Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 91 of 373
Found at i:28968728 original size:29 final size:29
Alignment explanation
Indices: 28968627--28968741 Score: 83
Period size: 29 Copynumber: 4.0 Consensus size: 29
28968617 TACCTGTATC
* *
28968627 TGGCCCATTA-AGCCC-AATCATATTCATA
1 TGGCCCATTACA-CCCAAATCACATTTATA
* * ** * *
28968655 TGACCCATCAGGCCCAAATCACCTGTATA
1 TGGCCCATTACACCCAAATCACATTTATA
**
28968684 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTACACCCAAATCACATTTATA
* * *
28968713 TGGCCCGTTACACCC-AGTCACATTCATA
1 TGGCCCATTACACCCAAATCACATTTATA
28968741 T
1 T
28968742 TCATGCTCAC
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
28 23 0.33
29 46 0.67
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (29 bp):
TGGCCCATTACACCCAAATCACATTTATA
Found at i:28976127 original size:101 final size:101
Alignment explanation
Indices: 28976008--28976202 Score: 250
Period size: 101 Copynumber: 1.9 Consensus size: 101
28975998 TTACATTAGT
* * * *
28976008 AGTGCCATAACCTAGTTAT-AGT-TTTATCATCAGAATGCCATAGCCCAGCCATGGTCTTGCATA
1 AGTGCCATAACCCAGTTATGA-TCTTT-TCATCAAAATGCCATAGCCCAACCATGGTCTTACATA
** * *
28976071 TAATTATTGTCATGGTCCAACCATGGTCTTATGTTCAA
64 TAAACACTGCCATGGTCCAACCATGGTCTTATGTTCAA
* * * *
28976109 AGTGGCATAACCCAGTTATGATCTTTTCATTAAAATGCCATAGCCCAACTATGGTCTTACATGTA
1 AGTGCCATAACCCAGTTATGATCTTTTCATCAAAATGCCATAGCCCAACCATGGTCTTACATATA
28976174 AACACTGCCATGGTCCAACCATGGTCTTA
66 AACACTGCCATGGTCCAACCATGGTCTTA
28976203 CCTATCAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
101 76 0.95
102 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (101 bp):
AGTGCCATAACCCAGTTATGATCTTTTCATCAAAATGCCATAGCCCAACCATGGTCTTACATATA
AACACTGCCATGGTCCAACCATGGTCTTATGTTCAA
Found at i:28976590 original size:124 final size:123
Alignment explanation
Indices: 28976353--28976604 Score: 400
Period size: 124 Copynumber: 2.0 Consensus size: 123
28976343 AAAGTTTAAC
* *
28976353 CATATGAACTTACCTGGGGTAGATTGTGGAAGTTGTAGTAATTCAGGGACTATTCGACTAATCTC
1 CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTCGACTAATCTC
*
28976418 CCTTTTTCTCGTTGGTCTACGAGCTCTTGATTTAAAATGTAAAATTTTTCATTCATTAG
66 CCTTTTTCTCGTTGGTCTACGAGCTCTTGATCTAAAATGTAAAATTTTT-ATTCATTAG
*
28976477 CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTC-AGCTAATTT
1 CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTCGA-CTAATCT
* * *
28976541 CCC-TTTTCTTGTTGGTTTACGGGCTCTTGATCTAAAATGTAAAATTTTTTATTCATTAG
65 CCCTTTTTCTCGTTGGTCTACGAGCTCTTGATCTAAAATGTAAAA-TTTTTATTCATTAG
28976600 CATAT
1 CATAT
28976605 ATTTCAATTT
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
123 52 0.44
124 67 0.56
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (123 bp):
CATATGAACTTACCTGGGGTAGATTGTGAAAATTGTAGTAATTCAGGGACTATTCGACTAATCTC
CCTTTTTCTCGTTGGTCTACGAGCTCTTGATCTAAAATGTAAAATTTTTATTCATTAG
Found at i:28980414 original size:29 final size:29
Alignment explanation
Indices: 28980359--28980416 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
28980349 TCTCGACATA
* * *
28980359 TACTGGGCCGAAGCCTTTCGTTTAACGGT
1 TACTAGGCCGAAGCCTTACGTTAAACGGT
28980388 TACTAGGCCGAAGCCTTAC-TGTAAACGGT
1 TACTAGGCCGAAGCCTTACGT-TAAACGGT
28980417 ATGACCCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (29 bp):
TACTAGGCCGAAGCCTTACGTTAAACGGT
Found at i:28980651 original size:25 final size:25
Alignment explanation
Indices: 28980623--28980692 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
28980613 CTATTTTAAT
*
28980623 AACTGGGGCAAAGCTCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
28980648 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
28980673 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
28980693 AGCACTTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:28981103 original size:109 final size:109
Alignment explanation
Indices: 28980921--28981127 Score: 351
Period size: 109 Copynumber: 1.9 Consensus size: 109
28980911 GGGTATCTCA
* * *
28980921 GTAATTCTACCTTACAAGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
* *
28980986 CTATAGGGGTATTTCAGTAATTCTACCTTACAATGGGTATTCCG
66 CTACAGGGGTATTTCAGTAATTCTACCCTACAATGGGTATTCCG
* *
28981030 GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCGGTAATTCTACC
1 GTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
28981095 CTACAGGGGTATTTCAGTAATTCTACCCTACAA
66 CTACAGGGGTATTTCAGTAATTCTACCCTACAA
28981128 GAGTATTTTA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 91 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (109 bp):
GTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACC
CTACAGGGGTATTTCAGTAATTCTACCCTACAATGGGTATTCCG
Found at i:28981143 original size:27 final size:27
Alignment explanation
Indices: 28980911--28981135 Score: 324
Period size: 27 Copynumber: 8.3 Consensus size: 27
28980901 TACCCCAAAA
* * *
28980911 GGGTATCTCAGTAATTCTACCTTACAA
1 GGGTATTTCAGTAATTCTACCCTACAG
*
28980938 GGGTATTTTAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
*
28980965 GGGTATTTCAGTAATTCTACCCTATAG
1 GGGTATTTCAGTAATTCTACCCTACAG
* *
28980992 GGGTATTTCAGTAATTCTACCTTACAAT
1 GGGTATTTCAGTAATTCTACCCTAC-AG
* *
28981020 GGGTATTCCGGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
*
28981047 GGGTATTTCAATAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
*
28981074 GGGTATTTCGGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
*
28981101 GGGTATTTCAGTAATTCTACCCTACAA
1 GGGTATTTCAGTAATTCTACCCTACAG
*
28981128 GAGTATTT
1 GGGTATTT
28981136 TAATAATTTT
Statistics
Matches: 176, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
27 153 0.87
28 23 0.13
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTACAG
Found at i:28981215 original size:81 final size:81
Alignment explanation
Indices: 28981130--28981360 Score: 204
Period size: 81 Copynumber: 2.9 Consensus size: 81
28981120 CCCTACAAGA
** * *
28981130 GTATTTTAATAATTTTGTC-AATTGAGGGTAAAACGGTAATTCTGTA-AATC-GAGGGTACTTT-
1 GTATTTTGGTAATTTTG-CAAACTGAGGGTAAAACGGTAATT-T-TACAAACTGAGGGTA-TTTC
28981191 GGTAATTTTACAAATCGA-GG
62 GGTAATTTTACAAA-CGAGGG
* ***
28981211 GTATTTCGGTAATTTTGCAAACTGAGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCGGTA
1 GTATTTTGGTAATTTTGCAAACTGAGGGTAAAACGGTAATTTTACAAACTGAGGGTATTTCGGTA
*
28981276 ATTTTACAAACTAGGG
66 ATTTTACAAACGAGGG
** ** **** *
28981292 GTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGT
1 GTATTTTGGTAATTTTGCAAACTGAGGGTAAAACGGTAATTTTACAAACTGA-GGGTATTTCGGT
28981356 AATTT
65 AATTT
28981361 GGTAAACTAA
Statistics
Matches: 128, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
79 2 0.02
80 11 0.09
81 115 0.90
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (81 bp):
GTATTTTGGTAATTTTGCAAACTGAGGGTAAAACGGTAATTTTACAAACTGAGGGTATTTCGGTA
ATTTTACAAACGAGGG
Found at i:28981320 original size:54 final size:54
Alignment explanation
Indices: 28981182--28981360 Score: 270
Period size: 54 Copynumber: 3.3 Consensus size: 54
28981172 TGTAAATCGA
* * *
28981182 GGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTGCAAACT-G
1 GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTCGGTAATTTTACAAACTAG
* *
28981235 AGGGTATTTCGGTAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAACTAG
1 -GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTCGGTAATTTTACAAACTAG
* * *
28981290 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTCGGTAATTTTACAAACTAG
28981344 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
28981361 GGTAAACTAA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 113 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACCGAGGGTATTTCGGTAATTTTACAAACTAG
Found at i:28981369 original size:27 final size:27
Alignment explanation
Indices: 28981182--28981360 Score: 222
Period size: 27 Copynumber: 6.6 Consensus size: 27
28981172 TGTAAATCGA
*
28981182 GGGTACTTT-GGTAATTTTACAAA-TCG
1 GGGTA-TTTCGGTAATTTTACAAACTAG
*
28981208 AGGGTATTTCGGTAATTTTGCAAACT-G
1 -GGGTATTTCGGTAATTTTACAAACTAG
28981235 AGGGTATTTCGGTAATTTTACAAACT-G
1 -GGGTATTTCGGTAATTTTACAAACTAG
28981262 AGGGTATTTCGGTAATTTTACAAACTAG
1 -GGGTATTTCGGTAATTTTACAAACTAG
* * * *
28981290 GGGTATTTTGGTAATTTTATAAACCAA
1 GGGTATTTCGGTAATTTTACAAACTAG
*
28981317 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTTACAAACTAG
*
28981344 GGGTATTTTGGTAATTT
1 GGGTATTTCGGTAATTT
28981361 GGTAAACTAA
Statistics
Matches: 140, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
26 3 0.02
27 135 0.96
28 2 0.01
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAACTAG
Found at i:28987918 original size:16 final size:16
Alignment explanation
Indices: 28987899--28987929 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28987889 CTTCTTCACT
28987899 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28987915 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28987930 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28987935 original size:20 final size:20
Alignment explanation
Indices: 28987896--28987935 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28987886 AAACTTCTTC
* *
28987896 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28987916 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28987936 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28988369 original size:55 final size:54
Alignment explanation
Indices: 28988121--28988375 Score: 215
Period size: 55 Copynumber: 4.8 Consensus size: 54
28988111 ACACGGGTAC
* * * **
28988121 CTTACC-ATTTCCATGACTTGTCATGGTCTTATGTGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * * * *
28988170 CTAACC-ATTGCCATGTCTCGACATTGTCTTACATGGTATCCTTACCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
* * * * *
28988223 CTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CATTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATC-CTTGCC-T-TAGAAA
* *
28988278 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * *
28988331 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTTTCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
28988376 AAACTCTAAT
Statistics
Matches: 165, Mismatches: 28, Indels: 20
0.77 0.13 0.09
Matches are distributed among these distances:
49 35 0.21
52 3 0.02
53 41 0.25
54 12 0.07
55 73 0.44
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
Found at i:28995519 original size:16 final size:16
Alignment explanation
Indices: 28995500--28995530 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28995490 CTTCTTCACT
28995500 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28995516 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28995531 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28995536 original size:20 final size:20
Alignment explanation
Indices: 28995497--28995536 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28995487 AAACTTCTTC
* *
28995497 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28995517 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28995537 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28995907 original size:108 final size:110
Alignment explanation
Indices: 28995770--28995970 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
28995760 ATCCTTTTGA
*
28995770 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTATG-AA-CTTACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTA-GAAACCTTACCAA
28995833 -TGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
* * * *
28995878 AACTTATCAATGCCATTTTTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTAGAAACCTTACCAAT
*
28995943 TTCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
28995971 TATCCTCAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.57
109 8 0.10
110 27 0.32
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTAGAAACCTTACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACATTTGCCTTATAGT
Found at i:28995971 original size:55 final size:54
Alignment explanation
Indices: 28995723--28995976 Score: 249
Period size: 55 Copynumber: 4.8 Consensus size: 54
28995713 ACACAGGTAC
* * * *
28995723 CTTACC-ATTGCCATGACTTGTCATGATCTTACGTGGTATCCTT---TT-GAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* *
28995772 CTTACC-ATTGCCATGTCTTGACATGGTCTTACATGGTACCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
* * * *
28995825 CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CATTTGCCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATC-CTTGCC-T-TAGAAA
* ***
28995880 CTTATCAA-TGCCATTTTTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* *
28995933 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCT
28995977 CAAACCCTAA
Statistics
Matches: 169, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
49 38 0.22
52 3 0.02
53 45 0.27
54 12 0.07
55 70 0.41
56 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
Found at i:29010423 original size:15 final size:15
Alignment explanation
Indices: 29010405--29010447 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
29010395 TCTGAGACAG
29010405 AGAAATCCAAGATAA
1 AGAAATCCAAGATAA
**
29010420 AGAAACTCCCAAGATTC
1 AGAAA-T-CCAAGATAA
29010437 AGAAATCCAAG
1 AGAAATCCAAG
29010448 TTACAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.51, C:0.21, G:0.14, T:0.14
Consensus pattern (15 bp):
AGAAATCCAAGATAA
Found at i:29014505 original size:40 final size:40
Alignment explanation
Indices: 29014407--29014749 Score: 476
Period size: 40 Copynumber: 8.6 Consensus size: 40
29014397 TCCTCGTTCA
* * * * *
29014407 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
29014446 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29014486 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
29014526 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29014566 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
29014606 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
29014646 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
29014686 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
29014726 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29014750 CAGCATTCAA
Statistics
Matches: 278, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 37 0.13
40 233 0.84
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:29020275 original size:20 final size:21
Alignment explanation
Indices: 29020250--29020291 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29020240 TCTTTGAAAC
29020250 AAGGC-ACACGCTCGTGTGGA
1 AAGGCAACACGCTCGTGTGGA
29020270 AAGGCAACACGCTCGTGTGGA
1 AAGGCAACACGCTCGTGTGGA
29020291 A
1 A
29020292 TTAATTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.29, C:0.24, G:0.33, T:0.14
Consensus pattern (21 bp):
AAGGCAACACGCTCGTGTGGA
Found at i:29022261 original size:45 final size:45
Alignment explanation
Indices: 29022142--29022264 Score: 187
Period size: 45 Copynumber: 2.7 Consensus size: 45
29022132 CATCCATTAT
* *
29022142 GAACTTGGACCAACTCCACAAGCTTGGA-TGCTTCACATATACCAC
1 GAACTTGGACCAACTCAACAAGCTTGGATTTC-TCACATATACCAC
*
29022187 GAACTTGGACCAACTCAACAAG-TTCGGATTTCTCACATATATCAC
1 GAACTTGGACCAACTCAACAAGCTT-GGATTTCTCACATATACCAC
29022232 GAACTTGGACCAACTCAACAAGCTTGGATTTCT
1 GAACTTGGACCAACTCAACAAGCTTGGATTTCT
29022265 TAATTCCTAG
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
44 2 0.03
45 66 0.92
46 4 0.06
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (45 bp):
GAACTTGGACCAACTCAACAAGCTTGGATTTCTCACATATACCAC
Found at i:29027014 original size:27 final size:27
Alignment explanation
Indices: 29026984--29027161 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29026974 ATATTGAGTC
* * * *
29026984 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29027011 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29027038 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29027066 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29027093 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29027120 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29027147 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29027162 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29027123 original size:82 final size:81
Alignment explanation
Indices: 29027005--29027160 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29026995 TGCTATATAA
* *
29027005 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29027070 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29027087 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29027151 CACTTAGTGC
65 CACTTAGTGC
29027161 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29036395 original size:43 final size:43
Alignment explanation
Indices: 29036348--29036461 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
29036338 TCACATATCG
* * * *
29036348 ATGCCACTGTCCTAGATAGCGTCTTACACAAAATCA-TATAACA
1 ATGCCAATGTCCCAGACAGCGTCTTACACAAAATCACAAT-ACA
** *
29036391 ATGCCAATGTCCCAGACATTGTCTTACACATAATCACAATACA
1 ATGCCAATGTCCCAGACAGCGTCTTACACAAAATCACAATACA
29036434 ATGCCAATGTCCCAGACATG-GTCTTACA
1 ATGCCAATGTCCCAGACA-GCGTCTTACA
29036462 TGTAACCACA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 59 0.97
44 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGCGTCTTACACAAAATCACAATACA
Found at i:29038711 original size:15 final size:15
Alignment explanation
Indices: 29038693--29038724 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29038683 CATTTCACTA
29038693 TTATGTATTTTATAT
1 TTATGTATTTTATAT
*
29038708 TTATGTCTTTTATAT
1 TTATGTATTTTATAT
29038723 TT
1 TT
29038725 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (15 bp):
TTATGTATTTTATAT
Found at i:29044615 original size:106 final size:107
Alignment explanation
Indices: 29044490--29044705 Score: 371
Period size: 106 Copynumber: 2.0 Consensus size: 107
29044480 GCATGCTCAT
* * * **
29044490 TTTTATTTTGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACTTGTCCAAGTATGGG
1 TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
29044555 CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTG-A
66 CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTGCA
29044596 TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
1 TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
*
29044661 CTGAAAATTTTGTTCATCAAATCCATAAACACTGTAGGTGCA
66 CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTGCA
29044703 TTT
1 TTT
29044706 GTCAAGTCGA
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 99 0.96
107 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (107 bp):
TTTTATTTCGAGAGTAAACCAAAATATCATCTATAAATACCATCACAAACCTGTCCAAATACAGG
CTGAAAATTTTGTTCATCAAATCCATAAACACTGCAGGTGCA
Found at i:29049499 original size:45 final size:45
Alignment explanation
Indices: 29049435--29049522 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
29049425 AAACATGTGC
*
29049435 CACATACATCATGAACTCAGACCACAACTCAATAAGTTTAGATGT
1 CACATACATCATGAACTCAGACCACAACTCAATAAGTTCAGATGT
* *
29049480 CACATATATCATGAACTCAGACCACAACTCAATGAGTTCAGAT
1 CACATACATCATGAACTCAGACCACAACTCAATAAGTTCAGAT
29049523 CACATAGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (45 bp):
CACATACATCATGAACTCAGACCACAACTCAATAAGTTCAGATGT
Found at i:29052755 original size:31 final size:29
Alignment explanation
Indices: 29052720--29052777 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
29052710 ACTAGTATTT
*
29052720 TATTAATTTAATATTAAAGTGATTATCTTAA
1 TATTAAATTAA-ATTAAA-TGATTATCTTAA
* *
29052751 TATTAAATTAAATTTAATGTTTATCTT
1 TATTAAATTAAATTAAATGATTATCTT
29052778 GTAGATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 5 0.21
31 10 0.42
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (29 bp):
TATTAAATTAAATTAAATGATTATCTTAA
Found at i:29056563 original size:31 final size:32
Alignment explanation
Indices: 29056528--29056593 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
29056518 TTTTATAGCT
* *
29056528 AAATTTGGCCATCAATCTTTT-AAAAAGAGTC
1 AAATTTGACCATCAACCTTTTGAAAAAGAGTC
**
29056559 AAATTTGACCATTGACCTTTTGAAAAAGAGTC
1 AAATTTGACCATCAACCTTTTGAAAAAGAGTC
29056591 AAA
1 AAA
29056594 ATGATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 17 0.57
32 13 0.43
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (32 bp):
AAATTTGACCATCAACCTTTTGAAAAAGAGTC
Found at i:29057445 original size:23 final size:23
Alignment explanation
Indices: 29057419--29057467 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29057409 ATTATTTGTA
29057419 AATATGTT-TAAACATATTCATTT
1 AATAT-TTGTAAACATATTCATTT
* *
29057442 AATATTTGTAAATATATTTATTT
1 AATATTTGTAAACATATTCATTT
29057465 AAT
1 AAT
29057468 TTCATGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
AATATTTGTAAACATATTCATTT
Found at i:29057757 original size:16 final size:18
Alignment explanation
Indices: 29057736--29057772 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29057726 TTTATAATAC
29057736 TTTT-TATATTATGTAAT
1 TTTTATATATTATGTAAT
29057753 TTTTATATATTATGTAAT
1 TTTTATATATTATGTAAT
29057771 TT
1 TT
29057773 ATAACACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTATATATTATGTAAT
Found at i:29057906 original size:26 final size:26
Alignment explanation
Indices: 29057839--29057907 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
29057829 ATATTAGAAT
* *
29057839 AATATTAAAATGATGATAAAAAAATTC
1 AATATTAAAATAAT-ATAAAAAAATTA
* **
29057866 AATAAATAAAA-AATATAAAATTATTA
1 AAT-ATTAAAATAATATAAAAAAATTA
29057892 AATATTAAAATAATAT
1 AATATTAAAATAATAT
29057908 CATATAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 6 0.18
26 17 0.50
27 5 0.15
28 6 0.18
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (26 bp):
AATATTAAAATAATATAAAAAAATTA
Found at i:29064981 original size:29 final size:30
Alignment explanation
Indices: 29064945--29065004 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29064935 TCCTTAACTC
29064945 AAACTTTT-CAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * * *
29064974 AAACTTTTGCATATTTACACTTTTTCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
29065004 A
1 A
29065005 GGCTTGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.30, C:0.25, G:0.03, T:0.42
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:29073691 original size:39 final size:39
Alignment explanation
Indices: 29073630--29073793 Score: 247
Period size: 39 Copynumber: 4.2 Consensus size: 39
29073620 GAAATGTGTA
29073630 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* * * *
29073669 TGGAAATATATCTGGGCCAAAGACCTGCAGGCTTCGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
29073708 TGGAAATGTATCCGGGCTAAAGACCCTCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
* *
29073747 TGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTGC
1 TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
*
29073786 TGGTAATA
1 TGGAAATA
29073794 AAATTTCGGG
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (39 bp):
TGGAAATATATCCGGGCTAAAGACCCGCAGGCTTTGTGC
Found at i:29098401 original size:27 final size:27
Alignment explanation
Indices: 29098369--29098473 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
29098359 AGGAAGTGTC
* *
29098369 CTGGTGGTTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
29098396 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
29098423 CTAGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* * *
29098450 CTTGTGACTCTGTCAC-ATTATCTG
1 CTGGTGGCTCTGCCACAATTATCTG
29098474 TTGTGGCAGC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.14
27 57 0.83
28 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:29099878 original size:24 final size:24
Alignment explanation
Indices: 29099851--29099909 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
29099841 ATGTTTAAGT
29099851 GAGCTATATTACGAAGCTCATAAA
1 GAGCTATATTACGAAGCTCATAAA
* * *
29099875 GAGCCTATATCAGGATGCTCATAAA
1 GAG-CTATATTACGAAGCTCATAAA
* *
29099900 AAGCTGTATT
1 GAGCTATATT
29099910 TGTGTCTGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
GAGCTATATTACGAAGCTCATAAA
Found at i:29103937 original size:21 final size:21
Alignment explanation
Indices: 29103908--29103952 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
29103898 TATAAACTAT
* *
29103908 ATTTCTTAATTAGTTTTTTAAA
1 ATTTCTTAATGA-TTTTTCAAA
29103930 ATTT-TTAATGATTTTTCAAA
1 ATTTCTTAATGATTTTTCAAA
29103950 ATT
1 ATT
29103953 AGAATAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 6 0.29
22 4 0.19
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTCTTAATGATTTTTCAAA
Found at i:29109254 original size:21 final size:21
Alignment explanation
Indices: 29109230--29109269 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29109220 ATTTAACATC
*
29109230 AATTTAATCCATTTCACACTT
1 AATTTAATCCAATTCACACTT
*
29109251 AATTTAATTCAATTCACAC
1 AATTTAATCCAATTCACAC
29109270 CCTAAGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTAATCCAATTCACACTT
Found at i:29110183 original size:39 final size:39
Alignment explanation
Indices: 29110129--29110206 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
29110119 CACTGAAAAC
29110129 GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
1 GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
*
29110168 GGGCTATTACATTTTCCAATGCAAATTCAAACAGTTAAT
1 GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
29110207 CAATCTTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (39 bp):
GGGCTATTACATTTTCCAATGCAAATTCAAACAATTAAT
Found at i:29111655 original size:25 final size:25
Alignment explanation
Indices: 29111627--29111685 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
29111617 CAGCTCGTAT
29111627 GAGCTTACCGTTATTCAGCTCAGAG
1 GAGCTTACCGTTATTCAGCTCAGAG
* *
29111652 GAGCTTACTGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCAGAG
*
29111677 GAACTTACC
1 GAGCTTACC
29111686 TTTTACAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCAGAG
Found at i:29113689 original size:22 final size:22
Alignment explanation
Indices: 29113663--29113706 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
29113653 AAAATAAATC
*
29113663 AAAATTAATTAAAATTTAATAT
1 AAAATTAATTAAAATTAAATAT
29113685 AAAATTAATTAAAATTAAATAT
1 AAAATTAATTAAAATTAAATAT
29113707 GTTAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATTAATTAAAATTAAATAT
Found at i:29113692 original size:11 final size:10
Alignment explanation
Indices: 29113653--29113702 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
29113643 AAATCTGTCG
* *
29113653 AAAATAAATC
1 AAAATTAATT
29113663 AAAATTAATT
1 AAAATTAATT
29113673 AAAATTTAATAT
1 AAAA-TTAAT-T
29113685 AAAATTAATT
1 AAAATTAATT
29113695 AAAATTAA
1 AAAATTAA
29113703 ATATGTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
10 21 0.58
11 10 0.28
12 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATTAATT
Found at i:29118824 original size:16 final size:16
Alignment explanation
Indices: 29118803--29118833 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29118793 AATTAATTTA
*
29118803 AATTAATTAATTTTCC
1 AATTAAATAATTTTCC
29118819 AATTAAATAATTTTC
1 AATTAAATAATTTTC
29118834 TCAACCCAAT
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:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTAAATAATTTTCC
Found at i:29129146 original size:17 final size:18
Alignment explanation
Indices: 29129120--29129153 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29129110 TTTTTGTTTA
29129120 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
29129137 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
29129154 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:29132234 original size:9 final size:9
Alignment explanation
Indices: 29132220--29132253 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
29132210 ATTTTATAAT
29132220 TAATTTTGG
1 TAATTTTGG
29132229 TAATTTTGG
1 TAATTTTGG
29132238 TTAATTTTGAG
1 -TAATTTTG-G
29132249 TAATT
1 TAATT
29132254 ATACTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 13 0.57
11 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (9 bp):
TAATTTTGG
Found at i:29132261 original size:20 final size:19
Alignment explanation
Indices: 29132213--29132261 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
29132203 TTAGTTAATT
29132213 TTATAATTAATTTTGGTAA
1 TTATAATTAATTTTGGTAA
* **
29132232 TTTTGGTTAATTTTGAGTAA
1 TTATAATTAATTTTG-GTAA
*
29132252 TTATACTTAA
1 TTATAATTAA
29132262 ATTATAATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (19 bp):
TTATAATTAATTTTGGTAA
Found at i:29134734 original size:58 final size:58
Alignment explanation
Indices: 29134641--29134763 Score: 146
Period size: 58 Copynumber: 2.1 Consensus size: 58
29134631 TTCTTGTTTT
* *
29134641 CATTTCCATTTT--TTTTAAAGAAAACCATATTCATTTCCT-AATGATTCC-ATTTTCTC
1 CATTT-CATTTTCATTTTAAAGAAAACCATAATCATTTCCTGAACGATTCCTA-TTTCTC
* * *
29134697 CAATTTCATTTTCATTTTGAAGTAAACCATAATCATTTCCTGAACGTTTCCTATTTCTC
1 C-ATTTCATTTTCATTTTAAAGAAAACCATAATCATTTCCTGAACGATTCCTATTTCTC
29134756 CATTTCAT
1 CATTTCAT
29134764 CAATTCTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
56 7 0.12
57 4 0.07
58 31 0.54
59 14 0.25
60 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.46
Consensus pattern (58 bp):
CATTTCATTTTCATTTTAAAGAAAACCATAATCATTTCCTGAACGATTCCTATTTCTC
Found at i:29136654 original size:20 final size:20
Alignment explanation
Indices: 29136629--29136669 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29136619 AGCATTGTAA
* *
29136629 TGAGGCACTGAAGTGCAAAC
1 TGAGGCACTAAAGTGAAAAC
29136649 TGAGGCACTAAAGTGAAAAC
1 TGAGGCACTAAAGTGAAAAC
29136669 T
1 T
29136670 CATACAAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (20 bp):
TGAGGCACTAAAGTGAAAAC
Found at i:29144004 original size:15 final size:15
Alignment explanation
Indices: 29143984--29144015 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29143974 TTAACTACAT
29143984 TTTCACAATCTATAG
1 TTTCACAATCTATAG
*
29143999 TTTCACAGTCTATAG
1 TTTCACAATCTATAG
29144014 TT
1 TT
29144016 CCAGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (15 bp):
TTTCACAATCTATAG
Found at i:29144746 original size:21 final size:21
Alignment explanation
Indices: 29144707--29144746 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29144697 GTCTTATGCC
*
29144707 ACAGTCCATAAAAATAATAAG
1 ACAGTCCATAAAAACAATAAG
29144728 ACAGTCC-TAAAATACAATA
1 ACAGTCCATAAAA-ACAATA
29144747 TAATAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.20
Consensus pattern (21 bp):
ACAGTCCATAAAAACAATAAG
Found at i:29163579 original size:27 final size:27
Alignment explanation
Indices: 29163549--29163726 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
29163539 ATATTGAGTC
* * * *
29163549 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29163576 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
29163603 CGCACACTTAGTGCTACATAGTCAACCT
1 CGCACACTTAGTGCTACATAGTCAA-AT
** * *
29163631 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29163658 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29163685 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29163712 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29163727 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29163688 original size:82 final size:81
Alignment explanation
Indices: 29163570--29163725 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
29163560 TGCTATATAA
* * *
29163570 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAACCTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAA-ATCGCA
29163635 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29163652 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29163716 CACTTAGTGC
65 CACTTAGTGC
29163726 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29170507 original size:71 final size:71
Alignment explanation
Indices: 29170430--29170606 Score: 300
Period size: 71 Copynumber: 2.5 Consensus size: 71
29170420 TCACCAGATA
29170430 CAGATATTGTGGCTAGGCCACCAGAACAAATATATATATGTGACGAAGTCACCGGATTGTAGCGA
1 CAGATATTGTGGCTAGGCCACCAGAACAAATATATATATGTGACGAAGTCACCGGATTGTAGCGA
29170495 GGCTGC
66 GGCTGC
*
29170501 CAGATATTGTGGCTAGGCCACCAGAACAAATATATATATGTGGCGAAGTCACCGGATTGTAGCGA
1 CAGATATTGTGGCTAGGCCACCAGAACAAATATATATATGTGACGAAGTCACCGGATTGTAGCGA
29170566 GGCTGC
66 GGCTGC
* * * * *
29170572 CAGATATTGTGACGAAGTCACCAGAACAGATATAT
1 CAGATATTGTGGCTAGGCCACCAGAACAAATATAT
29170607 GTGGCGAGGC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 100 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (71 bp):
CAGATATTGTGGCTAGGCCACCAGAACAAATATATATATGTGACGAAGTCACCGGATTGTAGCGA
GGCTGC
Found at i:29170642 original size:67 final size:68
Alignment explanation
Indices: 29170430--29170642 Score: 212
Period size: 71 Copynumber: 3.1 Consensus size: 68
29170420 TCACCAGATA
* * * * * * *
29170430 CAGATATTGTGGCTAGGCCACCAGAACAAATATATATATGTGACGAAGTCACCGGATTGTAGCGA
1 CAGATATTGTGACGAAGCCACCAGAAC--A-AGATATATGTGGCGAAGCCACCAGATTGTAGCGA
29170495 GGCTGC
63 GGCTGC
* * * * * *
29170501 CAGATATTGTGGCTAGGCCACCAGAACAAATATATATATGTGGCGAAGTCACCGGATTGTAGCGA
1 CAGATATTGTGACGAAGCCACCAGAAC--A-AGATATATGTGGCGAAGCCACCAGATTGTAGCGA
29170566 GGCTGC
63 GGCTGC
* * * *
29170572 CAGATATTGTGACGAAGTCACCAGAAC-AGATATATGTGGCGAGGCCACTAGATTGCAGCGAGGC
1 CAGATATTGTGACGAAGCCACCAGAACAAGATATATGTGGCGAAGCCACCAGATTGTAGCGAGGC
29170636 TGC
66 TGC
29170639 CAGA
1 CAGA
29170643 ACGCTTCCTC
Statistics
Matches: 131, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
67 38 0.29
71 93 0.71
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (68 bp):
CAGATATTGTGACGAAGCCACCAGAACAAGATATATGTGGCGAAGCCACCAGATTGTAGCGAGGC
TGC
Found at i:29176131 original size:45 final size:45
Alignment explanation
Indices: 29176046--29176131 Score: 100
Period size: 45 Copynumber: 1.9 Consensus size: 45
29176036 TATACGCCTA
** * *
29176046 AAATGAGTAAGACCATAGCTGAAAGATATTATGGCTTCATGATAT
1 AAATGAGTAAGACCATAGCTGAAAGATACCACGGCATCATGATAT
* * * *
29176091 AAATGTGTAAGACCCTGGCTGAAAGATGCCACGGCATCATG
1 AAATGAGTAAGACCATAGCTGAAAGATACCACGGCATCATG
29176132 GTAAATATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGATACCACGGCATCATGATAT
Found at i:29176398 original size:27 final size:28
Alignment explanation
Indices: 29176368--29176428 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
29176358 TGGCATCAAA
*
29176368 GATAGTCT-GACGGGA-TGTTAAACATGG
1 GATAGTCTCGACGAGACT-TTAAACATGG
29176395 GATAGT-TCGACGAGACTTTAAACATGG
1 GATAGTCTCGACGAGACTTTAAACATGG
29176422 GATAGTC
1 GATAGTC
29176429 CAATAGGACG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.03
27 28 0.93
28 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (28 bp):
GATAGTCTCGACGAGACTTTAAACATGG
Found at i:29176442 original size:27 final size:27
Alignment explanation
Indices: 29176384--29176445 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
29176374 CTGACGGGAT
* * *
29176384 GTTAAACATGGGATAGTTCGACGAGAC
1 GTTAAACATGGGATAGTCCAAAGAGAC
*
29176411 TTTAAACATGGGATAGTCCAATAG-GAC
1 GTTAAACATGGGATAGTCCAA-AGAGAC
29176438 GTTAAACA
1 GTTAAACA
29176446 CACGGCCATG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (27 bp):
GTTAAACATGGGATAGTCCAAAGAGAC
Found at i:29179158 original size:12 final size:12
Alignment explanation
Indices: 29179141--29179165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29179131 TCTGAAGTCG
29179141 TAATATTATTTT
1 TAATATTATTTT
29179153 TAATATTATTTT
1 TAATATTATTTT
29179165 T
1 T
29179166 GGTGTTTACA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TAATATTATTTT
Found at i:29179780 original size:28 final size:29
Alignment explanation
Indices: 29179749--29179804 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
29179739 AAAGTGATTT
*
29179749 TTGAAAAAAATGTCAATT-AGGGATTAAA
1 TTGAAAAAAATGTAAATTGAGGGATTAAA
* * *
29179777 TTGAGAAAAGTGTAAATTGAGGGGTTAA
1 TTGAAAAAAATGTAAATTGAGGGATTAA
29179805 TTTGTGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.29
Consensus pattern (29 bp):
TTGAAAAAAATGTAAATTGAGGGATTAAA
Found at i:29179804 original size:29 final size:28
Alignment explanation
Indices: 29179749--29179813 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
29179739 AAAGTGATTT
* *
29179749 TTGAAAAAAATGTCAATTAGGGATTAAA
1 TTGAGAAAAATGTAAATTAGGGATTAAA
* * *
29179777 TTGAGAAAAGTGTAAATTGAGGGGTTAAT
1 TTGAGAAAAATGTAAATT-AGGGATTAAA
*
29179806 TTGTGAAA
1 TTGAGAAA
29179814 TAAATGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.43, C:0.02, G:0.25, T:0.31
Consensus pattern (28 bp):
TTGAGAAAAATGTAAATTAGGGATTAAA
Found at i:29203341 original size:43 final size:43
Alignment explanation
Indices: 29203259--29203414 Score: 97
Period size: 43 Copynumber: 3.7 Consensus size: 43
29203249 TGTGATTACA
* * *
29203259 TGTAAGACCATTTCTGGGACATCGGCATTGTATTGCGATTAAG
1 TGTAAGACCATGTCTGGGACATCGGCATCGTAATGCGATTAAG
* * * **
29203302 TGTAAGATCATGTCTGGGACCTTGGCATCGTTAAT-CGATTTCG
1 TGTAAGACCATGTCTGGGACATCGGCATCG-TAATGCGATTAAG
* * * * * *
29203345 TATAAGACCCTTTCTAGGACAGT-GGCATCG-ATATGTGA-TAACA
1 TGTAAGACCATGTCTGGGACA-TCGGCATCGTA-ATGCGATTAA-G
* *
29203388 TGTAAGACCATATCTGGGATAT-GGCAT
1 TGTAAGACCATGTCTGGGACATCGGCAT
29203415 TGTATTGGCT
Statistics
Matches: 85, Mismatches: 23, Indels: 11
0.71 0.19 0.09
Matches are distributed among these distances:
41 1 0.01
42 9 0.11
43 71 0.84
44 4 0.05
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACATCGGCATCGTAATGCGATTAAG
Found at i:29206786 original size:46 final size:46
Alignment explanation
Indices: 29206733--29206861 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
29206723 TATTTGGGCA
*
29206733 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
*
29206779 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
29206825 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29206862 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:29213962 original size:13 final size:13
Alignment explanation
Indices: 29213944--29213976 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
29213934 ACCTTGTGTC
29213944 ACACACGACTGAG
1 ACACACGACTGAG
29213957 ACACACGACTGAG
1 ACACACGACTGAG
29213970 ACACACG
1 ACACACG
29213977 CCTGTGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.33, G:0.21, T:0.06
Consensus pattern (13 bp):
ACACACGACTGAG
Found at i:29215925 original size:13 final size:13
Alignment explanation
Indices: 29215907--29215931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29215897 CCAAGCACAC
29215907 GCCCGTGTCCTTT
1 GCCCGTGTCCTTT
29215920 GCCCGTGTCCTT
1 GCCCGTGTCCTT
29215932 CACATGGCCT
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:0.00, C:0.40, G:0.24, T:0.36
Consensus pattern (13 bp):
GCCCGTGTCCTTT
Found at i:29216564 original size:21 final size:21
Alignment explanation
Indices: 29216538--29216580 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29216528 ATCTCATGAA
29216538 ACATTCAAGCATGAAATGCAC
1 ACATTCAAGCATGAAATGCAC
*
29216559 ACATTCAAGCATGACATGCAC
1 ACATTCAAGCATGAAATGCAC
29216580 A
1 A
29216581 ATTAGTAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.19
Consensus pattern (21 bp):
ACATTCAAGCATGAAATGCAC
Found at i:29217575 original size:15 final size:15
Alignment explanation
Indices: 29217555--29217585 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29217545 AAGAACATGC
29217555 ATTTTTAAGTATATT
1 ATTTTTAAGTATATT
29217570 ATTTTTAAGTATATT
1 ATTTTTAAGTATATT
29217585 A
1 A
29217586 AGAGTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTTTTAAGTATATT
Found at i:29225383 original size:15 final size:15
Alignment explanation
Indices: 29225363--29225391 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29225353 AGAACATGCA
29225363 TTTTAAGTATATTAT
1 TTTTAAGTATATTAT
29225378 TTTTAAGTATATTA
1 TTTTAAGTATATTA
29225392 GGAGTTTACT
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:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTTAAGTATATTAT
Found at i:29231009 original size:27 final size:27
Alignment explanation
Indices: 29230977--29231031 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
29230967 CGTATCATAA
29230977 CTTCATCACCACCACTTCTCAATCGTT
1 CTTCATCACCACCACTTCTCAATCGTT
29231004 CTTCATCACCACCACTTCTCAATCGTT
1 CTTCATCACCACCACTTCTCAATCGTT
29231031 C
1 C
29231032 CCCTCTCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.42, G:0.04, T:0.33
Consensus pattern (27 bp):
CTTCATCACCACCACTTCTCAATCGTT
Found at i:29234689 original size:34 final size:34
Alignment explanation
Indices: 29234641--29234707 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
29234631 AGGTAGAGCA
*
29234641 ATCAAGAAGGTTAATGCAACCTCTGGAACTAACC
1 ATCAAGAAGGTTAATGCAACCTATGGAACTAACC
*
29234675 ATCAGGAAGGTTAATGCAACCTATGGAACTAAC
1 ATCAAGAAGGTTAATGCAACCTATGGAACTAAC
29234708 ACTTATCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (34 bp):
ATCAAGAAGGTTAATGCAACCTATGGAACTAACC
Found at i:29235771 original size:15 final size:17
Alignment explanation
Indices: 29235737--29235774 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
29235727 GTAAAATAAC
29235737 TTTTAACATATTTTAAT
1 TTTTAACATATTTTAAT
*
29235754 TTTTAA-AT-TTTTACT
1 TTTTAACATATTTTAAT
29235769 TTTTAA
1 TTTTAA
29235775 TATAGCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAACATATTTTAAT
Found at i:29240051 original size:27 final size:27
Alignment explanation
Indices: 29240013--29240070 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
29240003 ACTCCCACCC
29240013 CTAAAACCACAACACTTCAACCAGAGA
1 CTAAAACCACAACACTTCAACCAGAGA
29240040 CTAAAACCACAACACTTCAACCAGAGA
1 CTAAAACCACAACACTTCAACCAGAGA
29240067 CTAA
1 CTAA
29240071 GATTTAGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.48, C:0.33, G:0.07, T:0.12
Consensus pattern (27 bp):
CTAAAACCACAACACTTCAACCAGAGA
Found at i:29240808 original size:8 final size:8
Alignment explanation
Indices: 29240795--29240866 Score: 65
Period size: 8 Copynumber: 8.4 Consensus size: 8
29240785 CAAAATATGA
29240795 TTTTATAT
1 TTTTATAT
29240803 TTTTATAAT
1 TTTTAT-AT
*
29240812 TTTATATTGT
1 TTT-TA-TAT
29240822 TTTTATACT
1 TTTTATA-T
*
29240831 TTTTGTAAT
1 TTTTAT-AT
29240840 TGTTT-TAT
1 T-TTTATAT
29240848 TTTTATAT
1 TTTTATAT
29240856 TTTTATAT
1 TTTTATAT
29240864 TTT
1 TTT
29240867 CACTGAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
7 3 0.06
8 24 0.44
9 16 0.30
10 10 0.19
11 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.72
Consensus pattern (8 bp):
TTTTATAT
Found at i:29243705 original size:12 final size:12
Alignment explanation
Indices: 29243683--29243742 Score: 75
Period size: 12 Copynumber: 4.9 Consensus size: 12
29243673 ACAAAAAAAT
29243683 TGAAGTAAATAAG
1 TGAA-TAAATAAG
29243696 TGAATAAATAAG
1 TGAATAAATAAG
29243708 TGAATAAATAAG
1 TGAATAAATAAG
* *
29243720 TGAGTGAATAAG
1 TGAATAAATAAG
* *
29243732 TAAAAAAATAA
1 TGAATAAATAA
29243743 TTAAGAAGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
12 37 0.90
13 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.23
Consensus pattern (12 bp):
TGAATAAATAAG
Found at i:29244114 original size:9 final size:9
Alignment explanation
Indices: 29244100--29244132 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
29244090 TCGAGTTGAT
29244100 TCGATTAAC
1 TCGATTAAC
*
29244109 TCGATTAAT
1 TCGATTAAC
29244118 TCGATTAAC
1 TCGATTAAC
29244127 TCGATT
1 TCGATT
29244133 CGAATAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (9 bp):
TCGATTAAC
Found at i:29244121 original size:18 final size:18
Alignment explanation
Indices: 29244098--29244132 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29244088 ATTCGAGTTG
29244098 ATTCGATTAACTCGATTA
1 ATTCGATTAACTCGATTA
29244116 ATTCGATTAACTCGATT
1 ATTCGATTAACTCGATT
29244133 CGAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (18 bp):
ATTCGATTAACTCGATTA
Found at i:29249279 original size:68 final size:67
Alignment explanation
Indices: 29249233--29249390 Score: 280
Period size: 68 Copynumber: 2.3 Consensus size: 67
29249223 ATACTATATA
29249233 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
29249298 AAT
65 AAT
29249301 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACG-GAGAGATA
29249366 AAT
65 AAT
* *
29249369 GTAGCTAGGTCGCATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
29249391 TCCAAGTGAA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 88 1.00
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (67 bp):
GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGGAGAGATAA
AT
Found at i:29249464 original size:66 final size:67
Alignment explanation
Indices: 29249267--29249464 Score: 192
Period size: 68 Copynumber: 2.9 Consensus size: 67
29249257 GGGATGTATC
* * *
29249267 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATA-C--GGGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
* *
29249329 TGTATC-
62 AGGA-CA
*
29249335 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
29249400 AGGACA
62 AGGACA
* *
29249406 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
29249465 TTCACCATGT
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
66 24 0.21
67 9 0.08
68 55 0.47
69 1 0.01
70 1 0.01
71 26 0.22
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:29252905 original size:42 final size:43
Alignment explanation
Indices: 29252846--29252926 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
29252836 TGAGTTTACA
*
29252846 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTTTG
1 TGTAAGACCATAGCTGGGATATTGGCATCGATATGAGATTTTG
* *
29252888 TGTAAGACCATAGCTGGGCTATTGGCATCGATTTGAGAT
1 TGTAAGACCATAGCTGGGATATTGGCATCGATATGAGAT
29252927 CCCATATAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 19 0.54
43 16 0.46
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATAGCTGGGATATTGGCATCGATATGAGATTTTG
Found at i:29252937 original size:43 final size:42
Alignment explanation
Indices: 29252848--29252954 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 42
29252838 AGTTTACATG
* **** *
29252848 TAAGACCATATCTGGGATATGGCATCGATATGAGATTTTGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATGAGATCCCATA
* *
29252890 TAAGACCATAGCTGGGCTATTGGCATCGATTTGAGATCCCATA
1 TAAGACCATAGCTGGGATA-TGGCATCGATATGAGATCCCATA
**
29252933 TAAGACCATATTTGGGATATGG
1 TAAGACCATAGCTGGGATATGG
29252955 TATTGGTATG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 20 0.38
43 33 0.62
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (42 bp):
TAAGACCATAGCTGGGATATGGCATCGATATGAGATCCCATA
Found at i:29260220 original size:43 final size:42
Alignment explanation
Indices: 29260127--29260231 Score: 138
Period size: 43 Copynumber: 2.5 Consensus size: 42
29260117 TTTGAGTATA
* **
29260127 CATGTAAGACCATATCTGGGGTATGGCATCGATATGAGATTT
1 CATGTAAGACCATATCTGGGCTATGGCATCGATATGAGATCC
* * * *
29260169 CGTTTAAGACCATAGCTGGGCTATTGGCATCGATTTGAGATCC
1 CATGTAAGACCATATCTGGGCTA-TGGCATCGATATGAGATCC
29260212 CATGTAAGACCATATCTGGG
1 CATGTAAGACCATATCTGGG
29260232 ATGGTACTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
42 19 0.37
43 33 0.63
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (42 bp):
CATGTAAGACCATATCTGGGCTATGGCATCGATATGAGATCC
Found at i:29260337 original size:20 final size:20
Alignment explanation
Indices: 29260312--29260354 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29260302 CCATGTTAAA
**
29260312 GTTATGAAAGATTATGGTAT
1 GTTATGAAAGACAATGGTAT
*
29260332 GTTATGGAAGACAATGGTAT
1 GTTATGAAAGACAATGGTAT
29260352 GTT
1 GTT
29260355 GCAAGTTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (20 bp):
GTTATGAAAGACAATGGTAT
Found at i:29272788 original size:40 final size:40
Alignment explanation
Indices: 29272699--29272960 Score: 356
Period size: 40 Copynumber: 6.6 Consensus size: 40
29272689 TTGAATGATG
* *
29272699 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
29272738 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
29272778 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29272817 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
29272857 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
29272897 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
29272938 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
29272961 CGAACGAGGA
Statistics
Matches: 204, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
39 53 0.26
40 141 0.69
41 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29283941 original size:17 final size:17
Alignment explanation
Indices: 29283921--29283956 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29283911 TATTTTGCCT
29283921 GCCAGACAATACTATTC
1 GCCAGACAATACTATTC
* *
29283938 GCCATACAATACTGTTC
1 GCCAGACAATACTATTC
29283955 GC
1 GC
29283957 AGGGCAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.25
Consensus pattern (17 bp):
GCCAGACAATACTATTC
Found at i:29287169 original size:26 final size:26
Alignment explanation
Indices: 29287099--29287170 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 26
29287089 AACTGATACC
* * * * *
29287099 GGCAGCTTTGCTGTGTTACTGTTATT
1 GGCAGCTTTGCTGAGATATTATTACT
* * *
29287125 AGCAGCTCTGCTGAAATATTATTACT
1 GGCAGCTTTGCTGAGATATTATTACT
*
29287151 GGCAGCTTTGCTGCGATATT
1 GGCAGCTTTGCTGAGATATT
29287171 GGTGTGTTGG
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (26 bp):
GGCAGCTTTGCTGAGATATTATTACT
Found at i:29287566 original size:20 final size:19
Alignment explanation
Indices: 29287537--29287575 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29287527 TATTTTTTTG
*
29287537 TAATAGTTGTGTTTCCAAAA
1 TAATAATTGT-TTTCCAAAA
*
29287557 TAATAATTGTTTTTCAAAA
1 TAATAATTGTTTTCCAAAA
29287576 CACGTGTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (19 bp):
TAATAATTGTTTTCCAAAA
Found at i:29295596 original size:26 final size:26
Alignment explanation
Indices: 29295563--29295618 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
29295553 TTACTAAGTA
29295563 TTTTACATACTTACTCGGGTTACTAC
1 TTTTACATACTTACTCGGGTTACTAC
29295589 TTTTACATACTTACTCGGGTTACTAC
1 TTTTACATACTTACTCGGGTTACTAC
29295615 TTTT
1 TTTT
29295619 TTTTATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (26 bp):
TTTTACATACTTACTCGGGTTACTAC
Found at i:29300890 original size:15 final size:15
Alignment explanation
Indices: 29300870--29300899 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29300860 TTAATCTAAC
29300870 TTTAATTTTATTAAA
1 TTTAATTTTATTAAA
29300885 TTTAATTTTATTAAA
1 TTTAATTTTATTAAA
29300900 GTTGCAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAATTTTATTAAA
Found at i:29302026 original size:28 final size:28
Alignment explanation
Indices: 29301967--29302026 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
29301957 AGGCCGTGTG
* **
29301967 AGCCACACGGCAAGGACATGTGCGTATG
1 AGCCACACAGCAAGGACATGTGCGTAAC
*
29301995 AGCCACACAAGCAAGGACATG-GTGTAAC
1 AGCCACAC-AGCAAGGACATGTGCGTAAC
29302023 AGCC
1 AGCC
29302027 CCATTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.33, C:0.27, G:0.28, T:0.12
Consensus pattern (28 bp):
AGCCACACAGCAAGGACATGTGCGTAAC
Found at i:29315506 original size:42 final size:42
Alignment explanation
Indices: 29315451--29315568 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
29315441 TGCTTTAGAA
* *
29315451 CCACACAGCCAAGGACATGGGCATGTGCCCAGGCCGTGTGAG
1 CCACACAGGCAAGGACATGGGCATGTGCCCAGGCCGTGTAAG
* * *
29315493 CCACACGGGCAAGGACATGAGCGTGTGCCCAGGCCGTGTAAG
1 CCACACAGGCAAGGACATGGGCATGTGCCCAGGCCGTGTAAG
* * *
29315535 CCACACAAGCAAGGACATGGACATTTGCCCAGGC
1 CCACACAGGCAAGGACATGGGCATGTGCCCAGGC
29315569 TATGTAACTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.26, C:0.31, G:0.31, T:0.12
Consensus pattern (42 bp):
CCACACAGGCAAGGACATGGGCATGTGCCCAGGCCGTGTAAG
Found at i:29320346 original size:38 final size:37
Alignment explanation
Indices: 29320298--29320562 Score: 332
Period size: 38 Copynumber: 7.0 Consensus size: 37
29320288 TTGTTTGACA
**
29320298 ATTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCA
1 ATTCG-TTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
29320336 ATTCAGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
1 ATTC-GTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* *
29320374 TTTTGGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
1 -ATTCGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* * *
29320412 TTTCGATTGGATCAGCTCTTATGAGCTTTTGTTTGGCG
1 ATTCG-TTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* *
29320450 ATTCGATTGGATTAGCTCTTGTGAGCTTCTGTTTGGTG
1 ATTCG-TTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* * *
29320488 ATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTG
1 A-TTCGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
* * *
29320526 TTTCGGTTAGATCAGCTCTTATGAGCTTCTGTCTGGT
1 ATTC-GTTGGATCAGCTCTTATGAGCTTCTGTTTGGT
29320563 CTGTTCGGTT
Statistics
Matches: 200, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
37 6 0.03
38 188 0.94
39 6 0.03
ACGTcount: A:0.15, C:0.16, G:0.26, T:0.44
Consensus pattern (37 bp):
ATTCGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTG
Found at i:29320501 original size:114 final size:114
Alignment explanation
Indices: 29320299--29320557 Score: 412
Period size: 114 Copynumber: 2.3 Consensus size: 114
29320289 TGTTTGACAA
29320299 TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAGTTGGATCAGCTCTTATGAGCTT
1 TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAGTTGGATCAGCTCTTATGAGCTT
* * * *
29320364 CTGTTTGGTGTTTTGGTTGGATCAGCTCTTATGAGCTTCTGTTTGGTGT
66 CTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
* * * *
29320413 TTCGATTGGATCAGCTCTTATGAGCTTTTGTTTGGCGATTC-GATTGGATTAGCTCTTGTGAGCT
1 TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAG-TTGGATCAGCTCTTATGAGCT
29320477 TCTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
65 TCTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
* *
29320527 TTCGGTTAGATCAGCTCTTATGAGCTTCTGT
1 TTCGATTGGATCAGCTCTTATGAGCTTCTGT
29320558 CTGGTCTGTT
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 1 0.01
114 132 0.99
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (114 bp):
TTCGATTGGATCAGCTCTTATGAGCTTCTGTTTGGCAATTCAGTTGGATCAGCTCTTATGAGCTT
CTGTTTGGTGATTTAGTTCGATCAACTCTTATGAGCTTCTGTTTGGTGT
Found at i:29326230 original size:3 final size:3
Alignment explanation
Indices: 29326222--29326252 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29326212 AACACATTTT
29326222 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
29326253 TCCTACAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:29326431 original size:21 final size:21
Alignment explanation
Indices: 29326388--29326432 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29326378 CACATAATCG
**
29326388 CATTTCATTTTGTTAGATTCA
1 CATTTCATTTTGTTAGAGCCA
29326409 CATTTCATTTTGTTAGAGCCA
1 CATTTCATTTTGTTAGAGCCA
29326430 CAT
1 CAT
29326433 ATCACTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (21 bp):
CATTTCATTTTGTTAGAGCCA
Found at i:29342674 original size:72 final size:72
Alignment explanation
Indices: 29342587--29342747 Score: 191
Period size: 72 Copynumber: 2.2 Consensus size: 72
29342577 TGTGGGTCCA
* ** * *
29342587 GGTACTGAATTTGTGTATAAACTAGTGAGTAACTCGCTGAG-TGAGCA-TATCATGTTAATGCTT
1 GGTACTGACTTTGTGTATAAACTAGTGAGTAACTCAATGAGCGGA-CATTA-CATGATAATGCTT
29342650 TGGGGCCCG
64 TGGGGCCCG
* *
29342659 GGTACTGACTTTGTGTATAAACTTGTGAGTAGCTCAATGAGCGGACATTACATGATAATGCTTTG
1 GGTACTGACTTTGTGTATAAACTAGTGAGTAACTCAATGAGCGGACATTACATGATAATGCTTTG
**
29342724 GGGTTCG
66 GGGCCCG
**
29342731 GGTGTTGACTTTGTGTA
1 GGTACTGACTTTGTGTA
29342748 CAGACCCGTG
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
72 72 0.95
73 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.34
Consensus pattern (72 bp):
GGTACTGACTTTGTGTATAAACTAGTGAGTAACTCAATGAGCGGACATTACATGATAATGCTTTG
GGGCCCG
Found at i:29357304 original size:25 final size:25
Alignment explanation
Indices: 29357275--29357323 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
29357265 TTTTTGTGCG
29357275 AAGTCATGCTTTACGTTGTTATGCA
1 AAGTCATGCTTTACGTTGTTATGCA
* *
29357300 AAGTCATGCTTTACTTTTTTATGC
1 AAGTCATGCTTTACGTTGTTATGC
29357324 GAAGCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (25 bp):
AAGTCATGCTTTACGTTGTTATGCA
Found at i:29358659 original size:23 final size:23
Alignment explanation
Indices: 29358633--29358679 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
29358623 AATTTTCGCC
29358633 TTCAAATTACTTAAAGTTGGTGA
1 TTCAAATTACTTAAAGTTGGTGA
*
29358656 TTCAAATTGCTTAAAGTTGGTGA
1 TTCAAATTACTTAAAGTTGGTGA
29358679 T
1 T
29358680 CTCTCAGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (23 bp):
TTCAAATTACTTAAAGTTGGTGA
Found at i:29363124 original size:13 final size:13
Alignment explanation
Indices: 29363108--29363143 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
29363098 ATTTTTCGTG
29363108 AAAATTTCATTCA
1 AAAATTTCATTCA
29363121 AAAATTTCATTCA
1 AAAATTTCATTCA
29363134 AAAATTTCAT
1 AAAATTTCAT
29363144 CGATTGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATTTCATTCA
Found at i:29366267 original size:43 final size:43
Alignment explanation
Indices: 29366183--29366264 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
29366173 GTATTGTACA
* * *
29366183 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAAACACATATCG
*
29366226 ATGCCACTGTCCCAGACATGGTCTTAC-T-CAAACACATAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAAACACATAT
29366265 ATCAGAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 9 0.26
42 1 0.03
43 25 0.71
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGCAAACACATATCG
Found at i:29385034 original size:30 final size:30
Alignment explanation
Indices: 29385000--29385064 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
29384990 CCTGTCTGAG
29385000 ACTATGAAAGATGGAATTCCACAAAGGTGC
1 ACTATGAAAGATGGAATTCCACAAAGGTGC
*
29385030 ACTATGATAGATGGAATTCCACAAAGGTGC
1 ACTATGAAAGATGGAATTCCACAAAGGTGC
29385060 ACTAT
1 ACTAT
29385065 CTTAAAGACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (30 bp):
ACTATGAAAGATGGAATTCCACAAAGGTGC
Found at i:29388395 original size:33 final size:33
Alignment explanation
Indices: 29388353--29388419 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
29388343 ATCCATATGA
*
29388353 AAATAGACTCATTAAGCTTCAATTTCATAACTT
1 AAATAGACTCATCAAGCTTCAATTTCATAACTT
*
29388386 AAATAGACTCATCAAGCTTTAATTTCATAACTT
1 AAATAGACTCATCAAGCTTCAATTTCATAACTT
29388419 A
1 A
29388420 CTCATCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (33 bp):
AAATAGACTCATCAAGCTTCAATTTCATAACTT
Found at i:29398923 original size:59 final size:62
Alignment explanation
Indices: 29398851--29398973 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 62
29398841 TTATGTTCCC
*
29398851 AATGCTTATCATAAGCCTAAACG-A-CAT-TATCCCTGACTTATTGTATTTATCCATGATAT
1 AATGCTTATCATAAGCCTAAACGCATCATCAATCCCTGACTTATTGTATTTATCCATGATAT
*
29398910 AATGCTTATCATAAGCCTAAACGTCATCATCAATTCCTGACTTATTGTATTTATCCATGATAT
1 AATGCTTATCATAAGCCTAAACG-CATCATCAATCCCTGACTTATTGTATTTATCCATGATAT
29398973 A
1 A
29398974 GGTATATTCA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
59 23 0.40
61 1 0.02
62 3 0.05
63 31 0.53
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (62 bp):
AATGCTTATCATAAGCCTAAACGCATCATCAATCCCTGACTTATTGTATTTATCCATGATAT
Found at i:29400398 original size:24 final size:25
Alignment explanation
Indices: 29400371--29400422 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
29400361 CTCACCACAA
29400371 CTCGCATGAGCTTACCAAT-TTCAG
1 CTCGCATGAGCTTACCAATATTCAG
* *
29400395 CTCGTATGAGCTTACCAATATTTAG
1 CTCGCATGAGCTTACCAATATTCAG
29400420 CTC
1 CTC
29400423 AGAAAAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (25 bp):
CTCGCATGAGCTTACCAATATTCAG
Found at i:29409530 original size:40 final size:40
Alignment explanation
Indices: 29409366--29409530 Score: 190
Period size: 40 Copynumber: 4.1 Consensus size: 40
29409356 CAGAATTTAA
* ** * *
29409366 CCGGATATAGCAACTCGTTCAAATGCCTTCGGGCCATAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
29409406 CCGGTTATAGTAACTCGCACCAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29409446 CCGGATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
29409486 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29409526 CCGGA
1 CCGGA
29409531 CATCATTCGA
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.03
40 91 0.87
41 11 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29413487 original size:37 final size:37
Alignment explanation
Indices: 29413434--29413536 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
29413424 CGAATAGTCC
*
29413434 CCACACGTAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
29413471 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
29413508 CCACACGTAGTCATCGGGTCTTACCCGGA
1 CCACACGTAGTCATCGGGTCTTACCCGGA
29413537 ATATATTTCC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:29413734 original size:48 final size:48
Alignment explanation
Indices: 29413676--29414121 Score: 768
Period size: 48 Copynumber: 9.3 Consensus size: 48
29413666 ATATACACAC
* *
29413676 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* *
29413724 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACGTATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * *
29413772 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
29413820 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
29413868 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
29413916 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
*
29413964 ATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
* * * *
29414012 ATCTCATTCATATTTCACACTAGCTATTCGGCTTTACCATATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
29414060 ATCTCATACATA-TTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
29414107 ATCTCATACATATTT
1 ATCTCATACATATTT
29414122 ATCTTGTACA
Statistics
Matches: 377, Mismatches: 20, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
47 44 0.12
48 333 0.88
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:29417691 original size:40 final size:40
Alignment explanation
Indices: 29417624--29417711 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
29417614 CCTTCGGAGT
*
29417624 TTAG-CCGGATATAGCTACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCTACTAGCACAAATGCCTTCGGGAC
*
29417663 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGCT-ACTAGCACAAATGCCTTCGGGAC
29417703 TTAGCCCGG
1 TTAGCCCGG
29417712 GTATCAATCC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 5 0.11
40 40 0.89
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGCTACTAGCACAAATGCCTTCGGGAC
Found at i:29420771 original size:2 final size:2
Alignment explanation
Indices: 29420764--29420797 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29420754 ACTAATAGAC
29420764 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29420798 ATGGAATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29425996 original size:12 final size:11
Alignment explanation
Indices: 29425965--29426018 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
29425955 TATTTTACAG
29425965 GTTGTTTTTGGT
1 GTTG-TTTTGGT
* *
29425977 GCTATTTTGGGT
1 GTTGTTTT-GGT
29425989 GTTGTTTTGGT
1 GTTGTTTTGGT
* *
29426000 ATTGTTTTGAT
1 GTTGTTTTGGT
29426011 GTTGTTTT
1 GTTGTTTT
29426019 TAATGTTCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 23 0.68
12 11 0.32
ACGTcount: A:0.06, C:0.02, G:0.30, T:0.63
Consensus pattern (11 bp):
GTTGTTTTGGT
Found at i:29426019 original size:23 final size:24
Alignment explanation
Indices: 29425965--29426019 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
29425955 TATTTTACAG
* *
29425965 GTTGTTTTTGGTGCTATTTTGGGT
1 GTTGTTTTTGGTACTATTTTGGAT
* *
29425989 GTTG-TTTTGGTATTGTTTT-GAT
1 GTTGTTTTTGGTACTATTTTGGAT
29426011 GTTGTTTTT
1 GTTGTTTTT
29426020 AATGTTCTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.05, C:0.02, G:0.29, T:0.64
Consensus pattern (24 bp):
GTTGTTTTTGGTACTATTTTGGAT
Found at i:29429418 original size:20 final size:20
Alignment explanation
Indices: 29429393--29429513 Score: 76
Period size: 20 Copynumber: 6.1 Consensus size: 20
29429383 TAAATGTTTT
*
29429393 CAGGGGTACCAATGTACAAA
1 CAGGGGCACCAATGTACAAA
**
29429413 CAGGGGCACGTATG-AGCAAA
1 CAGGGGCACCAATGTA-CAAA
*
29429433 CA--GGCATGCCAAAGTACAAA
1 CAGGGGCA--CCAATGTACAAA
*
29429453 C-GGGGCACGC-ATGTGCAAA
1 CAGGGGCAC-CAATGTACAAA
* *
29429472 CAAGGGTACCGAA-GTACAAA
1 CAGGGGCACC-AATGTACAAA
29429492 CAGGGGCA-CATATGTACAAA
1 CAGGGGCACCA-ATGTACAAA
29429512 CA
1 CA
29429514 AAGGTACCGA
Statistics
Matches: 76, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
18 5 0.07
19 13 0.17
20 52 0.68
21 6 0.08
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.12
Consensus pattern (20 bp):
CAGGGGCACCAATGTACAAA
Found at i:29429450 original size:40 final size:39
Alignment explanation
Indices: 29429399--29429513 Score: 126
Period size: 39 Copynumber: 2.9 Consensus size: 39
29429389 TTTTCAGGGG
*
29429399 TACCAATGTACAAACAGGGGCACGTATGAGCAAACAGGCA
1 TACCAAAGTACAAACAGGGGCACGTATGAGCAAACAGG-A
* * * *
29429439 TGCCAAAGTACAAAC-GGGGCACGCATGTGCAAACAAGGG
1 TACCAAAGTACAAACAGGGGCACGTATGAGCAAAC-AGGA
* *
29429478 TACCGAAGTACAAACAGGGGCACATATGTA-CAAACA
1 TACCAAAGTACAAACAGGGGCACGTATG-AGCAAACA
29429514 AAGGTACCGA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 31 0.50
40 31 0.50
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (39 bp):
TACCAAAGTACAAACAGGGGCACGTATGAGCAAACAGGA
Found at i:29429471 original size:39 final size:40
Alignment explanation
Indices: 29429399--29429500 Score: 127
Period size: 39 Copynumber: 2.6 Consensus size: 40
29429389 TTTTCAGGGG
* *
29429399 TACCAATGTACAAACAGGGGCACGTATGAGCAAAC-AGGCA
1 TACCAAAGTACAAACAGGGGCACGCATGAGCAAACAAGG-A
* * *
29429439 TGCCAAAGTACAAAC-GGGGCACGCATGTGCAAACAAGGG
1 TACCAAAGTACAAACAGGGGCACGCATGAGCAAACAAGGA
*
29429478 TACCGAAGTACAAACAGGGGCAC
1 TACCAAAGTACAAACAGGGGCAC
29429501 ATATGTACAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 30 0.57
40 23 0.43
ACGTcount: A:0.38, C:0.24, G:0.27, T:0.11
Consensus pattern (40 bp):
TACCAAAGTACAAACAGGGGCACGCATGAGCAAACAAGGA
Found at i:29429514 original size:40 final size:40
Alignment explanation
Indices: 29429396--29429533 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
29429386 ATGTTTTCAG
29429396 GGGTACC-AATGTACAAACAGGGGCACGTATG-AGCAAAC-A
1 GGGTACCGAA-GTACAAACAGGGGCACGTATGTA-CAAACAA
* * * * *
29429435 GGCATGCCAAAGTACAAAC-GGGGCACGCATGTGCAAACAA
1 GG-GTACCGAAGTACAAACAGGGGCACGTATGTACAAACAA
*
29429475 GGGTACCGAAGTACAAACAGGGGCACATATGTACAAACAA
1 GGGTACCGAAGTACAAACAGGGGCACGTATGTACAAACAA
* *
29429515 AGGTACCGAAGAACAAACA
1 GGGTACCGAAGTACAAACA
29429534 TTCAACAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
39 31 0.38
40 49 0.60
41 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.11
Consensus pattern (40 bp):
GGGTACCGAAGTACAAACAGGGGCACGTATGTACAAACAA
Found at i:29440777 original size:20 final size:20
Alignment explanation
Indices: 29440752--29440797 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
29440742 TATTGACATG
*
29440752 CAAACAGGGGTACCGAAGTA
1 CAAACAGGGGTACCAAAGTA
*
29440772 CAAACAGGGGTCCCAAAGTA
1 CAAACAGGGGTACCAAAGTA
29440792 CAAACA
1 CAAACA
29440798 TTCAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.09
Consensus pattern (20 bp):
CAAACAGGGGTACCAAAGTA
Found at i:29444674 original size:30 final size:30
Alignment explanation
Indices: 29444599--29444679 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
29444589 AACTTTGATT
*
29444599 AAAATAACAAAACAATCACT-AAACTTAAA
1 AAAATAACAAAACAGTCACTAAAACTTAAA
* ** * **
29444628 AAAATTACAATTCAGTCACTAAAATTTAGG
1 AAAATAACAAAACAGTCACTAAAACTTAAA
*
29444658 AAAATAACAAACCAGTCACTAA
1 AAAATAACAAAACAGTCACTAA
29444680 CATTATCGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 16 0.39
30 25 0.61
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.21
Consensus pattern (30 bp):
AAAATAACAAAACAGTCACTAAAACTTAAA
Found at i:29446435 original size:38 final size:38
Alignment explanation
Indices: 29446388--29446464 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
29446378 TCAATGCATA
* * *
29446388 TGCTCTGTGTTGTCATGAATTCTCACTATTGATGTTAG
1 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
29446426 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
1 TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
29446464 T
1 T
29446465 ATTAACATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (38 bp):
TGCTATGTGTTGTCATAAATTCTCACCATTGATGTTAG
Found at i:29448563 original size:9 final size:9
Alignment explanation
Indices: 29448549--29448573 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29448539 ATTATATAAG
29448549 ATTATTATC
1 ATTATTATC
29448558 ATTATTATC
1 ATTATTATC
29448567 ATTATTA
1 ATTATTA
29448574 GGTAGCGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTATC
Found at i:29460099 original size:31 final size:31
Alignment explanation
Indices: 29460063--29460126 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
29460053 ATTGAGTTAG
*
29460063 AATCCAGTTGATGAGTAATACCAACTTAATA
1 AATCCAGTTGATGAATAATACCAACTTAATA
29460094 AATCCAGTTGATGAATAATACCAACTTAATA
1 AATCCAGTTGATGAATAATACCAACTTAATA
29460125 AA
1 AA
29460127 GAACTTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (31 bp):
AATCCAGTTGATGAATAATACCAACTTAATA
Found at i:29464710 original size:22 final size:22
Alignment explanation
Indices: 29464685--29464729 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29464675 TTTAATAAAG
29464685 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* * *
29464707 AAAATATTTATAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
29464729 A
1 A
29464730 CACTCCCCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:29470547 original size:6 final size:6
Alignment explanation
Indices: 29470530--29470562 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
29470520 ATTTTCTTTC
29470530 AATGATA AATGAA AATGAA AATGAA AATGAA AA
1 AATGA-A AATGAA AATGAA AATGAA AATGAA AA
29470563 AAAAAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (6 bp):
AATGAA
Done.