Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 19 of 211
Found at i:6001395 original size:24 final size:22
Alignment explanation
Indices: 6001331--6001386 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
6001321 TGAGAGTTTA
6001331 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
6001353 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
6001375 AGAGAATATTTG
1 AGAGAAT-TTTG
6001387 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:6002499 original size:27 final size:28
Alignment explanation
Indices: 6002464--6002551 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 28
6002454 TTAAGATGAT
*
6002464 TATATAAAAATTTTAATTAATAAAA-AA
1 TATATAAAAATTTTAAATAATAAAATAA
*
6002491 TATAT-AAAATTATTAAATATTAAAATAA
1 TATATAAAAATT-TTAAATAATAAAATAA
*
6002519 -A-ATAAATATTTTAAAATAAATTTAAAATAA
1 TATATAAAAATTTT-AAAT-AA--TAAAATAA
6002549 TAT
1 TAT
6002552 GGGCGGGCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 10 0.21
27 26 0.54
28 3 0.06
30 8 0.17
31 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TATATAAAAATTTTAAATAATAAAATAA
Found at i:6004442 original size:83 final size:83
Alignment explanation
Indices: 6004293--6004445 Score: 204
Period size: 83 Copynumber: 1.8 Consensus size: 83
6004283 GTCTCAAATT
* *
6004293 TTTTTCAAAAATAGCAATTAAGACCCTACTTTTTTTGCACCCAATTGAGTACTTGAACTTTCAAA
1 TTTTTCAAAAATAGCAATTAAGACCCTACTTTTTTTGCACCCAATTGAGTACTTGAAATTGCAAA
6004358 ATGCAAAGGCCCACAAGC
66 ATGCAAAGGCCCACAAGC
* * * *
6004376 TTTTTCAGAAAA-AGCAATTAAG-CCCCATTTTTTTTTGCACTCAATTGGGTACTT-AAATTGCT
1 TTTTTCA-AAAATAGCAATTAAGACCCTA-CTTTTTTTGCACCCAATTGAGTACTTGAAATTGC-
6004438 AAAATGCA
63 AAAATGCA
6004446 TAAAAAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
82 9 0.15
83 48 0.79
84 4 0.07
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (83 bp):
TTTTTCAAAAATAGCAATTAAGACCCTACTTTTTTTGCACCCAATTGAGTACTTGAAATTGCAAA
ATGCAAAGGCCCACAAGC
Found at i:6005001 original size:23 final size:22
Alignment explanation
Indices: 6004966--6005010 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
6004956 AAAGGTTGTA
*
6004966 AAAATTATTAAAT-TTTAATAAC
1 AAAATTATAAAATATTT-ATAAC
6004988 AAAATATATAAAATATTTATAAC
1 AAAAT-TATAAAATATTTATAAC
6005011 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 12 0.60
24 3 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTATAAAATATTTATAAC
Found at i:6005067 original size:11 final size:10
Alignment explanation
Indices: 6005011--6005087 Score: 59
Period size: 10 Copynumber: 7.8 Consensus size: 10
6005001 TATTTATAAC
*
6005011 TTATTAAAAA
1 TTATAAAAAA
6005021 TTATAAAAAA
1 TTATAAAAAA
6005031 -TAT-AAAAA
1 TTATAAAAAA
**
6005039 TCGTAAAAAA
1 TTATAAAAAA
** *
6005049 TTGCAAAAAT
1 TTATAAAAAA
6005059 TTATAAAAAAA
1 TTAT-AAAAAA
* *
6005070 TCATAAAATA
1 TTATAAAAAA
6005080 TTATAAAA
1 TTATAAAA
6005088 TATATAGAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
8 5 0.10
9 4 0.08
10 35 0.67
11 8 0.15
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.30
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:6005069 original size:21 final size:21
Alignment explanation
Indices: 6005015--6005087 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
6005005 TATAACTTAT
6005015 TAAAA-ATTAT-AAAAAAT-A
1 TAAAATATTATAAAAAAATCA
** *
6005033 TAAAA-ATCGTAAAAAATTGCA
1 TAAAATATTATAAAAAAAT-CA
6005054 -AAAAT-TTATAAAAAAATCA
1 TAAAATATTATAAAAAAATCA
6005073 TAAAATATTATAAAA
1 TAAAATATTATAAAA
6005088 TATATAGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 8 0.19
19 8 0.19
20 18 0.42
21 9 0.21
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (21 bp):
TAAAATATTATAAAAAAATCA
Found at i:6005118 original size:10 final size:9
Alignment explanation
Indices: 6004988--6005087 Score: 51
Period size: 9 Copynumber: 10.3 Consensus size: 9
6004978 TTTTAATAAC
6004988 AAAATATATA
1 AAAAT-TATA
6004998 AAATATT-TA
1 AAA-ATTATA
* *
6005007 TAACTTATTA
1 AAAATTA-TA
6005017 AAAATTATA
1 AAAATTATA
*
6005026 AAAAATATA
1 AAAATTATA
6005035 AAAATCGTA-A
1 AAAAT--TATA
**
6005045 AAAATTGCA
1 AAAATTATA
6005054 AAAATTTATAAA
1 AAAA-TTAT--A
*
6005066 AAAATCATA
1 AAAATTATA
6005075 AAATATTATA
1 AAA-ATTATA
6005085 AAA
1 AAA
6005088 TATATAGAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.04
9 27 0.39
10 27 0.39
11 7 0.10
12 5 0.07
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:6005688 original size:90 final size:89
Alignment explanation
Indices: 6005496--6005721 Score: 274
Period size: 90 Copynumber: 2.5 Consensus size: 89
6005486 GCCCCTTACC
* * * * * *
6005496 TTTTTGATGTATTTTAGCAGTTCAAGTATCTAATTGAGTG-AAAAAAAAGCAGGGGCTTAATTGG
1 TTTTTGATGTATTTTGGCAGTTCAAGTACCCAATTGAGTGAAAAAAAAAACAAGGGCTTAATTGC
*
6005560 TTTTTTTGAAAAAGTTTGAGCGCA
66 TTTTTTTGAAAAAGTTTGAGAGCA
* *
6005584 TTTTTGATGAATTTTGGCAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAACAAGGGCTTAATTG
1 TTTTTGATGTATTTTGGCAGTTCAAGTACCCAATTGAGTG-AAAAAAAAAACAAGGGCTTAATTG
* ***
6005649 CTTTTTTTTAAAAAGTTTGAGATTT
65 CTTTTTTTGAAAAAGTTTGAGAGCA
* ** * *
6005674 TTTTTTATGTATTTTGAAAGTTCAAATACCCAATTGAGTGTAAAAAAA
1 TTTTTGATGTATTTTGGCAGTTCAAGTACCCAATTGAGTGAAAAAAAA
6005722 GAGAGACTTA
Statistics
Matches: 116, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
88 35 0.30
89 7 0.06
90 74 0.64
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (89 bp):
TTTTTGATGTATTTTGGCAGTTCAAGTACCCAATTGAGTGAAAAAAAAAACAAGGGCTTAATTGC
TTTTTTTGAAAAAGTTTGAGAGCA
Found at i:6008329 original size:249 final size:246
Alignment explanation
Indices: 6007806--6008415 Score: 832
Period size: 249 Copynumber: 2.5 Consensus size: 246
6007796 ATTGACAGAA
* * * * *
6007806 ATTGCTCAAGGTAATGATAATCCAAGATGAATACCCT-TTCGTTTCCCAGTGCCTGCCATATAGT
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATACCCTATTGGCTT-CCATTGCCTGCCATATAGT
* *
6007870 GTTGTGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATGCATAAACTTGTTTTTCCT
65 GTTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCCT
* * * *
6007935 TTTTACCTTATAAAAATCTCGCAATCGCTGCTGCTTAAACTTTGCCTGTAGAAGCAGCAACGTTT
130 TTTTACCTTATAAAAATCTCGAAATCGCTGCTGCTTAAACTTTGCCTGTAGAACCAGCAACATTA
* * *
6008000 AAAATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
195 AAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCCAGGAAAGAC
* * * *
6008052 ATTGCTCAAGGCAATGGTGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGTCGTATAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATACCCTATTGGCTTCCATTGCCTGCCATATAGTG
*
6008117 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTG-TTTTCTTT
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCCTT
* * ** * * * * *
6008181 TTTACCTT-TATCAAATCTTGAAATTTCTGCCTG-TTATACTGCTTTTCCTTTAGGACCTGCAAA
131 TTTACCTTATA-AAAATCTCGAAATCGCTG-CTGCTTA-A--ACTTTGCCTGTAGAACCAGC-AA
*
6008244 CATTAAAAATATTGGATTCTAAGCTCAAACATTATATGTTATTAACCCAGGAAAGAC
190 CATTAAAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCCAGGAAAGAC
* *
6008301 ATTGCTCAAGGTAATGGTGATCCAAGATGAATACCCTATTGACTTCCATTGCCTGCCATCTAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATACCCTATTGGCTTCCATTGCCTGCCATATAGTG
* *
6008366 TTATGTATGTATTCATAAAGTAGTTAATTTTAAAGTAAAAGAAATACATA
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
6008416 TCTCTGCAAA
Statistics
Matches: 320, Mismatches: 37, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
244 2 0.01
245 31 0.10
246 108 0.34
247 5 0.02
248 14 0.04
249 160 0.50
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (246 bp):
ATTGCTCAAGGTAATGGTGATCCAAGATGAATACCCTATTGGCTTCCATTGCCTGCCATATAGTG
TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCCTT
TTTACCTTATAAAAATCTCGAAATCGCTGCTGCTTAAACTTTGCCTGTAGAACCAGCAACATTAA
AAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCCAGGAAAGAC
Found at i:6015622 original size:17 final size:17
Alignment explanation
Indices: 6015600--6015637 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
6015590 TAAAAAACAA
6015600 CATAACTCTTAACCTTT
1 CATAACTCTTAACCTTT
*
6015617 CATAACTCTTGACCTTT
1 CATAACTCTTAACCTTT
6015634 CATA
1 CATA
6015638 TAACATAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (17 bp):
CATAACTCTTAACCTTT
Found at i:6019960 original size:17 final size:17
Alignment explanation
Indices: 6019938--6019975 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
6019928 TAAAAAACAA
6019938 CATAACTCTTGACCTTT
1 CATAACTCTTGACCTTT
6019955 CATAACTCTTGACCTTT
1 CATAACTCTTGACCTTT
6019972 CATA
1 CATA
6019976 TAACATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (17 bp):
CATAACTCTTGACCTTT
Found at i:6022904 original size:19 final size:18
Alignment explanation
Indices: 6022868--6022914 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 18
6022858 AAAAAATATA
*
6022868 TAAAATAAATAAATATTT
1 TAAAATAAATAAAGATTT
6022886 TAAAATAATATAAAGATTT
1 TAAAATAA-ATAAAGATTT
6022905 TAAAATAAAT
1 TAAAATAAAT
6022915 TAAAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAATAAATAAAGATTT
Found at i:6030460 original size:14 final size:15
Alignment explanation
Indices: 6030436--6030474 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
6030426 AATGATGTGA
* *
6030436 AAAAATGAAAAGATG
1 AAAAATAAAAAAATG
6030451 -AAAATAAAAAAATG
1 AAAAATAAAAAAATG
6030465 AAAAATAAAA
1 AAAAATAAAA
6030475 TGGAGAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAAATG
Found at i:6030460 original size:22 final size:20
Alignment explanation
Indices: 6030435--6030475 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
6030425 AAATGATGTG
6030435 AAAAAATGAAAAGATGAAAATA
1 AAAAAATGAAAA-AT-AAAATA
6030457 AAAAAATGAAAAATAAAAT
1 AAAAAATGAAAAATAAAAT
6030476 GGAGAGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (20 bp):
AAAAAATGAAAAATAAAATA
Found at i:6031965 original size:132 final size:132
Alignment explanation
Indices: 6031723--6032232 Score: 711
Period size: 132 Copynumber: 3.9 Consensus size: 132
6031713 AGATACAAAC
* * * *
6031723 CTTGTCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCTCTGTGGTTACAG
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAG
* * *
6031788 TGGAGTACATTGAAGCCGGTAATTATA-CTTCCCTGGGCAGTAGCGGAATAGATTGAAGATTTCA
66 TGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCA
6031852 GAT
130 GAT
6031855 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCT-ATGGTTACA
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGA-GGTTACA
*
6031919 GTGGAGTACATTGAAGCCAGTAATTCTA-CTTTCCTGGGCAGCAGCGGAATAGATTGAAGATTTC
65 GTGGAGTACATTGAAGCCAGTAATTCTATC-TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTC
6031983 AGAT
129 AGAT
* * * * *
6031987 CTTGTCTCCCTAAGCAGTAGTGGAGCTGATCGAAGATAGCGGATTTTACCTCACTGAGGTTACAA
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAG
* * * *** * *
6032052 TGGAGTACATTAAAGCCAGTAATTCTATCTTCCTGGGTAATGGTGGAATAGATTGAAGATTACAG
66 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAG
6032117 AT
131 AT
* * ** * *
6032119 CTTATCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGATGTATTTTACCTCCCTGAGGTTGCAG
1 CTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAG
* *
6032184 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGTAGCAGTGGAAT
66 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGCGGAAT
6032233 CCCTAAGCAA
Statistics
Matches: 339, Mismatches: 36, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
132 337 0.99
133 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (132 bp):
CTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTACAG
TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAG
AT
Found at i:6032311 original size:107 final size:106
Alignment explanation
Indices: 6032125--6032322 Score: 333
Period size: 107 Copynumber: 1.9 Consensus size: 106
6032115 AGATCTTATC
* * *
6032125 TCCCTAAACAGTAGTGGAGCAGATCAAAGATGATGTATTTTACCTCCCTGAGGTTGCAGTGGAGT
1 TCCCTAAACAATAGTGGAGCAGATCAAAAATGATGGATTTTACCTCCCTGAGGTTGCAGTGGAGT
6032190 ACATTGAAGCCAGTAATTCTATCTCCCTGGGTAGCAGTGGAA
66 ACATTGAAGCCAGTAATTCTAT-TCCCTGGGTAGCAGTGGAA
* *
6032232 TCCCTAAGCAATAGTGGAGCAGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGT
1 TCCCTAAACAATAGTGGAGCAGATCAAAAATGATGGATTTTACCTCCCTGAGGTTGCAGTGGAGT
*
6032297 ATATTGAAGCCAGTAATTCTATTCCC
66 ACATTGAAGCCAGTAATTCTATTCCC
6032323 CCGGTCGGTA
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
106 4 0.05
107 81 0.95
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (106 bp):
TCCCTAAACAATAGTGGAGCAGATCAAAAATGATGGATTTTACCTCCCTGAGGTTGCAGTGGAGT
ACATTGAAGCCAGTAATTCTATTCCCTGGGTAGCAGTGGAA
Found at i:6033272 original size:4 final size:5
Alignment explanation
Indices: 6033242--6033270 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
6033232 CTATTCTTTC
6033242 TATTT TATTT TATTT TATTT TA-TT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT
6033271 ATAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:6035533 original size:9 final size:9
Alignment explanation
Indices: 6035519--6035655 Score: 57
Period size: 10 Copynumber: 14.3 Consensus size: 9
6035509 TTTTAATAAC
6035519 AAAATATAT
1 AAAATATAT
*
6035528 AAAATATTT
1 AAAATATAT
*
6035537 AAAACT-TGTT
1 AAAA-TAT-AT
6035547 AAAA-AT-T
1 AAAATATAT
*
6035554 AGAAAAATAT
1 A-AAATATAT
*
6035564 AAAAATCATAA
1 -AAAAT-ATAT
* *
6035575 AAAAAATTGT
1 AAAATA-TAT
*
6035585 AAAATTTTAT
1 AAAATAT-AT
6035595 AAAA-ATCAT
1 AAAATAT-AT
6035604 AAAATATTAT
1 AAAATA-TAT
6035614 AAAATATAT
1 AAAATATAT
6035623 AGAAATATAT
1 A-AAATATAT
* *
6035633 AAAAAATGAG
1 AAAATAT-AT
6035643 AAAATTATAT
1 AAAA-TATAT
6035653 AAA
1 AAA
6035656 GTTGCAAGAA
Statistics
Matches: 98, Mismatches: 15, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
7 2 0.02
8 3 0.03
9 34 0.35
10 52 0.53
11 7 0.07
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAATATAT
Found at i:6035579 original size:29 final size:29
Alignment explanation
Indices: 6035547--6035655 Score: 100
Period size: 29 Copynumber: 3.7 Consensus size: 29
6035537 AAAACTTGTT
6035547 AAAAATTAGAAAA-ATATAAAAATCATAAA
1 AAAAATTAGAAAATATATAAAAATCAT-AA
*
6035576 AAAAATT-GTAAAATTTTATAAAAATCAT-A
1 AAAAATTAG-AAAA-TATATAAAAATCATAA
* * *
6035605 AAATATTATAAAATATATAGAAAT-ATATA
1 AAAAATTAGAAAATATATAAAAATCATA-A
*
6035634 AAAAATGAGAAAATTATATAAA
1 AAAAATTAGAAAA-TATATAAA
6035656 GTTGCAAGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
27 2 0.03
28 10 0.16
29 33 0.52
30 7 0.11
31 12 0.19
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAAATTAGAAAATATATAAAAATCATAA
Found at i:6035597 original size:10 final size:10
Alignment explanation
Indices: 6035584--6035636 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
6035574 AAAAAAATTG
*
6035584 TAAAATTTTA
1 TAAAATATTA
*
6035594 TAAAA-ATCA
1 TAAAATATTA
6035603 TAAAATATTA
1 TAAAATATTA
6035613 TAAAATA-TA
1 TAAAATATTA
6035622 TAGAAATA-TA
1 TA-AAATATTA
6035632 TAAAA
1 TAAAA
6035637 AATGAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 14 0.37
10 24 0.63
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (10 bp):
TAAAATATTA
Found at i:6035598 original size:19 final size:19
Alignment explanation
Indices: 6035584--6035637 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
6035574 AAAAAAATTG
*
6035584 TAAAATTTTATAAAAATCA
1 TAAAATATTATAAAAATCA
6035603 TAAAATATTATAAAATAT-A
1 TAAAATATTATAAAA-ATCA
6035622 TAGAAATA-TATAAAAA
1 TA-AAATATTATAAAAA
6035638 ATGAGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.03
19 24 0.75
20 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAATATTATAAAAATCA
Found at i:6037252 original size:10 final size:11
Alignment explanation
Indices: 6037233--6037264 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
6037223 CTTTCTTCTA
6037233 TTTTATTTTTT
1 TTTTATTTTTT
6037244 TTTTATTTTTT
1 TTTTATTTTTT
6037255 TGTTTATTTT
1 T-TTTATTTT
6037265 CTACAACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:6038007 original size:3 final size:3
Alignment explanation
Indices: 6037999--6038029 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6037989 TTTAGCAACT
*
6037999 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6038030 CATTGCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6038016 original size:12 final size:12
Alignment explanation
Indices: 6037999--6038044 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
6037989 TTTAGCAACT
6037999 TTATTATTATTG
1 TTATTATTATTG
*
6038011 TTATTATTATTA
1 TTATTATTATTG
*
6038023 TTATTATCATTG
1 TTATTATTATTG
* *
6038035 CTACTATTAT
1 TTATTATTAT
6038045 ATAATTGCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:6050778 original size:46 final size:46
Alignment explanation
Indices: 6050711--6051385 Score: 308
Period size: 46 Copynumber: 15.7 Consensus size: 46
6050701 ATTATACAGG
* *
6050711 TCTTATCTCCCTGAGATTACAGTGGAGTAGACCGAAGAATTTCAAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
* * ** ** * *
6050757 TCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAG--CCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
*
6050801 TCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTACAAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
* * * *
6050847 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A-CAC-TA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
* *
6050890 TCCTATCTCTCTGAGATTACAGT-G-G-AG--C--AG-ATTA-AAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAA--A
* * * * * **
6050929 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATC---GTA-T-CAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATTACAAA
* * *
6050970 TCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
* * ** * *
6051016 TTTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-A-CAC-TA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
* *
6051059 TCCTATCTCTCTGAGATTACAGT-G-G-AG--CG--G-ATTA-AAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAA--A
* * ** * * **
6051098 TCTTATCTCTCTGA-AGTTACAGTAGAGTGGATC---GTA-T-CAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATTACAAA
* *
6051139 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
* * * **
6051185 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-A-TAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
* * *
6051229 TCCTATCTCCTTGAGATTACAGT-G-G-AG--TG--G-ATTA-AATGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAA--A
* * ** * * **
6051268 TCTTATCTCTCTGA-AGTTACAGTAGAGTGGATC---GTA-T-CAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGACCGAAGAATTACAAA
* *
6051309 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
*
6051355 TCTTATCTCCCTGAGATTACAGCGGAGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGA
6051386 TCAAATATAG
Statistics
Matches: 485, Mismatches: 89, Indels: 110
0.71 0.13 0.16
Matches are distributed among these distances:
36 5 0.01
37 5 0.01
38 7 0.01
39 61 0.13
40 7 0.01
41 85 0.18
42 10 0.02
43 51 0.11
44 72 0.15
45 6 0.01
46 176 0.36
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTACAAA
Found at i:6051038 original size:169 final size:170
Alignment explanation
Indices: 6050801--6051495 Score: 1092
Period size: 169 Copynumber: 4.1 Consensus size: 170
6050791 AAGCCAGAGA
* * *
6050801 TCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTACAAATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTA
*
6050866 CAGCGGAGCAGATCGAAGACACT-ATCCTATCTCTCTGAGATTACAGTGGAGCAGATTAAAGGAT
66 CAGCGGAGCAGATCAAAGACACTAATCCTATCTCTCTGAGATTACAGTGGAGCAGATTAAAGGAT
*
6050930 CTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
131 CTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
* *
6050970 TCTTATCTCCCTGAGATTACAGTGGAGCAGACTGAAGAATTGCAGATTTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTA
** *
6051035 CAGCGGAGCAGATTGAAGACACT-ATCCTATCTCTCTGAGATTACAGTGGAGCGGATTAAAGGAT
66 CAGCGGAGCAGATCAAAGACACTAATCCTATCTCTCTGAGATTACAGTGGAGCAGATTAAAGGAT
6051099 CTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
131 CTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
6051139 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTA
* * ** *
6051204 CAGCGGAGCAGATCAAAGATAGTAATCCTATCTC-CTTGAGATTACAGTGGAGTGGATTAAATGA
66 CAGCGGAGCAGATCAAAGACACTAATCCTATCTCTC-TGAGATTACAGTGGAGCAGATTAAAGGA
6051268 TCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
130 TCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
6051309 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTA
* * * * *
6051374 CAGCGGAGCAGATCAAATATAGTAATCTTATCTCTCTGA-AGTTACAGCGGAGCAGATTCAAACC
66 CAGCGGAGCAGATCAAAGACACTAATCCTATCTCTCTGAGA-TTACAGTGGAGCAGATT--AA--
*
6051438 ACAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
126 A-GGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
* *
6051484 CCTTATATCCCT
1 TCTTATCTCCCT
6051496 AATGTTGCAG
Statistics
Matches: 495, Mismatches: 22, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
169 247 0.50
170 191 0.39
171 1 0.00
172 2 0.00
174 1 0.00
175 53 0.11
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (170 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGACCGAAGAATTGCAGATCTTATCTCCCTGAGATTA
CAGCGGAGCAGATCAAAGACACTAATCCTATCTCTCTGAGATTACAGTGGAGCAGATTAAAGGAT
CTTATCTCTCTGAAGTTACAGTAGAGTGGATCGTATCAGG
Found at i:6054771 original size:9 final size:9
Alignment explanation
Indices: 6054757--6054793 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6054747 TATAGTTTGA
6054757 TATTCGAAT
1 TATTCGAAT
6054766 TATTCGAAT
1 TATTCGAAT
*
6054775 TATTCGAGT
1 TATTCGAAT
6054784 TATTCGAAT
1 TATTCGAAT
6054793 T
1 T
6054794 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6054864 original size:9 final size:9
Alignment explanation
Indices: 6054847--6054877 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6054837 TCGAGTTGAT
6054847 TCGAATAAC
1 TCGAATAAC
*
6054856 TCGATTAAC
1 TCGAATAAC
6054865 TCGAATAAC
1 TCGAATAAC
6054874 TCGA
1 TCGA
6054878 TTCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:6057841 original size:238 final size:242
Alignment explanation
Indices: 6057290--6057892 Score: 805
Period size: 238 Copynumber: 2.5 Consensus size: 242
6057280 ATTGTCAGAA
* * * * *
6057290 ATTGCTCAAGGTAATGATGATCCAAGATGAATACCCTA-TCGTTTAGCACTGCCTGCCATATAGT
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTCGCTT-CCATTGCCTGCCATATAGT
*
6057354 GTTGTGTATGTATTCATAAAGTAGTTAATTTGAAAAGG-AAAGAAATACATATAAACTTGTTTTT
65 GTTATGTATGTATTCATAAAGTAGTTAATTTG-AAAGGAAAAGAAATAC--ATAAACTTGTTTTT
*
6057418 CCTTTTTACCTTACAAAAATCTTGCAATTGCGGCTGGTTAAACTTTTCCTGTAGAACGCCAGCAA
127 CCTTTTTACCTTACAAAAATCTTCCAATTGCGGCTGGTTAAACTTTTCCTGTAGAAC-CCAGCAA
6057483 CGTTTAAAATATTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
191 CGTTTAAAATATTGG--TG-AAGCT--AACATTATATGTTATAAACCTAGGAAAGAG
* * * *
6057540 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCTTATTGGCTTCCATTGTCTGCTATATAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTCGCTTCCATTGCCTGCCATATAGTG
* * *
6057605 TTATGTATGTATTTAAAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTG-TTTTCTTT
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCCTT
* * **
6057669 TTTACCTTA-AACAAATCTTCCCAATT-CTGCTTGTTCCACTTCATTTCCTGTAGAA-CCAGCAA
131 TTTACCTTACAA-AAATCTT-CCAATTGCGGCTGGTTAAAC-T--TTTCCTGTAGAACCCAGCAA
*
6057731 CGTTTAAAATATT-G-G-A-CT-GCATTATATGTTATAAACCTAGGAAAGAG
191 CGTTTAAAATATTGGTGAAGCTAACATTATATGTTATAAACCTAGGAAAGAG
*
6057778 ATTGATCAAGGTAATGGTGATCCAAGATGAATGCCCTATTCGCTTCCATTGCCTGCCATATAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTCGCTTCCATTGCCTGCCATATAGTG
*
6057843 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAGATACATA
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
6057893 TCTCTGCAAA
Statistics
Matches: 319, Mismatches: 27, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
238 135 0.42
241 2 0.01
242 1 0.00
244 1 0.00
246 2 0.01
247 33 0.10
248 35 0.11
249 5 0.02
250 101 0.32
251 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (242 bp):
ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTCGCTTCCATTGCCTGCCATATAGTG
TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCCTT
TTTACCTTACAAAAATCTTCCAATTGCGGCTGGTTAAACTTTTCCTGTAGAACCCAGCAACGTTT
AAAATATTGGTGAAGCTAACATTATATGTTATAAACCTAGGAAAGAG
Found at i:6062724 original size:161 final size:162
Alignment explanation
Indices: 6062546--6062862 Score: 548
Period size: 161 Copynumber: 2.0 Consensus size: 162
6062536 CACCATTCAC
*
6062546 TTCCTTTCAAAAACTAATTTTCTAAAAAAATTATTAACTTTGTTGACATGACATATAC-TGGATT
1 TTCCTTTCAAAAACTAATTTTCTAAAAAAATTATTAACTTTGCTGACATGACATATACGTGGATT
6062610 ACCACATGAAAGATATGTAAAAATTTAATTAATTTTTTAAAAAATATTTTTTATACTTCTTTAAT
66 ACCACATGAAAGATATGTAAAAATTTAATTAATTTTTTAAAAAATATTTTTTATACTT-TTTAAT
6062675 GATTTTAAATTTTTAAAAAACAATTTTCACCAT
130 GATTTTAAATTTTTAAAAAACAATTTTCACCAT
**
6062708 TTCCTTTC-AAAACTAATTTTCTAAAAAGTTTATTAACTTTGCTGACATGACATATACGTGGATT
1 TTCCTTTCAAAAACTAATTTTCTAAAAAAATTATTAACTTTGCTGACATGACATATACGTGGATT
* * *
6062772 ACCACGTGAAAGATATGTCAACATTTAATTAATTTTTTAAAAAATATTTTTTATACTTTTTAATG
66 ACCACATGAAAGATATGTAAAAATTTAATTAATTTTTTAAAAAATATTTTTTATACTTTTTAATG
*
6062837 ATTTTGAATTTTTAAAAAACAATTTT
131 ATTTTAAATTTTTAAAAAACAATTTT
6062863 TCAAATTTTG
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
161 78 0.53
162 69 0.47
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (162 bp):
TTCCTTTCAAAAACTAATTTTCTAAAAAAATTATTAACTTTGCTGACATGACATATACGTGGATT
ACCACATGAAAGATATGTAAAAATTTAATTAATTTTTTAAAAAATATTTTTTATACTTTTTAATG
ATTTTAAATTTTTAAAAAACAATTTTCACCAT
Found at i:6063530 original size:18 final size:18
Alignment explanation
Indices: 6063509--6063543 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6063499 ATTTTGTAAT
*
6063509 TAGTTTGAATTTAATTTC
1 TAGTTTAAATTTAATTTC
*
6063527 TAGTTTAAATTTGATTT
1 TAGTTTAAATTTAATTT
6063544 TTAAGTTTTT
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:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:6064798 original size:43 final size:43
Alignment explanation
Indices: 6064702--6064865 Score: 199
Period size: 43 Copynumber: 3.8 Consensus size: 43
6064692 AGTGGGAGAG
* * * *
6064702 GCGCCGCTAAAGG-CCATGATCTTTAGCGGCGTTTGT-GTAAAA
1 GCGCCGCTAAAGGTCC-TGATCTATAGCGGCATTTATGGAAAAA
6064744 GCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTATGGAAAAA
1 GCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTATGGAAAAA
* * * *
6064787 GCGCCGCTAAAGGTACC-GATCTATAGCGGCATTTGTGGGAGAT
1 GCGCCGCTAAAGGT-CCTGATCTATAGCGGCATTTATGGAAAAA
* *
6064830 GCGCCGCTAAAGGTCATGATCTATAGCGGCGTTTAT
1 GCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTAT
6064866 TTCTAAAAAC
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
42 31 0.29
43 74 0.69
44 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (43 bp):
GCGCCGCTAAAGGTCCTGATCTATAGCGGCATTTATGGAAAAA
Found at i:6064865 original size:86 final size:84
Alignment explanation
Indices: 6064702--6064865 Score: 222
Period size: 86 Copynumber: 1.9 Consensus size: 84
6064692 AGTGGGAGAG
* * * *
6064702 GCGCCGCTAAAGGCCATGATCTTTAGCGGCGTTTGTGTAAAAGCGCCGCTAAAGGTCCTGATCTA
1 GCGCCGCTAAAGGCCA-GATCTATAGCGGCATTTGTGGAAAAGCGCCGCTAAAGGTCATGATCTA
6064767 TAGCGGCATTTATGGAAAAA
65 TAGCGGCATTTATGGAAAAA
* *
6064787 GCGCCGCTAAAGGTACC-GATCTATAGCGGCATTTGTGGGAGATGCGCCGCTAAAGGTCATGATC
1 GCGCCGCTAAAGG--CCAGATCTATAGCGGCATTTGT-GGAAAAGCGCCGCTAAAGGTCATGATC
*
6064851 TATAGCGGCGTTTAT
63 TATAGCGGCATTTAT
6064866 TTCTAAAAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 30 0.43
86 37 0.54
87 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (84 bp):
GCGCCGCTAAAGGCCAGATCTATAGCGGCATTTGTGGAAAAGCGCCGCTAAAGGTCATGATCTAT
AGCGGCATTTATGGAAAAA
Found at i:6068873 original size:23 final size:22
Alignment explanation
Indices: 6068822--6068875 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
6068812 TTCAAATGTC
6068822 TGATTTTGCGTATTTATACATT
1 TGATTTTGCGTATTTATACATT
* * *
6068844 GGGTTTTGTCGTATTTTTTAC-TT
1 TGATTTTG-CGTA-TTTATACATT
6068867 TGATTTTGC
1 TGATTTTGC
6068876 TTTTTTATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
22 7 0.28
23 12 0.48
24 6 0.24
ACGTcount: A:0.15, C:0.09, G:0.19, T:0.57
Consensus pattern (22 bp):
TGATTTTGCGTATTTATACATT
Found at i:6070288 original size:17 final size:17
Alignment explanation
Indices: 6070268--6070360 Score: 67
Period size: 17 Copynumber: 5.9 Consensus size: 17
6070258 TTATTTTCTA
6070268 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
6070285 TATAAGTTTTCTAAA-T
1 TATAAGTTTTCTAAATT
*
6070301 CAT---TTTTCTAAATT
1 TATAAGTTTTCTAAATT
* * **
6070315 TATTAG-TATAAAAATT
1 TATAAGTTTTCTAAATT
*
6070331 TAGT-AG-TAT-TAAATT
1 TA-TAAGTTTTCTAAATT
6070346 TATAAGTTTTCTAAA
1 TATAAGTTTTCTAAA
6070361 AAAATGTTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
13 9 0.15
14 4 0.07
15 9 0.15
16 19 0.31
17 20 0.33
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.49
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:6070295 original size:30 final size:30
Alignment explanation
Indices: 6070261--6070317 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
6070251 TATTGTTTTA
*
6070261 TTTTCTATATAAGTTTTCTAAATTTATAAG
1 TTTTCTAAATAAGTTTTCTAAATTTATAAG
* *
6070291 TTTTCTAAATCATTTTTCTAAATTTAT
1 TTTTCTAAATAAGTTTTCTAAATTTAT
6070318 TAGTATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTTCTAAATAAGTTTTCTAAATTTATAAG
Found at i:6070346 original size:15 final size:16
Alignment explanation
Indices: 6070309--6070347 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
6070299 ATCATTTTTC
*
6070309 TAAATTTATTAGTATA
1 TAAATTTAGTAGTATA
*
6070325 AAAATTTAGTAGTAT-
1 TAAATTTAGTAGTATA
6070340 TAAATTTA
1 TAAATTTA
6070348 TAAGTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (16 bp):
TAAATTTAGTAGTATA
Found at i:6070377 original size:61 final size:61
Alignment explanation
Indices: 6070279--6070393 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
6070269 ATAAGTTTTC
** * *
6070279 TAAATTTATAAGTTTTCTAAATCATTTTTCTAAATTTATTAGT-ATAAAAATTTAGTAGTAT
1 TAAATTTATAAGTTTTCTAAAAAAATGTTCTAAATTTATTAGTAAT-AAAATTTAGTAGTAT
* *
6070340 TAAATTTATAAGTTTTCTAAAAAAATGTTCTAGATTTATTATTAATAAAATTTA
1 TAAATTTATAAGTTTTCTAAAAAAATGTTCTAAATTTATTAGTAATAAAATTTA
6070394 TAATTATCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
61 45 0.96
62 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (61 bp):
TAAATTTATAAGTTTTCTAAAAAAATGTTCTAAATTTATTAGTAATAAAATTTAGTAGTAT
Found at i:6070414 original size:61 final size:61
Alignment explanation
Indices: 6070280--6070421 Score: 153
Period size: 61 Copynumber: 2.3 Consensus size: 61
6070270 TAAGTTTTCT
** * * *
6070280 AAATTTATAAGTTTTCTAAATCATTTTTCTAAATTTATTAGTATAAAAATTTAGTAGTATT
1 AAATTTATAAGTTTTCTAAAAAAATGTTCTAAATTTATTAGTATAAAAATTTAGTAGTATC
* * *
6070341 AAATTTATAAGTTTTCTAAAAAAATGTTCTAGATTTATTATTA-ATAAAATTTA-TAATTATC
1 AAATTTATAAGTTTTCTAAAAAAATGTTCTAAATTTATTAGTATA-AAAATTTAGT-AGTATC
* * *
6070402 AATTTTACAAGTTTTGTAAA
1 AAATTTATAAGTTTTCTAAA
6070422 TAATTATATT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 2 0.03
61 66 0.97
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (61 bp):
AAATTTATAAGTTTTCTAAAAAAATGTTCTAAATTTATTAGTATAAAAATTTAGTAGTATC
Found at i:6070662 original size:8 final size:7
Alignment explanation
Indices: 6070649--6070694 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
6070639 TAACTTATAT
6070649 ATAATAAC
1 ATAAT-AC
6070657 ATAATA-
1 ATAATAC
*
6070663 A-ATTAC
1 ATAATAC
6070669 ATAATAC
1 ATAATAC
6070676 ATAATAAC
1 ATAAT-AC
6070684 ATAATAC
1 ATAATAC
6070691 ATAA
1 ATAA
6070695 CTTTTATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 16 0.48
8 12 0.36
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAC
Found at i:6070682 original size:95 final size:95
Alignment explanation
Indices: 6070570--6070836 Score: 392
Period size: 95 Copynumber: 2.8 Consensus size: 95
6070560 AATCATTTGC
* * * *
6070570 TTACTTAATACATAATAACACAATACATAA-TTGGTATATAAGCTTGCATAACTTAGATAATAAC
1 TTACATAATACATAATAACATAATACATAACTT-ATATATAAGCTTGCATAACTTACATAATAAC
6070634 TTCCATAACTTATATATAATAACATAATAAA
65 TTCCATAACTTATATATAATAACATAATAAA
* *
6070665 TTACATAATACATAATAACATAATACATAACTTTTATATAAGCTTGTATAACTTACATAATAACT
1 TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
*** *
6070730 TCCATAACTTATATATAATCTGATAATACA
66 TCCATAACTTATATATAATAACATAATAAA
* *
6070760 TTACGTAATACATAATAACATAATACATAACTTATATTATAATCTTGCATAACTTACATAATAAC
1 TTACATAATACATAATAACATAATACATAACTTATA-TATAAGCTTGCATAACTTACATAATAAC
*
6070825 TTTCATAACTTA
65 TTCCATAACTTA
6070837 ATACACCACT
Statistics
Matches: 156, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
95 117 0.75
96 39 0.25
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.36
Consensus pattern (95 bp):
TTACATAATACATAATAACATAATACATAACTTATATATAAGCTTGCATAACTTACATAATAACT
TCCATAACTTATATATAATAACATAATAAA
Found at i:6070687 original size:15 final size:15
Alignment explanation
Indices: 6070649--6070694 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
6070639 TAACTTATAT
6070649 ATAATAACATAAT--
1 ATAATAACATAATAC
*
6070662 A-AATTACATAATAC
1 ATAATAACATAATAC
6070676 ATAATAACATAATAC
1 ATAATAACATAATAC
6070691 ATAA
1 ATAA
6070695 CTTTTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
14 1 0.04
15 16 0.57
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAACATAATAC
Found at i:6070801 original size:27 final size:27
Alignment explanation
Indices: 6070732--6070802 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 27
6070722 TAATAACTTC
***
6070732 CATAACTTATA-TATAATCTGATAATA
1 CATAACTTATATTATAATAACATAATA
* * *
6070758 CATTACGTA-ATACATAATAACATAATA
1 CATAACTTATAT-TATAATAACATAATA
6070785 CATAACTTATATTATAAT
1 CATAACTTATATTATAAT
6070803 CTTGCATAAC
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
25 1 0.03
26 7 0.21
27 23 0.70
28 2 0.06
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.37
Consensus pattern (27 bp):
CATAACTTATATTATAATAACATAATA
Found at i:6070833 original size:21 final size:21
Alignment explanation
Indices: 6070768--6070880 Score: 81
Period size: 21 Copynumber: 5.3 Consensus size: 21
6070758 CATTACGTAA
6070768 TACATAATAACATAATACATAACT
1 TACATAATAAC-T--TACATAACT
* * *
6070792 TATATTATAATCTTGCATAACT
1 TACATAATAA-CTTACATAACT
*
6070814 TACATAATAACTTTCATAACT
1 TACATAATAACTTACATAACT
** *
6070835 TA-ATACACCACTTAAATAACT
1 TACATA-ATAACTTACATAACT
*
6070856 TAC---ATAACTTACATAGCT
1 TACATAATAACTTACATAACT
6070874 TACATAA
1 TACATAA
6070881 CTCGTTATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
18 14 0.20
20 3 0.04
21 26 0.38
22 16 0.23
24 9 0.13
25 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.35
Consensus pattern (21 bp):
TACATAATAACTTACATAACT
Found at i:6070862 original size:9 final size:9
Alignment explanation
Indices: 6070844--6071630 Score: 507
Period size: 9 Copynumber: 89.1 Consensus size: 9
6070834 TTAATACACC
*
6070844 ACTTAAATA
1 ACTTACATA
6070853 ACTTACATA
1 ACTTACATA
6070862 ACTTACATA
1 ACTTACATA
*
6070871 GCTTACATA
1 ACTTACATA
*
6070880 ACTCGT-TATA
1 ACT--TACATA
6070890 A---ACATA
1 ACTTACATA
*
6070896 ACTTGCATA
1 ACTTACATA
6070905 ACTTACGTAATA
1 ACTTAC---ATA
*
6070917 ACATAACATA
1 AC-TTACATA
6070927 ACTTACATA
1 ACTTACATA
*
6070936 A--TACAAAAA
1 ACTTAC--ATA
6070945 ACTTACATA
1 ACTTACATA
*
6070954 ACTTAAATA
1 ACTTACATA
* * *
6070963 TCTGACACA
1 ACTTACATA
6070972 ACTTACATA
1 ACTTACATA
*
6070981 A--TACACA
1 ACTTACATA
6070988 ACTTACATA
1 ACTTACATA
* *
6070997 GCTTACTTA
1 ACTTACATA
6071006 A--TACATA
1 ACTTACATA
*
6071013 ATTTACATA
1 ACTTACATA
6071022 ACTT--ATA
1 ACTTACATA
*
6071029 CACGTACATA
1 -ACTTACATA
6071039 ACTTACATA
1 ACTTACATA
*
6071048 A--TATATAA
1 ACTTACAT-A
* *
6071056 ACATATATAGAA
1 AC-T-TACA-TA
*
6071068 ACTCACATA
1 ACTTACATA
* *
6071077 AATTAAATA
1 ACTTACATA
6071086 ACTTACATA
1 ACTTACATA
*
6071095 AATTA-AGTA
1 ACTTACA-TA
6071104 AC-T---TA
1 ACTTACATA
6071109 A-TTACATA
1 ACTTACATA
6071117 ACTTACATAA
1 ACTTACAT-A
*
6071127 ACTTGCATA
1 ACTTACATA
* *
6071136 AATTAAATA
1 ACTTACATA
6071145 ACTTACATA
1 ACTTACATA
6071154 ACTTACATA
1 ACTTACATA
*
6071163 ACCTACATA
1 ACTTACATA
* *
6071172 AATTAAATA
1 ACTTACATA
6071181 ACTTACATA
1 ACTTACATA
6071190 ACTTACATA
1 ACTTACATA
* *
6071199 AATTAAATA
1 ACTTACATA
6071208 ACTTACATA
1 ACTTACATA
* * * *
6071217 AATTCCGTGG
1 ACTTACAT-A
6071227 ACTTACATA
1 ACTTACATA
*
6071236 ACCTACATA
1 ACTTACATA
* *
6071245 AATTAAATA
1 ACTTACATA
6071254 ACTTACATA
1 ACTTACATA
6071263 ACTTACATA
1 ACTTACATA
* *
6071272 AATTAAATA
1 ACTTACATA
*
6071281 ATTTACATA
1 ACTTACATA
6071290 ACTTACATA
1 ACTTACATA
* *
6071299 AATTAAATA
1 ACTTACATA
6071308 ACTTACATA
1 ACTTACATA
6071317 ACTTACATA
1 ACTTACATA
*
6071326 AATTA-ATTA
1 ACTTACA-TA
6071335 ACTTACATA
1 ACTTACATA
6071344 ACTTACATAA
1 ACTTACAT-A
*
6071354 AC-TAAATA
1 ACTTACATA
6071362 ACTTACATA
1 ACTTACATA
*
6071371 GCTTACATAA
1 ACTTACAT-A
*
6071381 AC-TAAATA
1 ACTTACATA
6071389 ACTTACATA
1 ACTTACATA
*
6071398 ATTTACATA
1 ACTTACATA
* *
6071407 AATTAAATA
1 ACTTACATA
6071416 ACTTACATA
1 ACTTACATA
6071425 ACTTACATA
1 ACTTACATA
* *
6071434 AATTAAATA
1 ACTTACATA
6071443 ACTTACATA
1 ACTTACATA
6071452 ACTTACATA
1 ACTTACATA
* * * *
6071461 AATTTCGTGG
1 ACTTACAT-A
6071471 ACTTACATA
1 ACTTACATA
*
6071480 ACCTACATA
1 ACTTACATA
*
6071489 ACTTACATT
1 ACTTACATA
*
6071498 A--TACAGA
1 ACTTACATA
*
6071505 ACCTT-CTTA
1 A-CTTACATA
*
6071514 ACTTACATT
1 ACTTACATA
*
6071523 A--TACACA
1 ACTTACATA
*
6071530 ACTCACATA
1 ACTTACATA
6071539 A-TTA-AT-
1 ACTTACATA
* *
6071545 ATTATACACA
1 ACT-TACATA
6071555 ACTTACATA
1 ACTTACATA
*
6071564 A--TACATT
1 ACTTACATA
6071571 ACTTACATA
1 ACTTACATA
*
6071580 ACTTACATT
1 ACTTACATA
6071589 ACTTACAGT-
1 ACTTACA-TA
6071598 ACTTACATA
1 ACTTACATA
6071607 A--TACATA
1 ACTTACATA
6071614 A--TACATA
1 ACTTACATA
6071621 ACTTACATA
1 ACTTACATA
6071630 A
1 A
6071631 TACATAAAAA
Statistics
Matches: 596, Mismatches: 124, Indels: 116
0.71 0.15 0.14
Matches are distributed among these distances:
5 4 0.01
6 5 0.01
7 55 0.09
8 25 0.04
9 445 0.75
10 42 0.07
11 5 0.01
12 12 0.02
13 3 0.01
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:6071508 original size:25 final size:25
Alignment explanation
Indices: 6071474--6071595 Score: 99
Period size: 25 Copynumber: 4.9 Consensus size: 25
6071464 TTCGTGGACT
*
6071474 TACATAACCTACATAACTTACATTA
1 TACACAACCTACATAACTTACATTA
* * *
6071499 TACAGAACCTTCTTAACTTACATTA
1 TACACAACCTACATAACTTACATTA
*
6071524 TACACAA-CTCACATAA-TTAATATTA
1 TACACAACCT-ACATAACTT-ACATTA
*
6071549 TACACAACTTACATAA--TACATTA
1 TACACAACCTACATAACTTACATTA
* * *
6071572 CTTACATAACTTACATTACTTACA
1 --TACACAACCTACATAACTTACA
6071596 GTACTTACAT
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 5 0.06
24 5 0.06
25 64 0.81
26 1 0.01
27 4 0.05
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.34
Consensus pattern (25 bp):
TACACAACCTACATAACTTACATTA
Found at i:6071568 original size:66 final size:65
Alignment explanation
Indices: 6071474--6071634 Score: 166
Period size: 66 Copynumber: 2.4 Consensus size: 65
6071464 TTCGTGGACT
* *
6071474 TACATAACCTACATAACTTACATTATACAGAACCTT-CTTAACTTACATTA-TACACAACTCACA
1 TACATAA--TACATAACTTACATAATACAGAA-CTTACATAACTTACATTACTACACAACTCACA
6071537 TAA
63 TAA
* ** ** *
6071540 TTA-ATATTATACACAACTTACATAATACATTACTTACATAACTTACATTACTTACAGTACTTAC
1 -TACATA--ATACATAACTTACATAATACAGAACTTACATAACTTACATTAC-TACACAACTCAC
6071604 ATAA
62 ATAA
6071608 TACATAATACATAACTTACATAATACA
1 TACATAATACATAACTTACATAATACA
6071635 TAAAAATATA
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
65 3 0.04
66 55 0.70
67 4 0.05
68 17 0.22
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.33
Consensus pattern (65 bp):
TACATAATACATAACTTACATAATACAGAACTTACATAACTTACATTACTACACAACTCACATAA
Found at i:6071574 original size:16 final size:16
Alignment explanation
Indices: 6071555--6071635 Score: 85
Period size: 16 Copynumber: 4.9 Consensus size: 16
6071545 ATTATACACA
6071555 ACTTACATAATACATT
1 ACTTACATAATACATT
6071571 ACTTACATAACTTACATT
1 ACTTACATAA--TACATT
*
6071589 ACTTACAGTACTTACA-T
1 ACTTACA-TA-ATACATT
* *
6071606 A-ATACATAATACATA
1 ACTTACATAATACATT
6071621 ACTTACATAATACAT
1 ACTTACATAATACAT
6071636 AAAAATATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.07
15 3 0.06
16 26 0.48
17 2 0.04
18 17 0.31
19 2 0.04
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.35
Consensus pattern (16 bp):
ACTTACATAATACATT
Found at i:6071579 original size:41 final size:42
Alignment explanation
Indices: 6071513--6071628 Score: 123
Period size: 41 Copynumber: 2.8 Consensus size: 42
6071503 GAACCTTCTT
* * *
6071513 AACTTACATTATACACAACTCACATAA-TTAATATTA-TACAC
1 AACTTACATAATACATAACTCACATAACTT-ACATTACTACAC
* * *
6071554 AACTTACATAATACATTACTTACATAACTTACATTACTTACAG
1 AACTTACATAATACATAACTCACATAACTTACATTAC-TACAC
*
6071597 TACTTACATAATACATAA-T-ACATAACTTACAT
1 AACTTACATAATACATAACTCACATAACTTACAT
6071629 AATACATAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 41 0.64
42 3 0.05
43 20 0.31
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.34
Consensus pattern (42 bp):
AACTTACATAATACATAACTCACATAACTTACATTACTACAC
Found at i:6071613 original size:7 final size:7
Alignment explanation
Indices: 6071601--6071637 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
6071591 TTACAGTACT
6071601 TACATAA
1 TACATAA
6071608 TACATAA
1 TACATAA
6071615 TACATAA
1 TACATAA
6071622 CTTACATAA
1 --TACATAA
6071631 TACATAA
1 TACATAA
6071638 AAATATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 21 0.75
9 7 0.25
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:6077721 original size:42 final size:42
Alignment explanation
Indices: 6077571--6077901 Score: 315
Period size: 42 Copynumber: 7.8 Consensus size: 42
6077561 GTTTTTGTAC
* * * * * *
6077571 AAAAGCGCCACTAAAGAACATGTTCTGTAGCGGCGTTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAG
* * * * * *
6077613 AAAAAGCGCCGCTAAAGATCATGTTCTTCAGCGGAGTTTTTAT
1 AAAAA-CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAG
* * *
6077656 ACAAAGCGCCGTTAAAGAACATGTTCTTTAGTGGCGCTTAATA-
1 A-AAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT-ATAG
* *
6077699 AAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTATAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAG
* *
6077741 AAAAACGCCGCTAAAAAACATGTTCTTCAGCGGCGCTTATAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAG
* * * *
6077783 AAAAACGCCGTTAAAGAACATGTTCTTCAGCGACGCTTATAT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAG
* * * * **
6077825 AAAAACGCCGCTAAAGACCATGTT-TTTCAGTGGCGTTTTTCT
1 AAAAACGCCGCTAAAGAACATGTTCTTT-AGCGGCGCTTATAG
* * * *
6077867 CAAAGCGCCGTTAAAGAACATGATCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
6077902 TTTTTGGTTG
Statistics
Matches: 240, Mismatches: 43, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
41 5 0.02
42 168 0.70
43 62 0.26
44 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTATAG
Found at i:6077876 original size:126 final size:127
Alignment explanation
Indices: 6077571--6077901 Score: 362
Period size: 126 Copynumber: 2.6 Consensus size: 127
6077561 GTTTTTGTAC
* * * * * * *
6077571 AAAAGCGCCACTAAAGAACATGTTCTGTAGCGGCGTTTGTAAAAAAAGCGCCGCTAAAGATCATG
1 AAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAT-AGAAAAGCGCCGCTAAAGAACATG
* * * * * * * *
6077636 TTCTTCAGCGGAGTTTTTATACAAAGCGCCGTTAAAGAACATGTTCTTTAGTGGCGCTTAATA
65 TTCTTCAGCGGCGCTTATAGACAAAACGCCGTTAAAGAACATGTTCTTCAGCGACGCTTAATA
* * *
6077699 AAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTATAGAAAAACGCCGCTAAAAAACATGT
1 AAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTATAGAAAAGCGCCGCTAAAGAACATGT
6077764 TCTTCAGCGGCGCTTATAGA-AAAACGCCGTTAAAGAACATGTTCTTCAGCGACGCTT-ATA
66 TCTTCAGCGGCGCTTATAGACAAAACGCCGTTAAAGAACATGTTCTTCAGCGACGCTTAATA
* * * * *** *
6077824 TAAAAACGCCGCTAAAGACCATGTT-TTTCAGTGGCGTTTTTCTCAAAGCGCCGTTAAAGAACAT
1 -AAAAACGCCACTAAAGACCATGTTCTTT-AGCGGCGCTTATAGAAAAGCGCCGCTAAAGAACAT
* *
6077888 GATCTTTAGCGGCG
64 GTTCTTCAGCGGCG
6077902 TTTTTGGTTG
Statistics
Matches: 171, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
125 6 0.04
126 93 0.54
127 37 0.22
128 35 0.20
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (127 bp):
AAAAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTATAGAAAAGCGCCGCTAAAGAACATGT
TCTTCAGCGGCGCTTATAGACAAAACGCCGTTAAAGAACATGTTCTTCAGCGACGCTTAATA
Found at i:6078967 original size:17 final size:17
Alignment explanation
Indices: 6078942--6078988 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
6078932 GAATTCGATG
*
6078942 AATAAAAATATATTAAAT
1 AATATAAATAT-TTAAAT
* *
6078960 TAT-TAAATATTAAAAT
1 AATATAAATATTTAAAT
6078976 AATATAAATATTT
1 AATATAAATATTT
6078989 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
16 7 0.30
17 14 0.61
18 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAAATATTTAAAT
Found at i:6081226 original size:10 final size:10
Alignment explanation
Indices: 6081191--6081260 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
6081181 AAAAAATTTG
*
6081191 TAAAATTTTA
1 TAAAATATTA
*
6081201 TAAAA-ATCA
1 TAAAATATTA
6081210 TAAAATATTA
1 TAAAATATTA
6081220 TAAAATA-TA
1 TAAAATATTA
*
6081229 TAGAAATATAA
1 TA-AAATATTA
* *
6081240 AAAAAAATT-
1 TAAAATATTA
*
6081249 TAAAAAATTA
1 TAAAATATTA
6081259 TA
1 TA
6081261 TAAAGTTGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
9 19 0.40
10 27 0.56
11 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
TAAAATATTA
Found at i:6081294 original size:21 final size:21
Alignment explanation
Indices: 6081241--6081297 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
6081231 GAAATATAAA
*
6081241 AAAAAATTTAAA-AAA-TTAT
1 AAAAAATGTAAAGAAATTTAT
**
6081260 ATAAAGTTGT-AAGAAATTTAT
1 A-AAAAATGTAAAGAAATTTAT
6081281 AAAAAATGTAAAGAAAT
1 AAAAAATGTAAAGAAAT
6081298 ATAATATTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.10
20 14 0.48
21 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAAAATGTAAAGAAATTTAT
Found at i:6084431 original size:249 final size:249
Alignment explanation
Indices: 6083989--6084601 Score: 962
Period size: 249 Copynumber: 2.5 Consensus size: 249
6083979 ATTGTCAGAA
* * * * * *
6083989 ATTGCTCAAGGTAATGATGATCCAAGATGAATG-CCTTTTCGTTTAACAGTGCCTGCCATATTGT
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTT-ACATTGCCTGCCATATAGT
*
6084053 GTTGTGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTT
65 GTTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTT
* * *
6084118 TTTACCTCTATCAAATCTTGAAATTTCGGCTGGTTATACTGTTTTCCCTGTAGAACCTGCAAACG
130 TTTACCTCTATCAAATCTTGAAATTGCAGCTGCTTATACTGTTTTCCCTGTAGAACCTGCAAACG
*
6084183 TTTAAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
195 TTTAAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAC
* * *
6084238 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTAGTGGCTTCCATTGCCTGCCATATAGTC
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTACATTGCCTGCCATATAGTG
*
6084303 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAACGAAATACATAAACTTGTTTTCTTTT
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTT
* * *
6084368 TTACCTTTTTCAAATCTTGAAATTGCATCTGCTTATACTGATTTT-CCTGTAGAA-CTGGCAAAC
131 TTACCTCTATCAAATCTTGAAATTGCAGCTGCTTATACTG-TTTTCCCTGTAGAACCT-GCAAAC
6084431 GTTTAAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAC
194 GTTTAAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAC
* * *
6084487 ATTGCTCAAGGTAACGGTGATCCAAGATGAATGCCCTATTGACTTTCATTGCCTGCCATATAGTG
1 ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTACATTGCCTGCCATATAGTG
* * *
6084552 TTATGTATGTATTCATAAAGTAGTTAATTTTAAGGGAAAAGAGATACATA
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
6084602 TCTCTGCAAA
Statistics
Matches: 334, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
248 2 0.01
249 321 0.96
250 11 0.03
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (249 bp):
ATTGCTCAAGGTAATGGTGATCCAAGATGAATGCCCTATTGGCTTACATTGCCTGCCATATAGTG
TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTCTTTT
TTACCTCTATCAAATCTTGAAATTGCAGCTGCTTATACTGTTTTCCCTGTAGAACCTGCAAACGT
TTAAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAC
Found at i:6088729 original size:19 final size:20
Alignment explanation
Indices: 6088707--6088747 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6088697 AAAAAAAGAA
6088707 ATTATAAAA-ATCATA-AAAT
1 ATTATAAAATAT-ATAGAAAT
6088726 ATTATAAAATATATAGAAAT
1 ATTATAAAATATATAGAAAT
6088746 AT
1 AT
6088748 AGAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
ATTATAAAATATATAGAAAT
Found at i:6088734 original size:10 final size:10
Alignment explanation
Indices: 6088707--6088747 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
6088697 AAAAAAAGAA
6088707 ATTATAAAA-
1 ATTATAAAAT
*
6088716 ATCATAAAAT
1 ATTATAAAAT
6088726 ATTATAAAAT
1 ATTATAAAAT
6088736 A-TATAGAAAT
1 ATTATA-AAAT
6088746 AT
1 AT
6088748 AGAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 12 0.44
10 15 0.56
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (10 bp):
ATTATAAAAT
Found at i:6093197 original size:246 final size:248
Alignment explanation
Indices: 6092704--6093312 Score: 798
Period size: 246 Copynumber: 2.5 Consensus size: 248
6092694 ATTGTCAGAA
* * * * * *
6092704 ATTGCTCAAGGTAAT-GATGATCCAAGATGAATACCCT-TTCGTTTAGCGTTGCCTGCCTTATAG
1 ATTGCTCAAGGTAATGGA-GATCCAAGATGAATGCCCTATTGGCTT-CCATTGCCTGCCATATAG
* ***
6092767 TGTTGTGTATGTATTCATAAAGTAGTTAATTTGAAA-GAAAAAAAATACATAAACTTGTTTTTCC
64 TGTTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAAAAATACATAAACTAACTTTT-C
** * *
6092831 TTTTTACCTCAGAAAAATCTTGCAATTGCGGCTGGTTAAACTTCTTTTCCTGTAAAACTAGCAAC
128 TTTTTACCTCAGAAAAATCTCCCAATTGCGGCTGGTTAAACTTCATTTCCTGTAAAACCAGCAAC
* *
6092896 GTTTAAAATATTGGATTCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
193 GTTTAAAATATTGGATTCTAAACTCAAACATTATATGTTATAAACCTACGAAAGAG
*
6092952 ATTGCTCAAGGTAATGGAGATCAAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
1 ATTGCTCAAGGTAATGGAGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
* *
6093017 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAGAC-AACTTTT-TTT
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAAAAATACATAAACTAACTTTTCTTT
* * *** * ***
6093080 TTACCTTA-AACAAATCTCCCTATTTTTGTTGGTTCGGCTTCATTTCCTGTAAAACCAGCAACGT
131 TTACCTCAGAA-AAATCTCCCAATTGCGGCTGGTTAAACTTCATTTCCTGTAAAACCAGCAACGT
*
6093144 TTAAAATATTGGATTGTAAACTCAAACATTATATGTTATAAACCTACGAAAGAG
195 TTAAAATATTGGATTCTAAACTCAAACATTATATGTTATAAACCTACGAAAGAG
* * * * * * *
6093198 ATTGCTCAATGTAATGGTGATCCAAGATTAATGTCGTATTGGCTTCCATTGCTTGTCATATAGTG
1 ATTGCTCAAGGTAATGGAGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
* *
6093263 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAATAGATACATA
66 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAAAAATACATA
6093313 TATCTGCAAA
Statistics
Matches: 318, Mismatches: 39, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
245 2 0.01
246 207 0.65
248 86 0.27
249 23 0.07
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (248 bp):
ATTGCTCAAGGTAATGGAGATCCAAGATGAATGCCCTATTGGCTTCCATTGCCTGCCATATAGTG
TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAAAAATACATAAACTAACTTTTCTTT
TTACCTCAGAAAAATCTCCCAATTGCGGCTGGTTAAACTTCATTTCCTGTAAAACCAGCAACGTT
TAAAATATTGGATTCTAAACTCAAACATTATATGTTATAAACCTACGAAAGAG
Found at i:6102247 original size:43 final size:44
Alignment explanation
Indices: 6102168--6102255 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 44
6102158 GAAAGATATG
* *
6102168 TCTGTCGAAGCCTTTTTTTTTGGAAAAAGGCATCGACTTTTTAT
1 TCTGTCGAAACCTATTTTTTTGGAAAAAGGCATCGACTTTTTAT
* *
6102212 TCTGTCGAAACC-ATTTTTTTGTAAAAATGG-GTCGACTTTTTAT
1 TCTGTCGAAACCTATTTTTTTGGAAAAA-GGCATCGACTTTTTAT
6102255 T
1 T
6102256 TAAAAACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
43 26 0.67
44 13 0.33
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (44 bp):
TCTGTCGAAACCTATTTTTTTGGAAAAAGGCATCGACTTTTTAT
Found at i:6102369 original size:104 final size:104
Alignment explanation
Indices: 6102235--6102444 Score: 386
Period size: 104 Copynumber: 2.0 Consensus size: 104
6102225 TTTTTTTGTA
*
6102235 AAAATGGGTCGACTTTTTATTTAAAAACAAAAGCGAACATGGGAGTCGCCACCAATCCTTTTTGA
1 AAAATGGGTCGACTTTTTATTTAAAAACAAAAGCGAACATGGGAGTCACCACCAATCCTTTTTGA
*
6102300 TGAGGTGTGATC-AGGTCACCTCGAAGAGTGGTTATTTTT
66 TGAGGTGTAATCGA-GTCACCTCGAAGAGTGGTTATTTTT
6102339 AAAATGGGTCGACTTTTTATTTAAAAACAAAAGCGAACATGGGAGTCACCACCAATCCTTTTTGA
1 AAAATGGGTCGACTTTTTATTTAAAAACAAAAGCGAACATGGGAGTCACCACCAATCCTTTTTGA
6102404 TGAGGTGTAATCGAGTCACCTCGAAGAGTGGTTATTTTT
66 TGAGGTGTAATCGAGTCACCTCGAAGAGTGGTTATTTTT
6102443 AA
1 AA
6102445 TAAATAATTT
Statistics
Matches: 103, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
104 102 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (104 bp):
AAAATGGGTCGACTTTTTATTTAAAAACAAAAGCGAACATGGGAGTCACCACCAATCCTTTTTGA
TGAGGTGTAATCGAGTCACCTCGAAGAGTGGTTATTTTT
Found at i:6103174 original size:15 final size:15
Alignment explanation
Indices: 6103152--6103186 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6103142 ATGCAAATGG
*
6103152 CAAT-ATAACAATAA
1 CAATAATAACAACAA
6103166 CAATAATAACAACAA
1 CAATAATAACAACAA
6103181 CAATAA
1 CAATAA
6103187 ATATAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (15 bp):
CAATAATAACAACAA
Found at i:6107519 original size:50 final size:50
Alignment explanation
Indices: 6107395--6107628 Score: 258
Period size: 50 Copynumber: 4.7 Consensus size: 50
6107385 GATAATAACA
* * ** * * *
6107395 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * ** *
6107444 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
**
6107494 TGCCCAA-GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TG-CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
6107544 TGCCAATGCCATATCCCAGACATGGTCTTAGATGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
6107594 TGCCAATGTCATGTCCCAGACATGGTCTTATATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
6107629 AATCTCTTTA
Statistics
Matches: 157, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
48 1 0.01
49 42 0.27
50 110 0.70
51 4 0.03
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:6112905 original size:13 final size:13
Alignment explanation
Indices: 6112887--6112961 Score: 54
Period size: 13 Copynumber: 5.9 Consensus size: 13
6112877 ATTCTAGTTA
6112887 ATATATATATATT
1 ATATATATATATT
*
6112900 ATATATATGTA--
1 ATATATATATATT
6112911 AGTA-ATGAT-TATT
1 A-TATAT-ATATATT
*
6112924 AT-TA-ATATTTT
1 ATATATATATATT
6112935 ATATTATATTATATT
1 ATA-TATA-TATATT
6112950 ATATATATATAT
1 ATATATATATAT
6112962 CACAAAAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 20
0.68 0.04 0.28
Matches are distributed among these distances:
10 2 0.04
11 10 0.20
12 6 0.12
13 18 0.37
14 5 0.10
15 8 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (13 bp):
ATATATATATATT
Found at i:6113252 original size:13 final size:13
Alignment explanation
Indices: 6113234--6113265 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6113224 TTTCCAGCAA
6113234 TTATGAATTTATT
1 TTATGAATTTATT
6113247 TTATGAATTTATT
1 TTATGAATTTATT
*
6113260 TGATGA
1 TTATGA
6113266 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:6113459 original size:36 final size:37
Alignment explanation
Indices: 6113412--6113489 Score: 131
Period size: 36 Copynumber: 2.1 Consensus size: 37
6113402 TCCTTAAGAT
*
6113412 CATGAGAGGTCCCCTGTAAGA-ATGTCTGGGACATGG
1 CATGAGAGGTCCCATGTAAGACATGTCTGGGACATGG
6113448 CATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG
1 CATGAGAGGTCCCATGTAAGA-CATGTCTGGGACATGG
6113486 CATG
1 CATG
6113490 GGCACCGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 20 0.51
38 19 0.49
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.22
Consensus pattern (37 bp):
CATGAGAGGTCCCATGTAAGACATGTCTGGGACATGG
Found at i:6113526 original size:50 final size:50
Alignment explanation
Indices: 6113451--6113637 Score: 277
Period size: 50 Copynumber: 3.7 Consensus size: 50
6113441 GACATGGCAT
6113451 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* * *
6113501 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* * *
6113551 GAGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCAC
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GAC
**
6113601 GAGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
6113638 TTTGGCATGT
Statistics
Matches: 122, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
49 1 0.01
50 92 0.75
51 29 0.24
ACGTcount: A:0.26, C:0.25, G:0.31, T:0.18
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
Found at i:6115646 original size:12 final size:12
Alignment explanation
Indices: 6115629--6115653 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6115619 CATGTTATGT
6115629 GTATATATATAA
1 GTATATATATAA
6115641 GTATATATATAA
1 GTATATATATAA
6115653 G
1 G
6115654 AGTCAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (12 bp):
GTATATATATAA
Found at i:6116098 original size:13 final size:13
Alignment explanation
Indices: 6116080--6116107 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6116070 TGATCTCTTC
6116080 TGGGTATTCTATA
1 TGGGTATTCTATA
6116093 TGGGTATTCTATA
1 TGGGTATTCTATA
6116106 TG
1 TG
6116108 CTCTTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:6118344 original size:13 final size:13
Alignment explanation
Indices: 6118326--6118357 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6118316 TTTCCAGCAA
6118326 TTATGAATTTATT
1 TTATGAATTTATT
6118339 TTATGAATTTATT
1 TTATGAATTTATT
*
6118352 TGATGA
1 TTATGA
6118358 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:6118565 original size:50 final size:50
Alignment explanation
Indices: 6118452--6118743 Score: 397
Period size: 50 Copynumber: 5.7 Consensus size: 50
6118442 ATTTGGGTAA
* * *
6118452 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
6118508 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
6118558 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
6118608 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
6118658 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
6118708 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
6118744 TTTGGCATGT
Statistics
Matches: 216, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
49 1 0.00
50 141 0.65
51 29 0.13
52 1 0.00
53 3 0.01
55 2 0.01
56 39 0.18
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:6122759 original size:3 final size:3
Alignment explanation
Indices: 6122751--6122779 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6122741 AAATTAGTTA
6122751 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6122780 AAAGGATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6123115 original size:31 final size:31
Alignment explanation
Indices: 6123080--6123141 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6123070 AGGTAAATTA
6123080 CAAGACTAATTGAATCCTAATAAAACTCTTT
1 CAAGACTAATTGAATCCTAATAAAACTCTTT
*
6123111 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGACTAATTGAATCCTAATAAAACTCTTT
6123142 AAACTTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (31 bp):
CAAGACTAATTGAATCCTAATAAAACTCTTT
Found at i:6129240 original size:31 final size:31
Alignment explanation
Indices: 6129202--6129263 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
6129192 AGGCAAATTA
6129202 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
6129233 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
6129264 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:6129675 original size:31 final size:31
Alignment explanation
Indices: 6129637--6129698 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
6129627 TTCTGACGAG
6129637 TTAATGTTTCTCCCATACGAAACATTTTCAA
1 TTAATGTTTCTCCCATACGAAACATTTTCAA
6129668 TTAATGTTTCTCCCATACGAAACATTTTCAA
1 TTAATGTTTCTCCCATACGAAACATTTTCAA
6129699 CTAGTTGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (31 bp):
TTAATGTTTCTCCCATACGAAACATTTTCAA
Found at i:6132686 original size:38 final size:38
Alignment explanation
Indices: 6132596--6132700 Score: 97
Period size: 38 Copynumber: 2.7 Consensus size: 38
6132586 AAAAATGATT
**
6132596 AAATTTTAATAAAAATATATAAAATATTTAAAACTTGTTA
1 AAATTTT-ATAAAAATATA-AAAATATAAAAAACTTGTTA
* * * *
6132636 AAA-ATTAGAAAAATATAAAAATCGTAAAAAATTTG-TA
1 AAATTTTATAAAAATATAAAAAT-ATAAAAAACTTGTTA
6132673 AAATTTTATAAAAATCATAAAATATATA
1 AAATTTTATAAAAAT-ATAAAA-ATATA
6132701 GAAATATAGA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
37 10 0.19
38 27 0.52
39 10 0.19
40 5 0.10
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (38 bp):
AAATTTTATAAAAATATAAAAATATAAAAAACTTGTTA
Found at i:6132758 original size:19 final size:19
Alignment explanation
Indices: 6132719--6132793 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
6132709 GAAAAAATTT
*
6132719 AGAAAATTATATAAAGTTGTA
1 AGAAAATTATA-AAA-ATGTA
6132740 AGAAAATTATAAAAATGTA
1 AGAAAATTATAAAAATGTA
*
6132759 A-AGAAA-TATAAAATTCGTA
1 AGA-AAATTATAAAAAT-GTA
* *
6132778 AAAAAATTACAAAAAT
1 AGAAAATTATAAAAAT
6132794 TATTGTACCT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 9 0.20
19 15 0.33
20 11 0.24
21 11 0.24
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (19 bp):
AGAAAATTATAAAAATGTA
Found at i:6133320 original size:93 final size:88
Alignment explanation
Indices: 6133155--6133426 Score: 304
Period size: 93 Copynumber: 3.1 Consensus size: 88
6133145 GTCCCTGGCC
* *
6133155 TTTTTGATGCATTTTAGCAGTTCAAGTA-TCTAATTGAGTGAAAAAAAAAAAGCAAGGGCTTAAT
1 TTTTTTATGCATTTTAGCAGTTCAAGTACTC-AATTGAGTGAAAAAAAAAAAGCAAGGACTTAAT
6133219 TGCTTTTTTTTTGAAAAAGTTTGAGGGTA
65 TGC--TTTTTTTGAAAAAGTTTGA--G-A
* * *
6133248 TTTTTTATGAATTTTGGCAGTTTAAGTACTCAATTGAGTGAAAAAAAACAAAGCAAGGACTTAAT
1 TTTTTTATGCATTTTAGCAGTTCAAGTACTCAATTGAGTGAAAAAAAA-AAAGCAAGGACTTAAT
6133313 TGC-TTTTTTGAAAAAGTTTGAGA
65 TGCTTTTTTTGAAAAAGTTTGAGA
* ** * * *
6133336 TATTTTATGCATTTTAAAAGTTCAAATACCCAATTGAGTG-TAAAAAAAAAG--A-GACTTAATT
1 TTTTTTATGCATTTTAGCAGTTCAAGTACTCAATTGAGTGAAAAAAAAAAAGCAAGGACTTAATT
* * *
6133397 ACTTTTTTTGAAAAAATTTAAAGA
66 GCTTTTTTTGAAAAAGTTT-GAGA
6133421 TTTTTT
1 TTTTTT
6133427 TACAACTTTA
Statistics
Matches: 157, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
83 10 0.06
84 16 0.10
85 8 0.05
86 4 0.03
87 6 0.04
88 33 0.21
89 1 0.01
91 18 0.11
93 41 0.26
94 20 0.13
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (88 bp):
TTTTTTATGCATTTTAGCAGTTCAAGTACTCAATTGAGTGAAAAAAAAAAAGCAAGGACTTAATT
GCTTTTTTTGAAAAAGTTTGAGA
Found at i:6137897 original size:21 final size:20
Alignment explanation
Indices: 6137871--6137910 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
6137861 AAATCTTGAG
6137871 GTTTAGGATTCAAAGTTTAAT
1 GTTTAGGATTC-AAGTTTAAT
*
6137892 GTTTAGGGTTCAAGTTTAA
1 GTTTAGGATTCAAGTTTAA
6137911 GGTTCGGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (20 bp):
GTTTAGGATTCAAGTTTAAT
Found at i:6137908 original size:20 final size:20
Alignment explanation
Indices: 6137869--6137925 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
6137859 CTAAATCTTG
*
6137869 AGGTTTAGGATTCAAAGTTTA
1 AGGTTTAGGGTTC-AAGTTTA
*
6137890 ATGTTTAGGGTTCAAGTTTA
1 AGGTTTAGGGTTCAAGTTTA
**
6137910 AGGTTCGGGGTTCAAG
1 AGGTTTAGGGTTCAAG
6137926 GTAAAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (20 bp):
AGGTTTAGGGTTCAAGTTTA
Found at i:6143827 original size:77 final size:77
Alignment explanation
Indices: 6143700--6143853 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 77
6143690 CGAAGACCCC
* *
6143700 CTTGAAAATGCCGGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGGT-GAGGCTACCA
1 CTTGAAAATGCCAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAG-GGCTACCA
6143764 CCTATGAGAGAGG
65 CCTATGAGAGAGG
*
6143777 CTTGAAAATGCTAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAGGGCTACCAC
1 CTTGAAAATGCCAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAGGGCTACCAC
6143842 CTATGAGAGAGG
66 CTATGAGAGAGG
6143854 TGAGTTGTAA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
77 72 0.99
78 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (77 bp):
CTTGAAAATGCCAGAGGTGTGGCAAACCAATGTGAAGCATGTTGAGTTATCGATAGGGCTACCAC
CTATGAGAGAGG
Found at i:6145270 original size:15 final size:15
Alignment explanation
Indices: 6145250--6145279 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6145240 ATCACAAGTA
6145250 TAAAAGATGATCCAC
1 TAAAAGATGATCCAC
6145265 TAAAAGATGATCCAC
1 TAAAAGATGATCCAC
6145280 ATAATGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
TAAAAGATGATCCAC
Found at i:6150325 original size:34 final size:34
Alignment explanation
Indices: 6150282--6150351 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
6150272 CAAATAGGGT
* *
6150282 TTAGGGTTTAGGGTTTCAAATGCATACCAAACTA
1 TTAGGGTTTAGGGTTCCAAATACATACCAAACTA
6150316 TTAGGGTTTAGGGTTCCAAATACATACCAAACTA
1 TTAGGGTTTAGGGTTCCAAATACATACCAAACTA
6150350 TT
1 TT
6150352 TCTTTCACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (34 bp):
TTAGGGTTTAGGGTTCCAAATACATACCAAACTA
Found at i:6152976 original size:15 final size:14
Alignment explanation
Indices: 6152956--6152985 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6152946 TAATATATTT
6152956 TTATAAATTTTAAAA
1 TTATAAA-TTTAAAA
6152971 TTATAAATTTAAAA
1 TTATAAATTTAAAA
6152985 T
1 T
6152986 ATATTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTATAAATTTAAAA
Found at i:6155753 original size:22 final size:23
Alignment explanation
Indices: 6155715--6155758 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
6155705 ATAAAATTTA
6155715 AATGGTAATAAATAAATTTAAAC
1 AATGGTAATAAATAAATTTAAAC
*
6155738 AATGTTAAT-AATAAATTTAAA
1 AATGGTAATAAATAAATTTAAA
6155759 ATAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (23 bp):
AATGGTAATAAATAAATTTAAAC
Found at i:6155768 original size:23 final size:23
Alignment explanation
Indices: 6155720--6155793 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 23
6155710 ATTTAAATGG
* *
6155720 TAATAAATAAATTT-AAACAATGT
1 TAAT-AATAAATTTAAAATAATAT
6155743 TAATAATAAATTTAAAATAATAT
1 TAATAATAAATTTAAAATAATAT
*
6155766 TAAGCTTAAT-CA-TTAAAATAATAT
1 TAA---TAATAAATTTAAAATAATAT
6155790 TAAT
1 TAAT
6155794 TTTAAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 9 0.20
23 14 0.32
24 15 0.34
25 1 0.02
26 4 0.09
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (23 bp):
TAATAATAAATTTAAAATAATAT
Found at i:6158059 original size:132 final size:132
Alignment explanation
Indices: 6157830--6158444 Score: 838
Period size: 132 Copynumber: 4.7 Consensus size: 132
6157820 CGTTGCCTTC
* * * * *
6157830 GATCTGCTCCACTACTACTTAGGGAGACATGATTTACAATATTCAACCTACTCCACTACTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
** * * * * * *
6157895 GGGAGATATAATTTGTGGTTTAATTCTACTTCCCTACTACCTTAGGAAGATAAGATTCACCGTCT
66 GGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTAT
6157960 TT
131 TT
* * *
6157962 GATCTGCTCCACTACTGCTTAGGGAGACGGGATCTACATTCTTCAACCTACTCCACTGTTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
* *
6158027 AGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT-C
66 GGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTAT
6158091 TT
131 TT
6158093 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTT----C-A----ACTGCTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
* *
6158149 AGGAGATAGGACTGGTGGCTTAAA-CATGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTA
66 GGGAGATAGGATTGGTGGCTTAAATC-TGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTA
6158213 TTT
130 TTT
6158216 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
* * ** * *
6158281 GGGAGACAGGACTAATGGCTTAAACCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATAT
66 GGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTAT
6158346 TT
131 TT
* * * * *
6158348 GATCTGTTCCACTACTGCTTAGGGAGACAGGATCTAAAATCTTCAACTTACTCCACTACTACTCA
1 GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
* **
6158413 GGGAGATAGGATTGGTGGTTTCGATCTGCTTC
66 GGGAGATAGGATTGGTGGCTTAAATCTGCTTC
6158445 ACTGCCAGTA
Statistics
Matches: 431, Mismatches: 40, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
121 1 0.00
122 70 0.16
123 45 0.10
126 1 0.00
127 2 0.00
128 1 0.00
131 43 0.10
132 267 0.62
133 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
GATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCA
GGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTAT
TT
Found at i:6158270 original size:44 final size:44
Alignment explanation
Indices: 6158222--6158424 Score: 139
Period size: 44 Copynumber: 4.6 Consensus size: 44
6158212 ATTTGATCTG
6158222 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
* * * *
6158266 CTCCACTGCTGCTCAGGGAGACAGGA-CT--AATGGCTTAAACCTG
1 CTCCACTACTGCTTAGGGAGACAGGATCTACAAT--CTTCAACCTA
* * * * * ** * *
6158309 CTTCC-CTACTACCTT-GGGAAGATAAGAT-TCACCATATTTGATCTG
1 C-TCCACTACT-GCTTAGGG-AGACAGGATCT-ACAATCTTCAACCTA
* * *
6158354 TTCCACTACTGCTTAGGGAGACAGGATCTAAAATCTTCAACTTA
1 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
* * *
6158398 CTCCACTACTACTCAGGGAGATAGGAT
1 CTCCACTACTGCTTAGGGAGACAGGAT
6158425 TGGTGGTTTC
Statistics
Matches: 117, Mismatches: 30, Indels: 24
0.68 0.18 0.14
Matches are distributed among these distances:
41 3 0.03
43 18 0.15
44 79 0.68
45 15 0.13
47 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
Found at i:6158302 original size:254 final size:255
Alignment explanation
Indices: 6157923--6158395 Score: 804
Period size: 254 Copynumber: 1.9 Consensus size: 255
6157913 TTTAATTCTA
*
6157923 CTTCCCTACTACCTTAGGAAGATAAGATTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAG
1 CTTCCCTACTACCTTAGGAAGATAAGATTCACCGTATTTGATCTGCTCCACTACTGCTTAGGGAG
* * * * * ** *
6157988 ACGGGATCTACATTCTTCAACCTACTCCACTGTTGCTCAAGGAGATAGGATTGGTGGCTTAAATC
66 ACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAAGGAGACAGGACTAATGGCTTAAACC
*
6158053 TGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT-CTTGATCTGCTCCACTACTGCTTAGGG
131 TGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATACTTGATCTGCTCCACTACTGCTTAGGG
*
6158117 AGACAGGATCTACAATCTTCAACTGCTGCTCAAGGAGATAGGACTGGTGGCTTAAACATG
196 AGACAGGATCTAAAATCTTCAACTGCTGCTCAAGGAGATAGGACTGGTGGCTTAAACATG
*
6158177 CTTCCCTACTACCTTGGGAAGATAAGATTCACCGTATTTGATCTGCTCCACTACTGCTTAGGGAG
1 CTTCCCTACTACCTTAGGAAGATAAGATTCACCGTATTTGATCTGCTCCACTACTGCTTAGGGAG
*
6158242 ACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGACAGGACTAATGGCTTAAACC
66 ACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAAGGAGACAGGACTAATGGCTTAAACC
* *
6158307 TGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGTTCCACTACTGCTTAGGG
131 TGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATACTTGATCTGCTCCACTACTGCTTAGGG
6158372 AGACAGGATCTAAAATCTTCAACT
196 AGACAGGATCTAAAATCTTCAACT
6158396 TACTCCACTA
Statistics
Matches: 203, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
254 155 0.76
255 48 0.24
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (255 bp):
CTTCCCTACTACCTTAGGAAGATAAGATTCACCGTATTTGATCTGCTCCACTACTGCTTAGGGAG
ACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAAGGAGACAGGACTAATGGCTTAAACC
TGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATACTTGATCTGCTCCACTACTGCTTAGGG
AGACAGGATCTAAAATCTTCAACTGCTGCTCAAGGAGATAGGACTGGTGGCTTAAACATG
Found at i:6158632 original size:88 final size:88
Alignment explanation
Indices: 6158432--6158870 Score: 318
Period size: 88 Copynumber: 4.9 Consensus size: 88
6158422 GATTGGTGGT
* * * * * * ** ** * *
6158432 TTCGATCTGCTTCACTGCCAGTACAGAAAGACAAGATCTGATGTTTTTAGTCTATTCCACTGCAA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTCCAACCTACTCCACTGC-T
* * * **
6158497 ACTCAAGGAGGCAAGGCTTGCTATC
65 GCCCAAGGAGACAAGGCTTG-GGTC
* * * *
6158522 TTTGATCTACTTCGCTGCCAATACAGGAATACAAGATCTGTTATTTCCAACCTACTCTACTGCTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTCCAACCTACTCCACTGCTG
*
6158587 CCC-AGAGAGATAAGG-TTGGGGTC
66 CCCAAG-GAGACAAGGCTT-GGGTC
* * *
6158610 TTCGATCTACTTCGCTGCCAATACATGAAGACAAGATCTGCTATTTTCAACCTATTCCACTGCTG
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTCCAACCTACTCCACTGCTG
* * *
6158675 CTCAAGGAGACAAGGCTTGTGAC
66 CCCAAGGAGACAAGGCTTGGGTC
* * * * * * *
6158698 TTCAATCTACTTCGCTGCCAATACAGGAAGACAATATTTGCTATCTT-CGATCTACTTCGCTG-T
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-TTCCAACCTACTCCACTGCT
** * *
6158761 -CAATACAGGAAGACAA-GATCT-GCTAAC
65 GC-CCA-AGG-AGACAAGGCT-TGGGT--C
* *
6158788 TTCGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTT-CAACCTACTCCACTACT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-TTCCAACCTACTCCACTGCT
* * *
6158852 GCTCAGGGAGATAAGGCTT
65 GCCCAAGGAGACAAGGCTT
6158871 TGTGGTTTCA
Statistics
Matches: 274, Mismatches: 61, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
86 1 0.00
87 2 0.01
88 132 0.48
89 29 0.11
90 107 0.39
91 2 0.01
92 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (88 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTCCAACCTACTCCACTGCTG
CCCAAGGAGACAAGGCTTGGGTC
Found at i:6158752 original size:45 final size:45
Alignment explanation
Indices: 6158515--6158835 Score: 245
Period size: 45 Copynumber: 7.2 Consensus size: 45
6158505 AGGCAAGGCT
* *
6158515 TGCTATCTTTGATCTACTTCGCTGCCAATACAGGAATACAAGATC
1 TGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
* * * * *
6158560 TGTTAT-TTCCAACCTACTCTACTGCTGCC----CA-GAGAGATAAGGT-
1 TGCTATCTT-CGATCTACT-T-C-GCTGCCAATACAGGA-AGACAAGATC
*** *
6158603 TGGGGTCTTCGATCTACTTCGCTGCCAATACATGAAGACAAGATC
1 TGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
* * * * *** *
6158648 TGCTATTTTCAACCTA-TTCCACTGCTGCT-CAAGG-AGACAAG-GC
1 TGCTATCTTCGATCTACTT-CGCTGCCAATAC-AGGAAGACAAGATC
* * *
6158691 TTG-TGA-CTTCAATCTACTTCGCTGCCAATACAGGAAGACAATATT
1 -TGCT-ATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
*
6158736 TGCTATCTTCGATCTACTTCGCTGTCAATACAGGAAGACAAGATC
1 TGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
* *
6158781 TGCTAACTTCGATCTACTTCGCTGCCAATATAGGAAGACAAGATC
1 TGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
6158826 TGCTATCTTC
1 TGCTATCTTC
6158836 AACCTACTCC
Statistics
Matches: 211, Mismatches: 43, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
40 6 0.03
41 1 0.00
42 1 0.00
43 31 0.15
44 46 0.22
45 118 0.56
46 1 0.00
47 1 0.00
48 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (45 bp):
TGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
Found at i:6161141 original size:10 final size:10
Alignment explanation
Indices: 6161120--6161167 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
6161110 TGGCCTCTCA
6161120 TTTTTCTGTTC
1 TTTTTCT-TTC
6161131 TTTTTCTTTC
1 TTTTTCTTTC
*
6161141 TTTCTTTTTTC
1 TTT-TTCTTTC
*
6161152 TTTTTTTTTC
1 TTTTTCTTTC
*
6161162 ATTTTC
1 TTTTTC
6161168 ATTTTTGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 17 0.52
11 16 0.48
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:6161149 original size:15 final size:15
Alignment explanation
Indices: 6161122--6161154 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
6161112 GCCTCTCATT
6161122 TTTCTGTTCTTTTTC
1 TTTCTGTTCTTTTTC
6161137 TTTCT-TTCTTTTTTC
1 TTTCTGTTC-TTTTTC
6161152 TTT
1 TTT
6161155 TTTTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTCTGTTCTTTTTC
Found at i:6169634 original size:30 final size:31
Alignment explanation
Indices: 6169600--6169658 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
6169590 AGGTGGGATG
*
6169600 GGAAGGGAATAAAAGTTTT-AGGGGAAAAGT
1 GGAAGGGAATAAAAATTTTGAGGGGAAAAGT
* *
6169630 GGAAGGGAGTAAAAATTTTGGGGGGAAAA
1 GGAAGGGAATAAAAATTTTGAGGGGAAAA
6169659 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (31 bp):
GGAAGGGAATAAAAATTTTGAGGGGAAAAGT
Found at i:6169823 original size:30 final size:31
Alignment explanation
Indices: 6169763--6169823 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6169753 GGGTTGGGAG
** *
6169763 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTAAGGGAAAAGT
6169794 GGGA-AGGAGTAAAAGTTTTAAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTAAGGGAAAAGT
6169824 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTAAGGGAAAAGT
Found at i:6169875 original size:9 final size:9
Alignment explanation
Indices: 6169858--6169894 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6169848 AAATGTAAAA
6169858 TATTCGAAT
1 TATTCGAAT
*
6169867 TATTTGAAT
1 TATTCGAAT
*
6169876 TATTCGAGT
1 TATTCGAAT
6169885 TATTCGAAT
1 TATTCGAAT
6169894 T
1 T
6169895 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6169965 original size:9 final size:9
Alignment explanation
Indices: 6169948--6169978 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6169938 TCGAGTTGAT
6169948 TCGAATAAC
1 TCGAATAAC
*
6169957 TCGATTAAC
1 TCGAATAAC
6169966 TCGAATAAC
1 TCGAATAAC
6169975 TCGA
1 TCGA
6169979 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:6173872 original size:33 final size:32
Alignment explanation
Indices: 6173834--6173898 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
6173824 AAATTTTTAA
*
6173834 AAAATACAATA-CATCAAATATATTAAAAATATT
1 AAAATA-AATATCATC-AATAAATTAAAAATATT
*
6173867 AAAATAAATATTTATCAATAAATTAAAAATAT
1 AAAATAAATA-TCATCAATAAATTAAAAATAT
6173899 ACAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 4 0.14
33 21 0.75
34 3 0.11
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (32 bp):
AAAATAAATATCATCAATAAATTAAAAATATT
Found at i:6177595 original size:22 final size:23
Alignment explanation
Indices: 6177561--6177607 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
6177551 TATTTCGTTT
*
6177561 CTCATCTGG-AAAAGTTCTATAG
1 CTCATCTGGAAAAAGGTCTATAG
6177583 CTCAT-TGGAAAAAAGGTCTATAG
1 CTCATCTGG-AAAAAGGTCTATAG
6177606 CT
1 CT
6177608 AGTTTGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 5 0.23
23 14 0.64
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (23 bp):
CTCATCTGGAAAAAGGTCTATAG
Found at i:6191315 original size:6 final size:7
Alignment explanation
Indices: 6191297--6191321 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6191287 CCAAAATTCT
6191297 ATTTTTA
1 ATTTTTA
6191304 ATTTTTA
1 ATTTTTA
6191311 ATTTTTA
1 ATTTTTA
6191318 ATTT
1 ATTT
6191322 AAATTTACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:6197182 original size:23 final size:23
Alignment explanation
Indices: 6197140--6197183 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6197130 TAAATATTAT
*
6197140 TTTATTAATATTTTGCTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
6197163 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
6197184 AAAATGGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:6202659 original size:13 final size:13
Alignment explanation
Indices: 6202641--6202670 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6202631 TCCAGCAACT
6202641 ATGAATTTATTTC
1 ATGAATTTATTTC
*
6202654 ATGAATTTATTTG
1 ATGAATTTATTTC
6202667 ATGA
1 ATGA
6202671 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:6202840 original size:50 final size:50
Alignment explanation
Indices: 6202765--6202948 Score: 280
Period size: 50 Copynumber: 3.7 Consensus size: 50
6202755 ATTTGGGTAA
6202765 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATG
*
6202815 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATG
* * * *
6202865 AGAGGTCCTC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCC-CATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATG
**
6202915 AGAACATCCCATGTAAGACCATGTCTGGGACATG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATG
6202949 ACTTTGGCAC
Statistics
Matches: 123, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
50 96 0.78
51 27 0.22
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTCGGCACCGAGATG
Found at i:6213097 original size:10 final size:10
Alignment explanation
Indices: 6213082--6213115 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
6213072 CCATAATTAT
6213082 TTTTTTACAA
1 TTTTTTACAA
6213092 TTTTTTACAA
1 TTTTTTACAA
6213102 TTTTTTACAA
1 TTTTTTACAA
6213112 TTTT
1 TTTT
6213116 CCAAAATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTTTACAA
Found at i:6213570 original size:45 final size:45
Alignment explanation
Indices: 6213506--6213593 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
6213496 ACAGATACTC
* * *
6213506 GGTGGATTCATCACATAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGAATCAGCACATAGCAACCACCTTAATAATCAATGATGTCT
*
6213551 GGTGGAATCAGCACATAGCAACCAGCTTAATAATCAATGATGT
1 GGTGGAATCAGCACATAGCAACCACCTTAATAATCAATGATGT
6213594 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTAATAATCAATGATGTCT
Found at i:6213662 original size:51 final size:52
Alignment explanation
Indices: 6213604--6213739 Score: 224
Period size: 50 Copynumber: 2.7 Consensus size: 52
6213594 TCGGTTCACA
6213604 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA-TCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
* * *
6213655 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
6213705 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
6213740 CACTTTCACT
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
49 4 0.05
50 42 0.54
51 32 0.41
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCGATACACG
Found at i:6219644 original size:17 final size:16
Alignment explanation
Indices: 6219624--6219668 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
6219614 AACTTATAAG
6219624 AAATTATAATATTATTT
1 AAATTATAATATTA-TT
6219641 AAATTATAATA-TATT
1 AAATTATAATATTATT
*
6219656 -AATAATAATATTA
1 AAATTATAATATTA
6219669 ATATTCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 9 0.35
15 4 0.15
16 2 0.08
17 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTATAATATTATT
Found at i:6219669 original size:27 final size:27
Alignment explanation
Indices: 6219598--6219669 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 27
6219588 TTAATTCAAC
*
6219598 AATATA-TAA-AATAA-A-TAACTTAT
1 AATATATTAATAATAATATTAAATTAT
* * *
6219621 AAGAAATT-ATAATATTATTTAAATTAT
1 AATATATTAATAATAATA-TTAAATTAT
6219648 AATATATTAATAATAATATTAA
1 AATATATTAATAATAATATTAA
6219670 TATTCAAACC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
23 5 0.14
24 5 0.14
25 1 0.03
27 17 0.47
28 8 0.22
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (27 bp):
AATATATTAATAATAATATTAAATTAT
Found at i:6219919 original size:49 final size:48
Alignment explanation
Indices: 6219866--6219965 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 48
6219856 TTAATTATAT
* * *
6219866 CCATGAATCATGTAACAA-GTCAATAGCTTACATGCATTATATTAGCCAC
1 CCATGAATCATG-AAAAACGTC-ATAGCTTACATGCATAATATTAACCAC
*
6219915 CCATGAATCATGAAAAACTCGTCATAGCTTCCATGCATAATATTAACCAC
1 CCATGAATCATGAAAAA--CGTCATAGCTTACATGCATAATATTAACCAC
6219965 C
1 C
6219966 ATAATTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
48 4 0.09
49 12 0.27
50 25 0.57
51 3 0.07
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (48 bp):
CCATGAATCATGAAAAACGTCATAGCTTACATGCATAATATTAACCAC
Found at i:6220413 original size:12 final size:12
Alignment explanation
Indices: 6220396--6220421 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6220386 TTTCAAACAC
6220396 TTAGAAAATGTT
1 TTAGAAAATGTT
6220408 TTAGAAAATGTT
1 TTAGAAAATGTT
6220420 TT
1 TT
6220422 CAATTTGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTAGAAAATGTT
Found at i:6227285 original size:41 final size:41
Alignment explanation
Indices: 6227228--6227329 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
6227218 TTTAACATAT
* *
6227228 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAAA
* *
6227269 TCACCAGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAAA
6227310 TCACCGGCACTTAGCCTGCT
1 TCACCGGCACTTAGCCTGCT
6227330 GGACTTAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAAA
Found at i:6227509 original size:41 final size:41
Alignment explanation
Indices: 6227310--6227495 Score: 259
Period size: 41 Copynumber: 4.5 Consensus size: 41
6227300 CTGATTCAAA
* * * *
6227310 TCACCGGCACTT-AGCCTGCTGGACTTAAAGTCCG-AATCATT
1 TCACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAAT-AAT
*
6227351 TCACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
*
6227392 TCACCGGCATTAAGCCTGGTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
*
6227433 TCACCGGCGTTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
* *
6227474 TCACCGGTATTAAACCTGCTAG
1 TCACCGGCATTAAGCCTGCTAG
6227496 GCATCGAGCC
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 126 0.96
42 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
Found at i:6227929 original size:64 final size:64
Alignment explanation
Indices: 6227871--6228152 Score: 200
Period size: 64 Copynumber: 4.3 Consensus size: 64
6227861 AATTTCATTC
* *
6227871 AACTTACAAAACTCAGCATATATATATTCGGCTAAAAATATATAGAATTTATGCAATTTATTTT
1 AACTTACAAAACTCAACATATATATATTCGGCTAAAAATATATAGAATTCATGCAATTTATTTT
* * * * * * * **
6227935 ATCTTA-TAAACTCAA-ATATACATTGACTAAC-GC-ACATATATATATACAATTCATACGTTTT
1 AACTTACAAAACTCAACATATATA-T-A-T-TCGGCTA-A-AAATATATAGAATTCATGCAATTT
6227996 ATTTT
60 ATTTT
* * * * **
6228001 AACTTATAAAATTCAAAACATATATATACATTCGGCT-AACATATATATAATTCATTAAATTTCA
1 AACTTACAAAACTC--AACATATATAT--ATTCGGCTAAAAATATATAGAATTCATGCAATTT-A
*
6228065 -TTC
61 TTTT
* * ** *
6228068 AACTTACAAAACCCAACATATATATATTCGGCTAAATATATATAGAATTTTTGTAATTTATTTT
1 AACTTACAAAACTCAACATATATATATTCGGCTAAAAATATATAGAATTCATGCAATTTATTTT
*
6228132 AACTTATAAAACTCAA-ATATA
1 AACTTACAAAACTCAACATATA
6228153 CATTGACTAA
Statistics
Matches: 166, Mismatches: 36, Indels: 33
0.71 0.15 0.14
Matches are distributed among these distances:
62 6 0.04
63 22 0.13
64 42 0.25
65 15 0.09
66 29 0.17
67 36 0.22
68 3 0.02
69 6 0.04
70 7 0.04
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (64 bp):
AACTTACAAAACTCAACATATATATATTCGGCTAAAAATATATAGAATTCATGCAATTTATTTT
Found at i:6228053 original size:67 final size:67
Alignment explanation
Indices: 6227974--6228268 Score: 234
Period size: 67 Copynumber: 4.4 Consensus size: 67
6227964 ACGCACATAT
*
6227974 ATATATACAATTCATACGTTTTATTTTAACTTATAAAATTCAAAACATATATATACATTCGGCTA
1 ATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATATATACATTCGGCTA
6228039 AC
66 AC
* * * * * **
6228041 ATATATATAATTCATTAAATTTCA-TTCAACTTACAAAA--CCCAACATATATAT--ATTCGGCT
1 ATATATACAATTCA-TACATTTTATTTTAACTTATAAAATTCAAAACATATATATACATTCGGCT
*
6228101 AAAT
65 -AAC
* ** ** * *
6228105 ATATATAGAATTTTTGTAATTTATTTTAACTTATAAAACTCAAATATACAT-TGACTA-ACA--C
1 ATATATACAATTCATACATTTTATTTTAACTTATAAAATTC-AA-A-ACATAT-A-TATACATTC
* *
6228166 -AC-ATAT
61 GGCTA-AC
6228172 ATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATATATACATTCGGCTA
1 ATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATATATACATTCGGCTA
6228237 AC
66 AC
* *
6228239 ATTTTTATACAATTCATACCATTATATTTT
1 A--TATATACAATTCATA-CATTTTATTTT
6228269 TGCTTATAGA
Statistics
Matches: 174, Mismatches: 32, Indels: 41
0.70 0.13 0.17
Matches are distributed among these distances:
63 15 0.09
64 33 0.19
65 14 0.08
66 5 0.03
67 64 0.37
68 10 0.06
69 20 0.11
70 12 0.07
71 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (67 bp):
ATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATATATACATTCGGCTA
AC
Found at i:6228235 original size:198 final size:197
Alignment explanation
Indices: 6227829--6228240 Score: 725
Period size: 197 Copynumber: 2.1 Consensus size: 197
6227819 AATTCAATAC
* * * *
6227829 ATACATTCGGCTATCATATATGTAATTCATTAAATTTCATTCAACTTACAAAACTCAGCATATAT
1 ATACATTCGGCTAACATATATATAATTCATTAAATTTCATTCAACTTACAAAACCCAACATATAT
*
6227894 ATATTCGGCTAAAAATATATAGAATTTATGCAATTTATTTTATCTTATAAACTCAAATATACATT
66 ATATTCGGCTAAAAATATATAGAATTTATGCAATTTATTTTAACTTATAAACTCAAATATACATT
* *
6227959 GACTAACGCACATATATATATACAATTCATACGTTTTATTTTAACTTATAAAATTCAAAACATAT
131 GACTAACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATAT
6228024 AT
196 AT
6228026 ATACATTCGGCTAACATATATATAATTCATTAAATTTCATTCAACTTACAAAACCCAACATATAT
1 ATACATTCGGCTAACATATATATAATTCATTAAATTTCATTCAACTTACAAAACCCAACATATAT
* * *
6228091 ATATTCGGCTAAATATATATAGAATTTTTGTAATTTATTTTAACTTATAAAACTCAAATATACAT
66 ATATTCGGCTAAAAATATATAGAATTTATGCAATTTATTTTAACTTAT-AAACTCAAATATACAT
6228156 TGACTAACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATA
130 TGACTAACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATA
6228221 TAT
195 TAT
6228224 ATACATTCGGCTAACAT
1 ATACATTCGGCTAACAT
6228241 TTTTATACAA
Statistics
Matches: 204, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
197 105 0.51
198 99 0.49
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (197 bp):
ATACATTCGGCTAACATATATATAATTCATTAAATTTCATTCAACTTACAAAACCCAACATATAT
ATATTCGGCTAAAAATATATAGAATTTATGCAATTTATTTTAACTTATAAACTCAAATATACATT
GACTAACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATAT
AT
Found at i:6231802 original size:24 final size:24
Alignment explanation
Indices: 6231775--6231826 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
6231765 AGTTAATGTC
* *
6231775 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
6231799 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATACT
6231823 AAAT
1 AAAT
6231827 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:6237310 original size:41 final size:41
Alignment explanation
Indices: 6237229--6237320 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
6237219 ACCAGCTCTT
6237229 AGCCTGCTAGACCTATAGTCCGAAATATATCACCGACATTA
1 AGCCTGCTAGACCTATAGTCCGAAATATATCACCGACATTA
* * * * * *
6237270 AGCCTGCTAGACGTA-AGGTCTGAATTATTTTACCGGCATTA
1 AGCCTGCTAGACCTATA-GTCCGAAATATATCACCGACATTA
6237311 AGCCTGCTAG
1 AGCCTGCTAG
6237321 GCACATAGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 1 0.02
41 43 0.98
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACCTATAGTCCGAAATATATCACCGACATTA
Found at i:6237960 original size:21 final size:21
Alignment explanation
Indices: 6237934--6237973 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6237924 TCATAAAATC
6237934 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
*
6237955 AAATTCAGCTTATATAACA
1 AAATTCAGCTTATAGAACA
6237974 CACATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:6241113 original size:560 final size:559
Alignment explanation
Indices: 6240053--6241300 Score: 2081
Period size: 560 Copynumber: 2.2 Consensus size: 559
6240043 CATGCTATTA
* * * * * *
6240053 GAGCTTGTTGTAGCCCATACAACGCCTTTGTCAATCGACAAACAAGAGATTGCCCATCGACATCA
1 GAGCTTGTCGTAGCCCATACAAAGCCTTCGTCAATCGACAAACAAGAGGTTGCCCATCGGCATTA
* *
6240118 TGTTGAACATAT-TTGGAGGGTTGTTGCATGTATACTTCCTCAGTGGGCTCACCATTTAGGAATC
66 TGTTGAACATGTCAT-G-GGGTTGTTGCATGTATACTTCCTCAGTGGGCTCACCATTTAGGAATC
* *
6240182 ACTTTGAAGCTGTTTAATGTCTCTCTCAAATTGTGTTTTGACCATTCACTGAAACTGAATAAATC
129 ACTTTGAAGCTGTTTAATGTCTCTCTCAAATTGTGTTTTGACCATTCACTGAAACAGAATAAAAC
* * * *
6240247 AGTCAATTGCTTGAGATTTATGTTGAATGAGAAACAACTATGTAAAATAGCTAAAAACATCAACA
194 AGTCAATTGCTTGAGATTTACGTTGAATGAGAAACAACCATGTAAAACAGCTAAAAACATCAAAA
* *
6240312 AAAGAAACATAGTACCAGTAACCACTACAATCAACAGCTACAGGTCCCCATAAGTCTGAAATGAC
259 AAAGAAACATAGTACCAATAACCACTACAATCAACAGCTACAGGTCCCCATAAGTCTGAAACGAC
*
6240377 TAATTCAAATGGAAAGGTATACATAGTAGCAGATTTAGAAAATGAAAACTTATGTGGCTTTCCTT
324 TAATTCAAACGGAAAGGTATACATAGTAGCAGATTTAGAAAATGAAAACTTATGTGGCTTTCCTT
* *
6240442 TTTAACATGTAGTATAAACATGAACAATATTATTTTTATTTGTAACTACATTACAATATTTCAAA
389 TTTAACATGTAGTACAAACATGAACAATATTATTTTTATTTGTAACCACATTACAATATTTCAAA
* * *
6240507 ATAGTCTAAACTATAAGAGCTGAAGGATGACCCAAACGACGGTGCCAAAGTTTGATCATTTTATC
454 ACAATCTAAACTATAAGAGCTGAAGGATGACCCAAACGACGGTGCCAAAGTTTGAACATTTTATC
6240572 ATTTTAGGAACTTGGTCTT-AAAACTGCATTATGTGTTGACG
519 ATTTTAGGAACTTGGT-TTCAAAACTGCATTATGTGTTGACG
* *
6240613 GAGCTTGTCGTAGCCCATACAAAGCCTTCATCAATCGACAAATAAGAGGTTGCCCATCGGCATTA
1 GAGCTTGTCGTAGCCCATACAAAGCCTTCGTCAATCGACAAACAAGAGGTTGCCCATCGGCATTA
6240678 TGTTGAACATGTCCATGGGGTTGTTGCATGTATACTTCCTCAGTGGGCTCACCATTTAGGAATCA
66 TGTTGAACATGT-CATGGGGTTGTTGCATGTATACTTCCTCAGTGGGCTCACCATTTAGGAATCA
**
6240743 CTTTGAAGCTGTTTAATGTCTCTCTCAAATTGTGTTTTGACCATTTGCTGAAACAGAATAAAACA
130 CTTTGAAGCTGTTTAATGTCTCTCTCAAATTGTGTTTTGACCATTCACTGAAACAGAATAAAACA
6240808 GTCAATTGCTTGAGATTTACGTTGAATGAGAAACAACCATGTAAAACAGCTAAAAACATCAAAAA
195 GTCAATTGCTTGAGATTTACGTTGAATGAGAAACAACCATGTAAAACAGCTAAAAACATCAAAAA
*
6240873 AAGAAACATAGTACCAATAACCACTACAATCAATAGCTACAGGTCCCCATAAGTCTGAAACGACT
260 AAGAAACATAGTACCAATAACCACTACAATCAACAGCTACAGGTCCCCATAAGTCTGAAACGACT
* *
6240938 AATTCAAACGTAAAGGTATACATAGTATCAGATTTAGAAAATGAAAACTTATGTGGCTTTCCTTT
325 AATTCAAACGGAAAGGTATACATAGTAGCAGATTTAGAAAATGAAAACTTATGTGGCTTTCCTTT
*
6241003 TTGACATGTAGTACAAACATGAACAATATTATTTTTATTTGTAACCACATTACAATATTTCAAAA
390 TTAACATGTAGTACAAACATGAACAATATTATTTTTATTTGTAACCACATTACAATATTTCAAAA
* * *
6241068 CAATCTAAACTATACGAGCTGAAGGATGACCCAGACGATGGTGCCAAAGTTTGAACATTTTATCA
455 CAATCTAAACTATAAGAGCTGAAGGATGACCCAAACGACGGTGCCAAAGTTTGAACATTTTATCA
6241133 TTTTAGGAACTTGGTTTCAAAACTGCATTATGTGTTGACG
520 TTTTAGGAACTTGGTTTCAAAACTGCATTATGTGTTGACG
*
6241173 GAGCTTGTCGTAGCCCATA-AAACGCCTTCGTCAATCGACAAACAATAGGTTGCCCATCGGCATT
1 GAGCTTGTCGTAGCCCATACAAA-GCCTTCGTCAATCGACAAACAAGAGGTTGCCCATCGGCATT
* *
6241237 ATGTTGAACATGTC-TAGGGAGTTGTTGCATGTATACTTTCTCAGTGGGCTCAACATTTAGGAAT
65 ATGTTGAACATGTCAT-GGG-GTTGTTGCATGTATACTTCCTCAGTGGGCTCACCATTTAGGAAT
6241301 GCATTATTTA
Statistics
Matches: 644, Mismatches: 38, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
558 1 0.00
559 9 0.01
560 632 0.98
561 1 0.00
562 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (559 bp):
GAGCTTGTCGTAGCCCATACAAAGCCTTCGTCAATCGACAAACAAGAGGTTGCCCATCGGCATTA
TGTTGAACATGTCATGGGGTTGTTGCATGTATACTTCCTCAGTGGGCTCACCATTTAGGAATCAC
TTTGAAGCTGTTTAATGTCTCTCTCAAATTGTGTTTTGACCATTCACTGAAACAGAATAAAACAG
TCAATTGCTTGAGATTTACGTTGAATGAGAAACAACCATGTAAAACAGCTAAAAACATCAAAAAA
AGAAACATAGTACCAATAACCACTACAATCAACAGCTACAGGTCCCCATAAGTCTGAAACGACTA
ATTCAAACGGAAAGGTATACATAGTAGCAGATTTAGAAAATGAAAACTTATGTGGCTTTCCTTTT
TAACATGTAGTACAAACATGAACAATATTATTTTTATTTGTAACCACATTACAATATTTCAAAAC
AATCTAAACTATAAGAGCTGAAGGATGACCCAAACGACGGTGCCAAAGTTTGAACATTTTATCAT
TTTAGGAACTTGGTTTCAAAACTGCATTATGTGTTGACG
Found at i:6258017 original size:11 final size:10
Alignment explanation
Indices: 6257995--6258050 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 10
6257985 AAACTCTAAA
*
6257995 TTTTAAAATT
1 TTTTATAATT
6258005 TTTTATGAATT
1 TTTTAT-AATT
6258016 TTGTT-TATATT
1 TT-TTATA-ATT
*
6258027 TTTTATGATT
1 TTTTATAATT
6258037 TTTTAATAATT
1 TTTT-ATAATT
6258048 TTT
1 TTT
6258051 AAACTTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 15 0.39
11 21 0.55
12 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Done.