Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 11 of 378
Found at i:3225665 original size:19 final size:22
Alignment explanation
Indices: 3225626--3225665 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
3225616 AGAAACCCAA
3225626 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
3225648 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
3225666 GTGTGGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:3225765 original size:27 final size:27
Alignment explanation
Indices: 3225727--3225866 Score: 153
Period size: 27 Copynumber: 5.2 Consensus size: 27
3225717 AGCACGGCTG
* *
3225727 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
3225753 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
3225781 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
*
3225808 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* * *
3225835 CTAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
3225862 CCAGA
1 CCAGA
3225867 ACGCTTCCTC
Statistics
Matches: 102, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
26 5 0.05
27 80 0.78
28 17 0.17
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:3225791 original size:54 final size:54
Alignment explanation
Indices: 3225727--3225866 Score: 174
Period size: 54 Copynumber: 2.6 Consensus size: 54
3225717 AGCACGGCTG
* *
3225727 CCAGAACAGATA-ATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * *
3225781 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
* * * * *
3225835 CTAGATCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGACAGAGCCACCAGA
3225867 ACGCTTCCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
54 58 0.76
55 18 0.24
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:3227521 original size:26 final size:26
Alignment explanation
Indices: 3227485--3227645 Score: 270
Period size: 26 Copynumber: 6.2 Consensus size: 26
3227475 CATGAAATTC
*
3227485 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
3227511 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
3227537 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
3227563 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
3227589 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
3227615 TTA-CATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
3227640 TTATCA
1 TTATCA
3227646 ATTTGTATCA
Statistics
Matches: 131, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
25 24 0.18
26 107 0.82
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:3232536 original size:73 final size:72
Alignment explanation
Indices: 3232390--3232793 Score: 496
Period size: 73 Copynumber: 5.5 Consensus size: 72
3232380 GTTTTCAAAA
3232390 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC-GCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACAGCTGAGGTATTTTCAATTT
3232454 ATGTTTTTC
65 ATG-TTTTC
* * * *
3232463 AAAAATCAATTCATATTGCTAGAGGTGAATTGAGCCTCGGGTCACATGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACA-GCTGAGGTATTTTCAATT
3232528 TATG-TTTC
64 TATGTTTTC
3232536 AAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-ACACGCTGAGGTATTTTC
1 -----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACA-GCTGAGGTATTTTC
3232600 AATTTATGTTTTTC
60 AATTTATG-TTTTC
*
3232614 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC-GCTGAGGTATTTTCAAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACAGCTGAGGTATTTTCAATTT
3232677 ATGTTTTTC
65 ATG-TTTTC
* ** * * *
3232686 AAAAATCAATTCATATTGTTAGAGGTGAATTGAACCTCGGGTCACATGCCGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACA-GCTGAGGTATTTTCAATT
3232751 TATG-TTTC
64 TATGTTTTC
* *
3232759 AAAAAAATCAACTCATATTGCGAGAAGTAAGTTGA
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
3232794 AGTCTTGGCT
Statistics
Matches: 290, Mismatches: 23, Indels: 34
0.84 0.07 0.10
Matches are distributed among these distances:
72 70 0.24
73 84 0.29
74 2 0.01
75 68 0.23
76 24 0.08
78 42 0.14
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (72 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACAGCTGAGGTATTTTCAATTTA
TGTTTTC
Found at i:3232641 original size:72 final size:72
Alignment explanation
Indices: 3232391--3232793 Score: 486
Period size: 75 Copynumber: 5.4 Consensus size: 72
3232381 TTTTCAAAAA
3232391 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CACGCTGAGGTATTTTCAATTTA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTTTCAATTTA
3232455 TGTTTTTC
65 TGTTTTTC
* * * * *
3232463 AAAAATCAATTCATATTGCTAGAGGTGAATTGAGCCTCGGGTCACATGCCGAGGTATTTTCAATT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTATTTTCAATT
***
3232528 TATGTTTCAAAAAA
63 TATGTTT----TTC
3232542 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTAT
3232607 GTTTTTC
66 GTTTTTC
*
3232614 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CACGCTGAGGTATTTTCAAATTA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTATTTTCAATTTA
3232678 TGTTTTTC
65 TGTTTTTC
* ** * * * *
3232686 AAAAATCAATTCATATTGTTAGAGGTGAATTGAACCTCGGGTCACATGCCGAGGTATTTTCAATT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCTGAGGTATTTTCAATT
***
3232751 TATGTTTCAAA
63 TATGTTT-TTC
* *
3232762 AAAATCAACTCATATTGCGAGAAGTAAGTTGA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGA
3232794 AGTCTTGGCT
Statistics
Matches: 283, Mismatches: 34, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
72 73 0.26
73 69 0.24
75 77 0.27
76 27 0.10
78 37 0.13
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (72 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTAT
GTTTTTC
Found at i:3232827 original size:223 final size:221
Alignment explanation
Indices: 3232391--3232793 Score: 727
Period size: 223 Copynumber: 1.8 Consensus size: 221
3232381 TTTTCAAAAA
*
3232391 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTAT
*
3232456 GTTTTTCAAAAATCAATTCATATTGCTAGAGGTGAATTGAGCCTCGGGTCACATGCCGAGGTATT
66 GTTTTTCAAAAATCAATTCATATTGCTAGAGGTGAATTGAACCTCGGGTCACATGCCGAGGTATT
* *
3232521 TTCAATTTATGTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
131 TTCAATTTATGTTTC--AAAAAAAATCAACTCATATTGCGAGAAGTAAGTTGAGCCTCGGGACAC
*
3232586 GCTGAGGTATTTTCAATTTATGTTTTTC
194 GCTGAGCTATTTTCAATTTATGTTTTTC
3232614 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTAT
*
3232679 GTTTTTCAAAAATCAATTCATATTGTTAGAGGTGAATTGAACCTCGGGTCACATGCCGAGGTATT
66 GTTTTTCAAAAATCAATTCATATTGCTAGAGGTGAATTGAACCTCGGGTCACATGCCGAGGTATT
3232744 TTCAATTTATGTTTC-AAAAAAATCAACTCATATTGCGAGAAGTAAGTTGA
131 TTCAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTAAGTTGA
3232794 AGTCTTGGCT
Statistics
Matches: 175, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
220 33 0.19
223 142 0.81
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (221 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAATTAT
GTTTTTCAAAAATCAATTCATATTGCTAGAGGTGAATTGAACCTCGGGTCACATGCCGAGGTATT
TTCAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAAGTAAGTTGAGCCTCGGGACACGC
TGAGCTATTTTCAATTTATGTTTTTC
Found at i:3233373 original size:22 final size:22
Alignment explanation
Indices: 3233348--3233391 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3233338 CAATTTTGGC
* * *
3233348 CCCTTTATATTAAACCCTAAAA
1 CCCTTCATACTAAACCCCAAAA
3233370 CCCTTCATACTAAACCCCAAAA
1 CCCTTCATACTAAACCCCAAAA
3233392 ACCAACACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (22 bp):
CCCTTCATACTAAACCCCAAAA
Found at i:3234752 original size:2 final size:2
Alignment explanation
Indices: 3234745--3234775 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3234735 ACGTACATTT
3234745 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3234776 TTATCTACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3234848 original size:20 final size:22
Alignment explanation
Indices: 3234805--3234846 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3234795 CTCAACTTTA
* *
3234805 ATATATATTACGTATAGTATTT
1 ATATATAGTACGTATAGCATTT
3234827 ATATATAGTACGTATA-CATT
1 ATATATAGTACGTATAGCATT
3234847 ATGTATGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (22 bp):
ATATATAGTACGTATAGCATTT
Found at i:3235841 original size:21 final size:18
Alignment explanation
Indices: 3235817--3235861 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
3235807 ACATTTCTAA
3235817 TATGTATTTCTAATACTATAT
1 TATGTATTTC--ATA-TATAT
3235838 TATGT-TTTCATATATAT
1 TATGTATTTCATATATAT
3235855 TATGTAT
1 TATGTAT
3235862 ACACTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
20 4 0.17
21 5 0.22
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
TATGTATTTCATATATAT
Found at i:3236355 original size:24 final size:26
Alignment explanation
Indices: 3236327--3236377 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
3236317 GTGTGTATAG
*
3236327 ATATTATGTAAAT-TTTTTA-ATATT
1 ATATTATATAAATGTTTTTATATATT
*
3236351 ATATTATATATATGTTTTTATATATT
1 ATATTATATAAATGTTTTTATATATT
3236377 A
1 A
3236378 CGAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 11 0.48
25 6 0.26
26 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
ATATTATATAAATGTTTTTATATATT
Found at i:3236632 original size:9 final size:9
Alignment explanation
Indices: 3236618--3236644 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3236608 ATATATCTTT
3236618 CTATTATTA
1 CTATTATTA
3236627 CTATTATTA
1 CTATTATTA
3236636 CTATTATTA
1 CTATTATTA
3236645 TTAGTATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (9 bp):
CTATTATTA
Found at i:3236737 original size:23 final size:22
Alignment explanation
Indices: 3236704--3236747 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
3236694 TGTTATGTAT
3236704 GTATATATTATGTACCAATATTTA
1 GTATATATTATGTA--AATATTTA
3236728 GTAT-TATTATGTAAATATTT
1 GTATATATTATGTAAATATTT
3236748 TTCATTCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (22 bp):
GTATATATTATGTAAATATTTA
Found at i:3242813 original size:26 final size:26
Alignment explanation
Indices: 3242777--3242912 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
3242767 CATGATATTC
3242777 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3242803 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3242829 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3242855 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3242881 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3242907 TTATCA
1 TTATCA
3242913 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3244355 original size:23 final size:22
Alignment explanation
Indices: 3244325--3244368 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3244315 ATAGCTTAAT
*
3244325 ATAAATAATATATATAAAAATA
1 ATAAATAATATATAAAAAAATA
*
3244347 ATAATATAATATTTAAAAAAAT
1 ATAA-ATAATATATAAAAAAAT
3244369 GTTCATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
ATAAATAATATATAAAAAAATA
Found at i:3244437 original size:15 final size:14
Alignment explanation
Indices: 3244380--3244437 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
3244370 TTCATAAAAG
*
3244380 AGAAAATAAATAAA
1 AGAAAATAAACAAA
* *
3244394 ATATAATAAAACAAA
1 AGAAAAT-AAACAAA
*
3244409 ATGAAAATATACAAA
1 A-GAAAATAAACAAA
3244424 AGAAAATACAACAA
1 AGAAAATA-AACAA
3244438 GAAAAAATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.35
15 18 0.53
16 4 0.12
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (14 bp):
AGAAAATAAACAAA
Found at i:3244939 original size:24 final size:24
Alignment explanation
Indices: 3244912--3244957 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3244902 GGGGTGATTT
3244912 AGTAGGGTGATGGAATTAGTGGCA
1 AGTAGGGTGATGGAATTAGTGGCA
*
3244936 AGTAGGGTGATGGAGTTAGTGG
1 AGTAGGGTGATGGAATTAGTGG
3244958 TCGGTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.46, T:0.26
Consensus pattern (24 bp):
AGTAGGGTGATGGAATTAGTGGCA
Found at i:3251325 original size:25 final size:25
Alignment explanation
Indices: 3251291--3251341 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3251281 CCACAAAAGT
3251291 ATAGTAAAAAGATCATGAACCAACC
1 ATAGTAAAAAGATCATGAACCAACC
3251316 ATAGTAAAAAGATCATGAACCAACC
1 ATAGTAAAAAGATCATGAACCAACC
3251341 A
1 A
3251342 AAAGAAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.16
Consensus pattern (25 bp):
ATAGTAAAAAGATCATGAACCAACC
Found at i:3263517 original size:26 final size:26
Alignment explanation
Indices: 3263481--3263590 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
3263471 CATGAATTTC
3263481 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3263507 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
3263533 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3263559 TTATCATGGAATATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3263585 TTATCA
1 TTATCA
3263591 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3264481 original size:25 final size:27
Alignment explanation
Indices: 3264448--3264498 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
3264438 TTAACTATCT
*
3264448 AAATTTTTTA-TATTATTTAT-TTAAA
1 AAATATTTTATTATTATTTATCTTAAA
*
3264473 AAATATTTTATTGTTATTTATCTTAA
1 AAATATTTTATTATTATTTATCTTAA
3264499 GATTGCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.41
26 9 0.41
27 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
AAATATTTTATTATTATTTATCTTAAA
Found at i:3264562 original size:21 final size:21
Alignment explanation
Indices: 3264536--3264589 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
3264526 TATAATATTC
3264536 TTTATTTTAAATTTCTTAATA
1 TTTATTTTAAATTTCTTAATA
* *
3264557 TTTATTTCAAATTTCTTTATA
1 TTTATTTTAAATTTCTTAATA
3264578 TATTATTTTAAA
1 T-TTATTTTAAA
3264590 CTATTTTACC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTATTTTAAATTTCTTAATA
Found at i:3264627 original size:21 final size:21
Alignment explanation
Indices: 3264536--3264632 Score: 63
Period size: 21 Copynumber: 4.3 Consensus size: 21
3264526 TATAATATTC
*
3264536 TTTATTTTAAATTTCTTA-ATA
1 TTTATTTTAAACTT-TTACATA
* **
3264557 TTTATTTCAAA-TTTCTTTATA
1 TTTATTTTAAACTTT-TACATA
3264578 TATTATTTTAAACTATTTTACCTATTA
1 T-TTATTTTAAAC--TTTTA-C-A-TA
3264605 TTTATTTTAAACTTTTACATA
1 TTTATTTTAAACTTTTACATA
3264626 TTATATT
1 TT-TATT
3264633 ATAGATTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 18 0.30
22 14 0.23
23 1 0.02
24 6 0.10
25 3 0.05
26 12 0.20
27 3 0.05
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATTTTAAACTTTTACATA
Found at i:3264627 original size:24 final size:26
Alignment explanation
Indices: 3264576--3264634 Score: 86
Period size: 24 Copynumber: 2.3 Consensus size: 26
3264566 AATTTCTTTA
*
3264576 TATATTATTTTAAACTATTTTACCTAT
1 TATATTATTTTAAAC-ATTTTACATAT
3264603 TAT-TTATTTTAAAC-TTTTACATAT
1 TATATTATTTTAAACATTTTACATAT
3264627 TATATTAT
1 TATATTAT
3264635 AGATTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 12 0.40
25 4 0.13
26 11 0.37
27 3 0.10
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (26 bp):
TATATTATTTTAAACATTTTACATAT
Found at i:3264694 original size:23 final size:23
Alignment explanation
Indices: 3264664--3264710 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3264654 AGCTTAAACT
* *
3264664 ATTTTATATATTATTCACTTTAA
1 ATTTTATATAATATCCACTTTAA
*
3264687 ATTTTATATAATATCCATTTTAA
1 ATTTTATATAATATCCACTTTAA
3264710 A
1 A
3264711 ATGTTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTTATATAATATCCACTTTAA
Found at i:3264994 original size:25 final size:27
Alignment explanation
Indices: 3264944--3264995 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
3264934 TTTATTCTAT
*
3264944 ACATATTATTTATTTTAAGTTCCTTTTC
1 ACATATTATTTATTTTAAG-TACTTTTC
3264972 ACATATTATTTATTTT-AG-ACTTTT
1 ACATATTATTTATTTTAAGTACTTTT
3264996 TGTACACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
27 2 0.09
28 16 0.70
ACGTcount: A:0.27, C:0.12, G:0.04, T:0.58
Consensus pattern (27 bp):
ACATATTATTTATTTTAAGTACTTTTC
Found at i:3265006 original size:28 final size:27
Alignment explanation
Indices: 3264943--3265006 Score: 62
Period size: 28 Copynumber: 2.3 Consensus size: 27
3264933 TTTTATTCTA
*
3264943 TACA-TATTATTTATTTTAAGTTCCTTT
1 TACACTATTATTTATTTTAACTT-CTTT
3264970 T-CACATATTATTTATTTTAGACTT-TTT
1 TACAC-TATTATTTATTTTA-ACTTCTTT
3264997 GTACACTATT
1 -TACACTATT
3265007 TAATCCAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
26 2 0.06
27 4 0.13
28 19 0.61
29 6 0.19
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (27 bp):
TACACTATTATTTATTTTAACTTCTTT
Found at i:3266602 original size:12 final size:12
Alignment explanation
Indices: 3266585--3266609 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3266575 TATCATATAA
3266585 ATTTTCTTCTCT
1 ATTTTCTTCTCT
3266597 ATTTTCTTCTCT
1 ATTTTCTTCTCT
3266609 A
1 A
3266610 GAATATATAT
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:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTCTTCTCT
Found at i:3271694 original size:37 final size:37
Alignment explanation
Indices: 3271644--3271722 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
3271634 ATTAGTTGAA
3271644 GATTGAAGAAAAGGGTTTAATTAACGGAAGATTGTTT
1 GATTGAAGAAAAGGGTTTAATTAACGGAAGATTGTTT
*
3271681 GATTGAAGAAAAGGGTTTAATTGACGGAAGATTGTTT
1 GATTGAAGAAAAGGGTTTAATTAACGGAAGATTGTTT
3271718 GATTG
1 GATTG
3271723 GTGAGAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (37 bp):
GATTGAAGAAAAGGGTTTAATTAACGGAAGATTGTTT
Found at i:3271703 original size:18 final size:18
Alignment explanation
Indices: 3271645--3271704 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
3271635 TTAGTTGAAG
3271645 ATTGAAGAAAAGGGTTTA
1 ATTGAAGAAAAGGGTTTA
* ** *
3271663 ATT-AACGGAAGATTGTTTG
1 ATTGAA--GAAAAGGGTTTA
3271682 ATTGAAGAAAAGGGTTTA
1 ATTGAAGAAAAGGGTTTA
3271700 ATTGA
1 ATTGA
3271705 CGGAAGATTG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
17 2 0.06
18 16 0.52
19 11 0.35
20 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.27, T:0.32
Consensus pattern (18 bp):
ATTGAAGAAAAGGGTTTA
Found at i:3272994 original size:43 final size:43
Alignment explanation
Indices: 3272933--3273018 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
3272923 ATTGTTGGAA
*
3272933 AGAATGGCTAATTAATTGATAGCGAAGTTCAATAGATTTAAGG
1 AGAATGGCTAATTAATTGATAGCGAAATTCAATAGATTTAAGG
3272976 AGAATGGCTAATTAATTGATAGCGAAATTCAATAGATTTAAGG
1 AGAATGGCTAATTAATTGATAGCGAAATTCAATAGATTTAAGG
3273019 TTGAAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (43 bp):
AGAATGGCTAATTAATTGATAGCGAAATTCAATAGATTTAAGG
Found at i:3276385 original size:26 final size:26
Alignment explanation
Indices: 3276349--3276484 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
3276339 CATGATATTC
3276349 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
3276375 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3276401 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3276427 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
3276453 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
3276479 TTATCA
1 TTATCA
3276485 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:3277261 original size:17 final size:17
Alignment explanation
Indices: 3277239--3277272 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3277229 AAAAGCTAAA
3277239 ATCATCTAATAAATTAT
1 ATCATCTAATAAATTAT
3277256 ATCATCTAATAAATTAT
1 ATCATCTAATAAATTAT
3277273 CTTGGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
ATCATCTAATAAATTAT
Found at i:3279420 original size:7 final size:7
Alignment explanation
Indices: 3279408--3279433 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3279398 TATTACTTGA
3279408 ATTTAAT
1 ATTTAAT
3279415 ATTTAAT
1 ATTTAAT
3279422 ATTTAAT
1 ATTTAAT
3279429 ATTTA
1 ATTTA
3279434 TTTTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTAAT
Found at i:3280534 original size:10 final size:11
Alignment explanation
Indices: 3280518--3280559 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3280508 TGACCTTTCC
3280518 AAGGTATGGG-
1 AAGGTATGGGA
*
3280528 TAGGTATGGGA
1 AAGGTATGGGA
*
3280539 AAGGTATGGGC
1 AAGGTATGGGA
*
3280550 AAGGAATGGG
1 AAGGTATGGG
3280560 TATATTCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.31, C:0.02, G:0.48, T:0.19
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:3283138 original size:26 final size:26
Alignment explanation
Indices: 3283109--3283218 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
3283099 TGATACAAAT
3283109 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3283135 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
3283161 TAATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3283187 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3283213 TGATAA
1 TGATAA
3283219 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:3287731 original size:18 final size:18
Alignment explanation
Indices: 3287710--3287745 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3287700 GAACAGTACT
3287710 GTATACGTAAATAGTGCC
1 GTATACGTAAATAGTGCC
* *
3287728 GTATACTTGAATAGTGCC
1 GTATACGTAAATAGTGCC
3287746 ATAAATGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (18 bp):
GTATACGTAAATAGTGCC
Found at i:3288321 original size:11 final size:11
Alignment explanation
Indices: 3288282--3288335 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
3288272 TTGACCTTTC
3288282 CAAGGTATGGG
1 CAAGGTATGGG
*
3288293 -TAGGTATGGG
1 CAAGGTATGGG
* *
3288303 AAATGTATGGG
1 CAAGGTATGGG
*
3288314 CAAGGTATAGG
1 CAAGGTATGGG
*
3288325 CAAGGAATGGG
1 CAAGGTATGGG
3288336 TATATTCTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
10 9 0.26
11 25 0.74
ACGTcount: A:0.31, C:0.06, G:0.43, T:0.20
Consensus pattern (11 bp):
CAAGGTATGGG
Found at i:3288544 original size:2 final size:2
Alignment explanation
Indices: 3288537--3288564 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3288527 GAAGTCATGC
3288537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3288565 GATCAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3290849 original size:22 final size:22
Alignment explanation
Indices: 3290824--3290894 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
3290814 TAAAGAAACC
3290824 TATATAA-ATTACCCTATAATAT
1 TATATAATATT-CCCTATAATAT
*
3290846 TATATAATATTTCCTATAATAT
1 TATATAATATTCCCTATAATAT
* *
3290868 TATATAATATTTCATATAA-A-
1 TATATAATATTCCCTATAATAT
3290888 TATATAA
1 TATATAA
3290895 GCTTAAAGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.15
21 1 0.02
22 35 0.76
23 3 0.07
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATAATATTCCCTATAATAT
Found at i:3290865 original size:12 final size:11
Alignment explanation
Indices: 3290838--3290886 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
3290828 TAAATTACCC
3290838 TATAATATT-A
1 TATAATATTCA
*
3290848 TATAATATTTCC
1 TATAATA-TTCA
3290860 TATAATATT-A
1 TATAATATTCA
3290870 TATAATATTTCA
1 TATAATA-TTCA
3290882 TATAA
1 TATAA
3290887 ATATATAAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 14 0.42
11 6 0.18
12 13 0.39
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (11 bp):
TATAATATTCA
Found at i:3294878 original size:3 final size:3
Alignment explanation
Indices: 3294870--3294918 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
3294860 TACTTTAATT
3294870 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
3294916 TTA
1 TTA
3294919 GTGTATACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3295145 original size:12 final size:13
Alignment explanation
Indices: 3295117--3295148 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3295107 AAAACATTAT
3295117 TATTATTTTACCA
1 TATTATTTTACCA
3295130 TATTATTTTA-CA
1 TATTATTTTACCA
3295142 TATTATT
1 TATTATT
3295149 GCTGTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTATTTTACCA
Found at i:3295352 original size:20 final size:21
Alignment explanation
Indices: 3295314--3295352 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3295304 ATATATGTCG
*
3295314 TATATGTTTATGTATATATCA
1 TATATGTTTATGTAGATATCA
3295335 TATATGTTT-TGTAGATAT
1 TATATGTTTATGTAGATAT
3295353 TATGTACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (21 bp):
TATATGTTTATGTAGATATCA
Found at i:3295671 original size:23 final size:22
Alignment explanation
Indices: 3295640--3295695 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
3295630 ATTCATGTAT
3295640 TTTAT-TATATAT-GTATATATC
1 TTTATGTATATATAG-ATATATC
*
3295661 TTTAATGTATATATAGGTATATC
1 TTT-ATGTATATATAGATATATC
3295684 TTTATGTA-ATAT
1 TTTATGTATATAT
3295696 TAGTATTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 16 0.52
24 1 0.03
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.54
Consensus pattern (22 bp):
TTTATGTATATATAGATATATC
Found at i:3296025 original size:9 final size:9
Alignment explanation
Indices: 3296011--3296042 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3296001 ATATATCTTT
3296011 CTATTATTA
1 CTATTATTA
3296020 CTATTATTA
1 CTATTATTA
3296029 CTATTATTA
1 CTATTATTA
*
3296038 TTATT
1 CTATT
3296043 GTGTGTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (9 bp):
CTATTATTA
Found at i:3296102 original size:2 final size:2
Alignment explanation
Indices: 3296095--3296128 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3296085 TATGTTATGC
3296095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3296129 TATGTACCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3299085 original size:30 final size:30
Alignment explanation
Indices: 3299049--3299105 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3299039 TATAAATTTT
3299049 TTAATTTATTTTGATATT-TGAATTTAACGA
1 TTAATTTATTTTGAT-TTCTGAATTTAACGA
*
3299079 TTAATTTATTTTTATTTCTGAATTTAA
1 TTAATTTATTTTGATTTCTGAATTTAA
3299106 ATTAGTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.58
Consensus pattern (30 bp):
TTAATTTATTTTGATTTCTGAATTTAACGA
Found at i:3299803 original size:11 final size:12
Alignment explanation
Indices: 3299781--3299832 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
3299771 TATATACATC
3299781 ATAATAAAAAAT
1 ATAATAAAAAAT
3299793 ATAATAAAAATAT
1 ATAATAAAAA-AT
*
3299806 ATATACAAAACAAAT
1 ATA-A-TAAA-AAAT
3299821 ATAA-AAAAAAT
1 ATAATAAAAAAT
3299832 A
1 A
3299833 CCTTTTCGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 5 0.14
12 13 0.37
13 5 0.14
14 2 0.06
15 8 0.23
16 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (12 bp):
ATAATAAAAAAT
Found at i:3300694 original size:16 final size:15
Alignment explanation
Indices: 3300670--3300704 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
3300660 TAATTATTAT
3300670 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
3300686 TATTTTAATATTTTA
1 TATTCTAATATTTTA
3300701 TATT
1 TATT
3300705 ATTCACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:3302226 original size:25 final size:24
Alignment explanation
Indices: 3302173--3302227 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
3302163 ATTTGAATAT
* *
3302173 ATTT-TAATTATTAATTTAATTAT
1 ATTTATAAGTATTAATTTAATTAC
3302196 ATTTTATAAGTATTAATTTTAATTAC
1 A-TTTATAAGTATTAA-TTTAATTAC
3302222 ATTTAT
1 ATTTAT
3302228 TTAAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 3 0.11
25 14 0.52
26 9 0.33
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
ATTTATAAGTATTAATTTAATTAC
Found at i:3312883 original size:22 final size:22
Alignment explanation
Indices: 3312858--3312900 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3312848 ATTCAGCCTC
3312858 AATGGAGAAAGAAAAGAAGAAA
1 AATGGAGAAAGAAAAGAAGAAA
*
3312880 AATGGAGAAAGAAGAGAAGAA
1 AATGGAGAAAGAAAAGAAGAA
3312901 CAGAAGGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (22 bp):
AATGGAGAAAGAAAAGAAGAAA
Found at i:3322897 original size:43 final size:43
Alignment explanation
Indices: 3322864--3323009 Score: 211
Period size: 43 Copynumber: 3.4 Consensus size: 43
3322854 AAGACGAGAT
* *
3322864 TTTTAGCGGCATTTGTGAAAAAAACGCCTCTAAAAGTCACGTC
1 TTTTAGCGGCGTTTGTGAAAAAAACGCCGCTAAAAGTCACGTC
** ** *
3322907 TTTTAGCGATGTTTGTGGTAAAAGCGCCGCTAAAAGTCACGTC
1 TTTTAGCGGCGTTTGTGAAAAAAACGCCGCTAAAAGTCACGTC
3322950 TTTTAGCGGCGTTTGTGAAAAAAACGCCGCTAAAAGTCACGTC
1 TTTTAGCGGCGTTTGTGAAAAAAACGCCGCTAAAAGTCACGTC
*
3322993 TTTTGAGTGGCGTTTGT
1 TTTT-AGCGGCGTTTGT
3323010 AGGAAAAGCG
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 78 0.88
44 11 0.12
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (43 bp):
TTTTAGCGGCGTTTGTGAAAAAAACGCCGCTAAAAGTCACGTC
Found at i:3322932 original size:86 final size:86
Alignment explanation
Indices: 3322831--3323026 Score: 261
Period size: 86 Copynumber: 2.3 Consensus size: 86
3322821 AATTTGTGGC
* *
3322831 GTTTGTGGGAGAAGCGCCGCTAAAAGACGA-GAT-TTTTAGCGGCATTTGTGAAAAAAACGCCTC
1 GTTTGTGGGAAAAGCGCCGCTAAAAGAC-ACG-TCTTTTAGCGGCATTTGTGAAAAAAACGCCGC
3322894 TAAAAGTCACGTCTTTTAGCGAT
64 TAAAAGTCACGTCTTTTAGCGAT
* * *
3322917 GTTTGTGGTAAAAGCGCCGCTAAAAGTCACGTCTTTTAGCGGCGTTTGTGAAAAAAACGCCGCTA
1 GTTTGTGGGAAAAGCGCCGCTAAAAGACACGTCTTTTAGCGGCATTTGTGAAAAAAACGCCGCTA
* **
3322982 AAAGTCACGTCTTTTGAGTGGC
66 AAAGTCACGTCTTTT-AGCGAT
* *
3323004 GTTTGTAGGAAAAGCGCCACTAA
1 GTTTGTGGGAAAAGCGCCGCTAA
3323027 TTTTAGCAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
85 2 0.02
86 71 0.74
87 23 0.24
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (86 bp):
GTTTGTGGGAAAAGCGCCGCTAAAAGACACGTCTTTTAGCGGCATTTGTGAAAAAAACGCCGCTA
AAAGTCACGTCTTTTAGCGAT
Found at i:3323954 original size:22 final size:22
Alignment explanation
Indices: 3323929--3323972 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3323919 ATCCATCTTT
*
3323929 CTTCCTATGCGTAATCTCAAAA
1 CTTCCTATGCATAATCTCAAAA
*
3323951 CTTCCTATGCATAATCTTAAAA
1 CTTCCTATGCATAATCTCAAAA
3323973 AGCTGAAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (22 bp):
CTTCCTATGCATAATCTCAAAA
Found at i:3329119 original size:9 final size:9
Alignment explanation
Indices: 3329018--3329130 Score: 118
Period size: 9 Copynumber: 12.2 Consensus size: 9
3329008 TATGTAAGTT
*
3329018 GTTATGTAC
1 GTTATGTAA
*
3329027 GTTATGTGA
1 GTTATGTAA
3329036 GTTATGTAA
1 GTTATGTAA
*
3329045 ATTATGTAA
1 GTTATGTAA
*
3329054 GTTATGTGA
1 GTTATGTAA
3329063 GTTATGTAA
1 GTTATGTAA
3329072 GTTGTTATGTAA
1 ---GTTATGTAA
*
3329084 ATTATGTAA
1 GTTATGTAA
* *
3329093 GTTATATGA
1 GTTATGTAA
3329102 GTTATGTAA
1 GTTATGTAA
3329111 GTTATGTAA
1 GTTATGTAA
* *
3329120 TTTATTTAA
1 GTTATGTAA
3329129 GT
1 GT
3329131 AATGATCAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
9 76 0.89
12 9 0.11
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
GTTATGTAA
Found at i:3329130 original size:57 final size:57
Alignment explanation
Indices: 3329003--3329130 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 57
3328993 ATGTATTAGT
* ** * *
3329003 TAAGCTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * *
3329060 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
3329117 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
3329131 AATGATCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:3329597 original size:205 final size:205
Alignment explanation
Indices: 3329245--3329853 Score: 1155
Period size: 205 Copynumber: 3.0 Consensus size: 205
3329235 TAATTTGAAT
* *
3329245 ATAGTAATTTTTTAAGATTCATCATACGTGGCGTTGTTTCACCTAGGGAGGATCCATTATATCTT
1 ATAGTAATTTTTTAAGATTCATCGTACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTT
3329310 ACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
66 ACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
3329375 AAATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAA
131 AAATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAA
3329440 TAAATATTCA
196 TAAATATTCA
3329450 ATAGTAATTTTTTAAGATTCATCGTACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTT
1 ATAGTAATTTTTTAAGATTCATCGTACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTT
*
3329515 ACAGCTCGATATAAGACAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
66 ACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
* *
3329580 AAATAAAGTTAGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAA
131 AAATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAA
3329645 TAAATATTCA
196 TAAATATTCA
3329655 ATAGTAATTTTTTAAGATTCATCGTACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTT
1 ATAGTAATTTTTTAAGATTCATCGTACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTT
* *
3329720 ACAACTCGATATAAGGCAACCCGTTAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
66 ACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
3329785 AAATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAA
131 AAATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAA
3329850 TAAA
196 TAAA
3329854 ATTAATTCAT
Statistics
Matches: 394, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
205 394 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (205 bp):
ATAGTAATTTTTTAAGATTCATCGTACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTT
ACAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTA
AAATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTAATGGACAAGCAAGCTACATGGTAA
TAAATATTCA
Found at i:3330012 original size:23 final size:23
Alignment explanation
Indices: 3329986--3330035 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
3329976 GTTCAAGTTT
3329986 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
3330009 ATTTAAAGGGCTGCAATTCATAC
1 ATTTAAAGGGCTGCAATTCATAC
3330032 ATTT
1 ATTT
3330036 GATTAATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
ATTTAAAGGGCTGCAATTCATAC
Found at i:3330487 original size:23 final size:25
Alignment explanation
Indices: 3330442--3330490 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
3330432 AACACAAAAT
3330442 TCTCTAAATGTGTTATGAGTTCTAA
1 TCTCTAAATGTGTTATGAGTTCTAA
**
3330467 TCTCT-AATG-GTTATGTTTTCTAA
1 TCTCTAAATGTGTTATGAGTTCTAA
3330490 T
1 T
3330491 GTTCTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 4 0.18
25 5 0.23
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.49
Consensus pattern (25 bp):
TCTCTAAATGTGTTATGAGTTCTAA
Found at i:3335961 original size:17 final size:17
Alignment explanation
Indices: 3335918--3335961 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3335908 GAAATCTAGA
* *
3335918 AAATTATTGAAATTTTG
1 AAATTATTTAAAATTTG
*
3335935 AAATCA-TTAAAATTTG
1 AAATTATTTAAAATTTG
3335951 AAATTATTTAA
1 AAATTATTTAA
3335962 GATATATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (17 bp):
AAATTATTTAAAATTTG
Found at i:3336223 original size:44 final size:45
Alignment explanation
Indices: 3336174--3336269 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 45
3336164 TGAACCATGT
* *
3336174 CCCTTAACCCCTAAACCCTCAA-CCTTAAACCATATCCTCTTAAC
1 CCCTTAACCCATAAACCCTCAACCCCTAAACCATATCCTCTTAAC
* * * *
3336218 CCCTTAA-CTATTAACCTTTAACCCCTAAACCATATCCTCTTAAC
1 CCCTTAACCCATAAACCCTCAACCCCTAAACCATATCCTCTTAAC
3336262 CCCTTAAC
1 CCCTTAAC
3336270 TATTAACCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 9 0.20
44 35 0.80
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (45 bp):
CCCTTAACCCATAAACCCTCAACCCCTAAACCATATCCTCTTAAC
Found at i:3336240 original size:22 final size:22
Alignment explanation
Indices: 3336213--3336282 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
3336203 CCATATCCTC
3336213 TTAACCCCTTAACTATTAACCT
1 TTAACCCCTTAACTATTAACCT
* * *
3336235 TTAACCCCTAAACCA-TATCCT
1 TTAACCCCTTAACTATTAACCT
3336256 CTTAACCCCTTAACTATTAACCT
1 -TTAACCCCTTAACTATTAACCT
3336279 TTAA
1 TTAA
3336283 ATCTTAACCC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 5 0.12
22 30 0.75
23 5 0.12
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (22 bp):
TTAACCCCTTAACTATTAACCT
Found at i:3336270 original size:44 final size:44
Alignment explanation
Indices: 3336199--3336282 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
3336189 CCCTCAACCT
3336199 TAAACCATATCCTCTTAACCCCTTAACTATTAACCTTTAACCCC
1 TAAACCATATCCTCTTAACCCCTTAACTATTAACCTTTAACCCC
3336243 TAAACCATATCCTCTTAACCCCTTAACTATTAACCTTTAA
1 TAAACCATATCCTCTTAACCCCTTAACTATTAACCTTTAA
3336283 ATCTTAACCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (44 bp):
TAAACCATATCCTCTTAACCCCTTAACTATTAACCTTTAACCCC
Found at i:3336514 original size:14 final size:16
Alignment explanation
Indices: 3336497--3336533 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3336487 CATAATCAAC
*
3336497 AAACCATA-A-ACTCT
1 AAACCATATATACCCT
3336511 AAACCATATATACCCT
1 AAACCATATATACCCT
3336527 AAACCAT
1 AAACCAT
3336534 GCATAAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 11 0.55
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.22
Consensus pattern (16 bp):
AAACCATATATACCCT
Found at i:3337425 original size:41 final size:42
Alignment explanation
Indices: 3337329--3337429 Score: 134
Period size: 41 Copynumber: 2.4 Consensus size: 42
3337319 AATAGTTTAG
* *
3337329 ATCTATAGCGGCGTTTTTCCAATAAGCGCCGCTAAAACTTAA
1 ATCTATAGCGGCGTTTTTCCAATAAGCGCCACTAAAACTCAA
* * *
3337371 ATCTATTA-TGGCGTTTTTCTAA-AAGCGCCACTAAATCTCAA
1 ATCTA-TAGCGGCGTTTTTCCAATAAGCGCCACTAAAACTCAA
3337412 ATCTATAGCGGCGTTTTT
1 ATCTATAGCGGCGTTTTT
3337430 GAAGAAGCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.04
41 30 0.59
42 17 0.33
43 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.34
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTTCCAATAAGCGCCACTAAAACTCAA
Found at i:3338496 original size:7 final size:7
Alignment explanation
Indices: 3338484--3338531 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
3338474 TTGTTACTAT
3338484 AATTTTA
1 AATTTTA
3338491 AATTTTA
1 AATTTTA
*
3338498 ATATTTAA
1 A-ATTTTA
3338506 AATTTTA
1 AATTTTA
*
3338513 TATTTTA
1 AATTTTA
* *
3338520 AAATCTA
1 AATTTTA
3338527 AATTT
1 AATTT
3338532 AGAATTTTGG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
7 26 0.81
8 6 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (7 bp):
AATTTTA
Found at i:3338508 original size:15 final size:14
Alignment explanation
Indices: 3338485--3338523 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
3338475 TGTTACTATA
*
3338485 ATTTTAAATTTTAAT
1 ATTTAAAATTTT-AT
3338500 ATTTAAAATTTTAT
1 ATTTAAAATTTTAT
3338514 ATTTTAAAAT
1 A-TTTAAAAT
3338524 CTAAATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAAAATTTTAT
Found at i:3338528 original size:22 final size:22
Alignment explanation
Indices: 3338484--3338528 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3338474 TTGTTACTAT
* *
3338484 AATTTTAAATTTTAATATTTAA
1 AATTTTAAATTTTAAAATCTAA
*
3338506 AATTTTATATTTTAAAATCTAA
1 AATTTTAAATTTTAAAATCTAA
3338528 A
1 A
3338529 TTTAGAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTAAATTTTAAAATCTAA
Found at i:3346476 original size:20 final size:20
Alignment explanation
Indices: 3346435--3346476 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3346425 TATGTGTATT
*
3346435 TTATAAAGTTATAATGTTTA
1 TTATAAAGTTATAATATTTA
*
3346455 TTATAAA-TTATTATATTATA
1 TTATAAAGTTATAATATT-TA
3346475 TT
1 TT
3346477 CATTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTATAAAGTTATAATATTTA
Found at i:3357095 original size:20 final size:20
Alignment explanation
Indices: 3357070--3357136 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 20
3357060 CAACCCAGTC
3357070 TTTTTTTTATTTTTATTTATTT
1 TTTTTTTTATTTTTATTTA--T
3357092 TTTTCTTTTATTATTTA-TTAT
1 TTTT-TTTTATT-TTTATTTAT
*
3357113 TTTCTTTTATTTTTATTTTAT
1 TTTTTTTTATTTTTA-TTTAT
3357134 TTT
1 TTT
3357137 AGATAATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.10
20 7 0.17
21 11 0.28
22 4 0.10
23 10 0.25
24 4 0.10
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTTATTTTTATTTAT
Found at i:3357130 original size:16 final size:15
Alignment explanation
Indices: 3357073--3357137 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 15
3357063 CCCAGTCTTT
3357073 TTTTTATTTTTATTTA
1 TTTTTATTTTT-TTTA
3357089 TTTTT-TTCTTTTATTA
1 TTTTTATT-TTTT-TTA
3357105 TTTATTATTTTCTTTTA
1 TTT-TTATTTT-TTTTA
3357122 TTTTTATTTTATTTTA
1 TTTTTATTTT-TTTTA
3357138 GATAATTTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
15 3 0.07
16 26 0.60
17 10 0.23
18 4 0.09
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:3357317 original size:43 final size:42
Alignment explanation
Indices: 3357234--3357324 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
3357224 TCCATGCTGT
* * *
3357234 CAAACAGTTCTATTCCAGCCCAGAATACCATATCTCTGCAGC
1 CAAACAGTCCTATTCCAGCCCAGAATACCAAAACTCTGCAGC
* *
3357276 CAAACAGTCCTATTCCAGCCTTAGAATCCCCAAAAC-CTGCAGC
1 CAAACAGTCCTATTCCAGCC-CAGAAT-ACCAAAACTCTGCAGC
3357319 CAAACA
1 CAAACA
3357325 CCCCTTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 19 0.45
43 18 0.43
44 5 0.12
ACGTcount: A:0.34, C:0.35, G:0.11, T:0.20
Consensus pattern (42 bp):
CAAACAGTCCTATTCCAGCCCAGAATACCAAAACTCTGCAGC
Found at i:3358198 original size:118 final size:118
Alignment explanation
Indices: 3357990--3358220 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
3357980 TGTTTTCCAT
* *
3357990 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
3358055 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
3358108 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
3358173 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
3358221 ACCGGAAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:3358355 original size:7 final size:7
Alignment explanation
Indices: 3358325--3358386 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
3358315 ATTCCTAAGT
3358325 AAATAAA
1 AAATAAA
*
3358332 TAATAATA
1 AAATAA-A
3358340 AAATTTAAA
1 AAA--TAAA
3358349 AAATAAA
1 AAATAAA
*
3358356 AAAAAAA
1 AAATAAA
*
3358363 AAAAAAA
1 AAATAAA
*
3358370 AAAAAAA
1 AAATAAA
*
3358377 AAAGAAA
1 AAATAAA
3358384 AAA
1 AAA
3358387 ATAAGTACTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
7 38 0.79
8 3 0.06
9 4 0.08
10 3 0.06
ACGTcount: A:0.85, C:0.00, G:0.02, T:0.13
Consensus pattern (7 bp):
AAATAAA
Found at i:3358357 original size:1 final size:1
Alignment explanation
Indices: 3358346--3358387 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
3358336 AATAAAATTT
* *
3358346 AAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3358388 TAAGTACTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.95, C:0.00, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:3364017 original size:26 final size:26
Alignment explanation
Indices: 3363958--3364092 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
3363948 TGATACAAAT
3363958 TGATAATAGGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
3363983 TGATAATAGGTTAGATAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3364009 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3364035 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3364061 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3364087 TGATAA
1 TGATAA
3364093 GAATTTCATG
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 22 0.21
26 83 0.79
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:3368247 original size:43 final size:43
Alignment explanation
Indices: 3368200--3368283 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
3368190 TATTTAATCA
* * *
3368200 TTTTAGAAATAATAAAATTATAAGTTAATTTAGTGTAAAATAT
1 TTTTAAAAATAATAAAATTATAAATTAATATAGTGTAAAATAT
* *
3368243 TTTTAAAAATAATGAAATTATAAATTAATATATTGTAAAAT
1 TTTTAAAAATAATAAAATTATAAATTAATATAGTGTAAAAT
3368284 CACATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (43 bp):
TTTTAAAAATAATAAAATTATAAATTAATATAGTGTAAAATAT
Found at i:3377249 original size:14 final size:15
Alignment explanation
Indices: 3377224--3377253 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3377214 GTTTTGTAAA
3377224 TGGACATTTATTATT
1 TGGACATTTATTATT
3377239 TGGAC-TTTATTATT
1 TGGACATTTATTATT
3377253 T
1 T
3377254 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (15 bp):
TGGACATTTATTATT
Found at i:3379786 original size:10 final size:10
Alignment explanation
Indices: 3379771--3379809 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
3379761 TGCTTTTGTA
3379771 CATGATATGC
1 CATGATATGC
3379781 CATGATATGC
1 CATGATATGC
3379791 ACATGATATGC
1 -CATGATATGC
3379802 CATGATAT
1 CATGATAT
3379810 ATTGACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:3379795 original size:21 final size:21
Alignment explanation
Indices: 3379770--3379809 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3379760 CTGCTTTTGT
3379770 ACATGATATGCCATGATATGC
1 ACATGATATGCCATGATATGC
3379791 ACATGATATGCCATGATAT
1 ACATGATATGCCATGATAT
3379810 ATTGACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
ACATGATATGCCATGATATGC
Found at i:3383887 original size:9 final size:9
Alignment explanation
Indices: 3383865--3383963 Score: 60
Period size: 10 Copynumber: 10.6 Consensus size: 9
3383855 CATGTAATTT
*
3383865 TTTTTACAA
1 TTTTTATAA
3383874 TTTTTTATAA
1 -TTTTTATAA
3383884 TTTTTAATAA
1 TTTTT-ATAA
*
3383894 TTTTTAAATA
1 TTTTTATA-A
3383904 TTTTGTATTAA
1 TTTT-TA-TAA
* *
3383915 ATTTAATAA
1 TTTTTATAA
3383924 TTTTT-TAAA
1 TTTTTAT-AA
* *
3383933 ATTTTATTGA
1 TTTTTA-TAA
3383943 TTTTTAT--
1 TTTTTATAA
3383950 TTTTTATAA
1 TTTTTATAA
3383959 TTTTT
1 TTTTT
3383964 TTGCCGCATG
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
7 7 0.10
8 1 0.01
9 25 0.36
10 29 0.41
11 7 0.10
12 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3383907 original size:30 final size:30
Alignment explanation
Indices: 3383864--3383937 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
3383854 GCATGTAATT
* * *
3383864 TTTTTTACAATTTTTTA-TAATTTTTAATAA
1 TTTTTTAAAATTTTGTATTAA-ATTTAATAA
3383894 TTTTT-AAATATTTTGTATTAAATTTAATAA
1 TTTTTTAAA-ATTTTGTATTAAATTTAATAA
3383924 TTTTTTAAAATTTT
1 TTTTTTAAAATTTT
3383938 ATTGATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 2 0.05
30 30 0.79
31 6 0.16
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTTAAAATTTTGTATTAAATTTAATAA
Found at i:3385602 original size:3 final size:3
Alignment explanation
Indices: 3385589--3385754 Score: 70
Period size: 3 Copynumber: 54.3 Consensus size: 3
3385579 AAAGGTTAAT
* * * *
3385589 TAA TTA TAA TAA TAGA -AA AAA TAA TAA TAGT TAA -AA TAA TAG TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* * * * **
3385634 TAG TAA -ATA TAA TGA TAA TAAA TAA TAA TAA TGA TAG TCG TAA TAA
1 TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * * * * *
3385680 TGA TAA TGG CAA TAAA TAA TAA TAG TGAA AAA TAA TAA TAG GAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
3385727 TAA TGA TAA TATA TAA -AA TAA TAA TAA T
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T
3385755 GATAGCAAAA
Statistics
Matches: 117, Mismatches: 35, Indels: 22
0.67 0.20 0.13
Matches are distributed among these distances:
2 6 0.05
3 97 0.83
4 14 0.12
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3385614 original size:15 final size:15
Alignment explanation
Indices: 3385594--3385752 Score: 59
Period size: 16 Copynumber: 9.6 Consensus size: 15
3385584 TTAATTAATT
3385594 ATAATAATAGAAAAA
1 ATAATAATAGAAAAA
3385609 ATAATAATAGTTAAAATA
1 ATAATAATAG--AAAA-A
*
3385627 ATAGTAATAGTAAATATA
1 ATAATAATAG-AAA-A-A
*
3385645 ATGATAATA-AATAATA
1 ATAATAATAGAA-AA-A
* * *
3385661 ATAATGATAGTCGTAATA
1 ATAAT-A-A-TAGAAAAA
* * *
3385679 ATGATAATGGCAATAA
1 ATAATAATAG-AAAAA
*
3385695 ATAATAATAGTGAAAA
1 ATAATAATAG-AAAAA
3385711 ATAATAATAGGAATAATA
1 ATAATAATA-GAA-AA-A
* * *
3385729 ATGATAATATATAAA
1 ATAATAATAGAAAAA
3385744 ATAATAATA
1 ATAATAATA
3385753 ATGATAGCAA
Statistics
Matches: 109, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
15 21 0.19
16 35 0.32
17 15 0.14
18 35 0.32
19 2 0.02
20 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.30
Consensus pattern (15 bp):
ATAATAATAGAAAAA
Found at i:3385768 original size:24 final size:24
Alignment explanation
Indices: 3385722--3385768 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3385712 TAATAATAGG
* * *
3385722 AATAATAATGATAATATATAAAAT
1 AATAATAATGATAACAAAAAAAAT
*
3385746 AATAATAATGATAGCAAAAAAAA
1 AATAATAATGATAACAAAAAAAA
3385769 AGAAAATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (24 bp):
AATAATAATGATAACAAAAAAAAT
Found at i:3385823 original size:3 final size:3
Alignment explanation
Indices: 3385817--3385864 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
3385807 GGTGCTAACG
* *
3385817 ATA ATAA ATA ATA GTA GTAA ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
3385863 AT
1 AT
3385865 GCAAATAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3385919 original size:3 final size:3
Alignment explanation
Indices: 3385911--3385953 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3385901 GAAATTTAAG
3385911 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3385954 GGTAGAATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3394109 original size:30 final size:30
Alignment explanation
Indices: 3394075--3394137 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3394065 ACTTAACAAG
*
3394075 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
* *
3394105 CAAATGTCTTTAAAATAATAAAAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
3394135 CAA
1 CAA
3394138 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAAAAAAATTAA
Found at i:3394711 original size:20 final size:19
Alignment explanation
Indices: 3394682--3394728 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
3394672 CTTATAAATT
3394682 ATAAAATAAT--TA-TAAA
1 ATAAAATAATAATATTAAA
3394698 ATCAAAATAATAATATTAAA
1 AT-AAAATAATAATATTAAA
*
3394718 ATTAAATAATA
1 ATAAAATAATA
3394729 TAAAACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
19 10 0.38
20 6 0.23
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAATAATAATATTAAA
Found at i:3403303 original size:27 final size:27
Alignment explanation
Indices: 3403253--3403331 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
3403243 TTTGGGTCTT
* **
3403253 CCTCATCTTCTTCCTCAGTTGAAGAC-
1 CCTCTTCTTCTTCCTCAGAAGAAGACA
*
3403279 CCTTCTTCTTCTTCCTCAGAAGAAGTCA
1 CC-TCTTCTTCTTCCTCAGAAGAAGACA
* * *
3403307 CCTCTTCATCTTCTTCAGAGGAAGA
1 CCTCTTCTTCTTCCTCAGAAGAAGA
3403332 AGCGGCTGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.05
27 39 0.91
28 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTCTTCTTCTTCCTCAGAAGAAGACA
Found at i:3404002 original size:17 final size:18
Alignment explanation
Indices: 3403969--3404004 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3403959 AAAAAAACTA
3403969 TAAAAAAATATTGAAAAT
1 TAAAAAAATATTGAAAAT
*
3403987 TAAAAAAAT-TTTAAAAT
1 TAAAAAAATATTGAAAAT
3404004 T
1 T
3404005 TTAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TAAAAAAATATTGAAAAT
Found at i:3404083 original size:23 final size:23
Alignment explanation
Indices: 3404057--3404111 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3404047 AAACATAGAA
3404057 AAAAAAATTTAATA-AAAAACTAT
1 AAAAAAATTTAATATAAAAA-TAT
** * *
3404080 AAAAATTTTTTATATAGAAATAT
1 AAAAAAATTTAATATAAAAATAT
3404103 AAAAAAATT
1 AAAAAAATT
3404112 ATAAACATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAAATTTAATATAAAAATAT
Found at i:3404327 original size:18 final size:18
Alignment explanation
Indices: 3404290--3404323 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3404280 GATTAAAGGG
3404290 TATTTTTTATGCATTTTA
1 TATTTTTTATGCATTTTA
3404308 TATTTTTTATG-ATTTT
1 TATTTTTTATGCATTTT
3404324 TATAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (18 bp):
TATTTTTTATGCATTTTA
Found at i:3404333 original size:28 final size:27
Alignment explanation
Indices: 3404302--3404401 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 27
3404292 TTTTTTATGC
3404302 ATTTTATATTTTTTATGATTTTTATAAA
1 ATTTTATATTTTTTAT-ATTTTTATAAA
* *
3404330 ATTTTATATTTTTTTCTAACTTTTA-ATAA
1 ATTTTATA-TTTTTTAT-ATTTTTATA-AA
3404359 A-TTT-TATTTTTTATATTTTTATTAAA
1 ATTTTATATTTTTTATATTTTTA-TAAA
* *
3404385 ATTTAATCTTTTTTATA
1 ATTTTATATTTTTTATA
3404402 AACTTTTTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
25 6 0.10
26 10 0.17
27 5 0.08
28 22 0.37
29 16 0.27
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (27 bp):
ATTTTATATTTTTTATATTTTTATAAA
Found at i:3404671 original size:88 final size:87
Alignment explanation
Indices: 3404507--3404673 Score: 223
Period size: 88 Copynumber: 1.9 Consensus size: 87
3404497 TTATAACCAA
*
3404507 AGGGCCTTTTTGATGCATTTGACAGTTCAAGTATCCAATTGAGTGAAAAAAAAAATCAGGGCTTA
1 AGGGCCTTTTTGATGCATTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAAAAATCAGGGCTTA
**
3404572 ATTATTTTTTTTTTTAAGTTTG
66 ATTATGGTTTTTTTTAAGTTTG
* * *
3404594 AGGGTCTTTTTTATGCATTTTGAGAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAGT-AGGAG
1 AGGGCCTTTTTGATGCA-TTTGACAGTTCAAGTACCCAATTGAGTG-AAAAAAAAAA-TCAGG-G
3404658 CTTAA-T-TGGTTTTTTT
62 CTTAATTATGGTTTTTTT
3404674 AAATTTTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
87 15 0.21
88 34 0.49
89 14 0.20
90 7 0.10
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (87 bp):
AGGGCCTTTTTGATGCATTTGACAGTTCAAGTACCCAATTGAGTGAAAAAAAAAATCAGGGCTTA
ATTATGGTTTTTTTTAAGTTTG
Found at i:3407180 original size:13 final size:13
Alignment explanation
Indices: 3407162--3407187 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3407152 CACTAATTCT
3407162 ATCACCCCACTAA
1 ATCACCCCACTAA
3407175 ATCACCCCACTAA
1 ATCACCCCACTAA
3407188 CCCCATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (13 bp):
ATCACCCCACTAA
Found at i:3407210 original size:15 final size:15
Alignment explanation
Indices: 3407190--3407221 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3407180 CCCACTAACC
3407190 CCATTACCTCACTTG
1 CCATTACCTCACTTG
3407205 CCATTACCTCACTTG
1 CCATTACCTCACTTG
3407220 CC
1 CC
3407222 TAGGAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (15 bp):
CCATTACCTCACTTG
Found at i:3407774 original size:20 final size:21
Alignment explanation
Indices: 3407733--3407771 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
3407723 TTATGAACAT
3407733 TTTTTAAATATTATATTATTA
1 TTTTTAAATATTATATTATTA
3407754 TTTTT-AATA-TATATTATT
1 TTTTTAAATATTATATTATT
3407772 TATATTAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTAAATATTATATTATTA
Found at i:3414260 original size:64 final size:64
Alignment explanation
Indices: 3414184--3414309 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
3414174 ATTCATAGTG
* * *
3414184 CATCTAGTTAGGAGCATTTCATTCATTTTGATCATAGCATCCTAATTATTTGGCATAAGCATCA
1 CATCTAGCTAGGAGCATTTCATTCATTTCGATCATAGCATCCTAACTATTTGGCATAAGCATCA
* *
3414248 CATCTAGCTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAACTGTTTGGCATAAGCAT
1 CATCTAGCTAGGAGCATTTCATTCATTTCGATCATAGCATCCTAACTATTTGGCATAAGCAT
3414310 ATATACATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (64 bp):
CATCTAGCTAGGAGCATTTCATTCATTTCGATCATAGCATCCTAACTATTTGGCATAAGCATCA
Found at i:3414697 original size:133 final size:133
Alignment explanation
Indices: 3414421--3414669 Score: 315
Period size: 133 Copynumber: 1.9 Consensus size: 133
3414411 TACAAATTAT
* * *
3414421 AGATCTTACCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTATC
1 AGATCTTATCTCCATGTATCAGCTATGGAGCAGATCAGAAATGACGAGTCTTATCTCCATGTATC
** * *
3414486 GGCTATGGAACAGATTTTAGCCACAGGTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAAT
66 GGCTATGGAACAGATTTTAGCCACAGCCCTTATCCTCCTGAAGTAGCAAGAAGCAGACTGAAAAT
* *
3414551 TAC
131 AAA
* * *
3414554 AGATCTTATCTCCATGTATCAGCTATGGAGTAGATC-GAAAATGATGAGTTTTATCTCCATGTAT
1 AGATCTTATCTCCATGTATCAGCTATGGAGCAGATCAG-AAATGACGAGTCTTATCTCCATGTAT
** *
3414618 CGGCTATGGAGTAGATTTTAGCCACCA-CCCTTAT-CTCTCTGAGGTAGCAAGA
65 CGGCTATGGAACAGATTTTAGCCA-CAGCCCTTATCCTC-CTGAAGTAGCAAGA
3414670 GAGTAGGTTA
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
132 4 0.04
133 94 0.94
134 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (133 bp):
AGATCTTATCTCCATGTATCAGCTATGGAGCAGATCAGAAATGACGAGTCTTATCTCCATGTATC
GGCTATGGAACAGATTTTAGCCACAGCCCTTATCCTCCTGAAGTAGCAAGAAGCAGACTGAAAAT
AAA
Found at i:3414743 original size:178 final size:177
Alignment explanation
Indices: 3414512--3415174 Score: 1003
Period size: 178 Copynumber: 3.7 Consensus size: 177
3414502 TTAGCCACAG
*
3414512 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAA-TTACAGATCTTATCTCCATGTATCAG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCAG
* ** * *
3414576 CTATGGAGTAGATCGAAAATGATGAGTTTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCC
66 CTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
* * *
3414641 ACCACCCTTATCTCTCTGAGGTAGCAAGAGAGTAGGTTAAAGATAAAA
131 ACCAGCCTCATCTCTCTGAGGTAGCAAGAGAG-AGGTTAAAGATACAA
* * * *
3414689 GTTTTATCTTCCTGAAGTTGCAGAAAGCAGACTGGAAATTTACAGATTTTATCTCCATGTATC-G
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCAG
** *
3414753 ACTATGGAGCAGATAAAAAATGGTGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
66 -CTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
*
3414818 CACCAGCCTCATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAA-TTACAA
130 CACCAGCCTCATCTCTCTGAGGTAGCAAGAGAG-AGGTT-AAAGATACAA
3414867 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCAG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCAG
* *
3414932 CTATAGAGCAGATCGAAAATGGCGGGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
66 CTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
* * *
3414997 ACCAGCCTCATCTCTCTGAGGTAGCAAGAGAGCGGTTGAAGATACAG
131 ACCAGCCTCATCTCTCTGAGGTAGCAAGAGAGAGGTTAAAGATACAA
* * * * *
3415044 GTCTTATCTTCTTGAAGTTGTAGGAAGCAGACTAAAAAGTTACAGATCTTATCTCCATGTATCGG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCAG
3415109 CTATGGAGCAGATC-AGAAATGGCGAGTCTTATCTCCATGT-TCGGCTATGGAGCAGATTTTAGC
66 CTATGGAGCAGATCGA-AAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
3415172 CAC
130 CAC
3415175 TAGTCTTATC
Statistics
Matches: 444, Mismatches: 36, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
176 29 0.07
177 139 0.31
178 272 0.61
179 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (177 bp):
GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCAG
CTATGGAGCAGATCGAAAATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
ACCAGCCTCATCTCTCTGAGGTAGCAAGAGAGAGGTTAAAGATACAA
Found at i:3415205 original size:133 final size:134
Alignment explanation
Indices: 3415044--3415308 Score: 390
Period size: 133 Copynumber: 2.0 Consensus size: 134
3415034 GAAGATACAG
* * *
3415044 GTCTTATCTTCTTGAAGTTGTAGGAAGCAGACT-AAAAAGTTACAGATCTTATCTCCATGTATCG
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAAAA-TTACAGATCTTATCTCCATGTATCG
* * * * *
3415108 GCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGT-TCGGCTATGGAGCAGATTTTAGC
65 ACAATGGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
3415172 CACTA
130 CACTA
* *
3415177 GTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAGAATTACAGATTTTATCTCCATGTATCGA
1 GTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAAAATTACAGATCTTATCTCCATGTATCGA
* * *
3415242 CAATGGAGTAGATAAAAAATAGCGAGTTTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCC
66 CAATGGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
3415307 AC
131 AC
3415309 CGGCCTTATC
Statistics
Matches: 117, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
133 87 0.74
134 30 0.26
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (134 bp):
GTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAAAATTACAGATCTTATCTCCATGTATCGA
CAATGGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
ACTA
Found at i:3415220 original size:355 final size:355
Alignment explanation
Indices: 3414512--3415212 Score: 1041
Period size: 355 Copynumber: 2.0 Consensus size: 355
3414502 TTAGCCACAG
3414512 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCAGC
1 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCAGC
* * * * *
3414577 TATGGAGTAGATCGAAAATGATGAGTTTTATCTCCATGTATCGGCTATGGAGTAGATTTTAGCCA
66 TATAGAGCAGATCGAAAATGACGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
* *
3414642 CCACCCTTATCTCTCTGAGGTAGCAAGAGAGTAGGTTAAAGATAAAAGTTTTATCTTCCTGAAGT
131 CCACCCTCATCTCTCTGAGGTAGCAAGAGAGTAGGTTAAAGATAAAAGTCTTATCTTCCTGAAGT
** * *
3414707 TGCAGAAAGCAGACTGGAAATTTACAGATTTTATCTCCATGTATCGACTATGGAGCAGATAAAAA
196 TGCAGAAAGCAGACTAAAAAGTTACAGATCTTATCTCCATGTATCGACTATGGAGCAGATAAAAA
*
3414772 ATGGTGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTCATCTCTCTG
261 ATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTCATCTCTCTG
* ***
3414837 AGGTAGCAAGAGAGCAGGTTGAAATTACAA
326 AAGTAGCAAGAGAGCAAACTGAAATTACAA
*
3414867 GTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCAG
1 GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAA-TTACAGATCTTATCTCCATGTATCAG
* *
3414932 CTATAGAGCAGATCGAAAATGGCGGGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
65 CTATAGAGCAGATCGAAAATGACGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCC
* * * * * *
3414997 ACCAGCCTCATCTCTCTGAGGTAGCAAGAGAG-CGGTTGAAGATACAGGTCTTATCTTCTTGAAG
130 ACCACCCTCATCTCTCTGAGGTAGCAAGAGAGTAGGTTAAAGATAAAAGTCTTATCTTCCTGAAG
* * * * *
3415061 TTGTAGGAAGCAGACTAAAAAGTTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGA
195 TTGCAGAAAGCAGACTAAAAAGTTACAGATCTTATCTCCATGTATCGACTATGGAGCAGATAAAA
* * *
3415126 AATGGCGAGTCTTATCTCCATGT-TCGGCTATGGAGCAGATTTTAGCCACTAGTCTTATCT-TCC
260 AATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTCATCTCT-C
* *
3415189 TGAAGTTGCAGGA-AGCAAACTGAA
324 TGAAGTAGCAAGAGAGCAAACTGAA
3415213 GAATTACAGA
Statistics
Matches: 309, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
353 9 0.03
354 45 0.15
355 141 0.46
356 114 0.37
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (355 bp):
GTCTTATCCTCCTGAAGTTGCAGGAAGCAGACTGAAAATTACAGATCTTATCTCCATGTATCAGC
TATAGAGCAGATCGAAAATGACGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA
CCACCCTCATCTCTCTGAGGTAGCAAGAGAGTAGGTTAAAGATAAAAGTCTTATCTTCCTGAAGT
TGCAGAAAGCAGACTAAAAAGTTACAGATCTTATCTCCATGTATCGACTATGGAGCAGATAAAAA
ATGGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGCCTCATCTCTCTG
AAGTAGCAAGAGAGCAAACTGAAATTACAA
Found at i:3415363 original size:133 final size:133
Alignment explanation
Indices: 3415046--3415341 Score: 353
Period size: 133 Copynumber: 2.2 Consensus size: 133
3415036 AGATACAGGT
* * * * * * *
3415046 CTTATCTTCTTGAAGTTGTAGGAAGCAGACT-AAAAAGTTACAGATCTTATCTCCATGTATCGGC
1 CTTATCTTCCTGAAGTAGCAAGAAGCAAACTGAAGAA-TTACAGATCTTATCTCCATGTATCGAC
* * * *
3415110 TATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTTCGGCTATGGAGCAGATTTTAGCCAC
65 AATGGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTTCGGCTATGGAGCAGATTTTAGCCAC
* *
3415175 TAGT
130 CAGC
* * *
3415179 CTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAGAATTACAGATTTTATCTCCATGTATCGACA
1 CTTATCTTCCTGAAGTAGCAAGAAGCAAACTGAAGAATTACAGATCTTATCTCCATGTATCGACA
* * *
3415244 ATGGAGTAGATAAAAAATAGCGAGTTTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCAC
66 ATGGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGT-TCGGCTATGGAGCAGATTTTAGCCAC
*
3415309 CGGC
130 CAGC
*
3415313 CTTATCTAT-CTGAGGTAGCAAGAGAGCAA
1 CTTATCT-TCCTGAAGTAGCAAGA-AGCAA
3415342 GTTGAAGATA
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
133 85 0.61
134 49 0.35
135 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (133 bp):
CTTATCTTCCTGAAGTAGCAAGAAGCAAACTGAAGAATTACAGATCTTATCTCCATGTATCGACA
ATGGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTTCGGCTATGGAGCAGATTTTAGCCACC
AGC
Found at i:3415404 original size:310 final size:310
Alignment explanation
Indices: 3414866--3415510 Score: 958
Period size: 310 Copynumber: 2.1 Consensus size: 310
3414856 TGAAATTACA
*
3414866 AGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGAAAATTTACAGATCTTATCTCCATGTATCA
1 AGTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAAATTTACAGATCTTATCTCCATGTATCA
* ** * *
3414931 GCTATAGAGCAGATCGAAAATGGCGGGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
66 GCAATAGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
* *
3414996 CACCAGCCTCATCTCTCTGAGGTAGCAAGAGAGCGGTTGAAGATACAGGTCTTATCTTCTTGAAG
131 CACCAGCCTCATCTATCTGAGGTAGCAAGAGAGCAGTTGAAGATACAGGTCTTATCTTCTTGAAG
* * *
3415061 TTGTAGGAAGCAGACTAAAAAGTTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGA
196 TTGCAAGAAGCAGACTAAAAAGTTACAGATCTTATCTCCATATATCGGCTATGGAGCAGATCAGA
* *
3415126 AATGGCGAGTCTTATCTCCATGT-TCGGCTATGGAGCAGATTTTAGCCACT
261 AATGGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCA-T
*
3415176 AGTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAGAA-TTACAGATTTTATCTCCATGTATC
1 AGTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAA-AATTTACAGATCTTATCTCCATGTATC
* * * *
3415240 -GACAATGGAGTAGATAAAAAATAGCGAGTTTTATCTCTATGTATCGGCTATGGAGCAGATTTTA
65 AG-CAATAGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTA
* *
3415304 GCCACCGGCCTTATCTATCTGAGGTAGCAAGAGAGCAAGTTGAAGATACTA-GTCTTATCTTCTT
129 GCCACCAGCCTCATCTATCTGAGGTAGCAAGAGAGC-AGTTGAAGATAC-AGGTCTTATCTTCTT
* **
3415368 GAAGTTGCAAGAAGCAGACTGAAAA-TTATGGATCTTATCTCCATATATCGGCTATGGAGCAGAT
192 GAAGTTGCAAGAAGCAGACTAAAAAGTTACAGATCTTATCTCCATATATCGGCTATGGAGCAGAT
3415432 CAGAAATGGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAT
257 CAGAAATGGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAT
* * * *
3415486 TGACCTCATCTCCCTGAAGTTGCAG
1 AG-TCTTATCTTCCTGAAGTTGCAG
3415511 TGGAACAGGT
Statistics
Matches: 302, Mismatches: 27, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
309 1 0.00
310 208 0.69
311 92 0.30
312 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (310 bp):
AGTCTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAAATTTACAGATCTTATCTCCATGTATCA
GCAATAGAGCAGATAAAAAATAGCGAGTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGC
CACCAGCCTCATCTATCTGAGGTAGCAAGAGAGCAGTTGAAGATACAGGTCTTATCTTCTTGAAG
TTGCAAGAAGCAGACTAAAAAGTTACAGATCTTATCTCCATATATCGGCTATGGAGCAGATCAGA
AATGGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAT
Found at i:3415541 original size:177 final size:178
Alignment explanation
Indices: 3415179--3415552 Score: 423
Period size: 177 Copynumber: 2.1 Consensus size: 178
3415169 AGCCACTAGT
* * * *
3415179 CTTATCTTCCTGAAGTTGCAGGAAGCAAACTGAAGAATTACAGATTTTATCTCCATGTATCGACA
1 CTTATCTTCTTGAAGTTGCAAGAAGCAAACTGAAGAATTACAGATCTTATCTCCATATATCGACA
* * ** *
3415244 ATGGAGTAGATAAAAAATAGCGAGTTTTATCTCTATGTATCGGCTATGGAGCAGATTTTAGCCAC
66 ATGGAGCAGATAAAAAATAGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAC
* * * * * **
3415309 CGGCCTTATCTATCTGAGGTAGCAAGAGAGCAAGTTGAAGATACTAGT
131 CGACCTCATCTACCTGAAGTAGCAAGAGAACAAGTTGAAGATACTAAA
* ** * *
3415357 CTTATCTTCTTGAAGTTGCAAGAAGCAGACTGAA-AATTATGGATCTTATCTCCATATATCGGCT
1 CTTATCTTCTTGAAGTTGCAAGAAGCAAACTGAAGAATTACAGATCTTATCTCCATATATCGACA
* * * *
3415421 ATGGAGCAGATCAGAAATGGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAT
66 ATGGAGCAGATAAAAAATAGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAC
* * * * *
3415486 TGACCTCATCTCCCTGAAGTTGC-AGTGGAACAGGTTGAA-ATTAC-AAA
131 CGACCTCATCTACCTGAAGTAGCAAG-AGAACAAGTTGAAGA-TACTAAA
3415533 CGTTATCTTCTTGAAGTTGC
1 C-TTATCTTCTTGAAGTTGC
3415553 TGTAGGACTA
Statistics
Matches: 163, Mismatches: 30, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
176 5 0.03
177 127 0.78
178 31 0.19
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (178 bp):
CTTATCTTCTTGAAGTTGCAAGAAGCAAACTGAAGAATTACAGATCTTATCTCCATATATCGACA
ATGGAGCAGATAAAAAATAGCAAGTCCTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCAC
CGACCTCATCTACCTGAAGTAGCAAGAGAACAAGTTGAAGATACTAAA
Found at i:3415779 original size:17 final size:17
Alignment explanation
Indices: 3415757--3415791 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3415747 ACTAAACCGA
3415757 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
3415774 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
3415791 C
1 C
3415792 TATTTGCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.17
Consensus pattern (17 bp):
CCACTAACTCCATCACC
Found at i:3416409 original size:21 final size:22
Alignment explanation
Indices: 3416364--3416406 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3416354 TTTTATGAAC
3416364 ATTTTTTAAATATTATATTATT
1 ATTTTTTAAATATTATATTATT
*
3416386 ATTTTTATATATATTAT-TTAT
1 ATTTTT-TAAATATTATATTAT
3416407 ATTAAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTTTAAATATTATATTATT
Found at i:3423357 original size:23 final size:22
Alignment explanation
Indices: 3423313--3423362 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
3423303 AACCAATCAA
*
3423313 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
3423335 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
3423358 CATAT
1 CATAT
3423363 ACCCAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:3426629 original size:18 final size:18
Alignment explanation
Indices: 3426584--3426653 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
3426574 ACTCTTTAAT
*
3426584 AGTCAGTTATTCAGTAAC
1 AGTCAGTTATTCAGTAGC
* *
3426602 -GATAAATTATTCAGTAGC
1 AG-TCAGTTATTCAGTAGC
3426620 AGTCAGTTATTCAGTAGC
1 AGTCAGTTATTCAGTAGC
3426638 AGTCAGTTATTCAGTA
1 AGTCAGTTATTCAGTA
3426654 TTTTTATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
17 1 0.02
18 43 0.96
19 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (18 bp):
AGTCAGTTATTCAGTAGC
Found at i:3428206 original size:24 final size:24
Alignment explanation
Indices: 3428179--3428265 Score: 156
Period size: 24 Copynumber: 3.6 Consensus size: 24
3428169 CTTATTATGT
*
3428179 TCGCACACCTAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
3428203 TCGCACACACAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
3428227 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
3428251 TCGCACACATAGTGC
1 TCGCACACATAGTGC
3428266 AATTGATATT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:3430004 original size:6 final size:6
Alignment explanation
Indices: 3429986--3430021 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3429976 TAGGGCTGTC
* *
3429986 ACAGTA ACGGTA ACAGTA ACAGTA ACAGGA ACAGTA
1 ACAGTA ACAGTA ACAGTA ACAGTA ACAGTA ACAGTA
3430022 GTGATACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (6 bp):
ACAGTA
Found at i:3431213 original size:14 final size:14
Alignment explanation
Indices: 3431196--3431238 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
3431186 TCTTATAATA
3431196 TAATTATAATAAAT
1 TAATTATAATAAAT
3431210 TAATT-TAATATAAT
1 TAATTATAATA-AAT
*
3431224 TTATTACTAATAAAT
1 TAATTA-TAATAAAT
3431239 ATATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 12 0.48
15 3 0.12
16 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATTATAATAAAT
Found at i:3432049 original size:26 final size:26
Alignment explanation
Indices: 3432012--3432147 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
3432002 TGATACAAAT
*
3432012 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3432038 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3432064 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3432090 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3432116 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3432142 TGATAA
1 TGATAA
3432148 GAATATCATG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3434172 original size:137 final size:137
Alignment explanation
Indices: 3433926--3434212 Score: 547
Period size: 137 Copynumber: 2.1 Consensus size: 137
3433916 GAGTAGTCTC
3433926 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
3433991 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
3434056 ACTGTTA
131 ACTGTTA
*
3434063 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTGTGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
3434128 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
3434193 ACTGTTA
131 ACTGTTA
**
3434200 CCTGAATGGGCTT
1 CCCAAATGGGCTT
3434213 AGGCCCAATA
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 147 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:3438026 original size:26 final size:26
Alignment explanation
Indices: 3437939--3438072 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
3437929 TGATACAAAT
3437939 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3437965 TGATAAT-GGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
3437989 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3438015 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3438041 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3438067 TGATAA
1 TGATAA
3438073 GAATTCATGT
Statistics
Matches: 104, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
24 9 0.09
25 30 0.29
26 65 0.62
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:3442673 original size:26 final size:26
Alignment explanation
Indices: 3442604--3442738 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
3442594 TGATACAAAT
3442604 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3442630 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3442655 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3442681 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3442707 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3442733 TGATAA
1 TGATAA
3442739 GAATTCATGT
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
25 25 0.24
26 81 0.76
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:3444249 original size:26 final size:26
Alignment explanation
Indices: 3444220--3444272 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3444210 TTTACAGTTT
3444220 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
3444246 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
3444272 T
1 T
3444273 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:3444763 original size:134 final size:136
Alignment explanation
Indices: 3444520--3444803 Score: 527
Period size: 134 Copynumber: 2.1 Consensus size: 136
3444510 GAGTAGTCTC
3444520 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTA-TGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
3444585 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
65 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
3444650 ACTGTTA
130 ACTGTTA
3444657 CCCAAATGGGCTTGCATATG-TT-TGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCCAAATGGGCTTGCATATGTTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
3444720 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
3444785 CTGTTA
131 CTGTTA
**
3444791 CCTGAATGGGCTT
1 CCCAAATGGGCTT
3444804 AGGCCCAATA
Statistics
Matches: 145, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
134 123 0.85
136 2 0.01
137 20 0.14
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTTATGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Done.