Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 275 of 318
Found at i:88168410 original size:30 final size:30
Alignment explanation
Indices: 88168368--88168424 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
88168358 TCTCTATTTT
88168368 CAATTATATCCCTAA-ATTTCAAAATTTTCA
1 CAATTATATCCCTAATA-TTCAAAATTTTCA
*
88168398 CAATT-TAGTCCCTATTATTCAAAATTT
1 CAATTATA-TCCCTAATATTCAAAATTT
88168425 AAAATTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 2 0.08
30 21 0.88
31 1 0.04
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (30 bp):
CAATTATATCCCTAATATTCAAAATTTTCA
Found at i:88171319 original size:21 final size:21
Alignment explanation
Indices: 88171273--88171320 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
88171263 TAAAAATAAT
* *
88171273 AATTTTTTAACTTTCTTTATA
1 AATTTTTTAAATTTCTTTAAA
*
88171294 TATTTTTTAGAATTT-TTTAAA
1 AATTTTTTA-AATTTCTTTAAA
88171315 AATTTT
1 AATTTT
88171321 ATAATTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTTTTTAAATTTCTTTAAA
Found at i:88171396 original size:20 final size:20
Alignment explanation
Indices: 88171348--88171407 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
88171338 GAATTTTGGG
*
88171348 ATTTTTATAAA-TATTTTGA
1 ATTTTTAAAAATTATTTTGA
88171367 A-TTTTAAAAATTATTTTGA
1 ATTTTTAAAAATTATTTTGA
*
88171386 ATTTTTGAAAATTATTTTGA
1 ATTTTTAAAAATTATTTTGA
88171406 AT
1 AT
88171408 AATTTTGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.22
19 10 0.27
20 19 0.51
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTTTAAAAATTATTTTGA
Found at i:88172585 original size:23 final size:23
Alignment explanation
Indices: 88172558--88172601 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
88172548 AGTTCTAATT
88172558 CTAAAAATTTA-ATAAATTTATAC
1 CTAAAAATTTACA-AAATTTATAC
*
88172581 CTAAACATTTACAAAATTTAT
1 CTAAAAATTTACAAAATTTAT
88172602 CAATTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (23 bp):
CTAAAAATTTACAAAATTTATAC
Found at i:88178417 original size:44 final size:44
Alignment explanation
Indices: 88178304--88178562 Score: 283
Period size: 44 Copynumber: 5.8 Consensus size: 44
88178294 AGCGATATAT
* *
88178304 GTGATTTTCGTGTAAGACCATGTCTGGGACGTTGGCAGCGATATAC
1 GTGA-TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT-TAC
* ** *
88178350 GTGATTTCGTGTAAGCCCGCGTCTGGGATATTGGCATCGATTA-
1 GTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATTAC
* * *
88178393 GTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCAGCGATATAC
1 GTGA-TTTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT-TAC
* *
88178439 TTGATTTCGTGTAAGACCGA-GTCTGGGATATTGGCATCGATTA-
1 GTGATTTCGTGTAAGACC-ATGTCTGGGACATTGGCATCGATTAC
* *
88178482 GTGATTTACGTGTAAGACCATGTCTGGGACAGTGGCATCGA-TAT
1 GTGATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGATTAC
* * **
88178526 TTGATTACACGTAAGACCATGTCTGGGACATTGGCAT
1 GTGATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
88178563 TGTACGAGCT
Statistics
Matches: 183, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
43 40 0.22
44 70 0.38
45 65 0.36
46 8 0.04
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (44 bp):
GTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATTAC
Found at i:88178463 original size:89 final size:89
Alignment explanation
Indices: 88178304--88178562 Score: 382
Period size: 89 Copynumber: 2.9 Consensus size: 89
88178294 AGCGATATAT
* *
88178304 GTGATTTTCGTGTAAGACCATGTCTGGGACGTTGGCAGCGATATACGTGATTTCGTGTAAGCCCG
1 GTGATTTTCGTGTAAGACCATGTCTGGGACGTTGGCAGCGATATACTTGATTTCGTGTAAGACCG
*
88178369 CGTCTGGGATATTGGCATCGATTA
66 AGTCTGGGATATTGGCATCGATTA
*
88178393 GTGATTTTCGTGTAAGACCACGTCTGGGACGTTGGCAGCGATATACTTGATTTCGTGTAAGACCG
1 GTGATTTTCGTGTAAGACCATGTCTGGGACGTTGGCAGCGATATACTTGATTTCGTGTAAGACCG
88178458 AGTCTGGGATATTGGCATCGATTA
66 AGTCTGGGATATTGGCATCGATTA
* * * **
88178482 GTGATTTACGTGTAAGACCATGTCTGGGACAG-TGGCATCGATAT--TTGATTACACGTAAGACC
1 GTGATTTTCGTGTAAGACCATGTCTGGGAC-GTTGGCAGCGATATACTTGATTTCGTGTAAGACC
*
88178544 -ATGTCTGGGACATTGGCAT
65 GA-GTCTGGGATATTGGCAT
88178563 TGTACGAGCT
Statistics
Matches: 157, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
86 1 0.01
87 31 0.20
89 124 0.79
90 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (89 bp):
GTGATTTTCGTGTAAGACCATGTCTGGGACGTTGGCAGCGATATACTTGATTTCGTGTAAGACCG
AGTCTGGGATATTGGCATCGATTA
Found at i:88180902 original size:5 final size:5
Alignment explanation
Indices: 88180892--88180924 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
88180882 ATACATGCCA
*
88180892 ATATT ATATT ATATT ATGTT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATA
88180925 ATATTATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:88183498 original size:25 final size:25
Alignment explanation
Indices: 88183470--88183520 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
88183460 CTGAATGAGG
*
88183470 AAAGCCTCTACTTTCCTGATTTGCT
1 AAAGCCCCTACTTTCCTGATTTGCT
88183495 AAAGCCCCTACTTTCCTGATTTGCT
1 AAAGCCCCTACTTTCCTGATTTGCT
88183520 A
1 A
88183521 CTATCAGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (25 bp):
AAAGCCCCTACTTTCCTGATTTGCT
Found at i:88188833 original size:18 final size:19
Alignment explanation
Indices: 88188810--88188847 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
88188800 ATGTTTTATA
88188810 TAGTAA-ATTTCAAAAGTT
1 TAGTAATATTTCAAAAGTT
* *
88188828 TAGTAATGTTTCCAAAGTT
1 TAGTAATATTTCAAAAGTT
88188847 T
1 T
88188848 TCAGTCTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (19 bp):
TAGTAATATTTCAAAAGTT
Found at i:88189544 original size:6 final size:6
Alignment explanation
Indices: 88189535--88189559 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
88189525 CAGAAATACA
88189535 AATCAG AATCAG AATCAG AATCAG A
1 AATCAG AATCAG AATCAG AATCAG A
88189560 TATCCTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AATCAG
Found at i:88201897 original size:43 final size:41
Alignment explanation
Indices: 88201831--88201989 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 41
88201821 ATCGTATACA
* *
88201831 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAATGTCCCAGAAG-GGTCTTACACGTAATCAAA-ATCG
* * *
88201874 ATGCCACTGTCCCAGATAGGGTCTTACACGAAATC-AGATACG
1 ATGCCAATGTCCCAGA-AGGGTCTTACACGTAATCAAAAT-CG
* * *
88201916 ATGCCAATGTCCTAGACATGGTCTTACACGTAAAACAAAAGTCG
1 ATGCCAATGTCCCAGA-AGGGTCTTACACGT-AATCAAAA-TCG
* *
88201960 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAGAAG-GGTCTTACACG
88201990 ATATCACATA
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 32 0.34
44 30 0.32
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (41 bp):
ATGCCAATGTCCCAGAAGGGTCTTACACGTAATCAAAATCG
Found at i:88201989 original size:86 final size:86
Alignment explanation
Indices: 88201818--88201995 Score: 222
Period size: 85 Copynumber: 2.1 Consensus size: 86
88201808 GAATAGATCG
* * *
88201818 GAAATC-GTATACAATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAACATCGATGCCACT
1 GAAATCAGTATACAATGCCAATGTCCCAGACATGGTCTTACACGTAAACAAACATCGATGCCACT
88201882 GTCCCAGATAGGGTCTTACAC
66 GTCCCAGATAGGGTCTTACAC
* *
88201903 GAAATCAG-ATACGATGCCAATGTCCTAGACATGGTCTTACACGTAAAACAAA-AGTCGATGCCA
1 GAAATCAGTATACAATGCCAATGTCCCAGACATGGTCTTACACGT-AAACAAACA-TCGATGCC-
*
88201966 AC-GTCCCAGA-CGTGGTCTTACAC
63 ACTGTCCCAGATAG-GGTCTTACAC
*
88201989 GATATCA
1 GAAATCA
88201996 CATATCCAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
85 40 0.49
86 39 0.48
87 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (86 bp):
GAAATCAGTATACAATGCCAATGTCCCAGACATGGTCTTACACGTAAACAAACATCGATGCCACT
GTCCCAGATAGGGTCTTACAC
Found at i:88206772 original size:28 final size:29
Alignment explanation
Indices: 88206732--88206787 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
88206722 CACGGGCAAT
*
88206732 GACACGGGCGTGT-CTAGGCCTTGTGAAG
1 GACACGGGCGTGTGCTAGGCCGTGTGAAG
*
88206760 GACACGGGCGTGTGCTTGGCCGTGTGAA
1 GACACGGGCGTGTGCTAGGCCGTGTGAA
88206788 AACCCTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.16, C:0.21, G:0.41, T:0.21
Consensus pattern (29 bp):
GACACGGGCGTGTGCTAGGCCGTGTGAAG
Found at i:88223237 original size:51 final size:51
Alignment explanation
Indices: 88223181--88223321 Score: 126
Period size: 51 Copynumber: 2.8 Consensus size: 51
88223171 TATTTTTATA
*
88223181 TTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTATTATAAATAAT
1 TTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTAATATAAATAAT
* ** * * * * * **
88223232 TTG--TTTAGTTTAATGTTTATTGTGA-TTTGTTAGGTTATGAATGTAATTTTT
1 TTGTTTTTAATTT-AT-TTTAAAGTTATTTTGTTA-GTAATTAATATAAATAAT
*
88223283 TTATTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATT
1 TTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATT
88223322 TTTGTGATTA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
49 7 0.11
50 9 0.14
51 34 0.52
52 9 0.14
53 7 0.11
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (51 bp):
TTGTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTAATATAAATAAT
Found at i:88223297 original size:102 final size:105
Alignment explanation
Indices: 88223184--88223444 Score: 325
Period size: 110 Copynumber: 2.4 Consensus size: 105
88223174 TTTTATATTG
88223184 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTATTATAAATAATTTGTTTAGTTTAATGTT
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTATTATAAATAATTTGTTTAGTTTAATGTT
*
88223249 TATTGTGAT-TTGTTAGGTT-ATGAATGTAAT-TTTT-TTA-
66 TATTGTGATCTT-TTAGATTAAT-AATGTAATCTTTTATTAC
* **
88223286 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTTTTGTGATTAGGTTAATTGTTTGTTTAGT
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAA----T-T-ATTA--TAAATAATTTGTTTAGT
*
88223351 TTAATGTTTATTGTTATCTTTTAGATTAATAATGTAATCTTTTATTAC
58 TTAATGTTTATTGTGATCTTTTAGATTAATAATGTAATCTTTTATTAC
* *
88223399 TTTTTTAATTTATTTTAAAGTTATTTTGTTAGTAACTAATATAAAT
1 -TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTATTATAAAT
88223445 TTGAAAAAAA
Statistics
Matches: 137, Mismatches: 8, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
102 34 0.25
106 5 0.04
107 1 0.01
108 7 0.05
109 1 0.01
110 44 0.32
111 8 0.06
112 3 0.02
114 34 0.25
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (105 bp):
TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAATTATTATAAATAATTTGTTTAGTTTAATGTT
TATTGTGATCTTTTAGATTAATAATGTAATCTTTTATTAC
Found at i:88223356 original size:110 final size:113
Alignment explanation
Indices: 88223231--88223433 Score: 326
Period size: 110 Copynumber: 1.8 Consensus size: 113
88223221 TTATAAATAA
*
88223231 TTTGTTTAGTTTAATGTTTATTGTGAT-TTGTTAGGTT-ATGAATGTAAT-TTTT-TTA-TTTTT
1 TTTGTTTAGTTTAATGTTTATTGTGATCTT-TTAGATTAAT-AATGTAATCTTTTATTACTTTTT
88223291 AATTTATTTTAAAGTTATTTTGTTAGTAATTTTTGTGATTAGGTTAATTG
64 AATTTATTTTAAAGTTATTTTGTTAGTAATTTTTGTGATTAGGTTAATTG
*
88223341 TTTGTTTAGTTTAATGTTTATTGTTATCTTTTAGATTAATAATGTAATCTTTTATTACTTTTTTA
1 TTTGTTTAGTTTAATGTTTATTGTGATCTTTTAGATTAATAATGTAATCTTTTATTAC-TTTTTA
88223406 ATTTATTTTAAAGTTATTTTGTTAGTAA
65 ATTTATTTTAAAGTTATTTTGTTAGTAA
88223434 CTAATATAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 8
0.89 0.02 0.08
Matches are distributed among these distances:
110 40 0.47
111 8 0.09
112 3 0.04
114 34 0.40
ACGTcount: A:0.25, C:0.01, G:0.13, T:0.60
Consensus pattern (113 bp):
TTTGTTTAGTTTAATGTTTATTGTGATCTTTTAGATTAATAATGTAATCTTTTATTACTTTTTAA
TTTATTTTAAAGTTATTTTGTTAGTAATTTTTGTGATTAGGTTAATTG
Found at i:88226774 original size:25 final size:25
Alignment explanation
Indices: 88226746--88226793 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
88226736 TAAATAATCA
88226746 ATTAGATA-TACTTATTAATATATTT
1 ATTA-ATATTACTTATTAATATATTT
* *
88226771 ATTAATATTATTTATTATTATAT
1 ATTAATATTACTTATTAATATAT
88226794 GGAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTAATATTACTTATTAATATATTT
Found at i:88226784 original size:13 final size:12
Alignment explanation
Indices: 88226746--88226793 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
88226736 TAAATAATCA
*
88226746 ATTAGATATACTT
1 ATTA-ATATATTT
88226759 ATTAATATATTT
1 ATTAATATATTT
88226771 ATTAATATTATTT
1 ATTAATA-TATTT
*
88226784 ATTATTATAT
1 ATTAATATAT
88226794 GGAAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
12 17 0.53
13 15 0.47
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
ATTAATATATTT
Found at i:88227440 original size:12 final size:12
Alignment explanation
Indices: 88227423--88227451 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
88227413 TAAATAAATA
88227423 ATATTAATTAAT
1 ATATTAATTAAT
88227435 ATATTAATTAAT
1 ATATTAATTAAT
88227447 -TATTA
1 ATATTA
88227452 TATTTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATTAATTAAT
Found at i:88227446 original size:16 final size:16
Alignment explanation
Indices: 88227425--88227455 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88227415 AATAAATAAT
88227425 ATTAATTAATATATTA
1 ATTAATTAATATATTA
*
88227441 ATTAATTATTATATT
1 ATTAATTAATATATT
88227456 TAATCATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTAATTAATATATTA
Found at i:88227576 original size:12 final size:12
Alignment explanation
Indices: 88227559--88227592 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
88227549 TTGTTGAATA
88227559 ATATTAATAAAT
1 ATATTAATAAAT
88227571 ATATTAATAAAT
1 ATATTAATAAAT
*
88227583 ATGTTAATAA
1 ATATTAATAA
88227593 TTTATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (12 bp):
ATATTAATAAAT
Found at i:88227640 original size:21 final size:22
Alignment explanation
Indices: 88227607--88227647 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
88227597 TTTAAAAGGA
**
88227607 AAATAATTTATTTAT-TATTTG
1 AAATAATAAATTTATCTATTTG
88227628 AAATAATAAATTTATCTATT
1 AAATAATAAATTTATCTATT
88227648 AATTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATAATAAATTTATCTATTTG
Found at i:88228997 original size:18 final size:18
Alignment explanation
Indices: 88228974--88229008 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88228964 GGCCCAAAAA
88228974 GCCCACACGCCCGTGTGG
1 GCCCACACGCCCGTGTGG
* *
88228992 GCCCACATGCCTGTGTG
1 GCCCACACGCCCGTGTG
88229009 TCACACACAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.40, G:0.31, T:0.17
Consensus pattern (18 bp):
GCCCACACGCCCGTGTGG
Found at i:88229111 original size:12 final size:12
Alignment explanation
Indices: 88229090--88229119 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
88229080 CATGTATCGT
*
88229090 CACACAGCCTAC
1 CACACGGCCTAC
88229102 CACACGGCCTAC
1 CACACGGCCTAC
88229114 CACACG
1 CACACG
88229120 CTTGTATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.50, G:0.13, T:0.07
Consensus pattern (12 bp):
CACACGGCCTAC
Found at i:88241381 original size:652 final size:654
Alignment explanation
Indices: 88239978--88241609 Score: 2677
Period size: 652 Copynumber: 2.5 Consensus size: 654
88239968 GACAAGTGTT
88239978 ATAATAATTTTAATTATTATCAGATCCAAGCAGGAATTGATTTAATAACAACAGCTCAGCACGTA
1 ATAATAATTTTAATTATTATCAGATCCAAGCAGGAATTGATTTAATAACAACAGCTCAGCACGTA
*
88240043 CTTCAACATTAGAATTATAAACTTTGGACTGATGGAAGAAGTATAGTGGCTGATGATACTGAAAA
66 CTTCAACATTAGAATTATAAACTTTGGACTGATGGAAGAAGGATAGTGGCTGATGATACTGAAAA
*
88240108 TATCCAGAAAGATAGAGACGAAGAATCTCTGAAGCTGTTATAAAAGATAGCTGATATAGAGATTG
131 TATCCAGAAAGATAGAGACGAAGAATCTCTGAAGCTGTTAAAAAAGATAGCTGATATAGAGATTG
* * * * *
88240173 ATGATTTTCCGTTAGAAATAATAGAGGAAATCGAAAAAACGTGGGAGTCTTGGAATTCACCAAGA
196 ATGATTTTCCATAAAAAATAATAGAGGAAATCG-AAATACGTGGGAGACTTGGAATTCACCAAGA
* *
88240238 CTGTCATCAGATTTATTACACTTAGATGAAATAGAGTTACTGAATCTAGACAACATCCAAGAAGG
260 CTGTCATCAGATTCATTACACTTAGATGAAATAGAGTTAATGAATCTAGACAACATCCAAGAAGG
*
88240303 ATAAAGACAAAATAAGATAACCATGTGGAAGCACACCAAGAAATTCAAGATTGGTGGTAACTTAA
325 ATAAAGACAAAATAAGATAACCACGTGGAAGCACACCAAGAAATTCAAGATTGGTGGTAACTTAA
88240368 ACAACAAGGCATCTATAAGCAAACAAAAAGTTGTTGTGATATTGATGTGAAAAATGCCAGGCTAC
390 ACAACAAGGCATCTATAAGCAAAC-AAAA-------TGATATTGATGTGAAAAATGCCAGGCTAC
* * * *
88240433 GTGGAAGCTACAATCAGTTCATCACTATCAGAAATATTGTGCGAGATTGAAGAAGAATTGAATAG
447 ATGGAAGCTACAATCAATTCATCACTATCAGAAATACTGTGCGAGATTGAAGAAGAATTAAATAG
88240498 AGTTTAAGAATTTTACTATAAATAGCGATGTATGAAGCCTAAACAAGGCATCAAAAAATAGTTTA
512 AGTTTAAGAATTTTACTATAAATAGCGATGTATGAAGCCTAAACAAGGCATCAAAAAATAGTTTA
*
88240563 GAAATCTTTTCTTTTACTTTCAATATTCTCTCTTTGTCAATAATAAATATATTAATAAATTATTT
577 GAAATCTTTTCTTTTACTTTCAATACTCTCTCTTTGTCAATAATAAATATATTAATAAATTATTT
88240628 AAAAGACATTTTA
642 AAAAGACATTTTA
88240641 ATAATAATTTTAATTATTATCAGATCCAAGCAGGAATTGATTTAATAACAACAGCTCAGCACGTA
1 ATAATAATTTTAATTATTATCAGATCCAAGCAGGAATTGATTTAATAACAACAGCTCAGCACGTA
** * *
88240706 CTTCAACACCAGAATTTTAAACTTTGGACTGATGGAAGAAGGATAGTGGCTGATGATAATGGAAA
66 CTTCAACATTAGAATTATAAACTTTGGACTGATGGAAGAAGGATAGTGGCTGATGATACT-GAAA
*
88240771 A-ATCCAAAAAGATAGAGACGAAGAATCTCTGAAGCTGTTAAAAAAGATAGCTGATATAGAGATT
130 ATATCCAGAAAGATAGAGACGAAGAATCTCTGAAGCTGTTAAAAAAGATAGCTGATATAGAGATT
* *
88240835 GATGATTTTCCATAAAAAATAATAGAGGAAATCAGAAATACGTAGGAGACTTGGAATTCACCCAG
195 GATGATTTTCCATAAAAAATAATAGAGGAAATC-GAAATACGTGGGAGACTTGGAATTCACCAAG
* *
88240900 ACTGTCATCAGATTCATTAAACCTAGATGAAATAGAGTTAATGAATCTAGACAACATCCAAGAAG
259 ACTGTCATCAGATTCATTACACTTAGATGAAATAGAGTTAATGAATCTAGACAACATCCAAGAAG
* *
88240965 GATAAAGACAAAATAAGCTAGCCACGTGGAAGCACACCAAGAAATTCAAGATTGGTGGTAACTTA
324 GATAAAGACAAAATAAGATAACCACGTGGAAGCACACCAAGAAATTCAAGATTGGTGGTAACTTA
* * *
88241030 AACAACAAGGCATTTATAAGCAAAC-AAA-GA-GTTGATGTGAAAAATGGCAGGCTACATGGAAG
389 AACAACAAGGCATCTATAAGCAAACAAAATGATATTGATGTGAAAAATGCCAGGCTACATGGAAG
88241092 CTACAATCAATTCATC-CTTATCAGAAATACTGTGCCG-GATTGAAGTAA-AATTAAATAGAGTT
454 CTACAATCAATTCATCAC-TATCAGAAATACTGTG-CGAGATTGAAG-AAGAATTAAATAGAGTT
* * *
88241154 TAGGAATTTTGCTATAAATAGCGATGTATGAAGCCTAAACAAGGCATCGAAAAATAGTTTAGAAA
516 TAAGAATTTTACTATAAATAGCGATGTATGAAGCCTAAACAAGGCATCAAAAAATAGTTTAGAAA
88241219 TCTTTTCTTTTACTTTCAATACTCTCTCTTTGTCAATAATAAATATATTAATAAATTATTTAAAA
581 TCTTTTCTTTTACTTTCAATACTCTCTCTTTGTCAATAATAAATATATTAATAAATTATTTAAAA
*
88241284 GACCTTTTA
646 GACATTTTA
* *
88241293 ATAATAATTTTAATTATTATCAGATACAAGCAGGAATTGATTTAATAACAACAGCTCAGCACCTA
1 ATAATAATTTTAATTATTATCAGATCCAAGCAGGAATTGATTTAATAACAACAGCTCAGCACGTA
*
88241358 CTTCAACATTAGAATTATAAACTTTAGACTGATGGAAGAAGGATAGTGGCTGATGATACTGAAAA
66 CTTCAACATTAGAATTATAAACTTTGGACTGATGGAAGAAGGATAGTGGCTGATGATACTGAAAA
* * * *
88241423 TATCCAGAAAGATAGAGAAGAAGAATCTCTGAAGTTATTAAAAAAGATAGTTGATATAGAGATTG
131 TATCCAGAAAGATAGAGACGAAGAATCTCTGAAGCTGTTAAAAAAGATAGCTGATATAGAGATTG
*
88241488 ATGATTTTCTATAAAAAAATAATAGAGGAAATCTGAAATACGTGGGAGACTTGGAATTCACCAAG
196 ATGATTTTCCAT-AAAAAATAATAGAGGAAATC-GAAATACGTGGGAGACTTGGAATTCACCAAG
* *
88241553 ACTGTCATCA-ATTCATTACAGTTAGATGAAATAGAGTTAATGAATATAGACAACATC
259 ACTGTCATCAGATTCATTACACTTAGATGAAATAGAGTTAATGAATCTAGACAACATC
88241610 TGTAACACCC
Statistics
Matches: 909, Mismatches: 53, Indels: 25
0.92 0.05 0.03
Matches are distributed among these distances:
651 6 0.01
652 445 0.49
653 65 0.07
661 3 0.00
663 384 0.42
664 6 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (654 bp):
ATAATAATTTTAATTATTATCAGATCCAAGCAGGAATTGATTTAATAACAACAGCTCAGCACGTA
CTTCAACATTAGAATTATAAACTTTGGACTGATGGAAGAAGGATAGTGGCTGATGATACTGAAAA
TATCCAGAAAGATAGAGACGAAGAATCTCTGAAGCTGTTAAAAAAGATAGCTGATATAGAGATTG
ATGATTTTCCATAAAAAATAATAGAGGAAATCGAAATACGTGGGAGACTTGGAATTCACCAAGAC
TGTCATCAGATTCATTACACTTAGATGAAATAGAGTTAATGAATCTAGACAACATCCAAGAAGGA
TAAAGACAAAATAAGATAACCACGTGGAAGCACACCAAGAAATTCAAGATTGGTGGTAACTTAAA
CAACAAGGCATCTATAAGCAAACAAAATGATATTGATGTGAAAAATGCCAGGCTACATGGAAGCT
ACAATCAATTCATCACTATCAGAAATACTGTGCGAGATTGAAGAAGAATTAAATAGAGTTTAAGA
ATTTTACTATAAATAGCGATGTATGAAGCCTAAACAAGGCATCAAAAAATAGTTTAGAAATCTTT
TCTTTTACTTTCAATACTCTCTCTTTGTCAATAATAAATATATTAATAAATTATTTAAAAGACAT
TTTA
Found at i:88242932 original size:39 final size:39
Alignment explanation
Indices: 88242881--88242955 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
88242871 TGAATGAATA
*
88242881 AAATATCTTAATGTCTGTAATACCCGTATATGATATATG
1 AAATATCTTAATGACTGTAATACCCGTATATGATATATG
88242920 AAATATCTTAATGACTGTAATACCCGTATATGATAT
1 AAATATCTTAATGACTGTAATACCCGTATATGATAT
88242956 GTATATAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (39 bp):
AAATATCTTAATGACTGTAATACCCGTATATGATATATG
Found at i:88246506 original size:23 final size:23
Alignment explanation
Indices: 88246480--88246549 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 23
88246470 GATGGATTAT
88246480 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATTCTGGTGTGTTTGGGAGG
*
88246503 ATTATATGATACTGGTGTGTTTTGGAGG
1 A-T-TAT--T-CTGGTGTGTTTGGGAGG
*
88246531 ATTATACTGGTGTGTTTGG
1 ATTATTCTGGTGTGTTTGG
88246550 TTGGACATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 13 0.33
24 1 0.03
25 3 0.08
26 3 0.08
27 2 0.05
28 17 0.44
ACGTcount: A:0.17, C:0.04, G:0.34, T:0.44
Consensus pattern (23 bp):
ATTATTCTGGTGTGTTTGGGAGG
Found at i:88246506 original size:28 final size:28
Alignment explanation
Indices: 88246453--88246536 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
88246443 CACTTTGTGC
88246453 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
88246482 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
88246510 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
88246537 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:88246768 original size:22 final size:22
Alignment explanation
Indices: 88246740--88246782 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
88246730 GCTTTACTGA
88246740 TCAGGCACTTATGTGTCGTATG
1 TCAGGCACTTATGTGTCGTATG
88246762 TCAGGCACTTATGTGTCGTAT
1 TCAGGCACTTATGTGTCGTAT
88246783 TCTGATCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (22 bp):
TCAGGCACTTATGTGTCGTATG
Found at i:88255215 original size:3 final size:3
Alignment explanation
Indices: 88255207--88255257 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
88255197 GTTTATTTGT
* * *
88255207 TTA TTA TTA TTA TTA TTA TTA TTTA TTT TTA CTT- TTA TTT TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA
88255253 TTA TT
1 TTA TT
88255258 CTTCTTCCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (3 bp):
TTA
Found at i:88256389 original size:14 final size:14
Alignment explanation
Indices: 88256372--88256404 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
88256362 TCTGAATTGG
88256372 TACATCTGCATACA
1 TACATCTGCATACA
*
88256386 TACATTTGCATACA
1 TACATCTGCATACA
88256400 TACAT
1 TACAT
88256405 ACATATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (14 bp):
TACATCTGCATACA
Found at i:88256415 original size:18 final size:18
Alignment explanation
Indices: 88256380--88256415 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
88256370 GGTACATCTG
* *
88256380 CATACATACATTTGCATA
1 CATACATACATATACATA
88256398 CATACATACATATACATA
1 CATACATACATATACATA
88256416 AACTATTTTG
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:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (18 bp):
CATACATACATATACATA
Found at i:88263316 original size:38 final size:38
Alignment explanation
Indices: 88263274--88263347 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
88263264 GGGATTAAGC
88263274 TTTATAGCTTAGTAAGACCGTATGAAAATAATAAGCGT
1 TTTATAGCTTAGTAAGACCGTATGAAAATAATAAGCGT
*
88263312 TTTATAGCTTAGTAAGACTGTATGAAAATAATAAGC
1 TTTATAGCTTAGTAAGACCGTATGAAAATAATAAGC
88263348 AATTTATCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (38 bp):
TTTATAGCTTAGTAAGACCGTATGAAAATAATAAGCGT
Found at i:88264520 original size:45 final size:47
Alignment explanation
Indices: 88264412--88264627 Score: 167
Period size: 46 Copynumber: 4.6 Consensus size: 47
88264402 CGAGGCTGAC
*
88264412 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCTGTACCGAT
1 GCCATGTCCCAGACATGGTCTTACACTA---CACACATATCTGTACCGAT
*
88264462 GCCATGTCCCAGACATGGTCTTACACTA-ACACATCTC-GTAGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTACACACATATCTGTA-CCGAT
* * * * ** *
88264508 G-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTA-CACACATATCTGTACCGAT
* * * * * * *
88264554 GCCATGTCCTAGACATGTTCTTACACTGGCTCTCATA-ATGTGGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACT-ACACACATATCTGT-ACCGAT
*
88264602 G-CATGTCCTAGACAT-GTCTTACACTA
1 GCCATGTCCCAGACATGGTCTTACACTA
88264628 GCTCTCAATA
Statistics
Matches: 141, Mismatches: 17, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
44 11 0.08
45 17 0.12
46 34 0.24
47 29 0.21
48 22 0.16
50 28 0.20
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCATGTCCCAGACATGGTCTTACACTACACACATATCTGTACCGAT
Found at i:88264538 original size:94 final size:95
Alignment explanation
Indices: 88264414--88264634 Score: 270
Period size: 94 Copynumber: 2.3 Consensus size: 95
88264404 AGGCTGACGC
**
88264414 CATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCTGTACCGATGCCATGTCCCAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCACATATCAATACCGATGCCATGTCCCAGACATG
88264479 GTCTTACACTAACACATC-T-CGTAGCCGATG
65 GTCTTACACTAACAC-TCATACGTAGCCGATG
* * * * *
88264509 CATGTCCCAGACATGTCTTACACTAGCTCT--CGTCTCAATGCCGATGCCATGTCCTAGACATGT
1 CATGTCCCAGACATGTCTTACACTAGCTCTCACATATCAATACCGATGCCATGTCCCAGACATGG
** * * *
88264572 TCTTACACTGGCTCTCATAATGTGGCCGATG
66 TCTTACACTAACACTCAT-ACGTAGCCGATG
*
88264603 CATGTCCTAGACATGTCTTACACTAGCTCTCA
1 CATGTCCCAGACATGTCTTACACTAGCTCTCA
88264635 ATAACCCATA
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
91 2 0.02
92 38 0.35
94 54 0.50
95 14 0.13
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (95 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCACATATCAATACCGATGCCATGTCCCAGACATGG
TCTTACACTAACACTCATACGTAGCCGATG
Found at i:88264553 original size:46 final size:45
Alignment explanation
Indices: 88264412--88264638 Score: 203
Period size: 47 Copynumber: 4.8 Consensus size: 45
88264402 CGAGGCTGAC
* *
88264412 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCTGTACCGAT
1 GCCATGTCCCAGACAT-GTCTTACACTAGCTCTC-TATA-ATG--CCGAT
* * *
88264462 GCCATGTCCCAGACATGGTCTTACACTAACACATCTCGT-A-GCCGAT
1 GCCATGTCCCAGACAT-GTCTTACACTAGCTC-TCT-ATAATGCCGAT
*
88264508 G-CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGAT
1 GCCATGTCCCAGACATGTCTTACACTAGCTCTC-TAT-AATGCCGAT
* *
88264554 GCCATGTCCTAGACATGTTCTTACACTGGCTCTC-ATAATGTGGCCGAT
1 GCCATGTCCCAGACATG-TCTTACACTAGCTCTCTATAA--T-GCCGAT
* *
88264602 G-CATGTCCTAGACATGTCTTACACTAGCTCTCAATAA
1 GCCATGTCCCAGACATGTCTTACACTAGCTCTCTATAA
88264639 CCCATACATC
Statistics
Matches: 153, Mismatches: 12, Indels: 27
0.80 0.06 0.14
Matches are distributed among these distances:
43 3 0.02
44 14 0.09
45 17 0.11
46 29 0.19
47 34 0.22
48 23 0.15
50 30 0.20
51 3 0.02
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (45 bp):
GCCATGTCCCAGACATGTCTTACACTAGCTCTCTATAATGCCGAT
Found at i:88276155 original size:17 final size:19
Alignment explanation
Indices: 88276119--88276156 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
88276109 ATGCATACGT
88276119 AAAGAGTTGTGACCAATGTC
1 AAAGAGTTGTGA-CAATGTC
88276139 AAAGAGTTG-GA-AATGTC
1 AAAGAGTTGTGACAATGTC
88276156 A
1 A
88276157 CCAACAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (19 bp):
AAAGAGTTGTGACAATGTC
Found at i:88281985 original size:33 final size:34
Alignment explanation
Indices: 88281948--88282014 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
88281938 AATAAAAGTA
88281948 AAATCCATATAGAATTACACTTC-TTTATTTTAT
1 AAATCCATATAGAATTACACTTCTTTTATTTTAT
88281981 AAATCCATATAGAATTACACTTCTTTTATTTTAT
1 AAATCCATATAGAATTACACTTCTTTTATTTTAT
88282015 TTTAGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (34 bp):
AAATCCATATAGAATTACACTTCTTTTATTTTAT
Found at i:88283007 original size:15 final size:16
Alignment explanation
Indices: 88282987--88283016 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88282977 ATTTGAGAAA
88282987 AAATATTTTT-TTAAT
1 AAATATTTTTATTAAT
88283002 AAATATTTTTATTAA
1 AAATATTTTTATTAA
88283017 AGTAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTTTATTAAT
Found at i:88289277 original size:19 final size:18
Alignment explanation
Indices: 88289253--88289300 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
88289243 ACGTAAAAAG
88289253 TAAAAAGTAAAAGATGAAA
1 TAAAAA-TAAAAGATGAAA
88289272 TAAAAATAAAAAGATGAAA
1 TAAAAAT-AAAAGATGAAA
88289291 TAAAAATAAA
1 TAAAAATAAA
88289301 TAACAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAGATGAAA
Found at i:88310417 original size:40 final size:40
Alignment explanation
Indices: 88310362--88310442 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
88310352 AAAATAACAA
88310362 TAAAAAATAATACATTTTCTTTCTTTCTTATCTTCTCCCT
1 TAAAAAATAATACATTTTCTTTCTTTCTTATCTTCTCCCT
88310402 TAAAAAATAATACATTTTCTTTCTTTCTTATCTTCTCCCT
1 TAAAAAATAATACATTTTCTTTCTTTCTTATCTTCTCCCT
88310442 T
1 T
88310443 TCTTGTTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (40 bp):
TAAAAAATAATACATTTTCTTTCTTTCTTATCTTCTCCCT
Found at i:88312008 original size:18 final size:19
Alignment explanation
Indices: 88311975--88312013 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
88311965 GGTACTCTAT
88311975 ATCCTTCTAAGATTTT-AA
1 ATCCTTCTAAGATTTTCAA
* *
88311993 ATCCTTCTAGGTTTTTCAA
1 ATCCTTCTAAGATTTTCAA
88312012 AT
1 AT
88312014 GAATTTCACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (19 bp):
ATCCTTCTAAGATTTTCAA
Found at i:88315879 original size:32 final size:33
Alignment explanation
Indices: 88315819--88315881 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
88315809 TTTCATCTGT
*
88315819 TGGGATTAGGGTTTTTTAGGGTTGGGGTTAGGG
1 TGGGATTAGGGTTTTTTAGGGTTAGGGTTAGGG
*
88315852 TGGG-TTAGGG-TTTTTATGGTTTAGGGTTAG
1 TGGGATTAGGGTTTTTTA-GGGTTAGGGTTAG
88315882 ATTGTTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 17 0.63
33 4 0.15
ACGTcount: A:0.13, C:0.00, G:0.44, T:0.43
Consensus pattern (33 bp):
TGGGATTAGGGTTTTTTAGGGTTAGGGTTAGGG
Found at i:88315979 original size:16 final size:16
Alignment explanation
Indices: 88315939--88315976 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
88315929 GGTGTAAGAT
88315939 TAATTAATTAAATTAAA
1 TAATTAATTAAA-TAAA
88315956 T-ATTAATTAAA-AAA
1 TAATTAATTAAATAAA
88315970 TAATTAA
1 TAATTAA
88315977 ATTTGAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 5 0.25
16 10 0.50
17 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATTAATTAAATAAA
Found at i:88316229 original size:126 final size:123
Alignment explanation
Indices: 88316080--88316464 Score: 371
Period size: 126 Copynumber: 3.1 Consensus size: 123
88316070 TTTTTTGTTT
* * * * * * *
88316080 TTTTTCTTCAGTAGTATCTAGAAAAAAAATTTTAAGAAGAAGTTTCTGAAGAAATAGTATCCAAA
1 TTTTTCTACAGTGGTATCTAGAAAAAAAATTTTGAGAAGACGTTTCTGAAAAAATAGTGTCAAAA
* * *
88316145 ACGCTTCAAGCATGACGCATTGTCAGCAAAATTACTGAAAAATGCTTCCACGTGGACGCT-
66 ACACTTCAAGCA-GATGCATT-TCAGCAAAATTACTGAAAAA-GCTCCCACGTGGACGCTC
* * *
88316205 TTTTTCTACAGTGGTATCTA-AGAAAATAATTTTGAGAAGACGTTTTTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTGGTATCTAGA-AAAAAAATTTTGAGAAGACGTTTCTGAAAAAATAGTGTCAAA
* * * * * * * *
88316269 AACACTTTAAACAGGATGCACTCTCAGCAAAAATGCTGAAAAAAGCTCCCATGTGCATGCTC
65 AACACTTCAAGCA-GATGCA-TTTCAGCAAAATTACTG-AAAAAGCTCCCACGTGGACGCTC
** * * * * *
88316331 TTTTGATACAGTGGTATCT-GAAAAAATAATTGTGAGATGACCTTTCTGAACAAATACTGTCAAA
1 TTTTTCTACAGTGGTATCTAGAAAAAA-AATTTTGAGAAGACGTTTCTGAAAAAATAGTGTCAAA
* * *
88316395 AACACTTCATGCAGTATGCACTTTCAGTAAAATTACTGAGAAAAACTCCCACGTGGACGCTC
65 AACACTTCAAGCAG-ATGCA-TTTCAGCAAAATTACTGA-AAAAGCTCCCACGTGGACGCTC
88316457 TTTTTCTA
1 TTTTTCTA
88316465 TAGTAGTTCC
Statistics
Matches: 207, Mismatches: 45, Indels: 15
0.78 0.17 0.06
Matches are distributed among these distances:
124 1 0.00
125 99 0.48
126 107 0.52
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (123 bp):
TTTTTCTACAGTGGTATCTAGAAAAAAAATTTTGAGAAGACGTTTCTGAAAAAATAGTGTCAAAA
ACACTTCAAGCAGATGCATTTCAGCAAAATTACTGAAAAAGCTCCCACGTGGACGCTC
Found at i:88319594 original size:29 final size:29
Alignment explanation
Indices: 88319562--88319650 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
88319552 AAAACAACTT
88319562 TTATTTTATTAAAAATATAAAAGAGTAAA
1 TTATTTTATTAAAAATATAAAAGAGTAAA
* * *
88319591 TTA--TAATT-AAAATACTAAAA-A-CAACTT
1 TTATTTTATTAAAAATA-TAAAAGAGTAA--A
*
88319618 TTATTTTATTACAAATATAAAAGAGTAAA
1 TTATTTTATTAAAAATATAAAAGAGTAAA
88319647 TTAT
1 TTAT
88319651 AATTAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 2 0.04
26 7 0.16
27 12 0.27
29 16 0.36
30 6 0.13
31 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (29 bp):
TTATTTTATTAAAAATATAAAAGAGTAAA
Found at i:88319600 original size:27 final size:27
Alignment explanation
Indices: 88319573--88319666 Score: 79
Period size: 27 Copynumber: 3.4 Consensus size: 27
88319563 TATTTTATTA
88319573 AAAATA-TAAAAGAGTAAATTATAATT
1 AAAATACTAAAAGAGTAAATTATAATT
* * *
88319599 AAAATACTAAAA-A-CAACTTTTATTTTATT
1 AAAATACTAAAAGAGTAA--ATTA--TAATT
88319628 ACAAATA-TAAAAGAGTAAATTATAATT
1 A-AAATACTAAAAGAGTAAATTATAATT
*
88319655 AAAATATTAAAA
1 AAAATACTAAAA
88319667 ACAACTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
25 2 0.04
26 12 0.23
27 18 0.34
29 13 0.25
30 6 0.11
31 2 0.04
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (27 bp):
AAAATACTAAAAGAGTAAATTATAATT
Found at i:88319612 original size:56 final size:56
Alignment explanation
Indices: 88319552--88319686 Score: 252
Period size: 56 Copynumber: 2.4 Consensus size: 56
88319542 TTCCTTATTC
88319552 AAAACAACTTTTATTTTATTAAAAATATAAAAGAGTAAATTATAATTAAAATACTA
1 AAAACAACTTTTATTTTATTAAAAATATAAAAGAGTAAATTATAATTAAAATACTA
* *
88319608 AAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAATTATAATTAAAATATTA
1 AAAACAACTTTTATTTTATTAAAAATATAAAAGAGTAAATTATAATTAAAATACTA
88319664 AAAACAACTTTTATTTTATTAAA
1 AAAACAACTTTTATTTTATTAAA
88319687 TGAAAAAGTA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 76 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (56 bp):
AAAACAACTTTTATTTTATTAAAAATATAAAAGAGTAAATTATAATTAAAATACTA
Found at i:88319677 original size:27 final size:26
Alignment explanation
Indices: 88319591--88319677 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 26
88319581 AAAGAGTAAA
88319591 TTATAATTAAAATACTAAAAACAACTT
1 TTATAATTAAAATA-TAAAAACAACTT
* * *
88319618 TTATTTTATTACAAATATAAAAGAGTAA--A
1 TTA--TAATTA-AAATATAAAA-A-CAACTT
88319647 TTATAATTAAAATATTAAAAACAACTT
1 TTATAATTAAAATA-TAAAAACAACTT
88319674 TTAT
1 TTAT
88319678 TTTATTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
25 2 0.04
26 6 0.13
27 17 0.37
29 13 0.28
30 6 0.13
31 2 0.04
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (26 bp):
TTATAATTAAAATATAAAAACAACTT
Found at i:88320135 original size:18 final size:18
Alignment explanation
Indices: 88320104--88320138 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88320094 AAAAGGAAAC
*
88320104 ATATAAGGATTAGGATAT
1 ATATAAGGACTAGGATAT
*
88320122 ATATAAGGGCTAGGATA
1 ATATAAGGACTAGGATA
88320139 CGCACCTAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.29
Consensus pattern (18 bp):
ATATAAGGACTAGGATAT
Found at i:88320759 original size:7 final size:7
Alignment explanation
Indices: 88320749--88320802 Score: 99
Period size: 7 Copynumber: 7.7 Consensus size: 7
88320739 TTGTATACAT
88320749 AATACTA
1 AATACTA
88320756 AATACTA
1 AATACTA
88320763 AATACTA
1 AATACTA
88320770 AATACTA
1 AATACTA
88320777 AATACTA
1 AATACTA
*
88320784 AATATTA
1 AATACTA
88320791 AATACTA
1 AATACTA
88320798 AATAC
1 AATAC
88320803 GAAAGAGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:88321843 original size:48 final size:48
Alignment explanation
Indices: 88321746--88321843 Score: 144
Period size: 48 Copynumber: 2.0 Consensus size: 48
88321736 ATAAAATTAA
* **
88321746 AATTAAAATTGCATAAATGAAAAAAATATTAAATTGTATTGAAAAATT
1 AATTAAAATTACATAAATGAAAAAAATATTAAATACTATTGAAAAATT
*
88321794 AATTAAAATTACATAAATTAAAAAAATATTAAATACTATT-AAAATATT
1 AATTAAAATTACATAAATGAAAAAAATATTAAATACTATTGAAAA-ATT
88321842 AA
1 AA
88321844 AATTATCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 4 0.09
48 41 0.91
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (48 bp):
AATTAAAATTACATAAATGAAAAAAATATTAAATACTATTGAAAAATT
Found at i:88322009 original size:10 final size:10
Alignment explanation
Indices: 88321994--88322059 Score: 71
Period size: 10 Copynumber: 6.4 Consensus size: 10
88321984 TAAAGAGAGC
*
88321994 TTTGAGACAA
1 TTTGAGAGAA
88322004 TTTGAGAGAA
1 TTTGAGAGAA
*
88322014 TATGAGAGAA
1 TTTGAGAGAA
*
88322024 TATGAGAGAA
1 TTTGAGAGAA
88322034 TTTTTG-GAAGAA
1 --TTTGAG-AGAA
88322046 TTTGAGAGAA
1 TTTGAGAGAA
88322056 TTTG
1 TTTG
88322060 GATAGGAGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
10 40 0.82
11 2 0.04
12 7 0.14
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:88324026 original size:15 final size:15
Alignment explanation
Indices: 88324006--88324034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88323996 TATACATGCA
88324006 AAATACAAAAGACAG
1 AAATACAAAAGACAG
88324021 AAATACAAAAGACA
1 AAATACAAAAGACA
88324035 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.07
Consensus pattern (15 bp):
AAATACAAAAGACAG
Found at i:88328898 original size:22 final size:21
Alignment explanation
Indices: 88328873--88328913 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
88328863 GCCGTCTAGG
*
88328873 AAAATTATATATATCAAATTCC
1 AAAAATATATAT-TCAAATTCC
88328895 AAAAATATATATTCAAATT
1 AAAAATATATATTCAAATT
88328914 GAAACCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATATATATTCAAATTCC
Found at i:88343741 original size:20 final size:21
Alignment explanation
Indices: 88343702--88343741 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
88343692 TAACTCTGAC
*
88343702 TTTGACTCATGATAACTTTGG
1 TTTGACACATGATAACTTTGG
*
88343723 TTTGACACAT-ATCACTTTG
1 TTTGACACATGATAACTTTG
88343742 TAATTAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTGACACATGATAACTTTGG
Found at i:88346689 original size:22 final size:21
Alignment explanation
Indices: 88346664--88346705 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
88346654 ATTTTAAATC
88346664 TAATAAATAATAATATTAATTG
1 TAATAAATAATAATA-TAATTG
*
88346686 TAATAAGTAATAATATAATT
1 TAATAAATAATAATATAATT
88346706 ATATACTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TAATAAATAATAATATAATTG
Found at i:88362335 original size:27 final size:27
Alignment explanation
Indices: 88362305--88362364 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
88362295 ATTTCAATTT
*
88362305 TATTTTAATAATAA-ATTTTAAAAATAA
1 TATTTTAAAAATAATATTTT-AAAATAA
*
88362332 TATTTTAAAAATAATATTTTTAAATAA
1 TATTTTAAAAATAATATTTTAAAATAA
88362359 TATTTT
1 TATTTT
88362365 TCACATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATTTTAAAAATAATATTTTAAAATAA
Found at i:88362338 original size:14 final size:14
Alignment explanation
Indices: 88362305--88362364 Score: 88
Period size: 13 Copynumber: 4.4 Consensus size: 14
88362295 ATTTCAATTT
*
88362305 TATTTTAATAATAA
1 TATTTTAAAAATAA
88362319 -ATTTTAAAAATAA
1 TATTTTAAAAATAA
88362332 TATTTTAAAAATAA
1 TATTTTAAAAATAA
*
88362346 TATTTT-TAAATAA
1 TATTTTAAAAATAA
88362359 TATTTT
1 TATTTT
88362365 TCACATATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
13 24 0.56
14 19 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTTAAAAATAA
Found at i:88362365 original size:14 final size:14
Alignment explanation
Indices: 88362307--88362365 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 14
88362297 TTCAATTTTA
88362307 TTTTAATAATAA-AT
1 TTTTAA-AATAATAT
*
88362321 TTTAAAAATAATAT
1 TTTTAAAATAATAT
*
88362335 TTTAAAAATAATAT
1 TTTTAAAATAATAT
88362349 TTTT-AAATAATAT
1 TTTTAAAATAATAT
88362362 TTTT
1 TTTT
88362366 CACATATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
13 18 0.43
14 24 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTTAAAATAATAT
Found at i:88362400 original size:49 final size:48
Alignment explanation
Indices: 88362343--88362438 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 48
88362333 ATTTTAAAAA
*
88362343 TAATATTTTTA-AAT-AATATTT-TTCACATATTATTAAAAATATTCAATAT
1 TAATATTTTGATAATAAATATTTATT-ACA-ATTA-TAAAAATATT-AATAT
*
88362392 TAATATTTTGATAATAAATATTTATTACAATTATAAATATATTAATA
1 TAATATTTTGATAATAAATATTTATTACAATTATAAAAATATTAATA
88362439 ATAAATGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
48 4 0.10
49 19 0.45
50 7 0.17
51 10 0.24
52 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (48 bp):
TAATATTTTGATAATAAATATTTATTACAATTATAAAAATATTAATAT
Found at i:88370001 original size:13 final size:13
Alignment explanation
Indices: 88369979--88370011 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
88369969 AAGGGTTTGT
88369979 TTAT-TAAACTAA
1 TTATCTAAACTAA
88369991 TTATCTAAACTAA
1 TTATCTAAACTAA
*
88370004 TTAACTAA
1 TTATCTAA
88370012 TTTAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:88372929 original size:6 final size:6
Alignment explanation
Indices: 88372863--88372921 Score: 100
Period size: 6 Copynumber: 9.8 Consensus size: 6
88372853 CTTTATAACG
* *
88372863 AAAAAT AAACAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAGT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
88372911 AAAAAT AAAAA
1 AAAAAT AAAAA
88372922 AATAAAAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:88378306 original size:13 final size:13
Alignment explanation
Indices: 88378284--88378316 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
88378274 AAGGGTTTGT
88378284 TTAT-TAAACTAA
1 TTATCTAAACTAA
88378296 TTATCTAAACTAA
1 TTATCTAAACTAA
*
88378309 TTAACTAA
1 TTATCTAA
88378317 TTTAATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:88380795 original size:7 final size:7
Alignment explanation
Indices: 88380783--88380807 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
88380773 AGTAAATAGA
88380783 TATTTAT
1 TATTTAT
88380790 TATTTAT
1 TATTTAT
88380797 TATTTAT
1 TATTTAT
88380804 TATT
1 TATT
88380808 AAGTAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:88380818 original size:34 final size:37
Alignment explanation
Indices: 88380758--88380825 Score: 106
Period size: 34 Copynumber: 1.9 Consensus size: 37
88380748 ATGGATTTAA
88380758 ATTACTTATTATTTAAGTAAATAGATATTTATTATTT
1 ATTACTTATTATTTAAGTAAATAGATATTTATTATTT
*
88380795 ATTATTTATTA-TTAAGT-AA-AGATATTTATTA
1 ATTACTTATTATTTAAGTAAATAGATATTTATTA
88380826 ATTAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 12 0.40
35 2 0.07
36 6 0.20
37 10 0.33
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (37 bp):
ATTACTTATTATTTAAGTAAATAGATATTTATTATTT
Found at i:88380842 original size:34 final size:35
Alignment explanation
Indices: 88380765--88380842 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
88380755 TAAATTACTT
* *
88380765 ATTAT-TTAAGTAAATAGATATTTATTATTTATTA
1 ATTATATTAAGTAAATAGATATTTATTATTAAATA
*
88380799 TTTATTATTAAGT-AA-AGATATTTATTAATTAAATA
1 ATTA-TATTAAGTAAATAGATATTTATT-ATTAAATA
88380834 ATTATATTA
1 ATTATATTA
88380843 TAAGATTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
34 19 0.51
35 12 0.32
36 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (35 bp):
ATTATATTAAGTAAATAGATATTTATTATTAAATA
Found at i:88382134 original size:39 final size:39
Alignment explanation
Indices: 88382086--88382236 Score: 194
Period size: 39 Copynumber: 3.9 Consensus size: 39
88382076 TTAATAGGGG
*
88382086 TAAACTACTGTACTGAATAATTGATAGTTTCTGAATAAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * *
88382125 TAAATTACTGTATTGAATAATTGATAGTTATTGAATAAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * *
88382164 TAAACTACTGCACTGAATATTTGATAGTTACTGAATGAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * * * *
88382203 TAAATTACTATACTAAATAACTGATTGTTACTGA
1 TAAACTACTGTACTGAATAATTGATAGTTACTGA
88382237 TTAAATATGA
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 95 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (39 bp):
TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
Found at i:88382143 original size:21 final size:20
Alignment explanation
Indices: 88382117--88382173 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
88382107 TGATAGTTTC
88382117 TGAATAACTAAATTACTGTAT
1 TGAATAACTAAA-TACTGTAT
** *
88382138 TGAATAA-TTGATAGT-TAT
1 TGAATAACTAAATACTGTAT
88382156 TGAATAACTAAACTACTG
1 TGAATAACTAAA-TACTG
88382174 CACTGAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
18 10 0.37
19 5 0.19
20 5 0.19
21 7 0.26
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAATAACTAAATACTGTAT
Found at i:88382158 original size:18 final size:18
Alignment explanation
Indices: 88382099--88382162 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
88382089 ACTACTGTAC
88382099 TGAATAATTGATAGTT-T
1 TGAATAATTGATAGTTAT
** *
88382116 CTGAATAACTAAATTACTGTAT
1 -TGAATAA-TTGA-TAGT-TAT
88382138 TGAATAATTGATAGTTAT
1 TGAATAATTGATAGTTAT
88382156 TGAATAA
1 TGAATAA
88382163 CTAAACTACT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 17 0.47
19 5 0.14
20 5 0.14
21 8 0.22
22 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (18 bp):
TGAATAATTGATAGTTAT
Found at i:88383189 original size:76 final size:74
Alignment explanation
Indices: 88383103--88383263 Score: 220
Period size: 76 Copynumber: 2.2 Consensus size: 74
88383093 ACCGCAACTC
* *
88383103 TCATGAGCTTCTCGATTAATGGCTT-TCCGGAGCTTCCTGATATTGGCTCACT-TGAACTTCCCG
1 TCATGAGCTTCCCGATTAATGG-TTCTCCGAAGCTTCCTGATATTGGCTC-CTATGAACTTCCC-
88383166 ATTAAAGGCTTTT
63 ATTAAAGGC-TTT
*
88383179 TCATGAGCTTCCCGATTAATGGTTCTCCGAAGCTTCCTGATATTGGCTCGTATGAACTTCCCATT
1 TCATGAGCTTCCCGATTAATGGTTCTCCGAAGCTTCCTGATATTGGCTCCTATGAACTTCCCATT
* *
88383244 TACGGCTTT
66 AAAGGCTTT
88383253 T-ATGAGCTTCC
1 TCATGAGCTTCC
88383264 TGTTACATGG
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
73 10 0.13
74 4 0.05
75 10 0.13
76 54 0.69
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (74 bp):
TCATGAGCTTCCCGATTAATGGTTCTCCGAAGCTTCCTGATATTGGCTCCTATGAACTTCCCATT
AAAGGCTTT
Found at i:88386651 original size:43 final size:43
Alignment explanation
Indices: 88386603--88386761 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
88386593 AGCTCGTACA
* * *
88386603 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
* * * *
88386646 ATGCC-ACTGTCCCAGATAGGGTTTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAATCAAATATCG
* * *
88386688 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAA-GTCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATCA-AATATCG
* *
88386732 ATGCCAACATCCCAGACATGGTATTACACG
1 ATGCCAACGTCCCAGACATGGTCTTACACG
88386762 AGAACACATA
Statistics
Matches: 94, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 27 0.29
43 38 0.40
44 29 0.31
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCG
Found at i:88389321 original size:32 final size:33
Alignment explanation
Indices: 88389251--88389322 Score: 78
Period size: 32 Copynumber: 2.2 Consensus size: 33
88389241 ATTCACATAT
*
88389251 CTTAAATAGATATAACCATTCAAGTAAGACCTTA
1 CTTAAATAAATATAACCATTCAAGTAAGA-CTTA
* * *
88389285 --TAAATAAATATAACTATTCAATTAATA-TTA
1 CTTAAATAAATATAACCATTCAAGTAAGACTTA
88389315 CTTAAATA
1 CTTAAATA
88389323 GTTAGAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
30 3 0.09
32 29 0.91
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.35
Consensus pattern (33 bp):
CTTAAATAAATATAACCATTCAAGTAAGACTTA
Found at i:88394061 original size:28 final size:28
Alignment explanation
Indices: 88394029--88394112 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
88394019 AACTTCGATC
88394029 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
88394057 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
*
88394079 ACGTGTGTAATACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
88394107 ACGTGT
1 ACGTGT
88394113 ACCGGATAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
21 1 0.02
22 8 0.20
23 2 0.05
24 3 0.07
25 6 0.15
26 3 0.07
27 2 0.05
28 14 0.34
29 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:88394102 original size:50 final size:49
Alignment explanation
Indices: 88393981--88394170 Score: 227
Period size: 50 Copynumber: 3.8 Consensus size: 49
88393971 TGAGGTCGCA
* * * *
88393981 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCACG
* **
88394032 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
* * * *
88394082 TGTGTAATACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
88394131 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
88394171 CCTTGTCTAC
Statistics
Matches: 119, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
49 40 0.34
50 45 0.38
51 34 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:88397151 original size:14 final size:13
Alignment explanation
Indices: 88397126--88397194 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 13
88397116 TCGTATCTTG
88397126 GGTTTCTTTATTCT
1 GGTTT-TTTATTCT
88397140 GGATTTTTTATTCT
1 GG-TTTTTTATTCT
88397154 AGGTTTTTCTA-TCTT
1 -GGTTTTT-TATTC-T
88397169 GGATTTCTTTATTC-
1 GG-TTT-TTTATTCT
88397183 GGTTTTCTTATT
1 GGTTTT-TTATT
88397195 ATCTTTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
12 1 0.02
13 8 0.17
14 21 0.45
15 13 0.28
16 4 0.09
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (13 bp):
GGTTTTTTATTCT
Found at i:88399671 original size:50 final size:49
Alignment explanation
Indices: 88399550--88399739 Score: 227
Period size: 50 Copynumber: 3.8 Consensus size: 49
88399540 TGAGGTCGCA
* * * *
88399550 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCACG
* * **
88399601 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
* * *
88399651 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
88399700 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
88399740 CCTTGTCTAC
Statistics
Matches: 119, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
49 41 0.34
50 45 0.38
51 33 0.28
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:88401904 original size:29 final size:29
Alignment explanation
Indices: 88401870--88401943 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
88401860 CAAAAATAAT
*
88401870 ACAAAG-ATGCACTGAAGTGCAATAACAAA
1 ACAAAGTA-GCACCGAAGTGCAATAACAAA
* *
88401899 GCAAAGTAGCACCGAAGTGCAATACCAAA
1 ACAAAGTAGCACCGAAGTGCAATAACAAA
*
88401928 ACAAAGTAGCATCGAA
1 ACAAAGTAGCACCGAA
88401944 ATAGAATGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (29 bp):
ACAAAGTAGCACCGAAGTGCAATAACAAA
Found at i:88405314 original size:40 final size:41
Alignment explanation
Indices: 88405259--88405438 Score: 199
Period size: 40 Copynumber: 4.4 Consensus size: 41
88405249 CAATTATGTT
*
88405259 TGGCACTTAGTGTGCGAATTGGAATAGCTTCGGCTAT-ATA
1 TGGCACTTAGTGTGCGAATTGGAATAGCTTCAGCTATGATA
*
88405299 TGGCACTTAGTGTGCGAATCGGAATAGCTTCAGCTAT-ATA
1 TGGCACTTAGTGTGCGAATTGGAATAGCTTCAGCTATGATA
*
88405339 TGGCACTTAGTGTGCAAGAA-T-GAGATAGCTTCGGCTATGA-A
1 TGGCACTTAGTGTGC--GAATTGGA-ATAGCTTCAGCTATGATA
* * ** * * *
88405380 AGGCACTTAGTATGCGAGATTATAATAGCTTTAGCTATGCTT
1 TGGCACTTAGTGTGCGA-ATTGGAATAGCTTCAGCTATGATA
88405422 TGGCACTTAGTGTGCGA
1 TGGCACTTAGTGTGCGA
88405439 GATATTGAGT
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
39 2 0.02
40 56 0.47
41 41 0.34
42 20 0.17
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (41 bp):
TGGCACTTAGTGTGCGAATTGGAATAGCTTCAGCTATGATA
Found at i:88405370 original size:81 final size:82
Alignment explanation
Indices: 88405259--88405438 Score: 217
Period size: 81 Copynumber: 2.2 Consensus size: 82
88405249 CAATTATGTT
* * *
88405259 TGGCACTTAGTGTGCGAATTGGAATAGCTTCGGCTAT-ATATGGCACTTAGTGTGCGA-ATCGGA
1 TGGCACTTAGTGTGCGAATTGGAATAGCTTCGGCTATGA-AAGGCACTTAGTATGCGAGATCAGA
88405322 ATAGCTTCAGCTAT-ATA
65 ATAGCTTCAGCTATGATA
*
88405339 TGGCACTTAGTGTGCAAGAA-T-GAGATAGCTTCGGCTATGAAAGGCACTTAGTATGCGAGATTA
1 TGGCACTTAGTGTGC--GAATTGGA-ATAGCTTCGGCTATGAAAGGCACTTAGTATGCGAGATCA
* * * *
88405402 TAATAGCTTTAGCTATGCTT
63 GAATAGCTTCAGCTATGATA
88405422 TGGCACTTAGTGTGCGA
1 TGGCACTTAGTGTGCGA
88405439 GATATTGAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
80 17 0.20
81 33 0.38
82 20 0.23
83 16 0.19
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (82 bp):
TGGCACTTAGTGTGCGAATTGGAATAGCTTCGGCTATGAAAGGCACTTAGTATGCGAGATCAGAA
TAGCTTCAGCTATGATA
Found at i:88405557 original size:12 final size:12
Alignment explanation
Indices: 88405540--88405564 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88405530 AGAAGTTATG
88405540 AACTTGTTCATA
1 AACTTGTTCATA
88405552 AACTTGTTCATA
1 AACTTGTTCATA
88405564 A
1 A
88405565 GCATGATGTA
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
AACTTGTTCATA
Found at i:88409354 original size:31 final size:31
Alignment explanation
Indices: 88409311--88409378 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
88409301 GCATCAGTGC
*
88409311 GATATGTGCTTCTGTGAAAGACCATATCTGG
1 GATATGTACTTCTGTGAAAGACCATATCTGG
88409342 GATATGTACTTCTGTGAAAGACCATATCTGG
1 GATATGTACTTCTGTGAAAGACCATATCTGG
88409373 GATATG
1 GATATG
88409379 GCATCAGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (31 bp):
GATATGTACTTCTGTGAAAGACCATATCTGG
Found at i:88411960 original size:35 final size:35
Alignment explanation
Indices: 88411869--88412035 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
88411859 CATGGCAAAG
*
88411869 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
88411904 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
*
88411939 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTAAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGT
** * *
88411979 TAAGAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGT
**
88412014 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
88412036 TCAATGAGGA
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.71
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 28 0.25
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGT
Found at i:88411993 original size:75 final size:75
Alignment explanation
Indices: 88411869--88412039 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
88411859 CATGGCAAAG
* ** *
88411869 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTAAGTTAAGAAATGTAGGTATGGCATT-TC
*
88411928 CCATACTGAGC
65 CCATACCGAGC
88411939 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTAAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTAAGTTAAGAAATGTAGGTATGGCATTTCC
*
88412004 CATACCGAGT
66 CATACCGAGC
**
88412014 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
88412040 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTAAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:88436657 original size:21 final size:21
Alignment explanation
Indices: 88436631--88436689 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
88436621 ATAGACTCTT
88436631 GAAACGACGCCGTTTTGGGCC
1 GAAACGACGCCGTTTTGGGCC
88436652 GAAACGACGCCGTTTTGGGCC
1 GAAACGACGCCGTTTTGGGCC
* *
88436673 AAAACGACGTCGTTTTG
1 GAAACGACGCCGTTTTG
88436690 ATCCTTACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (21 bp):
GAAACGACGCCGTTTTGGGCC
Found at i:88437051 original size:3 final size:3
Alignment explanation
Indices: 88437043--88437118 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
88437033 TTAATTTTAA
* * *
88437043 TAT TAT TAT TAT TAC TAT TAT CTTT TAT TAT TAT CT-C TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT
* * * *
88437089 TAA CA- TAT TAT TAT TCT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
88437119 TTTGTTATCT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:88437225 original size:9 final size:9
Alignment explanation
Indices: 88437211--88437239 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
88437201 TTACAAGCTG
88437211 TTTTATTTA
1 TTTTATTTA
88437220 TTTTATTT-
1 TTTTATTTA
88437228 TTTTATTTA
1 TTTTATTTA
88437237 TTT
1 TTT
88437240 ACCTATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATTTA
Found at i:88439812 original size:26 final size:26
Alignment explanation
Indices: 88439765--88439818 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
88439755 TATTTAGTTA
*
88439765 TTATACATTATTTTAATATTTTACCC
1 TTATACATCATTTTAATATTTTACCC
88439791 TTATACATCATTTTAATATTTTACCC
1 TTATACATCATTTTAATATTTTACCC
88439817 TT
1 TT
88439819 TCTACTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATACATCATTTTAATATTTTACCC
Found at i:88439920 original size:3 final size:3
Alignment explanation
Indices: 88439909--88439988 Score: 51
Period size: 3 Copynumber: 27.7 Consensus size: 3
88439899 AAAAAATGAT
** * * *
88439909 TTA TT- TTA TTA TCG TTA TTA CTA TTA CTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
88439956 TT- TTG TCT- TTG CTA TT- TTA TTA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TT
88439989 TTAAAAAAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
2 7 0.12
3 51 0.86
4 1 0.02
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:88450327 original size:48 final size:48
Alignment explanation
Indices: 88450238--88450424 Score: 191
Period size: 48 Copynumber: 3.9 Consensus size: 48
88450228 TGATACTAGG
* * *
88450238 GTTATGTGAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGACTTT
1 GTTATGAGAGCTAGTGTAAGACCATGTCTAGG-ACATGGCATCGACTTT
* * * * *
88450286 GTTACGAGAGCTAGTGTAAGACCATGTCTAGGACATAGCATCGGCCTC
1 GTTATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACTTT
** * * * *
88450334 AATATGTGAGCTAATGTAAGACTATGTTTA-GAGCATGGCATC-AGCTTT
1 GTTATGAGAGCTAGTGTAAGACCATGTCTAGGA-CATGGCATCGA-CTTT
*
88450382 GTTATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GTTATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCG
88450425 GCATCTTACC
Statistics
Matches: 108, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
47 2 0.02
48 101 0.94
49 5 0.05
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (48 bp):
GTTATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACTTT
Found at i:88450404 original size:96 final size:96
Alignment explanation
Indices: 88450240--88450426 Score: 286
Period size: 96 Copynumber: 1.9 Consensus size: 96
88450230 ATACTAGGGT
* *
88450240 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACTTTGTTACGAGAGCTAGTGTAA
1 TATGTGAGCCAATGTAAGACCATGTTTAGAACATGGCATCGACTTTGTTACGAGAGCTAGTGTAA
88450305 GACCATGTCTAGGACATAGCATCGGCCTCAA
66 GACCATGTCTAGGACATAGCATCGGCCTCAA
* * * *
88450336 TATGTGAGCTAATGTAAGACTATGTTTAGAGCATGGCATC-AGCTTTGTTATGAGAGCTAGTGTA
1 TATGTGAGCCAATGTAAGACCATGTTTAGAACATGGCATCGA-CTTTGTTACGAGAGCTAGTGTA
* *
88450400 AGACCATGTCTGGGACATGGCATCGGC
65 AGACCATGTCTAGGACATAGCATCGGC
88450427 ATCTTACCCT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 1 0.01
96 81 0.99
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (96 bp):
TATGTGAGCCAATGTAAGACCATGTTTAGAACATGGCATCGACTTTGTTACGAGAGCTAGTGTAA
GACCATGTCTAGGACATAGCATCGGCCTCAA
Found at i:88454527 original size:75 final size:75
Alignment explanation
Indices: 88454433--88454642 Score: 298
Period size: 75 Copynumber: 2.8 Consensus size: 75
88454423 GGCACACAAC
* ** * * * *
88454433 CGTCGGTTTATCCGACTAGCGTTAGGCGCAATTA-CAGTTGGTTCATCCAACTAGAGCTGGGATC
1 CGTCGGTATATCCGACTAGCACTGGGTGCAAATATC-GTTGGTTTATCCAACTAGAGCTGGGATC
*
88454497 ACAATTATTAT
65 ACAATTACTAT
*
88454508 CGTCGGTATATCCGACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCA
1 CGTCGGTATATCCGACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGATCA
88454573 CAATTACTAT
66 CAATTACTAT
* *
88454583 CGTAGGTATACCCGACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGA-CTGGG
1 CGTCGGTATATCCGACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
88454643 CTTACATTTA
Statistics
Matches: 123, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
74 5 0.04
75 117 0.95
76 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (75 bp):
CGTCGGTATATCCGACTAGCACTGGGTGCAAATATCGTTGGTTTATCCAACTAGAGCTGGGATCA
CAATTACTAT
Found at i:88454533 original size:40 final size:38
Alignment explanation
Indices: 88454489--88454642 Score: 117
Period size: 35 Copynumber: 4.1 Consensus size: 38
88454479 CCAACTAGAG
*
88454489 CTGGGATCACAATTATTATCGTCGGTATATCCGACTAGCA
1 CTGGG-TCACAATTA-TATCGTAGGTATATCCGACTAGCA
* * * *
88454529 CTGGGT-GCAA--ATATCGTTGGTTTATCCAACTAG-A
1 CTGGGTCACAATTATATCGTAGGTATATCCGACTAGCA
*
88454563 GCTGGGCTCACAATTACTATCGTAGGTATACCCGACTAGCA
1 -CTGGG-TCACAATTA-TATCGTAGGTATATCCGACTAGCA
* * * *
88454604 CTGGGT-GCAA--ATATCGTTGGTTTATCCAACTAG-A
1 CTGGGTCACAATTATATCGTAGGTATATCCGACTAGCA
88454638 CTGGG
1 CTGGG
88454643 CTTACATTTA
Statistics
Matches: 93, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
34 7 0.08
35 42 0.45
36 3 0.03
37 3 0.03
38 6 0.06
39 3 0.03
40 28 0.30
41 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (38 bp):
CTGGGTCACAATTATATCGTAGGTATATCCGACTAGCA
Found at i:88454555 original size:35 final size:34
Alignment explanation
Indices: 88454505--88454642 Score: 132
Period size: 35 Copynumber: 3.8 Consensus size: 34
88454495 TCACAATTAT
* *
88454505 TATCGTCGGTATATCCGACTAGCACTGGGTGCAAA
1 TATCGTTGGTATATCCAACTAG-ACTGGGTGCAAA
* *
88454540 TATCGTTGGTTTATCCAACTAGAGCTGGGCTCACAATTA
1 TATCGTTGGTATATCCAACTAGA-CTGGG-T-GCAA--A
* * *
88454579 CTATCGTAGGTATACCCGACTAGCACTGGGTGCAAA
1 -TATCGTTGGTATATCCAACTAG-ACTGGGTGCAAA
*
88454615 TATCGTTGGTTTATCCAACTAGACTGGG
1 TATCGTTGGTATATCCAACTAGACTGGG
88454643 CTTACATTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
34 7 0.08
35 42 0.51
36 2 0.02
37 3 0.04
38 3 0.04
39 2 0.02
40 23 0.28
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (34 bp):
TATCGTTGGTATATCCAACTAGACTGGGTGCAAA
Found at i:88459137 original size:17 final size:16
Alignment explanation
Indices: 88459069--88459134 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 16
88459059 TAATCACATT
* *
88459069 AATATTAAATTAATAA
1 AATATTAAATTTATTA
*
88459085 AATATT--ATCTAGTTA
1 AATATTAAATTTA-TTA
* *
88459100 AATATTTAATTTAATTC
1 AATATTAAATTT-ATTA
88459117 AATATTAAATTTATTA
1 AATATTAAATTTATTA
88459133 AA
1 AA
88459135 ATAATATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
14 3 0.08
15 8 0.21
16 11 0.28
17 16 0.41
18 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (16 bp):
AATATTAAATTTATTA
Found at i:88459519 original size:41 final size:41
Alignment explanation
Indices: 88459446--88459653 Score: 301
Period size: 41 Copynumber: 5.1 Consensus size: 41
88459436 CATTTTACCA
* * *
88459446 AAAACGACGCTAAAAA-CAGAGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
88459486 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
* * *
88459527 AAAACGACGCTAAAAATAAGAGCATTAGTGACGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
* * ** *
88459568 AAAGCGCCACTAAAAATCGGAGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
*
88459609 AAAGCGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
88459650 AAAA
1 AAAA
88459654 TCAGTTGGAT
Statistics
Matches: 148, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 15 0.10
41 133 0.90
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (41 bp):
AAAACGCCGCTAAAAATAAGAGCATTAGCGGCGCTTTTGGT
Found at i:88460199 original size:14 final size:13
Alignment explanation
Indices: 88460176--88460205 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
88460166 ATTACTATAA
88460176 TAATTATATGAAG
1 TAATTATATGAAG
88460189 TAATATATATGAAG
1 TAAT-TATATGAAG
88460203 TAA
1 TAA
88460206 AATTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:88460584 original size:183 final size:183
Alignment explanation
Indices: 88460276--88460644 Score: 686
Period size: 183 Copynumber: 2.0 Consensus size: 183
88460266 GATATAGTTC
* *
88460276 CATGTGTCTATATTAGTGAATTAATGTTGTATATGTTTCAGTTACTGCTTCCTGCTTCTCCTGCA
1 CATGTGTCTATATTAGTGAATTAATGTTGTATATATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
88460341 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
88460406 G-TTTTCATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GATTTT-ATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
* *
88460459 CATGTGTCTGTATTAGTGAATTAATGTTGTATGTATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
1 CATGTGTCTATATTAGTGAATTAATGTTGTATATATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
88460524 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
66 ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
88460589 GATTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
131 GATTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
88460642 CAT
1 CAT
88460645 CTGTTCTAGG
Statistics
Matches: 181, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
183 177 0.98
184 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (183 bp):
CATGTGTCTATATTAGTGAATTAATGTTGTATATATTTCAGTTACTGCTTCCTGCTCCTCCTGCA
ACTATTGGTTCAACTGAAGCTGCCATTTAATCTTCGAATTAATATTTGGTACTGATATAGATAAA
GATTTTATATTTGCTTAAACTGAAATATATTTGGTGCTACTCTTATAATCTTA
Found at i:88460865 original size:15 final size:15
Alignment explanation
Indices: 88460845--88460873 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88460835 GGAGTAGACC
88460845 AGGTACGTTTTATTA
1 AGGTACGTTTTATTA
88460860 AGGTACGTTTTATT
1 AGGTACGTTTTATT
88460874 TAAAATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (15 bp):
AGGTACGTTTTATTA
Found at i:88462269 original size:357 final size:358
Alignment explanation
Indices: 88461096--88462334 Score: 2365
Period size: 358 Copynumber: 3.5 Consensus size: 358
88461086 CTTGTCCATT
* *
88461096 AAAATTACAACAATGGATGACTTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
*
88461161 ATAGGCTGGAAACCTGACAGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
88461226 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
131 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
88461291 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
196 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
*
88461356 ATTATTATATTCAAATTACTATTTTTTTGTATTAATAATGTTTGATTTTAATATTTAATATTTTT
261 ATTATTATATTCAAATTACTATTTTTTTGCATTAATAATGTTTGATTTTAATATTTAATATTTTT
88461421 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
326 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
88461454 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
*
88461519 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAACTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
88461584 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
131 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
*
88461649 TCATTTACTAGTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
196 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
*
88461714 ATTATTATATTCAAATTACTATTCTTTTGCATTAATAATGTTTGATTTTAATATTTAATATTTTT
261 ATTATTATATTCAAATTACTATTTTTTTGCATTAATAATGTTTGATTTTAATATTTAATATTTTT
88461779 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
326 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
88461812 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
88461877 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
88461942 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
131 GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
88462007 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTC-TTTTTTAT
196 TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
88462071 ATTATTATATTCAAATTACTATTTTTTTGCATTAATAATGTTTGATTTTAATATTTAATATTTTT
261 ATTATTATATTCAAATTACTATTTTTTTGCATTAATAATGTTTGATTTTAATATTTAATATTTTT
88462136 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
326 AAATGTCTTTAAAAGTTATAACTAATTTTTATC
* *
88462169 AAAATTACAACAATGGTTGGCCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
1 AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
88462234 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
66 ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
*
88462299 GTAACAATG-CAGCGTATGATGAATCTTAAAAAATTC
131 GTAACAACGCCA-CGTATGATGAATCTTAAAAAATTC
88462335 TCCGTTTTAT
Statistics
Matches: 867, Mismatches: 13, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
356 2 0.00
357 265 0.31
358 600 0.69
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (358 bp):
AAAATTACAACAATGGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTAT
ATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGCAAGATATAATGGATCCTCCCTAGGT
GTAACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGC
TCATTTACTATTGAATATTTATTTCCAATTTACTTATAAAAATTAAACTACGATTCTTTTTTTAT
ATTATTATATTCAAATTACTATTTTTTTGCATTAATAATGTTTGATTTTAATATTTAATATTTTT
AAATGTCTTTAAAAGTTATAACTAATTTTTATC
Found at i:88462588 original size:15 final size:15
Alignment explanation
Indices: 88462544--88462599 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
88462534 AACGACATGT
*
88462544 ATATTACTTAATTAAA
1 ATATTATTTAATT-AA
88462560 ATAATT-TTT-A-TAA
1 AT-ATTATTTAATTAA
88462573 ATATTATTTAATTAA
1 ATATTATTTAATTAA
88462588 ATATTATTTAAT
1 ATATTATTTAAT
88462600 CCCGCTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 7 0.20
14 2 0.06
15 16 0.46
16 4 0.11
17 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:88462744 original size:9 final size:9
Alignment explanation
Indices: 88462704--88462893 Score: 107
Period size: 9 Copynumber: 20.6 Consensus size: 9
88462694 TATTTGATAT
*
88462704 CATAATTTA
1 CATAACTTA
*
88462713 TATAACTTA
1 CATAACTTA
* *
88462722 CAAAACGTA
1 CATAACTTA
88462731 CATAACTTA
1 CATAACTTA
*
88462740 TATAACTTA
1 CATAACTTA
* *
88462749 GATAA-ATA
1 CATAACTTA
*
88462757 TATAACTTA
1 CATAACTTA
88462766 CATAACTTA
1 CATAACTTA
88462775 CATAATACTTA
1 CAT-A-ACTTA
* *
88462786 AATATATTTTATA
1 CATA-A--CT-TA
*
88462799 TCATAATTTA
1 -CATAACTTA
88462809 CATAACTTA
1 CATAACTTA
88462818 CATAACTTA
1 CATAACTTA
*
88462827 TATAACTTA
1 CATAACTTA
* *
88462836 GATAA-ATA
1 CATAACTTA
* *
88462844 TATAATTTA
1 CATAACTTA
*
88462853 CATAA-ATA
1 CATAACTTA
* * *
88462861 TATATCATA
1 CATAACTTA
88462870 TCATAACTTA
1 -CATAACTTA
88462880 CATAACTTA
1 CATAACTTA
88462889 CATAA
1 CATAA
88462894 TACTTAAATA
Statistics
Matches: 142, Mismatches: 29, Indels: 20
0.74 0.15 0.10
Matches are distributed among these distances:
8 17 0.12
9 97 0.68
10 12 0.08
11 9 0.06
12 1 0.01
13 3 0.02
14 3 0.02
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (9 bp):
CATAACTTA
Found at i:88462760 original size:17 final size:17
Alignment explanation
Indices: 88462738--88462893 Score: 93
Period size: 17 Copynumber: 8.9 Consensus size: 17
88462728 GTACATAACT
*
88462738 TATATAACTTAGATAAA
1 TATATAACTTACATAAA
*
88462755 TATATAACTTACATAACT
1 TATATAACTTACATAA-A
* *
88462773 TACATAA--TACTTAAA
1 TATATAACTTACATAAA
** *
88462788 TATAT-TTTATATCATAATT
1 TATATAACT-TA-CATAA-A
* *
88462807 TACATAACTTACATAACT
1 TATATAACTTACATAA-A
*
88462825 TATATAACTTAGATAAA
1 TATATAACTTACATAAA
*
88462842 TATATAATTTACATAAA
1 TATATAACTTACATAAA
* * *
88462859 TATATATCATATCATAACT
1 TATATAACTTA-CATAA-A
*
88462878 TACATAACTTACATAA
1 TATATAACTTACATAA
88462894 TACTTAAATA
Statistics
Matches: 105, Mismatches: 25, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
15 4 0.04
16 6 0.06
17 40 0.38
18 40 0.38
19 14 0.13
20 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (17 bp):
TATATAACTTACATAAA
Found at i:88462875 original size:96 final size:96
Alignment explanation
Indices: 88462677--88462884 Score: 231
Period size: 96 Copynumber: 2.1 Consensus size: 96
88462667 ATAAAAAACT
* *
88462677 TACATAATACATAAATATATTTGATATCATAATTTATATAACTTACAAAACGTACATAACTTATA
1 TACATAATACATAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTAGA
* * * *
88462742 TAACTTAGATAAATATATAACTTACATAACT
66 TAACATAGATAAATACATAACATACATAACA
* * * * *
88462773 TACATAATACTTAAATATATTTTATATCATAATTTACATAACTTACATAACTTATATAACTTAGA
1 TACATAATACATAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTAGA
* * * *
88462838 TAA-ATATATAATTTACATAA-ATATATATCA
66 TAACATAGATAA-ATACATAACATACATAACA
88462868 TATCATAACTTACATAA
1 TA-CATAA--TACATAA
88462885 CTTACATAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
95 14 0.15
96 72 0.78
98 6 0.07
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (96 bp):
TACATAATACATAAATATATTTGATATCATAATTTACATAACTTACAAAACGTACATAACTTAGA
TAACATAGATAAATACATAACATACATAACA
Found at i:88468120 original size:13 final size:14
Alignment explanation
Indices: 88468104--88468132 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88468094 TTCTAAATAT
88468104 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
88468117 TTATAATTGTTTAA
1 TTATAATTGTTTAA
88468131 TT
1 TT
88468133 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:88468569 original size:21 final size:21
Alignment explanation
Indices: 88468544--88468605 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
88468534 TTAGAGCGGA
88468544 GGCAGCAGAGAGGGAGGCAGC
1 GGCAGCAGAGAGGGAGGCAGC
*
88468565 GGCAGCA-ACGAGAGAGGCAGC
1 GGCAGCAGA-GAGGGAGGCAGC
*
88468586 GGCAGCAGCGAGGGAGGCAG
1 GGCAGCAGAGAGGGAGGCAG
88468606 AGCATAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.29, C:0.21, G:0.50, T:0.00
Consensus pattern (21 bp):
GGCAGCAGAGAGGGAGGCAGC
Found at i:88469007 original size:43 final size:43
Alignment explanation
Indices: 88468979--88469189 Score: 368
Period size: 43 Copynumber: 4.9 Consensus size: 43
88468969 TTTGTGGGAA
* *
88468979 AAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTTTCTTC
1 AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTC
* *
88469022 AAGCGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTATTC
1 AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTC
* *
88469065 AAACACCGCTAAAGGCCACGACTTTTAGCGGCTCTTTTTCTTC
1 AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTC
88469108 AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTC
1 AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTC
88469151 AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTT
1 AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTT
88469190 TTTAATAAAC
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 158 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGCCACGACTTTTAGCGGCGCTTTTTCTTC
Found at i:88470729 original size:17 final size:18
Alignment explanation
Indices: 88470692--88470731 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
88470682 TGAATAATTT
* *
88470692 AAAATAATATAATATTCA
1 AAAATAATATAATAATAA
88470710 AAAAT-ATATAATAATAA
1 AAAATAATATAATAATAA
88470727 AAAAT
1 AAAAT
88470732 TCAAACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAATATAATAATAA
Found at i:88472382 original size:13 final size:13
Alignment explanation
Indices: 88472364--88472388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88472354 GCTAAGTCCT
88472364 TAGTTCTATGATA
1 TAGTTCTATGATA
88472377 TAGTTCTATGAT
1 TAGTTCTATGAT
88472389 GTTCGGTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (13 bp):
TAGTTCTATGATA
Found at i:88478374 original size:3 final size:3
Alignment explanation
Indices: 88478359--88478571 Score: 83
Period size: 3 Copynumber: 71.0 Consensus size: 3
88478349 TTTCGTTTCT
* * *
88478359 TTA TTA ATA TTA TTA TTA TT- TCTA ATA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
** *
88478404 TTA TTA TTA AAA TTA GTGTA -TA TTT TTA TTA TATA TGTA -TA TATA
1 TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA T-TA T-TA TTA T-TA
* * *
88478449 TTTA TATA TT- TATA TATA GTA TTA TTT TTAA TTA CT- TTA TT- TTA
1 -TTA T-TA TTA T-TA T-TA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* ** *
88478493 ATA TTA TTA TTA -TA TTA -TA TT- TGC TT- TT- TGTA TT- TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* *
88478533 TTA TT- TCTA TTA TTA TTA TTA TTA TTA TCA TCA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
88478572 ACATATATAT
Statistics
Matches: 160, Mismatches: 27, Indels: 46
0.69 0.12 0.20
Matches are distributed among these distances:
2 19 0.12
3 117 0.73
4 21 0.13
5 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:88478703 original size:24 final size:22
Alignment explanation
Indices: 88478676--88478731 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
88478666 TTATTATTAT
88478676 TTATTATTTTCTTTATTCTGAATA
1 TTATTATTTT-TTTATTCT-AATA
*
88478700 TTATTGTTATTTTTATTCTAATA
1 TTATTATT-TTTTTATTCTAATA
88478723 TTA-TATTTT
1 TTATTATTTT
88478732 AACATTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 7 0.24
24 15 0.52
25 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.04, T:0.66
Consensus pattern (22 bp):
TTATTATTTTTTTATTCTAATA
Found at i:88492295 original size:43 final size:44
Alignment explanation
Indices: 88492207--88492295 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
88492197 TTATGCCTAA
* *
88492207 AACAAAAAAGATTAAGGTGAAAACCCGAAAAGGGCGTCTTGATG
1 AACAAAAAAGATTAAGGTGAAAACCCGAAAAGGGCGTCCTAATG
* * *
88492251 AACAAAAAGGATT-AGGATGAAAACCTG-AGAGGGCGTCCTAATG
1 AACAAAAAAGATTAAGG-TGAAAACCCGAAAAGGGCGTCCTAATG
88492294 AA
1 AA
88492296 GTAAACCTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 18 0.46
44 21 0.54
ACGTcount: A:0.45, C:0.13, G:0.26, T:0.16
Consensus pattern (44 bp):
AACAAAAAAGATTAAGGTGAAAACCCGAAAAGGGCGTCCTAATG
Found at i:88493163 original size:78 final size:77
Alignment explanation
Indices: 88493078--88493422 Score: 421
Period size: 78 Copynumber: 4.5 Consensus size: 77
88493068 TTCTGTTTTT
* * *
88493078 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTAAGGTATTTTTAGT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
*
88493143 TCCTAATTTTCAA
66 TTCTAATTTTC-A
* * * * *
88493156 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCAGATCACGCACTGAGGTATTTTCAA-
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
88493220 TT-T-ATGTTTCA
66 TTCTAAT-TTTCA
* * **
88493231 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACGCTGATGTATTTT-TGT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
*
88493295 TTCTATTTTTCA
66 TTCTAATTTTCA
* * *
88493307 AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACACGTTGAGGTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
* **
88493372 TTATGTTTTTTCA
66 TTCT-AATTTTCA
* *
88493385 AAAAAAT-AGACTCATATTGCGAGAAGTGAGTTAAGCCT
1 AAAAAATCA-ACTCATATTGCGAGAGGTGAGTTGAGCCT
88493423 TTTAGTTTCT
Statistics
Matches: 229, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
75 59 0.26
76 67 0.29
77 7 0.03
78 96 0.42
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (77 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAAT
TTCTAATTTTCA
Found at i:88493543 original size:135 final size:134
Alignment explanation
Indices: 88493288--88493551 Score: 338
Period size: 135 Copynumber: 2.0 Consensus size: 134
88493278 CGCTGATGTA
* *
88493288 TTTTTGTTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAC
** * *
88493353 ACGTTGAGGTATTTTCAATTTATGTTTTTTCAAAAAAATAGACTCATATTGCGAGA-AGTGAGTT
66 ACACTGAGGTATTTTCAATTTATGTTTTTTCAAAAAAATAGACTCATAATCCGAGAGA-TGAGTT
88493417 AAGCC
130 AAGCC
* ** *
88493422 TTTTAGTTTCTGTTTTTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCA
1 TTTTAGTTTCTATTTTTC-AAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACA
* * *
88493487 CACACTGAGTTATTTTCAATTGTTACT-TTTTTTC-AAATATTA-ACTCATAATCCGAGAGATGA
65 CACACTGAGGTATTTTCAA-T-TTA-TGTTTTTTCAAAAAAATAGACTCATAATCCGAGAGATGA
88493549 GTT
127 GTT
88493552 GAACGTCAGT
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
134 16 0.14
135 77 0.69
136 8 0.07
137 10 0.09
138 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (134 bp):
TTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACAC
ACACTGAGGTATTTTCAATTTATGTTTTTTCAAAAAAATAGACTCATAATCCGAGAGATGAGTTA
AGCC
Found at i:88494489 original size:21 final size:19
Alignment explanation
Indices: 88494445--88494490 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
88494435 CTAGAGTAAC
*
88494445 ACCAAATCAGAAGCACAAT
1 ACCAAATCAGAAGAACAAT
*
88494464 ACCAAATCAGAGGAACTAAGT
1 ACCAAATCAGAAGAAC-AA-T
88494485 ACCAAA
1 ACCAAA
88494491 AAATCAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.61
20 2 0.09
21 7 0.30
ACGTcount: A:0.52, C:0.24, G:0.13, T:0.11
Consensus pattern (19 bp):
ACCAAATCAGAAGAACAAT
Found at i:88494620 original size:14 final size:14
Alignment explanation
Indices: 88494601--88494634 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
88494591 TATTAAGCAA
*
88494601 AAAAAAAAGAAACT
1 AAAAAAAACAAACT
*
88494615 AAAAAAAACACACT
1 AAAAAAAACAAACT
88494629 AAAAAA
1 AAAAAA
88494635 GTACATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.79, C:0.12, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAAAAACAAACT
Found at i:88495196 original size:3 final size:3
Alignment explanation
Indices: 88495188--88495231 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
88495178 CTTTATTAAA
* *
88495188 TAT TAT TAT TAT TAT TAT TAT T-T CTAA TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
88495232 ATAAAATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:88495276 original size:8 final size:8
Alignment explanation
Indices: 88495254--88495287 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
88495244 TATATTTTTA
88495254 TTATATAT
1 TTATATAT
88495262 GTATATATAT
1 -T-TATATAT
88495272 TTATATAT
1 TTATATAT
88495280 TTATATAT
1 TTATATAT
88495288 AATATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
TTATATAT
Found at i:88495300 original size:26 final size:26
Alignment explanation
Indices: 88495244--88495329 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
88495234 AAAATTAGTG
* * *
88495244 TATATTTTTATTATATATGTATATATATT
1 TATATATTTA-TATATA-ATAT-TATTTT
88495273 TATATATTTATATATAATATTATTTT
1 TATATATTTATATATAATATTATTTT
* *
88495299 TA-ATTACTTTAT-TTTAATATTATTAT
1 TATA-TA-TTTATATATAATATTATTTT
88495325 TATAT
1 TATAT
88495330 TATATTTGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
25 1 0.02
26 24 0.49
27 9 0.18
28 6 0.12
29 9 0.18
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (26 bp):
TATATATTTATATATAATATTATTTT
Found at i:88495523 original size:23 final size:22
Alignment explanation
Indices: 88495485--88495550 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
88495475 TATTAGAACA
* *
88495485 TTATTTTATTATTATTATTTTT
1 TTATTCTAATATTATTATTTTT
* *
88495507 TTATTGTGAATATTATTGTTATTT
1 TTATTCT-AATATTATTATT-TTT
88495531 TTATTCTAATATTA-TATTTT
1 TTATTCTAATATTATTATTTT
88495551 AATATTTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.05
22 9 0.24
23 17 0.46
24 9 0.24
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (22 bp):
TTATTCTAATATTATTATTTTT
Done.