Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 200 of 210
Found at i:58830223 original size:18 final size:19
Alignment explanation
Indices: 58830185--58830223 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58830175 TTTTATTTAA
*
58830185 TTGAATTTTACCATTAATT
1 TTGAATTTTACCATAAATT
*
58830204 TTGAATTTTACTA-AAATT
1 TTGAATTTTACCATAAATT
58830222 TT
1 TT
58830224 CCACTAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (19 bp):
TTGAATTTTACCATAAATT
Found at i:58833515 original size:112 final size:111
Alignment explanation
Indices: 58833365--58833606 Score: 310
Period size: 112 Copynumber: 2.2 Consensus size: 111
58833355 TAAACTTTGG
* * * *
58833365 TGCCGCCATAC-TGTCAGGC-GGCACCCTTAAGCGCTTTTTCGGTTGCCAATTAAGAAAGGAAAT
1 TGCCGCCA-ACATGTCAAGCAGG-ACCCTTAAGCGCTTTTTCAGTTGCCAATTAAAAAAGAAAAT
* * * *
58833428 TTGCATATGAGGTCCCTAGAATTTTTAGATCATCACATTTTAGTCA-A
64 TTACAGATAAGGTCCCTAAAATTTTTAGATCATCACATTTTAGTCAGA
* *
58833475 GTGCTGCCAACATGTCAAGCAGGACCCTTCAAGCGTTTTTTCAGTTGCCAATTAAAAAAGAAAAT
1 -TGCCGCCAACATGTCAAGCAGGACCCTT-AAGCGCTTTTTCAGTTGCCAATTAAAAAAGAAAAT
* *
58833540 TTACAGATAAGGTCTCTAAAATTTTTAGATCATCACATTTTAGTCTGA
64 TTACAGATAAGGTCCCTAAAATTTTTAGATCATCACATTTTAGTCAGA
*
58833588 TGCCGCCAATATGTCAAGC
1 TGCCGCCAACATGTCAAGC
58833607 GACACCGTCA
Statistics
Matches: 113, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
110 2 0.02
111 20 0.18
112 90 0.80
113 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (111 bp):
TGCCGCCAACATGTCAAGCAGGACCCTTAAGCGCTTTTTCAGTTGCCAATTAAAAAAGAAAATTT
ACAGATAAGGTCCCTAAAATTTTTAGATCATCACATTTTAGTCAGA
Found at i:58838990 original size:20 final size:21
Alignment explanation
Indices: 58838952--58839000 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
58838942 TTTTAAAAAT
58838952 ATTTTTATATTTACTTTTAAA
1 ATTTTTATATTTACTTTTAAA
58838973 ATTTTTA-ATTTA-TATTT-AA
1 ATTTTTATATTTACT-TTTAAA
*
58838992 CTTTTTATA
1 ATTTTTATA
58839001 ATCCATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.36
20 9 0.36
21 7 0.28
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTTATATTTACTTTTAAA
Found at i:58840071 original size:14 final size:15
Alignment explanation
Indices: 58840052--58840083 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
58840042 CATGTTTCTC
58840052 TTTA-TTTTTAAATA
1 TTTATTTTTTAAATA
58840066 TTTATTTTTTAAATA
1 TTTATTTTTTAAATA
58840081 TTT
1 TTT
58840084 TACTATACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTTTTTAAATA
Found at i:58840727 original size:20 final size:22
Alignment explanation
Indices: 58840692--58840749 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
58840682 ACAAAATATA
58840692 TTTAT-ATTTA-ATTTTAAAC-T
1 TTTATAATTTATA-TTTAAACTT
58840712 TTT-TAATTTATATTT-AACTTT
1 TTTATAATTTATATTTAAAC-TT
58840733 TTTATAATTTATATTTA
1 TTTATAATTTATATTTA
58840750 CATTTTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.12
20 11 0.34
21 5 0.16
22 12 0.38
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATAATTTATATTTAAACTT
Found at i:58851455 original size:34 final size:33
Alignment explanation
Indices: 58851396--58851468 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
58851386 AAAAAAATGT
*
58851396 TATTTTTTTGTTGTTTTATTATTGTTTTGATGC
1 TATTTTTTTGTTGTTTTATTATTGTTTTGATAC
* * * *
58851429 TATTTTCTTTTTTGTTTTCTTGTTGTTTTGCTAC
1 TATTTT-TTTGTTGTTTTATTATTGTTTTGATAC
58851463 TATTTT
1 TATTTT
58851469 ACTATTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 6 0.18
34 28 0.82
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.71
Consensus pattern (33 bp):
TATTTTTTTGTTGTTTTATTATTGTTTTGATAC
Found at i:58857428 original size:17 final size:19
Alignment explanation
Indices: 58857393--58857456 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 19
58857383 ATTAATATCC
58857393 AAAT-AAGTAAATAAAAGA
1 AAATAAAGTAAATAAAAGA
58857411 AAATAAAGT-AAT-AAAGA
1 AAATAAAGTAAATAAAAGA
58857428 AAATAAAG-AAA-AATAA-A
1 AAATAAAGTAAATAA-AAGA
*
58857445 AAATAAAATAAA
1 AAATAAAGTAAA
58857457 AATTGGGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 24 0.60
18 12 0.30
19 4 0.10
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.16
Consensus pattern (19 bp):
AAATAAAGTAAATAAAAGA
Found at i:58857432 original size:9 final size:9
Alignment explanation
Indices: 58857401--58857444 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
58857391 CCAAATAAGT
58857401 AAATAAAAGA
1 AAAT-AAAGA
58857411 AAATAAAG-
1 AAATAAAGA
*
58857419 TAATAAAGA
1 AAATAAAGA
58857428 AAATAAAGAA
1 AAATAAAG-A
58857438 AAATAAA
1 AAATAAA
58857445 AAATAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.23
9 11 0.37
10 12 0.40
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (9 bp):
AAATAAAGA
Found at i:58857454 original size:22 final size:22
Alignment explanation
Indices: 58857401--58857457 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
58857391 CCAAATAAGT
* * *
58857401 AAATAAAAGAAAATAAAGTAAT
1 AAATAAAATAAAATAAAATAAA
*
58857423 AAAGAAAATAAAGA-AAAATAAA
1 AAATAAAATAAA-ATAAAATAAA
58857445 AAATAAAATAAAA
1 AAATAAAATAAAA
58857458 ATTGGGTTGC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.03
22 27 0.93
23 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (22 bp):
AAATAAAATAAAATAAAATAAA
Found at i:58870447 original size:71 final size:71
Alignment explanation
Indices: 58870331--58870490 Score: 239
Period size: 71 Copynumber: 2.3 Consensus size: 71
58870321 AATACTTCGT
* * *
58870331 TTTTGTCTTCGCATCATAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
1 TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTATGATGAAGTCAGACTATAAATAACAAT
58870396 GTTGAA
66 GTTGAA
* * *
58870402 TTTTGTCTTTGCATCTTAACTCATAAGCTAGTAGATTATGATGAAGTCAGACTTTAAATAACAGT
1 TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTATGATGAAGTCAGACTATAAATAACAAT
*
58870467 GTTGGA
66 GTTGAA
**
58870473 TTTTAACTTTGCATCTTA
1 TTTTGTCTTTGCATCTTA
58870491 TTGTATCAGT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 80 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (71 bp):
TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTATGATGAAGTCAGACTATAAATAACAAT
GTTGAA
Found at i:58874424 original size:37 final size:37
Alignment explanation
Indices: 58874374--58874450 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
58874364 TCAACAAGGC
58874374 TCAATGATGATGCATGGTTGTGACACTTTTGCTATGG
1 TCAATGATGATGCATGGTTGTGACACTTTTGCTATGG
58874411 TCAATGATGATGCATGGTTGTGACACTTTTGCTATGG
1 TCAATGATGATGCATGGTTGTGACACTTTTGCTATGG
58874448 TCA
1 TCA
58874451 TCTAAATTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (37 bp):
TCAATGATGATGCATGGTTGTGACACTTTTGCTATGG
Found at i:58882955 original size:162 final size:162
Alignment explanation
Indices: 58882681--58883218 Score: 880
Period size: 162 Copynumber: 3.3 Consensus size: 162
58882671 TGCGCCCAAT
* * * *
58882681 TTGCAAACTCTGAGGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAATACTCACAAGTATC
1 TTGCAAACTCTAAAGATAGAGAGCTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
58882746 AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
66 AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
58882811 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
58882843 TTGCAAACTCTAAAGATAGAGAGCTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
1 TTGCAAACTCTAAAGATAGAGAGCTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
* *
58882908 AACCATAAGCTTCCAATGCCTAAGGGAATTACAAGTCACAAAATGCAATAAATTGAAATTTCTCT
66 AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
*
58882973 TCTCAATGTGTGTTGCTAATAGTCTTGGGAAA
131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
* * *
58883005 TTACAAACTCTAAAGATAGAGAGGTGCTTTGGAATGGAAGAAATAATCCAAGACTTACAAGTATC
1 TTGCAAACTCTAAAGATAGAGAGCTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
* * *
58883070 TACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAGTTAAAATTTCTCT
66 AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
* *
58883135 TCCCAATGTGTGTTGCTAATAGTCTCGGGCAA
131 TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
* *** *
58883167 TTGCAAACTCTAAGGATAGAGAGCTG-TTCCCAATTGCAAGAAATAATCCAAG
1 TTGCAAACTCTAAAGATAGAGAGCTGCTTTGGAA-TGGAAGAAATAATCCAAG
58883219 GACCGGAAGT
Statistics
Matches: 350, Mismatches: 25, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
161 4 0.01
162 346 0.99
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (162 bp):
TTGCAAACTCTAAAGATAGAGAGCTGCTTTGGAATGGAAGAAATAATCCAAGACTCACAAGTATC
AACCATAAGCTTCCAATGCCTAAGGGAAGTACAAGTCACAGAATGCAATAAATTGAAATTTCTCT
TCCCAATGTGTGTTGCTAATAGTCTTGGGAAA
Found at i:58886623 original size:29 final size:29
Alignment explanation
Indices: 58886581--58886637 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
58886571 TCACTATACA
58886581 GAATGAAGATTCCTCACTCTTGTACCTTT
1 GAATGAAGATTCCTCACTCTTGTACCTTT
*
58886610 GAATGATGATTCCTCACTCTTGTACCTT
1 GAATGAAGATTCCTCACTCTTGTACCTT
58886638 CGAAGACTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (29 bp):
GAATGAAGATTCCTCACTCTTGTACCTTT
Found at i:58887303 original size:21 final size:20
Alignment explanation
Indices: 58887279--58887317 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58887269 TTTCTCTCAC
*
58887279 TTATCTATCTTTTTTTTAAAA
1 TTATCTAT-TTTTATTTAAAA
58887300 TTATCTATTTTTATTTAA
1 TTATCTATTTTTATTTAA
58887318 TTTTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATCTATTTTTATTTAAAA
Found at i:58906860 original size:36 final size:35
Alignment explanation
Indices: 58906783--58906861 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
58906773 GACAACTTGC
* *
58906783 ACTTAGTCAATCCTCCAGGCTTAAACAATACACCG
1 ACTTAGTCAATCCACCAGGCTTAAACAATACACAG
* * * *
58906818 AGCTTAGTCAATGCACTAGGCTTAGACAATACGTCAG
1 A-CTTAGTCAATCCACCAGGCTTAAACAATAC-ACAG
58906855 ACTTAGT
1 ACTTAGT
58906862 AAATACAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
35 1 0.03
36 32 0.89
37 3 0.08
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (35 bp):
ACTTAGTCAATCCACCAGGCTTAAACAATACACAG
Found at i:58906916 original size:19 final size:19
Alignment explanation
Indices: 58906877--58906916 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58906867 CAATATGCCA
**
58906877 GGTGTAGTCAATTACGTTG
1 GGTGTAGTCAATTACACTG
*
58906896 GGTGTAGTTAATTACACTG
1 GGTGTAGTCAATTACACTG
58906915 GG
1 GG
58906917 CTTAGTCCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.35
Consensus pattern (19 bp):
GGTGTAGTCAATTACACTG
Found at i:58910181 original size:72 final size:68
Alignment explanation
Indices: 58910045--58910182 Score: 188
Period size: 72 Copynumber: 2.0 Consensus size: 68
58910035 ATGTATATCG
* * *
58910045 TCTAGCTTATTCATTGGGGTAATATAATTTTCTTCATGATTCATCCAAAAATCACGTCAAAGAAT
1 TCTAGCTTATTCATTGCGGCAATATAATTTTCTTCATGATTCATCCAAAAATCACGCCAAAGAAT
58910110 CCT
66 CCT
*
58910113 TCTAGTTTATTCATTGCGGCAATATAACTTTT-TTCATGGGTGATTCATCCAAAAATCACGCCAA
1 TCTAGCTTATTCATTGCGGCAATATAA-TTTTCTTCA----TGATTCATCCAAAAATCACGCCAA
58910177 AGAATC
61 AGAATC
58910183 TTTTCTTACA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
68 28 0.46
69 4 0.07
72 29 0.48
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (68 bp):
TCTAGCTTATTCATTGCGGCAATATAATTTTCTTCATGATTCATCCAAAAATCACGCCAAAGAAT
CCT
Found at i:58910290 original size:13 final size:14
Alignment explanation
Indices: 58910267--58910299 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
58910257 ATCCAAAAAA
58910267 AAAATTAAAATTAT
1 AAAATTAAAATTAT
58910281 AAAATT-AAATTAT
1 AAAATTAAAATTAT
58910294 AAAATT
1 AAAATT
58910300 TTGAGAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTAAAATTAT
Found at i:58915108 original size:51 final size:51
Alignment explanation
Indices: 58915053--58915486 Score: 481
Period size: 50 Copynumber: 8.6 Consensus size: 51
58915043 CTGATACATG
* * *
58915053 TAGTAGCCTGCATATAATACTACACACGTGATCGAAGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
* * ** * * * *
58915104 TAGTAGCCTGCACATAGTACTACACATGCGA-CCCATC-ATTCTGGTGCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTC-GGTACGCA
58915154 TAGTAG-CTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
* * ** * * *
58915204 TAGTAGCCTGCACATAGTACTACACATGCGA-CCCATC-ATTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTA-TTCGGTACGCA
58915254 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
* * ** * * *
58915305 TAGTAACCTGCACATAGTACTACACATGTGA-CCCATC-ATTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTA-TTCGGTACGCA
58915355 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
* * ** * * *
58915406 TAGTAGCCTGCACATAGTACTACACATGCGA-CCCATC-ATTCAGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTC-GGTACGCA
58915456 TAGTAGCCTGCACATAGTACTACACACGTGA
1 TAGTAGCCTGCACATAGTACTACACACGTGA
58915487 CCATCACTTT
Statistics
Matches: 316, Mismatches: 56, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
49 31 0.10
50 148 0.47
51 135 0.43
52 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATTCGGTACGCA
Found at i:58915250 original size:50 final size:50
Alignment explanation
Indices: 58914992--58915497 Score: 456
Period size: 51 Copynumber: 10.0 Consensus size: 50
58914982 TCAATGATAC
* * * *
58914992 TCGGTTCACATAGTAGCCTACACATAGTACTACTCATGTGA-CCATTTCCATC
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCCA--T-CATT
* ** * * * ** *
58915044 T-GATACATGTAGTAGCCTGCATATAATACTACACACGTGATCGAAGC-TAT
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCCATCAT-T
* * *
58915094 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCCATCA-T
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCCATCATT
* * * ** *
58915143 TCTGGTGCACGTAGTAG-CTGCACATAGTACTACACACGTGATCGAAGC-TAT
1 TC-GGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCCATCAT-T
* *
58915194 TCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATT
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCCATCATT
* * ** *
58915244 TCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TAT
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCCATCAT-T
* *
58915295 TCGGTACGCATAGTAACCTGCACATAGTACTACACATGTGACCCATCATT
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCCATCATT
* * ** *
58915345 TCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TAT
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCCATCAT-T
* *
58915396 TCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCCATCA-T
1 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCCATCATT
* *
58915445 TCAGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCACTT
1 TC-GGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCCATCA-TT
58915496 TC
1 TC
58915498 ACTTTTACAT
Statistics
Matches: 360, Mismatches: 74, Indels: 41
0.76 0.16 0.09
Matches are distributed among these distances:
49 34 0.09
50 151 0.42
51 173 0.48
52 1 0.00
53 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (50 bp):
TCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCCATCATT
Found at i:58915510 original size:101 final size:101
Alignment explanation
Indices: 58915000--58915486 Score: 786
Period size: 101 Copynumber: 4.8 Consensus size: 101
58914990 ACTCGGTTCA
* * * * * *
58915000 CATAGTAGCCTACACATAGTACTACTCATGTGA-CCATTTCCATCT-GATACATGTAGTAGCCTG
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCCA--T-CATTTCGGTACACGTAGTAGCCTG
* * *
58915063 CATATAATACTACACACGTGATCGAAGCTATCCGGTACG
63 CACATAGTACTACACACGTGATCGAAGCTATTCGGTACG
*
58915102 CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCA-TTCTGGTGCACGTAGTAG-CTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTTC-GGTACACGTAGTAGCCTGCA
58915165 CATAGTACTACACACGTGATCGAAGCTATTCGGTACG
65 CATAGTACTACACACGTGATCGAAGCTATTCGGTACG
58915202 CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTTCGGTACACGTAGTAGCCTGCAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTTCGGTACACGTAGTAGCCTGCAC
58915267 ATAGTACTACACACGTGATCGAAGCTATTCGGTACG
66 ATAGTACTACACACGTGATCGAAGCTATTCGGTACG
* *
58915303 CATAGTAACCTGCACATAGTACTACACATGTGACCCATCATTTCGGTACACGTAGTAGCCTGCAC
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTTCGGTACACGTAGTAGCCTGCAC
58915368 ATAGTACTACACACGTGATCGAAGCTATTCGGTACG
66 ATAGTACTACACACGTGATCGAAGCTATTCGGTACG
58915404 CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCA-TTCAGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTTC-GGTACACGTAGTAGCCTGCA
58915468 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
58915487 CCATCACTTT
Statistics
Matches: 364, Mismatches: 15, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
99 1 0.00
100 97 0.27
101 233 0.64
102 30 0.08
103 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCCATCATTTCGGTACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATTCGGTACG
Found at i:58923955 original size:17 final size:18
Alignment explanation
Indices: 58923933--58923968 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
58923923 GAGACTTTAA
58923933 TGAAAGAGGTGA-AATGT
1 TGAAAGAGGTGACAATGT
*
58923950 TGAAAGTGGTGACAATGT
1 TGAAAGAGGTGACAATGT
58923968 T
1 T
58923969 TCCCTCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.36, C:0.03, G:0.33, T:0.28
Consensus pattern (18 bp):
TGAAAGAGGTGACAATGT
Found at i:58930016 original size:19 final size:19
Alignment explanation
Indices: 58929992--58930058 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
58929982 GACTTAGGAA
58929992 TCAATATCCAATGCCGATT
1 TCAATATCCAATGCCGATT
* **
58930011 TCAATATCCAATGCCTCAAA
1 TCAATATCCAATGCC-GATT
58930031 TCAATATCCAATGCCGATT
1 TCAATATCCAATGCCGATT
58930050 TCAATATCC
1 TCAATATCC
58930059 GATTTCTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.30
Consensus pattern (19 bp):
TCAATATCCAATGCCGATT
Found at i:58930036 original size:20 final size:19
Alignment explanation
Indices: 58929990--58930045 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
58929980 CTGACTTAGG
*
58929990 AATCAATATCCAATGCCGA
1 AATCAATATCCAATGCCCA
**
58930009 TTTCAATATCCAATGCCTCA
1 AATCAATATCCAATGCC-CA
58930029 AATCAATATCCAATGCC
1 AATCAATATCCAATGCC
58930046 GATTTCAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.27
Consensus pattern (19 bp):
AATCAATATCCAATGCCCA
Found at i:58934803 original size:18 final size:18
Alignment explanation
Indices: 58934774--58934808 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
58934764 ATTACTACAA
58934774 ATAAAAATTT-AATATTT
1 ATAAAAATTTAAATATTT
58934791 ATAAAATATTTAAATATT
1 ATAAAA-ATTTAAATATT
58934809 AAATATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAAAATTTAAATATTT
Found at i:58941034 original size:30 final size:29
Alignment explanation
Indices: 58940961--58941044 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 29
58940951 TACTTATCAC
*
58940961 ATAAAAATTCTAAATT-ATTTTTTATATT
1 ATAAAAATTCTAAATTAATTTATTATATT
* ** * *
58940989 TTAATATTTTATAAATTAACTTATTATATT
1 ATAA-AAATTCTAAATTAATTTATTATATT
58941019 AATAAAAATTCTAAATTAATTTATTA
1 -ATAAAAATTCTAAATTAATTTATTA
58941045 AATTTTATAA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
28 3 0.07
29 9 0.21
30 27 0.64
31 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAAAATTCTAAATTAATTTATTATATT
Found at i:58941046 original size:22 final size:22
Alignment explanation
Indices: 58941021--58941066 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
58941011 ATTATATTAA
* *
58941021 TAAAAATTCTAAATTAATTTAT
1 TAAAAATTATAAATTAACTTAT
**
58941043 TAAATTTTATAAATTAACTTAT
1 TAAAAATTATAAATTAACTTAT
58941065 TA
1 TA
58941067 TTAACTATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAAATTATAAATTAACTTAT
Found at i:58941195 original size:7 final size:7
Alignment explanation
Indices: 58941183--58941208 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
58941173 ATAATTGTTT
58941183 TTATTAA
1 TTATTAA
58941190 TTATTAA
1 TTATTAA
58941197 TTATTAA
1 TTATTAA
58941204 TTATT
1 TTATT
58941209 GATAATATAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATTAA
Found at i:58942428 original size:14 final size:15
Alignment explanation
Indices: 58942400--58942429 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58942390 ACATTGATTA
58942400 GAACAAGATTTTTTT
1 GAACAAGATTTTTTT
58942415 GAACAAGATTTTTTT
1 GAACAAGATTTTTTT
58942430 AACCTTTAAA
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:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
GAACAAGATTTTTTT
Found at i:58948883 original size:21 final size:20
Alignment explanation
Indices: 58948857--58948899 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
58948847 ACTTTTAAAA
*
58948857 TTTTAATTTATATTTAACTTT
1 TTTTAATTCATATTT-ACTTT
58948878 TTTTAATTCATATTTACTTT
1 TTTTAATTCATATTTACTTT
58948898 TT
1 TT
58948900 CTCATCAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATTCATATTTACTTT
Found at i:58950118 original size:16 final size:16
Alignment explanation
Indices: 58950097--58950127 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58950087 TGTTTCTCTT
58950097 TATTTTTAAATATTTA
1 TATTTTTAAATATTTA
58950113 TATTTTTAAATATTT
1 TATTTTTAAATATTT
58950128 TACTATACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAAATATTTA
Found at i:58951655 original size:20 final size:20
Alignment explanation
Indices: 58951621--58951670 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
58951611 AACTGGAAAT
*
58951621 AAATTTTATTTATTTT-TAAA
1 AAATTTTA-TAATTTTATAAA
*
58951641 AAATATTTATAATTTTATGAA
1 AAAT-TTTATAATTTTATAAA
58951662 AAATTTTAT
1 AAATTTTAT
58951671 TTACAGACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AAATTTTATAATTTTATAAA
Found at i:58954758 original size:16 final size:17
Alignment explanation
Indices: 58954737--58954768 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
58954727 ATCGTTTTCC
58954737 AAAAGAAAAA-AAAAGA
1 AAAAGAAAAATAAAAGA
58954753 AAAAGAAAAATAAAAG
1 AAAAGAAAAATAAAAG
58954769 CAACAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAATAAAAGA
Found at i:58957280 original size:26 final size:23
Alignment explanation
Indices: 58957251--58957298 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
58957241 TACTTAAAAA
58957251 TAATAAATTAATATATTATTAATAAT
1 TAATAAA--AATA-ATTATTAATAAT
*
58957277 TAATAAAAATAATTATTCATAA
1 TAATAAAAATAATTATTAATAA
58957299 AAAGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 4 0.19
26 7 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAAATAATTATTAATAAT
Found at i:58957432 original size:31 final size:31
Alignment explanation
Indices: 58957397--58957493 Score: 106
Period size: 31 Copynumber: 3.2 Consensus size: 31
58957387 AATAAGTTAA
58957397 TTTATAAAATATAATAAATTAATTTAGAATT
1 TTTATAAAATATAATAAATTAATTTAGAATT
** * * **
58957428 TTTATTGAATATAATAACTTAATTTATAAAA
1 TTTATAAAATATAATAAATTAATTTAGAATT
* * *
58957459 TAT-TAAAATATAAAAAAATAATTTAGAATT
1 TTTATAAAATATAATAAATTAATTTAGAATT
58957489 TTTAT
1 TTTAT
58957494 GTGATAAATA
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
30 21 0.43
31 28 0.57
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTATAAAATATAATAAATTAATTTAGAATT
Found at i:58970846 original size:37 final size:36
Alignment explanation
Indices: 58970745--58970858 Score: 95
Period size: 40 Copynumber: 3.0 Consensus size: 36
58970735 TTAAATCAAG
* * * *
58970745 TTTAATATTATTATATTGATAAT-AAATTTTATTTTT
1 TTTAATATTATTAAAAT-ATAATAAAATATTATATTT
* *
58970781 TTTAAAAATATTTAAAATATTAATATAAAATATTATATTT
1 TTTAATATTA-TTAAAATA-T-A-ATAAAATATTATATTT
*
58970821 TTTAATATTATTAAACATATAATAAATTATTTATATTT
1 TTTAATATTATTAAA-ATATAATAAAATA-TTATATTT
58970859 AGTCATATAA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
36 9 0.15
37 13 0.21
38 10 0.16
39 8 0.13
40 22 0.35
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (36 bp):
TTTAATATTATTAAAATATAATAAAATATTATATTT
Found at i:58971517 original size:14 final size:14
Alignment explanation
Indices: 58971498--58971533 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
58971488 GAAAAGTAAG
58971498 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
* *
58971512 TCATTTTCCGGAAG
1 TCATTTTCCAGAAA
58971526 TCATTTTC
1 TCATTTTC
58971534 AGTGAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:58973521 original size:22 final size:22
Alignment explanation
Indices: 58973496--58973622 Score: 182
Period size: 22 Copynumber: 5.8 Consensus size: 22
58973486 CCAAATTAAG
58973496 ACTAAGCTCTCATGTTTAACGT
1 ACTAAGCTCTCATGTTTAACGT
*
58973518 ACTAAGCTCTCATGTTTAACGA
1 ACTAAGCTCTCATGTTTAACGT
* * **
58973540 ACTAAACCCTCATGGCTAACGT
1 ACTAAGCTCTCATGTTTAACGT
**
58973562 ACTAAGCTCTCATGGCTAACGT
1 ACTAAGCTCTCATGTTTAACGT
*
58973584 ACTAAGCTCTCATGTTTCACGT
1 ACTAAGCTCTCATGTTTAACGT
58973606 ACTAAGCTCTCATGTTT
1 ACTAAGCTCTCATGTTT
58973623 GAACAATAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 94 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (22 bp):
ACTAAGCTCTCATGTTTAACGT
Found at i:58993480 original size:18 final size:18
Alignment explanation
Indices: 58993457--58993503 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
58993447 AATTACACTG
58993457 GGCTTAGTCAATATGCCA
1 GGCTTAGTCAATATGCCA
* * * *
58993475 GGCTTAGACAGTATGTCG
1 GGCTTAGTCAATATGCCA
58993493 GGCTTAGTCAA
1 GGCTTAGTCAA
58993504 CTCACCACTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (18 bp):
GGCTTAGTCAATATGCCA
Found at i:59009269 original size:109 final size:109
Alignment explanation
Indices: 59009073--59009291 Score: 411
Period size: 109 Copynumber: 2.0 Consensus size: 109
59009063 GAAAAGTAAA
*
59009073 CAAAGTTGATTAGAAATATCGTGTTGAACCATTCCTGATTAATTGTCAATGGGGGGCTCCATAGT
1 CAAAGTTGATTAGAAATATCGTGTTGAACCACTCCTGATTAATTGTCAATGGGGGGCTCCATAGT
*
59009138 TGTGATCCTACTGGAACCATACTTCGTTTACTTTGAAGTCTCCC
66 TGTGATCCTACTGGAACCATACTGCGTTTACTTTGAAGTCTCCC
59009182 CAAAGTTGATTAGAAATATCGTGTTGAACCACTCCTGATTAATTGTCAATGGGGGGCTCCATAGT
1 CAAAGTTGATTAGAAATATCGTGTTGAACCACTCCTGATTAATTGTCAATGGGGGGCTCCATAGT
*
59009247 TGTGATCCTACTGGAACTATACTGCGTTTACTTTGAAGTCTCCC
66 TGTGATCCTACTGGAACCATACTGCGTTTACTTTGAAGTCTCCC
59009291 C
1 C
59009292 TTATCATTTT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (109 bp):
CAAAGTTGATTAGAAATATCGTGTTGAACCACTCCTGATTAATTGTCAATGGGGGGCTCCATAGT
TGTGATCCTACTGGAACCATACTGCGTTTACTTTGAAGTCTCCC
Found at i:59010208 original size:122 final size:124
Alignment explanation
Indices: 59009922--59010387 Score: 783
Period size: 124 Copynumber: 3.8 Consensus size: 124
59009912 CGAGTTGATG
* * * * * *
59009922 TTTCTGATAAAATAGTATAAAATCGCTTTTAGCAGGATACTTTTTGAGAAGAATTTGTGAAATCG
1 TTTCTGAGAAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCA
* *
59009987 CGGCCTGGTGGACGCGCTTTTGCTATAGTAGGTCATGTAAGAAATAATTTTTTTCGACT
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACT
*
59010046 TTTCTGAGCAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCA
1 TTTCTGAGAAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCA
* *
59010111 CGGCCTCGTGGACGCGC-TTTGCTACAGTAGGTCATGTAATAAATAATTTTTTT-TACT
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACT
* *
59010168 TTTCTGAGAAAATAGTATAAAATCGCTTTTATCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGAGAAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCA
*
59010233 CGGCATCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACT
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACT
*
59010292 TTTCTGAGCAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCA
1 TTTCTGAGAAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCA
59010357 CGGCCTCGTGGACGCGCTTTTGCTACAGTAG
66 CGGCCTCGTGGACGCGCTTTTGCTACAGTAG
59010388 CATGTTTGGG
Statistics
Matches: 319, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
122 81 0.25
123 69 0.22
124 169 0.53
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (124 bp):
TTTCTGAGAAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCA
CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACT
Found at i:59010356 original size:246 final size:247
Alignment explanation
Indices: 59009922--59010387 Score: 862
Period size: 246 Copynumber: 1.9 Consensus size: 247
59009912 CGAGTTGATG
* *
59009922 TTTCTGATAAAATAGTATAAAATCGCTTTTAGCAGGATACTTTTTGAGAAGAATTTGTGAAATCG
1 TTTCTGAGAAAATAGTATAAAATCGCTTTTAGCAGGATACTATTTGAGAAGAATTTGTGAAATCG
* * *
59009987 CGGCCTGGTGGACGCGCTTTTGCTATAGTAGGTCATGTAAGAAATAATTTTTTTCGACTTTTCTG
66 CGGCATCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACTTTTCTG
59010052 AGCAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCACGGCCT
131 AGCAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCACGGCCT
59010117 CGTGGACGCGC-TTTGCTACAGTAGGTCATGTAATAAATAATTTTTTTTACT
196 CGTGGACGCGCTTTTGCTACAGTAGGTCATGTAATAAATAATTTTTTTTACT
* *
59010168 TTTCTGAGAAAATAGTATAAAATCGCTTTTATCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGAGAAAATAGTATAAAATCGCTTTTAGCAGGATACTATTTGAGAAGAATTTGTGAAATCG
59010233 CGGCATCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACTTTTCTG
66 CGGCATCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACTTTTCTG
59010298 AGCAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCACGGCCT
131 AGCAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCACGGCCT
59010363 CGTGGACGCGCTTTTGCTACAGTAG
196 CGTGGACGCGCTTTTGCTACAGTAG
59010388 CATGTTTGGG
Statistics
Matches: 212, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
246 199 0.94
247 13 0.06
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (247 bp):
TTTCTGAGAAAATAGTATAAAATCGCTTTTAGCAGGATACTATTTGAGAAGAATTTGTGAAATCG
CGGCATCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCGACTTTTCTG
AGCAAATAGTATAAAATCGCTTTTATCAAGATGCTATTTGAGAAGAATTTGTGAAATCACGGCCT
CGTGGACGCGCTTTTGCTACAGTAGGTCATGTAATAAATAATTTTTTTTACT
Found at i:59013333 original size:22 final size:22
Alignment explanation
Indices: 59013283--59013411 Score: 107
Period size: 22 Copynumber: 5.5 Consensus size: 22
59013273 AAATATGGAT
59013283 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
59013305 TTAAGAGAATTTTGGAAGGAAT
1 TTGAGAGAATTTTGGAAGGAAA
* * **
59013327 TTGAGAGGAA-ATTGAAATTAAATA
1 TTGAGA-GAATTTTGGAA-GGAA-A
59013351 TGGTTTTGAGAGAATTTTGGAAGGAAA
1 -----TTGAGAGAATTTTGGAAGGAAA
*
59013378 TTGAGAGAATTTTGGAAAGAAA
1 TTGAGAGAATTTTGGAAGGAAA
59013400 TTGAGAGGAATT
1 TTGAGA-GAATT
59013412 GAGAGGAAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 19
0.72 0.11 0.16
Matches are distributed among these distances:
22 57 0.68
23 10 0.12
27 1 0.01
28 5 0.06
29 11 0.13
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:59013333 original size:73 final size:73
Alignment explanation
Indices: 59013247--59013413 Score: 282
Period size: 73 Copynumber: 2.3 Consensus size: 73
59013237 TATTTTAAAA
59013247 AAAGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATTAAGAG
1 AAAGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATTAAGAG
59013312 AATTTTGG
66 AATTTTGG
* * * * *
59013320 AAGGAATTTGAGAGGAAATTGAAATTAAATATGGTTTTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AAAGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATTAAGAG
59013385 AATTTTGG
66 AATTTTGG
59013393 AAAGAAATTGAGAGG-AATTGA
1 AAAGAAATTGAGAGGAAATTGA
59013414 GAGGAAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
72 6 0.07
73 81 0.93
ACGTcount: A:0.44, C:0.01, G:0.28, T:0.28
Consensus pattern (73 bp):
AAAGAAATTGAGAGGAAATTGAAATCAAATATGGATTTGAGAGAATTTTGGAAGGAAATTAAGAG
AATTTTGG
Found at i:59013428 original size:12 final size:11
Alignment explanation
Indices: 59013396--59013428 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
59013386 ATTTTGGAAA
59013396 GAAATTGAGAG
1 GAAATTGAGAG
59013407 G-AATTGAGAG
1 GAAATTGAGAG
59013417 GAAATATGAGAG
1 GAAAT-TGAGAG
59013429 AGGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
11 4 0.20
12 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:59018044 original size:23 final size:24
Alignment explanation
Indices: 59018018--59018071 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
59018008 TATATATTAA
59018018 ATTAAAAA-GTAAATTGGTTTTTT
1 ATTAAAAATGTAAATTGGTTTTTT
* * * *
59018041 ATTAAAAATTTTATTTGTTTTTTT
1 ATTAAAAATGTAAATTGGTTTTTT
59018065 ATTAAAA
1 ATTAAAA
59018072 GTTGTTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (24 bp):
ATTAAAAATGTAAATTGGTTTTTT
Found at i:59019531 original size:3 final size:3
Alignment explanation
Indices: 59019523--59019553 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59019513 AATTGAACAC
59019523 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
59019554 GAAATGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59020602 original size:6 final size:6
Alignment explanation
Indices: 59020591--59020620 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
59020581 TACAACATTT
59020591 TTTTTC TTTTTC TTTTTC TTTTTC TGTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTT
59020621 TGCCATACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:59024595 original size:26 final size:24
Alignment explanation
Indices: 59024566--59024625 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
59024556 AAAAATATTT
59024566 ATTTTATTTTATTTTAATATTTAATA
1 ATTTTATTTTATTTT--TATTTAATA
**
59024592 ATTTTA-TACATTTTTATTTAATA
1 ATTTTATTTTATTTTTATTTAATA
59024615 ATTTT-TTTTAT
1 ATTTTATTTTAT
59024626 ATAGTCATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 17 0.59
25 6 0.21
26 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTTATTTTATTTTTATTTAATA
Found at i:59025410 original size:20 final size:21
Alignment explanation
Indices: 59025372--59025411 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59025362 TTTAAAATTT
*
59025372 TAATTTATATTTAACTTTTTA
1 TAATTCATATTTAACTTTTTA
59025393 TAATTCATATTT-ACTTTTT
1 TAATTCATATTTAACTTTTT
59025412 CTTATCAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTCATATTTAACTTTTTA
Found at i:59027639 original size:29 final size:28
Alignment explanation
Indices: 59027586--59027645 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
59027576 GTTTTTTACT
59027586 AAAATAATATAAAAATAATCAATTACGA
1 AAAATAATATAAAAATAATCAATTACGA
59027614 AAAAT-ATATAGAAAATAGAAT-AATTACGA
1 AAAATAATATA-AAAAT--AATCAATTACGA
59027643 AAA
1 AAA
59027646 TAGACATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 5 0.17
28 10 0.34
29 11 0.38
30 3 0.10
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (28 bp):
AAAATAATATAAAAATAATCAATTACGA
Found at i:59027646 original size:28 final size:26
Alignment explanation
Indices: 59027581--59027647 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 26
59027571 TAAGGGTTTT
*
59027581 TTACTAAAATAATATAAAAATAATCAA
1 TTACGAAAAT-ATATAAAAATAATCAA
59027608 TTACGAAAAATATATAGAAAATAGAAT-AA
1 TTACG-AAAATATATA-AAAAT--AATCAA
59027637 TTACGAAAATA
1 TTACGAAAATA
59027648 GACATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 9 0.26
28 16 0.46
29 7 0.20
30 3 0.09
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (26 bp):
TTACGAAAATATATAAAAATAATCAA
Found at i:59028275 original size:20 final size:21
Alignment explanation
Indices: 59028237--59028276 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59028227 TTTAAAATTT
*
59028237 TAATTTATATTTAACTTTTTA
1 TAATTCATATTTAACTTTTTA
59028258 TAATTCATATTT-ACTTTTT
1 TAATTCATATTTAACTTTTT
59028277 CTCATCAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATTCATATTTAACTTTTTA
Found at i:59028751 original size:13 final size:13
Alignment explanation
Indices: 59028733--59028758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59028723 AAAACAAACC
59028733 TTACGTGAAGCAA
1 TTACGTGAAGCAA
59028746 TTACGTGAAGCAA
1 TTACGTGAAGCAA
59028759 CTAAGGGAAG
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:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
TTACGTGAAGCAA
Found at i:59031220 original size:111 final size:111
Alignment explanation
Indices: 59030987--59031238 Score: 303
Period size: 111 Copynumber: 2.3 Consensus size: 111
59030977 CATTTTAAAC
* * * * *
59030987 TTTGGTGCCGCCATAC-TGTCAGGCGGCACCCTTAAGCGCTTTTTCGGTTGCCAATTAAGAAAGG
1 TTTGATGCCGCCA-ACATGTCAAGCGGCACCCTTAAGCGCTTTTTCAGTTGCCAATTAAAAAAGA
* * * * *
59031051 AAATTTGCATATGAGGTCCCTAGAATTTTTAGATCATCACATTTTAG
65 AAATTTACAAATAAGGTCCCTAAAATTTTCAGATCATCACATTTTAG
** * * *
59031098 -TCAAGTACCGCCAACATGTCAAGCGGGA-CCTTCAAGCGTTTTTTCAGTTGCCAATTAAAAAAG
1 TTTGA-TGCCGCCAACATGTCAAGCGGCACCCTT-AAGCGCTTTTTCAGTTGCCAATTAAAAAAG
59031161 AAAATTTACAAATAAGGTCCCTAAAATTTTCAGATCATCACATTTTAG
64 AAAATTTACAAATAAGGTCCCTAAAATTTTCAGATCATCACATTTTAG
* *
59031209 TTTGATGCCGCCAATATGTCAAGCGACACC
1 TTTGATGCCGCCAACATGTCAAGCGGCACC
59031239 GTCATAACAT
Statistics
Matches: 115, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
110 7 0.06
111 105 0.91
112 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (111 bp):
TTTGATGCCGCCAACATGTCAAGCGGCACCCTTAAGCGCTTTTTCAGTTGCCAATTAAAAAAGAA
AATTTACAAATAAGGTCCCTAAAATTTTCAGATCATCACATTTTAG
Found at i:59078088 original size:15 final size:16
Alignment explanation
Indices: 59078068--59078097 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59078058 AACCAAAACA
59078068 TTTTTTTAT-ATTTAC
1 TTTTTTTATAATTTAC
59078083 TTTTTTTATAATTTA
1 TTTTTTTATAATTTA
59078098 TATTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTATAATTTAC
Found at i:59078497 original size:11 final size:11
Alignment explanation
Indices: 59078483--59078509 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
59078473 TATTTAATTT
59078483 TAATTTTTTTA
1 TAATTTTTTTA
59078494 TAATTTTTTTA
1 TAATTTTTTTA
59078505 TAATT
1 TAATT
59078510 AGGACTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:59083732 original size:6 final size:6
Alignment explanation
Indices: 59083723--59083752 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59083713 GCTAGTGGTG
59083723 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA
1 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA
59083753 AGCTTAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
GTGGCA
Found at i:59084480 original size:2 final size:2
Alignment explanation
Indices: 59084473--59084499 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59084463 TCCCAATCTC
59084473 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59084500 CATTATAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59086419 original size:24 final size:24
Alignment explanation
Indices: 59086391--59086438 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
59086381 CTTGATGATG
59086391 AGCCACAAACTCTCAAATACGAAT
1 AGCCACAAACTCTCAAATACGAAT
59086415 AGCCACAAACTCTCAAATACGAAT
1 AGCCACAAACTCTCAAATACGAAT
59086439 CAATCTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.29, G:0.08, T:0.17
Consensus pattern (24 bp):
AGCCACAAACTCTCAAATACGAAT
Found at i:59090423 original size:71 final size:71
Alignment explanation
Indices: 59090294--59090453 Score: 266
Period size: 71 Copynumber: 2.3 Consensus size: 71
59090284 AATACTTCGT
* * *
59090294 TTTTTTCTTGGCATCATAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
1 TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
59090359 GTTGGA
66 GTTGGA
* *
59090365 TTTTGTCTTTGCATCTTAACTCATAAGCTAGTAGATTGTGATGAAGTCAGACTTTAAATAACAAT
1 TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
59090430 GTTGGA
66 GTTGGA
*
59090436 TTTTGACTTTGCATCTTA
1 TTTTGTCTTTGCATCTTA
59090454 TTGTATCAGT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 83 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (71 bp):
TTTTGTCTTTGCATCTTAACTCATAAGCTACTAGATTGTGATGAAGTCAGACTATAAATAACAAT
GTTGGA
Found at i:59092031 original size:3 final size:3
Alignment explanation
Indices: 59092023--59092053 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59092013 AATTGAACAC
59092023 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
59092054 GAAATGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59093101 original size:6 final size:6
Alignment explanation
Indices: 59093090--59093119 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
59093080 TACAACATTT
59093090 TTTTTC TTTTTC TTTTTC TTTTTC TGTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTT
59093120 TGCCATACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:59095396 original size:20 final size:20
Alignment explanation
Indices: 59095373--59095413 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
59095363 AAATATTCTA
59095373 AAAATAAGGTTTAAAAGGAG
1 AAAATAAGGTTTAAAAGGAG
59095393 AAAATAAGGTTTAAAAGGAG
1 AAAATAAGGTTTAAAAGGAG
59095413 A
1 A
59095414 TGTATATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (20 bp):
AAAATAAGGTTTAAAAGGAG
Found at i:59099711 original size:24 final size:25
Alignment explanation
Indices: 59099682--59099741 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
59099672 CTTTAAAAAT
*
59099682 TATTTTTATTTAATTACAA-TA-TA
1 TATTTTTATTTAATTAAAACTATTA
*
59099705 TATTTTTATTTTATTAAAACTATTTA
1 TATTTTTATTTAATTAAAACTA-TTA
59099731 TATTTTT-TTTA
1 TATTTTTATTTA
59099742 CAAATATAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 17 0.55
24 2 0.06
25 3 0.10
26 9 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTTTTATTTAATTAAAACTATTA
Found at i:59103554 original size:21 final size:21
Alignment explanation
Indices: 59103528--59103591 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
59103518 AGAACACGCC
*
59103528 AACAGAAGCTCGTGAGAGCTT
1 AACAGAAGCTCGTGAGAGCTG
*
59103549 AACAGAAGCTCGTTAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
* * *
59103570 AACAGAAACTCATAAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
59103591 A
1 A
59103592 TCCACCAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCGTGAGAGCTG
Found at i:59119013 original size:23 final size:22
Alignment explanation
Indices: 59118962--59119006 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
59118952 GGTAAAGTAC
*
59118962 AATTTAACTATATATTAATTTGT
1 AATTTAACTATATATT-ATTTAT
59118985 AATTTAACTATATATT-TTTAT
1 AATTTAACTATATATTATTTAT
59119006 A
1 A
59119007 TGATTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
23 16 0.76
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTAACTATATATTATTTAT
Found at i:59119749 original size:17 final size:17
Alignment explanation
Indices: 59119723--59119773 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
59119713 ATAATTATTC
59119723 ATTT-AATATTATAATT
1 ATTTAAATATTATAATT
*
59119739 ATTTAAATATTATAACT
1 ATTTAAATATTATAATT
59119756 ATTTAAATAGTTATAATT
1 ATTTAAATA-TTATAATT
59119774 CTTTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.13
17 20 0.65
18 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTAAATATTATAATT
Found at i:59119961 original size:122 final size:122
Alignment explanation
Indices: 59119744--59119994 Score: 475
Period size: 122 Copynumber: 2.1 Consensus size: 122
59119734 TAATTATTTA
*
59119744 AATATTATAACTATTTAAATAGTTATAATTCTTTTTTAAAAAATCAAATAATATAACTTTTAATT
1 AATATGATAACTATTTAAATAGTTATAATTCTTTTTTAAAAAATCAAATAATATAACTTTTAATT
* *
59119809 AATTATACATTTTTATTTATAGTTATTAAAACACTAAAAATATTTAAATATGTTCGT
66 AATTATACATTTTTATTTATAATTATTAAAACACTAAAAATATTTAAATACGTTCGT
59119866 AATATGATAACTATTTAAATAGTTATAATTCTTTTTTAAAAAATCAAATAATATAACTTTTAATT
1 AATATGATAACTATTTAAATAGTTATAATTCTTTTTTAAAAAATCAAATAATATAACTTTTAATT
59119931 AATTATACATTTTTATTTATAATTATTAAAACACTAAAAATATTTAAATACGTTCGT
66 AATTATACATTTTTATTTATAATTATTAAAACACTAAAAATATTTAAATACGTTCGT
59119988 AATATGA
1 AATATGA
59119995 CTCACTTGTG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 126 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (122 bp):
AATATGATAACTATTTAAATAGTTATAATTCTTTTTTAAAAAATCAAATAATATAACTTTTAATT
AATTATACATTTTTATTTATAATTATTAAAACACTAAAAATATTTAAATACGTTCGT
Found at i:59130971 original size:23 final size:22
Alignment explanation
Indices: 59130920--59130964 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
59130910 GGTAAAGTGC
*
59130920 AATTTAACTATATATTAATTTGT
1 AATTTAACTATATATT-ATTTAT
59130943 AATTTAACTATATATT-TTTAT
1 AATTTAACTATATATTATTTAT
59130964 A
1 A
59130965 TGATTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
23 16 0.76
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTAACTATATATTATTTAT
Found at i:59132948 original size:17 final size:17
Alignment explanation
Indices: 59132859--59133272 Score: 103
Period size: 17 Copynumber: 23.8 Consensus size: 17
59132849 TTTTTTTTGT
*
59132859 TTTTTAAAAAACGA-AA
1 TTTTTAAAACACGACAA
*
59132875 -TTTTAGAACACGA-AA
1 TTTTTAAAACACGACAA
* *
59132890 ATTTTAGAAACACGA-ATTTT
1 TTTTTA-AAACACGACA---A
59132910 TTTTTAAAACACGACAA
1 TTTTTAAAACACGACAA
* *
59132927 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGACAA
*
59132944 TTTTTCAAA-AC-ACAA
1 TTTTTAAAACACGACAA
* *
59132959 TTTTAAAAAAAAACATGACAA
1 TTTT----TAAAACACGACAA
* * * *
59132980 TTTGTGAAACATTAGTC-A
1 TTTTTAAAACA--CGACAA
*
59132998 --TTGAAAACACGGA-AA
1 TTTTTAAAACAC-GACAA
* *
59133013 TTTGTGAAAAAACGA-AA
1 TTT-TTAAAACACGACAA
*
59133030 TTTTTTGAAACACAGA-AA
1 -TTTTTAAAACAC-GACAA
59133048 TTTTTAGAAAACACGA-AA
1 TTTTT--AAAACACGACAA
* * * *
59133066 ATTTTGAATCACCG-GAA
1 TTTTTAAAACA-CGACAA
59133083 TTTTTGAAAACACGA-AGA
1 TTTTT-AAAACACGACA-A
*
59133101 TTTTTGAAACATCGA-AA
1 TTTTTAAAACA-CGACAA
**
59133118 TTTTTGAAAACACGTGAA
1 TTTTT-AAAACACGACAA
*
59133136 TTTTTGAAACAC-A-AA
1 TTTTTAAAACACGACAA
* *
59133151 TTTTTTTTGAAAATACGAAAA
1 ---TTTTT-AAAACACGACAA
59133172 TTTTTGAAAACACAGA-AA
1 TTTTT-AAAACAC-GACAA
* **
59133190 TTTTTAAAACAAGGGAA
1 TTTTTAAAACACGACAA
*
59133207 TTTTTGAAACACTGA-AA
1 TTTTTAAAACAC-GACAA
*
59133224 TTTTTGAAAACACGAGAA
1 TTTTT-AAAACACGACAA
* *
59133242 TTTTTTAAAACACAAAAA
1 -TTTTTAAAACACGACAA
*
59133260 TTTTTTAAACACG
1 TTTTTAAAACACG
59133273 GGAATTTTTT
Statistics
Matches: 303, Mismatches: 52, Indels: 85
0.69 0.12 0.19
Matches are distributed among these distances:
15 24 0.08
16 18 0.06
17 120 0.40
18 93 0.31
19 31 0.10
20 8 0.03
21 9 0.03
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGACAA
Found at i:59132948 original size:36 final size:35
Alignment explanation
Indices: 59132875--59132956 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
59132865 AAAAACGAAA
* *
59132875 TTTTAGAACACGAAAATTTTAGAAACACGAATTTTT
1 TTTTAAAACACGAAAATTTTAGAAACACGAA-TATT
* *
59132911 TTTTAAAACACGACAATTTTTGAAACACGAGA-ATT
1 TTTTAAAACACGAAAATTTTAGAAACACGA-ATATT
*
59132946 TTTCAAAACAC
1 TTTTAAAACAC
59132957 AATTTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 12 0.30
36 27 0.68
37 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (35 bp):
TTTTAAAACACGAAAATTTTAGAAACACGAATATT
Found at i:59133022 original size:18 final size:18
Alignment explanation
Indices: 59132998--59133281 Score: 222
Period size: 18 Copynumber: 16.1 Consensus size: 18
59132988 ACATTAGTCA
59132998 TTGAAAACACGGAAATTT
1 TTGAAAACACGGAAATTT
* *
59133016 GTGAAAAAAC-GAAATTTT
1 TTGAAAACACGGAAA-TTT
*
59133034 TTG-AAACACAGAAATTT
1 TTGAAAACACGGAAATTT
*
59133051 TTAGAAAACAC-GAAAATT
1 TT-GAAAACACGGAAATTT
*
59133069 TTG-AATCACCGG-AATTT
1 TTGAAAACA-CGGAAATTT
59133086 TTGAAAACAC-GAAGATTT
1 TTGAAAACACGGAA-ATTT
59133104 TTG-AAACATC-GAAATTT
1 TTGAAAACA-CGGAAATTT
59133121 TTGAAAACACGTG-AATTT
1 TTGAAAACACG-GAAATTT
59133139 TTG-AAACAC--AAATTTTTT
1 TTGAAAACACGGAAA---TTT
* *
59133157 TTGAAAATACGAAAATTT
1 TTGAAAACACGGAAATTT
*
59133175 TTGAAAACACAGAAATTT
1 TTGAAAACACGGAAATTT
* *
59133193 TT-AAAACAAGGGAATTT
1 TTGAAAACACGGAAATTT
*
59133210 TTG-AAACACTGAAATTT
1 TTGAAAACACGGAAATTT
59133227 TTGAAAACAC-GAGAATTT
1 TTGAAAACACGGA-AATTT
* **
59133245 TTTAAAACACAAAAATTT
1 TTGAAAACACGGAAATTT
* *
59133263 TT-TAAACACGGGAATTT
1 TTGAAAACACGGAAATTT
59133280 TT
1 TT
59133282 TTTTTTACAC
Statistics
Matches: 218, Mismatches: 24, Indels: 49
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.01
16 5 0.02
17 87 0.40
18 108 0.50
19 13 0.06
21 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (18 bp):
TTGAAAACACGGAAATTT
Found at i:59133048 original size:35 final size:34
Alignment explanation
Indices: 59133002--59133281 Score: 262
Period size: 35 Copynumber: 8.0 Consensus size: 34
59132992 TAGTCATTGA
* * *
59133002 AAACACGGAAATTTGTGAAAAAACGAAATTTTTTG
1 AAACACAGAAATTTTTGAAAACACGAAA-TTTTTG
*
59133037 AAACACAGAAATTTTTAGAAAACACGAAAATTTTG
1 AAACACAGAAATTTTT-GAAAACACGAAATTTTTG
* * *
59133072 AATCACCGGAATTTTTGAAAACACGAAGATTTTTG
1 AAACACAGAAATTTTTGAAAACACGAA-ATTTTTG
*
59133107 AAACATC-GAAATTTTTGAAAACACGTGAATTTTTG
1 AAACA-CAGAAATTTTTGAAAACACG-AAATTTTTG
* *
59133142 AAACACA-AATTTTTTTTGAAAATACGAAAATTTTTG
1 AAACACAGAA--ATTTTTGAAAACACG-AAATTTTTG
* *
59133178 AAAACACAGAAATTTTT-AAAACAAGGGAATTTTTG
1 -AAACACAGAAATTTTTGAAAAC-ACGAAATTTTTG
* *
59133213 AAACACTGAAATTTTTGAAAACACGAGAATTTTTTA
1 AAACACAGAAATTTTTGAAAACACGA-AA-TTTTTG
* * *
59133249 AAACACAAAAATTTTT-TAAACACGGGAATTTTT
1 AAACACAGAAATTTTTGAAAACAC-GAAATTTTT
59133282 TTTTTTACAC
Statistics
Matches: 204, Mismatches: 27, Indels: 29
0.78 0.10 0.11
Matches are distributed among these distances:
34 36 0.18
35 98 0.48
36 61 0.30
37 7 0.03
38 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (34 bp):
AAACACAGAAATTTTTGAAAACACGAAATTTTTG
Found at i:59133211 original size:53 final size:50
Alignment explanation
Indices: 59132998--59133281 Score: 218
Period size: 53 Copynumber: 5.4 Consensus size: 50
59132988 ACATTAGTCA
* * *
59132998 TTGAAAACACGGAAATTTGTGAAAAAACGAAATTTTTTGAAACACAGAAATTT
1 TTGAAAACAC-GAAATTTTTGAAAACACGAAA-TTTTTAAAACA-AGAAATTT
* * * *
59133051 TTAGAAAACACGAAAATTTTG-AATCACCGGAATTTTTGAAAACACGAAGATTT
1 TT-GAAAACACGAAATTTTTGAAAACA-CGAAATTTTT-AAAACAAGAA-ATTT
* **
59133104 TTG-AAACATCGAAATTTTTGAAAACACGTGAATTTTTGAAACACAA-ATTTTTT
1 TTGAAAACA-CGAAATTTTTGAAAACACG-AAATTTTT-AAA-ACAAGA-AATTT
* *
59133157 TTGAAAATACGAAAATTTTTGAAAACACAGAAATTTTTAAAACAAGGGAATTT
1 TTGAAAACACG-AAATTTTTGAAAACAC-GAAATTTTTAAAACAA-GAAATTT
*
59133210 TTG-AAACACTGAAATTTTTGAAAACACGAGAATTTTTTAAAACACAAAAATTT
1 TTGAAAACAC-GAAATTTTTGAAAACACGA-AA-TTTTTAAAACA-AGAAATTT
* *
59133263 TT-TAAACACGGGAATTTTT
1 TTGAAAACAC-GAAATTTTT
59133282 TTTTTTACAC
Statistics
Matches: 190, Mismatches: 22, Indels: 38
0.76 0.09 0.15
Matches are distributed among these distances:
51 7 0.04
52 51 0.27
53 92 0.48
54 39 0.21
55 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (50 bp):
TTGAAAACACGAAATTTTTGAAAACACGAAATTTTTAAAACAAGAAATTT
Found at i:59133278 original size:17 final size:17
Alignment explanation
Indices: 59133188--59133282 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 17
59133178 AAAACACAGA
* *
59133188 AATTTTTAAAACAAGGG
1 AATTTTTTAAACACGGG
* * *
59133205 AATTTTTGAAACACTGA
1 AATTTTTTAAACACGGG
* *
59133222 AATTTTTGAAAACACGAG
1 AATTTTT-TAAACACGGG
***
59133240 AATTTTTTAAAACACAAA
1 AATTTTTT-AAACACGGG
59133258 AATTTTTTAAACACGGG
1 AATTTTTTAAACACGGG
59133275 AATTTTTT
1 AATTTTTT
59133283 TTTTTACACA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
17 34 0.55
18 28 0.45
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (17 bp):
AATTTTTTAAACACGGG
Found at i:59133445 original size:19 final size:19
Alignment explanation
Indices: 59133403--59133449 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
59133393 TCGTTGCCTT
**
59133403 ATTTTTGAAAACACGACTA
1 ATTTTTGAAAACACGAAAA
* *
59133422 TTTTTTGAAGACACGAAAA
1 ATTTTTGAAAACACGAAAA
59133441 A-TTTTGAAA
1 ATTTTTGAAA
59133450 GATAGAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34
Consensus pattern (19 bp):
ATTTTTGAAAACACGAAAA
Found at i:59133839 original size:17 final size:16
Alignment explanation
Indices: 59133799--59133841 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
59133789 AATTGAACCT
*
59133799 TTTTTTTCCTTTTTCC
1 TTTTTTTCTTTTTTCC
59133815 TTTTTTTCTTTTTTCTC
1 TTTTTTTCTTTTTTC-C
59133832 TTTTTTTCTT
1 TTTTTTTCTT
59133842 CCCTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTTTTCC
Found at i:59133850 original size:15 final size:13
Alignment explanation
Indices: 59133831--59133864 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
59133821 TCTTTTTTCT
59133831 CTTTTTTTCTTCC
1 CTTTTTTTCTTCC
*
59133844 CTTTTTTTCTTCT
1 CTTTTTTTCTTCC
59133857 CTTTTTTT
1 CTTTTTTT
59133865 TTCTGGCCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTTTCTTCC
Found at i:59133861 original size:10 final size:8
Alignment explanation
Indices: 59133799--59133841 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
59133789 AATTGAACCT
59133799 TTTTTTTC
1 TTTTTTTC
* *
59133807 CTTTTTCC
1 TTTTTTTC
59133815 TTTTTTTC
1 TTTTTTTC
59133823 TTTTTTCTC
1 TTTTTT-TC
59133832 TTTTTTTC
1 TTTTTTTC
59133840 TT
1 TT
59133842 CCCTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:59134166 original size:4 final size:4
Alignment explanation
Indices: 59134157--59134225 Score: 60
Period size: 4 Copynumber: 18.5 Consensus size: 4
59134147 TTTCCTCCTT
* *
59134157 TTTC TTTC -TTC -TTC -TTC -TTC TTTC -TTC TTTC TCTC TTTT TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC
*
59134201 TTT- TTTC TTTC TTAC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
59134226 CCTCCCCGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
3 18 0.33
4 34 0.62
5 3 0.05
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:59134198 original size:27 final size:27
Alignment explanation
Indices: 59134157--59134209 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
59134147 TTTCCTCCTT
*
59134157 TTTCTTTCTTCTTCTTCTTCTTTCTTC
1 TTTCTCTCTTCTTCTTCTTCTTTCTTC
* *
59134184 TTTCTCTCTTTTTCTTCTTTTTTCTT
1 TTTCTCTCTTCTTCTTCTTCTTTCTT
59134210 TCTTACTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTCTCTCTTCTTCTTCTTCTTTCTTC
Found at i:59134218 original size:8 final size:7
Alignment explanation
Indices: 59134154--59134221 Score: 66
Period size: 7 Copynumber: 9.0 Consensus size: 7
59134144 TTTTTTCCTC
59134154 CTTT-TT
1 CTTTCTT
59134160 CTTTCTT
1 CTTTCTT
59134167 CTTCTTCTT
1 C-T-TTCTT
59134176 CTTTCTT
1 CTTTCTT
59134183 CTTTCTCT
1 CTTTCT-T
59134191 CTTTTTCTT
1 C--TTTCTT
*
59134200 CTTTTTT
1 CTTTCTT
59134207 CTTTCTT
1 CTTTCTT
59134214 ACTTTCTT
1 -CTTTCTT
59134222 TCTTCCTCCC
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
6 4 0.08
7 25 0.47
8 11 0.21
9 8 0.15
10 5 0.09
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (7 bp):
CTTTCTT
Found at i:59134223 original size:16 final size:15
Alignment explanation
Indices: 59134157--59134225 Score: 74
Period size: 17 Copynumber: 4.7 Consensus size: 15
59134147 TTTCCTCCTT
59134157 TTTCTTTC-TTCTTC
1 TTTCTTTCTTTCTTC
59134171 -TTC-TTCTTTCTTC
1 TTTCTTTCTTTCTTC
*
59134184 TTTCTCTCTTTTTCTTC
1 TTTCT-T-TCTTTCTTC
59134201 TTT-TTTCTTTCTTAC
1 TTTCTTTCTTTCTT-C
59134216 TTTCTTTCTT
1 TTTCTTTCTT
59134226 CCTCCCCGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
12 3 0.07
13 9 0.20
14 10 0.22
15 5 0.11
16 8 0.17
17 11 0.24
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTTTCTTTCTTC
Found at i:59134777 original size:30 final size:30
Alignment explanation
Indices: 59134729--59134864 Score: 136
Period size: 30 Copynumber: 4.6 Consensus size: 30
59134719 GTAATTTTAT
* *
59134729 AAAGTTTAGAGGTTAAAATATAATTTGGAGA
1 AAAGTTTAGGGGTCAAAATATAATTT-GAGA
* * *
59134760 ACA-TTTAGGGGTCAAAATGTAATTT-AAA
1 AAAGTTTAGGGGTCAAAATATAATTTGAGA
** *
59134788 AAAGTTTAGGGGTTGAAGTATAATTTTGAG-
1 AAAGTTTAGGGGTCAAAATATAA-TTTGAGA
*
59134818 AAAGTTTAGGGGTCAAAATGA-AATTTTAGA
1 AAAGTTTAGGGGTCAAAAT-ATAATTTGAGA
59134848 AAAGTTTAGGGGTCAAA
1 AAAGTTTAGGGGTCAAA
59134865 TGCAAAAAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 11
0.77 0.14 0.10
Matches are distributed among these distances:
28 4 0.05
29 20 0.24
30 57 0.67
31 4 0.05
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATATAATTTGAGA
Found at i:59134810 original size:59 final size:59
Alignment explanation
Indices: 59134708--59134860 Score: 193
Period size: 59 Copynumber: 2.6 Consensus size: 59
59134698 CAAAATTTTT
* * *
59134708 GGGG-CAAAAGTGTAATTTTATAAAGTTTAGAGGTTAAAATATAATTTGGAGAACA-TTTA
1 GGGGTCAAAA-TGTAATTTAAAAAAGTTTAGGGGTTAAAATATAATTTGGAGAA-AGTTTA
* * *
59134767 GGGGTCAAAATGTAATTTAAAAAAGTTTAGGGGTTGAAGTATAATTTTGAGAAAGTTTA
1 GGGGTCAAAATGTAATTTAAAAAAGTTTAGGGGTTAAAATATAATTTGGAGAAAGTTTA
* *
59134826 GGGGTCAAAATGAAATTTTAGAAAAGTTTAGGGGT
1 GGGGTCAAAATGTAA-TTTAAAAAAGTTTAGGGGT
59134861 CAAATGCAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
58 1 0.01
59 59 0.71
60 23 0.28
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (59 bp):
GGGGTCAAAATGTAATTTAAAAAAGTTTAGGGGTTAAAATATAATTTGGAGAAAGTTTA
Found at i:59139928 original size:24 final size:21
Alignment explanation
Indices: 59139901--59139964 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
59139891 AAAAAATGAG
59139901 TAAATTAGTCTTTATATATTATAA
1 TAAATTAGTCTTT-T-TATTA-AA
*
59139925 TAAACTAGTCTTTTTATTAAA
1 TAAATTAGTCTTTTTATTAAA
* *
59139946 AAAATTATTCATTTTTATT
1 TAAATTAGTC-TTTTTATT
59139965 GTTAAAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.26
22 13 0.37
23 1 0.03
24 12 0.34
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (21 bp):
TAAATTAGTCTTTTTATTAAA
Found at i:59141861 original size:24 final size:24
Alignment explanation
Indices: 59141834--59141879 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
59141824 AATTCAATTG
*
59141834 CTAAATTAAAATTTATCAACTCGA
1 CTAAATCAAAATTTATCAACTCGA
* *
59141858 CTAACTCAAAATTTATTAACTC
1 CTAAATCAAAATTTATCAACTC
59141880 AATTCGACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (24 bp):
CTAAATCAAAATTTATCAACTCGA
Found at i:59145615 original size:16 final size:16
Alignment explanation
Indices: 59145594--59145636 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
59145584 TGAGTTTAAG
59145594 AGTTTTAAGAGT-ATT
1 AGTTTTAAGAGTAATT
59145609 AAGTTTTAATGAGTAATT
1 -AGTTTTAA-GAGTAATT
*
59145627 AGATTTAAGA
1 AGTTTTAAGA
59145637 TTCAAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 11 0.46
18 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (16 bp):
AGTTTTAAGAGTAATT
Found at i:59145622 original size:17 final size:19
Alignment explanation
Indices: 59145580--59145623 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
59145570 ATTTTTAATA
59145580 TTAATGAGT-TTAAGAGTT
1 TTAATGAGTATTAAGAGTT
59145598 TTAA-GAGTATT-A-AGTT
1 TTAATGAGTATTAAGAGTT
59145614 TTAATGAGTA
1 TTAATGAGTA
59145624 ATTAGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.33
17 10 0.42
18 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (19 bp):
TTAATGAGTATTAAGAGTT
Found at i:59145778 original size:18 final size:18
Alignment explanation
Indices: 59145757--59145799 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
59145747 AATTGAATAT
*
59145757 AAAAATTGACTAAATCAA
1 AAAAATTGAATAAATCAA
*
59145775 AAAAACTGAATAAATCAA
1 AAAAATTGAATAAATCAA
59145793 AAAAATT
1 AAAAATT
59145800 AAGTAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAATTGAATAAATCAA
Found at i:59147173 original size:12 final size:12
Alignment explanation
Indices: 59147156--59147191 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
59147146 AGCTGGATCA
*
59147156 AAATTTTTTTAT
1 AAATTTTTTAAT
59147168 AAATTTTTTAAT
1 AAATTTTTTAAT
*
59147180 AAATTATTTAAT
1 AAATTTTTTAAT
59147192 TAGTTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AAATTTTTTAAT
Found at i:59160994 original size:3 final size:3
Alignment explanation
Indices: 59160976--59161018 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
59160966 ATAATAAACC
*
59160976 AGA A-A AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
59161019 GGATTACCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:59162594 original size:2 final size:2
Alignment explanation
Indices: 59162587--59162614 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59162577 CACCAATTAA
59162587 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
59162615 CTAACTATGA
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:59163445 original size:31 final size:31
Alignment explanation
Indices: 59163410--59163477 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
59163400 GGATCAAATT
*
59163410 AAAGTATAAGGACTAAACCCATAAGTTTTGC
1 AAAGTATAAGGACTAAACCCATAACTTTTGC
59163441 AAAGTATAAGGACTAAACCCATAACTTTTGC
1 AAAGTATAAGGACTAAACCCATAACTTTTGC
*
59163472 GAAGTA
1 AAAGTA
59163478 CAAGAGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (31 bp):
AAAGTATAAGGACTAAACCCATAACTTTTGC
Found at i:59164046 original size:42 final size:42
Alignment explanation
Indices: 59163987--59164077 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
59163977 GCTGGATTGA
59163987 TGTGGTGTGAGTAGATACTTATCTGAGTATTCTTGCTCTAAT
1 TGTGGTGTGAGTAGATACTTATCTGAGTATTCTTGCTCTAAT
*
59164029 TGTGGTGTGAGTAGATACTTATCTGAGTATTCTTGCTGTAAT
1 TGTGGTGTGAGTAGATACTTATCTGAGTATTCTTGCTCTAAT
*
59164071 AGTGGTG
1 TGTGGTG
59164078 CACATAACTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.21, C:0.10, G:0.27, T:0.42
Consensus pattern (42 bp):
TGTGGTGTGAGTAGATACTTATCTGAGTATTCTTGCTCTAAT
Found at i:59164602 original size:23 final size:25
Alignment explanation
Indices: 59164558--59164603 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
59164548 ATTTAACACG
*
59164558 TTTGAGTCTCCTTTTTTGTTGATAT
1 TTTGAGTCTCCTTTTCTGTTGATAT
*
59164583 TTTGATTCT-CTTTTCT-TTGAT
1 TTTGAGTCTCCTTTTCTGTTGAT
59164604 TTATTTTGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 6 0.32
25 8 0.42
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.63
Consensus pattern (25 bp):
TTTGAGTCTCCTTTTCTGTTGATAT
Found at i:59169148 original size:13 final size:12
Alignment explanation
Indices: 59169130--59169171 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
59169120 AAGTCGTAAC
59169130 TTAAAAAAATTAG
1 TTAAAAAAATT-G
*
59169143 TTAAAAATAATTT
1 TTAAAAA-AATTG
59169156 TTAAAAAAATT-
1 TTAAAAAAATTG
59169167 TTAAA
1 TTAAA
59169172 TTAATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 14 0.52
14 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (12 bp):
TTAAAAAAATTG
Found at i:59172457 original size:22 final size:24
Alignment explanation
Indices: 59172419--59172467 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
59172409 GTGTATATGT
*
59172419 ATATGTATTTACTAAAA-TA-AAA
1 ATATGTATGTACTAAAAGTATAAA
59172441 ATATGTATGTA-TAAAAAGTATAAA
1 ATATGTATGTACT-AAAAGTATAAA
59172465 ATA
1 ATA
59172468 CAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 2 0.09
24 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATGTATGTACTAAAAGTATAAA
Found at i:59173534 original size:5 final size:6
Alignment explanation
Indices: 59173514--59173551 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
59173504 TGAAACAAGT
59173514 AAATGAA AAATAA AAATAA AAATAA AAA-AGA AAATAA A
1 AAAT-AA AAATAA AAATAA AAATAA AAATA-A AAATAA A
59173552 GAAGATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.03
6 23 0.79
7 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:59174486 original size:13 final size:13
Alignment explanation
Indices: 59174468--59174493 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59174458 GGTTTTGAAA
59174468 AAAAAAATGTTAT
1 AAAAAAATGTTAT
59174481 AAAAAAATGTTAT
1 AAAAAAATGTTAT
59174494 TTTAGTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAAAAATGTTAT
Found at i:59174517 original size:8 final size:8
Alignment explanation
Indices: 59174499--59174532 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
59174489 GTTATTTTAG
59174499 TTATTTATT
1 TTATTT-TT
59174508 TTATTTTT
1 TTATTTTT
59174516 TTATTTTT
1 TTATTTTT
59174524 TTATTTTT
1 TTATTTTT
59174532 T
1 T
59174533 AGTCGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTATTTTT
Found at i:59174699 original size:19 final size:18
Alignment explanation
Indices: 59174651--59174721 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
59174641 ATTAATTTTT
*
59174651 AAAATTAAAAT-TTCAAA
1 AAAATTAAAATATTTAAA
59174668 AAAATATAAAAAAGTATTTAAA
1 AAAAT-T--AAAA-TATTTAAA
59174690 AAAATTAAAAT-TATTAAA
1 AAAATTAAAATAT-TTAAA
59174708 AAATATTAAAATAT
1 AAA-ATTAAAATAT
59174722 ATTATTTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
17 6 0.13
18 10 0.22
19 12 0.27
20 5 0.11
21 2 0.04
22 10 0.22
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAATTAAAATATTTAAA
Found at i:59174710 original size:11 final size:10
Alignment explanation
Indices: 59174666--59174725 Score: 63
Period size: 10 Copynumber: 6.1 Consensus size: 10
59174656 TAAAATTTCA
59174666 AAAAAATA-T
1 AAAAAATATT
59174675 AAAAAAGTATTT
1 AAAAAA-TA-TT
59174687 AAAAAA-ATT
1 AAAAAATATT
*
59174696 -AAAATTATT
1 AAAAAATATT
59174705 AAAAAATATT
1 AAAAAATATT
*
59174715 AAAATATATT
1 AAAAAATATT
59174725 A
1 A
59174726 TTTTTAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
8 4 0.09
9 11 0.26
10 21 0.49
12 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAAAATATT
Found at i:59175019 original size:21 final size:21
Alignment explanation
Indices: 59174985--59175028 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
59174975 TATCTAAATT
* *
59174985 AAAATCGAACCAAATTCAATA
1 AAAATCCAACCAAAATCAATA
* *
59175006 AAAATCCAATCAAAATCGATA
1 AAAATCCAACCAAAATCAATA
59175027 AA
1 AA
59175029 TTAAGTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAATCCAACCAAAATCAATA
Found at i:59175587 original size:25 final size:27
Alignment explanation
Indices: 59175559--59175617 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
59175549 TTTTTTTATT
*
59175559 AATTTGAT-TTT-TATTTTTTGAGTTA
1 AATTTGATCTTTATATTTTTTGAGCTA
* *
59175584 AATTTGGTCTTTATTTTTTTTGAGCTA
1 AATTTGATCTTTATATTTTTTGAGCTA
59175611 AATTTGA
1 AATTTGA
59175618 CCATTGACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.25
26 3 0.11
27 18 0.64
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (27 bp):
AATTTGATCTTTATATTTTTTGAGCTA
Found at i:59175803 original size:6 final size:6
Alignment explanation
Indices: 59175777--59175821 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
59175767 TTTAAAAATT
*
59175777 ATAAAA ATAAATA ATTTAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAA-A A-TAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
59175822 ATTAACATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 28 0.80
7 4 0.11
8 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
ATAAAA
Found at i:59176960 original size:36 final size:36
Alignment explanation
Indices: 59176913--59176986 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
59176903 TTTCAAGTAA
59176913 GATAATTGGCCAATGGGTAATTGAACTTGAAGATTG
1 GATAATTGGCCAATGGGTAATTGAACTTGAAGATTG
59176949 GATAATTGGCCAATGGGTAATTGAACTTGAAGATTG
1 GATAATTGGCCAATGGGTAATTGAACTTGAAGATTG
59176985 GA
1 GA
59176987 CTTGAGATCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (36 bp):
GATAATTGGCCAATGGGTAATTGAACTTGAAGATTG
Found at i:59178350 original size:29 final size:28
Alignment explanation
Indices: 59178317--59178384 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
59178307 ATTCTTAAAT
59178317 GATAGTCACTGCTAGA-CTCTTGTTTGGCG
1 GATAGTCACTGC--GACCTCTTGTTTGGCG
*
59178346 GATAGTTACTGCGACCTCTTGTTTGGCG
1 GATAGTCACTGCGACCTCTTGTTTGGCG
*
59178374 GATAATCACTG
1 GATAGTCACTG
59178385 TGAACTCTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.06
28 22 0.63
29 11 0.31
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (28 bp):
GATAGTCACTGCGACCTCTTGTTTGGCG
Found at i:59178392 original size:28 final size:28
Alignment explanation
Indices: 59178317--59178392 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
59178307 ATTCTTAAAT
* *
59178317 GATAGTCACTGCTAGACTCTTGTTTGGCG
1 GATAATCACTGCGA-ACTCTTGTTTGGCG
* * *
59178346 GATAGTTACTGCGACCTCTTGTTTGGCG
1 GATAATCACTGCGAACTCTTGTTTGGCG
*
59178374 GATAATCACTGTGAACTCT
1 GATAATCACTGCGAACTCT
59178393 CGATTTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 28 0.70
29 12 0.30
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (28 bp):
GATAATCACTGCGAACTCTTGTTTGGCG
Found at i:59178714 original size:15 final size:15
Alignment explanation
Indices: 59178680--59178717 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
59178670 CATGGATGCG
59178680 AACTCATATATGGAT
1 AACTCATATATGGAT
*
59178695 GACTCATATATGGCA-
1 AACTCATATATGG-AT
59178710 AACTCATA
1 AACTCATA
59178718 CATGCAGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (15 bp):
AACTCATATATGGAT
Found at i:59182592 original size:14 final size:15
Alignment explanation
Indices: 59182575--59182612 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
59182565 TTTCCAATTT
59182575 TATTTTTATTATT-C
1 TATTTTTATTATTCC
59182589 TATTTTT-TTATTCC
1 TATTTTTATTATTCC
*
59182603 GATTTTTATT
1 TATTTTTATT
59182613 TGATCCTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 5 0.24
14 14 0.67
15 2 0.10
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTTTATTATTCC
Found at i:59185321 original size:2 final size:2
Alignment explanation
Indices: 59185314--59185350 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
59185304 ATAATCTCAA
59185314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59185351 ACTATTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59189935 original size:29 final size:30
Alignment explanation
Indices: 59189889--59189949 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
59189879 TTCCTTTTTG
*
59189889 TTTTTTAATAATGGCCCAATAT-TTT-TAC
1 TTTTTTAATAATGACCCAATATGTTTATAC
*
59189917 TTTTTTCATAAATGACCCAATATGTTTATAC
1 TTTTTTAAT-AATGACCCAATATGTTTATAC
59189948 TT
1 TT
59189950 CTTCTTCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.29
29 12 0.43
30 3 0.11
31 5 0.18
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.49
Consensus pattern (30 bp):
TTTTTTAATAATGACCCAATATGTTTATAC
Found at i:59201326 original size:2 final size:2
Alignment explanation
Indices: 59201319--59201359 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
59201309 ATAAAGCTAT
59201319 TA TA TA TA TA 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 TA TA TA TA TA T
59201360 TACGTAACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59202507 original size:22 final size:22
Alignment explanation
Indices: 59202477--59202519 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59202467 ACACCAAAAC
* *
59202477 AGGCTTTTAGCGGTGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
59202499 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
59202520 AGCGCCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:59202663 original size:43 final size:41
Alignment explanation
Indices: 59202613--59202926 Score: 342
Period size: 43 Copynumber: 7.3 Consensus size: 41
59202603 TTTTATAAAT
* *
59202613 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCATTTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTC-CAC
59202656 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTT--CCAC
*
59202699 AAACGTCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTC-CAC
* *
59202742 AAACGCCGCTAAAAACCAAGACCTTTAGCGGCGCTTTAACCAT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTT--CCAC
* * * *
59202785 AAACGCCGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTT-CCAC
*
59202828 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTT--CCAC
* * * * * *
59202871 AAACGCTGCTAAAGAACATGATCTTTAGCGATG-GTTTTATCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCG--GCGCTTT-CCAC
59202914 AAACGCCGCTAAA
1 AAACGCCGCTAAA
59202927 AGTACAACTC
Statistics
Matches: 234, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
42 10 0.04
43 212 0.91
44 12 0.05
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (41 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCAC
Found at i:59202767 original size:129 final size:127
Alignment explanation
Indices: 59202613--59202950 Score: 382
Period size: 129 Copynumber: 2.6 Consensus size: 127
59202603 TTTTATAAAT
* *
59202613 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCGC-TTTCTCACAAACGCCGCTAAAGAACAAGAC
* * *
59202678 CTTTAGCGGCGCTTTAACCACAAACGTCGCTAAAGACCAAGACCTTTAGCGGCGCTTT-TCTCAC
64 CTTTAGCGGCGCTTTAACCACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAAC-CAC
* * * *
59202742 AAACGCCGCTAAAAACCAAGACCTTTAGCGGCGCTTTAAC-CATAAACGCCGCTATAGAACATGA
1 AAACGCCGCTAAAAA-CATGACCTTTAGCGGCGCTTT--CTCACAAACGCCGCTAAAGAACAAGA
* **
59202806 GCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAACCAC
63 CCTTTAGCGGCGCTTTAACCACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAACCAC
* * * * *
59202871 AAACGCTGCTAAAGAACATGATCTTTAGCGATG-GTTTTATCACAAACGCCGCTAAAAGTAC-A-
1 AAACGCCGCTAAA-AACATGACCTTTAGCG--GCGCTTTCTCACAAACGCCGCT-AAAGAACAAG
59202933 ACTCTTTAGCGGCG-TTTA
62 AC-CTTTAGCGGCGCTTTA
59202951 TAGAAAAACG
Statistics
Matches: 176, Mismatches: 23, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
128 8 0.05
129 154 0.88
130 13 0.07
131 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (127 bp):
AAACGCCGCTAAAAACATGACCTTTAGCGGCGCTTTCTCACAAACGCCGCTAAAGAACAAGACCT
TTAGCGGCGCTTTAACCACAAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAACCAC
Found at i:59202943 original size:86 final size:86
Alignment explanation
Indices: 59202613--59202926 Score: 475
Period size: 86 Copynumber: 3.7 Consensus size: 86
59202603 TTTTATAAAT
* *
59202613 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
59202678 CTTTAGCGGCGCTTTAACCAC
66 CTTTAGCGGCGCTTTAACCAC
* * * *
59202699 AAACGTCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAAACCAAGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
*
59202764 CTTTAGCGGCGCTTTAACCAT
66 CTTTAGCGGCGCTTTAACCAC
* * *
59202785 AAACGCCGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
*
59202850 CTTTAGCGACGCTTTAACCAC
66 CTTTAGCGGCGCTTTAACCAC
* * ** * *
59202871 AAACGCTGCTAAAGAACATGATCTTTAGCGATGGTTTTATCACAAACGCCGCTAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAA
59202927 AGTACAACTC
Statistics
Matches: 205, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 205 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
CTTTAGCGGCGCTTTAACCAC
Found at i:59204117 original size:86 final size:85
Alignment explanation
Indices: 59204020--59204207 Score: 277
Period size: 86 Copynumber: 2.2 Consensus size: 85
59204010 GGCATTAAGG
* * * *
59204020 CTAAATCTTCAATTTCTATAACGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTC
1 CTAAATTTTCAATTT-TATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
* *
59204085 ATGTATTTACCAAAAATCAGA
65 ATGCATTTACCAAAAAGCAGA
* *
59204106 CTAATTTTTCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTC
1 CTAAATTTTCAAT-TTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
*
59204171 ATGCATTTACCAACAAGCAGA
65 ATGCATTTACCAAAAAGCAGA
59204192 CTAAATTTTCAATTTT
1 CTAAATTTTCAATTTT
59204208 CAATTTTTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
85 3 0.03
86 86 0.95
87 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (85 bp):
CTAAATTTTCAATTTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTCA
TGCATTTACCAAAAAGCAGA
Done.