Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 276 of 279
Found at i:90184181 original size:344 final size:344
Alignment explanation
Indices: 90183554--90184242 Score: 1351
Period size: 344 Copynumber: 2.0 Consensus size: 344
90183544 ATTCCCAAAA
90183554 TCGTAGAATTTTCTTCTCATTCATATGCAATTCGATCGAGCTTTTGTTGAGCTATATAATTAGGC
1 TCGTAGAATTTTCTTCTCATTCATATGCAATTCGATCGAGCTTTTGTTGAGCTATATAATTAGGC
90183619 TCTATTGATTGCAATTATGTCTTCTGATAATTCTCAATTACTTAATCATGGAGTCAGTTCATAAT
66 TCTATTGATTGCAATTATGTCTTCTGATAATTCTCAATTACTTAATCATGGAGTCAGTTCATAAT
90183684 AAGTACCATCATTGTAATTATACTATTTACGAAAGTAATTTATCCATTGCTTTGTCCAATGACCT
131 AAGTACCATCATTGTAATTATACTATTTACGAAAGTAATTTATCCATTGCTTTGTCCAATGACCT
90183749 CGCCATGTATGTGTTACCCTCATATGATATCATTAATTCCTTTGAGTTAAATCTGTCCACTAAAT
196 CGCCATGTATGTGTTACCCTCATATGATATCATTAATTCCTTTGAGTTAAATCTGTCCACTAAAT
90183814 ACAATCCTATTTTATCTTATTGTCACCATTGTGTCTTCTTAATGATTATTATGATCACTGTCAAC
261 ACAATCCTATTTTATCTTATTGTCACCATTGTGTCTTCTTAATGATTATTATGATCACTGTCAAC
*
90183879 AAATGTAACAGCCCGATTT
326 AAATATAACAGCCCGATTT
90183898 TCGTAGAATTTTCTTCTCATTCATATGCAATTCGATCGAGCTTTTGTTGAGCTATATAATTAGGC
1 TCGTAGAATTTTCTTCTCATTCATATGCAATTCGATCGAGCTTTTGTTGAGCTATATAATTAGGC
90183963 TCTATTGATTGCAATTATGTCTTCTGATAATTCTCAATTACTTAATCATGGAGTCAGTTCATAAT
66 TCTATTGATTGCAATTATGTCTTCTGATAATTCTCAATTACTTAATCATGGAGTCAGTTCATAAT
90184028 AAGTACCATCATTGTAATTATACTATTTACGAAAGTAATTTATCCATTGCTTTGTCCAATGACCT
131 AAGTACCATCATTGTAATTATACTATTTACGAAAGTAATTTATCCATTGCTTTGTCCAATGACCT
* *
90184093 CGTCATGTGTGTGTTACCCTCATATGATATCATTAATTCCTTTGAGTTAAATCTGTCCACTAAAT
196 CGCCATGTATGTGTTACCCTCATATGATATCATTAATTCCTTTGAGTTAAATCTGTCCACTAAAT
90184158 ACAATCCTATTTTATCTTATTGTCACCATTGTGTCTTCTTAATGATTATTATGATCACTGTCAAC
261 ACAATCCTATTTTATCTTATTGTCACCATTGTGTCTTCTTAATGATTATTATGATCACTGTCAAC
90184223 AAATATAACAGCCCGATTT
326 AAATATAACAGCCCGATTT
90184242 T
1 T
90184243 GGGCCTAGTA
Statistics
Matches: 342, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
344 342 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (344 bp):
TCGTAGAATTTTCTTCTCATTCATATGCAATTCGATCGAGCTTTTGTTGAGCTATATAATTAGGC
TCTATTGATTGCAATTATGTCTTCTGATAATTCTCAATTACTTAATCATGGAGTCAGTTCATAAT
AAGTACCATCATTGTAATTATACTATTTACGAAAGTAATTTATCCATTGCTTTGTCCAATGACCT
CGCCATGTATGTGTTACCCTCATATGATATCATTAATTCCTTTGAGTTAAATCTGTCCACTAAAT
ACAATCCTATTTTATCTTATTGTCACCATTGTGTCTTCTTAATGATTATTATGATCACTGTCAAC
AAATATAACAGCCCGATTT
Found at i:90186689 original size:52 final size:52
Alignment explanation
Indices: 90186632--90186777 Score: 170
Period size: 52 Copynumber: 2.8 Consensus size: 52
90186622 GACGGAAAAG
* *
90186632 ATGTGATATGTGCTTCCGTATAAAACCATAGCTGGGCTATGGAATCGGTACA
1 ATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGAATCGGTACA
* * ***
90186684 ATGTGAT-TCGT-ATTCTCGTATAAGACCATAGCTAGGCTATGGCATCGGTGTG
1 ATGTGATAT-GTGATTC-CGTATAAGACCATAGCTGGGCTATGGAATCGGTACA
* *
90186736 ATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATG
1 ATGTGAT-ATGTGATTCCGTATAAGACCATAGCTGGGCTATG
90186778 ACATTGGTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
51 4 0.05
52 46 0.58
53 24 0.30
54 5 0.06
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (52 bp):
ATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGAATCGGTACA
Found at i:90194159 original size:53 final size:51
Alignment explanation
Indices: 90194010--90194164 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 51
90194000 TGACGAAAAA
*
90194010 GATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATTAGTGC
1 GATGTGATATGTG-TTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTGC
* * * *
90194062 AATGTGAT-TCGTGTTCCCGTATAAGACTATAGCTGGGCTATGGCATCGGTGT
1 GATGTGATAT-GTGTT-CCGTATAAGACCATAGCTGGGCTATGGCATCAGTGC
* *
90194114 GATGTGATAATGTGATTCCATATAAGACCATATG-TGGGATATGGCATCAGT
1 GATGTGAT-ATGTG-TTCCGTATAAGACCATA-GCTGGGCTATGGCATCAGT
90194165 ATGATATGTG
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
51 3 0.03
52 49 0.56
53 31 0.36
54 4 0.05
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (51 bp):
GATGTGATATGTGTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTGC
Found at i:90194979 original size:20 final size:20
Alignment explanation
Indices: 90194954--90194991 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
90194944 ACCCCATGGG
90194954 CAGGCCACACGGGCATGTCC
1 CAGGCCACACGGGCATGTCC
90194974 CAGGCCACACGGGCATGT
1 CAGGCCACACGGGCATGT
90194992 GCCCCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.37, G:0.32, T:0.11
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTCC
Found at i:90198580 original size:30 final size:30
Alignment explanation
Indices: 90198545--90198604 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
90198535 AATTTGAGTT
*
90198545 TAAAAATATTAAAGCAAAATTTCGAATTTA
1 TAAAAATATTAAAGAAAAATTTCGAATTTA
* *
90198575 TAAAAATATTAGAGAAAAATTTTGAATTTA
1 TAAAAATATTAAAGAAAAATTTCGAATTTA
90198605 AATGAAGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.35
Consensus pattern (30 bp):
TAAAAATATTAAAGAAAAATTTCGAATTTA
Found at i:90199612 original size:26 final size:27
Alignment explanation
Indices: 90199582--90199636 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
90199572 AATCACGTAA
*
90199582 TATTTTAATTGAA-AAATTAATGATAT
1 TATTTTAATTGAATAAATTAATAATAT
* *
90199608 TA-TTTATTTGAATTAATTAATAATAT
1 TATTTTAATTGAATAAATTAATAATAT
90199634 TAT
1 TAT
90199637 AAAAATATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (27 bp):
TATTTTAATTGAATAAATTAATAATAT
Found at i:90202200 original size:18 final size:18
Alignment explanation
Indices: 90202177--90202214 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
90202167 AGCATGAAAG
*
90202177 AGGCATAGTTCGAGTATA
1 AGGCATAGTTCGAGAATA
90202195 AGGCATAGTTCGAGAATA
1 AGGCATAGTTCGAGAATA
90202213 AG
1 AG
90202215 AAAAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (18 bp):
AGGCATAGTTCGAGAATA
Found at i:90202678 original size:47 final size:48
Alignment explanation
Indices: 90202609--90202732 Score: 162
Period size: 47 Copynumber: 2.6 Consensus size: 48
90202599 GGTATAATGC
* * *
90202609 CAATGCCATATCCCAGACATGGTCTTACACTGGCTCATC-CATC-AAGT
1 CAATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCAAATCGAAGT
*
90202656 CAATGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCGAGGT
1 CAATGCCATGTCCCAGACATGGTCTTACACTGACTATC-AAATCGAAGT
* *
90202705 CGACGCCATGTCCCAGACATGGTCTTAC
1 CAATGCCATGTCCCAGACATGGTCTTAC
90202733 TGTAACACCC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
46 3 0.04
47 33 0.49
48 3 0.04
49 29 0.43
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (48 bp):
CAATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAATCGAAGT
Found at i:90204311 original size:68 final size:65
Alignment explanation
Indices: 90204105--90204326 Score: 220
Period size: 68 Copynumber: 3.4 Consensus size: 65
90204095 CATAATTTTG
* *
90204105 GCTCTCTTGTACACATGGTGTACACATAGTATCACCCATGTAACCTAGC--CGCTTTA-TCTCGT
1 GCTCTCTTGTACACATGGTGTACACATAGTATCACCCATGCAACCTAGCTAC-CTCTATTCTCGT
90204167 A
65 A
** * * * * * * *
90204168 GCTCTCTTGTTTACATGGTGTCCTTCACCTGGAACCACACATGCAACCTAGCTACATCTA-TCTC
1 GCTCTCTTGTACACATGGTG---TACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTC
90204232 GTA
63 GTA
*
90204235 GCTCTCTTGT-CTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACCTCATAATGTCT
1 GCTCTCTTGTAC-ACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTC-T-AT-TCT
90204299 CGTA
62 CGTA
*
90204303 GCTCTCTTGTACACATGGTATACA
1 GCTCTCTTGTACACATGGTGTACA
90204327 TCCCATATTA
Statistics
Matches: 127, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
63 18 0.14
64 27 0.21
65 1 0.01
66 23 0.18
67 28 0.22
68 29 0.23
69 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (65 bp):
GCTCTCTTGTACACATGGTGTACACATAGTATCACCCATGCAACCTAGCTACCTCTATTCTCGTA
Found at i:90210043 original size:18 final size:17
Alignment explanation
Indices: 90209996--90210033 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
90209986 TTTTAAAAGG
*
90209996 AAAACAAATGAATCTTA
1 AAAACAAATGAAACTTA
90210013 AAAACAAATGAAACTTA
1 AAAACAAATGAAACTTA
90210030 AAAA
1 AAAA
90210034 ATTAATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (17 bp):
AAAACAAATGAAACTTA
Found at i:90211996 original size:29 final size:29
Alignment explanation
Indices: 90211964--90212052 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
90211954 CATAATTTGC
90211964 ATATTACTCAATAATAACCACAAAGCATA
1 ATATTACTCAATAATAACCACAAAGCATA
* * **
90211993 ATATT--TCATGATATTAATCATC-TTGC---
1 ATATTACTCA--ATAATAACCA-CAAAGCATA
90212019 ATATTACTCAATAATAACCACAAAGCATA
1 ATATTACTCAATAATAACCACAAAGCATA
90212048 ATATT
1 ATATT
90212053 TCATGATATT
Statistics
Matches: 43, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
25 1 0.02
26 15 0.35
27 3 0.07
28 3 0.07
29 20 0.47
30 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (29 bp):
ATATTACTCAATAATAACCACAAAGCATA
Found at i:90212025 original size:55 final size:55
Alignment explanation
Indices: 90211960--90212069 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
90211950 CACACATAAT
90211960 TTGCATATTACTCAATAATAACCACAAAGCATAATATTTCATGATATTAATCATC
1 TTGCATATTACTCAATAATAACCACAAAGCATAATATTTCATGATATTAATCATC
90212015 TTGCATATTACTCAATAATAACCACAAAGCATAATATTTCATGATATTAATCATC
1 TTGCATATTACTCAATAATAACCACAAAGCATAATATTTCATGATATTAATCATC
90212070 ATATCATATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (55 bp):
TTGCATATTACTCAATAATAACCACAAAGCATAATATTTCATGATATTAATCATC
Found at i:90212046 original size:26 final size:26
Alignment explanation
Indices: 90211962--90212047 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
90211952 CACATAATTT
90211962 GCATATTACTCAATAATAACCACAAA
1 GCATATTACTCAATAATAACCACAAA
* * * * **
90211988 GCATAATATTTCATGATATTAATCATC-TT
1 GCATATTA-CTCA--ATAATAACCA-CAAA
90212017 GCATATTACTCAATAATAACCACAAA
1 GCATATTACTCAATAATAACCACAAA
90212043 GCATA
1 GCATA
90212048 ATATTTCATG
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 1 0.02
26 20 0.47
27 3 0.07
28 3 0.07
29 15 0.35
30 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (26 bp):
GCATATTACTCAATAATAACCACAAA
Found at i:90217134 original size:23 final size:23
Alignment explanation
Indices: 90217052--90217138 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
90217042 ACCGATCAGT
*
90217052 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
90217074 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
90217094 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
90217117 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
90217139 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:90217534 original size:15 final size:15
Alignment explanation
Indices: 90217509--90217566 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
90217499 TCATATATAT
90217509 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
90217525 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
90217540 AATAATTTCAATCAA
1 TATAAATTCAATCAA
90217555 TATAAATTCAAT
1 TATAAATTCAAT
90217567 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:90218883 original size:8 final size:8
Alignment explanation
Indices: 90218870--90218898 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
90218860 TATTTTTATT
90218870 ATATAATA
1 ATATAATA
90218878 ATATAATA
1 ATATAATA
90218886 ATATAATA
1 ATATAATA
90218894 ATATA
1 ATATA
90218899 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:90219394 original size:21 final size:21
Alignment explanation
Indices: 90219368--90219452 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 21
90219358 ACTCCTAAAC
* *
90219368 CTTAAACCCTAAACCTTATAT
1 CTTAAACCATAAACCATATAT
*
90219389 CTTAAACCATAATTAACTCATAAACCT
1 CTTAAACCAT-A--AAC-CATATA--T
*
90219416 GCTTAAACCCTAAACCATATAT
1 -CTTAAACCATAAACCATATAT
90219438 CTTAAACCATAAACC
1 CTTAAACCATAAACC
90219453 TTAAACTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
21 23 0.45
22 2 0.04
24 8 0.16
25 7 0.14
27 2 0.04
28 9 0.18
ACGTcount: A:0.42, C:0.28, G:0.01, T:0.28
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:90219445 original size:14 final size:14
Alignment explanation
Indices: 90219419--90219463 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
90219409 TAAACCTGCT
*
90219419 TAAACCCTAAACCA
1 TAAACCTTAAACCA
* *
90219433 TATATCTTAAACCA
1 TAAACCTTAAACCA
*
90219447 TAAACCTTAAACTA
1 TAAACCTTAAACCA
90219461 TAA
1 TAA
90219464 TGATAATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:90219678 original size:41 final size:41
Alignment explanation
Indices: 90219621--90219797 Score: 227
Period size: 41 Copynumber: 4.4 Consensus size: 41
90219611 GTTATATGAC
* *
90219621 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATTCCCTGGT
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGGT
* * **
90219662 TTTTAGTGGCGTTTTACCAAAAGCGCAACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGGT
*
90219703 TTTTAGCGGCGTTTTA-TCAAAAGCGCCGCTACTGCTCTGGT
1 TTTTAGCGGCGTTTTACT-AAAAGCGCCGCTAATGCTCTGGT
*
90219744 TTTTAGTGGCGTTTTACCT-AAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTA-CTAAAAGCGCCGCTAATGCTCTGGT
*
90219784 TTTTAG-AGCGTTTT
1 TTTTAGCGGCGTTTT
90219798 TTGTAAAACG
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
39 7 0.06
40 8 0.07
41 103 0.87
43 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTCTGGT
Found at i:90219758 original size:82 final size:81
Alignment explanation
Indices: 90219621--90219797 Score: 259
Period size: 82 Copynumber: 2.2 Consensus size: 81
90219611 GTTATATGAC
*
90219621 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATTCCCTGGTTTTTAGTGGCGTTTTACCAAAAGC
1 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCCCTGGTTTTTAGTGGCGTTTTACCAAAAGC
90219686 GCAACTAATGCTCTGGT
66 GCAACTAATGCTCT-GT
* * *
90219703 TTTTAGCGGCGTTTTA-TCAAAAGCGCCGCTACTGCTCTGGTTTTTAGTGGCGTTTTACCTAAAG
1 TTTTAGCGGCGTTTTACT-AAAAGCGCCGCTAATGCCCTGGTTTTTAGTGGCGTTTTACCAAAAG
**
90219767 CGCCGCTAATGCTCTGT
65 CGCAACTAATGCTCTGT
*
90219784 TTTTAG-AGCGTTTT
1 TTTTAGCGGCGTTTT
90219798 TTGTAAAACG
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
80 7 0.08
81 9 0.10
82 71 0.82
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (81 bp):
TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCCCTGGTTTTTAGTGGCGTTTTACCAAAAGC
GCAACTAATGCTCTGT
Found at i:90219822 original size:39 final size:40
Alignment explanation
Indices: 90219621--90219821 Score: 190
Period size: 41 Copynumber: 5.0 Consensus size: 40
90219611 GTTATATGAC
* * *
90219621 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATTCCCTGGT
1 TTTTAGCGGCGTTTTATTAAAA-CGCCGCTAATGCTCTGGT
* ** **
90219662 TTTTAGTGGCGTTTTACCAAAAGCGCAACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTATTAAAA-CGCCGCTAATGCTCTGGT
* *
90219703 TTTTAGCGGCGTTTTATCAAAAGCGCCGCTACTGCTCTGGT
1 TTTTAGCGGCGTTTTATTAAAA-CGCCGCTAATGCTCTGGT
* * *
90219744 TTTTAGTGGCGTTTTACCTAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTA-TTAAAACGCCGCTAATGCTCTGGT
* * * *
90219784 TTTTAG-AGCGTTTTTTGTAAAACGCCGTTATTGCTCTG
1 TTTTAGCGGCGTTTTAT-TAAAACGCCGCTAATGCTCTG
90219822 TATTTTAAAT
Statistics
Matches: 135, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
39 24 0.18
40 8 0.06
41 100 0.74
42 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTATTAAAACGCCGCTAATGCTCTGGT
Found at i:90220901 original size:38 final size:38
Alignment explanation
Indices: 90220855--90220951 Score: 167
Period size: 38 Copynumber: 2.6 Consensus size: 38
90220845 CTTATGTTGG
*
90220855 TATACATGGCTGCTGGTATACTGTTGCTTAACATATGT
1 TATACATGGTTGCTGGTATACTGTTGCTTAACATATGT
* *
90220893 TATACATGGTTGCTGGTATATTGTTGCTTAATATATGT
1 TATACATGGTTGCTGGTATACTGTTGCTTAACATATGT
90220931 TATACATGGTTGCTGGTATAC
1 TATACATGGTTGCTGGTATAC
90220952 ATGGCTAACC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (38 bp):
TATACATGGTTGCTGGTATACTGTTGCTTAACATATGT
Found at i:90221526 original size:46 final size:46
Alignment explanation
Indices: 90221460--90221549 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
90221450 TGTAGGGAAT
* *
90221460 TTTACAAATAACTTCTGTGACTATGCCTAAGTTTATCAACAGTAAA
1 TTTACAAAAAACTTCAGTGACTATGCCTAAGTTTATCAACAGTAAA
90221506 TTTACAAAAAACTTCAGTGACTATGCCTAAGTTTATCAACAGTA
1 TTTACAAAAAACTTCAGTGACTATGCCTAAGTTTATCAACAGTA
90221550 GCAATCATAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (46 bp):
TTTACAAAAAACTTCAGTGACTATGCCTAAGTTTATCAACAGTAAA
Found at i:90222700 original size:3 final size:3
Alignment explanation
Indices: 90222692--90222746 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
90222682 TTAAATAAAA
* * *
90222692 AAT AAT AAT TAT AAT AAT -AT AAT AAT -AT AAT AAT ATAT ATGT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT AAT
90222737 AAT AAT AAT A
1 AAT AAT AAT A
90222747 GAATAAAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.09
3 34 0.79
4 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:90222714 original size:8 final size:8
Alignment explanation
Indices: 90222693--90222743 Score: 66
Period size: 8 Copynumber: 6.1 Consensus size: 8
90222683 TAAATAAAAA
90222693 ATAATAATT
1 ATAATAA-T
90222702 ATAATAAT
1 ATAATAAT
90222710 ATAATAAT
1 ATAATAAT
90222718 ATAATAAT
1 ATAATAAT
**
90222726 ATATATGTT
1 ATA-ATAAT
90222735 ATAATAAT
1 ATAATAAT
90222743 A
1 A
90222744 ATAGAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
8 24 0.65
9 13 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
ATAATAAT
Found at i:90224287 original size:20 final size:20
Alignment explanation
Indices: 90224262--90224301 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
90224252 GCCTCATGGC
*
90224262 CATGTCCCAGGCCACACGGG
1 CATGTCCCAGACCACACGGG
*
90224282 CATGTCCCAGACTACACGGG
1 CATGTCCCAGACCACACGGG
90224302 TGTGTGCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.12
Consensus pattern (20 bp):
CATGTCCCAGACCACACGGG
Found at i:90224813 original size:40 final size:40
Alignment explanation
Indices: 90224741--90224883 Score: 232
Period size: 40 Copynumber: 3.5 Consensus size: 40
90224731 AAAAAAATAG
* *
90224741 TCACTGCATACATATTAAAAAAATAGGCAACACATCAACAA
1 TCACTGCATGCATATT-AAAAAATAGGCAACACACCAACAA
90224782 TCACTGCATGCATATTAAAAAATAGGCAACACACCAACAA
1 TCACTGCATGCATATTAAAAAATAGGCAACACACCAACAA
* *
90224822 TCACTGCATGCATATTAAAAAATAGTCAACACGCCAACAA
1 TCACTGCATGCATATTAAAAAATAGGCAACACACCAACAA
*
90224862 TCAGTGCATGCATATTAAAAAA
1 TCACTGCATGCATATTAAAAAA
90224884 CATTTACTAA
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
40 82 0.85
41 15 0.15
ACGTcount: A:0.48, C:0.22, G:0.10, T:0.20
Consensus pattern (40 bp):
TCACTGCATGCATATTAAAAAATAGGCAACACACCAACAA
Found at i:90226553 original size:15 final size:15
Alignment explanation
Indices: 90226533--90226578 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
90226523 TATGCATCAC
90226533 TATCACTACTAGACA
1 TATCACTACTAGACA
*
90226548 TATCACTACCAGACA
1 TATCACTACTAGACA
*
90226563 CATCACTACTAGACA
1 TATCACTACTAGACA
90226578 T
1 T
90226579 GTTTTCTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.39, C:0.30, G:0.07, T:0.24
Consensus pattern (15 bp):
TATCACTACTAGACA
Found at i:90227109 original size:22 final size:21
Alignment explanation
Indices: 90227058--90227109 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
90227048 CATTAATAAC
90227058 AAATAAAATCGAAATCAAAATA
1 AAAT-AAATCGAAATCAAAATA
** *
90227080 ACCCTAAATCGAAATCCAAATCA
1 A-AATAAATCGAAATCAAAAT-A
90227103 AAATAAA
1 AAATAAA
90227110 AAACAAATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.62, C:0.17, G:0.04, T:0.17
Consensus pattern (21 bp):
AAATAAATCGAAATCAAAATA
Found at i:90227164 original size:42 final size:42
Alignment explanation
Indices: 90227083--90227164 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
90227073 CAAAATAACC
*
90227083 CTAAATCGAAATCCAAATCAAAATAAAAAACAAATTCTAATT
1 CTAAATCGAAATCCAAATCAAAATAAAAAACAAAATCTAATT
* * ** * *
90227125 CTAAATCGAGATCGAAATTGAAATTAAAATCAAAATCTAA
1 CTAAATCGAAATCCAAATCAAAATAAAAAACAAAATCTAA
90227165 ATCAGAATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (42 bp):
CTAAATCGAAATCCAAATCAAAATAAAAAACAAAATCTAATT
Found at i:90227201 original size:12 final size:12
Alignment explanation
Indices: 90227184--90227238 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
90227174 AGTGAGTGTT
* *
90227184 TCAAAATTGTAA
1 TCAAAATCGAAA
90227196 TCAAAATCGAAA
1 TCAAAATCGAAA
*
90227208 TCAAAATCAAAA
1 TCAAAATCGAAA
*
90227220 TCAAAATCAAAA
1 TCAAAATCGAAA
90227232 TCAAAAT
1 TCAAAAT
90227239 TAAAATTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.60, C:0.15, G:0.04, T:0.22
Consensus pattern (12 bp):
TCAAAATCGAAA
Found at i:90227245 original size:6 final size:6
Alignment explanation
Indices: 90227194--90227244 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
90227184 TCAAAATTGT
* *
90227194 AATCAA AATCGA AATCAA AATCAA AATCAA AATCAA AATCAA AATTAA
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA AATCAA
90227242 AAT
1 AAT
90227245 TGAAACCGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.20
Consensus pattern (6 bp):
AATCAA
Found at i:90230719 original size:12 final size:12
Alignment explanation
Indices: 90230704--90230728 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90230694 AAAATGTCTC
90230704 AAAAAAATATTT
1 AAAAAAATATTT
90230716 AAAAAAATATTT
1 AAAAAAATATTT
90230728 A
1 A
90230729 TATTAATTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAAAATATTT
Found at i:90231571 original size:29 final size:29
Alignment explanation
Indices: 90231539--90231621 Score: 69
Period size: 31 Copynumber: 2.8 Consensus size: 29
90231529 AAATAAAATC
*
90231539 AAAATATTATATAAAAATTGAAAAATTGAA
1 AAAATATTATATAAAAATTGAAAAAAT-AA
* ** * *
90231569 AAAATATAAATATAAATTTTTAAAAAAT-C
1 AAAATAT-TATATAAAAATTGAAAAAATAA
* *
90231598 AAAATATTTTGTAAAAATTGAAAA
1 AAAATATTATATAAAAATTGAAAA
90231622 TTTGTCATTA
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
28 11 0.28
29 7 0.17
30 7 0.17
31 15 0.38
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATATTATATAAAAATTGAAAAAATAA
Found at i:90231676 original size:29 final size:29
Alignment explanation
Indices: 90231629--90231690 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
90231619 AAATTTGTCA
90231629 TTAACTTTTAGATATTTAGATATATATTTT
1 TTAACTTTTAGATATTTAGA-ATATATTTT
* * *
90231659 TTAATTTTTAGA-ATTTAGAATTTCTTTT
1 TTAACTTTTAGATATTTAGAATATATTTT
90231687 TTAA
1 TTAA
90231691 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 11 0.38
29 7 0.24
30 11 0.38
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (29 bp):
TTAACTTTTAGATATTTAGAATATATTTT
Found at i:90231763 original size:22 final size:23
Alignment explanation
Indices: 90231729--90231784 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
90231719 TTATATAATA
*
90231729 ATTT-TATTCTTTA-AAATTTAT
1 ATTTATATTTTTTAGAAATTTAT
*
90231750 ATTTATATTTTTTAGAATTTTAT
1 ATTTATATTTTTTAGAAATTTAT
90231773 ATTTTATATTTT
1 A-TTTATATTTT
90231785 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 8 0.27
23 8 0.27
24 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTTATATTTTTTAGAAATTTAT
Found at i:90231778 original size:7 final size:7
Alignment explanation
Indices: 90231745--90231791 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
90231735 TTCTTTAAAA
90231745 TTTATAT
1 TTTATAT
*
90231752 TTATATTT
1 TT-TATAT
*
90231760 TTTAGAAT
1 TTTA-TAT
90231768 TTTATAT
1 TTTATAT
90231775 TTTATAT
1 TTTATAT
90231782 TTTATAT
1 TTTATAT
90231789 TTT
1 TTT
90231792 TAAACTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 23 0.68
8 11 0.32
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (7 bp):
TTTATAT
Found at i:90231785 original size:22 final size:20
Alignment explanation
Indices: 90231729--90231785 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
90231719 TTATATAATA
90231729 ATTTTATTCTTTAAAATTTAT
1 ATTTTATT-TTTAAAATTTAT
*
90231750 ATTTATATTTTTTAGAATTTTAT
1 ATTT-TA-TTTTTA-AAATTTAT
90231773 ATTTTATATTTTA
1 ATTTTAT-TTTTA
90231786 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.16
22 13 0.42
23 13 0.42
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
ATTTTATTTTTAAAATTTAT
Found at i:90231793 original size:15 final size:15
Alignment explanation
Indices: 90231745--90231793 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
90231735 TTCTTTAAAA
90231745 TTTATA-TTTATATTT
1 TTTATATTTTATA-TT
*
90231760 TTTAGAATTTTATA-T
1 TTTA-TATTTTATATT
90231775 TTTATATTTTATATT
1 TTTATATTTTATATT
90231790 TTTA
1 TTTA
90231794 AACTCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 8 0.28
15 14 0.48
16 1 0.03
17 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTATATTTTATATT
Found at i:90232138 original size:37 final size:37
Alignment explanation
Indices: 90232091--90232163 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
90232081 ACACTGTTAC
90232091 AAAAAAGTTAAACAAGATAACGGAAGGATAGTTTAAA
1 AAAAAAGTTAAACAAGATAACGGAAGGATAGTTTAAA
**
90232128 AAAAAAGTTAAACCGGATAACGGAAGGATAGTTTAA
1 AAAAAAGTTAAACAAGATAACGGAAGGATAGTTTAA
90232164 GTATAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (37 bp):
AAAAAAGTTAAACAAGATAACGGAAGGATAGTTTAAA
Found at i:90235000 original size:29 final size:34
Alignment explanation
Indices: 90234967--90235029 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 34
90234957 TTTTATTTCA
90234967 ATACTTT-A-ATTTTTAATT-T-AAATAA-AAAT
1 ATACTTTAATATTTTTAATTATAAAATAACAAAT
90234996 ATACTTTAATATTTTTAATTATAAAATAACAAAT
1 ATACTTTAATATTTTTAATTATAAAATAACAAAT
90235030 TTTAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 7 0.24
30 1 0.03
31 10 0.34
32 1 0.03
33 6 0.21
34 4 0.14
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (34 bp):
ATACTTTAATATTTTTAATTATAAAATAACAAAT
Found at i:90235875 original size:22 final size:22
Alignment explanation
Indices: 90235850--90235915 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 22
90235840 GTCAAAGTGT
90235850 AATTTTACCTTTACTAATTTAA
1 AATTTTACCTTTACTAATTTAA
* * *
90235872 AATTTTTCC---A--AA-GTAT
1 AATTTTACCTTTACTAATTTAA
90235888 AATTTTACCTTTACTAATTTAA
1 AATTTTACCTTTACTAATTTAA
90235910 AATTTT
1 AATTTT
90235916 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
16 10 0.31
17 2 0.06
19 2 0.06
21 2 0.06
22 16 0.50
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (22 bp):
AATTTTACCTTTACTAATTTAA
Found at i:90235885 original size:38 final size:38
Alignment explanation
Indices: 90235842--90235916 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
90235832 TTAAGAGGGT
*
90235842 CAAAGTGTAATTTTACCTTTACTAATTTAAAATTTTTC
1 CAAAGTATAATTTTACCTTTACTAATTTAAAATTTTTC
90235880 CAAAGTATAATTTTACCTTTACTAATTTAAAATTTTT
1 CAAAGTATAATTTTACCTTTACTAATTTAAAATTTTT
90235917 AAAAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (38 bp):
CAAAGTATAATTTTACCTTTACTAATTTAAAATTTTTC
Found at i:90239387 original size:14 final size:14
Alignment explanation
Indices: 90239352--90239396 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
90239342 CTTGGGCACC
*
90239352 TAATT-TAATTTCT
1 TAATTCTAATTTTT
90239365 TAA-TCTAATTTTT
1 TAATTCTAATTTTT
90239378 TAATTCTAATTATTT
1 TAATTCTAATT-TTT
90239393 TAAT
1 TAAT
90239397 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 13 0.46
14 7 0.25
15 7 0.25
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATTCTAATTTTT
Found at i:90239794 original size:6 final size:6
Alignment explanation
Indices: 90239783--90239821 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
90239773 AGAGTTGTGA
90239783 ACAGCC ACAGCC ACAGCC ACAGCC ACAGCC ACAGCC ACA
1 ACAGCC ACAGCC ACAGCC ACAGCC ACAGCC ACAGCC ACA
90239822 TATCCCTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.36, C:0.49, G:0.15, T:0.00
Consensus pattern (6 bp):
ACAGCC
Found at i:90242798 original size:17 final size:17
Alignment explanation
Indices: 90242776--90242808 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
90242766 CTCCCCATTG
*
90242776 AATGTCCATTGGTAGAT
1 AATGTCCATTGATAGAT
90242793 AATGTCCATTGATAGA
1 AATGTCCATTGATAGA
90242809 GACTCAGCGG
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:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (17 bp):
AATGTCCATTGATAGAT
Found at i:90244477 original size:27 final size:27
Alignment explanation
Indices: 90244447--90244501 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
90244437 AATAAAAGTT
90244447 ATATTAAA-TTTTAATAAAAATATAGAA
1 ATATTAAATTTTTAATAAAAAT-TAGAA
*
90244474 ATATTAAATTTTTATTAAAAATTAGAA
1 ATATTAAATTTTTAATAAAAATTAGAA
90244501 A
1 A
90244502 AAATTATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
ATATTAAATTTTTAATAAAAATTAGAA
Found at i:90244513 original size:19 final size:19
Alignment explanation
Indices: 90244489--90244541 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
90244479 AAATTTTTAT
*
90244489 TAAAAATTAGAAAAAATTA
1 TAAAAATTAGAAAAAAATA
* *
90244508 TAAAAATCATAAAAAAATA
1 TAAAAATTAGAAAAAAATA
90244527 TAAAATATATAGAAA
1 TAAAA-AT-TAGAAA
90244542 TATAGAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 21 0.78
20 2 0.07
21 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
TAAAAATTAGAAAAAAATA
Found at i:90244565 original size:10 final size:10
Alignment explanation
Indices: 90244484--90244569 Score: 52
Period size: 10 Copynumber: 8.8 Consensus size: 10
90244474 ATATTAAATT
90244484 TTTATTAAAAA
1 TTTA-TAAAAA
*
90244495 -TTAGAAAAA
1 TTTATAAAAA
*
90244504 ATTATAAAAA
1 TTTATAAAAA
*
90244514 -TCATAAAAA
1 TTTATAAAAA
**
90244523 AATAT-AAAA
1 TTTATAAAAA
* *
90244532 TATATAGAAA
1 TTTATAAAAA
* *
90244542 TATAGAAAAA
1 TTTATAAAAA
*
90244552 TTTATAAAAT
1 TTTATAAAAA
90244562 TTTATAAA
1 TTTATAAA
90244570 GTCGTAAGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
9 21 0.35
10 39 0.65
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:90245138 original size:85 final size:85
Alignment explanation
Indices: 90244992--90245180 Score: 195
Period size: 85 Copynumber: 2.2 Consensus size: 85
90244982 ATCCGCCCTT
* * * * * *
90244992 GGCCTTTTTAATGTATTTTGGCAATTTAAGTACTCAGTTGAATGAAAAAAAAAGGGACTTAATTG
1 GGCCTTTTT-ATGCATTTTGACAATTCAAATACCCAATTGAATGAAAAAAAAAGGGACTTAATTG
90245057 TTTTCTTTGAAAAAG-TATGAG
65 TTTT-TTTGAAAAAGATATGAG
**
90245078 GGCCTTTTTATGCATTTTGACAATTCAAATACCCAATT-AAGTGAAAAAAATTGAGG-CTTAATT
1 GGCCTTTTTATGCATTTTGACAATTCAAATACCCAATTGAA-TGAAAAAAAAAG-GGACTTAATT
** *
90245141 GTTTTTTTTTAAAAGATTTGAG
64 GTTTTTTTGAAAAAGATATGAG
* *
90245163 AGCATTTTTTATGCATTT
1 GGC-CTTTTTATGCATTT
90245181 AAAAGTTGAA
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
84 10 0.12
85 52 0.60
86 24 0.28
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (85 bp):
GGCCTTTTTATGCATTTTGACAATTCAAATACCCAATTGAATGAAAAAAAAAGGGACTTAATTGT
TTTTTTGAAAAAGATATGAG
Found at i:90245639 original size:10 final size:10
Alignment explanation
Indices: 90245624--90245648 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
90245614 TAGATATAAA
90245624 AAAATTTATG
1 AAAATTTATG
90245634 AAAATTTATG
1 AAAATTTATG
90245644 AAAAT
1 AAAAT
90245649 GTAAAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (10 bp):
AAAATTTATG
Found at i:90247781 original size:21 final size:21
Alignment explanation
Indices: 90247757--90247798 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
90247747 TTCTATTAAA
*
90247757 CTCTTATGAGTTTCTGTTCAG
1 CTCTTATGAGCTTCTGTTCAG
90247778 CTCTTATGAGCTTCTGTTCAG
1 CTCTTATGAGCTTCTGTTCAG
90247799 TTTTCGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.45
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAG
Found at i:90252377 original size:12 final size:12
Alignment explanation
Indices: 90252360--90252401 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
90252350 ATAAATTTAC
*
90252360 AATAAATATAAT
1 AATAAATATAAA
*
90252372 AATAAATTTAAA
1 AATAAATATAAA
*
90252384 AATATATATAAA
1 AATAAATATAAA
90252396 AA-AAAT
1 AATAAAT
90252402 TGTTGGTGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 3 0.12
12 22 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAATATAAA
Found at i:90252392 original size:24 final size:22
Alignment explanation
Indices: 90252350--90252402 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
90252340 AAAAACTCAG
*
90252350 ATAAATTTACAATAAATATAATA
1 ATAAATTTAAAATAAATATAA-A
*
90252373 ATAAATTTAAAAATATATATAAA
1 ATAAATTT-AAAATAAATATAAA
*
90252396 AAAAATT
1 ATAAATT
90252403 GTTGGTGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAATTTAAAATAAATATAAA
Found at i:90255823 original size:26 final size:24
Alignment explanation
Indices: 90255793--90255842 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
90255783 AAATAAAAAA
*
90255793 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
90255819 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
90255843 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:90255862 original size:21 final size:21
Alignment explanation
Indices: 90255813--90255871 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
90255803 ATAATAAATC
*
90255813 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
90255833 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
90255855 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
90255872 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:90255948 original size:15 final size:16
Alignment explanation
Indices: 90255918--90255950 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
90255908 AAATGGTTAT
90255918 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
90255935 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
90255950 A
1 A
90255951 ATATATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:90258450 original size:22 final size:22
Alignment explanation
Indices: 90258420--90258462 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
90258410 TATCTAAATG
90258420 ATAACAATAAAATAATAGCAAC
1 ATAACAATAAAATAATAGCAAC
* *
90258442 ATAATAATAAAATGATAGCAA
1 ATAACAATAAAATAATAGCAA
90258463 AACAACATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAATAGCAAC
Found at i:90259137 original size:30 final size:30
Alignment explanation
Indices: 90259101--90259193 Score: 150
Period size: 30 Copynumber: 3.1 Consensus size: 30
90259091 ACTTATTTTA
*
90259101 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
* *
90259131 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
*
90259161 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
90259191 TTG
1 TTG
90259194 CTTGTTAAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:90262473 original size:9 final size:9
Alignment explanation
Indices: 90262461--90262497 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
90262451 GTTTATTGCG
90262461 TTTTTC-TT
1 TTTTTCTTT
90262469 TTTTTCTTT
1 TTTTTCTTT
90262478 TTTTTCTTT
1 TTTTTCTTT
90262487 TTTTT-TTT
1 TTTTTCTTT
90262495 TTT
1 TTT
90262498 GGTTTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 12 0.43
9 16 0.57
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:90262474 original size:8 final size:8
Alignment explanation
Indices: 90262461--90262497 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
90262451 GTTTATTGCG
90262461 TTTTTCTT
1 TTTTTCTT
90262469 TTTTTCTTT
1 TTTTTC-TT
90262478 TTTTTCTT
1 TTTTTCTT
90262486 TTTTT-TT
1 TTTTTCTT
90262493 TTTTT
1 TTTTT
90262498 GGTTTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.25
8 13 0.46
9 8 0.29
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (8 bp):
TTTTTCTT
Found at i:90262483 original size:17 final size:16
Alignment explanation
Indices: 90262461--90262497 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
90262451 GTTTATTGCG
90262461 TTTTTCTTTTTTTCTTT
1 TTTTTCTTTTTTT-TTT
90262478 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTT
90262494 TTTT
1 TTTT
90262498 GGTTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTT
Found at i:90269884 original size:76 final size:76
Alignment explanation
Indices: 90269758--90269909 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
90269748 CTTTTAGGGA
*
90269758 GATAATAAACAATTCTAAGCCTTCTACTTATTACTACCTCCTTTTCTAACTCTAAGCAGTCAACA
1 GATAATAAACAATTCTAAGCCTTCTACTTATTACAACCTCCTTTTCTAACTCTAAGCAGTCAACA
90269823 TGACTTGCAAT
66 TGACTTGCAAT
* *
90269834 GATAATAAACAATTTTAAGCCTTCTACTTATTACAACCTCCTTTTCTAACTCTAAGCAGTCGACA
1 GATAATAAACAATTCTAAGCCTTCTACTTATTACAACCTCCTTTTCTAACTCTAAGCAGTCAACA
90269899 TGACTTGCAAT
66 TGACTTGCAAT
90269910 ACAGAGGGTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (76 bp):
GATAATAAACAATTCTAAGCCTTCTACTTATTACAACCTCCTTTTCTAACTCTAAGCAGTCAACA
TGACTTGCAAT
Found at i:90274255 original size:6 final size:6
Alignment explanation
Indices: 90274244--90274274 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
90274234 TTTTCTGTTG
90274244 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA T
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA T
90274275 ACTAAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (6 bp):
TCAAAA
Found at i:90274289 original size:6 final size:6
Alignment explanation
Indices: 90274280--90274326 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
90274270 AAAATACTAA
90274280 AATACT AATACT AATACT AATACT AATACT AATACT AATACT AATAC
1 AATACT AATACT AATACT AATACT AATACT AATACT AATACT AATAC
90274327 ATTAGTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (6 bp):
AATACT
Found at i:90281906 original size:3 final size:3
Alignment explanation
Indices: 90281900--90281935 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
90281890 GAAAAAAATA
90281900 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
90281936 GAAGGTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:90283456 original size:29 final size:34
Alignment explanation
Indices: 90283394--90283456 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 34
90283384 TATATTTAAA
90283394 ATTTGTTATTTTATAATTAAAAATATTAAAGTAT
1 ATTTGTTATTTTATAATTAAAAATATTAAAGTAT
90283428 ATTT-TTA-TTTA-AATT-AAAA-ATTAAAGTAT
1 ATTTGTTATTTTATAATTAAAAATATTAAAGTAT
90283457 TGAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.34
30 4 0.14
31 4 0.14
32 4 0.14
33 3 0.10
34 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (34 bp):
ATTTGTTATTTTATAATTAAAAATATTAAAGTAT
Found at i:90288156 original size:7 final size:7
Alignment explanation
Indices: 90288144--90288172 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
90288134 TGTCTATGTG
90288144 TTGGGAC
1 TTGGGAC
90288151 TTGGGAC
1 TTGGGAC
90288158 TTGGGAC
1 TTGGGAC
90288165 TTGGGAC
1 TTGGGAC
90288172 T
1 T
90288173 GGTTAGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.41, T:0.31
Consensus pattern (7 bp):
TTGGGAC
Found at i:90288378 original size:30 final size:30
Alignment explanation
Indices: 90288310--90288380 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
90288300 TCAATAATCT
*
90288310 ATATCTTTATAATTTTTAAAGGATTAAATTA
1 ATAT-TTTATTATTTTTAAAGGATTAAATTA
*
90288341 ATTTTTTATTATTTTTAAGAGG-TTAAATTA
1 ATATTTTATTATTTTTAA-AGGATTAAATTA
90288371 CA-ATTTTATT
1 -ATATTTTATT
90288381 TTTACTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 28 0.80
31 7 0.20
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (30 bp):
ATATTTTATTATTTTTAAAGGATTAAATTA
Found at i:90289303 original size:29 final size:30
Alignment explanation
Indices: 90289271--90289329 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
90289261 TATAGTTTAA
90289271 TGTGTAATTGTATACA-AAAATTTTGATTT
1 TGTGTAATTGTATACATAAAATTTTGATTT
*
90289300 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGTAATTGTATACATAAAATTTTGATTT
90289330 AATCCAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (30 bp):
TGTGTAATTGTATACATAAAATTTTGATTT
Found at i:90290119 original size:26 final size:25
Alignment explanation
Indices: 90290064--90290122 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
90290054 CGCGTTTATT
* * **
90290064 TATTTTAATTTAATTAATTATATATT
1 TATTTT-ACTTAATTAATTAAATAAC
90290090 TATTTTACTTAATTAATTTAAATAAC
1 TATTTTACTTAATTAA-TTAAATAAC
90290116 TATTTTA
1 TATTTTA
90290123 AAAAATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTTTACTTAATTAATTAAATAAC
Found at i:90290362 original size:111 final size:109
Alignment explanation
Indices: 90290009--90290370 Score: 413
Period size: 111 Copynumber: 3.3 Consensus size: 109
90289999 TTTTTAAATG
* * * ** * ** *
90290009 TTTAAAATTTATTTA-TTTCTTAAATCACGTGCCCATGTCCATTGACGCGTTTATTTATTTTAAT
1 TTTAAAAATTA-TTAGTTTCTTAAATCACGTGCACACGTATATTGATGTATCTATTTATTTTAAT
* * *
90290073 TTAATTAATTATATATTTATTTTACTTAATTAATTTAAATAACTAT
65 TTAA-TAATTATATATTTATTTTACTCAATTAATGTAAATAATTAT
* * * *
90290119 TTTAAAAAATTATTAGTTTCTCAAATAACGTGCGCACGTATATTGATGTATTTATTTATTTTAAT
1 TTT-AAAAATTATTAGTTTCTTAAATCACGTGCACACGTATATTGATGTATCTATTTATTTTAAT
*
90290184 TTAATAACTATATATTTATTTTACTCAATTAATGTAAATAATTATTT
65 TTAATAATTATATATTTATTTTACTCAATTAATGTAAATAATTA--T
* * * * *
90290231 TTTAAAAGTTATTAATTTCTTAAATCACGTGCACACTTATATT-ATCGTGTCTATTTGTTTTAAT
1 TTTAAAAATTATTAGTTTCTTAAATCACGTGCACACGTATATTGAT-GTATCTATTTATTTTAAT
*
90290295 TTAATAATTATATATTTATTTTACTCAATTAAAGTAAATAATTAT
65 TTAATAATTATATATTTATTTTACTCAATTAATGTAAATAATTAT
* *
90290340 TTTAAAATTTTCATTAGTTTCTTAATTCACG
1 TTTAAAA-ATT-ATTAGTTTCTTAAATCACG
90290371 CACGTATATT
Statistics
Matches: 217, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
109 8 0.04
110 46 0.21
111 159 0.73
112 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (109 bp):
TTTAAAAATTATTAGTTTCTTAAATCACGTGCACACGTATATTGATGTATCTATTTATTTTAATT
TAATAATTATATATTTATTTTACTCAATTAATGTAAATAATTAT
Found at i:90290397 original size:111 final size:108
Alignment explanation
Indices: 90290059--90290414 Score: 332
Period size: 111 Copynumber: 3.2 Consensus size: 108
90290049 ATTGACGCGT
* * *
90290059 TTATTTATTTTAATTTAATTAATTATATATTTATTTTACTTAATTAATTTAAATAACTATTTTAA
1 TTATTTATTTTAATTTAA-TAATTATATATTTATTTTACTCAATTAATGTAAATAATTATTTT-A
* * *
90290124 AAAATTATTAGTTTCTCAAATAACGTGCGCACGTATA-TT--GA-TGTA
64 AAAATTATTAGTTTCT-TAAT-TC--ACGCACGTATATTTACGAGTGTA
*
90290169 TTTATTTATTTTAATTTAATAACTATATATTTATTTTACTCAATTAATGTAAATAATTATTTTTT
1 -TTATTTATTTTAATTTAATAATTATATATTTATTTTACTCAATTAATGTAAATAATTA--TTTT
* * * *
90290234 AAAAGTTATTAATTTCTTAAATCACGTGCACACT-TATATTATC--GTGT-
63 AAAAATTATTAGTTTCTTAATTCAC--GCAC-GTATAT-TTA-CGAGTGTA
* * *
90290281 CTATTTGTTTTAATTTAATAATTATATATTTATTTTACTCAATTAAAGTAAATAATTATTTTAAA
1 TTATTTATTTTAATTTAATAATTATATATTTATTTTACTCAATTAATGTAAATAATTATTTTAAA
* *
90290346 ATTTTCATTAGTTTCTTAATTCACGCACGTATATTTACGAGTTTAA
66 A-ATT-ATTAGTTTCTTAATTCACGCACGTATATTTACGAGTGT-A
*
90290392 TTATTTTAATTTAATTTATATAA
1 TTA-TTTATTTTAATTTA-ATAA
90290415 ATAATTATTT
Statistics
Matches: 202, Mismatches: 23, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
107 2 0.01
108 4 0.02
109 25 0.12
110 41 0.20
111 107 0.53
112 16 0.08
113 7 0.03
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.51
Consensus pattern (108 bp):
TTATTTATTTTAATTTAATAATTATATATTTATTTTACTCAATTAATGTAAATAATTATTTTAAA
AATTATTAGTTTCTTAATTCACGCACGTATATTTACGAGTGTA
Found at i:90291720 original size:27 final size:27
Alignment explanation
Indices: 90291673--90291724 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
90291663 ATGCTCATAC
* *
90291673 GAGTTGTGAAAATGGGTCTGCTCACGT
1 GAGTTGTGAAAACGGGCCTGCTCACGT
*
90291700 GAGTTGTGAAAACGTGCCTGCTCAC
1 GAGTTGTGAAAACGGGCCTGCTCAC
90291725 ACAAGCTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (27 bp):
GAGTTGTGAAAACGGGCCTGCTCACGT
Found at i:90294481 original size:29 final size:29
Alignment explanation
Indices: 90294441--90294508 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
90294431 TATTCGAAAG
* * *
90294441 TTTTTATTTAAGATAGCAGACTATTAAGT
1 TTTTTTTTTAAGATAGCAAACTAATAAGT
*
90294470 TTTTTTTTTAAGATAGTAAACTAATAAGT
1 TTTTTTTTTAAGATAGCAAACTAATAAGT
90294499 TTTTTTTTTA
1 TTTTTTTTTA
90294509 TTTTAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.53
Consensus pattern (29 bp):
TTTTTTTTTAAGATAGCAAACTAATAAGT
Found at i:90295667 original size:3 final size:3
Alignment explanation
Indices: 90295653--90295687 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
90295643 CTTGGCCAGG
* *
90295653 TCA TCT TCA TCA TCA TCA TCA TTA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
90295688 TTCTTCTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:90296314 original size:51 final size:51
Alignment explanation
Indices: 90296218--90296314 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 51
90296208 TATTTTTTTT
* * * *
90296218 TAATTTGGAGGTTTGACTATGTAAGTGAATATTCTAGAATAAAAAAAATTA
1 TAATTCGGAAGTTTGACTATGTAAGTGAAGATTCTAGAACAAAAAAAATTA
* * *
90296269 TAATTCGGAAGTTTGATTGTGTAAGTGAAGATTCTAGAACCAAAAA
1 TAATTCGGAAGTTTGACTATGTAAGTGAAGATTCTAGAACAAAAAA
90296315 TTTGAATCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (51 bp):
TAATTCGGAAGTTTGACTATGTAAGTGAAGATTCTAGAACAAAAAAAATTA
Found at i:90303180 original size:23 final size:22
Alignment explanation
Indices: 90303143--90303185 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
90303133 TTTACCATCA
*
90303143 ATTATTTACTTTTATGTTATAT
1 ATTATTTACTATTATGTTATAT
*
90303165 ATTATTTTACTATTATTTTAT
1 ATTA-TTTACTATTATGTTAT
90303186 TCATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTATTTACTATTATGTTATAT
Found at i:90303679 original size:21 final size:21
Alignment explanation
Indices: 90303653--90303692 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
90303643 TAACGGGACC
90303653 GCTGATGTAGCAAGTTAACCA
1 GCTGATGTAGCAAGTTAACCA
*
90303674 GCTGATGTGGCAAGTTAAC
1 GCTGATGTAGCAAGTTAAC
90303693 TTGCCACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (21 bp):
GCTGATGTAGCAAGTTAACCA
Found at i:90304167 original size:6 final size:6
Alignment explanation
Indices: 90304158--90304197 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
90304148 ATTTAGGGTT
* * *
90304158 ATTTCG ATTTTA ATTTTG ATTTTG ATTTCG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
90304198 CAATTTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.20, C:0.05, G:0.12, T:0.62
Consensus pattern (6 bp):
ATTTTG
Found at i:90304178 original size:12 final size:12
Alignment explanation
Indices: 90304158--90304311 Score: 73
Period size: 12 Copynumber: 12.8 Consensus size: 12
90304148 ATTTAGGGTT
*
90304158 ATTTCGATTTTA
1 ATTTCGATTTTG
*
90304170 ATTTTGATTTTG
1 ATTTCGATTTTG
90304182 ATTTCGATTTTG
1 ATTTCGATTTTG
*
90304194 ATTTCAATTTTG
1 ATTTCGATTTTG
** **
90304206 A-AAC-ACTCACTG
1 ATTTCGA-T-TTTG
*
90304218 A-TTCTGATTCTG
1 ATTTC-GATTTTG
90304230 A-TTCTGATTTTG
1 ATTTC-GATTTTG
*
90304242 ATTTTGATTTTG
1 ATTTCGATTTTG
** *
90304254 ATTTTAATTTCG
1 ATTTCGATTTTG
* **
90304266 ATCTCGATTTAA
1 ATTTCGATTTTG
* *
90304278 ATTTAGATTTAG
1 ATTTCGATTTTG
*
90304290 ATTTAGATTTTG
1 ATTTCGATTTTG
*
90304302 ATTTCTATTT
1 ATTTCGATTT
90304312 AGGGTTATTT
Statistics
Matches: 111, Mismatches: 26, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
10 1 0.01
11 2 0.02
12 104 0.94
13 3 0.03
14 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (12 bp):
ATTTCGATTTTG
Found at i:90304184 original size:18 final size:18
Alignment explanation
Indices: 90304158--90304203 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
90304148 ATTTAGGGTT
*
90304158 ATTTCGATTTTAATTTTG
1 ATTTCGATTTCAATTTTG
* *
90304176 ATTTTGATTTCGATTTTG
1 ATTTCGATTTCAATTTTG
*
90304194 ATTTCAATTT
1 ATTTCGATTT
90304204 TGAAACACTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.61
Consensus pattern (18 bp):
ATTTCGATTTCAATTTTG
Found at i:90304257 original size:6 final size:6
Alignment explanation
Indices: 90304216--90304305 Score: 72
Period size: 6 Copynumber: 15.0 Consensus size: 6
90304206 AAACACTCAC
* * * *
90304216 TGATTC TGATTC TGATTC TGATTT TGATTT TGATTT TGATTT TAATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
* * * ** * * *
90304264 CGATCT CGATTT AAATTT AGATTT AGATTT AGATTT TGATTT
1 TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT TGATTT
90304306 CTATTTAGGG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.23, C:0.07, G:0.14, T:0.56
Consensus pattern (6 bp):
TGATTT
Found at i:90304790 original size:15 final size:15
Alignment explanation
Indices: 90304772--90304811 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
90304762 TGTCTAGTAT
**
90304772 TGATGTGTCTGGCAG
1 TGATGTGTCTGAAAG
*
90304787 TGATGTATCTGAAAG
1 TGATGTGTCTGAAAG
90304802 TGATGTGTCT
1 TGATGTGTCT
90304812 AATAGGATAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.38
Consensus pattern (15 bp):
TGATGTGTCTGAAAG
Found at i:90306535 original size:40 final size:40
Alignment explanation
Indices: 90306475--90306572 Score: 153
Period size: 40 Copynumber: 2.5 Consensus size: 40
90306465 ATGAATGTTC
*
90306475 TTTAATATGCATGCACTGATTGTTGGTATGTTGA-CTATTT
1 TTTAATATGCATGCAGTGATTGTTGGTATGTT-ACCTATTT
* *
90306515 TTTAATATACATGCAGTGATTGTTGGTGTGTTACCTATTT
1 TTTAATATGCATGCAGTGATTGTTGGTATGTTACCTATTT
90306555 TTTAATATGCATGCAGTG
1 TTTAATATGCATGCAGTG
90306573 GGTATTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 1 0.02
40 52 0.98
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.46
Consensus pattern (40 bp):
TTTAATATGCATGCAGTGATTGTTGGTATGTTACCTATTT
Found at i:90306609 original size:29 final size:28
Alignment explanation
Indices: 90306552--90306611 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
90306542 GTGTTACCTA
**
90306552 TTTTTTAATATGCATGCAGTGGGTATTT
1 TTTTTTAATATGCATGCAGTGACTATTT
*
90306580 TTTTTATAATATGCATGTAGTGACT-TTT
1 TTTTT-TAATATGCATGCAGTGACTATTT
90306608 TTTT
1 TTTT
90306612 AGGAAGGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.55
Consensus pattern (28 bp):
TTTTTTAATATGCATGCAGTGACTATTT
Found at i:90308052 original size:38 final size:36
Alignment explanation
Indices: 90308010--90308095 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
90308000 GTTAGCCATT
* **
90308010 TATACCAGCAACCATGTATAACATATGTTAAGCAACAA
1 TATACTAGCAACCATGTATAACA-A-CATAAGCAACAA
* *
90308048 TATACTAGCAGCCATGTATACCAACATAAGCAACAA
1 TATACTAGCAACCATGTATAACAACATAAGCAACAA
90308084 TATACTAGCAAC
1 TATACTAGCAAC
90308096 AATATTACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 21 0.50
37 1 0.02
38 20 0.48
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.22
Consensus pattern (36 bp):
TATACTAGCAACCATGTATAACAACATAAGCAACAA
Found at i:90308110 original size:36 final size:36
Alignment explanation
Indices: 90308038--90308114 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
90308028 TAACATATGT
* * * *
90308038 TAAGCAACAATATACTAGCAGCCATGTATACCAACA
1 TAAGCAACAATATACTAGCAACAATATATACAAACA
90308074 TAAGCAACAATATACTAGCAACAATAT-TACAAAACA
1 TAAGCAACAATATACTAGCAACAATATATAC-AAACA
90308110 TAAGC
1 TAAGC
90308115 TGGTTTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 3 0.08
36 33 0.92
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.19
Consensus pattern (36 bp):
TAAGCAACAATATACTAGCAACAATATATACAAACA
Found at i:90308474 original size:19 final size:19
Alignment explanation
Indices: 90308447--90308483 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
90308437 CTTCAGGCAT
90308447 CTCCATTTTTCCTCTTCTC
1 CTCCATTTTTCCTCTTCTC
* *
90308466 CTCCTTTTTTCTTCTTCT
1 CTCCATTTTTCCTCTTCT
90308484 TTTTCTTTTT
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:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (19 bp):
CTCCATTTTTCCTCTTCTC
Found at i:90309960 original size:28 final size:28
Alignment explanation
Indices: 90309902--90309961 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
90309892 TCACTGCTAA
* *
90309902 TTATCAATATTTTATTTTATTATGTTGT
1 TTATCAATATTTTATTTTATTATATTAT
90309930 TTATCATATATTATTATTTTA-TA-ATTAT
1 TTATCA-ATATT-TTATTTTATTATATTAT
90309958 TTAT
1 TTAT
90309962 TTTTTAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.46
29 7 0.25
30 8 0.29
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (28 bp):
TTATCAATATTTTATTTTATTATATTAT
Found at i:90318392 original size:81 final size:81
Alignment explanation
Indices: 90318252--90318414 Score: 236
Period size: 81 Copynumber: 2.0 Consensus size: 81
90318242 GCATGATAGA
* ** *
90318252 ATGACGAGCACCATCTAAATGAACTATAGAGTATCACTATAAACAACTCTACATTGGTCAGGTGT
1 ATGACGAGCACCATCTAAATGAACTATAGAATATCACTATAAACAACTCTACAGCGGTCAAGTGT
*
90318317 GAGCACTATATTTAAG
66 GAACACTATATTTAAG
* * *
90318333 ATGATGAGCACCATCTAAATGAACTGTAGAATTTCACTATAAACAACTCTACAGCGGTCAAGTGT
1 ATGACGAGCACCATCTAAATGAACTATAGAATATCACTATAAACAACTCTACAGCGGTCAAGTGT
* *
90318398 GAACATTGTATTTAAG
66 GAACACTATATTTAAG
90318414 A
1 A
90318415 CAGGTAATGA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (81 bp):
ATGACGAGCACCATCTAAATGAACTATAGAATATCACTATAAACAACTCTACAGCGGTCAAGTGT
GAACACTATATTTAAG
Found at i:90320784 original size:33 final size:33
Alignment explanation
Indices: 90320746--90320809 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
90320736 CTAAGTGGGA
90320746 GTGTTTGGTTGCTGGACAGGAGCTGGAATGTGG
1 GTGTTTGGTTGCTGGACAGGAGCTGGAATGTGG
*
90320779 GTGTTTTGTTGCTGGACAGGAGCTGGAATGT
1 GTGTTTGGTTGCTGGACAGGAGCTGGAATGT
90320810 CAAGAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.09, G:0.42, T:0.33
Consensus pattern (33 bp):
GTGTTTGGTTGCTGGACAGGAGCTGGAATGTGG
Found at i:90336148 original size:24 final size:23
Alignment explanation
Indices: 90336086--90336156 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 23
90336076 CAGTAGCCCC
* *
90336086 TTAAATCTTTTAAAAAAATACAA
1 TTAAATATTTTAAAAAATTACAA
* * *
90336109 TT--ATACTTTAACAAATTACTAT
1 TTAAATATTTTAAAAAATTAC-AA
90336131 TTAAATATTTTAAAAAATTA-AA
1 TTAAATATTTTAAAAAATTACAA
90336153 TTAA
1 TTAA
90336157 TAAAAATAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
21 13 0.35
22 8 0.22
23 2 0.05
24 14 0.38
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAATATTTTAAAAAATTACAA
Found at i:90336210 original size:15 final size:17
Alignment explanation
Indices: 90336176--90336209 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
90336166 AATTATACTT
90336176 TAATCCCTAAAAAAATA
1 TAATCCCTAAAAAAATA
90336193 TAATCCCTAAAAAAATA
1 TAATCCCTAAAAAAATA
90336210 AAAATTCATA
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:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TAATCCCTAAAAAAATA
Found at i:90340244 original size:83 final size:85
Alignment explanation
Indices: 90340157--90340329 Score: 264
Period size: 83 Copynumber: 2.1 Consensus size: 85
90340147 TTTTTAAAAA
90340157 AAATTTTGATGTCC-AAAATACGAGTATTT-AAAAAAAATAGTGTTGGCCTGTCAATGGCCGGCA
1 AAATTTTGATGTCCGAAAATACGAGTATTTAAAAAAAAATAGTGTTGGCCTGTCAATGGCCGGCA
90340220 CCAAGTACAAAAAAAAAATC
66 CCAAGTACAAAAAAAAAATC
* * * *
90340240 AAA--TTGATTTCCGAAAATACGAGTTTTTAAAAAAAAATTGTGTTGGCCTGTTAATGGCCGGCA
1 AAATTTTGATGTCCGAAAATACGAGTATTTAAAAAAAAATAGTGTTGGCCTGTCAATGGCCGGCA
* *
90340303 CCAAGTACAAAAAAAAATTT
66 CCAAGTACAAAAAAAAAATC
90340323 AAATTTT
1 AAATTTT
90340330 TTTGGTGCTG
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
81 8 0.10
82 14 0.17
83 56 0.70
85 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (85 bp):
AAATTTTGATGTCCGAAAATACGAGTATTTAAAAAAAAATAGTGTTGGCCTGTCAATGGCCGGCA
CCAAGTACAAAAAAAAAATC
Found at i:90340343 original size:138 final size:139
Alignment explanation
Indices: 90340182--90340525 Score: 367
Period size: 141 Copynumber: 2.4 Consensus size: 139
90340172 AAATACGAGT
*
90340182 ATTTAAAAAAAATA-GTGTTGGCCTGTCAATGGCCGGCACCAAGTACAAAAAAAAAATCAAATTG
1 ATTTAAAAAAAATAGGTGCTGGCCTGTCAATGGCCGGCACCAA-TACAAAAAAAAAA--AAATTG
* * * **
90340246 AT-TTCCGAAAATACGAGTTTTTAAAAAAAAA-TT-GTGTTGGCCTGTTAATGGCCGGCACCAAG
63 ATATT-CGAAAATACAAGTTTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATAACCGGCACCAAG
90340308 TAC-AAAAAA-AA
127 TACAAAAAAATAA
***** * * ****
90340319 ATTTAAATTTTTTTGGTGCTGGCCTGTCAATGGCAGGCACCAATACGAGTTTTTTAAAAAAAATT
1 ATTTAAAAAAAATAGGTGCTGGCCTGTCAATGGCCGGCACCAATAC-A---AAAAAAAAAAAATT
90340384 GATATTCGAAAATACAAGTTTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATAACCGGCACCAAG
62 GATATTCGAAAATACAAGTTTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATAACCGGCACCAAG
90340449 TACAAAAAAATTAA
127 TACAAAAAAA-TAA
* * *
90340463 ATTTAAAAAAAATAGGTGTTGGCCTGTCAATGGCCAGCACCAAATACAAAAAAATTAAAAATT
1 ATTTAAAAAAAATAGGTGCTGGCCTGTCAATGGCCGGCACC-AATACAAAAAAA-AAAAAATT
90340526 CGTATCTGGT
Statistics
Matches: 163, Mismatches: 31, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
137 11 0.07
138 27 0.17
139 33 0.20
140 4 0.02
141 35 0.21
142 13 0.08
144 35 0.21
145 5 0.03
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (139 bp):
ATTTAAAAAAAATAGGTGCTGGCCTGTCAATGGCCGGCACCAATACAAAAAAAAAAAAATTGATA
TTCGAAAATACAAGTTTTTAAAAAAAAATTTGGTGCTGGCCTGTCAATAACCGGCACCAAGTACA
AAAAAATAA
Found at i:90340486 original size:58 final size:59
Alignment explanation
Indices: 90340408--90340521 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 59
90340398 CAAGTTTTTA
* * *
90340408 AAAAAAAATTTGGTGCTGGCCTGTCAATAACCGGCACCAAGTACAAAAAAATTAAATTT
1 AAAAAAAATTAGGTGCTGGCCTGTCAATAACCAGCACCAAATACAAAAAAATTAAATTT
* **
90340467 AAAAAAAA-TAGGTGTTGGCCTGTCAATGGCCAGCACCAAATACAAAAAAATTAAA
1 AAAAAAAATTAGGTGCTGGCCTGTCAATAACCAGCACCAAATACAAAAAAATTAAA
90340522 AATTCGTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 41 0.84
59 8 0.16
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (59 bp):
AAAAAAAATTAGGTGCTGGCCTGTCAATAACCAGCACCAAATACAAAAAAATTAAATTT
Found at i:90342239 original size:103 final size:104
Alignment explanation
Indices: 90342060--90342311 Score: 409
Period size: 103 Copynumber: 2.4 Consensus size: 104
90342050 ACCGTTATTA
* * * *
90342060 GTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAA
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
** *
90342125 TCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATACG
66 TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
90342163 GTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGGA
90342227 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
65 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
*
90342267 GTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCAC
1 GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCAC
90342312 ACAACAACCT
Statistics
Matches: 138, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
102 1 0.01
103 81 0.59
104 55 0.40
105 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (104 bp):
GTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAA
TCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACG
Found at i:90345808 original size:21 final size:20
Alignment explanation
Indices: 90345784--90345832 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
90345774 AATGAAGTTG
* *
90345784 AAATGAATTAAAATTAAAATA
1 AAATGAATGAAAATGAAAA-A
*
90345805 AAATGAGATGAAAATGAAAAG
1 AAATGA-ATGAAAATGAAAAA
90345826 AAATGAA
1 AAATGAA
90345833 AAAAAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.20
Consensus pattern (20 bp):
AAATGAATGAAAATGAAAAA
Found at i:90348637 original size:141 final size:141
Alignment explanation
Indices: 90348353--90348714 Score: 511
Period size: 142 Copynumber: 2.6 Consensus size: 141
90348343 CAAACTCATA
* *
90348353 TTGGTGCCACCCATTGACAGGCC-A-TCAA-TTTTTTTTTAAAACTCGTATTTTCGGAA-ATC-A
1 TTGGTGCCAGCCATTGACAGGCCAACACAATTTTTTTTTTAAAACTCGTATTTTC-GAACATCAA
* *
90348413 AATTTTTTTTAAAAAACTCGTATTGGTGCTGACCATTGACAGGCCAGCACCAAAAAAATTTGAAT
65 AATTTTTTTAAAAAAACTCGTATTGGTGCAGACCATTGACAGGCCAGCACCAAAAAAATTTGAAT
90348478 TTTTTTTTGTAC
130 TTTTTTTTGTAC
* * * *
90348490 TTGGTGCCGGCCATTGACAGGCCAACACAATTTTTTTTTTAAAAATTCGTACTTTCAAACATCAA
1 TTGGTGCCAGCCATTGACAGGCCAACACAATTTTTTTTTT-AAAACTCGTATTTTCGAACATCAA
*
90348555 AATTTTTTTAAAAAAACTCGTATTGGTGCAGGCCATTGACAGGCCAGCACCAAAAAAATTTG-AT
65 AATTTTTTTAAAAAAACTCGTATTGGTGCAGACCATTGACAGGCCAGCACCAAAAAAATTTGAAT
90348619 TTTTTTTTGTAC
130 TTTTTTTTGTAC
** *
90348631 TTGGTGCCAGCCATTGACAGGCCAACACCAAAATTTTCATTTTAAAACTCGTATTTTCGGACAAT
1 TTGGTGCCAGCCATTGACAGGCCAACA-C--AATTTTTTTTTTAAAACTCGTATTTTCGAAC-AT
*
90348696 AAAAATTTTTTTAAAAAAA
62 CAAAATTTTTTTAAAAAAA
90348715 ATTGATTTTT
Statistics
Matches: 198, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
137 21 0.11
138 1 0.01
139 3 0.02
140 11 0.06
141 56 0.28
142 61 0.31
143 15 0.08
144 30 0.15
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (141 bp):
TTGGTGCCAGCCATTGACAGGCCAACACAATTTTTTTTTTAAAACTCGTATTTTCGAACATCAAA
ATTTTTTTAAAAAAACTCGTATTGGTGCAGACCATTGACAGGCCAGCACCAAAAAAATTTGAATT
TTTTTTTGTAC
Found at i:90348782 original size:101 final size:102
Alignment explanation
Indices: 90348606--90348814 Score: 282
Period size: 101 Copynumber: 2.1 Consensus size: 102
90348596 GGCCAGCACC
*
90348606 AAAAAAATTTGATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACACCAAAATTTTCAT
1 AAAAAAAATTGATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACACCAAAATTTTCAT
* *
90348671 TTTAAAACTCGTATTTTCGGACAATAAAAATTTTTTT
66 TTTAAAACTCGAATTTTCAGACAATAAAAATTTTTTT
* *
90348708 AAAAAAAATTGA-TTTTTTTTGTACTTGGTGCCAGCCATT-ACAGGCCAGCACC-AAATTTT-TT
1 AAAAAAAATTGATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACACCAAAATTTTCAT
* * *
90348769 TTTAAAAAAACTCGAATTTTCAGATATTAAAATTTTTTTT
66 TTT---AAAACTCGAATTTTCAGACAATAAAAATTTTTTT
*
90348809 TAAAAA
1 AAAAAA
90348815 CTTGTATTGG
Statistics
Matches: 95, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
98 4 0.04
99 7 0.07
100 12 0.13
101 61 0.64
102 11 0.12
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (102 bp):
AAAAAAAATTGATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACACCAAAATTTTCAT
TTTAAAACTCGAATTTTCAGACAATAAAAATTTTTTT
Found at i:90348924 original size:244 final size:243
Alignment explanation
Indices: 90348464--90348944 Score: 659
Period size: 244 Copynumber: 2.0 Consensus size: 243
90348454 GGCCAGCACC
* *
90348464 AAAAAAATTTGAATTTTTTTTTGTACTTGGTGCCGGCCATTGACAGGCCAACACAATTTTTTTTT
1 AAAAAAAATTGAATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACACAATTTTTTTTT
* * * *
90348529 TAAAAATTCGTACTTTCAAACATCAAAATTTTTTTAAAAAAACTCGTATTGGTGCAGGCCATTGA
66 AAAAAACTCGAACTTTCAAACATCAAAATTTTTTTAAAAAAACTCGTATTGGTGCAGACCATTGA
*
90348594 CAGGCCAGCACCAAAAAAATTTGATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACAC
131 CAGGCCAGCACCAAAAAAATTTGAATTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACAC
*
90348659 CAAAATTTTCATTTTAAAACTCGTATTTTCGGACAATAAAAATTTTTTT
196 C-AAATTTTCATTTTAAAACTCGTATTTTCAGACAATAAAAATTTTTTT
*
90348708 AAAAAAAATTG-A-TTTTTTTTGTACTTGGTGCCAGCCATT-ACAGGCCAGCACCAAATTTTTTT
1 AAAAAAAATTGAATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACA-C-AATTTTTTT
* * * * ** * *
90348770 TTAAAAAAACTCGAATTTTCAGATATTAAAATTTTTTTTTAAAAACTTGTATTGGTGCCGACCAT
64 TT-AAAAAACTCGAACTTTCAAACATCAAAATTTTTTTAAAAAAACTCGTATTGGTGCAGACCAT
* *
90348835 TGACAGGGCAGCACCAAAAAAATTTGAATTTTTTTT-TACTTGGTGCCGGCCATTGACAGGCCAA
128 TGACAGGCCAGCACCAAAAAAATTTGAATTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAA
* *
90348899 CACC-AATTTT-TTTTTAAAAAAAACTCGTATTTTCAGACATTAAAAA
193 CACCAAATTTTCATTTT----AAAACTCGTATTTTCAGACAATAAAAA
90348945 AAATTTAATT
Statistics
Matches: 209, Mismatches: 21, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
240 4 0.02
241 16 0.08
242 27 0.13
243 43 0.21
244 119 0.57
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (243 bp):
AAAAAAAATTGAATTTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACACAATTTTTTTTT
AAAAAACTCGAACTTTCAAACATCAAAATTTTTTTAAAAAAACTCGTATTGGTGCAGACCATTGA
CAGGCCAGCACCAAAAAAATTTGAATTTTTTTTGTACTTGGTGCCAGCCATTGACAGGCCAACAC
CAAATTTTCATTTTAAAACTCGTATTTTCAGACAATAAAAATTTTTTT
Found at i:90349087 original size:105 final size:99
Alignment explanation
Indices: 90348943--90349126 Score: 253
Period size: 105 Copynumber: 1.8 Consensus size: 99
90348933 AGACATTAAA
* *
90348943 AAAAATTTAATTTTTTTTTTGTATTTGGTGTCGGCCATTGACAGGCCAGCACCAAAAAGAAAAAC
1 AAAAATTTAATTTTTTTTTTGTACTTGGTGTCGGCCATTGACAGGCCAGCAAC-AAAA-AAAAA-
90349008 TTAAAAAACTCATATTTTCGGACATCAAAAAAAAATTT
63 TT-AAAAACTCATATTTTCGGACATCAAAAAAAAATTT
* *
90349046 AAAAATTTGAATTTTTTTATTTTTACTTGGTG-CTGGTCATTGACAGGCCAGCAACAAAAAAAAA
1 AAAAATTT-AATTTTTTT-TTTGTACTTGGTGTC-GGCCATTGACAGGCCAGCAACAAAAAAAAA
*
90349110 TTAAAAACTCGTATTTT
63 TTAAAAACTCATATTTT
90349127 ATATACCAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
101 14 0.19
102 2 0.03
103 13 0.18
104 14 0.19
105 30 0.41
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (99 bp):
AAAAATTTAATTTTTTTTTTGTACTTGGTGTCGGCCATTGACAGGCCAGCAACAAAAAAAAATTA
AAAACTCATATTTTCGGACATCAAAAAAAAATTT
Found at i:90349947 original size:8 final size:8
Alignment explanation
Indices: 90349936--90350002 Score: 73
Period size: 9 Copynumber: 8.0 Consensus size: 8
90349926 TTTTTCTTTA
90349936 ATTTTTTT
1 ATTTTTTT
90349944 ATTTTTTT
1 ATTTTTTT
90349952 AATTTTTTT
1 -ATTTTTTT
90349961 A-TTTTTT
1 ATTTTTTT
* *
90349968 CTTATTTT
1 ATTTTTTT
90349976 ATTTTGTTT
1 ATTTT-TTT
90349985 ATTTTGTTT
1 ATTTT-TTT
90349994 ATTTATTTT
1 ATTT-TTTT
90350003 TTGTTATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
7 6 0.12
8 17 0.33
9 27 0.53
10 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.03, T:0.81
Consensus pattern (8 bp):
ATTTTTTT
Found at i:90349949 original size:9 final size:9
Alignment explanation
Indices: 90349926--90350010 Score: 66
Period size: 9 Copynumber: 9.2 Consensus size: 9
90349916 AACTTTTGTC
90349926 TTTTTCTTTA
1 TTTTT-TTTA
*
90349936 ATTTTTTTA
1 TTTTTTTTA
90349945 -TTTTTTTA
1 TTTTTTTTA
*
90349953 ATTTTTTTA
1 TTTTTTTTA
90349962 TTTTTTCTTA
1 TTTTTT-TTA
*
90349972 TTTTATTTTG
1 TTTT-TTTTA
*
90349982 TTTATTTT-
1 TTTTTTTTA
* *
90349990 GTTTATTTA
1 TTTTTTTTA
90349999 TTTTTTGTTA
1 TTTTTT-TTA
90350009 TT
1 TT
90350011 AATTTTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
8 13 0.21
9 25 0.41
10 21 0.34
11 2 0.03
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:90349954 original size:17 final size:16
Alignment explanation
Indices: 90349936--90350002 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 16
90349926 TTTTTCTTTA
90349936 ATTTTTTTATTTTTTT
1 ATTTTTTTATTTTTTT
90349952 AATTTTTTTA-TTTTTT
1 -ATTTTTTTATTTTTTT
* *
90349968 CTTATTTTATTTTGTTT
1 ATTTTTTTATTTT-TTT
90349985 ATTTTGTTTATTTATTTT
1 ATTTT-TTTATTT-TTTT
90350003 TTGTTATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 7 0.17
16 9 0.21
17 15 0.36
18 10 0.24
19 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.03, T:0.81
Consensus pattern (16 bp):
ATTTTTTTATTTTTTT
Found at i:90349957 original size:14 final size:13
Alignment explanation
Indices: 90349926--90350002 Score: 59
Period size: 13 Copynumber: 5.8 Consensus size: 13
90349916 AACTTTTGTC
* *
90349926 TTTTTCTTTAATT
1 TTTTTATTTTATT
90349939 TTTTTATTTT-TT
1 TTTTTATTTTATT
*
90349951 TAATTT-TTTTATTT
1 T-TTTTATTTTA-TT
90349965 TTTCTTATTTTATT
1 TTT-TTATTTTATT
*
90349979 TTGTTTATTTTGTT
1 TT-TTTATTTTATT
*
90349993 TATTTATTTT
1 TTTTTATTTT
90350003 TTGTTATTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 7 0.13
13 20 0.38
14 19 0.37
15 6 0.12
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:90349967 original size:37 final size:37
Alignment explanation
Indices: 90349926--90350017 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 37
90349916 AACTTTTGTC
*
90349926 TTTTTCTTTAATTT-TTTTATTT-TTTTAATTTTTTTAT
1 TTTTTC-TTAATTTATTTTATTTATTTT-ATTTATTTAT
* * *
90349963 TTTTTCTTATTTTATTTTGTTTATTTTGTTTATTTAT
1 TTTTTCTTAATTTATTTTATTTATTTTATTTATTTAT
* *
90350000 TTTTTGTT-ATTAATTTTA
1 TTTTTCTTAATTTATTTTA
90350018 AAAATTTGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
36 13 0.29
37 28 0.62
38 4 0.09
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.78
Consensus pattern (37 bp):
TTTTTCTTAATTTATTTTATTTATTTTATTTATTTAT
Found at i:90350003 original size:14 final size:13
Alignment explanation
Indices: 90349937--90350016 Score: 65
Period size: 13 Copynumber: 6.0 Consensus size: 13
90349927 TTTTCTTTAA
90349937 TTTT-TTTATTTT
1 TTTTATTTATTTT
*
90349949 TTTAATTT-TTTT
1 TTTTATTTATTTT
*
90349961 ATTTTTTCTTATTTT
1 -TTTTAT-TTATTTT
*
90349976 ATTTTGTTTATTTT
1 -TTTTATTTATTTT
*
90349990 GTTTATTTATTTT
1 TTTTATTTATTTT
*
90350003 TTGTTATTAATTTT
1 TT-TTATTTATTTT
90350017 AAAAATTTGA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
12 7 0.13
13 19 0.35
14 19 0.35
15 10 0.18
ACGTcount: A:0.15, C:0.01, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTATTTATTTT
Found at i:90350009 original size:23 final size:23
Alignment explanation
Indices: 90349940--90350010 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
90349930 TCTTTAATTT
* *
90349940 TTTTATTTTTTTAATTTTT-TTA
1 TTTTATTTATTTATTTTTTGTTA
* *
90349962 TTTTTTCTTATTT-TATTTTGTTTA
1 TTTTAT-TTATTTATTTTTTG-TTA
*
90349986 TTTTGTTTATTTATTTTTTGTTA
1 TTTTATTTATTTATTTTTTGTTA
90350009 TT
1 TT
90350011 AATTTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
22 9 0.23
23 16 0.41
24 14 0.36
ACGTcount: A:0.14, C:0.01, G:0.04, T:0.80
Consensus pattern (23 bp):
TTTTATTTATTTATTTTTTGTTA
Found at i:90350103 original size:34 final size:35
Alignment explanation
Indices: 90350065--90350145 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
90350055 ATATTTTTTA
*
90350065 AAATTTTAAATTAT-TTTTTTAAATT-ATGTCTTAT
1 AAATTTTAAATTATATTTTTGAAATTAAT-TCTTAT
* * *
90350099 AAATTTTAAAATATATTTTTGAAATTAATTTTTCT
1 AAATTTTAAATTATATTTTTGAAATTAATTCTTAT
90350134 AAATTTTAAATT
1 AAATTTTAAATT
90350146 TTAAATATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
34 13 0.32
35 25 0.62
36 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (35 bp):
AAATTTTAAATTATATTTTTGAAATTAATTCTTAT
Found at i:90350173 original size:14 final size:14
Alignment explanation
Indices: 90350148--90350176 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90350138 TTTAAATTTT
90350148 AAATATATTTTTAA
1 AAATATATTTTTAA
90350162 AAATATATTTTTAA
1 AAATATATTTTTAA
90350176 A
1 A
90350177 CAAAATGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATTTTTAA
Found at i:90350240 original size:21 final size:20
Alignment explanation
Indices: 90350207--90350248 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
90350197 TTTAAATATT
*
90350207 ATTTTTAAATTATTTTTTAA
1 ATTTTGAAATTATTTTTTAA
90350227 ATTTTGAATATTATTTTTTAA
1 ATTTTGAA-ATTATTTTTTAA
90350248 A
1 A
90350249 ATTATGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTGAAATTATTTTTTAA
Found at i:90350304 original size:163 final size:163
Alignment explanation
Indices: 90350056--90350486 Score: 805
Period size: 163 Copynumber: 2.7 Consensus size: 163
90350046 TTATAATATA
* *
90350056 TATTTTTTAAAATTTT-AA-ATTATTTTTTTAAATTATGTCTTATAAATTTT-AAAATATATTTT
1 TATTTTTT-AAATTTTGAATATTATTTTTTAAAATTATGTCTTATAAATTTTAAAAATATATATT
90350118 TGAAATTAATTTTTCTAAATTTTAAATTTTAAATATATTTTTAAAAATATATTTTTAAACAAAAT
65 TGAAATTAATTTTTCTAAATTTTAAATTTTAAATATATTTTTAAAAATATATTTTTAAACAAAAT
90350183 GAAATAATTTCAATTTTAAATATTATTTTTAAAT
130 GAAATAATTTCAATTTTAAATATTATTTTTAAAT
90350217 TATTTTTTAAATTTTGAATATTATTTTTTAAAATTATGTCTTATAAATTTTAAAAATATATATTT
1 TATTTTTTAAATTTTGAATATTATTTTTTAAAATTATGTCTTATAAATTTTAAAAATATATATTT
90350282 GAAATTAATTTTTCTAAATTTTAAATTTTAAATATATTTTTAAAAATATATTTTTAAACAAAATG
66 GAAATTAATTTTTCTAAATTTTAAATTTTAAATATATTTTTAAAAATATATTTTTAAACAAAATG
90350347 AAATAATTTCAATTTTAAATATTATTTTTAAAT
131 AAATAATTTCAATTTTAAATATTATTTTTAAAT
90350380 TATTTTTTAAATTTTGAATATTATTTTTTAAAATTATGTCTTATAAATTTTAAAAATATATATTT
1 TATTTTTTAAATTTTGAATATTATTTTTTAAAATTATGTCTTATAAATTTTAAAAATATATATTT
90350445 GAAATTAATTTTTCTAAATTTTAAATTTTAAATATATATTTT
66 GAAATTAATTTTTCTAAATTTTAAATTTTAAATATAT-TTTT
90350487 TGAAATTATT
Statistics
Matches: 264, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
160 7 0.03
161 10 0.04
162 31 0.12
163 212 0.80
164 4 0.02
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (163 bp):
TATTTTTTAAATTTTGAATATTATTTTTTAAAATTATGTCTTATAAATTTTAAAAATATATATTT
GAAATTAATTTTTCTAAATTTTAAATTTTAAATATATTTTTAAAAATATATTTTTAAACAAAATG
AAATAATTTCAATTTTAAATATTATTTTTAAAT
Found at i:90350328 original size:14 final size:14
Alignment explanation
Indices: 90350311--90350339 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90350301 TTTAAATTTT
90350311 AAATATATTTTTAA
1 AAATATATTTTTAA
90350325 AAATATATTTTTAA
1 AAATATATTTTTAA
90350339 A
1 A
90350340 CAAAATGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATTTTTAA
Found at i:90350403 original size:21 final size:20
Alignment explanation
Indices: 90350370--90350411 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
90350360 TTTAAATATT
*
90350370 ATTTTTAAATTATTTTTTAA
1 ATTTTGAAATTATTTTTTAA
90350390 ATTTTGAATATTATTTTTTAA
1 ATTTTGAA-ATTATTTTTTAA
90350411 A
1 A
90350412 ATTATGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTGAAATTATTTTTTAA
Found at i:90350450 original size:36 final size:35
Alignment explanation
Indices: 90350357--90350545 Score: 147
Period size: 36 Copynumber: 5.3 Consensus size: 35
90350347 AAATAATTTC
* * *
90350357 AATTTTAAATAT-TAT-TTTTAAATTATT-TTTTA
1 AATTTTAAAAATATATATTTGAAATTATTCTTATA
* * * *
90350389 AATTTTGAATAT-TATTTTTTAAAATTATGTCTTATA
1 AATTTTAAAAATATA-TATTTGAAATTAT-TCTTATA
* *
90350425 AATTTTAAAAATATATATTTGAAATTAATTTTTCTA
1 AATTTTAAAAATATATATTTGAAATT-ATTCTTATA
90350461 AATTTTAAATTTTAAATATATATTTTTGAAATTATTTCTTATA
1 AATTTT-AA----AAATATATA--TTTGAAATTA-TTCTTATA
*
90350504 AATTTTAAAAATATATTTTTGAAATTATT-TT-TA
1 AATTTTAAAAATATATATTTGAAATTATTCTTATA
90350537 AATTTTAAA
1 AATTTTAAA
90350546 TATTATTTTA
Statistics
Matches: 131, Mismatches: 12, Indels: 27
0.77 0.07 0.16
Matches are distributed among these distances:
32 13 0.10
33 12 0.09
34 12 0.09
35 3 0.02
36 44 0.34
37 6 0.05
38 8 0.06
41 9 0.07
42 3 0.02
43 21 0.16
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (35 bp):
AATTTTAAAAATATATATTTGAAATTATTCTTATA
Found at i:90350470 original size:43 final size:41
Alignment explanation
Indices: 90350423--90350546 Score: 161
Period size: 36 Copynumber: 3.1 Consensus size: 41
90350413 TTATGTCTTA
*
90350423 TAAATTTTAAAAATATATATTTGAAATTAATTTTTCTAAATTT
1 TAAATTTTAAAAATATATTTTTGAAATT-A-TTTTCTAAATTT
* *
90350466 TAAATTTTAAATATATATTTTTGAAATTA-TTTC----TTA
1 TAAATTTTAAAAATATATTTTTGAAATTATTTTCTAAATTT
90350502 TAAATTTTAAAAATATATTTTTGAAATTATTTT-TAAATTT
1 TAAATTTTAAAAATATATTTTTGAAATTATTTTCTAAATTT
90350542 TAAAT
1 TAAAT
90350547 ATTATTTTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
36 30 0.42
37 3 0.04
40 11 0.15
42 1 0.01
43 26 0.37
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (41 bp):
TAAATTTTAAAAATATATTTTTGAAATTATTTTCTAAATTT
Found at i:90350553 original size:12 final size:12
Alignment explanation
Indices: 90350538--90350562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90350528 TTATTTTTAA
90350538 ATTTTAAATATT
1 ATTTTAAATATT
90350550 ATTTTAAATATT
1 ATTTTAAATATT
90350562 A
1 A
90350563 AATATATTTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTAAATATT
Found at i:90350554 original size:19 final size:19
Alignment explanation
Indices: 90350527--90350577 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
90350517 TATTTTTGAA
*
90350527 ATTATTTTTAAATTTTAAAT
1 ATTA-TTTTAAATATTAAAT
90350547 ATTATTTTAAATATTAAAT
1 ATTATTTTAAATATTAAAT
*
90350566 A-TATTTTTAATA
1 ATTATTTTAAATA
90350578 ATATTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 10 0.34
19 15 0.52
20 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTATTTTAAATATTAAAT
Done.