Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 9 of 175
Found at i:2611263 original size:9 final size:9
Alignment explanation
Indices: 2611185--2611282 Score: 63
Period size: 9 Copynumber: 10.4 Consensus size: 9
2611175 CATGTGACAA
2611185 AAAAATTAT
1 AAAAATTAT
*
2611194 AAAAA-AAT
1 AAAAATTAT
*
2611202 AAAAATCAAT
1 AAAAAT-TAT
*
2611212 AAAAGTTAT
1 AAAAATTAT
*
2611221 AACAATTAT
1 AAAAATTAT
* *
2611230 TAAATTATATT
1 AAAAAT-TA-T
* *
2611241 AAAAAATAGA
1 AAAAATTA-T
2611251 AAAAATTAT
1 AAAAATTAT
*
2611260 AAAAATCAT
1 AAAAATTAT
2611269 AAAAAATTAT
1 -AAAAATTAT
2611279 AAAA
1 AAAA
2611283 TGCATAAAAA
Statistics
Matches: 67, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
8 7 0.10
9 29 0.43
10 27 0.40
11 4 0.06
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2611288 original size:19 final size:19
Alignment explanation
Indices: 2611185--2611294 Score: 79
Period size: 19 Copynumber: 5.8 Consensus size: 19
2611175 CATGTGACAA
*
2611185 AAAAATTATAAAAAA--AT
1 AAAAATCATAAAAAATTAT
*
2611202 AAAAATCA-ATAAAAGTTAT
1 AAAAATCATA-AAAAATTAT
* * *
2611221 AACAATTATTAAATTATATTA-
1 AAAAATCA-TAAA--AAATTAT
*
2611242 AAAAAT-AGAAAAAATTAT
1 AAAAATCATAAAAAATTAT
2611260 AAAAATCATAAAAAATTAT
1 AAAAATCATAAAAAATTAT
2611279 -AAAATGCATAAAAAAT
1 AAAAAT-CATAAAAAAT
2611295 GTCATTTAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
16 1 0.01
17 16 0.22
18 11 0.15
19 32 0.44
20 3 0.04
21 6 0.08
22 4 0.05
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (19 bp):
AAAAATCATAAAAAATTAT
Found at i:2611543 original size:10 final size:10
Alignment explanation
Indices: 2611528--2611569 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
2611518 TTTTTACGAC
2611528 TTTATAAAAT
1 TTTATAAAAT
2611538 TTTATAAAAT
1 TTTATAAAAT
* *
2611548 TTTAT-GATT
1 TTTATAAAAT
2611557 TTTATAAAAT
1 TTTATAAAAT
2611567 TTT
1 TTT
2611570 TAAGATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:2611570 original size:20 final size:20
Alignment explanation
Indices: 2611537--2611628 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
2611527 CTTTATAAAA
2611537 TTTTATAAAA-TTTTATGAT
1 TTTTATAAAATTTTTATGAT
*
2611556 TTTTATAAAATTTTTAAGAT
1 TTTTATAAAATTTTTATGAT
* * ** * *
2611576 ATTTGTAATTTTTTTCTAAT
1 TTTTATAAAATTTTTATGAT
* **
2611596 TTTAATAAAATTTAAAT-AT
1 TTTTATAAAATTTTTATGAT
2611615 TTTTATTAAAATTT
1 TTTTA-TAAAATTT
2611629 AATATATATA
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
19 16 0.30
20 38 0.70
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTATAAAATTTTTATGAT
Found at i:2611586 original size:29 final size:29
Alignment explanation
Indices: 2611528--2611628 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
2611518 TTTTTACGAC
*
2611528 TTTATAAAATTTTATAAAATTTTATGATT
1 TTTATAAAATTTTATAAAATTTTATAATT
* *
2611557 TTTATAAAATTTT-TAAGATATTTGTAATT
1 TTTATAAAATTTTATAAAAT-TTTATAATT
* ** *
2611586 TTTTTCTAATTTTAATAAAA-TTTAAATATT
1 TTTATAAAATTTT-ATAAAATTTTATA-ATT
2611616 TTTATTAAAATTT
1 TTTA-TAAAATTT
2611629 AATATATATA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
28 5 0.09
29 34 0.62
30 6 0.11
31 10 0.18
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTATAAAATTTTATAAAATTTTATAATT
Found at i:2611629 original size:20 final size:21
Alignment explanation
Indices: 2611595--2611635 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2611585 TTTTTTCTAA
2611595 TTTTAATAAAATTTAA-ATAT
1 TTTTAATAAAATTTAATATAT
*
2611615 TTTTATTAAAATTTAATATAT
1 TTTTAATAAAATTTAATATAT
2611636 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAATAAAATTTAATATAT
Found at i:2611640 original size:19 final size:20
Alignment explanation
Indices: 2611601--2611640 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2611591 CTAATTTTAA
* *
2611601 TAAAATTTAAATATTTTTAT
1 TAAAATTTAAATATATATAT
2611621 TAAAATTT-AATATATATAT
1 TAAAATTTAAATATATATAT
2611640 T
1 T
2611641 TTTTATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAATTTAAATATATATAT
Found at i:2611916 original size:91 final size:90
Alignment explanation
Indices: 2611749--2611986 Score: 265
Period size: 91 Copynumber: 2.7 Consensus size: 90
2611739 TACCCAATTA
** * ** *
2611749 AGTGC-AAAAAAAGGCAGGGGCTTAATTG-TTTTTTTT-TTAAATTTTGAGGGCCTTTTTATGCA
1 AGTGCAAAAAAAAATCAAGGGCTTAATTGATTTTTTTTGAAAAAATTTGAGGGCCTTTTTATGCA
* * *
2611811 TTTTGAAAGTTCAAGTGGCCAATTG
66 TTGTGAAAGCTCAAGTGGCCAAGTG
* *
2611836 AGTGCAAAAAAGAAAT-AATGGCTTAATTGATTTTTTTTGAAAAAATTTGAGGG-TTATTTTGAT
1 AGTGCAAAAAA-AAATCAAGGGCTTAATTGATTTTTTTTGAAAAAATTTGAGGGCCT-TTTT-AT
*
2611899 GCATTGTGAAAGCTCAAGTGTCCAAGTG
63 GCATTGTGAAAGCTCAAGTGGCCAAGTG
* *
2611927 AGTGCAAAAAAAAATGCAAGGGCTTAATT-ACTTTTTTTGAAAAAATTTGAGAG-CTTTTTA
1 AGTGCAAAAAAAAAT-CAAGGGCTTAATTGATTTTTTTTGAAAAAATTTGAGGGCCTTTTTA
2611987 CACGAAAAAT
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
87 5 0.04
88 16 0.13
89 12 0.09
90 23 0.18
91 60 0.47
92 11 0.09
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.37
Consensus pattern (90 bp):
AGTGCAAAAAAAAATCAAGGGCTTAATTGATTTTTTTTGAAAAAATTTGAGGGCCTTTTTATGCA
TTGTGAAAGCTCAAGTGGCCAAGTG
Found at i:2613739 original size:21 final size:21
Alignment explanation
Indices: 2613715--2613820 Score: 69
Period size: 21 Copynumber: 5.0 Consensus size: 21
2613705 TATATATTAC
* *
2613715 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
*
2613736 AATAAATCAAAAGAAAGAAAG
1 AATAAAACAAAAGAAAGAAAG
*
2613757 -ATAGAAACGAAACGGAAAGAAA-
1 AATA-AAAC-AAA-AGAAAGAAAG
*
2613779 AAGAAAA-AGAAAGAAAGAAAAG
1 AATAAAACA-AAAGAAAG-AAAG
*
2613801 AA-AAGAA-AAAGGAAAGAAAG
1 AATAA-AACAAAAGAAAGAAAG
2613821 GAAGGAGAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
20 13 0.19
21 35 0.51
22 11 0.16
23 10 0.14
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.06
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:2613752 original size:4 final size:4
Alignment explanation
Indices: 2613745--2613820 Score: 57
Period size: 4 Copynumber: 18.0 Consensus size: 4
2613735 GAATAAATCA
* *
2613745 AAAG AAAG AAAG ATAG AAACG AAACGG AAAG AAA- AAGAA AAAG AAAG
1 AAAG AAAG AAAG AAAG AAA-G AAA--G AAAG AAAG AA-AG AAAG AAAG
*
2613792 AAAG AAAAG AAAAG AAA- AAGG AAAG AAAG
1 AAAG -AAAG -AAAG AAAG AAAG AAAG AAAG
2613821 GAAGGAGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
3 4 0.07
4 37 0.62
5 15 0.25
6 4 0.07
ACGTcount: A:0.72, C:0.03, G:0.24, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:2614746 original size:41 final size:39
Alignment explanation
Indices: 2614701--2614831 Score: 108
Period size: 40 Copynumber: 3.3 Consensus size: 39
2614691 ACTTCGAGTT
2614701 GATGAGACACTAGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACT-GGTGTCAATTTA-TACTTCGGATTAATTC
* * * * *
2614742 GATGAGGCACTGGATG-CAAATT-TACTTCTGTTTAA-CC
1 GATGAGACACTGG-TGTCAATTTATACTTCGGATTAATTC
* * *
2614779 GATGAGACAATGGGTGTCAATTTATTATTTCGAATT-ATTC
1 GATGAGACACT-GGTGTCAATTTA-TACTTCGGATTAATTC
*
2614819 GATGAGGCACTGG
1 GATGAGACACTGG
2614832 GAGCCAAACT
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
37 12 0.17
38 18 0.26
39 3 0.04
40 24 0.35
41 12 0.17
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (39 bp):
GATGAGACACTGGTGTCAATTTATACTTCGGATTAATTC
Found at i:2615740 original size:46 final size:46
Alignment explanation
Indices: 2615676--2615944 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
2615666 TTTGAGTACT
* * *
2615676 TCTGATCAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
2615722 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
2615768 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
2615820 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTTATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCGGCTACACTTA
**
2615872 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
2615918 TTTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
2615945 GCTACACTTA
Statistics
Matches: 204, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
46 109 0.53
52 95 0.47
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:2615801 original size:52 final size:52
Alignment explanation
Indices: 2615736--2615933 Score: 291
Period size: 52 Copynumber: 3.9 Consensus size: 52
2615726 ATCAAGTGAC
2615736 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
*
2615788 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* * *
2615840 AAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGTGAC------
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* * *
2615886 AAAGTGATAAGTGATAGCTTTAGCTACACTTATTTGATCAAGAGACAA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
2615934 AGTGATAAGT
Statistics
Matches: 135, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
46 40 0.30
52 95 0.70
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (52 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:2615952 original size:37 final size:37
Alignment explanation
Indices: 2615908--2616017 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
2615898 GATAGCTTTA
*
2615908 GCTACACTTATTTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
2615945 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
2615982 GCTACACTTATCTGATCAAGGGA-TAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
2616018 ATCATACGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
36 12 0.18
37 56 0.82
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:2624183 original size:73 final size:73
Alignment explanation
Indices: 2624075--2624228 Score: 229
Period size: 73 Copynumber: 2.1 Consensus size: 73
2624065 TGGGTTTAGA
* * *
2624075 GGAAGGAAAAGAAAGGTTTGAAAGGAAACTAGTTTCATTTTTGCTTTTTTTTTTGGTAGAAGGAA
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAA-GAA
2624140 A-ATAAGAG
65 AGATAAGAG
* *
2624148 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCCTTTTTTCCTTTTTCTTTGGTAGAAGAAA
1 GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAAGAAA
*
2624213 GATAGGAG
66 GATAAGAG
*
2624221 GGAGGGAA
1 GGAAGGAA
2624229 GGAAGGAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 4 0.05
73 69 0.95
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (73 bp):
GGAAGGAAAAGAAAGATTTGAAAGGAAACTAGTTTCATTTTTGCCTTTTTCTTTGGTAGAAGAAA
GATAAGAG
Found at i:2625121 original size:17 final size:18
Alignment explanation
Indices: 2625096--2625207 Score: 69
Period size: 18 Copynumber: 6.3 Consensus size: 18
2625086 TAAGAGAGAA
*
2625096 AGAAAGAAC-TGAAAAGG
1 AGAAGGAACGTGAAAAGG
2625113 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
* *
2625131 A-AAGGGAGAAG-G-AACGCG
1 AGAA-GGA-ACGTGAAAAG-G
2625149 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
* *
2625167 A-AAGGGAGAAG-G-AACGCG
1 AGAA-GGA-ACGTGAAAAG-G
2625185 AGAAGGAACGTGAAAAGG
1 AGAAGGAACGTGAAAAGG
2625203 A-AAGG
1 AGAAGG
2625208 GAGAAGGCTG
Statistics
Matches: 73, Mismatches: 9, Indels: 26
0.68 0.08 0.24
Matches are distributed among these distances:
17 26 0.36
18 33 0.45
19 14 0.19
ACGTcount: A:0.50, C:0.07, G:0.39, T:0.04
Consensus pattern (18 bp):
AGAAGGAACGTGAAAAGG
Found at i:2625132 original size:12 final size:12
Alignment explanation
Indices: 2625112--2625214 Score: 107
Period size: 12 Copynumber: 8.6 Consensus size: 12
2625102 AACTGAAAAG
2625112 GAGAAGGAACGT
1 GAGAAGGAACGT
* * *
2625124 GAAAAGGAAAGG
1 GAGAAGGAACGT
*
2625136 GAGAAGGAACGC
1 GAGAAGGAACGT
2625148 GAGAAGGAACGT
1 GAGAAGGAACGT
* * *
2625160 GAAAAGGAAAGG
1 GAGAAGGAACGT
*
2625172 GAGAAGGAACGC
1 GAGAAGGAACGT
2625184 GAGAAGGAACGT
1 GAGAAGGAACGT
* * *
2625196 GAAAAGGAAAGG
1 GAGAAGGAACGT
2625208 GAGAAGG
1 GAGAAGG
2625215 CTGAAAGCAA
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 73 1.00
ACGTcount: A:0.48, C:0.07, G:0.43, T:0.03
Consensus pattern (12 bp):
GAGAAGGAACGT
Found at i:2625138 original size:24 final size:24
Alignment explanation
Indices: 2625106--2625214 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
2625096 AGAAAGAACT
*
2625106 GAAAAGGAGAAGGAACGTGAAAAG
1 GAAAGGGAGAAGGAACGTGAAAAG
* *
2625130 GAAAGGGAGAAGGAACGCGAGAAG
1 GAAAGGGAGAAGGAACGTGAAAAG
* * * * * *
2625154 GAACGTGAAAAGGAAAGGGAGAAG
1 GAAAGGGAGAAGGAACGTGAAAAG
* *
2625178 GAACGCGAGAAGGAACGTGAAAAG
1 GAAAGGGAGAAGGAACGTGAAAAG
2625202 GAAAGGGAGAAGG
1 GAAAGGGAGAAGG
2625215 CTGAAAGCAA
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.49, C:0.06, G:0.42, T:0.03
Consensus pattern (24 bp):
GAAAGGGAGAAGGAACGTGAAAAG
Found at i:2625152 original size:36 final size:36
Alignment explanation
Indices: 2625112--2625214 Score: 206
Period size: 36 Copynumber: 2.9 Consensus size: 36
2625102 AACTGAAAAG
2625112 GAGAAGGAACGTGAAAAGGAAAGGGAGAAGGAACGC
1 GAGAAGGAACGTGAAAAGGAAAGGGAGAAGGAACGC
2625148 GAGAAGGAACGTGAAAAGGAAAGGGAGAAGGAACGC
1 GAGAAGGAACGTGAAAAGGAAAGGGAGAAGGAACGC
2625184 GAGAAGGAACGTGAAAAGGAAAGGGAGAAGG
1 GAGAAGGAACGTGAAAAGGAAAGGGAGAAGG
2625215 CTGAAAGCAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.48, C:0.07, G:0.43, T:0.03
Consensus pattern (36 bp):
GAGAAGGAACGTGAAAAGGAAAGGGAGAAGGAACGC
Found at i:2626977 original size:25 final size:25
Alignment explanation
Indices: 2626943--2626993 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2626933 TTTTCTTGAG
2626943 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
2626968 ATCATATAATGAACCTGATTAGTTT
1 ATCATATAATGAACCTGATTAGTTT
2626993 A
1 A
2626994 GTTGTTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (25 bp):
ATCATATAATGAACCTGATTAGTTT
Found at i:2628874 original size:6 final size:6
Alignment explanation
Indices: 2628853--2628907 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
2628843 AAAAACAATG
* * *
2628853 TTTTG- TTTTAGA TTTTGA TTTTGA TTTTGA TTTTTA GTTTGA GTTTGA
1 TTTTGA TTTT-GA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
*
2628901 GTTTGA T
1 TTTTGA T
2628908 AAGTAGAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
5 4 0.09
6 36 0.82
7 4 0.09
ACGTcount: A:0.16, C:0.00, G:0.20, T:0.64
Consensus pattern (6 bp):
TTTTGA
Found at i:2634211 original size:4 final size:4
Alignment explanation
Indices: 2634204--2634240 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
2634194 TGCATGCATC
* *
2634204 TATG TATG TATA TATG TATG TCTG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T
2634241 TTTGCAGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2634219 original size:12 final size:12
Alignment explanation
Indices: 2634188--2634238 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
2634178 ACATCATATA
*
2634188 TATATATGCATG
1 TATATATGTATG
* *
2634200 CATCTATGTATG
1 TATATATGTATG
2634212 TATATATGTATG
1 TATATATGTATG
* *
2634224 TCTGTATGTATG
1 TATATATGTATG
2634236 TAT
1 TAT
2634239 GTTTTGCAGG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (12 bp):
TATATATGTATG
Found at i:2636936 original size:21 final size:24
Alignment explanation
Indices: 2636903--2636950 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 24
2636893 ATTGGTAGGT
2636903 ATTTAATTATT-AA-TA-AAAAAA
1 ATTTAATTATTAAATTATAAAAAA
* *
2636924 ATTTAGTTGTTAAATTATAAAAAA
1 ATTTAATTATTAAATTATAAAAAA
2636948 ATT
1 ATT
2636951 ATAAAATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 2 0.09
24 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTTAATTATTAAATTATAAAAAA
Found at i:2638223 original size:38 final size:38
Alignment explanation
Indices: 2638181--2638294 Score: 228
Period size: 38 Copynumber: 3.0 Consensus size: 38
2638171 ATTATCGGGT
2638181 TAATTGCAATAAAACTCCCAAACTCGTCCATATTCTCA
1 TAATTGCAATAAAACTCCCAAACTCGTCCATATTCTCA
2638219 TAATTGCAATAAAACTCCCAAACTCGTCCATATTCTCA
1 TAATTGCAATAAAACTCCCAAACTCGTCCATATTCTCA
2638257 TAATTGCAATAAAACTCCCAAACTCGTCCATATTCTCA
1 TAATTGCAATAAAACTCCCAAACTCGTCCATATTCTCA
2638295 AATGATCTCT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (38 bp):
TAATTGCAATAAAACTCCCAAACTCGTCCATATTCTCA
Found at i:2649103 original size:27 final size:27
Alignment explanation
Indices: 2649073--2649139 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
2649063 TAAGTTTCGT
*
2649073 GGGACAGTCCACCATATAGGTGTTTGC
1 GGGACAGTCCACCAAATAGGTGTTTGC
* ** *
2649100 GGGACATTCCATAAAATAGGTGTTTGT
1 GGGACAGTCCACCAAATAGGTGTTTGC
2649127 GGGACAGTCCACC
1 GGGACAGTCCACC
2649140 GTTTAGCCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (27 bp):
GGGACAGTCCACCAAATAGGTGTTTGC
Found at i:2651132 original size:33 final size:33
Alignment explanation
Indices: 2651092--2651157 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2651082 TCAATCTCTA
2651092 AAACATAACTCCATCGAGTTTCGAAAAGAGCCT
1 AAACATAACTCCATCGAGTTTCGAAAAGAGCCT
2651125 AAACATAACTCCATCGAGTTTCGAAAAGAGCCT
1 AAACATAACTCCATCGAGTTTCGAAAAGAGCCT
2651158 TATACACAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (33 bp):
AAACATAACTCCATCGAGTTTCGAAAAGAGCCT
Found at i:2651984 original size:27 final size:27
Alignment explanation
Indices: 2651933--2652007 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
2651923 CTTTCTTTAG
* *
2651933 AATATGCCACGAAGGCGTTTCTTTTCATA
1 AATAT-CCACAAAGGC-TTCCTTTTCATA
*
2651962 AATCAT-TACAAAGGCTTCCTTTTCATA
1 AAT-ATCCACAAAGGCTTCCTTTTCATA
*
2651989 GATATCCACAAAGGCTTCC
1 AATATCCACAAAGGCTTCC
2652008 CTTCTTTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.05
27 25 0.64
28 7 0.18
29 3 0.08
30 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (27 bp):
AATATCCACAAAGGCTTCCTTTTCATA
Found at i:2652017 original size:27 final size:27
Alignment explanation
Indices: 2651969--2652036 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 27
2651959 ATAAATCATT
2651969 ACAAAGGCTT-CCTTTTCATAGATAT-CC
1 ACAAAGGCTTCCCTTTT-ATAGAT-TGCC
2651996 ACAAAGGCTTCCCTTCTT-TAGATTGCC
1 ACAAAGGCTTCCCTT-TTATAGATTGCC
2652023 ACAAAGGCTTCCCT
1 ACAAAGGCTTCCCT
2652037 CACCTTTCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.03
27 31 0.82
28 4 0.11
29 2 0.05
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.31
Consensus pattern (27 bp):
ACAAAGGCTTCCCTTTTATAGATTGCC
Found at i:2652195 original size:50 final size:50
Alignment explanation
Indices: 2652112--2652211 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
2652102 TCTTTTAGTC
* * * * * *
2652112 CTTTCTATATTATGTCATAACCCACCAGTTATGGTCTTATATAATATGGT
1 CTTTCCATATGATGCCATAACCCACCAGCTATGGTCTTACACAATATGGT
*
2652162 CTTTCCATATGATGCCATAGCCCACCAGCTATGGTCTTACACAATATGGT
1 CTTTCCATATGATGCCATAACCCACCAGCTATGGTCTTACACAATATGGT
2652212 GCCATGGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (50 bp):
CTTTCCATATGATGCCATAACCCACCAGCTATGGTCTTACACAATATGGT
Found at i:2653709 original size:14 final size:14
Alignment explanation
Indices: 2653690--2653718 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2653680 AAGATACCCC
2653690 ATTGGAAATGCTAA
1 ATTGGAAATGCTAA
2653704 ATTGGAAATGCTAA
1 ATTGGAAATGCTAA
2653718 A
1 A
2653719 GGTACATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (14 bp):
ATTGGAAATGCTAA
Found at i:2663091 original size:105 final size:105
Alignment explanation
Indices: 2662909--2663227 Score: 620
Period size: 105 Copynumber: 3.0 Consensus size: 105
2662899 CTGGTGCGAG
2662909 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
2662974 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
* *
2663014 TCAAACAATGTGAAGTTGCCTGATCTTGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTCGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
2663079 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
2663119 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
1 TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
2663184 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
66 AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
2663224 TCAA
1 TCAA
2663228 CTTATACTCA
Statistics
Matches: 210, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 210 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (105 bp):
TCAAACAATGTGAAGTTGCCTGATCTCGTGGAGTCCACTTTAAATCAGGTCTATCCGCCTTGTGC
AACTAAGGTTAAGAAGTTGGTTGAGGACTTGAAGAGTACA
Found at i:2668582 original size:15 final size:15
Alignment explanation
Indices: 2668539--2668582 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2668529 AATGAATACA
* *
2668539 AATAA-AAACATAAC
1 AATAATAAAAATAAT
2668553 AATAATAAAAATAAT
1 AATAATAAAAATAAT
*
2668568 AATGATAAAAATAAT
1 AATAATAAAAATAAT
2668583 TAGCTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAATAAAAATAAT
Found at i:2669815 original size:46 final size:46
Alignment explanation
Indices: 2669759--2669854 Score: 165
Period size: 46 Copynumber: 2.1 Consensus size: 46
2669749 TATTTTGAGT
*
2669759 TTGGTTCTGTAATGGGCTAGGCTAGTTGGGTCTGAGTTATTTGGGC
1 TTGGTTCTGTAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGC
* *
2669805 TTGGTTCTGTAATGGGCTAGGTTAGTTAGGTCTGGGTTATTTGGGC
1 TTGGTTCTGTAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGC
2669851 TTGG
1 TTGG
2669855 GCAATAATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.12, C:0.09, G:0.38, T:0.41
Consensus pattern (46 bp):
TTGGTTCTGTAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGC
Found at i:2669867 original size:46 final size:46
Alignment explanation
Indices: 2669768--2669868 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
2669758 TTTGGTTCTG
* * **
2669768 TAATGGGCTAGGCTAGTTGGGTCTGAGTTATTTGGGCTTGGTTCTG
1 TAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGCTTGGTGCAA
* *
2669814 TAATGGGCTAGGTTAGTTAGGTCTGGGTTATTTGGGCTTGG-GCAA
1 TAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGCTTGGTGCAA
2669859 TAATTGGGCT
1 TAA-TGGGCT
2669869 TGTACAATCC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
45 4 0.08
46 44 0.92
ACGTcount: A:0.16, C:0.10, G:0.37, T:0.38
Consensus pattern (46 bp):
TAATGGGCTAGGCTAGTTAGGTCTGAGTTATTTGGGCTTGGTGCAA
Found at i:2676437 original size:106 final size:102
Alignment explanation
Indices: 2676309--2676541 Score: 278
Period size: 106 Copynumber: 2.2 Consensus size: 102
2676299 AAAATATATA
* * *
2676309 TTTTTTACTTTTGGTT--TGTCAATGTCCGGCACCAGTATACGAAAAAAGT-AAAAAAAAAA-A-
1 TTTTTTACTTTT--TTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAAGAT
*
2676369 TTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATTGGAATTTT
64 TTGGTGGTGGCCTGCCAATGGCCGACACCA---GTA----AATTTT
2676415 TTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAAAGATT
1 TTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGT-AAAAAAAAAAAGA-T
* *
2676480 TTGGTGGTGGCCTGCCAATGGTCGGCACCAGTAAATTTT
64 TTGGTGGTGGCCTGCCAATGGCCGACACCAGTAAATTTT
2676519 TTTTTTACTTTTTTCGTGTCAAT
1 TTTTTTACTTTTTTCGTGTCAAT
2676542 AGCCGGCCCA
Statistics
Matches: 114, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
104 31 0.27
106 42 0.37
108 12 0.11
109 1 0.01
111 28 0.25
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (102 bp):
TTTTTTACTTTTTTCGTGTCAATGGCAGGCACCAGTATACAAAAAAAGTAAAAAAAAAAAGATTT
GGTGGTGGCCTGCCAATGGCCGACACCAGTAAATTTT
Found at i:2678185 original size:113 final size:103
Alignment explanation
Indices: 2678061--2678318 Score: 284
Period size: 113 Copynumber: 2.4 Consensus size: 103
2678051 TGGCAAGCCA
* *
2678061 TTTTTTTTACTTTTTTCGTATACTGGTGCCTTCTATTGACACAAAAAAAGTAAAAAAAATATTTT
1 TTTTTTTTACTTTTTTCGTATACTGGTGCCGTCCATTGACACAAAAAAAGTAAAAAAAA-A----
* *
2678126 TTTCCAATAAAGGTGGTGCTGGCCATTGGTAGGCCATCACCA-AAAAT
61 -TT-CAAAAAAGGTGGTGCTGGCCATTGGCAGG-C--CACCATAAAAT
* ** *
2678173 TTTTTTATTACTTTTTTCGTATACTGGTGCCGTCCATTGACAGACCAAAAGTAAAAAAAAATTGA
1 TTTTTT-TTACTTTTTTCGTATACTGGTGCCGTCCATTGACACAAAAAAAGTAAAAAAAAATTCA
*
2678238 AAAAAGGTGGTGCTGGCCATTGGCAGGCCACCATTAAATT
65 AAAAAGGTGGTGCTGGCCATTGGCAGGCCACCA-TAAAAT
* ** *
2678278 TTTTTTTTACTTTTTTCGTATTCTGGTATCGACCATTGACA
1 TTTTTTTTACTTTTTTCGTATACTGGTGCCGTCCATTGACA
2678319 GACTAATACC
Statistics
Matches: 130, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
103 5 0.04
104 31 0.24
105 11 0.08
106 26 0.20
107 2 0.02
112 7 0.05
113 48 0.37
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (103 bp):
TTTTTTTTACTTTTTTCGTATACTGGTGCCGTCCATTGACACAAAAAAAGTAAAAAAAAATTCAA
AAAAGGTGGTGCTGGCCATTGGCAGGCCACCATAAAAT
Found at i:2678334 original size:104 final size:105
Alignment explanation
Indices: 2678134--2678336 Score: 266
Period size: 104 Copynumber: 1.9 Consensus size: 105
2678124 TTTTTCCAAT
*
2678134 AAAGGTGGTGCTGGCCATTGGTAGGCCATCACCAAAAATTTTTTTATTACTTTTTTCGTATACTG
1 AAAGGTGGTGCTGGCCATTGGCAGGCCA-CACCAAAAATTTTTTTATTACTTTTTTCGTATACTG
* * **
2678199 GTGCCGTCCATTGACAGACCAAAAGTAAAAAAAAATTGAAA
65 GTACCGACCATTGACAGACCAAAACCAAAAAAAAATTGAAA
* * *
2678240 AAAGGTGGTGCTGGCCATTGGCAGG-C-CACCATTAAATTTTTTTTTTACTTTTTTCGTATTCTG
1 AAAGGTGGTGCTGGCCATTGGCAGGCCACACCA-AAAATTTTTTTATTACTTTTTTCGTATACTG
* * * *
2678303 GTATCGACCATTGACAGACTAATACCCAAAAAAA
65 GTACCGACCATTGACAGACCAAAACCAAAAAAAA
2678337 TATTTTTTCG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
103 5 0.06
104 54 0.64
105 1 0.01
106 24 0.29
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (105 bp):
AAAGGTGGTGCTGGCCATTGGCAGGCCACACCAAAAATTTTTTTATTACTTTTTTCGTATACTGG
TACCGACCATTGACAGACCAAAACCAAAAAAAAATTGAAA
Found at i:2683013 original size:21 final size:21
Alignment explanation
Indices: 2682987--2683027 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2682977 AGACGAGCAA
* *
2682987 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2683008 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2683028 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2692356 original size:22 final size:21
Alignment explanation
Indices: 2692317--2692365 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2692307 CTATTTAATT
*
2692317 CTTTTCTTTTATGTTCTTTTAA
1 CTTTTCTTTTATGTTCTTCT-A
*
2692339 CTTTTTTTTTAT-TCTCTTCTA
1 CTTTTCTTTTATGT-TCTTCTA
2692360 CTTTTC
1 CTTTTC
2692366 CCTCTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.69
Consensus pattern (21 bp):
CTTTTCTTTTATGTTCTTCTA
Found at i:2702162 original size:18 final size:19
Alignment explanation
Indices: 2702091--2702164 Score: 57
Period size: 18 Copynumber: 4.0 Consensus size: 19
2702081 TTTTGTCACT
2702091 ATATATTTTGAAAT-T-AAA
1 ATATATTTT-AAATATAAAA
* *
2702109 ATATATATTAAATGTAAAA
1 ATATATTTTAAATATAAAA
* **
2702128 ATGTGATTTTTTA-ATAAAA
1 ATAT-ATTTTAAATATAAAA
2702147 AT-TATTTTAAATATAAAA
1 ATATATTTTAAATATAAAA
2702165 TGTGAAATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
17 10 0.23
18 16 0.36
19 13 0.30
20 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATATATTTTAAATATAAAA
Found at i:2713041 original size:61 final size:61
Alignment explanation
Indices: 2712937--2713117 Score: 308
Period size: 61 Copynumber: 3.0 Consensus size: 61
2712927 CCTTTGTCTA
* * **
2712937 CCCTTGGCTAGGCTATATTCTATCCACGTGTTTTTGAGCGAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
*
2712998 CCCTTAGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
*
2713059 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTTAATCTAATTCGATTTTTTT
1 CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTT
2713118 TGTTTGTATA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 113 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (61 bp):
CCCTTGGCTAGGCTATAATCTATCCACGTGTTTCTGATTGAATCTAATTCGATTTTTTTGT
Found at i:2729699 original size:27 final size:26
Alignment explanation
Indices: 2729657--2729707 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
2729647 GAAAATCTGA
*
2729657 TTTTTTTCTATTCTCTTTCTCTCTAT
1 TTTTTTTCTATTCTCTCTCTCTCTAT
2729683 TTTTTTTCT-TTAGCTCTCTCTCTCT
1 TTTTTTTCTATT--CTCTCTCTCTCT
2729708 GCCGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 2 0.09
26 9 0.41
27 11 0.50
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTTTTCTATTCTCTCTCTCTCTAT
Found at i:2730647 original size:17 final size:16
Alignment explanation
Indices: 2730625--2730658 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2730615 AAATCCAGGG
2730625 ATTAAAGTGAAAAGAAT
1 ATTAAA-TGAAAAGAAT
*
2730642 ATTAAATTAAAAGAAT
1 ATTAAATGAAAAGAAT
2730658 A
1 A
2730659 AATGTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (16 bp):
ATTAAATGAAAAGAAT
Found at i:2738422 original size:19 final size:20
Alignment explanation
Indices: 2738389--2738436 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
2738379 AAAATTAGTA
* *
2738389 TTTATTTGTG-TTTTTATTT
1 TTTATTTCTGATTTTCATTT
2738408 TTTATTTCTGATTTTCCAATTT
1 TTTATTTCTGATTTT-C-ATTT
2738430 TTTATTT
1 TTTATTT
2738437 TTACTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
22 11 0.46
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTATTTCTGATTTTCATTT
Found at i:2749980 original size:14 final size:15
Alignment explanation
Indices: 2749946--2749974 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2749936 TAACTTTCTG
2749946 AATATATATTTATTT
1 AATATATATTTATTT
2749961 AATATA-ATTTATTT
1 AATATATATTTATTT
2749975 TTTATAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATATATTTATTT
Found at i:2757528 original size:15 final size:16
Alignment explanation
Indices: 2757498--2757530 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2757488 TGGTTAATTA
2757498 ATTTTATAATTATTTT
1 ATTTTATAATTATTTT
*
2757514 ATTTT-TAATTTTTTT
1 ATTTTATAATTATTTT
2757529 AT
1 AT
2757531 ATCCATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTATAATTATTTT
Found at i:2759387 original size:24 final size:24
Alignment explanation
Indices: 2759360--2759411 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2759350 TTAGTAAGTC
*
2759360 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2759384 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2759408 AAAT
1 AAAT
2759412 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2761356 original size:24 final size:24
Alignment explanation
Indices: 2761329--2761380 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2761319 TTAGTAAGTC
*
2761329 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2761353 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2761377 AAAT
1 AAAT
2761381 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2762991 original size:16 final size:16
Alignment explanation
Indices: 2762970--2763006 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2762960 CTACAATAAC
* *
2762970 AATTAATTAATTTTTA
1 AATTAATTAATATTAA
2762986 AATTAATTAATATTAA
1 AATTAATTAATATTAA
2763002 AATTA
1 AATTA
2763007 CTCTTTATAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTAATATTAA
Found at i:2766807 original size:3 final size:3
Alignment explanation
Indices: 2766799--2766825 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2766789 CAGTGCATCA
2766799 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2766826 TGTCACTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2767568 original size:31 final size:30
Alignment explanation
Indices: 2767532--2767610 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
2767522 TCTATTGGTA
2767532 GTAAAATTTTAAATTAATCCCTTCTTAAAA-TT
1 GTAAAATTTTAAATTAAT-CC-T-TTAAAAGTT
* *
2767564 -TAAAATTCATAACTTAATCCTTTAAAAGTT
1 GTAAAATT-TTAAATTAATCCTTTAAAAGTT
*
2767594 GTAAAATTTTACATTAA
1 GTAAAATTTTAAATTAA
2767611 AATAATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
29 6 0.15
30 9 0.23
31 16 0.41
32 8 0.21
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (30 bp):
GTAAAATTTTAAATTAATCCTTTAAAAGTT
Found at i:2774883 original size:31 final size:31
Alignment explanation
Indices: 2774843--2774908 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
2774833 AAAATCTCAA
* *
2774843 AATTTGAAAAGTACAATGG-CTAAAATTGACC
1 AATTCGAAAAGCACAA-GGACTAAAATTGACC
* *
2774874 AATTCGAAAAGCATAAGGACTAAAATTGATC
1 AATTCGAAAAGCACAAGGACTAAAATTGACC
2774905 AATT
1 AATT
2774909 AATGTATAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
AATTCGAAAAGCACAAGGACTAAAATTGACC
Found at i:2775206 original size:51 final size:51
Alignment explanation
Indices: 2775125--2775241 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
2775115 TTAGGTATAA
* * *
2775125 TAACAAATTTAGCTCTCAAAATTTACACATTTTGTCAA-TTTGATCTTGATT
1 TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTG-TCTTGATT
* * *
2775176 TAACAAATTTAGC-CAACAATATTTATACATTCTATTAATTTTGTCTTGATT
1 TAACAAATTTAGCTC-ACAAAATTTACACATTCTATCAATTTTGTCTTGATT
*
2775227 TAGCAAATTTAGCTC
1 TAACAAATTTAGCTC
2775242 GTGATATTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
50 1 0.02
51 50 0.89
52 5 0.09
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (51 bp):
TAACAAATTTAGCTCACAAAATTTACACATTCTATCAATTTTGTCTTGATT
Found at i:2783301 original size:72 final size:73
Alignment explanation
Indices: 2783175--2783330 Score: 174
Period size: 72 Copynumber: 2.2 Consensus size: 73
2783165 AGAATCAACC
* * * * * * * **
2783175 GAAGGCCAATGTGTGAGGTCTCATCCCTTTGAGGGATTGGCAAAGTTGTTAGGTCTTGT-CCCTT
1 GAAGACCAAGGTGTGAGGTATCATCCCATTGAGGAATTGGCAAAGATGTAAGGTCTCATCCCCTT
*
2783239 TTGCCCTT
66 ATGCCCTT
*
2783247 G-AGACCAAGGTGTGAGGTATCATCTTCATTGAGGAATTGGCTAAA-ATGTAAGGTCTCATCCCC
1 GAAGACCAAGGTGTGAGGTATCATC-CCATTGAGGAATTGGC-AAAGATGTAAGGTCTCATCCCC
2783310 TTATGCCCTT
64 TTATGCCCTT
2783320 GAAGACCAAGG
1 GAAGACCAAGG
2783331 CGAGAGGTCT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
71 20 0.29
72 24 0.35
73 16 0.23
74 9 0.13
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (73 bp):
GAAGACCAAGGTGTGAGGTATCATCCCATTGAGGAATTGGCAAAGATGTAAGGTCTCATCCCCTT
ATGCCCTT
Found at i:2783741 original size:19 final size:19
Alignment explanation
Indices: 2783717--2783759 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2783707 GTTGCTCACC
2783717 CTCTTCATAACAAAATTAT
1 CTCTTCATAACAAAATTAT
2783736 CTCTTCATAACAAAATTAT
1 CTCTTCATAACAAAATTAT
2783755 CTCTT
1 CTCTT
2783760 TAGGCTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (19 bp):
CTCTTCATAACAAAATTAT
Found at i:2788212 original size:121 final size:120
Alignment explanation
Indices: 2787974--2788272 Score: 377
Period size: 121 Copynumber: 2.5 Consensus size: 120
2787964 TACAACAACG
* *
2787974 ACCTAATGACTTAAATAAAAACTTTTGAATAGTTTAGTGACTATTTTGTAACTTTTTGAAGTTAC
1 ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGAC-ATTTTGTAAC-TTTTGAAGCTAC
*
2788039 AAATAACGATTTTAACTTTCTGCGAAGAGAGAAGGCTATACAACAATAATTTTAACA
64 AAATAACAATTTTAACTTTCTGCGAAGAGAGAAGGCTATACAACAATAATTTTAACA
** * *
2788096 ACCTAATGAATTAAATAAAAACTTTAAAATAGTTTAATGATCATTTTGTAACTTTTGAAGCTGCA
1 ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGA-CATTTTGTAACTTTTGAAGCTACA
* * * * *
2788161 AATAATAATTTTAACTTTTTGC-AGATAGAGAAGGCTATACAATAATGATTTTAACA
65 AATAACAATTTTAACTTTCTGCGA-AGAGAGAAGGCTATACAACAATAATTTTAACA
* * ***
2788217 GCTTAAT-AATTTAAATAAATTTTTTTGAATAGTTTAGTGACCATTTTGTAACTTTT
1 ACCTAATGAA-TTAAATAAAAACTTTTGAATAGTTTAGTGA-CATTTTGTAACTTTT
2788273 TAAAGTTGAA
Statistics
Matches: 153, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
120 3 0.02
121 103 0.67
122 46 0.30
123 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (120 bp):
ACCTAATGAATTAAATAAAAACTTTTGAATAGTTTAGTGACATTTTGTAACTTTTGAAGCTACAA
ATAACAATTTTAACTTTCTGCGAAGAGAGAAGGCTATACAACAATAATTTTAACA
Found at i:2795030 original size:30 final size:30
Alignment explanation
Indices: 2794991--2795065 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
2794981 TTAAATTAAT
* *
2794991 AATAGTAAAATTATACTTTAACCTCTCAAA
1 AATAATAAAATTATAATTTAACCTCTCAAA
* * * *
2795021 AATGATAAAAATT-TAATTTAAGCTTTTAAA
1 AATAAT-AAAATTATAATTTAACCTCTCAAA
*
2795051 AATAATAAAAATATA
1 AATAATAAAATTATA
2795066 GACGATTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
29 5 0.14
30 24 0.69
31 6 0.17
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (30 bp):
AATAATAAAATTATAATTTAACCTCTCAAA
Found at i:2795440 original size:18 final size:17
Alignment explanation
Indices: 2795412--2795445 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2795402 TTTTTTTTCT
*
2795412 TTTTAAATTTAGTTTAA
1 TTTTAAATTTAATTTAA
2795429 TTTTAAATTTTAATTTA
1 TTTTAAA-TTTAATTTA
2795446 CTACTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTAATTTAA
Found at i:2800802 original size:23 final size:23
Alignment explanation
Indices: 2800771--2800821 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2800761 ACCTACTTCC
* *
2800771 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
2800794 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
2800817 TTACA
1 TTACA
2800822 TTTCTCCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:2814835 original size:5 final size:5
Alignment explanation
Indices: 2814825--2814863 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
2814815 ATATGGTAAA
2814825 AAAAT AAAAT AAAAT AAAAT AAAAT ATTAAA- AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT A--AAAT AAAAT AAA
2814864 CATGTGAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.10
5 24 0.77
6 1 0.03
7 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:2814845 original size:15 final size:15
Alignment explanation
Indices: 2814821--2814863 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
2814811 TATAATATGG
2814821 TAAAAAAATAAAATA
1 TAAAAAAATAAAATA
2814836 -AAATAAAATAAAATA
1 TAAA-AAAATAAAATA
2814851 TTAAAAAAATAAA
1 -TAAAAAAATAAA
2814864 CATGTGAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 11 0.44
16 8 0.32
17 3 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAAAAATAAAATA
Found at i:2816971 original size:13 final size:14
Alignment explanation
Indices: 2816943--2816971 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2816933 AAATAATTTT
2816943 AATATTTATCCTAA
1 AATATTTATCCTAA
2816957 AATATTTAT-CTAA
1 AATATTTATCCTAA
2816970 AA
1 AA
2816972 CGAATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATTTATCCTAA
Found at i:2822468 original size:3 final size:3
Alignment explanation
Indices: 2822453--2822566 Score: 111
Period size: 3 Copynumber: 38.0 Consensus size: 3
2822443 TTTAAGATTT
* * ** * * * * * *
2822453 TTA TTA TTG TTA TTA TTA TTA TTA ATA CCA TCA TCA TCA TCA TCA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
2822501 TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2822549 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
2822567 AATTGTTTTA
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:2828863 original size:40 final size:40
Alignment explanation
Indices: 2828793--2828868 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2828783 ATATCAACAC
* * *
2828793 TTATATGCACGAAATTAACAAAATTGAATAATCCAACAAT
1 TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
*
2828833 TTATATGCAAC-AAATTAATAAAAATAAATAACCCAA
1 TTATATGC-ACGAAATTAACAAAAATAAATAACCCAA
2828869 AGGCAAAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.26
Consensus pattern (40 bp):
TTATATGCACGAAATTAACAAAAATAAATAACCCAACAAT
Found at i:2831867 original size:28 final size:28
Alignment explanation
Indices: 2831811--2831893 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
2831801 CACAGGAATA
*
2831811 AGTTGCTCACACAAGCTAACAGTATATTAG
1 AGTTCCTCACACAAGCTAACA-T-TATTAG
* * *
2831841 GGTTCCTCACACAAGTTGACATTATTAG
1 AGTTCCTCACACAAGCTAACATTATTAG
* *
2831869 AGTTGCTCACGCAAGCTAACATTAT
1 AGTTCCTCACACAAGCTAACATTAT
2831894 ATTGAGGTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 26 0.59
29 1 0.02
30 17 0.39
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (28 bp):
AGTTCCTCACACAAGCTAACATTATTAG
Found at i:2832983 original size:18 final size:18
Alignment explanation
Indices: 2832957--2832991 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2832947 TTGTCAGGCT
*
2832957 ATCTACCCAAGTTTGAAA
1 ATCTACCCAAATTTGAAA
*
2832975 ATCTGCCCAAATTTGAA
1 ATCTACCCAAATTTGAA
2832992 GGGTTCCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ATCTACCCAAATTTGAAA
Found at i:2833507 original size:14 final size:14
Alignment explanation
Indices: 2833476--2833515 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2833466 TATGAAATTT
*
2833476 AATTAAATATTTAAA
1 AATTAAA-ATTAAAA
2833491 AATTAAAATTAAAA
1 AATTAAAATTAAAA
*
2833505 AATAAAAATTA
1 AATTAAAATTA
2833516 CCTCCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATTAAAATTAAAA
Found at i:2845269 original size:10 final size:10
Alignment explanation
Indices: 2845254--2845365 Score: 57
Period size: 10 Copynumber: 10.7 Consensus size: 10
2845244 TTTATATATA
*
2845254 TTTTTAGATT
1 TTTTTAAATT
2845264 TTTTTAAA-T
1 TTTTTAAATT
* *
2845273 TTATTATATT
1 TTTTTAAATT
*
2845283 TTTTAAAATAT
1 TTTTTAAAT-T
*
2845294 AAATTTTGAAATT
1 ---TTTTTAAATT
*
2845307 TTTATAAATT
1 TTTTTAAATT
2845317 TTTTTAAA-T
1 TTTTTAAATT
* *
2845326 TTTATAAATA
1 TTTTTAAATT
**
2845336 TTTTTATTTT
1 TTTTTAAATT
2845346 ATTTTTATAATT
1 -TTTTTA-AATT
2845358 TTTGTTAA
1 TTT-TTAA
2845366 GAGATAGATC
Statistics
Matches: 75, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
9 15 0.20
10 35 0.47
11 11 0.15
12 5 0.07
13 1 0.01
14 8 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:2845328 original size:19 final size:18
Alignment explanation
Indices: 2845261--2845341 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
2845251 ATATTTTTAG
*
2845261 ATTTTTTTAAATTTAT-T
1 ATTTTTTTAAATTTATAA
*
2845278 ATATTTTTTAAA-ATATAA
1 AT-TTTTTTAAATTTATAA
*
2845296 A--TTTTGAAATTTTTATAA
1 ATTTTTTTAAA--TTTATAA
2845314 ATTTTTTTAAATTTTATAA
1 ATTTTTTTAAA-TTTATAA
*
2845333 ATATTTTTA
1 ATTTTTTTA
2845342 TTTTATTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.14
17 5 0.10
18 16 0.31
19 16 0.31
20 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (18 bp):
ATTTTTTTAAATTTATAA
Found at i:2845336 original size:43 final size:43
Alignment explanation
Indices: 2845247--2845333 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
2845237 AACTTTCTTT
* * * * * *
2845247 ATATATATTTTTAGATTTTTTTAAATTTATTATATTTTTTAAA
1 ATATAAATTTTGAAATTTTTATAAATTTATTAAATTTTATAAA
*
2845290 ATATAAATTTTGAAATTTTTATAAATTTTTTTAAATTTTATAAA
1 ATATAAATTTTGAAATTTTTATAAA-TTTATTAAATTTTATAAA
2845334 TATTTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 21 0.58
44 15 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (43 bp):
ATATAAATTTTGAAATTTTTATAAATTTATTAAATTTTATAAA
Found at i:2847479 original size:29 final size:28
Alignment explanation
Indices: 2847432--2847510 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 28
2847422 GTGAATGTTT
* * *
2847432 TCAATTTAGTCTTTATATTTTAATTTGA
1 TCAATTTAGTTTTTGTATTTTAAATTGA
*
2847460 TCATATTTAGTTTTTGTATTTTTAAATTGG
1 TCA-ATTTAGTTTTTGTA-TTTTAAATTGA
*
2847490 TCAATTTTAGTTTATGTATTT
1 TCAA-TTTAGTTTTTGTATTT
2847511 AAAAAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.07
29 16 0.37
30 24 0.56
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.59
Consensus pattern (28 bp):
TCAATTTAGTTTTTGTATTTTAAATTGA
Found at i:2854059 original size:27 final size:29
Alignment explanation
Indices: 2854003--2854060 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
2853993 TAAATAAGAA
* * *
2854003 AATATAAAATTTTAAAAATTATAATTTTT
1 AATATAAAATTATAAAAATGATAATCTTT
2854032 AATA-AAAATTATAAAAATGA-AATCTTT
1 AATATAAAATTATAAAAATGATAATCTTT
2854059 AA
1 AA
2854061 AATTCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 14 0.54
29 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
AATATAAAATTATAAAAATGATAATCTTT
Found at i:2854351 original size:16 final size:17
Alignment explanation
Indices: 2854330--2854367 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2854320 TAAACATTAA
2854330 TATTTATATA-AT-TTTT
1 TATTTA-ATACATATTTT
2854346 TATTTAATACATATTTT
1 TATTTAATACATATTTT
2854363 TATTT
1 TATTT
2854368 TCGTAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 8 0.40
17 9 0.45
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTAATACATATTTT
Found at i:2857119 original size:16 final size:18
Alignment explanation
Indices: 2857088--2857125 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2857078 AAAATTCACG
2857088 AAATTGAAACATTAAAAA
1 AAATTGAAACATTAAAAA
*
2857106 AAATT-AAA-ATTAAAAC
1 AAATTGAAACATTAAAAA
2857122 AAAT
1 AAAT
2857126 CTTCACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATTGAAACATTAAAAA
Found at i:2867054 original size:11 final size:12
Alignment explanation
Indices: 2867028--2867060 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2867018 AACCAATTCA
2867028 ATTAAATAAATT
1 ATTAAATAAATT
*
2867040 ATTAAA-AATTT
1 ATTAAATAAATT
2867051 ATTAAATAAA
1 ATTAAATAAA
2867061 AAATATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTAAATAAATT
Found at i:2872963 original size:2 final size:2
Alignment explanation
Indices: 2872958--2872989 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2872948 TGTTGTGCAA
2872958 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2872990 TCCTTGTTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2877265 original size:47 final size:47
Alignment explanation
Indices: 2877197--2877337 Score: 176
Period size: 47 Copynumber: 3.0 Consensus size: 47
2877187 TTCGTTTTCT
** *
2877197 CGATGCCATAGACCA-ACTATGGTCTTACATGGAATCACATATCACAC
1 CGATGCCATATCCCAGA-TATGGTCTTACACGGAATCACATATCACAC
* * * *
2877244 CGATGTCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
* *
2877291 TGATGCCATATCCCAGATATGATCTTACACGGAAATCACATATCACA
1 CGATGCCATATCCCAGATATGGTCTTACACGG-AATCACATATCACA
2877338 TATTGCCATG
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
47 66 0.84
48 13 0.16
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
Found at i:2894833 original size:19 final size:19
Alignment explanation
Indices: 2894806--2894845 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
2894796 TTTTCTTTTA
2894806 TTTTAAAATTTTAAA-TAT
1 TTTTAAAATTTTAAATTAT
2894824 TTTTATAAATTTTAAATTAT
1 TTTTA-AAATTTTAAATTAT
2894844 TT
1 TT
2894846 GATGATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.25
19 10 0.50
20 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAAATTTTAAATTAT
Found at i:2908300 original size:2 final size:2
Alignment explanation
Indices: 2908295--2908326 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2908285 AAAACAAGGA
2908295 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2908327 TTGCACAACA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2945310 original size:2 final size:2
Alignment explanation
Indices: 2945305--2945336 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2945295 TGTTGTGCAA
2945305 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2945337 TCCTTGTTTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2949657 original size:47 final size:47
Alignment explanation
Indices: 2949589--2949729 Score: 176
Period size: 47 Copynumber: 3.0 Consensus size: 47
2949579 TTCGTTTTCT
** *
2949589 CGATGCCATAGACCA-ACTATGGTCTTACATGGAATCACATATCACAC
1 CGATGCCATATCCCAGA-TATGGTCTTACACGGAATCACATATCACAC
* * * *
2949636 CGATGTCATATCCCAGATATGGTCTTACACAGTAGCACATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
* *
2949683 TGATGCCATATCCCAGATATGATCTTACACGGAAATCACATATCACA
1 CGATGCCATATCCCAGATATGGTCTTACACGG-AATCACATATCACA
2949730 TATTGCCATG
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
47 66 0.84
48 13 0.16
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACGGAATCACATATCACAC
Found at i:2961739 original size:20 final size:20
Alignment explanation
Indices: 2961701--2961739 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2961691 TGAACCAAAA
*
2961701 TTTTAATATTTTTTATAATT
1 TTTTAATATTTATTATAATT
2961721 TTTTAATGATTTATT-TAAT
1 TTTTAAT-ATTTATTATAAT
2961740 CAAATCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTAATATTTATTATAATT
Found at i:2967743 original size:31 final size:31
Alignment explanation
Indices: 2967708--2967766 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2967698 CAATCCAATA
*
2967708 ACTTAAATAAAAACTTTCGAATAATTTAATG
1 ACTTAAATAAAAACTTTCAAATAATTTAATG
* * *
2967739 ACTTAAATGAGAACTTTTAAATAATTTA
1 ACTTAAATAAAAACTTTCAAATAATTTA
2967767 CTGATCATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTTAATG
Found at i:2968424 original size:17 final size:18
Alignment explanation
Indices: 2968404--2968439 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2968394 GAGAGAAAGG
*
2968404 AGAAGAAG-AGAAGGAAA
1 AGAAGAAGAAGAAAGAAA
2968421 AGAAGAAGAAGAAAGAAA
1 AGAAGAAGAAGAAAGAAA
2968439 A
1 A
2968440 AAAAAAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAGAAAGAAA
Found at i:2968434 original size:14 final size:14
Alignment explanation
Indices: 2968388--2968431 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
2968378 TAGAGAAAAA
2968388 AAAAGAGAGAGAAAGG
1 AAAAGA-AGAG-AAGG
*
2968404 AGAAGAAGAGAAGG
1 AAAAGAAGAGAAGG
2968418 AAAAGAAGAAGAAG
1 AAAAGAAG-AGAAG
2968432 AAAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAGAAGG
Found at i:2968441 original size:20 final size:20
Alignment explanation
Indices: 2968390--2968440 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2968380 GAGAAAAAAA
* *
2968390 AAGAG-AGAGAAAGGAGAAG
1 AAGAGAAGAAAAAGAAGAAG
*
2968409 AAGAGAAGGAAAAGAAGAAG
1 AAGAGAAGAAAAAGAAGAAG
2968429 AAGA-AAGAAAAA
1 AAGAGAAGAAAAA
2968441 AAAAAGGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
AAGAGAAGAAAAAGAAGAAG
Found at i:2968646 original size:40 final size:38
Alignment explanation
Indices: 2968596--2968786 Score: 122
Period size: 41 Copynumber: 4.7 Consensus size: 38
2968586 TATAGTTTAG
* * *
2968596 ATTAGAATTTTGTATGAATATTTTAAATTTTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGT-AA-TGTTGTATGAAT
*
2968636 ATTATAATTTTTTATGAATATTGTAATGTTGTATGAAT
1 ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
* * *
2968674 ATTGTAATTATTTTAT-AATTAAATTTGTATTTATAGTT-T-TG--G
1 ATTATAATT-TTGTATGAA-T--A-TTGTA---AT-GTTGTATGAAT
*
2968716 ATTAGTAATTTTTTGTATGAATATTGTAATTTTGTATGAAT
1 ATTA-TAA--TTTTGTATGAATATTGTAATGTTGTATGAAT
2968757 ATTATAAATTTTTTGTATGAATATTGTAAT
1 ATTAT-AA--TTTTGTATGAATATTGTAAT
2968787 ATTATAGTTT
Statistics
Matches: 123, Mismatches: 10, Indels: 35
0.73 0.06 0.21
Matches are distributed among these distances:
37 2 0.02
38 24 0.20
39 11 0.09
40 22 0.18
41 34 0.28
42 9 0.07
43 3 0.02
44 8 0.07
45 7 0.06
46 3 0.02
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (38 bp):
ATTATAATTTTGTATGAATATTGTAATGTTGTATGAAT
Found at i:2968651 original size:19 final size:19
Alignment explanation
Indices: 2968596--2968786 Score: 102
Period size: 19 Copynumber: 9.4 Consensus size: 19
2968586 TATAGTTTAG
* *
2968596 ATTAGAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
2968615 ATTTTAAATTTTTGTATGAAT
1 ATTAT-AATTTTT-TATGAAT
2968636 ATTATAATTTTTTATGAAT
1 ATTATAATTTTTTATGAAT
* * *
2968655 ATTGTAATGTTGTATGAAT
1 ATTATAATTTTTTATGAAT
*
2968674 ATTGTAATTATTTTAT--A-
1 ATTATAATT-TTTTATGAAT
**
2968691 ATTA-AATTTGTATTTATAGTTTT
1 ATTATAA-TT-T-TTTAT-G-AAT
2968714 GGATTAGTAATTTTTTGTATGAAT
1 --ATTA-TAA-TTTTT-TATGAAT
* *
2968738 ATTGTAATTTTGTATGAAT
1 ATTATAATTTTTTATGAAT
2968757 ATTATAAATTTTTTGTATGAAT
1 ATTAT-AA-TTTTT-TATGAAT
*
2968779 ATTGTAAT
1 ATTATAAT
2968787 ATTATAGTTT
Statistics
Matches: 135, Mismatches: 19, Indels: 35
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.01
17 6 0.04
18 6 0.04
19 45 0.33
20 25 0.19
21 20 0.15
22 14 0.10
24 1 0.01
25 7 0.05
26 4 0.03
27 5 0.04
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (19 bp):
ATTATAATTTTTTATGAAT
Found at i:2968679 original size:49 final size:46
Alignment explanation
Indices: 2968596--2969003 Score: 240
Period size: 49 Copynumber: 8.5 Consensus size: 46
2968586 TATAGTTTAG
* * *
2968596 ATTAGAATTTTGTATGAATATTTTAAATTT-T-TG--TA-TG-AAT
1 ATTATAATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAAT
* *
2968636 ATTATAATTTTTTATGAATATTGTAATGTTGTATGAATATTGTAATT
1 ATTATAATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAA-T
*** * * * * * *
2968683 ATTTTATAATTAAATTTGTAT-TTATAGTTTTGGATTAGTAATTTTTTGTATGAAT
1 A--TTATAATTTTGTATGAATATTGTAATTTTGTA-T-G-AA--TATTG--T-AAT
* *
2968738 ATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAAT
1 ATTATAATTTTGTATGAATATTGT-AA--TTTTGTATGAATATTGTAAT
* * * *
2968787 ATTATAGTTTTGTATGAATATTGCAATTTTTTTGCATGAATATTATAAT
1 ATTATAATTTTGTATGAATATTGTAA---TTTTGTATGAATATTGTAAT
* * * * *
2968836 TTTGTAATTTTGTATGAATATTATATTTTTTTGTATGAATGTTGTAAT
1 ATTATAATTTTGTATGAATATTGTA--ATTTTGTATGAATATTGTAAT
*
2968884 ATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAAT
1 ATTATAATTTTGTATGAATATTGTAA---TTTTGTATGAATATTGTAAT
* * * * *
2968933 TTTGTAATTTTGTATGAATAATGTAA-TGTG-AGGATATATTGTAAT
1 ATTATAATTTTGTATGAATATTGTAATTTTGTATGA-ATATTGTAAT
*
2968978 ATTGTAATTTTTTGTATGAATATTGT
1 ATTATAA--TTTTGTATGAATATTGT
2969004 GATTATTTTA
Statistics
Matches: 285, Mismatches: 53, Indels: 53
0.73 0.14 0.14
Matches are distributed among these distances:
40 25 0.09
41 1 0.00
42 2 0.01
44 5 0.02
45 21 0.07
46 2 0.01
47 18 0.06
48 49 0.17
49 118 0.41
50 2 0.01
51 2 0.01
52 4 0.01
53 16 0.06
54 6 0.02
55 5 0.02
56 3 0.01
57 6 0.02
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (46 bp):
ATTATAATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAAT
Found at i:2968773 original size:22 final size:22
Alignment explanation
Indices: 2968603--2968935 Score: 180
Period size: 22 Copynumber: 15.1 Consensus size: 22
2968593 TAGATTAGAA
*
2968603 TTTTGTATGAATATTTTAAA-T
1 TTTTGTATGAATATTGTAAATT
*
2968624 TTTTGTATGAATATTAT-AA-T
1 TTTTGTATGAATATTGTAAATT
2968644 TTTT-TATGAATATTGT-AA--
1 TTTTGTATGAATATTGTAAATT
*
2968662 TGTTGTATGAATATTGT-AATT
1 TTTTGTATGAATATTGTAAATT
* *
2968683 ATTTTATAATTAA-ATTTGT--ATT
1 -TTTTGT-ATGAATA-TTGTAAATT
* * * * *
2968705 TATAGTTTTGGAT-TAGT-AATT
1 TTTTG-TATGAATATTGTAAATT
2968726 TTTTGTATGAATATTGT-AA--
1 TTTTGTATGAATATTGTAAATT
*
2968745 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAAATT
2968767 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAA-A-T-T
* *
2968792 AGTTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAAATT
* * *
2968816 TTTTGCATGAATATTATAATTTTGT
1 TTTTGTATGAATATTGTAA--AT-T
* *
2968841 AATTTTGTATGAATATTAT-ATTT
1 --TTTTGTATGAATATTGTAAATT
*
2968864 TTTTGTATGAATGTTGTAATATTAT
1 TTTTGTATGAATATTGTAA-A-T-T
* *
2968889 AATTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAAATT
2968913 TTTTGTATGAATATTGT-AATT
1 TTTTGTATGAATATTGTAAATT
2968934 TT
1 TT
2968936 GTAATTTTGT
Statistics
Matches: 249, Mismatches: 34, Indels: 58
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.01
19 43 0.17
20 17 0.07
21 51 0.20
22 60 0.24
23 10 0.04
24 8 0.03
25 5 0.02
26 1 0.00
27 51 0.20
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.55
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAAATT
Found at i:2968803 original size:27 final size:25
Alignment explanation
Indices: 2968735--2968959 Score: 188
Period size: 27 Copynumber: 9.1 Consensus size: 25
2968725 TTTTTGTATG
*
2968735 AATATTGTAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
2968762 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
2968784 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
* * *
2968810 CA-ATTT-TTTTGCATGAATATTAT
1 AATATTTATTTTGTATGAATATTGT
*
2968833 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
*
2968858 -ATATTT-TTTTGTATGAATGTTGT
1 AATATTTATTTTGTATGAATATTGT
2968881 AATATTATAATTTTGTATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
2968907 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
* *
2968930 AATTTTGTAATTTTGTATGAATAATGT
1 AATATT-T-ATTTTGTATGAATATTGT
2968957 AAT
1 AAT
2968960 GTGAGGATAT
Statistics
Matches: 163, Mismatches: 14, Indels: 42
0.74 0.06 0.19
Matches are distributed among these distances:
21 12 0.07
22 49 0.30
23 5 0.03
24 17 0.10
25 12 0.07
26 4 0.02
27 64 0.39
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.53
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:2968899 original size:97 final size:98
Alignment explanation
Indices: 2968739--2968952 Score: 376
Period size: 97 Copynumber: 2.2 Consensus size: 98
2968729 TGTATGAATA
*
2968739 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
2968804 ATATTGCAATTTTTTTGCATGAATATTATAATT
66 ATATTGCAATTTTTTTGCATGAATATTATAATT
* *
2968837 TTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATGTTGTAATATTATAATTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
* *
2968901 ATATTGCAATTTTTTTGTATGAATATTGTAATT
66 ATATTGCAATTTTTTTGCATGAATATTATAATT
2968934 TTGTAATTTTGTATGAATA
1 TTGTAATTTTGTATGAATA
2968953 ATGTAATGTG
Statistics
Matches: 111, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 88 0.79
98 23 0.21
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (98 bp):
TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
ATATTGCAATTTTTTTGCATGAATATTATAATT
Found at i:2969200 original size:38 final size:38
Alignment explanation
Indices: 2969155--2969228 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
2969145 CATATAAAGT
2969155 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
2969193 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTT
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTT
2969229 GGGTTTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:2969379 original size:15 final size:15
Alignment explanation
Indices: 2969338--2969379 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
2969328 GTTAACTTAT
2969338 TTAAATTTTATATAA
1 TTAAATTTTATATAA
*
2969353 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
2969369 TTAAATTTTAT
1 TTAAATTTTAT
2969380 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:2971207 original size:16 final size:18
Alignment explanation
Indices: 2971186--2971222 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2971176 CCTAATTTTT
2971186 TTCTTTT-TT-TCCTTCC
1 TTCTTTTCTTCTCCTTCC
*
2971202 TTCTTTTCTTCTGCTTCC
1 TTCTTTTCTTCTCCTTCC
2971220 TTC
1 TTC
2971223 CTTCTTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (18 bp):
TTCTTTTCTTCTCCTTCC
Found at i:2971236 original size:18 final size:18
Alignment explanation
Indices: 2971186--2971237 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 18
2971176 CCTAATTTTT
2971186 TTCTT-TTT-TTCCTTCC
1 TTCTTCTTTCTTCCTTCC
2971202 TTCTTTTCTTCTGCTTCCTTCC
1 TTC--TTCTT-T-CTTCCTTCC
2971224 TTCTTCTTTCTTCC
1 TTCTTCTTTCTTCC
2971238 GTTTTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.10
18 7 0.23
19 3 0.10
20 6 0.20
22 11 0.37
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (18 bp):
TTCTTCTTTCTTCCTTCC
Found at i:2971394 original size:27 final size:27
Alignment explanation
Indices: 2971294--2971396 Score: 129
Period size: 27 Copynumber: 3.8 Consensus size: 27
2971284 AAAATCACAG
2971294 CATTGGCGCCTCCTA-ATATGGCACCAC
1 CATTGGCGCCTCCTAGATA-GGCACCAC
*
2971321 CATTGGCGACTCCTAGATAGGCACCAC
1 CATTGGCGCCTCCTAGATAGGCACCAC
* * *
2971348 CATTGGCGCCTCCCAAATAGGCACCTC
1 CATTGGCGCCTCCTAGATAGGCACCAC
*
2971375 CGTTGGCGCCTTCC-AGATAGGC
1 CATTGGCGCC-TCCTAGATAGGC
2971397 GCCAATACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
27 61 0.91
28 6 0.09
ACGTcount: A:0.21, C:0.36, G:0.22, T:0.20
Consensus pattern (27 bp):
CATTGGCGCCTCCTAGATAGGCACCAC
Found at i:2971912 original size:6 final size:7
Alignment explanation
Indices: 2971879--2971910 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2971869 ATAAAAATAT
2971879 ATTTTT-
1 ATTTTTA
2971885 ATTTTTA
1 ATTTTTA
2971892 ATTTTTA
1 ATTTTTA
2971899 ATTTTTA
1 ATTTTTA
2971906 ATTTT
1 ATTTT
2971911 AAAATACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
ATTTTTA
Found at i:2971963 original size:20 final size:21
Alignment explanation
Indices: 2971919--2971963 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2971909 TTAAAATACT
* *
2971919 TTTAAAATAAATTTTTTTATT
1 TTTAAAATAAATTTTTTAATG
2971940 TTTAAAAT-AATTTTTTAATG
1 TTTAAAATAAATTTTTTAATG
2971960 TTTA
1 TTTA
2971964 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAAATAAATTTTTTAATG
Found at i:2973103 original size:8 final size:9
Alignment explanation
Indices: 2973084--2973117 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2973074 TTAATTTTTG
2973084 AAAATTTAA
1 AAAATTTAA
2973093 AAAATTTAA
1 AAAATTTAA
*
2973102 AAAAATTATA
1 AAAATTTA-A
2973112 AAAATT
1 AAAATT
2973118 ATTTTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:2977411 original size:30 final size:29
Alignment explanation
Indices: 2977354--2977416 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
2977344 CGCGGAAAAT
2977354 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCGGTAAATAATTAAAAAACC
* *
2977383 GGCCCATTTCGGTAAAT-TTTGAAAAAAACC
1 GGCCCATTCCGGTAAATAATT--AAAAAACC
2977413 GGCC
1 GGCC
2977417 TTTTTTGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 16 0.53
30 12 0.40
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATAATTAAAAAACC
Found at i:2977538 original size:25 final size:26
Alignment explanation
Indices: 2977484--2977553 Score: 124
Period size: 25 Copynumber: 2.7 Consensus size: 26
2977474 AAAAATAAAA
2977484 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATA-TATAACTTTTTTT
2977511 ATTTACCAAAATATATAA-TTTTTTT
1 ATTTACCAAAATATATAACTTTTTTT
2977536 ATTTACCAAAATATATAA
1 ATTTACCAAAATATATAA
2977554 AAAAACTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 25 0.58
26 5 0.12
27 13 0.30
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTACCAAAATATATAACTTTTTTT
Found at i:2977714 original size:4 final size:4
Alignment explanation
Indices: 2977705--2977851 Score: 106
Period size: 4 Copynumber: 36.0 Consensus size: 4
2977695 GAAGGAGAGG
* * * *
2977705 GAAA GAAA GAAA GAAA GAGA GAAA GAAA GGAA GAAA GGAGAG GGAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA
* * *
2977755 G-AA -AAA GAAG GAAA GAAA GGGAAA G-GA GAAGA GAAA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA --GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
* *
2977803 G-AA GAAGA GAAG GAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 GAAA GAA-A GAAA G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
2977852 AGGAAAGGAG
Statistics
Matches: 112, Mismatches: 18, Indels: 26
0.72 0.12 0.17
Matches are distributed among these distances:
3 12 0.11
4 77 0.69
5 18 0.16
6 5 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2977796 original size:26 final size:27
Alignment explanation
Indices: 2977766--2977876 Score: 99
Period size: 26 Copynumber: 4.2 Consensus size: 27
2977756 AAAAAGAAGG
2977766 AAAGAAAGGGAAAGGAGAAGAGAA-AA
1 AAAGAAAGGGAAAGGAGAAGAGAAGAA
* *
2977792 AAAGAAA--GAAAGAAGAAGAGAAGGA
1 AAAGAAAGGGAAAGGAGAAGAGAAGAA
** *
2977817 AAAGAGAAGAAAAAAGA-AAGA-AAGAA
1 AAAGA-AAGGGAAAGGAGAAGAGAAGAA
*
2977843 GGAAAGAAAAGGAAAGGAGAAGAGAA-AA
1 --AAAGAAAGGGAAAGGAGAAGAGAAGAA
2977871 AAAGAA
1 AAAGAA
2977877 GAAGAAGAAG
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
24 14 0.21
25 6 0.09
26 19 0.28
27 11 0.16
28 15 0.22
29 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (27 bp):
AAAGAAAGGGAAAGGAGAAGAGAAGAA
Found at i:2977807 original size:3 final size:3
Alignment explanation
Indices: 2977801--2977893 Score: 53
Period size: 3 Copynumber: 33.3 Consensus size: 3
2977791 AAAAGAAAGA
2977801 AAG AAG AAG -AG AAGG AA- AAG -AG AAG AA- AA- AAG AAAG AAAG AAG
1 AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG -AAG -AAG AAG
* * * *
2977844 GA- AAG AA- AAG GA- AAG GAG AAG -AG AA- AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2977887 AAG AAG A
1 AAG AAG A
2977894 GGGAAGGAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
2 18 0.25
3 44 0.61
4 10 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2977836 original size:81 final size:81
Alignment explanation
Indices: 2977696--2977918 Score: 248
Period size: 79 Copynumber: 2.8 Consensus size: 81
2977686 GGGAGGGCAG
* * * ***
2977696 AAGGAG-AGGGAAAGAAAGAAAGAAAGAGAGAA-AGAAAGGAAGAA-AGGAGAGGGAAGAAAGAA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGA-AGAAGAG-AAGGAA-AAGAGAAGAAAAAAGAAAGAA
*
2977758 AAAGAAGGAAAGAAAGGGA
63 AAAGAAGGAAAGAAAAGGA
2977777 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAAG--AAA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAAGAAAAA
2977840 GAAGGAAAGAAAAGGA
66 GAAGGAAAGAAAAGGA
** *
2977856 AAGGAGAAGAGAAAAAAAG-AAG-AAGAAGAAGAAGAAGAGGGAAG-GAAGGAAAAA-AAAGAAA
1 AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAG-AGAAG-GAAAAGAGAAGAAAAAAGAAAGAAA
2977917 AA
64 AA
2977919 AATGTAATTT
Statistics
Matches: 125, Mismatches: 10, Indels: 16
0.83 0.07 0.11
Matches are distributed among these distances:
77 13 0.10
78 17 0.14
79 44 0.35
80 2 0.02
81 28 0.22
82 21 0.17
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (81 bp):
AAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAAGAAAAA
GAAGGAAAGAAAAGGA
Found at i:2977865 original size:16 final size:15
Alignment explanation
Indices: 2977714--2977888 Score: 60
Period size: 14 Copynumber: 12.4 Consensus size: 15
2977704 GGAAAGAAAG
2977714 AAAGAAA-GAG-AG-
1 AAAGAAAGGAGAAGA
2977726 AAAGAAA-G-GAAGA
1 AAAGAAAGGAGAAGA
* *
2977739 AAGGAGAGG-GAAG-
1 AAAGAAAGGAGAAGA
* *
2977752 AAAGAAA-AAGAAGG
1 AAAGAAAGGAGAAGA
2977766 AAAGAAAGG-GAA-A
1 AAAGAAAGGAGAAGA
** *
2977779 GGAG-AA-GAGAAAA
1 AAAGAAAGGAGAAGA
2977792 AAAGAAA-GA-AAGA
1 AAAGAAAGGAGAAGA
*
2977805 AGAAGAGAAGGAAAAGA
1 A-AAGA-AAGGAGAAGA
* **
2977822 GAAGAAAAAAGAA-A
1 AAAGAAAGGAGAAGA
2977836 GAAAG-AAGGA-AAGA
1 -AAAGAAAGGAGAAGA
2977850 AAAGGAAAGGAGAAGA
1 AAA-GAAAGGAGAAGA
* *
2977866 GAAAAAAAGAAGAAGA
1 -AAAGAAAGGAGAAGA
2977882 AGAAGAA
1 A-AAGAA
2977889 GAAGAGGGAA
Statistics
Matches: 121, Mismatches: 22, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
11 2 0.02
12 15 0.12
13 28 0.23
14 29 0.24
15 16 0.13
16 24 0.20
17 7 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGAAAGGAGAAGA
Found at i:2977869 original size:34 final size:33
Alignment explanation
Indices: 2977705--2977894 Score: 107
Period size: 34 Copynumber: 5.8 Consensus size: 33
2977695 GAAGGAGAGG
*
2977705 GAAAGAA-AGAAAGAAAGAGAGAA-AGAAAGGAA
1 GAAAGAAGAGAAAGAAA-AGAGAAGAGAAAGAAA
* * * *
2977737 GAAAGGAGAGGGAAG-AAAGA-AAAAGAAGGAAA
1 GAAAGAAGA-GAAAGAAAAGAGAAGAGAAAGAAA
* *
2977769 GAAAG--G-GAAAGGAGAAGAGAA-AAAAAGAAA
1 GAAAGAAGAGAAA-GAAAAGAGAAGAGAAAGAAA
*
2977799 GAAAGAAGAAGAGAAGGAAAAGAGAAGAAAAAAGAAA
1 GAAAGAAG-AGA-AA-GAAAAGAGAAG-AGAAAGAAA
2977836 GAAAGAAG-GAAAGAAAAG-GAAAGGAGAAGAGAAA
1 GAAAGAAGAGAAAGAAAAGAG-AA-GAGAA-AGAAA
* *
2977870 AAAAGAAGA-AGAAGAAGA-AGAAGAG
1 GAAAGAAGAGA-AAGAAAAGAGAAGAG
2977895 GGAAGGAAGG
Statistics
Matches: 127, Mismatches: 12, Indels: 37
0.72 0.07 0.21
Matches are distributed among these distances:
28 3 0.02
29 1 0.01
30 17 0.13
31 4 0.03
32 23 0.18
33 17 0.13
34 24 0.19
35 21 0.17
37 17 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (33 bp):
GAAAGAAGAGAAAGAAAAGAGAAGAGAAAGAAA
Found at i:2977909 original size:37 final size:40
Alignment explanation
Indices: 2977699--2977910 Score: 151
Period size: 41 Copynumber: 5.3 Consensus size: 40
2977689 AGGGCAGAAG
* * *
2977699 GAGAGGGAAAGAAAGAAAGAAAGAGAGAAAGAA-AGGAAGAAA
1 GAGAAGGAAA-AAAGAAAGAAAGA-AG-AAGAAGAAGAGGAAA
* * *
2977741 GGAGAGGGAAGAAAG-AA-AAAGAAGGA-AAGAA-AGGGAAA
1 -GAGAAGGAAAAAAGAAAGAAAGAAGAAGAAGAAGA-GGAAA
*
2977779 GGAGAAGAGAAAAAAAGAAAGAAAGAAGAAG-AGAAG-GAAAA
1 -GAGAAG-G-AAAAAAGAAAGAAAGAAGAAGAAGAAGAGGAAA
* *
2977820 GAGAA-GAAAAAAGAAAGAAAGAAGGA-AAGAAAAGGAAA
1 GAGAAGGAAAAAAGAAAGAAAGAAGAAGAAGAAGAGGAAA
*
2977858 GGAGAAGAGAAAAAA-AGAAG-AAGAAGAAGAAGAAGAGGGAA
1 -GAGAAG-GAAAAAAGA-AAGAAAGAAGAAGAAGAAGAGGAAA
2977899 G-GAAGGAAAAAA
1 GAGAAGGAAAAAA
2977911 AAGAAAAAAA
Statistics
Matches: 140, Mismatches: 14, Indels: 35
0.74 0.07 0.19
Matches are distributed among these distances:
37 26 0.19
38 24 0.17
39 12 0.09
40 25 0.18
41 28 0.20
42 16 0.11
43 9 0.06
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (40 bp):
GAGAAGGAAAAAAGAAAGAAAGAAGAAGAAGAAGAGGAAA
Found at i:2977995 original size:14 final size:13
Alignment explanation
Indices: 2977972--2978009 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
2977962 TATTTAAAAT
2977972 TTATGTTATTTCA
1 TTATGTTATTTCA
2977985 TTATAGTTATTTCA
1 TTAT-GTTATTTCA
*
2977999 TTATTTTATTT
1 TTATGTTATTT
2978010 AGCATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (13 bp):
TTATGTTATTTCA
Found at i:2984326 original size:15 final size:12
Alignment explanation
Indices: 2984289--2984319 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2984279 AAAAAAATTT
*
2984289 ATACTCAAAATA
1 ATACACAAAATA
2984301 ATACACAAAATA
1 ATACACAAAATA
2984313 ATACACA
1 ATACACA
2984320 CTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:2984510 original size:3 final size:3
Alignment explanation
Indices: 2984502--2984536 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2984492 TCTTAATACT
2984502 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2984537 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2984541 original size:3 final size:3
Alignment explanation
Indices: 2984535--2984572 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
2984525 CAACAACAAC
*
2984535 AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AACT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
2984573 CTATTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2984871 original size:54 final size:54
Alignment explanation
Indices: 2984787--2984889 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
2984777 ATAATACGAG
**
2984787 TGGTGCCGCCAATTAGTATGGCACCATTGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATTAGTATGGCACCATTGGTGCCGCCAATCCCATTGGCACCAT
* * *
2984841 TGGTGCCGCCAA-TGGTTTTGGCACCTTTGGTGCCGCCAATCCCATTGGC
1 TGGTGCCGCCAATTAG-TATGGCACCATTGGTGCCGCCAATCCCATTGGC
2984890 GTGACCAGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.05
54 41 0.95
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (54 bp):
TGGTGCCGCCAATTAGTATGGCACCATTGGTGCCGCCAATCCCATTGGCACCAT
Found at i:2984888 original size:27 final size:27
Alignment explanation
Indices: 2984787--2984889 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
2984777 ATAATACGAG
* *
2984787 TGGTGCCGCCAATTAGTA-TGGCACCAT
1 TGGTGCCGCCAA-TGGCATTGGCACCAT
2984814 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
2984841 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
2984868 TGGTGCCGCCAATCCCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
2984890 GTGACCAGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 3 0.05
27 63 0.95
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:2984971 original size:25 final size:25
Alignment explanation
Indices: 2984943--2984992 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2984933 TTTTTTTGGT
**
2984943 TTTTTTGATATATTTTGGTAAATAA
1 TTTTTTGATATATTTTAATAAATAA
*
2984968 TTTTTTTATATATTTTAATAAATAA
1 TTTTTTGATATATTTTAATAAATAA
2984993 ATAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTTTTGATATATTTTAATAAATAA
Found at i:2992279 original size:24 final size:25
Alignment explanation
Indices: 2992218--2992279 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
2992208 GACACACCAT
2992218 AGCTCGTATGAGCTTACCGATATTC
1 AGCTCGTATGAGCTTACCGATATTC
* * *
2992243 AGCTCGGAGGAGCTTACCG-TTTATC
1 AGCTCGTATGAGCTTACCGATAT-TC
2992268 -GCTCGTATGAGC
1 AGCTCGTATGAGC
2992280 ATACATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATATTC
Found at i:2994101 original size:17 final size:15
Alignment explanation
Indices: 2994071--2994104 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
2994061 TAACTTTAGA
2994071 AAGTTATTTTTTTAT
1 AAGTTATTTTTTTAT
2994086 AAGTGTATTATTTTTAT
1 AAGT-TATT-TTTTTAT
2994103 AA
1 AA
2994105 TATAGCACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (15 bp):
AAGTTATTTTTTTAT
Found at i:3001262 original size:5 final size:6
Alignment explanation
Indices: 3001247--3001271 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3001237 CATATTTTTA
3001247 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
3001272 TCAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Done.