Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 128 of 141
Found at i:41055518 original size:23 final size:23
Alignment explanation
Indices: 41055492--41055542 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
41055482 ATACTAGACT
41055492 TGTTTTAGGAGTTTTTTTTCTTC
1 TGTTTTAGGAGTTTTTTTTCTTC
41055515 TGTTTTAGGAGTTTTTTTTCTTC
1 TGTTTTAGGAGTTTTTTTTCTTC
41055538 T-TTTT
1 TGTTTT
41055543 GTAAGTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.08, C:0.08, G:0.16, T:0.69
Consensus pattern (23 bp):
TGTTTTAGGAGTTTTTTTTCTTC
Found at i:41058852 original size:27 final size:27
Alignment explanation
Indices: 41058822--41058879 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
41058812 TCGATTTTTT
*
41058822 TATTTTTTATATAAATTT-TAATAAATA
1 TATTTATTATATAAATTTGT-ATAAATA
*
41058849 TATTTATTATATAAATTTGTATATATA
1 TATTTATTATATAAATTTGTATAAATA
41058876 TATT
1 TATT
41058880 AATAATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TATTTATTATATAAATTTGTATAAATA
Found at i:41058887 original size:27 final size:27
Alignment explanation
Indices: 41058830--41058887 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
41058820 TTTATTTTTT
* *
41058830 ATATAAATTTTAATAAATATATTTATT
1 ATATAAATTTTAATAAATATATTAATA
*
41058857 ATATAAATTTGT-ATATATATATTAATA
1 ATATAAATTT-TAATAAATATATTAATA
41058884 ATAT
1 ATAT
41058888 GATTGGTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
ATATAAATTTTAATAAATATATTAATA
Found at i:41059807 original size:2 final size:2
Alignment explanation
Indices: 41059802--41059833 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41059792 GTGTGTGTAC
41059802 AT AT 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 AT AT
41059834 CACTTGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41062639 original size:76 final size:76
Alignment explanation
Indices: 41062513--41062665 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
41062503 ATTTTACTAA
41062513 GGTAGTCTGCTATGTTGTACAGTTATACCATGACCACTGAATTTCACTGAATTTCTAGGAGGAAT
1 GGTAGTCTGCTATGTTGTACAGTTATACCATGACCACTGAATTTCACTGAATTTCTAGGAGGAAT
41062578 AATATCTACTT
66 AATATCTACTT
41062589 GGTAGTCTGCTATGTTGTACAGTTATACCATGACCACTGAATTTCACTGAATTTCTAGGAGGAAT
1 GGTAGTCTGCTATGTTGTACAGTTATACCATGACCACTGAATTTCACTGAATTTCTAGGAGGAAT
41062654 AATATCTACTT
66 AATATCTACTT
41062665 G
1 G
41062666 TCTTTTTCAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (76 bp):
GGTAGTCTGCTATGTTGTACAGTTATACCATGACCACTGAATTTCACTGAATTTCTAGGAGGAAT
AATATCTACTT
Found at i:41067431 original size:12 final size:12
Alignment explanation
Indices: 41067414--41067438 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41067404 CAGCAGAAAG
41067414 GAGTGAAGAGAA
1 GAGTGAAGAGAA
41067426 GAGTGAAGAGAA
1 GAGTGAAGAGAA
41067438 G
1 G
41067439 GCATTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:41076986 original size:16 final size:15
Alignment explanation
Indices: 41076967--41076997 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
41076957 CCCGTATTAA
41076967 TTTTTTATAT-TATT
1 TTTTTTATATATATT
41076981 TTTTTTATATATATT
1 TTTTTTATATATATT
41076996 TT
1 TT
41076998 AAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTATATATATT
Found at i:41084985 original size:26 final size:27
Alignment explanation
Indices: 41084931--41084985 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
41084921 GCAATGTAAA
*
41084931 TTGTAAATTTTGTATATAATATTTTTC
1 TTGTAAATTTTGTATATAATATTTCTC
41084958 TTGT-AATTTTGTATAT-ATATATTCTC
1 TTGTAAATTTTGTATATAATAT-TTCTC
41084984 TT
1 TT
41084986 TCCATAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 18 0.69
27 4 0.15
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.60
Consensus pattern (27 bp):
TTGTAAATTTTGTATATAATATTTCTC
Found at i:41094432 original size:3 final size:3
Alignment explanation
Indices: 41094424--41094449 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41094414 AGGGTACCTT
41094424 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
41094450 TATCTTCTCA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:41104283 original size:278 final size:277
Alignment explanation
Indices: 41103779--41104327 Score: 638
Period size: 278 Copynumber: 2.0 Consensus size: 277
41103769 ATTATCTCAT
* * * **
41103779 GGTCACCATTGTATCTGTTACAAAGAAAATGGTCATTACTCAAATTAGTAATGATGAAATCATTT
1 GGTCACCATTGTATCTGTTACAAAGAAAATGATCATTACACAAATTAGTAATGAAGAAATCAGGT
* * * * * * *
41103844 GTCCCAGACAAATTACCCGTAACTAGGTTCTATTTTTATAATCCATACAATGTCAGTAAGACTAT
66 GTCCCAAACAAATGACCCATAACCAGGTTCTATTTTCATAATCCATACAATCTCAGTAAGACGAT
* * * * * *
41103909 ACCATTTACTCTTTTATCGAGCTATGATTCCACTACGGTGAGTGAAGCCATATCATGTATAAGTC
131 ACCATTTACTCATTTAACAAGCCATGATTCCACTACGGTGAGTGAAGCCATATCATGCATAAGTA
** * *
41103974 ATGTACCCAACATACCAAATTCCGGTCCACTATCATTAGAGCAAATGTTTTCAATATATCAAAGC
196 ATGTACCCAACATACCAAATTCCAATCCACTATCATCAGAGC--ATATTTTCAATATATCAAAGC
41104039 ACAT-AGTTACACCCATAA
259 ACATGAGTTACACCCATAA
* * *
41104057 GGTCACCATTGTATCT-TTCACAATA-AAAATGATCATTACACAATTTATTAATGAAGAAATTAG
1 GGTCACCATTGTATCTGTT-ACAA-AGAAAATGATCATTACACAAATTAGTAATGAAGAAATCAG
* * ** * * *
41104120 GTGTCCTAAACAAATGACCTATGGCCAGGTTCTATTTTCATAATTCATACAATACT-AGTGAGAG
64 GTGTCCCAAACAAATGACCCATAACCAGGTTCTATTTTCATAATCCATACAAT-CTCAGTAAGAC
** ** ** *
41104184 GATATTATTTACTCATTTAACAAGCCATGATTCCACTATTGTGAGTGACTCTATATCATGCATAA
128 GATACCATTTACTCATTTAACAAGCCATGATTCCACTACGGTGAGTGAAGCCATATCATGCATAA
* * * *
41104249 GTAATGTACCTAACATACCAACTTCCAATCCACTATCATCAGCGCATATTTTCACTATATCAAAG
193 GTAATGTACCCAACATACCAAATTCCAATCCACTATCATCAGAGCATATTTTCAATATATCAAAG
41104314 CACATGAGTTACAC
258 CACATGAGTTACAC
41104328 AAACATGGTC
Statistics
Matches: 224, Mismatches: 43, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
276 23 0.10
277 10 0.04
278 189 0.84
279 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (277 bp):
GGTCACCATTGTATCTGTTACAAAGAAAATGATCATTACACAAATTAGTAATGAAGAAATCAGGT
GTCCCAAACAAATGACCCATAACCAGGTTCTATTTTCATAATCCATACAATCTCAGTAAGACGAT
ACCATTTACTCATTTAACAAGCCATGATTCCACTACGGTGAGTGAAGCCATATCATGCATAAGTA
ATGTACCCAACATACCAAATTCCAATCCACTATCATCAGAGCATATTTTCAATATATCAAAGCAC
ATGAGTTACACCCATAA
Found at i:41104926 original size:17 final size:19
Alignment explanation
Indices: 41104904--41104938 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
41104894 CTAAAATAGT
41104904 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
41104921 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
41104939 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:41105843 original size:11 final size:11
Alignment explanation
Indices: 41105813--41105875 Score: 92
Period size: 11 Copynumber: 5.6 Consensus size: 11
41105803 CTCTGCTCAT
41105813 TTTTAATAAATA
1 TTTTAA-AAATA
*
41105825 -TTAAAAAATTA
1 TTTTAAAAA-TA
41105836 TTTTAAAAATA
1 TTTTAAAAATA
41105847 TTTTAAAAATA
1 TTTTAAAAATA
41105858 TTTTAAAAATA
1 TTTTAAAAATA
41105869 TTTTAAA
1 TTTTAAA
41105876 TTTTAAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
10 3 0.06
11 37 0.79
12 7 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:41105847 original size:22 final size:21
Alignment explanation
Indices: 41105813--41105933 Score: 103
Period size: 22 Copynumber: 5.9 Consensus size: 21
41105803 CTCTGCTCAT
41105813 TTTTAATAAATATTAAAAAATTA
1 TTTTAA-AAATATTAAAAAA-TA
*
41105836 TTTTAAAAATATTTTAAAAATA
1 TTTTAAAAATA-TTAAAAAATA
**
41105858 TTTTAAAAATATT--TTAA-A
1 TTTTAAAAATATTAAAAAATA
*
41105876 TTTT-AAAAT-TTAAAAAAAA
1 TTTTAAAAATATTAAAAAATA
**
41105895 TTAAAAAAATATGTAAAAAATA
1 TTTTAAAAATAT-TAAAAAATA
41105917 TTTT-AAAAT-TTAAAAAA
1 TTTTAAAAATATTAAAAAA
41105934 AATATATTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.02
17 5 0.06
18 7 0.09
19 12 0.15
20 6 0.07
21 8 0.10
22 28 0.35
23 13 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (21 bp):
TTTTAAAAATATTAAAAAATA
Found at i:41105894 original size:11 final size:11
Alignment explanation
Indices: 41105880--41105936 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
41105870 TTTAAATTTT
41105880 AAAATTTAAAA
1 AAAATTTAAAA
41105891 AAAA-TTAAAA
1 AAAATTTAAAA
*
41105901 AAATATGTAAAA
1 AAA-ATTTAAAA
* *
41105913 AATATTT---T
1 AAAATTTAAAA
41105921 AAAATTTAAAA
1 AAAATTTAAAA
41105932 AAAAT
1 AAAAT
41105937 ATATTTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
8 6 0.17
10 9 0.26
11 13 0.37
12 7 0.20
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:41120237 original size:17 final size:16
Alignment explanation
Indices: 41120213--41120407 Score: 144
Period size: 17 Copynumber: 11.2 Consensus size: 16
41120203 ATATATATTT
41120213 TATTTTTAATCAAATA
1 TATTTTTAATCAAATA
41120229 TACTTTTTAATCAAATA
1 TA-TTTTTAATCAAATA
* *
41120246 TATATTAAAT-ATATATA
1 TATTTTTAATCA-A-ATA
41120263 TTTTATTTTTAATCAAATA
1 ---TATTTTTAATCAAATA
41120282 TACTTTTTAATCAAATA
1 TA-TTTTTAATCAAATA
* *
41120299 TATATTAAAT-ATATATA
1 TATTTTTAATCA-A-ATA
41120316 TTTTATTTTTAATCAAATA
1 ---TATTTTTAATCAAATA
41120335 TACTTTTTAATCAAATA
1 TA-TTTTTAATCAAATA
* *
41120352 TATATTAAAT-ATATATA
1 TATTTTTAATCA-A-ATA
41120369 TTTTATTTTTAATCAAATA
1 ---TATTTTTAATCAAATA
41120388 TACTTTTTAATCAAATA
1 TA-TTTTTAATCAAATA
41120405 TAT
1 TAT
41120408 ATTAAATATA
Statistics
Matches: 145, Mismatches: 12, Indels: 44
0.72 0.06 0.22
Matches are distributed among these distances:
15 3 0.02
16 30 0.21
17 73 0.50
19 9 0.06
20 27 0.19
21 3 0.02
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTTTAATCAAATA
Found at i:41120270 original size:53 final size:53
Alignment explanation
Indices: 41120191--41120419 Score: 458
Period size: 53 Copynumber: 4.3 Consensus size: 53
41120181 CGGCCCGAAT
41120191 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
1 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
41120244 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
1 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
41120297 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
1 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
41120350 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
1 TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
41120403 TATATATTAAATATATA
1 TATATATTAAATATATA
41120420 CTTTTTTGGT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 176 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (53 bp):
TATATATTAAATATATATATTTTATTTTTAATCAAATATACTTTTTAATCAAA
Found at i:41120276 original size:36 final size:35
Alignment explanation
Indices: 41120232--41120389 Score: 119
Period size: 36 Copynumber: 4.5 Consensus size: 35
41120222 TCAAATATAC
41120232 TTTTTAATCAAATATATATTAAATATATATATTTTA
1 TTTTTAATCAAATATATATTAAATATA-ATATTTTA
* *
41120268 TTTTTAATCAAATATACTTTTTAATCA-AATA---TA
1 TTTTTAATCAAATATA-TATTAAAT-ATAATATTTTA
* * * * ** * * *
41120301 TATTAAAT-ATATATATTTTATTTTTAATCAAATATA
1 TTTTTAATCAAATATATATTAAATATAAT--ATTTTA
41120337 CTTTTTAATCAAATATATATTAAATATATATATTTTA
1 -TTTTTAATCAAATATATATTAAATATA-ATATTTTA
41120374 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
41120390 CTTTTTAATC
Statistics
Matches: 93, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
31 8 0.09
32 6 0.06
33 9 0.10
36 37 0.40
37 17 0.18
38 14 0.15
39 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (35 bp):
TTTTTAATCAAATATATATTAAATATAATATTTTA
Found at i:41121770 original size:31 final size:31
Alignment explanation
Indices: 41121687--41121766 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
41121677 TTTAACGGTA
* * *
41121687 GAGTAACTAAAATTGACAACTTATCTACCAG
1 GAGTGACTAAAATTAACAATTTATCTACCAG
**
41121718 GAGTGACTAAAATTAACAATTTATCTATTAG
1 GAGTGACTAAAATTAACAATTTATCTACCAG
41121749 GAGTGACTAAAA-TAACAA
1 GAGTGACTAAAATTAACAA
41121767 ATTTTTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 6 0.14
31 38 0.86
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (31 bp):
GAGTGACTAAAATTAACAATTTATCTACCAG
Found at i:41123503 original size:120 final size:120
Alignment explanation
Indices: 41123379--41123610 Score: 464
Period size: 120 Copynumber: 1.9 Consensus size: 120
41123369 AAAGTTTTTA
41123379 TTTAAGTCATTGGACTGTTAAGTTTTTTATTTTTAAAAAAAAGTCTAGCTAGCGAGCTCCAAGTG
1 TTTAAGTCATTGGACTGTTAAGTTTTTTATTTTTAAAAAAAAGTCTAGCTAGCGAGCTCCAAGTG
41123444 ACTATCGATATGGTGGATCAGTACCTATCAACAAATAGAATAACATAGAAAGTTT
66 ACTATCGATATGGTGGATCAGTACCTATCAACAAATAGAATAACATAGAAAGTTT
41123499 TTTAAGTCATTGGACTGTTAAGTTTTTTATTTTTAAAAAAAAGTCTAGCTAGCGAGCTCCAAGTG
1 TTTAAGTCATTGGACTGTTAAGTTTTTTATTTTTAAAAAAAAGTCTAGCTAGCGAGCTCCAAGTG
41123564 ACTATCGATATGGTGGATCAGTACCTATCAACAAATAGAATAACATA
66 ACTATCGATATGGTGGATCAGTACCTATCAACAAATAGAATAACATA
41123611 CATTAAATCC
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (120 bp):
TTTAAGTCATTGGACTGTTAAGTTTTTTATTTTTAAAAAAAAGTCTAGCTAGCGAGCTCCAAGTG
ACTATCGATATGGTGGATCAGTACCTATCAACAAATAGAATAACATAGAAAGTTT
Found at i:41123659 original size:120 final size:118
Alignment explanation
Indices: 41123413--41123661 Score: 270
Period size: 120 Copynumber: 2.1 Consensus size: 118
41123403 TTTTATTTTT
41123413 AAAAAAAAGTCTAGCTAGCGAGCTCCAAGTGACTATCGATATGGTGGATCAGTACCTATCAACAA
1 AAAAAAAAGTCTAGCTAGCGAGCTCCAAGTGACTATCGATATGGTGGATCAGTACCTATCAACAA
* * ** * * ***** ***
41123478 ATAGAATAACATAGAAAGTTTTTTAAGTCATTGGACTGTTAAGTTTTTTATTTTT
66 ATAGAATAACATACAAA--TATCCAAATCATTGGACTATTAAGTCGAAGATTCAG
41123533 AAAAAAAAGTCTAGCTAGCGAGCTCCAAGTGACTATCGATATGGTGGATCAGTACCTATCAACAA
1 AAAAAAAAGTCTAGCTAGCGAGCTCCAAGTGACTATCGATATGGTGGATCAGTACCTATCAACAA
*
41123598 ATAGAATAACATACATTAA-ATCCAAATCAATCT-GACTATCTATGTCGAAGA-TCAG
66 ATAGAATAACATACA--AATATCCAAATC-AT-TGGACTAT-TAAGTCGAAGATTCAG
*
41123653 ATAAAAAAG
1 AAAAAAAAG
41123662 CTGTTTGGAT
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
119 5 0.05
120 95 0.88
121 6 0.06
122 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (118 bp):
AAAAAAAAGTCTAGCTAGCGAGCTCCAAGTGACTATCGATATGGTGGATCAGTACCTATCAACAA
ATAGAATAACATACAAATATCCAAATCATTGGACTATTAAGTCGAAGATTCAG
Found at i:41126606 original size:22 final size:22
Alignment explanation
Indices: 41126565--41126606 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41126555 TACAACACGA
* *
41126565 ATATACTAACATATCAAAATCT
1 ATATACTAAAAGATCAAAATCT
*
41126587 ATATACTAAAAGATCGAAAT
1 ATATACTAAAAGATCAAAAT
41126607 GATTAGGGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (22 bp):
ATATACTAAAAGATCAAAATCT
Found at i:41132770 original size:26 final size:26
Alignment explanation
Indices: 41132734--41132783 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
41132724 CACTGTCAAA
41132734 TAAATGAAGAGAACAGTAAAAAAAGG
1 TAAATGAAGAGAACAGTAAAAAAAGG
41132760 TAAATGAAGAGAACAGTAAAAAAA
1 TAAATGAAGAGAACAGTAAAAAAA
41132784 AGCACAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.64, C:0.04, G:0.20, T:0.12
Consensus pattern (26 bp):
TAAATGAAGAGAACAGTAAAAAAAGG
Found at i:41136654 original size:4 final size:4
Alignment explanation
Indices: 41136645--41136670 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41136635 AGGATTATAG
41136645 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
41136671 TATTCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:41140048 original size:26 final size:26
Alignment explanation
Indices: 41140012--41140064 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
41140002 ATACGTAATA
* *
41140012 CCTGCTAAACAAACATCGGCTCAAAG
1 CCTGCCAAACAAACACCGGCTCAAAG
*
41140038 CCTGCCAAACAATCACCGGCTCAAAG
1 CCTGCCAAACAAACACCGGCTCAAAG
41140064 C
1 C
41140065 TTACTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.36, C:0.36, G:0.15, T:0.13
Consensus pattern (26 bp):
CCTGCCAAACAAACACCGGCTCAAAG
Found at i:41140083 original size:22 final size:22
Alignment explanation
Indices: 41140055--41140098 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41140045 AACAATCACC
*
41140055 GGCTCAAAGCTTACTAAATAAT
1 GGCTCAAAGCCTACTAAATAAT
41140077 GGCTCAAAGCCTACTAAATAAT
1 GGCTCAAAGCCTACTAAATAAT
41140099 CGCTAGCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (22 bp):
GGCTCAAAGCCTACTAAATAAT
Found at i:41140114 original size:26 final size:26
Alignment explanation
Indices: 41140028--41140253 Score: 244
Period size: 26 Copynumber: 8.8 Consensus size: 26
41140018 AAACAAACAT
* * * *
41140028 CGGCTCAAAGCCTGCCAAACAATCAC
1 CGGCTCAAGGCCTACTAAATAATCAC
* *
41140054 CGGCTCAAAGCTTACTAAATAAT---
1 CGGCTCAAGGCCTACTAAATAATCAC
* *
41140077 -GGCTCAAAGCCTACTAAATAATCGC
1 CGGCTCAAGGCCTACTAAATAATCAC
** * *
41140102 TAGCTCAAGGCCTGCTAAATAAACAC
1 CGGCTCAAGGCCTACTAAATAATCAC
*
41140128 CGGCTCAAGGCCTGCTAAATAATCAC
1 CGGCTCAAGGCCTACTAAATAATCAC
* *
41140154 CGGCTCAAGGCTTACTAAATGATCAC
1 CGGCTCAAGGCCTACTAAATAATCAC
41140180 CGGCTCAAGGCCTACTAAATAATCAC
1 CGGCTCAAGGCCTACTAAATAATCAC
* * *
41140206 TGGCTTAAGGCCTACCAAATAATCAC
1 CGGCTCAAGGCCTACTAAATAATCAC
* *
41140232 CGGCTCAAGGTCTGCTAAATAA
1 CGGCTCAAGGCCTACTAAATAA
41140254 ACAATATACT
Statistics
Matches: 170, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
22 21 0.12
26 149 0.88
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (26 bp):
CGGCTCAAGGCCTACTAAATAATCAC
Found at i:41141463 original size:37 final size:39
Alignment explanation
Indices: 41141419--41141518 Score: 123
Period size: 37 Copynumber: 2.6 Consensus size: 39
41141409 CGGAGCAAAG
*
41141419 TTGATACCCAGTGTCTCATCG-GCCTAGCCGAAGT-AAA
1 TTGATACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAA
* * *
41141456 TTGATACCCAGTATCTCATCGAATCTATCCGAAGTAAAA
1 TTGATACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAA
*
41141495 TAGTGACACCCAGTGTCTCATCGA
1 T--TGATACCCAGTGTCTCATCGA
41141519 CTCGAGGTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 20 0.38
38 10 0.19
39 4 0.08
41 19 0.36
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (39 bp):
TTGATACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAA
Found at i:41141644 original size:18 final size:17
Alignment explanation
Indices: 41141610--41141663 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
41141600 TTTCCAATTC
41141610 TCATTTCAAATTCACTT
1 TCATTTCAAATTCACTT
*
41141627 TCATTTCAAAATTTACTT
1 TCATTTC-AAATTCACTT
*
41141645 TCAATATCAAATTCACTT
1 TC-ATTTCAAATTCACTT
41141663 T
1 T
41141664 TTCATTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.22
18 21 0.66
19 4 0.12
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.46
Consensus pattern (17 bp):
TCATTTCAAATTCACTT
Found at i:41142226 original size:29 final size:30
Alignment explanation
Indices: 41142178--41142240 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 30
41142168 TTACTCAATT
41142178 CTAATCAATAATTCTATCAA-ATAAACCC-
1 CTAATCAATAATTCTATCAACATAAACCCA
* *
41142206 CTAATTCAATCATT-TATTCAACATGAACCCA
1 CTAA-TCAATAATTCTA-TCAACATAAACCCA
41142237 CTAA
1 CTAA
41142241 AAAATCTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 6 0.21
29 12 0.41
30 7 0.24
31 4 0.14
ACGTcount: A:0.43, C:0.25, G:0.02, T:0.30
Consensus pattern (30 bp):
CTAATCAATAATTCTATCAACATAAACCCA
Found at i:41142289 original size:21 final size:20
Alignment explanation
Indices: 41142250--41142290 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
41142240 AAAAATCTAC
41142250 TAAATTTCAAAATTTCAACT
1 TAAATTTCAAAATTTCAACT
41142270 TAAA-TTCAATAATATTCAACT
1 TAAATTTCAA-AAT-TTCAACT
41142291 CTAGGACTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 7 0.37
21 7 0.37
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAATTTCAAAATTTCAACT
Found at i:41142657 original size:18 final size:18
Alignment explanation
Indices: 41142634--41142681 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
41142624 TAATAATAAA
*
41142634 AATAATAATTAT-TATTAT
1 AATAATAAATATCTATT-T
41142652 AATAATAAATATCTATTT
1 AATAATAAATATCTATTT
*
41142670 AATAACAAATAT
1 AATAATAAATAT
41142682 AAATATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATAAATATCTATTT
Found at i:41142815 original size:33 final size:32
Alignment explanation
Indices: 41142767--41142838 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
41142757 TATTTATCAT
*
41142767 ATAAAA-ATCTTTTACTAATTA-ATAATAAATA
1 ATAAAATATCTTTTACTAAATATAT-ATAAATA
41142798 ATAAAATATCTTTTTACTAAATATATATAAATA
1 ATAAAATATC-TTTTACTAAATATATATAAATA
41142831 ATACAAAT
1 ATA-AAAT
41142839 GTACTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 6 0.17
32 3 0.08
33 21 0.58
34 6 0.17
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (32 bp):
ATAAAATATCTTTTACTAAATATATATAAATA
Found at i:41142952 original size:29 final size:29
Alignment explanation
Indices: 41142897--41142953 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
41142887 GTTTTTTCTT
* **
41142897 AATTTATTTCATAATATAATATTATAATC
1 AATTTATTTCATAATATAAGAAAATAATC
41142926 AATTTAATTT-ATAATATAAGAAAATAAT
1 AATTT-ATTTCATAATATAAGAAAATAAT
41142954 AACAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (29 bp):
AATTTATTTCATAATATAAGAAAATAATC
Found at i:41150044 original size:33 final size:33
Alignment explanation
Indices: 41150007--41150073 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
41149997 AAGAAGAAAG
*
41150007 AAAAGAAGAAGAAATTAGAAAAATAAATTAATA
1 AAAAGAAGAAGAAAATAGAAAAATAAATTAATA
*
41150040 AAAAGAAGAATAAAATAGAAAAATAAATTAATA
1 AAAAGAAGAAGAAAATAGAAAAATAAATTAATA
41150073 A
1 A
41150074 CTTGTTAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (33 bp):
AAAAGAAGAAGAAAATAGAAAAATAAATTAATA
Found at i:41153186 original size:2 final size:2
Alignment explanation
Indices: 41153179--41153207 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41153169 GGTGTTTAGA
41153179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41153208 GGTCATGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41153490 original size:20 final size:20
Alignment explanation
Indices: 41153444--41153482 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41153434 ACTTTATATC
*
41153444 ACAA-TTATCAAAATTTCTA
1 ACAATTTATCAAAATTTCAA
*
41153463 ACAATTTATCATAATTTCAA
1 ACAATTTATCAAAATTTCAA
41153483 TACATTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (20 bp):
ACAATTTATCAAAATTTCAA
Found at i:41153582 original size:20 final size:20
Alignment explanation
Indices: 41153553--41153604 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
41153543 AACCTATGCC
*
41153553 AAAATATCTAACGATTTACCA
1 AAAAT-TCTAACAATTTACCA
41153574 AAAATTCTAGA-AATTTACCA
1 AAAATTCTA-ACAATTTACCA
* *
41153594 ATATTTCTAAC
1 AAAATTCTAAC
41153605 CTATACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 19 0.73
21 6 0.23
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTCTAACAATTTACCA
Found at i:41154120 original size:29 final size:29
Alignment explanation
Indices: 41154077--41154134 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
41154067 ACTTATAACG
41154077 TCAATTCCATAAACATTAACCATATCATA
1 TCAATTCCATAAACATTAACCATATCATA
*
41154106 TCAATTCCATGAACATTAACCATATCATA
1 TCAATTCCATAAACATTAACCATATCATA
41154135 CAAATAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (29 bp):
TCAATTCCATAAACATTAACCATATCATA
Found at i:41155219 original size:241 final size:242
Alignment explanation
Indices: 41154752--41155244 Score: 810
Period size: 241 Copynumber: 2.0 Consensus size: 242
41154742 GGTCATGGGG
41154752 AGACTAGGGATGGCAGCAATAGGACATTTGCAAATTATCCGAATTTGAATTCAAATTTAATATCA
1 AGACTAGGGATGGCAGCAATAGGACATTTGCAAATTATCCGAATTTGAATTCAAATTTAATATCA
* *
41154817 TTATTTGTTGAATATATGACTCTGCATTCATTATTTAGATAAAAAATTCAGATTTGAATATTTGG
66 TTATTTGTTGAATATATGACTCCGCATTCATTATTCAGATAAAAAATTC-----T-AATATTTGG
* *
41154882 CAATCTCTAATGTGTTGATATCAATTGTGCCTCATTATTTCCATGAATCATTTTTCTAGATAGAA
125 CAATCTCTAATGTGTTGATATCAATGGTGCCTCATTATTTCCATGAATCATTTTTCCAGATAGAA
* * *
41154947 GAAAATTATGTAAATATTTACTCAAAATCTTGTTTATCAGATTCCATTGTGGA
190 GAAAATTATGTAAACACTTACTCAAAATCTTGCTTATCAGATTCCATTGTGGA
* * *
41155000 AGACTAGGGATGGCAGCGATAGGATATTTGCAAATTATCCGAATTTGAATTCAAATTTAATATCT
1 AGACTAGGGATGGCAGCAATAGGACATTTGCAAATTATCCGAATTTGAATTCAAATTTAATATCA
*
41155065 TTATTTGTTGAATATATGACTCCGCATTCGTTATTCAGATAAAAAATTC-AA-ATTTGGACAATC
66 TTATTTGTTGAATATATGACTCCGCATTCATTATTCAGATAAAAAATTCTAATATTTGG-CAATC
41155128 TCTAATGTGTTGATATCAATGGTGCCTCATTATTTCCATGAATCATTTTTCCAGATAGAAGAAAA
130 TCTAATGTGTTGATATCAATGGTGCCTCATTATTTCCATGAATCATTTTTCCAGATAGAAGAAAA
41155193 TTATGTAAACACTTACTCAAAATCTTGCTTATCAGATTCCATTGTGGA
195 TTATGTAAACACTTACTCAAAATCTTGCTTATCAGATTCCATTGTGGA
41155241 AGAC
1 AGAC
41155245 ATTGTTTTTC
Statistics
Matches: 233, Mismatches: 11, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
240 6 0.03
241 119 0.51
248 108 0.46
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (242 bp):
AGACTAGGGATGGCAGCAATAGGACATTTGCAAATTATCCGAATTTGAATTCAAATTTAATATCA
TTATTTGTTGAATATATGACTCCGCATTCATTATTCAGATAAAAAATTCTAATATTTGGCAATCT
CTAATGTGTTGATATCAATGGTGCCTCATTATTTCCATGAATCATTTTTCCAGATAGAAGAAAAT
TATGTAAACACTTACTCAAAATCTTGCTTATCAGATTCCATTGTGGA
Found at i:41156082 original size:14 final size:14
Alignment explanation
Indices: 41156063--41156091 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41156053 TCATCTCATG
41156063 TATATTAATATATT
1 TATATTAATATATT
41156077 TATATTAATATATT
1 TATATTAATATATT
41156091 T
1 T
41156092 CGATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATTAATATATT
Found at i:41156132 original size:3 final size:3
Alignment explanation
Indices: 41156115--41156225 Score: 65
Period size: 3 Copynumber: 36.3 Consensus size: 3
41156105 TATATTTCTA
*
41156115 TAT TATT TAT T-T TAT TAT T-C TAT CTAT TAT TA- TAT TAT CTAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT
* *
41156160 TA- TAT TAT TCT TA- TAA TAT TAT TA- TAT ATAT TAT TAT T-T CTATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TA-T
41156204 TAGT TAT TATT TAGT TAT TAT T
1 TA-T TAT TA-T TA-T TAT TAT T
41156226 TATATTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
2 12 0.14
3 51 0.59
4 23 0.26
5 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:41156197 original size:29 final size:29
Alignment explanation
Indices: 41156141--41156194 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
41156131 ATTCTATCTA
*
41156141 TTATTATATTATCTATTATTATATTATTC
1 TTATAATATTATCTATTATTATATTATTC
41156170 TTATAATATTAT-TA-TA-TATATTATT
1 TTATAATATTATCTATTATTATATTATT
41156195 ATTTCTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 2 0.08
29 11 0.46
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (29 bp):
TTATAATATTATCTATTATTATATTATTC
Found at i:41156216 original size:11 final size:11
Alignment explanation
Indices: 41156200--41156227 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41156190 TTATTATTTC
41156200 TATTTAGTTAT
1 TATTTAGTTAT
41156211 TATTTAGTTAT
1 TATTTAGTTAT
41156222 TATTTA
1 TATTTA
41156228 TATTTAGTCT
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:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (11 bp):
TATTTAGTTAT
Found at i:41156275 original size:20 final size:20
Alignment explanation
Indices: 41156250--41156289 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41156240 TTAGAATTTT
*
41156250 TTATTATTTCATTTAAGTTA
1 TTATTATTTAATTTAAGTTA
41156270 TTATTATTTAATTTAAGTTA
1 TTATTATTTAATTTAAGTTA
41156290 AATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (20 bp):
TTATTATTTAATTTAAGTTA
Found at i:41156310 original size:31 final size:33
Alignment explanation
Indices: 41156275--41156345 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
41156265 AGTTATTATT
*
41156275 ATTTAATTTAAGT-TAAATAGAA-AAATTAATA
1 ATTTAATTTAAGTATAAATAAAATAAATTAATA
* *
41156306 ATTTAATTTAAGTATAATTAAAATAAATTATTA
1 ATTTAATTTAAGTATAAATAAAATAAATTAATA
41156339 ATTTAAT
1 ATTTAAT
41156346 AATTTAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 13 0.37
32 7 0.20
33 15 0.43
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (33 bp):
ATTTAATTTAAGTATAAATAAAATAAATTAATA
Found at i:41157253 original size:4 final size:4
Alignment explanation
Indices: 41157244--41157272 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
41157234 TTTTTTTACT
41157244 TTAA TTAA TTAA TTAA TTAA TTAA -TAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
41157273 CGAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:41169677 original size:19 final size:19
Alignment explanation
Indices: 41169645--41169681 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41169635 TATAAACTTG
*
41169645 TAATTCTTTCAAATATTTA
1 TAATTCTTTAAAATATTTA
*
41169664 TAATTTTTTAAAATATTT
1 TAATTCTTTAAAATATTT
41169682 TTTTGAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTCTTTAAAATATTTA
Found at i:41169828 original size:18 final size:18
Alignment explanation
Indices: 41169807--41169841 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41169797 ATATATTATA
41169807 ATCTTAAAAATTAAGATG
1 ATCTTAAAAATTAAGATG
41169825 ATCTTAAAAATTAAGAT
1 ATCTTAAAAATTAAGAT
41169842 TTTTAGGCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (18 bp):
ATCTTAAAAATTAAGATG
Found at i:41170952 original size:43 final size:43
Alignment explanation
Indices: 41170904--41171075 Score: 344
Period size: 43 Copynumber: 4.0 Consensus size: 43
41170894 TAATTACCGA
41170904 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
1 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
41170947 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
1 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
41170990 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
1 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
41171033 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
1 AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
41171076 CCCGAAGTCG
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 129 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (43 bp):
AATGGGCCAACTATTTAATTATTTACCGGATTGATCCATTTTC
Found at i:41171281 original size:12 final size:11
Alignment explanation
Indices: 41171264--41171299 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
41171254 AACAAATCCT
41171264 CTCTCATATTTC
1 CTCTCA-ATTTC
*
41171276 CTCTCAATTTT
1 CTCTCAATTTC
41171287 CTCTCAATTTC
1 CTCTCAATTTC
41171298 CT
1 CT
41171300 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:41171310 original size:22 final size:23
Alignment explanation
Indices: 41171263--41171311 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
41171253 AAACAAATCC
**
41171263 TCTCTCATATTTCCTCTCAATTT
1 TCTCTCATATTTCCTCTCAAAAT
41171286 TCTCTCA-ATTTCCT-TCCAAAAT
1 TCTCTCATATTTCCTCT-CAAAAT
41171308 TCTC
1 TCTC
41171312 ATAAATCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 15 0.65
23 7 0.30
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (23 bp):
TCTCTCATATTTCCTCTCAAAAT
Found at i:41171344 original size:51 final size:51
Alignment explanation
Indices: 41171279--41171402 Score: 187
Period size: 51 Copynumber: 2.4 Consensus size: 51
41171269 ATATTTCCTC
* * *
41171279 TCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTC-TCAAACCCATATTTAATT
*
41171330 TCAATTTCCTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
*
41171381 TCAATTTGCTCTCAATTTCCTT
1 TCAATTTCCTCTCAATTTCCTT
41171403 TTTTAAAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.30, C:0.26, G:0.01, T:0.44
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAATT
Found at i:41192003 original size:82 final size:83
Alignment explanation
Indices: 41191844--41192006 Score: 222
Period size: 82 Copynumber: 2.0 Consensus size: 83
41191834 TGGACTTTGG
* *
41191844 TTTGTAGATTCATGACATTCAAGTTGTTTTATAAAAAAAATAAATTGCAAAAGAGAAGGGAAATG
1 TTTGTAGATTCATGACATTAAAGTTATTTTAT--AAAAAATAAATTGCAAAAGAGAAGGGAAATG
*
41191909 AGTGCTTGCGGTTGGTGCGT
64 AGAGCTTGCGGTTGGTGCGT
* *
41191929 TTTGTAGATTCATGACGTTTAAAGTTATTTTAT-AAAAAT-AATTGCAAAAGAGAAGGGAAATTA
1 TTTGTAGATTCATGAC-ATTAAAGTTATTTTATAAAAAATAAATTGCAAAAGAGAAGGGAAATGA
* *
41191992 GAGTTTTCGGTTGGT
65 GAGCTTGCGGTTGGT
41192007 ACATGTGATG
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
82 35 0.50
83 6 0.09
85 16 0.23
86 13 0.19
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (83 bp):
TTTGTAGATTCATGACATTAAAGTTATTTTATAAAAAATAAATTGCAAAAGAGAAGGGAAATGAG
AGCTTGCGGTTGGTGCGT
Found at i:41193336 original size:14 final size:14
Alignment explanation
Indices: 41193317--41193344 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41193307 CGGAGATAGG
41193317 ATAATGAAGTCTAA
1 ATAATGAAGTCTAA
41193331 ATAATGAAGTCTAA
1 ATAATGAAGTCTAA
41193345 TATTTAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
ATAATGAAGTCTAA
Found at i:41196714 original size:20 final size:20
Alignment explanation
Indices: 41196689--41196730 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41196679 TTTCTTACAT
41196689 TTTCTTCAT-ATTTTCAATAA
1 TTTCTTC-TCATTTTCAATAA
*
41196709 TTTCTTCTCATTTTCCATAA
1 TTTCTTCTCATTTTCAATAA
41196729 TT
1 TT
41196731 GATATTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.24, C:0.19, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTCTTCTCATTTTCAATAA
Found at i:41209649 original size:23 final size:24
Alignment explanation
Indices: 41209613--41209673 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
41209603 CCATACTATT
41209613 TTTTACTTTTTTTTAA-ATATT-TA
1 TTTTA-TTTTTTTTAATATATTATA
*
41209636 TTTTATTTTATTTTAATATTTTATA
1 TTTTATTTT-TTTTAATATATTATA
*
41209661 TTTTATATTTTTT
1 TTTTATTTTTTTT
41209674 GAAAGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 4 0.12
23 11 0.33
24 8 0.24
25 10 0.30
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTATTTTTTTTAATATATTATA
Found at i:41209653 original size:22 final size:23
Alignment explanation
Indices: 41209613--41209656 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
41209603 CCATACTATT
41209613 TTTTACTTTTTTTTAAATATTTA
1 TTTTACTTTTTTTTAAATATTTA
41209636 TTTTA-TTTTATTTT-AATATTT
1 TTTTACTTTT-TTTTAAATATTT
41209657 TATATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTACTTTTTTTTAAATATTTA
Found at i:41209663 original size:7 final size:7
Alignment explanation
Indices: 41209639--41209671 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
41209629 ATATTTATTT
41209639 TATTTTA
1 TATTTTA
*
41209646 T-TTTAA
1 TATTTTA
41209652 TATTTTA
1 TATTTTA
41209659 TATTTTA
1 TATTTTA
41209666 TATTTT
1 TATTTT
41209672 TTGAAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TATTTTA
Found at i:41211322 original size:9 final size:9
Alignment explanation
Indices: 41211310--41211416 Score: 63
Period size: 10 Copynumber: 11.0 Consensus size: 9
41211300 TTTTATGATT
41211310 TTTTTATAA
1 TTTTTATAA
41211319 TTTTTAT-A
1 TTTTTATAA
*
41211327 TGTTTATATTGA
1 T-TTT-TA-TAA
41211339 TTTTTAATAA
1 TTTTT-ATAA
* *
41211349 TTTTAAATAT
1 TTTT-TATAA
*
41211359 TTTTTTTATA
1 TTTTTATA-A
*
41211369 TTTTTATGA
1 TTTTTATAA
41211378 TTTTTATAA
1 TTTTTATAA
*
41211387 GTTTTTAAGAA
1 -TTTTT-ATAA
41211398 TTTTTATACA
1 TTTTTATA-A
*
41211408 TTATTATAA
1 TTTTTATAA
41211417 AATTTATATT
Statistics
Matches: 76, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
8 2 0.03
9 24 0.32
10 40 0.53
11 8 0.11
12 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:41211343 original size:21 final size:20
Alignment explanation
Indices: 41211319--41211382 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
41211309 TTTTTTATAA
41211319 TTTTTATATGTTTATATTGAT
1 TTTTTATAT-TTTATATTGAT
*
41211340 TTTTAATAATTTTAAATATT--T
1 TTTTTAT-ATTTT--ATATTGAT
41211361 TTTTTATATTTT-TA-TGAT
1 TTTTTATATTTTATATTGAT
41211379 TTTT
1 TTTT
41211383 ATAAGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
16 1 0.03
17 2 0.06
18 5 0.14
20 5 0.14
21 16 0.44
22 2 0.06
23 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTATATTTTATATTGAT
Found at i:41211392 original size:20 final size:19
Alignment explanation
Indices: 41211299--41211405 Score: 65
Period size: 20 Copynumber: 5.4 Consensus size: 19
41211289 TCAATTCAAG
* *
41211299 TTTTTATGATTTTTTTATAA
1 TTTTTAT-AATTTTTTATGA
*
41211319 TTTTTAT-ATGTTTATATTGA
1 TTTTTATAAT-TTTTTA-TGA
**
41211339 TTTTTAATAATTTTAAAT-A
1 TTTTT-ATAATTTTTTATGA
* *
41211358 TTTTTTTTATATTTTTATGA
1 TTTTTATAAT-TTTTTATGA
* *
41211378 TTTTTATAAGTTTTTAAGAA
1 TTTTTATAATTTTTTATG-A
41211398 TTTTTATA
1 TTTTTATA
41211406 CATTATTATA
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.06
19 23 0.34
20 32 0.47
21 7 0.10
22 2 0.03
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTATAATTTTTTATGA
Found at i:41212079 original size:19 final size:19
Alignment explanation
Indices: 41212055--41212109 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
41212045 ATTTTTACAC
*
41212055 TAAAAATCATAAAAAATTA
1 TAAAAAACATAAAAAATTA
** *
41212074 TAAAAAACATTGAAACTTA
1 TAAAAAACATAAAAAATTA
*
41212093 TAAAAAAACAGAAAAAA
1 T-AAAAAACATAAAAAA
41212110 AAAATATAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (19 bp):
TAAAAAACATAAAAAATTA
Found at i:41212210 original size:30 final size:30
Alignment explanation
Indices: 41212124--41212210 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
41212114 TATAAACAAA
*
41212124 CTAATAAATAT-TAAAATTATAAAAAATAAT
1 CTAATAAATTTATAAAATTAT-AAAAATAAT
* * *
41212154 CTCATATATATTATAAAAATATAAAAAT-AT
1 CTAATAAAT-TTATAAAATTATAAAAATAAT
41212184 CTAATAAATTTATAAAATTAATAAAAA
1 CTAATAAATTTATAAAATT-ATAAAAA
41212211 CACATTTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 9 0.19
30 23 0.49
31 7 0.15
32 8 0.17
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (30 bp):
CTAATAAATTTATAAAATTATAAAAATAAT
Found at i:41212316 original size:18 final size:17
Alignment explanation
Indices: 41212278--41212312 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41212268 ATTAGAAATC
* *
41212278 ATTAAAAACTATTGAAA
1 ATTAAAAAATATTAAAA
41212295 ATTAAAAAATATTAAAA
1 ATTAAAAAATATTAAAA
41212312 A
1 A
41212313 ATTATTGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
ATTAAAAAATATTAAAA
Found at i:41212348 original size:9 final size:9
Alignment explanation
Indices: 41212334--41212543 Score: 79
Period size: 10 Copynumber: 21.9 Consensus size: 9
41212324 CGATACAAAT
41212334 TTATAAAAA
1 TTATAAAAA
41212343 TTATAAAAAAA
1 TTAT--AAAAA
*
41212354 TCATAAAAA
1 TTATAAAAA
**
41212363 CTTATAAGTA
1 -TTATAAAAA
*
41212373 TTGTAAAAA
1 TTATAAAAA
41212382 GTTATAAAAA
1 -TTATAAAAA
*
41212392 TCTA-ATAAA
1 T-TATAAAAA
*
41212401 TTATTAAAA
1 TTATAAAAA
*
41212410 TTAT-ACAA
1 TTATAAAAA
41212418 TTA-AAAATA
1 TTATAAAA-A
* *
41212427 TATTTAAAAT
1 T-TATAAAAA
41212437 TGTATAAAAA
1 T-TATAAAAA
*
41212447 CTTATAAAAT
1 -TTATAAAAA
41212457 TTCATAAAAACA
1 TT-AT-AAAA-A
*
41212469 TTA-AATAA
1 TTATAAAAA
41212477 -TATAATAAA
1 TTATAA-AAA
*
41212486 TTCTAAAACA
1 TTATAAAA-A
*
41212496 TTATAAGATA
1 TTATAA-AAA
**
41212506 TTATCCAAA
1 TTATAAAAA
41212515 TTACTAAAAA
1 TTA-TAAAAA
41212525 GTTTATAAAAA
1 --TTATAAAAA
*
41212536 TCATAAAA
1 TTATAAAA
41212544 GCATTAAAAA
Statistics
Matches: 148, Mismatches: 31, Indels: 44
0.66 0.14 0.20
Matches are distributed among these distances:
7 2 0.01
8 13 0.09
9 51 0.34
10 52 0.35
11 25 0.17
12 5 0.03
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:41213189 original size:18 final size:18
Alignment explanation
Indices: 41213163--41213210 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
41213153 CCATTTCGAT
41213163 TAAATAAAACATT-AAAAAG
1 TAAA-AAAA-ATTAAAAAAG
*
41213182 TAAAAAAATTTAAAAAAG
1 TAAAAAAAATTAAAAAAG
*
41213200 TAAAAACAATT
1 TAAAAAAAATT
41213211 CAAACGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 19 0.76
19 4 0.16
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (18 bp):
TAAAAAAAATTAAAAAAG
Found at i:41213418 original size:22 final size:21
Alignment explanation
Indices: 41213393--41213446 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
41213383 TTTTAATTTA
41213393 TTTTAATGAACTTTTTATAAGTTT
1 TTTTAA-GAA-TTTTTATAAG-TT
*
41213417 TTTTAAGAATTTTTATACGTT
1 TTTTAAGAATTTTTATAAGTT
41213438 TTTATAAGA
1 TTT-TAAGA
41213447 TTTCAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 14 0.50
23 3 0.11
24 6 0.21
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTTAAGAATTTTTATAAGTT
Found at i:41213491 original size:49 final size:47
Alignment explanation
Indices: 41213438--41213536 Score: 105
Period size: 47 Copynumber: 2.1 Consensus size: 47
41213428 TTTATACGTT
*
41213438 TTTATAAGATTTCAAATATG-TTTTGT-TAATA-TTATTATTTTTTTTATAA
1 TTTATAAGAATT--AATATGATTTT-TATAATATTTATTA--TTTTTTATAA
* *
41213487 TTTATTAGAATTAATTTGATTTTTATAATATTTATTATTTTTTATAA
1 TTTATAAGAATTAATATGATTTTTATAATATTTATTATTTTTTATAA
41213534 TTT
1 TTT
41213537 TTATAACTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
47 19 0.43
48 9 0.20
49 16 0.36
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (47 bp):
TTTATAAGAATTAATATGATTTTTATAATATTTATTATTTTTTATAA
Found at i:41213530 original size:19 final size:18
Alignment explanation
Indices: 41213506--41213577 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 18
41213496 ATTAATTTGA
41213506 TTTTTATAATATTTATTAT
1 TTTTTATAAT-TTTATTAT
* *
41213525 TTTTTATAATTTTTATAAC
1 TTTTTATAA-TTTTATTAT
* *
41213544 TTTCTATCAATTTAATTATT
1 TTTTTAT-AATTTTATTA-T
*
41213564 TTTTTATATTTTTA
1 TTTTTATAATTTTA
41213578 ATAATTTCTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 32 0.78
20 9 0.22
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTATAATTTTATTAT
Found at i:41213537 original size:9 final size:9
Alignment explanation
Indices: 41213478--41213584 Score: 58
Period size: 10 Copynumber: 11.3 Consensus size: 9
41213468 ATTATTATTT
41213478 TTTTTATAA
1 TTTTTATAA
*
41213487 TTTATTAGAA
1 TTT-TTATAA
* *
41213497 TTAATT-TGA
1 TT-TTTATAA
41213506 TTTTTATAA
1 TTTTTATAA
* *
41213515 TATTTATTAT
1 TTTTTA-TAA
41213525 TTTTTATAA
1 TTTTTATAA
41213534 TTTTTATAA
1 TTTTTATAA
*
41213543 CTTTCTATCAA
1 -TTTTTAT-AA
*
41213554 TTTAATTAT-T
1 TTT--TTATAA
41213564 TTTTTAT-A
1 TTTTTATAA
41213572 TTTTTAATAA
1 TTTTT-ATAA
41213582 TTT
1 TTT
41213585 CTTTTATTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
8 11 0.15
9 26 0.35
10 32 0.43
11 2 0.03
12 3 0.04
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:41213594 original size:19 final size:20
Alignment explanation
Indices: 41213554--41213594 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41213544 TTTCTATCAA
* *
41213554 TTTAATTATTTTTTTATATT
1 TTTAATAATTTCTTTATATT
41213574 TTTAATAATTTCTTT-TATT
1 TTTAATAATTTCTTTATATT
41213593 TT
1 TT
41213595 ATGAGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTAATAATTTCTTTATATT
Found at i:41214640 original size:10 final size:9
Alignment explanation
Indices: 41214625--41214711 Score: 51
Period size: 9 Copynumber: 9.6 Consensus size: 9
41214615 TATTTTCTCA
41214625 TAAAAACTAT
1 TAAAAA-TAT
41214635 TAAAAATCAT
1 TAAAAAT-AT
*
41214645 AAAAAATTAT
1 TAAAAA-TAT
41214655 TAAAAATCAT
1 TAAAAAT-AT
41214665 T--AAAT-T
1 TAAAAATAT
41214671 TATAAAAT-T
1 TA-AAAATAT
41214680 TATAAAATTAT
1 TA-AAAA-TAT
*
41214691 T--AAATAA
1 TAAAAATAT
41214698 TAAAAATAT
1 TAAAAATAT
41214707 TAAAA
1 TAAAA
41214712 CTGATAGAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
8 7 0.11
9 24 0.38
10 24 0.38
11 3 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATAT
Found at i:41214646 original size:19 final size:20
Alignment explanation
Indices: 41214622--41214664 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41214612 TAATATTTTC
41214622 TCAT-AAAAACTATTAAAAA
1 TCATAAAAAACTATTAAAAA
*
41214641 TCATAAAAAATTATTAAAAA
1 TCATAAAAAACTATTAAAAA
41214661 TCAT
1 TCAT
41214665 TAAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (20 bp):
TCATAAAAAACTATTAAAAA
Found at i:41218736 original size:17 final size:17
Alignment explanation
Indices: 41218714--41218747 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41218704 TCGGCTACCT
41218714 CTACTTTCCCATCCCAA
1 CTACTTTCCCATCCCAA
41218731 CTACTTTCCCATCCCAA
1 CTACTTTCCCATCCCAA
41218748 ATGTATTATT
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:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (17 bp):
CTACTTTCCCATCCCAA
Found at i:41223552 original size:31 final size:31
Alignment explanation
Indices: 41223425--41223552 Score: 77
Period size: 31 Copynumber: 4.2 Consensus size: 31
41223415 ATATGATATT
* * *
41223425 TAAATAA-TTAATATTATGATACATTAAATA
1 TAAATAATTTAATATAATGATATATAAAATA
* * * *
41223455 TAAATTATTT-GTAAAAT-TTATA-AAAATA
1 TAAATAATTTAATATAATGATATATAAAATA
* * * * * *
41223483 TTTTAATAATCTAATATAATAATAAATTATAT-
1 --TAAATAATTTAATATAATGATATATAAAATA
41223515 TCAAATAATTTAATATAATGATATATAAAATA
1 T-AAATAATTTAATATAATGATATATAAAATA
41223547 TAAATA
1 TAAATA
41223553 GCTAACATAA
Statistics
Matches: 68, Mismatches: 22, Indels: 15
0.65 0.21 0.14
Matches are distributed among these distances:
28 5 0.07
29 3 0.04
30 18 0.26
31 35 0.51
32 4 0.06
33 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (31 bp):
TAAATAATTTAATATAATGATATATAAAATA
Found at i:41224046 original size:22 final size:22
Alignment explanation
Indices: 41224018--41224060 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41224008 ATGTTACAAT
41224018 TAAATGACT-TATAAACTTTCAC
1 TAAATGACTAT-TAAACTTTCAC
41224040 TAAATGACTATTAAACTTTCA
1 TAAATGACTATTAAACTTTCA
41224061 TTAGCTAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (22 bp):
TAAATGACTATTAAACTTTCAC
Found at i:41229579 original size:16 final size:16
Alignment explanation
Indices: 41229558--41229596 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
41229548 AATTATGGAG
*
41229558 ATATATGAAAGCATGT
1 ATATATAAAAGCATGT
*
41229574 ATATATAAAAGTATGT
1 ATATATAAAAGCATGT
41229590 ATATATA
1 ATATATA
41229597 TGTATACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGCATGT
Found at i:41229849 original size:13 final size:13
Alignment explanation
Indices: 41229831--41229856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41229821 ATCATAAAAC
41229831 ATAAAATACATAT
1 ATAAAATACATAT
41229844 ATAAAATACATAT
1 ATAAAATACATAT
41229857 TTTAAGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAATACATAT
Found at i:41229921 original size:3 final size:3
Alignment explanation
Indices: 41229913--41229975 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
41229903 ATATAAAAGC
* *
41229913 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41229961 AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT A
41229976 GTTAACTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:41230943 original size:25 final size:24
Alignment explanation
Indices: 41230908--41230955 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
41230898 CTTTTTTGTT
*
41230908 TTTGGGTTTGGGCTAGGTTTGGGTA
1 TTTGGGCTTGGG-TAGGTTTGGGTA
*
41230933 TTTGGGCTTGGGTAGTTTTGGGT
1 TTTGGGCTTGGGTAGGTTTGGGT
41230956 CTGTTTGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.06, C:0.04, G:0.44, T:0.46
Consensus pattern (24 bp):
TTTGGGCTTGGGTAGGTTTGGGTA
Found at i:41235105 original size:3 final size:3
Alignment explanation
Indices: 41235097--41235189 Score: 93
Period size: 3 Copynumber: 31.3 Consensus size: 3
41235087 TTCTGTAATT
* * * *
41235097 TTA TTA TTA TTA TTA TTA TT- TTG TTA TTA TTA TTT TTA TCA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
41235144 TTA TTA TT- TATA TTA TTG TTA CTTA TCA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
41235189 T
1 T
41235190 ATAATAGCTT
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
2 4 0.05
3 66 0.89
4 4 0.05
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41235125 original size:14 final size:14
Alignment explanation
Indices: 41235106--41235132 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41235096 TTTATTATTA
41235106 TTATTATTATTTTG
1 TTATTATTATTTTG
41235120 TTATTATTATTTT
1 TTATTATTATTTT
41235133 TATCATTTTT
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:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
TTATTATTATTTTG
Found at i:41235470 original size:16 final size:16
Alignment explanation
Indices: 41235449--41235487 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
41235439 NNNNNNNNNN
41235449 TATATAT-TAAAGTATG
1 TATATATATAAA-TATG
*
41235465 TATATATATATATATG
1 TATATATATAAATATG
41235481 TATATAT
1 TATATAT
41235488 GTATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (16 bp):
TATATATATAAATATG
Found at i:41235478 original size:8 final size:8
Alignment explanation
Indices: 41235461--41235493 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
41235451 TATATTAAAG
41235461 TATGTATA
1 TATGTATA
*
41235469 TATATATA
1 TATGTATA
41235477 TATGTATA
1 TATGTATA
41235485 TATGTATA
1 TATGTATA
41235493 T
1 T
41235494 TTTATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:41236179 original size:108 final size:107
Alignment explanation
Indices: 41235945--41236346 Score: 564
Period size: 108 Copynumber: 3.8 Consensus size: 107
41235935 TTCAAAAAGG
* * * ** *
41235945 AAAATATTTCAAATTAAGGCAATATTTAGCGTTTGGAAATTCGAGAAAACACGCCCTAAGGTGCT
1 AAAAT-TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACT
* * *
41236010 GGGTGTCGATTTTTCTCGTT-A--AATAG-CTAAATATCC--TTCA
64 GGGTTTCGA--TTTCTCGTTCACCAATTGACTTAATATCCTTTTCA
41236050 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
41236115 GTTTCGATTTCTCGTTCCACCAATTGACTTAATATCCTTTTCA
66 GTTTCGATTTCTCGTT-CACCAATTGACTTAATATCCTTTTCA
* *
41236158 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTATTGA
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
*
41236223 GTTTCGATTTCTCGTTCGACCAAATGACTTAATATCCTTTTCA
66 GTTTCGATTTCTCGTTC-ACCAATTGACTTAATATCCTTTTCA
* * *
41236266 AAAATTTTCTAAATAAGTCAATATTTTGCATTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
*
41236331 GTTTCGATTTCACGTT
66 GTTTCGATTTCTCGTT
41236347 TAGTCAAATT
Statistics
Matches: 271, Mismatches: 18, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
101 9 0.03
103 24 0.09
104 37 0.14
105 9 0.03
106 9 0.03
107 1 0.00
108 182 0.67
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (107 bp):
AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCACCAATTGACTTAATATCCTTTTCA
Found at i:41237783 original size:19 final size:19
Alignment explanation
Indices: 41237759--41237805 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
41237749 AACGTCTCTT
*
41237759 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
41237778 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
41237797 TATGCATTA
1 TTTGCATTA
41237806 GATTTTCACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:41240406 original size:9 final size:9
Alignment explanation
Indices: 41240392--41240462 Score: 87
Period size: 8 Copynumber: 8.3 Consensus size: 9
41240382 TTCAGACTCA
41240392 AAAAAAATC
1 AAAAAAATC
41240401 AAAAAAATC
1 AAAAAAATC
41240410 AAAAAAATC
1 AAAAAAATC
41240419 AAAAAAATC
1 AAAAAAATC
41240428 -AAAAAAT-
1 AAAAAAATC
*
41240435 TAAAAAAT-
1 AAAAAAATC
*
41240443 TAAAAAAT-
1 AAAAAAATC
*
41240451 TAAAAAATC
1 AAAAAAATC
41240460 AAA
1 AAA
41240463 GTCAAAATAG
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
8 30 0.51
9 29 0.49
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAAAATC
Found at i:41242453 original size:88 final size:88
Alignment explanation
Indices: 41242309--41242922 Score: 1054
Period size: 88 Copynumber: 7.0 Consensus size: 88
41242299 TGAAAACAAC
* * * * *
41242309 AGATCTTGCCTTTCTGCATTGACAGTGAAGCAGGTTGAAG-CACCAAACCTTGCCTCTCTCGGTT
1 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACA-CAAACCTTGCCTCTCTCGATT
* * *
41242373 GTGATGAAGCTGGTTGAAGACAAC
65 GTGATGGAGCTGGTTGAAGAAAAA
*
41242397 AGATCTTG-CCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATT
1 AGATCTTGCCCTT-CTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATT
41242461 GTGATGGAGCTGGTTGAAGAAAAA
65 GTGATGGAGCTGGTTGAAGAAAAA
41242485 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
*
41242550 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGAAAAA
* * * *
41242573 AGATCCTG-TCTTCCTGCATTGATAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATT
1 AGATCTTGCCCTT-CTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATT
41242637 GTGATGGAGCTGGTTGAAGAAAAA
65 GTGATGGAGCTGGTTGAAGAAAAA
41242661 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
41242726 TGATGGAGCTGGTTGAAGAAAAA
66 TGATGGAGCTGGTTGAAGAAAAA
41242749 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
41242814 TGATGGAGCTGGTTGAAGAAAAA
66 TGATGGAGCTGGTTGAAGAAAAA
41242837 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
1 AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
41242902 TGATGGAGCTGGTTGAAGAAA
66 TGATGGAGCTGGTTGAAGAAA
41242923 TCCATTTCAT
Statistics
Matches: 503, Mismatches: 18, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
87 6 0.01
88 488 0.97
89 9 0.02
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCCTTCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGATTG
TGATGGAGCTGGTTGAAGAAAAA
Found at i:41246470 original size:88 final size:88
Alignment explanation
Indices: 41246300--41246924 Score: 1097
Period size: 88 Copynumber: 7.1 Consensus size: 88
41246290 CTTGTCCCCT
* * * * * *
41246300 TCGGTTGTGATTGAGGTGGTTGAAAACAAAAAATCTTGCCTTCACTGCATTGACAGCGAAGCAGG
1 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTT-TCTGTATTGACAGCGAAGCAGG
41246365 TCGAAGACACAAACCTTGCCTCTC
65 TCGAAGACACAAACCTTGCCTCTC
41246389 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
1 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
41246454 CGAAGACACAAACCTTGCCTCTC
66 CGAAGACACAAACCTTGCCTCTC
* * *
41246477 TCGGTTGTGATGGAGCTGGTTGAAGAAAAAAGATTTTGCCTTCCTGTATTGACAGCGAAGCAGGT
1 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
41246542 CGAAGACACAAACCTTGCCTCTC
66 CGAAGACACAAACCTTGCCTCTC
*
41246565 TCGGTTGTGATGGAGCTGGTTGAAGAAAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
1 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
41246630 CGAAGACACAAACCTTGCCTCTC
66 CGAAGACACAAACCTTGCCTCTC
*
41246653 TCGGTTGTGATGGAGCTGGTTGAAGACAATAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
1 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
41246718 CGAAGACACAAACCTTGCCTCTC
66 CGAAGACACAAACCTTGCCTCTC
* *
41246741 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGTGAAGCAGGT
1 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
41246806 CGAAGACACAAACCTTGCCTCTC
66 CGAAGACACAAACCTTGCCTCTC
*
41246829 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGTGAAGCAGGT
1 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
*
41246894 CGAAGACACAAACCTTGCCTTTC
66 CGAAGACACAAACCTTGCCTCTC
*
41246917 TCGATTGT
1 TCGGTTGT
41246925 ATAATATACA
Statistics
Matches: 517, Mismatches: 19, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
88 479 0.93
89 38 0.07
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (88 bp):
TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGT
CGAAGACACAAACCTTGCCTCTC
Found at i:41257727 original size:3 final size:3
Alignment explanation
Indices: 41257719--41257757 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
41257709 CCTACTGCTG
41257719 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41257758 TTCCTAGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41262949 original size:18 final size:18
Alignment explanation
Indices: 41262926--41262970 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
41262916 AATAATAACT
41262926 CTTGCCATTAATTTTGCC
1 CTTGCCATTAATTTTGCC
41262944 CTTGCCATTAATTTTGCC
1 CTTGCCATTAATTTTGCC
*
41262962 ATTGCCATT
1 CTTGCCATT
41262971 GAACCCTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.44
Consensus pattern (18 bp):
CTTGCCATTAATTTTGCC
Found at i:41269386 original size:2 final size:2
Alignment explanation
Indices: 41269374--41269402 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41269364 ATTGGTGAAA
41269374 AT AT A- 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 AT
41269403 CTTTGGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41269695 original size:17 final size:17
Alignment explanation
Indices: 41269669--41269701 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41269659 AATTTTAAAT
*
41269669 TCATTTTATTATATTAA
1 TCATTATATTATATTAA
41269686 TCATTATATTATATTA
1 TCATTATATTATATTA
41269702 GTATCGTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TCATTATATTATATTAA
Found at i:41272759 original size:17 final size:17
Alignment explanation
Indices: 41272723--41272762 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41272713 AATTTTACTA
*
41272723 ACAAAATGTTAGATTTT
1 ACAAAATGTTAGATTGT
41272740 ACAAAATGTT-GATTGGT
1 ACAAAATGTTAGATT-GT
41272757 ACAAAA
1 ACAAAA
41272763 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
ACAAAATGTTAGATTGT
Found at i:41272799 original size:16 final size:16
Alignment explanation
Indices: 41272780--41272836 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
41272770 AATTTGATAC
*
41272780 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
41272796 AATTTTGATAACAATT
1 AATTTTAATAACAATT
41272812 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
41272828 AGTTTTAAT
1 AATTTTAAT
41272837 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:41272862 original size:23 final size:23
Alignment explanation
Indices: 41272810--41272873 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
41272800 TTGATAACAA
* * * *
41272810 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATC
41272832 TTAATTTTAATAAAAAAATAATC
1 TTAATTTTAATAAAAAAATAATC
41272855 TTAATTTTAATTAAAAAAA
1 TTAATTTTAA-TAAAAAAA
41272874 CGGGCCGGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.31
23 17 0.47
24 8 0.22
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATC
Found at i:41274588 original size:18 final size:18
Alignment explanation
Indices: 41274565--41274599 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41274555 GTTCAAGGTG
*
41274565 TAATTAATTGAAAACTTT
1 TAATTAATTAAAAACTTT
41274583 TAATTAATTAAAAACTT
1 TAATTAATTAAAAACTT
41274600 ATTTTCATCC
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:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATTAATTAAAAACTTT
Found at i:41274989 original size:96 final size:96
Alignment explanation
Indices: 41274825--41275101 Score: 529
Period size: 96 Copynumber: 2.9 Consensus size: 96
41274815 AAAATCATTG
*
41274825 TGGTTGAAAGTGTGAAAA-TAAGGAAGTGTTCAAAATCTTGTGCTCAATTTAAACATTTAATTTT
1 TGGTTGAAAGTGT-AAAAGTGAGGAAGTGTTCAAAATCTTGTGCTCAATTTAAACATTTAATTTT
41274889 AAGCATTATTTTTCAAAACCATTAATGTGGAT
65 AAGCATTATTTTTCAAAACCATTAATGTGGAT
41274921 TGGTTGAAAGTGTAAAAGTGAGGAAGTGTTCAAAATCTTGTGCTCAATTTAAACATTTAATTTTA
1 TGGTTGAAAGTGTAAAAGTGAGGAAGTGTTCAAAATCTTGTGCTCAATTTAAACATTTAATTTTA
41274986 AGCATTATTTTTCAAAACCATTAATGTGGAT
66 AGCATTATTTTTCAAAACCATTAATGTGGAT
41275017 TGGTTGAAAGTGTAAAAGTGAGGAAGTGTTCAAAATCTTGTGCTCAATTTAAACATTTAATTTTA
1 TGGTTGAAAGTGTAAAAGTGAGGAAGTGTTCAAAATCTTGTGCTCAATTTAAACATTTAATTTTA
41275082 AGCATTATTTTTCAAAACCA
66 AGCATTATTTTTCAAAACCA
41275102 CTCTCCTTGA
Statistics
Matches: 179, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
95 4 0.02
96 175 0.98
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (96 bp):
TGGTTGAAAGTGTAAAAGTGAGGAAGTGTTCAAAATCTTGTGCTCAATTTAAACATTTAATTTTA
AGCATTATTTTTCAAAACCATTAATGTGGAT
Found at i:41278714 original size:18 final size:18
Alignment explanation
Indices: 41278687--41278723 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41278677 GATTCTAAAT
*
41278687 TTAATTGATTTAATTCGG
1 TTAATCGATTTAATTCGG
*
41278705 TTAATCGATTTAGTTCGG
1 TTAATCGATTTAATTCGG
41278723 T
1 T
41278724 CAGAAGTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.49
Consensus pattern (18 bp):
TTAATCGATTTAATTCGG
Found at i:41281455 original size:44 final size:44
Alignment explanation
Indices: 41281405--41281492 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
41281395 AAATTTAATT
41281405 TTTTATCGAATTTTTCGAATTGAATCGAATTTTACTCATCTCTA
1 TTTTATCGAATTTTTCGAATTGAATCGAATTTTACTCATCTCTA
*
41281449 TTTTATCGAATTTTTCGCATTGAATCGAATTTTACTCATCTCTA
1 TTTTATCGAATTTTTCGAATTGAATCGAATTTTACTCATCTCTA
41281493 ATAAGGAGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (44 bp):
TTTTATCGAATTTTTCGAATTGAATCGAATTTTACTCATCTCTA
Found at i:41288070 original size:12 final size:12
Alignment explanation
Indices: 41288055--41288096 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
41288045 TCAAGTCTTG
41288055 AATCAATTCATA
1 AATCAATTCATA
* * *
41288067 AATCAAGTCTTG
1 AATCAATTCATA
41288079 AATCAATTCATA
1 AATCAATTCATA
41288091 AATCAA
1 AATCAA
41288097 GCTCTCATCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.31
Consensus pattern (12 bp):
AATCAATTCATA
Found at i:41288076 original size:24 final size:24
Alignment explanation
Indices: 41288044--41288097 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
41288034 CATTTTAACC
41288044 ATCAAGTCTTGAATCAATTCATAA
1 ATCAAGTCTTGAATCAATTCATAA
41288068 ATCAAGTCTTGAATCAATTCATAA
1 ATCAAGTCTTGAATCAATTCATAA
41288092 ATCAAG
1 ATCAAG
41288098 CTCTCATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (24 bp):
ATCAAGTCTTGAATCAATTCATAA
Found at i:41318923 original size:15 final size:16
Alignment explanation
Indices: 41318898--41318929 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41318888 AATTTATTTT
41318898 TATATAAAAATATTAA
1 TATATAAAAATATTAA
41318914 TATA-AAAAATATTAA
1 TATATAAAAATATTAA
41318929 T
1 T
41318930 GTGGATTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATAAAAATATTAA
Found at i:41322746 original size:88 final size:88
Alignment explanation
Indices: 41322597--41322773 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
41322587 GGTCTTTCTG
41322597 TTAAAAATTGATTCCTGTAAATCAATATGAGTTACTCATGACACGCCACATTTCACTGTCTAGTT
1 TTAAAAATTGATTCCTGTAAATCAATATGAGTTACTCATGACACGCCACATTTCACTGTCTAGTT
41322662 ATTCCATCAACCTTGTCAAATTT
66 ATTCCATCAACCTTGTCAAATTT
41322685 TTAAAAATTGATTCCTGTAAATCAATATGAGTTACTCATGACACGCCACATTTCACTGTCTAGTT
1 TTAAAAATTGATTCCTGTAAATCAATATGAGTTACTCATGACACGCCACATTTCACTGTCTAGTT
41322750 ATTCCATCAACCTTGTCAAATTT
66 ATTCCATCAACCTTGTCAAATTT
41322773 T
1 T
41322774 AACAATACAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (88 bp):
TTAAAAATTGATTCCTGTAAATCAATATGAGTTACTCATGACACGCCACATTTCACTGTCTAGTT
ATTCCATCAACCTTGTCAAATTT
Found at i:41325543 original size:17 final size:17
Alignment explanation
Indices: 41325496--41325543 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
41325486 AGTAAAATAC
41325496 AATTT-TATCATTTTAAT
1 AATTTCTATCATTTT-AT
41325513 AA--TCTAT-ATCTTTAT
1 AATTTCTATCAT-TTTAT
41325528 AATTTCTATCATTTTA
1 AATTTCTATCATTTTA
41325544 GGGGGGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
15 7 0.27
16 6 0.23
17 11 0.42
18 2 0.08
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTCTATCATTTTAT
Found at i:41326066 original size:10 final size:9
Alignment explanation
Indices: 41326042--41326090 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
41326032 TATCAAGTGC
41326042 AAAATTTATT
1 AAAATTT-TT
*
41326052 TAAATCTTTT
1 AAAAT-TTTT
41326062 AAAATTTTT
1 AAAATTTTT
41326071 AAAATTTTT
1 AAAATTTTT
41326080 --AATTTTT
1 AAAATTTTT
41326087 AAAA
1 AAAA
41326091 ATAAAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.21
9 15 0.44
10 10 0.29
11 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
AAAATTTTT
Found at i:41327144 original size:16 final size:15
Alignment explanation
Indices: 41327126--41327185 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
41327116 AGAATATATA
41327126 TATATAAATTATAAG
1 TATATAAATTATAAG
*
41327141 -ATATAAAAATATAAG
1 TATAT-AAATTATAAG
* * *
41327156 TATTTACATGTATATG
1 TATATAAAT-TATAAG
*
41327172 TATATAGATTATAA
1 TATATAAATTATAA
41327186 AATACAAGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
14 4 0.12
15 15 0.44
16 15 0.44
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (15 bp):
TATATAAATTATAAG
Found at i:41327152 original size:30 final size:31
Alignment explanation
Indices: 41327088--41327153 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 31
41327078 TATATGTATG
41327088 TATATACATAAAATTATGTAAATATGAAAGAA
1 TATATACATAAAATTA-GTAAATATGAAAGAA
*
41327120 TATATATATATAAATTA-TAAGATAT-AAA-AA
1 TATATACATA-AAATTAGTAA-ATATGAAAGAA
41327150 TATA
1 TATA
41327154 AGTATTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 6 0.19
31 6 0.19
32 13 0.42
33 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (31 bp):
TATATACATAAAATTAGTAAATATGAAAGAA
Found at i:41327202 original size:16 final size:16
Alignment explanation
Indices: 41327177--41327217 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
41327167 ATATGTATAT
41327177 AGAT-TATAAAATACA
1 AGATATATAAAATACA
*
41327192 AGATATATAAAATATA
1 AGATATATAAAATACA
41327208 AGAGTATATA
1 AGA-TATATA
41327218 CATATATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.17
16 13 0.57
17 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (16 bp):
AGATATATAAAATACA
Found at i:41327624 original size:3 final size:3
Alignment explanation
Indices: 41327610--41327653 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
41327600 ACAATAACAT
*
41327610 TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA CTAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -T-AA TAA TAA
41327654 AGGAAACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 33 0.89
4 2 0.05
5 2 0.05
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:41328441 original size:19 final size:19
Alignment explanation
Indices: 41328419--41328456 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41328409 TAAATACTAA
*
41328419 AGAAACTGAAAAATAAAAG
1 AGAAACAGAAAAATAAAAG
*
41328438 AGAAACAGAGAAATAAAAG
1 AGAAACAGAAAAATAAAAG
41328457 TTGAAATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.18, T:0.08
Consensus pattern (19 bp):
AGAAACAGAAAAATAAAAG
Found at i:41332144 original size:20 final size:20
Alignment explanation
Indices: 41332119--41332158 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41332109 AAAAAATCTG
41332119 TACAAATAATTGAATCAAGA
1 TACAAATAATTGAATCAAGA
41332139 TACAAATAATTGAATCAAGA
1 TACAAATAATTGAATCAAGA
41332159 ACTACAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (20 bp):
TACAAATAATTGAATCAAGA
Found at i:41332781 original size:2 final size:2
Alignment explanation
Indices: 41332774--41332809 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41332764 ATTGGAGTAC
41332774 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41332810 AAATTCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41340894 original size:307 final size:305
Alignment explanation
Indices: 41340272--41340902 Score: 1102
Period size: 307 Copynumber: 2.1 Consensus size: 305
41340262 TTATTATCAC
* * *
41340272 TATTTTCCGCTCAATTTGGACAAATATCATACCGGGTTCCATGAAACTTTTTCTTTCTCAATGAA
1 TATTTTCCACTCAATTTGGACAAATATCACACCAGGTTCCATGAAACTTTTTCTTTCTCAATGAA
* *
41340337 AGATCACAAACTTCAAACAACGTTCTCATAAAAATAAATAAACAAACAAAATTAAATCGCTAGCA
66 AGATCACAAACTTCAAACAACGTTCTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCA
41340402 ACCAGATAGCACAATCCTCGATTACTAACCAAACCGTGATGAAATTCAATAAGATCTTGATCACA
131 ACCAGATAGCACAATCCTCGATTACTAACCAAACCGTGATGAAATTCAATAAGATCTTGATCACA
* **
41340467 AAAAAAACCATCAAAATAAAAATGAAAATTTCAATGAAAATGAAGCTTGAATATACCTGAAATCG
196 AAAAAAACCATCAAAATAAAAATGAAAATTTAAATGAAAATGAAGCTCCAATATACCTGAAATCG
*
41340532 GCATCCGAAGATTGCCGAGTTACGGTAGAAAACAACATATGCTCA
261 GCATCCGAAGACTGCCGAGTTACGGTAGAAAACAACATATGCTCA
41340577 TATTTTCCACTCAATTTGGACAAATATCACACCAGGTTCCATGAAACTTTTT-TTTCTCAATGAA
1 TATTTTCCACTCAATTTGGACAAATATCACACCAGGTTCCATGAAACTTTTTCTTTCTCAATGAA
41340641 AGATCACAAACTTCAAACAACGTTCTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCA
66 AGATCACAAACTTCAAACAACGTTCTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCA
41340706 ACCAGATAGCACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATCAC
131 ACCAGATAGCACAATCCTCGATTACT-AACCAAACCGTGATGAAATTCAATAAGATCTTGATCAC
* * *
41340771 AAAAAAAAAATCATCAAAATAAAAATGAAATTTTAAATGAAAATGGAGCTCCAATATACCTGAAA
195 --AAAAAAAACCATCAAAATAAAAATGAAAATTTAAATGAAAATGAAGCTCCAATATACCTGAAA
*
41340836 TCGGCATCCGAAGACTGCCGAGTTACGTTAGAAAACAACATATGCTCA
258 TCGGCATCCGAAGACTGCCGAGTTACGGTAGAAAACAACATATGCTCA
41340884 TATTTTCCACTCAAATTTG
1 TATTTTCCACTC-AATTTG
41340903 TTTTCAAAAG
Statistics
Matches: 309, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
304 101 0.33
305 87 0.28
307 115 0.37
308 6 0.02
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (305 bp):
TATTTTCCACTCAATTTGGACAAATATCACACCAGGTTCCATGAAACTTTTTCTTTCTCAATGAA
AGATCACAAACTTCAAACAACGTTCTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCA
ACCAGATAGCACAATCCTCGATTACTAACCAAACCGTGATGAAATTCAATAAGATCTTGATCACA
AAAAAAACCATCAAAATAAAAATGAAAATTTAAATGAAAATGAAGCTCCAATATACCTGAAATCG
GCATCCGAAGACTGCCGAGTTACGGTAGAAAACAACATATGCTCA
Found at i:41343044 original size:13 final size:13
Alignment explanation
Indices: 41343026--41343051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41343016 ATAATTTCAA
41343026 AATAAAATAAAAT
1 AATAAAATAAAAT
41343039 AATAAAATAAAAT
1 AATAAAATAAAAT
41343052 TCGAGACGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAATAAAAT
Found at i:41343750 original size:6 final size:6
Alignment explanation
Indices: 41343741--41343775 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
41343731 TTAAAGTGCG
* *
41343741 AACCGT AACCGT AACCGT AACCGT GACCGT GACCG
1 AACCGT AACCGT AACCGT AACCGT AACCGT AACCG
41343776 CCACAGCCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (6 bp):
AACCGT
Found at i:41351112 original size:21 final size:21
Alignment explanation
Indices: 41351083--41351125 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41351073 GAAAAATCAA
*
41351083 ATTTTCAACTTTTTCCTCCTG
1 ATTTCCAACTTTTTCCTCCTG
41351104 ATTTCCAACTTTTTCCTCCTG
1 ATTTCCAACTTTTTCCTCCTG
41351125 A
1 A
41351126 AAATTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.30, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTCCAACTTTTTCCTCCTG
Found at i:41351131 original size:24 final size:23
Alignment explanation
Indices: 41351081--41351132 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
41351071 ACGAAAAATC
*
41351081 AAATTTTCAACTTTTTCCTCCTG
1 AAATTTCCAACTTTTTCCTCCTG
41351104 --ATTTCCAACTTTTTCCTCCTG
1 AAATTTCCAACTTTTTCCTCCTG
41351125 AAAATTTC
1 -AAATTTC
41351133 AAATCCAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 20 0.80
24 5 0.20
ACGTcount: A:0.23, C:0.27, G:0.04, T:0.46
Consensus pattern (23 bp):
AAATTTCCAACTTTTTCCTCCTG
Found at i:41356106 original size:13 final size:13
Alignment explanation
Indices: 41356090--41356115 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41356080 ATTGCAGTGT
41356090 CTGATTCTATTAA
1 CTGATTCTATTAA
41356103 CTGATTCTATTAA
1 CTGATTCTATTAA
41356116 TGGTTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
CTGATTCTATTAA
Found at i:41357974 original size:45 final size:45
Alignment explanation
Indices: 41357922--41358176 Score: 366
Period size: 45 Copynumber: 5.4 Consensus size: 45
41357912 CTTTAGGCAC
*
41357922 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACT
*
41357967 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACTTGT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCAC---T
*
41358015 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
1 ---TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACT
*
41358063 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACTTGT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCAC---T
41358111 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACT
1 ---TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACT
41358159 TGATCAGATAAGTGTAGC
1 TGATCAGATAAGTGTAGC
41358177 ACTTATCACT
Statistics
Matches: 191, Mismatches: 7, Indels: 24
0.86 0.03 0.11
Matches are distributed among these distances:
45 102 0.53
48 4 0.02
51 85 0.45
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (45 bp):
TGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCCACT
Done.