Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 112 of 185
Found at i:35056683 original size:81 final size:81
Alignment explanation
Indices: 35056547--35056700 Score: 247
Period size: 81 Copynumber: 1.9 Consensus size: 81
35056537 TTTTGGGGCA
* *
35056547 TTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTTGATAAAGCG
1 TTTAGCGGCATTTTGGAAAAAGCGCCGCTAATGC-CTGACCTTTAGCGGCGTTTTTGAAAAAGCG
35056612 CCGCTAATGCTCTTGCC
65 CCGCTAATGCTCTTGCC
* *
35056629 TTTAGCGGCGTTTCTGGAAAAAGCGCCGCTAATG-CTGACCTTTAGTGGCGTTTTTGAAAAAGCG
1 TTTAGCGGCATTT-TGGAAAAAGCGCCGCTAATGCCTGACCTTTAGCGGCGTTTTTGAAAAAGCG
35056693 CCGCTAAT
65 CCGCTAAT
35056701 AATAAAATCT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
81 36 0.54
82 12 0.18
83 19 0.28
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (81 bp):
TTTAGCGGCATTTTGGAAAAAGCGCCGCTAATGCCTGACCTTTAGCGGCGTTTTTGAAAAAGCGC
CGCTAATGCTCTTGCC
Found at i:35060394 original size:48 final size:48
Alignment explanation
Indices: 35060320--35060419 Score: 191
Period size: 48 Copynumber: 2.1 Consensus size: 48
35060310 TAACAGTTCA
35060320 TCTTTCATCAGAAAGGGTAGTACCTTTGAGTAACCAATTCTTATATTT
1 TCTTTCATCAGAAAGGGTAGTACCTTTGAGTAACCAATTCTTATATTT
*
35060368 TCTTTCATCAGAAAGGGTAGTTCCTTTGAGTAACCAATTCTTATATTT
1 TCTTTCATCAGAAAGGGTAGTACCTTTGAGTAACCAATTCTTATATTT
35060416 TCTT
1 TCTT
35060420 CTTTTTTAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (48 bp):
TCTTTCATCAGAAAGGGTAGTACCTTTGAGTAACCAATTCTTATATTT
Found at i:35061615 original size:42 final size:42
Alignment explanation
Indices: 35061478--35061718 Score: 315
Period size: 42 Copynumber: 5.7 Consensus size: 42
35061468 ATTAGGTTGT
* ** *
35061478 CTAAAGGTCATGGTCTTTAGCGGCGTTTGTTTAAAAAAGCGCTG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTG--TGGAAAAGCGCCG
* * *
35061522 CTAAAGGTCATGGTCTTTAGCGACGTTTGT--ATAAAGCACCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGA-AAAGCGCCG
*
35061563 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAGCGCCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAGCGCCG
* * *
35061605 CTAAAAGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAGCGCTG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAGCGCCG
* *
35061647 TTAAAGGTCTTGGTTTTTAGCGGCGTTTGTGGAAAAGCGCCG
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAGCGCCG
*
35061689 CTAAAGGTCTTGTTCTTTAGCGGCGTTTGT
1 CTAAAGGTCTTGGTCTTTAGCGGCGTTTGT
35061719 TTCTAAAACC
Statistics
Matches: 177, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
40 1 0.01
41 35 0.20
42 113 0.64
44 28 0.16
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.32
Consensus pattern (42 bp):
CTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGAAAAGCGCCG
Found at i:35064069 original size:23 final size:23
Alignment explanation
Indices: 35064039--35064087 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
35064029 GCATGGTATA
*
35064039 TGTAATGAC-CTGATAGTCAGGGG
1 TGTAATGACTC-GATAGTCACGGG
35064062 TGTAATGACTCGATAGTCACGGG
1 TGTAATGACTCGATAGTCACGGG
35064085 TGT
1 TGT
35064088 CTAAAAGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (23 bp):
TGTAATGACTCGATAGTCACGGG
Found at i:35064650 original size:5 final size:5
Alignment explanation
Indices: 35064371--35064634 Score: 528
Period size: 5 Copynumber: 52.8 Consensus size: 5
35064361 TTATTAACTA
35064371 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35064421 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35064471 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35064521 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35064571 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
35064621 TATAT TATAT TATA
1 TATAT TATAT TATA
35064635 ATAAGTAAAT
Statistics
Matches: 259, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 259 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:35064680 original size:20 final size:20
Alignment explanation
Indices: 35064650--35064693 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35064640 TAAATATAAT
35064650 AAATAAAAGAAACA-AAAAG
1 AAATAAAAGAAACATAAAAG
*
35064669 AAATAGAAAGAAACATAATAG
1 AAATA-AAAGAAACATAAAAG
35064690 AAAT
1 AAAT
35064694 TAAACAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 9 0.41
21 8 0.36
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (20 bp):
AAATAAAAGAAACATAAAAG
Found at i:35064734 original size:13 final size:15
Alignment explanation
Indices: 35064707--35064746 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
35064697 ACAGGGAGAA
35064707 AAAGAAA-GA-AAAG
1 AAAGAAAGGAGAAAG
35064720 AAA-AAAGG-GAAAG
1 AAAGAAAGGAGAAAG
35064733 AAAGAAAGGAGAAA
1 AAAGAAAGGAGAAA
35064747 TTAGAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 5 0.22
15 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAGAAAGGAGAAAG
Found at i:35066784 original size:43 final size:44
Alignment explanation
Indices: 35066710--35066813 Score: 102
Period size: 43 Copynumber: 2.4 Consensus size: 44
35066700 TCGAAAGTAT
* ** *
35066710 ATGGCACTAAGTATGCGAAGTTAAGATAGCTTCGACTGAAT-AA
1 ATGGCACTAAGTGTGCGAAGCCAAGAGAGCTTCGACTGAATGAA
* * ** * **
35066753 ATGGCACTAAGTGTGCGATGCCGAGAGAGCTTCGGTTTAATGTG
1 ATGGCACTAAGTGTGCGAAGCCAAGAGAGCTTCGACTGAATGAA
35066797 ATGGCACTAAGTGTGCG
1 ATGGCACTAAGTGTGCG
35066814 GCATCGTTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
43 32 0.65
44 17 0.35
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (44 bp):
ATGGCACTAAGTGTGCGAAGCCAAGAGAGCTTCGACTGAATGAA
Found at i:35073209 original size:18 final size:18
Alignment explanation
Indices: 35073186--35073239 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
35073176 AATTTTTATG
35073186 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
35073204 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
35073222 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
35073240 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:35077548 original size:25 final size:25
Alignment explanation
Indices: 35077520--35077611 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 25
35077510 TATCGATATT
*
35077520 TGGCTCTCACGAGCTTCCCAATTAA
1 TGGCTCTCATGAGCTTCCCAATTAA
* *
35077545 TGGCTCTCTTGAGCTTCCCGA-TAA
1 TGGCTCTCATGAGCTTCCCAATTAA
* *
35077569 TTGGCTCGT-ATGAGCTTTCCAATTTA
1 -TGGCTC-TCATGAGCTTCCCAATTAA
*
35077595 TGGCTCTTATGAGCTTC
1 TGGCTCTCATGAGCTTC
35077612 TCGATATACA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
24 4 0.07
25 48 0.87
26 3 0.05
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (25 bp):
TGGCTCTCATGAGCTTCCCAATTAA
Found at i:35077584 original size:50 final size:50
Alignment explanation
Indices: 35077499--35077617 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 50
35077489 ACACCATAGT
* ** *
35077499 TCTTATGAGCATATCGATATTTGGCTCTCACGAGCTTCCCAATTAATGGC
1 TCTTATGAGCTTCCCGATAATTGGCTCTCACGAGCTTCCCAATTAATGGC
* * *
35077549 TCTCT-TGAGCTTCCCGATAATTGGCTCGT-ATGAGCTTTCCAATTTATGGC
1 TCT-TATGAGCTTCCCGATAATTGGCTC-TCACGAGCTTCCCAATTAATGGC
*
35077599 TCTTATGAGCTTCTCGATA
1 TCTTATGAGCTTCCCGATA
35077618 TACAACTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.02
50 55 0.95
51 2 0.03
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (50 bp):
TCTTATGAGCTTCCCGATAATTGGCTCTCACGAGCTTCCCAATTAATGGC
Found at i:35077708 original size:25 final size:25
Alignment explanation
Indices: 35077653--35077708 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
35077643 TACAGCTCAC
*
35077653 ATGAGCTTCCTGTTACATGGCTTGA
1 ATGAGCTTCATGTTACATGGCTTGA
* *
35077678 AAGAGCTTCATGTTTACAT-GCTTGT
1 ATGAGCTTCATG-TTACATGGCTTGA
35077703 ATGAGC
1 ATGAGC
35077709 ATACCTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (25 bp):
ATGAGCTTCATGTTACATGGCTTGA
Found at i:35084254 original size:24 final size:24
Alignment explanation
Indices: 35084227--35084291 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
35084217 CTCGTTATTG
35084227 GCTCATAT-GAGCTTCCCATTAATA
1 GCTC-TATGGAGCTTCCCATTAATA
*
35084251 GCTCTTTGGAGCTTCCCATTAATA
1 GCTCTATGGAGCTTCCCATTAATA
*
35084275 GCTCTCTGGAGCTTCCC
1 GCTCTATGGAGCTTCCC
35084292 GTTACATGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 2 0.05
24 36 0.95
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (24 bp):
GCTCTATGGAGCTTCCCATTAATA
Found at i:35087587 original size:71 final size:71
Alignment explanation
Indices: 35087471--35087613 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
35087461 CACCGCTCTT
* *
35087471 CCTATCTTCCCCCACCGCACCTCACTTCTCCCTTCATCATCCCTTCATGTCCATCGAACCCCCGC
1 CCTATCTTCCCCAACCCCACCTCACTTCTCCCTTCATCATCCCTTCATGTCCATCGAACCCCCGC
35087536 CACCGG
66 CACCGG
*
35087542 CCTATCTTCCCCAACCCCACCTCACTTCTCCCTTCATCATCCCTTCATGTCCATCGAACCCCTGC
1 CCTATCTTCCCCAACCCCACCTCACTTCTCCCTTCATCATCCCTTCATGTCCATCGAACCCCCGC
35087607 CACCGG
66 CACCGG
35087613 C
1 C
35087614 TACGCCGCAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.16, C:0.52, G:0.08, T:0.24
Consensus pattern (71 bp):
CCTATCTTCCCCAACCCCACCTCACTTCTCCCTTCATCATCCCTTCATGTCCATCGAACCCCCGC
CACCGG
Found at i:35088964 original size:14 final size:14
Alignment explanation
Indices: 35088945--35088986 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
35088935 ATTTTTAACT
35088945 CTTATTATAATACA
1 CTTATTATAATACA
*
35088959 CTTATTATAATACT
1 CTTATTATAATACA
*
35088973 CTTATTATTATACA
1 CTTATTATAATACA
35088987 TTGAGTAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (14 bp):
CTTATTATAATACA
Found at i:35099694 original size:121 final size:118
Alignment explanation
Indices: 35099536--35099762 Score: 310
Period size: 121 Copynumber: 1.9 Consensus size: 118
35099526 TCGAAAATCC
* * * *
35099536 GATGATATTCGGACCCACACTCGTATCTGACACTTACAAGTAGGTTACTGGGTTTAAGTCGACAC
1 GATGATATTCAGACCCACACTCATATCTGACACTTACAAGTAGGTTACTAGGTTTAA-TAGA-AC
* * * *
35099601 ATGGATATGCAGATATGGCTTTGAAACATGAAAAAATGTAGAAATGTAGAAAAAAT
64 ATCGATATGCAGATATGACCTCGAAACATG-AAAAATGTAGAAATGTAGAAAAAAT
* ** *
35099657 GATGATATTCAGACCCATACTCATATCTGACGGTTACAAGTAGGTTACTAGGTTTAATATAACAT
1 GATGATATTCAGACCCACACTCATATCTGACACTTACAAGTAGGTTACTAGGTTTAATAGAACAT
*
35099722 CGATATGCGGATATGACCTCGAAACATGAAAAATGTAGAAA
66 CGATATGCAGATATGACCTCGAAACATGAAAAATGTAGAAA
35099763 ATCCGACTAC
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
118 13 0.14
119 27 0.29
120 2 0.02
121 51 0.55
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (118 bp):
GATGATATTCAGACCCACACTCATATCTGACACTTACAAGTAGGTTACTAGGTTTAATAGAACAT
CGATATGCAGATATGACCTCGAAACATGAAAAATGTAGAAATGTAGAAAAAAT
Found at i:35102942 original size:5 final size:5
Alignment explanation
Indices: 35102932--35102958 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
35102922 ATAGACGATA
35102932 TATTG TATTG TATTG TATTG TATTG TA
1 TATTG TATTG TATTG TATTG TATTG TA
35102959 AAATACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (5 bp):
TATTG
Found at i:35113382 original size:26 final size:26
Alignment explanation
Indices: 35113330--35113397 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
35113320 CTAACAAACA
* *
35113330 AAAAAAAATTTAAGACAAAGGACAAC
1 AAAAAAAATTCAAAACAAAGGACAAC
* * *
35113356 AAAAAAAATTCAAAAGAAATGATAAC
1 AAAAAAAATTCAAAACAAAGGACAAC
*
35113382 AGCAGAAAAATTCAAA
1 A--AAAAAAATTCAAA
35113398 TAAAGAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 22 0.65
28 12 0.35
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.13
Consensus pattern (26 bp):
AAAAAAAATTCAAAACAAAGGACAAC
Found at i:35114773 original size:16 final size:16
Alignment explanation
Indices: 35114752--35114787 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
35114742 AAACGGAAAG
35114752 TATATAGATATACATA
1 TATATAGATATACATA
35114768 TATATAGATATACATA
1 TATATAGATATACATA
35114784 TATA
1 TATA
35114788 AAAAAGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TATATAGATATACATA
Found at i:35115519 original size:14 final size:13
Alignment explanation
Indices: 35115490--35115515 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35115480 TACAAAAGTT
35115490 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
35115503 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
35115516 AGAACCCCCC
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:35117714 original size:26 final size:26
Alignment explanation
Indices: 35117685--35117737 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
35117675 GAAGGGGAGG
35117685 AATGCCAGAGTCGAAGGAAGCAAGAA
1 AATGCCAGAGTCGAAGGAAGCAAGAA
*
35117711 AATGCCGGAGTCGAAGGAAGCAAGAA
1 AATGCCAGAGTCGAAGGAAGCAAGAA
35117737 A
1 A
35117738 TGGCTACTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.15, G:0.32, T:0.08
Consensus pattern (26 bp):
AATGCCAGAGTCGAAGGAAGCAAGAA
Found at i:35121845 original size:26 final size:26
Alignment explanation
Indices: 35121813--35121866 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
35121803 ACATAGTTTT
35121813 TATATTAT-TTATAAAGGTTATAATAA
1 TATATTATATTATAAA-GTTATAATAA
*
35121839 TATATTATATTATAAAGTTATTATAA
1 TATATTATATTATAAAGTTATAATAA
35121865 TA
1 TA
35121867 AAAGACAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
TATATTATATTATAAAGTTATAATAA
Found at i:35124457 original size:46 final size:46
Alignment explanation
Indices: 35124390--35124529 Score: 201
Period size: 46 Copynumber: 3.0 Consensus size: 46
35124380 ACAATGCTAT
* * * *
35124390 AACTCAATATGGTTTCCTTCACTGAAATACCATACCTACTTTTCTC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
35124436 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTATTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
35124482 AACTTAGTATGAGTTTT-TTCACTGAAACACTATACCTACTTTTCAC
1 AACTCAGTATG-GTTTTCTTCACTGAAACACCATACCTACTTTTCAC
35124528 AA
1 AA
35124530 TTTTCCATGG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
46 80 0.94
47 5 0.06
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:35125777 original size:17 final size:17
Alignment explanation
Indices: 35125755--35125802 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
35125745 AAATTCTTTT
35125755 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
35125772 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
35125789 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
35125803 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:35126011 original size:44 final size:43
Alignment explanation
Indices: 35125958--35126074 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 43
35125948 TATGTGTTAT
* * * *
35125958 CATGTAAGACCACGTCTAGGACGTTGGCATCGTTTTATGATTTG
1 CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGA-TTA
* *
35126002 CGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTA
1 CATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATATGATTA
35126045 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CATGTAAGACCACGTCTGGGACGTTGGCAT
35126075 TGTACCAACT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.02
43 28 0.45
44 32 0.52
45 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACGTTGGCATCGATATATGATTA
Found at i:35126062 original size:43 final size:43
Alignment explanation
Indices: 35125948--35126074 Score: 143
Period size: 43 Copynumber: 2.9 Consensus size: 43
35125938 AGGATTCCGT
* *
35125948 TATGTG-TTATCATGTAAGACCACGTCTAGGACGTTGGCATCGT
1 TATGTGATTA-CATGTAAGACCACGTCTGGGACGTTGGCATCGA
* * * *
35125991 TTTATGATTTGCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA
1 TATGTGA-TTACATGTAAGACCAC-GTCTGGGAC-GTTGGCATCGA
35126035 TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
35126075 TGTACCAACT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
42 1 0.01
43 32 0.47
44 32 0.47
45 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (43 bp):
TATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATCGA
Found at i:35132590 original size:43 final size:43
Alignment explanation
Indices: 35132523--35132793 Score: 276
Period size: 43 Copynumber: 6.3 Consensus size: 43
35132513 TTTTAGACAT
* * * ***
35132523 AAACGCAGCTAAA-AATCATGACTTTTAGCGGCGTTTTTTTCAC
1 AAACGCCGCTAAAGAA-CATGACCTTTAGCGGCGCTTTACCCAC
* * * * **
35132566 AAACACCGCTATAGATCATGACTTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* * * *
35132609 AAACGTCGCTATAGAACATGAGCTTTAACGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* *
35132652 AAATGCCGCTAAAGAACATGACCTTTAACGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* *
35132695 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTACCCAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
** * * * *
35132738 AAATACCGCTAAAGAACGTGATCTTTAGCTGCGCTTTTA-TCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGC-TTTACCCAC
35132781 AAACGCCGCTAAA
1 AAACGCCGCTAAA
35132794 AGTACGATTC
Statistics
Matches: 195, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
43 190 0.97
44 5 0.03
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
Found at i:35133827 original size:34 final size:34
Alignment explanation
Indices: 35133784--35133852 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
35133774 TTCAAGCAAG
35133784 ACATACACACAATAAGTACTGGAAAATTAAGCCA
1 ACATACACACAATAAGTACTGGAAAATTAAGCCA
35133818 ACATACACACAATAAGTACTGGAAAATTAAGCCA
1 ACATACACACAATAAGTACTGGAAAATTAAGCCA
35133852 A
1 A
35133853 TACTAACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (34 bp):
ACATACACACAATAAGTACTGGAAAATTAAGCCA
Found at i:35134062 original size:40 final size:40
Alignment explanation
Indices: 35133999--35134083 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
35133989 TAGCTTGAAT
* * *
35133999 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
35134039 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
35134079 ATCAA
1 ATCAA
35134084 TCTTACAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:35134277 original size:87 final size:86
Alignment explanation
Indices: 35134149--35134428 Score: 384
Period size: 86 Copynumber: 3.2 Consensus size: 86
35134139 GGCAATAGGG
* * *
35134149 CTAAATCTTCAATTTCTATAACGATTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
1 CTAAATTTTCAATTT-TATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
* * *
35134214 CATGTATTTACCAAAAATCAGA
65 CATGCATTTACCAACAACCAGA
* *
35134236 CTAATTTTTCAATATTTATAACAACTTATATGCAACAAATTAGC-AAAAATAAATGGTTCAAGTT
1 CTAAATTTTCAAT-TTTATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
*
35134300 CATGCATTTACCAACAAGCAGA
65 CATGCATTTACCAACAACCAGA
* **
35134322 CTAAATTTTCAATTTTTATAACAACTTATGTGCAACAAATTAG-AAAAAATCAACAGTTCAAGTT
1 CTAAATTTTCAA-TTTTATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTT
*
35134386 CATGCATTCACCAACAACCAGA
65 CATGCATTTACCAACAACCAGA
*
35134408 CCAAATTTTCAACTTTTATAA
1 CTAAATTTTCAA-TTTTATAA
35134429 AGTAGAAAAA
Statistics
Matches: 173, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
86 133 0.77
87 38 0.22
88 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.32
Consensus pattern (86 bp):
CTAAATTTTCAATTTTATAACAACTTATATGCAACAAATTAGCAAAAAATCAATGGTTCAAGTTC
ATGCATTTACCAACAACCAGA
Found at i:35138145 original size:14 final size:14
Alignment explanation
Indices: 35138053--35138179 Score: 57
Period size: 14 Copynumber: 8.9 Consensus size: 14
35138043 ACATAAATTA
35138053 TAAATCCTT-AACTCC
1 TAAA-CCTTAAAC-CC
35138068 TAAATCC-TAAACCC
1 TAAA-CCTTAAACCC
*
35138082 TAACCCTTAAACCC
1 TAAACCTTAAACCC
* * *
35138096 ATAATCCATAAACCT
1 -TAAACCTTAAACCC
* *
35138111 TAAGA--TAATAACTCT
1 TAA-ACCTTA-AAC-CC
35138126 TAAACCTTAAACCC
1 TAAACCTTAAACCC
* * *
35138140 TAAACCATATATCC
1 TAAACCTTAAACCC
35138154 TAAA-CTATAAACCC
1 TAAACCT-TAAACCC
*
35138168 TAAACCCTAAAC
1 TAAACCTTAAAC
35138180 TATAATGATA
Statistics
Matches: 86, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
13 4 0.05
14 50 0.58
15 30 0.35
16 2 0.02
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:35138164 original size:21 final size:21
Alignment explanation
Indices: 35138126--35138184 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
35138116 TAATAACTCT
* **
35138126 TAAACCTTAAACCCTAAACCA
1 TAAACCCTAAACTATAAACCA
* * *
35138147 TATATCCTAAACTATAAACCC
1 TAAACCCTAAACTATAAACCA
35138168 TAAACCCTAAACTATAA
1 TAAACCCTAAACTATAA
35138185 TGATAATTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAACTATAAACCA
Found at i:35138268 original size:8 final size:7
Alignment explanation
Indices: 35138230--35138278 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
35138220 CTAGTTACTC
*
35138230 TAAACCT
1 TAAACCA
35138237 TAAACCA
1 TAAACCA
35138244 TAAACC-
1 TAAACCA
*
35138250 TAAACCC
1 TAAACCA
35138257 TAAAACCA
1 T-AAACCA
35138265 TAAACTCA
1 TAAAC-CA
35138273 TAAACC
1 TAAACC
35138279 CTTAACACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 6 0.16
7 18 0.49
8 13 0.35
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:35138328 original size:7 final size:7
Alignment explanation
Indices: 35138316--35138362 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
35138306 CCCCAGCCTT
35138316 TAAACCA
1 TAAACCA
35138323 TAAACCA
1 TAAACCA
*
35138330 TAAATCA
1 TAAACCA
*
35138337 TAACCCA
1 TAAACCA
35138344 TAAACCCA
1 TAAA-CCA
*
35138352 TAATCCA
1 TAAACCA
35138359 TAAA
1 TAAA
35138363 TCTTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:35138399 original size:14 final size:14
Alignment explanation
Indices: 35138380--35138413 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35138370 ATGGTAACAC
*
35138380 CTAAACCTTAAACT
1 CTAAACCATAAACT
*
35138394 CTAAACCATATACT
1 CTAAACCATAAACT
35138408 CTAAAC
1 CTAAAC
35138414 TAAAAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
CTAAACCATAAACT
Found at i:35138667 original size:14 final size:14
Alignment explanation
Indices: 35138575--35138701 Score: 57
Period size: 14 Copynumber: 8.9 Consensus size: 14
35138565 ACATAAATTA
35138575 TAAATCCTT-AACTCC
1 TAAA-CCTTAAAC-CC
35138590 TAAATCC-TAAACCC
1 TAAA-CCTTAAACCC
*
35138604 TAACCCTTAAACCC
1 TAAACCTTAAACCC
* * *
35138618 ATAATCCATAAACCT
1 -TAAACCTTAAACCC
* *
35138633 TAAGA--TAATAACTCT
1 TAA-ACCTTA-AAC-CC
35138648 TAAACCTTAAACCC
1 TAAACCTTAAACCC
* * *
35138662 TAAACCATATATCC
1 TAAACCTTAAACCC
35138676 TAAA-CTATAAACCC
1 TAAACCT-TAAACCC
*
35138690 TAAACCCTAAAC
1 TAAACCTTAAAC
35138702 TATAATGATA
Statistics
Matches: 86, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
13 4 0.05
14 50 0.58
15 30 0.35
16 2 0.02
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:35138686 original size:21 final size:21
Alignment explanation
Indices: 35138648--35138706 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
35138638 TAATAACTCT
* **
35138648 TAAACCTTAAACCCTAAACCA
1 TAAACCCTAAACTATAAACCA
* * *
35138669 TATATCCTAAACTATAAACCC
1 TAAACCCTAAACTATAAACCA
35138690 TAAACCCTAAACTATAA
1 TAAACCCTAAACTATAA
35138707 TGATAATTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAACTATAAACCA
Found at i:35138790 original size:8 final size:7
Alignment explanation
Indices: 35138752--35138800 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
35138742 CTAGTTACTC
*
35138752 TAAACCT
1 TAAACCA
35138759 TAAACCA
1 TAAACCA
35138766 TAAACC-
1 TAAACCA
*
35138772 TAAACCC
1 TAAACCA
35138779 TAAAACCA
1 T-AAACCA
35138787 TAAACTCA
1 TAAAC-CA
35138795 TAAACC
1 TAAACC
35138801 CTTAACACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 6 0.16
7 18 0.49
8 13 0.35
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCA
Found at i:35138850 original size:7 final size:7
Alignment explanation
Indices: 35138838--35138884 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
35138828 CCCCAGCCTT
35138838 TAAACCA
1 TAAACCA
35138845 TAAACCA
1 TAAACCA
*
35138852 TAAATCA
1 TAAACCA
*
35138859 TAACCCA
1 TAAACCA
35138866 TAAACCCA
1 TAAA-CCA
*
35138874 TAATCCA
1 TAAACCA
35138881 TAAA
1 TAAA
35138885 TCTTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCA
Found at i:35138921 original size:14 final size:14
Alignment explanation
Indices: 35138902--35138935 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35138892 ATGGTAACAC
*
35138902 CTAAACCTTAAACT
1 CTAAACCATAAACT
*
35138916 CTAAACCATATACT
1 CTAAACCATAAACT
35138930 CTAAAC
1 CTAAAC
35138936 TAAAAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
CTAAACCATAAACT
Found at i:35138941 original size:522 final size:522
Alignment explanation
Indices: 35137952--35139100 Score: 2280
Period size: 522 Copynumber: 2.2 Consensus size: 522
35137942 TAATTTAAAC
* *
35137952 TACAATTATATAAGAAATTATTTAATATATAAATTAAAAAACACTAATCAATCTAAACCCCTAAC
1 TACAGTTATATAAGAAATTATTTAATATATAAATTAAAAAAGACTAATCAATCTAAACCCCTAAC
35138017 CCTATCCCTAAACCCTGAATCATAAAACATAAATTATAAATCCTTAACTCCTAAATCCTAAACCC
66 CCTATCCCTAAACCCTGAATCATAAAACATAAATTATAAATCCTTAACTCCTAAATCCTAAACCC
35138082 TAACCCTTAAACCCATAATCCATAAACCTTAAGATAATAACTCTTAAACCTTAAACCCTAAACCA
131 TAACCCTTAAACCCATAATCCATAAACCTTAAGATAATAACTCTTAAACCTTAAACCCTAAACCA
35138147 TATATCCTAAACTATAAACCCTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATT
196 TATATCCTAAACTATAAACCCTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATT
35138212 AGAAAACACTAGTTACTCTAAACCTTAAACCATAAACCTAAACCCTAAAACCATAAACTCATAAA
261 AGAAAACACTAGTTACTCTAAACCTTAAACCATAAACCTAAACCCTAAAACCATAAACTCATAAA
35138277 CCCTTAACACATAACCTCTAAATTTTAAACCCCAGCCTTTAAACCATAAACCATAAATCATAACC
326 CCCTTAACACATAACCTCTAAATTTTAAACCCCAGCCTTTAAACCATAAACCATAAATCATAACC
35138342 CATAAACCCATAATCCATAAATCTTAAAATGGTAACACCTAAACCTTAAACTCTAAACCATATAC
391 CATAAACCCATAATCCATAAATCTTAAAATGGTAACACCTAAACCTTAAACTCTAAACCATATAC
35138407 TCTAAACTAAAAACCCTAAATTGTAGTGATAATTAATTTAATATTTTAAAATTAATACTATCTCT
456 TCTAAACTAAAAACCCTAAATTGTAGTGATAATTAATTTAATATTTTAAAATTAATACTATCTCT
35138472 TT
521 TT
35138474 TACAGTTATATAAGAAATTATTTAATATATAAATTAAAAAAGACTAATCAATCTAAACCCCTAAC
1 TACAGTTATATAAGAAATTATTTAATATATAAATTAAAAAAGACTAATCAATCTAAACCCCTAAC
35138539 CCTATCCCTAAACCCTGAATCATAAAACATAAATTATAAATCCTTAACTCCTAAATCCTAAACCC
66 CCTATCCCTAAACCCTGAATCATAAAACATAAATTATAAATCCTTAACTCCTAAATCCTAAACCC
35138604 TAACCCTTAAACCCATAATCCATAAACCTTAAGATAATAACTCTTAAACCTTAAACCCTAAACCA
131 TAACCCTTAAACCCATAATCCATAAACCTTAAGATAATAACTCTTAAACCTTAAACCCTAAACCA
35138669 TATATCCTAAACTATAAACCCTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATT
196 TATATCCTAAACTATAAACCCTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATT
35138734 AGAAAACACTAGTTACTCTAAACCTTAAACCATAAACCTAAACCCTAAAACCATAAACTCATAAA
261 AGAAAACACTAGTTACTCTAAACCTTAAACCATAAACCTAAACCCTAAAACCATAAACTCATAAA
35138799 CCCTTAACACATAACCTCTAAATTTTAAACCCCAGCCTTTAAACCATAAACCATAAATCATAACC
326 CCCTTAACACATAACCTCTAAATTTTAAACCCCAGCCTTTAAACCATAAACCATAAATCATAACC
35138864 CATAAACCCATAATCCATAAATCTTAAAATGGTAACACCTAAACCTTAAACTCTAAACCATATAC
391 CATAAACCCATAATCCATAAATCTTAAAATGGTAACACCTAAACCTTAAACTCTAAACCATATAC
35138929 TCTAAACTAAAAACCCTAAATTGTAGTGATAATTAATTTAATATTTTAAAATTAATACTATCTCT
456 TCTAAACTAAAAACCCTAAATTGTAGTGATAATTAATTTAATATTTTAAAATTAATACTATCTCT
35138994 TT
521 TT
35138996 TACAGTTATATAAGAAATTATTTAATATATAAATTAAAAAAGACTAATCAATCTAAACCCCTAAC
1 TACAGTTATATAAGAAATTATTTAATATATAAATTAAAAAAGACTAATCAATCTAAACCCCTAAC
35139061 CCTATCCCTAAACCCTGAATCATAAAACATAAATTATAAA
66 CCTATCCCTAAACCCTGAATCATAAAACATAAATTATAAA
35139101 CTTTAAAATT
Statistics
Matches: 625, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
522 625 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (522 bp):
TACAGTTATATAAGAAATTATTTAATATATAAATTAAAAAAGACTAATCAATCTAAACCCCTAAC
CCTATCCCTAAACCCTGAATCATAAAACATAAATTATAAATCCTTAACTCCTAAATCCTAAACCC
TAACCCTTAAACCCATAATCCATAAACCTTAAGATAATAACTCTTAAACCTTAAACCCTAAACCA
TATATCCTAAACTATAAACCCTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATT
AGAAAACACTAGTTACTCTAAACCTTAAACCATAAACCTAAACCCTAAAACCATAAACTCATAAA
CCCTTAACACATAACCTCTAAATTTTAAACCCCAGCCTTTAAACCATAAACCATAAATCATAACC
CATAAACCCATAATCCATAAATCTTAAAATGGTAACACCTAAACCTTAAACTCTAAACCATATAC
TCTAAACTAAAAACCCTAAATTGTAGTGATAATTAATTTAATATTTTAAAATTAATACTATCTCT
TT
Found at i:35139407 original size:41 final size:41
Alignment explanation
Indices: 35139296--35139526 Score: 222
Period size: 41 Copynumber: 5.8 Consensus size: 41
35139286 AATAGTTTTT
* * **
35139296 GCGGCGCTTTTTCAAAAACGTCGCTAAA-AATAGAGCATT-
1 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTA
* **
35139335 GC-G--TTTTTTCAAAAACGCCGCTAAA-AATAGAGCATTA
1 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTA
* * **
35139372 GAGTCACTTTTTCAAAAACGATGCTAAAGCCTAGAGCATTA
1 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTA
* * * *
35139413 GCGGCACCTTTTCACAAATGCCGCTAAAGCCCAGAGCATTA
1 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTA
* ** *
35139454 GCGGCGCTTTTTCAAAAACGCCGCTAAATTCTCGAGCATTA
1 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTA
* * *
35139495 GTGGCATTTTTTCAAAAACGCCGCTAACGCCT
1 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCT
35139527 CAAAAAGCTG
Statistics
Matches: 156, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
36 31 0.20
37 1 0.01
38 1 0.01
39 2 0.01
40 19 0.12
41 102 0.65
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
GCGGCACTTTTTCAAAAACGCCGCTAAAGCCTAGAGCATTA
Found at i:35145000 original size:6 final size:6
Alignment explanation
Indices: 35144981--35145037 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
35144971 ATTATTGGGC
* * * * * *
35144981 CATGAT CATAGT CATGGT CACGGT CATGGC CATGAT CACGGT CATGGT
1 CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT CATGGT
*
35145029 CATAGT CAT
1 CATGGT CAT
35145038 AGCCATAGCC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (6 bp):
CATGGT
Found at i:35145014 original size:18 final size:18
Alignment explanation
Indices: 35144993--35145027 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35144983 TGATCATAGT
*
35144993 CATGGTCACGGTCATGGC
1 CATGATCACGGTCATGGC
35145011 CATGATCACGGTCATGG
1 CATGATCACGGTCATGG
35145028 TCATAGTCAT
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:0.20, C:0.26, G:0.31, T:0.23
Consensus pattern (18 bp):
CATGATCACGGTCATGGC
Found at i:35145037 original size:30 final size:30
Alignment explanation
Indices: 35144978--35145043 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
35144968 TCTATTATTG
* *
35144978 GGCCATGATCATAGTCATGGTCACGGTCAT
1 GGCCATGATCACAGTCATGGTCACAGTCAT
* *
35145008 GGCCATGATCACGGTCATGGTCATAGTCAT
1 GGCCATGATCACAGTCATGGTCACAGTCAT
*
35145038 AGCCAT
1 GGCCAT
35145044 AGCCATAGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (30 bp):
GGCCATGATCACAGTCATGGTCACAGTCAT
Found at i:35145076 original size:6 final size:6
Alignment explanation
Indices: 35145029--35145063 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
35145019 CGGTCATGGT
*
35145029 CATAGT CATAGC CATAGC CATAGC CATAGC CATAG
1 CATAGC CATAGC CATAGC CATAGC CATAGC CATAG
35145064 TGATCATAGT
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:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (6 bp):
CATAGC
Found at i:35151389 original size:21 final size:21
Alignment explanation
Indices: 35151357--35151397 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
35151347 GAACATTTGG
35151357 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
35151378 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
35151398 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:35157589 original size:18 final size:18
Alignment explanation
Indices: 35157566--35157601 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35157556 AGACCAATCT
35157566 GTTATTCGAATTATTCGA
1 GTTATTCGAATTATTCGA
* *
35157584 GTTATTTGAGTTATTCGA
1 GTTATTCGAATTATTCGA
35157602 ATTGTAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (18 bp):
GTTATTCGAATTATTCGA
Found at i:35159626 original size:21 final size:21
Alignment explanation
Indices: 35159591--35159653 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
35159581 CAAATGTGCA
35159591 AGCTCACCAAAGCATGAGAGCG
1 AGCTCACC-AAGCATGAGAGCG
35159613 AGCTCACCAAGCATGAGAGCG
1 AGCTCACCAAGCATGAGAGCG
35159634 AGCTCACCAAGCATGAGAGC
1 AGCTCACCAAGCATGAGAGC
35159654 TTACCTGCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 33 0.80
22 8 0.20
ACGTcount: A:0.35, C:0.29, G:0.27, T:0.10
Consensus pattern (21 bp):
AGCTCACCAAGCATGAGAGCG
Found at i:35159891 original size:16 final size:16
Alignment explanation
Indices: 35159870--35159903 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
35159860 AACTATGCAT
*
35159870 CAGTTTTTTAATGAAA
1 CAGTTTTTTAACGAAA
35159886 CAGTTTTTTAACGAAA
1 CAGTTTTTTAACGAAA
35159902 CA
1 CA
35159904 ATTCACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
CAGTTTTTTAACGAAA
Found at i:35161521 original size:4 final size:4
Alignment explanation
Indices: 35161512--35161545 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
35161502 AAGTTTTATT
35161512 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
35161546 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:35161553 original size:22 final size:22
Alignment explanation
Indices: 35161495--35161554 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
35161485 AAGTGGCCCA
*
35161495 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
35161519 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
35161540 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
35161555 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:35172785 original size:4 final size:4
Alignment explanation
Indices: 35172776--35172802 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
35172766 AGTTATAAAG
35172776 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
35172803 CTTAGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:35191566 original size:42 final size:42
Alignment explanation
Indices: 35191507--35191589 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
35191497 GACATGGTTT
*
35191507 AGCAGTTCCTGTTTTGTAATAGAGAGACCATAGATTGGATCC
1 AGCAGTTCCTGTTTTGTAAGAGAGAGACCATAGATTGGATCC
35191549 AGCAGTTCCTGTTTTGTAAGAGAGAGACCATAGATTGGATC
1 AGCAGTTCCTGTTTTGTAAGAGAGAGACCATAGATTGGATC
35191590 AAGAAGTCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (42 bp):
AGCAGTTCCTGTTTTGTAAGAGAGAGACCATAGATTGGATCC
Found at i:35193502 original size:16 final size:16
Alignment explanation
Indices: 35193464--35193502 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
35193454 TTTGGTTCAG
*
35193464 TGTAATGGAATAGAGC
1 TGTAATTGAATAGAGC
*
35193480 TGTAATTGAATAGAGT
1 TGTAATTGAATAGAGC
35193496 TGTAATT
1 TGTAATT
35193503 AGTAATTCAA
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:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (16 bp):
TGTAATTGAATAGAGC
Found at i:35193803 original size:21 final size:23
Alignment explanation
Indices: 35193774--35193822 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
35193764 ATATAATTAT
35193774 TATATTAAT-TA-AAAAATCATA
1 TATATTAATATATAAAAATCATA
35193795 -ATATATAATACTATAAAAATCATA
1 TATAT-TAATA-TATAAAAATCATA
35193819 TATA
1 TATA
35193823 ATCTACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
23 2 0.09
24 10 0.43
25 3 0.13
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (23 bp):
TATATTAATATATAAAAATCATA
Found at i:35200962 original size:49 final size:49
Alignment explanation
Indices: 35200878--35202070 Score: 2203
Period size: 49 Copynumber: 24.6 Consensus size: 49
35200868 TATTTGAATA
* *
35200878 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35200925 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
35200974 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201021 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
35201068 AATGTGAAAGTGTATATATGTGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201117 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201166 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201215 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201264 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201313 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201362 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201411 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201460 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201509 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201558 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201607 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201656 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201705 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201754 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201803 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201852 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201901 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
35201950 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
35201997 AATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
35202044 GATGTGAAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
35202071 TCCCGAAGGG
Statistics
Matches: 1125, Mismatches: 15, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
47 199 0.18
48 1 0.00
49 925 0.82
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:35212429 original size:15 final size:15
Alignment explanation
Indices: 35212404--35212438 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
35212394 GACTCTATTT
*
35212404 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
35212418 TAATTAATATTAAGA
1 TAATTAATATTAAGA
35212433 TAATTA
1 TAATTA
35212439 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:35218004 original size:46 final size:46
Alignment explanation
Indices: 35217937--35218030 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
35217927 GGTTCCGAGA
35217937 GTAAGTCTTTTCTATTACTTCATTTCATGAAAGTATTTAAATATGT
1 GTAAGTCTTTTCTATTACTTCATTTCATGAAAGTATTTAAATATGT
35217983 GTAAGTCTTTTCTATTACTTCATTTCATGAAAGTATTTAAATATGT
1 GTAAGTCTTTTCTATTACTTCATTTCATGAAAGTATTTAAATATGT
35218029 GT
1 GT
35218031 TTTTATTAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.48
Consensus pattern (46 bp):
GTAAGTCTTTTCTATTACTTCATTTCATGAAAGTATTTAAATATGT
Found at i:35219321 original size:14 final size:14
Alignment explanation
Indices: 35219302--35219328 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35219292 TGAAACTTGG
35219302 TTAAGTGTTTTTAT
1 TTAAGTGTTTTTAT
35219316 TTAAGTGTTTTTA
1 TTAAGTGTTTTTA
35219329 CCTTCATGAT
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:0.15, T:0.63
Consensus pattern (14 bp):
TTAAGTGTTTTTAT
Found at i:35225622 original size:260 final size:259
Alignment explanation
Indices: 35225162--35225682 Score: 848
Period size: 260 Copynumber: 2.0 Consensus size: 259
35225152 CTAACTATAA
* *
35225162 AACTTGCAAAACATAATTACATGCCATTAACAAATTCTACTTAATATCACAATATAGAAAAATAT
1 AACTTGCAAAACATAATTACATGCCATTAACAAATTCTACTCAACATCACAATATAGAAAAATAT
* *
35225227 AAAGGACTCCACTAGGTACTTGCCAATTAACTAACACAATAATTTCACCAACTTTATTGAGTCCT
66 AAAGGACTCCACTAGGTACATGCCAATTAACTAACACAATAATTTCACCAACTTTATTGAGTCCC
* * * *
35225292 AGATTATGCCTGGATGCTGATGTTGATATCCAGGATCACCTATTAACCTAACTTGCTCATAGAAA
131 AAATTATGCCTGGATGCTGATGTTGATATCCAGGATCACCTATTAACCTAACCTGCGCAGAGAAA
* * *
35225357 ACAAAA-TCGTAACATGAGTAATAAACTCAGTTGTATTTTAACAATTCAGAGATCAATGCAAATT
196 ACAAAACT-GTAACATAAGTAATAAACTCAGTTGTATTTCAACAATTCAAAGATCAATGCAAATT
*
35225421 AACTTGCAAAACATAATTACATGTCATTAACAAATTCTACTCAACATCACAATATAGAAAAAATA
1 AACTTGCAAAACATAATTACATGCCATTAACAAATTCTACTCAACATCACAATATAG-AAAAATA
* *
35225486 TAAAGGACTTCACTAGGTGCATGCCAATTAACTAACACAATAATTTCACCAACTTTATTGAGTCC
65 TAAAGGACTCCACTAGGTACATGCCAATTAACTAACACAATAATTTCACCAACTTTATTGAGTCC
* *
35225551 CAAATTATGCCTGGATGCTGATGTTGATATTCAGGATCACGTATTAACCTAACCTGCGCACGA-A
130 CAAATTATGCCTGGATGCTGATGTTGATATCCAGGATCACCTATTAACCTAACCTGCGCA-GAGA
*
35225615 AAACAAAACTGTAACCTAAGTAATAAACTCAGTTGTATTTCAACAATTCAAAGATCAATGCAAAT
194 AAACAAAACTGTAACATAAGTAATAAACTCAGTTGTATTTCAACAATTCAAAGATCAATGCAAAT
35225680 T
259 T
35225681 AA
1 AA
35225683 GCTAAAATAT
Statistics
Matches: 242, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
259 54 0.22
260 186 0.77
261 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (259 bp):
AACTTGCAAAACATAATTACATGCCATTAACAAATTCTACTCAACATCACAATATAGAAAAATAT
AAAGGACTCCACTAGGTACATGCCAATTAACTAACACAATAATTTCACCAACTTTATTGAGTCCC
AAATTATGCCTGGATGCTGATGTTGATATCCAGGATCACCTATTAACCTAACCTGCGCAGAGAAA
ACAAAACTGTAACATAAGTAATAAACTCAGTTGTATTTCAACAATTCAAAGATCAATGCAAATT
Found at i:35228044 original size:17 final size:17
Alignment explanation
Indices: 35228004--35228050 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
35227994 CTTGTTTAGA
*
35228004 AATTATTTTTTCTATACT
1 AATTAATTTTT-TATACT
*
35228022 AA-TAATTTTTTATAGT
1 AATTAATTTTTTATACT
35228038 AATTAATTTTTTA
1 AATTAATTTTTTA
35228051 ATATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 17 0.65
18 2 0.08
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (17 bp):
AATTAATTTTTTATACT
Found at i:35228838 original size:31 final size:31
Alignment explanation
Indices: 35228798--35228863 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
35228788 TATATCTGAC
* * * *
35228798 CATGTTTGCTAAAAATTTACTCCTTTTGCGA
1 CATGCTTGCTAAAAAATTACTCCATTTGCCA
*
35228829 CATGCTTGCTAAAAAATTGCTCCATTTGCCA
1 CATGCTTGCTAAAAAATTACTCCATTTGCCA
35228860 CATG
1 CATG
35228864 TATCTATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (31 bp):
CATGCTTGCTAAAAAATTACTCCATTTGCCA
Found at i:35235935 original size:18 final size:18
Alignment explanation
Indices: 35235909--35235943 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35235899 TGACGTGGAA
* *
35235909 GAGAGAAGTTGTAAGGGT
1 GAGAAAAGTAGTAAGGGT
35235927 GAGAAAAGTAGTAAGGG
1 GAGAAAAGTAGTAAGGG
35235944 CAAGAAGCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (18 bp):
GAGAAAAGTAGTAAGGGT
Found at i:35239524 original size:27 final size:27
Alignment explanation
Indices: 35239490--35239667 Score: 139
Period size: 28 Copynumber: 6.5 Consensus size: 27
35239480 TTCGCCATGT
*
35239490 AGGCTTCCATTTCATAGATTGCCACAAA
1 AGGCTTCCATTTCATAGATAGCCAC-AA
* * *
35239518 AGG-TTCCCTTTTCACAAATCA-CCACAA
1 AGGCTT-CCATTTCATAGAT-AGCCACAA
* * *
35239545 AGGCTTCCCTTTTCATATATCA-CCATAA
1 AGGCTT-CCATTTCATAGAT-AGCCACAA
*
35239573 AAGCTT-CATTTCCATAGATAGCCACAA
1 AGGCTTCCATTT-CATAGATAGCCACAA
* * *
35239600 AAGCTTCCCTTTTCATAGATAGACACAA
1 AGGCTT-CCATTTCATAGATAGCCACAA
* **
35239628 AGGCTTCCATTTCATAAATTTCCACAA
1 AGGCTTCCATTTCATAGATAGCCACAA
35239655 AGGCTTCCATTTC
1 AGGCTTCCATTTC
35239668 TCTGGCATGT
Statistics
Matches: 124, Mismatches: 19, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
26 5 0.04
27 53 0.43
28 62 0.50
29 4 0.03
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (27 bp):
AGGCTTCCATTTCATAGATAGCCACAA
Found at i:35239551 original size:55 final size:54
Alignment explanation
Indices: 35239490--35239667 Score: 148
Period size: 55 Copynumber: 3.3 Consensus size: 54
35239480 TTCGCCATGT
* *
35239490 AGGCTT-CCATTTCATAGATTGCCACAAAAGGTTCCCTTTTCACAAATCACCACAA
1 AGGCTTCCCATTTCATAGATAGCCACAAAAGGTT-CCTTTTCATAAAT-ACCACAA
* * * * * * *
35239545 AGGCTTCCCTTTTCATATATCA-CCATAAAAGCTTCATTTCCATAGATAGCCACAA
1 AGGCTTCCCATTTCATAGAT-AGCCACAAAAGGTTCCTTTTCATAAATA-CCACAA
* * * * *
35239600 AAGCTTCCCTTTTCATAGATAGACAC-AAAGGCTTCCATTTCATAAATTTCCACAA
1 AGGCTTCCCATTTCATAGATAGCCACAAAAGG-TTCCTTTTCATAAA-TACCACAA
35239655 AGGCTT-CCATTTC
1 AGGCTTCCCATTTC
35239668 TCTGGCATGT
Statistics
Matches: 96, Mismatches: 21, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
54 12 0.12
55 62 0.65
56 22 0.23
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (54 bp):
AGGCTTCCCATTTCATAGATAGCCACAAAAGGTTCCTTTTCATAAATACCACAA
Found at i:35239627 original size:83 final size:82
Alignment explanation
Indices: 35239492--35239667 Score: 212
Period size: 83 Copynumber: 2.1 Consensus size: 82
35239482 CGCCATGTAG
* * * *
35239492 GCTTCCATTTCATAGATTGCCACAAAAGGTTCCCTTTTCACAAATCACCACAAAGGCTTCCCTTT
1 GCTTCCATTTCATAGATAGCCACAAAAGCTTCCCTTTTCACAAATCAACACAAAGGCTT-CCATT
35239557 TCATATATCACCATAAAA
65 TCATATATCACCATAAAA
* *
35239575 GCTT-CATTTCCATAGATAGCCACAAAAGCTTCCCTTTTCATAGAT-AGACACAAAGGCTTCCAT
1 GCTTCCATTT-CATAGATAGCCACAAAAGCTTCCCTTTTCACAAATCA-ACACAAAGGCTTCCAT
* ** * *
35239638 TTCATAAATTTCCACAAAG
64 TTCATATATCACCATAAAA
35239657 GCTTCCATTTC
1 GCTTCCATTTC
35239668 TCTGGCATGT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
82 28 0.35
83 51 0.65
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.31
Consensus pattern (82 bp):
GCTTCCATTTCATAGATAGCCACAAAAGCTTCCCTTTTCACAAATCAACACAAAGGCTTCCATTT
CATATATCACCATAAAA
Found at i:35244704 original size:5 final size:5
Alignment explanation
Indices: 35244696--35244724 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35244686 TGAATGAAAT
35244696 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
35244725 TTTAATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:35246051 original size:18 final size:17
Alignment explanation
Indices: 35246030--35246064 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35246020 TTATTATTAA
*
35246030 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35246048 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35246065 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35246178 original size:162 final size:163
Alignment explanation
Indices: 35245944--35246238 Score: 547
Period size: 162 Copynumber: 1.8 Consensus size: 163
35245934 TGGTAAATGA
* * *
35245944 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAGTAATAAATATTTTAATCATA
1 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATA
*
35246009 TTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT-ATAA
66 TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
35246073 TTAGCAGAAATTTGTTTTGGTAAATTATTATTG
131 TTAGCAGAAATTTGTTTTGGTAAATTATTATTG
35246106 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATA
1 TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATA
35246171 TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
66 TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
35246236 TTA
131 TTA
35246239 ATATTCTTAT
Statistics
Matches: 128, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
162 121 0.95
163 7 0.05
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (163 bp):
TTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAATAAATAATTTAATCATA
TTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAGCAGAAATTTGTTTTGGTAAATTATTATTG
Found at i:35246209 original size:16 final size:16
Alignment explanation
Indices: 35246172--35246213 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35246162 TTAATCATAT
*
35246172 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
35246188 TT-AAATATATTATAA
1 TTAAAATATATTATAA
35246203 TTAAAATATAT
1 TTAAAATATAT
35246214 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:35246220 original size:14 final size:15
Alignment explanation
Indices: 35246181--35246222 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35246171 TTTAAACATA
*
35246181 ATTATTATTAAATAT
1 ATTATAATTAAATAT
35246196 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
35246210 A-TATAATTTAATA
1 ATTATAATTAAATA
35246223 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:35246272 original size:61 final size:61
Alignment explanation
Indices: 35246207--35246394 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
35246197 TTATAATTAA
35246207 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * *
35246268 AATATATGATACT-ATAAAA-T-AT-A-AATTAACATAATTATTAT-TAAATATA-TTATAATTA
1 AATATATAAT-TTAATAAAATTCTTAATAATT-A-AT-ATTCTTATATGAATTTACTCA-AATCA
*
35246326 A
61 T
35246327 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
35246388 AATATAT
1 AATATAT
35246395 GATACTATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
57 4 0.04
58 5 0.05
59 28 0.29
60 16 0.16
61 35 0.36
62 5 0.05
63 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:35246340 original size:14 final size:15
Alignment explanation
Indices: 35246291--35246342 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35246281 ATAAAATATA
35246291 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35246306 TATTAAATATATTAT
1 AATTAAATATATTAT
35246321 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
35246334 AATTTAATA
1 AATTAAATA
35246343 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35246388 original size:120 final size:121
Alignment explanation
Indices: 35246170--35246467 Score: 521
Period size: 120 Copynumber: 2.5 Consensus size: 121
35246160 ATTTAATCAT
*
35246170 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
35246235 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
35246292 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
35246355 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* * *
35246411 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
35246468 TAAAATAATT
Statistics
Matches: 170, Mismatches: 4, Indels: 6
0.94 0.02 0.03
Matches are distributed among these distances:
119 3 0.02
120 162 0.95
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:35250577 original size:23 final size:23
Alignment explanation
Indices: 35250550--35250595 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35250540 GCCTTTCAAA
35250550 TTTTCAAAAATACAAAATACATT
1 TTTTCAAAAATACAAAATACATT
*
35250573 TTTTCAAAAATACAGAATACATT
1 TTTTCAAAAATACAAAATACATT
35250596 CAAAATTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (23 bp):
TTTTCAAAAATACAAAATACATT
Found at i:35251239 original size:13 final size:13
Alignment explanation
Indices: 35251221--35251247 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35251211 TAAAAACAAC
35251221 TATATTGTTTAAA
1 TATATTGTTTAAA
35251234 TATATTGTTTAAA
1 TATATTGTTTAAA
35251247 T
1 T
35251248 TAAACCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TATATTGTTTAAA
Found at i:35257022 original size:23 final size:22
Alignment explanation
Indices: 35256996--35257042 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
35256986 CTTCCACTTT
35256996 TTATTCT-ATAATTTATTTATTTA
1 TTATTCTGAT-ATTTATTT-TTTA
*
35257019 TTATTTTGATATTTATTTTTTA
1 TTATTCTGATATTTATTTTTTA
35257041 TT
1 TT
35257043 CTAAAATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 14 0.64
24 2 0.09
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TTATTCTGATATTTATTTTTTA
Found at i:35259066 original size:28 final size:28
Alignment explanation
Indices: 35259007--35259154 Score: 92
Period size: 28 Copynumber: 5.2 Consensus size: 28
35258997 TTTCTCCAGG
*
35259007 AGGCTTTCCTTTCCAAAGATAGCCACAG
1 AGGCTTTCCTTTCCAAAGATAGCCACAA
*
35259035 AGGCTTTCCTTT-CAAAGTCTCA-CCACAA
1 AGGCTTTCCTTTCCAAAG-AT-AGCCACAA
* * * *
35259063 AGGC-GTCCTTTTAACAGAGATTGCCAC-A
1 AGGCTTTCC-TTT-CCAAAGATAGCCACAA
**
35259091 AGGC-TTCCTTTTAATAGAGATAGCCACAA
1 AGGCTTTCCTTTCCA-A-AGATAGCCACAA
* *
35259120 AGGC-TTCCTTTTAACAAGGATAGCCACAA
1 AGGCTTTCC-TTT-CCAAAGATAGCCACAA
35259149 AGGCTT
1 AGGCTT
35259155 CATTTTAACA
Statistics
Matches: 94, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
26 1 0.01
27 11 0.12
28 42 0.45
29 30 0.32
30 9 0.10
31 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (28 bp):
AGGCTTTCCTTTCCAAAGATAGCCACAA
Found at i:35259091 original size:29 final size:29
Alignment explanation
Indices: 35259057--35259234 Score: 215
Period size: 29 Copynumber: 6.3 Consensus size: 29
35259047 CAAAGTCTCA
* *
35259057 CCACAAAGGCGTCCTTTTAACAGAGATTG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
*
35259086 CCAC-AAGGCTTCCTTTTAATAGAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
35259114 CCACAAAGGCTTCCTTTTAACA-AGGATAG
1 CCACAAAGGCTTCCTTTTAACAGA-GATAG
* *
35259143 CCACAAAGGCTTCATTTTAACAGAGATAA
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * *
35259172 CCACTAAGGCTTCCGTTTAAGAGAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
*
35259201 CCACAAAGGCGT-CTTTTCAA-A-A-ATAG
1 CCACAAAGGCTTCCTTTT-AACAGAGATAG
35259227 CCACAAAG
1 CCACAAAG
35259235 AAATACTTTC
Statistics
Matches: 131, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
26 12 0.09
27 1 0.01
28 31 0.24
29 86 0.66
30 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (29 bp):
CCACAAAGGCTTCCTTTTAACAGAGATAG
Found at i:35259201 original size:87 final size:83
Alignment explanation
Indices: 35259057--35259234 Score: 241
Period size: 86 Copynumber: 2.1 Consensus size: 83
35259047 CAAAGTCTCA
* ** * *
35259057 CCACAAAGGCGTCCTTTTAACAGAGATTGCCACAAGGCTTCCTTTTAATAGAGATAGCCACAAAG
1 CCACAAAGGCGTCATTTTAACAGAGATAACCACAAGGCTTCCGTTTAAGAGAGATAGCCACAAAG
*
35259122 GCTTCCTTTT-AACAAGGATAG
66 GCGT-CTTTTCAA-AA--ATAG
*
35259143 CCACAAAGGCTTCATTTTAACAGAGATAACCACTAAGGCTTCCGTTTAAGAGAGATAGCCACAAA
1 CCACAAAGGCGTCATTTTAACAGAGATAACCAC-AAGGCTTCCGTTTAAGAGAGATAGCCACAAA
35259208 GGCGTCTTTTCAAAAATAG
65 GGCGTCTTTTCAAAAATAG
35259227 CCACAAAG
1 CCACAAAG
35259235 AAATACTTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
84 12 0.14
86 36 0.43
87 35 0.42
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (83 bp):
CCACAAAGGCGTCATTTTAACAGAGATAACCACAAGGCTTCCGTTTAAGAGAGATAGCCACAAAG
GCGTCTTTTCAAAAATAG
Found at i:35261283 original size:54 final size:54
Alignment explanation
Indices: 35261218--35261322 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
35261208 TGAGTTAGGT
* * * *
35261218 CACACGACCGTGTCGCAGGTCGTGTACTAGACTGTGTAACTCATTGACTTGCGA
1 CACACGACCGTGTCGCAAGCCATGTACTAGACCGTGTAACTCATTGACTTGCGA
* * * *
35261272 CACACGGCCGTGTCGCAAGCCATGTGCTAGGCCGTGTAACTTATTGACTTG
1 CACACGACCGTGTCGCAAGCCATGTACTAGACCGTGTAACTCATTGACTTG
35261323 ATACACATAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.26
Consensus pattern (54 bp):
CACACGACCGTGTCGCAAGCCATGTACTAGACCGTGTAACTCATTGACTTGCGA
Found at i:35268589 original size:19 final size:17
Alignment explanation
Indices: 35268542--35268592 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
35268532 TATCATTAGC
35268542 TTAAGTTAATTAA-AGA
1 TTAAGTTAATTAATAGA
35268558 TTAAGGTTTAATTAATCATGA
1 TTAA-G-TTAATTAAT-A-GA
35268579 TTAAGTTAATTAAT
1 TTAAGTTAATTAAT
35268593 TAAGCTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.13
17 1 0.03
18 8 0.27
19 9 0.30
20 2 0.07
21 6 0.20
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (17 bp):
TTAAGTTAATTAATAGA
Found at i:35269758 original size:38 final size:38
Alignment explanation
Indices: 35269713--35269801 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
35269703 TTCGTACGCT
* *
35269713 AGTATGCACTTTGTGTGCCAGGATACATTTTGTGTGCC
1 AGTATGCACTTTGTGTGCCAGGATACACTTAGTGTGCC
** * * *
35269751 ACG-ATGCACTTCATGTGTCAGGATGCACTTAGTGTGCT
1 A-GTATGCACTTTGTGTGCCAGGATACACTTAGTGTGCC
35269789 AGTATGCACTTTG
1 AGTATGCACTTTG
35269802 CACAGTAGTG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
37 1 0.03
38 38 0.95
39 1 0.03
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (38 bp):
AGTATGCACTTTGTGTGCCAGGATACACTTAGTGTGCC
Found at i:35269786 original size:19 final size:19
Alignment explanation
Indices: 35269716--35269799 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 19
35269706 GTACGCTAGT
*
35269716 ATGCACTTTGTGTGCCAGG
1 ATGCACTTAGTGTGCCAGG
* * * *
35269735 ATACATTTTGTGTGCCACG
1 ATGCACTTAGTGTGCCAGG
*
35269754 ATGCACTTCA-TGTGTCAGG
1 ATGCACTT-AGTGTGCCAGG
* *
35269773 ATGCACTTAGTGTGCTAGT
1 ATGCACTTAGTGTGCCAGG
35269792 ATGCACTT
1 ATGCACTT
35269800 TGCACAGTAG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 1 0.02
19 51 0.98
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (19 bp):
ATGCACTTAGTGTGCCAGG
Found at i:35273096 original size:89 final size:90
Alignment explanation
Indices: 35272934--35273146 Score: 254
Period size: 89 Copynumber: 2.4 Consensus size: 90
35272924 TACAGTGGAT
* * **
35272934 CAGCACATAGC-ACCACCCTTATAATCAACT-ATATTCGGTGGAATCAGCACATAGCAACCACCT
1 CAGCACATAGCAACCACCATTATAATCAA-TGGTACCCGGTGGAATCAGCACATAGCAACCACCT
** *** *
35272997 TTATTTTCAATGATTTTCGGTGGAGC
65 TTATAATCAATGATACCCGGTGGAAC
*
35273023 CAGC-CTATAGCAACCACCATTATAAT-AATGGTACCCGGTGGAATTAGCACATAGCAACCACCT
1 CAGCAC-ATAGCAACCACCATTATAATCAATGGTACCCGGTGGAATCAGCACATAGCAACCACCT
* *
35273086 TTATAATCAATGGTACCCGGTGGAAT
65 TTATAATCAATGATACCCGGTGGAAC
*
35273112 CAGCACATAGCAACCACCTTTATAATCAATGGTAC
1 CAGCACATAGCAACCACCATTATAATCAATGGTAC
35273147 TCAGTACACG
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
88 2 0.02
89 81 0.77
90 22 0.21
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (90 bp):
CAGCACATAGCAACCACCATTATAATCAATGGTACCCGGTGGAATCAGCACATAGCAACCACCTT
TATAATCAATGATACCCGGTGGAAC
Found at i:35273143 original size:45 final size:45
Alignment explanation
Indices: 35272928--35273146 Score: 259
Period size: 45 Copynumber: 4.9 Consensus size: 45
35272918 TCGTTATACA
* * **
35272928 GTGG-ATCAGCACATAGC-ACCACCCTTATAATCAACT-ATATTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAA-TGGTACCCG
** * ***
35272971 GTGGAATCAGCACATAGCAACCACCTTTATTTTCAATGATTTTCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCCG
** *
35273016 GTGGAGCCAGC-CTATAGCAACCACCATTATAAT-AATGGTACCCG
1 GTGGAATCAGCAC-ATAGCAACCACCTTTATAATCAATGGTACCCG
*
35273060 GTGGAATTAGCACATAGCAACCACCTTTATAATCAATGGTACCCG
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCCG
35273105 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTAC
1 GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTAC
35273147 TCAGTACACG
Statistics
Matches: 152, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
43 4 0.03
44 49 0.32
45 99 0.65
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACCCG
Found at i:35278353 original size:29 final size:29
Alignment explanation
Indices: 35278317--35278468 Score: 150
Period size: 29 Copynumber: 5.3 Consensus size: 29
35278307 AAGAAGTGCA
*
35278317 TTTGTGGCTATCTCTGTTAAAAAGAAGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
* *
35278346 TTTTTGGCTATCTCTATTAAAAGGAAGCC
1 TTTGTGGCTATCTCTGTTAAAAGGAAGCC
* * *
35278375 TTTATGG-TGATCTCTATTAAAAGGAA-AC
1 TTTGTGGCT-ATCTCTGTTAAAAGGAAGCC
* * *
35278403 TTGTGTGGCGATCTTTGTTAAAAGGAAGTC
1 TT-TGTGGCTATCTCTGTTAAAAGGAAGCC
* *
35278433 TTTGTGGCAATCTCTGTCAAAA-GACA-CC
1 TTTGTGGCTATCTCTGTTAAAAGGA-AGCC
35278461 TTTGTGGC
1 TTTGTGGC
35278469 GAGACTCTGA
Statistics
Matches: 104, Mismatches: 14, Indels: 11
0.81 0.11 0.09
Matches are distributed among these distances:
28 15 0.14
29 86 0.83
30 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (29 bp):
TTTGTGGCTATCTCTGTTAAAAGGAAGCC
Found at i:35285693 original size:12 final size:12
Alignment explanation
Indices: 35285676--35285703 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
35285666 CACTTAAGAA
35285676 TATACTATTAAG
1 TATACTATTAAG
35285688 TATACTATTAAG
1 TATACTATTAAG
35285700 TATA
1 TATA
35285704 TTTAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
TATACTATTAAG
Found at i:35288415 original size:40 final size:40
Alignment explanation
Indices: 35288332--35288594 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
35288322 TTGAATGCTG
* * * * * *
35288332 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
35288372 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
35288412 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
35288452 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
35288492 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
35288532 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
35288571 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35288595 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:35288614 original size:79 final size:80
Alignment explanation
Indices: 35288371--35288629 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
35288361 AAGTGAATAT
* * * * * *
35288371 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
35288435 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
35288451 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
35288516 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
35288531 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
35288595 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
35288610 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
35288630 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:35296368 original size:40 final size:40
Alignment explanation
Indices: 35296285--35296547 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
35296275 TTGAATGCTG
* * * * * *
35296285 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
35296325 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
35296365 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
35296405 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
35296445 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
35296485 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
35296524 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35296548 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:35296567 original size:79 final size:80
Alignment explanation
Indices: 35296324--35296582 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
35296314 AAGTGAATAT
* * * * * *
35296324 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
35296388 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
35296404 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
35296469 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
35296484 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
35296548 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
35296563 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
35296583 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:35300183 original size:20 final size:19
Alignment explanation
Indices: 35300158--35300196 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35300148 TATCAAATTA
*
35300158 CAAAATGATATAAATATTTT
1 CAAAATAAT-TAAATATTTT
*
35300178 CAAAATAATTATATATTTT
1 CAAAATAATTAAATATTTT
35300197 TATAGGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (19 bp):
CAAAATAATTAAATATTTT
Found at i:35300912 original size:3 final size:3
Alignment explanation
Indices: 35300904--35300947 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
35300894 ATACTATCAT
35300904 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
35300948 TTTTCCCTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:35305400 original size:16 final size:17
Alignment explanation
Indices: 35305365--35305410 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
35305355 ATTATAAAAT
**
35305365 AAAATTAAACCAATACA
1 AAAATTAAATAAATACA
35305382 AAACA-TAAATAAATA-A
1 AAA-ATTAAATAAATACA
35305398 AAAATTAAATAAA
1 AAAATTAAATAAA
35305411 ATAATTAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 1 0.04
16 12 0.48
17 11 0.44
18 1 0.04
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATTAAATAAATACA
Found at i:35306724 original size:22 final size:23
Alignment explanation
Indices: 35306683--35306725 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
35306673 GGAAAGATTT
*
35306683 AATTACAATGAAGAGTAAAAAAG
1 AATTACAATGAAAAGTAAAAAAG
35306706 AATTACAAT-AAAAGTAAAAA
1 AATTACAATGAAAAGTAAAAA
35306726 TATTAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.19
Consensus pattern (23 bp):
AATTACAATGAAAAGTAAAAAAG
Found at i:35309947 original size:3 final size:3
Alignment explanation
Indices: 35309939--35310022 Score: 150
Period size: 3 Copynumber: 28.0 Consensus size: 3
35309929 ATTTTTGTAC
*
35309939 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
35309987 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35310023 GTATACCTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:35310908 original size:70 final size:70
Alignment explanation
Indices: 35310795--35310928 Score: 214
Period size: 70 Copynumber: 1.9 Consensus size: 70
35310785 TCCTTTCAAA
** *
35310795 CTCAAGTTTTAAACGATCTCGGGAATTAAGAGGAGGTCGTGTCCTAACTTACTGGGCATGATCCT
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCT
35310860 TTTTT
66 TTTTT
* * *
35310865 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAAAGATTGTGTCCTAACTTATTGGGCATGATCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
35310929 CCTTTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (70 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCT
TTTTT
Found at i:35311654 original size:17 final size:17
Alignment explanation
Indices: 35311632--35311665 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
35311622 CTGTACCTAT
35311632 GTCTTCGTGAGATTTTC
1 GTCTTCGTGAGATTTTC
35311649 GTCTTCGTGAGATTTTC
1 GTCTTCGTGAGATTTTC
35311666 ATCTCCGTAT
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:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (17 bp):
GTCTTCGTGAGATTTTC
Found at i:35316618 original size:24 final size:24
Alignment explanation
Indices: 35316591--35316643 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
35316581 CCCAAAGTAT
*
35316591 AGTGGATTGAACCTTAAAGATTAC
1 AGTGGATTAAACCTTAAAGATTAC
*
35316615 AGTGGATTAAACCTTGAAGATTAC
1 AGTGGATTAAACCTTAAAGATTAC
35316639 AGTGG
1 AGTGG
35316644 GGGAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (24 bp):
AGTGGATTAAACCTTAAAGATTAC
Found at i:35316852 original size:62 final size:62
Alignment explanation
Indices: 35316778--35316955 Score: 304
Period size: 62 Copynumber: 2.9 Consensus size: 62
35316768 ATTTAGCATT
* *
35316778 CATTCATACACATTTAGTTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAG
1 CATTCACACACATCTAGTTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAG
* *
35316840 CATTCACACACATCTAGTTAGGAGATTTTGGTTCATTCCGATCATAATATCCTAATCACTAG
1 CATTCACACACATCTAGTTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAG
35316902 CATTCACACAC-TGCTAGTTAGGAGATTTTGATTCATTCCGATCATAACATCCTA
1 CATTCACACACAT-CTAGTTAGGAGATTTTGATTCATTCCGATCATAACATCCTA
35316956 GTCATTAGGC
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
61 1 0.01
62 108 0.99
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (62 bp):
CATTCACACACATCTAGTTAGGAGATTTTGATTCATTCCGATCATAACATCCTAATCACTAG
Found at i:35317219 original size:44 final size:44
Alignment explanation
Indices: 35317082--35318353 Score: 599
Period size: 44 Copynumber: 28.8 Consensus size: 44
35317072 AGATGACAAA
* * *
35317082 TCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAAT-AA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA---AAATCAAG
* * **
35317127 ACCTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAT-CAAG
* *
35317171 TCTTAT-TCCCCTGAAGTTGTAGTGGGGCAGATTGAATAAATCAA-
1 TCTTATCT-CCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCAAG
* *
35317215 TCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGAAA--ATAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCA-AG
* * * *
35317259 ACTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCAAG
* * * *
35317304 TCTTATC-CCTCTGAAGTTGCAGTGG-GCCAAACT-AAAGTTATGAA-
1 TCTTATCTCC-CTGAAGTTGCAGTGGAG-CAGATTGAAA--AATCAAG
* *
35317348 TCTTATCTCCCTGAAGCTGCATTGGAGCAGATT-AAAGCCAAT-AA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AATCAAG
* * * * * * *
35317392 CCTTATCTCCCTGGAGTTGCAGCGAAGCAGGTT-AAAGCTACCAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA--AATCAAG
* * **
35317436 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAATTAATGGA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA--AATCAAG
* * * * * ** * *
35317480 TATTATCTCTCTAAAGTTGTAGTAGAATAGATCG---CATC-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAATCAAG
* * * ** *
35317520 ATCTTATCTCCCGGAAGTTGCAATGGGGCAGATTGAAGTTAT-AAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCAAG
* * * * * **
35317565 TCCTATCTCCCTAAAGTTGTAGTAGAGCGGATT-AAAATGAT-GGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAA--ATCAAG
* * * * *
35317609 TCTTATCTCCCTAAAGTTACAGTGGAGTAGACTGAATAAACCAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCAAG
* * * ** * ** *
35317653 CCTTATGTCCCTAAAGTTGCAGTAAAGCTGATT-AAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAT-CAAG
* * **
35317697 TCTTATCTCCCTGAAGTTACAGTGGAGCGGATT-AAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAT-CAAG
*
35317741 TCTTAT-TCCCCTGAAGTTGCAGTGGGGCAGATTGAATAAATCAA-
1 TCTTATCT-CCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCAAG
* *
35317785 TCTTATCTCCCTGAAGTTGAAGTGAAGCAGATT-AAAGCCAAT-AA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AATCAAG
* * *
35317829 TCCTACCTCCCTGAAGTTGCAGTGAAGCAGATT-AAAGCCAAT-AA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AATCAAG
* * **
35317873 TCCTATCTCCCTGAAATTGCAGTGGAGCAGATT-AAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAT-CAAG
* * * *
35317917 TCTTATCTTCCTGAAGTTGCAGTAGAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCAAG
* ** * * * *
35317962 TCTTATCCCCCTGAAGTTGCA-AAGAGGCAAACTG-AAGATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTGAAAAAT--CAAG
* *
35318007 TCTTATCTCCCTAAAGTTGCAGTGGAGCAAATT-AAAGCCAAT-AA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AATCAAG
* * **
35318051 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAT-CAAG
* *
35318095 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-AAATCAAG
* * * * * *
35318140 TCTTATCCCCCTGAAGTTGCAGAGGGGCAGACT-AAAGATGTTGAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-A--ATCAAG
* * * * *
35318185 TCTTATCTCTCTAAAGTTACAGTGGAGTATATT-AAAGCCAAT-AA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA---AATCAAG
* * **
35318229 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAAT-CAAG
** * * *
35318273 TCTTATCTCATTGAAGTTGCAGTGGAGCTGACTGAAAAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AAAAATCAAG
* * * *
35318318 TCTTATCCCCCTGAAGTTGTAGTGGGGCAGACTGAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
35318354 GATAACATAT
Statistics
Matches: 944, Mismatches: 214, Indels: 139
0.73 0.16 0.11
Matches are distributed among these distances:
39 1 0.00
40 2 0.00
41 28 0.03
42 3 0.00
43 26 0.03
44 621 0.66
45 244 0.26
46 16 0.02
47 1 0.00
48 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAAATCAAG
Found at i:35317399 original size:177 final size:176
Alignment explanation
Indices: 35317083--35317412 Score: 375
Period size: 177 Copynumber: 1.9 Consensus size: 176
35317073 GATGACAAAT
* * *
35317083 CTTATCTTCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAATAAACCTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAG-CAAACAAACCTATCTCCCTGAAGTTGCA
* * * * * * *
35317148 GTGGAGCAGATTAAAGTTACAAGTCTTATTCCCCTGAAGTTGTAGTGGGGCAGATTGAATAAATC
65 GTGGAGCAAACTAAAGTTACAAGTCTTATTCCCCTGAAGCTGCAGTGGAGCAGATTAAACAAATC
*
35317213 AATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGAAAATAGA
130 AACCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGAAAATAGA
* * *
35317260 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG-AAAGCAAGTCTTATC-CCTCTGAAGTTG
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGCAAA-CAA-ACCTATCTCC-CTGAAGTTG
* *
35317323 CAGTGG-GCCAAACTAAAGTTATGAA-TCTTA-TCTCCCTGAAGCTGCATTGGAGCAGATTAAAG
63 CAGTGGAG-CAAACTAAAGTTA-CAAGTCTTATTC-CCCTGAAGCTGCAGTGGAGCAGATTAAA-
* **
35317385 CCAAT-AACCTTATCTCCCTGGAGTTGCA
124 CAAATCAACCTTATCTCCCTAAAGTTGCA
35317413 GCGAAGCAGG
Statistics
Matches: 127, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
175 3 0.02
176 7 0.06
177 112 0.88
178 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (176 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGCAAACAAACCTATCTCCCTGAAGTTGCAG
TGGAGCAAACTAAAGTTACAAGTCTTATTCCCCTGAAGCTGCAGTGGAGCAGATTAAACAAATCA
ACCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGAAAATAGA
Found at i:35318238 original size:222 final size:222
Alignment explanation
Indices: 35317130--35318360 Score: 652
Period size: 222 Copynumber: 5.6 Consensus size: 222
35317120 CAAATAAACC
** * * *
35317130 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACA-AGTCTTAT-TCCCCTGAAGTTGTAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATAATCCTATCT-CCCTGAAGTTGCAG
* * * * * *
35317193 TGGGGCAGATTGAATAAATCAA-TCTTATCTCCCTAAAGTTGCAATGGAGCAGATTGAAGAAA-A
64 TGGAGCAGATTAAAGAAA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACA
* * * * * * *
35317256 TAGACTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAAAGCAAGTCTTATCCCTCTGAAGT
128 -AGTCTTATCCCCCTGAAGTTGCAGTAGAGCAGACTAAAGAAAGCAAGTCTTATCCCCCTAAAGT
* ** *
35317321 TGCAGTG-GGCCAAACTAAAGTTATG---AATCT
192 TACAAAGAGG-CAAACTGAAG--ATGCCAAATCT
* * * *
35317351 TATCTCCCTGAAGCTGCATTGGAGCAGATTAAAGCCAATAA-CCTTATCTCCCTGGAGTTGCAGC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCC-TATCTCCCTGAAGTTGCAGT
* * * * * * * * ** **
35317415 GAAGCAGGTTAAAGCTACCAA-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAATTAA-TG
65 GGAGCAGATTAAAG-AAACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAA
* * * * * ** * * * * **
35317478 GATATTATCTCTCTAAAGTTGTAGTAGAATAGA-T--CG-CATC-AGATCTTATCTCCCGGAAGT
129 G-TCTTATCCCCCTGAAGTTGCAGTAGAGCAGACTAAAGAAAGCAAG-TCTTATCCCCCTAAAGT
* * * * * *** *
35317538 TGCAATGGGGCAGATTGAAG-TTATAAATCC
192 TACAAAGAGGCAAACTGAAGATGCCAAATCT
* * * * *** ** * * *
35317568 TATCTCCCTAAAGTTGTAGTAGAGCGGATTAAA-ATGATGGGTCTTATCTCCCTAAAGTTACAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT-AATCCTATCTCCCTGAAGTTGCAGT
* * * * * * * ** * * * **
35317632 GGAGTAGACTGAATAAACCAA-CCTTATGTCCCTAAAGTTGCAGTAAAGCTGATTAAAGTTACAA
65 GGAGCAGATTAAAGAAA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAA
* * * * * * ** * * *
35317696 ATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGTTA-CAAGTCTTATTCCCCTGAAGTTG
129 GTCTTATCCCCCTGAAGTTGCAGTAGAGCAGACTAAAGAAAGCAAGTCTTATCCCCCTAAAGTTA
** * * * * ***
35317760 CAGTGGGGCAGATTGAATAAATC-AATCT
194 CAAAGAGGCAAACTGAAGATGCCAAATCT
* * *
35317788 TATCTCCCTGAAGTTGAAGTGAAGCAGATTAAAGCCAATAATCCTACCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTG
* * * * * * * **
35317853 AAGCAGATTAAAGCCAATAA-TCCTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAG
66 GAGCAGATTAAAG-AAACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
** * * *
35317917 TCTTATCTTCCTGAAGTTGCAGTAGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGC
130 TCTTATCCCCCTGAAGTTGCAGTAGAGCAGACTAAAGAAAGCAAGTCTTATCCCCCTAAAGTTAC
*
35317982 AAAGAGGCAAACTGAAGATGGCAAATCT
195 AAAGAGGCAAACTGAAGATGCCAAATCT
* *
35318010 TATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTG
* **
35318075 GAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
66 GAGCAGATTAAAGAAACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAG
* * * * *
35318140 TCTTATCCCCCTGAAGTTGCAG-AGGGGCAGACTAAAG-ATGTTGAA-TCTTATCTCTCTAAAGT
130 TCTTATCCCCCTGAAGTTGCAGTA-GAGCAGACTAAAGAAAG--CAAGTCTTATCCCCCTAAAGT
** * * * *
35318202 TACAGTG-GAGTATA-TTAA-A-GCCAATAATCC
192 TACAAAGAG-GCAAACTGAAGATGCC-A-AATCT
* ** * * **
35318232 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTTACA-AGTCTTATCTCATTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATAATCCTATCTCCCTGAAGTTGCAGT
* * * * *
35318296 GGAGCTGACTGAAA-AAAGCAAGTCTTATCCCCCTGAAGTTGTAGTGGGGCAGACTGAAGATAAC
65 GGAGCAGA-TTAAAGAAA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AAC
35318360 A
127 A
35318361 TATCTTGTCT
Statistics
Matches: 776, Mismatches: 198, Indels: 70
0.74 0.19 0.07
Matches are distributed among these distances:
214 1 0.00
216 5 0.01
217 140 0.18
218 5 0.01
220 169 0.22
221 166 0.21
222 184 0.24
223 102 0.13
224 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (222 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTG
GAGCAGATTAAAGAAACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAGT
CTTATCCCCCTGAAGTTGCAGTAGAGCAGACTAAAGAAAGCAAGTCTTATCCCCCTAAAGTTACA
AAGAGGCAAACTGAAGATGCCAAATCT
Found at i:35318347 original size:178 final size:177
Alignment explanation
Indices: 35317654--35318356 Score: 910
Period size: 178 Copynumber: 4.0 Consensus size: 177
35317644 ATAAACCAAC
* ** ** ** * *
35317654 CTTATGTCCCTAAAGTTGCAGTAAAGCTGATTAAAGTTACA-AATCTTATCTCCCTGAAGTTACA
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCA-ATAATCCTATCTCCCTGAAGTTGCA
* * * *
35317718 GTGGAGCGGATTAAAGTTACAAGTCTTAT-TCCCCTGAAGTTGCAGTGGGGCAGATTGAATAAAT
65 GTGGAGCGGATTAAAGTTACAAGTCTTATCT-CCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAG
* * * * * ***
35317782 CAA-TCTTATCTCCCTGAAGTTGAAGTGAAGCAGATTAAAGCCAATAAT
129 CAAGTCTTATCCCCCTGAAGTTGCAGAGAGGCAGACTAAAGATGATAAT
* * * * * *
35317830 CCTACCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAATTGCAG
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAG
* * *
35317895 TGGAGCAGATTAAAGTTACAAGTCTTATCTTCCTGAAGTTGCAGTAGAGCAGACTGAAGAAAGCA
66 TGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA
* * *
35317960 AGTCTTATCCCCCTGAAGTTGCAAAGAGGCAAACTGAAGATGGCA-AAT
131 AGTCTTATCCCCCTGAAGTTGCAGAGAGGCAGACTAAAGAT-G-ATAAT
35318008 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAG
35318073 TGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA
66 TGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA
* *
35318138 AGTCTTATCCCCCTGAAGTTGCAGAGGGGCAGACTAAAGATGTTGAAT
131 AGTCTTATCCCCCTGAAGTTGCAGAGAGGCAGACTAAAGATGAT-AAT
* * * *
35318186 CTTATCTCTCTAAAGTTACAGTGGAGTATATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAG
** * *
35318251 TGGAGCGGATTAAAGTTACAAGTCTTATCTCATTGAAGTTGCAGTGGAGCTGACTGAAAAAAGCA
66 TGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA
* * * *
35318316 AGTCTTATCCCCCTGAAGTTGTAGTGGGGCAGACTGAAGAT
131 AGTCTTATCCCCCTGAAGTTGCAGAGAGGCAGACTAAAGAT
35318357 AACATATCTT
Statistics
Matches: 466, Mismatches: 54, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
175 1 0.00
176 109 0.23
177 31 0.07
178 324 0.70
179 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (177 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAG
TGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA
AGTCTTATCCCCCTGAAGTTGCAGAGAGGCAGACTAAAGATGATAAT
Found at i:35318485 original size:89 final size:89
Alignment explanation
Indices: 35318338--35318610 Score: 386
Period size: 89 Copynumber: 3.1 Consensus size: 89
35318328 CTGAAGTTGT
* * *
35318338 AGTGGGGCAGACTGAAGATAACATATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGACA
1 AGTGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACA
* *
35318403 CCAACCTTGCCTCTCTGAGTTTGT
66 CCAGCCTTGCCTCTCTGAGTTTGC
* *
35318427 AGTGGAGCAGATTGAAGATAACAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGACA
1 AGTGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACA
*
35318492 CCAGCCTTGCCTCCCTGAG-TTGC
66 CCAGCCTTGCCTCTCTGAGTTTGC
* * * * ** * *
35318515 AGTGGAGCAGACTAAAAATAGCAGATCTTGTCTTCCTGTACTGGCAATGAAGAAGATCGAAAACA
1 AGTGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACA
*
35318580 CCAGCCTTGCCTCTCTTAGTTTGC
66 CCAGCCTTGCCTCTCTGAGTTTGC
35318604 AGTGGAG
1 AGTGGAG
35318611 TAGGTTGAAG
Statistics
Matches: 163, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
88 75 0.46
89 88 0.54
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (89 bp):
AGTGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACA
CCAGCCTTGCCTCTCTGAGTTTGC
Found at i:35318772 original size:132 final size:131
Alignment explanation
Indices: 35318602--35319008 Score: 515
Period size: 132 Copynumber: 3.1 Consensus size: 131
35318592 CTCTTAGTTT
*
35318602 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTTTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGT-GATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * * *
35318667 -AGTGAATCTTATCTTTCCAAGGTAGTAGGGAAGTAGATTTAAGCCACTAGTCCTATCTCCCTAA
65 GA-CGAATCTTATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAA
35318731 GTA
129 GTA
* * *
35318734 GCAGTAGAGTAGGTTGAAGATTGTCGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GCAGTGGAGTAGGTTGAAGATTGT-GATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* * * * *
35318799 GACGAATCTTATCCTCCCGAGATAGTA-GGAAGCAGATTTAAGCCACCAGTCCTATCTCTCTGAG
65 GACGAATCTTATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAG
*
35318863 CA
130 TA
* *
35318865 GTAGTGGAGTAGGTTG--GA----GATCCTGTCTCCCTAAGCAGTAGTGAAGCAGATCAAAGACG
1 GCAGTGGAGTAGGTTGAAGATTGTGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACG
* * * **
35318924 ACGAGTCTTATCTTCCCGAGGTACTAGGGAAATAGATTTAAGCCACCAGTTTTATCTCCCTGAAG
66 ACGAATCTTATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCT-AAG
*
35318989 TT
130 TA
*
35318991 GCAGTGGAGCAGGTTGAA
1 GCAGTGGAGTAGGTTGAA
35319009 ATTACCAATT
Statistics
Matches: 236, Mismatches: 34, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
124 60 0.25
125 29 0.12
126 16 0.07
129 2 0.01
131 48 0.20
132 80 0.34
133 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (131 bp):
GCAGTGGAGTAGGTTGAAGATTGTGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACG
ACGAATCTTATCTTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGT
A
Found at i:35318924 original size:124 final size:126
Alignment explanation
Indices: 35318626--35319007 Score: 446
Period size: 124 Copynumber: 3.0 Consensus size: 126
35318616 TGAAGATTGT
* * * *
35318626 AGATCCTGTTTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC-AGTGAATCTTATCTTTCCAAGGT
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGA-CGAATCTTATCTTCCCGAGGT
* *
35318690 AGTAGGGAAGTAGATTTAAGCCACTAGTCCTATCTCCCTAAGTAGCAGTAGAGTAGGTTGAAG
65 AGTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTAGAGTAGGTTG-AG
* * *
35318753 ATTGTCGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCCTCCCG
1 A-----GATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCG
* * * * * *
35318818 AGATAGTA-GGAAGCAGATTTAAGCCACCAGTCCTATCTCTCTGAGCAGTAGTGGAGTAGGTTG-
61 AGGTAGTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTAGAGTAGGTTGA
35318881 G
126 G
* *
35318882 AGATCCTGTCTCCCTAAGCAGTAGTGAAGCAGATCAAAGACGACGAGTCTTATCTTCCCGAGGTA
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCGAGGTA
* * ** ** * *
35318947 CTAGGGAAATAGATTTAAGCCACCAGTTTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGA
66 GTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCT-AAGCAGCAGTAGAGTAGGTTGA
35319008 AATTACCAAT
Statistics
Matches: 214, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
124 60 0.28
125 29 0.14
126 16 0.07
127 1 0.00
129 2 0.01
131 48 0.22
132 57 0.27
133 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (126 bp):
AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTTATCTTCCCGAGGTA
GTAGGGAAGTAGATTTAAGCCACCAGTCCTATCTCCCTAAGCAGCAGTAGAGTAGGTTGAG
Found at i:35319820 original size:8 final size:8
Alignment explanation
Indices: 35319809--35319839 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
35319799 TATTTATCCA
35319809 TTTAATTG
1 TTTAATTG
35319817 TTTAATTG
1 TTTAATTG
35319825 TTTAATTG
1 TTTAATTG
35319833 TTTAATT
1 TTTAATT
35319840 ATTCTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.65
Consensus pattern (8 bp):
TTTAATTG
Found at i:35325899 original size:22 final size:22
Alignment explanation
Indices: 35325871--35325967 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 22
35325861 ACACCACACT
*
35325871 AGAGAGCACTGTAGTGCTAAAA
1 AGAGAGCACTGAAGTGCTAAAA
*
35325893 AGAGAGCACTGAAGTGCTAAAT
1 AGAGAGCACTGAAGTGCTAAAA
* * * * *
35325915 AGAGGGTACCGAAGTGCTGAAC
1 AGAGAGCACTGAAGTGCTAAAA
* ** * *
35325937 AGAGAACACAAAAGTGCTGAAT
1 AGAGAGCACTGAAGTGCTAAAA
35325959 AGAGAGCAC
1 AGAGAGCAC
35325968 AAAAGTTCTA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.14
Consensus pattern (22 bp):
AGAGAGCACTGAAGTGCTAAAA
Found at i:35325968 original size:22 final size:22
Alignment explanation
Indices: 35325883--35325979 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 22
35325873 AGAGCACTGT
* **
35325883 AGTGCTAAAAAGAGAGCACTGA
1 AGTGCTAAATAGAGAGCACAAA
* * **
35325905 AGTGCTAAATAGAGGGTACCGA
1 AGTGCTAAATAGAGAGCACAAA
* * *
35325927 AGTGCTGAACAGAGAACACAAA
1 AGTGCTAAATAGAGAGCACAAA
*
35325949 AGTGCTGAATAGAGAGCACAAA
1 AGTGCTAAATAGAGAGCACAAA
*
35325971 AGTTCTAAA
1 AGTGCTAAA
35325980 CCCGTATAAG
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.15
Consensus pattern (22 bp):
AGTGCTAAATAGAGAGCACAAA
Found at i:35345665 original size:40 final size:39
Alignment explanation
Indices: 35345628--35345719 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
35345618 GCTACTCGTT
*
35345628 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
35345668 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
35345707 CAAATGCCTTCGG
1 CAAATGCCTTCGG
35345720 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:35345699 original size:39 final size:40
Alignment explanation
Indices: 35345609--35345772 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
35345599 CGGAATTTAA
** *
35345609 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
35345649 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
35345688 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
35345728 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
35345768 CCGGA
1 CCGGA
35345773 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:35367900 original size:41 final size:41
Alignment explanation
Indices: 35367741--35367893 Score: 200
Period size: 41 Copynumber: 3.7 Consensus size: 41
35367731 AAAATCTTAA
*
35367741 TATGAAACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGT
1 TATGATACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGT
*
35367782 TATGATACACCGGCAATAAGCCCGCTAGGCGTAAAGCCTGT
1 TATGATACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGT
* * * * *
35367823 TATGGTACATCGGCATTAAGCTTGCTAGGCGTAAAGCCTGA
1 TATGATACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGT
* * *
35367864 TATAATTCACCGGC-ATAATGCTTGCTAGGC
1 TATGATACACCGGCAATAA-GCCTGCTAGGC
35367894 AGAAAGCGCG
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
40 3 0.03
41 95 0.97
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (41 bp):
TATGATACACCGGCAATAAGCCTGCTAGGCGTAAAGCCTGT
Found at i:35371779 original size:16 final size:16
Alignment explanation
Indices: 35371750--35371782 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
35371740 TCACCATAAT
35371750 TAATCAATAATTAAAA
1 TAATCAATAATTAAAA
*
35371766 TAAT-AATAATTTAAA
1 TAATCAATAATTAAAA
35371781 TA
1 TA
35371783 TGAAACATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATCAATAATTAAAA
Found at i:35372587 original size:14 final size:14
Alignment explanation
Indices: 35372568--35372599 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
35372558 AGGTCATTTA
35372568 GCCCAACCAAACTG
1 GCCCAACCAAACTG
35372582 GCCCAACCAAACTG
1 GCCCAACCAAACTG
35372596 GCCC
1 GCCC
35372600 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:35377714 original size:14 final size:14
Alignment explanation
Indices: 35377695--35377724 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
35377685 GTCATTTAGG
35377695 CCAACCAAACTGGC
1 CCAACCAAACTGGC
35377709 CCAACCAAACTGGC
1 CCAACCAAACTGGC
35377723 CC
1 CC
35377725 GGTGATTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.47, G:0.13, T:0.07
Consensus pattern (14 bp):
CCAACCAAACTGGC
Found at i:35398321 original size:16 final size:18
Alignment explanation
Indices: 35398285--35398321 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35398275 TTTACCCTTG
*
35398285 TTACAAATATTAATTTAT
1 TTACAAATATAAATTTAT
35398303 TTACAAAT-TAAATTT-T
1 TTACAAATATAAATTTAT
35398319 TTA
1 TTA
35398322 TTGTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 8 0.44
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TTACAAATATAAATTTAT
Found at i:35399454 original size:6 final size:6
Alignment explanation
Indices: 35399434--35399511 Score: 88
Period size: 6 Copynumber: 12.7 Consensus size: 6
35399424 TTTACGTCAA
*
35399434 AATTTT AATTAAT AATTAT AAATTA- AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATT-AT AATTAT -AATTAT AATTAT AATTAT AATTAT AATTAT
*
35399483 AATT-T AATTTAT AATTATT AATTAA AATT
1 AATTAT AA-TTAT AATTA-T AATTAT AATT
35399512 TTGACGTAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
5 8 0.12
6 37 0.58
7 19 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Done.