAAT
1 TATTAAAATATTAAT
*
20004 TATTAAGATATTAAT
1 TATTAAAATATTAAT
20019 GTTTCAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TATTAAAATATTAAT
Found at i:20537 original size:12 final size:12
Alignment explanation
Indices: 20522--20570 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
20512 TTAGATTAAA
20522 AAATTTATTATT
1 AAATTTATTATT
*
20534 AAATCT-TTA-T
1 AAATTTATTATT
*
20544 AAA-GTATTATAT
1 AAATTTATTAT-T
20556 AAATTTATTATT
1 AAATTTATTATT
20568 AAA
1 AAA
20571 ACAGTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
9 1 0.03
10 7 0.23
11 3 0.10
12 13 0.43
13 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (12 bp):
AAATTTATTATT
Found at i:22525 original size:22 final size:23
Alignment explanation
Indices: 22476--22575 Score: 93
Period size: 22 Copynumber: 4.4 Consensus size: 23
22466 TTGATTTTAA
* * *
22476 TTAAATTTAAGTGATTTGAATTAT
1 TTAAATTTAAATAATTTTAA-TAT
22500 TTAAATTTAAAT-ATTTTAATAT
1 TTAAATTTAAATAATTTTAATAT
22522 TTAAA-TTAAATAATTTATAA-AT
1 TTAAATTTAAATAATTT-TAATAT
*
22544 TT-AA-TAAAATTAATTTTAATAT
1 TTAAATTTAAA-TAATTTTAATAT
22566 TTATAATTTA
1 TTA-AATTTA
22576 TTTTTAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
21 15 0.23
22 26 0.40
23 9 0.14
24 13 0.20
25 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
TTAAATTTAAATAATTTTAATAT
Found at i:22648 original size:14 final size:14
Alignment explanation
Indices: 22630--22670 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
22620 AATAATTTTT
22630 ATTAAATAAATAAA
1 ATTAAATAAATAAA
* *
22644 TTTAATTAAATAAA
1 ATTAAATAAATAAA
*
22658 ATAAAATAAATAA
1 ATTAAATAAATAA
22671 TTTTTATCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATTAAATAAATAAA
Found at i:22651 original size:18 final size:18
Alignment explanation
Indices: 22616--22662 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
22606 TTAAATAAAA
* *
22616 AAAT-AATAATTTTTATT
1 AAATAAATAAATTTAATT
22633 AAATAAATAAATTTAATT
1 AAATAAATAAATTTAATT
22651 AAATAAAATAAA
1 AAAT-AAATAAA
22663 ATAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 4 0.15
18 15 0.58
19 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAAATAAATTTAATT
Found at i:22689 original size:45 final size:44
Alignment explanation
Indices: 22597--22712 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 44
22587 TAAATATTTA
22597 AAATTAAAGTTAAAT-AAA-AAAAT-AATAATTTTTATTAAATAAAT
1 AAATTAAA-TTAAATAAAATAAAATAAATAATTTTTATTAAAT--AT
*
22641 AAATTTAATTAAATAAAATAAAATAAATAATTTTTATCTTAAAT-T
1 AAATTAAATTAAATAAAATAAAATAAATAATTTTTA--TTAAATAT
* *
22686 AAATTAAAATATAA-AAAATAAATTAAA
1 AAATTAAATTA-AATAAAATAAAATAAA
22713 GTACGTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
43 6 0.10
44 10 0.16
45 27 0.44
46 13 0.21
48 6 0.10
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (44 bp):
AAATTAAATTAAATAAAATAAAATAAATAATTTTTATTAAATAT
Found at i:34850 original size:20 final size:20
Alignment explanation
Indices: 34827--34897 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
34817 GGCCCAGAAA
*
34827 TATCGATACATATTGCTTTG
1 TATCGATACATATTGCATTG
* * *
34847 TATCGATACATGTT-CGTTA
1 TATCGATACATATTGCATTG
** *
34866 TATCGATACATAAAGAATTG
1 TATCGATACATATTGCATTG
34886 TATCGATACATA
1 TATCGATACATA
34898 AAACTGGCAG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 14 0.34
20 27 0.66
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (20 bp):
TATCGATACATATTGCATTG
Found at i:34871 original size:19 final size:20
Alignment explanation
Indices: 34826--34877 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
34816 AGGCCCAGAA
*
34826 ATATCGATACATATTGCTTT
1 ATATCGATACATATTGCGTT
* *
34846 GTATCGATACATGTT-CGTT
1 ATATCGATACATATTGCGTT
34865 ATATCGATACATA
1 ATATCGATACATA
34878 AAGAATTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATATCGATACATATTGCGTT
Found at i:39705 original size:68 final size:67
Alignment explanation
Indices: 39632--39770 Score: 170
Period size: 67 Copynumber: 2.1 Consensus size: 67
39622 CACTCATTTT
* * * *
39632 TATGCTAAAATGTCGAGCAGACCTTTGAAGTCATTTATTAAAATAGATTACTTGGTGTCACTTGC
1 TATGCTAAAATGTC-AACAAAACTTTGAAGTCATTTATTAAAATAGATGACTTGGTGTCACTTGC
39697 TTA
65 TTA
* * * ** * *
39700 TATGCTAAATTGTCAATAAAACTTTGAGGTTGTTTATTAACATAGGTGACTTGGTGTCACTTGCT
1 TATGCTAAAATGTCAACAAAACTTTGAAGTCATTTATTAAAATAGATGACTTGGTGTCACTTGCT
39765 TA
66 TA
39767 TATG
1 TATG
39771 TTGAGATGTC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
67 47 0.78
68 13 0.22
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (67 bp):
TATGCTAAAATGTCAACAAAACTTTGAAGTCATTTATTAAAATAGATGACTTGGTGTCACTTGCT
TA
Found at i:45146 original size:13 final size:13
Alignment explanation
Indices: 45128--45153 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45118 TACAGCAAGT
45128 ATGTATCGATACA
1 ATGTATCGATACA
45141 ATGTATCGATACA
1 ATGTATCGATACA
45154 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:47360 original size:21 final size:21
Alignment explanation
Indices: 47327--47371 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
47317 TTGCAAGTTG
*
47327 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
47349 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
47369 AAA
1 AAA
47372 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:49195 original size:15 final size:15
Alignment explanation
Indices: 49175--49205 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
49165 TAAAAATGTC
*
49175 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
49190 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
49205 C
1 C
49206 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:51302 original size:13 final size:13
Alignment explanation
Indices: 51284--51309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51274 ACATTTTTCT
51284 TTGTATCGATACA
1 TTGTATCGATACA
51297 TTGTATCGATACA
1 TTGTATCGATACA
51310 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:53874 original size:13 final size:13
Alignment explanation
Indices: 53856--53881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53846 TACAGCAAGT
53856 ATGTATCGATACA
1 ATGTATCGATACA
53869 ATGTATCGATACA
1 ATGTATCGATACA
53882 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:57517 original size:11 final size:10
Alignment explanation
Indices: 57501--57540 Score: 62
Period size: 11 Copynumber: 3.8 Consensus size: 10
57491 TCTTCCTTTA
57501 AAAAAAAAACC
1 AAAAAAAAA-C
57512 AAAAAAAAAC
1 AAAAAAAAAC
57522 AAAAAAACAAC
1 AAAAAAA-AAC
57533 AAAAAAAA
1 AAAAAAAA
57541 GAAAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:57526 original size:22 final size:21
Alignment explanation
Indices: 57500--57540 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
57490 ATCTTCCTTT
57500 AAAAAAAAAACCAAAAAAAAAC
1 AAAAAAAAAA-CAAAAAAAAAC
*
57522 AAAAAAACAACAAAAAAAA
1 AAAAAAAAAACAAAAAAAA
57541 GAAAAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAAAC
Found at i:57546 original size:21 final size:20
Alignment explanation
Indices: 57500--57547 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
57490 ATCTTCCTTT
57500 AAAAAAAAAACCAAAAAAAA
1 AAAAAAAAAACCAAAAAAAA
57520 ACAAAAAAACAA-CAAAAAAAA
1 A-AAAAAAA-AACCAAAAAAAA
57541 GAAAAAA
1 -AAAAAA
57548 GAGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAACCAAAAAAAA
Found at i:57556 original size:20 final size:19
Alignment explanation
Indices: 57503--57559 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
57493 TTCCTTTAAA
*
57503 AAAAAAACCAAAAAAAAAC
1 AAAAAAACAAAAAAAAAAC
*
57522 AAAAAAACAACAAAAAAAAG
1 AAAAAAACAA-AAAAAAAAC
*
57542 AAAAAAGAGAAAAAAAAA
1 AAAAAA-ACAAAAAAAAA
57560 CCTGCTTAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.27
20 21 0.64
21 3 0.09
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAAAC
Found at i:58707 original size:61 final size:61
Alignment explanation
Indices: 58522--58969 Score: 471
Period size: 61 Copynumber: 7.3 Consensus size: 61
58512 AAACCTTTTA
* * *
58522 ACCTTTCAGTCATCAAAAAGCAGAACATCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGC
1 ACCTTTCAGTCCTCAAAGAGCAGGACATCTTTTCC-TTTTAAAGCCCACACAAGTTGGTGGC
* * * * *
58584 ACCTTTTAGTCCTTAAAGAGTAGGACACTTCTTTT-CTATTAAAGCCCACACAAGTCGGTGGC
1 ACCTTTCAGTCCTCAAAGAGCAGGACA--TCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
* * *
58646 ACC-TTCTAATCCTCAAAGAGCAGGACATCTTTTCATTTTAAAGTCCACACAAGTTGGTGGC
1 ACCTTTC-AGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
* * *
58707 ACCTTTCAGTCCAT-AAAAAGTAGG--ATGCTTTTTCCTTTTAAAGCCCACACAAGTTCGTGGC
1 ACCTTTCAGTCC-TCAAAGAGCAGGACAT-C-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
* * *** *
58768 ACCTTTCAATCCTCAAAGACCAGGATGCCTTTTCCTTTTAAAG-CGACACAAGTTGGTGGC
1 ACCTTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
** **
58828 ACCTTTCAGTCCTCAAAGAGCAGGATGTCTTTTCCTTTTAAAGCTGACACAAGTTGGTGGC
1 ACCTTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
* * ** * *
58889 ACTTTTCAGTTCTCAAAGAGCAGGACGCCTTGCTT--TTTTAAAGCCCACACAAGTTAGTGAC
1 ACCTTTCAGTCCTCAAAGAGCAGGACATCTT--TTCCTTTTAAAGCCCACACAAGTTGGTGGC
* *
58950 ACCTTTTAGTCCCCAAAGAG
1 ACCTTTCAGTCCTCAAAGAG
58970 TAGGGCATGC
Statistics
Matches: 326, Mismatches: 46, Indels: 29
0.81 0.11 0.07
Matches are distributed among these distances:
59 2 0.01
60 63 0.19
61 182 0.56
62 70 0.21
63 3 0.01
64 6 0.02
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (61 bp):
ACCTTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGC
Found at i:58848 original size:182 final size:184
Alignment explanation
Indices: 58522--58955 Score: 490
Period size: 182 Copynumber: 2.4 Consensus size: 184
58512 AAACCTTTTA
* * ** *
58522 ACCTTTCAGTCATCAAAAAGCAGAACATC-TTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCAC
1 ACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTTTCC-TTTTAAAGCCCACACAAGTTAGTGGCAC
* * * **
58586 CTTTTAGTCCTTAAAGAGTAGGACACTTCTTTTCTATTAAAGCCCACACAAGTCGGTGGCACCTT
65 CTTTCAATCCTCAAAGACCAGGACAC-TCTTTTCTATTAAAGCCCACACAAGTCGGTGGCACCTT
58651 CTAATCCTCAAAGAGCAGGACATCTTTTCATTTTAAAG-TCCACACAAGTTGGTGGC
129 CTAATCCTCAAAGAGCAGGACATCTTTTCATTTTAAAGCT-CACACAAGTTGGTGGC
* * *
58707 ACCTTTCAGTCCAT-AAAAAGTAGGATG-CTTTTTCCTTTTAAAGCCCACACAAGTTCGTGGCAC
1 ACCTTTCAGTCC-TCAAAAAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCAC
** * * *
58770 CTTTCAATCCTCAAAGACCAGGATGC-CTTTTCCTTTTAAAG-CGACACAAGTTGGTGGCACCTT
65 CTTTCAATCCTCAAAGACCAGGACACTCTTTT-CTATTAAAGCCCACACAAGTCGGTGGCACCTT
* ** * *
58833 -TCAGTCCTCAAAGAGCAGGATGTCTTTTCCTTTTAAAGCTGACACAAGTTGGTGGC
129 CT-AATCCTCAAAGAGCAGGACATCTTTTCATTTTAAAGCTCACACAAGTTGGTGGC
* * * * *
58889 ACTTTTCAGTTCTCAAAGAGCAGGACGCCTTGCTT--TTTTAAAGCCCACACAAGTTAGTGACAC
1 ACCTTTCAGTCCTCAAAAAGCAGGACGCCTT-TTTCCTTTTAAAGCCCACACAAGTTAGTGGCAC
58952 CTTT
65 CTTT
58956 TAGTCCCCAA
Statistics
Matches: 212, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
181 2 0.01
182 122 0.58
183 12 0.06
184 49 0.23
185 26 0.12
186 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (184 bp):
ACCTTTCAGTCCTCAAAAAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCACC
TTTCAATCCTCAAAGACCAGGACACTCTTTTCTATTAAAGCCCACACAAGTCGGTGGCACCTTCT
AATCCTCAAAGAGCAGGACATCTTTTCATTTTAAAGCTCACACAAGTTGGTGGC
Found at i:58882 original size:121 final size:122
Alignment explanation
Indices: 58522--58973 Score: 499
Period size: 121 Copynumber: 3.7 Consensus size: 122
58512 AAACCTTTTA
* * * * **
58522 ACCTTTCAGTCATCAAAAAGCAGAACATCTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACC
1 ACCTTTCAATCCTCAAAGAGCAGGACGCCTTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
58587 TTTTAGTCCTTAAAGAGTAGGACACT-TCTTTT-CTATTAAAGCCCACACAAG-TCGGTGGC
65 TTTCAGTCCTCAAAGAGTAGG--A-TGTCTTTTCCTTTTAAAGCCCACACAAGTTC-GTGGC
** * *
58646 ACC-TTCTAATCCTCAAAGAGCAGGACATCTTTTCATTTTAAAGTCCACACAAGTTGGTGGCACC
1 ACCTTTC-AATCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
58710 TTTCAGTCCAT-AAAAAGTAGGATG-CTTTTTCCTTTTAAAGCCCACACAAGTTCGTGGC
65 TTTCAGTCC-TCAAAGAGTAGGATGTC-TTTTCCTTTTAAAGCCCACACAAGTTCGTGGC
* * *
58768 ACCTTTCAATCCTCAAAGACCAGGATGCCTTTTCCTTTTAAAG-CGACACAAGTTGGTGGCACCT
1 ACCTTTCAATCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* ** *
58832 TTCAGTCCTCAAAGAGCAGGATGTCTTTTCCTTTTAAAGCTGACACAAGTTGGTGGC
66 TTCAGTCCTCAAAGAGTAGGATGTCTTTTCCTTTTAAAGCCCACACAAGTTCGTGGC
* * * * *
58889 ACTTTTCAGTTCTCAAAGAGCAGGACGCCTTGCTT--TTTTAAAGCCCACACAAGTTAGTGACAC
1 ACCTTTCAATCCTCAAAGAGCAGGACGCCTT--TTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* *
58952 CTTTTAGTCCCCAAAGAGTAGG
64 CTTTCAGTCCTCAAAGAGTAGG
58974 GCATGCTTTA
Statistics
Matches: 285, Mismatches: 31, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
120 3 0.01
121 107 0.38
122 93 0.33
123 55 0.19
124 27 0.09
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (122 bp):
ACCTTTCAATCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
TTCAGTCCTCAAAGAGTAGGATGTCTTTTCCTTTTAAAGCCCACACAAGTTCGTGGC
Found at i:59013 original size:44 final size:41
Alignment explanation
Indices: 58952--59119 Score: 119
Period size: 42 Copynumber: 4.0 Consensus size: 41
58942 TTAGTGACAC
* *
58952 CTTTTAGTCCCCAAAGAGTAGG-GCATGCTTTAATTTCCTTCTTTT
1 CTTTT-GTCCTCAAAGAGCAGGAGCAT--TTT-ATTTCCTT-TTTT
58997 CTTTTGTCCTCAAAGAGCAGGACGCATTTTATTTCCTTTTTT
1 CTTTTGTCCTCAAAGAGCAGGA-GCATTTTATTTCCTTTTTT
* ** * * * *
59039 CCTTTGTCCTCATGGAGCAAGACTCATTTCA-TT-CTCTTTT
1 CTTTTGTCCTCAAAGAGCAGGA-GCATTTTATTTCCTTTTTT
* * *
59079 CCTTTGTCCTCAAAGAGCAAGA-CATATTCTTTTTCCTTTTT
1 CTTTTGTCCTCAAAGAGCAGGAGCAT-TT-TATTTCCTTTTT
59120 CCTTGAAGAA
Statistics
Matches: 103, Mismatches: 14, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
38 3 0.03
39 2 0.02
40 26 0.25
41 4 0.04
42 34 0.33
43 8 0.08
44 17 0.17
45 5 0.05
46 4 0.04
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (41 bp):
CTTTTGTCCTCAAAGAGCAGGAGCATTTTATTTCCTTTTTT
Found at i:59045 original size:42 final size:42
Alignment explanation
Indices: 58984--59123 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 42
58974 GCATGCTTTA
* * *
58984 ATTTCCTTCTTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTT
1 ATTTCCTT-TTTTCCTTTGTCCTCAAAGAGCAAGACACATTTT
** * *
59027 ATTTCCTTTTTTCCTTTGTCCTCATGGAGCAAGACTCATTTC
1 ATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAAGACACATTTT
* *
59069 A-TT-CTCTTTTCCTTTGTCCTCAAAGAGCAAGACATATTCTT
1 ATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAAGACACATT-TT
59110 -TTTCC-TTTTTCCTT
1 ATTTCCTTTTTTCCTT
59124 GAAGAACAGG
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
40 30 0.37
41 13 0.16
42 30 0.37
43 8 0.10
ACGTcount: A:0.18, C:0.25, G:0.11, T:0.46
Consensus pattern (42 bp):
ATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAAGACACATTTT
Found at i:59090 original size:40 final size:42
Alignment explanation
Indices: 58984--59101 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 42
58974 GCATGCTTTA
* * *
58984 ATTTCCTTCTTTTCTTTTGTCCTCAAAGAGCAGGACGCATTTT
1 ATTTCC-TCTTTTCCTTTGTCCTCAAAGAGCAAGACGCATTTC
* ** *
59027 ATTTCCTTTTTTCCTTTGTCCTCATGGAGCAAGACTCATTTC
1 ATTTCCTCTTTTCCTTTGTCCTCAAAGAGCAAGACGCATTTC
59069 A-TT-CTCTTTTCCTTTGTCCTCAAAGAGCAAGAC
1 ATTTCCTCTTTTCCTTTGTCCTCAAAGAGCAAGAC
59102 ATATTCTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 27 0.42
41 2 0.03
42 30 0.46
43 6 0.09
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (42 bp):
ATTTCCTCTTTTCCTTTGTCCTCAAAGAGCAAGACGCATTTC
Found at i:59114 original size:34 final size:34
Alignment explanation
Indices: 59034--59160 Score: 101
Period size: 34 Copynumber: 3.6 Consensus size: 34
59024 TTTATTTCCT
**
59034 TTTTTCCTTTGTCCTCATGGAGCAAGACTCATTTCATTC
1 TTTTTCCTTTGTCCTCAAAGAGCAAGA--CA--T-ATTC
59073 TCTTTTCCTTTGTCCTCAAAGAGCAAGACATATTC
1 T-TTTTCCTTTGTCCTCAAAGAGCAAGACATATTC
* ** * * * *
59108 TTTTTCCTTTTTCCTTGAAGAACAGGACGTCTTC
1 TTTTTCCTTTGTCCTCAAAGAGCAAGACATATTC
* *
59142 CTTTTCCTTTGTCATCAAA
1 TTTTTCCTTTGTCCTCAAA
59161 AAGTAAGATG
Statistics
Matches: 73, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
34 40 0.55
35 5 0.07
36 1 0.01
38 2 0.03
39 1 0.01
40 24 0.33
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (34 bp):
TTTTTCCTTTGTCCTCAAAGAGCAAGACATATTC
Found at i:59840 original size:50 final size:50
Alignment explanation
Indices: 59760--59858 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
59750 ACAATTTGTA
* *
59760 TCGATACATTCTTCATTGTATCGATACATTATAGGTTTTACCCAGATGTG
1 TCGATACATTCTTCATTATATCAATACATTATAGGTTTTACCCAGATGTG
* * * *
59810 TCGATATATTTTTCATTATATCAATGCATTATGGGTTTTACCCAGATGT
1 TCGATACATTCTTCATTATATCAATACATTATAGGTTTTACCCAGATGT
59859 ATCAATCCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (50 bp):
TCGATACATTCTTCATTATATCAATACATTATAGGTTTTACCCAGATGTG
Found at i:61667 original size:79 final size:79
Alignment explanation
Indices: 61569--62292 Score: 604
Period size: 79 Copynumber: 9.3 Consensus size: 79
61559 CACCATTGGA
* ** ** * *
61569 GATACTCTAACCCCATTATTTCCAAGGGGATACTCCAACCCTGGTTTTATTTCAAAAACATCAAT
1 GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGAT
*
61634 TTTTCACCATCAGG
66 TTTTCACAATCAGG
* * *
61648 GATACTCCAACCCTGTTATTTCTAAGGGGATACTCCAACCCC-GATTTTATTTTCAAAACATCAA
1 GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAG-TTTTATTTCCAAAACATCGA
*
61712 TTTTTCATAATC-GG
65 TTTTTCACAATCAGG
* * * *
61726 AGATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAA--CC-----TCTTTCCAAAACATTGA
1 -GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGA
* *
61784 TTTTCCATAA-CTAGG
65 TTTTTCACAATC-AGG
* * * * * * ** * * * *
61799 GATAATCTAATCTTGTTATTTTCGAGAAGATACTCTAACCCTAATTTTATTTCCAAAACATTGAT
1 GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGAT
*
61864 TTTTCATAATCAGG
66 TTTTCACAATCAGG
* * * *
61878 GATACTCTAACCCTGTTATTTTCAAAGGGATACTCCAACCCC-GATTTTATTTCTAAAACATCGA
1 GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAG-TTTTATTTCCAAAACATCGA
* *
61942 TTTTCCATAATC-GAG
65 TTTTTCACAATCAG-G
* * * * *
61957 GATACTCCAA-CCTCATTA-TTCTGAA-GGGATACTCCAACCTCGGTTTTATTTTCAAAACATCG
1 GATACTCCAACCCT-GTTATTTC-CAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCG
* * *
62019 ATTTTCCATAAT-TGTG
64 ATTTTTCACAATCAG-G
* * * * *
62035 GATACTCCAA-CCTCGTTATTTTCGAA-AGGATACTCTAACCCTAGTTTTATTTCCAAAACATCA
1 GATACTCCAACCCT-GTTA-TTTCCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCG
**
62098 ATTTTTCACAATTGGG
64 ATTTTTCACAATCAGG
* * * * * *
62114 GATACTCTAACCCCGTTATTTCTAAAGGGATACACCAACCCCAGTTTTATTTCCAAAACA-CTAA
1 GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATC-GA
*
62178 TTTTTCACAATCGGG
65 TTTTTCACAATCAGG
*** * *
62193 GATACTGTGACCTTGTTATTTCCAAGGGGATACTCTAACCCCAGTTTTATTTCCAAAACATCGAT
1 GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGAT
* **
62258 TTTTCACCATTGGG
66 TTTTCACAATCAGG
*
62272 GATACTCCAACCCAGTTATTT
1 GATACTCCAACCCTGTTATTT
62293 TTGAGGGGGG
Statistics
Matches: 533, Mismatches: 87, Indels: 50
0.80 0.13 0.07
Matches are distributed among these distances:
71 1 0.00
72 49 0.09
73 2 0.00
74 1 0.00
77 2 0.00
78 79 0.15
79 391 0.73
80 8 0.02
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCTGTTATTTCCAAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGAT
TTTTCACAATCAGG
Found at i:62118 original size:236 final size:234
Alignment explanation
Indices: 61596--62293 Score: 810
Period size: 236 Copynumber: 3.0 Consensus size: 234
61586 ATTTCCAAGG
* * * * *
61596 GGATACTCCAACCCTGGTTTTATTTCAAAAACATCAATTTTTCACCATCAGGGATACTCCAACCC
1 GGATACTCTAACCCTAGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGGATACTCTAACCC
*
61661 TGTTATTTCTAAGGGGATACTCCAACCCCGATTTTATTT-TCAAAACATCAATTTTTCATAATCG
66 TGTTATTTCTAAAGGGATACTCCAACCCCGATTTTATTTCT-AAAACATCAATTTTTCATAATCG
* * *
61725 GAGATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAACCTC------TTTCCAAAACATTGA
130 G-GATACTCCAACCTCGTTA-TTCTAAAGGGATACTCCAACCTCGTTTTATTTCCAAAACATCGA
* * * * *
61784 TTTTCCATAACTAGGGATAATCTAATCTTGTTATTTTCGAGAA
193 TTTTCCATAA-TTGGGATACTCCAACCTCGTTATTTTCGAGAA
* ** *
61827 -GATACTCTAACCCTAATTTTATTTCCAAAACATTGATTTTTCATAATCAGGGATACTCTAACCC
1 GGATACTCTAACCCTAGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGGATACTCTAACCC
* *
61891 TGTTATTT-TCAAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCATAATCG
66 TGTTATTTCT-AAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCG
* * *
61955 AGGATACTCCAACCTCATTATTCTGAAGGGATACTCCAACCTCGGTTTTATTTTCAAAACATCGA
130 -GGATACTCCAACCTCGTTATTCTAAAGGGATACTCCAACCTC-GTTTTATTTCCAAAACATCGA
62020 TTTTCCATAATTGTGGATACTCCAACCTCGTTATTTTCGA-AA
193 TTTTCCATAATTG-GGATACTCCAACCTCGTTATTTTCGAGAA
**
62062 GGATACTCTAACCCTAGTTTTATTTCCAAAACATCAATTTTTCACAATTGGGGATACTCTAACCC
1 GGATACTCTAACCCTAGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGGATACTCTAACCC
* * * *
62127 CGTTATTTCTAAAGGGATACACCAACCCC-AGTTTTATTTCCAAAACA-CTAATTTTTCACAATC
66 TGTTATTTCTAAAGGGATACTCCAACCCCGA-TTTTATTTCTAAAACATC-AATTTTTCATAATC
*** * * * * *
62190 GGGGATACTGTGACCTTGTTATTTCCAAGGGGATACTCTAACCCCAGTTTTATTTCCAAAACATC
129 -GGGATACTCCAACCTCGTTA-TTCTAAAGGGATACTCCAACCTC-GTTTTATTTCCAAAACATC
* **
62255 GATTTTTCACCATTGGGGATACTCCAACC-CAGTTATTTT
191 GATTTTCCATAATT-GGGATACTCCAACCTC-GTTATTTT
62294 TGAGGGGGGA
Statistics
Matches: 398, Mismatches: 50, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
229 22 0.06
230 128 0.32
231 2 0.01
235 6 0.02
236 169 0.42
237 70 0.18
238 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (234 bp):
GGATACTCTAACCCTAGTTTTATTTCCAAAACATCAATTTTTCACAATCAGGGATACTCTAACCC
TGTTATTTCTAAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGG
GATACTCCAACCTCGTTATTCTAAAGGGATACTCCAACCTCGTTTTATTTCCAAAACATCGATTT
TCCATAATTGGGATACTCCAACCTCGTTATTTTCGAGAA
Found at i:62313 original size:158 final size:157
Alignment explanation
Indices: 61569--62344 Score: 694
Period size: 158 Copynumber: 5.0 Consensus size: 157
61559 CACCATTGGA
* * * * * *
61569 GATACTCTAACCCCATTATTTCCAAGGGGATACTCCAACCCTGGTTTTATTTCAAAAACATCAAT
1 GATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAACCC-CGTTTTATTTCCAAAACATCGAT
* ** * *
61634 TTTTCACCATCAGGGATACTCCAACCCTGTTATTTCTAAGGGGATACTCCAACCCC-GATTTTAT
65 TTTTCACAATTGGGGATACTCCAACCCAGTTATTTCTGAGGGGATACTCCAACCCCAG-TTTTAT
* *
61698 TTTCAAAACATCAATTTTTCATAATCGGA
129 TTCCAAAACATCAATTTTTCATAATCGGG
* *
61727 GATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAA--CC----TCTTTCCAAAACATTGATT
1 GATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAACCCCGTTTTATTTCCAAAACATCGATT
* * * * * * * ** ** * * *
61786 TTCCATAACTAGGGATAATCTAATCTTGTTATTT-TCGAGAAGATACTCTAACCCTAATTTTATT
66 TTTCACAATTGGGGATACTCCAACCCAGTTATTTCT-GAGGGGATACTCCAACCCCAGTTTTATT
** *
61850 TCCAAAACATTGATTTTTCATAATCAGG
130 TCCAAAACATCAATTTTTCATAATCGGG
* * * *
61878 GATACTCTAACCCTGTTATTTTCAAAGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGAT
1 GATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAACCCCG-TTTTATTTCCAAAACATCGAT
* * * * * * *
61943 TTTCCATAATCGAGGATACTCCAACCTCA-TTA-TTCTGAAGGGATACTCCAACCTCGGTTTTAT
65 TTTTCACAATTGGGGATACTCCAACC-CAGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTAT
* * * * *
62006 TTTCAAAACATCGATTTTCCATAATTGTG
129 TTCCAAAACATCAATTTTTCATAATCGGG
* * * * *
62035 GATACTCCAACCTCGTTATTTTCGAAA-GGATACTCTAACCCTAGTTTTATTTCCAAAACATCAA
1 GATACTCCAACCCCGTTA-TTTCCAAAGGGATACTCCAACCC-CGTTTTATTTCCAAAACATCGA
* * * * *
62099 TTTTTCACAATTGGGGATACTCTAACCCCGTTATTTCTAAAGGGATACACCAACCCCAGTTTTAT
64 TTTTTCACAATTGGGGATACTCCAACCCAGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTAT
*
62164 TTCCAAAACA-CTAATTTTTCACAATCGGG
129 TTCCAAAACATC-AATTTTTCATAATCGGG
*** ** * *
62193 GATACTGTGACCTTGTTATTTCCAAGGGGATACTCTAACCCCAGTTTTATTTCCAAAACATCGAT
1 GATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAACCCC-GTTTTATTTCCAAAACATCGAT
* * ** ** * *
62258 TTTTCACCATTGGGGATACTCCAACCCAGTTATTTTTGAGGGGGGACTCTGACCCCATTTTTATC
65 TTTTCACAATTGGGGATACTCCAACCCAGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTATT
* *
62323 TCCAAAATATTAAATTTTTCAT
130 TCCAAAACA-TCAATTTTTCAT
62345 CGATAAATGT
Statistics
Matches: 492, Mismatches: 106, Indels: 39
0.77 0.17 0.06
Matches are distributed among these distances:
150 1 0.00
151 119 0.24
153 2 0.00
156 2 0.00
157 122 0.25
158 237 0.48
159 9 0.02
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (157 bp):
GATACTCCAACCCCGTTATTTCCAAAGGGATACTCCAACCCCGTTTTATTTCCAAAACATCGATT
TTTCACAATTGGGGATACTCCAACCCAGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTATTT
CCAAAACATCAATTTTTCATAATCGGG
Found at i:66280 original size:78 final size:78
Alignment explanation
Indices: 66030--66515 Score: 433
Period size: 79 Copynumber: 6.2 Consensus size: 78
66020 TCATTCATGT
* * ** * ** * ***
66030 TTTTATTTCTAAAATATCAATTTTCCACCATCAGGGATACTCCAACCCCATTATTTCTGATAAGA
1 TTTTATTTCCAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCAATTATTT-TGAGGGGA
**
66095 TACTCCAACCCTGG
65 TACTCCAACCCCAG
* * * * ***
66109 TTTTATTTCCAAAACATTAATTATCCACAATCAAGGATACTCCAACCTC-ATTATTTTCGAGGGG
1 TTTTATTTCCAAAACATTGATTTTTCACCATTGGGGATACTCCAACC-CAATTATTTT-GAGGGG
66173 ATACTCCAACCCC-G
64 ATACTCCAACCCCAG
* * ** *
66187 ATTTTATTTCTAAAACATTAATTTTTCATAATTGGGGATAGTCCAACCCAATTATTTTGAGGGGA
1 -TTTTATTTCCAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCAATTATTTTGAGGGGA
*
66252 TACTTCAACCCCAG
65 TACTCCAACCCCAG
* **** *
66266 TTTTATTTCCAAAACATTGATTTTTCACCATCGGGGATACTCCAACTTTGTTATTTTTGAAGGGA
1 TTTTATTTCCAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCAATTA-TTTTGAGGGGA
*
66331 TACTCCAACCCTAG
65 TACTCCAACCCCAG
* * * * *
66345 TTTTATTTCCAAAACATTGATTTTCCACCA-TCGGGATACTCCAACCCAGTTATTTCTAAAGGGA
1 TTTTATTTCCAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCAATTATTT-TGAGGGGA
** *
66409 TACTCTGACCTTC-G
65 TACTCCAACC-CCAG
* * * *
66423 TTTTATTTTCAAAACATCGATTTTTCACCATTGGGGATACTCCAACCCTATTATTTTCAAGGGGA
1 TTTTATTTCCAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCAATTATTTT-GAGGGGA
*
66488 TACTCCAACCCTA-
65 TACTCCAACCCCAG
*
66501 TTTTTTTCTCCAAAA
1 TTTTATT-TCCAAAA
66516 TATGAAATTT
Statistics
Matches: 339, Mismatches: 56, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
77 3 0.01
78 131 0.39
79 204 0.60
80 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (78 bp):
TTTTATTTCCAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCAATTATTTTGAGGGGAT
ACTCCAACCCCAG
Found at i:66320 original size:157 final size:158
Alignment explanation
Indices: 66030--66498 Score: 518
Period size: 157 Copynumber: 3.0 Consensus size: 158
66020 TCATTCATGT
* * * * *
66030 TTTTATTTCTAAAATATCAATTTTCCACCATCAGGGATACTCCAACCCCATTATTTCTGATA-AG
1 TTTTATTTCTAAAACATTAATTTTCCACCATTAGGGATACTCCAACCCAATTATTTCTGA-AGGG
* * * * * * ** *
66094 ATACTCCAACCCTGGTTTTATTTCCAAAACATTAATTATCCACAATCAAGGATACTCCAACCTCA
65 ATACTTCAACCC-CGTTTTATTTCCAAAACATTGATTTTTCACCATCGGGGATACTCCAACCTTA
66159 TTATTTTCGAGGGGATACTCCAACCCCGA-
129 TTATTTTCGAGGGGATACTCCAACCCCGAG
* ** * * *
66188 TTTTATTTCTAAAACATTAATTTTTCATAATTGGGGATAGTCCAACCCAATTATTT-TGAGGGGA
1 TTTTATTTCTAAAACATTAATTTTCCACCATTAGGGATACTCCAACCCAATTATTTCTGAAGGGA
* *
66252 TACTTCAACCCCAGTTTTATTTCCAAAACATTGATTTTTCACCATCGGGGATACTCCAACTTTGT
66 TACTTCAACCCC-GTTTTATTTCCAAAACATTGATTTTTCACCATCGGGGATACTCCAACCTTAT
* * *
66317 TATTTTTGAAGGGATACTCCAA-CCCTAG
130 TATTTTCGAGGGGATACTCCAACCCCGAG
* * * * *
66345 TTTTATTTCCAAAACATTGATTTTCCACCA-TCGGGATACTCCAACCCAGTTATTTCTAAAGGGA
1 TTTTATTTCTAAAACATTAATTTTCCACCATTAGGGATACTCCAACCCAATTATTTCTGAAGGGA
* * * * * *
66409 TAC-TCTGACCTTCGTTTTATTTTCAAAACATCGATTTTTCACCATTGGGGATACTCCAACCCTA
66 TACTTC-AACC-CCGTTTTATTTCCAAAACATTGATTTTTCACCATCGGGGATACTCCAACCTTA
*
66473 TTATTTTCAAGGGGATACTCCAACCC
129 TTATTTTCGAGGGGATACTCCAACCC
66499 TATTTTTTTC
Statistics
Matches: 258, Mismatches: 46, Indels: 14
0.81 0.14 0.04
Matches are distributed among these distances:
156 28 0.11
157 180 0.70
158 50 0.19
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (158 bp):
TTTTATTTCTAAAACATTAATTTTCCACCATTAGGGATACTCCAACCCAATTATTTCTGAAGGGA
TACTTCAACCCCGTTTTATTTCCAAAACATTGATTTTTCACCATCGGGGATACTCCAACCTTATT
ATTTTCGAGGGGATACTCCAACCCCGAG
Found at i:66495 original size:28 final size:28
Alignment explanation
Indices: 66455--66508 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
66445 TTTCACCATT
66455 GGGGATACTCCAACCCTATTATTTTCAA
1 GGGGATACTCCAACCCTATTATTTTCAA
*
66483 GGGGATACTCCAACCCTATTTTTTTC
1 GGGGATACTCCAACCCTATTATTTTC
66509 TCCAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (28 bp):
GGGGATACTCCAACCCTATTATTTTCAA
Found at i:67437 original size:20 final size:19
Alignment explanation
Indices: 67393--67443 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
67383 TGTATCAATA
**
67393 CATTGTAT-GATACATGTT
1 CATTGTATCGATACATACT
67411 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
67430 CAATTGTATCGATA
1 C-ATTGTATCGATA
67444 ATGAAACTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 8 0.28
19 9 0.31
20 12 0.41
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:67519 original size:20 final size:20
Alignment explanation
Indices: 67476--67527 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
67466 TAAGTGAAAT
* **
67476 GTATCAATACATGGGACATT
1 GTATCAATACATGGGAAAAA
*
67496 GTATCAATACATGGTAAAAA
1 GTATCAATACATGGGAAAAA
*
67516 GTATCGATACAT
1 GTATCAATACAT
67528 TATGCCCAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (20 bp):
GTATCAATACATGGGAAAAA
Found at i:67950 original size:23 final size:23
Alignment explanation
Indices: 67923--67966 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
67913 GCATTCAACC
*
67923 TTGGGTTATAATCTCTT-AAGAAT
1 TTGGGGTATAAT-TCTTGAAGAAT
67946 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTATAATTCTTGAAGA
67967 GATTGAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGGGGTATAATTCTTGAAGAAT
Found at i:69748 original size:4 final size:4
Alignment explanation
Indices: 69739--69820 Score: 155
Period size: 4 Copynumber: 20.5 Consensus size: 4
69729 ATTAAGGTGC
69739 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
69787 TTAT TTAT TCAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
69821 TGTTTTGTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 76 1.00
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:74785 original size:13 final size:13
Alignment explanation
Indices: 74767--74791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74757 ATTTTGCTTA
74767 GTATCGATACATT
1 GTATCGATACATT
74780 GTATCGATACAT
1 GTATCGATACAT
74792 AAACTAGCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:79546 original size:33 final size:32
Alignment explanation
Indices: 79493--79556 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
79483 ACAAGCTATT
*
79493 TATCGATACATTTCTTCATGTATCTATACAATG
1 TATCGATACATTTC-TCATGTATCGATACAATG
79526 TATCGATACATTGTAC-CATGTATCGATACAA
1 TATCGATACATT-T-CTCATGTATCGATACAA
79557 ATAGTGATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (32 bp):
TATCGATACATTTCTCATGTATCGATACAATG
Found at i:79631 original size:19 final size:20
Alignment explanation
Indices: 79606--79659 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
79596 ACAAATTATC
*
79606 CATGTATCGATACATTG-AA
1 CATGTATCGATACATGGCAA
* *
79625 TATGTATCGATACAAGGCAA
1 CATGTATCGATACATGGCAA
79645 CATGTATCGATACAT
1 CATGTATCGATACAT
79660 CTGGGGGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACATGGCAA
Found at i:80237 original size:18 final size:19
Alignment explanation
Indices: 80214--80252 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
80204 CTTAAATGAT
80214 TATCTTCT-CCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
*
80232 TATCTTTTCCCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
80251 TA
1 TA
80253 AAAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.13, C:0.31, G:0.00, T:0.56
Consensus pattern (19 bp):
TATCTTCTCCCCCTTTTTA
Found at i:82258 original size:20 final size:18
Alignment explanation
Indices: 82233--82273 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
82223 CTATAGACCC
82233 TAATTCAAGTCAAACAAACA
1 TAATTCAA-TCAAAC-AACA
*
82253 TAATTCAATCATACAACA
1 TAATTCAATCAAACAACA
82271 TAA
1 TAA
82274 CAAACATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.24
Consensus pattern (18 bp):
TAATTCAATCAAACAACA
Found at i:86046 original size:21 final size:21
Alignment explanation
Indices: 86020--86059 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
86010 ATGCAAGTTT
* *
86020 TTATTTTTCTTAGCTAATTCA
1 TTATTTTTATTAGCCAATTCA
86041 TTATTTTTATTAGCCAATT
1 TTATTTTTATTAGCCAATT
86060 TTTCAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTTTTATTAGCCAATTCA
Found at i:88300 original size:13 final size:13
Alignment explanation
Indices: 88282--88312 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
88272 ACATTTCTTC
88282 ATGTATCGATACA
1 ATGTATCGATACA
88295 ATGTATCGATACA
1 ATGTATCGATACA
*
88308 TTGTA
1 ATGTA
88313 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:88300 original size:33 final size:33
Alignment explanation
Indices: 88262--88328 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
88252 ATTACAAGCT
88262 ATGTATCCATACATT-T-CTTCATGTATCGATACA
1 ATGTATCCATACATTGTAC--CATGTATCGATACA
*
88295 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCCATACATTGTACCATGTATCGATACA
88328 A
1 A
88329 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (33 bp):
ATGTATCCATACATTGTACCATGTATCGATACA
Found at i:88423 original size:20 final size:20
Alignment explanation
Indices: 88378--88430 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
88368 ACAATTTATC
**
88378 CATGTATCGATACATTGAAT
1 CATGTATCGATACAAGGAAT
*
88398 -ATGTATCGATACAAGGCAT
1 CATGTATCGATACAAGGAAT
88417 CATGTATCGATACA
1 CATGTATCGATACA
88431 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAAGGAAT
Found at i:91179 original size:17 final size:16
Alignment explanation
Indices: 91133--91172 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 16
91123 CTTTTTTCTT
91133 AAAAAAAATAAAATTA
1 AAAAAAAATAAAATTA
91149 AAAATAAAATAAAATTA
1 AAAA-AAAATAAAATTA
91166 AAAAAAA
1 AAAAAAA
91173 GAAAAAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAAAAATAAAATTA
Found at i:92355 original size:61 final size:61
Alignment explanation
Indices: 92161--92548 Score: 374
Period size: 61 Copynumber: 6.4 Consensus size: 61
92151 CCTTTTATCT
* *
92161 TTTCAGTCCTCAATGAGTAAGACGCCTTTTCCTTTTAAAG-CCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * ** * *
92221 TTTCAGTCTTTAAAGAGCAACACGCCTTTTTTTCTTTTAGAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGTAGGACGCC--TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
92284 TTTCGGTCCTCAAAGAGTAGGATGCCTTTTCCTTCTAAAGCCCACACAAATTGGTAGCACC
1 TTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * * *
92345 TTTTAATCCTCAAAGAGCAGGAAG-CTGTTTCCTTTTAAAGCCCACACAACTGGGTGGCATC
1 TTTCAGTCCTCAAAGAGTAGGACGCCT-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
92406 TTCCAGTCCTCAAAAAGTAGG-GGGC-TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * * **
92465 -TTCTAGTCCTTAAA-ATGTAAGACTCATTTTTCTTGCAAAGCCCACACAAGTTGGTGGCACC
1 TTTC-AGTCCTCAAAGA-GTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
92526 TTTTAGTCCTCAAAGAGCAGGAC
1 TTTCAGTCCTCAAAGAGTAGGAC
92549 ACACTTCATT
Statistics
Matches: 265, Mismatches: 52, Indels: 21
0.78 0.15 0.06
Matches are distributed among these distances:
58 3 0.01
59 43 0.16
60 24 0.09
61 141 0.53
62 15 0.06
63 39 0.15
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (61 bp):
TTTCAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:92505 original size:120 final size:120
Alignment explanation
Indices: 92161--92539 Score: 372
Period size: 120 Copynumber: 3.1 Consensus size: 120
92151 CCTTTTATCT
** * * *
92161 TTTCAGTCCTCAATGAGTAAGACGCCTTTTCCTTTTAAAG-CCACACAAGTTGGTGGCACCTTTC
1 TTTCAGTCCTCAAAAAGTAGGAGGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-
* * *
92225 AGTCTTTAAAGAGCAACACGCCTTTTTTTCTTTTAGAGCCCACACAAGTTGGTGGCACC
65 AGTCCTTAAAGAGCAAGAC-CC--TTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
92284 TTTCGGTCCTCAAAGAGTAGGATGCCTTTTCC-TTCTAAAGCCCACACAAATTGGTAGCACCTTT
1 TTTCAGTCCTCAAAAAGTAGGAGGCCTTTTCCTTTC-AAAGCCCACACAAGTTGGTGGCACC-TT
* * * ** * * * *
92348 TAATCCTCAAAGAGCAGGAAGCTGTTTCCTTTTAAAGCCCACACAACTGGGTGGCATC
64 TAGTCCTTAAAGAGCAAGACCCT-TTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
* *
92406 TTCCAGTCCTCAAAAAGTAGG-GGGC-TTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCT
1 TTTCAGTCCTCAAAAAGTAGGAGGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-T
* * **
92469 AGTCCTTAAA-ATGTAAGACTCATTTTTCTTGCAAAGCCCACACAAGTTGGTGGCACC
65 AGTCCTTAAAGA-GCAAGAC-CCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
92526 TTTTAGTCCTCAAA
1 TTTCAGTCCTCAAA
92540 GAGCAGGACA
Statistics
Matches: 207, Mismatches: 41, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
119 3 0.01
120 81 0.39
121 7 0.03
122 49 0.24
123 33 0.16
124 31 0.15
125 3 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (120 bp):
TTTCAGTCCTCAAAAAGTAGGAGGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTA
GTCCTTAAAGAGCAAGACCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:92706 original size:42 final size:42
Alignment explanation
Indices: 92525--92795 Score: 232
Period size: 41 Copynumber: 6.5 Consensus size: 42
92515 TTGGTGGCAC
* *
92525 CTTTTAGTCCTCAAAGAGCAGGACACACTTCATTTTCTTCATT-T
1 CTTTT-GTCCTCAAAGAGCAGGACACACTTTATTTCCTT--TTCT
*
92569 CCTTTTTGTCCTCAAAGAGCATGACACACTTTATTTCCTTTTC-
1 -C-TTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCT
* * * ** *
92612 CCTTTGTCTTCAAAGAGCAAGATGCACTTTATTTCTTTTTC-
1 CTTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCT
* * * *
92653 CCTTTATCCTCAAAGAGTAGGACGCACTTTATTTCCTTTTCT
1 CTTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCT
* *
92695 CTTTTGTCCTCAAAGAGTAGGACACA-TTTAATTTCCTTCTTTT
1 CTTTTGTCCTCAAAGAGCAGGACACACTTT-ATTTCCTT-TTCT
* * * * *
92738 CCTTTGTCTTCAAAGAGTAGGACGCATTTTATTT--TTTT-T
1 CTTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCT
**
92777 CTTTTGTCCTTGAAGAGCA
1 CTTTTGTCCTCAAAGAGCA
92796 AGATGTACTC
Statistics
Matches: 193, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
39 15 0.08
40 2 0.01
41 74 0.38
42 32 0.17
43 32 0.17
44 3 0.02
45 31 0.16
46 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (42 bp):
CTTTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTCT
Found at i:93491 original size:50 final size:50
Alignment explanation
Indices: 93426--93557 Score: 187
Period size: 50 Copynumber: 2.7 Consensus size: 50
93416 ATTTGTATTG
* * *
93426 ATACATCCTTTATTGTATCGATACATTCTAGGTTTTACCCAGATGTATCA
1 ATACATTCTTCATTGTATTGATACATTCTAGGTTTTACCCAGATGTATCA
* *
93476 ATACATTCTTCATTGTATTGATACATTCTGGGTTTTACCCAGATGTATCG
1 ATACATTCTTCATTGTATTGATACATTCTAGGTTTTACCCAGATGTATCA
*
93526 ATACATT-TCTCAATGTATTGATACATTC-AGGT
1 ATACATTCT-TCATTGTATTGATACATTCTAGGT
93558 ATTTTTGACC
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 4 0.05
50 70 0.95
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (50 bp):
ATACATTCTTCATTGTATTGATACATTCTAGGTTTTACCCAGATGTATCA
Found at i:95992 original size:79 final size:79
Alignment explanation
Indices: 95798--96204 Score: 406
Period size: 79 Copynumber: 5.2 Consensus size: 79
95788 TCATTCATAT
* * * * * * * *
95798 TTTTATTTCTAAAATACCGATTTTTCACCATTGGGGATACTCCAACCCCATTGTTTCTGAGGG-A
1 TTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGAA
* * *
95862 TACTCTAACTCCGG
66 TACTCCAACCCCGA
* * * * * * ** * *
95876 TTTTATTTCTAAAATACCGATTGTCCATAATCAGGGATACTTCAACCCCGTTATTTCTAAGGGAA
1 TTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGAA
* * *
95941 TACTCCAACTCTGG
66 TACTCCAACCCCGA
* * * * *
95955 TTTTATTTCCAAAACATCAATTTTCCACCATCGGGGATACTCTAACCCTGTTATTTC-GAGGGGA
1 TTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGAA
*
96019 TACTCTAACCCCGA
66 TACTCCAACCCCGA
* * *
96033 TTTTATTTTCAAAACATCAATTTTTCACCATCGAGGATACTCCAACCCCGTTATTTCCAA-GGAG
1 TTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGA-
*
96097 ATACTGCAACCCCGA
65 ATACTCCAACCCCGA
** * * * *
96112 TTTTATTTTTAAAACATCAATTTTTCACCATTGGGGATACTCCAACCCTGTTATTTTTAAGGGGA
1 TTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGAA
*
96177 TACTCCAACCCCGT
66 TACTCCAACCCCGA
*
96191 TTTTATCTCCAAAA
1 TTTTATTTCCAAAA
96205 TATTAAATTT
Statistics
Matches: 275, Mismatches: 50, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
78 122 0.44
79 151 0.55
80 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (79 bp):
TTTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTCTAAGGGAA
TACTCCAACCCCGA
Found at i:96084 original size:157 final size:158
Alignment explanation
Indices: 95798--96196 Score: 457
Period size: 157 Copynumber: 2.5 Consensus size: 158
95788 TCATTCATAT
* * * ** *
95798 TTTTATTTCTAAAATACCGATTTTTCACCATTGGGGATACTCCAACCCCATTGTTTCTGA-GGGA
1 TTTTATTTCTAAAACATCAATTTTTCACCATTGGGGATACTCCAACCCTGTTATTTC-GAGGGGA
* * * * * *
95862 TACTCTAACTCCGGTTTTA-TTTCTAAAATACCGATTGTCCATAATCAGGGATACTTCAACCCCG
65 TACTCTAACCCCGATTTTATTTTCTAAAACACCAATTGTCCACAATCAGGGATACTCCAACCCCG
* * * *
95926 TTATTTCTAAGG-GAATACTCCAACTCTGG
130 TTATTTCCAAGGAG-ATACTCCAACCCCGA
* * * *
95955 TTTTATTTCCAAAACATCAATTTTCCACCATCGGGGATACTCTAACCCTGTTATTTCGAGGGGAT
1 TTTTATTTCTAAAACATCAATTTTTCACCATTGGGGATACTCCAACCCTGTTATTTCGAGGGGAT
* * * *
96020 ACTCTAACCCCGATTTTATTTTC-AAAACATCAATTTTTCACCATC-GAGGATACTCCAACCCCG
66 ACTCTAACCCCGATTTTATTTTCTAAAACACCAATTGTCCACAATCAG-GGATACTCCAACCCCG
*
96083 TTATTTCCAAGGAGATACTGCAACCCCGA
130 TTATTTCCAAGGAGATACTCCAACCCCGA
* **
96112 TTTTATTTTTAAAACATCAATTTTTCACCATTGGGGATACTCCAACCCTGTTATTTTTAAGGGGA
1 TTTTATTTCTAAAACATCAATTTTTCACCATTGGGGATACTCCAACCCTGTTA-TTTCGAGGGGA
* *
96177 TACTCCAACCCCGTTTTTAT
65 TACTCTAACCCCGATTTTAT
96197 CTCCAAAATA
Statistics
Matches: 203, Mismatches: 34, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
156 3 0.01
157 168 0.83
158 32 0.16
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (158 bp):
TTTTATTTCTAAAACATCAATTTTTCACCATTGGGGATACTCCAACCCTGTTATTTCGAGGGGAT
ACTCTAACCCCGATTTTATTTTCTAAAACACCAATTGTCCACAATCAGGGATACTCCAACCCCGT
TATTTCCAAGGAGATACTCCAACCCCGA
Found at i:97263 original size:20 final size:20
Alignment explanation
Indices: 97238--97304 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
97228 TTATCGATAC
97238 AATGTATCGATACAGAGTAT
1 AATGTATCGATACAGAGTAT
97258 AATGTATCGATAC-------
1 AATGTATCGATACAGAGTAT
*
97271 AATGTATCGATATAGAGTAT
1 AATGTATCGATACAGAGTAT
97291 AATGTATCGATACA
1 AATGTATCGATACA
97305 TCTGGATGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 12 0.32
20 26 0.68
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACAGAGTAT
Found at i:97271 original size:33 final size:33
Alignment explanation
Indices: 97229--97304 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
97219 AATGAACATT
97229 TATCGATACAATGTATCGATACAGAGTATAATG
1 TATCGATACAATGTATCGATACAGAGTATAATG
*
97262 TATCGATACAATGTATCGATATAGAGTATAATG
1 TATCGATACAATGTATCGATACAGAGTATAATG
97295 TATCGATACA
1 TATCGATACA
97305 TCTGGATGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (33 bp):
TATCGATACAATGTATCGATACAGAGTATAATG
Found at i:97290 original size:13 final size:13
Alignment explanation
Indices: 97229--97282 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
97219 AATGAACATT
97229 TATCGATACAATG
1 TATCGATACAATG
97242 TATCGATAC-A-G
1 TATCGATACAATG
*
97253 -A--G-TATAATG
1 TATCGATACAATG
97262 TATCGATACAATG
1 TATCGATACAATG
97275 TATCGATA
1 TATCGATA
97283 TAGAGTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
10 2 0.06
11 1 0.03
12 2 0.06
13 23 0.70
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:98788 original size:21 final size:23
Alignment explanation
Indices: 98759--98801 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
98749 TTGGCCCACC
98759 AGATGATTTTTCC-AAAATTTTT
1 AGATGATTTTTCCTAAAATTTTT
98781 AGAT-ATTTTTCCTAAAATTTT
1 AGATGATTTTTCCTAAAATTTT
98802 CATGAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (23 bp):
AGATGATTTTTCCTAAAATTTTT
Found at i:99926 original size:24 final size:24
Alignment explanation
Indices: 99869--99929 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
99859 TGATATATTG
*
99869 CTATTCATGTATCACTGTTCATCA
1 CTATTCATGTATCACTATTCATCA
* *
99893 TTGTTCATGTATCACTATTCATCA
1 CTATTCATGTATCACTATTCATCA
*
99917 CTATTTATGTATC
1 CTATTCATGTATC
99930 GATACATAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (24 bp):
CTATTCATGTATCACTATTCATCA
Found at i:100029 original size:20 final size:20
Alignment explanation
Indices: 99983--100029 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
99973 AATTTCAAAT
* *
99983 GCATGTATCGATACATTATA
1 GCATGTATCGATACATAAGA
*
100003 -AATTGTATCGATACATAAGA
1 GCA-TGTATCGATACATAAGA
100023 GCATGTA
1 GCATGTA
100030 AGTGCGAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.05
20 19 0.90
21 1 0.05
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (20 bp):
GCATGTATCGATACATAAGA
Found at i:100430 original size:36 final size:34
Alignment explanation
Indices: 100385--100477 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 34
100375 CTAAGTGATT
100385 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCC-TTGAAAAAGATA-GGA
*
100421 GAGAGGTTCTATCTTAGCCCGTG-AAAAGATAGGA
1 GAGAGGTTCTATCTTAG-CCTTGAAAAAGATAGGA
*
100455 -AG-GTTTCTATCTTAGCCTTGAAA
1 GAGAGGTTCTATCTTAGCCTTGAAA
100478 GATAATGTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
31 4 0.08
32 14 0.27
33 2 0.04
34 3 0.06
35 8 0.15
36 19 0.37
37 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (34 bp):
GAGAGGTTCTATCTTAGCCTTGAAAAAGATAGGA
Found at i:100812 original size:21 final size:21
Alignment explanation
Indices: 100788--100830 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
100778 TTGGTTATCT
*
100788 CGAGATA-ATTGATGGCAATTA
1 CGAGATACATTG-TGACAATTA
*
100809 CGAGGTACATTGTGACAATTA
1 CGAGATACATTGTGACAATTA
100830 C
1 C
100831 ATTTTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (21 bp):
CGAGATACATTGTGACAATTA
Found at i:103182 original size:33 final size:32
Alignment explanation
Indices: 103145--103212 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
103135 CGTTACAAGC
*
103145 CAATGTATCGATACATTTTATGATGTATCGATA
1 CAATGTATCGATACATATTATG-TGTATCGATA
* *
103178 CAATGTATCGATACATATTGTGTGTATTGATA
1 CAATGTATCGATACATATTATGTGTATCGATA
103210 CAA
1 CAA
103213 ATTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (32 bp):
CAATGTATCGATACATATTATGTGTATCGATA
Found at i:103185 original size:13 final size:13
Alignment explanation
Indices: 103167--103192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
103157 ACATTTTATG
103167 ATGTATCGATACA
1 ATGTATCGATACA
103180 ATGTATCGATACA
1 ATGTATCGATACA
103193 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:103274 original size:20 final size:20
Alignment explanation
Indices: 103249--103297 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
103239 TGACTTGTAA
**
103249 CGATACATTTTTTCAAGTAT
1 CGATACATTTAGTCAAGTAT
*
103269 CGATACATTTAGTCATGTAT
1 CGATACATTTAGTCAAGTAT
103289 CGATACATT
1 CGATACATT
103298 GTATCGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (20 bp):
CGATACATTTAGTCAAGTAT
Found at i:103302 original size:13 final size:13
Alignment explanation
Indices: 103284--103320 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
103274 CATTTAGTCA
103284 TGTATCGATACAT
1 TGTATCGATACAT
103297 TGTATCGATACAT
1 TGTATCGATACAT
103310 TGTATCGATAC
1 TGTATCGATAC
103321 TGTGCAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:103918 original size:22 final size:21
Alignment explanation
Indices: 103876--103919 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
103866 TTTTCTTTTC
*
103876 TCTCCCCCTTAATCAAAAATT
1 TCTCCCCCTTAATAAAAAATT
*
103897 TCTCCCCCTTAGTAAAACAATT
1 TCTCCCCCTTAATAAAA-AATT
103919 T
1 T
103920 AACACTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAAAATT
Found at i:105631 original size:20 final size:21
Alignment explanation
Indices: 105602--105642 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
105592 TGTTTTTGAT
105602 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
105621 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
105643 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:105792 original size:13 final size:13
Alignment explanation
Indices: 105774--105824 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
105764 ATAATCCCCT
105774 TGTATCGATACAG
1 TGTATCGATACAG
*
105787 TGTATCGATACAA
1 TGTATCGATACAG
105800 TGTATCGATACAG
1 TGTATCGATACAG
105813 TGTATCGATACA
1 TGTATCGATACA
105825 TCTGCATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:111945 original size:13 final size:13
Alignment explanation
Indices: 111927--111952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
111917 AAATTTTATG
111927 ATGTATCGATACA
1 ATGTATCGATACA
111940 ATGTATCGATACA
1 ATGTATCGATACA
111953 TATTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:111968 original size:32 final size:33
Alignment explanation
Indices: 111905--111972 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
111895 CGTTACAAGC
*
111905 CAATGTATCGATAAATTTTATGATGTATCGATA
1 CAATGTATCGATAAATATTATGATGTATCGATA
* *
111938 CAATGTATCGATACATATTGT-ATGTATCGATA
1 CAATGTATCGATAAATATTATGATGTATCGATA
111970 CAA
1 CAA
111973 ATTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATAAATATTATGATGTATCGATA
Found at i:112030 original size:20 final size:20
Alignment explanation
Indices: 112005--112057 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
111995 CCAATGACTT
**
112005 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
112025 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
112045 GTATCGATACATT
1 GTATCGATACATT
112058 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:112481 original size:13 final size:13
Alignment explanation
Indices: 112463--112489 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
112453 ACATTATGCT
112463 TTGTATCGATACA
1 TTGTATCGATACA
112476 TTGTATCGATACA
1 TTGTATCGATACA
112489 T
1 T
112490 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:112499 original size:19 final size:19
Alignment explanation
Indices: 112475--112530 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
112465 GTATCGATAC
**
112475 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
112494 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
112514 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
112531 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:112518 original size:20 final size:20
Alignment explanation
Indices: 112475--112529 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
112465 GTATCGATAC
**
112475 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
112494 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
112514 ATTGTATCGATACATG
1 ATTGTATCGATACATG
112530 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:121323 original size:13 final size:13
Alignment explanation
Indices: 121305--121331 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
121295 ACATTATGCT
121305 TTGTATCGATACA
1 TTGTATCGATACA
121318 TTGTATCGATACA
1 TTGTATCGATACA
121331 T
1 T
121332 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:121341 original size:19 final size:19
Alignment explanation
Indices: 121317--121372 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
121307 GTATCGATAC
**
121317 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
121336 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
121356 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
121373 GATTGGCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:121360 original size:20 final size:20
Alignment explanation
Indices: 121317--121371 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
121307 GTATCGATAC
**
121317 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
121336 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
121356 ATTGTATCGATACATG
1 ATTGTATCGATACATG
121372 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:121442 original size:33 final size:33
Alignment explanation
Indices: 121400--121469 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
121390 CTACCACTGT
121400 TTGTATCGATACATG-GAACAATGTATCAATACA
1 TTGTATCGATACATGAGAA-AATGTATCAATACA
* *
121433 TTGTATCGATACATGATGAAATTGTATCGATACA
1 TTGTATCGATACATGA-GAAAATGTATCAATACA
121467 TTG
1 TTG
121470 CTTGTAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 15 0.45
34 15 0.45
35 3 0.09
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATGAGAAAATGTATCAATACA
Found at i:123352 original size:20 final size:21
Alignment explanation
Indices: 123327--123366 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
123317 ATTATTTTTC
123327 TATCAT-AATTTTATATAAAA
1 TATCATAAATTTTATATAAAA
123347 TATCATAAATTTTATATAAA
1 TATCATAAATTTTATATAAA
123367 TATTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
TATCATAAATTTTATATAAAA
Found at i:123379 original size:8 final size:8
Alignment explanation
Indices: 123366--123429 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
123356 TTTTATATAA
123366 ATATTAAT
1 ATATTAAT
123374 ATATTAAT
1 ATATTAAT
*
123382 A-ATTTAT
1 ATATTAAT
123389 ATTATATAA-
1 A-TAT-TAAT
*
123398 ATTTTAAT
1 ATATTAAT
*
123406 ATATTTAT
1 ATATTAAT
*
123414 ATATTCAT
1 ATATTAAT
*
123422 ATAATAAT
1 ATATTAAT
123430 TATGTTTTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
7 9 0.20
8 30 0.68
9 3 0.07
10 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (8 bp):
ATATTAAT
Found at i:123837 original size:13 final size:13
Alignment explanation
Indices: 123803--123856 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
123793 ATTTTTTATA
123803 ATTT-AATTATATT
1 ATTTAAATTAT-TT
*
123816 ATATAAAATTATTT
1 AT-TTAAATTATTT
123830 ATTTAAA-TATTT
1 ATTTAAATTATTT
123842 A-TTAAATATATTT
1 ATTTAAAT-TATTT
123855 AT
1 AT
123857 ATATATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 5 0.15
12 6 0.18
13 12 0.35
14 5 0.15
15 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTAAATTATTT
Found at i:123842 original size:12 final size:13
Alignment explanation
Indices: 123805--123856 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
123795 TTTTTATAAT
*
123805 TTAATTATATTATA
1 TTAAATATATT-TA
*
123819 TAAAAT-TATTTA
1 TTAAATATATTTA
*
123831 TTTAA-ATATTTA
1 TTAAATATATTTA
123843 TTAAATATATTTA
1 TTAAATATATTTA
123856 T
1 T
123857 ATATATTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 15 0.48
13 12 0.39
14 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATATATTTA
Found at i:123847 original size:25 final size:27
Alignment explanation
Indices: 123803--123856 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
123793 ATTTTTTATA
*
123803 ATTTAATTATATTATATAAA-ATTATTT
1 ATTTAAATATATTATATAAATA-TATTT
123830 ATTTAAATAT-TTAT-TAAATATATTT
1 ATTTAAATATATTATATAAATATATTT
123855 AT
1 AT
123857 ATATATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 11 0.44
26 5 0.20
27 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTAAATATATTATATAAATATATTT
Found at i:123853 original size:21 final size:20
Alignment explanation
Indices: 123829--123916 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
123819 TAAAATTATT
123829 TATTTAAATATTTATTAAATA
1 TATTTAAATATTT-TTAAATA
* * *
123850 TATTTATATATATTTATATA
1 TATTTAAATATTTTTAAATA
* *
123870 TAATTAACTATATTTTTAATTTA
1 TATTTAA--ATATTTTTAA-ATA
* *
123893 AAATTAAATA-TTTTAAATA
1 TATTTAAATATTTTTAAATA
123912 TATTT
1 TATTT
123917 TCTCGTAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 5 0.10
20 17 0.33
21 14 0.27
22 8 0.15
23 8 0.15
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTAAATATTTTTAAATA
Found at i:123862 original size:10 final size:10
Alignment explanation
Indices: 123847--123884 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
123837 TATTTATTAA
123847 ATATATTTAT
1 ATATATTTAT
123857 ATATATTTAT
1 ATATATTTAT
*
123867 ATATAATTA-
1 ATATATTTAT
123876 ACTATATTT
1 A-TATATTT
123885 TTAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 1 0.04
10 24 0.96
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATATTTAT
Found at i:123871 original size:12 final size:12
Alignment explanation
Indices: 123814--123869 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
123804 TTTAATTATA
123814 TTATATAAAATTAT
1 TTATAT-AAA-TAT
*
123828 TTATTTAAATAT
1 TTATATAAATAT
123840 TTAT-TAAATAT
1 TTATATAAATAT
*
123851 ATT-TATATATAT
1 -TTATATAAATAT
123863 TTATATA
1 TTATATA
123870 TAATTAACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 10 0.27
12 19 0.51
13 3 0.08
14 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTATATAAATAT
Found at i:125062 original size:28 final size:28
Alignment explanation
Indices: 125005--125077 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
124995 TTTTTTTATA
*
125005 AATTTTAATT-AATATTATTAAAAAATT
1 AATTTTAATTAAATTTTATTAAAAAATT
*
125032 AATTTTAAATTAAATTTTATTAAATAA-T
1 AATTTT-AATTAAATTTTATTAAAAAATT
*
125060 AATTATTTATTAAATTTT
1 AATT-TTAATTAAATTTT
125078 GTATATAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 6 0.15
28 19 0.47
29 15 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTTTAATTAAATTTTATTAAAAAATT
Done.