Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011525.1 Kokia drynarioides strain JFW-HI SEQ_126511, 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: 121833
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 470 characters in sequence are not A, C, G, or T
Found at i:4885 original size:22 final size:22
Alignment explanation
Indices: 4829--4910 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
4819 TAAGTCATGA
* * *
4829 TTCACATATCACTTTAGCATAAA
1 TTCACATATCAC-ATGGCATAAG
* * *
4852 TTCGCATGTCACATGGCATAGG
1 TTCACATATCACATGGCATAAG
* *
4874 TTCACATATCACTTAGCATAAG
1 TTCACATATCACATGGCATAAG
4896 TTCACATATCACATG
1 TTCACATATCACATG
4911 ACAGTCACAC
Statistics
Matches: 46, Mismatches: 13, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
22 36 0.78
23 10 0.22
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (22 bp):
TTCACATATCACATGGCATAAG
Found at i:5177 original size:21 final size:21
Alignment explanation
Indices: 5151--5268 Score: 67
Period size: 21 Copynumber: 5.5 Consensus size: 21
5141 ATAAGGAATG
*
5151 GGTTCACATGTACGGTGATAA
1 GGTTCACATGTAAGGTGATAA
* **
5172 GGTTCATATGTAAGGTGATGG
1 GGTTCACATGTAAGGTGATAA
* * * *
5193 GGTTCACATACT-AGATGAGAG
1 GGTTCACAT-GTAAGGTGATAA
* ** *
5214 GGTTCTCATGTAACATGATAG
1 GGTTCACATGTAAGGTGATAA
* * *
5235 GGTTTACATGTTAGGTGATAG
1 GGTTCACATGTAAGGTGATAA
5256 GGTTTGCACATGT
1 GG-TT-CACATGT
5269 CTTTGGTGAT
Statistics
Matches: 74, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.01
21 64 0.86
22 3 0.04
23 6 0.08
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.32
Consensus pattern (21 bp):
GGTTCACATGTAAGGTGATAA
Found at i:5258 original size:42 final size:41
Alignment explanation
Indices: 5150--5259 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
5140 TATAAGGAAT
* ** *
5150 GGGTTCACATGTACGGTGATAAGGTTCATATGTAAGGTGATG
1 GGGTTCACATGTA-GGTGATAGGGTTCATATGTAACATGATA
* * *
5192 GGGTTCACATACTAGATGAGAGGGTTC-TCATGTAACATGATA
1 GGGTTCACAT-GTAGGTGATAGGGTTCAT-ATGTAACATGATA
*
5234 GGGTTTACATGTTAGGTGATAGGGTT
1 GGGTTCACATG-TAGGTGATAGGGTT
5260 TGCACATGTC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
41 1 0.02
42 51 0.94
43 2 0.04
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.32
Consensus pattern (41 bp):
GGGTTCACATGTAGGTGATAGGGTTCATATGTAACATGATA
Found at i:12618 original size:17 final size:17
Alignment explanation
Indices: 12598--12630 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12588 ACTTTTTAAA
*
12598 ATTTTTATAATATTTTT
1 ATTTTTAAAATATTTTT
12615 ATTTTTAAAATATTTT
1 ATTTTTAAAATATTTT
12631 GTGAATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTAAAATATTTTT
Found at i:12642 original size:28 final size:26
Alignment explanation
Indices: 12590--12642 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12580 AATTAACGAC
*
12590 TTTTTAAAATTTTTATAATATTTTTA
1 TTTTTAAAATTTTTATAATACTTTTA
*
12616 TTTTTAAAATATTTTGTGAATACTTTT
1 TTTTTAAAAT-TTTTAT-AATACTTTT
12643 CAATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 5 0.22
28 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTTTAAAATTTTTATAATACTTTTA
Found at i:18534 original size:59 final size:58
Alignment explanation
Indices: 18456--18763 Score: 235
Period size: 59 Copynumber: 5.2 Consensus size: 58
18446 CTTTTAATCT
* *
18456 GATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGATTGACACCTTCTTTTTGTCA
1 GATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGTTGACACC-TCTTTTT-TCA
** ** ** * * *
18516 GAT-AAAAAATTTAATTTTTTTATGTTGGTCATGCCATGGCTGACA-CTCTTATTTATCT
1 GATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGTTGACACCTCTT-TTT-TCA
* * *
18574 GATAAAAAAATCAAATTTTTTTGTGTTGACCATGCAATGGTCGACACCCCTTTTTTCA
1 GATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGTTGACACCTCTTTTTTCA
* ** * * *
18632 GATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATTGC-ATGGCCGACACCCCTTTTATCT
1 GATAAAAAAA--TCAAA-TTTTTTGGTGTTGACCA-TGCAATGGTTGACACCTCTTTTTTCA
* * ** * ** *
18693 GAATAAAAAAATCAAATTATTGGGTGTTGGTCATGCCATGGCCGACACCCCCTTTTTTGTCA
1 G-ATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGTTGACA-CCTC-TTTTT-TCA
18755 GATAAAAAA
1 GATAAAAAA
18764 TTCGATTTTT
Statistics
Matches: 204, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
57 4 0.02
58 24 0.12
59 93 0.46
60 21 0.10
61 47 0.23
62 15 0.07
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (58 bp):
GATAAAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGTTGACACCTCTTTTTTCA
Found at i:18575 original size:118 final size:116
Alignment explanation
Indices: 18432--18809 Score: 436
Period size: 120 Copynumber: 3.2 Consensus size: 116
18422 TGGCCACTGT
* *
18432 ATGGTCGACACCCCCTTTTAATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGAT
1 ATGGCCGACA-CCCCTTTT-ATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGGT
* *
18497 TGACACCTTCTTTTTGTCAGATAAAAAATTTAATTTTTTTATGTTGGTCATGCC
64 CGACACC-CCTTTTTGTCAGATAAAAAATTTAATTTTTTTATGTTGGTCATGCC
* * * **
18551 ATGGCTGACACTCTTATTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGACCATGCAATGGTC
1 ATGGCCGACACCCCT-TTTATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGGTC
* *
18616 GACACCCCTTTTT-TCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATTG-C
65 GACACCCCTTTTTGTCAGAT-AAAAAATTT--AATTTTTTT-ATGTTGGTCA-TGCC
* ** * *
18671 ATGGCCGACACCCCTTTTATCTGAATAAAAAAATCAAATTATTGGGTGTTGGTCATGCCATGGCC
1 ATGGCCGACACCCCTTTTATCTG-ATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGGTC
* *
18736 GACACCCCCTTTTTTGTCAGATAAAAAATTCGATTTTTTTTTATGTTGGTCATGCC
65 GACA-CCCC-TTTTTGTCAGATAAAAAATT-TA-ATTTTTTTATGTTGGTCATGCC
**
18792 ATGATCGACACCCCTTTT
1 ATGGCCGACACCCCTTTT
18810 TTGTCAGATA
Statistics
Matches: 219, Mismatches: 27, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
116 6 0.03
117 15 0.07
118 51 0.23
119 28 0.13
120 61 0.28
121 32 0.15
122 20 0.09
123 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (116 bp):
ATGGCCGACACCCCTTTTATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGGTCG
ACACCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTATGTTGGTCATGCC
Found at i:19008 original size:60 final size:59
Alignment explanation
Indices: 18900--19068 Score: 180
Period size: 60 Copynumber: 2.8 Consensus size: 59
18890 CAAATGGTCG
* ** * * * * * *
18900 ACACCAAAAAAATTGAAATTTTTTATCTGAAAAAAGAGGGTGTTGGCCATTGCATGGCCT
1 ACACCAAAAAATTTGATTTTTTTTATCAGATAAAAG-GAGTGTCGGCCATTGCATGACCA
*
18960 ACACCAAAAAATTTGATTTTTTTTATCAGATAAATAGGAATGTCGGCCATTGCATGACCA
1 ACACCAAAAAATTTGATTTTTTTTATCAGATAAA-AGGAGTGTCGGCCATTGCATGACCA
* *
19020 ACACC--CAAATTTAATTTTTTTTATCAGATTAAAAGGGAGTGTCGGCCAT
1 ACACCAAAAAATTTGATTTTTTTTATCAGA-TAAAA-GGAGTGTCGGCCAT
19069 GAAATGGCCA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 22 0.24
59 17 0.18
60 52 0.56
61 2 0.02
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (59 bp):
ACACCAAAAAATTTGATTTTTTTTATCAGATAAAAGGAGTGTCGGCCATTGCATGACCA
Found at i:19037 original size:58 final size:60
Alignment explanation
Indices: 18944--19068 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 60
18934 AGAGGGTGTT
* * *
18944 GGCCATTGCATGGCCTACACCAAAAAATTTGATTTTTTTTATCAGA-TAAATA-GGAATGTC
1 GGCCATTGCATGACCAACACC-AAAAATTTAATTTTTTTTATCAGATTAAA-AGGGAATGTC
* *
19004 GGCCATTGCATGACCAACACC-CAAATTTAATTTTTTTTATCAGATTAAAAGGGAGTGTC
1 GGCCATTGCATGACCAACACCAAAAATTTAATTTTTTTTATCAGATTAAAAGGGAATGTC
19063 GGCCAT
1 GGCCAT
19069 GAAATGGCCA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
58 22 0.38
59 17 0.29
60 19 0.33
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (60 bp):
GGCCATTGCATGACCAACACCAAAAATTTAATTTTTTTTATCAGATTAAAAGGGAATGTC
Found at i:19080 original size:59 final size:58
Alignment explanation
Indices: 18968--19082 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 58
18958 CTACACCAAA
* *
18968 AAATTTGATTTTTTTTATCAGATAAATAGGAATGTCGGCCATTGCATGACCAACACCC
1 AAATTTAATTTTTTTTATCAGATAAATAGGAATGTCGGCCATTGAATGACCAACACCC
* *
19026 AAATTTAATTTTTTTTATCAGATTAAA-AGGGAGTGTCGGCCA-TGAAATGGCCAACAC
1 AAATTTAATTTTTTTTATCAGA-TAAATA-GGAATGTCGGCCATTG-AATGACCAACAC
19083 TAATTTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
58 24 0.48
59 26 0.52
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (58 bp):
AAATTTAATTTTTTTTATCAGATAAATAGGAATGTCGGCCATTGAATGACCAACACCC
Found at i:19775 original size:21 final size:21
Alignment explanation
Indices: 19751--19790 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19741 CTACTTTTCA
19751 AAAGAAATTATATTATTTTTT
1 AAAGAAATTATATTATTTTTT
* * *
19772 AAAGTATTTTTATTATTTT
1 AAAGAAATTATATTATTTT
19791 ATATAGGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
AAAGAAATTATATTATTTTTT
Found at i:24534 original size:96 final size:96
Alignment explanation
Indices: 24357--24541 Score: 239
Period size: 96 Copynumber: 1.9 Consensus size: 96
24347 GAAGAGGATG
* * * ** *
24357 TTCGATTATCTCGATTTGAGGAAAGATTGCACCTAGTAAGTTAAGGCGTAAATTTTTAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAAATTTTGAGAATCGA
**
24422 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAAAAACATTGCCTCGATTAAGGGTA
* *
24453 TTCGATTATTTTGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAAATTTTCGA-AACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAAATTTT-GAGAA-TC
*
24517 GAA-ATAAAAAAATATTGCCTCGATT
64 GAAGATAAAAAAACATTGCCTCGATT
24542 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
96 70 0.92
97 6 0.08
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAATAAGTTAAGGCACAAATTTTGAGAATCGA
AGATAAAAAAACATTGCCTCGATTAAGGGTA
Found at i:24845 original size:30 final size:30
Alignment explanation
Indices: 24803--25083 Score: 181
Period size: 29 Copynumber: 9.6 Consensus size: 30
24793 TTTCGGAGGC
* *
24803 AAAATGGTAATTTTGGGAAATTTCGAGGTTA
1 AAAATGG-AATTTTTGGAAATTTCGAGGTCA
* *
24834 AAAATGGAATTTTTAGACA-TTCGAGG--A
1 AAAATGGAATTTTTGGAAATTTCGAGGTCA
* * * *
24861 AAAAGGGTAA-TTTT-GAGAGTTTCAAGGTCG
1 AAAATGG-AATTTTTGGA-AATTTCGAGGTCA
** * *
24891 AAAATGGGGTTTTTGGACA-TTCGAGGGC-
1 AAAATGGAATTTTTGGAAATTTCGAGGTCA
* *
24919 AAAATGGTAATTTTT-GAAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAA-TTTCGAGGTCA
* * **
24950 AAAATGGAAATTTTAG-AGGTTCGAGGTCA
1 AAAATGGAATTTTTGGAAATTTCGAGGTCA
* *
24979 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAATTTCGAGGTCA
* * * *
25009 AAAATGGAATTTTTGGAAGTTTTGGGGT-T
1 AAAATGGAATTTTTGGAAATTTCGAGGTCA
* * *
25038 AAAATGGAATTTCTGG-AAGTTCTGGGGT-A
1 AAAATGGAATTTTTGGAAATTTC-GAGGTCA
25067 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
25084 CAGTTTAAGG
Statistics
Matches: 197, Mismatches: 38, Indels: 31
0.74 0.14 0.12
Matches are distributed among these distances:
26 2 0.01
27 11 0.06
28 21 0.11
29 76 0.39
30 70 0.36
31 17 0.09
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAATTTCGAGGTCA
Found at i:24932 original size:28 final size:28
Alignment explanation
Indices: 24771--24932 Score: 87
Period size: 28 Copynumber: 5.6 Consensus size: 28
24761 GATACCCGAG
* * **
24771 GGGCAAAGTGGTAATTTTGAATTTTCG-
1 GGGCAAAATGGTAATTTTGGACATTCGA
*
24798 GAGGCAAAATGGTAATTTTGGGAAATTTCGA
1 G-GGCAAAATGGTAATTTT-GGACA-TTCGA
** *
24829 GGTTAAAAATGG-AATTTTTAGACATTCGA
1 GG-GCAAAATGGTAA-TTTTGGACATTCGA
* * ** *
24858 -GGAAAAAGGGTAATTTTGAGAGTTTCAA
1 GGGCAAAATGGTAATTTTG-GACATTCGA
* ***
24886 GGTCGAAAATGGGGTTTTTGGACATTCGA
1 GGGC-AAAATGGTAATTTTGGACATTCGA
24915 GGGCAAAATGGTAATTTT
1 GGGCAAAATGGTAATTTT
24933 TGAAAGTTTT
Statistics
Matches: 98, Mismatches: 27, Indels: 19
0.68 0.19 0.13
Matches are distributed among these distances:
27 12 0.12
28 36 0.37
29 17 0.17
30 21 0.21
31 12 0.12
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (28 bp):
GGGCAAAATGGTAATTTTGGACATTCGA
Found at i:24954 original size:59 final size:59
Alignment explanation
Indices: 24800--25085 Score: 246
Period size: 59 Copynumber: 4.9 Consensus size: 59
24790 AATTTTCGGA
* * * *
24800 GGCAAAATGGTAATTTTGGGAAA-TTTCGAGGTTAAAAATGGAATTTTTAGACATTCGA-
1 GGCAAAATGGTAATTTT-TGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGACATTCGAG
* * * ** * **
24858 GGAAAAAGGGTAA-TTTTGAGAGTTTCAAGGTCGAAAATGGGGTTTTTGGACATTCGAG
1 GGCAAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGACATTCGAG
* * * **
24916 GGCAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAAATTTTAGAGGTTCGAG
1 GGCAAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGACATTCGAG
* * *
24975 GTCAAAAATGG-AATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGGA-AGTTTTG-G
1 GGC-AAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGACA--TTCGAG
* * * * *
25034 GGTTAAAATGG-AATTTCTGGAAGTTCTGGGGT-AAAAATGGAATTTTTGGACA
1 GG-CAAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGACA
25086 GTTTAAGGAC
Statistics
Matches: 185, Mismatches: 35, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
56 3 0.02
57 32 0.17
58 40 0.22
59 100 0.54
60 10 0.05
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (59 bp):
GGCAAAATGGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGACATTCGAG
Found at i:25042 original size:29 final size:30
Alignment explanation
Indices: 24919--25089 Score: 213
Period size: 29 Copynumber: 5.7 Consensus size: 30
24909 ATTCGAGGGC
*
24919 AAAATGGTAATTTTTGAAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTCA
* * * * *
24950 AAAATGGAAATTTTAG-AGGTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
*
24979 AAAATGGAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
*
25009 AAAATGGAATTTTTGGAAGTTTTGGGGT-T
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
* *
25038 AAAATGGAATTTCTGGAAGTTCTGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
25067 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
25090 AAGGACCTTT
Statistics
Matches: 121, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
29 66 0.55
30 48 0.40
31 7 0.06
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTCA
Found at i:26172 original size:3 final size:3
Alignment explanation
Indices: 26166--26225 Score: 102
Period size: 3 Copynumber: 19.7 Consensus size: 3
26156 TAATTAATGC
*
26166 TAT TAT TAA TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26212 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
26226 AAAATATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:26946 original size:6 final size:6
Alignment explanation
Indices: 26935--27009 Score: 66
Period size: 6 Copynumber: 12.8 Consensus size: 6
26925 TATAATAAGT
* *
26935 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** **
26983 -ACAAA TTTAAA -TTAAA AATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
27010 TTTCAAAATC
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 13 0.24
6 36 0.65
7 6 0.11
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:26958 original size:18 final size:18
Alignment explanation
Indices: 26935--27009 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
26925 TATAATAAGT
26935 TTTAAATTTAAATATAAA
1 TTTAAATTTAAATATAAA
*
26953 TCTAAATTTAAAT-TAAA
1 TTTAAATTTAAATATAAA
*
26970 TTTAAATTTTAAA-ACAAA
1 TTTAAA-TTTAAATATAAA
*
26988 TTTAAA-TTAAAAATAAA
1 TTTAAATTTAAATATAAA
27005 TTTAA
1 TTTAA
27010 TTTCAAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.10
17 18 0.36
18 27 0.54
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTAAATTTAAATATAAA
Found at i:26969 original size:29 final size:29
Alignment explanation
Indices: 26936--26998 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
26926 ATAATAAGTT
*
26936 TTAAATTTAAA-TATAAATCTAAATTTAAA
1 TTAAATTTAAATTATAAAAC-AAATTTAAA
*
26965 TTAAATTTAAATTTTAAAACAAATTTAAA
1 TTAAATTTAAATTATAAAACAAATTTAAA
26994 TTAAA
1 TTAAA
26999 AATAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
TTAAATTTAAATTATAAAACAAATTTAAA
Found at i:27009 original size:12 final size:12
Alignment explanation
Indices: 26937--26998 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 12
26927 TAATAAGTTT
26937 TAAATTTAAATA
1 TAAATTTAAATA
* *
26949 TAAATCTAAATT
1 TAAATTTAAATA
*
26961 TAAA-TTAAATT
1 TAAATTTAAATA
26972 TAAATTTTAAA-A
1 TAAA-TTTAAATA
*
26984 CAAATTTAAAT-
1 TAAATTTAAATA
26995 TAAA
1 TAAA
26999 AATAAATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 19 0.46
12 17 0.41
13 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:27017 original size:17 final size:16
Alignment explanation
Indices: 26939--27044 Score: 86
Period size: 17 Copynumber: 6.1 Consensus size: 16
26929 ATAAGTTTTA
*
26939 AATTTAAATATAAATCTA
1 AATTTAAA-ATAAAT-TT
*
26957 AATTTAAATTAAATTT
1 AATTTAAAATAAATTT
*
26973 AAATTTTAAAACAAATTT
1 -AA-TTTAAAATAAATTT
*
26991 AAATTAAAAATAAATTT
1 -AATTTAAAATAAATTT
*
27008 AATTTCAAAATCAATTT
1 AATTT-AAAATAAATTT
*
27025 ATTCTTAAAATAAATCTT
1 AAT-TTAAAATAAAT-TT
27043 AA
1 AA
27045 AATGGGTTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
16 5 0.07
17 39 0.54
18 28 0.39
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTAAAATAAATTT
Found at i:27879 original size:200 final size:199
Alignment explanation
Indices: 27457--28003 Score: 644
Period size: 200 Copynumber: 2.8 Consensus size: 199
27447 GTTTCCTCAG
** * * * *
27457 GAAGACGGGTTTGGTTCACTTCTCCGTATCTCATCAGGAAACTAACCTTTTTATTGTTTC-ACCT
1 GAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACC-
* * *
27521 TGTTTCTCAGTATCTCATCAGGAAGCTGGGGTCGAAGATTT-GT---TT-A-CATTGAGTTGGTA
65 TGCTTCTCAGTATCTCATCAGGAAGCTGGGGTCGAAGATTTGGTCCATTGAGCCTCGAGTTGGTA
** ** * * * *
27580 TACTTCTCTGTATCTTATCAGGAAGATGATCGCCTTACTTGTTTCAATCCGCTTCTCTATATCTC
130 TACTTCTCTACATCCCATCAGGAAGATAAACGCCTTACTTGTTTCAATACGCTTCTCTATACCTC
*
27645 ATCAG
195 ATCAA
* * *
27650 GAAGACGAATTTGATCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGTCCT
1 GAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCT
*
27715 GCTTCTCAGTGTCTCATCAGGAAGCTGGGGTCGAAGATTTGGTCGCATTGAGCCTCGAGTTGGTA
66 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTCGAAGATTTGGTC-CATTGAGCCTCGAGTTGGTA
* * * * * *
27780 TTCTTCTCTACGTCCCATTAGGAAGATAAACGTCTTACTTGTTTCAATATGCTTCTCTGTACCTC
130 TACTTCTCTACATCCCATCAGGAAGATAAACGCCTTACTTGTTTCAATACGCTTCTCTATACCTC
*
27845 ATTAA
195 ATCAA
* *
27850 GAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGTTAACC-TTTTATTGCTTCGCCCT
1 GAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCT
* ** * *
27914 GCTTCTCAATATCTCATCAGGAAGCTGGATTCGAAGATTTGCTCACATCGAGCC-CTGAGTTGGT
66 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTCGAAGATTTGGTC-CATTGAGCCTC-GAGTTGGT
** *
27978 ATACTTCTCTGTATCTCATCAGGAAG
129 ATACTTCTCTACATCCCATCAGGAAG
28004 CTGACCATTT
Statistics
Matches: 300, Mismatches: 45, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
193 92 0.31
194 4 0.01
198 3 0.01
199 92 0.31
200 109 0.36
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (199 bp):
GAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCT
GCTTCTCAGTATCTCATCAGGAAGCTGGGGTCGAAGATTTGGTCCATTGAGCCTCGAGTTGGTAT
ACTTCTCTACATCCCATCAGGAAGATAAACGCCTTACTTGTTTCAATACGCTTCTCTATACCTCA
TCAA
Found at i:28162 original size:123 final size:123
Alignment explanation
Indices: 27858--28249 Score: 511
Period size: 123 Copynumber: 3.3 Consensus size: 123
27848 AAGAAGACGA
* * *
27858 ATTTGGTAC-ACTTCTCAGTATCTCATCAGGAAGTTAACC-TTTTATTG-CTTCGCCCTGCTTCT
1 ATTTGGT-CTACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTA-TGCCTTCGACCTGCTTCT
* * * * *
27920 CAATATCTCATCAGGAAGCT-GGATTCGAAGATTTGCTCACATCGAG-C-C----C--TG
64 CAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTG
* * * * *
27971 AGTTGGTATACTTCTCTGTATCTCATCAGGAAGCTGACCATTTTATGCCTTCGACGTGCTTCTTA
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATGCCTTCGACCTGCTTCTCA
*
28036 GTATTTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTG
66 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTG
* * * *
28094 ATTTTGTCTACTTCTCAATATCTCATCAGGAAGCTGACCATTTTATGCCTTCGACTTGTTTCTCA
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATGCCTTCGACCTGCTTCTCA
*
28159 GTATCTCATCAGGAAGCTGGGGTTCGAGGATTTGCTCGCTTTGAGCCTCGTTTCATTG
66 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTG
28217 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAG
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAG
28250 ATGATCGCAT
Statistics
Matches: 241, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
113 35 0.15
114 35 0.15
115 22 0.09
116 1 0.00
117 1 0.00
121 1 0.00
123 146 0.61
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (123 bp):
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATGCCTTCGACCTGCTTCTCA
GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCCTCGTTTCATTG
Found at i:35491 original size:17 final size:18
Alignment explanation
Indices: 35467--35511 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
35457 NNNNNNNNNN
35467 TAAATTTAAAT-TTAAAA
1 TAAATTTAAATCTTAAAA
*
35484 TCAATTT-AATCTTAAAA
1 TAAATTTAAATCTTAAAA
35501 TAAATCTTAAA
1 TAAAT-TTAAA
35512 ATGGGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 2 0.09
19 2 0.09
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATCTTAAAA
Found at i:37110 original size:30 final size:30
Alignment explanation
Indices: 37076--37147 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
37066 AAATTGAATC
37076 AAATCAAAATTTCATATATAAAATTACACA-
1 AAATCAAAATTT-ATATATAAAATTACACAT
* * *
37106 AAATCAAAATTTATGTATACAATTATACATT
1 AAATCAAAATTTATATATAAAATTACACA-T
37137 AAATCAAAATT
1 AAATCAAAATT
37148 CATGTATTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.38
30 12 0.32
31 11 0.30
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.33
Consensus pattern (30 bp):
AAATCAAAATTTATATATAAAATTACACAT
Found at i:37129 original size:29 final size:30
Alignment explanation
Indices: 37076--37154 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
37066 AAATTGAATC
*
37076 AAATCAAAATTTCATATATAAAATTACACA-
1 AAATCAAAATTT-ATGTATAAAATTACACAT
* *
37106 AAATCAAAATTTATGTATACAATTATACATT
1 AAATCAAAATTTATGTATAAAATTACACA-T
*
37137 AAATCAAAATTCATGTAT
1 AAATCAAAATTTATGTAT
37155 TCTCCTTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.33
30 12 0.28
31 17 0.40
ACGTcount: A:0.52, C:0.11, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTTATGTATAAAATTACACAT
Found at i:39309 original size:19 final size:19
Alignment explanation
Indices: 39287--39331 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39277 TTATATTAAG
39287 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
39306 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
39325 ATTTAAT
1 ATTTAAT
39332 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:40181 original size:21 final size:22
Alignment explanation
Indices: 40141--40201 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
40131 TTCGACTTCC
*
40141 CTATTTTCTATTTCTTTTT-ATT
1 CTATTTTCT-TTTATTTTTAATT
*
40163 TTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
40185 CTA-TTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
40202 CCTTAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:41401 original size:1 final size:1
Alignment explanation
Indices: 41395--41420 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
41385 ATGAGTGAAG
41395 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
41421 GAGAAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:44158 original size:10 final size:10
Alignment explanation
Indices: 44143--44173 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
44133 AATTTTTTCA
44143 TTTAAAATTT
1 TTTAAAATTT
*
44153 TTTAAAAATT
1 TTTAAAATTT
44163 TTTAAAATTT
1 TTTAAAATTT
44173 T
1 T
44174 AAATTAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTAAAATTT
Found at i:44993 original size:54 final size:52
Alignment explanation
Indices: 44870--45005 Score: 148
Period size: 54 Copynumber: 2.5 Consensus size: 52
44860 ATTTTATTTG
* * * *
44870 TGAGAGTTAGGATTAGGGATTTAGTTGAGAGTTAGATTAGGCTCCCTTTTGGT
1 TGAGAGTTAGG-TTAGAGATTTAGTTGGGAGTTAGATTAAGCTCCCTTTTAGT
* * *
44923 TGATAGTTAGGGTTAGAGATTTAGTTGGGAGTTAGGGTTAAGCT-GCTTTATAGT
1 TGAGAGTTA-GGTTAGAGATTTAGTTGGGAGTTA-GATTAAGCTCCCTTT-TAGT
*
44977 TGAGAGTTAGTGTTAGAGATTTAGATGGG
1 TGAGAGTTAG-GTTAGAGATTTAGTTGGG
45006 GTTTGAGAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
53 33 0.47
54 37 0.53
ACGTcount: A:0.24, C:0.04, G:0.34, T:0.38
Consensus pattern (52 bp):
TGAGAGTTAGGTTAGAGATTTAGTTGGGAGTTAGATTAAGCTCCCTTTTAGT
Found at i:45274 original size:25 final size:25
Alignment explanation
Indices: 45246--45293 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
45236 CCACGTTAGC
45246 AATTAATTAAAT-TTTTTTAAAAAAT
1 AATT-ATTAAATATTTTTTAAAAAAT
* *
45271 AATTTTTATATATTTTTTAAAAA
1 AATTATTAAATATTTTTTAAAAA
45294 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTATTAAATATTTTTTAAAAAAT
Found at i:45304 original size:12 final size:12
Alignment explanation
Indices: 45289--45313 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45279 TATATTTTTT
45289 AAAAATTTTAAA
1 AAAAATTTTAAA
45301 AAAAATTTTAAA
1 AAAAATTTTAAA
45313 A
1 A
45314 TTTTTTTGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATTTTAAA
Found at i:46296 original size:39 final size:42
Alignment explanation
Indices: 46221--46299 Score: 110
Period size: 39 Copynumber: 1.9 Consensus size: 42
46211 AAATTGAGTG
* *
46221 TATGTAATGACAAATTATTGATGAATGATTACAATGATAAAAA
1 TATGTAATGAC-AATTATTGATCAATGATTAAAATGATAAAAA
46264 TATGTAATGAC-ATTA-TGA-CAATGATTAAAATGATAA
1 TATGTAATGACAATTATTGATCAATGATTAAAATGATAA
46300 TAGTATGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 16 0.47
40 3 0.09
41 4 0.12
43 11 0.32
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (42 bp):
TATGTAATGACAATTATTGATCAATGATTAAAATGATAAAAA
Found at i:51465 original size:23 final size:23
Alignment explanation
Indices: 51431--51484 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
51421 ACGCTAGCGC
51431 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
51454 GCTTACTTTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
51477 GCCTACTG
1 GCTTACTG
51485 GATTGCACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.09, C:0.26, G:0.20, T:0.44
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:52352 original size:23 final size:23
Alignment explanation
Indices: 52326--52383 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
52316 ACGCTAGCGC
*
52326 GCTTATTATTTCGCACTTTGTGT
1 GCTTACTATTTCGCACTTTGTGT
*
52349 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTATTTCGCACTTTGTGT
*
52372 ACTTACTGATTT
1 GCTTACT-ATTT
52384 GCGCTATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 27 0.90
24 3 0.10
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.50
Consensus pattern (23 bp):
GCTTACTATTTCGCACTTTGTGT
Found at i:52393 original size:23 final size:23
Alignment explanation
Indices: 52333--52424 Score: 89
Period size: 23 Copynumber: 4.0 Consensus size: 23
52323 CGCGCTTATT
*
52333 ATTTCGCACTTTGTGTGCTTACTG
1 ATTT-GCACTATGTGTGCTTACTG
* *
52357 -TTTCGCACTTTGTGTACTTACTG
1 ATTT-GCACTATGTGTGCTTACTG
* * * *
52380 ATTTGCGCTATGTGCGCCTATTG
1 ATTTGCACTATGTGTGCTTACTG
52403 A-TTGCACTATGTGTGCTTACTG
1 ATTTGCACTATGTGTGCTTACTG
52425 TTTCCCCAGC
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.30
23 36 0.64
24 3 0.05
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (23 bp):
ATTTGCACTATGTGTGCTTACTG
Found at i:59060 original size:38 final size:38
Alignment explanation
Indices: 59010--59083 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
59000 ACGTTATTTC
*
59010 TAATAATAGAGAACTCTATGATTGCCTCTTTTCGTTGA
1 TAATAATAGAGAACTCAATGATTGCCTCTTTTCGTTGA
59048 TAATAATAGAGAACTCAATGATTGCCTCTTTTCGTT
1 TAATAATAGAGAACTCAATGATTGCCTCTTTTCGTT
59084 TATCAACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (38 bp):
TAATAATAGAGAACTCAATGATTGCCTCTTTTCGTTGA
Found at i:68158 original size:25 final size:25
Alignment explanation
Indices: 68130--68177 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
68120 CCTACTATTT
*
68130 CCCAACACTTATGTGCTTCTGTTTC
1 CCCAACACTTATGCGCTTCTGTTTC
*
68155 CCCACCACTTATGCGCTTCTGTT
1 CCCAACACTTATGCGCTTCTGTT
68178 AAGTACTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.15, C:0.35, G:0.12, T:0.38
Consensus pattern (25 bp):
CCCAACACTTATGCGCTTCTGTTTC
Found at i:69050 original size:19 final size:19
Alignment explanation
Indices: 69028--69074 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
69018 CTACATCAAC
*
69028 AAATATTTAAAAATTAA-AA
1 AAAT-TTTAAAAATAAATAA
*
69047 AAATCTTAAAAATAAATAA
1 AAATTTTAAAAATAAATAA
69066 AAATTTTAA
1 AAATTTTAA
69075 TAATCACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTTTAAAAATAAATAA
Found at i:69057 original size:18 final size:19
Alignment explanation
Indices: 69034--69074 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
69024 CAACAAATAT
*
69034 TTAAAAATTAA-AAAAATC
1 TTAAAAATAAATAAAAATC
*
69052 TTAAAAATAAATAAAAATT
1 TTAAAAATAAATAAAAATC
69071 TTAA
1 TTAA
69075 TAATCACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAATAAATAAAAATC
Found at i:69678 original size:9 final size:9
Alignment explanation
Indices: 69640--69679 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
69630 TTTTGGATGG
69640 TTTTAATAAT
1 TTTTAAT-AT
69650 TTTT-AT-T
1 TTTTAATAT
69657 TTTT-ATAT
1 TTTTAATAT
69665 TTTTAATAT
1 TTTTAATAT
69674 TTTTAA
1 TTTTAA
69680 ATAATCCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.25
8 5 0.18
9 12 0.43
10 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTAATAT
Found at i:71671 original size:29 final size:29
Alignment explanation
Indices: 71637--71697 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
71627 AAATGAGACT
*
71637 TTTTGGA-TACTCGGGGGGTAAAATGGTAA
1 TTTTGGACT-CTCGAGGGGTAAAATGGTAA
71666 TTTTGGACTCTCGAGGGGTAAAATGGTAA
1 TTTTGGACTCTCGAGGGGTAAAATGGTAA
71695 TTT
1 TTT
71698 AGGAAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.31, T:0.34
Consensus pattern (29 bp):
TTTTGGACTCTCGAGGGGTAAAATGGTAA
Found at i:71741 original size:59 final size:58
Alignment explanation
Indices: 71678--71853 Score: 173
Period size: 59 Copynumber: 3.0 Consensus size: 58
71668 TTGGACTCTC
*
71678 GAGGGGT-AAAATGGTAATTTAGGAAAATTTGGGGTTAAAAATGGAACTTTTGGAAGTTT
1 GAGGGGTAAAAAT-GTAATTTA-GAAAATTTGGGGTCAAAAATGGAACTTTTGGAAGTTT
** * *
71737 GA-GGGTAAAAATGTAATTTTTAGAAGTTTTGGGGTCAAGAATGGAATTTTTGGAAGTTT
1 GAGGGGTAAAAATGTAA--TTTAGAAAATTTGGGGTCAAAAATGGAACTTTTGGAAGTTT
* * *
71796 G-GGGGTAAAAATGTAATTTTTAG-AAGTTTCAGGGTC-AAAATGGAATTTTTGGACAGTT
1 GAGGGGTAAAAATGTAA--TTTAGAAAATTT-GGGGTCAAAAATGGAACTTTTGGA-AGTT
71854 CAGGGACCTT
Statistics
Matches: 102, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
58 28 0.27
59 70 0.69
60 4 0.04
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.35
Consensus pattern (58 bp):
GAGGGGTAAAAATGTAATTTAGAAAATTTGGGGTCAAAAATGGAACTTTTGGAAGTTT
Found at i:71757 original size:29 final size:28
Alignment explanation
Indices: 71680--71853 Score: 163
Period size: 29 Copynumber: 6.0 Consensus size: 28
71670 GGACTCTCGA
* *
71680 GGGGT-AAAATGGTAA-TTTAGGAAAATTT
1 GGGGTAAAAATGG-AATTTTTGG-AAGTTT
*
71708 GGGGTTAAAAATGGAACTTTTGGAAGTTT
1 GGGG-TAAAAATGGAATTTTTGGAAGTTT
* *
71737 GAGGGTAAAAATGTAATTTTTAGAAGTTTT
1 G-GGGTAAAAATGGAATTTTTGGAAG-TTT
*
71767 GGGGTCAAGAATGGAATTTTTGGAAGTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTT
* *
71796 GGGGGTAAAAATGTAATTTTTAGAAGTTT
1 -GGGGTAAAAATGGAATTTTTGGAAGTTT
* *
71825 CAGGGTCAAAATGGAATTTTTGGACAGTT
1 -GGGGTAAAAATGGAATTTTTGGA-AGTT
71854 CAGGGACCTT
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.03
29 73 0.60
30 45 0.37
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTT
Found at i:72921 original size:15 final size:16
Alignment explanation
Indices: 72903--72938 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
72893 TACTATTAAC
*
72903 ATTATTACTAATA-TT
1 ATTATTAATAATATTT
72918 ATTATTAATAATATTT
1 ATTATTAATAATATTT
72934 ATTAT
1 ATTAT
72939 ATTATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATTAATAATATTT
Found at i:72941 original size:21 final size:20
Alignment explanation
Indices: 72917--72961 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
72907 TTACTAATAT
* *
72917 TATTATTAATAATATTTATTA
1 TATTATAAATAA-AATTATTA
72938 TATTATAAATAAAATTATTA
1 TATTATAAATAAAATTATTA
72958 -ATTA
1 TATTA
72962 CTATTAATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 7 0.32
21 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAAATAAAATTATTA
Found at i:78069 original size:36 final size:36
Alignment explanation
Indices: 78016--78089 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 36
78006 GGTGAGTAAT
78016 AAAACATAACAATAATGTAA-AATATGTAATATGTATA
1 AAAACATAACAATAATGTAATAAT-T-TAATATGTATA
*
78053 AAAACATAATAA-AATGTAATTAATTTAATATGTATA
1 AAAACATAACAATAATGTAA-TAATTTAATATGTATA
78089 A
1 A
78090 TAGAAATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 19 0.56
37 12 0.35
38 3 0.09
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (36 bp):
AAAACATAACAATAATGTAATAATTTAATATGTATA
Found at i:80423 original size:28 final size:28
Alignment explanation
Indices: 80376--80429 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
80366 TATTTGCACA
80376 AAAATTTTAAACTGGTTC-TTAAAATTT
1 AAAATTTTAAACTGGTTCTTTAAAATTT
*
80403 AAAATATTTAAATTGAG-TCTTTAAAAT
1 AAAAT-TTTAAACTG-GTTCTTTAAAAT
80430 ATTATTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.22
28 10 0.43
29 8 0.35
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (28 bp):
AAAATTTTAAACTGGTTCTTTAAAATTT
Found at i:83419 original size:20 final size:20
Alignment explanation
Indices: 83391--83443 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
83381 CCACCCTAGG
* * *
83391 ACTTCTACCGGTAGAACTTC
1 ACTTTTACCGATACAACTTC
*
83411 ACTTTTACCTATACAACTTC
1 ACTTTTACCGATACAACTTC
*
83431 AATTTTACCGATA
1 ACTTTTACCGATA
83444 TAAGTATGCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.08, T:0.36
Consensus pattern (20 bp):
ACTTTTACCGATACAACTTC
Found at i:84851 original size:61 final size:61
Alignment explanation
Indices: 84778--84896 Score: 150
Period size: 61 Copynumber: 2.0 Consensus size: 61
84768 CTCAATTTGT
* ** * *
84778 ATTATATATTGTAATTATTTTA-ATTTATTTTTACGTAATTAATATTTAGATACTATTTACA
1 ATTATATATTGTAATCA-TTTAGATTTATTTTTACCAAAGTAATATTTAAATACTATTTACA
* * *
84839 ATTATATTTTGTAATCATTTAGTTTTATTTTTGCCAAAGTAATATTTAAATACTATTT
1 ATTATATATTGTAATCATTTAGATTTATTTTTACCAAAGTAATATTTAAATACTATTT
84897 TATGTTAGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 4 0.08
61 45 0.92
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (61 bp):
ATTATATATTGTAATCATTTAGATTTATTTTTACCAAAGTAATATTTAAATACTATTTACA
Found at i:85675 original size:17 final size:17
Alignment explanation
Indices: 85652--85761 Score: 123
Period size: 17 Copynumber: 6.4 Consensus size: 17
85642 CAAGCCCCCC
85652 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
* *
85670 -TTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
85687 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
85704 TTTAAATGTATTTTAAA
1 TTTAAATTTATTTTAAA
*
85721 TTTAAATTTATTATCAAA
1 TTTAAATTTATT-TTAAA
* * *
85739 TTTAAAATTATTATGAA
1 TTTAAATTTATTTTAAA
85756 TTTAAA
1 TTTAAA
85762 ATAAATAAAG
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
17 50 0.64
18 28 0.36
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:85691 original size:35 final size:34
Alignment explanation
Indices: 85652--85744 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 34
85642 CAAGCCCCCC
* *
85652 TTTAAATTTATTTTAAGA-TTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAA-ATTTAAATGTATTT-AAAA
*
85687 TTTAAATTTATTTTAAATTTAAATGTATTTTAAA
1 TTTAAATTTATTTTAAATTTAAATGTATTTAAAA
*
85721 TTTAAATTTATTATCAAATTTAAA
1 TTTAAATTTATT-TTAAATTTAAA
85745 ATTATTATGA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
34 16 0.31
35 36 0.69
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATGTATTTAAAA
Found at i:85695 original size:6 final size:6
Alignment explanation
Indices: 85684--85730 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
85674 ATTTGTTTAA
* * *
85684 AAATTT AAATTT -ATTTT AAATTT AAATGT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
85730 A
1 A
85731 TTATCAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 26 0.79
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:85716 original size:52 final size:52
Alignment explanation
Indices: 85652--85761 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 52
85642 CAAGCCCCCC
* * * *
85652 TTTAAATTTATTTTAAGA-TTAAATTTGTT-TAAAAATTTAAATTTATTTTAAA
1 TTTAAATGTATTTTAA-ATTTAAATTTATTAT-AAAATTTAAAATTATTATAAA
* *
85704 TTTAAATGTATTTTAAATTTAAATTTATTATCAAATTTAAAATTATTATGAA
1 TTTAAATGTATTTTAAATTTAAATTTATTATAAAATTTAAAATTATTATAAA
85756 TTTAAA
1 TTTAAA
85762 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 1 0.02
52 48 0.96
53 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (52 bp):
TTTAAATGTATTTTAAATTTAAATTTATTATAAAATTTAAAATTATTATAAA
Found at i:86513 original size:21 final size:19
Alignment explanation
Indices: 86470--86521 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
86460 AAATATTTAT
86470 ATAATAATAATTAACAATA
1 ATAATAATAATTAACAATA
* *
86489 ATAATAATAATACTGACACTA
1 ATAATAATAAT--TAACAATA
86510 ATAATAATAATT
1 ATAATAATAATT
86522 TTTAATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAATAATAATTAACAATA
Found at i:86779 original size:22 final size:23
Alignment explanation
Indices: 86753--86796 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
86743 AAAGTTAAAT
86753 AAAACGGTTTTCAA-AAAAAGGG
1 AAAACGGTTTTCAACAAAAAGGG
* *
86775 AAAACGTTTTTTAACAAAAAGG
1 AAAACGGTTTTCAACAAAAAGG
86797 AGTACTGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (23 bp):
AAAACGGTTTTCAACAAAAAGGG
Found at i:87635 original size:30 final size:29
Alignment explanation
Indices: 87591--87798 Score: 140
Period size: 30 Copynumber: 7.1 Consensus size: 29
87581 TTAAATTGTT
*
87591 CAAAAATCCATTTTTAAACCCGAAACTTC
1 CAAAAATTCATTTTTAAACCCGAAACTTC
** *
87620 CAAAAATATCATTTTTACCCCCG-AAC-TA
1 CAAAAAT-TCATTTTTAAACCCGAAACTTC
* * *
87648 CAAAAATCCCATTTTTAACCCCGAAACTTT
1 CAAAAAT-TCATTTTTAAACCCGAAACTTC
* * *
87678 CAAAAATTCCAATTTTAACCCCAAAACTTC
1 CAAAAATT-CATTTTTAAACCCGAAACTTC
*
87708 CAAAAATTTCATTTTT--ACCTCTG-AACTAC
1 CAAAAA-TTCATTTTTAAACC-C-GAAACTTC
* *
87737 CAAAAATCTCATTTTT-AACCTCGAAGCTTT
1 CAAAAAT-TCATTTTTAAACC-CGAAACTTC
* * * *
87767 CAAAAATTCCAATTTTAACCCCAAAAATTC
1 CAAAAATT-CATTTTTAAACCCGAAACTTC
87797 CA
1 CA
87799 TTTTTACCCT
Statistics
Matches: 142, Mismatches: 25, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
28 24 0.17
29 35 0.25
30 78 0.55
31 5 0.04
ACGTcount: A:0.39, C:0.27, G:0.03, T:0.30
Consensus pattern (29 bp):
CAAAAATTCATTTTTAAACCCGAAACTTC
Found at i:87741 original size:59 final size:56
Alignment explanation
Indices: 87591--87978 Score: 199
Period size: 59 Copynumber: 6.8 Consensus size: 56
87581 TTAAATTGTT
* * * *
87591 CAAAAA-TCCATTTTTAAACCC-GAAACTTCCAAAAATAT-CATTTTTACCCCCGAAC-TA
1 CAAAAATTCCATTTTT--ACCCTG-AACTACCAAAAAT-TCCA-TTTTAACCCCAAACTTC
* * **
87648 CAAAAATCCCATTTTTAACCCCGAAACTTTCAAAAATTCCAATTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCTG-AACTACCAAAAATTCC-ATTTTAACCCC-AAACTTC
* * * *
87708 CAAAAATTTCATTTTTACCTCTGAACTACCAAAAA-TCTCATTTTTAACCTCGAAGCTTT
1 CAAAAATTCCATTTTTACC-CTGAACTACCAAAAATTC-CA-TTTTAACC-CCAAACTTC
* * * *
87767 CAAAAATTCCA-ATTT----T-AAC-CCCAAAAATTCCATTTTTACCCTCAAACTAC
1 CAAAAATTCCATTTTTACCCTGAACTACCAAAAATTCCATTTTAACCC-CAAACTTC
* ** * * *
87817 CAAAAATCCCATTTTTAACCCTGAAGCTTTCAAAAATTCCATTTTTACCCTCGAACCTC
1 CAAAAATTCCATTTTT-ACCCTGAA-CTACCAAAAATTCCATTTTAACCC-CAAACTTC
* ** * *
87876 CAAAAATCCCATTTTTGACCCAAAAACTACCAAAAATCCCATTTTAACCCCAAAACTTT
1 CAAAAATTCCATTTTT-ACCC-TGAACTACCAAAAATTCCATTTTAACCCC-AAACTTC
* * * * *
87935 CAAAAGGTT-CATTTTTACCCCCGAACTTCTAAAAATCCCATTTT
1 CAAAA-ATTCCATTTTTA-CCCTGAACTACCAAAAATTCCATTTT
87979 TGACCCTGAA
Statistics
Matches: 262, Mismatches: 44, Indels: 49
0.74 0.12 0.14
Matches are distributed among these distances:
49 1 0.00
50 21 0.08
51 12 0.05
52 5 0.02
53 1 0.00
56 1 0.00
57 14 0.05
58 60 0.23
59 126 0.48
60 21 0.08
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (56 bp):
CAAAAATTCCATTTTTACCCTGAACTACCAAAAATTCCATTTTAACCCCAAACTTC
Found at i:87801 original size:20 final size:22
Alignment explanation
Indices: 87766--87812 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
87756 CTCGAAGCTT
87766 TCAAAAATTCCAATTTTAACCC
1 TCAAAAATTCCAATTTTAACCC
*
87788 -CAAAAATTCC-ATTTTTACCC
1 TCAAAAATTCCAATTTTAACCC
87808 TCAAA
1 TCAAA
87813 CTACCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (22 bp):
TCAAAAATTCCAATTTTAACCC
Found at i:87801 original size:51 final size:50
Alignment explanation
Indices: 87736--87837 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 50
87726 CTCTGAACTA
* ** *
87736 CCAAAAATCTCATTTTTAACCTCGAAGCTTTCAAAAATTCCAATTTTAACC
1 CCAAAAATCTCATTTTTAACCTC-AAACTACCAAAAATCCCAATTTTAACC
* *
87787 CCAAAAAT-TCCATTTTTACCCTCAAACTACCAAAAATCCCATTTTTAACC
1 CCAAAAATCT-CATTTTTAACCTCAAACTACCAAAAATCCCAATTTTAACC
87837 C
1 C
87838 TGAAGCTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 24 0.55
51 20 0.45
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.31
Consensus pattern (50 bp):
CCAAAAATCTCATTTTTAACCTCAAACTACCAAAAATCCCAATTTTAACC
Found at i:87829 original size:29 final size:29
Alignment explanation
Indices: 87787--88000 Score: 180
Period size: 29 Copynumber: 7.3 Consensus size: 29
87777 AATTTTAACC
* *
87787 CCAAAAATTCCATTTTTACCCTCAAACTA
1 CCAAAAATCCCATTTTTACCCTCAAACTT
* *
87816 CCAAAAATCCCATTTTTAACCCTGAAGCTT
1 CCAAAAATCCCATTTTT-ACCCTCAAACTT
* * * *
87846 TCAAAAATTCCATTTTTACCCTCGAACCT
1 CCAAAAATCCCATTTTTACCCTCAAACTT
** *
87875 CCAAAAATCCCATTTTTGACCCAAAAACTA
1 CCAAAAATCCCATTTTT-ACCCTCAAACTT
*
87905 CCAAAAATCCCATTTTAACCC-CAAAACTT
1 CCAAAAATCCCATTTTTACCCTC-AAACTT
* * * * *
87934 TCAAAAGGT-TCATTTTTACCCCCGAACTT
1 CCAAAA-ATCCCATTTTTACCCTCAAACTT
* * **
87963 CTAAAAATCCCATTTTTGACCCTGAATTTT
1 CCAAAAATCCCATTTTT-ACCCTCAAACTT
87993 CCAAAAAT
1 CCAAAAAT
88001 TACCGTTTCA
Statistics
Matches: 143, Mismatches: 35, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
28 1 0.01
29 79 0.55
30 63 0.44
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.30
Consensus pattern (29 bp):
CCAAAAATCCCATTTTTACCCTCAAACTT
Found at i:88027 original size:88 final size:87
Alignment explanation
Indices: 87783--87984 Score: 203
Period size: 88 Copynumber: 2.3 Consensus size: 87
87773 TTCCAATTTT
* ** * * ** *
87783 AACC-CCAAAAATTCCATTTTT-ACCCTCAAACTACCAAAAATCCCATTTTTAACCCTGAAGCTT
1 AACCTCCAAAAATCCCATTTTTGACCCAAAAACTACCAAAAATACCA-TTTCAACCCCAAAAC-T
* * *
87846 TCAAAA-ATTCCATTTTTACCCTCG
64 CCAAAAGGTT-CATTTTTACCCCCG
* * *
87870 AACCTCCAAAAATCCCATTTTTGACCCAAAAACTACCAAAAATCCCATTTTAACCCCAAAACTTT
1 AACCTCCAAAAATCCCATTTTTGACCCAAAAACTACCAAAAATACCATTTCAACCCCAAAAC-TC
87935 CAAAAGGTTCATTTTTACCCCCG
65 CAAAAGGTTCATTTTTACCCCCG
* *
87958 AACTTCTAAAAATCCCATTTTTGACCC
1 AACCTCCAAAAATCCCATTTTTGACCC
87985 TGAATTTTCC
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
87 4 0.04
88 74 0.73
89 24 0.24
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (87 bp):
AACCTCCAAAAATCCCATTTTTGACCCAAAAACTACCAAAAATACCATTTCAACCCCAAAACTCC
AAAAGGTTCATTTTTACCCCCG
Found at i:88067 original size:29 final size:29
Alignment explanation
Indices: 88012--88068 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
88002 ACCGTTTCAT
*
88012 CCCCGAGAATCCAAAATTATCACTTTTGC
1 CCCCGAGAATCCAAAAGTATCACTTTTGC
*
88041 CCCCGAGAATCCGAAAAGTCTCA-TTTTG
1 CCCCGAGAATCC-AAAAGTATCACTTTTG
88069 AACTCCGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
CCCCGAGAATCCAAAAGTATCACTTTTGC
Found at i:89978 original size:8 final size:8
Alignment explanation
Indices: 89965--89993 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
89955 TAAATGGTAA
89965 ACAAAAAT
1 ACAAAAAT
89973 ACAAAAAT
1 ACAAAAAT
89981 AC-AAAAT
1 ACAAAAAT
89988 ACAAAA
1 ACAAAA
89994 TAACACGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.76, C:0.14, G:0.00, T:0.10
Consensus pattern (8 bp):
ACAAAAAT
Found at i:90107 original size:27 final size:28
Alignment explanation
Indices: 90077--90136 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
90067 AAAATGAGAC
*
90077 TTTGG-ATACCCG-GGGTAAAATGATAAT
1 TTTGGAAT-CCCGAGGGCAAAATGATAAT
* *
90104 TTTGGAATCTCGAGGGCAAAATGGTAAT
1 TTTGGAATCCCGAGGGCAAAATGATAAT
90132 TTTGG
1 TTTGG
90137 GAAAGTTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (28 bp):
TTTGGAATCCCGAGGGCAAAATGATAAT
Found at i:90362 original size:59 final size:58
Alignment explanation
Indices: 90239--90401 Score: 213
Period size: 58 Copynumber: 2.8 Consensus size: 58
90229 CATCTAAGGG
* * * *
90239 TAAAATGGTAATTTTTGAAAGCTTC-AGCGTAAAAAATGGAATTTTTGGAAGTTCATGGA
1 TAAAATGG-AATTTTGGAAAGTTTCGAG-GTTAAAAATGGAATTTTTGGAAATTCATGGA
90298 TAAAATGGAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAATTCATGGA
1 TAAAATGGAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAATTCATGGA
* * * *
90356 TAAAAATGGAATTTCGAAAAGTTT-GTGGGTAAAAATGGAATTTTTG
1 T-AAAATGGAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTG
90402 AAAGTTCGGG
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
58 64 0.68
59 30 0.32
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (58 bp):
TAAAATGGAATTTTGGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGAAATTCATGGA
Found at i:90414 original size:29 final size:29
Alignment explanation
Indices: 90236--90419 Score: 153
Period size: 29 Copynumber: 6.3 Consensus size: 29
90226 GGACATCTAA
*
90236 GGGT-AAAATGGTAATTTTTGAAAGCTTC-A
1 GGGTAAAAATGG-AATTTTTGAAAG-TTCGT
* * *
90265 GCGTAAAAAATGGAATTTTTGGAAGTTCAT
1 GGGT-AAAAATGGAATTTTTGAAAGTTCGT
* * *
90295 GGAT-AAAATGGAATTTTGGAAAGTTTCGA
1 GGGTAAAAATGGAATTTTTGAAAG-TTCGT
* *
90324 GGTTAAAAATGGAATTTTTGGAAA-TTCAT
1 GGGTAAAAATGGAATTTTT-GAAAGTTCGT
* * *
90353 GGATAAAAATGGAA-TTTCGAAAAGTTTGT
1 GGGTAAAAATGGAATTTTTG-AAAGTTCGT
*
90382 GGGTAAAAATGGAATTTTTGAAAGTTCGG
1 GGGTAAAAATGGAATTTTTGAAAGTTCGT
*
90411 GGGTCAAAA
1 GGGTAAAAA
90420 CATAATTTTT
Statistics
Matches: 124, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 23 0.19
29 59 0.48
30 30 0.24
31 11 0.09
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGAAAGTTCGT
Found at i:91509 original size:16 final size:15
Alignment explanation
Indices: 91485--91532 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
91475 TCTTTTTATT
*
91485 TATTTATATTATTTAA
1 TATTAATATTA-TTAA
*
91501 TATTAATATTA--AT
1 TATTAATATTATTAA
91514 TATTAATATTATTAA
1 TATTAATATTATTAA
91529 TATT
1 TATT
91533 TTTCATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 12 0.44
15 5 0.19
16 10 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTAATATTATTAA
Found at i:92245 original size:30 final size:30
Alignment explanation
Indices: 92204--92275 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
92194 TCTTTTGAGT
92204 TAATT-GGTTTGGGCCAATTTGGGCCATTG
1 TAATTGGGTTTGGGCCAATTTGGGCCATTG
92233 TAATTGGGTTTGGGCCAATTTGGGCCATTG
1 TAATTGGGTTTGGGCCAATTTGGGCCATTG
92263 TAATTGGGTTTGG
1 TAATTGGGTTTGG
92276 TGCTTAGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 5 0.12
30 37 0.88
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.39
Consensus pattern (30 bp):
TAATTGGGTTTGGGCCAATTTGGGCCATTG
Found at i:92395 original size:11 final size:11
Alignment explanation
Indices: 92379--92421 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
92369 AAATTATTTC
92379 AAATTTAAACT
1 AAATTTAAACT
*
92390 AAATTTAAATTT
1 AAATTTAAA-CT
*
92402 AAATTTAAAGT
1 AAATTTAAACT
92413 AAATTTAAA
1 AAATTTAAA
92422 TTTAGAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AAATTTAAACT
Found at i:92399 original size:17 final size:18
Alignment explanation
Indices: 92395--92439 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
92385 AAACTAAATT
*
92395 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
92412 TAAATTTAAATTTAGAAA
1 TAAATTTAAATTTAGAAA
92430 TAAATTTAAA
1 TAAATTTAAA
92440 ATAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:92400 original size:6 final size:6
Alignment explanation
Indices: 92343--92439 Score: 69
Period size: 6 Copynumber: 16.3 Consensus size: 6
92333 ATGGACTTTG
* * * *
92343 AATTTA ATTTTA AAGTTTA AGTTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA A-ATTTA AATTTA AATTT-A AATTTA AATTTA
* *
92391 AATTTA AATTTA AATTTA AA-GTA AATTTA AATTTA GAA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA
92438 AA
1 AA
92440 ATAATTTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
4 3 0.04
5 10 0.14
6 41 0.59
7 16 0.23
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:92409 original size:23 final size:23
Alignment explanation
Indices: 92374--92425 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
92364 TTTTAAAATT
92374 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATTTAAACTAAATTTAA
*
92398 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATTTAAACTAAATTTAA
92421 ATTTA
1 ATTTA
92426 GAAATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTTAAATTTAAACTAAATTTAA
Found at i:92410 original size:18 final size:18
Alignment explanation
Indices: 92343--92439 Score: 69
Period size: 17 Copynumber: 5.4 Consensus size: 18
92333 ATGGACTTTG
*
92343 AATTTAATTTTAAAGTTTA
1 AATTTAAATTTAAA-TTTA
* *
92362 AGTTTTAAAATT--ATTTCA
1 A-ATTTAAATTTAAATTT-A
*
92380 AATTTAAA-CTAAATTTA
1 AATTTAAATTTAAATTTA
*
92397 AATTTAAATTTAAA-GTA
1 AATTTAAATTTAAATTTA
*
92414 AATTTAAATTTAGAA-ATA
1 AATTTAAATTTA-AATTTA
92432 AATTTAAA
1 AATTTAAA
92440 ATAATTTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
16 1 0.02
17 32 0.50
18 23 0.36
19 1 0.02
20 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
AATTTAAATTTAAATTTA
Found at i:92433 original size:23 final size:23
Alignment explanation
Indices: 92374--92433 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
92364 TTTTAAAATT
*
92374 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATATAAACTAAATTTAA
* *
92398 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATATAAACTAAATTTAA
92421 ATTTAGAA-ATAAA
1 ATTTA-AATATAAA
92434 TTTAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 27 0.82
24 6 0.18
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (23 bp):
ATTTAAATATAAACTAAATTTAA
Found at i:92447 original size:10 final size:11
Alignment explanation
Indices: 92379--92449 Score: 55
Period size: 12 Copynumber: 6.8 Consensus size: 11
92369 AAATTATTTC
*
92379 AAATTTAAACT
1 AAATTTAAAAT
*
92390 AAATTTAAATTT
1 AAATTTAAA-AT
*
92402 AAATTTAAAGT
1 AAATTTAAAAT
92413 AAA-TT----T
1 AAATTTAAAAT
92419 AAATTTAGAAAT
1 AAATTTA-AAAT
92431 AAATTTAAAAT
1 AAATTTAAAAT
92442 -AATTTAAA
1 AAATTTAAA
92450 CTCAAAAGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
10 10 0.20
11 17 0.33
12 18 0.35
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:94863 original size:26 final size:24
Alignment explanation
Indices: 94826--94873 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
94816 AAGTGTTGAC
94826 AAAAAATAAATTAAATTAAAATTTT
1 AAAAAATAAATTAAA-TAAAATTTT
*
94851 AAAACAATTAATTAAATAAAATT
1 AAAA-AATAAATTAAATAAAATT
94874 CTATTTCCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAAATAAATTAAATAAAATTTT
Found at i:95610 original size:7 final size:7
Alignment explanation
Indices: 95598--95631 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
95588 TTAATAATAA
95598 AAATATG
1 AAATATG
95605 AAATATG
1 AAATATG
95612 AAATATG
1 AAATATG
95619 AAATATG
1 AAATATG
95626 AAATAT
1 AAATAT
95632 ATAAACTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (7 bp):
AAATATG
Found at i:95791 original size:23 final size:21
Alignment explanation
Indices: 95748--95796 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
95738 CTGTTTGGAG
95748 TAAAATTAAAATTTGAAAATT
1 TAAAATTAAAATTTGAAAATT
*
95769 ATAAAGATT-AAATTTGACCAATT
1 -TAAA-ATTAAAATTTGA-AAATT
95792 TAAAA
1 TAAAA
95797 AGTATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (21 bp):
TAAAATTAAAATTTGAAAATT
Found at i:96820 original size:17 final size:19
Alignment explanation
Indices: 96800--96836 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
96790 AGAAAAAATT
96800 TAAATAAAT-AT-AATTTA
1 TAAATAAATAATCAATTTA
96817 TAAATAAATAATCAATTTA
1 TAAATAAATAATCAATTTA
96836 T
1 T
96837 TATATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 2 0.11
19 7 0.39
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATAAATAATCAATTTA
Found at i:98059 original size:19 final size:20
Alignment explanation
Indices: 98035--98083 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
98025 TTTAAATTAG
98035 TTTAAATTTAT-TTTTTAAA
1 TTTAAATTTATCTTTTTAAA
98054 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTATCTTTTTAAA
98074 TTTAAATTTA
1 TTTAAATTTA
98084 ATCAAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAAATTTATCTTTTTAAA
Found at i:99987 original size:29 final size:29
Alignment explanation
Indices: 99946--100299 Score: 314
Period size: 29 Copynumber: 12.1 Consensus size: 29
99936 GAGGTCCCTA
* *
99946 AACTGTCCGAAAATTCCATTTTTACCCTTG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
*
99976 AACTTCCAAAAATTCCATTTTTACCCTTG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
100005 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
100034 AAACTATCTAAAAATTCCATTTTTACCCTCG
1 -AACT-TCCAAAAATTCCATTTTTACCCTCG
* * *
100065 AACTTCTAAAAATTTCATTTTAACCC-CG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
100093 AAACTTCCAAAAATTCCATTTTTACCTTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* **
100123 AACTTCAAAAAATTCCA-TTTTACCCCCTAA
1 AACTTCCAAAAATTCCATTTTTA--CCCTCG
* *
100153 AACTTCCAAAAATTCCATTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* *
100182 AACTTCTAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* ** *
100211 AACCTCC-AAAATCTCCATTCTCGA-CCTCAA
1 AACTTCCAAAAAT-TCCATT-TTTACCCTC-G
*
100241 AAC-TCTC-AAAATTACC-TTGTTACCCTCG
1 AACTTC-CAAAAATT-CCATTTTTACCCTCG
* *
100269 AA-TGTCTAAAAATTCCATTTTTAACCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
100298 AA
1 AA
100300 TTTTTCCAAA
Statistics
Matches: 271, Mismatches: 32, Indels: 43
0.78 0.09 0.12
Matches are distributed among these distances:
28 17 0.06
29 179 0.66
30 49 0.18
31 26 0.10
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:100098 original size:89 final size:87
Alignment explanation
Indices: 99955--100206 Score: 330
Period size: 89 Copynumber: 2.9 Consensus size: 87
99945 AAACTGTCCG
* * *
99955 AAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTACCCTTG-AACTTCCAAAAATT
1 AAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTAACCC-CGAAACTTCCAAAAATT
*
100019 CCATTTTTGACC-TCGAAACTATCTA
65 CCATTTTT-ACCTTCG-AACT-TCAA
* * *
100044 AAAATTCCATTTTTACCCTCGAACTTCTAAAAATTTCATTTTAACCCCGAAACTTCCAAAAATTC
1 AAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAATTC
100109 CATTTTTACCTTCGAACTTCAA
66 CATTTTTACCTTCGAACTTCAA
* * * *
100131 AAAATTCCA-TTTTACCCCCTAAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCTAAAAAT
1 AAAATTCCATTTTTA--CCCTAGAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAAT
100195 TCCATTTTTACC
64 TCCATTTTTACC
100207 CCCGAACCTC
Statistics
Matches: 146, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
86 5 0.03
87 12 0.08
88 61 0.42
89 68 0.47
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (87 bp):
AAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAATTC
CATTTTTACCTTCGAACTTCAA
Found at i:100243 original size:88 final size:87
Alignment explanation
Indices: 99976--100244 Score: 258
Period size: 88 Copynumber: 3.0 Consensus size: 87
99966 TTTACCCTTG
* ***
99976 AACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTA
1 AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCTCG-AAC-A
* ** *
100040 TCTAAAAATTCCATTTTTACCCTC-G
63 TCAAAAAATTCCATTTCCA-CCTCAA
* * * * *
100065 AACTTCTAAAAATTTCATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCTTCGAACTTCA
1 AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACATCA
*
100130 AAAAATTCCATTTTACCCCCT-AA
66 AAAAATTCCA-TTT-CCACCTCAA
* * * *
100153 AACTTCCAAAAATTCCATTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACCTC-
1 AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACATCA
* *
100217 CAAAATCTCCATTCTCGACCTCAA
66 AAAAAT-TCCATT-TCCACCTCAA
100241 AACT
1 AACT
100245 CTCAAAATTA
Statistics
Matches: 149, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
87 23 0.15
88 77 0.52
89 49 0.33
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACATCA
AAAAATTCCATTTCCACCTCAA
Found at i:100251 original size:88 final size:86
Alignment explanation
Indices: 99976--100291 Score: 236
Period size: 88 Copynumber: 3.6 Consensus size: 86
99966 TTTACCCTTG
** * * *
99976 AACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTA
1 AACTTCCAAAAATTCCA-TTTTACCC-CAAACTTCTAAAAATTCCATTTTT-ACCCCCG-AAC-C
* * **
100040 TCTAAAAATTCCATTTTTA-C-CCTCG
61 TCAAAAAATTCCA-TTCTACCACCTAA
* * * ** *
100065 AACTTCTAAAAATTTCATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCTTCGAACTTCA
1 AACTTCCAAAAATTCCATTTT-ACCCC-AAACTTCTAAAAATTCCATTTTTACCCCCGAACCTCA
* *
100130 AAAAATTCCATTTTACCCCCTAA
64 AAAAATTCCATTCTACCACCTAA
100153 AACTTCCAAAAATTCCATTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACCTC-
1 AACTTCCAAAAATTCCATTTT-ACCCC-AAACTTCTAAAAATTCCATTTTTACCCCCGAACCTCA
* *
100217 CAAAATCTCCATTCT-CGACCTCAA
64 AAAAAT-TCCATTCTACCACCT-AA
*
100241 AAC-TCTC-AAAATTACC-TTGTTACCCTCGAA-TGTCTAAAAATTCCATTTTTA
1 AACTTC-CAAAAATT-CCATT-TTACCC-CAAACT-TCTAAAAATTCCATTTTTA
100292 ACCTCGAATT
Statistics
Matches: 193, Mismatches: 22, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
86 6 0.03
87 57 0.30
88 85 0.44
89 45 0.23
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (86 bp):
AACTTCCAAAAATTCCATTTTACCCCAAACTTCTAAAAATTCCATTTTTACCCCCGAACCTCAAA
AAATTCCATTCTACCACCTAA
Found at i:102146 original size:19 final size:20
Alignment explanation
Indices: 102122--102170 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
102112 TTTAAATTAG
102122 TTTAAATTTAT-TTTTTAAA
1 TTTAAATTTATCTTTTTAAA
102141 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTATCTTTTTAAA
102161 TTTAAATTTA
1 TTTAAATTTA
102171 ATCAAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAAATTTATCTTTTTAAA
Found at i:104074 original size:29 final size:29
Alignment explanation
Indices: 104033--104386 Score: 314
Period size: 29 Copynumber: 12.1 Consensus size: 29
104023 GAGGTCCCTA
* *
104033 AACTGTCCGAAAATTCCATTTTTACCCTTG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
*
104063 AACTTCCAAAAATTCCATTTTTACCCTTG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
104092 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
*
104121 AAACTATCTAAAAATTCCATTTTTACCCTCG
1 -AACT-TCCAAAAATTCCATTTTTACCCTCG
* * *
104152 AACTTCTAAAAATTTCATTTTAACCC-CG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
104180 AAACTTCCAAAAATTCCATTTTTACCTTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* **
104210 AACTTCAAAAAATTCCA-TTTTACCCCCTAA
1 AACTTCCAAAAATTCCATTTTTA--CCCTCG
* *
104240 AACTTCCAAAAATTCCATTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTTACCCTC-G
* *
104269 AACTTCTAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* ** *
104298 AACCTCC-AAAATCTCCATTCTCGA-CCTCAA
1 AACTTCCAAAAAT-TCCATT-TTTACCCTC-G
*
104328 AAC-TCTC-AAAATTACC-TTGTTACCCTCG
1 AACTTC-CAAAAATT-CCATTTTTACCCTCG
* *
104356 AA-TGTCTAAAAATTCCATTTTTAACCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
104385 AA
1 AA
104387 TTTTTCCAAA
Statistics
Matches: 271, Mismatches: 32, Indels: 43
0.78 0.09 0.12
Matches are distributed among these distances:
28 17 0.06
29 179 0.66
30 49 0.18
31 26 0.10
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:104185 original size:89 final size:87
Alignment explanation
Indices: 104042--104293 Score: 330
Period size: 89 Copynumber: 2.9 Consensus size: 87
104032 AAACTGTCCG
* * *
104042 AAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTACCCTTG-AACTTCCAAAAATT
1 AAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTAACCC-CGAAACTTCCAAAAATT
*
104106 CCATTTTTGACC-TCGAAACTATCTA
65 CCATTTTT-ACCTTCG-AACT-TCAA
* * *
104131 AAAATTCCATTTTTACCCTCGAACTTCTAAAAATTTCATTTTAACCCCGAAACTTCCAAAAATTC
1 AAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAATTC
104196 CATTTTTACCTTCGAACTTCAA
66 CATTTTTACCTTCGAACTTCAA
* * * *
104218 AAAATTCCA-TTTTACCCCCTAAAACTTCCAAAAATTCCATTTTGACCCCAAAACTTCTAAAAAT
1 AAAATTCCATTTTTA--CCCTAGAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAAT
104282 TCCATTTTTACC
64 TCCATTTTTACC
104294 CCCGAACCTC
Statistics
Matches: 146, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
86 5 0.03
87 12 0.08
88 61 0.42
89 68 0.47
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (87 bp):
AAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCCATTTTAACCCCGAAACTTCCAAAAATTC
CATTTTTACCTTCGAACTTCAA
Found at i:104330 original size:88 final size:87
Alignment explanation
Indices: 104063--104331 Score: 258
Period size: 88 Copynumber: 3.0 Consensus size: 87
104053 TTTACCCTTG
* ***
104063 AACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTA
1 AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCTCG-AAC-A
* ** *
104127 TCTAAAAATTCCATTTTTACCCTC-G
63 TCAAAAAATTCCATTTCCA-CCTCAA
* * * * *
104152 AACTTCTAAAAATTTCATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCTTCGAACTTCA
1 AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACATCA
*
104217 AAAAATTCCATTTTACCCCCT-AA
66 AAAAATTCCA-TTT-CCACCTCAA
* * * *
104240 AACTTCCAAAAATTCCATTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACCTC-
1 AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACATCA
* *
104304 CAAAATCTCCATTCTCGACCTCAA
66 AAAAAT-TCCATT-TCCACCTCAA
104328 AACT
1 AACT
104332 CTCAAAATTA
Statistics
Matches: 149, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
87 23 0.15
88 77 0.52
89 49 0.33
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCGAACATCA
AAAAATTCCATTTCCACCTCAA
Found at i:104338 original size:88 final size:86
Alignment explanation
Indices: 104063--104378 Score: 236
Period size: 88 Copynumber: 3.6 Consensus size: 86
104053 TTTACCCTTG
** * * *
104063 AACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTA
1 AACTTCCAAAAATTCCA-TTTTACCC-CAAACTTCTAAAAATTCCATTTTT-ACCCCCG-AAC-C
* * **
104127 TCTAAAAATTCCATTTTTA-C-CCTCG
61 TCAAAAAATTCCA-TTCTACCACCTAA
* * * ** *
104152 AACTTCTAAAAATTTCATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCTTCGAACTTCA
1 AACTTCCAAAAATTCCATTTT-ACCCC-AAACTTCTAAAAATTCCATTTTTACCCCCGAACCTCA
* *
104217 AAAAATTCCATTTTACCCCCTAA
64 AAAAATTCCATTCTACCACCTAA
104240 AACTTCCAAAAATTCCATTTTGACCCCAAAACTTCTAAAAATTCCATTTTTACCCCCGAACCTC-
1 AACTTCCAAAAATTCCATTTT-ACCCC-AAACTTCTAAAAATTCCATTTTTACCCCCGAACCTCA
* *
104304 CAAAATCTCCATTCT-CGACCTCAA
64 AAAAAT-TCCATTCTACCACCT-AA
*
104328 AAC-TCTC-AAAATTACC-TTGTTACCCTCGAA-TGTCTAAAAATTCCATTTTTA
1 AACTTC-CAAAAATT-CCATT-TTACCC-CAAACT-TCTAAAAATTCCATTTTTA
104379 ACCTCGAATT
Statistics
Matches: 193, Mismatches: 22, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
86 6 0.03
87 57 0.30
88 85 0.44
89 45 0.23
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (86 bp):
AACTTCCAAAAATTCCATTTTACCCCAAACTTCTAAAAATTCCATTTTTACCCCCGAACCTCAAA
AAATTCCATTCTACCACCTAA
Found at i:106817 original size:13 final size:13
Alignment explanation
Indices: 106799--106823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106789 CCGTACCTGT
106799 CCCGTAAAACTCC
1 CCCGTAAAACTCC
106812 CCCGTAAAACTC
1 CCCGTAAAACTC
106824 AAGATCCACT
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:0.44, G:0.08, T:0.16
Consensus pattern (13 bp):
CCCGTAAAACTCC
Found at i:107310 original size:546 final size:546
Alignment explanation
Indices: 106272--107337 Score: 2024
Period size: 546 Copynumber: 2.0 Consensus size: 546
106262 GTATTTATTG
* *
106272 AAACTCAAGATCCACTCTTCATACCTGTCCCGTAAAACTCCCCCAGCAGTTGTATTTCCTGAAGT
1 AAACTCAAGATCCACTCTCCATACCTGTCCCGTAAAACTCCCCCAGCAGTTGCATTTCCTGAAGT
*
106337 CACTTGAATGGCACCGTCAGTGTTGAGGAAAAACCAGCCTTTTGACAAAGATGGAGCAAGAAGGG
66 CACTTGAATGGCACCGTCAGTGTTGAGGAAAAACCAGCCTTCTGACAAAGATGGAGCAAGAAGGG
*
106402 ACTCGAGATCTTTAACCACATTCTCTCTATTTGTCGAGGAGAAATGCTTAGCTCAACTTGCCGAT
131 ACTCGAGATCTTTAACCACATTCTCTCTATTTGTCGAGGAGAAATGCTTAGCCCAACTTGCCGAT
106467 GTCTTGATTATCTCTGTAGAGCTCCACGATTTTCCTTGAAAAATGAGTAGATTACGATTCTTCCA
196 GTCTTGATTATCTCTGTAGAGCTCCACGATTTTCCTTGAAAAATGAGTAGATTACGATTCTTCCA
106532 TAAGCGCCAAGACAGAAGCCCGAAGAGACACGCTCAACTAGTTTCCCCACTGCGAGGTTTTGAGG
261 TAAGCGCCAAGACAGAAGCCCGAAGAGACACGCTCAACTAGTTTCCCCACTGCGAGGTTTTGAGG
*
106597 AATCCTGCAAATTACCTGCTAGCCATTCGGGTAGGGTGTTAGAGAAAAAAATAAAGTGTTGAGCT
326 AATCCTGCAAATTACCTACTAGCCATTCGGGTAGGGTGTTAGAGAAAAAAATAAAGTGTTGAGCT
*
106662 CTCGGGATTACCTAATTCCAAACTTCCTTAGCCAAAGTACAGTCTCGAATGATGTGTATGACGTC
391 CTCGAGATTACCTAATTCCAAACTTCCTTAGCCAAAGTACAGTCTCGAATGATGTGTATGACGTC
* *
106727 CTCTAGCTCATGGCCACACACAAGGCATGATGGGTCCGTTGCAATGCCACGTCTGGTTCTCTCCG
456 CTCTAGCTCATGGCCACACACAAGGCATGACGGGTCCGTTACAATGCCACGTCTGGTTCTCTCCG
106792 TACCTGTCCCGTAAAACTCCCCCGTA
521 TACCTGTCCCGTAAAACTCCCCCGTA
106818 AAACTCAAGATCCACTCTCCATACCTGTCCCGTAAAACTCCCCCAGCAGTTGCATTTCCTGAAGT
1 AAACTCAAGATCCACTCTCCATACCTGTCCCGTAAAACTCCCCCAGCAGTTGCATTTCCTGAAGT
106883 CACTTGAATGGCACCGTCAGTGTTGAGGAAAAACCAGCCTTCTGACAAAGATGGAGCAAGAAGGG
66 CACTTGAATGGCACCGTCAGTGTTGAGGAAAAACCAGCCTTCTGACAAAGATGGAGCAAGAAGGG
*
106948 ACTCGAGATCTTTAACCACATTCTCTCTATTTGTTGAGGAGAAATGCTTAGCCCAACTTGCCGAT
131 ACTCGAGATCTTTAACCACATTCTCTCTATTTGTCGAGGAGAAATGCTTAGCCCAACTTGCCGAT
*
107013 GTCTTGATTATCTCTGTAGAGCTCCACGATTTTCCTTGAAAAATGAGTAGATTATGATTCTTCCA
196 GTCTTGATTATCTCTGTAGAGCTCCACGATTTTCCTTGAAAAATGAGTAGATTACGATTCTTCCA
107078 TAAGCGCCAAGACAGAAGCCCGAAGAGACACGCTCAACTAGTTTCCCCACTGCGAGGTTTTGAGG
261 TAAGCGCCAAGACAGAAGCCCGAAGAGACACGCTCAACTAGTTTCCCCACTGCGAGGTTTTGAGG
*
107143 AATCCTGCAAATTACCTACTAGCCATTCGGGTTGGGTGTTAGAGAAAAAAATAAAGTGTTGAGCT
326 AATCCTGCAAATTACCTACTAGCCATTCGGGTAGGGTGTTAGAGAAAAAAATAAAGTGTTGAGCT
*
107208 CTCGAGATTACCTAATTCCAAACTTCCTTAGCCAAAGTACATTCTCGAATGATGTGTATGACGTC
391 CTCGAGATTACCTAATTCCAAACTTCCTTAGCCAAAGTACAGTCTCGAATGATGTGTATGACGTC
107273 CTCTAGCTCATGGCCACACACAAGGCATGACGGGTCCGTTACAATGCCACGTCTGGTTCTCTCCG
456 CTCTAGCTCATGGCCACACACAAGGCATGACGGGTCCGTTACAATGCCACGTCTGGTTCTCTCCG
107338 CGTTGGTAAG
Statistics
Matches: 508, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
546 508 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (546 bp):
AAACTCAAGATCCACTCTCCATACCTGTCCCGTAAAACTCCCCCAGCAGTTGCATTTCCTGAAGT
CACTTGAATGGCACCGTCAGTGTTGAGGAAAAACCAGCCTTCTGACAAAGATGGAGCAAGAAGGG
ACTCGAGATCTTTAACCACATTCTCTCTATTTGTCGAGGAGAAATGCTTAGCCCAACTTGCCGAT
GTCTTGATTATCTCTGTAGAGCTCCACGATTTTCCTTGAAAAATGAGTAGATTACGATTCTTCCA
TAAGCGCCAAGACAGAAGCCCGAAGAGACACGCTCAACTAGTTTCCCCACTGCGAGGTTTTGAGG
AATCCTGCAAATTACCTACTAGCCATTCGGGTAGGGTGTTAGAGAAAAAAATAAAGTGTTGAGCT
CTCGAGATTACCTAATTCCAAACTTCCTTAGCCAAAGTACAGTCTCGAATGATGTGTATGACGTC
CTCTAGCTCATGGCCACACACAAGGCATGACGGGTCCGTTACAATGCCACGTCTGGTTCTCTCCG
TACCTGTCCCGTAAAACTCCCCCGTA
Found at i:109791 original size:7 final size:7
Alignment explanation
Indices: 109779--109806 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
109769 GGATGGAGAT
109779 ATGGCAA
1 ATGGCAA
109786 ATGGCAA
1 ATGGCAA
109793 ATGGCAA
1 ATGGCAA
109800 ATGGCAA
1 ATGGCAA
109807 TGCAATAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (7 bp):
ATGGCAA
Done.