Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 9 of 126
Found at i:2977420 original size:21 final size:21
Alignment explanation
Indices: 2977356--2977421 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
2977346 AAGAAAAGCA
2977356 AAATTGAAAAAGAGAAAGATT
1 AAATTGAAAAAGAGAAAGATT
*
2977377 AAATT-ATCAAAGA-AAAGCA--
1 AAATTGA-AAAAGAGAAAG-ATT
2977396 AAATTGAAAAAGAGAAAGATT
1 AAATTGAAAAAGAGAAAGATT
2977417 AAATT
1 AAATT
2977422 ACACAATGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
19 11 0.30
20 10 0.27
21 16 0.43
ACGTcount: A:0.62, C:0.03, G:0.15, T:0.20
Consensus pattern (21 bp):
AAATTGAAAAAGAGAAAGATT
Found at i:2978095 original size:18 final size:18
Alignment explanation
Indices: 2978063--2978114 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
2978053 TTAGGACGAG
2978063 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
2978079 AATAAATTTAATTAATTA
1 AATAAATTTAATTAATTA
*
2978097 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
2978115 CACTTTGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 18 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:2978947 original size:16 final size:16
Alignment explanation
Indices: 2978926--2978956 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2978916 TATATATTAT
2978926 TTTTAAAAAAAATAAA
1 TTTTAAAAAAAATAAA
*
2978942 TTTTAAAAAATATAA
1 TTTTAAAAAAAATAA
2978957 TATATCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTTAAAAAAAATAAA
Found at i:2979119 original size:11 final size:11
Alignment explanation
Indices: 2979077--2979110 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
2979067 AAATACCTCG
2979077 AAAATAATAAT
1 AAAATAATAAT
2979088 AAAATTAATAAT
1 AAAA-TAATAAT
2979100 AAAATAATAAT
1 AAAATAATAAT
2979111 TATATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:2982941 original size:16 final size:16
Alignment explanation
Indices: 2982905--2982961 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2982895 GAAAAAAAGC
*
2982905 TTTTAGTAATTTTTATAT
1 TTTTAATAA-TTTT-TAT
*
2982923 TTTTAATAGTTTTTAT
1 TTTTAATAATTTTTAT
* *
2982939 TTTTTATAATTTTAAGT
1 TTTTAATAATTTTTA-T
2982956 TTTTAA
1 TTTTAA
2982962 AATATATGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
16 15 0.47
17 10 0.31
18 7 0.22
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (16 bp):
TTTTAATAATTTTTAT
Found at i:2982944 original size:25 final size:23
Alignment explanation
Indices: 2982914--2982960 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
2982904 CTTTTAGTAA
*
2982914 TTTTTATATTTTTAATAGTTTTTAT
1 TTTTTATAATTTT-A-AGTTTTTAT
2982939 TTTTTATAATTTTAAGTTTTTA
1 TTTTTATAATTTTAAGTTTTTA
2982961 AAATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 12 0.57
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTATAATTTTAAGTTTTTAT
Found at i:2985099 original size:28 final size:30
Alignment explanation
Indices: 2985069--2985124 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
2985059 TTTATGGAAC
* *
2985069 AAATTTT-TAATATAAATTCAACACTTGCA
1 AAATTTTGCAATAAAAATTCAACACTTGCA
*
2985098 AAATTTTGCAATAAAAATTCAGCACTT
1 AAATTTTGCAATAAAAATTCAACACTT
2985125 AATTTTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (30 bp):
AAATTTTGCAATAAAAATTCAACACTTGCA
Found at i:2997324 original size:17 final size:17
Alignment explanation
Indices: 2997302--2997340 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2997292 AGGTGGAGAA
* *
2997302 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
2997319 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
2997336 CTTGT
1 CTTGT
2997341 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:3002725 original size:16 final size:16
Alignment explanation
Indices: 3002704--3002740 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3002694 CGTCATCATG
3002704 TCATTGAGACAAAGCT
1 TCATTGAGACAAAGCT
* *
3002720 TCATTGAGACAGAGTT
1 TCATTGAGACAAAGCT
3002736 TCATT
1 TCATT
3002741 AAACTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (16 bp):
TCATTGAGACAAAGCT
Found at i:3013767 original size:3 final size:3
Alignment explanation
Indices: 3013759--3013799 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3013749 CTACCAAAAT
3013759 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3013800 AAACAAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3014756 original size:16 final size:16
Alignment explanation
Indices: 3014732--3014769 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
3014722 TTTACTTTTA
*
3014732 TTTACTATCATCAAAT
1 TTTATTATCATCAAAT
3014748 TTTATTATCATCAAAT
1 TTTATTATCATCAAAT
3014764 TTTATT
1 TTTATT
3014770 TCTCTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATTATCATCAAAT
Found at i:3016567 original size:3 final size:3
Alignment explanation
Indices: 3016559--3016590 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3016549 TATATGTCAT
3016559 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3016591 TTAAGACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3018716 original size:29 final size:29
Alignment explanation
Indices: 3018660--3018717 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
3018650 TATTTTATAT
* *
3018660 ATTTTATAATTAAATTTAAATTTAAAAAC
1 ATTTTATAATTAAATTGAAATATAAAAAC
*
3018689 ATTTTATTATTTAAATTGAAATATAAAAA
1 ATTTTA-TAATTAAATTGAAATATAAAAA
3018718 TACTTGACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
ATTTTATAATTAAATTGAAATATAAAAAC
Found at i:3020339 original size:61 final size:60
Alignment explanation
Indices: 3020274--3020404 Score: 138
Period size: 61 Copynumber: 2.1 Consensus size: 60
3020264 ATCTTGAATA
* * * * * *
3020274 TAAAATATTCAAAAAATTTAACCCTCAATGTTTACAAAAT-TTATCATTTTAGTTCTAATTC
1 TAAAAAATT-AAAAAATTTAACCCTCAATATTTACAAAATCAT-TCAATTTAGTCCTAACTC
* ** *
3020335 TAAAAAAATTAATAAATTTGGCCCTCAATATTTATAAAATCATTCAATTTAGTCCTAACTC
1 T-AAAAAATTAAAAAATTTAACCCTCAATATTTACAAAATCATTCAATTTAGTCCTAACTC
3020396 TAAAAAATT
1 TAAAAAATT
3020405 TTTAAAGTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
60 8 0.14
61 42 0.72
62 8 0.14
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (60 bp):
TAAAAAATTAAAAAATTTAACCCTCAATATTTACAAAATCATTCAATTTAGTCCTAACTC
Found at i:3022869 original size:13 final size:12
Alignment explanation
Indices: 3022851--3022901 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
3022841 TAAAATATCC
3022851 TAATTTTTTTATA
1 TAATTTTTTT-TA
3022864 TAATTTATTTTGTA
1 TAATTT-TTTT-TA
* *
3022878 -AATTTATTTTG
1 TAATTTTTTTTA
3022889 TAATTTTTTTTA
1 TAATTTTTTTTA
3022901 T
1 T
3022902 TTATATTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 1 0.03
12 13 0.42
13 11 0.35
14 6 0.19
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (12 bp):
TAATTTTTTTTA
Found at i:3031474 original size:29 final size:28
Alignment explanation
Indices: 3031438--3031630 Score: 95
Period size: 28 Copynumber: 6.7 Consensus size: 28
3031428 TTGACTTTCG
*
3031438 AGGGTAAAAATGTGATTTTGGAAAATTT
1 AGGGTTAAAATGTGATTTTGGAAAATTT
* * *** *
3031466 AGGGTTAAAATGGGATTTTAGATGGTTCG
1 AGGGTTAAAATGTGATTTTGGAAAATT-T
* **
3031495 AGGG-TAAAATGGTAATTTTTGGTAAAATCG
1 AGGGTTAAAAT-GTGA-TTTTGG-AAAATTT
* * *
3031525 A-GGTTAAAATGGGATTTTGGAAAGTTC
1 AGGGTTAAAATGTGATTTTGGAAAATTT
* * *
3031552 AGGGGTAAAATGGTAATTTTAGGTAAATTT
1 AGGGTTAAAAT-GTGATTTT-GGAAAATTT
* *
3031582 GGGGTTAAAAATG-GAATTTTGGAAAGTTT
1 AGGGTT-AAAATGTG-ATTTTGGAAAATTT
* * *
3031611 GGGGGTAAAATAGTAATTTT
1 AGGGTTAAAAT-GTGATTTT
3031631 TGGTGAAATT
Statistics
Matches: 121, Mismatches: 32, Indels: 23
0.69 0.18 0.13
Matches are distributed among these distances:
27 5 0.04
28 46 0.38
29 34 0.28
30 29 0.24
31 7 0.06
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.35
Consensus pattern (28 bp):
AGGGTTAAAATGTGATTTTGGAAAATTT
Found at i:3031627 original size:59 final size:59
Alignment explanation
Indices: 3031496--3031928 Score: 554
Period size: 59 Copynumber: 7.4 Consensus size: 59
3031486 GATGGTTCGA
* * * *
3031496 GGGTAAAATGGTAATTTTTGGTAAAATCGAGGTT-AAAATGGGATTTTGGAAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
3031554 GGGTAAAATGGTAATTTTAGGT-AAATTTGGGGTTAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * * * *
3031613 GGGTAAAATAGTAATTTTTGGTGAAATTGTGGTTAAAAATGAAATCTTGGAAAGTTTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
*
3031672 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* ** * * *
3031731 AGGTAAAAT-AAAATTTTTGGTAAAATCGGGGTT-AAAATGGAATTTAGGAAAGATTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTTAG
** *
3031789 GGGTAAAAATGGTAA-TTTTGGATGAAATTAGGGTTAAAAATGGAATCTTGGAAAGTTT-G
1 GGGT-AAAATGGTAATTTTTGG-TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
*
3031848 GGAGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GG-GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
*
3031908 GGGTAAAATGGTAAGTTTTGG
1 GGGTAAAATGGTAATTTTTGG
3031929 AAGTTTTGGG
Statistics
Matches: 323, Mismatches: 41, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
57 21 0.07
58 54 0.17
59 203 0.63
60 28 0.09
61 17 0.05
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:3031826 original size:177 final size:176
Alignment explanation
Indices: 3031495--3031917 Score: 622
Period size: 177 Copynumber: 2.4 Consensus size: 176
3031485 AGATGGTTCG
* * * * *
3031495 AGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTT-AAAATGGGATTTTGGAAAGTTCAGGGGTA
1 AGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
** * * *
3031559 AAATGGTAATTTTAGGTAAATTTGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATAG
66 AAATGAAAATTTTAGGTAAAATCGGGGTTAAAAATGGAATTTAGGAAAGTTTGGGGGTAAAATAG
3031624 TAATTTTTGGTGAAATTGTGGTTAAAAATGAAATCTTGGAAAGTTT
131 TAATTTTTGGTGAAATTGTGGTTAAAAATGAAATCTTGGAAAGTTT
*
3031670 AAGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGAGGT
1 -AGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*
3031735 AAAAT-AAAATTTTTGGTAAAATCGGGGTT-AAAATGGAATTTAGGAAAGATTTGGGGGTAAAAA
65 AAAATGAAAATTTTAGGTAAAATCGGGGTTAAAAATGGAATTTAGGAAAG-TTTGGGGGT-AAAA
* *
3031798 TGGTAA-TTTTGGATGAAATTAG-GGTTAAAAATGGAATCTTGGAAAGTTT
128 TAGTAATTTTTGG-TGAAATT-GTGGTTAAAAATGAAATCTTGGAAAGTTT
*
3031847 GGGAGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AGG-GTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
3031912 AAAATG
65 AAAATG
3031918 GTAAGTTTTG
Statistics
Matches: 224, Mismatches: 16, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
175 18 0.08
176 68 0.30
177 137 0.61
178 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.29, T:0.33
Consensus pattern (176 bp):
AGGGTAAAATGGTAATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
AAATGAAAATTTTAGGTAAAATCGGGGTTAAAAATGGAATTTAGGAAAGTTTGGGGGTAAAATAG
TAATTTTTGGTGAAATTGTGGTTAAAAATGAAATCTTGGAAAGTTT
Found at i:3031994 original size:29 final size:28
Alignment explanation
Indices: 3031438--3031996 Score: 133
Period size: 29 Copynumber: 19.1 Consensus size: 28
3031428 TTGACTTTCG
* * * *
3031438 AGGGTAAAAATGTGATTTTGGAAAATTT
1 AGGGTTAAAATGTAATTTTTGAAAGTTT
** * ** *
3031466 AGGGTTAAAATGGGATTTTAGATGGTTCG
1 AGGGTTAAAATGTAATTTTTGAAAGTT-T
* **
3031495 AGGG-TAAAATGGTAATTTTTGGTAAAATCG
1 AGGGTTAAAAT-GTAATTTTT-G-AAAGTTT
** * *
3031525 A-GGTTAAAATGGGATTTTGGAAAGTTC
1 AGGGTTAAAATGTAATTTTTGAAAGTTT
* *
3031552 AGGGGTAAAATGGTAATTTTAGGTAAA-TTT
1 AGGGTTAAAAT-GTAATTTT-TG-AAAGTTT
* * *
3031582 GGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGTT-AAAATGTAATTTTTGAAAGTTT
* *
3031611 GGGGGTAAAATAGTAATTTTTGGTGAAA--TT
1 AGGGTTAAAAT-GTAA-TTTT--TGAAAGTTT
* * *
3031641 -GTGGTTAAAAATGAAATCTTGGAAAGTTT
1 AG-GGTT-AAAATGTAATTTTTGAAAGTTT
*
3031670 AAGGG-TAAAATGGTAATTTTGGGTGAAA--TC
1 -AGGGTTAAAAT-GTAATTTT---TGAAAGTTT
* * *
3031700 GGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGTT-AAAATGTAATTTTTGAAAGTTT
** * *
3031729 AGAGG-TAAAATAAAATTTTTGGTAAA-ATC
1 AG-GGTTAAAATGTAATTTTT-G-AAAGTTT
* * **
3031758 GGGGTTAAAATGGAATTTAGGAAAGATTT
1 AGGGTTAAAATGTAATTTTTGAAAG-TTT
* *
3031787 GGGGGTAAAAATGGTAATTTTGGATGAAA--TT
1 -AGGGTTAAAAT-GTAATTTT---TGAAAGTTT
* * *
3031818 AGGGTTAAAAATGGAATCTTGGAAAGTTT
1 AGGGTT-AAAATGTAATTTTTGAAAGTTT
* *
3031847 -GGGAGTAAAATGGTAATTTTGGGTGAAA--TC
1 AGGG-TTAAAAT-GTAATTTT---TGAAAGTTT
* * *
3031877 GGGGTTAAAAATGGAATTTTGGAAAGTTT
1 AGGGTT-AAAATGTAATTTTTGAAAGTTT
* * *
3031906 AGGGGTAAAATGGTAAGTTTTGGAAGTTT
1 AGGGTTAAAAT-GTAATTTTTGAAAGTTT
* * * ** *
3031935 TGGGTCAAAATATAATTTTCCAAATTTTT
1 AGGGTTAAAATGTAATTTTTGAAA-GTTT
3031964 AGGGTTAAAATGTAATTTTTGAATAGTTT
1 AGGGTTAAAATGTAATTTTTGAA-AGTTT
3031993 AGGG
1 AGGG
3031997 ACTTATACAC
Statistics
Matches: 382, Mismatches: 94, Indels: 109
0.65 0.16 0.19
Matches are distributed among these distances:
27 24 0.06
28 84 0.22
29 134 0.35
30 82 0.21
31 42 0.11
32 12 0.03
34 4 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (28 bp):
AGGGTTAAAATGTAATTTTTGAAAGTTT
Found at i:3033945 original size:6 final size:6
Alignment explanation
Indices: 3033930--3033988 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
3033920 TTAAATTTGA
* * *
3033930 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
3033978 ATAAAT TTAAA
1 TTAAAT TTAAA
3033989 ACCCATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:3033964 original size:14 final size:14
Alignment explanation
Indices: 3033945--3033972 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3033935 CTTAAATTTA
3033945 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
3033959 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
3033973 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:3034096 original size:28 final size:26
Alignment explanation
Indices: 3034065--3034152 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 26
3034055 TTCAAGCCCA
*
3034065 AAACAGAGTAATGCTCTTATCGAGCCAG
1 AAACAGAAT-ATGCTCTT-TCGAGCCAG
*
3034093 AAACAGAATCACGCTCCTTTCGAGCCAG
1 AAACAGAAT-ATGCT-CTTTCGAGCCAG
* *
3034121 AATCAGAATATCGCTCTTTCAAGCCAG
1 AAACAGAATAT-GCTCTTTCGAGCCAG
3034148 AAACA
1 AAACA
3034153 AAACTTTGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 16 0.31
28 32 0.63
29 3 0.06
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (26 bp):
AAACAGAATATGCTCTTTCGAGCCAG
Found at i:3034147 original size:27 final size:27
Alignment explanation
Indices: 3034077--3034152 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 27
3034067 ACAGAGTAAT
3034077 GCTCTTATCGAGCCAGAAACAGAATCAC
1 GCTCTT-TCGAGCCAGAAACAGAATCAC
*
3034105 GCTCCTTTCGAGCCAGAATCAGAAT-ATC
1 GCT-CTTTCGAGCCAGAAACAGAATCA-C
*
3034133 GCTCTTTCAAGCCAGAAACA
1 GCTCTTTCGAGCCAGAAACA
3034153 AAACTTTGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 16 0.37
28 24 0.56
29 3 0.07
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (27 bp):
GCTCTTTCGAGCCAGAAACAGAATCAC
Found at i:3038667 original size:6 final size:6
Alignment explanation
Indices: 3038645--3038700 Score: 78
Period size: 6 Copynumber: 9.2 Consensus size: 6
3038635 TTAAATTGAT
*
3038645 TTTAAA TTTAATTA TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3038694 TTTAAA T
1 TTTAAA T
3038701 ACTAAACATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
5 4 0.09
6 35 0.78
8 6 0.13
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:3038675 original size:11 final size:11
Alignment explanation
Indices: 3038635--3038700 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
3038625 TAATTTGGAG
* *
3038635 TTAAATTGATT
1 TTAAATTTAAT
3038646 TTAAATTTAATTAT
1 TTAAATTT-A--AT
*
3038660 TTAAATTTACT
1 TTAAATTTAAT
3038671 TTAAATTTAAAT
1 TTAAATTT-AAT
3038683 TTAAATTTAAAT
1 TTAAATTT-AAT
3038695 TTAAAT
1 TTAAAT
3038701 ACTAAACATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
11 16 0.34
12 21 0.45
13 1 0.02
14 9 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:3040650 original size:30 final size:30
Alignment explanation
Indices: 3040599--3040867 Score: 271
Period size: 30 Copynumber: 9.0 Consensus size: 30
3040589 CCCTAAATTG
* * *
3040599 TCCAGAAATTACATTTCGACCCTAAGACTTT
1 TCCA-AAATTATATTTTGACCCTAAAACTTT
** *
3040630 TTGAAAATTATATCTTGACCCTAAAAC-TT
1 TCCAAAATTATATTTTGACCCTAAAACTTT
* * *
3040659 TCTGAAAATTACATTTTAACCCCT-AAACTTT
1 TC-CAAAATTATATTTTGA-CCCTAAAACTTT
3040690 TCCAAAATTATATTTTGACCCTAAAACTTT
1 TCCAAAATTATATTTTGACCCTAAAACTTT
*
3040720 TCCAAAATTAAATTTTGACCCTAAAACTTT
1 TCCAAAATTATATTTTGACCCTAAAACTTT
* *
3040750 CCCAAAATTATATTTTGACCCCAAAAC-TT
1 TCCAAAATTATATTTTGACCCTAAAACTTT
* * *
3040779 TCTAAAAATTACATTTTAACCC-AAAACTTT
1 TC-CAAAATTATATTTTGACCCTAAAACTTT
*
3040809 TCCAAAATTACATTTTGACTCC-AAAACTTT
1 TCCAAAATTATATTTTGAC-CCTAAAACTTT
* * * *
3040839 TTCAAAATTATACTTTAACCC-GAAACTTT
1 TCCAAAATTATATTTTGACCCTAAAACTTT
3040868 GAAAAATTAC
Statistics
Matches: 203, Mismatches: 28, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
29 39 0.19
30 154 0.76
31 10 0.05
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCTAAAACTTT
Found at i:3040670 original size:60 final size:60
Alignment explanation
Indices: 3040604--3040867 Score: 313
Period size: 60 Copynumber: 4.4 Consensus size: 60
3040594 AATTGTCCAG
** * ** * *
3040604 AAATTACATTTCGACCCTAAGACTTTTTGAAAATTATATCTTGACCCTAAAACTTTCTGA
1 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTCA
3040664 AAATTACATTTTAACCCCT-AAACTTTTCCAAAATTATATTTTGACCCTAAAACTTT-TCCA
1 AAATTACATTTTAA-CCCTAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCT-CA
* * * * *
3040724 AAATTAAATTTTGACCCTAAAACTTTCCCAAAATTATATTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTCA
* *
3040784 AAATTACATTTTAACCC-AAAACTTTTCCAAAATTACATTTTGACTCC-AAAACTTTTTCA
1 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTTGAC-CCTAAAACTTTCTCA
* * *
3040843 AAATTATACTTTAACCC-GAAACTTT
1 AAATTACATTTTAACCCTAAAACTTT
3040868 GAAAAATTAC
Statistics
Matches: 178, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
59 62 0.35
60 111 0.62
61 5 0.03
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.37
Consensus pattern (60 bp):
AAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTCTCA
Found at i:3040742 original size:90 final size:90
Alignment explanation
Indices: 3040589--3040867 Score: 325
Period size: 90 Copynumber: 3.1 Consensus size: 90
3040579 CTTTATAAGT
* * * ** * *
3040589 CCCTAAA-TTGTCCAGAAATTACATTTCGACCCTAAGACTTTTTGAAAATTATATCTTGACCCTA
1 CCCTAAACTTTTCCA-AAATTACATTTTGACCCTAAAACTTTTCCAAAATTAAATTTTGACCCTA
* *
3040653 AAACTTTCTGAAAATTACATTTTAAC
65 AAACTTTCTCAAAATTATATTTTAAC
*
3040679 CCCTAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTTCCAAAATTAAATTTTGACCCTAA
1 CCCTAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTAAATTTTGACCCTAA
* *
3040744 AACTTTCCCAAAATTATATTTTGAC
66 AACTTTCTCAAAATTATATTTTAAC
* * * *
3040769 CCCAAAAC-TTTCTAAAAATTACATTTTAACCC-AAAACTTTTCCAAAATTACATTTTGACTCC-
1 CCCTAAACTTTTC-CAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTAAATTTTGAC-CCT
* *
3040831 AAAACTTTTTCAAAATTATACTTTAA-
64 AAAACTTTCTCAAAATTATATTTTAAC
*
3040857 CCCGAAACTTT
1 CCCTAAACTTT
3040868 GAAAAATTAC
Statistics
Matches: 163, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
88 7 0.04
89 54 0.33
90 96 0.59
91 6 0.04
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.36
Consensus pattern (90 bp):
CCCTAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAAAATTAAATTTTGACCCTAA
AACTTTCTCAAAATTATATTTTAAC
Found at i:3040892 original size:59 final size:59
Alignment explanation
Indices: 3040633--3040895 Score: 244
Period size: 60 Copynumber: 4.4 Consensus size: 59
3040623 AGACTTTTTG
* * * * * * *
3040633 AAAATTATATCTTGACCCTAAAACTTTCTGAAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACACTTTAA-CCCAAAACTTTTCA
* * * * * * * *
3040693 AAAATTATATTTTGACCCTAAAACTTT-TCCAAAATTAAATTTTGACCCTAAAACTTTCCC
1 AAAATTACATTTTGACCCCAAAACTTTCT-AAAAATTACACTTTAACCC-AAAACTTTTCA
* * *
3040753 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTAACCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACACTTTAACCCAAAACTTTTCA
* * * * * *
3040812 AAAATTACATTTTGACTCCAAAACTTTTTCAAAATTATACTTTAACCCGAAAC-TTTGA
1 AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACACTTTAACCCAAAACTTTTCA
*
3040870 AAAATTACCATTTT-ACCCCCAAACTT
1 AAAATTA-CATTTTGACCCCAAAACTT
3040896 CCCTAAATCC
Statistics
Matches: 177, Mismatches: 22, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
58 20 0.11
59 66 0.37
60 90 0.51
61 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAATTACATTTTGACCCCAAAACTTTCTAAAAATTACACTTTAACCCAAAACTTTTCA
Found at i:3052898 original size:69 final size:68
Alignment explanation
Indices: 3052783--3053545 Score: 1019
Period size: 69 Copynumber: 10.9 Consensus size: 68
3052773 ATCATTTCCT
* *
3052783 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCGAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAAC
3052848 GTC
66 GTC
* **
3052851 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAA
3052916 CGTC
65 CGTC
* *
3052920 ATCCTCTTGAAATTGAAGTAGAGTGGATACCACGCCTTTATCTTTGAAATTGAAGTAAGAGCAA-
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAAC
3052984 GATC
66 G-TC
* *
3052988 ATTTCCTATCCCCTTGAAATTGAGGTAGAGTGGATAATACGCCTTTATCTCTGAAATTGAAGTAA
1 A--TCC--T---CTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAA
* * * *
3053053 GAACGACATA
59 GAGCAACGTC
* * **
3053063 ATCCGCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAA
3053128 CGTC
65 CGTC
* ** * *
3053132 ATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAA
3053197 CGTC
65 CGTC
*
3053201 ATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAA-
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAAC
3053265 GATC
66 G-TC
3053269 ATTTCCTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAA
1 A--TCC--T---CTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAA
*
3053334 GAGCGACGTC
59 GAGCAACGTC
**
3053344 AT-CTGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCT-CTTGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCA
3053408 ACGTC
64 ACGTC
* ** * *
3053413 ATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAA
3053478 CGTC
65 CGTC
*
3053482 ATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAA
3053546 GATTACCGAT
Statistics
Matches: 622, Mismatches: 51, Indels: 44
0.87 0.07 0.06
Matches are distributed among these distances:
67 2 0.00
68 173 0.28
69 315 0.51
70 9 0.01
72 3 0.00
73 4 0.01
75 115 0.18
76 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (68 bp):
ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:3053136 original size:212 final size:205
Alignment explanation
Indices: 3052783--3053545 Score: 1055
Period size: 212 Copynumber: 3.6 Consensus size: 205
3052773 ATCATTTCCT
* *
3052783 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCGAC
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAACGAC
* *
3052848 GTCATCCGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAG
66 ATCATCCGCTTGAAATTGAAGTAGAG-TGGATAACACACCTTTATCTCTGAAATTGAAGTAAGAG
* **
3052913 CAACGTCATCCTCTTGAAATTGAAGTAGAG-TGGATACCACGCCTTTATCTTTGAAATTGAAGTA
130 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTTTGAAATTGAAGTA
3052977 AGAGCAA-GATC
195 AGAGCAACG-TC
* *
3052988 ATTTCCTATCCCCTTGAAATTGAGGTAGAGTGGATAATACGCCTTTATCTCTGAAATTGAAGTAA
1 A--TCC--T---CTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAA
* * *
3053053 GAACGACATAATCCGCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTCTGAAATTGAA
59 GAACGACATCATCCGCTTGAAATTGAAGTAGAG-TGGATAACACACCTTTATCTCTGAAATTGAA
*
3053118 GTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAAT
123 GTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTTTGAAAT
*
3053183 TGAAGAAAGAGCAACGTC
188 TGAAGTAAGAGCAACGTC
* *
3053201 ATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCAAG
1 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGA--ACG
* *
3053266 ATCATTTCCTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAG
64 A-CA--T-C-ATCCGCTTGAAATTGAAGTAGAGTGGATAACACACCTTTATCTCTGAAATTGAAG
* *
3053331 TAAGAGCGACGTCAT-CTGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAAT
124 TAAGAGCAACGTCATCCT-CTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTTTGAAAT
3053395 TGAAGTAAGAGCAACGTC
188 TGAAGTAAGAGCAACGTC
* ** * * * *
3053413 ATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAACGA
* * * *
3053478 CGTCATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAG
65 CATCATCCGCTTGAAATTGAAGTAGAGTGGATAACACACCTTTATCTCTGAAATTGAAGTAAGAG
3053543 CAA
130 CAA
3053546 GATTACCGAT
Statistics
Matches: 502, Mismatches: 38, Indels: 35
0.87 0.07 0.06
Matches are distributed among these distances:
205 1 0.00
206 113 0.23
207 4 0.01
208 4 0.01
209 3 0.01
210 1 0.00
211 7 0.01
212 274 0.55
213 94 0.19
214 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (205 bp):
ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAACGAC
ATCATCCGCTTGAAATTGAAGTAGAGTGGATAACACACCTTTATCTCTGAAATTGAAGTAAGAGC
AACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTTTGAAATTGAAGTAA
GAGCAACGTC
Found at i:3053146 original size:31 final size:31
Alignment explanation
Indices: 3053108--3053217 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
3053098 TCTTTATCTC
3053108 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
* * * *
3053139 TGAAATTGAAGTAAAGTTGGATAAC-ACATCTTTATCTT
1 TGAAATTGAAGT-AAG--AG-CAACGTCATC---CTC-T
*
3053177 TGAAATTGAAGAAAGAGCAACGTCATCCTCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
3053208 TGAAATTGAA
1 TGAAATTGAA
3053218 TTAGAGTGGA
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
31 23 0.38
32 5 0.08
34 8 0.13
35 8 0.13
37 5 0.08
38 12 0.20
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCTCT
Found at i:3053249 original size:37 final size:37
Alignment explanation
Indices: 3053208--3053538 Score: 145
Period size: 37 Copynumber: 9.4 Consensus size: 37
3053198 GTCATCCTCT
*
3053208 TGAAATTGAATTAGAGTGGATAACACGCCTTTATCTC
1 TGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTC
* * ** *
3053245 TGAAATTGAAGTA-AGAGCA-AGATCATTTCC--TATCCCC
1 TGAAATTGAAGTAGAGTGGATA-A-CA-CGCCTTTAT-CTC
3053282 TTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTC
1 -TGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTC
* *
3053320 TGAAATTGAAGTA-A---G--AGCGACG---TCATCTGC
1 TGAAATTGAAGTAGAGTGGATAAC-ACGCCTTTATCT-C
**
3053350 TTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTC
1 -TGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTC
** * * **
3053389 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTC
* ** *
3053420 TGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTT
1 TGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTC
* ** * * **
3053458 TGAAATTGAAG-A-A--AGAGCA-ACGTCATCCTCT-
1 TGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTC
*
3053489 TGAAATTGAATTAGAGTGGATAACACGCCTTTATCTC
1 TGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTC
3053526 TGAAATTGAAGTA
1 TGAAATTGAAGTA
3053539 AGAGCAAGAT
Statistics
Matches: 215, Mismatches: 44, Indels: 70
0.65 0.13 0.21
Matches are distributed among these distances:
29 5 0.02
30 1 0.00
31 38 0.18
32 22 0.10
33 8 0.04
35 4 0.02
36 22 0.10
37 55 0.26
38 45 0.21
39 9 0.04
40 6 0.03
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (37 bp):
TGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTC
Found at i:3053313 original size:281 final size:281
Alignment explanation
Indices: 3052783--3053548 Score: 1363
Period size: 281 Copynumber: 2.7 Consensus size: 281
3052773 ATCATTTCCT
* ** *
3052783 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGCCTTTATCTCTGAAATTGAAGTAAGAGCGA
1 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
* * * *
3052847 CGTCATCCGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGA
66 CGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGA
* * *
3052912 GCAACGTCATCCTCTTGAAATTGAAGTAGAGTGGATACCACGCCTTTATCTTTGAAATTGAAGTA
131 GCAACGTCATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTA
* *
3052977 AGAGCAAGATCATTTCCTATCCCCTTGAAATTGAGGTAGAGTGGATAATACGCCTTTATCTCTGA
196 AGAGCAAGATCATTTCCTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGA
3053042 AATTGAAGTAAGAACGACATA
261 AATTGAAGTAAGAACGACATA
*
3053063 ATCCGCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
3053128 CGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGA
66 CGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGA
3053193 GCAACGTCATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTA
131 GCAACGTCATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTA
3053258 AGAGCAAGATCATTTCCTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGA
196 AGAGCAAGATCATTTCCTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGA
* * *
3053323 AATTGAAGTAAGAGCGACGTC
261 AATTGAAGTAAGAACGACATA
*
3053344 ATCTGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
3053409 CGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGA
66 CGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGA
3053474 GCAACGTCATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTA
131 GCAACGTCATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTA
3053539 AGAGCAAGAT
196 AGAGCAAGAT
3053549 TACCGATATT
Statistics
Matches: 466, Mismatches: 19, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
280 21 0.05
281 445 0.95
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (281 bp):
ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAA
CGTCATCCTCTTGAAATTGAAGTAAAGTTGGATAACACATCTTTATCTTTGAAATTGAAGAAAGA
GCAACGTCATCCTCTTGAAATTGAATTAGAGTGGATAACACGCCTTTATCTCTGAAATTGAAGTA
AGAGCAAGATCATTTCCTATCCCCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGA
AATTGAAGTAAGAACGACATA
Found at i:3053427 original size:31 final size:31
Alignment explanation
Indices: 3053389--3053498 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
3053379 TCTTTATCTC
3053389 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
* * * *
3053420 TGAAATTGAAGTAAAGTTGGATAAC-ACATCTTTATCTT
1 TGAAATTGAAGT-AAG--AG-CAACGTCATC---CTC-T
*
3053458 TGAAATTGAAGAAAGAGCAACGTCATCCTCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
3053489 TGAAATTGAA
1 TGAAATTGAA
3053499 TTAGAGTGGA
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
31 23 0.38
32 5 0.08
34 8 0.13
35 8 0.13
37 5 0.08
38 12 0.20
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCTCT
Found at i:3055512 original size:6 final size:6
Alignment explanation
Indices: 3055493--3055570 Score: 74
Period size: 6 Copynumber: 13.3 Consensus size: 6
3055483 AGTTAAATTG
3055493 ATTTAA ATTT-- ATTTAA ATTTAA ATTT-A ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
3055538 TTATTTTA A-TTAA ATTAAA ATTAAA ATTAAA AT
1 --ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
3055571 ACTAAACATT
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
4 4 0.06
5 9 0.14
6 45 0.71
8 5 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:3055525 original size:17 final size:17
Alignment explanation
Indices: 3055493--3055539 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
3055483 AGTTAAATTG
3055493 ATTTAAATTT-ATTTAA
1 ATTTAAATTTAATTTAA
3055509 ATTTAAATTTAATTTAA
1 ATTTAAATTTAATTTAA
3055526 ATTTAAATTTAATT
1 ATTTAAATTTAATT
3055540 ATTTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:3058558 original size:31 final size:31
Alignment explanation
Indices: 3058505--3058567 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
3058495 TATCTATATC
*
3058505 TTTATAATTTTTAAAGGATTAAATTA-AATT
1 TTTATAATTTTTAAAGGATTAAAATACAATT
**
3058535 TTTATAATTTTTAGGGGGATTAAAATACAATT
1 TTTATAATTTTTA-AAGGATTAAAATACAATT
3058567 T
1 T
3058568 CCCTTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 13 0.46
31 10 0.36
32 5 0.18
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGATTAAAATACAATT
Found at i:3059001 original size:3 final size:3
Alignment explanation
Indices: 3058993--3059024 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3058983 TATATGTCAT
3058993 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3059025 TTAAGACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3061134 original size:29 final size:30
Alignment explanation
Indices: 3061101--3061162 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3061091 GATGTTTTAT
*
3061101 ATATTTTA-TAATTAAATTTAAATTTAAAA
1 ATATTTTATTAATTAAATTGAAATTTAAAA
*
3061130 ATATTTTATTATTTAAATTGAAATTTAAAA
1 ATATTTTATTAATTAAATTGAAATTTAAAA
3061160 ATA
1 ATA
3061163 CTTATTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATTTTATTAATTAAATTGAAATTTAAAA
Found at i:3062797 original size:61 final size:61
Alignment explanation
Indices: 3062721--3062846 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 61
3062711 TCTTGAATAT
* * * * *
3062721 AAAAAATTCAAAAATTTAACCTTCAATATTTACAAAAT-TTATCATTTTAGTTCTAATTCTA
1 AAAAAATTCAAAAATTTAACCCTCAATATTTACAAAATCAT-TCAATTTAGTCCTAACTCTA
** *
3062782 AAAAAATT-AATAAATTTGGCCCTCAATATTTATAAAATCATTCAATTTAGTCCTAACTCTA
1 AAAAAATTCAA-AAATTTAACCCTCAATATTTACAAAATCATTCAATTTAGTCCTAACTCTA
3062843 AAAA
1 AAAA
3062847 TTTTTTAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 2 0.04
61 52 0.95
62 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.37
Consensus pattern (61 bp):
AAAAAATTCAAAAATTTAACCCTCAATATTTACAAAATCATTCAATTTAGTCCTAACTCTA
Found at i:3064979 original size:22 final size:22
Alignment explanation
Indices: 3064934--3064976 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3064924 AAAATCTATC
* *
3064934 TATATAATTTACTTTTAATTTA
1 TATATAATTTAATTATAATTTA
3064956 TATATAATTTCAATTATAATT
1 TATATAATTT-AATTATAATT
3064977 ATAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATAATTTAATTATAATTTA
Found at i:3070178 original size:26 final size:26
Alignment explanation
Indices: 3070148--3070202 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
3070138 CCTAAACACT
*
3070148 AAAATCCCAATCAATGGCCGGCATTA
1 AAAATCCCAATCAATGGCCGGCAGTA
*
3070174 AAAATCCCCATCAATGGCCGGCAGTA
1 AAAATCCCAATCAATGGCCGGCAGTA
3070200 AAA
1 AAA
3070203 GTCCACCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.16
Consensus pattern (26 bp):
AAAATCCCAATCAATGGCCGGCAGTA
Found at i:3070430 original size:17 final size:18
Alignment explanation
Indices: 3070391--3070435 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
3070381 TTTCGTTTTT
*
3070391 ATTTTTAAATATATATTA
1 ATTTTTAAATATATAATA
3070409 ATTTTTAAAT-TA-AATA
1 ATTTTTAAATATATAATA
*
3070425 ATTTTTTAATA
1 ATTTTTAAATA
3070436 GCTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 12 0.50
17 2 0.08
18 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTAAATATATAATA
Found at i:3071395 original size:27 final size:27
Alignment explanation
Indices: 3071343--3071397 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3071333 ACAAAAAAAA
* * *
3071343 TCAAAATTTTGTAATAATTTTTAAATT
1 TCAAAATTTTATAATAAATTTAAAATT
3071370 TCAAAATATTTATAA-AAATTTAAAATT
1 TCAAAAT-TTTATAATAAATTTAAAATT
3071397 T
1 T
3071398 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (27 bp):
TCAAAATTTTATAATAAATTTAAAATT
Found at i:3071403 original size:23 final size:24
Alignment explanation
Indices: 3071375--3071442 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
3071365 AAATTTCAAA
3071375 ATATTTATAAAAATTTAAA-ATTT
1 ATATTTATAAAAATTTAAAGATTT
*
3071398 ATATTTTTAAAAAATTATAAAGATTT
1 ATATTTAT-AAAAATT-TAAAGATTT
*
3071424 -TATTTA-AAAAATCTAAAGA
1 ATATTTATAAAAATTTAAAGA
3071443 ATGTATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 6 0.15
23 13 0.33
24 7 0.18
25 9 0.23
26 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (24 bp):
ATATTTATAAAAATTTAAAGATTT
Found at i:3078649 original size:17 final size:17
Alignment explanation
Indices: 3078627--3078665 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3078617 CTCCACCTTG
* *
3078627 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
3078644 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
3078661 ACAAG
1 ACAAG
3078666 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:3089906 original size:36 final size:36
Alignment explanation
Indices: 3089851--3089921 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
3089841 TGCCCACCAC
* *
3089851 GCGTGAAAAAGTAAAATAAAAAAGAAATTATTTAAT
1 GCGTGAAAAAATAAAATAAAAAAGAAATTACTTAAT
*
3089887 GCGTGAAAAAATAATATAAAAAAGAAATTACTTAA
1 GCGTGAAAAAATAAAATAAAAAAGAAATTACTTAA
3089922 CATAATGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (36 bp):
GCGTGAAAAAATAAAATAAAAAAGAAATTACTTAAT
Found at i:3105357 original size:3 final size:3
Alignment explanation
Indices: 3105349--3105373 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3105339 AAGTTTCACT
3105349 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3105374 AATCTTGTTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3106608 original size:23 final size:25
Alignment explanation
Indices: 3106582--3106627 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3106572 CCAATTAAGG
3106582 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
3106605 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
3106628 TAGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:3114591 original size:17 final size:17
Alignment explanation
Indices: 3114569--3114607 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3114559 AGGTGGAGAA
* *
3114569 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
3114586 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
3114603 CTTGT
1 CTTGT
3114608 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:3116199 original size:24 final size:24
Alignment explanation
Indices: 3116169--3116214 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3116159 TATGCATTTA
*
3116169 TTTATATATAGTATAAAAATAAAT
1 TTTATATATAATATAAAAATAAAT
*
3116193 TTTATATCTAATATAAAAATAA
1 TTTATATATAATATAAAAATAA
3116215 TTGTGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTATATATAATATAAAAATAAAT
Found at i:3126177 original size:14 final size:14
Alignment explanation
Indices: 3126141--3126178 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3126131 GTTATTTGAC
3126141 AAATTG-TTTTTTA
1 AAATTGTTTTTTTA
**
3126154 AAATAATTTTTTTA
1 AAATTGTTTTTTTA
3126168 AAATTGTTTTT
1 AAATTGTTTTT
3126179 AGTAAAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (14 bp):
AAATTGTTTTTTTA
Found at i:3127754 original size:16 final size:17
Alignment explanation
Indices: 3127733--3127809 Score: 56
Period size: 16 Copynumber: 4.6 Consensus size: 17
3127723 CAATGATAAG
3127733 TTATATTAATAA-TATA
1 TTATATTAATAAGTATA
* * *
3127749 TTATATTATTAATTAAA
1 TTATATTAATAAGTATA
*
3127766 TATATATGT-TTAAGTATA
1 T-TATAT-TAATAAGTATA
3127784 TTATATT-ATAA-TAT-
1 TTATATTAATAAGTATA
3127798 TTATTATTAATA
1 TTA-TATTAATA
3127810 TTTTAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
14 3 0.06
15 7 0.14
16 18 0.35
17 9 0.18
18 13 0.25
19 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTATATTAATAAGTATA
Found at i:3127862 original size:6 final size:6
Alignment explanation
Indices: 3127846--3127879 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3127836 TTAAAGATGG
* *
3127846 TGGTGA GGGTGA TGGTGA TGATGA TGGTGA TGGT
1 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA TGGT
3127880 ACAAGCCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (6 bp):
TGGTGA
Found at i:3131327 original size:24 final size:24
Alignment explanation
Indices: 3131298--3131345 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3131288 TATGCATTTA
*
3131298 TTTATATCTAGTATAAAAATAATT
1 TTTATATCTAATATAAAAATAATT
3131322 TTTATATCTAATATAAAAATAATT
1 TTTATATCTAATATAAAAATAATT
3131346 ATGATGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTATATCTAATATAAAAATAATT
Found at i:3140347 original size:3 final size:3
Alignment explanation
Indices: 3140339--3140377 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3140329 AAGCTTCACT
3140339 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3140378 TCTTGTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3140758 original size:14 final size:14
Alignment explanation
Indices: 3140736--3140769 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3140726 TGTTTCACTT
*
3140736 AAAACAATTTTTAA
1 AAAATAATTTTTAA
*
3140750 AAAATAATTTTTGA
1 AAAATAATTTTTAA
3140764 AAAATA
1 AAAATA
3140770 GATTGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (14 bp):
AAAATAATTTTTAA
Found at i:3142323 original size:46 final size:45
Alignment explanation
Indices: 3142270--3142407 Score: 197
Period size: 46 Copynumber: 3.0 Consensus size: 45
3142260 TCAATCCTTA
*
3142270 AATGTTAATATCCACATTAAGCTTTTAAACGTGTTTTCATTTTGTT
1 AATGTTAATATCCACATTAA-CTTTTAAATGTGTTTTCATTTTGTT
*
3142316 AATGTTAATATCCACATTAAACTTTTAAATGTGTTTACATTTTGTT
1 AATGTTAATATCCACATT-AACTTTTAAATGTGTTTTCATTTTGTT
* *
3142362 CATGTTAATATCCACAATGAACTTTTAAATGTGTTTGT-ATTTTGTT
1 AATGTTAATATCCAC-ATTAACTTTTAAATGTGTTT-TCATTTTGTT
3142408 CTCGTCTATT
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
46 80 0.95
47 4 0.05
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.48
Consensus pattern (45 bp):
AATGTTAATATCCACATTAACTTTTAAATGTGTTTTCATTTTGTT
Found at i:3142657 original size:22 final size:24
Alignment explanation
Indices: 3142621--3142667 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
3142611 ATTTTCACCA
*
3142621 AAAAAAATAATTTTTTAACTTTTT
1 AAAAAAATAATTTTTTAACTATTT
3142645 AAAAAAAT-A-TTTTTAACTATTT
1 AAAAAAATAATTTTTTAACTATTT
3142667 A
1 A
3142668 TTATCATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
23 1 0.05
24 8 0.36
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAAAAATAATTTTTTAACTATTT
Found at i:3145999 original size:58 final size:58
Alignment explanation
Indices: 3145935--3146054 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 58
3145925 ACCCATTAAC
*
3145935 AAACTAAACCCAAATATTTTTAAAACT-AAATATAATTTCATTCTTTAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTT-AAACTCAAATATAATTTCATTC-CTAAATAACACTCAT
* *
3145993 AAACTAAACCGAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCCTAAATAACACTCAT
3146051 AAAC
1 AAAC
3146055 AACTCCTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
57 9 0.16
58 48 0.84
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:3147183 original size:23 final size:23
Alignment explanation
Indices: 3147140--3147183 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3147130 AAGAAATATA
*
3147140 AACAAAATGAAAAGTAGGGAATT
1 AACAAAATGAAAAGAAGGGAATT
*
3147163 AACAAAAT-CAAAGAAGAGGAA
1 AACAAAATGAAAAGAAG-GGAA
3147184 CCTAGTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.61, C:0.07, G:0.20, T:0.11
Consensus pattern (23 bp):
AACAAAATGAAAAGAAGGGAATT
Found at i:3149599 original size:32 final size:31
Alignment explanation
Indices: 3149532--3149689 Score: 94
Period size: 32 Copynumber: 5.2 Consensus size: 31
3149522 TGAACCCAAA
* *
3149532 AAGTTTAAGTACCAACTTAAAATAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
*
3149563 AAGTTTAGGTACCAAATTAAAAAAAAAGTGAT-
1 AAGTTTAAGTACCAAATT-AAAAAAAAGTG-TC
* * * **
3149595 AAGTTTGAGTATCAAATTTGATCAAAA-----
1 AAGTTTAAGTACCAAA-TTAAAAAAAAGTGTC
* * ** *
3149622 AATTTTAAATATTAAATTAAGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
* **
3149653 AAGATTTAAATATTAAATTAAAAAAAAGTGTC
1 AAG-TTTAAGTACCAAATTAAAAAAAAGTGTC
3149685 AAGTT
1 AAGTT
3149690 CAAATATCAA
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
26 7 0.07
27 12 0.12
31 20 0.20
32 58 0.58
33 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
Found at i:3149695 original size:31 final size:32
Alignment explanation
Indices: 3149628--3149701 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
3149618 AAAAAATTTT
* *
3149628 AAATATTAAATTAAGAAAAAGTGTCAAGATTT
1 AAATATTAAATTAAAAAAAAGTGTCAAGATTC
3149660 AAATATTAAATTAAAAAAAAGTGTCAAG-TTC
1 AAATATTAAATTAAAAAAAAGTGTCAAGATTC
*
3149691 AAATATCAAAT
1 AAATATTAAAT
3149702 ATTATATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 12 0.31
32 27 0.69
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.30
Consensus pattern (32 bp):
AAATATTAAATTAAAAAAAAGTGTCAAGATTC
Found at i:3154430 original size:12 final size:12
Alignment explanation
Indices: 3154414--3154460 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
3154404 CTCGTTTAAA
3154414 AGCTCATTTATT
1 AGCTCATTTATT
* * *
3154426 GGCTCGTTTATA
1 AGCTCATTTATT
*
3154438 AGCTCGTTTA-T
1 AGCTCATTTATT
3154449 AGCTCATTTATT
1 AGCTCATTTATT
3154461 TATTAATGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (12 bp):
AGCTCATTTATT
Found at i:3154591 original size:24 final size:24
Alignment explanation
Indices: 3154546--3154591 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3154536 TCATTAACAT
* *
3154546 TGTTTGTGAACGTATTCAATTATA
1 TGTTCGTGAACATATTCAATTATA
* *
3154570 TGTTCGTGAACATGTTCGATTA
1 TGTTCGTGAACATATTCAATTA
3154592 AGTTAAATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAACATATTCAATTATA
Found at i:3154718 original size:40 final size:41
Alignment explanation
Indices: 3154656--3154736 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 41
3154646 TTTAAATAAA
* ** *
3154656 CGAACATGAATAAAATTTAAAAT-TCTTAACGAACACGAAC
1 CGAACATGAATAAAATTAAAAATAAATAAACGAACACGAAC
*
3154696 CGAACATGAAT-AACTTCAAAAATAAATAAACGAACACGAAC
1 CGAACATGAATAAAATT-AAAAATAAATAAACGAACACGAAC
3154737 GAAGGTTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 4 0.12
40 16 0.47
41 14 0.41
ACGTcount: A:0.53, C:0.19, G:0.10, T:0.19
Consensus pattern (41 bp):
CGAACATGAATAAAATTAAAAATAAATAAACGAACACGAAC
Found at i:3154844 original size:6 final size:6
Alignment explanation
Indices: 3154835--3154884 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
3154825 CAAATTTATT
** *
3154835 TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA TTT-AC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
3154883 TT
1 TT
3154885 CAATCAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 4 0.11
6 28 0.78
7 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:3154858 original size:19 final size:19
Alignment explanation
Indices: 3154826--3154884 Score: 97
Period size: 19 Copynumber: 3.3 Consensus size: 19
3154816 AAATTGATTC
3154826 AAATTTAT-TTTTAAATTT
1 AAATTTATCTTTTAAATTT
3154844 AAATTTATCTTTTAAATTT
1 AAATTTATCTTTTAAATTT
3154863 AAATTTA-C-TTTAAATTT
1 AAATTTATCTTTTAAATTT
3154880 AAATT
1 AAATT
3154885 CAATCAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
17 14 0.35
18 9 0.22
19 17 0.43
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTTATCTTTTAAATTT
Found at i:3155672 original size:3 final size:3
Alignment explanation
Indices: 3155664--3155715 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
3155654 TTAATAGGAT
* * *
3155664 TAA TAA TAA TAA TTAA TAT TAA TAA -AG TCAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
3155710 TAA TAA
1 TAA TAA
3155716 GGAAATCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 1 0.02
3 35 0.85
4 5 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3155676 original size:28 final size:30
Alignment explanation
Indices: 3155645--3155709 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
3155635 TTACTGTTTT
*
3155645 TAATAAATATTAAT-AG-GATTAATAATAA
1 TAATAAATATTAATAAGTCATTAATAATAA
*
3155673 TAATTAATATTAATAAAGTCATTAATAATAA
1 TAATAAATATTAAT-AAGTCATTAATAATAA
3155704 TAATAA
1 TAATAA
3155710 TAATAAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 13 0.42
30 2 0.06
31 16 0.52
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (30 bp):
TAATAAATATTAATAAGTCATTAATAATAA
Found at i:3156068 original size:27 final size:28
Alignment explanation
Indices: 3156021--3156083 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
3156011 GTTTTGTTTT
*
3156021 AAAAGAAAAAAAAATGAAAAAAAAGAA-
1 AAAAGAGAAAAAAATGAAAAAAAAGAAG
* *
3156048 ATAAAGAGAAAAAGATG-AAAAAGAGAAG
1 A-AAAGAGAAAAAAATGAAAAAAAAGAAG
3156076 AAAAGAGA
1 AAAAGAGA
3156084 GAAGAGACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (28 bp):
AAAAGAGAAAAAAATGAAAAAAAAGAAG
Found at i:3156785 original size:30 final size:30
Alignment explanation
Indices: 3156746--3156945 Score: 135
Period size: 30 Copynumber: 6.7 Consensus size: 30
3156736 CCTTAAACTG
*
3156746 TCTAGAAATTAAATTTTGACCCCTAAACTTT
1 TCTA-AAATTAAATTTTGACCCCAAAACTTT
* * *
3156777 TTTAAAATT-ATTTTTAACCCCAAAACATTT
1 TCTAAAATTAAATTTTGACCCCAAAAC-TTT
** * *
3156807 AGT-AAATTACATTTTGACCCCTAAACTTT
1 TCTAAAATTAAATTTTGACCCCAAAACTTT
* * *
3156836 TCCAAAATTATATTTTAACCCCAAAACTTT
1 TCTAAAATTAAATTTTGACCCCAAAACTTT
* * **
3156866 T-TGAAAATTACCA-TTTCACCCTTAAAC-TT
1 TCT-AAAATTA-AATTTTGACCCCAAAACTTT
*
3156895 TCT-AAATTATATTTTGACCCCAAAAC-TT
1 TCTAAAATTAAATTTTGACCCCAAAACTTT
* * *
3156923 TCCAACAATTACATTTTTACCCC
1 TCTAA-AATTAAATTTTGACCCC
3156946 CAAGTTTTCC
Statistics
Matches: 132, Mismatches: 28, Indels: 19
0.74 0.16 0.11
Matches are distributed among these distances:
27 1 0.01
28 21 0.16
29 26 0.20
30 80 0.61
31 4 0.03
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
TCTAAAATTAAATTTTGACCCCAAAACTTT
Found at i:3156821 original size:59 final size:60
Alignment explanation
Indices: 3156751--3156974 Score: 235
Period size: 59 Copynumber: 3.8 Consensus size: 60
3156741 AACTGTCTAG
* * *
3156751 AAATTAAATTTTGACCCCTAAACTTTTTTAAAATTAT-TTTTAACCCCAAAACATTTAGT
1 AAATTACATTTTGACCCCTAAACTTTTCTAAAATTATATTTTAACCCCAAAACATTTAGA
* * *
3156810 AAATTACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTTGA
1 AAATTACATTTTGACCCCTAAACTTTTCTAAAATTATATTTTAACCCCAAAACATTTAGA
* * * **
3156870 AAATTACCA-TTTCACCCTTAAAC-TTTCT-AAATTATATTTTGACCCCAAAAC-TTTCCA
1 AAATTA-CATTTTGACCCCTAAACTTTTCTAAAATTATATTTTAACCCCAAAACATTTAGA
* * * * * *
3156927 ACAATTACATTTTTACCCC-CAAGTTTTCCAAAATTCTATTTTTACCCC
1 A-AATTACATTTTGACCCCTAAACTTTTCTAAAATTATATTTTAACCCC
3156975 CGATTTCACC
Statistics
Matches: 140, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
57 9 0.06
58 38 0.27
59 54 0.39
60 37 0.26
61 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (60 bp):
AAATTACATTTTGACCCCTAAACTTTTCTAAAATTATATTTTAACCCCAAAACATTTAGA
Found at i:3156971 original size:29 final size:29
Alignment explanation
Indices: 3156817--3156975 Score: 99
Period size: 30 Copynumber: 5.4 Consensus size: 29
3156807 AGTAAATTAC
* * *
3156817 ATTTTGACCCCTAAACTTTTCCAAAATTAT
1 ATTTTTACCCCCAAAC-TTTCCAAAATTCT
* * ** *
3156847 ATTTTAACCCCAAAACTTTTTGAAAATTACC
1 ATTTTTACCCCCAAAC-TTTCCAAAATT-CT
* ** * *
3156878 A-TTTCACCCTTAAACTTT-CTAAATTAT
1 ATTTTTACCCCCAAACTTTCCAAAATTCT
* *
3156905 ATTTTGACCCCAAAACTTTCCAACAATTAC-
1 ATTTTTACCCCCAAACTTTCCAA-AATT-CT
**
3156935 ATTTTTACCCCCAAGTTTTCCAAAATTCT
1 ATTTTTACCCCCAAACTTTCCAAAATTCT
3156964 ATTTTTACCCCC
1 ATTTTTACCCCC
3156976 GATTTCACCA
Statistics
Matches: 101, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
27 1 0.01
28 20 0.20
29 21 0.21
30 58 0.57
31 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTTTTACCCCCAAACTTTCCAAAATTCT
Found at i:3161761 original size:37 final size:34
Alignment explanation
Indices: 3161720--3161797 Score: 86
Period size: 37 Copynumber: 2.2 Consensus size: 34
3161710 ATCATACATA
*
3161720 TTTTATATGTTATT-TTTAATTATTTTCAAATCATAC
1 TTTTATAT-TTATTGTAT-ATTATTTTCAAAT-ATAC
*
3161756 GTTTTATTATTTATTGTATATTATTTTTAAATATAC
1 -TTTTA-TATTTATTGTATATTATTTTCAAATATAC
3161792 TTTTAT
1 TTTTAT
3161798 TCTAAATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
34 1 0.03
35 5 0.14
36 4 0.11
37 22 0.59
38 5 0.14
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (34 bp):
TTTTATATTTATTGTATATTATTTTCAAATATAC
Found at i:3164228 original size:32 final size:34
Alignment explanation
Indices: 3164169--3164235 Score: 102
Period size: 32 Copynumber: 2.0 Consensus size: 34
3164159 CTTAATCTGA
3164169 TGTATTTATATATTTAAATTTCGTTTTACTCACAAT
1 TGTATTTATATATTT--ATTTCGTTTTACTCACAAT
3164205 TGTATTTATAT-TTT-TTTCGTTTTACTCACAA
1 TGTATTTATATATTTATTTCGTTTTACTCACAA
3164236 AATTTTAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 17 0.55
35 3 0.10
36 11 0.35
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (34 bp):
TGTATTTATATATTTATTTCGTTTTACTCACAAT
Found at i:3166905 original size:6 final size:6
Alignment explanation
Indices: 3166889--3166924 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
3166879 GGGACGCAAT
*
3166889 GAAGAGG GAAGGG GAAGGG GAAGGG GAAAGG GAAGG
1 GAAG-GG GAAGGG GAAGGG GAAGGG GAAGGG GAAGG
3166925 AGAAAGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:3166929 original size:12 final size:12
Alignment explanation
Indices: 3166893--3166935 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
3166883 CGCAATGAAG
3166893 AGGGAAGGGGAA
1 AGGGAAGGGGAA
*
3166905 GGGGAAGGGGAA
1 AGGGAAGGGGAA
*
3166917 AGGGAAGGAGAA
1 AGGGAAGGGGAA
*
3166929 AGAGAAG
1 AGGGAAG
3166936 AGCGTTTAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (12 bp):
AGGGAAGGGGAA
Found at i:3171263 original size:47 final size:48
Alignment explanation
Indices: 3171205--3171307 Score: 156
Period size: 47 Copynumber: 2.2 Consensus size: 48
3171195 CATAAAGAAA
* *
3171205 AAAAT-ATATAAAGATTAGTGGTATAATTTAACCTAAAA-TTTTATTT
1 AAAATAATATAAAAATTAGTGGTATAATTTAACCTAAAATTTTTATCT
* *
3171251 GAAATAATATAAAAATTAGTGGTATAATTTAATCTAAAATTTTTATCT
1 AAAATAATATAAAAATTAGTGGTATAATTTAACCTAAAATTTTTATCT
3171299 AAAATAATA
1 AAAATAATA
3171308 ATTTAATACG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 4 0.08
47 31 0.62
48 15 0.30
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.40
Consensus pattern (48 bp):
AAAATAATATAAAAATTAGTGGTATAATTTAACCTAAAATTTTTATCT
Found at i:3182539 original size:15 final size:14
Alignment explanation
Indices: 3182515--3182544 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3182505 GTTAAATTAA
3182515 AATTAAAATTAATT
1 AATTAAAATTAATT
3182529 AATTCAAAATTAATT
1 AATT-AAAATTAATT
3182544 A
1 A
3182545 TACAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTAAAATTAATT
Found at i:3183323 original size:6 final size:6
Alignment explanation
Indices: 3183305--3183362 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
3183295 GGGACGCAAT
* * * * *
3183305 GAAGGA GGAAGGA GAAGGA AAAGGG GAAGGG GAAGGG GAAGGA AAAGGA
1 GAAGGA -GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA
*
3183354 GAAAGA GAA
1 GAAGGA GAA
3183363 AAGCGTTTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
6 38 0.86
7 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:3183339 original size:24 final size:25
Alignment explanation
Indices: 3183305--3183352 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
3183295 GGGACGCAAT
3183305 GAAGGAGGAAGGAGAAGGAAAAGGG
1 GAAGGAGGAAGGAGAAGGAAAAGGG
*
3183330 GAAGG-GGAAGGGGAAGGAAAAGG
1 GAAGGAGGAAGGAGAAGGAAAAGG
3183353 AGAAAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (25 bp):
GAAGGAGGAAGGAGAAGGAAAAGGG
Found at i:3183693 original size:20 final size:20
Alignment explanation
Indices: 3183670--3183712 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3183660 TTAGATATAA
* *
3183670 TTTTTAACATTATATTTATG
1 TTTTGAACATTAGATTTATG
* *
3183690 TTTTGAAGATTAGATTTGTG
1 TTTTGAACATTAGATTTATG
3183710 TTT
1 TTT
3183713 GTTTATTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (20 bp):
TTTTGAACATTAGATTTATG
Found at i:3188263 original size:15 final size:15
Alignment explanation
Indices: 3188243--3188288 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
3188233 ATGTCGAAAT
3188243 TTGAATTCATTCTAA
1 TTGAATTCATTCTAA
*
3188258 TTGAATTCATTCTAG
1 TTGAATTCATTCTAA
*
3188273 TTGAATTCATTTTAA
1 TTGAATTCATTCTAA
3188288 T
1 T
3188289 AATTTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (15 bp):
TTGAATTCATTCTAA
Found at i:3195735 original size:48 final size:48
Alignment explanation
Indices: 3195667--3195765 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
3195657 TAAAGAATAA
* * *
3195667 AATATAAAGATTAGTGGTATAATTTAACCTAAAATTTTTATCTGAAAT
1 AATATAAAAATTAGTAGTATAATTTAACCTAAAACTTTTATCTGAAAT
3195715 AATATAAAAATTAGTAGTATAATTTAACCTAAAACTTTTATCTGAAAT
1 AATATAAAAATTAGTAGTATAATTTAACCTAAAACTTTTATCTGAAAT
3195763 AAT
1 AAT
3195766 GATTTACTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.38
Consensus pattern (48 bp):
AATATAAAAATTAGTAGTATAATTTAACCTAAAACTTTTATCTGAAAT
Found at i:3200878 original size:33 final size:33
Alignment explanation
Indices: 3200800--3200879 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
3200790 TTAAATTTGC
* *
3200800 AAAAATCGAATAAACTTTCTAAACCATTTAACT
1 AAAAATCGAACAGACTTTCTAAACCATTTAACT
*
3200833 AAAAATCGAACAGACTTTCTAAACCATTTAGCT
1 AAAAATCGAACAGACTTTCTAAACCATTTAACT
*
3200866 AAAAATCTAACAGA
1 AAAAATCGAACAGA
3200880 AAACCCAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.26
Consensus pattern (33 bp):
AAAAATCGAACAGACTTTCTAAACCATTTAACT
Found at i:3200890 original size:33 final size:33
Alignment explanation
Indices: 3200820--3200891 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
3200810 TAAACTTTCT
**** *
3200820 AAACCATTTAACTAAAAATCGAACAGACTTTCT
1 AAACCATTTAACTAAAAATCGAACAGAAAACCC
* *
3200853 AAACCATTTAGCTAAAAATCTAACAGAAAACCC
1 AAACCATTTAACTAAAAATCGAACAGAAAACCC
3200886 AAACCA
1 AAACCA
3200892 AAAATAGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.21
Consensus pattern (33 bp):
AAACCATTTAACTAAAAATCGAACAGAAAACCC
Found at i:3201122 original size:22 final size:23
Alignment explanation
Indices: 3201097--3201142 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
3201087 GAAAAATTAC
3201097 ACATATGGTA-TTT-GATACAAAT
1 ACATAT-GTAGTTTAGATACAAAT
*
3201119 ACATATGTAGTTTAGATGCAAAT
1 ACATATGTAGTTTAGATACAAAT
3201142 A
1 A
3201143 AAGTTGCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 9 0.43
23 9 0.43
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (23 bp):
ACATATGTAGTTTAGATACAAAT
Found at i:3201185 original size:24 final size:23
Alignment explanation
Indices: 3201158--3201228 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
3201148 GCAGATGCTG
3201158 ATACAGACATAAATATAGATACAA
1 ATACAGA-ATAAATATAGATACAA
*
3201182 ATACAG-ATACAGATATAGATACAG
1 ATACAGAATA-A-ATATAGATACAA
3201206 ATACA-AATACATATATAGATACA
1 ATACAGAATA-A-ATATAGATACA
3201229 TATCCTACTC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.07
23 1 0.02
24 38 0.90
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (23 bp):
ATACAGAATAAATATAGATACAA
Found at i:3201191 original size:6 final size:6
Alignment explanation
Indices: 3201174--3201228 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
3201164 ACATAAATAT
* * * * *
3201174 AGATAC AAATAC AGATAC AGATAT AGATAC AGATAC AAATAC ATATAT
1 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC
3201222 AGATAC A
1 AGATAC A
3201229 TATCCTACTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.22
Consensus pattern (6 bp):
AGATAC
Found at i:3201231 original size:12 final size:12
Alignment explanation
Indices: 3201170--3201228 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
3201160 ACAGACATAA
*
3201170 ATATAGATACAA
1 ATATAGATACAG
*
3201182 ATACAGATACAG
1 ATATAGATACAG
3201194 ATATAGATACAG
1 ATATAGATACAG
* * *
3201206 ATACAAATACAT
1 ATATAGATACAG
3201218 ATATAGATACA
1 ATATAGATACA
3201229 TATCCTACTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (12 bp):
ATATAGATACAG
Found at i:3203529 original size:13 final size:14
Alignment explanation
Indices: 3203508--3203536 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3203498 ATTGATTAAA
3203508 AATTAAAATTAACT
1 AATTAAAATTAACT
3203522 AATT-AAATTAACT
1 AATTAAAATTAACT
3203535 AA
1 AA
3203537 AGACCGCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAAATTAACT
Found at i:3207951 original size:31 final size:31
Alignment explanation
Indices: 3207904--3207969 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3207894 GTAATTGAAT
* *
3207904 TATTTAAAAGTTTTCATTTAAGTCATTAAAC
1 TATTCAAAAGTTTTCATATAAGTCATTAAAC
* *
3207935 TATTCAAATGTTTTCATATAAGTCATTGAAC
1 TATTCAAAAGTTTTCATATAAGTCATTAAAC
3207966 TATT
1 TATT
3207970 TGAAAGTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATATAAGTCATTAAAC
Found at i:3212317 original size:16 final size:17
Alignment explanation
Indices: 3212291--3212336 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
3212281 ATTTAGTGAC
3212291 TAAAT-TATAATTTAAA
1 TAAATATATAATTTAAA
* *
3212307 T-CATATATAA-TTAAC
1 TAAATATATAATTTAAA
3212322 TAAATATATAATTTA
1 TAAATATATAATTTA
3212337 TCCAAAGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 7 0.29
16 14 0.58
17 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATATAATTTAAA
Found at i:3212744 original size:21 final size:20
Alignment explanation
Indices: 3212718--3212767 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
3212708 AATTCCCATA
3212718 TTTTTTTTGAACAATTTAAAT
1 TTTTTTTTGAAC-ATTTAAAT
** *
3212739 TTTTTTTATGTTCTTTTAAAT
1 TTTTTTT-TGAACATTTAAAT
3212760 TTTTTTTT
1 TTTTTTTT
3212768 TCTTTCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTTTTGAACATTTAAAT
Found at i:3217960 original size:21 final size:21
Alignment explanation
Indices: 3217934--3217977 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3217924 AGTATTTATG
3217934 CATACCATGGAGAAAAGAATC
1 CATACCATGGAGAAAAGAATC
3217955 CATACCATGGAGAAAAGAATC
1 CATACCATGGAGAAAAGAATC
3217976 CA
1 CA
3217978 AGCTTCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (21 bp):
CATACCATGGAGAAAAGAATC
Found at i:3223993 original size:19 final size:18
Alignment explanation
Indices: 3223960--3224015 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
3223950 CTAATTCTGG
3223960 TTATTCTTTAGAAATTTTT
1 TTATTCTTTA-AAATTTTT
*
3223979 TTATCTCTTTAAAATATTT
1 TTAT-TCTTTAAAATTTTT
* *
3223998 GTATTATTTAAAAATTTT
1 TTATTCTTT-AAAATTTT
3224016 GGTGTAGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.13
19 21 0.68
20 6 0.19
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (18 bp):
TTATTCTTTAAAATTTTT
Found at i:3235934 original size:30 final size:31
Alignment explanation
Indices: 3235873--3235937 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 31
3235863 AATCAATGAT
3235873 TGTTTTGTCACTTTTCAATAACGTTAGTGAC
1 TGTTTTGTCACTTTTCAATAACGTTAGTGAC
3235904 TGTTTTGTCACATTTTC-A-AA-GTTGAGTGAC
1 TGTTTTGTCAC-TTTTCAATAACGTT-AGTGAC
3235934 TGTT
1 TGTT
3235938 GTGTTAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.09
30 12 0.38
31 12 0.38
32 5 0.16
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (31 bp):
TGTTTTGTCACTTTTCAATAACGTTAGTGAC
Found at i:3236141 original size:31 final size:31
Alignment explanation
Indices: 3236082--3236143 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3236072 GCTGAAATGT
**
3236082 AAATCAAGTGACTATTTATTTCTCCATGTCA
1 AAATCAAGTGACTATTTATTAATCCATGTCA
*
3236113 AAATTAAGTGACTATTTATGTAAT-CATGTCA
1 AAATCAAGTGACTATTTAT-TAATCCATGTCA
3236144 CTGTTCCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (31 bp):
AAATCAAGTGACTATTTATTAATCCATGTCA
Found at i:3236164 original size:141 final size:141
Alignment explanation
Indices: 3235996--3236277 Score: 519
Period size: 141 Copynumber: 2.0 Consensus size: 141
3235986 CGTCAACTGC
*
3235996 CATGTCACTGTTTCGTGACGTCTGTGACGGAAAATATGAAAAAATGACTATTTTGTCACATTTTC
1 CATGTCACTGTTCCGTGACGTCTGTGACGGAAAATATGAAAAAATGACTATTTTGTCACATTTTC
3236061 AAAGTTCAGTGGCTGAAATGTAAATCAAGTGACTATTTATTTCTCCATGTCAAAATTAAGTGACT
66 AAAGTTCAGTGGCTGAAATGTAAATCAAGTGACTATTTATTTCTCCATGTCAAAATTAAGTGACT
3236126 ATTTATGTAAT
131 ATTTATGTAAT
*
3236137 CATGTCACTGTTCCGTGACGTTTGTGACGGAAAATATGAAAAAATGACTATTTTGTCACATTTTC
1 CATGTCACTGTTCCGTGACGTCTGTGACGGAAAATATGAAAAAATGACTATTTTGTCACATTTTC
* * *
3236202 AAAGTTGAGTGGCTGAAATGTAAATCAAGTGACTATTTGTTTCTCCATGTCAAAATTAAGTGATT
66 AAAGTTCAGTGGCTGAAATGTAAATCAAGTGACTATTTATTTCTCCATGTCAAAATTAAGTGACT
3236267 ATTTATGTAAT
131 ATTTATGTAAT
3236278 TTATCCTTAA
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 136 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (141 bp):
CATGTCACTGTTCCGTGACGTCTGTGACGGAAAATATGAAAAAATGACTATTTTGTCACATTTTC
AAAGTTCAGTGGCTGAAATGTAAATCAAGTGACTATTTATTTCTCCATGTCAAAATTAAGTGACT
ATTTATGTAAT
Found at i:3236829 original size:57 final size:57
Alignment explanation
Indices: 3236757--3236869 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
3236747 TTTAAAAAAG
*
3236757 AAGAAGATATTCGTATGATTCTAAAGCACCTTGAAAGCCAACAAGAAGGCGAGTTAA
1 AAGAAGATATTCGTATGATTCTAAAGCACCTTGAAAGCCAACAAGAAGACGAGTTAA
*
3236814 AAGAAGATATTCGTATGGTTCTAAAGCACCTTGAAAGCCAACAAGAAGACGAGTTA
1 AAGAAGATATTCGTATGATTCTAAAGCACCTTGAAAGCCAACAAGAAGACGAGTTA
3236870 GGACCGTTGC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (57 bp):
AAGAAGATATTCGTATGATTCTAAAGCACCTTGAAAGCCAACAAGAAGACGAGTTAA
Found at i:3248072 original size:13 final size:13
Alignment explanation
Indices: 3248054--3248085 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3248044 ATTAAATCAA
3248054 ATTTTTTAAAATT
1 ATTTTTTAAAATT
3248067 ATTTTTTAAAATT
1 ATTTTTTAAAATT
3248080 ATTTTT
1 ATTTTT
3248086 CCAAAGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTTTTAAAATT
Found at i:3255473 original size:6 final size:6
Alignment explanation
Indices: 3255464--3255496 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3255454 TTAACACTGC
3255464 CTTTTT CTTTTT C-TTTT CTTTTT CTTTTT -TTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
3255497 GTTCAATCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
CTTTTT
Found at i:3255482 original size:11 final size:11
Alignment explanation
Indices: 3255466--3255496 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3255456 AACACTGCCT
3255466 TTTTCTTTTTC
1 TTTTCTTTTTC
3255477 TTTTCTTTTTC
1 TTTTCTTTTTC
3255488 TTTT-TTTTT
1 TTTTCTTTTT
3255497 GTTCAATCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:3255486 original size:17 final size:16
Alignment explanation
Indices: 3255464--3255496 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3255454 TTAACACTGC
3255464 CTTTTTCTTTTTCTTTT
1 CTTTTTCTTTTT-TTTT
3255481 CTTTTTCTTTTTTTTT
1 CTTTTTCTTTTTTTTT
3255497 GTTCAATCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
CTTTTTCTTTTTTTTT
Found at i:3255518 original size:75 final size:76
Alignment explanation
Indices: 3255400--3255555 Score: 287
Period size: 75 Copynumber: 2.1 Consensus size: 76
3255390 AACACTGCCT
3255400 TTTTCTTTTTCTTTTTTTTTTTGTTCAATCACTAACACTACTGCCTTTTTCTTTTTAACACTGCC
1 TTTTCTTTTTC-TTTTTTTTTTGTTCAATCACTAACACTACTGCCTTTTTCTTTTTAACACTGCC
3255465 TTTTTCTTTTTC
65 TTTTTCTTTTTC
*
3255477 TTTTCTTTTTC-TTTTTTTTTGTTCAATCGCTAACACTACTGCCTTTTTCTTTTTAACACTGCCT
1 TTTTCTTTTTCTTTTTTTTTTGTTCAATCACTAACACTACTGCCTTTTTCTTTTTAACACTGCCT
3255541 TTTTCTTTTTC
66 TTTTCTTTTTC
3255552 TTTT
1 TTTT
3255556 TTGTTGTTCA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
75 67 0.86
77 11 0.14
ACGTcount: A:0.12, C:0.22, G:0.04, T:0.62
Consensus pattern (76 bp):
TTTTCTTTTTCTTTTTTTTTTGTTCAATCACTAACACTACTGCCTTTTTCTTTTTAACACTGCCT
TTTTCTTTTTC
Found at i:3255520 original size:55 final size:55
Alignment explanation
Indices: 3255459--3255632 Score: 210
Period size: 64 Copynumber: 3.0 Consensus size: 55
3255449 TCTTTTTAAC
3255459 ACTGCCTTTTTCTTTTTCTTTTCTTTTTCTTTTTTTTTGTTCAATCGCTAACACT
1 ACTGCCTTTTTCTTTTTCTTTTCTTTTTCTTTTTTTTTGTTCAATCGCTAACACT
*
3255514 ACTGCCTTTTTCTTTTTAACACTGCCTTTTTCTTTTTCTTTTTTGTTGTTCAATCGCTAACACT
1 ACTGCCTTTTTC-TTTT-----T--C-TTTTCTTTTTCTTTTTTTTTGTTCAATCGCTAACACT
3255578 ACTGCC-TTTTC-TTTTCTTTTC-TTTTCTTTTCTTTTTTGGTTCAATCGCTAACACT
1 ACTGCCTTTTTCTTTTTCTTTTCTTTTTC-TTT-TTTTTT-GTTCAATCGCTAACACT
3255633 GCTTTAGCTG
Statistics
Matches: 105, Mismatches: 2, Indels: 24
0.80 0.02 0.18
Matches are distributed among these distances:
52 5 0.05
53 8 0.08
54 6 0.06
55 29 0.28
56 5 0.05
61 4 0.04
63 6 0.06
64 42 0.40
ACGTcount: A:0.12, C:0.23, G:0.07, T:0.58
Consensus pattern (55 bp):
ACTGCCTTTTTCTTTTTCTTTTCTTTTTCTTTTTTTTTGTTCAATCGCTAACACT
Found at i:3255593 original size:5 final size:5
Alignment explanation
Indices: 3255583--3255612 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3255573 ACACTACTGC
3255583 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
3255613 TTGGTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:3255847 original size:56 final size:58
Alignment explanation
Indices: 3255772--3255888 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 58
3255762 ATAATGGTAG
* * * *
3255772 TGTCGGTGAG-AA-AGCGAGAGAGGATAGTGAATTTTGAATATCAAATAATAATTATT
1 TGTCGGTGAGAAAGAGAGAGAGAGGATAGTAAATATTGAATATCAAATAAAAATTATT
*
3255828 TGTCGGTGGGAAAGAGAGAGAGAGGATAGTAAATATTGAATATCAAATAAAAATTATT
1 TGTCGGTGAGAAAGAGAGAGAGAGGATAGTAAATATTGAATATCAAATAAAAATTATT
3255886 TGT
1 TGT
3255889 AGATTTTGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 9 0.17
57 2 0.04
58 43 0.80
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.29
Consensus pattern (58 bp):
TGTCGGTGAGAAAGAGAGAGAGAGGATAGTAAATATTGAATATCAAATAAAAATTATT
Found at i:3266494 original size:31 final size:30
Alignment explanation
Indices: 3266416--3266502 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 30
3266406 TGATTTTATT
3266416 TACAATTGTATACATG-AACTTTAATTTGG
1 TACAATTGTATACATGAAACTTTAATTTGG
* * * * *
3266445 TGCAATTATACACGTGAAACTCTAATTGTGG
1 TACAATTGTATACATGAAACTTTAATT-TGG
* *
3266476 TACAAATGTATACTTGAAACTTTAATT
1 TACAATTGTATACATGAAACTTTAATT
3266503 ATACACATTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 12 0.27
30 9 0.20
31 24 0.53
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Consensus pattern (30 bp):
TACAATTGTATACATGAAACTTTAATTTGG
Found at i:3279107 original size:21 final size:21
Alignment explanation
Indices: 3279078--3279117 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3279068 GAATAATTTC
*
3279078 ATTTGATTTGACTCGATTTAA
1 ATTTGATTTCACTCGATTTAA
*
3279099 ATTTTATTTCACTCGATTT
1 ATTTGATTTCACTCGATTT
3279118 TTTTCGAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
ATTTGATTTCACTCGATTTAA
Found at i:3282396 original size:38 final size:38
Alignment explanation
Indices: 3282354--3282432 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
3282344 CTCATAATTC
3282354 ATTTGGTTTATTGATAGAGTTAAAACATATATTTATAA
1 ATTTGGTTTATTGATAGAGTTAAAACATATATTTATAA
3282392 ATTTGGTTTATTGATAGAGTTAAAACATATATTTATAA
1 ATTTGGTTTATTGATAGAGTTAAAACATATATTTATAA
3282430 ATT
1 ATT
3282433 AAATGTAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.46
Consensus pattern (38 bp):
ATTTGGTTTATTGATAGAGTTAAAACATATATTTATAA
Found at i:3285006 original size:18 final size:16
Alignment explanation
Indices: 3284971--3285025 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
3284961 ATATTATTTA
*
3284971 TATATTTATATTAT-AT
1 TATAATTATATT-TGAT
3284987 TATAAATTATCATTTGAT
1 TAT-AATTAT-ATTTGAT
3285005 TATAATTATATTT-A-
1 TATAATTATATTTGAT
3285019 TATAATT
1 TATAATT
3285026 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
14 7 0.20
15 1 0.03
16 7 0.20
17 12 0.34
18 8 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TATAATTATATTTGAT
Found at i:3285214 original size:3 final size:3
Alignment explanation
Indices: 3285206--3285243 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3285196 ATGTTAATGC
3285206 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3285244 CCCACTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3295430 original size:17 final size:18
Alignment explanation
Indices: 3295399--3295441 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3295389 GGTAATGAAA
3295399 AAAAATAAAACATTT-AT
1 AAAAATAAAACATTTGAT
* *
3295416 AAAAATAATAGATTTGAT
1 AAAAATAAAACATTTGAT
3295434 AAATAATA
1 AAA-AATA
3295442 TATAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 5 0.23
19 4 0.18
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATAAAACATTTGAT
Found at i:3303465 original size:29 final size:29
Alignment explanation
Indices: 3303432--3303491 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
3303422 TCACTTAATT
3303432 ATTCGACTTTTTCTTTTAAACTTGGCATA
1 ATTCGACTTTTTCTTTTAAACTTGGCATA
*
3303461 ATTCGACTTTTTCTTTTAAATTTGGCATA
1 ATTCGACTTTTTCTTTTAAACTTGGCATA
3303490 AT
1 AT
3303492 AGCAACTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (29 bp):
ATTCGACTTTTTCTTTTAAACTTGGCATA
Found at i:3305413 original size:27 final size:29
Alignment explanation
Indices: 3305352--3305417 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 29
3305342 TATAAGGATT
* *
3305352 TAATTATGTTAAAGAAATCTGAAAGAACC
1 TAATTATGTTAAAGAAATCGGAAACAACC
* *
3305381 TCATTATG-TAAAGAAAT-GGTAACAACC
1 TAATTATGTTAAAGAAATCGGAAACAACC
3305408 TAATTA-GTTA
1 TAATTATGTTA
3305418 TTAAACTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 14 0.45
28 9 0.29
29 7 0.23
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (29 bp):
TAATTATGTTAAAGAAATCGGAAACAACC
Found at i:3312755 original size:2 final size:2
Alignment explanation
Indices: 3312748--3312776 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3312738 GTTGAGCTTG
3312748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3312777 GCTTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3316631 original size:51 final size:51
Alignment explanation
Indices: 3316555--3316656 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
3316545 TCAAAACAAG
3316555 GGCAGTTTTTCTTAACACTGGGGATGCAGTATTCATACAGTTTCATGCAAA
1 GGCAGTTTTTCTTAACACTGGGGATGCAGTATTCATACAGTTTCATGCAAA
*
3316606 GGCAGTTTTTCTTAACACTTGGGATGCAGTATTCATACAGTTTCATGCAAA
1 GGCAGTTTTTCTTAACACTGGGGATGCAGTATTCATACAGTTTCATGCAAA
3316657 CTCCAGAGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (51 bp):
GGCAGTTTTTCTTAACACTGGGGATGCAGTATTCATACAGTTTCATGCAAA
Done.