Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 54 of 135
Found at i:21985583 original size:24 final size:24
Alignment explanation
Indices: 21985538--21985585 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21985528 CAAGAACCAT
*
21985538 ATAACGGGAAGCTCATGAGAGCTA
1 ATAACGGGAAGCTCATCAGAGCTA
* * *
21985562 ATAACGGGATGCTCTTCCGAGCTA
1 ATAACGGGAAGCTCATCAGAGCTA
21985586 TGGTGTGTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (24 bp):
ATAACGGGAAGCTCATCAGAGCTA
Found at i:21987246 original size:21 final size:20
Alignment explanation
Indices: 21987220--21987275 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
21987210 CATGTTTACT
21987220 TTTTGTTTAGCTCTCACGAGC
1 TTTTGTTTAGCTCT-ACGAGC
* * *
21987241 TTTTGTTTAACTCATATGAGT
1 TTTTGTTTAGCTC-TACGAGC
*
21987262 TTTTGTTCAGCTCT
1 TTTTGTTTAGCTCT
21987276 TTTGAGCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTTGTTTAGCTCTACGAGC
Found at i:21987292 original size:42 final size:42
Alignment explanation
Indices: 21987246--21987325 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
21987236 CGAGCTTTTG
* ** * *
21987246 TTTAACTCATATGAGTTTTTGTTCAGCTCTTTTGAGCTACTA
1 TTTAACCCATATGAGTTTCCGTTCAACTCTTATGAGCTACTA
* *
21987288 TTTAACCCTTATGGGTTTCCGTTCAACTCTTATGAGCT
1 TTTAACCCATATGAGTTTCCGTTCAACTCTTATGAGCT
21987326 TCCGTTCAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (42 bp):
TTTAACCCATATGAGTTTCCGTTCAACTCTTATGAGCTACTA
Found at i:21987321 original size:21 final size:21
Alignment explanation
Indices: 21987291--21987348 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
21987281 GCTACTATTT
21987291 AACCCTTATGGGTTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
* * *
21987312 AACTCTTATGAGCTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
21987333 AACCCTTATGGGTTTC
1 AACCCTTATGGGTTTC
21987349 TGTTTAGCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTC
Found at i:21988817 original size:14 final size:14
Alignment explanation
Indices: 21988798--21988838 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
21988788 TAGGTGATAT
21988798 GTGTGAAAAATTTC
1 GTGTGAAAAATTTC
21988812 GTGTGAAAAATTTC
1 GTGTGAAAAATTTC
21988826 GTGTGAAAAATTT
1 GTGTGAAAAATTT
21988839 ATTGTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (14 bp):
GTGTGAAAAATTTC
Found at i:21990825 original size:2 final size:2
Alignment explanation
Indices: 21990813--21990849 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
21990803 AATTGTATGG
*
21990813 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21990850 GTAACATGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21992892 original size:103 final size:104
Alignment explanation
Indices: 21992761--21992967 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 104
21992751 TTGACATAAA
21992761 AATTCAAATATGAAAAAAAAATAAAAATATAACTTAAATTTTACTATATCTAATAGTGGAATGAA
1 AATTCAAATATGAAAAAAAAATAAAAATATAACTTAAATTTTACTATATCTAATAGTGGAATGAA
21992826 TTTATAATTTTTCTTATTAGTAACTTTTTTTATAATTTC
66 TTTATAATTTTTCTTATTAGTAACTTTTTTTATAATTTC
21992865 AATTCAAATA-GAAAAAAAAATAAAAATATAACTTAAATTTTACTATATCTAATAGTGGAATGAA
1 AATTCAAATATGAAAAAAAAATAAAAATATAACTTAAATTTTACTATATCTAATAGTGGAATGAA
21992929 TTTATAATTTTTCTTATTAGTAACTTTTTTTATAATTTC
66 TTTATAATTTTTCTTATTAGTAACTTTTTTTATAATTTC
21992968 TAAAATTTTT
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 93 0.90
104 10 0.10
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (104 bp):
AATTCAAATATGAAAAAAAAATAAAAATATAACTTAAATTTTACTATATCTAATAGTGGAATGAA
TTTATAATTTTTCTTATTAGTAACTTTTTTTATAATTTC
Found at i:21997777 original size:16 final size:16
Alignment explanation
Indices: 21997756--21997790 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21997746 AAAAATATCA
21997756 TCTTTTCTA-TTTTCTT
1 TCTTTT-TATTTTTCTT
21997772 TCTTTTTATTTTTCTT
1 TCTTTTTATTTTTCTT
21997788 TCT
1 TCT
21997791 AACCAATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTTATTTTTCTT
Found at i:22002472 original size:3 final size:3
Alignment explanation
Indices: 22002464--22002489 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
22002454 TATACGAACA
22002464 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
22002490 ACGAGGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22004658 original size:32 final size:31
Alignment explanation
Indices: 22004596--22004655 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
22004586 ATCAGAACAA
22004596 GCAAGGCCTGGGAAGGGCGAAGTCAAAAATT
1 GCAAGGCCTGGGAAGGGCGAAGTCAAAAATT
*
22004627 GCAAGGCCTGGGGAAGGGTGAAG-CAAAAA
1 GCAAGGCCT-GGGAAGGGCGAAGTCAAAAA
22004656 ATTTATTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.37, C:0.15, G:0.38, T:0.10
Consensus pattern (31 bp):
GCAAGGCCTGGGAAGGGCGAAGTCAAAAATT
Found at i:22016003 original size:52 final size:52
Alignment explanation
Indices: 22015946--22016050 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
22015936 TTTAACCATG
22015946 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
1 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
22015998 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
1 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
22016050 T
1 T
22016051 GTTAAGTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (52 bp):
TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
Found at i:22017957 original size:18 final size:17
Alignment explanation
Indices: 22017919--22017960 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
22017909 ATATTTAATA
22017919 TATTATTTTAATTTAAC
1 TATTATTTTAATTTAAC
*
22017936 --TTATTTTAATTATTAC
1 TATTATTTTAATT-TAAC
22017952 TATTATTTT
1 TATTATTTT
22017961 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 11 0.52
16 3 0.14
18 7 0.33
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTTTAATTTAAC
Found at i:22019214 original size:17 final size:17
Alignment explanation
Indices: 22019181--22019214 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22019171 TTTATAATAC
*
22019181 TTTATATTATGTTATTT
1 TTTATATTATGTAATTT
*
22019198 TTTATATTTTGTAATTT
1 TTTATATTATGTAATTT
22019215 AAAACACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATATTATGTAATTT
Found at i:22021012 original size:28 final size:28
Alignment explanation
Indices: 22020979--22021044 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
22020969 TTTTTTTGGT
**
22020979 ATATTTTGGTAAATAAAAAAATTTTAAA
1 ATATTTTGGTAAATAAAAAAAAGTTAAA
*
22021007 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTAAA
22021035 ATATTTTGGT
1 ATATTTTGGT
22021045 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTAAA
Found at i:22025016 original size:73 final size:73
Alignment explanation
Indices: 22024939--22025112 Score: 217
Period size: 73 Copynumber: 2.4 Consensus size: 73
22024929 TGTATAACGA
* * *
22024939 GAAGCTCATAAGAGCCATA-ATCGGGAAGCTCATGCGAGCCAATAACGAGTAGCTCCAAATAGCC
1 GAAGCTCATAAGAGCCATATATCGGGAAGCTCAAGCGAGCC-ATAACGAGAAGCTCCAAAGAGCC
22025003 ATTAATCAG
65 ATTAATCAG
* * * * **
22025012 GAAGCTC-TAGATAGCCATATATCGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGGAGAGCC
1 GAAGCTCATA-AGAGCCATATATCGGGAAGCTCAAGCGAGCCATAACGAGAAGCTCCAAAGAGCC
22025076 ATTAATCAG
65 ATTAATCAG
*
22025085 GAAGCTCACGAAGAGCCATATATCGGGA
1 GAAGCTCA-TAAGAGCCATATATCGGGA
22025113 CACTCATAAG
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
72 2 0.02
73 48 0.56
74 35 0.41
75 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (73 bp):
GAAGCTCATAAGAGCCATATATCGGGAAGCTCAAGCGAGCCATAACGAGAAGCTCCAAAGAGCCA
TTAATCAG
Found at i:22025018 original size:25 final size:24
Alignment explanation
Indices: 22024939--22025104 Score: 74
Period size: 25 Copynumber: 6.8 Consensus size: 24
22024929 TGTATAACGA
*
22024939 GAAGCT-CATAAGAGCCATAATCGG
1 GAAGCTCCA-AAGAGCCATAATCAG
**
22024963 GAAGCT-CATGCGAGCCAATAA-C-G
1 GAAGCTCCA-AAGAGCC-ATAATCAG
* *
22024986 AGTAGCTCCAAATAGCCATTAATCAG
1 -GAAGCTCCAAAGAGCCA-TAATCAG
* * * *
22025012 GAAGCTCTAGATAGCCATATATCGG
1 GAAGCTCCAAAGAGCCATA-ATCAG
* * *
22025037 GAAG-TTCAAGCGAGCCAT-ATCGG
1 GAAGCTCCAA-AGAGCCATAATCAG
**
22025060 GAAGCTCCGGAGAGCCATTAATCAG
1 GAAGCTCCAAAGAGCCA-TAATCAG
*
22025085 GAAGCTCACGAAGAGCCATA
1 GAAGCTC-CAAAGAGCCATA
22025105 TATCGGGACA
Statistics
Matches: 109, Mismatches: 21, Indels: 23
0.71 0.14 0.15
Matches are distributed among these distances:
23 17 0.16
24 34 0.31
25 48 0.44
26 10 0.09
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (24 bp):
GAAGCTCCAAAGAGCCATAATCAG
Found at i:22025028 original size:49 final size:48
Alignment explanation
Indices: 22024932--22025104 Score: 113
Period size: 48 Copynumber: 3.5 Consensus size: 48
22024922 TCTAGGTTGT
* *
22024932 ATAACGAGAAGCTCATAAGAGCCATAATCGGGAAGCTCATGCGAGCCA
1 ATAACGAGAAGCTCATAAGAGCCATAATCAGGAAGCTCATGAGAGCCA
* * *
22024980 ATAACGAGTAGCTCCA-AATAGCCATTAATCAGGAAGCTC-TAGATAGCCA
1 ATAACGAGAAGCT-CATAAGAGCCA-TAATCAGGAAGCTCAT-GAGAGCCA
* * * * * **
22025029 TATATCGGGAAGTTCA-AGCGAGCCAT-ATCGGGAAGCTCCGGAGAGCCA
1 -ATAACGAGAAGCTCATA-AGAGCCATAATCAGGAAGCTCATGAGAGCCA
* *
22025077 TTAATC-AGGAAGCTCACGAAGAGCCATA
1 ATAA-CGA-GAAGCTCA-TAAGAGCCATA
22025105 TATCGGGACA
Statistics
Matches: 95, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
47 2 0.02
48 46 0.48
49 32 0.34
50 15 0.16
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (48 bp):
ATAACGAGAAGCTCATAAGAGCCATAATCAGGAAGCTCATGAGAGCCA
Found at i:22025074 original size:23 final size:23
Alignment explanation
Indices: 22025030--22025105 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
22025020 AGATAGCCAT
* ** *
22025030 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGCTCCGGAGAGCC
22025053 ATATCGGGAAGCTCCGGAGAGCC
1 ATATCGGGAAGCTCCGGAGAGCC
* *
22025076 ATTAATCAGGAAGCTCACGAAGAGCC
1 A-T-ATCGGGAAGCTC-CGGAGAGCC
22025102 ATAT
1 ATAT
22025106 ATCGGGACAC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
23 20 0.45
24 3 0.07
25 12 0.27
26 9 0.20
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (23 bp):
ATATCGGGAAGCTCCGGAGAGCC
Found at i:22025215 original size:25 final size:25
Alignment explanation
Indices: 22025186--22025249 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
22025176 GAAGAGCTAT
* *
22025186 TAACGGGAAGCTCGTAATAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
*
22025211 TAACGAGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
22025236 TAACGAGG-AGCTCG
1 TAACG-GGAAGCTCG
22025250 AAAGGGCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 33 0.97
26 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (25 bp):
TAACGGGAAGCTCGCAAGAACCATA
Found at i:22026844 original size:17 final size:17
Alignment explanation
Indices: 22026813--22026852 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
22026803 TTTTATATTG
22026813 AATTGAATGTATGTGA-
1 AATTGAATGTATGTGAT
*
22026829 AATTGTAATTTATGTGAT
1 AATTG-AATGTATGTGAT
22026847 AATTGA
1 AATTGA
22026853 GTATTGGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (17 bp):
AATTGAATGTATGTGAT
Found at i:22035760 original size:43 final size:42
Alignment explanation
Indices: 22035623--22035783 Score: 159
Period size: 43 Copynumber: 3.8 Consensus size: 42
22035613 ATCACATACA
* * * * *
22035623 ATGCCATATCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
* *
22035665 ATG-CATGTATCCCAAACAGGGTCTTACACG-AA--TCATATACG
1 ATGCCATG--TCCCAGACATGGTCTTACACGTAATCTCATAT-CG
*
22035706 GTGCCAATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
1 ATGCC-ATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
* *
22035749 ATGCCAATGTCCTAGACATGGTCTTACACGAAATC
1 ATGCC-ATGTCCCAGACATGGTCTTACACGTAATC
22035784 ACACCTCGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
40 5 0.05
41 26 0.27
42 7 0.07
43 54 0.55
44 6 0.06
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
ATGCCATGTCCCAGACATGGTCTTACACGTAATCTCATATCG
Found at i:22037188 original size:33 final size:33
Alignment explanation
Indices: 22037146--22037344 Score: 148
Period size: 33 Copynumber: 5.5 Consensus size: 33
22037136 ATCGGTGGAT
*
22037146 TCAGCACTTAGCAACCACCAATGAGACGGGGAA
1 TCAGCACTTAGCAACCACCAATGATACGGGGAA
* * *
22037179 TCAGCACTTAGCAACCCCTTTCACATTTAAGATATGGTGGGA
1 TCAGCACTTAGCAACCAC---CA-A--T--GATACGG-GGAA
*
22037221 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATACGGGGAA
* *
22037254 TCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTAGAA
1 TCAGCACTTAGCAA-CCAC--CA-A--T--GATACGG-GGAA
22037296 TCAGCACTTAGCAACCACCAATGAGT-CGGGGAA
1 TCAGCACTTAGCAACCACCAATGA-TACGGGGAA
*
22037329 TCAACACTTAGCAACC
1 TCAGCACTTAGCAACC
22037345 CCTTTCACAT
Statistics
Matches: 133, Mismatches: 14, Indels: 38
0.72 0.08 0.21
Matches are distributed among these distances:
33 52 0.39
34 13 0.10
35 1 0.01
36 6 0.05
37 2 0.02
38 2 0.02
39 6 0.05
41 14 0.11
42 37 0.28
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGATACGGGGAA
Found at i:22037262 original size:75 final size:75
Alignment explanation
Indices: 22037138--22037386 Score: 417
Period size: 75 Copynumber: 3.3 Consensus size: 75
22037128 TTACCGTTAT
* *
22037138 CGGTGGATTCAGCACTTAGCAACCACCAATGAGACGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
22037203 ATTTAAGATA
66 ATTTAAGATA
* * * *
22037213 TGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
22037278 ATTTAAGATA
66 ATTTAAGATA
* *
22037288 CGGTAGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAACACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
22037353 ATTTAAGATA
66 ATTTAAGATA
*
22037363 CGGTGGAATCAGCACTTAGAAACC
1 CGGTGGAATCAGCACTTAGCAACC
22037387 CCTTGGGGGA
Statistics
Matches: 160, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 160 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTTAAGATA
Found at i:22037310 original size:42 final size:42
Alignment explanation
Indices: 22037250--22037388 Score: 161
Period size: 42 Copynumber: 3.5 Consensus size: 42
22037240 AATGATTCGG
22037250 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
* * *
22037292 AGAATCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
* *
22037325 GGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
*
22037367 GGAATCAGCACTTAGAAACCCC
1 GGAATCAGCACTTAGCAACCCC
22037389 TTGGGGGAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
33 16 0.21
34 5 0.06
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 6 0.08
42 37 0.47
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
Found at i:22040873 original size:26 final size:26
Alignment explanation
Indices: 22040843--22040915 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
22040833 GCAACTCTTA
*
22040843 TGAGCGTCCC-ATTATATGGCTCTTCG
1 TGAGCGTCCCGATTA-AAGGCTCTTCG
* *
22040869 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCGTCCCGATTAAAGGCTCTTCG
* * *
22040895 TGAGCTTCCTGATTAATGGCT
1 TGAGCGTCCCGATTAAAGGCT
22040916 TTCCGAAGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAGCGTCCCGATTAAAGGCTCTTCG
Found at i:22043126 original size:21 final size:21
Alignment explanation
Indices: 22043102--22043302 Score: 183
Period size: 21 Copynumber: 9.6 Consensus size: 21
22043092 GAAGCCCGAA
* *
22043102 AGCTGAACATAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAG
*
22043123 AGCTAAACAGAAACTCATAAG
1 AGCTGAACAGAAACTCATAAG
*
22043144 AGCTAAACAGAAACTCATAAG
1 AGCTGAACAGAAACTCATAAG
* * * *
22043165 GGTTGAACAGAAGCTTATAAG
1 AGCTGAACAGAAACTCATAAG
*
22043186 AGCTGAATAGAAAC-CTATAAG
1 AGCTGAACAGAAACTC-ATAAG
22043207 AGCTGAACAGAAAC-CATAAG
1 AGCTGAACAGAAACTCATAAG
* * * *
22043227 GGTTGAATAGAAGCTCGA-AAG
1 AGCTGAACAGAAACTC-ATAAG
* *
22043248 AGTTGAACAGAAACTCATATG
1 AGCTGAACAGAAACTCATAAG
* * *
22043269 AGTTAAACAGAAACTCGTAAG
1 AGCTGAACAGAAACTCATAAG
* *
22043290 AGCTAAATAGAAA
1 AGCTGAACAGAAA
22043303 GTAAAACATG
Statistics
Matches: 149, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.11
21 132 0.89
22 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (21 bp):
AGCTGAACAGAAACTCATAAG
Found at i:22043260 original size:62 final size:64
Alignment explanation
Indices: 22043105--22043289 Score: 227
Period size: 63 Copynumber: 3.0 Consensus size: 64
22043095 GCCCGAAAGC
* * *
22043105 TGAACATAAGCTCATAAGAGCTAAACAGAAA-CTCATAAGAGCTAAACAGAAACTCATAAGGGT
1 TGAACAGAAGCTGATAAGAGCTGAACAGAAACCTCATAAGAGCTAAACAGAAACTCATAAGGGT
* * *
22043168 TGAACAGAAGCTTATAAGAGCTGAATAGAAACCT-ATAAGAGCTGAACAGAAAC-CATAAGGGT
1 TGAACAGAAGCTGATAAGAGCTGAACAGAAACCTCATAAGAGCTAAACAGAAACTCATAAGGGT
* * * * *
22043230 TGAATAGAAGCTCGA-AAGAGTTGAACAGAAA-CTCATATGAGTTAAACAGAAACTCGTAAG
1 TGAACAGAAGCT-GATAAGAGCTGAACAGAAACCTCATAAGAGCTAAACAGAAACTCATAAG
22043290 AGCTAAATAG
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
61 2 0.02
62 50 0.48
63 51 0.49
64 2 0.02
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (64 bp):
TGAACAGAAGCTGATAAGAGCTGAACAGAAACCTCATAAGAGCTAAACAGAAACTCATAAGGGT
Found at i:22045236 original size:5 final size:5
Alignment explanation
Indices: 22045226--22045253 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
22045216 GAAAATTTTT
22045226 GATTC GATTC GATTC GATTC GATTC GAT
1 GATTC GATTC GATTC GATTC GATTC GAT
22045254 CGAATGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
GATTC
Found at i:22055625 original size:44 final size:44
Alignment explanation
Indices: 22055549--22055632 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
22055539 TAGAGTGTGG
* *
22055549 AATGCCATGTTATCTTAAGAAAAACGGTATCAAATTTATCACGA
1 AATGCCATATTATCTTAAGAAAAACGGTATCAAAATTATCACGA
* *
22055593 AATGTCATATTAT-TTAAGGAAAAATGGTATCAAAATTATC
1 AATGCCATATTATCTTAA-GAAAAACGGTATCAAAATTATC
22055633 GCTTGATCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 4 0.11
44 31 0.89
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (44 bp):
AATGCCATATTATCTTAAGAAAAACGGTATCAAAATTATCACGA
Found at i:22075621 original size:26 final size:26
Alignment explanation
Indices: 22075546--22075627 Score: 130
Period size: 26 Copynumber: 3.2 Consensus size: 26
22075536 GCACACCTTA
**
22075546 GCTCTTT-TGAGCTTCCTGATTAAAA
1 GCTCTTTGTGAGCTTCCTGATTAATG
*
22075571 GCTTTTTGTGAGCTTCCTGATTAATG
1 GCTCTTTGTGAGCTTCCTGATTAATG
22075597 GCTCTTTGTGAGCTTCCTGATTAATG
1 GCTCTTTGTGAGCTTCCTGATTAATG
22075623 GCTCT
1 GCTCT
22075628 CCGGAGCTTC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 6 0.12
26 46 0.88
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.43
Consensus pattern (26 bp):
GCTCTTTGTGAGCTTCCTGATTAATG
Found at i:22075683 original size:23 final size:23
Alignment explanation
Indices: 22075634--22075690 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
22075624 CTCTCCGGAG
* * *
22075634 CTTCCCGATACGACTCTCTAGAG
1 CTTCCCGATATGACTCGCTAGAA
* *
22075657 CTTCCCGATATGGCTCGCTTGAA
1 CTTCCCGATATGACTCGCTAGAA
*
22075680 CTTCCTGATAT
1 CTTCCCGATAT
22075691 AGGGCTATCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.32, G:0.18, T:0.32
Consensus pattern (23 bp):
CTTCCCGATATGACTCGCTAGAA
Found at i:22078471 original size:15 final size:15
Alignment explanation
Indices: 22078435--22078474 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
22078425 CAAAACTTAG
* *
22078435 ATTATTATTACTATT
1 ATTATTGTTACTATC
22078450 ATTATTGTTACTATC
1 ATTATTGTTACTATC
22078465 ATTATTGTTA
1 ATTATTGTTA
22078475 TTTATATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (15 bp):
ATTATTGTTACTATC
Found at i:22082547 original size:7 final size:7
Alignment explanation
Indices: 22082537--22082561 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22082527 AAAAAAAGTA
22082537 AAAATAT
1 AAAATAT
22082544 AAAATAT
1 AAAATAT
22082551 AAAATAT
1 AAAATAT
22082558 AAAA
1 AAAA
22082562 AAATAATATT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:22082560 original size:22 final size:21
Alignment explanation
Indices: 22082535--22082575 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
22082525 CAAAAAAAAG
*
22082535 TAAAAATATAAAATATAAAATA
1 TAAAAAAATAAAAT-TAAAATA
*
22082557 TAAAAAAATAATATTAAAA
1 TAAAAAAATAAAATTAAAA
22082576 GCTAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAAAAAATAAAATTAAAATA
Found at i:22105567 original size:24 final size:24
Alignment explanation
Indices: 22105533--22105578 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
22105523 TATATGAAAT
* *
22105533 ATAAATTTTAAATATTTTTAAGTA
1 ATAAATATTAAATATTTATAAGTA
*
22105557 ATAAATATTAATTATTTATAAG
1 ATAAATATTAAATATTTATAAG
22105579 ATTTAATTAG
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAGTA
Found at i:22110213 original size:2 final size:2
Alignment explanation
Indices: 22110206--22110233 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22110196 CTAATGTACC
22110206 AT 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 AT
22110234 TTGTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22117076 original size:22 final size:22
Alignment explanation
Indices: 22117049--22117090 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22117039 ATTATATATA
22117049 TATTTAATATGT-TATATTTTAT
1 TATTTAATATGTAT-TATTTTAT
*
22117071 TATTTATTATGTATTATTTT
1 TATTTAATATGTATTATTTT
22117091 TAAACACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TATTTAATATGTATTATTTTAT
Found at i:22117077 original size:14 final size:15
Alignment explanation
Indices: 22117038--22117089 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
22117028 TTTATTTTAA
*
22117038 TATTATATATATATT
1 TATTATTTATATATT
*
22117053 TAATATGTTATAT-TT
1 TATTAT-TTATATATT
*
22117068 TATTATTTAT-TATG
1 TATTATTTATATATT
22117082 TATTATTT
1 TATTATTT
22117090 TTAAACACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 1 0.03
14 13 0.42
15 12 0.39
16 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TATTATTTATATATT
Found at i:22118042 original size:30 final size:31
Alignment explanation
Indices: 22118001--22118080 Score: 121
Period size: 30 Copynumber: 2.7 Consensus size: 31
22117991 AAAAAAATAG
*
22118001 AAAATTAAAAAAGTATTTTTAAAATATTTTT
1 AAAAATAAAAAAGTATTTTTAAAATATTTTT
22118032 -AAAATAAAAAAGTA-TTTTAAAATATTTTT
1 AAAAATAAAAAAGTATTTTTAAAATATTTTT
*
22118061 AAAAATAAAAAA-TATATTTA
1 AAAAATAAAAAAGTATTTTTA
22118081 TTATATTCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (31 bp):
AAAAATAAAAAAGTATTTTTAAAATATTTTT
Found at i:22118049 original size:19 final size:17
Alignment explanation
Indices: 22118021--22118055 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
22118011 AAGTATTTTT
22118021 AAAATATTTTTAAAATAA
1 AAAATA-TTTTAAAATAA
22118039 AAAAGTATTTTAAAATA
1 AAAA-TATTTTAAAATA
22118056 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAATATTTTAAAATAA
Found at i:22118066 original size:12 final size:11
Alignment explanation
Indices: 22118009--22118064 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
22117999 AGAAAATTAA
22118009 AAAAGTATTTTT
1 AAAA-TATTTTT
22118021 AAAATATTTTT
1 AAAATATTTTT
*
22118032 AAAATA----A
1 AAAATATTTTT
22118039 AAAAGTA-TTTT
1 AAAA-TATTTTT
22118050 AAAATATTTTT
1 AAAATATTTTT
22118061 AAAA
1 AAAA
22118065 ATAAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
7 4 0.11
8 2 0.05
10 2 0.05
11 25 0.68
12 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:22118509 original size:2 final size:2
Alignment explanation
Indices: 22118504--22118531 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22118494 TAAAAAACAC
22118504 AT 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 AT
22118532 TTGGCAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22118875 original size:16 final size:17
Alignment explanation
Indices: 22118848--22118879 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
22118838 GAAACAACAT
22118848 AATTAAACAATTAAATA
1 AATTAAACAATTAAATA
22118865 AATTAAA-AATTAAAT
1 AATTAAACAATTAAAT
22118880 TGGAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAACAATTAAATA
Found at i:22122183 original size:3 final size:3
Alignment explanation
Indices: 22122167--22122208 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
22122157 GGAAGAAGGT
* * *
22122167 GAA GGA GAA G-A GAA GAA GAA GAA GAA AAA GAA GGA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
22122209 GGACTGAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:22122407 original size:6 final size:6
Alignment explanation
Indices: 22122391--22122426 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
22122381 AGGCCAGTAG
*
22122391 CCCAGC TCCAGC CCCAGC CCCAGC CCCAGC CCCAGC
1 CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC CCCAGC
22122427 AGCTGAGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.64, G:0.17, T:0.03
Consensus pattern (6 bp):
CCCAGC
Found at i:22133384 original size:17 final size:17
Alignment explanation
Indices: 22133362--22133395 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22133352 AATGGTTTTG
22133362 GGATGCAAACAATGACA
1 GGATGCAAACAATGACA
22133379 GGATGCAAACAATGACA
1 GGATGCAAACAATGACA
22133396 ATGTTACTTA
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:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (17 bp):
GGATGCAAACAATGACA
Found at i:22147348 original size:18 final size:18
Alignment explanation
Indices: 22147325--22147365 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
22147315 AATGAGCATA
* *
22147325 AATTTTGTATTTCAATTT
1 AATTTTATATTTCAATAT
*
22147343 AATTTTATATTTTAATAT
1 AATTTTATATTTCAATAT
22147361 AATTT
1 AATTT
22147366 ATTTCGTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
AATTTTATATTTCAATAT
Found at i:22169868 original size:26 final size:26
Alignment explanation
Indices: 22169806--22169862 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
22169796 GCACACAACA
* *
22169806 GCTCTT-ATGAGCGTCCCGTTATATG
1 GCTCTTCATGAGCTTCCCGTTATAAG
22169831 GCTCTTCATGAGCTTCCCGATTA-AAG
1 GCTCTTCATGAGCTTCCCG-TTATAAG
22169857 GCTCTT
1 GCTCTT
22169863 TGTGAGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 6 0.21
26 19 0.68
27 3 0.11
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (26 bp):
GCTCTTCATGAGCTTCCCGTTATAAG
Found at i:22174633 original size:42 final size:42
Alignment explanation
Indices: 22174569--22174673 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
22174559 TCGTGTTTAT
* * * * *
22174569 TTTCCATTTAGTTCTCACGAGCTTCTGTTTAACTCATATGAG
1 TTTCCATTCAGCTCTTATGAGCTTCTGTTTAACCCATATGAG
* * * *
22174611 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCCATTCAGCTCTTATGAGCTTCTGTTTAACCCATATGAG
*
22174653 TTTCCATTTAGCTCTTATGAG
1 TTTCCATTCAGCTCTTATGAG
22174674 TTTCCGTTCA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (42 bp):
TTTCCATTCAGCTCTTATGAGCTTCTGTTTAACCCATATGAG
Found at i:22174705 original size:42 final size:42
Alignment explanation
Indices: 22174610--22174711 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
22174600 ACTCATATGA
* * * * *
22174610 GTTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGG
1 GTTTCCGTTTAGCTCTTATGAGCTTCCGTTCAACCCTTACGG
* * *
22174652 GTTTCCATTTAGCTCTTATGAGTTTCCGTTCAACCTTTACGG
1 GTTTCCGTTTAGCTCTTATGAGCTTCCGTTCAACCCTTACGG
* *
22174694 GTTTCTGTTTAGCACTTA
1 GTTTCCGTTTAGCTCTTA
22174712 CGTGCTTCTG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (42 bp):
GTTTCCGTTTAGCTCTTATGAGCTTCCGTTCAACCCTTACGG
Found at i:22174712 original size:21 final size:21
Alignment explanation
Indices: 22174688--22174740 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
22174678 CGTTCAACCT
*
22174688 TTACGGGTTTCTGTTTAGCAC
1 TTACGGGCTTCTGTTTAGCAC
*
22174709 TTACGTGCTTCTGTTTAGC-C
1 TTACGGGCTTCTGTTTAGCAC
*
22174729 TT-CAGGCTTCTG
1 TTACGGGCTTCTG
22174741 AAAATGATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.29
20 3 0.11
21 17 0.61
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (21 bp):
TTACGGGCTTCTGTTTAGCAC
Found at i:22174726 original size:63 final size:63
Alignment explanation
Indices: 22174589--22174727 Score: 145
Period size: 63 Copynumber: 2.2 Consensus size: 63
22174579 GTTCTCACGA
* * * * *
22174589 GCTTCTGTTTAACTCATATGAGTTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGG
1 GCTTCTGTTTAGCTCATATGAGTTTCCGTTCAACTCTTTCGAGCTTCTGTTTAACACTTACGG
* ** * * * * *
22174652 GTTTCCATTTAGCTCTTATGAGTTTCCGTTCAAC-CTTTACGGGTTTCTGTTTAGCACTTACGT
1 GCTTCTGTTTAGCTCATATGAGTTTCCGTTCAACTCTTT-CGAGCTTCTGTTTAACACTTACGG
22174715 GCTTCTGTTTAGC
1 GCTTCTGTTTAGC
22174728 CTTCAGGCTT
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
62 4 0.07
63 55 0.93
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (63 bp):
GCTTCTGTTTAGCTCATATGAGTTTCCGTTCAACTCTTTCGAGCTTCTGTTTAACACTTACGG
Found at i:22178976 original size:67 final size:67
Alignment explanation
Indices: 22178867--22179174 Score: 287
Period size: 67 Copynumber: 4.6 Consensus size: 67
22178857 ATGGGCTGTA
* * * * *
22178867 ATGGGGTATAATGTGCAAGACCATAGCTCGACTATGGTAACATAAAGAGTCCATTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGATTATGGCAACATAGAGAGTCCACTAGGACATTAA
22178932 ACT
66 A-T
* * ** *
22178935 -TGGGGTATAATATGTAAGTCCGGAGCTCGATTATGGCAACATAGAGAGTCCGCTAGGACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGATTATGGCAACATAGAGAGTCCACTAGGACATTAA
22178999 AT
66 AT
* * * ** *
22179001 ATAGAGTATAATGTGTAAGACCTTAGCTCGATTATGGCAACATAGAGAG-CCTGTCAAGACATTA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGATTATGGCAACATAGAGAGTCCACT-AGGACATTA
*
22179065 AAC
65 AAT
* * * * * * * * * *
22179068 ATGGGCTATGATGTGTAAGACCACAGCTCAACTAAGGCAACATTGAGAGTCTACCAGAACATTAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGATTATGGCAACATAGAGAGTCCACTAGGACATTAA
*
22179133 AC
66 AT
* * * * *
22179135 ATTGGGTATGATTTGTAAGACTATAGCTCGACTATGGCAA
1 ATGGGGTATAATGTGTAAGACCATAGCTCGATTATGGCAA
22179175 AATATGAAGT
Statistics
Matches: 194, Mismatches: 43, Indels: 7
0.80 0.18 0.03
Matches are distributed among these distances:
66 4 0.02
67 189 0.97
68 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (67 bp):
ATGGGGTATAATGTGTAAGACCATAGCTCGATTATGGCAACATAGAGAGTCCACTAGGACATTAA
AT
Found at i:22179116 original size:134 final size:134
Alignment explanation
Indices: 22178872--22179174 Score: 324
Period size: 134 Copynumber: 2.3 Consensus size: 134
22178862 CTGTAATGGG
* * * * *
22178872 GTATAATGTGCAAGACCATAGCTCGACTATGGTAACATAAAGAGTCCATTAGGACATTAAACTTG
1 GTATAATGTGTAAGACCTTAGCTCGACTATGGCAACATAAAGAGTCCATTAAGACATTAAACATG
* * ** * * * * * * *
22178937 GGGTATAATATGTAAGTCCGGAGCTCGATTATGGCAACATAGAGAGTCCGCTAGGACATTAAATA
66 GGCTATAATATGTAAGACCACAGCTCAACTAAGGCAACATAGAGAGTCCACCAGAACATTAAACA
22179002 TAGA
131 TAGA
* *
22179006 GTATAATGTGTAAGACCTTAGCTCGATTATGGCAACATAGAGAG-CC-TGTCAAGACATTAAACA
1 GTATAATGTGTAAGACCTTAGCTCGACTATGGCAACATAAAGAGTCCAT-T-AAGACATTAAACA
* * * *
22179069 TGGGCTATGATGTGTAAGACCACAGCTCAACTAAGGCAACATTGAGAGTCTACCAGAACATTAAA
64 TGGGCTATAATATGTAAGACCACAGCTCAACTAAGGCAACATAGAGAGTCCACCAGAACATTAAA
* *
22179134 CATTGG
129 CATAGA
* *
22179140 GTATGATTTGTAAGA-CTATAGCTCGACTATGGCAA
1 GTATAATGTGTAAGACCT-TAGCTCGACTATGGCAA
22179175 AATATGAAGT
Statistics
Matches: 139, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
132 1 0.01
133 5 0.04
134 133 0.96
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (134 bp):
GTATAATGTGTAAGACCTTAGCTCGACTATGGCAACATAAAGAGTCCATTAAGACATTAAACATG
GGCTATAATATGTAAGACCACAGCTCAACTAAGGCAACATAGAGAGTCCACCAGAACATTAAACA
TAGA
Found at i:22179212 original size:27 final size:27
Alignment explanation
Indices: 22179182--22179241 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
22179172 CAAAATATGA
* **
22179182 AGTCCGTTGGGACAATAAATGTGGGAT
1 AGTCCGCTGGGACAATAAAAATGGGAT
* *
22179209 AGTCCACTGGGACAATAAAAATGGGGT
1 AGTCCGCTGGGACAATAAAAATGGGAT
22179236 AGTCCG
1 AGTCCG
22179242 ACAAGATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.22
Consensus pattern (27 bp):
AGTCCGCTGGGACAATAAAAATGGGAT
Found at i:22186545 original size:12 final size:13
Alignment explanation
Indices: 22186528--22186556 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
22186518 CCCCCCACCT
22186528 TTTCAAAGG-TCC
1 TTTCAAAGGTTCC
22186540 TTTCAAAGGTTCC
1 TTTCAAAGGTTCC
22186553 TTTC
1 TTTC
22186557 TTTTTTTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (13 bp):
TTTCAAAGGTTCC
Found at i:22193327 original size:10 final size:10
Alignment explanation
Indices: 22193294--22193357 Score: 67
Period size: 10 Copynumber: 6.3 Consensus size: 10
22193284 AAGAATAAAT
22193294 AAAAAGAAAG
1 AAAAAGAAAG
*
22193304 AAAAAAAAACG
1 AAAAAGAAA-G
*
22193315 AAACAGAAAG
1 AAAAAGAAAG
22193325 AAAAAGAAAG
1 AAAAAGAAAG
* *
22193335 AAAGA-AAAT
1 AAAAAGAAAG
22193344 AAAAAGGAAAG
1 AAAAA-GAAAG
22193355 AAA
1 AAA
22193358 GGAAGGAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
9 7 0.16
10 22 0.51
11 14 0.33
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:22193337 original size:20 final size:20
Alignment explanation
Indices: 22193298--22193357 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
22193288 ATAAATAAAA
*
22193298 AGAAAGAAAAAAAAACGAAAC
1 AGAAAGAAAAAGAAA-GAAAC
*
22193319 AGAAAGAAAAAGAAAGAAAG
1 AGAAAGAAAAAGAAAGAAAC
*
22193339 A-AAATAAAAAGGAAAGAAA
1 AGAAAGAAAAA-GAAAGAAA
22193358 GGAAGGAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.23
20 13 0.37
21 14 0.40
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAAGAAAGAAAC
Found at i:22193358 original size:20 final size:18
Alignment explanation
Indices: 22193283--22193358 Score: 68
Period size: 17 Copynumber: 4.2 Consensus size: 18
22193273 ATTATAAAAT
* *
22193283 AAAGAATAAATAA-AAAG
1 AAAGAAAAAAAAAGAAAG
22193300 AAAGAAAAAAAAACG-AA-
1 AAAGAAAAAAAAA-GAAAG
* *
22193317 ACAGAAAGAAAAAGAAAG
1 AAAGAAAAAAAAAGAAAG
22193335 AAAGAAAATAAAAAGGAAAG
1 AAAGAAAA-AAAAA-GAAAG
22193355 AAAG
1 AAAG
22193359 GAAGGAGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
16 1 0.02
17 24 0.51
18 8 0.17
19 5 0.11
20 9 0.19
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.04
Consensus pattern (18 bp):
AAAGAAAAAAAAAGAAAG
Found at i:22194769 original size:41 final size:40
Alignment explanation
Indices: 22194724--22194837 Score: 108
Period size: 38 Copynumber: 2.9 Consensus size: 40
22194714 CTTCGAGTCG
*
22194724 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTAATTCA
1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTAACT-A
* * * ** * *
22194765 ATGAGGCACTGAGTG-CCAA-T-TTACTTCGGTTTAGCTG
1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTAACTA
* *
22194802 ATGAGAAACTGGGTGTCAAGTTATTACTTCGAATTA
1 ATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
22194838 TCCGATTAGG
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
37 12 0.22
38 14 0.25
39 2 0.04
40 14 0.25
41 13 0.24
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTATTACTTCGAATTAACTA
Found at i:22194853 original size:40 final size:39
Alignment explanation
Indices: 22194722--22194856 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
22194712 GACTTCGAGT
* *
22194722 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAATT
1 CGATGAGGCACTGGGTGTC-AATTATTACTTCGAATT-ATC
* * * ** *
22194763 CAATGAGGCACTGAGTGCCAA-T-TTACTTCGGTTTAGC
1 CGATGAGGCACTGGGTGTCAATTATTACTTCGAATTATC
* **
22194800 TGATGAGAAACTGGGTGTCAAGTTATTACTTCGAATTATC
1 CGATGAGGCACTGGGTGTCAA-TTATTACTTCGAATTATC
*
22194840 CGATTAGGCACTGGGTG
1 CGATGAGGCACTGGGTG
22194857 CCAAACTGGT
Statistics
Matches: 70, Mismatches: 21, Indels: 7
0.71 0.21 0.07
Matches are distributed among these distances:
37 16 0.23
38 10 0.14
39 2 0.03
40 27 0.39
41 15 0.21
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGTCAATTATTACTTCGAATTATC
Found at i:22196097 original size:19 final size:19
Alignment explanation
Indices: 22196075--22196159 Score: 66
Period size: 19 Copynumber: 4.3 Consensus size: 19
22196065 AAAATTAAAA
*
22196075 AAAAAGAAAAAAA-TATTTT
1 AAAAACAAAAAAATTA-TTT
**
22196094 AAAAATCATTAAAATTATTT
1 AAAAA-CAAAAAAATTATTT
*
22196114 AAAAATAAAAAAATTATTT
1 AAAAACAAAAAAATTATTT
22196133 AAAAA-AATCATTAAAATTATTT
1 AAAAACAA--A--AAAATTATTT
22196155 AAAAA
1 AAAAA
22196160 TTATAACTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.04
19 21 0.39
20 14 0.26
21 2 0.04
22 15 0.28
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAAACAAAAAAATTATTT
Found at i:22196107 original size:22 final size:20
Alignment explanation
Indices: 22196083--22196160 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
22196073 AAAAAAAGAA
22196083 AAAAATATTTTAAAAATCATT
1 AAAAATA-TTTAAAAATCATT
* *
22196104 AAAATTATTTAAAAAT-A-A
1 AAAAATATTTAAAAATCATT
22196122 AAAAATTATTTAAAAAAATCATT
1 AAAAA-TATTT--AAAAATCATT
*
22196145 AAAATTATTTAAAAAT
1 AAAAATATTTAAAAAT
22196161 TATAACTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.09
19 6 0.13
20 15 0.32
21 12 0.26
22 6 0.13
23 4 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATATTTAAAAATCATT
Found at i:22196108 original size:39 final size:41
Alignment explanation
Indices: 22196065--22196151 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 41
22196055 TTAAATTTTA
*
22196065 AAAATTAAAAAAAAAGAAAAAAA-TATTT-TAAAAATCATT
1 AAAATTAAAAAAAAAGAAAAAAATTATTTAAAAAAATCATT
*** *
22196104 AAAATTATTTAAAAATAAAAAAATTATTTAAAAAAATCATT
1 AAAATTAAAAAAAAAGAAAAAAATTATTTAAAAAAATCATT
22196145 AAAATTA
1 AAAATTA
22196152 TTTAAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
39 19 0.46
40 5 0.12
41 17 0.41
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (41 bp):
AAAATTAAAAAAAAAGAAAAAAATTATTTAAAAAAATCATT
Found at i:22196139 original size:41 final size:39
Alignment explanation
Indices: 22196075--22196160 Score: 136
Period size: 41 Copynumber: 2.2 Consensus size: 39
22196065 AAAATTAAAA
* *
22196075 AAAAAGAAAAAAATATTTTAAAAATCATTAAAATTATTT
1 AAAAATAAAAAAATATTTAAAAAATCATTAAAATTATTT
22196114 AAAAATAAAAAAATTATTTAAAAAAATCATTAAAATTATTT
1 AAAAATAAAAAAA-TATTT-AAAAAATCATTAAAATTATTT
22196155 AAAAAT
1 AAAAAT
22196161 TATAACTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 12 0.28
40 5 0.12
41 26 0.60
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (39 bp):
AAAAATAAAAAAATATTTAAAAAATCATTAAAATTATTT
Found at i:22196171 original size:22 final size:20
Alignment explanation
Indices: 22196091--22196174 Score: 73
Period size: 22 Copynumber: 4.0 Consensus size: 20
22196081 AAAAAAATAT
*
22196091 TTTAAAAATCATTA-AAATTA
1 TTTAAAAAT-ATAATAAATTA
*
22196111 TTTAAAAATA-AAAAAATTA
1 TTTAAAAATATAATAAATTA
* *
22196130 TTTAAAAAAATCATTAAAATTA
1 TTTAAAAATAT-AAT-AAATTA
22196152 TTTAAAAATTATAACTAAATTA
1 TTTAAAAA-TATAA-TAAATTA
22196174 T
1 T
22196175 AAAAGTTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 1 0.02
19 16 0.31
20 9 0.17
21 1 0.02
22 22 0.42
23 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAATATAATAAATTA
Found at i:22207072 original size:7 final size:7
Alignment explanation
Indices: 22207060--22207097 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
22207050 AAAATATTTT
22207060 AAAATTA
1 AAAATTA
22207067 AAAATTA
1 AAAATTA
22207074 AAAATTA
1 AAAATTA
*
22207081 AAAAATA
1 AAAATTA
22207088 AAAA-TA
1 AAAATTA
22207094 AAAA
1 AAAA
22207098 AATATATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATTA
Found at i:22223172 original size:21 final size:20
Alignment explanation
Indices: 22223138--22223188 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
22223128 GAAACAGAAA
22223138 AAAACTC-CAAACAAAGTT-C
1 AAAACTCACAAAC-AAGTTAC
22223157 AAAACTCACAACACAAGTTAC
1 AAAACTCACAA-ACAAGTTAC
22223178 ACAAA-TCACAA
1 A-AAACTCACAA
22223189 GCAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
20 8 0.29
21 10 0.36
22 3 0.11
ACGTcount: A:0.55, C:0.27, G:0.04, T:0.14
Consensus pattern (20 bp):
AAAACTCACAAACAAGTTAC
Found at i:22224264 original size:3 final size:3
Alignment explanation
Indices: 22224244--22224338 Score: 91
Period size: 3 Copynumber: 31.7 Consensus size: 3
22224234 TTAATTTTAA
* * * * * * * * *
22224244 TAT TTT TAT TAT TGT TAT TAT TAT TAA TAC CAT CAT CAT CAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
22224292 TAT TAT TAA TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
22224339 AATTGTTTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:22228788 original size:5 final size:5
Alignment explanation
Indices: 22228754--22228803 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
22228744 ATGTTTTAAA
* *
22228754 TATAT TAT-T T-TAT TATAT AATATAA TATAT TATAT TGTAT TATAT TATAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATAT
22228804 AAATTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 28 0.76
7 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:22228794 original size:27 final size:25
Alignment explanation
Indices: 22228752--22228805 Score: 81
Period size: 27 Copynumber: 2.1 Consensus size: 25
22228742 TTATGTTTTA
22228752 AATATATTATTTTATTATATAATAT
1 AATATATTATTTTATTATATAATAT
*
22228777 AATATATTATATTGTATTATATTATAT
1 AATATATTAT-TT-TATTATATAATAT
22228804 AA
1 AA
22228806 ATTAAATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 10 0.38
26 2 0.08
27 14 0.54
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
AATATATTATTTTATTATATAATAT
Found at i:22229419 original size:22 final size:24
Alignment explanation
Indices: 22229391--22229434 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
22229381 TATGGCAAGA
22229391 AATTAAG-TAGAAAAG-AAGTATG
1 AATTAAGCTAGAAAAGTAAGTATG
22229413 AATTAAGCTAGAAAAGTAAGTA
1 AATTAAGCTAGAAAAGTAAGTA
22229435 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 8 0.40
24 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.23
Consensus pattern (24 bp):
AATTAAGCTAGAAAAGTAAGTATG
Found at i:22230239 original size:17 final size:17
Alignment explanation
Indices: 22230167--22230292 Score: 57
Period size: 17 Copynumber: 7.4 Consensus size: 17
22230157 AAAAAGAAGA
*
22230167 AATTTTTGAAACACGAA
1 AATTTTTGAAACACGAG
22230184 AATTTTAT-AAACACG-G
1 AATTTT-TGAAACACGAG
* ** *
22230200 -TTTGTTTTTAACACGAC
1 AATT-TTTGAAACACGAG
*
22230217 AGTTTTTGAAACACGAG
1 AATTTTTGAAACACGAG
* **
22230234 AATTTTTTTCAAAACATAAG
1 AA--TTTTT-GAAACACGAG
*
22230254 AA-TTTTAAAACACGA-
1 AATTTTTGAAACACGAG
*
22230269 ACATTTGTGAAACAC-AG
1 A-ATTTTTGAAACACGAG
22230286 AATTTTT
1 AATTTTT
22230293 TTTTGAAAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 23
0.67 0.14 0.19
Matches are distributed among these distances:
15 4 0.05
16 22 0.27
17 38 0.47
18 3 0.04
19 5 0.06
20 9 0.11
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (17 bp):
AATTTTTGAAACACGAG
Found at i:22230419 original size:18 final size:16
Alignment explanation
Indices: 22230372--22230543 Score: 74
Period size: 17 Copynumber: 9.5 Consensus size: 16
22230362 AAATCACCGG
22230372 AATTTTTGAAAACACGAA
1 AATTTTTG-AAACACG-A
**
22230390 AATCCTTGAAACACTGA
1 AATTTTTGAAACAC-GA
*
22230407 AATTTTTGAAAACATGA
1 AATTTTTG-AAACACGA
* *
22230424 GGATTTTTGAAATACGA
1 -AATTTTTGAAACACGA
* *
22230441 AATTTTTTTGAGAATAGGA
1 AA--TTTTTGA-AACACGA
22230460 AGATTTTTTTTTTGAAAACACGGA
1 A-A-----TTTTTG-AAACAC-GA
* *
22230484 AATTTTTAAAACACGGG
1 AATTTTTGAAACAC-GA
22230501 AATTTTTGAAACACGA
1 AATTTTTGAAACACGA
*
22230517 AATTTTTTTTAAACACGA
1 AA--TTTTTGAAACACGA
22230535 CAATTTTTG
1 -AATTTTTG
22230544 GAATACGAGA
Statistics
Matches: 121, Mismatches: 18, Indels: 31
0.71 0.11 0.18
Matches are distributed among these distances:
16 4 0.03
17 47 0.39
18 44 0.36
19 9 0.07
20 1 0.01
23 12 0.10
24 4 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (16 bp):
AATTTTTGAAACACGA
Found at i:22230434 original size:35 final size:34
Alignment explanation
Indices: 22230372--22230447 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 34
22230362 AAATCACCGG
22230372 AATTTTTGAAAACACGAAAATCCTTGAAACACTGA
1 AATTTTTGAAAACACGAAAATCCTTGAAACAC-GA
* ** ** *
22230407 AATTTTTGAAAACATGAGGATTTTTGAAATACGA
1 AATTTTTGAAAACACGAAAATCCTTGAAACACGA
22230441 AATTTTT
1 AATTTTT
22230448 TTGAGAATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 9 0.26
35 26 0.74
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (34 bp):
AATTTTTGAAAACACGAAAATCCTTGAAACACGA
Found at i:22230449 original size:19 final size:20
Alignment explanation
Indices: 22230427--22230469 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
22230417 AACATGAGGA
22230427 TTTTTGA-AATACGAA-ATT
1 TTTTTGAGAATACGAAGATT
*
22230445 TTTTTGAGAATAGGAAGATT
1 TTTTTGAGAATACGAAGATT
22230465 TTTTT
1 TTTTT
22230470 TTTGAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (20 bp):
TTTTTGAGAATACGAAGATT
Found at i:22230488 original size:23 final size:23
Alignment explanation
Indices: 22230443--22230490 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
22230433 AAATACGAAA
* *
22230443 TTTTTTTGAGAATAGGAAGATTT
1 TTTTTTTGAAAACAGGAAGATTT
22230466 TTTTTTTGAAAACACGGAA-ATTT
1 TTTTTTTGAAAACA-GGAAGATTT
22230489 TT
1 TT
22230491 AAAACACGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.48
Consensus pattern (23 bp):
TTTTTTTGAAAACAGGAAGATTT
Found at i:22230524 original size:111 final size:113
Alignment explanation
Indices: 22230351--22230562 Score: 261
Period size: 111 Copynumber: 1.9 Consensus size: 113
22230341 GAATTTTTTC
* *
22230351 TTTTTTTTTTTAAATCACCGGAATTTTTGAAAACACGAAAATCCTTGAAACACTGAAATTTTTGA
1 TTTTTTTTTTGAAAACACCGGAATTTTTGAAAACACGAAAATCCTTGAAACACTGAAATTTTTGA
* **
22230416 AAACATGAGGATTTTTGAAATAC-GAAATTTTTTTGAGAATAGGAAGA
66 AAACACGACAATTTTTGAAATACAGAAATTTTTTTGAGAATAGGAAGA
** **
22230463 TTTTTTTTTTGAAAACA-CGGAAATTTTT-AAAACACGGGAATTTTTGAAACAC-GAAATTTTTT
1 TTTTTTTTTTGAAAACACCGG-AATTTTTGAAAACACGAAAATCCTTGAAACACTGAAA-TTTTT
** *
22230525 TTAAACACGACAATTTTTGGAATACGAGAAATTTTTTT
64 GAAAACACGACAATTTTTGAAATAC-AGAAATTTTTTT
22230563 TTTAAACTAC
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
110 4 0.05
111 47 0.56
112 22 0.26
113 11 0.13
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (113 bp):
TTTTTTTTTTGAAAACACCGGAATTTTTGAAAACACGAAAATCCTTGAAACACTGAAATTTTTGA
AAACACGACAATTTTTGAAATACAGAAATTTTTTTGAGAATAGGAAGA
Found at i:22230525 original size:35 final size:35
Alignment explanation
Indices: 22230468--22230562 Score: 97
Period size: 35 Copynumber: 2.7 Consensus size: 35
22230458 GAAGATTTTT
**
22230468 TTTTTGAAAACACGGAAA--TTTTTAAAACACGGGAA
1 TTTTTG-AAACAC-GAAATTTTTTTAAAACACGACAA
*
22230503 TTTTTGAAACACGAAATTTTTTTTAAACACGACAA
1 TTTTTGAAACACGAAATTTTTTTAAAACACGACAA
22230538 TTTTTGGAATACGA-GAAATTTTTTT
1 TTTTT-GAA-AC-ACGAAATTTTTTT
22230563 TTTAAACTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
33 4 0.08
34 6 0.12
35 25 0.48
36 3 0.06
37 13 0.25
38 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (35 bp):
TTTTTGAAACACGAAATTTTTTTAAAACACGACAA
Found at i:22230525 original size:94 final size:92
Alignment explanation
Indices: 22230374--22230606 Score: 217
Period size: 94 Copynumber: 2.5 Consensus size: 92
22230364 ATCACCGGAA
* ** * * * * *
22230374 TTTTTGAAAACACGAAAATCCTTGAAACACTGAAATTTTTGAAAACATGAGGATTTTTGAAATAC
1 TTTTTGAAAACACGGAAATTTTTGAAACACGGGAATTTTTG-AAACACGAGAATTTTTGAAACAC
22230439 GA-AATTTTTTTGAGAATA-G-GAAGATTTTT
65 GACAA--TTTTTG-GAATACGAGAA-ATTTTT
* *
22230468 TTTTTGAAAACACGGAAATTTTTAAAACACGGGAATTTTTGAAACACGA-AATTTTTTTTAAACA
1 TTTTTGAAAACACGGAAATTTTTGAAACACGGGAATTTTTGAAACACGAGAA--TTTTTGAAACA
22230532 CGACAATTTTTGGAATACGAGAAATTTTT
64 CGACAATTTTTGGAATACGAGAAATTTTT
* * * * *
22230561 TTTTT--AAACTACGGAATTTTTTGAAATACGAGAATATTAGAAACAC
1 TTTTTGAAAAC-ACGGAAATTTTTGAAACACGGGAATTTTTGAAACAC
22230607 TAAAATAATG
Statistics
Matches: 117, Mismatches: 16, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
91 4 0.03
92 36 0.31
93 25 0.21
94 50 0.43
95 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (92 bp):
TTTTTGAAAACACGGAAATTTTTGAAACACGGGAATTTTTGAAACACGAGAATTTTTGAAACACG
ACAATTTTTGGAATACGAGAAATTTTT
Found at i:22230539 original size:19 final size:18
Alignment explanation
Indices: 22230427--22230542 Score: 69
Period size: 18 Copynumber: 6.2 Consensus size: 18
22230417 AACATGAGGA
*
22230427 TTTTTGAAATACGAAATT
1 TTTTTGAAACACGAAATT
* *
22230445 TTTTTGAGAATAGGAAGATTTTT
1 TTTTTGA-AACACGAA-A---TT
22230468 TTTTTGAAAACACGGAAA--
1 TTTTTG-AAACAC-GAAATT
* *
22230486 TTTTTAAAACACGGGAA--
1 TTTTTGAAACAC-GAAATT
22230503 TTTTTGAAACACGAAATT
1 TTTTTGAAACACGAAATT
*
22230521 TTTTTTAAACACGACAATT
1 TTTTTGAAACACGA-AATT
22230540 TTT
1 TTT
22230543 GGAATACGAG
Statistics
Matches: 80, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.04
17 21 0.26
18 25 0.31
19 14 0.17
20 1 0.01
23 12 0.15
24 4 0.05
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (18 bp):
TTTTTGAAACACGAAATT
Found at i:22230579 original size:39 final size:40
Alignment explanation
Indices: 22230519--22230594 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
22230509 AAACACGAAA
*
22230519 TTTTTTTTAAACACGACAA-TTTTTGGAATACGAGAAATT
1 TTTTTTTTAAACACGACAATTTTTTGAAATACGAGAAATT
*
22230558 TTTTTTTTAAACTACG-GAATTTTTTGAAATACGAGAA
1 TTTTTTTTAAAC-ACGACAATTTTTTGAAATACGAGAA
22230595 TATTAGAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (40 bp):
TTTTTTTTAAACACGACAATTTTTTGAAATACGAGAAATT
Found at i:22230582 original size:18 final size:18
Alignment explanation
Indices: 22230427--22230595 Score: 62
Period size: 18 Copynumber: 9.0 Consensus size: 18
22230417 AACATGAGGA
22230427 TTTTTGAAATACGA-AATT
1 TTTTTGAAATACGAGAA-T
* *
22230445 TTTTTGAGAATAGGAAGATTTTT
1 TTTTTGA-AATACG-AGA---AT
* *
22230468 TTTTTGAAAACACG-GAAA
1 TTTTTG-AAATACGAGAAT
* * *
22230486 TTTTTAAAACACGGGAA-
1 TTTTTGAAATACGAGAAT
*
22230503 TTTTTGAAACACGA-AATT
1 TTTTTGAAATACGAGAA-T
* * *
22230521 TTTTTTAAACACGACAA-
1 TTTTTGAAATACGAGAAT
*
22230538 TTTTTGGAATACGAGAAATTTT
1 TTTTTGAAATACGAG-AA---T
*
22230560 TTTTTTAAACTACG-GAAT
1 TTTTTGAAA-TACGAGAAT
22230578 TTTTTGAAATACGAGAAT
1 TTTTTGAAATACGAGAAT
22230596 ATTAGAAACA
Statistics
Matches: 116, Mismatches: 17, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.02
17 34 0.29
18 43 0.37
19 7 0.06
20 1 0.01
21 5 0.04
22 8 0.07
23 15 0.13
24 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTTTGAAATACGAGAAT
Found at i:22230582 original size:40 final size:39
Alignment explanation
Indices: 22230486--22230594 Score: 111
Period size: 35 Copynumber: 2.9 Consensus size: 39
22230476 AACACGGAAA
* ** *
22230486 TTTTTAAAACACGGGAATTTTTGAAACAC--GAAA--TT
1 TTTTTTAAACACGACAATTTTTGAAATACGAGAAATTTT
*
22230521 TTTTTTAAACACGACAATTTTTGGAATACGAGAAATTTT
1 TTTTTTAAACACGACAATTTTTGAAATACGAGAAATTTT
*
22230560 TTTTTTAAACTACGGA-ATTTTTTGAAATACGAGAA
1 TTTTTTAAAC-AC-GACAATTTTTGAAATACGAGAA
22230595 TATTAGAAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
35 24 0.39
37 4 0.07
39 12 0.20
40 19 0.31
41 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (39 bp):
TTTTTTAAACACGACAATTTTTGAAATACGAGAAATTTT
Found at i:22230854 original size:25 final size:25
Alignment explanation
Indices: 22230823--22230901 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
22230813 AAAACTCGAC
22230823 TATTTTTGAAATACGAGAAATTTAT
1 TATTTTTGAAATACGAGAAATTTAT
* * *
22230848 TATTTTTAAAAGAAC-ACG-AATATAT
1 TATTTTTGAAA-TACGA-GAAATTTAT
*
22230873 T-TTTTTGAAATACGAGAAGTTTTAT
1 TATTTTTGAAATACGAGAA-ATTTAT
22230898 TATT
1 TATT
22230902 ATTATTTTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
23 3 0.07
24 10 0.24
25 23 0.56
26 5 0.12
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (25 bp):
TATTTTTGAAATACGAGAAATTTAT
Found at i:22231237 original size:3 final size:3
Alignment explanation
Indices: 22231229--22231262 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
22231219 TGCATTAAAA
22231229 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22231263 TAAAAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22231652 original size:10 final size:10
Alignment explanation
Indices: 22231645--22231707 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
22231635 CCTTTTTTGT
22231645 TTTCTTTTTC
1 TTTCTTTTTC
22231655 TTTCTTTTTC
1 TTTCTTTTTC
22231665 TCTT-TTTTT-
1 T-TTCTTTTTC
22231674 TTTCTTTTTCC
1 TTTCTTTTT-C
* *
22231685 CTTCTTCTTC
1 TTTCTTTTTC
* *
22231695 TTCCCTTTTC
1 TTTCTTTTTC
22231705 TTT
1 TTT
22231708 TTTCTGTCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
8 2 0.05
9 6 0.14
10 25 0.60
11 9 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:22231670 original size:23 final size:22
Alignment explanation
Indices: 22231636--22231680 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
22231626 TTATTATTCC
*
22231636 CTTTTTTGTTTTCTTTTTCTTT
1 CTTTTTTCTTTTCTTTTTCTTT
*
22231658 CTTTTTCTCTTTTTTTTTTCTTT
1 CTTTTT-TCTTTTCTTTTTCTTT
22231681 TTCCCTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (22 bp):
CTTTTTTCTTTTCTTTTTCTTT
Found at i:22231690 original size:30 final size:30
Alignment explanation
Indices: 22231636--22231695 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
22231626 TTATTATTCC
* *
22231636 CTTTTTTGTTTTCTTTTTCTTTCTTTTTCT
1 CTTTTTTGTTTTCTTTTTCCTTCTTCTTCT
22231666 CTTTTTT-TTTTCTTTTTCCCTTCTTCTTCT
1 CTTTTTTGTTTTCTTTTT-CCTTCTTCTTCT
22231696 TCCCTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (30 bp):
CTTTTTTGTTTTCTTTTTCCTTCTTCTTCT
Found at i:22231692 original size:14 final size:13
Alignment explanation
Indices: 22231673--22231709 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
22231663 TCTCTTTTTT
22231673 TTTTCTTTTTCCC
1 TTTTCTTTTTCCC
*
22231686 TTCTTCTTCTTCCC
1 TT-TTCTTTTTCCC
22231700 TTTTCTTTTT
1 TTTTCTTTTT
22231710 TCTGTCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCTTTTTCCC
Found at i:22232900 original size:17 final size:17
Alignment explanation
Indices: 22232850--22232902 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
22232840 ACTAATCCCT
* *
22232850 ATACATCACTTAGGTAT
1 ATACATTACTTAGGTAC
*
22232867 ATACATTACCTAGGTAC
1 ATACATTACTTAGGTAC
*
22232884 ATATATTACTTAGGTAC
1 ATACATTACTTAGGTAC
22232901 AT
1 AT
22232903 GCCACGTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (17 bp):
ATACATTACTTAGGTAC
Found at i:22235290 original size:24 final size:24
Alignment explanation
Indices: 22235184--22235508 Score: 557
Period size: 24 Copynumber: 13.5 Consensus size: 24
22235174 ATACGGAACA
* *
22235184 AATA-CAGAGAGCACAAATGTGCT
1 AATATCAGAGAGCACCAACGTGCT
***
22235207 AA-A-CAGAGAGCACTGGCGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235229 AAATATCAGAGAGCACCAACGTGCT
1 -AATATCAGAGAGCACCAACGTGCT
22235254 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
22235279 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235303 AATAATCAGAGAGCACCAACGTGCT
1 AAT-ATCAGAGAGCACCAACGTGCT
22235328 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235352 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235376 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235400 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235424 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235448 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235472 AATATCAGAGAGCACCAACGTGCT
1 AATATCAGAGAGCACCAACGTGCT
22235496 AATATCAGAGAGC
1 AATATCAGAGAGC
22235509 GCGCTAAAGT
Statistics
Matches: 290, Mismatches: 7, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
22 16 0.06
23 4 0.01
24 206 0.71
25 64 0.22
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (24 bp):
AATATCAGAGAGCACCAACGTGCT
Found at i:22236158 original size:13 final size:13
Alignment explanation
Indices: 22236129--22236166 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
22236119 CCCGTTTTGC
22236129 TCTCTGTTTCT-T
1 TCTCTGTTTCTAT
22236141 TCTCTGTTTCTAT
1 TCTCTGTTTCTAT
*
22236154 TCTCTTTTTCTAT
1 TCTCTGTTTCTAT
22236167 CCTTTCTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (13 bp):
TCTCTGTTTCTAT
Found at i:22237036 original size:30 final size:29
Alignment explanation
Indices: 22237002--22237129 Score: 96
Period size: 30 Copynumber: 4.3 Consensus size: 29
22236992 GGGGCCAAGC
*
22237002 ATAATTTTGAGAAAATTTAGGGGTCAAAAT
1 ATAATTTT-AGAAAATTGAGGGGTCAAAAT
* * * *
22237032 ATAATTTCA-AGAAGTTGATGGGCCAAAAT
1 ATAATTTTAGA-AAATTGAGGGGTCAAAAT
* * * *
22237061 GTAATTTTAGGAAAGTTTAGGGGTGAAAAT
1 ATAATTTTA-GAAAATTGAGGGGTCAAAAT
* *
22237091 ATAATTTTTAAAAAAGTTGAGGGGTTAAAAT
1 ATAA-TTTTAGAAAA-TTGAGGGGTCAAAAT
*
22237122 GTAATTTT
1 ATAATTTT
22237130 TATTTTTGTT
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
28 1 0.01
29 22 0.29
30 31 0.41
31 22 0.29
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (29 bp):
ATAATTTTAGAAAATTGAGGGGTCAAAAT
Found at i:22237084 original size:59 final size:60
Alignment explanation
Indices: 22237003--22237129 Score: 159
Period size: 59 Copynumber: 2.1 Consensus size: 60
22236993 GGGCCAAGCA
* * *
22237003 TAATTTTGAGAAAATTTAGGGGTCAAAATATAA-TTTCAAGAAGTTGATGGGCCAAAATG
1 TAATTTTGAGAAAATTTAGGGGTCAAAATATAATTTTAAAAAAGTTGAGGGGCCAAAATG
* * **
22237062 TAATTTT-AGGAAAGTTTAGGGGTGAAAATATAATTTTTAAAAAAGTTGAGGGGTTAAAATG
1 TAATTTTGA-GAAAATTTAGGGGTCAAAATATAA-TTTTAAAAAAGTTGAGGGGCCAAAATG
22237123 TAATTTT
1 TAATTTT
22237130 TATTTTTGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.02
59 29 0.50
61 28 0.48
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (60 bp):
TAATTTTGAGAAAATTTAGGGGTCAAAATATAATTTTAAAAAAGTTGAGGGGCCAAAATG
Found at i:22237107 original size:31 final size:31
Alignment explanation
Indices: 22237002--22237131 Score: 106
Period size: 31 Copynumber: 4.3 Consensus size: 31
22236992 GGGGCCAAGC
* * *
22237002 ATAATTTTGAGAAAA-TTTAGGGGTCAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
* * * *
22237032 ATAA--TTTCAAGAAGTTGATGGGCCAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
* ** * *
22237061 GTAA-TTTTAGGAAAGTTTAGGGGTGAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
*
22237091 ATAATTTTTAAAAAAGTTGAGGGGTTAAAAT
1 ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
*
22237122 GTAATTTTTA
1 ATAATTTTTA
22237132 TTTTTGTTTT
Statistics
Matches: 75, Mismatches: 22, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
28 5 0.07
29 15 0.20
30 24 0.32
31 31 0.41
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (31 bp):
ATAATTTTTAAAAAAGTTGAGGGGTCAAAAT
Found at i:22237466 original size:24 final size:26
Alignment explanation
Indices: 22237412--22237465 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
22237402 TCTAATGCTT
**
22237412 TATTGGTGTGTTTGGGAGGATATGATA
1 TATTGGTGTGTTAAGGAGGATAT-ATA
*
22237439 TATTGGTGTGTTAAGGAGGATTTATA
1 TATTGGTGTGTTAAGGAGGATATATA
22237465 T
1 T
22237466 TATCCCGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (26 bp):
TATTGGTGTGTTAAGGAGGATATATA
Found at i:22248205 original size:17 final size:17
Alignment explanation
Indices: 22248183--22248221 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
22248173 AGATTATCGG
*
22248183 AAGCTCTGACGGGTTGA
1 AAGCTCGGACGGGTTGA
*
22248200 AAGCTCGGATGGGTTGA
1 AAGCTCGGACGGGTTGA
22248217 AAGCT
1 AAGCT
22248222 TGTCGGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (17 bp):
AAGCTCGGACGGGTTGA
Found at i:22249931 original size:12 final size:11
Alignment explanation
Indices: 22249904--22249941 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
22249894 GAAAATAGTC
22249904 AAAATTAATA-
1 AAAATTAATAT
22249914 AAAATTAACTAT
1 AAAATTAA-TAT
22249926 AAAATTAAT-T
1 AAAATTAATAT
22249936 AAAATT
1 AAAATT
22249942 CATCATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:22251454 original size:22 final size:25
Alignment explanation
Indices: 22251405--22251460 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
22251395 TATATTATAT
* *
22251405 AATAATAATAATAATAAGTAAATGA
1 AATAATAATAACAATAAGCAAATGA
22251430 AATAATAATAACAA-AA-CAAAT-A
1 AATAATAATAACAATAAGCAAATGA
22251452 AATAGATAA
1 AATA-ATAA
22251461 AAGAAATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.18
23 8 0.29
24 2 0.07
25 13 0.46
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (25 bp):
AATAATAATAACAATAAGCAAATGA
Found at i:22251476 original size:12 final size:12
Alignment explanation
Indices: 22251451--22251502 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
22251441 CAAAACAAAT
22251451 AAATAGATAAAAG
1 AAATAGA-AAAAG
22251464 AAATAGAAAAAG
1 AAATAGAAAAAG
* * *
22251476 AAACAGAGATAG
1 AAATAGAAAAAG
22251488 AAAT-GAAAACAG
1 AAATAGAAAA-AG
22251500 AAA
1 AAA
22251503 GGCAAAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 3 0.09
12 22 0.69
13 7 0.22
ACGTcount: A:0.69, C:0.04, G:0.17, T:0.10
Consensus pattern (12 bp):
AAATAGAAAAAG
Found at i:22252423 original size:37 final size:38
Alignment explanation
Indices: 22252356--22252427 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
22252346 GGTGTCAATT
** *
22252356 ATTTACTTTGGATTAATTCGATGAGGCACTGGGTGCCA
1 ATTTACTTTGGATTAAGCCGATGAGACACTGGGTGCCA
*
22252394 ATTTACTTTGG-TTTAGCCGATGAGACACTGGGTG
1 ATTTACTTTGGATTAAGCCGATGAGACACTGGGTG
22252428 TTTGTCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 19 0.63
38 11 0.37
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (38 bp):
ATTTACTTTGGATTAAGCCGATGAGACACTGGGTGCCA
Found at i:22255650 original size:12 final size:14
Alignment explanation
Indices: 22255610--22255641 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
22255600 TCAATAATGG
22255610 CCTCCTTATGCAAA
1 CCTCCTTATGCAAA
22255624 CCTCCTTATGCAAA
1 CCTCCTTATGCAAA
22255638 CCTC
1 CCTC
22255642 TATGAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.41, G:0.06, T:0.28
Consensus pattern (14 bp):
CCTCCTTATGCAAA
Found at i:22261970 original size:24 final size:23
Alignment explanation
Indices: 22261943--22261996 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
22261933 TTATTAACAT
22261943 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* * **
22261967 TGTTCATGAACGTGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
22261990 TGTTCGT
1 TGTTCGT
22261997 AAATATTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:22264330 original size:27 final size:25
Alignment explanation
Indices: 22264282--22264332 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
22264272 ATTATATATT
*
22264282 AAATATATATTTTTTATTTTTAATC
1 AAATATATATTTTTTATATTTAATC
22264307 AAATATATATTTTATATATATTTAAT
1 AAATATATATTTT-T-TATATTTAAT
22264333 ATGGGCCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 1 0.04
27 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATATATTTTTTATATTTAATC
Found at i:22265550 original size:25 final size:25
Alignment explanation
Indices: 22265522--22265571 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
22265512 ATATAGTTTT
*
22265522 TATATTAT-TTATAAATGTTATAATA
1 TATATTATATTAT-AATGTTAAAATA
22265547 TATATTATATTATAATGTTAAAATA
1 TATATTATATTATAATGTTAAAATA
22265572 AAACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TATATTATATTATAATGTTAAAATA
Found at i:22266050 original size:43 final size:43
Alignment explanation
Indices: 22265977--22266105 Score: 158
Period size: 43 Copynumber: 3.0 Consensus size: 43
22265967 CATAGGATTC
*
22265977 CGATATGTGTTTTCGTGTAAGAC-CTCGTCTGGGACGTTGGCAT
1 CGATATGTGTTTACGTGTAAGACACT-GTCTGGGACGTTGGCAT
22266020 CGACT-TGTGTTTACGTGTAAGACACTGTCTGGGACAG-TGGCAT
1 CGA-TATGTGTTTACGTGTAAGACACTGTCTGGGAC-GTTGGCAT
* * *
22266063 CGATATGTGATTACATGTAAGACCAC-GTCCGGGACGTTGGCAT
1 CGATATGTGTTTACGTGTAAGA-CACTGTCTGGGACGTTGGCAT
22266106 TGTACGAGCC
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
42 2 0.03
43 67 0.88
44 7 0.09
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
CGATATGTGTTTACGTGTAAGACACTGTCTGGGACGTTGGCAT
Found at i:22269295 original size:71 final size:70
Alignment explanation
Indices: 22269164--22269320 Score: 208
Period size: 71 Copynumber: 2.2 Consensus size: 70
22269154 CAACTCTTAA
* * *
22269164 AACCGAATGTATATTCACTATAAACATGAATAGCCGAATGCTTATATACATATATGCTTAACAAG
1 AACCAAATGTATATACACTATAAACATGAATAGCCGAATGCTTATATACATATA-GCTTAACAAA
22269229 TATTAG
65 TATTAG
** * *
22269235 CTCCAAATGTATATACACTTTGAACATGAATAGCCGAATGCATATATATACATATA-CTTAACAA
1 AACCAAATGTATATACACTATAAACATGAATAGCCGAATGC-T-TATATACATATAGCTTAACAA
*
22269299 ATATTAT
64 ATATTAG
22269306 AACCAAATGTATATA
1 AACCAAATGTATATA
22269321 TGTATTTATC
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 61 0.82
72 1 0.01
73 12 0.16
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (70 bp):
AACCAAATGTATATACACTATAAACATGAATAGCCGAATGCTTATATACATATAGCTTAACAAAT
ATTAG
Found at i:22269825 original size:41 final size:41
Alignment explanation
Indices: 22269791--22270019 Score: 323
Period size: 41 Copynumber: 5.6 Consensus size: 41
22269781 ACCGACAATT
* * * * *
22269791 AGCCTGTTAGACGTAAAGCCCGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
22269832 AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
22269873 AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
** * * *
22269914 AGCCTGCTAGACATAAAGTCCAAAATATTTCACTGGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
** * *
22269955 AGCCTGCTAGATGTAAAGTCTGAAACATTTCACCAGCATTA
1 AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
*
22269996 AGCCTGCTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACATAAAGTCTGAA
22270020 TCATCTTACT
Statistics
Matches: 170, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 170 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
Found at i:22269958 original size:123 final size:123
Alignment explanation
Indices: 22269791--22270019 Score: 359
Period size: 123 Copynumber: 1.9 Consensus size: 123
22269781 ACCGACAATT
* * *
22269791 AGCCTGTTAGACGTAAAGCCCGAAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAA
1 AGCCTGCTAGACATAAAGCCCAAAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAA
*
22269856 ACATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
66 ACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
* * * **
22269914 AGCCTGCTAGACATAAAGTCCAAAATATTTCACTGGCATTAAGCCTGCTAGATGTAAAGTCTGAA
1 AGCCTGCTAGACATAAAGCCCAAAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAA
* *
22269979 ACATTTCACCAGCATTAAGCCTGCTAGACGTAAAGTCTGAA
66 ACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTCTGAA
22270020 TCATCTTACT
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 95 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (123 bp):
AGCCTGCTAGACATAAAGCCCAAAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAA
ACATTTCACCAGCATCAAGCCTGCTAGACATAAAGTCTGAAACATTTCACCGGCATCA
Found at i:22270360 original size:88 final size:88
Alignment explanation
Indices: 22270268--22270433 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
22270258 AACATACACC
* * * *
22270268 TATATAAGTTCATATAC-CAT-TTC-AATACAAGATCTTATACATGTACATATATACATATTCGA
1 TATATAA-TTC-TATACTCATATTCGAA-ACAAGAACTTATACATGTACACACATACATATTCAA
22270330 ATCTAACAAATATATATACATATATA
63 ATCTAACAAATATATATACATATATA
* * * *
22270356 TATATAATTCTATACTTATATTCGAAACAAGAACTTATACCTGTATACACATACATATTCAAATT
1 TATATAATTCTATACTCATATTCGAAACAAGAACTTATACATGTACACACATACATATTCAAATC
*
22270421 TAACATATATATA
66 TAACAAATATATA
22270434 AGTATAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
86 5 0.08
87 5 0.08
88 54 0.82
89 2 0.03
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (88 bp):
TATATAATTCTATACTCATATTCGAAACAAGAACTTATACATGTACACACATACATATTCAAATC
TAACAAATATATATACATATATA
Found at i:22270642 original size:113 final size:113
Alignment explanation
Indices: 22270512--22270732 Score: 433
Period size: 113 Copynumber: 2.0 Consensus size: 113
22270502 TTATACAAAT
22270512 ATTTTATACACACACATATATATATATATCTATTCAGACATCTTGTAAACATATATAACAAACAA
1 ATTTTATACACACACATATATATATATATCTATTCAGACATCTTGTAAACATATATAACAAACAA
22270577 CATTAATTAAATTCAAATATTATTTACACATATACATACATATGTTCG
66 CATTAATTAAATTCAAATATTATTTACACATATACATACATATGTTCG
22270625 ATTTTATACACACACATATATATATATATCTATTCAGACATCTTGTAAACATATATAACAAACAA
1 ATTTTATACACACACATATATATATATATCTATTCAGACATCTTGTAAACATATATAACAAACAA
*
22270690 CATTAATTAAATTCACATATTATTTACACATATACATACATAT
66 CATTAATTAAATTCAAATATTATTTACACATATACATACATAT
22270733 ATACTGATTT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (113 bp):
ATTTTATACACACACATATATATATATATCTATTCAGACATCTTGTAAACATATATAACAAACAA
CATTAATTAAATTCAAATATTATTTACACATATACATACATATGTTCG
Found at i:22273589 original size:23 final size:23
Alignment explanation
Indices: 22273563--22273644 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 23
22273553 TTAATGTTCA
*
22273563 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TGAACATTAAT
*
22273586 CGAACATGTTCATGAACATTAAA
1 CGAACATGTTCATGAACATTAAT
*
22273609 CAAACATGTTCATGAACATATAAT
1 CGAACATGTTCATGAACAT-TAAT
*
22273633 TGAACATGTTCA
1 CGAACATGTTCA
22273645 CGAATAATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 4 0.08
23 34 0.67
24 13 0.25
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (23 bp):
CGAACATGTTCATGAACATTAAT
Found at i:22277124 original size:2 final size:2
Alignment explanation
Indices: 22277117--22277142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22277107 TTAATAAAAT
22277117 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
22277143 CATACACATT
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):
TA
Found at i:22285144 original size:20 final size:21
Alignment explanation
Indices: 22285110--22285150 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
22285100 GACCGAAAGG
22285110 CTGTTCGGATCTCTG-CACAT
1 CTGTTCGGATCTCTGTCACAT
* *
22285130 CTGTTCGGTTTTCTGTCACAT
1 CTGTTCGGATCTCTGTCACAT
22285151 TTTATATAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.12, C:0.27, G:0.20, T:0.41
Consensus pattern (21 bp):
CTGTTCGGATCTCTGTCACAT
Found at i:22288965 original size:2 final size:2
Alignment explanation
Indices: 22288958--22288983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22288948 TGTCATACAT
22288958 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
22288984 CCATTTGCAT
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):
TA
Found at i:22292899 original size:19 final size:19
Alignment explanation
Indices: 22292877--22292913 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22292867 TCTCGAAAAT
*
22292877 TGACCAAATTACCATTTTA
1 TGACAAAATTACCATTTTA
22292896 TGACAAAATTACCATTTT
1 TGACAAAATTACCATTTT
22292914 GCCCCACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (19 bp):
TGACAAAATTACCATTTTA
Found at i:22294251 original size:3 final size:3
Alignment explanation
Indices: 22294243--22294279 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
22294233 TCTTTATTAA
22294243 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
22294280 TATTGCTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22330711 original size:2 final size:2
Alignment explanation
Indices: 22330704--22330734 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22330694 ATTTTAAATT
*
22330704 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22330735 CTCATTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22338259 original size:59 final size:59
Alignment explanation
Indices: 22338137--22338290 Score: 159
Period size: 59 Copynumber: 2.6 Consensus size: 59
22338127 AACAATTCAA
* *** *
22338137 TATAATTGGATGACTAAAAAAGAAAAAATTTGAATAGTTAAGTGATCGTTTTGCAACCTTT
1 TATAGTTGGATGACTAAAAAAGAAAAAA--ACCATAGTTAAGTGATCATTTTGCAACCTTT
* **
22338198 TATAGTTGGATGACTAAAAAAGAAAAAAACCATAGTTAAGTGA-CTATTTTGTAATTTTT
1 TATAGTTGGATGACTAAAAAAGAAAAAAACCATAGTTAAGTGATC-ATTTTGCAACCTTT
* * *
22338257 TATAGTT-AAGTGACAAAAAAAGAAAATAACCATA
1 TATAGTTGGA-TGACTAAAAAAGAAAAAAACCATA
22338291 ATTGGGTAAG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
58 2 0.03
59 51 0.64
61 27 0.34
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (59 bp):
TATAGTTGGATGACTAAAAAAGAAAAAAACCATAGTTAAGTGATCATTTTGCAACCTTT
Done.