Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001476.1 Hibiscus syriacus cultivar Beakdansim tig00002866_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 310879
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:7302 original size:18 final size:17
Alignment explanation
Indices: 7275--7354 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 17
7265 AAGAAGAAAT
7275 AAAA-GAGAAAAAATAAA
1 AAAATGAGAAAAAA-AAA
*
7292 AAAATGAG-AAAAAAGA
1 AAAATGAGAAAAAAAAA
7308 AAAATGATGGAAAAAACAAA
1 AAAATGA--GAAAAAA-AAA
*
7328 AAGAA--AGAAAAGAAAA
1 AA-AATGAGAAAAAAAAA
7344 AAAATG-GAAAA
1 AAAATGAGAAAA
7355 GGGAAGAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
15 2 0.04
16 19 0.37
17 15 0.29
18 4 0.08
19 6 0.12
20 4 0.08
21 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (17 bp):
AAAATGAGAAAAAAAAA
Found at i:7345 original size:17 final size:17
Alignment explanation
Indices: 7268--7346 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
7258 TTGCTTGAAG
7268 AAGAAATAAAAGAGAAAA
1 AAGAAA-AAAAGAGAAAA
*
7286 AATAAAAAAATGAGAAAA
1 AAGAAAAAAA-GAGAAAA
* *
7304 AAG-AAAAATGATGGAAA
1 AAGAAAAAAAGA-GAAAA
*
7321 AA-ACAAAAAGA-AAGAA
1 AAGAAAAAAAGAGAA-AA
7337 AAGAAAAAAA
1 AAGAAAAAAA
7347 ATGGAAAAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 1 0.02
16 6 0.12
17 27 0.56
18 14 0.29
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.06
Consensus pattern (17 bp):
AAGAAAAAAAGAGAAAA
Found at i:7347 original size:36 final size:35
Alignment explanation
Indices: 7281--7349 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
7271 AAATAAAAGA
* *
7281 GAAAAAATAAAAAAATGAGAAAAAAGAAAAATGATG
1 GAAAAAACAAAAAAA-GAGAAAAAAAAAAAATGATG
7317 GAAAAAACAAAAAGAA-AGAAAAGAAAAAAAATG
1 GAAAAAACAAAAA-AAGAGAAAA-AAAAAAAATG
7350 GAAAAGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 6 0.21
36 21 0.72
37 2 0.07
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.07
Consensus pattern (35 bp):
GAAAAAACAAAAAAAGAGAAAAAAAAAAAATGATG
Found at i:7355 original size:16 final size:17
Alignment explanation
Indices: 7281--7354 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 17
7271 AAATAAAAGA
* *
7281 GAAAAAATAAAAAAATG
1 GAAAAAACAAAAAGATG
*
7298 AGAAAAAAGAAAAATGATG
1 -GAAAAAACAAAAA-GATG
**
7317 GAAAAAACAAAAAGAAA
1 GAAAAAACAAAAAGATG
7334 GAAAAGAA-AAAAA-ATG
1 GAAAA-AACAAAAAGATG
7350 GAAAA
1 GAAAA
7355 GGGAAGAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 6 0.13
17 12 0.26
18 26 0.55
19 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (17 bp):
GAAAAAACAAAAAGATG
Found at i:7390 original size:10 final size:10
Alignment explanation
Indices: 7372--7411 Score: 53
Period size: 10 Copynumber: 3.7 Consensus size: 10
7362 AAACGTATAA
7372 AAAACAAAAAG
1 AAAA-AAAAAG
7383 AAAAAAAAAAG
1 -AAAAAAAAAG
7394 AAAAAAAAAG
1 AAAAAAAAAG
7404 AAATAAAA
1 AAA-AAAA
7412 GGAGGGTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 13 0.48
11 10 0.37
12 4 0.15
ACGTcount: A:0.88, C:0.03, G:0.07, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:7392 original size:12 final size:12
Alignment explanation
Indices: 7370--7402 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7360 GAAAACGTAT
7370 AAAAAACAAAAAG
1 AAAAAA-AAAAAG
7383 -AAAAAAAAAAG
1 AAAAAAAAAAAG
7394 AAAAAAAAA
1 AAAAAAAAA
7403 GAAATAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:8862 original size:107 final size:109
Alignment explanation
Indices: 8736--9363 Score: 673
Period size: 107 Copynumber: 5.8 Consensus size: 109
8726 GTTGAAGATT
* * * * *
8736 GAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACAAGTTTTGTTGAAGA-TT-GAGTCCTATAC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCAGTTTTGTTGAAGATTTCGAGTTCTATAC
** *
8799 TCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
66 TCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
*
8843 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCAGTTTTGTTGAAGA-T-TTCGAGTTCTAT
* * *
8908 ACTCCCTGAACGAATAGGGAGCGGACCCGTTT-TATAAAGATTGTTC
64 ACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTC
8954 GAGTTCTATA--CTCTGAAGGAATAGAGAGCGGACCCA--TTTGTTG-AGATTGTTCGAGTTCTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGA-CCAGTTTTGTTGAAGA-T-TTCGAGTTCTA
* * *
9014 TACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
63 TACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
* *
9061 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-ATGAAGATTGCTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCAGTTTTGTTGAAGATT--TCGAGTTCTAT
* * *
9125 ACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGA---TT-
64 ACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
* * * * *
9167 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATTTTCCGAGTTCTAT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCAGTTTTGTTGAAGA-TTT-CGAGTTCTAT
* *
9231 ACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
64 ACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGTTC
* * * * *
9278 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACA-TTTT-ATGATGATGGTTCGAG-TCT
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGAC-CAGTTTTGTTGAAGAT--TTCGAGTTC-
*
9339 TAAACT-TCCTGAAGGAATAGGGAGC
61 TATACTCT-CTGAAGGAATAGGGAGC
9364 AGACTCGTCA
Statistics
Matches: 450, Mismatches: 42, Indels: 54
0.82 0.08 0.10
Matches are distributed among these distances:
105 4 0.01
106 76 0.17
107 129 0.29
108 11 0.02
109 47 0.10
110 63 0.14
111 114 0.25
112 6 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (109 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCAGTTTTGTTGAAGATTTCGAGTTCTATAC
TCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
Found at i:8874 original size:55 final size:55
Alignment explanation
Indices: 8736--9363 Score: 707
Period size: 55 Copynumber: 11.6 Consensus size: 55
8726 GTTGAAGATT
* * **
8736 GAGTCCTATACTCTCTGAAGGAATAGGGAGTGGACAAGTTTTGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGTTC
* ** *
8788 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
*
8843 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGTTC
* * *
8899 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTT-TATAAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTC
* *
8954 GAGTTCTATA--CTCTGAAGGAATAGAGAGCGGACCCATTTGTTG-AGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
* * *
9006 GAGTTCTATACTCCCTGAACGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
* *
9061 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGCTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTC
* * *
9116 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTAAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
* * * *
9167 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGATT-TTCC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTT-C
* *
9222 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCG-TTTGTTGAAGATTGTTC
* * * * * * * *
9278 AAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACACATTT-TATGATGATGGTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGTTC
*
9333 GAG-TCTTAAACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
9364 AGACTCGTCA
Statistics
Matches: 503, Mismatches: 52, Indels: 39
0.85 0.09 0.07
Matches are distributed among these distances:
51 52 0.10
52 57 0.11
53 28 0.06
54 35 0.07
55 233 0.46
56 96 0.19
57 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTC
Found at i:16204 original size:21 final size:22
Alignment explanation
Indices: 16164--16204 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16154 AATATATAGT
16164 AACCTAATACAATAATTTAATA
1 AACCTAATACAATAATTTAATA
16186 AACCTTAAT-CAAT-ATTTAA
1 AACC-TAATACAATAATTTAA
16205 AATAGTAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (22 bp):
AACCTAATACAATAATTTAATA
Found at i:16703 original size:18 final size:18
Alignment explanation
Indices: 16667--16703 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16657 AACAACACTC
*
16667 TATAATCAAAGGACTATT
1 TATAATCAAAGGACCATT
*
16685 TATAATCAAATGACCATT
1 TATAATCAAAGGACCATT
16703 T
1 T
16704 GTAACAGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (18 bp):
TATAATCAAAGGACCATT
Found at i:28905 original size:21 final size:21
Alignment explanation
Indices: 28828--28905 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
28818 TCTATACCAT
*
28828 ACCCTAAAACCTTAAATTATAA
1 ACCCT-AAACCTTAAATCATAA
28850 ACCCTAAA-CTCTAAATCAT-A
1 ACCCTAAACCT-TAAATCATAA
* *
28870 ACCCATAATCTTTAAATCATAA
1 ACCC-TAAACCTTAAATCATAA
28892 ACCCTAAACCTTAA
1 ACCCTAAACCTTAA
28906 TTTAAGATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.15
21 29 0.62
22 11 0.23
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
ACCCTAAACCTTAAATCATAA
Found at i:29799 original size:2 final size:2
Alignment explanation
Indices: 29792--29823 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29782 CATAAATTCC
29792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29824 ACTCCATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37339 original size:29 final size:28
Alignment explanation
Indices: 37243--37340 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 28
37233 ATTAACTCCT
*
37243 TCAACTATTAAAAGTAATAAAATGGTCA
1 TCAACTATTAAAAGTTATAAAATGGTCA
* ** * *
37271 TTCAACTA-TAAAATGCTACTTCATTGAATCTA
1 -TCAACTATTAAAA-GTTA-TAAAATG-GTC-A
*
37303 TCGACTATTAAAAGTTATAAAATGGTCA
1 TCAACTATTAAAAGTTATAAAATGGTCA
37331 CTCAACTATT
1 -TCAACTATT
37341 CATTATGTTC
Statistics
Matches: 50, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
28 6 0.12
29 19 0.38
30 8 0.16
31 11 0.22
32 6 0.12
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (28 bp):
TCAACTATTAAAAGTTATAAAATGGTCA
Found at i:39770 original size:61 final size:60
Alignment explanation
Indices: 39671--39791 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 60
39661 AACAATGGCG
39671 AAACCCACAAAGCAACGATTTCTCGGAAATGGAACTAGACGTGGCTCGCCAGCTGATTCA
1 AAACCCACAAAGCAACGATTTCTCGGAAATGGAACTAGACGTGGCTCGCCAGCTGATTCA
39731 AAACCCACAAAGCAACGATTTTCTCGGAAATGGAACTAGACGTGGCTCGCCAGCTGATTCA
1 AAACCCACAAAGCAACGA-TTTCTCGGAAATGGAACTAGACGTGGCTCGCCAGCTGATTCA
39792 GCTCTGCGAG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 18 0.30
61 42 0.70
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (60 bp):
AAACCCACAAAGCAACGATTTCTCGGAAATGGAACTAGACGTGGCTCGCCAGCTGATTCA
Found at i:40697 original size:29 final size:29
Alignment explanation
Indices: 40651--40714 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
40641 GCAACATTCT
* *
40651 ATAGTCAATGGACTATTTTATAACTTTTA
1 ATAGTCAATGGACCATTTTATAACTTTAA
*
40680 ATAGTCAGAT-GACCATTTTGTAACTTTAA
1 ATAGTCA-ATGGACCATTTTATAACTTTAA
40709 ATAGTC
1 ATAGTC
40715 GATAGGCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (29 bp):
ATAGTCAATGGACCATTTTATAACTTTAA
Found at i:40753 original size:89 final size:89
Alignment explanation
Indices: 40600--40767 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
40590 AATAATCGAG
* * * *
40600 TGACCATCTTGTAACTTTTAATAGTCGGCGGACTCAACAAAGCAACATTCTATAGTCAATGGACT
1 TGACCATCTTGTAACTTTAAATAGTCGGAGGACTCAACAAAACAACATTCTATAGTCAAAGGACT
40665 ATTTTATAACTTTTAATAGTCAGA
66 ATTTTATAACTTTTAATAGTCAGA
* *
40689 TGACCATTTTGTAACTTTAAATAGTCGATAGG-CTCAACAAAACAAC-TCTCTATAGTCAAAGGA
1 TGACCATCTTGTAACTTTAAATAGTCG-GAGGACTCAACAAAACAACAT-TCTATAGTCAAAGGA
40752 CTATTTTATAACTTTT
64 CTATTTTATAACTTTT
40768 GAAATAATGT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 1 0.01
89 68 0.96
90 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (89 bp):
TGACCATCTTGTAACTTTAAATAGTCGGAGGACTCAACAAAACAACATTCTATAGTCAAAGGACT
ATTTTATAACTTTTAATAGTCAGA
Found at i:41765 original size:48 final size:48
Alignment explanation
Indices: 41692--41939 Score: 268
Period size: 48 Copynumber: 5.2 Consensus size: 48
41682 TTTTCGTAAC
** * * **
41692 TGTTTGGTTGATGCTCATAATCTGGGAAAAAGTGAGCTTGCTGTGAAAA
1 TGTTTGGACGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTG-GGGAA
** *
41741 T-TTTGGGTGATGTTGAGAATCTGGGAAAAAGTGAGCTTGCT-GGGAA
1 TGTTTGGACGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGGAA
* * ***
41787 TTGTTCGGATGATGCTGAGAATCTGGGAAAAAGTCTTCTTGCTGGGGAA
1 -TGTTTGGACGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGGAA
*** *
41836 TGTTTGGACGATGCTGAGAATCTGGGAAAAAGTCTTCTTGCTGGGGAT
1 TGTTTGGACGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGGAA
* *
41884 TGTTTGGACGATGCTGAGAATCTGGGAAAAGGTGAGCTTTCT-GGGAA
1 TGTTTGGACGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGGAA
41931 TTGTTTGGA
1 -TGTTTGGA
41940 TGGAAGGAAA
Statistics
Matches: 174, Mismatches: 21, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
46 3 0.02
47 5 0.03
48 160 0.92
49 6 0.03
ACGTcount: A:0.25, C:0.10, G:0.33, T:0.31
Consensus pattern (48 bp):
TGTTTGGACGATGCTGAGAATCTGGGAAAAAGTGAGCTTGCTGGGGAA
Found at i:48086 original size:31 final size:31
Alignment explanation
Indices: 48048--48120 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
48038 AAATTATAGA
*
48048 TTTAGTATCTAAACTATCAGTTTT-GATTCGT
1 TTTAGTATCTAAACTATCAATTTTAG-TTCGT
*
48079 TTTAGTATCTAAATTATCAATTTTAGTTCGT
1 TTTAGTATCTAAACTATCAATTTTAGTTCGT
48110 TTTAGTA-CTAA
1 TTTAGTATCTAA
48121 CTTTTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
30 4 0.10
31 34 0.87
32 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (31 bp):
TTTAGTATCTAAACTATCAATTTTAGTTCGT
Found at i:48484 original size:101 final size:101
Alignment explanation
Indices: 48309--48504 Score: 392
Period size: 101 Copynumber: 1.9 Consensus size: 101
48299 ACGCGTTAAG
48309 TTTTTAACGACATGTACTGAAATGAAATGAAAACTAAACGTTAGGTAAGCTTTTAGAAAAATTGA
1 TTTTTAACGACATGTACTGAAATGAAATGAAAACTAAACGTTAGGTAAGCTTTTAGAAAAATTGA
48374 AAGTTTAGATACTAAAACAGACCAAAAATAATTTGA
66 AAGTTTAGATACTAAAACAGACCAAAAATAATTTGA
48410 TTTTTAACGACATGTACTGAAATGAAATGAAAACTAAACGTTAGGTAAGCTTTTAGAAAAATTGA
1 TTTTTAACGACATGTACTGAAATGAAATGAAAACTAAACGTTAGGTAAGCTTTTAGAAAAATTGA
48475 AAGTTTAGATACTAAAACAGACCAAAAATA
66 AAGTTTAGATACTAAAACAGACCAAAAATA
48505 GTAGTTTAGG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (101 bp):
TTTTTAACGACATGTACTGAAATGAAATGAAAACTAAACGTTAGGTAAGCTTTTAGAAAAATTGA
AAGTTTAGATACTAAAACAGACCAAAAATAATTTGA
Found at i:51353 original size:2 final size:2
Alignment explanation
Indices: 51346--51382 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
51336 TATGGATTTA
51346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51383 TTAATAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51387 original size:7 final size:7
Alignment explanation
Indices: 51344--51388 Score: 51
Period size: 6 Copynumber: 6.7 Consensus size: 7
51334 AATATGGATT
51344 TAATATA
1 TAATATA
51351 T-ATATA
1 TAATATA
51357 T-ATATA
1 TAATATA
51363 T-ATATA
1 TAATATA
51369 TATATATA
1 TA-ATATA
*
51377 TAATATT
1 TAATATA
51384 TAATA
1 TAATA
51389 ATTTTAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
6 18 0.51
7 10 0.29
8 7 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (7 bp):
TAATATA
Found at i:53684 original size:181 final size:181
Alignment explanation
Indices: 53462--53805 Score: 449
Period size: 182 Copynumber: 1.9 Consensus size: 181
53452 GCTTATACAT
* * * * *
53462 TAAAAAATAGGAGATATTTTAATATGACTATCGATCTTTTAA-ATTTTCCAACCAAATCACTTAA
1 TAAAAAATACGAGAGATTTTAATATGACCATCGATCTTTTAATATTTTCAAACCAAACCACTTAA
* **
53526 CTATTTAAATAATTTCAGTCAAGCCATAC-ACCATTAACATTCGATAAAGGAGTTGACATGACGG
66 CTATTTAAATAATTTCAATCAAGCCAT-CTACCATTAACATTCGATAAAGGAGTTGACATGACAA
* *
53590 TTAATAAAATTAATATAATTACGCATTTAATCCTTATCACTACACATTCTAC
130 TTAACAAAATTAATATAATTACACATTTAATCCTTATCACTACACATTCTAC
* * * * * *
53642 TAAAAAATTACGAGAGATTTTAATTTGACCATTGGTCTTTTAATTTTTTTAAACCAGACCACTTA
1 TAAAAAA-TACGAGAGATTTTAATATGACCATCGATCTTTTAATATTTTCAAACCAAACCACTTA
* * ** * *
53707 ACTATTTAAATAATTTCAATCAAGCCATCTAGCATTAACATTTGATGGAGGAGTTGACGTGATAA
65 ACTATTTAAATAATTTCAATCAAGCCATCTACCATTAACATTCGATAAAGGAGTTGACATGACAA
*
53772 TTAACAAAATTAATATAATTACACATTTAGTCCT
130 TTAACAAAATTAATATAATTACACATTTAATCCT
53806 CAGTACTTAT
Statistics
Matches: 138, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
180 7 0.05
181 30 0.22
182 101 0.73
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (181 bp):
TAAAAAATACGAGAGATTTTAATATGACCATCGATCTTTTAATATTTTCAAACCAAACCACTTAA
CTATTTAAATAATTTCAATCAAGCCATCTACCATTAACATTCGATAAAGGAGTTGACATGACAAT
TAACAAAATTAATATAATTACACATTTAATCCTTATCACTACACATTCTAC
Found at i:54590 original size:183 final size:183
Alignment explanation
Indices: 54282--54643 Score: 670
Period size: 183 Copynumber: 2.0 Consensus size: 183
54272 TGCATGTATT
54282 TGAGTAAAAATAGTAATTTTAATTATTTAAATATTAAAACATGTCATTTATCAGAATCAAATACA
1 TGAGTAAAAATAGTAATTTTAATTATTTAAATATTAAAACATGTCATTTATCAGAATCAAATACA
* *
54347 TAAACACGGTAACCAAAGATCATGCTAGAAGCATTCGGTAATTCAGATATCGTGTGATCAAAATA
66 TAAACACGGTAACCAAAGATCATGCTAGAAGCATTCGGTAATTCAGATATCATATGATCAAAATA
54412 TAAAATTAAAATTTTTAAACAGTTCAGACAGATAATCAAAATAGTACTACAAA
131 TAAAATTAAAATTTTTAAACAGTTCAGACAGATAATCAAAATAGTACTACAAA
*
54465 TGAGTAAAAATAGTAATTTTAATTATTTAAATATTAAAACATGTCATTTATCAGAATCAGATACA
1 TGAGTAAAAATAGTAATTTTAATTATTTAAATATTAAAACATGTCATTTATCAGAATCAAATACA
* *
54530 TAAACACGGTAACCAAAGATCATGCTAGAAGCATTCGGTGATTTAGATATCATATGATCAAAATA
66 TAAACACGGTAACCAAAGATCATGCTAGAAGCATTCGGTAATTCAGATATCATATGATCAAAATA
*
54595 TAAAATTAGAATTTTTAAACAGTTCAGACAGATAATCAAAATAGTACTA
131 TAAAATTAAAATTTTTAAACAGTTCAGACAGATAATCAAAATAGTACTA
54644 TAACATCAAT
Statistics
Matches: 173, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 173 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (183 bp):
TGAGTAAAAATAGTAATTTTAATTATTTAAATATTAAAACATGTCATTTATCAGAATCAAATACA
TAAACACGGTAACCAAAGATCATGCTAGAAGCATTCGGTAATTCAGATATCATATGATCAAAATA
TAAAATTAAAATTTTTAAACAGTTCAGACAGATAATCAAAATAGTACTACAAA
Found at i:72870 original size:25 final size:24
Alignment explanation
Indices: 72837--72901 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
72827 TCCATTTTAT
*
72837 TTTAAACGAACATGTTCGCGAACG
1 TTTAAACGAACATGTTCGCGAACA
*
72861 TTATAAACGAA-ATGTTCGCTAACA
1 TT-TAAACGAACATGTTCGCGAACA
*
72885 TTTAAACGGACATGTTC
1 TTTAAACGAACATGTTC
72902 ACTAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 7 0.19
24 21 0.58
25 8 0.22
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (24 bp):
TTTAAACGAACATGTTCGCGAACA
Found at i:72906 original size:24 final size:24
Alignment explanation
Indices: 72837--72919 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
72827 TCCATTTTAT
* * *
72837 TTTAAACGAACATGTTCGCGAACG
1 TTTAAACGGACATGTTCGCTAACA
*
72861 TTATAAAC-GAAATGTTCGCTAACA
1 TT-TAAACGGACATGTTCGCTAACA
* *
72885 TTTAAACGGACATGTTCACTAATA
1 TTTAAACGGACATGTTCGCTAACA
*
72909 -TTAAACTGACA
1 TTTAAACGGACA
72920 CGTTTACGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
23 15 0.31
24 29 0.59
25 5 0.10
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (24 bp):
TTTAAACGGACATGTTCGCTAACA
Found at i:72935 original size:23 final size:23
Alignment explanation
Indices: 72886--72936 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
72876 TCGCTAACAT
* *
72886 TTAAACGGACATGTTCACTAATA
1 TTAAACGGACACGTTCACGAATA
* * *
72909 TTAAACTGACACGTTTACGAATG
1 TTAAACGGACACGTTCACGAATA
72932 TTAAA
1 TTAAA
72937 TAAAAGAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (23 bp):
TTAAACGGACACGTTCACGAATA
Found at i:75511 original size:2 final size:2
Alignment explanation
Indices: 75499--75533 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
75489 TGTTTTGGTT
75499 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75534 GGCAACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:76652 original size:13 final size:13
Alignment explanation
Indices: 76636--76660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76626 TTGGGATCAG
76636 ATTTTATCATATA
1 ATTTTATCATATA
76649 ATTTTATCATAT
1 ATTTTATCATAT
76661 CTCATACAAT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTATCATATA
Found at i:79886 original size:8 final size:8
Alignment explanation
Indices: 79767--79884 Score: 218
Period size: 8 Copynumber: 14.8 Consensus size: 8
79757 TGATTTACAT
*
79767 ATACATAC
1 ATACATGC
79775 ATACATGC
1 ATACATGC
79783 ATACATGC
1 ATACATGC
79791 ATACATGC
1 ATACATGC
79799 ATACATGC
1 ATACATGC
79807 ATACATGC
1 ATACATGC
79815 ATACATGC
1 ATACATGC
79823 ATACATGC
1 ATACATGC
79831 ATACATGC
1 ATACATGC
79839 ATACATGC
1 ATACATGC
79847 ATACATGC
1 ATACATGC
79855 ATACATGC
1 ATACATGC
79863 ATACATGC
1 ATACATGC
*
79871 ATACATAC
1 ATACATGC
79879 ATACAT
1 ATACAT
79885 ACTATAAGAA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 108 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (8 bp):
ATACATGC
Found at i:82378 original size:32 final size:31
Alignment explanation
Indices: 82328--82397 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 31
82318 TACTTAGATG
*
82328 AAAAAA-ATATTTTAGGTACTTATTTTGACC
1 AAAAAATATATTTTAGGTACTTATTGTGACC
*
82358 AAAAAATATATATTTAGGTACTTATTGTGATC
1 AAAAAATATAT-TTTAGGTACTTATTGTGACC
82390 AAAAAATA
1 AAAAAATA
82398 CTTTTGGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 6 0.17
31 4 0.11
32 26 0.72
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (31 bp):
AAAAAATATATTTTAGGTACTTATTGTGACC
Found at i:87743 original size:60 final size:58
Alignment explanation
Indices: 87646--87777 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 58
87636 GCATCATATG
* * * *
87646 TCCTCAAACTATGAATCATTTTAAATTGTTCTCTAAACTTTTGAATATACCAATTTCA
1 TCCTCAAACTATGAATCATTATAAATTGTCCTCTAAACTTTTGAACATACCAAATTCA
*
87704 TCCTCAAACTAT-AATTTTCATTATAAATTAGTCCT-TAAACTTTTGAACATTCCAAATTCA
1 TCCTCAAACTATGAA---TCATTATAAATT-GTCCTCTAAACTTTTGAACATACCAAATTCA
*
87764 TCCTCAAAATATGA
1 TCCTCAAACTATGA
87778 CCCTCATTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
57 2 0.03
58 12 0.19
60 44 0.70
61 5 0.08
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (58 bp):
TCCTCAAACTATGAATCATTATAAATTGTCCTCTAAACTTTTGAACATACCAAATTCA
Found at i:87785 original size:60 final size:60
Alignment explanation
Indices: 87661--87807 Score: 145
Period size: 60 Copynumber: 2.5 Consensus size: 60
87651 AAACTATGAA
* * * * * ***
87661 TCATTTTAAATTGTTCTCTAAACTTTTGAATATACCAATTTCATCCTCAAACTATAATTT
1 TCATTATAAATTGTCCTCTAAACTTTTGAACATACCAAATTCATCCTCAAAATATAACCC
* *
87721 TCATTATAAATTAGTCCT-TAAACTTTTGAACATTCCAAATTCATCCTCAAAATATGACCC
1 TCATTATAAATT-GTCCTCTAAACTTTTGAACATACCAAATTCATCCTCAAAATATAACCC
* * *
87781 TCATTTTGAATCTGTCC-CCAAACTTTT
1 TCATTATAAAT-TGTCCTCTAAACTTTT
87808 AAATCTTTCA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
60 66 0.93
61 5 0.07
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (60 bp):
TCATTATAAATTGTCCTCTAAACTTTTGAACATACCAAATTCATCCTCAAAATATAACCC
Found at i:88833 original size:18 final size:17
Alignment explanation
Indices: 88799--88837 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
88789 TTATAATTTG
**
88799 TTAAAAATAATTTTTAA
1 TTAAAAATAATAATTAA
88816 TTAAAAATACATAATTAA
1 TTAAAAATA-ATAATTAA
88834 TTAA
1 TTAA
88838 TCTTAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATAATAATTAA
Found at i:92385 original size:31 final size:31
Alignment explanation
Indices: 92341--92410 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
92331 GTAACTTTTA
92341 ATAGTCGAAAGATTTAATAAAGCAGTACCCT
1 ATAGTCGAAAGATTTAATAAAGCAGTACCCT
* *
92372 ATAGTTGAGAGATTTAATAAAGCAGTACCCT
1 ATAGTCGAAAGATTTAATAAAGCAGTACCCT
92403 ATAGTCGA
1 ATAGTCGA
92411 GGGACCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (31 bp):
ATAGTCGAAAGATTTAATAAAGCAGTACCCT
Found at i:102834 original size:38 final size:38
Alignment explanation
Indices: 102787--102864 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
102777 ATACCTAAAG
102787 TTTAATTTTTGTTTCA-TTTTAGTACCC-GCCTTTAAAAT
1 TTTAATTTTTGTTTCATTTTTAGTACCCTG--TTTAAAAT
*
102825 TTTAGTTTTTGTTTCATTTTTAGTACCCTGTTTAAAAT
1 TTTAATTTTTGTTTCATTTTTAGTACCCTGTTTAAAAT
102863 TT
1 TT
102865 AACATTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 25 0.68
39 11 0.30
40 1 0.03
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (38 bp):
TTTAATTTTTGTTTCATTTTTAGTACCCTGTTTAAAAT
Found at i:106252 original size:21 final size:20
Alignment explanation
Indices: 106166--106323 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
106156 AAATGACCAA
**
106166 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
106185 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
106205 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
106225 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
106246 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
106267 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
106287 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
106308 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
106324 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:106352 original size:20 final size:20
Alignment explanation
Indices: 106291--106680 Score: 448
Period size: 20 Copynumber: 19.4 Consensus size: 20
106281 GATTTTCAAT
* ** *
106291 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
106311 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
106331 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
106351 AAACGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
106371 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
106391 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
106411 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
106431 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
106452 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
106472 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
106492 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
106512 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
106532 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
106552 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
106572 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
106592 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
106612 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
106632 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
106652 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
106672 AATCACAAC
1 AATCGCAAC
106681 ACTGAAATTT
Statistics
Matches: 317, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.01
20 294 0.93
21 18 0.06
22 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:107393 original size:24 final size:24
Alignment explanation
Indices: 107354--107400 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
107344 AAATTTGGTC
107354 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
107378 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
107401 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:107592 original size:12 final size:12
Alignment explanation
Indices: 107575--107599 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
107565 ATATAATCCT
107575 GAAGAAGAAAAA
1 GAAGAAGAAAAA
107587 GAAGAAGAAAAA
1 GAAGAAGAAAAA
107599 G
1 G
107600 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:109901 original size:19 final size:19
Alignment explanation
Indices: 109879--110133 Score: 316
Period size: 19 Copynumber: 14.4 Consensus size: 19
109869 CGGAAAATAC
*
109879 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
109898 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
109912 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
109932 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
109946 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
109965 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
109984 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
109998 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
110017 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
110036 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
110055 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
110074 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
110088 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
110107 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
110126 AATCGCAA
1 AATCGCAA
110134 CGAGATAATC
Statistics
Matches: 207, Mismatches: 8, Indels: 42
0.81 0.03 0.16
Matches are distributed among these distances:
14 40 0.19
15 2 0.01
16 11 0.05
17 10 0.05
18 3 0.01
19 128 0.62
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:109966 original size:33 final size:33
Alignment explanation
Indices: 109879--110114 Score: 210
Period size: 33 Copynumber: 6.8 Consensus size: 33
109869 CGGAAAATAC
* * *
109879 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
109912 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* *
109946 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * * *
109978 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
*
110017 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G
*
110054 AAATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 -AATCGCAATGCGAAATGAAAATCGCAACGAGAG
110088 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
110115 TGCGAAATGA
Statistics
Matches: 172, Mismatches: 15, Indels: 32
0.79 0.07 0.15
Matches are distributed among these distances:
31 7 0.04
32 7 0.04
33 64 0.37
34 30 0.17
35 3 0.02
36 6 0.03
38 41 0.24
39 7 0.04
40 7 0.04
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:109994 original size:52 final size:53
Alignment explanation
Indices: 109907--110133 Score: 306
Period size: 52 Copynumber: 4.2 Consensus size: 53
109897 AAATCCCAAC
109907 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
109960 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
*
110012 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAGA--G-AATCGCAATGCGAA
*
110069 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAGAATCGCAATGCGAA
110121 ATGAAAATCGCAA
1 ATGAAAATCGCAA
110134 CGAGATAATC
Statistics
Matches: 163, Mismatches: 3, Indels: 17
0.89 0.02 0.09
Matches are distributed among these distances:
52 107 0.66
53 16 0.10
54 6 0.04
55 6 0.04
56 1 0.01
57 27 0.17
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAGAATCGCAATGCGAA
Found at i:110062 original size:90 final size:89
Alignment explanation
Indices: 109879--110155 Score: 394
Period size: 90 Copynumber: 3.2 Consensus size: 89
109869 CGGAAAATAC
* * *
109879 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATCGCAATGC
*
109941 G--A-GAGAATCGCAATGCGAAATGAA
64 GAAATGAAAATCGCAATGCGAAATG-A
109965 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
110030 AATGAAAATCGCAATGCGAAATGGA
66 AATGAAAATCGCAATGCGAAAT-GA
*
110055 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
*
110120 AATGAAAATCGCAA--CGAGAT--
66 AATGAAAATCGCAATGCGAAATGA
110140 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
110156 TATAAACGCA
Statistics
Matches: 178, Mismatches: 6, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
85 32 0.18
86 39 0.22
87 3 0.02
88 5 0.03
89 1 0.01
90 97 0.54
91 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (89 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAAAATCGCAATGCGAAATGA
Found at i:110134 original size:52 final size:55
Alignment explanation
Indices: 109879--110155 Score: 290
Period size: 52 Copynumber: 5.3 Consensus size: 55
109869 CGGAAAATAC
* *
109879 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
109932 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
109984 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
110036 AATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
110088 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
110140 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
110156 TATAAACGCA
Statistics
Matches: 207, Mismatches: 6, Indels: 23
0.88 0.03 0.10
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 133 0.64
53 24 0.12
54 3 0.01
55 5 0.02
56 1 0.00
57 28 0.14
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:110252 original size:19 final size:19
Alignment explanation
Indices: 110162--110244 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
110152 AAATTATAAA
110162 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
110181 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
110201 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
110217 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
110234 CGCATTGCGAT
1 CGCATTGCGAT
110245 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:110370 original size:14 final size:14
Alignment explanation
Indices: 110351--110387 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
110341 CATCAATTAC
110351 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
110365 ACAAATCATCTTTT
1 ACAAATCAACTTTT
110379 ACAAATCAA
1 ACAAATCAA
110388 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:112368 original size:33 final size:33
Alignment explanation
Indices: 112322--112414 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
112312 GCGAAACCAA
*
112322 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
112355 AATCGCAATGCGAAATGAAAATCGAAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
112388 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
112415 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:112397 original size:14 final size:14
Alignment explanation
Indices: 112341--112397 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
112331 GCGAAATGAA
*
112341 AATCGCAACGACAG
1 AATCGCAACGAAAG
112355 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
112372 AAAATCGAAACGAAAG
1 --AATCGCAACGAAAG
112388 AATCGCAACG
1 AATCGCAACG
112398 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:112412 original size:19 final size:19
Alignment explanation
Indices: 112285--112419 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
112275 TAGTTTACTT
* *
112285 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
112305 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
112324 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
112343 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
112357 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
112376 TCG-AA-ACGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
112390 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
112409 TCGCAATGCGA
1 TCGCAACGCGA
112420 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 13 0.14
15 2 0.02
16 11 0.12
17 11 0.12
18 2 0.02
19 44 0.46
20 12 0.13
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:112431 original size:19 final size:19
Alignment explanation
Indices: 112415--112510 Score: 103
Period size: 19 Copynumber: 5.3 Consensus size: 19
112405 AAAATCGCAA
112415 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
112434 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
112448 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
112467 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
112486 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
112506 TGCGA
1 TGCGA
112511 AAGTAAACTA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
14 11 0.17
16 1 0.02
17 1 0.02
18 1 0.02
19 37 0.58
20 13 0.20
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:112724 original size:92 final size:92
Alignment explanation
Indices: 112554--113024 Score: 915
Period size: 92 Copynumber: 5.1 Consensus size: 92
112544 TTGAATGGAT
112554 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
112619 AGTTTAGCAGAATTGGCAGCAACCGAAC
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
112647 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
112712 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
112739 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
112804 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
112831 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
112896 GTTTAGCAGAATTGGCAGCAACCGAAC
66 GTTTAGCAGAATTGGCAGCAACCGAAC
112923 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
*
112988 AGTTTAGCAGAATTGGCAGCAACCGAAT
65 AGTTTAGCAGAATTGGCAGCAACCGAAC
113016 AAATTTACT
1 AAATTTACT
113025 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 276 0.73
93 100 0.27
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (92 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:114747 original size:14 final size:14
Alignment explanation
Indices: 114728--114817 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
114718 TTGAAATGAA
114728 AATCGCAACGAGAG
1 AATCGCAACGAGAG
114742 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
114759 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
114775 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
114794 AATCGCAACGAGAG
1 AATCGCAACGAGAG
114808 AATCGCAACG
1 AATCGCAACG
114818 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:114765 original size:33 final size:33
Alignment explanation
Indices: 114720--114834 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
114710 TCTTTTGGTT
114720 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
114753 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
114786 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
114819 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
114835 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:114766 original size:19 final size:18
Alignment explanation
Indices: 114727--114839 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
114717 GTTGAAATGA
114727 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
114742 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
114759 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
114775 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
114792 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
114808 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
114825 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
114840 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:114870 original size:14 final size:14
Alignment explanation
Indices: 114851--114905 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
114841 TTTGGTTTCG
114851 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
114865 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
114884 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
114898 CGTTGCGA
1 CGTTGCGA
114906 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:114883 original size:33 final size:33
Alignment explanation
Indices: 114835--114905 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
114825 AAAATCGCAA
**
114835 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
114868 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
114901 TGCGA
1 TGCGA
114906 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:114913 original size:33 final size:33
Alignment explanation
Indices: 114846--114927 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
114836 GCGATTTTGG
***
114846 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
114879 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
114912 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
114928 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:114932 original size:20 final size:20
Alignment explanation
Indices: 114858--114946 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
114848 TCGCGTTGCG
114858 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
114878 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
114891 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
114911 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
114931 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
114947 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:115068 original size:33 final size:33
Alignment explanation
Indices: 115026--115096 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
115016 AATACTAACT
*
115026 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
115059 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
115092 TGAAA
1 TGAAA
115097 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:115330 original size:22 final size:22
Alignment explanation
Indices: 115278--115332 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
115268 TGGTTGTGAG
**
115278 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
115300 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
115322 GGATTTCTTCG
1 GGATTTCTTCG
115333 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:115503 original size:20 final size:20
Alignment explanation
Indices: 115478--115670 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
115468 CTTTAAATAT
115478 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
115498 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
115520 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
115539 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
115559 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
115579 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
115599 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
115619 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
115639 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
115659 CGCGTTGCGATT
1 CGCGTTGCGATT
115671 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:115665 original size:60 final size:60
Alignment explanation
Indices: 115478--115670 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
115468 CTTTAAATAT
**
115478 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
115539 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
115599 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
115659 CGCGTTGCGATT
1 CGCGTTGCGATT
115671 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:123763 original size:21 final size:21
Alignment explanation
Indices: 123729--123787 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
123719 TGTTACGGTG
* *
123729 CTAACATAACAGTCCATTGTA
1 CTAACATGACAGTCCACTGTA
* **
123750 CTGATGTGACAGTCCACTGTA
1 CTAACATGACAGTCCACTGTA
123771 CTAACATGACAGTCCAC
1 CTAACATGACAGTCCAC
123788 AATGGTTGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.25
Consensus pattern (21 bp):
CTAACATGACAGTCCACTGTA
Found at i:124295 original size:40 final size:40
Alignment explanation
Indices: 124244--124349 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
124234 ATAAACGCGG
*
124244 TAAATACTTGTACTTTAGTGGTGTTTTTATATAAA-ACCCGC
1 TAAATA-TTGTACTTTAGTGGTGTTTTTATATAAACA-ACGC
* * * * *
124285 TAAATATTGTACTTTTGTGGCGTTTTTGTGTAAACAACTC
1 TAAATATTGTACTTTAGTGGTGTTTTTATATAAACAACGC
*
124325 TAAATATTGTACTTTAGCGGTGTTT
1 TAAATATTGTACTTTAGTGGTGTTT
124350 GTGTGGCGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
40 48 0.87
41 7 0.13
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (40 bp):
TAAATATTGTACTTTAGTGGTGTTTTTATATAAACAACGC
Found at i:124567 original size:41 final size:41
Alignment explanation
Indices: 124373--124581 Score: 129
Period size: 41 Copynumber: 5.0 Consensus size: 41
124363 AGCACAAATA
* * * *
124373 CCGCTAAATACTCTTACTTTAGTGGCT-TTTTTATATAAACG
1 CCGCTAAAGAATCGTACTTTAGTGG-TGTTTTTATACAAACG
* * * *
124414 CCG-TCAAAGAGTTGTATTTTAGTGGCGTTTTTATACAAACG
1 CCGCT-AAAGAATCGTACTTTAGTGGTGTTTTTATACAAACG
* * * * * *
124455 TCGATAAAGAATCATACTTTAGTAG-CTTTTTATACAAACA
1 CCGCTAAAGAATCGTACTTTAGTGGTGTTTTTATACAAACG
* ** * * *
124495 TCATTGAAGAATCGTGA-TTTAATGGTATTTTTATACAAACG
1 CCGCTAAAGAATCGT-ACTTTAGTGGTGTTTTTATACAAACG
* * *
124536 CCGCTAAAGACTCGTACTTTTGTAGTGTTTTTTAAATACAAACG
1 CCGCTAAAGAATCGTACTTTAGTGGTG-TTTTT--ATACAAACG
124580 CC
1 CC
124582 ACTATATTAC
Statistics
Matches: 127, Mismatches: 32, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
40 32 0.25
41 78 0.61
42 6 0.05
44 11 0.09
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (41 bp):
CCGCTAAAGAATCGTACTTTAGTGGTGTTTTTATACAAACG
Found at i:128874 original size:21 final size:21
Alignment explanation
Indices: 128850--128919 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
128840 TAAACTTTGA
*
128850 TTTATTATTATGGATTTCAAG
1 TTTATTGTTATGGATTTCAAG
*
128871 TTTACTGTTATGGATTTCAAG
1 TTTATTGTTATGGATTTCAAG
* *
128892 TTTGTTGTTATGGATGTCAAG
1 TTTATTGTTATGGATTTCAAG
128913 TTTATTG
1 TTTATTG
128920 GATAATGCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (21 bp):
TTTATTGTTATGGATTTCAAG
Found at i:129156 original size:44 final size:42
Alignment explanation
Indices: 129108--129199 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 42
129098 TTTTACATTC
* *
129108 ACAAACGCCACTATAT-TCTATAACATTTAGCGGT-GTTTTTGGG
1 ACAAACGCAACTATATGTC-AGAACATTTAGC--TCGTTTTTGGG
*
129151 AACAAACGCAACTATATGTCAGAATATTTAGCTCGTTTTTGGG
1 -ACAAACGCAACTATATGTCAGAACATTTAGCTCGTTTTTGGG
129194 ACAAAC
1 ACAAAC
129200 AACCACAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
42 7 0.16
43 9 0.21
44 25 0.58
45 2 0.05
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (42 bp):
ACAAACGCAACTATATGTCAGAACATTTAGCTCGTTTTTGGG
Found at i:131637 original size:29 final size:29
Alignment explanation
Indices: 131595--131653 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
131585 ATTTTCACCT
131595 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
131624 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
131653 A
1 A
131654 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:136315 original size:29 final size:29
Alignment explanation
Indices: 136273--136331 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
136263 ATTTTCACCT
136273 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
136302 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
136331 A
1 A
136332 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:139367 original size:46 final size:46
Alignment explanation
Indices: 139302--139402 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 46
139292 CATTTCTTCT
* * * * *
139302 TTTATTATTTGCCGCTATATCTTTCTTTCGTCGCAAAAACTATTTTC
1 TTTATT-TTTGCCCCTATATCTTCCTATCATAGCAAAAACTATTTTC
* * * *
139349 TTTATTTTTTCCCCTATATCTTCCTATCATAGCTACAATTATTTTC
1 TTTATTTTTGCCCCTATATCTTCCTATCATAGCAAAAACTATTTTC
139395 TTTATTTT
1 TTTATTTT
139403 CGCCGCAAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 39 0.87
47 6 0.13
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (46 bp):
TTTATTTTTGCCCCTATATCTTCCTATCATAGCAAAAACTATTTTC
Found at i:139465 original size:73 final size:73
Alignment explanation
Indices: 139327--139479 Score: 200
Period size: 73 Copynumber: 2.1 Consensus size: 73
139317 TATATCTTTC
* * * * *
139327 TTTCGTCGCAAAAACTATTTTCTTTATTTTTTCCCCTATATCTTCCTATCATAGCTACAATTATT
1 TTTCGCCGCAAAAACTATTTTCTTTATTTTTTCCCATATATCTTCCTATCACAGCTAAAACTATT
139392 TTCTTTAT
66 TTCTTTAT
* * * * *
139400 TTTCGCCGCAAGAACTATTTTCTTTATTTTTTCCCATATATATTTCTTTTGACA-CTAAAACTAT
1 TTTCGCCGCAAAAACTATTTTCTTTATTTTTTCCCATATAT-CTTCCTATCACAGCTAAAACTAT
139464 TTTCTTTAT
65 TTTCTTTAT
139473 TTTCGCC
1 TTTCGCC
139480 CGCTATATCT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
73 62 0.90
74 7 0.10
ACGTcount: A:0.23, C:0.22, G:0.05, T:0.50
Consensus pattern (73 bp):
TTTCGCCGCAAAAACTATTTTCTTTATTTTTTCCCATATATCTTCCTATCACAGCTAAAACTATT
TTCTTTAT
Found at i:139535 original size:50 final size:47
Alignment explanation
Indices: 139412--139817 Score: 266
Period size: 50 Copynumber: 8.4 Consensus size: 47
139402 TCGCCGCAAG
* * * * *
139412 AACTATTTTCTTTATTTTTTC-C--CATATATATTTCTTTTGACACTAA
1 AACTATTTTCTTT-TATTTTCACTGC-TATATCTTTCTTTCGTCGCTAA
* * *
139458 AACTATTTTC-TTTATTTTCGCCCGCTATATCTTTGTTTTCGTCGCTAA
1 AACTATTTTCTTTTATTTTC-ACTGCTATATCTTT-CTTTCGTCGCTAA
* * *
139506 AACATATTTTCTTTTATCTTTCACTGCTATATCTTTGTTTTCGACGCTAT
1 AAC-TATTTTCTTTTAT-TTTCACTGCTATATCTTT-CTTTCGTCGCTAA
* *
139556 AACATATTTTCTTTAATATTTTGC-C-GCTATATATTTCTTTCGTCTCTAA
1 AAC-TATTTTCTTT--TATTTT-CACTGCTATATCTTTCTTTCGTCGCTAA
* *
139605 AAGTATTTTC-TTTATTTTCACCGCTATATATCTTTCTTTCGTCGCT--
1 AACTATTTTCTTTTATTTTCACTGC--TATATCTTTCTTTCGTCGCTAA
* * * * *
139651 --CCATTTTC-CTTATTTTCACTGCTATATCTTTGTTTTCGTTGCTAG
1 AACTATTTTCTTTTATTTTCACTGCTATATCTTT-CTTTCGTCGCTAA
*
139696 AACATATTTTCTTTTATCTTTCGTCTTTCGCCGCTATATCTTTCTTTCGTCGCT-A
1 AAC-TATTTTCTTTTAT-TTTC-AC--T----GCTATATCTTTCTTTCGTCGCTAA
* * *
139751 AATTATTTTCTTTTATCTTTCA-TCGCTATATCTTTCTTTCGTCCCTAT
1 AACTATTTTCTTTTAT-TTTCACT-GCTATATCTTTCTTTCGTCGCTAA
139799 AACTATTTTC-TTTATTTTC
1 AACTATTTTCTTTTATTTTC
139818 GCCGCTCTAA
Statistics
Matches: 294, Mismatches: 35, Indels: 62
0.75 0.09 0.16
Matches are distributed among these distances:
42 9 0.03
43 9 0.03
44 25 0.09
45 9 0.03
46 17 0.06
47 38 0.13
48 53 0.18
49 22 0.07
50 58 0.20
51 9 0.03
52 4 0.01
53 1 0.00
54 18 0.06
55 2 0.01
56 9 0.03
57 11 0.04
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (47 bp):
AACTATTTTCTTTTATTTTCACTGCTATATCTTTCTTTCGTCGCTAA
Found at i:139597 original size:99 final size:94
Alignment explanation
Indices: 139415--139635 Score: 241
Period size: 99 Copynumber: 2.3 Consensus size: 94
139405 CCGCAAGAAC
**
139415 TATTTTCTTTATTTTTTCC-CATATATATTTCTTTTGACACTAAAACTATTTTCTTTATTTTCGC
1 TATTTTCTTTATTTTCACCGC-TATATATTTCTTTTGACACTAAAACTATTTTCTTTATTTTCGC
* *
139479 CCGCTATATCTTTGTTTTCGTCGCTAAAACA
65 CCGCTATATATTTGCTTTCGTCGCTAAAA-A
* * * * *
139510 TATTTTCTTTTATCTTTCACTGCTATATCTTTGTTTTCGACGCTATAACATATTTTCTTTAATAT
1 TATTTTC-TTTAT-TTTCACCGCTATATATTTCTTTT-GACACTAAAAC-TATTTTCTTT-AT-T
* * *
139575 TTTG-CCGCTATATATTT-CTTTCGTCTCTAAAAG
60 TTCGCCCGCTATATATTTGCTTTCGTCGCTAAAAA
139608 TATTTTCTTTATTTTCACCGCTATATAT
1 TATTTTCTTTATTTTCACCGCTATATAT
139636 CTTTCTTTCG
Statistics
Matches: 105, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
95 7 0.07
96 19 0.18
97 21 0.20
98 17 0.16
99 23 0.22
100 14 0.13
101 4 0.04
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (94 bp):
TATTTTCTTTATTTTCACCGCTATATATTTCTTTTGACACTAAAACTATTTTCTTTATTTTCGCC
CGCTATATATTTGCTTTCGTCGCTAAAAA
Found at i:139612 original size:147 final size:141
Alignment explanation
Indices: 139393--139817 Score: 418
Period size: 147 Copynumber: 2.9 Consensus size: 141
139383 ACAATTATTT
* * * * * *
139393 TCTTTATTTTCGCCGCAAGAAC-TATTTTCTTT-ATTTTTTCC-CATATATATTTCTTTTGACAC
1 TCTTTGTTTTCGACGCTAGAACATATTTTCTTTAATTTTTGCCGC-TATATATTTCTTTCGTCAC
* *
139455 TAAAACTATTTTCTTTATTTTCGCCCGCTATATCTTTGTTTTCGTCGCTAAAACATATTTTCTTT
65 TAAAACTATTTTCTTTATTTTC-ACCGCTATATCTTT-CTTTCGTCGCT-AAAC-TATTTTCTTT
139520 TATCTTTCACTGCTATA
126 TAT-TTTCACTGCTATA
* *
139537 TCTTTGTTTTCGACGCTATAACATATTTTCTTTAATATTTTGCCGCTATATATTTCTTTCGTCTC
1 TCTTTGTTTTCGACGCTAGAACATATTTTCTTTAAT-TTTTGCCGCTATATATTTCTTTCGTCAC
* * *
139602 TAAAAGTATTTTCTTTATTTTCACCGCTATATATCTTTCTTTCGTCGCT---CCATTTTC-CTTA
65 TAAAACTATTTTCTTTATTTTCACCGC--TATATCTTTCTTTCGTCGCTAAACTATTTTCTTTTA
139663 TTTTCACTGCTATA
128 TTTTCACTGCTATA
** * *
139677 TCTTTGTTTTCGTTGCTAGAACATATTTTCTTTTATCTTTCGTCTTTCGCCGCTATATCTTTCTT
1 TCTTTGTTTTCGACGCTAGAACATATTTTC-TTTA---AT--T-TTT-GCCGCTATATATTTCTT
* * * *
139742 TCGTCGCT-AAATTATTTTCTTTTATCTTTCATCGCTATATCTTTCTTTCGTCCCTATAACTATT
58 TCGTCACTAAAACTATTTTC-TTTAT-TTTCACCGCTATATCTTTCTTTCGTCGCTA-AACTATT
139806 TTC-TTTATTTTC
120 TTCTTTTATTTTC
139818 GCCGCTCTAA
Statistics
Matches: 237, Mismatches: 25, Indels: 32
0.81 0.09 0.11
Matches are distributed among these distances:
140 40 0.17
141 8 0.03
142 6 0.03
143 1 0.00
144 19 0.08
145 11 0.05
146 38 0.16
147 81 0.34
148 18 0.08
150 15 0.06
ACGTcount: A:0.19, C:0.21, G:0.08, T:0.52
Consensus pattern (141 bp):
TCTTTGTTTTCGACGCTAGAACATATTTTCTTTAATTTTTGCCGCTATATATTTCTTTCGTCACT
AAAACTATTTTCTTTATTTTCACCGCTATATCTTTCTTTCGTCGCTAAACTATTTTCTTTTATTT
TCACTGCTATA
Found at i:139813 original size:47 final size:46
Alignment explanation
Indices: 139412--139823 Score: 296
Period size: 48 Copynumber: 8.5 Consensus size: 46
139402 TCGCCGCAAG
** * * * *
139412 AACTATTTTCTTTATTTTTTCC-CATATATATTTCTTTTGACACTAA
1 AACTATTTTCTTTATTTTCACCGC-TATATCTTTCTTTCGTCGCTAA
* *
139458 AACTATTTTCTTTATTTTCGCCCGCTATATCTTTGTTTTCGTCGCTAA
1 AACTATTTTCTTTATTTTC-ACCGCTATATCTTT-CTTTCGTCGCTAA
* * * *
139506 AACATATTTTCTTTTATCTTTCACTGCTATATCTTTGTTTTCGACGCTAT
1 AAC-TATTTTC-TTTAT-TTTCACCGCTATATCTTT-CTTTCGTCGCTAA
** * *
139556 AACATATTTTCTTTAATATTTTGCCGCTATATATTTCTTTCGTCTCTAA
1 AAC-TATTTTCTTT-AT-TTTCACCGCTATATCTTTCTTTCGTCGCTAA
*
139605 AAGTATTTTCTTTATTTTCACCGCTATATATCTTTCTTTCGTCGCT--
1 AACTATTTTCTTTATTTTCACCGC--TATATCTTTCTTTCGTCGCTAA
* * * * * *
139651 --CCATTTTCCTTATTTTCACTGCTATATCTTTGTTTTCGTTGCTAG
1 AACTATTTTCTTTATTTTCACCGCTATATCTTT-CTTTCGTCGCTAA
*
139696 AACATATTTTCTTTTATCTTTCGTCTTTCGCCGCTATATCTTTCTTTCGTCGCT-A
1 AAC-TATTTTC-TTTA-------T-TTTCACCGCTATATCTTTCTTTCGTCGCTAA
* * * *
139751 AATTATTTTCTTTTATCTTTCATCGCTATATCTTTCTTTCGTCCCTAT
1 AACTATTTTC-TTTAT-TTTCACCGCTATATCTTTCTTTCGTCGCTAA
*
139799 AACTATTTTCTTTATTTTCGCCGCT
1 AACTATTTTCTTTATTTTCACCGCT
139824 CTAACTATTT
Statistics
Matches: 295, Mismatches: 46, Indels: 50
0.75 0.12 0.13
Matches are distributed among these distances:
42 9 0.03
43 9 0.03
44 18 0.06
46 33 0.11
47 46 0.16
48 56 0.19
49 24 0.08
50 56 0.19
51 4 0.01
54 12 0.04
55 2 0.01
56 10 0.03
57 16 0.05
ACGTcount: A:0.18, C:0.22, G:0.08, T:0.52
Consensus pattern (46 bp):
AACTATTTTCTTTATTTTCACCGCTATATCTTTCTTTCGTCGCTAA
Found at i:139813 original size:194 final size:191
Alignment explanation
Indices: 139462--139823 Score: 462
Period size: 194 Copynumber: 1.9 Consensus size: 191
139452 CACTAAAACT
* *
139462 ATTTTCTTTATTTTCGCCCGCTATATCTTTGTTTTCGTCGCTAAAACATATTTTCTTTTATCTTT
1 ATTTTCCTTATTTTCGACCGCTATATCTTTGTTTTCGTCGCTAAAACATATTTTCTTTTATCTTT
* **
139527 CACTGCTATATCTTTGTTTTCGACGCTATAACATATTTTCTTTAATATTTTGCCGCTATATATTT
66 CACTGCTATATCTTTGCTTTCGACGCTATAACATATTTTCTTTAATATTTCACCGCTATATATTT
* *
139592 CTTTCGTCTCTAAAAGTATTTTCTTTATTTTCACCGCTATATATCTTTCTTTCGTCGCTCC
131 CTTTCGTCCCTAAAACTATTTTCTTTATTTTCACCGCTATATATCTTTCTTTCGTCGCTCC
* * *
139653 ATTTTCCTTATTTTC-ACTGCTATATCTTTGTTTTCGTTGCTAGAACATATTTTCTTTTATCTTT
1 ATTTTCCTTATTTTCGACCGCTATATCTTTGTTTTCGTCGCTAAAACATATTTTCTTTTATCTTT
* * * * * *
139717 CGTCTTTCGCCGCTATATCTTT-CTTTCGTCGCTA-AA-TTATTTTCTTTTATCTTTCATCGCTA
66 C-AC--T----GCTATATCTTTGCTTTCGACGCTATAACATATTTTCTTTAATATTTCACCGCTA
* * *
139779 TATCTTTCTTTCGTCCCTATAACTATTTTCTTTATTTTCGCCGCT
124 TATATTTCTTTCGTCCCTAAAACTATTTTCTTTATTTTCACCGCT
139824 CTAACTATTT
Statistics
Matches: 145, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
190 46 0.32
191 15 0.10
193 1 0.01
194 60 0.41
195 2 0.01
196 10 0.07
197 11 0.08
ACGTcount: A:0.17, C:0.22, G:0.08, T:0.52
Consensus pattern (191 bp):
ATTTTCCTTATTTTCGACCGCTATATCTTTGTTTTCGTCGCTAAAACATATTTTCTTTTATCTTT
CACTGCTATATCTTTGCTTTCGACGCTATAACATATTTTCTTTAATATTTCACCGCTATATATTT
CTTTCGTCCCTAAAACTATTTTCTTTATTTTCACCGCTATATATCTTTCTTTCGTCGCTCC
Found at i:139818 original size:27 final size:27
Alignment explanation
Indices: 139787--139853 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
139777 TATATCTTTC
139787 TTTCGTCC-CTATAACTATTTTCTTTAT
1 TTTCG-CCGCTATAACTATTTTCTTTAT
*
139814 TTTCGCCGCTCTAACTATTTTCTTTAT
1 TTTCGCCGCTATAACTATTTTCTTTAT
* *
139841 TTCCGCTGCTATA
1 TTTCGCCGCTATA
139854 TCTTTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.16, C:0.25, G:0.07, T:0.51
Consensus pattern (27 bp):
TTTCGCCGCTATAACTATTTTCTTTAT
Found at i:139949 original size:46 final size:47
Alignment explanation
Indices: 139826--140111 Score: 260
Period size: 46 Copynumber: 6.0 Consensus size: 47
139816 TCGCCGCTCT
* ** * * *
139826 AACTATTTTC-TTTATTTCCGCTGCTATATCTTTGTTTTTGTCACTAA
1 AACTATTTTCTTTTATTTTCGCCACTATATCTTT-CTTTCGTCGCTAA
139873 AAC-ATTCCTTCTTTTATTTTTCGCCACTATATCTTTCTTTCGTCGCTAA
1 AACTATT--TTCTTTTA-TTTTCGCCACTATATCTTTCTTTCGTCGCTAA
* *
139922 AACTA-TTTCCTTTATTTTCGCCTCTATATCTTTCTTTCGTCGCTAA
1 AACTATTTTCTTTTATTTTCGCCACTATATCTTTCTTTCGTCGCTAA
* * * * *
139968 AATTATTTTCTTTTAATTTTTGACACTATATGTTTCCTTCGTCGCTAA
1 AACTATTTTCTTTT-ATTTTCGCCACTATATCTTTCTTTCGTCGCTAA
* * * *
140016 AACTA-TTT-TTTTATTTTCGCCGCTATAGCTTTCTCTCCGTCACTAA
1 AACTATTTTCTTTTATTTTCGCCACTATATCTTTCT-TTCGTCGCTAA
* * * *
140062 AATGTATTTTCTTTTATTTTTCACC-GTATATCTTTTCCTTCGTCGCTAA
1 AA-CTATTTTCTTTTA-TTTTCGCCACTATATC-TTTCTTTCGTCGCTAA
140111 A
1 A
140112 GGTCATTTTT
Statistics
Matches: 195, Mismatches: 31, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
45 16 0.08
46 53 0.27
47 22 0.11
48 38 0.19
49 38 0.19
50 28 0.14
ACGTcount: A:0.20, C:0.22, G:0.08, T:0.50
Consensus pattern (47 bp):
AACTATTTTCTTTTATTTTCGCCACTATATCTTTCTTTCGTCGCTAA
Found at i:140014 original size:94 final size:92
Alignment explanation
Indices: 139826--140111 Score: 326
Period size: 94 Copynumber: 3.0 Consensus size: 92
139816 TCGCCGCTCT
* * * *
139826 AACTATTTTCTTTATTTCCG-CTGCTATATCTTTGTTTTTGTCACTAAAA-CATTCCTTCTTTTA
1 AACTA-TTTCTTTATTTTCGCCT-CTATATCTTT-CTTTCGTCACTAAAATTATT--TTCTTTTA
* *
139889 TTTTTCGCCACTATATCTTTCTTTCGTCGCTAA
61 TTTTT-GACACTATATCTTTCCTTCGTCGCTAA
*
139922 AACTATTTCCTTTATTTTCGCCTCTATATCTTTCTTTCGTCGCTAAAATTATTTTCTTTTAATTT
1 AACTATTT-CTTTATTTTCGCCTCTATATCTTTCTTTCGTCACTAAAATTATTTTCTTTT-ATTT
*
139987 TTGACACTATATGTTTCCTTCGTCGCTAA
64 TTGACACTATATCTTTCCTTCGTCGCTAA
* * * *
140016 AACTATTTTTTTATTTTCGCCGCTATAGCTTTCTCTCCGTCACTAAAATGTATTTTCTTTTATTT
1 AACTATTTCTTTATTTTCGCCTCTATATCTTTCT-TTCGTCACTAAAAT-TATTTTCTTTTATTT
*
140081 TTCAC-CGTATATCTTTTCCTTCGTCGCTAA
64 TTGACAC-TATATC-TTTCCTTCGTCGCTAA
140111 A
1 A
140112 GGTCATTTTT
Statistics
Matches: 167, Mismatches: 15, Indels: 17
0.84 0.08 0.09
Matches are distributed among these distances:
93 24 0.14
94 64 0.38
95 49 0.29
96 28 0.17
97 2 0.01
ACGTcount: A:0.20, C:0.22, G:0.08, T:0.50
Consensus pattern (92 bp):
AACTATTTCTTTATTTTCGCCTCTATATCTTTCTTTCGTCACTAAAATTATTTTCTTTTATTTTT
GACACTATATCTTTCCTTCGTCGCTAA
Found at i:140913 original size:44 final size:45
Alignment explanation
Indices: 140839--140928 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
140829 GTGTGTTTTC
* * * *
140839 TTTTATCTATGTATCTGAACGTAAACTATTAAAACCGGTTGTAACA
1 TTTTATC-ATGTATCTGAACATAAAATATTAAAACCGATCGTAACA
140885 TTTTATC-TGTATCTGAACATAAAATATTAAAACCGATCGTAACA
1 TTTTATCATGTATCTGAACATAAAATATTAAAACCGATCGTAACA
140929 CGATGTTACG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 33 0.82
46 7 0.17
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (45 bp):
TTTTATCATGTATCTGAACATAAAATATTAAAACCGATCGTAACA
Found at i:153208 original size:33 final size:33
Alignment explanation
Indices: 153144--153209 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
153134 CATCATGTCA
*
153144 CATTCAGAGCTAATTCATCCAAAGCCTCTTAAT
1 CATTCAGAGCTAATTCATCCAAAGCCCCTTAAT
* * *
153177 CATTCAGCGCTTAA-TCATTCAGAGCCCCTTAAT
1 CATTCAGAGC-TAATTCATCCAAAGCCCCTTAAT
153210 AATTGATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (33 bp):
CATTCAGAGCTAATTCATCCAAAGCCCCTTAAT
Found at i:157631 original size:30 final size:33
Alignment explanation
Indices: 157596--157680 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 33
157586 TAAAAACTAG
* *
157596 GTTTAATTAAAATTTTTTAAAATT-TGAGA-GA
1 GTTTAATTAAAATTATTTAAAATTACGAGAGGA
* * *
157627 -TTTAATGAGAATTATTTCAAATTACGAGAGGA
1 GTTTAATTAAAATTATTTAAAATTACGAGAGGA
* *
157659 GTTTAATTAAAAATATTCAAAA
1 GTTTAATTAAAATTATTTAAAA
157681 AAATTAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
30 19 0.46
31 4 0.10
32 2 0.05
33 16 0.39
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.39
Consensus pattern (33 bp):
GTTTAATTAAAATTATTTAAAATTACGAGAGGA
Found at i:170138 original size:16 final size:16
Alignment explanation
Indices: 170113--170145 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
170103 TACCGAATTT
*
170113 TAGGTGATGTCGTTTA
1 TAGGTAATGTCGTTTA
170129 TAGGTAATGTCGTTTA
1 TAGGTAATGTCGTTTA
170145 T
1 T
170146 GCAATGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.27, T:0.45
Consensus pattern (16 bp):
TAGGTAATGTCGTTTA
Found at i:174479 original size:31 final size:32
Alignment explanation
Indices: 174441--174505 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
174431 AATTCTATAT
*
174441 ATTATTAGTGAAT-AAATGATGTCACATCATC
1 ATTATTAGTGAATCAAATGATATCACATCATC
* *
174472 ATTATTAGTGAATCATATGATATCTCATCATC
1 ATTATTAGTGAATCAAATGATATCACATCATC
174504 AT
1 AT
174506 ACCTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (32 bp):
ATTATTAGTGAATCAAATGATATCACATCATC
Found at i:176038 original size:5 final size:5
Alignment explanation
Indices: 176028--176053 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
176018 ACAAAGAGTA
176028 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
176054 TGAATAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:180089 original size:20 final size:21
Alignment explanation
Indices: 180042--180089 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
180032 AATTATGTAA
180042 AATTATTA-CAAAATGATATT
1 AATTATTATCAAAATGATATT
* *
180062 AAAT-TTATCAAAATGTTA-T
1 AATTATTATCAAAATGATATT
180081 AATTATTAT
1 AATTATTAT
180090 AACATCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (21 bp):
AATTATTATCAAAATGATATT
Found at i:182152 original size:65 final size:65
Alignment explanation
Indices: 182048--182181 Score: 225
Period size: 65 Copynumber: 2.1 Consensus size: 65
182038 TTGTGACAAT
*
182048 ATTGGTACTTAAACTCTCACATTCACTCTTCTCCTAAGATTGATTTTCCA-TAAAATCCACTCAA
1 ATTGGTACTAAAACTCTCACATTCACTCTTCTCCTAAGATTGATTTT-CATTAAAATCCACTCAA
182112 A
65 A
* *
182113 ATTGGTACTAAAACTCTCACGTTCACTCTTCTCCTAAGATTTATTTTCATTAAAATCCACTCAAA
1 ATTGGTACTAAAACTCTCACATTCACTCTTCTCCTAAGATTGATTTTCATTAAAATCCACTCAAA
182178 ATTG
1 ATTG
182182 ATGAAATTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 2 0.03
65 63 0.97
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (65 bp):
ATTGGTACTAAAACTCTCACATTCACTCTTCTCCTAAGATTGATTTTCATTAAAATCCACTCAAA
Found at i:184138 original size:14 final size:14
Alignment explanation
Indices: 184119--184145 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
184109 AACATTGAAC
184119 GCTCACACCTCTGA
1 GCTCACACCTCTGA
184133 GCTCACACCTCTG
1 GCTCACACCTCTG
184146 GCATTCCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.44, G:0.15, T:0.22
Consensus pattern (14 bp):
GCTCACACCTCTGA
Found at i:187461 original size:16 final size:16
Alignment explanation
Indices: 187437--187477 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
187427 GATTTAAACT
*
187437 TAAAATAATT-TCATA
1 TAAAATAATTAGCATA
187452 TAAAAGTAATTAGCATA
1 TAAAA-TAATTAGCATA
187469 TAAAATAAT
1 TAAAATAAT
187478 CTAAATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (16 bp):
TAAAATAATTAGCATA
Found at i:188692 original size:31 final size:32
Alignment explanation
Indices: 188615--188675 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
188605 AAACCATTTT
188615 GTAAC-TTTAATAGTC-AGAGGACTTAATAAA
1 GTAACTTTTAATAGTCGAGAGGACTTAATAAA
188645 GTAACTTTTAATAGTCGAGA-GACTTAATAAA
1 GTAACTTTTAATAGTCGAGAGGACTTAATAAA
188676 TCAATTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 5 0.17
31 21 0.72
32 3 0.10
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (32 bp):
GTAACTTTTAATAGTCGAGAGGACTTAATAAA
Found at i:188945 original size:3 final size:3
Alignment explanation
Indices: 188937--188961 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
188927 TTGACCTAAC
188937 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
188962 TATAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:190250 original size:24 final size:24
Alignment explanation
Indices: 190223--190310 Score: 115
Period size: 24 Copynumber: 3.6 Consensus size: 24
190213 AATTTAATGA
*
190223 TTTTTAGGTACCTTTTATTACTTG
1 TTTTTAGTTACCTTTTATTACTTG
* **
190247 TTTTTAGTTACC-TTTATTTCCATAA
1 TTTTTAGTTACCTTTTA-TTAC-TTG
190272 TTTTTAGTTACCTTTTATTACTTG
1 TTTTTAGTTACCTTTTATTACTTG
190296 TTTTTAGTTACCTTT
1 TTTTTAGTTACCTTT
190311 ATTTCCATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
23 4 0.07
24 30 0.56
25 16 0.30
26 4 0.07
ACGTcount: A:0.18, C:0.14, G:0.08, T:0.60
Consensus pattern (24 bp):
TTTTTAGTTACCTTTTATTACTTG
Found at i:190275 original size:25 final size:25
Alignment explanation
Indices: 190247--190323 Score: 95
Period size: 24 Copynumber: 3.1 Consensus size: 25
190237 TTATTACTTG
190247 TTTTTAGTTACCTTTATTTCCATAA
1 TTTTTAGTTACCTTTATTTCCATAA
* **
190272 TTTTTAGTTACCTTT-TATTAC-TTG
1 TTTTTAGTTACCTTTAT-TTCCATAA
190296 TTTTTAGTTACCTTTATTTCCATTAA
1 TTTTTAGTTACCTTTATTTCCA-TAA
190322 TT
1 TT
190324 CAATCAACCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
24 20 0.48
25 19 0.45
26 3 0.07
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (25 bp):
TTTTTAGTTACCTTTATTTCCATAA
Found at i:190284 original size:49 final size:50
Alignment explanation
Indices: 190222--190323 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 50
190212 AAATTTAATG
190222 ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCA-TA
1 ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
*
190271 ATTTTTAGTTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
1 ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
190321 ATT
1 ATT
190324 CAATCAACCT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 46 0.90
50 5 0.10
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (50 bp):
ATTTTTAGGTACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTA
Found at i:190334 original size:49 final size:48
Alignment explanation
Indices: 190232--190339 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 48
190222 ATTTTTAGGT
* * *
190232 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATAATTTTTAGTT
1 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATAA-TTTCAATA
190281 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATTAA-TTCAATCA
1 ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCA-TAATTTCAAT-A
190330 ACCTTTTATT
1 ACCTTTTATT
190340 TATGTGCATT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
48 4 0.07
49 47 0.87
50 3 0.06
ACGTcount: A:0.22, C:0.17, G:0.05, T:0.56
Consensus pattern (48 bp):
ACCTTTTATTACTTGTTTTTAGTTACCTTTATTTCCATAATTTCAATA
Found at i:196461 original size:4 final size:4
Alignment explanation
Indices: 196452--196478 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
196442 ATGCATAACC
196452 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
196479 GCCTGCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:205720 original size:54 final size:54
Alignment explanation
Indices: 205638--205800 Score: 281
Period size: 54 Copynumber: 3.0 Consensus size: 54
205628 CGAGTCTCGA
* * * * *
205638 ATACGAGAATGTGTCCGGCATGTGTATGACGTCTCGAATATGGGAATGTGTCCG
1 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
205692 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
1 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
205746 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
1 ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
205800 A
1 A
205801 ATAGAGAATG
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (54 bp):
ATACGAGTACGTGTCTGACATGTGTATGATGTCTCGAATATGGGAATGTGTCCG
Found at i:205815 original size:18 final size:20
Alignment explanation
Indices: 205717--205821 Score: 66
Period size: 17 Copynumber: 5.7 Consensus size: 20
205707 TGACATGTGT
*
205717 ATGATGTCTCGAATATGGGA
1 ATGATGTCTCGAATATGAGA
* *
205737 ATG-TGTC-CG-ATACGAGT
1 ATGATGTCTCGAATATGAGA
* * * *
205754 ACG-TGTCT-G-ACATGTGT
1 ATGATGTCTCGAATATGAGA
*
205771 ATGATGTCTCGAATATGGGA
1 ATGATGTCTCGAATATGAGA
205791 ATG-TGTC-CGAATA-GAGA
1 ATGATGTCTCGAATATGAGA
*
205808 ATGATGTCTGGAAT
1 ATGATGTCTCGAAT
205822 TTGAACTTGT
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
17 25 0.38
18 17 0.26
19 13 0.20
20 11 0.17
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (20 bp):
ATGATGTCTCGAATATGAGA
Found at i:209498 original size:57 final size:57
Alignment explanation
Indices: 209437--209585 Score: 208
Period size: 58 Copynumber: 2.6 Consensus size: 57
209427 GGCACGTTAT
* * *
209437 GAAGATTTAATGCTTTGGGGTTTGAGCTAAAAACTAACATCTCGTGGAGTGCGTTGC
1 GAAGACTTAATGCTTTGGGGTTTGAGCTAAAAACTAACATCTCGTGGAGAGCGCTGC
* *
209494 GAAGACTTACTGCTTTGGGGTTTGAGTTAAAAAACTAACATCTCGTGGAGAGCGCTGC
1 GAAGACTTAATGCTTTGGGGTTTGAGCT-AAAAACTAACATCTCGTGGAGAGCGCTGC
* * * *
209552 AAAGGCTTAATGCTCTGGGGTTTGAGCTTAAAAC
1 GAAGACTTAATGCTTTGGGGTTTGAGCTAAAAAC
209586 ATCACGTGGG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
57 30 0.38
58 50 0.62
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (57 bp):
GAAGACTTAATGCTTTGGGGTTTGAGCTAAAAACTAACATCTCGTGGAGAGCGCTGC
Found at i:215600 original size:24 final size:22
Alignment explanation
Indices: 215552--215601 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
215542 ACTATTATTC
215552 TTATTTTATTTTAATTTTTTAA
1 TTATTTTATTTTAATTTTTTAA
215574 TTATTATT-TTTTATATTATTTTAA
1 TTATT-TTATTTTA-ATT-TTTTAA
215598 TTAT
1 TTAT
215602 ACGTTGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.40
23 5 0.20
24 10 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATTTTATTTTAATTTTTTAA
Found at i:220115 original size:3 final size:3
Alignment explanation
Indices: 220107--220673 Score: 905
Period size: 3 Copynumber: 191.0 Consensus size: 3
220097 TTTTATCCAT
220107 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
220155 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
220203 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
220251 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
220299 -TA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
220343 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
220391 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
220439 -TA TTA TTA TCA TTA TTA TCA TTA TTA TCA TTA TTA TCA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
220486 TTA TTA TCA TTA TTA TCA TTA TTA TCA TTA TTA TCA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
220534 TTA TCA TTA TTA TCA TTA TTA TCA TTA TTA TCA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
220582 TCA TTA TTA TCA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
220629 -TA TTA TTA TTA -TA TT- TTA TTA ATA TTA TTA TTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
220674 AATATATTAA
Statistics
Matches: 518, Mismatches: 38, Indels: 16
0.91 0.07 0.03
Matches are distributed among these distances:
2 14 0.03
3 501 0.97
4 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:221441 original size:13 final size:13
Alignment explanation
Indices: 221423--221451 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
221413 ACCACCGTTA
221423 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
221436 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
221449 CGG
1 CGG
221452 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:222042 original size:19 final size:19
Alignment explanation
Indices: 222004--222039 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
221994 CAATTTAGTC
222004 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
222023 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
222040 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:233422 original size:1 final size:1
Alignment explanation
Indices: 233416--233453 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
233406 ATTATGCTTG
* *
233416 AAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
233454 GGGGTCAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:234470 original size:52 final size:52
Alignment explanation
Indices: 234392--235054 Score: 1200
Period size: 52 Copynumber: 12.7 Consensus size: 52
234382 TATGTGCTCA
*
234392 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
234444 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
234496 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
234548 ATAGCATCTTCTGGAAGTGTTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
234601 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
234653 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
234705 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
234757 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
234809 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTTGAATAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
234861 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
234913 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
234965 ATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGATGGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
235017 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
235055 CGAAGAAGTG
Statistics
Matches: 590, Mismatches: 20, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
52 539 0.91
53 51 0.09
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:235742 original size:113 final size:113
Alignment explanation
Indices: 235615--236623 Score: 1651
Period size: 113 Copynumber: 8.9 Consensus size: 113
235605 GATTCAAATT
* * * *
235615 CATCATTTGATGGATCATCATTACCCGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
235680 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
* * * *
235728 CATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
235793 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
235841 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
235906 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
235954 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
***
236019 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
*
236067 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
236132 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAACC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
236180 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
236245 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
*
236293 CATCATTTGGTGGATCATCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
236358 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
*
236406 CATCATTTGGTGGATCATATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *** * *
236471 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTGTTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC-CTTTTACCTGAATC
* * * ** *
236520 CATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGG
*
236585 AAGAAGAAGTTCATAATGAGAA-AAGCTTGTTCAACCTTT
65 AAGAAGAAGTTCATAATGAGAAGAA-TTTGTTCAACCTTT
236624 GTTTGATATC
Statistics
Matches: 844, Mismatches: 49, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
113 742 0.88
114 44 0.05
115 58 0.07
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (113 bp):
CATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
Found at i:236926 original size:3 final size:3
Alignment explanation
Indices: 236918--237075 Score: 280
Period size: 3 Copynumber: 52.7 Consensus size: 3
236908 TTTTTATCCA
236918 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
236966 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
237014 TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
237062 TAT TTT TAT TAT TA
1 TAT TAT TAT TAT TA
237076 AATATATTAA
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 147 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:237845 original size:13 final size:13
Alignment explanation
Indices: 237827--237855 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
237817 ACCACCGTTA
237827 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
237840 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
237853 CGG
1 CGG
237856 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:238456 original size:19 final size:19
Alignment explanation
Indices: 238418--238453 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
238408 CAATTTAGTC
238418 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
238437 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
238454 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:240311 original size:205 final size:206
Alignment explanation
Indices: 239959--240370 Score: 763
Period size: 205 Copynumber: 2.0 Consensus size: 206
239949 TTCTACCAAA
* *
239959 TTCCATTCATCAGTCTTTCAGTTCAAGGAAACAAAATCTGAATTAAACTCACTTTAGTTATTTCC
1 TTCCATTCATCAGTCTTTCAGTTCAAGGAAACAAAAGCTGAATTAAACTCACTTTAGTTAGTTCC
*
240024 AACCAAAAGTTTGTTCATTTGCCCCTCACAATAGATATACTTAAGAATTGAACAAAAAATGCAGT
66 AACCAAAAGTTTGTTCATTTGCCCCTCACAATAGATATACTTAAGAATTGAACAAAAAACGCAGT
240089 ATTGCATTTCAACGTTACTA-GTGAGAAAAATAAATTGAAATCAAGAATGTTTAGTTGACTGTAA
131 ATTGCATTTCAACGTTACTATGTGAGAAAAATAAATTGAAATCAAGAATGTTTAGTTGACTGTAA
240153 AATCAATTTAC
196 AATCAATTTAC
*
240164 TTCCATTCATCAGTCTTTCAGTTCAAGGAAACAAAAGCTGATTTAAACTCACTTTAGTTAGTTCC
1 TTCCATTCATCAGTCTTTCAGTTCAAGGAAACAAAAGCTGAATTAAACTCACTTTAGTTAGTTCC
240229 AACCAAAAGTTTGTTCATTTGCCCCTCACAATAGATATACTTAAGAATTGAACAAAAAACGCAGT
66 AACCAAAAGTTTGTTCATTTGCCCCTCACAATAGATATACTTAAGAATTGAACAAAAAACGCAGT
240294 ATTGCATTTCAACGTTACTACTTGTGAGAAAAATAAATTGAAATCAAGAATGTTTAGTTGACTGT
131 ATTGCATTTCAACGTTACTA--TGTGAGAAAAATAAATTGAAATCAAGAATGTTTAGTTGACTGT
240359 AAAATCAATTTA
194 AAAATCAATTTA
240371 AGAGTGATAA
Statistics
Matches: 200, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
205 146 0.73
208 54 0.27
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.33
Consensus pattern (206 bp):
TTCCATTCATCAGTCTTTCAGTTCAAGGAAACAAAAGCTGAATTAAACTCACTTTAGTTAGTTCC
AACCAAAAGTTTGTTCATTTGCCCCTCACAATAGATATACTTAAGAATTGAACAAAAAACGCAGT
ATTGCATTTCAACGTTACTATGTGAGAAAAATAAATTGAAATCAAGAATGTTTAGTTGACTGTAA
AATCAATTTAC
Found at i:243344 original size:60 final size:60
Alignment explanation
Indices: 243251--243370 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
243241 ACAAAATAAG
243251 TGGTTCTACTTTTATATAGACTAATTATGCTATAATCGATATTAGTTTTCATTTCTGATC
1 TGGTTCTACTTTTATATAGACTAATTATGCTATAATCGATATTAGTTTTCATTTCTGATC
*
243311 TGGTTCTACTTTTATATAGACTAATTATGCTATAATCGATGTTAGTTTTCATTTCTGATC
1 TGGTTCTACTTTTATATAGACTAATTATGCTATAATCGATATTAGTTTTCATTTCTGATC
243371 AACTTTGAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.48
Consensus pattern (60 bp):
TGGTTCTACTTTTATATAGACTAATTATGCTATAATCGATATTAGTTTTCATTTCTGATC
Found at i:245573 original size:16 final size:16
Alignment explanation
Indices: 245554--245610 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
245544 AAACACTTCA
*
245554 AACCGAAATTAACTCG
1 AACCGAAAATAACTCG
245570 AACC-AAAAGTAAC-CTG
1 AACCGAAAA-TAACTC-G
*
245586 AACCGAAAATAACTTG
1 AACCGAAAATAACTCG
*
245602 AATCGAAAA
1 AACCGAAAA
245611 GCAACCTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 4 0.12
16 26 0.76
17 4 0.12
ACGTcount: A:0.51, C:0.21, G:0.12, T:0.16
Consensus pattern (16 bp):
AACCGAAAATAACTCG
Found at i:245599 original size:32 final size:33
Alignment explanation
Indices: 245554--245617 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
245544 AAACACTTCA
* *
245554 AACCGAAATTAACTCGAA-CCAAAAGTAACCTG
1 AACCGAAAATAACTCGAATCCAAAAGCAACCTG
* *
245586 AACCGAAAATAACTTGAATCGAAAAGCAACCT
1 AACCGAAAATAACTCGAATCCAAAAGCAACCT
245618 AAATCGAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.16
Consensus pattern (33 bp):
AACCGAAAATAACTCGAATCCAAAAGCAACCTG
Found at i:246772 original size:27 final size:29
Alignment explanation
Indices: 246742--246808 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
246732 TTAATATTTA
*
246742 TAATAATATA-ATATTCTA-TTTTTAGTT
1 TAATAATATAGATATTATATTTTTTAGTT
*
246769 TAATAATATAAGATATTATATTTTTTATTT
1 TAATAATAT-AGATATTATATTTTTTAGTT
246799 TAATAATATA
1 TAATAATATA
246809 TAATAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 9 0.26
28 1 0.03
29 8 0.23
30 17 0.49
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
TAATAATATAGATATTATATTTTTTAGTT
Found at i:246818 original size:27 final size:29
Alignment explanation
Indices: 246736--246835 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
246726 TATTTATTAA
* *
246736 TATTTATAATAATATAATAT-TCTA-TTTT
1 TATTT-TAATAATATAAGATATATATTTTT
*
246764 TAGTTTAATAATATAAGATATTATATTTTT
1 TATTTTAATAATATAAGATA-TATATTTTT
*
246794 TATTTTAATAATATATA-ATAAAT-TTTTT
1 TATTTTAATAATATA-AGATATATATTTTT
246822 ATATATTTAATAAT
1 -TAT-TTTAATAAT
246836 GAATAATATT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
27 13 0.21
28 9 0.15
29 8 0.13
30 30 0.49
31 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (29 bp):
TATTTTAATAATATAAGATATATATTTTT
Found at i:246831 original size:30 final size:29
Alignment explanation
Indices: 246722--246867 Score: 89
Period size: 30 Copynumber: 5.0 Consensus size: 29
246712 AAATATTTAA
*
246722 AATATATTTATTA-ATATTT-ATAATAATAT
1 AATA-ATTTTTTATATATTTAATAAT-ATAT
246751 AAT-ATTCTATTT-T-TAGTTTAATAATATA-
1 AATAATT-T-TTTATATA-TTTAATAATATAT
246779 AGATATTATATTTTT-TAT-TTTAATAATATAT
1 A-ATA--AT-TTTTTATATATTTAATAATATAT
246810 AATAAATTTTTTATATATTTAATAATGA-AT
1 AAT-AATTTTTTATATATTTAATAAT-ATAT
* *
246840 AAT-ATTATTTATATATTTAA-AACATAT
1 AATAATTTTTTATATATTTAATAATATAT
246867 A
1 A
246868 CTAGTAAAGA
Statistics
Matches: 97, Mismatches: 3, Indels: 36
0.71 0.02 0.26
Matches are distributed among these distances:
26 1 0.01
27 8 0.08
28 25 0.26
29 18 0.19
30 33 0.34
31 7 0.07
32 4 0.04
33 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (29 bp):
AATAATTTTTTATATATTTAATAATATAT
Found at i:246859 original size:28 final size:27
Alignment explanation
Indices: 246776--246867 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 27
246766 GTTTAATAAT
* *
246776 ATAAGATATTATATTTTT-TAT-TTTA
1 ATAATATATAATATTTTTATATATTTA
246801 ATAATATATAATAAATTTTTTATATATTTA
1 ATAATATATAAT--A-TTTTTATATATTTA
246831 ATAATGA-ATAATATTATTTATATATTTA
1 ATAAT-ATATAATATT-TTTATATATTTA
*
246859 A-AACATATA
1 ATAATATATA
246868 CTAGTAAAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
25 10 0.18
26 1 0.02
27 8 0.14
28 19 0.34
29 3 0.05
30 14 0.25
31 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (27 bp):
ATAATATATAATATTTTTATATATTTA
Found at i:246893 original size:23 final size:23
Alignment explanation
Indices: 246852--246913 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
246842 TATTATTTAT
*
246852 ATATTTAAAACATATACTAGTAAAG
1 ATATTT-AAA-ATATACTAATAAAG
* *
246877 ATATTTAAAATATACTAATTAAT
1 ATATTTAAAATATACTAATAAAG
*
246900 ATTTTTAAAATATA
1 ATATTTAAAATATA
246914 ATATAACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 24 0.73
24 3 0.09
25 6 0.18
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (23 bp):
ATATTTAAAATATACTAATAAAG
Found at i:246994 original size:90 final size:85
Alignment explanation
Indices: 246882--247050 Score: 198
Period size: 90 Copynumber: 1.9 Consensus size: 85
246872 TAAAGATATT
* * * * *
246882 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTACTTTAATAAATAATTAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATA-TA-TTTAAT-AATAAATAA
246945 TATAATTTATAATATTTTATTTCAC
63 -ATAATTT-TAATATTTTATTTCAC
*
246970 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATATATTTAATAATAAATAAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATATATTTAATAATAAATAAA
*
247035 TTATTTTAATATTTTA
64 TAATTTTAATATTTTA
247051 AAATAATAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
87 10 0.14
88 15 0.21
89 10 0.14
90 19 0.27
91 8 0.11
92 8 0.11
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.46
Consensus pattern (85 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATATATTTAATAATAAATAAATA
ATTTTAATATTTTATTTCAC
Found at i:247252 original size:20 final size:20
Alignment explanation
Indices: 247194--247243 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
247184 TTTCCAGATG
247194 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
247214 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
247234 TTTTCCAGAA
1 TTTTCCAGAA
247244 TTCAAATTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Done.