Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 313 of 356
Found at i:101522840 original size:21 final size:21
Alignment explanation
Indices: 101522798--101522841 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
101522788 TTTATTACTT
* *
101522798 TATATATTCTAAAATTTTATA
1 TATATATTCTAAAATATAATA
101522819 TATATATT-TAAAATAATAATA
1 TATATATTCTAAAAT-ATAATA
101522840 TA
1 TA
101522842 AATAACATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATTCTAAAATATAATA
Found at i:101525123 original size:17 final size:16
Alignment explanation
Indices: 101525079--101525134 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 16
101525069 TTCAATAAAT
*
101525079 AAAAAAATAAA-AATA
1 AAAAAAATAAATATTA
* *
101525094 AAAATATTAAATATTA
1 AAAAAAATAAATATTA
*
101525110 AAATAAAATAAATATTT
1 AAA-AAAATAAATATTA
101525127 AAAAAAAT
1 AAAAAAAT
101525135 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 9 0.27
16 11 0.33
17 13 0.39
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAAATAAATATTA
Found at i:101525139 original size:18 final size:17
Alignment explanation
Indices: 101525093--101525139 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
101525083 AAATAAAAAT
101525093 AAAAATATTAAATATTAA
1 AAAAAT-TTAAATATTAA
*
101525111 AATAAA-ATAAATATTTAA
1 AA-AAATTTAAATA-TTAA
101525129 AAAAATTTAAA
1 AAAAATTTAAA
101525140 AATAATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATTTAAATATTAA
Found at i:101528208 original size:7 final size:7
Alignment explanation
Indices: 101528196--101528225 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
101528186 ATTATTTTTA
101528196 ATTCAAT
1 ATTCAAT
101528203 ATTCAAT
1 ATTCAAT
101528210 ATTCAAT
1 ATTCAAT
*
101528217 ATTTAAT
1 ATTCAAT
101528224 AT
1 AT
101528226 ATCTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (7 bp):
ATTCAAT
Found at i:101529760 original size:3 final size:3
Alignment explanation
Indices: 101529742--101529796 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
101529732 AACCCTTTTC
* *
101529742 TCT TAT TCT GCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
101529790 TCT TCT T
1 TCT TCT T
101529797 TTGTTCCAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:101537041 original size:133 final size:133
Alignment explanation
Indices: 101536853--101537143 Score: 307
Period size: 133 Copynumber: 2.2 Consensus size: 133
101536843 TGAAAAAGCG
*** ** * * ** **
101536853 CAACCCAGCACGATAGGGCACGATTCTTGAATTACCAAACATCGAACATCACCTTTGTTTTAAAG
1 CAACCCAGCACGATAGGGCACGATTCCCAAATTGTCGAACACCGAGTATTGCCTTTGTTTTAAAG
* * *
101536918 GGTTTTCTTAAAAAACATGAGTGAAAACCT-AAAGGATTATTCGATTGTTTTGAA-CAAACGAGA
66 GATTTTCTTAAAAAACATGACTGAAAACCTGAAAGGA-TATTCGATTATTTT-AAGCAAACGAGA
101536981 AATCA
129 AATCA
* *
101536986 CAACCCAGCATGATAGGGCATGATTCCCAAATTGTCGAACACCGAGTATTGCCTTTGTTTTAAAG
1 CAACCCAGCACGATAGGGCACGATTCCCAAATTGTCGAACACCGAGTATTGCCTTTGTTTTAAAG
* * * *** * *
101537051 GATTTTTTTAGAAGACATGACTGAAATTTTGAAGGGATATTTGATTATTTTAAGCAAACGAGAAA
66 GATTTTCTTAAAAAACATGACTGAAAACCTGAAAGGATATTCGATTATTTTAAGCAAACGAGAAA
**
101537116 TTG
131 TCA
*
101537119 CAACCCAGCACGTTAGGGCACGATT
1 CAACCCAGCACGATAGGGCACGATT
101537144 TCGCGAACTG
Statistics
Matches: 127, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
132 2 0.02
133 120 0.94
134 5 0.04
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (133 bp):
CAACCCAGCACGATAGGGCACGATTCCCAAATTGTCGAACACCGAGTATTGCCTTTGTTTTAAAG
GATTTTCTTAAAAAACATGACTGAAAACCTGAAAGGATATTCGATTATTTTAAGCAAACGAGAAA
TCA
Found at i:101539590 original size:23 final size:23
Alignment explanation
Indices: 101539564--101539609 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
101539554 CTGTTGCTGT
101539564 GTTTGTCTTGTTCACAGGTACGG
1 GTTTGTCTTGTTCACAGGTACGG
101539587 GTTTGTCTTGTTCACAGGTACGG
1 GTTTGTCTTGTTCACAGGTACGG
101539610 AGCAGAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.17, G:0.30, T:0.39
Consensus pattern (23 bp):
GTTTGTCTTGTTCACAGGTACGG
Found at i:101563414 original size:20 final size:20
Alignment explanation
Indices: 101563389--101563426 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
101563379 AAGACAAGGG
101563389 TTGTTCTTGCACATATGTCA
1 TTGTTCTTGCACATATGTCA
101563409 TTGTTCTTGCACATATGT
1 TTGTTCTTGCACATATGT
101563427 GAGTTCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (20 bp):
TTGTTCTTGCACATATGTCA
Found at i:101563660 original size:16 final size:16
Alignment explanation
Indices: 101563641--101563689 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
101563631 AAATTTTAGT
101563641 TATTCGTAACAAAAGC
1 TATTCGTAACAAAAGC
*
101563657 TATTC-T--CAAATG-
1 TATTCGTAACAAAAGC
*
101563669 AATTCGTAACAAAAGC
1 TATTCGTAACAAAAGC
101563685 TATTC
1 TATTC
101563690 TCAAATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
15 6 0.24
16 9 0.36
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (16 bp):
TATTCGTAACAAAAGC
Found at i:101563682 original size:28 final size:28
Alignment explanation
Indices: 101563642--101563698 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
101563632 AATTTTAGTT
101563642 ATTCGTAACAAAAGCTATTCTCAAATGA
1 ATTCGTAACAAAAGCTATTCTCAAATGA
101563670 ATTCGTAACAAAAGCTATTCTCAAATGA
1 ATTCGTAACAAAAGCTATTCTCAAATGA
101563698 A
1 A
101563699 ATGTACACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.28
Consensus pattern (28 bp):
ATTCGTAACAAAAGCTATTCTCAAATGA
Found at i:101566261 original size:12 final size:12
Alignment explanation
Indices: 101566244--101566286 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
101566234 TGTTGATGAT
101566244 TATTATCATTTA
1 TATTATCATTTA
*
101566256 TATTATCATTTC
1 TATTATCATTTA
101566268 TATTATCA-TTA
1 TATTATCATTTA
101566279 TTATTATC
1 -TATTATC
101566287 CATGCATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 2 0.07
12 26 0.93
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATCATTTA
Found at i:101578088 original size:44 final size:44
Alignment explanation
Indices: 101578025--101578193 Score: 173
Period size: 44 Copynumber: 3.8 Consensus size: 44
101578015 TATCATGGCG
101578025 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATAT
* * * * *
101578069 ATCTTATCTCACTGAAGTTGCAATAGAGAAGATTGAAGCCATGA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCAT-AT
* * ** *
101578113 ACCTTATGTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG--TTACT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATA-T
* * *
101578156 AGTCTCATCTCCCTAAAGTTGCAGTGGAGCTGACTGAA
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
101578194 AAGAGCGAAT
Statistics
Matches: 101, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 1 0.01
44 97 0.96
45 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGCCATAT
Found at i:101583032 original size:39 final size:40
Alignment explanation
Indices: 101582931--101583115 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
101582921 TCGAATGATG
* * * *
101582931 TCCGGGCTAAGTCCCGAAGGC-TCTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
101582970 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
101583011 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
101583050 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
101583089 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
101583116 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.29
40 78 0.64
41 9 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:101583137 original size:79 final size:79
Alignment explanation
Indices: 101582984--101583148 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
101582974 GGACTAAGAT
* * **
101582984 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
101583049 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
101583063 CCGAAGGCATTTGTACGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTACGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
101583126 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
101583142 CCGAAGG
1 CCGAAGG
101583149 TACGTGATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTACGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:101585909 original size:46 final size:47
Alignment explanation
Indices: 101585857--101585995 Score: 199
Period size: 46 Copynumber: 2.9 Consensus size: 47
101585847 GCTTTCTGAA
** *
101585857 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-T
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
101585903 ATGAAATGAATAAGACCATGGTTGAAAGATATACCATGGCAACATGACG
1 ATGAAATGAATAAGACCATGGTTGAAAG--ATACCATGGCAACATGACG
** *
101585952 GGGAAATGAATAAGACCATGGTTGAAAGATACCATAGCAACATG
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
101585996 GCAGTAAATG
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
46 26 0.31
47 15 0.18
48 17 0.20
49 26 0.31
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.21
Consensus pattern (47 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACG
Found at i:101586026 original size:46 final size:46
Alignment explanation
Indices: 101585867--101586026 Score: 196
Period size: 46 Copynumber: 3.4 Consensus size: 46
101585857 ATGAAATGTG
*
101585867 TAAGACCATGGTTGAAAGATACCATGGCAACATGATA-TGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGT-AAATGAA
* *
101585913 TAAGACCATGGTTGAAAGATATACCATGGCAACATGACGGGGAAATGAA
1 TAAGACCATGGTTGAAAG--ATACCATGGCAACATGAC-AGTAAATGAA
* * *
101585962 TAAGACCATGGTTGAAAGATACCATAGCAACATGGCAGTAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGTAAATGAA
* * *
101586008 TAATACCATAGTTCAAAGA
1 TAAGACCATGGTTGAAAGA
101586027 CATTATGGCA
Statistics
Matches: 99, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
46 41 0.41
47 16 0.16
48 17 0.17
49 25 0.25
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGTAAATGAA
Found at i:101587031 original size:3 final size:3
Alignment explanation
Indices: 101587023--101587060 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
101587013 ATTCGTACAC
101587023 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
101587061 TCTATTGTTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:101591072 original size:23 final size:21
Alignment explanation
Indices: 101591018--101591076 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
101591008 ACTTTATCTA
101591018 TGTTTTATTTATT-TTTTACTT
1 TGTTTTA-TTATTATTTTACTT
*
101591039 AGTTATT-TTATTATTATTACTT
1 TGTT-TTATTATTATT-TTACTT
101591061 TGTTCTTATTATTATT
1 TGTT-TTATTATTATT
101591077 CTAACCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.16
21 5 0.16
22 13 0.42
23 8 0.26
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.69
Consensus pattern (21 bp):
TGTTTTATTATTATTTTACTT
Found at i:101594221 original size:21 final size:21
Alignment explanation
Indices: 101594181--101594221 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
101594171 CAAATCTGAC
* * *
101594181 AAAGATTGAAGAGTTGAAGGG
1 AAAGATAGAAGAGCTCAAGGG
101594202 AAAGATAGAAGAGCTCAAGG
1 AAAGATAGAAGAGCTCAAGG
101594222 CCGCATTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.34, T:0.15
Consensus pattern (21 bp):
AAAGATAGAAGAGCTCAAGGG
Found at i:101602740 original size:22 final size:22
Alignment explanation
Indices: 101602710--101602755 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
101602700 CTACACCCCT
*
101602710 AAAGTCGTAGTGGGATGGATTG
1 AAAGCCGTAGTGGGATGGATTG
101602732 AAAGCCGTAGTGGGATGGATTG
1 AAAGCCGTAGTGGGATGGATTG
101602754 AA
1 AA
101602756 TCTACCATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.39, T:0.24
Consensus pattern (22 bp):
AAAGCCGTAGTGGGATGGATTG
Found at i:101602963 original size:44 final size:44
Alignment explanation
Indices: 101602766--101602953 Score: 229
Period size: 44 Copynumber: 4.3 Consensus size: 44
101602756 TCTACCATAG
101602766 CAAATCTTATCT-CACTGAAGATGTA-A-TGGAGCAAATTAAAGCTA
1 CAAATCTTATCTCCA-TGAA-AT-TACAGTGGAGCAAATTAAAGCTA
* * *
101602810 CAAATCATATCTCCCTGAAATTACAGTGAAGCAAATTAAAGCTA
1 CAAATCTTATCTCCATGAAATTACAGTGGAGCAAATTAAAGCTA
* * * * *
101602854 CAAAACTTATCTCCTTGAAATTGCAGTGGAGCGAATTGAAGCTA
1 CAAATCTTATCTCCATGAAATTACAGTGGAGCAAATTAAAGCTA
* * *
101602898 CAAATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTAAAGCTA
1 CAAATCTTATCTCCATGAAATTACAGTGGAGCAAATTAAAGCTA
101602942 CAAATCTTATCT
1 CAAATCTTATCT
101602954 TGCTAAAGTT
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
42 2 0.02
43 3 0.02
44 119 0.95
45 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCATGAAATTACAGTGGAGCAAATTAAAGCTA
Found at i:101604368 original size:13 final size:13
Alignment explanation
Indices: 101604350--101604377 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
101604340 TCTATCTTAT
101604350 TTAGATTTAATCC
1 TTAGATTTAATCC
101604363 TTAGATTTAATCC
1 TTAGATTTAATCC
101604376 TT
1 TT
101604378 TATATTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (13 bp):
TTAGATTTAATCC
Found at i:101604714 original size:21 final size:21
Alignment explanation
Indices: 101604690--101604730 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
101604680 TTAAACATGA
101604690 CATTAATTA-AATCATTATCAT
1 CATT-ATTATAATCATTATCAT
*
101604711 CATTATTATTATCATTATCA
1 CATTATTATAATCATTATCA
101604731 ATTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (21 bp):
CATTATTATAATCATTATCAT
Found at i:101608634 original size:60 final size:60
Alignment explanation
Indices: 101608541--101608660 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
101608531 TGCTTGCTTG
101608541 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
1 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
101608601 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
1 TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
101608661 GATGACAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (60 bp):
TAGCAGCTTTAATGTTCAAGGTTGTTTCTTTCCTGAATAGGGGCCTAATGGTAATGCATC
Found at i:101609509 original size:3 final size:3
Alignment explanation
Indices: 101609503--101609540 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
101609493 GAAGCATACG
*
101609503 AGA AGA AGA AGA AGA AGA AGA GGA AG- AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
101609541 GAAAATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:101609532 original size:17 final size:18
Alignment explanation
Indices: 101609507--101609541 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
101609497 CATACGAGAA
101609507 GAAGAAGAAGAAGAAGAG
1 GAAGAAGAAGAAGAAGAG
101609525 GAAG-AGAAGAAGAAGAG
1 GAAGAAGAAGAAGAAGAG
101609542 AAAATTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAAGAAGAG
Found at i:101610304 original size:29 final size:31
Alignment explanation
Indices: 101610248--101610318 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
101610238 GGAGAAGAAG
* *
101610248 AAGTATAAACATATTGGGCCATTTATG-TAAA
1 AAGTAAAAAAATATTGGGCCA-TTATGTTAAA
101610279 AAGTAAAAAAATATTGGGCCA-TATGTTAAA
1 AAGTAAAAAAATATTGGGCCATTATGTTAAA
101610309 AACG-AAAAAA
1 AA-GTAAAAAA
101610319 GAAGGACGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 4 0.11
30 12 0.33
31 20 0.56
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.25
Consensus pattern (31 bp):
AAGTAAAAAAATATTGGGCCATTATGTTAAA
Found at i:101611854 original size:24 final size:24
Alignment explanation
Indices: 101611826--101611871 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
101611816 TTTTTTTGGT
*
101611826 ATTTTATATGTTCAATTATTTTTA
1 ATTTTATATATTCAATTATTTTTA
* *
101611850 ATTTTATTTATTTAATTATTTT
1 ATTTTATATATTCAATTATTTT
101611872 ATTAATTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
ATTTTATATATTCAATTATTTTTA
Found at i:101612162 original size:27 final size:27
Alignment explanation
Indices: 101612073--101612162 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
101612063 AATTGAACTT
*
101612073 AAAAAAAATCTTAGGTATCAAATTAGAA
1 AAAAAAAAT-TTAGGTACCAAATTAGAA
* * * * **
101612101 AAAATGCCAAGTTTAGGTACTAAATTGGCC
1 AAAA---AAAATTTAGGTACCAAATTAGAA
*
101612131 CAAAAAAATTTAGGTACCAAATTAGAA
1 AAAAAAAATTTAGGTACCAAATTAGAA
101612158 AAAAA
1 AAAAA
101612163 GGGTCAAGTT
Statistics
Matches: 44, Mismatches: 15, Indels: 7
0.67 0.23 0.11
Matches are distributed among these distances:
27 21 0.48
28 4 0.09
30 16 0.36
31 3 0.07
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.23
Consensus pattern (27 bp):
AAAAAAAATTTAGGTACCAAATTAGAA
Found at i:101612185 original size:59 final size:57
Alignment explanation
Indices: 101612074--101612199 Score: 139
Period size: 59 Copynumber: 2.2 Consensus size: 57
101612064 ATTGAACTTA
* * * * *
101612074 AAAAAAATCTTAGGTATCAAATTAGAAAAAATGCCAAGTTTAGGTACTAAATTG-GCCC
1 AAAAAAAT-TTAGGTACCAAATTAGAAAAAAGGCCAAGTTCAGATACTAAATTGAG-AC
*
101612132 AAAAAAATTTAGGTACCAAATTAGAAAAAAAGGGTCAAGTTCAGATA-TCAAATTGAGAC
1 AAAAAAATTTAGGTACCAAATTAG-AAAAAA-GGCCAAGTTCAGATACT-AAATTGAGAC
101612191 AAAAAAATT
1 AAAAAAATT
101612200 AATAACAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
57 15 0.26
58 15 0.26
59 27 0.47
60 1 0.02
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (57 bp):
AAAAAAATTTAGGTACCAAATTAGAAAAAAGGCCAAGTTCAGATACTAAATTGAGAC
Found at i:101613783 original size:3 final size:3
Alignment explanation
Indices: 101613777--101613804 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
101613767 GTAACAAAAC
101613777 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
101613805 AATCTAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:101614394 original size:42 final size:42
Alignment explanation
Indices: 101614347--101614432 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
101614337 AAGGCCAAAA
101614347 CGATGCCGTTTTGGGCTATTGGAATCAGCCCCTAAACAACAT
1 CGATGCCGTTTTGGGCTATTGGAATCAGCCCCTAAACAACAT
101614389 CGATGCCGTTTTGGGCTATTGGAATCAGCCCCTAAACAACAT
1 CGATGCCGTTTTGGGCTATTGGAATCAGCCCCTAAACAACAT
101614431 CG
1 CG
101614433 TTTTACAGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (42 bp):
CGATGCCGTTTTGGGCTATTGGAATCAGCCCCTAAACAACAT
Found at i:101620500 original size:5 final size:5
Alignment explanation
Indices: 101620490--101620523 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
101620480 ATCTGTGTTC
101620490 TTTAT TTTAT TTTATT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTT
101620524 CACAAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:101620511 original size:16 final size:16
Alignment explanation
Indices: 101620490--101620523 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
101620480 ATCTGTGTTC
101620490 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
101620506 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
101620522 TT
1 TT
101620524 CACAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:101626591 original size:20 final size:21
Alignment explanation
Indices: 101626546--101626597 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
101626536 CAAAAGATAA
* *
101626546 ATAATAAAATTATATTATTTT
1 ATAATAAAATTATATTATGTG
101626567 A-AATAAAATTA-ATTATGTG
1 ATAATAAAATTATATTATGTG
101626586 ATAAT-AAATTAT
1 ATAATAAAATTAT
101626598 TATTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.48
20 13 0.48
21 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
ATAATAAAATTATATTATGTG
Found at i:101636329 original size:6 final size:6
Alignment explanation
Indices: 101636318--101636360 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
101636308 TTGTGTGTTC
*
101636318 TTTATT TTTATT TTTATC TTTATT TTTA-T TTTA-T TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
101636361 CTCACCCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:101636339 original size:18 final size:17
Alignment explanation
Indices: 101636316--101636360 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
101636306 ATTTGTGTGT
101636316 TCTTTATTTTTATTTTTA
1 TCTTTATTTTTA-TTTTA
101636334 TCTTTATTTTTATTTTA
1 TCTTTATTTTTATTTTA
101636351 T-TTTATTTTT
1 TCTTTATTTTT
101636361 CTCACCCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 12 0.44
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTATTTTTATTTTA
Found at i:101637204 original size:18 final size:18
Alignment explanation
Indices: 101637181--101637222 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
101637171 ACAATTACAT
101637181 AGAATATCTCATATATTA
1 AGAATATCTCATATATTA
101637199 AGAATATCTCATATATTA
1 AGAATATCTCATATATTA
*
101637217 ATAATA
1 AGAATA
101637223 GTTTAATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (18 bp):
AGAATATCTCATATATTA
Found at i:101638117 original size:80 final size:82
Alignment explanation
Indices: 101638015--101638172 Score: 248
Period size: 80 Copynumber: 2.0 Consensus size: 82
101638005 ATAAGGTAAT
* *
101638015 ATTTAACTTAAAGGGACCATGAATATCCTATGAGGGTAATACACATATGACAAGTTCATTGGAT-
1 ATTTAACCTAAAGGGACCATGAATATCCTATGAGGATAATACACATATGACAAGTTCATTGGATA
101638079 AAA-TTTAATTAAGTAG
66 AAAGTTTAATTAAGTAG
* * * *
101638095 ATTTAACCTAAATGGATCATGAATATCCTATGAGGATAATACATATATGACAAGTTTATTGGATA
1 ATTTAACCTAAAGGGACCATGAATATCCTATGAGGATAATACACATATGACAAGTTCATTGGATA
101638160 AAAGTTTAATTAA
66 AAAGTTTAATTAA
101638173 TCAAGATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
80 58 0.83
81 3 0.04
82 9 0.13
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (82 bp):
ATTTAACCTAAAGGGACCATGAATATCCTATGAGGATAATACACATATGACAAGTTCATTGGATA
AAAGTTTAATTAAGTAG
Found at i:101640145 original size:21 final size:21
Alignment explanation
Indices: 101640116--101640156 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
101640106 AATTAAGTAA
*
101640116 AATAAGATTAATTAGAATTAG
1 AATAAGATTAATTAAAATTAG
*
101640137 AATATGATTAATTAAAATTA
1 AATAAGATTAATTAAAATTA
101640157 ATTTAATGTT
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:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (21 bp):
AATAAGATTAATTAAAATTAG
Found at i:101654201 original size:78 final size:79
Alignment explanation
Indices: 101654091--101654383 Score: 340
Period size: 81 Copynumber: 3.7 Consensus size: 79
101654081 CCCTCCGTTT
* * * * * * * *
101654091 TGGTGAAGGTGTATCATTTCTCG--CCCTTCGTTTCCGAGGTGGTGACAGATCAG-CACCTGCTC
1 TGGTGAAGGTGTGTCA-TTC-CGAACCCTCCGTTTCCTAGGAGGAGATAAATCAGACATCTGCTC
*
101654153 TGTTTGCTAAAGGTTC
64 TGTTTACTAAAGGTTC
* *
101654169 TGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTTGGAGGAGATAAATCAGTACCATCTGTTC
1 TGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGAGATAAATCAG-A-CATCTGCTC
*
101654234 GGTTTACTAAAGGTTC
64 TGTTTACTAAAGGTTC
**
101654250 TGGTGAAGGTGTGTCATTCCGAACCCTATGTTTCCTAGGAGGAGATAAATCAGTACCATCTGCTC
1 TGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGAGATAAATCAG-A-CATCTGCTC
101654315 TGTTTACTAAAGGTTC
64 TGTTTACTAAAGGTTC
* * * * *
101654331 TGGTGAGGGTGTGCCATTCCTAACCCTCCGCTTCCAAGGAGGAGATAAATCAG
1 TGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGAGATAAATCAG
101654384 TACCACCTCT
Statistics
Matches: 186, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
76 2 0.01
77 3 0.02
78 38 0.20
81 143 0.77
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (79 bp):
TGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGAGATAAATCAGACATCTGCTCTG
TTTACTAAAGGTTC
Found at i:101654258 original size:81 final size:81
Alignment explanation
Indices: 101654147--101654388 Score: 376
Period size: 81 Copynumber: 3.0 Consensus size: 81
101654137 AGATCAGCAC
* * *
101654147 CTGCTCTGTTTGCTAAAGGTTCTGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTTGGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGA
101654212 GATAAATCAGTACCAT
66 GATAAATCAGTACCAT
* **
101654228 CTGTTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCCGAACCCTATGTTTCCTAGGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGA
101654293 GATAAATCAGTACCAT
66 GATAAATCAGTACCAT
* * * * * *
101654309 CTGCTCTGTTTACTAAAGGTTCTGGTGAGGGTGTGCCATTCCTAACCCTCCGCTTCCAAGGAGGA
1 CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGA
101654374 GATAAATCAGTACCA
66 GATAAATCAGTACCA
101654389 CCTCTAGAAG
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 146 1.00
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (81 bp):
CTGCTCGGTTTACTAAAGGTTCTGGTGAAGGTGTGTCATTCCGAACCCTCCGTTTCCTAGGAGGA
GATAAATCAGTACCAT
Found at i:101658637 original size:21 final size:21
Alignment explanation
Indices: 101658613--101658652 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
101658603 TTAACGGGAC
*
101658613 AGCTGATGTGGCAAGTTAATT
1 AGCTGATATGGCAAGTTAATT
*
101658634 AGCTGATATGGCCAGTTAA
1 AGCTGATATGGCAAGTTAA
101658653 CTTGCCACGT
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:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (21 bp):
AGCTGATATGGCAAGTTAATT
Found at i:101658698 original size:3 final size:3
Alignment explanation
Indices: 101658692--101658736 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
101658682 AATAATAGAG
*
101658692 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
101658737 GAAAAATGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:101660240 original size:19 final size:21
Alignment explanation
Indices: 101660216--101660288 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 21
101660206 TCTCATTTTT
101660216 TATTTGTTTTT-TG-TTTTAA
1 TATTTGTTTTTATGATTTTAA
101660235 TATTTGTTTTTATGATTTTAAA
1 TATTTGTTTTTATGATTTT-AA
101660257 TGTATTTGATTTATTAT-ATTTTAA
1 --TATTTG-TTT-TTATGATTTTAA
101660281 -ATTT-TTTT
1 TATTTGTTTT
101660289 ATTTAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
18 1 0.02
19 14 0.30
20 2 0.04
21 8 0.17
22 2 0.04
24 8 0.17
25 8 0.17
26 4 0.09
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.68
Consensus pattern (21 bp):
TATTTGTTTTTATGATTTTAA
Found at i:101660279 original size:25 final size:24
Alignment explanation
Indices: 101660216--101660282 Score: 74
Period size: 25 Copynumber: 3.0 Consensus size: 24
101660206 TCTCATTTTT
101660216 TATTTGTTTTT-TG-TTTT-AA--
1 TATTTGTTTTTATGATTTTAAATG
101660235 TATTTGTTTTTATGATTTTAAATG
1 TATTTGTTTTTATGATTTTAAATG
101660259 TATTTGATTTATTAT-ATTTTAAAT
1 TATTTG-TTT-TTATGATTTTAAAT
101660283 TTTTTTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.27
20 2 0.05
21 4 0.10
22 2 0.05
24 6 0.15
25 12 0.29
26 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (24 bp):
TATTTGTTTTTATGATTTTAAATG
Found at i:101663341 original size:63 final size:63
Alignment explanation
Indices: 101663238--101663360 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 63
101663228 AAATGGTACC
* * *
101663238 AATATCATATTGTAGTAGCTATGGAACTTTTATAAAACGATTTGGATCGGATATATATATACG
1 AATATCATATTGTAGTAGCTATGAAACTTTTACAAAACGATTTGGATCGGATATACATATACG
* * * *
101663301 AATATCATGTTGTAGTAGCTATGAAATTTTTACAATACGATTTGGATTGGATATACATAT
1 AATATCATATTGTAGTAGCTATGAAACTTTTACAAAACGATTTGGATCGGATATACATAT
101663361 TGATCTCTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (63 bp):
AATATCATATTGTAGTAGCTATGAAACTTTTACAAAACGATTTGGATCGGATATACATATACG
Found at i:101664997 original size:28 final size:28
Alignment explanation
Indices: 101664966--101665054 Score: 160
Period size: 28 Copynumber: 3.2 Consensus size: 28
101664956 GTCCCTGGCC
*
101664966 CGTGTCCCTCACACGGCCTAGACACGCT
1 CGTGTCCCGCACACGGCCTAGACACGCT
101664994 CGTGTCCCGCACACGGCCTAGACACGCT
1 CGTGTCCCGCACACGGCCTAGACACGCT
*
101665022 CGTGTCCCGCACACGGCCTAGACACGCC
1 CGTGTCCCGCACACGGCCTAGACACGCT
101665050 CGTGT
1 CGTGT
101665055 TGTCACCAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.17, C:0.43, G:0.25, T:0.16
Consensus pattern (28 bp):
CGTGTCCCGCACACGGCCTAGACACGCT
Found at i:101676600 original size:40 final size:40
Alignment explanation
Indices: 101676545--101676628 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
101676535 TAACCGATCG
101676545 ACTAACCCATGTGAGATATTATAATAAGAAGAAAAAAAAA
1 ACTAACCCATGTGAGATATTATAATAAGAAGAAAAAAAAA
101676585 ACTAACCCATGTGAGATATTATAATAAGAAGAAAAAAAAA
1 ACTAACCCATGTGAGATATTATAATAAGAAGAAAAAAAAA
101676625 ACTA
1 ACTA
101676629 TCCTCTTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.57, C:0.11, G:0.12, T:0.20
Consensus pattern (40 bp):
ACTAACCCATGTGAGATATTATAATAAGAAGAAAAAAAAA
Found at i:101678291 original size:20 final size:20
Alignment explanation
Indices: 101678244--101678293 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
101678234 TTCATTTTTC
*
101678244 TTTT-GTACTCCCTAATAGT
1 TTTTGGTACTCCCTAATAAT
*
101678263 TTTTAGGTACTCCCTTATAAT
1 TTTT-GGTACTCCCTAATAAT
101678284 TTTTGGTACT
1 TTTTGGTACT
101678294 TTTTAGTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 4 0.15
20 6 0.22
21 17 0.63
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTTGGTACTCCCTAATAAT
Found at i:101679287 original size:72 final size:71
Alignment explanation
Indices: 101679206--101679338 Score: 194
Period size: 72 Copynumber: 1.9 Consensus size: 71
101679196 TTCGAATCCT
* * * * *
101679206 TGAAAAGGTTGAAAAGGAAGTTATTCGCAAGGGATAACACATGGAAATGATGTATTTGAAAAAGA
1 TGAAAAGGTTGAAAAGGAAGTTATTCGAAAAGGATAACAAATGAAAATGATGT-GTTGAAAAAGA
101679271 TATCAAA
65 TATCAAA
* *
101679278 TGAAAAGGTTGAAAAGGATGTTATTCGAAAAGGATGACAAATGAAAATGATGTGTTGAAAA
1 TGAAAAGGTTGAAAAGGAAGTTATTCGAAAAGGATAACAAATGAAAATGATGTGTTGAAAA
101679339 GGGAATCATG
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
71 7 0.13
72 47 0.87
ACGTcount: A:0.46, C:0.05, G:0.25, T:0.24
Consensus pattern (71 bp):
TGAAAAGGTTGAAAAGGAAGTTATTCGAAAAGGATAACAAATGAAAATGATGTGTTGAAAAAGAT
ATCAAA
Found at i:101680064 original size:30 final size:30
Alignment explanation
Indices: 101680030--101680089 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
101680020 TTTTTGAATG
101680030 ATTTTAGTATTCGATTTGATCCCAGGTTGT
1 ATTTTAGTATTCGATTTGATCCCAGGTTGT
101680060 ATTTTAGTATTCGATTTGATCCCAGGTTGT
1 ATTTTAGTATTCGATTTGATCCCAGGTTGT
101680090 TTCCAAACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (30 bp):
ATTTTAGTATTCGATTTGATCCCAGGTTGT
Found at i:101682240 original size:46 final size:46
Alignment explanation
Indices: 101682176--101682295 Score: 222
Period size: 46 Copynumber: 2.6 Consensus size: 46
101682166 ATCCGAACTT
101682176 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGCACACCCGAGCTC
1 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGCACACCCGAGCTC
*
101682222 GTTGAGTTGAGTCTGAGTTCACTTATGGATGCGCACACCCGAGCTC
1 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGCACACCCGAGCTC
*
101682268 ATTGAGTTGAGTCCGAGTTCACTTATGG
1 GTTGAGTTGAGTCCGAGTTCACTTATGG
101682296 GTGGGTTACA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (46 bp):
GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGCACACCCGAGCTC
Found at i:101685147 original size:37 final size:37
Alignment explanation
Indices: 101685106--101685179 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
101685096 ATTTCATGTT
*
101685106 GATGATTTTGTTAGATAGATGTTACTTGCAAAAGTGG
1 GATGATTTTGGTAGATAGATGTTACTTGCAAAAGTGG
101685143 GATGATTTTGGTAGATAGATGTTACTTGCAAAAGTGG
1 GATGATTTTGGTAGATAGATGTTACTTGCAAAAGTGG
101685180 TACACTCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.36
Consensus pattern (37 bp):
GATGATTTTGGTAGATAGATGTTACTTGCAAAAGTGG
Found at i:101685388 original size:6 final size:6
Alignment explanation
Indices: 101685379--101685405 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
101685369 AAATGGGACT
101685379 GGGAGG GGGAGG GGGAGG GGGAGG GGG
1 GGGAGG GGGAGG GGGAGG GGGAGG GGG
101685406 GCCTATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.85, T:0.00
Consensus pattern (6 bp):
GGGAGG
Found at i:101694483 original size:11 final size:11
Alignment explanation
Indices: 101694467--101694494 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
101694457 TTAGGTTATA
101694467 TATATAAATAT
1 TATATAAATAT
101694478 TATATAAATAT
1 TATATAAATAT
101694489 TATATA
1 TATATA
101694495 TAATTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATAAATAT
Found at i:101694483 original size:13 final size:12
Alignment explanation
Indices: 101694463--101694502 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
101694453 TTATTTAGGT
101694463 TATATATATAAA
1 TATATATATAAA
101694475 TAT-TATATAAA
1 TATATATATAAA
*
101694486 TATTATATATAAT
1 TA-TATATATAAA
101694499 TATA
1 TATA
101694503 AACCATCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 10 0.40
12 6 0.24
13 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATATAAA
Found at i:101694530 original size:3 final size:3
Alignment explanation
Indices: 101694522--101694559 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
101694512 TATGGTTTTA
* *
101694522 TAT TAT TAT TAT TAT TAG TAT TGT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
101694560 AATGAAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:101696457 original size:23 final size:23
Alignment explanation
Indices: 101696427--101696515 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 23
101696417 GCTTTACTGA
* *
101696427 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
101696450 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
* *
101696471 TCAGACACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
101696493 T-AGGCACTTTTATGTGTCGTATT
1 TCAGGCAC-CTCATGTGTCGTATT
101696516 CTGATCAGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
21 24 0.44
22 10 0.19
23 20 0.37
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:101697767 original size:3 final size:3
Alignment explanation
Indices: 101697759--101697793 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
101697749 TTACTTCATT
* *
101697759 TAA TAA TAA TAA CAA TAC TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
101697794 TAAAACCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:101699082 original size:3 final size:3
Alignment explanation
Indices: 101699074--101699102 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
101699064 TGTCATTAGA
101699074 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
101699103 AGTCATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:101699239 original size:3 final size:3
Alignment explanation
Indices: 101699233--101699307 Score: 55
Period size: 3 Copynumber: 24.3 Consensus size: 3
101699223 ATTATTTCAC
* * * *
101699233 TAT TAT TAT CAT TAT TAT CAT ATAG TAT TAT TAAT TGAA TAT T-T T-T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT T-AT TAT TAT TAT
*
101699279 TAT TAT TGT TAT TAT TATT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
101699308 GTGTTCATTA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.07
3 44 0.77
4 9 0.16
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:101699317 original size:22 final size:22
Alignment explanation
Indices: 101699272--101699318 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
101699262 ATTAATTGAA
* *
101699272 TATTTTTTATTATTGTTATTAT
1 TATTTATTATTATTGTTATCAT
101699294 TATTTATTATTATTGTGT-TCAT
1 TATTTATTATTATTGT-TATCAT
101699316 TAT
1 TAT
101699319 AGTATTGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (22 bp):
TATTTATTATTATTGTTATCAT
Found at i:101704644 original size:39 final size:40
Alignment explanation
Indices: 101704601--101704705 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
101704591 TTCCATTATG
101704601 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
101704640 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
101704685 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
101704706 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:101704699 original size:45 final size:44
Alignment explanation
Indices: 101704599--101704708 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
101704589 TTTTCCATTA
101704599 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
101704638 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
101704683 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
101704709 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:101704708 original size:16 final size:16
Alignment explanation
Indices: 101704689--101704740 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
101704679 GATTTGCTAT
* *
101704689 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
101704705 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
101704721 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
101704737 TACA
1 TACA
101704741 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:101720600 original size:22 final size:21
Alignment explanation
Indices: 101720575--101720616 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
101720565 TTTGTTTTGG
101720575 TATCAAATAA-GATAAATATTTT
1 TATC-AATAATGATAAA-ATTTT
*
101720597 TATCTATAATGATAAAATTT
1 TATCAATAATGATAAAATTT
101720617 ATTACTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
TATCAATAATGATAAAATTTT
Found at i:101722455 original size:38 final size:38
Alignment explanation
Indices: 101722411--101722507 Score: 97
Period size: 39 Copynumber: 2.5 Consensus size: 38
101722401 TGAAACCAAT
*
101722411 TACCAGCACAAGCCTGCGGGAATTTAAACCCGG-TATAA
1 TACCAGCACAAGCCTGCGGGAATTT-AACCCGGACATAA
** * * *
101722449 TACCAGCTTGAAGCCTGCGGGACTTTAGCCCGGACATAT
1 TACCAGC-ACAAGCCTGCGGGAATTTAACCCGGACATAA
*
101722488 TTCCAGCACATAGCCTGCGG
1 TACCAGCACA-AGCCTGCGG
101722508 ACCCTAAGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
38 14 0.30
39 33 0.70
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.21
Consensus pattern (38 bp):
TACCAGCACAAGCCTGCGGGAATTTAACCCGGACATAA
Found at i:101722561 original size:39 final size:39
Alignment explanation
Indices: 101722478--101722562 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
101722468 GGACTTTAGC
* *
101722478 CCGGACATATTTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
101722517 CCGGATATAATTCCAGCACATAGCCTGTGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
101722556 CCGGATA
1 CCGGATA
101722563 CACATCAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:101726949 original size:7 final size:7
Alignment explanation
Indices: 101726937--101726961 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
101726927 AGAAGAGGGA
101726937 TGGAAAG
1 TGGAAAG
101726944 TGGAAAG
1 TGGAAAG
101726951 TGGAAAG
1 TGGAAAG
101726958 TGGA
1 TGGA
101726962 TTTAGGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (7 bp):
TGGAAAG
Found at i:101730912 original size:24 final size:23
Alignment explanation
Indices: 101730864--101730934 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
101730854 AAGGTCTTTT
* *
101730864 AAGAAAATGATAAATAAAGACAAA
1 AAGAAAA-GAAAAATAAAAACAAA
* *
101730888 AAGAAATGCAAAAATAAAAATAAA
1 AAGAAAAG-AAAAATAAAAACAAA
* *
101730912 AATAAAAGAAAAAGAAAAACAAA
1 AAGAAAAGAAAAATAAAAACAAA
101730935 TCGAAAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
23 14 0.37
24 24 0.63
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (23 bp):
AAGAAAAGAAAAATAAAAACAAA
Found at i:101740604 original size:20 final size:20
Alignment explanation
Indices: 101740575--101740628 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
101740565 AGGGGCACAC
101740575 GCCCGTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGGACAT
*
101740595 GCCTGTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGGACAT
*
101740615 GCCCATGTGGCCTG
1 GCCCGTGTGGCCTG
101740629 CCCATGGGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.09, C:0.30, G:0.39, T:0.22
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGGACAT
Found at i:101741491 original size:53 final size:52
Alignment explanation
Indices: 101741422--101741575 Score: 177
Period size: 52 Copynumber: 2.9 Consensus size: 52
101741412 ACATAACATG
* *
101741422 CCGATGCCATATCCCAGATATGGTCTTATACGGAATCACATTATCACATCACA
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACA-TATCACATCACA
* * ***
101741475 CCGATGCCATAGCCCAGCTATGGTCTTATATGGGAACTC-GA-ATCACATTGTA
1 CCGATGCCATAGCCCAGCTATGGTCTTATA-CGGAA-TCACATATCACATCACA
* * *
101741527 CCAATGCCATAGTCCAGCTATGGTCTTATACGGAAGCACATATCACATC
1 CCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATC
101741576 TTTTCCGTCA
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
50 1 0.01
51 5 0.06
52 43 0.51
53 28 0.33
54 5 0.06
55 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (52 bp):
CCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATATCACATCACA
Found at i:101748926 original size:52 final size:51
Alignment explanation
Indices: 101748779--101748930 Score: 162
Period size: 52 Copynumber: 2.9 Consensus size: 51
101748769 TAACATGCCG
* * * *
101748779 ATGCCATATCCCAGATATGGTCTTATATGGAATCACATTATCACATCACACCG
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAA-CACA-TATCACATCACACCA
* * ***
101748832 ATGTCATAGCCCAGCTATGGTCTTATACGGGAACTCGA-ATCACATTGTACCA
1 ATGCCATAGCCCAGCTATGGTCTTATAC-GGAACAC-ATATCACATCACACCA
*
101748884 ATGCCATAGCCCAGCTATGGTCTTATACAGAAGCACATATCACATCA
1 ATGCCATAGCCCAGCTATGGTCTTATACGGAA-CACATATCACATCA
101748931 TTTCCATCAA
Statistics
Matches: 81, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
51 4 0.05
52 46 0.57
53 26 0.32
54 5 0.06
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (51 bp):
ATGCCATAGCCCAGCTATGGTCTTATACGGAACACATATCACATCACACCA
Found at i:101749089 original size:22 final size:22
Alignment explanation
Indices: 101749062--101749103 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
101749052 ATTATACTTA
101749062 AAAACAATAATATTT-TCATAAC
1 AAAACAATAA-ATTTGTCATAAC
*
101749084 AAAACATTAAATTTGTCATA
1 AAAACAATAAATTTGTCATA
101749104 TGAGCTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAACAATAAATTTGTCATAAC
Found at i:101755280 original size:14 final size:14
Alignment explanation
Indices: 101755261--101755287 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
101755251 ATATTTGACT
101755261 TATTCTTAATTATA
1 TATTCTTAATTATA
101755275 TATTCTTAATTAT
1 TATTCTTAATTAT
101755288 TGTTTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTCTTAATTATA
Found at i:101768904 original size:24 final size:24
Alignment explanation
Indices: 101768860--101768909 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
101768850 GTTGTTTCAT
101768860 AAAAAAAACTGAACTGGAAAAGAG
1 AAAAAAAACTGAACTGGAAAAGAG
* *
101768884 AAAAAAAA-TCGAATTGTAAAAGAG
1 AAAAAAAACT-GAACTGGAAAAGAG
101768908 AA
1 AA
101768910 GGAGAATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.64, C:0.06, G:0.18, T:0.12
Consensus pattern (24 bp):
AAAAAAAACTGAACTGGAAAAGAG
Found at i:101769976 original size:185 final size:184
Alignment explanation
Indices: 101769543--101770096 Score: 1054
Period size: 185 Copynumber: 3.0 Consensus size: 184
101769533 AATCGGTAAG
*
101769543 AAAATTAATCCATCCAACCAATTGTTTCAACCGATTCCTCCCCTTACTGTTAATGCTAAAGGACT
1 AAAATTAATCCATCCAACCAACTGTTTCAACCGATTCCTCCCCTTACTGTTAATGCTAAAGGACT
101769608 AGAGCTCATCAATATAAACTATGGTTGTTTGGACTATTCCTTTTCCTAAAGAAACTTTACTATGA
66 AGAGCTCATCAATATAAACTATGGTTGTTTGGACTATTCCTTTTCCTAAAGAAACTTTACTATGA
101769673 TTTTTTTTAATTACAATAACAAGGAAAAGTGTGAACAACAAATGCGTTTAACGC
131 TTTTTTTTAATTACAATAACAAGGAAAAGTGTGAACAACAAATGCGTTTAACGC
*
101769727 AAAATTAATCCATTCAACCAACTGTTTCAACCGATTCCTCCCCTTACTGTTAATGCTAAAGGACT
1 AAAATTAATCCATCCAACCAACTGTTTCAACCGATTCCTCCCCTTACTGTTAATGCTAAAGGACT
*
101769792 AGAGCTCATCAATATAAACTATGGTTGTTTGGACTATTCGTTTTCCTAAAGAAACTTTACTATGA
66 AGAGCTCATCAATATAAACTATGGTTGTTTGGACTATTCCTTTTCCTAAAGAAACTTTACTATGA
101769857 TTTTTTTTAAATTACAATAACAAGGAAAAGTGTGAACAACAAATGCGTTTAACGC
131 TTTTTTTT-AATTACAATAACAAGGAAAAGTGTGAACAACAAATGCGTTTAACGC
101769912 AAAATTAATCCATCCAACCAACTGTTTCAACCGATTCCTCCCCTTACTGTTAATGCTAAAGGACT
1 AAAATTAATCCATCCAACCAACTGTTTCAACCGATTCCTCCCCTTACTGTTAATGCTAAAGGACT
101769977 AGAGCTCATCAATATAAACTATGGTTGTTTGGACTATTCCTTTTCCTAAAGAAACTTTACTATGA
66 AGAGCTCATCAATATAAACTATGGTTGTTTGGACTATTCCTTTTCCTAAAGAAACTTTACTATGA
*
101770042 TTTTTTTTTAATTACAATAACAAGAAAAAGTGTGAACAACAAATGCGTTTAACGC
131 -TTTTTTTTAATTACAATAACAAGGAAAAGTGTGAACAACAAATGCGTTTAACGC
101770097 GACTCAAATT
Statistics
Matches: 362, Mismatches: 6, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
184 135 0.37
185 219 0.60
186 8 0.02
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (184 bp):
AAAATTAATCCATCCAACCAACTGTTTCAACCGATTCCTCCCCTTACTGTTAATGCTAAAGGACT
AGAGCTCATCAATATAAACTATGGTTGTTTGGACTATTCCTTTTCCTAAAGAAACTTTACTATGA
TTTTTTTTAATTACAATAACAAGGAAAAGTGTGAACAACAAATGCGTTTAACGC
Found at i:101774222 original size:30 final size:30
Alignment explanation
Indices: 101774188--101774248 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
101774178 ATCAAAAGAA
101774188 GAAGAAAGTTAATCAAAGAAATAAGACTAT
1 GAAGAAAGTTAATCAAAGAAATAAGACTAT
101774218 GAAGAAAGTTAATCAAAGAAATAAGACTAT
1 GAAGAAAGTTAATCAAAGAAATAAGACTAT
101774248 G
1 G
101774249 CATATCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.07, G:0.18, T:0.20
Consensus pattern (30 bp):
GAAGAAAGTTAATCAAAGAAATAAGACTAT
Found at i:101775981 original size:30 final size:32
Alignment explanation
Indices: 101775922--101775984 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
101775912 ATTATTTTTA
* *
101775922 AATTTTTGGAAAGTTTAATATGAAAATTTTCT
1 AATTTTTAGAAAGTATAATATGAAAATTTTCT
*
101775954 AATTTTTAGAAAGTATGAT-TG-AAATTTTCT
1 AATTTTTAGAAAGTATAATATGAAAATTTTCT
101775984 A
1 A
101775985 GTAATTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 10 0.36
31 2 0.07
32 16 0.57
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (32 bp):
AATTTTTAGAAAGTATAATATGAAAATTTTCT
Found at i:101776460 original size:9 final size:9
Alignment explanation
Indices: 101776446--101776552 Score: 56
Period size: 9 Copynumber: 11.7 Consensus size: 9
101776436 CTACTCTAAT
101776446 TAAAAATTA
1 TAAAAATTA
*
101776455 TAAAAATAA
1 TAAAAATTA
**
101776464 TAAATTTTA
1 TAAAAATTA
*
101776473 GAAAAATTA
1 TAAAAATTA
**
101776482 TTAAATTTTAA
1 -TAAAAATT-A
101776493 TAAAAA-TA
1 TAAAAATTA
101776501 TAATAAATTA
1 TAA-AAATTA
***
101776511 TAATTTTTTA
1 TAA-AAATTA
*
101776521 TAAAAATTG
1 TAAAAATTA
*
101776530 TAAAAA-AA
1 TAAAAATTA
*
101776538 TAAAAATTG
1 TAAAAATTA
101776547 TAAAAA
1 TAAAAA
101776553 ATAGCGACCC
Statistics
Matches: 70, Mismatches: 23, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
8 10 0.14
9 38 0.54
10 21 0.30
11 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:101776478 original size:19 final size:20
Alignment explanation
Indices: 101776456--101776509 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
101776446 TAAAAATTAT
101776456 AAAAATAATAAATTTT-AGA
1 AAAAATAATAAATTTTAAGA
* * *
101776475 AAAATTATTAAATTTTAATA
1 AAAAATAATAAATTTTAAGA
101776495 AAAATATAATAAATT
1 AAAA-ATAATAAATT
101776510 ATAATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 14 0.50
20 6 0.21
21 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAAATAATAAATTTTAAGA
Found at i:101776540 original size:17 final size:17
Alignment explanation
Indices: 101776520--101776553 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
101776510 ATAATTTTTT
101776520 ATAAAAATTGTAAAAAA
1 ATAAAAATTGTAAAAAA
101776537 ATAAAAATTGTAAAAAA
1 ATAAAAATTGTAAAAAA
101776554 TAGCGACCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
ATAAAAATTGTAAAAAA
Found at i:101776759 original size:10 final size:9
Alignment explanation
Indices: 101776732--101776828 Score: 51
Period size: 8 Copynumber: 10.7 Consensus size: 9
101776722 ACTTTATAAA
*
101776732 ATTTTAAAT
1 ATTTTATAT
*
101776741 -TTTTTTAT
1 ATTTTATAT
101776749 ATTTCTATAT
1 ATTT-TATAT
101776759 ATTTTATA-
1 ATTTTATAT
101776767 ATTTT-TACT
1 ATTTTATA-T
*
101776776 ATTTTTATGAA
1 A-TTTTAT-AT
* *
101776787 ATTTAACA-
1 ATTTTATAT
*
101776795 ATTTTTTAT
1 ATTTTATAT
101776804 GAATTTTATAT
1 --ATTTTATAT
101776815 ATTTTATAT
1 ATTTTATAT
101776824 -TTTTA
1 ATTTTA
101776829 ATAAATTTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
7 2 0.03
8 21 0.31
9 18 0.26
10 16 0.24
11 10 0.15
12 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (9 bp):
ATTTTATAT
Found at i:101776790 original size:28 final size:25
Alignment explanation
Indices: 101776724--101776828 Score: 75
Period size: 28 Copynumber: 3.8 Consensus size: 25
101776714 TTCTTACAAC
101776724 TTTATAAAATTTTAAATTTTTTTATATT
1 TTTAT-AAATTTTAAA--TTTTTATATT
* *
101776752 TCTATATATTTTATAATTTTTACTATT
1 TTTATAAATTTTA-AATTTTTA-TATT
* *
101776779 TTTATGAAATTTAACAATTTTTTATGAAT
1 TTTAT-AAATTTTA-AA-TTTTTAT-ATT
* *
101776808 TTTATATATTTTATATTTTTA
1 TTTATAAATTTTAAATTTTTA
101776829 ATAAATTTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
26 12 0.19
27 16 0.26
28 21 0.34
29 13 0.21
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTATAAATTTTAAATTTTTATATT
Found at i:101776798 original size:56 final size:53
Alignment explanation
Indices: 101776724--101776828 Score: 140
Period size: 56 Copynumber: 1.9 Consensus size: 53
101776714 TTCTTACAAC
*
101776724 TTTATAAAATTTTAAATTTTTT-TATATTTCTATATATTTTATAATTTTTACTATT
1 TTTATAAAATTTAAAATTTTTTATA-ATTT-TATATATTTTAT-ATTTTTACTATT
*
101776779 TTTATGAAATTTAACAATTTTTTATGAATTTTATATATTTTATATTTTTA
1 TTTATAAAATTTAA-AATTTTTTAT-AATTTTATATATTTTATATTTTTA
101776829 ATAAATTTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
55 19 0.42
56 20 0.44
57 5 0.11
58 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (53 bp):
TTTATAAAATTTAAAATTTTTTATAATTTTATATATTTTATATTTTTACTATT
Found at i:101776818 original size:20 final size:19
Alignment explanation
Indices: 101776731--101776819 Score: 57
Period size: 20 Copynumber: 4.8 Consensus size: 19
101776721 AACTTTATAA
*
101776731 AATTTTAAAT-TTTTTTAT
1 AATTTTATATATTTTTTAT
101776749 -ATTTCTATATA--TTTTAT
1 AATTT-TATATATTTTTTAT
101776766 AATTTT-TACTA-TTTTTAT
1 AATTTTATA-TATTTTTTAT
* *
101776784 GAAATTTA-ACAATTTTTTAT
1 -AATTTTATA-TATTTTTTAT
101776804 GAATTTTATATATTTT
1 -AATTTTATATATTTT
101776820 ATATTTTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.04
17 13 0.23
18 14 0.25
19 8 0.14
20 19 0.33
21 1 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTATATATTTTTTAT
Found at i:101776835 original size:27 final size:26
Alignment explanation
Indices: 101776795--101776909 Score: 79
Period size: 27 Copynumber: 4.2 Consensus size: 26
101776785 AAATTTAACA
* *
101776795 ATTTTTTATGAATTTTATATATTTTAT
1 ATTTTTAATAAATTTTA-ATATTTTAT
* * *
101776822 ATTTTTAATAAATTTGTAATAATTGAA
1 ATTTTTAATAAATTT-TAATATTTTAT
* *
101776849 ATTTTTATTAAAATTTAATAATATTTAT
1 ATTTTTAATAAATTTTAAT-AT-TTTAT
** *
101776877 AACTTTTT-ATTGATTTTAATTTTTTAT
1 -A-TTTTTAATAAATTTTAATATTTTAT
101776904 ATTTTT
1 ATTTTT
101776910 TTCTAATTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
25 5 0.07
26 5 0.07
27 38 0.56
28 6 0.09
29 9 0.13
30 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (26 bp):
ATTTTTAATAAATTTTAATATTTTAT
Found at i:101777049 original size:91 final size:90
Alignment explanation
Indices: 101776924--101777156 Score: 261
Period size: 92 Copynumber: 2.5 Consensus size: 90
101776914 AATTTTTAAT
* * * *
101776924 AAAAGCAGAGGCCTAATTGTGTTTTTTTTAAAAAAGTTTAAGGGCCTTTTTGGTGTATTTTGAAA
1 AAAAGCAAAGGCTTAA-T-TGTTTTTTTT-AAAAAGTTTAAGGGCCTTTTTGATGCATTTTGAAA
*
101776989 GTTCAAGAACCCAATTGAATGCAAAAAA
63 GTTCAAGAACCCAAATGAATGCAAAAAA
* * * * * *
101777017 AAAAGTTAAAGGCTTTATTGTTTTTATTAAAAAGGTTTGAGGGCATTTTTTATGCATTTTGAAAG
1 AAAAG-CAAAGGCTTAATTGTTTTTTTTAAAAA-GTTTAAGGGCCTTTTTGATGCATTTTGAAAG
* * *
101777082 TTCAAGTACCCAAATGAGTGTAAAAAA
64 TTCAAGAACCCAAATGAATGCAAAAAA
** *
101777109 AAAAGCAGGGGCTTAATTGTTTTTTTTAAAAAGTTTTAGGG-CTTTTTG
1 AAAAGCAAAGGCTTAATTGTTTTTTTTAAAAAGTTTAAGGGCCTTTTTG
101777157 CATCAAACTT
Statistics
Matches: 116, Mismatches: 22, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
89 5 0.04
90 8 0.07
91 27 0.23
92 63 0.54
93 6 0.05
94 7 0.06
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (90 bp):
AAAAGCAAAGGCTTAATTGTTTTTTTTAAAAAGTTTAAGGGCCTTTTTGATGCATTTTGAAAGTT
CAAGAACCCAAATGAATGCAAAAAA
Found at i:101778340 original size:12 final size:12
Alignment explanation
Indices: 101778325--101778350 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
101778315 AACTAAATTG
101778325 AATAGACTTCAA
1 AATAGACTTCAA
101778337 AATAGACTTCAA
1 AATAGACTTCAA
101778349 AA
1 AA
101778351 CCTAGAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AATAGACTTCAA
Found at i:101781023 original size:19 final size:18
Alignment explanation
Indices: 101780987--101781032 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
101780977 TTAAAAGATA
101780987 TTTTTTTTAATTATTTTC
1 TTTTTTTTAATTATTTTC
101781005 TTTTCTTTTACATTATTTCTC
1 TTTT-TTTTA-ATTATTT-TC
101781026 TCTTTTT
1 T-TTTTT
101781033 ATTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.17
19 5 0.21
20 7 0.29
21 5 0.21
22 3 0.12
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTTAATTATTTTC
Found at i:101784980 original size:23 final size:22
Alignment explanation
Indices: 101784950--101784993 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
101784940 AAATTCTACT
* *
101784950 TCATAATGCTTTGTTTACTAAAA
1 TCATAATGATTTGCTT-CTAAAA
101784973 TCATAATGATTTGCTTCTAAA
1 TCATAATGATTTGCTTCTAAA
101784994 GTTAGGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (22 bp):
TCATAATGATTTGCTTCTAAAA
Found at i:101786071 original size:22 final size:20
Alignment explanation
Indices: 101786046--101786086 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
101786036 GTTCTGATCC
101786046 TTTAATATTTATAAAATTTTAA
1 TTTAATATTT-T-AAATTTTAA
101786068 TTTAATATTTTAAATTTTA
1 TTTAATATTTTAAATTTTA
101786087 TAAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAATATTTTAAATTTTAA
Found at i:101790161 original size:2 final size:2
Alignment explanation
Indices: 101790154--101790179 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
101790144 ACAAAAATAT
101790154 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
101790180 AAGCAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:101793340 original size:21 final size:21
Alignment explanation
Indices: 101793316--101793358 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
101793306 TAACTCTAAC
*
101793316 AATTTCATTTGATTCGACTCG
1 AATTTCATTTCATTCGACTCG
*
101793337 AATTTCATTTCATTTGACTCG
1 AATTTCATTTCATTCGACTCG
101793358 A
1 A
101793359 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (21 bp):
AATTTCATTTCATTCGACTCG
Found at i:101794881 original size:18 final size:18
Alignment explanation
Indices: 101794858--101794892 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
101794848 GGCCTGAAAC
*
101794858 CCCAAACTCAAACATTAA
1 CCCAAACCCAAACATTAA
101794876 CCCAAACCCAAACATTA
1 CCCAAACCCAAACATTA
101794893 TGTTTGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.37, G:0.00, T:0.14
Consensus pattern (18 bp):
CCCAAACCCAAACATTAA
Found at i:101801350 original size:104 final size:104
Alignment explanation
Indices: 101801171--101801373 Score: 246
Period size: 104 Copynumber: 2.0 Consensus size: 104
101801161 CCACACTGCC
* * * * * ** *
101801171 AGGGATATGGGCGTGTGCCCAGGCCGTGTGAGCTACACGGGCAAAGACATGGGCATGTGTTTAGT
1 AGGGACATGGGCATGTGCCCAGGCCGTGTAAGCCACACAGGCAAAGACATGGGCATGTGTCCAGG
** *
101801236 CCATGTAACTCACTATTTACGCTTTAGAACCACATGGCT
66 CCATACAACTCACTATTTACGATTTAGAACCACATGGCT
* *
101801275 AGGGACATGGGCATGTGCCTAGGCCGTGTAAGCCACACAGG-AAAGGACATGGGCGTGTGTCCAG
1 AGGGACATGGGCATGTGCCCAGGCCGTGTAAGCCACACAGGCAAA-GACATGGGCATGTGTCCAG
* * *
101801339 GCTATACAACTCACTGTTTATGATTTAGAACCACA
65 GCCATACAACTCACTATTTACGATTTAGAACCACA
101801374 CGGATGTGTG
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
103 3 0.04
104 79 0.96
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (104 bp):
AGGGACATGGGCATGTGCCCAGGCCGTGTAAGCCACACAGGCAAAGACATGGGCATGTGTCCAGG
CCATACAACTCACTATTTACGATTTAGAACCACATGGCT
Found at i:101804365 original size:11 final size:11
Alignment explanation
Indices: 101804350--101804389 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
101804340 GCTTTCTCCA
101804350 TATTTTGCTAT
1 TATTTTGCTAT
* *
101804361 CATTTTACTAT
1 TATTTTGCTAT
*
101804372 TATGTTGCTAT
1 TATTTTGCTAT
101804383 TATTTTG
1 TATTTTG
101804390 TTGTTATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (11 bp):
TATTTTGCTAT
Found at i:101805403 original size:42 final size:42
Alignment explanation
Indices: 101805277--101805450 Score: 168
Period size: 42 Copynumber: 4.1 Consensus size: 42
101805267 ACACAGCCAG
* * * * *
101805277 GGACATGGGCGTGTGCCCAAGCCGTATGAGCCACACGAGCAA
1 GGACATAGGCATGTGCCCAGGCCGTGTGAGCCACACGGGCAA
* * * * **
101805319 AGACATGGGCATGTGTCTAGGCCGTGTGAGCCACACATGCAA
1 GGACATAGGCATGTGCCCAGGCCGTGTGAGCCACACGGGCAA
* * *
101805361 GGACATAGGCATGTGCCCAGGCCGTTTGAGCCATATGGGCAA
1 GGACATAGGCATGTGCCCAGGCCGTGTGAGCCACACGGGCAA
* * * * **
101805403 GGATATAGACGTATGCAGAGGCCGTGTGAGCCACACGGGCAA
1 GGACATAGGCATGTGCCCAGGCCGTGTGAGCCACACGGGCAA
101805445 GGACAT
1 GGACAT
101805451 GTGTGTGTGT
Statistics
Matches: 105, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.16
Consensus pattern (42 bp):
GGACATAGGCATGTGCCCAGGCCGTGTGAGCCACACGGGCAA
Found at i:101809152 original size:24 final size:26
Alignment explanation
Indices: 101809119--101809173 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
101809109 AACAAAATAA
101809119 AAAAATAAACAAAAAGAA-GAAACAC
1 AAAAATAAACAAAAAGAAGGAAACAC
* * *
101809144 AAAAA-AAACGAAAGGAAGGAAACTC
1 AAAAATAAACAAAAAGAAGGAAACAC
101809169 AAAAA
1 AAAAA
101809174 GAAAAGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.73, C:0.11, G:0.13, T:0.04
Consensus pattern (26 bp):
AAAAATAAACAAAAAGAAGGAAACAC
Found at i:101814654 original size:10 final size:10
Alignment explanation
Indices: 101814639--101814666 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
101814629 TAAATACATT
101814639 TAATTAAAGA
1 TAATTAAAGA
101814649 TAATTAAAGA
1 TAATTAAAGA
101814659 TAATTAAA
1 TAATTAAA
101814667 AAAAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:101816155 original size:21 final size:23
Alignment explanation
Indices: 101816114--101816155 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
101816104 TAACAGATAG
*
101816114 GCACCGGGTGTCAACTTATTTTA
1 GCACCGGGCGTCAACTTATTTTA
101816137 GCACCGGGCG-CAA-TTATTT
1 GCACCGGGCGTCAACTTATTT
101816156 GCTTTGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 3 0.17
23 9 0.50
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACCGGGCGTCAACTTATTTTA
Found at i:101817685 original size:43 final size:43
Alignment explanation
Indices: 101817602--101817685 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
101817592 GTTTCCAACA
**
101817602 TGTGATTACATGTAAAACCATGTCATGGACATTGGCATTGTAT
1 TGTGATTACATGTAAAACCATGTCATGGACATTGAAATTGTAT
* *
101817645 TGTGATTACGTGTAAGACCATGTC-TGGGACATTGAAATTGT
1 TGTGATTACATGTAAAACCATGTCAT-GGACATTGAAATTGT
101817686 TAACCGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (43 bp):
TGTGATTACATGTAAAACCATGTCATGGACATTGAAATTGTAT
Found at i:101824645 original size:43 final size:44
Alignment explanation
Indices: 101824548--101824700 Score: 138
Period size: 43 Copynumber: 3.5 Consensus size: 44
101824538 ACCAAGATGT
* *
101824548 GATTACATGTAAGACCATGTCTGAGACATTGGCA-C-TGTATTTT
1 GATTACATGTAAGACCATGTCTG-GACATTGGCATCGTGTATATC
101824591 GATTACATGTAAGACCATGTCTAGGACATTGGCATCGT-TA-ATC
1 GATTACATGTAAGACCATGTCT-GGACATTGGCATCGTGTATATC
* * * * * *
101824634 GATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG-ATATGT-
1 GATTACATGTAAGACCATGTCT-GGACATTGGCATCGTGTATATC
* * *
101824677 GATAATATGTAAGACCATATCTGG
1 GATTACATGTAAGACCATGTCTGG
101824701 GATGTGGCAT
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
42 2 0.02
43 83 0.91
44 5 0.05
45 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (44 bp):
GATTACATGTAAGACCATGTCTGGACATTGGCATCGTGTATATC
Found at i:101829972 original size:7 final size:7
Alignment explanation
Indices: 101829955--101829987 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
101829945 TAATAGTAGT
101829955 TTAAA-A
1 TTAAATA
101829961 TTAAATA
1 TTAAATA
101829968 TTAAATA
1 TTAAATA
101829975 TTAAATA
1 TTAAATA
101829982 TTAAAT
1 TTAAAT
101829988 TGTTTGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATA
Found at i:101836639 original size:28 final size:28
Alignment explanation
Indices: 101836599--101836656 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
101836589 AATTCTATCG
101836599 TTTGATTTTTATTTTACGCAATAAAGAC
1 TTTGATTTTTATTTTACGCAATAAAGAC
101836627 TTTGATTTTTATTTTACGCAATAAAGAC
1 TTTGATTTTTATTTTACGCAATAAAGAC
101836655 TT
1 TT
101836657 AGATATTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (28 bp):
TTTGATTTTTATTTTACGCAATAAAGAC
Found at i:101838332 original size:15 final size:18
Alignment explanation
Indices: 101838294--101838340 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
101838284 TCTTACTTTT
101838294 ATAATTAAATATATTTAA
1 ATAATTAAATATATTTAA
101838312 ATAATTAAA-AT-TTTAA
1 ATAATTAAATATATTTAA
*
101838328 A-AATTAAGTATAT
1 ATAATTAAATATAT
101838341 ACTCTTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 3 0.12
18 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAATTAAATATATTTAA
Found at i:101838576 original size:15 final size:14
Alignment explanation
Indices: 101838549--101838575 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
101838539 GTATATAATA
101838549 AAATATTTAAAAAT
1 AAATATTTAAAAAT
101838563 AAATATTTAAAAA
1 AAATATTTAAAAA
101838576 AAGAGACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATTTAAAAAT
Found at i:101839526 original size:25 final size:23
Alignment explanation
Indices: 101839468--101839533 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
101839458 AACCACCTTT
101839468 TTTTATATTAAAATA-TTTTTTTA
1 TTTT-TATTAAAATATTTTTTTTA
* * *
101839491 GTTTAAATAAAATATTATTATTTTA
1 TTTTTATTAAAATATT-TT-TTTTA
101839516 TTTTTATTAAAAATATTT
1 TTTTTATT-AAAATATTT
101839534 AAATATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
22 8 0.24
23 4 0.12
24 2 0.06
25 11 0.33
26 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTTATTAAAATATTTTTTTTA
Found at i:101839841 original size:60 final size:60
Alignment explanation
Indices: 101839770--101839888 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
101839760 AATTTTTTAA
* *
101839770 TAATTATTTTAAAATTAATTTGTTAGTAATTTAAGATTATATTATAAATTGATGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAATAATTTAAGATTATATTATAAATTGATGTGTTTG
* * *
101839830 TAATTATTTTAAAATTAATTTATTAATAATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAATAATTTAAGATTATATTATAAATTGATGTGTTT
101839889 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAATAATTTAAGATTATATTATAAATTGATGTGTTTG
Found at i:101839965 original size:84 final size:79
Alignment explanation
Indices: 101839871--101840045 Score: 220
Period size: 72 Copynumber: 2.2 Consensus size: 79
101839861 TAGGATTATG
*
101839871 TTATAAATTGTTGTGTTTAGTTTAGTATTTGATGAGTTTTTAGTAATGTAAAATTATTTTATTAA
1 TTATAAATTGTTGTGTTT--TCT-G-ATTTG-TGAGTTTTTAGTAATGTAAAATTATTTTATTAA
*
101839936 ATATTTTGTTGGTAATTTA
61 ATATTTTGTTAGTAATTTA
* *
101839955 TTATAAA----T-TG--TTCTGCTTTGTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATT
1 TTATAAATTGTTGTGTTTTCTGATTTGTGAGTTTTTAGTAATGTAAAATTATTTTATTAAATATT
101840013 TTGTTAGTAATTTA
66 TTGTTAGTAATTTA
101840027 TTATAAATTGTTGTGTTTT
1 TTATAAATTGTTGTGTTTT
101840046 GTGAGTTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 19
0.78 0.04 0.18
Matches are distributed among these distances:
72 57 0.71
73 4 0.05
74 1 0.01
75 2 0.03
76 1 0.01
77 3 0.04
79 4 0.05
80 1 0.01
84 7 0.09
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (79 bp):
TTATAAATTGTTGTGTTTTCTGATTTGTGAGTTTTTAGTAATGTAAAATTATTTTATTAAATATT
TTGTTAGTAATTTA
Found at i:101839989 original size:38 final size:37
Alignment explanation
Indices: 101839947--101840061 Score: 96
Period size: 38 Copynumber: 3.1 Consensus size: 37
101839937 TATTTTGTTG
101839947 GTAATTTATTATAAATTGTTCTGCTTTGTGAGTTTTTA
1 GTAATTTATTATAAATTGTTCTG-TTTGTGAGTTTTTA
* * * ** *
101839985 GTAA--T-GTA-AAATTATTTTGTTAAAT-ATTTTGTTA
1 GTAATTTATTATAAATTGTTCTGTT-TGTGAGTTT-TTA
*
101840019 GTAATTTATTATAAATTGTTGTGTTTTGTGAGTTTTTA
1 GTAATTTATTATAAATTGTTCTG-TTTGTGAGTTTTTA
101840057 GTAAT
1 GTAAT
101840062 GTAAATTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
33 6 0.11
34 17 0.30
35 2 0.04
36 2 0.04
37 2 0.04
38 22 0.39
39 6 0.11
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.55
Consensus pattern (37 bp):
GTAATTTATTATAAATTGTTCTGTTTGTGAGTTTTTA
Found at i:101840020 original size:34 final size:34
Alignment explanation
Indices: 101839910--101840023 Score: 88
Period size: 34 Copynumber: 3.2 Consensus size: 34
101839900 TGATGAGTTT
*
101839910 TTAGTAATGTAAAATTATTTTATTAAATATTTTG
1 TTAGTAATGTAAAATTATTTTGTTAAATATTTTG
* * * * ** *
101839944 TTGGTAATTTATTATAAATTGTTCTGCTT-TGTGAGTTT-
1 TTAGTAA--T-GTA-AAATTATTTTG-TTAAAT-ATTTTG
101839982 TTAGTAATGTAAAATTATTTTGTTAAATATTTTG
1 TTAGTAATGTAAAATTATTTTGTTAAATATTTTG
101840016 TTAGTAAT
1 TTAGTAAT
101840024 TTATTATAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 16
0.65 0.17 0.18
Matches are distributed among these distances:
33 6 0.11
34 24 0.42
35 2 0.04
36 2 0.04
37 2 0.04
38 15 0.26
39 6 0.11
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.54
Consensus pattern (34 bp):
TTAGTAATGTAAAATTATTTTGTTAAATATTTTG
Found at i:101840023 original size:72 final size:72
Alignment explanation
Indices: 101839898--101840066 Score: 293
Period size: 72 Copynumber: 2.3 Consensus size: 72
101839888 TAGTTTAGTA
*
101839898 TTTGATGAGTTTTTAGTAATGTAAAATTATTTTATTAAATATTTTGTTGGTAATTTATTATAAAT
1 TTTG-TGAGTTTTTAGTAATGTAAAATTATTTTATTAAATATTTTGTTAGTAATTTATTATAAAT
101839963 TGTTCTGC
65 TGTTCTGC
*
101839971 TTTGTGAGTTTTTAGTAATGTAAAATTATTTTGTTAAATATTTTGTTAGTAATTTATTATAAATT
1 TTTGTGAGTTTTTAGTAATGTAAAATTATTTTATTAAATATTTTGTTAGTAATTTATTATAAATT
* *
101840036 GTTGTGT
66 GTTCTGC
101840043 TTTGTGAGTTTTTAGTAATGTAAA
1 TTTGTGAGTTTTTAGTAATGTAAA
101840067 TTTTTAAAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
72 88 0.96
73 4 0.04
ACGTcount: A:0.30, C:0.01, G:0.15, T:0.54
Consensus pattern (72 bp):
TTTGTGAGTTTTTAGTAATGTAAAATTATTTTATTAAATATTTTGTTAGTAATTTATTATAAATT
GTTCTGC
Found at i:101840137 original size:27 final size:27
Alignment explanation
Indices: 101840099--101840155 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
101840089 ATTTTGTTCA
** *
101840099 ACCAGTCGCGCCTGTCAGATAGGCTCC
1 ACCAGTCGCGCCTACCAGATAGGCGCC
101840126 ACCAGTCGCGCCTACCAGATAGGCGCC
1 ACCAGTCGCGCCTACCAGATAGGCGCC
101840153 ACC
1 ACC
101840156 TACCCCCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.40, G:0.25, T:0.14
Consensus pattern (27 bp):
ACCAGTCGCGCCTACCAGATAGGCGCC
Found at i:101850687 original size:2 final size:2
Alignment explanation
Indices: 101850680--101850705 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
101850670 CAACTTAAAC
101850680 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
101850706 CTTCTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101856212 original size:20 final size:21
Alignment explanation
Indices: 101856169--101856214 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
101856159 ATTTAAAAAA
101856169 TAAA-ATAAAGAATGAAAACG
1 TAAATATAAAGAATGAAAACG
*
101856189 -AAATATAAAGAAT-AAAATG
1 TAAATATAAAGAATGAAAACG
101856208 TAAATAT
1 TAAATAT
101856215 GCACATTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (21 bp):
TAAATATAAAGAATGAAAACG
Found at i:101860768 original size:10 final size:10
Alignment explanation
Indices: 101860751--101860793 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
101860741 ATAATTATTA
101860751 TTTA-TTAAT
1 TTTATTTAAT
101860760 TTTATTTAAATT
1 TTTATTT-AA-T
101860772 TTTATATTAAT
1 TTTAT-TTAAT
101860783 TTTATTTAAT
1 TTTATTTAAT
101860793 T
1 T
101860794 ATTTGATACT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.13
10 8 0.27
11 8 0.27
12 8 0.27
13 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTATTTAAT
Found at i:101860787 original size:32 final size:33
Alignment explanation
Indices: 101860732--101860793 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
101860722 TAATATTAAT
*
101860732 TTTAAATTTATAATTATTATTTA-TTAATTTTA
1 TTTAAATTTATAATTAATATTTATTTAATTTTA
*
101860764 TTTAAATTTTTATATTAAT-TTTATTTAATT
1 TTTAAATTTATA-ATTAATATTTATTTAATT
101860794 ATTTGATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTAAATTTATAATTAATATTTATTTAATTTTA
Found at i:101860797 original size:13 final size:13
Alignment explanation
Indices: 101860725--101860790 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
101860715 ATAAATTTAA
101860725 TATTAATTTTAAATT
1 TATTAATTTT--ATT
101860740 TA-TAATTATTATT
1 TATTAATT-TTATT
101860753 TATTAATTTTATT
1 TATTAATTTTATT
*
101860766 TA--AATTTT-TA
1 TATTAATTTTATT
101860776 TATTAATTTTATT
1 TATTAATTTTATT
101860789 TA
1 TA
101860791 ATTATTTGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 6 0.14
13 15 0.34
14 10 0.23
15 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTAATTTTATT
Done.