Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 93 of 295
Found at i:29626819 original size:31 final size:31
Alignment explanation
Indices: 29626781--29626859 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
29626771 TTTAACGATT
*
29626781 ACTGGGCCGAAGGCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
29626812 ACTGGGCCAAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
29626843 ACTGGGCTGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
29626860 ACTGTAAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:29626930 original size:42 final size:42
Alignment explanation
Indices: 29626883--29626974 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
29626873 TGGCCTATAG
* ** *
29626883 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
29626925 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
29626967 GCCCATTT
1 GCCCATTT
29626975 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:29627171 original size:26 final size:26
Alignment explanation
Indices: 29627119--29627268 Score: 212
Period size: 26 Copynumber: 5.8 Consensus size: 26
29627109 CCTCTTTAAT
29627119 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
** **
29627144 AACTGGGGCATAAATCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
29627170 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
**
29627196 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* *
29627222 AATTGGGGCATAAGCCATTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
*
29627248 AACTAGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
29627269 GCACTTCCTC
Statistics
Matches: 107, Mismatches: 17, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
25 10 0.09
26 97 0.91
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:29627192 original size:52 final size:52
Alignment explanation
Indices: 29627119--29627268 Score: 239
Period size: 52 Copynumber: 2.9 Consensus size: 52
29627109 CCTCTTTAAT
*
29627119 AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCATAAATCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAACCCTTTTCAATA
*
29627170 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAACCCTTTTCAATA
* * * *
29627222 AATTGGGGCATAAGCCATTTTCGGTAAACTAGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAACCCTTTT
29627269 GCACTTCCTC
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 10 0.11
52 83 0.89
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (52 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAACCCTTTTCAATA
Found at i:29628161 original size:27 final size:27
Alignment explanation
Indices: 29628070--29628153 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
29628060 GGGCATATTC
* *
29628070 GTCATTTTACCATACAGGGG-TATTACG
1 GTCACTTTACCCTACAGGGGCT-TTACG
29628097 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
*
29628124 ATCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCCTACAGGGGCTTTACG
29628151 GTC
1 GTC
29628154 TTTTTACCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 51 0.98
28 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCCTACAGGGGCTTTACG
Found at i:29628245 original size:27 final size:27
Alignment explanation
Indices: 29628192--29628253 Score: 52
Period size: 27 Copynumber: 2.3 Consensus size: 27
29628182 TTTCATCCTA
* * *
29628192 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * **
29628219 CAAAGGTATTTTAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
29628246 CAATGGTA
1 CAAGGGTA
29628254 ATTCTATAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:29628263 original size:27 final size:27
Alignment explanation
Indices: 29628215--29628266 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
29628205 GTAAATCTAC
*
29628215 AAACCAAAGGTATTTTAGTAATTTTGT
1 AAACCAAAGGTATTCTAGTAATTTTGT
*
29628242 AAACCAATGGTAATTCTA-TAATTTT
1 AAACCAAAGGT-ATTCTAGTAATTTT
29628267 TAGAAGGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTCTAGTAATTTTGT
Found at i:29628318 original size:27 final size:27
Alignment explanation
Indices: 29628302--29628430 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
29628292 CTTTGTAAAT
29628302 TAGGGGTATTTTGGTAATTTTACAAA-
1 TAGGGGTATTTTGGTAATTTTACAAAC
* * *
29628328 TTGAGGGTATTTCGGTAATTTCACAAAC
1 TAG-GGGTATTTTGGTAATTTTACAAAC
* *
29628356 CAAGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
29628383 TAGGGGTATTTTGGTAATTTTACAAAC
1 TAGGGGTATTTTGGTAATTTTACAAAC
* ** *
29628410 CAATGGTATTTTAGTAATTTT
1 TAGGGGTATTTTGGTAATTTT
29628431 GTAAATCGAG
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
26 2 0.02
27 85 0.98
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
TAGGGGTATTTTGGTAATTTTACAAAC
Found at i:29628363 original size:54 final size:54
Alignment explanation
Indices: 29628305--29628444 Score: 192
Period size: 54 Copynumber: 2.6 Consensus size: 54
29628295 TGTAAATTAG
29628305 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
* * *
29628359 GGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTGA-GGGTATTTCGGTAATTTCACAAACCAA
* * ** *
29628413 TGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTA
29628445 AAATAGTAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
53 1 0.01
54 73 0.97
55 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:29628443 original size:81 final size:80
Alignment explanation
Indices: 29628192--29628444 Score: 204
Period size: 81 Copynumber: 3.1 Consensus size: 80
29628182 TTTCATCCTA
* * * ** * **
29628192 CAAGGGTGTTTTGGTAAATCTACAAACCAAAGGTATTTTAGTAATTTTGTAAACCAATGGTAATT
1 CAAGGGTATTTTGGTAAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAATGGT-ATT
*
29628257 CTA-TAATTTTTAGAAGGT
65 TTAGTAATTTTTA-AA--T
* * ** * *** *
29628275 CAATGGTATTTCT-GTAACTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATT
1 CAAGGGTATTT-TGGTAAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAATGGTATT
** ** *
29628339 TCGGTAATTTCACAAAC
65 TTAGTAATTT-TTAAAT
*
29628356 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAATGGTATTT
1 CAAGGGTATTTTGGTAAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAATGGTATTT
29628421 TAGTAATTTTGTAAAT
66 TAGTAATTTT-TAAAT
*
29628437 CGAGGGTA
1 CAAGGGTA
29628445 AAATAGTAAT
Statistics
Matches: 127, Mismatches: 38, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
80 1 0.01
81 71 0.56
82 3 0.02
83 50 0.39
84 2 0.02
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (80 bp):
CAAGGGTATTTTGGTAAATTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAATGGTATTT
TAGTAATTTTTAAAT
Found at i:29628444 original size:27 final size:27
Alignment explanation
Indices: 29628223--29628498 Score: 128
Period size: 27 Copynumber: 10.1 Consensus size: 27
29628213 ACAAACCAAA
* * *
29628223 GGTATTTTAGTAATTTTGTAAACCAAT
1 GGTATTTTAGTAATTTTATAAATCAAG
* *
29628250 GGTAATTCTA-TAATTTT-TAGAAGGTCAAT
1 GGT-ATTTTAGTAATTTTATA-AA--TCAAG
* * * *
29628279 GGTATTTCT-GTAACTTTGTAAATTAGG
1 GGTATTT-TAGTAATTTTATAAATCAAG
* * **
29628306 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTTAGTAATTTTATAAATCAAG
** * * *
29628333 GGTATTTCGGTAATTTCACAAACCAAG
1 GGTATTTTAGTAATTTTATAAATCAAG
* * *
29628360 GGTATTTTGGTAATTTTACAAA-CTAGG
1 GGTATTTTAGTAATTTTATAAATC-AAG
* * * *
29628387 GGTATTTTGGTAATTTTACAAACCAAT
1 GGTATTTTAGTAATTTTATAAATCAAG
* *
29628414 GGTATTTTAGTAATTTTGTAAATCGAG
1 GGTATTTTAGTAATTTTATAAATCAAG
*** * *
29628441 GGTAAAATAGTAATTCTGTAAATCAAG
1 GGTATTTTAGTAATTTTATAAATCAAG
**** * *
29628468 GGTAAAACAGTAATTCTATAAATCGAG
1 GGTATTTTAGTAATTTTATAAATCAAG
29628495 GGTA
1 GGTA
29628499 AAATGGTAAT
Statistics
Matches: 203, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.02
27 172 0.85
28 9 0.04
29 16 0.08
30 2 0.01
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (27 bp):
GGTATTTTAGTAATTTTATAAATCAAG
Found at i:29628454 original size:54 final size:54
Alignment explanation
Indices: 29628305--29628509 Score: 162
Period size: 54 Copynumber: 3.8 Consensus size: 54
29628295 TGTAAATTAG
* * * ** *
29628305 GGGTATTTTGGTAATTTTACAAATTGAGGGT-ATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTAGTAATTTTATAAATCGAGGGTAAAAT-GGTAATTTTACAAACCAA
* * * ***
29628359 GGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAACCAA
1 GGGTATTTTAGTAATTTTATAAATCGA-GGGTAAAATGGTAATTTTACAAACCAA
* * * * ** *
29628413 TGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAATAGTAATTCTGTAAATCAA
1 GGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTACAAACCAA
**** *
29628467 GGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATT
1 GGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGGTAATT
29628510 CTGTAAATCG
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
53 1 0.01
54 117 0.95
55 5 0.04
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTTATAAATCGAGGGTAAAATGGTAATTTTACAAACCAA
Found at i:29628499 original size:27 final size:27
Alignment explanation
Indices: 29628422--29628687 Score: 329
Period size: 27 Copynumber: 9.9 Consensus size: 27
29628412 ATGGTATTTT
* *
29628422 AGTAATTTTGTAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
29628449 AGTAATTCTGTAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
29628476 AGTAATTCTATAAATCGAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
29628503 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
29628530 GGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
29628557 -GATAATTCTCTAAATCGAGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
*
29628584 AGTAATTCTGTAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
29628611 -GATAATTATGTAAATCGGGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * * *
29628638 GGGAATTATGTAAATCGGGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
29628665 GGTAATTCTGTAAATCGGGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
29628688 CTTTGGTAAT
Statistics
Matches: 214, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.01
27 210 0.98
28 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.27
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:29628724 original size:54 final size:54
Alignment explanation
Indices: 29628666--29628788 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
29628656 GGGTAAAACG
* * * *
29628666 GTAATTCTGTAAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTGTAAATCGGGGGTA-TTTCAGTAATTTTACAAATCAAAGGTATTTCA
** * * *
29628720 GTAATTTTACAAATCGGGGGTATTTCAGTATTTTTACAAATTAAAGGTATTTCG
1 GTAATTTTGTAAATCGGGGGTATTTCAGTAATTTTACAAATCAAAGGTATTTCA
29628774 GTAATTTTAGTAAAT
1 GTAATTTT-GTAAAT
29628789 TAAAATATTC
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
53 3 0.05
54 49 0.88
55 4 0.07
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
GTAATTTTGTAAATCGGGGGTATTTCAGTAATTTTACAAATCAAAGGTATTTCA
Found at i:29628741 original size:27 final size:27
Alignment explanation
Indices: 29628676--29628760 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
29628666 GTAATTCTGT
*
29628676 AAATCGGGGGTACTTT-GGTAATTTTAC
1 AAATCGGGGGTA-TTTCAGTAATTTTAC
* **
29628703 AAGTCGAAGGTATTTCAGTAATTTTAC
1 AAATCGGGGGTATTTCAGTAATTTTAC
*
29628730 AAATCGGGGGTATTTCAGTATTTTTAC
1 AAATCGGGGGTATTTCAGTAATTTTAC
29628757 AAAT
1 AAAT
29628761 TAAAGGTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 3 0.06
27 46 0.94
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (27 bp):
AAATCGGGGGTATTTCAGTAATTTTAC
Found at i:29628789 original size:28 final size:27
Alignment explanation
Indices: 29628693--29628792 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
29628683 GGGTACTTTG
* **
29628693 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATTAAAGGTATTTCA
****
29628720 GTAATTTTACAAATCGGGGGTATTTCA
1 GTAATTTTACAAATTAAAGGTATTTCA
* *
29628747 GTATTTTTACAAATTAAAGGTATTTCG
1 GTAATTTTACAAATTAAAGGTATTTCA
*
29628774 GTAATTTTAGTAAATTAAA
1 GTAATTTTA-CAAATTAAA
29628793 ATATTCTAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 53 0.87
28 8 0.13
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATTAAAGGTATTTCA
Found at i:29633987 original size:36 final size:37
Alignment explanation
Indices: 29633914--29634059 Score: 219
Period size: 36 Copynumber: 4.1 Consensus size: 37
29633904 CTTTAGCTCA
* *
29633914 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
29633951 GACAAAATCTCCACACGTAGTCATC-GGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
29633987 GACATAATCTTCACA--TAGTCATCGGGTCTTACCC-
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
29634021 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
29634058 GA
1 GA
29634060 ATATATTTCC
Statistics
Matches: 100, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
34 22 0.22
35 10 0.10
36 43 0.43
37 25 0.25
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (37 bp):
GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:29634325 original size:47 final size:47
Alignment explanation
Indices: 29634264--29634448 Score: 280
Period size: 47 Copynumber: 3.9 Consensus size: 47
29634254 TACATATATT
* ** * *
29634264 TCACATTAGCCATTCGGATTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
29634311 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
29634358 TCACATTGGCCATTTGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
**
29634405 TCACATTGGCCATTCGGCCTTATCACATATATGCACATTCACAT
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACAT
29634449 CACAATTATC
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 125 1.00
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:29634384 original size:22 final size:22
Alignment explanation
Indices: 29634357--29634432 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
29634347 GCTCACATTC
29634357 ATCACATTGGCCATTTGGCCTT
1 ATCACATTGGCCATTTGGCCTT
* ** *
29634379 ATCACATATATG-CATGTTCACATT
1 ATCACAT-T-GGCCAT-TTGGCCTT
*
29634403 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTTGGCCTT
29634426 ATCACAT
1 ATCACAT
29634433 ATATGCACAT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 10 0.25
25 7 0.17
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTTGGCCTT
Found at i:29638250 original size:25 final size:25
Alignment explanation
Indices: 29638215--29638264 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29638205 GGAATTCGCA
29638215 CACACACAGTGC-CTCTAATCATTCG
1 CACACACAGTGCTCT-TAATCATTCG
* *
29638240 CACACATAGTGCTCTTATTCATTCG
1 CACACACAGTGCTCTTAATCATTCG
29638265 TATTTGTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (25 bp):
CACACACAGTGCTCTTAATCATTCG
Found at i:29638474 original size:40 final size:40
Alignment explanation
Indices: 29638440--29638939 Score: 842
Period size: 40 Copynumber: 12.6 Consensus size: 40
29638430 CCAGCATGAT
** * * *
29638440 TGCTCTTCGGGACCCAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
29638480 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
29638520 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
29638560 TGCTCTTCGGGGCTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
29638600 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
29638640 TGCTCTTCGGG-CTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
29638679 TGCTCTTCGGG-CTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
29638718 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
29638758 TGCTCTTCGGGGCTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
29638798 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
29638838 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
29638878 TGCTCTTCGGGGCTTAGCCCGGATACATCACTAGCACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
29638918 TGCTCTTCAGGACTTAGCCCGG
1 TGCTCTTCGGGACTTAGCCCGG
29638940 GTATACCACT
Statistics
Matches: 436, Mismatches: 23, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
39 77 0.18
40 359 0.82
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:29640331 original size:35 final size:36
Alignment explanation
Indices: 29640215--29640358 Score: 236
Period size: 36 Copynumber: 4.0 Consensus size: 36
29640205 CTTTAGCTCA
* *
29640215 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCC
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
29640251 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
* *
29640287 GACATAATCTTCACACGTAGTCATCGGGTCTTA-CC
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
*
29640322 GACATAATCTCCACACGTAGTCATCGGGTCTTACCC
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
29640358 G
1 G
29640359 GAATATATTT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 34 0.33
36 68 0.67
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (36 bp):
GACAAAATCTCCACACGTAGTCATCGGGTCTTACCC
Found at i:29640344 original size:71 final size:72
Alignment explanation
Indices: 29640215--29640358 Score: 236
Period size: 71 Copynumber: 2.0 Consensus size: 72
29640205 CTTTAGCTCA
*
29640215 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCGACAAAATCTCCACACGTAGTCATCGGGT
1 GACAAAATCTCCACACGAAGTCATCGGGTCTTACCCGACAAAATCTCCACACGTAGTCATCGGGT
29640280 CTTACCC
66 CTTACCC
* * * *
29640287 GACATAATCTTCACACGTAGTCATCGGGTCTTA-CCGACATAATCTCCACACGTAGTCATCGGGT
1 GACAAAATCTCCACACGAAGTCATCGGGTCTTACCCGACAAAATCTCCACACGTAGTCATCGGGT
29640351 CTTACCC
66 CTTACCC
29640358 G
1 G
29640359 GAATATATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 38 0.57
72 29 0.43
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (72 bp):
GACAAAATCTCCACACGAAGTCATCGGGTCTTACCCGACAAAATCTCCACACGTAGTCATCGGGT
CTTACCC
Found at i:29640626 original size:47 final size:47
Alignment explanation
Indices: 29640565--29640749 Score: 289
Period size: 47 Copynumber: 3.9 Consensus size: 47
29640555 TACATATATT
* * * *
29640565 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
29640612 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
29640659 TCACATTGGCCATTTGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
**
29640706 TCACATTGGCCATTCGGCCTTATCACATATATGCACATTCACAT
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACAT
29640750 CACAATTATC
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 126 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:29640685 original size:22 final size:22
Alignment explanation
Indices: 29640658--29640733 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
29640648 GCTCACATTC
29640658 ATCACATTGGCCATTTGGCCTT
1 ATCACATTGGCCATTTGGCCTT
* ** *
29640680 ATCACATATATG-CATGTTCACATT
1 ATCACAT-T-GGCCAT-TTGGCCTT
*
29640704 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTTGGCCTT
29640727 ATCACAT
1 ATCACAT
29640734 ATATGCACAT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 10 0.25
25 7 0.17
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTTGGCCTT
Found at i:29658752 original size:44 final size:43
Alignment explanation
Indices: 29658665--29658784 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 43
29658655 AAATGTGTTA
* *
29658665 TCGTGTAAGACCACGTCTGGGACGTTGGCATC-AACTTCTATTT
1 TCGTGTAAGACCATGTCTGGGACATTGGCATCGAAC-TCTATTT
* *
29658708 TACGTGTAAGACCATGTCTTGGACATTGGCATCGTA-TCTGATTT
1 T-CGTGTAAGACCATGTCTGGGACATTGGCATCGAACTCT-ATTT
* *
29658752 T-GTGTAAGA-CATTGTCTGGGAAAGTGGCATCGA
1 TCGTGTAAGACCA-TGTCTGGGACATTGGCATCGA
29658785 TGTTTGATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
41 2 0.03
42 25 0.38
43 4 0.06
44 33 0.51
45 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACATTGGCATCGAACTCTATTT
Found at i:29660419 original size:50 final size:50
Alignment explanation
Indices: 29660346--29660581 Score: 230
Period size: 50 Copynumber: 4.7 Consensus size: 50
29660336 TGAATACATG
* * *
29660346 TGTGTAGTACTAAGTGTAGGCTACTACATGTATCATACTG-TTAAGTCGCA
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGA-TGATTAAGTCACA
* * * * * *
29660396 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTTA-ATGACTT-CGATCACG
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTA-TCAGATGA-TTAAG-TCACA
* * * *
29660447 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGATGAGGTCACG
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGATTAAGTCACA
* * *
29660497 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATTG-TTGA-TCACA
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGA-TGATTAAGTCACA
* *
29660546 TGTGTAGTACTAAGTGTAGGCTACTATGCGTATCAG
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAG
29660582 GTAGCTTCGG
Statistics
Matches: 155, Mismatches: 24, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
49 38 0.25
50 73 0.47
51 44 0.28
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGATTAAGTCACA
Found at i:29660579 original size:99 final size:100
Alignment explanation
Indices: 29660346--29660581 Score: 280
Period size: 101 Copynumber: 2.4 Consensus size: 100
29660336 TGAATACATG
* * * *
29660346 TGTGTAGTACTAAGTGTAGGCTACTACATGTATCATACTGTTAAGTCGCATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGACTGTGAAGTCACATGTGTAGTACTAAGT
* ** *
29660411 GCAGGCTACTATGCGTACTTAATGACTTCGATCACG
66 GCAGGCTACTACGCGTACGGAATGA-TTCGATCACA
* * *
29660447 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGATGAGGTCACGTGTGTAGTACTAAG
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGACTG-TGAAGTCACATGTGTAGTACTAAG
* * *
29660511 TGTAGGCTACTACGTGTACCGGATTG-TT-GATCACA
65 TGCAGGCTACTACGCGTA-CGGAATGATTCGATCACA
* *
29660546 TGTGTAGTACTAAGTGTAGGCTACTATGCGTATCAG
1 TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAG
29660582 GTAGCTTCGG
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
99 39 0.34
100 4 0.03
101 69 0.59
102 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (100 bp):
TGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGACTGTGAAGTCACATGTGTAGTACTAAGT
GCAGGCTACTACGCGTACGGAATGATTCGATCACA
Found at i:29660700 original size:27 final size:26
Alignment explanation
Indices: 29660670--29660721 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
29660660 GGGAAAATCG
29660670 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGT-G-AATATGTGCAAAGTTATT
* *
29660697 ATAAGGTGAATATGTGCAAATTTAT
1 ATAAAGTGAATATGTGCAAAGTTAT
29660722 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 8 0.36
26 8 0.36
27 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (26 bp):
ATAAAGTGAATATGTGCAAAGTTATT
Found at i:29667991 original size:42 final size:43
Alignment explanation
Indices: 29667891--29668039 Score: 135
Period size: 43 Copynumber: 3.5 Consensus size: 43
29667881 TGTGTTATCG
* * **
29667891 TGTAAGACCACGTCTCGGACGTTGGCATCGACT-TCT-ATTTTACA
1 TGTAAGACCATGTCTGGGACAATGGCATCGA-TATCTGA--TTACA
* * *
29667935 TGTAAGACCATGTCTTGGAC-ATCGGCATC-ATATCTGATTCCG
1 TGTAAGACCATGTCTGGGACAAT-GGCATCGATATCTGATTACA
* * *
29667977 TGTAAGACCCTGTCTGGGACAATGGCATCGATGTTTGATTACA
1 TGTAAGACCATGTCTGGGACAATGGCATCGATATCTGATTACA
*
29668020 TGTAAGACCACGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
29668040 GTTGGCGTTG
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
42 28 0.32
43 34 0.39
44 25 0.29
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAATGGCATCGATATCTGATTACA
Found at i:29671920 original size:86 final size:85
Alignment explanation
Indices: 29671807--29671967 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 85
29671797 GGATTTCCGA
* *
29671807 TATTTGAGTTCATGTAAGACCACGTCTGGGACGCTGGCATCGAT-TTGAGATTTACATGTAAGAC
1 TATTTGAGTTCATGTAAGACCACGTCTGGGACACTGGAATCGATATT-AGA-TTACATGTAAGAC
*
29671871 CATGTCTGGGACATCGGCATCG
64 CACGTCTGGGACATCGGCATCG
* * * *
29671893 TATTTGATTTCGTGTAAGACC-CTGTCTGGGATACTGGAATCGATATTTGATTACATGTAAGACC
1 TATTTGAGTTCATGTAAGACCAC-GTCTGGGACACTGGAATCGATATTAGATTACATGTAAGACC
29671957 ACGTCTGGGAC
65 ACGTCTGGGAC
29671968 GTTGGCATTG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 25 0.38
86 39 0.59
87 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (85 bp):
TATTTGAGTTCATGTAAGACCACGTCTGGGACACTGGAATCGATATTAGATTACATGTAAGACCA
CGTCTGGGACATCGGCATCG
Found at i:29671941 original size:43 final size:43
Alignment explanation
Indices: 29671804--29671967 Score: 192
Period size: 43 Copynumber: 3.8 Consensus size: 43
29671794 ATAGGATTTC
* *
29671804 CGATATTTGAGTTCATGTAAGACCACGTCTGGGACGCTGGCAT
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGACACTGGCAT
* *
29671847 CGAT-TTGAGATTTACATGTAAGACCATGTCTGGGACA-TCGGCAT
1 CGATATT-TGATTT-CATGTAAGACCACGTCTGGGACACT-GGCAT
* * *
29671891 CG-TATTTGATTTCGTGTAAGACC-CTGTCTGGGATACTGGAAT
1 CGATATTTGATTTCATGTAAGACCAC-GTCTGGGACACTGGCAT
*
29671933 CGATATTTGATTACATGTAAGACCACGTCTGGGAC
1 CGATATTTGATTTCATGTAAGACCACGTCTGGGAC
29671968 GTTGGCATTG
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
42 27 0.27
43 43 0.43
44 31 0.31
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
CGATATTTGATTTCATGTAAGACCACGTCTGGGACACTGGCAT
Found at i:29672915 original size:13 final size:13
Alignment explanation
Indices: 29672897--29672921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29672887 CGTGTGTGAC
29672897 ACATGGCCATGTT
1 ACATGGCCATGTT
29672910 ACATGGCCATGT
1 ACATGGCCATGT
29672922 GTCCCTTGGG
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (13 bp):
ACATGGCCATGTT
Found at i:29673227 original size:23 final size:24
Alignment explanation
Indices: 29673196--29673245 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
29673186 AGCGTGTGAC
*
29673196 CTATGATTCCTTGAAATT-TTTTT
1 CTATAATTCCTTGAAATTATTTTT
29673219 CTATAATTCCTTGAAATTATTTTT
1 CTATAATTCCTTGAAATTATTTTT
29673243 CTA
1 CTA
29673246 AGTGTCGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (24 bp):
CTATAATTCCTTGAAATTATTTTT
Found at i:29674736 original size:24 final size:24
Alignment explanation
Indices: 29674709--29674785 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
29674699 AGCTCTCGTT
29674709 ATATGGCTCTTTGTGAGCTTCCCA
1 ATATGGCTCTTTGTGAGCTTCCCA
* *
29674733 ATATGGTTCTTTGTGAACTTCCCGA
1 ATATGGCTCTTTGTGAGCTTCCC-A
* *
29674758 TTATGGCTC-TTATGAGCTTCCCA
1 ATATGGCTCTTTGTGAGCTTCCCA
*
29674781 TTATG
1 ATATG
29674786 TAGCCCGGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 6 0.13
24 32 0.70
25 8 0.17
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.40
Consensus pattern (24 bp):
ATATGGCTCTTTGTGAGCTTCCCA
Found at i:29689560 original size:7 final size:7
Alignment explanation
Indices: 29689537--29689628 Score: 130
Period size: 7 Copynumber: 12.7 Consensus size: 7
29689527 TTGGGAATTT
29689537 TTTTTAAA
1 TTTTT-AA
*
29689545 TTTTGAA
1 TTTTTAA
*
29689552 TATTTAA
1 TTTTTAA
*
29689559 TATTTAA
1 TTTTTAA
29689566 TTTTTAA
1 TTTTTAA
29689573 TTTTTTAA
1 -TTTTTAA
29689581 TTTTTTAA
1 -TTTTTAA
29689589 TTTTTAA
1 TTTTTAA
29689596 TTTTTAA
1 TTTTTAA
29689603 TTTTTAA
1 TTTTTAA
29689610 TTTTTAA
1 TTTTTAA
29689617 TTTTTAA
1 TTTTTAA
29689624 TTTTT
1 TTTTT
29689629 TTTGAAGATT
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
7 60 0.76
8 19 0.24
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (7 bp):
TTTTTAA
Found at i:29689595 original size:37 final size:36
Alignment explanation
Indices: 29689536--29689628 Score: 134
Period size: 37 Copynumber: 2.6 Consensus size: 36
29689526 TTTGGGAATT
* *
29689536 TTTTTTAAATTTTGAATATTTAATATTTAATTTTTAA
1 TTTTTT-AATTTTTAATTTTTAATATTTAATTTTTAA
*
29689573 TTTTTTAATTTTTTAATTTTTAATTTTTAATTTTTAA
1 TTTTTTAA-TTTTTAATTTTTAATATTTAATTTTTAA
29689610 -TTTTTAATTTTTAATTTTT
1 TTTTTTAATTTTTAATTTTT
29689629 TTTGAAGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
35 12 0.23
36 9 0.17
37 31 0.60
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (36 bp):
TTTTTTAATTTTTAATTTTTAATATTTAATTTTTAA
Found at i:29690238 original size:21 final size:21
Alignment explanation
Indices: 29690214--29690312 Score: 62
Period size: 22 Copynumber: 4.6 Consensus size: 21
29690204 AACCCCAACT
29690214 CTTAAACCATAAACCATAATC
1 CTTAAACCATAAACCATAATC
* * *
29690235 CTTAAACCTATAATCCACAAAC
1 CTTAAACC-ATAAACCATAATC
29690257 CTTAAA--ATAGTAACTCATACA-C
1 CTTAAACCATA--AAC-CATA-ATC
* *
29690279 TTTAAACCCTAAACCAT-ATAC
1 CTTAAACCATAAACCATAAT-C
*
29690300 CCTAAACCATAAA
1 CTTAAACCATAAA
29690313 TCCTAAACTA
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
19 4 0.07
21 24 0.41
22 28 0.47
23 1 0.02
24 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.24
Consensus pattern (21 bp):
CTTAAACCATAAACCATAATC
Found at i:29690303 original size:14 final size:14
Alignment explanation
Indices: 29690281--29690325 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
29690271 TCATACACTT
29690281 TAAACCCTAAACCA
1 TAAACCCTAAACCA
*
29690295 TATACCCTAAACCA
1 TAAACCCTAAACCA
* *
29690309 TAAATCCTAAACTA
1 TAAACCCTAAACCA
29690323 TAA
1 TAA
29690326 TGATAATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:29690431 original size:7 final size:7
Alignment explanation
Indices: 29690419--29690525 Score: 74
Period size: 7 Copynumber: 15.0 Consensus size: 7
29690409 ACTAATTAAT
29690419 CTAAACC
1 CTAAACC
29690426 CTAAACTC
1 CTAAAC-C
*
29690434 CTAATCC
1 CTAAACC
*
29690441 TTAAACC
1 CTAAACC
*
29690448 TTAAACC
1 CTAAACC
*
29690455 CTAAATC
1 CTAAACC
*
29690462 CTAAAAC
1 CTAAACC
*
29690469 ATAAACC
1 CTAAACC
*
29690476 CTTAACC
1 CTAAACC
*
29690483 CTTAACCC
1 C-TAAACC
29690491 CT-AACAC
1 CTAAAC-C
29690498 CTAAACC
1 CTAAACC
*
29690505 TTAAACC
1 CTAAACC
*
29690512 C-CAACC
1 CTAAACC
29690518 CTTAAACC
1 C-TAAACC
29690526 ACTCTTAAAC
Statistics
Matches: 77, Mismatches: 17, Indels: 11
0.73 0.16 0.10
Matches are distributed among these distances:
6 7 0.09
7 52 0.68
8 18 0.23
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:29690452 original size:29 final size:28
Alignment explanation
Indices: 29690420--29690512 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
29690410 CTAATTAATC
*
29690420 TAAACCCTAAACTCCTAATCCTTAAACCT
1 TAAACCCTAAACTCCTAA-CCATAAACCT
*
29690449 TAAACCCTAAA-TCCTAAAACATAAACCCT
1 TAAACCCTAAACTCCT-AACCATAAA-CCT
* * *
29690478 T-AACCCTTAACCCCTAACACCTAAACCT
1 TAAACCCTAAACTCCTAAC-CATAAACCT
29690506 TAAACCC
1 TAAACCC
29690513 CAACCCTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
28 23 0.43
29 30 0.57
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.23
Consensus pattern (28 bp):
TAAACCCTAAACTCCTAACCATAAACCT
Found at i:29690479 original size:36 final size:36
Alignment explanation
Indices: 29690439--29690525 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 36
29690429 AACTCCTAAT
*
29690439 CCTTAAACCTTAAACCCTAA-ATCCTAAAACATAAAC
1 CCTTAACCCTTAAACCCTAACA-CCTAAAACATAAAC
* * *
29690475 CCTTAACCCTTAACCCCTAACACCTAAACCTTAAAC
1 CCTTAACCCTTAAACCCTAACACCTAAAACATAAAC
*
29690511 CC-CAACCCTTAAACC
1 CCTTAACCCTTAAACC
29690526 ACTCTTAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 11 0.25
36 32 0.73
37 1 0.02
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.21
Consensus pattern (36 bp):
CCTTAACCCTTAAACCCTAACACCTAAAACATAAAC
Found at i:29691472 original size:88 final size:88
Alignment explanation
Indices: 29691323--29691503 Score: 208
Period size: 88 Copynumber: 2.1 Consensus size: 88
29691313 GCAGTGTTTT
* * *
29691323 TTTAAGATCTCAACCTTCAAACTTCAAAGATTTTCAAACTCTTAGACTTAACGATTTAAGATCGC
1 TTTAAGATCTCAACATTCAAACTTCAAAGATTTTCAAACTCTTAGACTTAACAACTTAAGATCGC
**
29691388 AACACT-CCTTTAAGGTTTTTTGA
66 AAC-CTCCCTTTAAGGTTCATTGA
* *
29691411 TTTAAGAT-TGCAACATTCAAACTTCAAGGATTTTCAGAA-TCTTAG-CGTTAGCAACTTAAGAT
1 TTTAAGATCT-CAACATTCAAACTTCAAAGATTTTCA-AACTCTTAGAC-TTAACAACTTAAGAT
* * *
29691473 TGCGACTTCCCTTTAAGGTTCATTGA
63 CGCAACCTCCCTTTAAGGTTCATTGA
29691499 TTTAA
1 TTTAA
29691504 TGTAACAACC
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
87 3 0.04
88 74 0.94
89 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (88 bp):
TTTAAGATCTCAACATTCAAACTTCAAAGATTTTCAAACTCTTAGACTTAACAACTTAAGATCGC
AACCTCCCTTTAAGGTTCATTGA
Found at i:29696605 original size:35 final size:35
Alignment explanation
Indices: 29696527--29696597 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
29696517 ATATATAACC
*
29696527 TCAATATAAACTCACATGTAACCAAATACACATGT
1 TCAATATAAACTCACATGTAACCAAATACACAAGT
* * *
29696562 TCAATATAAATTCACATGTAACCGAATACTCAAGT
1 TCAATATAAACTCACATGTAACCAAATACACAAGT
29696597 T
1 T
29696598 TGATATAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.28
Consensus pattern (35 bp):
TCAATATAAACTCACATGTAACCAAATACACAAGT
Found at i:29696860 original size:41 final size:41
Alignment explanation
Indices: 29696799--29696877 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
29696789 TGAAATTCAT
*
29696799 TCACCGGCACTAAGCCTGCTAGGCACGAAGCCCGAACAAAG
1 TCACCGGCACTAAGCCTGCTAGGCACAAAGCCCGAACAAAG
* *
29696840 TCACCGGCAC-AAGGCTTGCTAGGCTCAAAGCCCGAACA
1 TCACCGGCACTAA-GCCTGCTAGGCACAAAGCCCGAACA
29696878 TCACAAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.11
Consensus pattern (41 bp):
TCACCGGCACTAAGCCTGCTAGGCACAAAGCCCGAACAAAG
Found at i:29704861 original size:28 final size:28
Alignment explanation
Indices: 29704829--29704928 Score: 146
Period size: 28 Copynumber: 3.6 Consensus size: 28
29704819 ATATTCGACG
*
29704829 TCTCGCACACTAAGTGCCATACTCAACA
1 TCTCGCACACTAAGTGCCATACTCAATA
* *
29704857 TCTCGCACACTAAGTGCCATTCTCAATG
1 TCTCGCACACTAAGTGCCATACTCAATA
* *
29704885 TTTCGTACACTAAGTGCCATACTCAATA
1 TCTCGCACACTAAGTGCCATACTCAATA
*
29704913 TCTCACACACTAAGTG
1 TCTCGCACACTAAGTG
29704929 TCGTACATAG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27
Consensus pattern (28 bp):
TCTCGCACACTAAGTGCCATACTCAATA
Found at i:29704965 original size:40 final size:40
Alignment explanation
Indices: 29704918--29705050 Score: 137
Period size: 40 Copynumber: 3.3 Consensus size: 40
29704908 CAATATCTCA
* *
29704918 CACACTAAGTG-TCGTACATAGCCGAAGTTATCTCAAATCG
1 CACACTAAGTGCT-GTACATAGCCGAAGCTATCTCAAACCG
* * * *
29704958 TACACTAAGTGCTGTACATAGCTGACGCTATCTCGAACCG
1 CACACTAAGTGCTGTACATAGCCGAAGCTATCTCAAACCG
* *
29704998 CACACTAAGTGC--CACATTTAGCCGAAGCTATTTTCAAACCG
1 CACACTAAGTGCTGTACA--TAGCCGAAGCTA-TCTCAAACCG
29705039 CACACTAAGTGC
1 CACACTAAGTGC
29705051 CATATTTAGT
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
38 3 0.04
40 53 0.69
41 21 0.27
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (40 bp):
CACACTAAGTGCTGTACATAGCCGAAGCTATCTCAAACCG
Found at i:29706522 original size:18 final size:18
Alignment explanation
Indices: 29706499--29706533 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29706489 TAACAGATAT
29706499 ACTTAAAATCTAGTTGGC
1 ACTTAAAATCTAGTTGGC
*
29706517 ACTTAAAATCTGGTTGG
1 ACTTAAAATCTAGTTGG
29706534 ACTGCCACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (18 bp):
ACTTAAAATCTAGTTGGC
Found at i:29706881 original size:19 final size:20
Alignment explanation
Indices: 29706857--29706902 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
29706847 CATCCAAACA
29706857 CCAGAAAAGTAAATCA-TTT
1 CCAGAAAAGTAAATCATTTT
*
29706876 CCAGAAAAGTAAATTATTTT
1 CCAGAAAAGTAAATCATTTT
29706896 CCAGAAA
1 CCAGAAA
29706903 TTATCTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:29706918 original size:15 final size:14
Alignment explanation
Indices: 29706886--29706923 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
29706876 CCAGAAAAGT
29706886 AAATTATTTTCCAG
1 AAATTATTTTCCAG
29706900 AAATTATCTTT-CAG
1 AAATTAT-TTTCCAG
*
29706914 AAAATATTTT
1 AAATTATTTT
29706924 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (14 bp):
AAATTATTTTCCAG
Found at i:29707563 original size:47 final size:47
Alignment explanation
Indices: 29707466--29707589 Score: 140
Period size: 47 Copynumber: 2.6 Consensus size: 47
29707456 GATAAGTACA
* * * ** * *
29707466 TATATCATGGCCCGTAGCCAAATTAAGGTAACTTATCCCGGAGTACC
1 TATACCATGGCCCGTAGCCAAATTAAGGTAACTCATCACAAAATAAC
* * *
29707513 TATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTTACAAAATAAC
1 TATACCATGGCCCGTAGCCAAATTAAGGTAACTCATCACAAAATAAC
* *
29707560 TATACCGTGGCCCATAGCCAAATTAAGGTA
1 TATACCATGGCCCGTAGCCAAATTAAGGTA
29707590 TTTACTCACA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (47 bp):
TATACCATGGCCCGTAGCCAAATTAAGGTAACTCATCACAAAATAAC
Found at i:29711777 original size:21 final size:22
Alignment explanation
Indices: 29711737--29711778 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29711727 GCCTAAATGG
29711737 TCACACGAGCGTGTTGCCCCTC
1 TCACACGAGCGTGTTGCCCCTC
*
29711759 TCACACGGGCGTG-TGCCCCT
1 TCACACGAGCGTGTTGCCCCT
29711779 ATGTCAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.12, C:0.40, G:0.26, T:0.21
Consensus pattern (22 bp):
TCACACGAGCGTGTTGCCCCTC
Found at i:29720916 original size:15 final size:15
Alignment explanation
Indices: 29720858--29720937 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
29720848 TAAAGATAAC
*
29720858 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
*
29720872 AAGAAATTCA-AGATA
1 AAGAAATCCAGA-ATA
*
29720887 GAA-AAACCCAGAATA
1 -AAGAAATCCAGAATA
*
29720902 AAGAAATCTAGAATA
1 AAGAAATCCAGAATA
*
29720917 AA-AAGATCCAGGATA
1 AAGAA-ATCCAGAATA
29720932 AAGAAA
1 AAGAAA
29720938 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
14 12 0.24
15 34 0.67
16 5 0.10
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.12
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:29732019 original size:46 final size:46
Alignment explanation
Indices: 29731966--29732138 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
29731956 TAGTTGAGCA
*
29731966 TCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
29732012 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
29732057 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
29732105 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
29732139 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29732122 original size:93 final size:93
Alignment explanation
Indices: 29731963--29732133 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
29731953 GGATAGTTGA
*
29731963 GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
29732028 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
29732056 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
29732121 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29732134 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTCAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:29738297 original size:25 final size:23
Alignment explanation
Indices: 29738265--29738312 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
29738255 AAATTTATAA
**
29738265 TTTTAAAATGTAAAAGAATTAAAT
1 TTTTAAAATAAAAAAG-ATTAAAT
29738289 TTTTAAAAATAAAAAAGATTAAAT
1 TTTT-AAAATAAAAAAGATTAAAT
29738313 CTCAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (23 bp):
TTTTAAAATAAAAAAGATTAAAT
Found at i:29753461 original size:46 final size:46
Alignment explanation
Indices: 29753301--29753514 Score: 202
Period size: 46 Copynumber: 4.6 Consensus size: 46
29753291 TTGTGTGCTC
* *
29753301 GTGTAAGACATGTCTGGGGCATGCATCAGCCTCTTGATGTAAGCTA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCTCTTGATGTAAGCTA
* * * * *
29753347 GTGTAAGACCATGTCTGGGACATGGCATTGGCAT-TGAGACGAAAGCTA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCT-TGATGTAAGCTA
* *
29753395 GTGTAAGACATGTCTGGGACATGCATCGGCCTCTTCATGTAAGCCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCTCTTGATGTAAGCTA
* * * * *
29753441 ATGTAAGACATGTCTAGGACATGCATCAGCTTCATGATGT--G-TCA
1 GTGTAAGACATGTCTGGGACATGCATCGGCCTCTTGATGTAAGCT-A
* *
29753485 GTATAAGACCATGTCTGGAACATGGCATCG
1 GTGTAAGA-CATGTCTGGGACAT-GCATCG
29753515 ACGTAACGTG
Statistics
Matches: 135, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
44 8 0.06
45 12 0.09
46 62 0.46
47 29 0.21
48 24 0.18
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (46 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCCTCTTGATGTAAGCTA
Found at i:29754542 original size:28 final size:28
Alignment explanation
Indices: 29754502--29754567 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
29754492 ACACGGACTA
29754502 GGACACGGGCATGTAATGGCCATGTAAG
1 GGACACGGGCATGTAATGGCCATGTAAG
* *
29754530 GGACACGGGCATGTCATGGCCATGTCAG
1 GGACACGGGCATGTAATGGCCATGTAAG
29754558 GGACACGGGC
1 GGACACGGGC
29754568 CATGGACACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.24, C:0.23, G:0.38, T:0.15
Consensus pattern (28 bp):
GGACACGGGCATGTAATGGCCATGTAAG
Found at i:29754757 original size:21 final size:22
Alignment explanation
Indices: 29754718--29754758 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29754708 TCAAATTAGT
29754718 CACACAGGCGTGTTGCCCCTCC
1 CACACAGGCGTGTTGCCCCTCC
29754740 CACACAGGCGTG-TGCCCCT
1 CACACAGGCGTGTTGCCCCT
29754759 ATGTCTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.15, C:0.44, G:0.24, T:0.17
Consensus pattern (22 bp):
CACACAGGCGTGTTGCCCCTCC
Found at i:29761065 original size:94 final size:92
Alignment explanation
Indices: 29760865--29761040 Score: 221
Period size: 94 Copynumber: 1.9 Consensus size: 92
29760855 ATGTTTGTGT
* ** * *
29760865 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCTTGATGTAAGCTAATGTAATACCATGTC
1 GCTAGTGTAAGACATGTCT-GGACATGCATCAGCCTCACGATGT-AGCTAATATAAGACCATGTC
* *
29760930 TGGGACATGGCATTGGCATTGAGACGAGA
64 TGGGACATAGCATCGGCATTGAGACGAGA
* *
29760959 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCTTCACGATGT-G-TCAGTATAAGACCATGTC
1 GCTAGTGTAAGACATGTCT-GGACATGCATCAGCCTCACGATGTAGCT-AATATAAGACCATGTC
29761022 TGGGACATAGCATCGGCAT
64 TGGGACATAGCATCGGCAT
29761041 GAATACATGG
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
91 1 0.01
92 31 0.44
94 39 0.55
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.26
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCTGGACATGCATCAGCCTCACGATGTAGCTAATATAAGACCATGTCTG
GGACATAGCATCGGCATTGAGACGAGA
Found at i:29764526 original size:34 final size:35
Alignment explanation
Indices: 29764488--29764561 Score: 98
Period size: 34 Copynumber: 2.1 Consensus size: 35
29764478 TGATAAAATA
29764488 TTATTAATA-TAAAATAAAAATAATTATAACTAT-T
1 TTATTAATAGTAAAAT-AAAATAATTATAACTATCT
* * *
29764522 TTATTAATAGTAATATAAAATAATTTTAATTATCT
1 TTATTAATAGTAAAATAAAATAATTATAACTATCT
29764557 TTATT
1 TTATT
29764562 TTATTAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 24 0.69
35 11 0.31
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (35 bp):
TTATTAATAGTAAAATAAAATAATTATAACTATCT
Found at i:29766414 original size:17 final size:17
Alignment explanation
Indices: 29766389--29766425 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29766379 TTCAATTATC
*
29766389 TAAAAATATTTAAATTT
1 TAAAAATATTAAAATTT
*
29766406 TAAAGATATTAAAATTT
1 TAAAAATATTAAAATTT
29766423 TAA
1 TAA
29766426 TTTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAAAATATTAAAATTT
Found at i:29766425 original size:24 final size:25
Alignment explanation
Indices: 29766391--29766438 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
29766381 CAATTATCTA
29766391 AAAATATTTAAATTTTAAA-GATATT
1 AAAATATTT-AATTTTAAATGATATT
29766416 AAAAT-TTTAATTTTAAATGATAT
1 AAAATATTTAATTTTAAATGATAT
29766439 ATTTAAAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 8 0.36
25 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
AAAATATTTAATTTTAAATGATATT
Found at i:29766708 original size:13 final size:13
Alignment explanation
Indices: 29766690--29766719 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29766680 TTTTTGAGTT
29766690 AATCGAGTTTATG
1 AATCGAGTTTATG
*
29766703 AATCGAGTTTTTG
1 AATCGAGTTTATG
29766716 AATC
1 AATC
29766720 CTAACTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (13 bp):
AATCGAGTTTATG
Found at i:29769711 original size:90 final size:91
Alignment explanation
Indices: 29769540--29769849 Score: 455
Period size: 90 Copynumber: 3.4 Consensus size: 91
29769530 ATTAAAAATT
*** * *
29769540 AATTAATATAATAGTATGGTAGCATAAATTAAACAAAAAAAAAGTATGTTAAACTACATTTTAAA
1 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTATGTTAAGCTACAGTTTAAA
29769605 CTTTAAAGTTAGTTAATTGAAGCCTA
66 CTTTAAAGTTAGTTAATTGAAGCCTA
*
29769631 AATTAATATAATAGTACAATAGCATAAATTAAAC-AAAAAAAAGTCTGTTAAGCTATC-GTTTAA
1 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTATGTTAAGCTA-CAGTTTAA
29769694 ACTTTAAAGTTAGTTAATTGAAGCCTA
65 ACTTTAAAGTTAGTTAATTGAAGCCTA
* *
29769721 AATTAATATAATAGTACAAGTACAACAACATAAATTAAACAAAAAAAAAGTATGTT-AGACCACA
1 AATTAATATAATAGTACAA-T-----AGCATAAATTAAACAAAAAAAAAGTATGTTAAG-CTACA
29769785 GTTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
59 GTTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
29769818 AATTAATATAATAGTACAATAGCATAAATTAA
1 AATTAATATAATAGTACAATAGCATAAATTAA
29769850 TTAATTAAAG
Statistics
Matches: 199, Mismatches: 10, Indels: 20
0.87 0.04 0.09
Matches are distributed among these distances:
90 70 0.35
91 44 0.22
96 17 0.09
97 68 0.34
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (91 bp):
AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTATGTTAAGCTACAGTTTAAA
CTTTAAAGTTAGTTAATTGAAGCCTA
Found at i:29769826 original size:97 final size:90
Alignment explanation
Indices: 29769540--29769849 Score: 435
Period size: 97 Copynumber: 3.4 Consensus size: 90
29769530 ATTAAAAATT
*** * *
29769540 AATTAATATAATAGTATGGTAGCATAAATTAAACAAAAAAAAAGTATGTTAAACTACATTTTAAA
1 AATTAATATAATAGTACAATAACATAAATTAAACAAAAAAAAAGTATGTT-AACTACAGTTTAAA
29769605 CTTTAAAGTTAGTTAATTGAAGCCTA
65 CTTTAAAGTTAGTTAATTGAAGCCTA
* *
29769631 AATTAATATAATAGTACAATAGCATAAATTAAAC-AAAAAAAAGTCTGTTAAGCTATC-GTTTAA
1 AATTAATATAATAGTACAATAACATAAATTAAACAAAAAAAAAGTATGTTAA-CTA-CAGTTTAA
29769694 ACTTTAAAGTTAGTTAATTGAAGCCTA
64 ACTTTAAAGTTAGTTAATTGAAGCCTA
*
29769721 AATTAATATAATAGTACAAGTACAACAACATAAATTAAACAAAAAAAAAGTATGTTAGACCACAG
1 AATTAATATAATAGTACAA-T-----AACATAAATTAAACAAAAAAAAAGTATGTTA-ACTACAG
29769786 TTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
59 TTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
*
29769818 AATTAATATAATAGTACAATAGCATAAATTAA
1 AATTAATATAATAGTACAATAACATAAATTAA
29769850 TTAATTAAAG
Statistics
Matches: 199, Mismatches: 9, Indels: 22
0.87 0.04 0.10
Matches are distributed among these distances:
89 2 0.01
90 68 0.34
91 44 0.22
96 15 0.08
97 69 0.35
98 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (90 bp):
AATTAATATAATAGTACAATAACATAAATTAAACAAAAAAAAAGTATGTTAACTACAGTTTAAAC
TTTAAAGTTAGTTAATTGAAGCCTA
Found at i:29773223 original size:47 final size:48
Alignment explanation
Indices: 29773168--29773299 Score: 185
Period size: 47 Copynumber: 2.8 Consensus size: 48
29773158 CTCAATCGAT
* *
29773168 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATC-CCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCACCA
* * * *
29773215 GAGTACCTATACCATGGCCCGTAGCCAAAACAAGGTAACTCCTCACTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCACCA
* *
29773263 AAATACCTATACCATGGCCCATAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
29773300 TCACTCGCAC
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 40 0.54
48 34 0.46
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.20
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCACCA
Found at i:29780658 original size:27 final size:28
Alignment explanation
Indices: 29780621--29780697 Score: 113
Period size: 27 Copynumber: 2.8 Consensus size: 28
29780611 ACATATATCA
*
29780621 TATAGGGGCAAAATAGTCATTTTACC-C
1 TATAAGGGCAAAATAGTCATTTTACCAC
*
29780648 TATAAGGGCAAAACAGTCATTTTACCAC
1 TATAAGGGCAAAATAGTCATTTTACCAC
*
29780676 -ATAAGGGTAAAATAGTCATTTT
1 TATAAGGGCAAAATAGTCATTTT
29780698 GTCAATTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 44 0.98
28 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (28 bp):
TATAAGGGCAAAATAGTCATTTTACCAC
Found at i:29791032 original size:15 final size:15
Alignment explanation
Indices: 29791012--29791041 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29791002 AATTTCATGC
*
29791012 TTCAATCACCGTGTT
1 TTCAATCACCATGTT
29791027 TTCAATCACCATGTT
1 TTCAATCACCATGTT
29791042 ATCACTTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.10, T:0.40
Consensus pattern (15 bp):
TTCAATCACCATGTT
Found at i:29801967 original size:215 final size:215
Alignment explanation
Indices: 29801589--29802017 Score: 840
Period size: 215 Copynumber: 2.0 Consensus size: 215
29801579 ACAAAATCTT
* *
29801589 CCGTTTGTTGAATTAATTCCTGCTCGATCATTCTTCTTTTACTCAATTCTATCCAACAAACAGGT
1 CCGTTTATTGAATTAATTCCTGCTCGATCATTCTTCTTTCACTCAATTCTATCCAACAAACAGGT
29801654 GACCAGCACCTACAACCGTATAAGGCTTAATACGGAGCCATTTGAATACTCAATTGAAAACTATT
66 GACCAGCACCTACAACCGTATAAGGCTTAATACGGAGCCATTTGAATACTCAATTGAAAACTATT
29801719 ATTATAAACAAATTCAGCCAAAGGTAAGTAACGCTCCCAACCTGATTCAAAATCAATAACACAAG
131 ATTATAAACAAATTCAGCCAAAGGTAAGTAACGCTCCCAACCTGATTCAAAATCAATAACACAAG
29801784 TACGAAACATGTCTTCCAAG
196 TACGAAACATGTCTTCCAAG
29801804 CCGTTTATTGAATTAATTCCTGCTCGATCATTCTTCTTTCACTCAATTCTATCCAACAAACAGGT
1 CCGTTTATTGAATTAATTCCTGCTCGATCATTCTTCTTTCACTCAATTCTATCCAACAAACAGGT
29801869 GACCAGCACCTACAACCGTATAAGGCTTAATACGGAGCCATTTGAATACTCAATTGAAAACTATT
66 GACCAGCACCTACAACCGTATAAGGCTTAATACGGAGCCATTTGAATACTCAATTGAAAACTATT
29801934 ATTATAAACAAATTCAGCCAAAGGTAAGTAACGCTCCCAACCTGATTCAAAATCAATAACACAAG
131 ATTATAAACAAATTCAGCCAAAGGTAAGTAACGCTCCCAACCTGATTCAAAATCAATAACACAAG
29801999 TACGAAACATGTCTTCCAA
196 TACGAAACATGTCTTCCAA
29802018 AATCTGAATA
Statistics
Matches: 212, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
215 212 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (215 bp):
CCGTTTATTGAATTAATTCCTGCTCGATCATTCTTCTTTCACTCAATTCTATCCAACAAACAGGT
GACCAGCACCTACAACCGTATAAGGCTTAATACGGAGCCATTTGAATACTCAATTGAAAACTATT
ATTATAAACAAATTCAGCCAAAGGTAAGTAACGCTCCCAACCTGATTCAAAATCAATAACACAAG
TACGAAACATGTCTTCCAAG
Found at i:29804441 original size:12 final size:12
Alignment explanation
Indices: 29804424--29804497 Score: 61
Period size: 12 Copynumber: 6.5 Consensus size: 12
29804414 GTTTGTCTCC
29804424 TTCTTTCCTCTT
1 TTCTTTCCTCTT
29804436 TTCTTTCC-CTTT
1 TTCTTTCCTC-TT
29804448 TTCTTT--TCTT
1 TTCTTTCCTCTT
29804458 TTCTTTCCT-TT
1 TTCTTTCCTCTT
* * *
29804469 TTGTTTCGTTTT
1 TTCTTTCCTCTT
29804481 TATCTTT-CT-TT
1 T-TCTTTCCTCTT
29804492 TTCTTT
1 TTCTTT
29804498 TACTTATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
10 13 0.25
11 14 0.27
12 21 0.40
13 4 0.08
ACGTcount: A:0.01, C:0.23, G:0.03, T:0.73
Consensus pattern (12 bp):
TTCTTTCCTCTT
Found at i:29804487 original size:34 final size:34
Alignment explanation
Indices: 29804424--29804497 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
29804414 GTTTGTCTCC
29804424 TTCTTTCCTCTTTTCTTTCCCTTTTTCTTT-TCTT
1 TTCTTTCCTCTTTTCTTTCCCTTTTTCTTTCT-TT
* **
29804458 TTCTTTCCT-TTTTGTTTCGTTTTTATCTTTCTTT
1 TTCTTTCCTCTTTTCTTTCCCTTTT-TCTTTCTTT
29804492 TTCTTT
1 TTCTTT
29804498 TACTTATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 12 0.34
34 22 0.63
35 1 0.03
ACGTcount: A:0.01, C:0.23, G:0.03, T:0.73
Consensus pattern (34 bp):
TTCTTTCCTCTTTTCTTTCCCTTTTTCTTTCTTT
Found at i:29810636 original size:21 final size:21
Alignment explanation
Indices: 29810606--29810656 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
29810596 AAGCAGCTAA
* * *
29810606 GGTTCGCATATAATTTCTATG
1 GGTTCACATATAACTTCTACG
29810627 GGTTCACATATAACTTCTACG
1 GGTTCACATATAACTTCTACG
*
29810648 TGTTCACAT
1 GGTTCACAT
29810657 TACAATTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (21 bp):
GGTTCACATATAACTTCTACG
Found at i:29816282 original size:25 final size:25
Alignment explanation
Indices: 29816254--29816314 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
29816244 AGCCAAACAT
* *
29816254 AGCCTTTGTGGCAAGTTAT-TTGTAA
1 AGCCTTTGTGGCAAATTATCTT-AAA
*
29816279 AGCCCTTGTGGCAAATTATCTTAAA
1 AGCCTTTGTGGCAAATTATCTTAAA
*
29816304 AGACTTTGTGG
1 AGCCTTTGTGG
29816315 TGTATTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 28 0.93
26 2 0.07
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (25 bp):
AGCCTTTGTGGCAAATTATCTTAAA
Found at i:29821852 original size:21 final size:22
Alignment explanation
Indices: 29821826--29821879 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
29821816 CAGCCTGTAG
*
29821826 CACGGGCGTGTCCCATGG-TCA
1 CACGGGCGTGTCCCATGGACCA
* *
29821847 CACGGGCATGTCCCTTGGACCA
1 CACGGGCGTGTCCCATGGACCA
*
29821869 CACGGGTGTGT
1 CACGGGCGTGT
29821880 GAGCTCTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.20
Consensus pattern (22 bp):
CACGGGCGTGTCCCATGGACCA
Found at i:29839671 original size:39 final size:40
Alignment explanation
Indices: 29839594--29839740 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
29839584 TAGCTCCTCG
* * *
29839594 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
29839634 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
29839673 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
29839713 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
29839741 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:29839751 original size:80 final size:80
Alignment explanation
Indices: 29839640--29839820 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
29839630 CTCATTCAAT
* * *
29839640 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
29839703 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
29839719 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
29839783 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
29839800 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29839821 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:29839780 original size:40 final size:40
Alignment explanation
Indices: 29839637--29839820 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
29839627 TAACTCATTC
* *
29839637 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
29839677 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
29839717 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
29839757 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
29839798 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29839821 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:29847452 original size:39 final size:40
Alignment explanation
Indices: 29847375--29847480 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 40
29847365 TAGCTCCTCG
* * *
29847375 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
29847415 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
29847454 CACGAATGCC-TCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
29847481 ATTAGTATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
39 42 0.74
40 15 0.26
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:29847504 original size:79 final size:80
Alignment explanation
Indices: 29847421--29847600 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 80
29847411 CTCATTCAAT
* * *
29847421 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAATGCC-TCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA
29847482 TTAGT-A-TCTAGCACAAA
64 -TAGTCACT-TAGCACAAA
**
29847499 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATAT
29847564 AGTCACTTAGCACAAA
65 AGTCACTTAGCACAAA
*
29847580 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
29847601 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
78 4 0.04
79 38 0.43
80 35 0.39
81 11 0.12
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:29847519 original size:40 final size:40
Alignment explanation
Indices: 29847418--29847600 Score: 178
Period size: 40 Copynumber: 4.6 Consensus size: 40
29847408 TAACTCATTC
* * * *
29847418 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGTAACTAGCACA
*
29847458 AATGCC-TCGGGACTTAACCCGGAATTAGTATCTAGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAACTAGCACA
* * *
29847497 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAACTAGCACA
* ** *
29847537 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAGTAAC-TAGCACA
*
29847578 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29847601 CAGCATTCAA
Statistics
Matches: 118, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
38 3 0.03
39 34 0.29
40 70 0.59
41 11 0.09
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTAACTAGCACA
Found at i:29853206 original size:20 final size:20
Alignment explanation
Indices: 29853181--29853252 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
29853171 GTGTGGTCAC
*
29853181 ACACGCCCATGTGGCATGGG
1 ACACGCCCGTGTGGCATGGG
29853201 ACACGCCCGTGTGGCATGGG
1 ACACGCCCGTGTGGCATGGG
29853221 ACACGCCCGTGTGGCATGGG
1 ACACGCCCGTGTGGCATGGG
29853241 ACACGCCCGTGT
1 ACACGCCCGTGT
29853253 CCTCAGCCTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.17, C:0.32, G:0.36, T:0.15
Consensus pattern (20 bp):
ACACGCCCGTGTGGCATGGG
Found at i:29855867 original size:44 final size:44
Alignment explanation
Indices: 29855792--29855877 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
29855782 TACATGTATC
29855792 GCATCCATAATGAACTCAGACCAACTCAACAAACTCAGATGCTG
1 GCATCCATAATGAACTCAGACCAACTCAACAAACTCAGATGCTG
* * * *
29855836 GCATCCATAATGAACT-AGGACTAACTGAACAAGCTCGGATGC
1 GCATCCATAATGAACTCA-GACCAACTCAACAAACTCAGATGC
29855878 CTCATACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.03
44 36 0.97
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (44 bp):
GCATCCATAATGAACTCAGACCAACTCAACAAACTCAGATGCTG
Found at i:29860849 original size:64 final size:65
Alignment explanation
Indices: 29860694--29860866 Score: 174
Period size: 68 Copynumber: 2.6 Consensus size: 65
29860684 TGGATGATAC
* * * * *
29860694 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTAAGTGCACATCATGTGTACAAGAGAGCTACA
1 AGATA-TATGTAGCTAGGTCGCATGGATGATACTAAGTGCACACCATGTGTACAAGAGAGCTAC-
29860759 AG
64 AG
* * * *
29860761 ACATTATGATGTAGCTAGGTCGCATGGATGATACTATGTGTACACCATGTAG-ATAAGAGAGCTA
1 AGA-TAT-ATGTAGCTAGGTCGCATGGATGATACTAAGTGCACACCATGT-GTACAAGAGAGCTA
29860825 C-G
63 CAG
29860827 AGATATATGTAGCTAGGTCGCAT--ATGTAGTACTAAGTGCA
1 AGATATATGTAGCTAGGTCGCATGGATG-A-TACTAAGTGCA
29860867 GGCTACTATG
Statistics
Matches: 89, Mismatches: 12, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
62 3 0.03
63 1 0.01
64 26 0.29
65 3 0.03
66 3 0.03
67 3 0.03
68 49 0.55
69 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (65 bp):
AGATATATGTAGCTAGGTCGCATGGATGATACTAAGTGCACACCATGTGTACAAGAGAGCTACAG
Found at i:29860911 original size:51 final size:49
Alignment explanation
Indices: 29860851--29860986 Score: 184
Period size: 51 Copynumber: 2.8 Consensus size: 49
29860841 AGGTCGCATA
* *
29860851 TGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTTGATCACGTG
1 TGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA--TTGATCACATG
* * * * *
29860902 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATG
1 TGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGATCACATG
29860951 TGTAGTACTAAGTGCA-GCTACTATGCGTACCAGATA
1 TGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
29860987 GTTTGGCTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
48 17 0.22
49 24 0.32
51 35 0.46
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (49 bp):
TGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGATCACATG
Found at i:29865770 original size:20 final size:20
Alignment explanation
Indices: 29865745--29865784 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
29865735 AAAATTAGAT
29865745 GAAATATTTTATTATTTTAA
1 GAAATATTTTATTATTTTAA
29865765 GAAATATTTTATTATTTTAA
1 GAAATATTTTATTATTTTAA
29865785 CTTATATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
GAAATATTTTATTATTTTAA
Found at i:29871466 original size:2 final size:2
Alignment explanation
Indices: 29871459--29871487 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29871449 TCATTTGCAG
29871459 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
29871488 CAATCCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:29873283 original size:23 final size:23
Alignment explanation
Indices: 29873256--29873315 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
29873246 TACTTAAATT
29873256 TATTTCAAATATATAA-AATTATA
1 TATTT-AAATATATAATAATTATA
*
29873279 TATTTAAATTTATAATAATTATA
1 TATTTAAATATATAATAATTATA
29873302 T-TTTAAATTATATA
1 TATTTAAA-TATATA
29873316 TTCAAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTTAAATATATAATAATTATA
Found at i:29873286 original size:14 final size:13
Alignment explanation
Indices: 29873271--29873324 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
29873261 CAAATATATA
29873271 AAATTATATATTT
1 AAATTATATATTT
*
29873284 AAATT-TATA-AT
1 AAATTATATATTT
29873295 -AATTATAT-TTT
1 AAATTATATATTT
*
29873306 AAATTATATATTC
1 AAATTATATATTT
29873319 AAATTA
1 AAATTA
29873325 AATTTTACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 4 0.12
11 5 0.15
12 12 0.35
13 13 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTATATATTT
Found at i:29873292 original size:22 final size:23
Alignment explanation
Indices: 29873256--29873315 Score: 79
Period size: 22 Copynumber: 2.6 Consensus size: 23
29873246 TACTTAAATT
*
29873256 TATTTCAAATATATAA-AATTATA
1 TATTT-AAATTTATAATAATTATA
29873279 TATTTAAATTTATAATAATTATA
1 TATTTAAATTTATAATAATTATA
29873302 T-TTTAAATTATATA
1 TATTTAAATT-TATA
29873316 TTCAAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTTAAATTTATAATAATTATA
Found at i:29873399 original size:19 final size:19
Alignment explanation
Indices: 29873375--29873411 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29873365 TTATATTTCA
*
29873375 TATTTTAAAATAATTTTAC
1 TATTTTAAAATAAATTTAC
*
29873394 TATTTTAATATAAATTTA
1 TATTTTAAAATAAATTTA
29873412 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTAAAATAAATTTAC
Found at i:29873764 original size:29 final size:29
Alignment explanation
Indices: 29873733--29873788 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
29873723 TTGTAAACTT
29873733 TTTTTTATTTCTT-T-AATTTTGATTTATA
1 TTTTTTATTT-TTATAAATTTTGATTTATA
29873761 TTTTTTATTTTTATAAATTTTGATTTAT
1 TTTTTTATTTTTATAAATTTTGATTTAT
29873789 TTGTTGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 2 0.08
28 11 0.42
29 13 0.50
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (29 bp):
TTTTTTATTTTTATAAATTTTGATTTATA
Found at i:29880029 original size:21 final size:21
Alignment explanation
Indices: 29879997--29880096 Score: 54
Period size: 21 Copynumber: 5.0 Consensus size: 21
29879987 ATTATATTAT
* *
29879997 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
29880018 AATAAATA-AAAAGAAAGAAAG
1 AATAAA-ACAAAAGAAAGAAAG
** *
29880039 -ATAGAAA-TGAA-ACAGAAAG
1 AATA-AAACAAAAGAAAGAAAG
*
29880058 -A-AAAA-GAAAGAAAGAAAG
1 AATAAAACAAAAGAAAGAAAG
*
29880076 AATAGAAA-AAAGGAAAGAAAG
1 AATA-AAACAAAAGAAAGAAAG
29880097 GAAGGAGAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
17 5 0.08
18 8 0.13
19 9 0.14
20 7 0.11
21 33 0.52
22 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:29880034 original size:4 final size:4
Alignment explanation
Indices: 29880027--29880096 Score: 65
Period size: 4 Copynumber: 17.0 Consensus size: 4
29880017 GAATAAATAA
*
29880027 AAAG AAAG AAAG ATAG AAATG AAACAG AAAG -AA- AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG AAAG
29880076 AATAG AAA- AAAGG AAAG AAAG
1 AA-AG AAAG AAA-G AAAG AAAG
29880097 GAAGGAGAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
3 7 0.12
4 35 0.62
5 10 0.18
6 3 0.05
7 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.23, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:29880091 original size:17 final size:17
Alignment explanation
Indices: 29880022--29880094 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 17
29880012 ATAAAGAATA
*
29880022 AATAAAAAGAAAGAAAG
1 AATAGAAAGAAAGAAAG
29880039 -ATAGAAATGAAACAGAAAG
1 AATAGAAA-G-AA-AGAAAG
*
29880058 AAAAAGAAAGAAAGAAAG
1 -AATAGAAAGAAAGAAAG
29880076 AATAGAAA-AAAGGAAAG
1 AATAGAAAGAAA-GAAAG
29880093 AA
1 AA
29880095 AGGAAGGAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
16 9 0.19
17 15 0.32
18 8 0.17
19 8 0.17
20 1 0.02
21 6 0.13
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (17 bp):
AATAGAAAGAAAGAAAG
Found at i:29883751 original size:40 final size:40
Alignment explanation
Indices: 29883630--29883769 Score: 137
Period size: 40 Copynumber: 3.5 Consensus size: 40
29883620 GACTTCAAGT
* * *
29883630 CGATGAGACACTGGGTGTCAATTTA-CTACTTCGGATTAATT
1 CGATGAGACACTGGGTGCCAAATTATC-ACTTCGGATT-ATC
* * *
29883671 CGATGATG-CACTGGATGCCAAA-T-T-ACTTCGGTTTAGC
1 CGATGA-GACACTGGGTGCCAAATTATCACTTCGGATTATC
* *
29883708 CGATGAGACACTGGGTGTCAAATTATCACTTCGAATTATC
1 CGATGAGACACTGGGTGCCAAATTATCACTTCGGATTATC
*
29883748 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGCCAAA
29883770 CTGGTGTGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 13
0.75 0.12 0.12
Matches are distributed among these distances:
36 1 0.01
37 19 0.24
38 10 0.12
39 1 0.01
40 31 0.39
41 17 0.21
42 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTGGGTGCCAAATTATCACTTCGGATTATC
Found at i:29885909 original size:7 final size:7
Alignment explanation
Indices: 29885897--29885922 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29885887 TTTCATCATT
29885897 TCATATC
1 TCATATC
29885904 TCATATC
1 TCATATC
29885911 TCATATC
1 TCATATC
29885918 TCATA
1 TCATA
29885923 ATTCAATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (7 bp):
TCATATC
Found at i:29887597 original size:19 final size:19
Alignment explanation
Indices: 29887573--29887628 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
29887563 AAAATTGAGG
29887573 TTTGGGGGAAAGTAAAAGT
1 TTTGGGGGAAAGTAAAAGT
*
29887592 TTTGGGGGAAAGCAAAAGT
1 TTTGGGGGAAAGTAAAAGT
29887611 TTTGGGGGAAAGTAAAAG
1 TTTGGGGGAAAGTAAAAG
29887629 GAATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.38, C:0.02, G:0.38, T:0.23
Consensus pattern (19 bp):
TTTGGGGGAAAGTAAAAGT
Found at i:29887709 original size:31 final size:31
Alignment explanation
Indices: 29887674--29887732 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
29887664 TTGGAGAGAA
*
29887674 AGTAAAAGGGAAAAAGTTTTGGGGGTTTGGG
1 AGTAAAAGGAAAAAAGTTTTGGGGGTTTGGG
29887705 AGTAAAAGGAAAAAAGTTTTGGGGGTTT
1 AGTAAAAGGAAAAAAGTTTTGGGGGTTT
29887733 AGGGGAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.37, T:0.27
Consensus pattern (31 bp):
AGTAAAAGGAAAAAAGTTTTGGGGGTTTGGG
Found at i:29891308 original size:19 final size:19
Alignment explanation
Indices: 29891270--29891308 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29891260 TAATTTTATT
* * *
29891270 TATCATATTATAATGTACA
1 TATCATATTAAAAAGAACA
29891289 TATCATATTAAAAAGAACA
1 TATCATATTAAAAAGAACA
29891308 T
1 T
29891309 TTCAATAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (19 bp):
TATCATATTAAAAAGAACA
Found at i:29894739 original size:25 final size:25
Alignment explanation
Indices: 29894688--29894767 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
29894678 GTCATTAGGG
* * * *
29894688 TTACCGAT-TCCAACTCTTATGATC
1 TTACCGATATTCAGCTCGTATGAGC
29894712 TTACCGATATTCAGCTCGTATGAGC
1 TTACCGATATTCAGCTCGTATGAGC
* * *
29894737 TTACTGTTATTCAGCTCAG-AGGAGC
1 TTACCGATATTCAGCTC-GTATGAGC
29894762 TTACCG
1 TTACCG
29894768 TTTATACCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
24 8 0.17
25 37 0.80
26 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (25 bp):
TTACCGATATTCAGCTCGTATGAGC
Found at i:29899865 original size:8 final size:8
Alignment explanation
Indices: 29899854--29899879 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29899844 CATTTTAATC
29899854 ACTCTTAT
1 ACTCTTAT
29899862 ACTCTTAT
1 ACTCTTAT
29899870 ACTCTTAT
1 ACTCTTAT
29899878 AC
1 AC
29899880 CATGTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (8 bp):
ACTCTTAT
Found at i:29901423 original size:43 final size:43
Alignment explanation
Indices: 29901375--29901459 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
29901365 CACATGTACT
*
29901375 GCATCCATTATGAACTCAGACCACTCAACGAGCTCGGATGCTC
1 GCATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGCTC
* *
29901418 GCATCCATAATGAACTCGGACCACTCAATGAGCTCGGATGCT
1 GCATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGCT
29901460 ACATATATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (43 bp):
GCATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGCTC
Found at i:29916479 original size:23 final size:22
Alignment explanation
Indices: 29916435--29916489 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
29916425 TTGAAAGAAA
* *
29916435 AATAATAATATACATATAAAAAG
1 AATAATAA-AAACATATAAAAAC
*
29916458 AATAATAAAAACATCATTAAAAC
1 AATAATAAAAACAT-ATAAAAAC
29916481 AAT-ATAAAA
1 AATAATAAAA
29916490 TAAAAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (22 bp):
AATAATAAAAACATATAAAAAC
Found at i:29916837 original size:147 final size:146
Alignment explanation
Indices: 29916632--29916907 Score: 344
Period size: 147 Copynumber: 1.9 Consensus size: 146
29916622 GAAGCAACAT
* * * * * *
29916632 AAAATAAAAATTACAAATGTGAGTAGTAAATGAATAAAACTCGAGACTCAATGTTGTAATTACAA
1 AAAATAAAAAATAAAAATATGAGTAGTAAATGAATAAAACTCGAGACTAAAGGATGTAATTACAA
* * * *
29916697 CTATCT-TACTATCTAACGAAAA-AATTAATATCTTAAAAAATATTAATTAAAAAATTAAAAAGC
66 CTAACTAAACAATCTAAC-AAAAGAACTAATATCTT-AAAAA-ATTAATTAAAAAATTAAAAAGC
29916760 TTGAAGTAACATTAAATAA
128 TTGAAGTAACATTAAATAA
* * *
29916779 AAAATAAAAAATAAAAATATGAGTAAG-AGAA-GAATTAAATTCGAGACTAAAGGATGTAATTGC
1 AAAATAAAAAATAAAAATATGAGT-AGTA-AATGAATAAAACTCGAGACTAAAGGATGTAATTAC
* *
29916842 AACTAACTAAACAATCTAACAAAAGAACTAATATGTTAAAAAATTAATTAAAAATTTAAAAAGCT
64 AACTAACTAAACAATCTAACAAAAGAACTAATATCTTAAAAAATTAATTAAAAAATTAAAAAGCT
29916907 T
129 T
29916908 AATATGAAAT
Statistics
Matches: 110, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
146 23 0.21
147 64 0.58
148 23 0.21
ACGTcount: A:0.54, C:0.09, G:0.10, T:0.27
Consensus pattern (146 bp):
AAAATAAAAAATAAAAATATGAGTAGTAAATGAATAAAACTCGAGACTAAAGGATGTAATTACAA
CTAACTAAACAATCTAACAAAAGAACTAATATCTTAAAAAATTAATTAAAAAATTAAAAAGCTTG
AAGTAACATTAAATAA
Found at i:29917188 original size:40 final size:40
Alignment explanation
Indices: 29917133--29917221 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 40
29917123 GTATCAACAA
*
29917133 AGTAATCTAATTTTATGTATTTGTTTATCATAGAATCACG
1 AGTAATCTAATTTTATGCATTTGTTTATCATAGAATCACG
* *
29917173 AGTAATCTAATTTTATGCATTTGTTTATCGTGGAATCACG
1 AGTAATCTAATTTTATGCATTTGTTTATCATAGAATCACG
*
29917213 TGTAATCTA
1 AGTAATCTA
29917222 GTTGCTTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (40 bp):
AGTAATCTAATTTTATGCATTTGTTTATCATAGAATCACG
Found at i:29921379 original size:16 final size:16
Alignment explanation
Indices: 29921358--29921389 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29921348 ACTTGAAATT
29921358 AACTCACAATTGATGA
1 AACTCACAATTGATGA
29921374 AACTCACAATTGATGA
1 AACTCACAATTGATGA
29921390 CAATGCAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
AACTCACAATTGATGA
Found at i:29926278 original size:29 final size:28
Alignment explanation
Indices: 29926237--29926297 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
29926227 TATTAAATAT
* * *
29926237 TAAAAATATTAAAATTTATATAAACTTA
1 TAAAAATATTAAAAATAATAGAAACTTA
29926265 TAAAAATTATTAAAAATAATAGAAACTTA
1 TAAAAA-TATTAAAAATAATAGAAACTTA
29926294 TAAA
1 TAAA
29926298 TTTTAGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (28 bp):
TAAAAATATTAAAAATAATAGAAACTTA
Found at i:29926344 original size:9 final size:9
Alignment explanation
Indices: 29926167--29926574 Score: 76
Period size: 9 Copynumber: 43.6 Consensus size: 9
29926157 ATATTTTTTC
29926167 ATAAAATATT
1 ATAAAA-ATT
*
29926177 AAAAAAATT
1 ATAAAAATT
*
29926186 -TAAAAATA
1 ATAAAAATT
* *
29926194 AAAAAAAAT
1 ATAAAAATT
29926203 A-AAAAATGT
1 ATAAAAAT-T
*
29926212 ATAAAAAGT
1 ATAAAAATT
*
29926221 AT-TAAA-T
1 ATAAAAATT
*
29926228 AT-TAAA-T
1 ATAAAAATT
29926235 ATTAAAAA-T
1 A-TAAAAATT
*
29926244 ATTAAAATTT
1 A-TAAAAATT
*
29926254 ATATAAACTT
1 ATA-AAAATT
29926264 ATAAAAATT
1 ATAAAAATT
*
29926273 ATTAAAAATA
1 A-TAAAAATT
*
29926283 ATAGAAACTT
1 ATA-AAAATT
**
29926293 ATAAATTTT
1 ATAAAAATT
29926302 AGTAAAAGTATT
1 A-TAAAA--ATT
*
29926314 -TAAAAAAT
1 ATAAAAATT
* *
29926322 CTAATAACTT
1 ATAA-AAATT
29926332 ATAAAAATT
1 ATAAAAATT
*
29926341 AT-AAATTT
1 ATAAAAATT
29926349 AATAAAGCATATT
1 -ATAAA--A-ATT
*
29926362 -TAAAGTATT
1 ATAAA-AATT
*
29926371 -TAAAATTTT
1 ATAAAA-ATT
29926380 ATAAAAATTCT
1 ATAAAAA-T-T
* * *
29926391 TTTAAACTT
1 ATAAAAATT
*
29926400 ATAAAAAATC
1 AT-AAAAATT
29926410 ATAAAAA-T
1 ATAAAAATT
*
29926418 ATAAAAA-A
1 ATAAAAATT
*
29926426 ATTAAATATT
1 A-TAAAAATT
* *
29926436 ACAAATATT
1 ATAAAAATT
*
29926445 AT-TAAATT
1 ATAAAAATT
* *
29926453 -TTAAATTT
1 ATAAAAATT
*
29926461 GATATAAACTT
1 -ATA-AAAATT
29926472 ATAAAAATT
1 ATAAAAATT
*
29926481 ATTAAACAGATC
1 A-TAAA-A-ATT
29926493 ATAAAAACTT
1 ATAAAAA-TT
*
29926503 ATAAATATT
1 ATAAAAATT
29926512 ATAAAAA-T
1 ATAAAAATT
29926520 ATAAAAATCT
1 ATAAAAAT-T
*
29926530 AATAAATTATTT
1 -ATAAA--AATT
*
29926542 ATAAAATTT
1 ATAAAAATT
29926551 ATAAAATATAT
1 ATAAAA-AT-T
*
29926562 TTAAAAATT
1 ATAAAAATT
29926571 -TAAA
1 ATAAA
29926575 CCTCTAAAAT
Statistics
Matches: 298, Mismatches: 59, Indels: 84
0.68 0.13 0.19
Matches are distributed among these distances:
7 10 0.03
8 50 0.17
9 106 0.36
10 86 0.29
11 35 0.12
12 7 0.02
13 4 0.01
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAAAAATT
Found at i:29926557 original size:21 final size:21
Alignment explanation
Indices: 29926505--29926572 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
29926495 AAAAACTTAT
29926505 AAATATTATAAAA-ATA--TAA
1 AAAT-TTATAAAATATATTTAA
*
29926524 AAATCTA-ATAAAT-TATTTATA
1 AAATTTATA-AAATATATTTA-A
29926545 AAATTTATAAAATATATTTAA
1 AAATTTATAAAATATATTTAA
29926566 AAATTTA
1 AAATTTA
29926573 AACCTCTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
17 1 0.03
18 7 0.17
19 4 0.10
20 2 0.05
21 19 0.47
22 7 0.17
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTTATAAAATATATTTAA
Found at i:29926789 original size:12 final size:12
Alignment explanation
Indices: 29926772--29926796 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29926762 AGGGGTTTAA
29926772 ATTTTTAAATAT
1 ATTTTTAAATAT
29926784 ATTTTTAAATAT
1 ATTTTTAAATAT
29926796 A
1 A
29926797 CTTGAGTAAC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTTAAATAT
Found at i:29933820 original size:26 final size:26
Alignment explanation
Indices: 29933729--29933821 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
29933719 AAATTTATCA
* *
29933729 AATCGAATTGAGTAAGATGAAATTAG
1 AATCGAATCGAATAAGATGAAATTAG
* * * *
29933755 AATTGAATCGAGTAAAGCTGGAATTAG
1 AATCGAATCGAAT-AAGATGAAATTAG
** * *
29933782 AATAAAATTGAATAAGATGAAATTTG
1 AATCGAATCGAATAAGATGAAATTAG
29933808 AATCGAATCGAATA
1 AATCGAATCGAATA
29933822 TATTTATTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
26 32 0.62
27 20 0.38
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.27
Consensus pattern (26 bp):
AATCGAATCGAATAAGATGAAATTAG
Found at i:29934270 original size:18 final size:18
Alignment explanation
Indices: 29934236--29934270 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29934226 AAAATTAGGG
* *
29934236 TTTGGGAAGAAATAAAAT
1 TTTGGGAAAAAACAAAAT
29934254 TTTGGGAAAAAACAAAA
1 TTTGGGAAAAAACAAAA
29934271 GAAAAAAATT
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:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (18 bp):
TTTGGGAAAAAACAAAAT
Found at i:29936219 original size:16 final size:15
Alignment explanation
Indices: 29936170--29936213 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
29936160 ACTAATTTTG
29936170 AATATTAAAATATCA
1 AATATTAAAATATCA
*
29936185 CAT-TTAACAATAATCA
1 AATATTAA-AAT-ATCA
29936201 AATATTAAAATAT
1 AATATTAAAATAT
29936214 TAAAATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 9 0.38
17 4 0.17
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (15 bp):
AATATTAAAATATCA
Found at i:29936296 original size:6 final size:6
Alignment explanation
Indices: 29936286--29936320 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
29936276 CTCATCTTTT
*
29936286 TATTCT TATTCC TATTCC TATTCC TATTCC TATTC
1 TATTCC TATTCC TATTCC TATTCC TATTCC TATTC
29936321 ATGGTTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
TATTCC
Found at i:29938964 original size:12 final size:12
Alignment explanation
Indices: 29938939--29938972 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
29938929 TTTAAATTTT
*
29938939 AAAAATTAT-TA
1 AAAAATTATAAA
29938950 AAAAATTATAAA
1 AAAAATTATAAA
29938962 AAAAATTATAA
1 AAAAATTATAA
29938973 TTATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:29939057 original size:38 final size:39
Alignment explanation
Indices: 29939013--29939130 Score: 141
Period size: 38 Copynumber: 3.0 Consensus size: 39
29939003 CTGGGTGTTG
*
29939013 AAAATCTTATGAACATTAAAATTTAATAGTTGGATATT-
1 AAAATCTTATGACCATTAAAATTTAATAGTTGGATATTA
* ** *
29939051 AAAATCTTATGACCATTAAAATTTAATTGTTAAAAATTA
1 AAAATCTTATGACCATTAAAATTTAATAGTTGGATATTA
29939090 AAAATACTGTTATGACCATTAAAATTTAA-AGGTTGGATATT
1 AAAAT-C--TTATGACCATTAAAATTTAATA-GTTGGATATT
29939131 GTTATTTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
38 33 0.50
39 5 0.08
40 1 0.02
42 27 0.41
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (39 bp):
AAAATCTTATGACCATTAAAATTTAATAGTTGGATATTA
Found at i:29939695 original size:15 final size:15
Alignment explanation
Indices: 29939675--29939706 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29939665 GAGTAAACTA
29939675 TACTAGCCATTTTAT
1 TACTAGCCATTTTAT
29939690 TACTAGCCATTTTAT
1 TACTAGCCATTTTAT
29939705 TA
1 TA
29939707 TCAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TACTAGCCATTTTAT
Found at i:29944987 original size:42 final size:42
Alignment explanation
Indices: 29944878--29945036 Score: 164
Period size: 42 Copynumber: 3.8 Consensus size: 42
29944868 TACCAATGCC
* *
29944878 ATATCCTAGATATGGTCTTACACGTAATCTCGTATCGATGCTA
1 ATATCCCAGATATGGTCTTACACGTAATCTCATATCGATG-TA
* * *
29944921 ATAGCCCA-ACTATGATCTTACACG-AAGTCTCATATCGATGTT
1 ATATCCCAGA-TATGGTCTTACACGTAA-TCTCATATCGATGTA
* *
29944963 GTATCCCAGATATGGTCTTACACG-AAGTCTCATATCGAT-TCC
1 ATATCCCAGATATGGTCTTACACGTAA-TCTCATATCGATGT-A
**
29945005 ATATCATAGATATGGTCTTACACGTAATCTCA
1 ATATCCCAGATATGGTCTTACACGTAATCTCA
29945037 GTAATCCTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.01
42 64 0.65
43 34 0.34
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (42 bp):
ATATCCCAGATATGGTCTTACACGTAATCTCATATCGATGTA
Found at i:29955946 original size:42 final size:42
Alignment explanation
Indices: 29955840--29956003 Score: 179
Period size: 42 Copynumber: 3.9 Consensus size: 42
29955830 TACCGTACCA
* * * * *
29955840 ATGCCATATCCTAGATATGGTGTTACATGTAA-TCTCGTATCA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCATATCG
* * *
29955882 ATGCCAATAGCCTAGCTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
** *
29955925 ATGCTGTATCCCAGATATGGTCTTACACGAAGTCTTATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
*
29955967 ATGCCATATCTCAGATATGGTCTTACACGTAA-TCTCA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCA
29956004 GTAACCCTAA
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 69 0.67
43 34 0.33
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Done.