Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 184 of 185
Found at i:56145040 original size:25 final size:25
Alignment explanation
Indices: 56145012--56145085 Score: 112
Period size: 25 Copynumber: 3.0 Consensus size: 25
56145002 TTTTATAAAA
*
56145012 TTTAAATTAGGAATTTTATTAGGAC
1 TTTAAATTAGGAATTATATTAGGAC
* *
56145037 TTTAAATTAGGAATTCTACTAGGAC
1 TTTAAATTAGGAATTATATTAGGAC
*
56145062 TTTAAATTAGGAATTAGATTAGGA
1 TTTAAATTAGGAATTATATTAGGA
56145086 TTTTCCCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (25 bp):
TTTAAATTAGGAATTATATTAGGAC
Found at i:56149954 original size:48 final size:47
Alignment explanation
Indices: 56149735--56149954 Score: 142
Period size: 48 Copynumber: 4.6 Consensus size: 47
56149725 CATAGTAGGG
* * * * **
56149735 TGCCAATGCCATATCCCAAATATGGTCTTATATGAGACCACTTATCGA
1 TGCCAATGCCATAT-CCAGATATGGTCTTACATGGGATCAAATATCGA
* * * * *
56149783 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCACACAT--A
1 TGCCAATGCCATAT-CCAGATATGGTCTTACATGGGATCAAATATCGA
* * * * * * **
56149829 T--CAAAGCCGATAGCCCAGCTATGGTCTTACACGATGTTCTCATATCGA
1 TGCCAATGCC-ATA-TCCAGATATGGTCTTACATG-GGATCAAATATCGA
* * *
56149877 TGCCAATGCCATGTCACAGACATGCTCTTACATGGGATCAAATATCGA
1 TGCCAATGCCATATC-CAGATATGGTCTTACATGGGATCAAATATCGA
*
56149925 TGCCGATGCCATATCCTAGATATGGTCTTA
1 TGCCAATGCCATATCC-AGATATGGTCTTA
56149955 TACGAGATCT
Statistics
Matches: 130, Mismatches: 33, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
44 6 0.05
45 17 0.13
46 9 0.07
47 1 0.01
48 75 0.58
49 16 0.12
50 6 0.05
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (47 bp):
TGCCAATGCCATATCCAGATATGGTCTTACATGGGATCAAATATCGA
Found at i:56155588 original size:30 final size:28
Alignment explanation
Indices: 56155548--56155613 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
56155538 CCAATAACTT
* *
56155548 AAATAAAACTTTTGAATAATTTAGTGACCA
1 AAATATAACTTTT--ATAATTAAGTGACCA
* *
56155578 AATTATAACTTTTTTAATTAAGTGACCA
1 AAATATAACTTTTATAATTAAGTGACCA
56155606 AAATATAA
1 AAATATAA
56155614 ATTTACCCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 20 0.65
30 11 0.35
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (28 bp):
AAATATAACTTTTATAATTAAGTGACCA
Found at i:56157499 original size:6 final size:6
Alignment explanation
Indices: 56157473--56157536 Score: 83
Period size: 6 Copynumber: 10.3 Consensus size: 6
56157463 TCTAAATAAA
*
56157473 TTCATT TCTCATT TCTCATT TTCATT TTCATT TTCATT TTCATT TCCATT
1 TTCATT T-TCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TTCATT
* *
56157523 TCCATT TCCATT TT
1 TTCATT TTCATT TT
56157537 GAGAAAACCA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
6 42 0.76
7 13 0.24
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (6 bp):
TTCATT
Found at i:56160136 original size:21 final size:21
Alignment explanation
Indices: 56160098--56160137 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
56160088 AATCACAATA
56160098 ATTTTTAATCATGGATTAATT
1 ATTTTTAATCATGGATTAATT
*
56160119 ATTTATTAATC-TGTATTAA
1 ATTT-TTAATCATGGATTAA
56160138 CACGAGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTTTTAATCATGGATTAATT
Found at i:56160778 original size:59 final size:59
Alignment explanation
Indices: 56160686--56160811 Score: 207
Period size: 59 Copynumber: 2.1 Consensus size: 59
56160676 CATGATAAAC
* *
56160686 ATGCCATACTTCTAATTCTTATTCGCATGTAAAGCATGCTTACTGAAATTATGTTCTAT
1 ATGCCATACTTCTAATTCCTATCCGCATGTAAAGCATGCTTACTGAAATTATGTTCTAT
* * *
56160745 ATGCCATACTTCTGATTCCTATCCGTATGTAAAGCATGCTTACTGAAATTATGTTCTGT
1 ATGCCATACTTCTAATTCCTATCCGCATGTAAAGCATGCTTACTGAAATTATGTTCTAT
56160804 ATGCCATA
1 ATGCCATA
56160812 TCATATGCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (59 bp):
ATGCCATACTTCTAATTCCTATCCGCATGTAAAGCATGCTTACTGAAATTATGTTCTAT
Found at i:56161343 original size:19 final size:18
Alignment explanation
Indices: 56161319--56161357 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
56161309 TTTAGTTGCT
*
56161319 TTGGACTTTGGTTTTGGAC
1 TTGGACTTT-CTTTTGGAC
56161338 TTGGACTTTCTTTTGGAC
1 TTGGACTTTCTTTTGGAC
56161356 TT
1 TT
56161358 TGGATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.10, C:0.13, G:0.26, T:0.51
Consensus pattern (18 bp):
TTGGACTTTCTTTTGGAC
Found at i:56161360 original size:19 final size:20
Alignment explanation
Indices: 56161317--56161361 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
56161307 TGTTTAGTTG
*
56161317 CTTTGGACTTTGGTTTTGGA
1 CTTTGGACTTTGCTTTTGGA
56161337 C-TTGGACTTT-CTTTTGGA
1 CTTTGGACTTTGCTTTTGGA
56161355 CTTTGGA
1 CTTTGGA
56161362 TTTATTGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 14 0.61
20 1 0.04
ACGTcount: A:0.11, C:0.13, G:0.27, T:0.49
Consensus pattern (20 bp):
CTTTGGACTTTGCTTTTGGA
Found at i:56167752 original size:18 final size:18
Alignment explanation
Indices: 56167721--56167763 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
56167711 GGTTTTGGAC
*
56167721 TTGGATTTTCTTGTGGATT
1 TTGGA-TTTATTGTGGATT
**
56167740 TTGGATTTATTGTGTTTT
1 TTGGATTTATTGTGGATT
56167758 TTGGAT
1 TTGGAT
56167764 GGTTTTGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.12, C:0.02, G:0.26, T:0.60
Consensus pattern (18 bp):
TTGGATTTATTGTGGATT
Found at i:56169105 original size:19 final size:21
Alignment explanation
Indices: 56169081--56169123 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56169071 GTAATCATTA
56169081 CTTTTTTTC-A-AAGTATAAC
1 CTTTTTTTCTAGAAGTATAAC
*
56169100 CTTTTTTTCTAGAAGTCTAAC
1 CTTTTTTTCTAGAAGTATAAC
56169121 CTT
1 CTT
56169124 ATAAGTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 11 0.52
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.49
Consensus pattern (21 bp):
CTTTTTTTCTAGAAGTATAAC
Found at i:56171373 original size:39 final size:39
Alignment explanation
Indices: 56171319--56171401 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
56171309 ATAGAGAGAT
*
56171319 TATTTACACAACTTCCAGAATAACGATTGTGCCATTTTC
1 TATTTACACAACTTCCAGAATAACAATTGTGCCATTTTC
56171358 TATTTACACAACTTCCAGAATAACAATTGTGCCATTTTC
1 TATTTACACAACTTCCAGAATAACAATTGTGCCATTTTC
56171397 TATTT
1 TATTT
56171402 GAGAAGAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (39 bp):
TATTTACACAACTTCCAGAATAACAATTGTGCCATTTTC
Found at i:56172928 original size:18 final size:18
Alignment explanation
Indices: 56172907--56172951 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
56172897 CAAAATAATC
56172907 TTAAAAAAC-TAAAAATTA
1 TTAAAAAACTTAAAAA-TA
*
56172925 TTAAAAATCTTAAAAATA
1 TTAAAAAACTTAAAAATA
56172943 TATAAAAAA
1 T-TAAAAAA
56172952 ATACTAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAAACTTAAAAATA
Found at i:56172931 original size:19 final size:19
Alignment explanation
Indices: 56172909--56172952 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
56172899 AAATAATCTT
*
56172909 AAAAAACTAAAAAT-TATT
1 AAAAAACTAAAAATATATA
*
56172927 AAAAATCTTAAAAATATATA
1 AAAAAAC-TAAAAATATATA
56172947 AAAAAA
1 AAAAAA
56172953 TACTAAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 8 0.38
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAAACTAAAAATATATA
Found at i:56172982 original size:22 final size:23
Alignment explanation
Indices: 56172947--56172990 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
56172937 AAAATATATA
* *
56172947 AAAAAATACTAAATGATAATTTT
1 AAAAAATACAAAATGAAAATTTT
56172970 AAAAAAT-CAAAATGAAAATTT
1 AAAAAATACAAAATGAAAATTT
56172991 GAGGACTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (23 bp):
AAAAAATACAAAATGAAAATTTT
Found at i:56178364 original size:18 final size:17
Alignment explanation
Indices: 56178316--56178367 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
56178306 GCTCACAACA
*
56178316 TATTTCACATTTCATTT
1 TATTTCACATATCATTT
* *
56178333 TCAATCCACTATATCATTT
1 T-ATTTCAC-ATATCATTT
56178352 CTATTTCACATATCAT
1 -TATTTCACATATCAT
56178368 GCCATTTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.44
19 13 0.48
20 1 0.04
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTTCACATATCATTT
Found at i:56179499 original size:17 final size:17
Alignment explanation
Indices: 56179460--56179499 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
56179450 ACATCTTCTC
56179460 TTCTTTCT-TTTT-TTA
1 TTCTTTCTCTTTTATTA
56179475 TTCTTTCTCTTTTATT-
1 TTCTTTCTCTTTTATTA
56179491 TTCTATTCT
1 TTCT-TTCT
56179500 AATTGTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 8 0.36
17 6 0.27
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTTCTCTTTTATTA
Found at i:56181032 original size:15 final size:15
Alignment explanation
Indices: 56180999--56181041 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
56180989 CACCCCAATC
*
56180999 ACAGAAACA-AAAT-
1 ACAGATACAGAAATA
56181012 ACAGATACAGAAATA
1 ACAGATACAGAAATA
*
56181027 ACAGATACAGTAATA
1 ACAGATACAGAAATA
56181042 TCACGATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 8 0.31
14 4 0.15
15 14 0.54
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (15 bp):
ACAGATACAGAAATA
Found at i:56187306 original size:25 final size:27
Alignment explanation
Indices: 56187269--56187321 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
56187259 TCCAACATGC
56187269 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
56187295 ATTTCGGT-AATTTAACTCTTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
56187321 A
1 A
56187322 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:56198053 original size:14 final size:14
Alignment explanation
Indices: 56198034--56198063 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
56198024 GATTTTATTC
56198034 AACAATAGATCCAT
1 AACAATAGATCCAT
56198048 AACAATAGATCCAT
1 AACAATAGATCCAT
56198062 AA
1 AA
56198064 TTTTATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (14 bp):
AACAATAGATCCAT
Found at i:56199193 original size:25 final size:25
Alignment explanation
Indices: 56199165--56199234 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
56199155 CTCTTTTAAT
*
56199165 AACTGGGGTAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
56199190 AACTGGGGCAAAGCCCTATTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
56199215 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
56199235 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:56199475 original size:27 final size:27
Alignment explanation
Indices: 56199453--56199741 Score: 393
Period size: 27 Copynumber: 10.7 Consensus size: 27
56199443 TTTACCCCAA
* * *
56199453 AAGGGTATCTCGGTAATTCTACCTTAC
1 AAGGGTATTTCAGTAATTCTACCCTAC
*
56199480 AAGGGTATTTTAGTAATTCTACCCTAC
1 AAGGGTATTTCAGTAATTCTACCCTAC
*
56199507 AGGGGTATTTCAGTAATTCTACCCTAC
1 AAGGGTATTTCAGTAATTCTACCCTAC
* * *
56199534 AGGGGTATTTCATTAATTCTACCCTAT
1 AAGGGTATTTCAGTAATTCTACCCTAC
*
56199561 AGGGGTATTTCAGTAATTCTACCCTAC
1 AAGGGTATTTCAGTAATTCTACCCTAC
*
56199588 AATGGGTATTTCAGTATTTCTACCCTAC
1 AA-GGGTATTTCAGTAATTCTACCCTAC
* *
56199616 AAGGGTATTCCGGTAATTCTACCCTAC
1 AAGGGTATTTCAGTAATTCTACCCTAC
*
56199643 AAGGGTATTTCAATAATTCTACCCTAC
1 AAGGGTATTTCAGTAATTCTACCCTAC
*
56199670 AGGGGTATTTCAGTAATTCTACCCTAC
1 AAGGGTATTTCAGTAATTCTACCCTAC
*
56199697 -AGAGGTATTTCGGTAATTCTACCCTAC
1 AAG-GGTATTTCAGTAATTCTACCCTAC
*
56199724 -AGGAGTATTTCAATAATT
1 AAGG-GTATTTCAGTAATT
56199742 TTGTCAATTG
Statistics
Matches: 235, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
26 2 0.01
27 207 0.88
28 26 0.11
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (27 bp):
AAGGGTATTTCAGTAATTCTACCCTAC
Found at i:56199704 original size:136 final size:136
Alignment explanation
Indices: 56199455--56199724 Score: 423
Period size: 136 Copynumber: 2.0 Consensus size: 136
56199445 TACCCCAAAA
* * ** * *
56199455 GGGTATCTCGGTAATTCTACCTTACAAGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCAG
1 GGGTATCTCAGTAATTCTACCCTACAAGGGTATTCCAGTAATTCTACCCTACAAGGGTATTTCAA
* * *
56199520 TAATTCTACCCTACAGGGGTATTTCATTAATTCTACCCTATAGGGGTATTTCAGTAATTCTACCC
66 TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGAGGTATTTCAGTAATTCTACCC
56199585 TACAAT
131 TACAAT
* * *
56199591 GGGTATTTCAGTATTTCTACCCTACAAGGGTATTCCGGTAATTCTACCCTACAAGGGTATTTCAA
1 GGGTATCTCAGTAATTCTACCCTACAAGGGTATTCCAGTAATTCTACCCTACAAGGGTATTTCAA
*
56199656 TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGAGGTATTTCGGTAATTCTACCC
66 TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGAGGTATTTCAGTAATTCTACCC
56199721 TACA
131 TACA
56199725 GGAGTATTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
136 121 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (136 bp):
GGGTATCTCAGTAATTCTACCCTACAAGGGTATTCCAGTAATTCTACCCTACAAGGGTATTTCAA
TAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCTACAGAGGTATTTCAGTAATTCTACCC
TACAAT
Found at i:56199803 original size:27 final size:27
Alignment explanation
Indices: 56199778--56199984 Score: 238
Period size: 27 Copynumber: 7.7 Consensus size: 27
56199768 TCTGTAAATT
* *
56199778 AGGGGTACTTTGGTAATTTTACAAATC
1 AGGGGTATTTTGGTAATTTTACAAACC
** *
56199805 -GAGGGTATTTCAGTAATTTTACAAACT
1 AG-GGGTATTTTGGTAATTTTACAAACC
* *
56199832 AAGGGTATTTCGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* **
56199859 AGTGGTATTTTGGTAATTTTGTAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
*
56199886 AAGGGTATTTT-GTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* **
56199912 GGGGGTATTTTGGTAATTTTGTAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
56199939 AAGGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
*
56199966 AGGGGTATTTTGGTGATTT
1 AGGGGTATTTTGGTAATTT
56199985 GGTAAACTAA
Statistics
Matches: 149, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
26 23 0.15
27 126 0.85
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACC
Found at i:56199809 original size:54 final size:54
Alignment explanation
Indices: 56199751--56199856 Score: 124
Period size: 54 Copynumber: 2.0 Consensus size: 54
56199741 TTTGTCAATT
** * *
56199751 GAGGGTAAAACAGTAATTCTGTAAATTAGGGGTACTTT-GGTAATTTTACAAATC
1 GAGGGTAAAACAGTAATTCTACAAACTAAGGGTA-TTTCGGTAATTTTACAAATC
*** *
56199805 GAGGGTATTTCAGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAA
1 GAGGGTAAAACAGTAATTCTACAAACTAAGGGTATTTCGGTAATTTTACAAA
56199857 CCAGTGGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 3 0.07
54 40 0.93
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (54 bp):
GAGGGTAAAACAGTAATTCTACAAACTAAGGGTATTTCGGTAATTTTACAAATC
Found at i:56199866 original size:54 final size:53
Alignment explanation
Indices: 56199780--56199991 Score: 273
Period size: 54 Copynumber: 3.9 Consensus size: 53
56199770 TGTAAATTAG
* ** ** *
56199780 GGGTACTTTGGTAATTTTACAAATC-GAGGGTATTTCAGTAATTTTACAAACTAA
1 GGGTA-TTTGGTAATTTTACAAACCAG-GGGTATTTTGGTAATTTTGTAAACCAA
*
56199834 GGGTATTTCGGTAATTTTACAAACCAGTGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTT-GGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
* *
56199888 GGGTATTTTGTAATTTTACAAACCGGGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
* * *
56199941 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTGATTTGGTAAAC
1 GGGTA-TTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAAC
56199992 TAAAGTATTC
Statistics
Matches: 140, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
53 50 0.36
54 89 0.64
55 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.39
Consensus pattern (53 bp):
GGGTATTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
Found at i:56199927 original size:80 final size:80
Alignment explanation
Indices: 56199780--56199977 Score: 245
Period size: 80 Copynumber: 2.5 Consensus size: 80
56199770 TGTAAATTAG
* * * * *
56199780 GGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACTAAGGGTATTTCGG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTT-TGTAATTTTACAAACCAAGGGTATTTCGG
56199845 TAATTTTACAAACC-A
65 TAATTTTACAAACCAA
** ** *
56199860 GTGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGTAATTTTACAAACCGGGGGTATTTTGG
1 G-GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGTAATTTTACAAACCAAGGGTATTTCGG
**
56199925 TAATTTTGTAAACCAA
65 TAATTTTACAAACCAA
* *
56199941 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTG
56199978 GTGATTTGGT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
80 69 0.69
81 31 0.31
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGTAATTTTACAAACCAAGGGTATTTCGGT
AATTTTACAAACCAA
Found at i:56199943 original size:107 final size:108
Alignment explanation
Indices: 56199780--56199991 Score: 300
Period size: 107 Copynumber: 2.0 Consensus size: 108
56199770 TGTAAATTAG
* *
56199780 GGGTACTTTGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACTAAGGGTATTTCGG
1 GGGTACTTTGGTAATTTTACAAACCGAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTCGG
* *
56199845 TAATTTTACAAACCAGTGGTATTTTGGTAATTTTGTAAACCAA
66 TAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACCAA
* * ** ** *
56199888 GGGTA-TTTTGTAATTTTACAAACCGGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGG
1 GGGTACTTTGGTAATTTTACAAACCGAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTCGG
* *
56199952 TAATTTTACAAACTAGGGGTATTTTGGTGATTTGGTAAAC
66 TAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAAC
56199992 TAAAGTATTC
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
107 86 0.95
108 5 0.05
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.39
Consensus pattern (108 bp):
GGGTACTTTGGTAATTTTACAAACCGAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTCGG
TAATTTTACAAACCAGGGGTATTTTGGTAATTTGGTAAACCAA
Found at i:56200895 original size:25 final size:25
Alignment explanation
Indices: 56200865--56200917 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
56200855 AAGCTTTAAC
*
56200865 TGTCCTAACATATTGTCCCAACTGT
1 TGTCCTAACATATTATCCCAACTGT
* * *
56200890 TGTCCTAACTTGTTATCCCAAGTGT
1 TGTCCTAACATATTATCCCAACTGT
56200915 TGT
1 TGT
56200918 TTGAGTAAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (25 bp):
TGTCCTAACATATTATCCCAACTGT
Found at i:56201366 original size:23 final size:23
Alignment explanation
Indices: 56201340--56201389 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
56201330 AAAGTATATT
*
56201340 TAAAA-AATTCAAAACATAAATTA
1 TAAAATAATTAAAAAC-TAAATTA
*
56201363 TAAAATAATTAAAAACTAATTTA
1 TAAAATAATTAAAAACTAAATTA
56201386 TAAA
1 TAAA
56201390 GTAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAATAATTAAAAACTAAATTA
Found at i:56204674 original size:162 final size:162
Alignment explanation
Indices: 56204390--56204713 Score: 497
Period size: 162 Copynumber: 2.0 Consensus size: 162
56204380 AGTTAATAAG
* * *
56204390 TGTTTATACAAGCTTAAAATATCAAAACGGCTGAAAGATTATGAAAATCTTTTGTAGACAATTAT
1 TGTTGATACAAACTTAAAATATCAAAACGGCTGAAAGATTATGAAAATATTTTGTAGACAATTAT
* * *
56204455 TTTATGTTTAATTGAATTTACTGAAATTAAATCGAGTATAATATTGTGAATTTATATTTTTATGT
66 TTTATGTTTAATTGAATTTACTGAAATTAAATCAAGTATAATATTGTGAAATTATATTTATATGT
** *
56204520 TTGAAATTTGTGG-TTTAGATAAGAAAGTAAA
131 TTGAAAAATGTGGTTTTAGACAAGAAAGTAAA
** * *
56204551 TGTTGATACAAACTTAAAATATTGAAACGGTTGAAAGATTATGAAAATTATTTTGTAGACACTTA
1 TGTTGATACAAACTTAAAATATCAAAACGGCTGAAAGATTATGAAAA-TATTTTGTAGACAATTA
*
56204616 TTTTATGTTTAATTGAATTTATTGAAATTAAATCAAGTATAATATTGTGAAATTATATTTATATG
65 TTTTATGTTTAATTGAATTTACTGAAATTAAATCAAGTATAATATTGTGAAATTATATTTATATG
*
56204681 TTTGAAAAATGTGGTTTTAGACAAGTAAGTAAA
130 TTTGAAAAATGTGGTTTTAGACAAGAAAGTAAA
56204714 GTTTAACTGT
Statistics
Matches: 146, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
161 42 0.29
162 88 0.60
163 16 0.11
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.41
Consensus pattern (162 bp):
TGTTGATACAAACTTAAAATATCAAAACGGCTGAAAGATTATGAAAATATTTTGTAGACAATTAT
TTTATGTTTAATTGAATTTACTGAAATTAAATCAAGTATAATATTGTGAAATTATATTTATATGT
TTGAAAAATGTGGTTTTAGACAAGAAAGTAAA
Found at i:56206659 original size:21 final size:21
Alignment explanation
Indices: 56206635--56206696 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
56206625 TGGCTTTTCG
56206635 TTTAGCTCTTTTGAGCTTCTA
1 TTTAGCTCTTTTGAGCTTCTA
* * *
56206656 TTTAAC-CTTTATGGGTTTCTA
1 TTTAGCTCTTT-TGAGCTTCTA
* * *
56206677 TTCAGCTCCTATGAGCTTCT
1 TTTAGCTCTTTTGAGCTTCT
56206697 GTTCAACTCT
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 4 0.13
21 24 0.80
22 2 0.07
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.48
Consensus pattern (21 bp):
TTTAGCTCTTTTGAGCTTCTA
Found at i:56207204 original size:2 final size:2
Alignment explanation
Indices: 56207199--56207239 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
56207189 TGTATATATA
*
56207199 TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
56207240 TTGTAAGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:56212307 original size:2 final size:2
Alignment explanation
Indices: 56212296--56212453 Score: 309
Period size: 2 Copynumber: 79.5 Consensus size: 2
56212286 AAAATTTGTA
56212296 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56212337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56212379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56212421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56212454 CACTATAGCA
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
1 1 0.01
2 154 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56239265 original size:104 final size:105
Alignment explanation
Indices: 56239085--56239352 Score: 441
Period size: 104 Copynumber: 2.6 Consensus size: 105
56239075 TAACCGTTAT
* **
56239085 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
56239150 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* *
56239189 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCTTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
56239254 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
56239294 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
56239353 TTATATACAA
Statistics
Matches: 152, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
104 81 0.53
105 70 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:56239721 original size:30 final size:30
Alignment explanation
Indices: 56239687--56239744 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
56239677 CCACCCAACT
56239687 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
*** * *
56239717 TTTTGCGTAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
56239745 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:56255492 original size:124 final size:124
Alignment explanation
Indices: 56255268--56255515 Score: 460
Period size: 124 Copynumber: 2.0 Consensus size: 124
56255258 ACTTTGGAAG
56255268 AACAGGAACATTTTCATCTTCCAAGATATCAATTGGACGGCTTATGAGATCATTAAAACCTCCCT
1 AACAGGAACATTTTCATCTTCCAAGATATCAATTGGACGGCTTATGAGATCATTAAAACCTCCCT
56255333 CAGCTGGGCTCAACATTTTGAATTAACTCTAGGTGCAGCCGGTTCCACTGTAACTTGTT
66 CAGCTGGGCTCAACATTTTGAATTAACTCTAGGTGCAGCCGGTTCCACTGTAACTTGTT
*
56255392 AACAGGAACCTTTTCATCTTCCAAGATATCAATTGGACGGCTTATGAGATCATTAAAACCTCCCT
1 AACAGGAACATTTTCATCTTCCAAGATATCAATTGGACGGCTTATGAGATCATTAAAACCTCCCT
* * *
56255457 CAGCTGGGCTTAACATTTTGAATTGACTCTGGGTGCAGCCGGTTCCACTGTAACTTGTT
66 CAGCTGGGCTCAACATTTTGAATTAACTCTAGGTGCAGCCGGTTCCACTGTAACTTGTT
56255516 CTGAAACTTC
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (124 bp):
AACAGGAACATTTTCATCTTCCAAGATATCAATTGGACGGCTTATGAGATCATTAAAACCTCCCT
CAGCTGGGCTCAACATTTTGAATTAACTCTAGGTGCAGCCGGTTCCACTGTAACTTGTT
Found at i:56256572 original size:19 final size:19
Alignment explanation
Indices: 56256550--56256604 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 19
56256540 AAACATAAAT
56256550 TAAAATTAAAAAATATATA
1 TAAAATTAAAAAATATATA
* *
56256569 T-AAATT-CAAAATTTAT-
1 TAAAATTAAAAAATATATA
*
56256585 TAAAAATTATAAAATATATA
1 T-AAAATTAAAAAATATATA
56256605 AAATACTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
16 1 0.04
17 8 0.29
18 10 0.36
19 9 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATTAAAAAATATATA
Found at i:56256573 original size:18 final size:17
Alignment explanation
Indices: 56256550--56256626 Score: 59
Period size: 19 Copynumber: 4.3 Consensus size: 17
56256540 AAACATAAAT
56256550 TAAAATTAAAAAATATA
1 TAAAATTAAAAAATATA
* *
56256567 TATAAATT-CAAAATTTA
1 TA-AAATTAAAAAATATA
*
56256584 TTAAAAATTATAAAATATA
1 -T-AAAATTAAAAAATATA
56256603 TAAAATACTCAAAAAAT-TA
1 TAAAAT--T-AAAAAATATA
56256622 TAAAA
1 TAAAA
56256627 GAAATATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
17 14 0.29
18 12 0.25
19 16 0.33
20 6 0.12
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATTAAAAAATATA
Found at i:56259330 original size:13 final size:13
Alignment explanation
Indices: 56259312--56259336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56259302 CAAAAGTGAC
56259312 TATTTTAATAATT
1 TATTTTAATAATT
56259325 TATTTTAATAAT
1 TATTTTAATAAT
56259337 AATAATACTA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:56259630 original size:17 final size:18
Alignment explanation
Indices: 56259608--56259659 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
56259598 CAATTTTCAA
56259608 AAAAAAAAATAAAAAAT-
1 AAAAAAAAATAAAAAATG
* *
56259625 AAAAAAATATTTTAAAAATG
1 AAAAAAA-A-ATAAAAAATG
*
56259645 AAAATAAAATAAAAA
1 AAAAAAAAATAAAAA
56259660 GAATATTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
17 7 0.26
18 6 0.22
19 8 0.30
20 6 0.22
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAAAATAAAAAATG
Found at i:56259642 original size:32 final size:31
Alignment explanation
Indices: 56259600--56259674 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
56259590 CGTATTTTCA
56259600 ATTTTCAAAAAAAAAAATAAAAAATAAAAA-AAT
1 ATTTT-AAAAAAAAAAAT--AAAATAAAAAGAAT
**
56259633 ATTTTAAAAATGAAAATAAAATAAAAAGAAT
1 ATTTTAAAAAAAAAAATAAAATAAAAAGAAT
*
56259664 ATTTTCAAAAA
1 ATTTTAAAAAA
56259675 TGGGGAGCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.27
31 12 0.32
32 10 0.27
33 5 0.14
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (31 bp):
ATTTTAAAAAAAAAAATAAAATAAAAAGAAT
Found at i:56259675 original size:32 final size:32
Alignment explanation
Indices: 56259600--56259676 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
56259590 CGTATTTTCA
**
56259600 ATTTTCAAAAAAAAAAATAAAAAATAAAAAAAT
1 ATTTTCAAAAATGAAAAT-AAAAATAAAAAAAT
56259633 ATTTT-AAAAATGAAAAT-AAAATAAAAAGAAT
1 ATTTTCAAAAATGAAAATAAAAATAAAAA-AAT
56259664 ATTTTCAAAAATG
1 ATTTTCAAAAATG
56259677 GGGAGCCTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 10 0.25
31 8 0.20
32 17 0.43
33 5 0.12
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.26
Consensus pattern (32 bp):
ATTTTCAAAAATGAAAATAAAAATAAAAAAAT
Found at i:56274426 original size:13 final size:14
Alignment explanation
Indices: 56274398--56274426 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56274388 AAATCTGTAT
56274398 TTTTAAAATATATA
1 TTTTAAAATATATA
56274412 TTTTAAAAT-TATA
1 TTTTAAAATATATA
56274425 TT
1 TT
56274427 ATTTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTAAAATATATA
Found at i:56280614 original size:3 final size:3
Alignment explanation
Indices: 56280578--56280670 Score: 57
Period size: 3 Copynumber: 31.3 Consensus size: 3
56280568 TTTATCCCTG
* * * *
56280578 TTA TCA TTA TTA TCA TTA TT- TTA TCTA CTTA TTA TTA TGA -TA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA
* * * * * *
56280623 TTA CTA ATA TTA TTA ATA TTA TTA TTA TAA TTA -CA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56280670 T
1 T
56280671 AGTATTCCTT
Statistics
Matches: 66, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
2 4 0.06
3 57 0.86
4 4 0.06
5 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:56299993 original size:22 final size:24
Alignment explanation
Indices: 56299941--56299994 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
56299931 TTTTTGATGA
56299941 TTAAATTATTGTTATTAAATATGCT
1 TTAAATTATTGTTATT-AATATGCT
*
56299966 TGAAATTATTG-TATT-ATAT-CTT
1 TTAAATTATTGTTATTAATATGC-T
56299988 TTAAATT
1 TTAAATT
56299995 GAATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 11 0.42
24 4 0.15
25 10 0.38
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
TTAAATTATTGTTATTAATATGCT
Found at i:56307217 original size:23 final size:25
Alignment explanation
Indices: 56307167--56307218 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
56307157 ATCCTTTTGC
56307167 ATTTTAATTTTTACAATTTCATTTT
1 ATTTTAATTTTTACAATTTCATTTT
* *
56307192 ATTTTTATTTTTA-AA-TTGATTTT
1 ATTTTAATTTTTACAATTTCATTTT
56307215 ATTT
1 ATTT
56307219 ATAAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.44
24 2 0.08
25 12 0.48
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTTAATTTTTACAATTTCATTTT
Found at i:56307904 original size:23 final size:23
Alignment explanation
Indices: 56307838--56307907 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
56307828 TTTGTATTTT
* * *
56307838 TGCATGAAATGATAATGTGTATA
1 TGCATGAAATGTTAAAGTATATA
* ** *
56307861 TTCATGTTAT-TTATAATTATATA
1 TGCATGAAATGTTA-AAGTATATA
56307884 TGCATGAAATGTTAAAGTATATA
1 TGCATGAAATGTTAAAGTATATA
56307907 T
1 T
56307908 ATTGTAAGAT
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
22 2 0.06
23 29 0.85
24 3 0.09
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (23 bp):
TGCATGAAATGTTAAAGTATATA
Found at i:56312170 original size:15 final size:16
Alignment explanation
Indices: 56312140--56312170 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56312130 ACAGCTCAAA
56312140 AGAAATCTATTTTTTT
1 AGAAATCTATTTTTTT
56312156 AGAAATCTATTTTTT
1 AGAAATCTATTTTTT
56312171 GTAGGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
AGAAATCTATTTTTTT
Found at i:56313096 original size:134 final size:134
Alignment explanation
Indices: 56312892--56313134 Score: 378
Period size: 134 Copynumber: 1.8 Consensus size: 134
56312882 TTGGAATACA
* * *
56312892 TCAAACAGATCGATGATTTATGATCACGATTGGAATTATTAAAGCTTGTTGATTTATGATCACAA
1 TCAAACAGATCGATGATTTACGATCACGACTGGAATTATTAAAACTTGTTGATTTATGATCACAA
*
56312957 CTTAAGTTCAGTGATTTACGATCATAAATAGTTCATTTTGAGTTTGCTAATTTACGATCGCAACT
66 CTTAAGTTCAATGATTTACGATCATAAATAGTTCATTTTGAGTTTGCTAATTTACGATCGCAACT
56313022 CCAT
131 CCAT
* * * * *
56313026 TCAAACAGTTCGTTGATTTACGATCCCGACTGGTATTATTAAAACTTGTTGATTTATTATCACAA
1 TCAAACAGATCGATGATTTACGATCACGACTGGAATTATTAAAACTTGTTGATTTATGATCACAA
* * *
56313091 TTTAAGTTCAATGATTTATGATCATGAATAGTTCATTTTGAGTT
66 CTTAAGTTCAATGATTTACGATCATAAATAGTTCATTTTGAGTT
56313135 CGTTGATTTA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
134 97 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (134 bp):
TCAAACAGATCGATGATTTACGATCACGACTGGAATTATTAAAACTTGTTGATTTATGATCACAA
CTTAAGTTCAATGATTTACGATCATAAATAGTTCATTTTGAGTTTGCTAATTTACGATCGCAACT
CCAT
Found at i:56313205 original size:99 final size:99
Alignment explanation
Indices: 56313032--56313243 Score: 262
Period size: 99 Copynumber: 2.1 Consensus size: 99
56313022 CCATTCAAAC
* * * * ** *
56313032 AGTTCGTTGATTTACGATCCCGACTGGTATTATTAAAACTTGTTGATTTATTATCACAATTTAAG
1 AGTTCGTTGATTTACAATCACAACTGGTATTATTAAAACTTGCTGATTTACAATCACAACTTAAG
* * * *
56313097 TTCAATGATTTATGATCATGAATAGTTCATTTTG
66 TTCAATGATTTACGATCATGAACAATTCATTTTA
* * * *
56313131 AGTTCGTTGATTTACAATCACAACTGGTATTATTAAAGCTTGCTGATTTGCAATCATAGCTTAAG
1 AGTTCGTTGATTTACAATCACAACTGGTATTATTAAAACTTGCTGATTTACAATCACAACTTAAG
*
56313196 TTCATTGATTTACGATCATGAACAATTCATTTTA
66 TTCAATGATTTACGATCATGAACAATTCATTTTA
**
56313230 AGTTCACTGATTTA
1 AGTTCGTTGATTTA
56313244 TGGTCGCAAC
Statistics
Matches: 95, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.42
Consensus pattern (99 bp):
AGTTCGTTGATTTACAATCACAACTGGTATTATTAAAACTTGCTGATTTACAATCACAACTTAAG
TTCAATGATTTACGATCATGAACAATTCATTTTA
Found at i:56313300 original size:134 final size:134
Alignment explanation
Indices: 56313138--56313722 Score: 710
Period size: 134 Copynumber: 4.4 Consensus size: 134
56313128 TTGAGTTCGT
* * * * * *
56313138 TGATTTACAATCACAACTGGTATTATTAAAGCTTGCTGATTTGCAATCATAGCTTAAGTTCATTG
1 TGATTTACGATCACAACTGGTATTATTAAAGCTTGTTGATTTACGATCACAACTTAAGTTCATTG
* * ***
56313203 ATTTACGATCATGAACAATTCATTTTAAGTTCACTGATTTATGGTCGCAACTCTATTCAAATAGT
66 ATTTACGATCATGAACAATTTATTTTGAGTTCACTGATTTACAATCGCAACTCTATTCAAATAGT
56313268 TCAC
131 TCAC
* * * *
56313272 TGATTTACGAACACGATTGGTATTATTAAAGCTTGTTTATTTACGATCACAACTTAAGTTCATTG
1 TGATTTACGATCACAACTGGTATTATTAAAGCTTGTTGATTTACGATCACAACTTAAGTTCATTG
* * * * *
56313337 ATTTACGATCATGAACAATTTATTTTTAGTTC-GTCAATTTACGATC-CAAACTCCATTCAAATA
66 ATTTACGATCATGAACAATTTATTTTGAGTTCACT-GATTTACAATCGC-AACTCTATTCAAATA
56313400 GTTCAC
129 GTTCAC
* * *
56313406 TGATTTACGATCACAATTGGTATTATTAAAACTTGTTGATTTACGATCACAATTTAAGTTCATTG
1 TGATTTACGATCACAACTGGTATTATTAAAGCTTGTTGATTTACGATCACAACTTAAGTTCATTG
* * * * * *
56313471 ATTTACGATTATGAACAGTTTATTTTGAGTTCGCTGATTTACAATTGCAACTTTATTCAAAAAGT
66 ATTTACGATCATGAACAATTTATTTTGAGTTCACTGATTTACAATCGCAACTCTATTCAAATAGT
56313536 TCAC
131 TCAC
* ** * * * *
56313540 TGATTTATGATCACGGCTAGTATTACTAAAGCTT-TCTGATTTACGATCACAGCTTAAGTTCGTT
1 TGATTTACGATCACAACTGGTATTATTAAAGCTTGT-TGATTTACGATCACAACTTAAGTTCATT
* * * **
56313604 GATTTACAATCATGAACAATTTATTTTGAGTTTACTGATTTACAATCACAAC-CTCATTCAAACG
65 GATTTACGATCATGAACAATTTATTTTGAGTTCACTGATTTACAATCGCAACTCT-ATTCAAATA
56313668 GTTCAC
129 GTTCAC
* * *
56313674 TGATTTATGATTACAACTGGTATTATTAAAGCTTGTTGATTTACAATCA
1 TGATTTACGATCACAACTGGTATTATTAAAGCTTGTTGATTTACGATCA
56313723 TGAACAGTTT
Statistics
Matches: 386, Mismatches: 58, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
133 4 0.01
134 379 0.98
135 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (134 bp):
TGATTTACGATCACAACTGGTATTATTAAAGCTTGTTGATTTACGATCACAACTTAAGTTCATTG
ATTTACGATCATGAACAATTTATTTTGAGTTCACTGATTTACAATCGCAACTCTATTCAAATAGT
TCAC
Found at i:56313323 original size:233 final size:233
Alignment explanation
Indices: 56312926--56313370 Score: 584
Period size: 233 Copynumber: 1.9 Consensus size: 233
56312916 CACGATTGGA
* ** * *
56312926 ATTATTAAAGCTTGTTGATTTATGATCACAACTTAAGTTCAGTGATTTACGATCATAAATAGTTC
1 ATTATTAAAGCTTGCTGATTTACAATCACAACTTAAGTTCAGTGATTTACGATCATAAACAATTC
* ** ** * *
56312991 ATTTTGAGTTTGCTAATTTACGATCGCAACTCCATTCAAACAGTTCGTTGATTTACGATCCCGAC
66 ATTTTAAGTTCACTAATTTACGATCGCAACTCCATTCAAACAGTTCACTGATTTACGAACACGAC
** * * *
56313056 TGGTATTATTAAAACTTGTTGATTTATTATCACAATTTAAGTTCAATGATTTATGATCATGAATA
131 TGGTATTATTAAAACTTGTTGATTTACGATCACAACTTAAGTTCAATGATTTACGATCATGAACA
*
56313121 GTTCATTTTGAGTTCGTTGATTTACAATCACAACTGGT
196 ATTCATTTTGAGTTCGTTGATTTACAATCACAACTGGT
* * * * *
56313159 ATTATTAAAGCTTGCTGATTTGCAATCATAGCTTAAGTTCATTGATTTACGATCATGAACAATTC
1 ATTATTAAAGCTTGCTGATTTACAATCACAACTTAAGTTCAGTGATTTACGATCATAAACAATTC
* * * * * *
56313224 ATTTTAAGTTCACTGATTTATGGTCGCAACTCTATTCAAATAGTTCACTGATTTACGAACACGAT
66 ATTTTAAGTTCACTAATTTACGATCGCAACTCCATTCAAACAGTTCACTGATTTACGAACACGAC
* * *
56313289 TGGTATTATTAAAGCTTGTTTATTTACGATCACAACTTAAGTTCATTGATTTACGATCATGAACA
131 TGGTATTATTAAAACTTGTTGATTTACGATCACAACTTAAGTTCAATGATTTACGATCATGAACA
* *
56313354 ATTTATTTTTAGTTCGT
196 ATTCATTTTGAGTTCGT
56313371 CAATTTACGA
Statistics
Matches: 178, Mismatches: 34, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
233 178 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (233 bp):
ATTATTAAAGCTTGCTGATTTACAATCACAACTTAAGTTCAGTGATTTACGATCATAAACAATTC
ATTTTAAGTTCACTAATTTACGATCGCAACTCCATTCAAACAGTTCACTGATTTACGAACACGAC
TGGTATTATTAAAACTTGTTGATTTACGATCACAACTTAAGTTCAATGATTTACGATCATGAACA
ATTCATTTTGAGTTCGTTGATTTACAATCACAACTGGT
Found at i:56313325 original size:71 final size:70
Alignment explanation
Indices: 56313250--56313457 Score: 170
Period size: 71 Copynumber: 3.0 Consensus size: 70
56313240 TTTATGGTCG
*
56313250 CAACTCTATTCAAATAGTTCACTGATTTACGAACACGATTGGTATTATTAAAGCTTGTTTATTTA
1 CAACTCTATTCAAATAGTTCACTGATTTACGAACAC-ATTGGTATTATTAAAGCTTGTTAATTTA
56313315 CGATCA
65 CGATCA
* * * * * *
56313321 CAACT-TAAGTTC--ATTGATTTAC-GA-TCATGAACA-ATT--TATT-TT-TAG-TTCGTCAAT
1 CAACTCT-A-TTCAAATAG-TTCACTGATTTACGAACACATTGGTATTATTAAAGCTT-GTTAAT
56313375 TTACGATC-
62 TTACGATCA
* * * *
56313383 CAAACTCCATTCAAATAGTTCACTGATTTACGATCACAATTGGTATTATTAAAACTTGTTGATTT
1 C-AACTCTATTCAAATAGTTCACTGATTTACGAACAC-ATTGGTATTATTAAAGCTTGTTAATTT
56313448 ACGATCA
64 ACGATCA
56313455 CAA
1 CAA
56313458 TTTAAGTTCA
Statistics
Matches: 102, Mismatches: 17, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
62 6 0.06
63 23 0.23
64 7 0.07
65 10 0.10
67 6 0.06
69 11 0.11
70 8 0.08
71 25 0.25
72 6 0.06
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (70 bp):
CAACTCTATTCAAATAGTTCACTGATTTACGAACACATTGGTATTATTAAAGCTTGTTAATTTAC
GATCA
Found at i:56313339 original size:63 final size:63
Alignment explanation
Indices: 56313265--56313479 Score: 166
Period size: 63 Copynumber: 3.3 Consensus size: 63
56313255 CTATTCAAAT
* *
56313265 AGTTCACTGATTTACGAACACGATTGGTATTATTAAAGCTTGTTTATTTACGATCACAACTTA
1 AGTTCACTGATTTACGATCACGATTGGTATTATTAAAGCTTGTTAATTTACGATCACAACTTA
* * **** ** *
56313328 AGTTCATTGATTTACGATCATGAACAAT-TTATTTTTAG-TTCGTCAATTTACGATC-CAAACTC
1 AGTTCACTGATTTACGATCACGATTGGTATTA-TTAAAGCTT-GTTAATTTACGATCAC-AA---
56313390 CATTCAAA
60 C-TT---A
* * * *
56313398 TAGTTCACTGATTTACGATCACAATTGGTATTATTAAAACTTGTTGATTTACGATCACAATTTA
1 -AGTTCACTGATTTACGATCACGATTGGTATTATTAAAGCTTGTTAATTTACGATCACAACTTA
*
56313462 AGTTCATTGATTTACGAT
1 AGTTCACTGATTTACGAT
56313480 TATGAACAGT
Statistics
Matches: 113, Mismatches: 25, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
62 6 0.05
63 56 0.50
64 1 0.01
66 1 0.01
67 4 0.04
70 1 0.01
71 38 0.34
72 6 0.05
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (63 bp):
AGTTCACTGATTTACGATCACGATTGGTATTATTAAAGCTTGTTAATTTACGATCACAACTTA
Found at i:56319663 original size:16 final size:16
Alignment explanation
Indices: 56319632--56319674 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 16
56319622 TTTATTAATT
56319632 TAATATTAAACTAATTATC
1 TAATATTAAA-T--TTATC
56319651 TTAATATTAAATTTATC
1 -TAATATTAAATTTATC
56319668 TAATATT
1 TAATATT
56319675 TATCTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
19 1 0.04
20 10 0.43
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATTAAATTTATC
Found at i:56320933 original size:15 final size:16
Alignment explanation
Indices: 56320904--56320933 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56320894 TAATCGCTGT
56320904 ATTACATGAAATGTGG
1 ATTACATGAAATGTGG
56320920 ATTACATG-AATGTG
1 ATTACATGAAATGTG
56320934 CTCTTAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (16 bp):
ATTACATGAAATGTGG
Found at i:56324368 original size:10 final size:10
Alignment explanation
Indices: 56324353--56324378 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56324343 AAAAATATCA
56324353 CAACAGCTTT
1 CAACAGCTTT
56324363 CAACAGCTTT
1 CAACAGCTTT
56324373 CAACAG
1 CAACAG
56324379 ATTCGTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.23
Consensus pattern (10 bp):
CAACAGCTTT
Found at i:56327768 original size:5 final size:5
Alignment explanation
Indices: 56327758--56327793 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
56327748 CGTGTCTCAG
*
56327758 AATTT AATTT AATTT AATTT ATAATT AATTT AATTT
1 AATTT AATTT AATTT AATTT A-ATTT AATTT AATTT
56327794 TTACAATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:56328058 original size:7 final size:7
Alignment explanation
Indices: 56328046--56328070 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56328036 ATCAATTGTT
56328046 TAAAAAA
1 TAAAAAA
56328053 TAAAAAA
1 TAAAAAA
56328060 TAAAAAA
1 TAAAAAA
56328067 TAAA
1 TAAA
56328071 TTCAACCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:56328743 original size:15 final size:15
Alignment explanation
Indices: 56328715--56328752 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
56328705 TTCATTCGAA
56328715 AATTAAAA--AAATT
1 AATTAAAATTAAATT
56328728 AATTAAAATTAAATT
1 AATTAAAATTAAATT
*
56328743 AACTAAAATT
1 AATTAAAATT
56328753 GAGTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
15 14 0.64
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTAAAATTAAATT
Found at i:56330734 original size:84 final size:84
Alignment explanation
Indices: 56330585--56330894 Score: 282
Period size: 84 Copynumber: 3.7 Consensus size: 84
56330575 TCATTGTAAC
* * * * * * * * ** *
56330585 AGGCTTAGTAGTGGTAAGAAGCAAACTAGTTGCAAGAATCTGAGTGGTTGCATGCTAGTTTAGGG
1 AGGCTTAGTAGTGGTAGGAAGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTTTTGGTTTAGGG
56330650 CCTTAATTATTGATGCATG
66 CCTTAATTATTGATGCATG
* * *
56330669 AGGCTTAGTAGTGGCAGGAAACAAATTGGTTGTAGGAGTTTGGGTGGTTGCTTTTTGGTTTAGGG
1 AGGCTTAGTAGTGGTAGGAAGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTTTTGGTTTAGGG
* **
56330734 CCTT-AGTAGTTGATGCAAA
66 CCTTAATTA-TTGATGCATG
* * * ** * * *
56330753 AAGCTTAATAGTGGTAGGATGCCGATTGGTTGTAGGAGTTTGAGTGATTGCTTTCTGGTTTAAGG
1 AGGCTTAGTAGTGGTAGGAAGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTTTTGGTTTAGGG
* * * *
56330818 CCTCAATTGTTGCTACATG
66 CCTTAATTATTGATGCATG
* * * * *
56330837 AGGCTTAGTGGTGGTA-GAAGGCAAATTGGATGTAAGAATTTGAGTGGTTGCTTGTTGG
1 AGGCTTAGTAGTGGTAGGAA-GCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTTTTGG
56330895 CTGGTTTAGG
Statistics
Matches: 176, Mismatches: 47, Indels: 6
0.77 0.21 0.03
Matches are distributed among these distances:
83 5 0.03
84 169 0.96
85 2 0.01
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (84 bp):
AGGCTTAGTAGTGGTAGGAAGCAAATTGGTTGTAGGAGTTTGAGTGGTTGCTTTTTGGTTTAGGG
CCTTAATTATTGATGCATG
Found at i:56339698 original size:22 final size:22
Alignment explanation
Indices: 56339673--56339714 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56339663 GTTACAAACC
* *
56339673 CTTATTGTAAGCTTAAATAATA
1 CTTACTGTAAACTTAAATAATA
56339695 CTTACTGTAAACTTAAATAA
1 CTTACTGTAAACTTAAATAA
56339715 AGGTAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (22 bp):
CTTACTGTAAACTTAAATAATA
Found at i:56341399 original size:37 final size:37
Alignment explanation
Indices: 56341349--56341464 Score: 142
Period size: 37 Copynumber: 3.1 Consensus size: 37
56341339 TTACAAAACT
* * * *
56341349 TTTGCAAAGAATCTTCACTATTAATCTCCGTCTTTTC
1 TTTGCAGAGAATCTTTACTATTGATCTCCATCTTTTC
* * * *
56341386 TTTGTATATAATCTTTACTATTGATCTCCATCTTTTA
1 TTTGCAGAGAATCTTTACTATTGATCTCCATCTTTTC
* *
56341423 TTTGCAGAGAATCTTTACTGTTGATCTCCATTTTTTC
1 TTTGCAGAGAATCTTTACTATTGATCTCCATCTTTTC
56341460 TTTGC
1 TTTGC
56341465 TTGTCTTGGC
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (37 bp):
TTTGCAGAGAATCTTTACTATTGATCTCCATCTTTTC
Found at i:56341552 original size:37 final size:37
Alignment explanation
Indices: 56341473--56341552 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
56341463 GCTTGTCTTG
* *
56341473 GCTTTGCAAGGAACCACCCCAGTTCATTTCTATCTTT
1 GCTTTGCAAGGAACCACCCCAGTTCATCTCTATCATT
* * * *
56341510 ACTTTGCAAGGAATCACCCCTA-TTTATCTCTGTCATT
1 GCTTTGCAAGGAACCACCCC-AGTTCATCTCTATCATT
56341547 GCTTTG
1 GCTTTG
56341553 TTGCAAAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
37 34 0.97
38 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.38
Consensus pattern (37 bp):
GCTTTGCAAGGAACCACCCCAGTTCATCTCTATCATT
Found at i:56343075 original size:24 final size:23
Alignment explanation
Indices: 56343041--56343095 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
56343031 GATGTTTTAC
* *
56343041 AAATTTATAAAAAATTAATTTTTT
1 AAATTT-TAAAAAATAAAATTTTT
56343065 ATAATTTTAAAAAATAAAATTTTT
1 A-AATTTTAAAAAATAAAATTTTT
56343089 AAATTTT
1 AAATTTT
56343096 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 17 0.61
25 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATTTTAAAAAATAAAATTTTT
Found at i:56343093 original size:37 final size:37
Alignment explanation
Indices: 56343052--56343123 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
56343042 AATTTATAAA
56343052 AAATTAATTTTTTATAA-TTTTAAAAAATAAAATTTTT
1 AAATT-ATTTTTTATAATTTTTAAAAAATAAAATTTTT
* * *
56343089 AAATTTTTTTTTTTAATTTTTAAAAAATTAAATTT
1 AAATTATTTTTTATAATTTTTAAAAAATAAAATTT
56343124 GAAATGAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (37 bp):
AAATTATTTTTTATAATTTTTAAAAAATAAAATTTTT
Found at i:56348050 original size:29 final size:30
Alignment explanation
Indices: 56347992--56348050 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
56347982 GGGTGGGATG
*
56347992 GGAAGGAAGTAAAAGTTTTAGGGGGAAAAT
1 GGAAGGAAGTAAAAGTTTTAGGAGGAAAAT
*
56348022 GGAAGGGAGTAAAAG-TTTAGGAGGAAAAT
1 GGAAGGAAGTAAAAGTTTTAGGAGGAAAAT
56348051 AAAAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.44, C:0.00, G:0.37, T:0.19
Consensus pattern (30 bp):
GGAAGGAAGTAAAAGTTTTAGGAGGAAAAT
Found at i:56348276 original size:9 final size:9
Alignment explanation
Indices: 56348262--56348298 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
56348252 TATAGTTTGA
56348262 TATTCGAAT
1 TATTCGAAT
56348271 TATTCGAAT
1 TATTCGAAT
*
56348280 TATTCGAGT
1 TATTCGAAT
56348289 TATTCGAAT
1 TATTCGAAT
56348298 T
1 T
56348299 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:56349159 original size:13 final size:13
Alignment explanation
Indices: 56349143--56349212 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
56349133 TCATACAACA
56349143 ATTTCATGTAATC
1 ATTTCATGTAATC
* *
56349156 ATTTCATATAACC
1 ATTTCATGTAATC
*
56349169 ATTTCATCTAAAT-
1 ATTTCATGT-AATC
*
56349182 ATTTCATTTACA-C
1 ATTTCATGTA-ATC
56349195 ATTTAACATGTAATC
1 ATTT--CATGTAATC
56349210 ATT
1 ATT
56349213 CTGTATATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 1 0.02
13 32 0.71
14 3 0.07
15 9 0.20
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (13 bp):
ATTTCATGTAATC
Found at i:56349172 original size:26 final size:26
Alignment explanation
Indices: 56349133--56349212 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
56349123 TATAACCAAA
* *
56349133 TCATACAACAATTTCATGTAATCATT
1 TCATATAACCATTTCATGTAATCATT
*
56349159 TCATATAACCATTTCATCTAAAT-ATT
1 TCATATAACCATTTCATGT-AATCATT
*
56349185 TCAT-TTACACATTTAACATGTAATCATT
1 TCATATAAC-CATTT--CATGTAATCATT
56349213 CTGTATATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 3 0.07
26 28 0.64
27 6 0.14
28 7 0.16
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (26 bp):
TCATATAACCATTTCATGTAATCATT
Found at i:56357862 original size:32 final size:32
Alignment explanation
Indices: 56357798--56357865 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
56357788 TATTCAAGCA
* * *
56357798 ATATTACTTGAATAGTTATATTTATTTAAAAG
1 ATATTAATTGAATAGTTATAGTCATTTAAAAG
*
56357830 ATATTAATTGAATAGTTAT-GTCACTTTTAAAG
1 ATATTAATTGAATAGTTATAGTCA-TTTAAAAG
56357862 ATAT
1 ATAT
56357866 GATTATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (32 bp):
ATATTAATTGAATAGTTATAGTCATTTAAAAG
Found at i:56367896 original size:23 final size:23
Alignment explanation
Indices: 56367870--56367967 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
56367860 ATAAGTGCCA
56367870 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
56367893 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
56367916 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
56367938 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
56367961 CACTGAT
1 CACTGAT
56367968 CAATAACACT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:56367935 original size:45 final size:45
Alignment explanation
Indices: 56367877--56367965 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
56367867 CCACACTGAT
* *
56367877 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
56367922 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
56367966 ATCAATAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:56371905 original size:29 final size:30
Alignment explanation
Indices: 56371868--56371924 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
56371858 TCCGAGCCTT
*
56371868 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
56371897 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
56371925 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Found at i:56372154 original size:13 final size:13
Alignment explanation
Indices: 56372136--56372167 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
56372126 TTTCCAGCAA
56372136 TTATGAATTTATT
1 TTATGAATTTATT
56372149 TTATGAATTTATT
1 TTATGAATTTATT
*
56372162 TGATGA
1 TTATGA
56372168 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:56372441 original size:101 final size:101
Alignment explanation
Indices: 56372266--56372707 Score: 875
Period size: 101 Copynumber: 4.4 Consensus size: 101
56372256 GGGTAAAGAG
56372266 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
56372331 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
56372367 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
56372432 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
56372468 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
56372533 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
56372569 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
56372634 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
*
56372670 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
56372708 TGTTATTATC
Statistics
Matches: 340, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 340 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (101 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAAGACC
ATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
Found at i:56379455 original size:2 final size:2
Alignment explanation
Indices: 56379448--56379474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56379438 TATTGGTTTT
56379448 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
56379475 TGGGCATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:56390182 original size:6 final size:6
Alignment explanation
Indices: 56390171--56390224 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
56390161 AGGTAGAAAA
* * * *
56390171 AGTGAC AGTGAC GGTGAC AGTGAC GGTGAC TGTGAC AGTGAT AGTGAC
1 AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC AGTGAC
56390219 AGTGAC
1 AGTGAC
56390225 CGAGTTTCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.28, C:0.15, G:0.37, T:0.20
Consensus pattern (6 bp):
AGTGAC
Found at i:56396400 original size:32 final size:32
Alignment explanation
Indices: 56396364--56396424 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
56396354 TTACGTGACA
*
56396364 AAGTGAGGCGTGCCT-TAATCATTTTCTGTGAT
1 AAGTGAGGCGTG-CTATAATCAATTTCTGTGAT
*
56396396 AAGTGAGGTGTGCTATAATCAATTTCTGT
1 AAGTGAGGCGTGCTATAATCAATTTCTGT
56396425 TAAATTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (32 bp):
AAGTGAGGCGTGCTATAATCAATTTCTGTGAT
Found at i:56398496 original size:36 final size:36
Alignment explanation
Indices: 56398429--56398511 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
56398419 AGGATAACCC
* * * *
56398429 TGAGGGGGATATCCTCCAGGTGGATGGTGTCCTACA
1 TGAGGGGGATACCCTCCAGGAGGAAGATGTCCTACA
* *
56398465 TGAGGGGGATACCCTCCAGGAGTAAGATGTCCTCCA
1 TGAGGGGGATACCCTCCAGGAGGAAGATGTCCTACA
* *
56398501 TGTGGTGGATA
1 TGAGGGGGATA
56398512 TCCTGGGTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (36 bp):
TGAGGGGGATACCCTCCAGGAGGAAGATGTCCTACA
Found at i:56399693 original size:27 final size:27
Alignment explanation
Indices: 56399657--56399708 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
56399647 GAAGGGGGGT
56399657 GTGGTGCCTATCCGATAGGCGGCACTG
1 GTGGTGCCTATCCGATAGGCGGCACTG
*
56399684 GTGGTGCCTATCTGATAGGCGGCAC
1 GTGGTGCCTATCCGATAGGCGGCAC
56399709 ACCTAGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (27 bp):
GTGGTGCCTATCCGATAGGCGGCACTG
Found at i:56399820 original size:14 final size:15
Alignment explanation
Indices: 56399795--56399823 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56399785 GGAGAAGAGA
56399795 AGAAAGAAAGAAAAG
1 AGAAAGAAAGAAAAG
56399810 AGAAA-AAAGAAAAG
1 AGAAAGAAAGAAAAG
56399824 GTATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAGAAAGAAAAG
Found at i:56399947 original size:39 final size:42
Alignment explanation
Indices: 56399902--56399984 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 42
56399892 TATTATATAG
*
56399902 TTTGTTTAGTGTTATTT-TTA-T-GTTTTGT-TTTAAAGTTAT
1 TTTGTTTAGTGTGATTTGTTAGTAGTTTTGTGTTTAAA-TTAT
*
56399941 TTTGTTTATTGTGATTTGTTAGTAAGTTTTGTGTTTAAATTAT
1 TTTGTTTAGTGTGATTTGTTAGT-AGTTTTGTGTTTAAATTAT
56399984 T
1 T
56399985 GAGAATGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
39 15 0.41
40 3 0.08
41 1 0.03
43 12 0.32
44 6 0.16
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (42 bp):
TTTGTTTAGTGTGATTTGTTAGTAGTTTTGTGTTTAAATTAT
Found at i:56403373 original size:33 final size:33
Alignment explanation
Indices: 56403336--56403410 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
56403326 TGTTGTGGTG
56403336 GATACGACCCAGGAGGAGTAG-AATACTGCGGTA
1 GATACGACCCAGGAGGAGT-GTAATACTGCGGTA
* ** * *
56403369 GATACGAGCTGGGAGGAGTGTTATACTGCGGTG
1 GATACGACCCAGGAGGAGTGTAATACTGCGGTA
56403402 GATACGACC
1 GATACGACC
56403411 TAAAGATATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.28, C:0.17, G:0.36, T:0.19
Consensus pattern (33 bp):
GATACGACCCAGGAGGAGTGTAATACTGCGGTA
Found at i:56403560 original size:24 final size:24
Alignment explanation
Indices: 56403523--56403579 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
56403513 GCGATCGCTT
*
56403523 GAGCTCGGGCTCCGACTGTGGCTC
1 GAGCTCGGGATCCGACTGTGGCTC
*
56403547 GGGCTCGGGATCCGACTGTGGCTC
1 GAGCTCGGGATCCGACTGTGGCTC
56403571 GAGCTCGGG
1 GAGCTCGGG
56403580 CTCGGCCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.09, C:0.30, G:0.42, T:0.19
Consensus pattern (24 bp):
GAGCTCGGGATCCGACTGTGGCTC
Found at i:56406173 original size:9 final size:8
Alignment explanation
Indices: 56406156--56406214 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
56406146 CCTTCCCGCC
*
56406156 CTCTCCTT
1 CTCTTCTT
56406164 CTCATTCTT
1 CTC-TTCTT
56406173 CTTCTTCTT
1 C-TCTTCTT
56406182 CTCTTCTT
1 CTCTTCTT
*
56406190 TTCTTC-T
1 CTCTTCTT
56406197 CT-TTCTCT
1 CTCTTCT-T
*
56406205 TTCTTCTT
1 CTCTTCTT
56406213 CT
1 CT
56406215 TCACTCGCGG
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
6 3 0.07
7 2 0.05
8 19 0.46
9 15 0.37
10 2 0.05
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.63
Consensus pattern (8 bp):
CTCTTCTT
Found at i:56406176 original size:3 final size:3
Alignment explanation
Indices: 56406168--56406216 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
56406158 CTCCTTCTCA
56406168 TTC TTC TTC TTC TTC -TC TTC TT- TTC TTC -TC TT- TCTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC -TTC TTC
56406211 TTC TTC
1 TTC TTC
56406217 ACTCGCGGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 7 0.17
3 30 0.75
4 2 0.05
5 1 0.03
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:56425294 original size:21 final size:21
Alignment explanation
Indices: 56425268--56425319 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
56425258 GCTCAAAGTG
56425268 TATGTGACGGATAATGTGGAA
1 TATGTGACGGATAATGTGGAA
56425289 TATGTGACGGATAATGTGGAA
1 TATGTGACGGATAATGTGGAA
56425310 TA-GTTGACGG
1 TATG-TGACGG
56425320 GTAGAGATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.31, C:0.06, G:0.35, T:0.29
Consensus pattern (21 bp):
TATGTGACGGATAATGTGGAA
Found at i:56427712 original size:18 final size:20
Alignment explanation
Indices: 56427689--56427728 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
56427679 CCCTTTTTAC
56427689 ATATATTA-TTATA-TAAAT
1 ATATATTATTTATATTAAAT
56427707 ATATATTATTTATATTAAAT
1 ATATATTATTTATATTAAAT
56427727 AT
1 AT
56427729 TTCATTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATTATTTATATTAAAT
Found at i:56440017 original size:24 final size:26
Alignment explanation
Indices: 56439970--56440020 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
56439960 AAAATTTTAA
56439970 TAAATAAAAAAATAATTTATTAAATAT
1 TAAATAAAAAAATAA-TTATTAAATAT
*
56439997 TAAATTAAAAAATAA-TA-TAAATAT
1 TAAATAAAAAAATAATTATTAAATAT
56440021 ATTTTTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 2 0.09
27 14 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAATAAAAAAATAATTATTAAATAT
Found at i:56448843 original size:48 final size:49
Alignment explanation
Indices: 56448790--56448887 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 49
56448780 TTTATATGTC
56448790 AAATAT-TTACT-TTTCGACCTATATTGTGGGTATCATAAATTCTAATAT
1 AAATATATTACTCTTTC-ACCTATATTGTGGGTATCATAAATTCTAATAT
** *
56448838 AAATATAATTGTTCTTTCACCTATATTGTGGGTATGATAAATTCTAATAT
1 AAATAT-ATTACTCTTTCACCTATATTGTGGGTATCATAAATTCTAATAT
56448888 TATAAATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
48 6 0.14
50 34 0.77
51 4 0.09
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (49 bp):
AAATATATTACTCTTTCACCTATATTGTGGGTATCATAAATTCTAATAT
Found at i:56451017 original size:32 final size:33
Alignment explanation
Indices: 56450976--56451098 Score: 113
Period size: 33 Copynumber: 3.5 Consensus size: 33
56450966 ATATAAAGGG
56450976 GGTTGCTAAGTGCTGATTCCCCG-CTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* * *
56451008 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG---GT
* *
56451050 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
56451083 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
56451099 ATCCATCGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
32 19 0.26
33 20 0.27
36 3 0.04
37 2 0.03
38 3 0.04
39 2 0.03
40 1 0.01
41 3 0.04
42 20 0.27
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
Found at i:56452061 original size:85 final size:85
Alignment explanation
Indices: 56451918--56452258 Score: 664
Period size: 85 Copynumber: 4.0 Consensus size: 85
56451908 ATATGTTTAC
56451918 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
1 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
56451983 ACTTGGACAAAGTCAGGAAA
66 ACTTGGACAAAGTCAGGAAA
56452003 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
1 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
56452068 ACTTGGACAAAGTCAGGAAA
66 ACTTGGACAAAGTCAGGAAA
56452088 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
1 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
56452153 ACTTGGACAAAGTCAGGAAA
66 ACTTGGACAAAGTCAGGAAA
*
56452173 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGACATCAGCCAGTTCGAA
1 TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
*
56452238 ACTTGGACGAAGTCAGGAAA
66 ACTTGGACAAAGTCAGGAAA
56452258 T
1 T
56452259 CATCCACACT
Statistics
Matches: 254, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 254 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (85 bp):
TTACTAAGCTATATGCTTACTCGTTTGTATTTTCCCTTGATTATAGTGATATCAGCCAGTTCGAA
ACTTGGACAAAGTCAGGAAA
Found at i:56454066 original size:50 final size:50
Alignment explanation
Indices: 56453996--56454174 Score: 225
Period size: 51 Copynumber: 3.5 Consensus size: 50
56453986 TATCATTCGA
* * *
56453996 TACACGTAGTAGCATTCACATAGTACTACACACGTGATCAAACTTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATCCGG
* * *
56454046 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TATCCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCA--AACTATCCGG
* *
56454097 TACACGTAGTAGCCTGCACATAGTACTACACGCGTGATCGAAGCTATCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATC-AAACTATCCGG
* * *
56454148 TACGCATAGTAGTCTGCACATAGTACT
1 TACACGTAGTAGCCTGCACATAGTACT
56454175 GCATATGCGA
Statistics
Matches: 111, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
50 37 0.33
51 71 0.64
52 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATCCGG
Found at i:56454119 original size:51 final size:51
Alignment explanation
Indices: 56453996--56454234 Score: 210
Period size: 51 Copynumber: 4.8 Consensus size: 51
56453986 TATCATTCGA
* * * *
56453996 TACACGTAGTAGCATTCACATAGTACTACACACGTGATCA--AACTTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TATCCGG
* *
56454046 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGG
* * *
56454097 TACACGTAGTAGCCTGCACATAGTACTACACGCGTGATCGA--AGCTATCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATTA-ATATCCGG
* * * * * * * * *
56454148 TACGCATAGTAGTCTGCACATAGTACTGCATATGCGACCTTTCAT-TCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGG
*
56454198 TACAC-----AGCCTACACATAGTACTACACACGTGACCATT
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATT
56454235 CTTTCACTTA
Statistics
Matches: 152, Mismatches: 31, Indels: 17
0.76 0.16 0.09
Matches are distributed among these distances:
45 25 0.16
50 47 0.31
51 76 0.50
52 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGG
Found at i:56454202 original size:101 final size:100
Alignment explanation
Indices: 56453988--56454229 Score: 271
Period size: 101 Copynumber: 2.5 Consensus size: 100
56453978 TTAACTATTA
* * * * *
56453988 TCATT-CGATACACGTAGTAGCATTCACATAGTACTACACACGTGATCAAACTTTCCGGTTCACG
1 TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAACTATCCGGTACACA
*
56454052 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
66 TAGTAGCCTGCACATAGTACTACACACGCGACCAT
* * * * *
56454087 TAATATCCGATACACGTAGTAGCCTGCACATAGTACTACACGCGTGATCGAAGCTATCCGGTACG
1 TCAT-TCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATC-AAACTATCCGGTACA
* * * * *
56454152 CATAGTAGTCTGCACATAGTACTGCATATGCGACCTT
64 CATAGTAGCCTGCACATAGTACTACACACGCGACCAT
*
56454189 TCATTCCGGTACAC-----AGCCTACACATAGTACTACACACGTGA
1 TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGA
56454230 CCATTCTTTC
Statistics
Matches: 121, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
96 25 0.21
99 3 0.02
100 1 0.01
101 48 0.40
102 44 0.36
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (100 bp):
TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAACTATCCGGTACACA
TAGTAGCCTGCACATAGTACTACACACGCGACCAT
Found at i:56455503 original size:9 final size:9
Alignment explanation
Indices: 56455489--56455531 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
56455479 GTTTTCGAAT
56455489 TCGAATAAC
1 TCGAATAAC
*
56455498 TCGAATAAT
1 TCGAATAAC
56455507 TCGAATAAC
1 TCGAATAAC
*
56455516 TCGAATAAT
1 TCGAATAAC
56455525 TCGAATA
1 TCGAATA
56455532 TCAAACCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (9 bp):
TCGAATAAC
Found at i:56455507 original size:18 final size:18
Alignment explanation
Indices: 56455486--56455531 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
56455476 TGAGTTTTCG
56455486 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
56455504 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
56455522 AATTCGAATA
1 AATTCGAATA
56455532 TCAAACCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:56456815 original size:27 final size:27
Alignment explanation
Indices: 56456779--56456846 Score: 95
Period size: 26 Copynumber: 2.5 Consensus size: 27
56456769 AATATATAAT
56456779 AAATATTTTTTTTATTTTTTTA-TTTTA
1 AAATA-TTTTTTTATTTTTTTATTTTTA
56456806 AAATATTTTTTTA-TTTTTTATTTTTA
1 AAATATTTTTTTATTTTTTTATTTTTA
*
56456832 AAATAAATTTTTTAT
1 AAAT-ATTTTTTTAT
56456847 GTTTATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 7 0.19
26 17 0.46
27 13 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
AAATATTTTTTTATTTTTTTATTTTTA
Found at i:56456851 original size:26 final size:25
Alignment explanation
Indices: 56456786--56456853 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
56456776 AATAAATATT
* *
56456786 TTTTTTATTTTTTTATTTTAAAATAT
1 TTTTTTATTTTTAT-TTTTAAAATAA
56456812 TTTTTTATTTTTTATTTTTAAAATAAA
1 TTTTTTA-TTTTTATTTTTAAAAT-AA
*
56456839 TTTTTTATGTTTATT
1 TTTTTTATTTTTATT
56456854 AAAAAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.72
Consensus pattern (25 bp):
TTTTTTATTTTTATTTTTAAAATAA
Found at i:56476657 original size:52 final size:52
Alignment explanation
Indices: 56476572--56476675 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
56476562 GATCATAGAC
*
56476572 ATGTAATCTACTCTAATATTATGTTAACGAATTTTAAAACTATTGGATAATT
1 ATGTAATCTACTCTAATATTATGTTAACGAATTTTAAAACTAGTGGATAATT
* * * *
56476624 ATGTAATCTATTTTAATATTATGTTGACTAATTTTAAAACTAGTGGATAATT
1 ATGTAATCTACTCTAATATTATGTTAACGAATTTTAAAACTAGTGGATAATT
56476676 CAAAATCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.44
Consensus pattern (52 bp):
ATGTAATCTACTCTAATATTATGTTAACGAATTTTAAAACTAGTGGATAATT
Found at i:56477046 original size:36 final size:36
Alignment explanation
Indices: 56476996--56477064 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
56476986 ATTATCATCA
56476996 TCTTCATCTCCATCT-CAATCTCCATATTCATCTACT
1 TCTTCATCTCCATCTCCAATCT-CATATTCATCTACT
* * * *
56477032 TCTTGATCTTCATCTCCAATGTTATATTCATCT
1 TCTTCATCTCCATCTCCAATCTCATATTCATCT
56477065 TGTTATTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 23 0.82
37 5 0.18
ACGTcount: A:0.22, C:0.30, G:0.03, T:0.45
Consensus pattern (36 bp):
TCTTCATCTCCATCTCCAATCTCATATTCATCTACT
Found at i:56494856 original size:3 final size:3
Alignment explanation
Indices: 56494848--56494878 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56494838 GTCACTCTTA
56494848 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
56494879 TTTTATTTAT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:56497972 original size:36 final size:36
Alignment explanation
Indices: 56497922--56497993 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
56497912 TAAGCTCAAA
* *
56497922 ACTTGACTATCATATCCGTAAGTTATTCCGAATAAT
1 ACTTGACTACCATATCCATAAGTTATTCCGAATAAT
*
56497958 ACTTGACTACCATATCCATAAGTTATTCTGAATAAT
1 ACTTGACTACCATATCCATAAGTTATTCCGAATAAT
56497994 TTCATCTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (36 bp):
ACTTGACTACCATATCCATAAGTTATTCCGAATAAT
Found at i:56499036 original size:18 final size:17
Alignment explanation
Indices: 56499001--56499041 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
56498991 CATTAAAAAT
*
56499001 AAAATATAATTTACAAA
1 AAAATATAAATTACAAA
**
56499018 AAAATATAAATTATGAA
1 AAAATATAAATTACAAA
56499035 AAAATAT
1 AAAATAT
56499042 TAAAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATATAAATTACAAA
Found at i:56500550 original size:16 final size:16
Alignment explanation
Indices: 56500529--56500584 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
56500519 GTAAATATTT
56500529 TTTTTTAT-ATTTTGTA
1 TTTTTTATAATTTT-TA
56500545 TTTTTTATAATTTTTA
1 TTTTTTATAATTTTTA
*
56500561 TTTTTTGTAATTTTATA
1 TTTTTTATAATTTT-TA
56500578 TTATTTT
1 TT-TTTT
56500585 TGAAACATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 23 0.64
17 9 0.25
18 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (16 bp):
TTTTTTATAATTTTTA
Found at i:56500566 original size:25 final size:26
Alignment explanation
Indices: 56500530--56500585 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
56500520 TAAATATTTT
*
56500530 TTTTTATATTTTGT-ATTTTTTATAA
1 TTTTTATATTTTGTAATTTTATATAA
* *
56500555 TTTTTATTTTTTGTAATTTTATATTA
1 TTTTTATATTTTGTAATTTTATATAA
56500581 TTTTT
1 TTTTT
56500586 GAAACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (26 bp):
TTTTTATATTTTGTAATTTTATATAA
Found at i:56500782 original size:20 final size:21
Alignment explanation
Indices: 56500759--56500810 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
56500749 ACTTTTAAAT
* *
56500759 TTTTTTTATAATTTTTATGA-
1 TTTTTATATAATTTTAATGAC
56500779 TTTTCTATA-AATTTTAATGAC
1 TTTT-TATATAATTTTAATGAC
56500800 TTTTTATATAA
1 TTTTTATATAA
56500811 AATACCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTTATATAATTTTAATGAC
Found at i:56508497 original size:25 final size:25
Alignment explanation
Indices: 56508462--56508550 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
56508452 ACACACCACA
*
56508462 GCTCTCTTGAGCTTCCCGATACTTG
1 GCTCTCATGAGCTTCCCGATACTTG
*
56508487 GCTCTCATGAGCTTCCCGATA-TACG
1 GCTCTCATGAGCTTCCCGATACT-TG
* * *
56508512 GCTCGT-ATGAGTTTCCCGTTACTTA
1 GCTC-TCATGAGCTTCCCGATACTTG
* *
56508537 GCTCACACGAGCTT
1 GCTCTCATGAGCTT
56508551 TCCGTTATTC
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 1 0.02
25 48 0.94
26 2 0.04
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.33
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATACTTG
Found at i:56508566 original size:50 final size:50
Alignment explanation
Indices: 56508469--56508577 Score: 119
Period size: 50 Copynumber: 2.2 Consensus size: 50
56508459 ACAGCTCTCT
* * * *
56508469 TGAGCTTCCCGATACTTGGCTCTCATGAGCTTCCCGATATACGGCTCGTA
1 TGAGCTTCCCGATACTTAGCTCACACGAGCTTCCCGATATACAGCTCGTA
* * * * * *
56508519 TGAGTTTCCCGTTACTTAGCTCACACGAGCTTTCCGTTATTCAGCTCGAA
1 TGAGCTTCCCGATACTTAGCTCACACGAGCTTCCCGATATACAGCTCGTA
*
56508569 AGAGCTTCC
1 TGAGCTTCC
56508578 TGTTTACATG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.31
Consensus pattern (50 bp):
TGAGCTTCCCGATACTTAGCTCACACGAGCTTCCCGATATACAGCTCGTA
Found at i:56516360 original size:3 final size:3
Alignment explanation
Indices: 56516352--56516381 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
56516342 CTAAGAATCC
56516352 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
56516382 AGAACCGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:56522559 original size:14 final size:14
Alignment explanation
Indices: 56522540--56522575 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
56522530 TGGTTCAAGA
56522540 GCTGAAAGGCAGCG
1 GCTGAAAGGCAGCG
*
56522554 GCTGAAA-GCAGTG
1 GCTGAAAGGCAGCG
56522567 GCTGAAAGG
1 GCTGAAAGG
56522576 GAGAAGGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.17, G:0.42, T:0.11
Consensus pattern (14 bp):
GCTGAAAGGCAGCG
Found at i:56533831 original size:17 final size:15
Alignment explanation
Indices: 56533789--56533836 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
56533779 AGATCTGACA
*
56533789 CCTTCTCTTCTTTTT
1 CCTTCTTTTCTTTTT
56533804 CCTTCTTTTCTTTTT
1 CCTTCTTTTCTTTTT
*
56533819 CTCTCTTTTTTCTTTTT
1 C-CT-TCTTTTCTTTTT
56533836 C
1 C
56533837 ATGTTTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.52
16 2 0.07
17 12 0.41
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
CCTTCTTTTCTTTTT
Found at i:56559297 original size:16 final size:17
Alignment explanation
Indices: 56559272--56559309 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
56559262 ATATGTTCTG
*
56559272 TATATGATATGATTTAA
1 TATATGATATGATATAA
*
56559289 TATAT-ATATGCTATAA
1 TATATGATATGATATAA
56559305 TATAT
1 TATAT
56559310 TTTAATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (17 bp):
TATATGATATGATATAA
Found at i:56570461 original size:41 final size:40
Alignment explanation
Indices: 56570326--56570460 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
56570316 ACTATGTCTG
** * * *
56570326 GCACTTAGTGTGCGTTTTGAGATAGCTTTGTCTATATAAA
1 GCACTTAGTGTGCGGATTGAGATAGCTTTGGCTATATGAT
* * *
56570366 ACACTTATTGTGC-GATTCG-GAGTAGCTTCGGCTATATG-T
1 GCACTTAGTGTGCGGATT-GAGA-TAGCTTTGGCTATATGAT
*
56570405 GGCACTTAGTGTGCGAGATTGAGATAGCTTTGGCTATGTGAT
1 -GCACTTAGTGTGCG-GATTGAGATAGCTTTGGCTATATGAT
56570447 GCACTTAGTGTGCG
1 GCACTTAGTGTGCG
56570461 ACATTATAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
39 4 0.05
40 36 0.47
41 29 0.38
42 7 0.09
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (40 bp):
GCACTTAGTGTGCGGATTGAGATAGCTTTGGCTATATGAT
Found at i:56572540 original size:15 final size:17
Alignment explanation
Indices: 56572510--56572541 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
56572500 TTGATACTTG
56572510 TGAATGTGAGTTTGGTA
1 TGAATGTGAGTTTGGTA
56572527 TGAAT-TGA-TTTGGTA
1 TGAATGTGAGTTTGGTA
56572542 AATTATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TGAATGTGAGTTTGGTA
Found at i:56599612 original size:12 final size:13
Alignment explanation
Indices: 56599586--56599614 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
56599576 GCTTCGATAC
56599586 TAAATTTATAAAA
1 TAAATTTATAAAA
56599599 TAAATTTA-AAAA
1 TAAATTTATAAAA
56599611 TAAA
1 TAAA
56599615 AAACAGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATTTATAAAA
Found at i:56599829 original size:19 final size:19
Alignment explanation
Indices: 56599807--56599843 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
56599797 CATTCAATAG
*
56599807 AAACCAAAAAGTTCAACAA
1 AAACCAAAAACTTCAACAA
*
56599826 AAACCCAAAACTTCAACA
1 AAACCAAAAACTTCAACA
56599844 GAAATAGATT
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:0.59, C:0.27, G:0.03, T:0.11
Consensus pattern (19 bp):
AAACCAAAAACTTCAACAA
Found at i:56600094 original size:17 final size:18
Alignment explanation
Indices: 56600066--56600115 Score: 84
Period size: 17 Copynumber: 2.8 Consensus size: 18
56600056 TAATAAATAA
*
56600066 AATTATCCAACCCAACCC
1 AATTACCCAACCCAACCC
56600084 AATTA-CCAACCCAACCC
1 AATTACCCAACCCAACCC
56600101 AATTACCCAACCCAA
1 AATTACCCAACCCAA
56600116 TAAAACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.42, C:0.44, G:0.00, T:0.14
Consensus pattern (18 bp):
AATTACCCAACCCAACCC
Found at i:56600110 original size:13 final size:13
Alignment explanation
Indices: 56600092--56600116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56600082 CCAATTACCA
56600092 ACCCAACCCAATT
1 ACCCAACCCAATT
56600105 ACCCAACCCAAT
1 ACCCAACCCAAT
56600117 AAAACTAAAA
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Done.