Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 211 of 292
Found at i:62310279 original size:15 final size:15
Alignment explanation
Indices: 62310259--62310315 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
62310249 ATTCAATATT
62310259 AATATTTTAATAATA
1 AATATTTTAATAATA
*
62310274 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
62310293 AATATATTAATAATA
1 AATATTTTAATAATA
*
62310308 AATGTTTT
1 AATATTTT
62310316 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:62310789 original size:14 final size:14
Alignment explanation
Indices: 62310770--62310799 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62310760 CCAGAAAAGT
62310770 AAATCATTTTCCAA
1 AAATCATTTTCCAA
*
62310784 AAATCATTTTCTAA
1 AAATCATTTTCCAA
62310798 AA
1 AA
62310800 GTAATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAA
Found at i:62311550 original size:3 final size:3
Alignment explanation
Indices: 62311542--62311587 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
62311532 CGTGTTGCCC
62311542 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
62311588 CATTATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62312288 original size:38 final size:38
Alignment explanation
Indices: 62312240--62312315 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
62312230 AACTTATAAC
62312240 TATATACATATTCACAAGACATTCAAAATGCCAAATTA
1 TATATACATATTCACAAGACATTCAAAATGCCAAATTA
62312278 TATATACATATTCACAAGACATTCAAAATGCCAAATTA
1 TATATACATATTCACAAGACATTCAAAATGCCAAATTA
62312316 GTCCAAGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.29
Consensus pattern (38 bp):
TATATACATATTCACAAGACATTCAAAATGCCAAATTA
Found at i:62315567 original size:1 final size:1
Alignment explanation
Indices: 62315561--62315588 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
62315551 ATTTAACAAC
62315561 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
62315589 GGAGAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:62318535 original size:19 final size:20
Alignment explanation
Indices: 62318508--62318545 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62318498 TTATAAAGGT
*
62318508 TATATTTTA-ATATTTAAAA
1 TATAGTTTATATATTTAAAA
62318527 TATAGTTTATATATTTAAA
1 TATAGTTTATATATTTAAA
62318546 TTAACTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATAGTTTATATATTTAAAA
Found at i:62322034 original size:126 final size:126
Alignment explanation
Indices: 62321809--62322047 Score: 406
Period size: 126 Copynumber: 1.9 Consensus size: 126
62321799 GTTTTAGCCT
*
62321809 TAAGAGGATATTTGAATATTCAAAACAAACAAAAAAAGCAAAACCCAATACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAAAAAGCAAAACCCAATACGTTAGGGCACGATT
* * *
62321874 TTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTTAAAGTGAACTGG
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTTTAAAGTGAACTGG
* * * *
62321935 TAAGAGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAAAAAGCAAAACCCAATACGTTAGGGCACGATT
62322000 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTT
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTT
62322048 GAGAGAAGAT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 105 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (126 bp):
TAAGAGGATATTCGAATATTCAAAACAAACAAAAAAAGCAAAACCCAATACGTTAGGGCACGATT
CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTAAAAAATTTTTAAAGTGAACTGG
Found at i:62322185 original size:13 final size:12
Alignment explanation
Indices: 62322153--62322202 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
62322143 AACCATATAT
62322153 AAATAA-TAA-A
1 AAATAATTAATA
62322163 AAATAA-TAATA
1 AAATAATTAATA
*
62322174 ATAGTAATTAATA
1 A-AATAATTAATA
62322187 GAAATAATTAATA
1 -AAATAATTAATA
62322200 AAA
1 AAA
62322203 CAACAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 9 0.26
11 2 0.06
12 7 0.21
13 15 0.44
14 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (12 bp):
AAATAATTAATA
Found at i:62322936 original size:18 final size:18
Alignment explanation
Indices: 62322913--62322948 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
62322903 ATAACAAGTA
*
62322913 GGGTGATAGAGTTAGTGG
1 GGGTGATAGAGGTAGTGG
*
62322931 GGGTGATGGAGGTAGTGG
1 GGGTGATAGAGGTAGTGG
62322949 ATGGTTTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.56, T:0.25
Consensus pattern (18 bp):
GGGTGATAGAGGTAGTGG
Found at i:62322967 original size:29 final size:29
Alignment explanation
Indices: 62322931--62322993 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
62322921 GAGTTAGTGG
62322931 GGGTGATGGAGGTAGTGGAT-GGTTTAGTA
1 GGGTGATGGAGGTAGTGG-TCGGTTTAGTA
* *
62322960 GGGTGATGGAGTTAGTGGTCGGTTTAGTG
1 GGGTGATGGAGGTAGTGGTCGGTTTAGTA
62322989 GGGTG
1 GGGTG
62322994 TTTAATTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.16, C:0.02, G:0.51, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGTCGGTTTAGTA
Found at i:62332735 original size:30 final size:31
Alignment explanation
Indices: 62332670--62332739 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
62332660 GGACCTCAAA
*
62332670 TTTTTAAAAATTTTCATTAAACGATTAAAAG
1 TTTTTAAAAATTTTAATTAAACGATTAAAAG
* * **
62332701 -TTTTAAAATTTTTAATTAAAC-CTTCTAAG
1 TTTTTAAAAATTTTAATTAAACGATTAAAAG
62332730 TTTTTAAAAA
1 TTTTTAAAAA
62332740 ATTCTCATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTTTAAAAATTTTAATTAAACGATTAAAAG
Found at i:62335787 original size:2 final size:2
Alignment explanation
Indices: 62335780--62335810 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62335770 ATCAATAATA
62335780 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 A
62335811 GATAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62335855 original size:17 final size:18
Alignment explanation
Indices: 62335830--62335863 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
62335820 AGGATCTATA
62335830 AAAAAAATAATA-ATATG
1 AAAAAAATAATATATATG
*
62335847 AAAACAATAATATATAT
1 AAAAAAATAATATATAT
62335864 ACATATGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAAAATAATATATATG
Found at i:62340082 original size:34 final size:34
Alignment explanation
Indices: 62340039--62340107 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
62340029 TTTTTTATCC
62340039 AATATAAAATAATCCAACATATTACTACAAACAT
1 AATATAAAATAATCCAACATATTACTACAAACAT
62340073 AATATAAAATAATCCAACATATTACTACAAACAT
1 AATATAAAATAATCCAACATATTACTACAAACAT
62340107 A
1 A
62340108 TTTAGCAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (34 bp):
AATATAAAATAATCCAACATATTACTACAAACAT
Found at i:62340766 original size:8 final size:8
Alignment explanation
Indices: 62340755--62340780 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
62340745 TCTAATTTTC
62340755 AAATTTAA
1 AAATTTAA
62340763 AAATTTAA
1 AAATTTAA
62340771 AAATTTAA
1 AAATTTAA
62340779 AA
1 AA
62340781 GTGTAATTGT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATTTAA
Found at i:62345771 original size:2 final size:2
Alignment explanation
Indices: 62345764--62345795 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
62345754 AATTTTAAAC
62345764 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
62345796 TTAAATCCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62351204 original size:16 final size:17
Alignment explanation
Indices: 62351183--62351223 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
62351173 TTTATAAAAA
*
62351183 TTTTAAAATT-TATTTT
1 TTTTAAAATTATAATTT
62351199 TTTTAAAAATTATAATTT
1 TTTT-AAAATTATAATTT
62351217 TTTTAAA
1 TTTTAAA
62351224 TCTAAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATTATAATTT
Found at i:62351209 original size:17 final size:18
Alignment explanation
Indices: 62351183--62351223 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
62351173 TTTATAAAAA
*
62351183 TTTT-AAAATT-TATTTT
1 TTTTAAAAATTATAATTT
62351199 TTTTAAAAATTATAATTT
1 TTTTAAAAATTATAATTT
62351217 TTTTAAA
1 TTTTAAA
62351224 TCTAAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 6 0.27
18 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAAAATTATAATTT
Found at i:62351845 original size:7 final size:8
Alignment explanation
Indices: 62351807--62351849 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
62351797 TGAAAATATT
62351807 TATTTTAA
1 TATTTTAA
62351815 TATTTTTAA
1 TA-TTTTAA
*
62351824 TATATTATA
1 TATTTTA-A
62351833 TATTTTAA
1 TATTTTAA
62351841 T-TTTTAA
1 TATTTTAA
62351848 TA
1 TA
62351850 CGATCCGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.23
8 8 0.27
9 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:62357691 original size:14 final size:14
Alignment explanation
Indices: 62357672--62357760 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
62357662 CTCCTCTGGT
62357672 CTTCTGCTTCGCTG
1 CTTCTGCTTCGCTG
* *
62357686 CTTCTGTTGTCTCCATTG
1 CTTCTGCT-TC-GC--TG
62357704 TCTTCTGCTTCGCTG
1 -CTTCTGCTTCGCTG
62357719 CTTCTGCGGTCTC-CATTG
1 CTTCTGC--T-TCGC--TG
62357737 TCTTCTGCTTCGCTG
1 -CTTCTGCTTCGCTG
62357752 CTTCTGCTT
1 CTTCTGCTT
62357761 TCTCCTTCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
14 23 0.39
15 6 0.10
16 5 0.08
17 5 0.08
18 6 0.10
19 14 0.24
ACGTcount: A:0.02, C:0.33, G:0.19, T:0.46
Consensus pattern (14 bp):
CTTCTGCTTCGCTG
Found at i:62357712 original size:33 final size:33
Alignment explanation
Indices: 62357670--62357765 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
62357660 GGCTCCTCTG
62357670 GTCTTCTGCTTCGCTGCTTCTGTTGTCTCCATT
1 GTCTTCTGCTTCGCTGCTTCTGTTGTCTCCATT
**
62357703 GTCTTCTGCTTCGCTGCTTCTGCGGTCTCCATT
1 GTCTTCTGCTTCGCTGCTTCTGTTGTCTCCATT
62357736 GTCTTCTGCTTCGCTGCTTCTGCTT-TCTCC
1 GTCTTCTGCTTCGCTGCTTCTG-TTGTCTCC
62357766 TTCATGCTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.02, C:0.33, G:0.19, T:0.46
Consensus pattern (33 bp):
GTCTTCTGCTTCGCTGCTTCTGTTGTCTCCATT
Found at i:62359901 original size:18 final size:20
Alignment explanation
Indices: 62359860--62359908 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
62359850 ATATTTTATG
*
62359860 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
62359879 ATTATTTTAATGAGATAT-T
1 ATTATTTTAATGAGATATAT
62359898 -TTATTATTAAT
1 ATTATT-TTAAT
62359909 AATTTAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 5 0.19
19 10 0.37
20 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:62362098 original size:46 final size:46
Alignment explanation
Indices: 62362046--62362319 Score: 307
Period size: 46 Copynumber: 6.0 Consensus size: 46
62362036 AGTGTGCTCT
* * *
62362046 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATAGCAGC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * * *
62362092 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGT
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * * * *
62362138 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAGC
* ** * *
62362184 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * *
62362230 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * * * *
62362276 ATGACA-GAAAAAGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGACATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
62362320 TCATGTCAAA
Statistics
Matches: 200, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 1 0.00
46 199 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAGC
Found at i:62362305 original size:138 final size:138
Alignment explanation
Indices: 62362061--62362309 Score: 367
Period size: 138 Copynumber: 1.8 Consensus size: 138
62362051 ATGAAATGTG
* **
62362061 TAAGACCATGGTTGAAAGATACCATAGCAGCCTGATATGAAACGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATAGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGA
* * * * *
62362126 TACCATGGCAGTCTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGACAACATGACGG
66 TACCATGGCAGACTGACATGAAAAGAGTAAGACCATAGTTGAAAGATACCATGACAACATGACGG
62362191 GAAATAAA
131 GAAATAAA
* * *
62362199 TAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATAGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGA
62362264 TACCATGGCA-ACATGACA-GAAAAAGAGTAAGACCATAGTTGAAAGA
66 TACCATGGCAGAC-TGACATG-AAAAGAGTAAGACCATAGTTGAAAGA
62362310 CACTATGGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
137 2 0.02
138 96 0.98
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (138 bp):
TAAGACCATGGTTGAAAGATACCATAGCAGCCTGACATGAAACGAATAAGACCATGGTTGAAAGA
TACCATGGCAGACTGACATGAAAAGAGTAAGACCATAGTTGAAAGATACCATGACAACATGACGG
GAAATAAA
Found at i:62366080 original size:42 final size:42
Alignment explanation
Indices: 62366034--62366131 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
62366024 CATAGTTCAA
** * * *
62366034 CTATGGTCTTACACATCTTCATATATCGATGTCATAGCCCAG
1 CTATGGTCTTACACATAATCACATATCGATGCCACAGCCCAG
* *
62366076 CTATGGCCTTACACGTAATCACATATCGATGCCACAGCCCAG
1 CTATGGTCTTACACATAATCACATATCGATGCCACAGCCCAG
* *
62366118 TTATAGTCTTACAC
1 CTATGGTCTTACAC
62366132 GAATCGCATA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (42 bp):
CTATGGTCTTACACATAATCACATATCGATGCCACAGCCCAG
Found at i:62366132 original size:42 final size:41
Alignment explanation
Indices: 62366056--62366143 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 41
62366046 ACATCTTCAT
* * *
62366056 ATATCGATGTCATAGCCCAGCTATGGCCTTACACGTAATCAC
1 ATATCGATGCCACAGCCCAGCTATAGCCTTACACG-AATCAC
* * *
62366098 ATATCGATGCCACAGCCCAGTTATAGTCTTACACGAATCGC
1 ATATCGATGCCACAGCCCAGCTATAGCCTTACACGAATCAC
62366139 ATATC
1 ATATC
62366144 TCACTGATGC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 10 0.25
42 30 0.75
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (41 bp):
ATATCGATGCCACAGCCCAGCTATAGCCTTACACGAATCAC
Found at i:62366163 original size:46 final size:46
Alignment explanation
Indices: 62366102--62366214 Score: 120
Period size: 47 Copynumber: 2.4 Consensus size: 46
62366092 AATCACATAT
* * * * *
62366102 CGATGCCACAGCCCAGTTATAGTCTTACACGAATCGC-ATATCTCAC
1 CGATGCCATATCCCAGATATAGTCTTACAC-AATAGCAATATCACAC
* * * *
62366148 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATAGTCTTACACAATAGCA-ATATCACAC
62366195 CGATGCCATATCCCAGATAT
1 CGATGCCATATCCCAGATAT
62366215 GATCTTATAC
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
45 4 0.07
46 24 0.44
47 27 0.49
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATAGTCTTACACAATAGCAATATCACAC
Found at i:62366299 original size:31 final size:31
Alignment explanation
Indices: 62366243--62366390 Score: 169
Period size: 31 Copynumber: 4.8 Consensus size: 31
62366233 CTTGTCACTT
*
62366243 GTAGCC-GAAGCTACCAC-ATTCACTGATCAG
1 GTAGCCAG-AGCTACCACTTTTCACTGATCAG
*
62366273 GTAGCCAGAGCTACCATTTTTCACTGATCAG
1 GTAGCCAGAGCTACCACTTTTCACTGATCAG
* * *
62366304 GTAGTCGGAGTTACCACTTTTCACTGATCAG
1 GTAGCCAGAGCTACCACTTTTCACTGATCAG
*
62366335 GTAG-CAGAAGCTACCACTTTTCACTAATCAG
1 GTAGCCAG-AGCTACCACTTTTCACTGATCAG
* *
62366366 GTAGCC-GAAGCTATCACTTATCACT
1 GTAGCCAG-AGCTACCACTTTTCACT
62366391 TTCACTTGTC
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.16
31 86 0.83
32 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCAGAGCTACCACTTTTCACTGATCAG
Found at i:62366384 original size:62 final size:62
Alignment explanation
Indices: 62366243--62366390 Score: 201
Period size: 62 Copynumber: 2.4 Consensus size: 62
62366233 CTTGTCACTT
* * *
62366243 GTAGCCGAAGCTACCAC-ATTCACTGATCAGGTAGCCAGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAGGTAGCCAGAGCTACCACTTTTCACTAATCAG
* * *
62366304 GTAGTCGGAGTTACCACTTTTCACTGATCAGGTAG-CAGAAGCTACCACTTTTCACTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAGGTAGCCAG-AGCTACCACTTTTCACTAATCAG
* *
62366366 GTAGCCGAAGCTATCACTTATCACT
1 GTAGCCGAAGCTACCACTTTTCACT
62366391 TTCACTTGTC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
61 17 0.23
62 57 0.77
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (62 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAGGTAGCCAGAGCTACCACTTTTCACTAATCAG
Found at i:62372851 original size:23 final size:23
Alignment explanation
Indices: 62372821--62372867 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
62372811 CTCTTGGGAC
62372821 CTTTTGTATGTCCACTCCCCATT
1 CTTTTGTATGTCCACTCCCCATT
62372844 CTTTTGTATGTCCACTCCCCATT
1 CTTTTGTATGTCCACTCCCCATT
62372867 C
1 C
62372868 ATTCTTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.09, T:0.43
Consensus pattern (23 bp):
CTTTTGTATGTCCACTCCCCATT
Found at i:62387292 original size:16 final size:16
Alignment explanation
Indices: 62387271--62387303 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
62387261 CAAGTAAAGT
62387271 GGGTAATGAATTTAGA
1 GGGTAATGAATTTAGA
62387287 GGGTAATGAATTTAGA
1 GGGTAATGAATTTAGA
62387303 G
1 G
62387304 CCTGTTATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (16 bp):
GGGTAATGAATTTAGA
Found at i:62389223 original size:17 final size:17
Alignment explanation
Indices: 62389203--62389235 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
62389193 TTAAAAATTA
62389203 TAAA-AATATAAATTATT
1 TAAATAATA-AAATTATT
62389220 TAAATAATAAAATTAT
1 TAAATAATAAAATTAT
62389236 ATTTTTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAATAAAATTATT
Found at i:62390896 original size:5 final size:5
Alignment explanation
Indices: 62390880--62390909 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
62390870 TTTTTCCCAA
62390880 TGTTT T-TTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T
62390910 TTAAGAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TGTTT
Found at i:62400198 original size:32 final size:29
Alignment explanation
Indices: 62400118--62400198 Score: 69
Period size: 30 Copynumber: 2.7 Consensus size: 29
62400108 CAAATAGTTC
62400118 AATG-GTCAAATTGTAACTTTTTTTTAATTA
1 AATGAGTCAAATT-TAACTTTTTTTT-ATTA
**
62400148 AATGA-TCAAATTCGACTTTTTTTT-TTAA
1 AATGAGTCAAATTTAACTTTTTTTTATT-A
62400176 AGATTGAAGTCAAATTTAACTTT
1 A-A-TG-AGTCAAATTTAACTTT
62400199 AAAAAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
27 2 0.05
28 2 0.05
29 11 0.27
30 13 0.32
31 1 0.02
32 12 0.29
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.47
Consensus pattern (29 bp):
AATGAGTCAAATTTAACTTTTTTTTATTA
Found at i:62401658 original size:4 final size:4
Alignment explanation
Indices: 62401649--62401679 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
62401639 TCCAATTACA
62401649 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
62401680 ATATAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:62409597 original size:11 final size:11
Alignment explanation
Indices: 62409574--62409607 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
62409564 ATGTCAAATC
*
62409574 ATCAAGAATAA
1 ATCAAGAACAA
*
62409585 ATTAAGAACAA
1 ATCAAGAACAA
62409596 ATCAAGAACAA
1 ATCAAGAACAA
62409607 A
1 A
62409608 ACTAGATGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.12, G:0.09, T:0.15
Consensus pattern (11 bp):
ATCAAGAACAA
Found at i:62411158 original size:2 final size:2
Alignment explanation
Indices: 62411153--62411185 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
62411143 TTATCTTATG
*
62411153 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62411186 TGAAAGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:62411831 original size:26 final size:26
Alignment explanation
Indices: 62411797--62411869 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
62411787 TTTTTTTTAA
* *
62411797 TTTTCAAAATTAAATATAAAAATTAT
1 TTTTTAAAATTAAATATAAAAATAAT
* * *
62411823 TTTTTAAAAAT-AAGATACAAATAAT
1 TTTTTAAAATTAAATATAAAAATAAT
*
62411848 TTTAGTAAAATTTAAATATAAA
1 TTT-TTAAAA-TTAAATATAAA
62411870 TATGGGCGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 14 0.40
26 14 0.40
27 1 0.03
28 6 0.17
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (26 bp):
TTTTTAAAATTAAATATAAAAATAAT
Found at i:62414475 original size:23 final size:23
Alignment explanation
Indices: 62414449--62414501 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
62414439 TAATGCAATT
*
62414449 CATTCTGACA-CTTCGGTGTGATC
1 CATTCTGACATCTT-GGTGGGATC
* *
62414472 CATTCTGGCATCTTGGTGGGATT
1 CATTCTGACATCTTGGTGGGATC
62414495 CATTCTG
1 CATTCTG
62414502 TGGAGTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (23 bp):
CATTCTGACATCTTGGTGGGATC
Found at i:62415233 original size:117 final size:117
Alignment explanation
Indices: 62415027--62415258 Score: 401
Period size: 117 Copynumber: 2.0 Consensus size: 117
62415017 ATGTGCTTAC
* *
62415027 CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTTTTAGTGACGTT
1 CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
*
62415092 TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTATTACATATCGTATGGT
66 TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTAGTACATATCGTATGGT
*
62415144 CTTGATAGGTTATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
1 CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
* * *
62415209 TTGAACATGTCTTGGGTGTTTTGGATGATTTTAGTAGTACATATCGTATG
66 TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTAGTACATATCGTATG
62415259 TTTAATGACT
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.40
Consensus pattern (117 bp):
CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTAGTACATATCGTATGGT
Found at i:62415731 original size:6 final size:6
Alignment explanation
Indices: 62415720--62415751 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
62415710 TTAAAAAATA
*
62415720 TATATT TATATT TATATT TATATT AATATT TA
1 TATATT TATATT TATATT TATATT TATATT TA
62415752 ATAATTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:62418661 original size:17 final size:18
Alignment explanation
Indices: 62418639--62418674 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
62418629 TTGACCCGAA
62418639 TAATAACAAT-TAAAATT
1 TAATAACAATATAAAATT
*
62418656 TAATAATAATATAAAATT
1 TAATAACAATATAAAATT
62418674 T
1 T
62418675 CACTCTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAACAATATAAAATT
Found at i:62418978 original size:21 final size:21
Alignment explanation
Indices: 62418939--62418984 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
62418929 GCGGTGGTTG
* * *
62418939 TGAGATTAATTATTATAGCGA
1 TGAGATTAAATACTATAGCAA
*
62418960 TGAGATTAAATACTGTAGCAA
1 TGAGATTAAATACTATAGCAA
62418981 TGAG
1 TGAG
62418985 GTCAAAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (21 bp):
TGAGATTAAATACTATAGCAA
Found at i:62421089 original size:12 final size:11
Alignment explanation
Indices: 62421061--62421099 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
62421051 GAAGAGGAGG
62421061 AAAAATAAAAA
1 AAAAATAAAAA
62421072 AGAAAATAAAAA
1 A-AAAATAAAAA
*
62421084 GAAAAACAAAAA
1 -AAAAATAAAAA
62421096 AAAA
1 AAAA
62421100 GTATAATAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 5 0.20
12 19 0.76
13 1 0.04
ACGTcount: A:0.87, C:0.03, G:0.05, T:0.05
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:62421682 original size:24 final size:24
Alignment explanation
Indices: 62421637--62421683 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
62421627 TAAACTCAAT
* ** *
62421637 TTTTTTGAAAAATTAAATTAAAAG
1 TTTTATGAAAAACAAAAATAAAAG
62421661 TTTTATGAAAAACAAAAATAAAA
1 TTTTATGAAAAACAAAAATAAAA
62421684 TAAAGGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (24 bp):
TTTTATGAAAAACAAAAATAAAAG
Found at i:62422041 original size:16 final size:17
Alignment explanation
Indices: 62422001--62422042 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
62421991 TTAATTAATT
*
62422001 AATTAAAAATTCATAAT
1 AATTAAAAATTCATAAA
* *
62422018 AATAAAAAATT-TTAAA
1 AATTAAAAATTCATAAA
62422034 AATTAAAAA
1 AATTAAAAA
62422043 AATTATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAAAATTCATAAA
Found at i:62425023 original size:93 final size:93
Alignment explanation
Indices: 62424913--62425085 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
62424903 CGCCCATAAG
* *
62424913 CGAACTTGGACTTAACTCAACGAGCTCGGGA-GTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACGTTCGCATCCATAAGTGAACTCGGACTCAACTC
62424977 AACGAGCTCGGATGCCTAGTTACATCTCA
65 AACGAGCTCGGATGCCTAGTTACATCTCA
*
62425006 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
62425071 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
62425086 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 3 0.04
93 72 0.96
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:62425081 original size:46 final size:46
Alignment explanation
Indices: 62424906--62425081 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
62424896 TGTAACCCGC
* *
62424906 CCATAAGCGAACTTGGACTTAACTCAACGAGCTCGGGA-GTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GGACGTTCGCAT
* *
62424952 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* *
62425002 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
62425045 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
62425082 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 5 0.05
46 60 0.55
47 28 0.25
48 2 0.02
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:62428574 original size:26 final size:26
Alignment explanation
Indices: 62428538--62428590 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
62428528 TACTTTTGAA
62428538 AACATTTACTTAAACACCTTGTATGC
1 AACATTTACTTAAACACCTTGTATGC
62428564 AACATTTACTTAAACACCTTGTATGC
1 AACATTTACTTAAACACCTTGTATGC
62428590 A
1 A
62428591 TGTTTTCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (26 bp):
AACATTTACTTAAACACCTTGTATGC
Found at i:62431115 original size:21 final size:21
Alignment explanation
Indices: 62431088--62431152 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
62431078 AATCATCCTG
62431088 AAGGCCATTGCTTTCAATGTC
1 AAGGCCATTGCTTTCAATGTC
* * * *
62431109 GAGGCCATTTCCTTCTATGTC
1 AAGGCCATTGCTTTCAATGTC
* * *
62431130 AAGGCTATTGCTGTCAATATC
1 AAGGCCATTGCTTTCAATGTC
62431151 AA
1 AA
62431153 TGTCGTTCCC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (21 bp):
AAGGCCATTGCTTTCAATGTC
Found at i:62431472 original size:24 final size:24
Alignment explanation
Indices: 62431445--62431494 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
62431435 TTAGTCTTTA
62431445 TATACCATAAAAAGGACATGAAAC
1 TATACCATAAAAAGGACATGAAAC
62431469 TATACCATAAAAAGGACATGAAAC
1 TATACCATAAAAAGGACATGAAAC
62431493 TA
1 TA
62431495 CCTTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (24 bp):
TATACCATAAAAAGGACATGAAAC
Found at i:62432510 original size:25 final size:25
Alignment explanation
Indices: 62432482--62432529 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
62432472 TTCACTAACT
62432482 CAACTTTATCATTTAAATCTAGACC
1 CAACTTTATCATTTAAATCTAGACC
62432507 CAACTTTATCATTTAAATCTAGA
1 CAACTTTATCATTTAAATCTAGA
62432530 TCTGTTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (25 bp):
CAACTTTATCATTTAAATCTAGACC
Found at i:62432845 original size:15 final size:15
Alignment explanation
Indices: 62432805--62432848 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
62432795 AAATTTCAAT
*
62432805 AAATAAAAAATATCA
1 AAATAAAAAATATTA
* **
62432820 AATTATTAAATATTA
1 AAATAAAAAATATTA
62432835 AAATAAAAAATATT
1 AAATAAAAAATATT
62432849 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:62438758 original size:15 final size:16
Alignment explanation
Indices: 62438732--62438767 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
62438722 TAAATAAAAG
*
62438732 TAAATCAAAATTTAAT
1 TAAATCAAAATTGAAT
62438748 TAAAT-AAAATTGAAT
1 TAAATCAAAATTGAAT
62438763 TAAAT
1 TAAAT
62438768 TAATTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAATCAAAATTGAAT
Found at i:62438789 original size:20 final size:22
Alignment explanation
Indices: 62438766--62438805 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
62438756 ATTGAATTAA
*
62438766 ATTAATTGA-AAAT-ATTCTCC
1 ATTAAGTGATAAATAATTCTCC
62438786 ATTAAGTGATAAATAATTCT
1 ATTAAGTGATAAATAATTCT
62438806 TATCTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTAAGTGATAAATAATTCTCC
Found at i:62441031 original size:117 final size:118
Alignment explanation
Indices: 62440902--62441136 Score: 436
Period size: 118 Copynumber: 2.0 Consensus size: 118
62440892 TTTTGATGAG
62440902 AATGTTATATGTCG-AAAAAAATATTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
1 AATGTTATATGTCGAAAAAAAATATTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
62440966 AAACTCAACACTTTATTAAAATGATGCTTATTATAATGTCTTCCAAATTTATT
66 AAACTCAACACTTTATTAAAATGATGCTTATTATAATGTCTTCCAAATTTATT
*
62441019 AATGTTATATGTCGAAAAAAAATGTTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
1 AATGTTATATGTCGAAAAAAAATATTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
* *
62441084 ACATTCAACACTTTATTAAAATGATGCTTATTATAATGTCTTCCAAATTTATT
66 AAACTCAACACTTTATTAAAATGATGCTTATTATAATGTCTTCCAAATTTATT
62441137 TTTTTTAACT
Statistics
Matches: 114, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
117 14 0.12
118 100 0.88
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.37
Consensus pattern (118 bp):
AATGTTATATGTCGAAAAAAAATATTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
AAACTCAACACTTTATTAAAATGATGCTTATTATAATGTCTTCCAAATTTATT
Found at i:62453670 original size:26 final size:25
Alignment explanation
Indices: 62453616--62453674 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
62453606 TTAAAAACAT
62453616 TTTTTATAATTTAAATTTTTATAGAA
1 TTTTTA-AATTTAAATTTTTATAGAA
* *
62453642 TTTTTAAATTATATATATTTTATA-TA
1 TTTTTAAATT-TAAAT-TTTTATAGAA
62453668 TTTTTAA
1 TTTTTAA
62453675 TAATTTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 4 0.14
26 18 0.62
27 7 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTTAAATTTAAATTTTTATAGAA
Found at i:62456151 original size:52 final size:52
Alignment explanation
Indices: 62456073--62456175 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
62456063 TTAACGTTTA
62456073 CATATTTTATCAAAATGATCCTAATTGTATTTTTAAGCATTTTTTTGCTATT
1 CATATTTTATCAAAATGATCCTAATTGTATTTTTAAGCATTTTTTTGCTATT
*
62456125 CATATTTTATCAAAATGATCCTAATTGTATTTTTAAGTATTTTTTTGCTAT
1 CATATTTTATCAAAATGATCCTAATTGTATTTTTAAGCATTTTTTTGCTAT
62456176 CAACCTTTGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (52 bp):
CATATTTTATCAAAATGATCCTAATTGTATTTTTAAGCATTTTTTTGCTATT
Found at i:62459468 original size:25 final size:25
Alignment explanation
Indices: 62459433--62459481 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
62459423 AGGTAAAATT
62459433 ATTTCTGCCTTTGCATTTTTTTTTA
1 ATTTCTGCCTTTGCATTTTTTTTTA
*
62459458 ATTTCTTCCTTTGCATTTTTTTTT
1 ATTTCTGCCTTTGCATTTTTTTTT
62459482 CTTTTTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.10, C:0.16, G:0.06, T:0.67
Consensus pattern (25 bp):
ATTTCTGCCTTTGCATTTTTTTTTA
Found at i:62467724 original size:24 final size:24
Alignment explanation
Indices: 62467694--62467743 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
62467684 CCAAAGGCAG
62467694 AAAACCAAATGCAACCATAAATAA
1 AAAACCAAATGCAACCATAAATAA
62467718 AAAACCAAATGCAACCATAAATAA
1 AAAACCAAATGCAACCATAAATAA
62467742 AA
1 AA
62467744 GGCAGAAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.64, C:0.20, G:0.04, T:0.12
Consensus pattern (24 bp):
AAAACCAAATGCAACCATAAATAA
Found at i:62480806 original size:27 final size:23
Alignment explanation
Indices: 62480752--62480811 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
62480742 ATACACGGAT
62480752 TCCAACCAAACACATTGAAATAA
1 TCCAACCAAACACATTGAAATAA
62480775 TCCAACCAAACACATTGAAATAA
1 TCCAACCAAACACATTGAAATAA
*
62480798 TCCACCCAAACACA
1 TCCAACCAAACACA
62480812 CTAGAACGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.50, C:0.32, G:0.03, T:0.15
Consensus pattern (23 bp):
TCCAACCAAACACATTGAAATAA
Found at i:62481015 original size:24 final size:23
Alignment explanation
Indices: 62480967--62481016 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
62480957 TATTCAATTT
62480967 TCATATTTCAATTCAATCACTTTC
1 TCATATTTCAATTCAATCAC-TTC
*
62480991 TCATATTTTCCATTCAAATCA-TTC
1 TCATA-TTTCAATTC-AATCACTTC
62481015 TC
1 TC
62481017 CATTTAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 10 0.43
25 8 0.35
26 5 0.22
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (23 bp):
TCATATTTCAATTCAATCACTTC
Found at i:62481841 original size:16 final size:16
Alignment explanation
Indices: 62481822--62481854 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
62481812 GAATAGTCTC
62481822 TGTTTCTTTTCTTCTT
1 TGTTTCTTTTCTTCTT
*
62481838 TGTTTCTTTTGTTCTT
1 TGTTTCTTTTCTTCTT
62481854 T
1 T
62481855 TACTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTTCTTCTT
Found at i:62485110 original size:71 final size:71
Alignment explanation
Indices: 62485026--62485189 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
62485016 CGATTTGTCT
62485026 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
62485091 CTTTCA
66 CTTTCA
* *
62485097 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
62485162 CTTTCA
66 CTTTCA
62485168 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
62485190 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:62485227 original size:71 final size:70
Alignment explanation
Indices: 62485026--62485223 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
62485016 CGATTTGTCT
* * * * *
62485026 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
62485091 CTTTCA
65 CTTTCA
* * * *
62485097 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
62485162 CTTTCA
65 CTTTCA
* *
62485168 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
62485224 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:62492150 original size:70 final size:71
Alignment explanation
Indices: 62492067--62492229 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
62492057 CGATTTGTCT
62492067 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
62492131 CTTTCA
66 CTTTCA
*
62492137 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
62492202 CTTTCA
66 CTTTCA
62492208 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
62492230 GATACATCTC
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
70 51 0.56
71 40 0.44
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:62492267 original size:71 final size:70
Alignment explanation
Indices: 62492067--62492263 Score: 249
Period size: 70 Copynumber: 2.8 Consensus size: 70
62492057 CGATTTGTCT
* * * *
62492067 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
62492131 CTTTCA
65 CTTTCA
* * * *
62492137 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
62492202 CTTTCA
65 CTTTCA
* *
62492208 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
62492264 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 52 0.44
71 43 0.36
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:62493906 original size:2 final size:2
Alignment explanation
Indices: 62493899--62493928 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
62493889 TTAAAAGATA
62493899 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
62493929 CCCATAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62499228 original size:18 final size:17
Alignment explanation
Indices: 62499207--62499250 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
62499197 TTTAATAAAA
62499207 TATAAATTTTAAAATTTT
1 TATAAATTTT-AAATTTT
*
62499225 TATAAATATTTTAATTTT
1 TATAAAT-TTTAAATTTT
*
62499243 TAAAAATT
1 TATAAATT
62499251 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.83
19 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAAATTTTAAATTTT
Found at i:62499262 original size:20 final size:20
Alignment explanation
Indices: 62499219--62499283 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
62499209 TAAATTTTAA
*
62499219 AATTTTTATAAA-TATTTT-
1 AATTTTTAAAAATTATTTTG
62499237 AATTTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
*
62499257 AATTTTTGAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
62499277 AATTTTT
1 AATTTTT
62499284 TTTGTAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.26
19 6 0.14
20 26 0.60
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:62504397 original size:46 final size:47
Alignment explanation
Indices: 62504335--62504467 Score: 180
Period size: 46 Copynumber: 2.9 Consensus size: 47
62504325 TTATCTTTGA
* * * * *
62504335 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTTCATAT
62504381 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTTCATAT
* **
62504427 CAGGTTGCCATGGCATCTTTCAACCATGGTCTTACACATTT
1 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTT
62504468 CATTTCAGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
45 4 0.05
46 71 0.92
47 2 0.03
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (47 bp):
CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTTCATAT
Found at i:62509242 original size:29 final size:29
Alignment explanation
Indices: 62509168--62509286 Score: 109
Period size: 29 Copynumber: 4.2 Consensus size: 29
62509158 TACATACATG
*
62509168 CATATGGCCCACTAGGCCC-AATCTTATT
1 CATATGGCCCACTAGGCCCAAATCATATT
* * * **
62509196 CAAATTGCTCATCT-GGCCCAGTTCATATT
1 CATATGGCCCA-CTAGGCCCAAATCATATT
* * *
62509225 CTTATGGCCCACTAGGCCCAATTCACATT
1 CATATGGCCCACTAGGCCCAAATCATATT
* *
62509254 CATACGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCCAAATCATATT
62509283 -ATAT
1 CATAT
62509287 TCATGCTCAC
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
28 18 0.26
29 52 0.74
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.29
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAAATCATATT
Found at i:62513565 original size:89 final size:89
Alignment explanation
Indices: 62513414--62513578 Score: 249
Period size: 89 Copynumber: 1.9 Consensus size: 89
62513404 TATTGACAAT
*
62513414 TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGGCAACTTTTAGCTGCAAATATGTT
1 TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGACAACTTTTAGCTGCAAATATGTT
62513479 GTGCATCCACAGCCTGTTGGCAGC
66 GTGCATCCACAGCCTGTTGGCAGC
* * * * * * * *
62513503 TTAATAATTTGCAACATTGGTGGTTCATCCATAAATTACTGATAGCTTTTATCTGCAAATATGTT
1 TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGACAACTTTTAGCTGCAAATATGTT
62513568 GTGCATCCACA
66 GTGCATCCACA
62513579 ACAAGTGGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 67 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (89 bp):
TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGACAACTTTTAGCTGCAAATATGTT
GTGCATCCACAGCCTGTTGGCAGC
Found at i:62513689 original size:99 final size:99
Alignment explanation
Indices: 62513518--62513696 Score: 308
Period size: 99 Copynumber: 1.8 Consensus size: 99
62513508 AATTTGCAAC
62513518 ATTGGTGGTTCATCCATAAATTACTGATAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAA
1 ATTGGTGGTTCATCCATAAATTACTGATAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAA
62513583 GTGGTAGCTTGTCTGTGAACTATTTTTTTAAAAT
66 GTGGTAGCTTGTCTGTGAACTATTTTTTTAAAAT
* *
62513617 ATTGGTGGTTCATCCATAAATTACT-AGTTGCTTTTATCTGCAAATATGTTGTGCA-CCTACAAT
1 ATTGGTGGTTCATCCATAAATTACTGA-TAGCTTTTATCTGCAAATATGTTGTGCATCC-ACAAC
62513680 AAGTGGTAGCTTGTCTG
64 AAGTGGTAGCTTGTCTG
62513697 CAAACTGTTT
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
98 3 0.04
99 73 0.96
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (99 bp):
ATTGGTGGTTCATCCATAAATTACTGATAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAA
GTGGTAGCTTGTCTGTGAACTATTTTTTTAAAAT
Found at i:62513740 original size:99 final size:97
Alignment explanation
Indices: 62513522--62513732 Score: 291
Period size: 99 Copynumber: 2.2 Consensus size: 97
62513512 TGCAACATTG
*
62513522 GTGGTTCATCCATAAATTACTGATAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAAGTGG
1 GTGGTTCATCCATAAATTACTG-TTGCTTTTATCTGCAAATATGTTGTGCATCCACAACAAGTGG
** * * *
62513587 TAGCTTGTCTGTGAACTATTTTTTTAAAATATTG
65 TAGCTTGTCTGCAAAC-ATGTTTTTAAAATACTA
*
62513621 GTGGTTCATCCATAAATTACTAGTTGCTTTTATCTGCAAATATGTTGTGCA-CCTACAATAAGTG
1 GTGGTTCATCCATAAATTACT-GTTGCTTTTATCTGCAAATATGTTGTGCATCC-ACAACAAGTG
62513685 GTAGCTTGTCTGCAAAC-TGTTTTTAAAATACTA
64 GTAGCTTGTCTGCAAACATGTTTTTAAAATACTA
* *
62513718 GTTGTTTATCCATAA
1 GTGGTTCATCCATAA
62513733 TTTTTACTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
97 26 0.26
98 2 0.02
99 72 0.71
100 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (97 bp):
GTGGTTCATCCATAAATTACTGTTGCTTTTATCTGCAAATATGTTGTGCATCCACAACAAGTGGT
AGCTTGTCTGCAAACATGTTTTTAAAATACTA
Found at i:62515058 original size:25 final size:27
Alignment explanation
Indices: 62515015--62515065 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
62515005 CATAATAAAC
*
62515015 AAAATAAAAATCACGAAAAATATGGAT
1 AAAATAAAAACCACGAAAAATATGGAT
*
62515042 AAAAT-AAAACCAC-AAAATTATGGA
1 AAAATAAAAACCACGAAAAATATGGA
62515066 CAGAAACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.18
Consensus pattern (27 bp):
AAAATAAAAACCACGAAAAATATGGAT
Found at i:62518508 original size:29 final size:28
Alignment explanation
Indices: 62518423--62518512 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
62518413 AATATCTATA
* *
62518423 ATTAAATTAAAATTTTA-AGTATCCATTTAA
1 ATTAAATTAAAATTTTATA-TAT--AATTAC
** *
62518453 ATTATAATTAAAATTTCGTATGTAATTAC
1 ATTA-AATTAAAATTTTATATATAATTAC
62518482 ATTAAATTAAAATTTATATATATAATTAC
1 ATTAAATTAAAATTT-TATATATAATTAC
62518511 AT
1 AT
62518513 ATTTTAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 11 0.22
29 20 0.41
30 4 0.08
31 13 0.27
32 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (28 bp):
ATTAAATTAAAATTTTATATATAATTAC
Found at i:62519321 original size:18 final size:18
Alignment explanation
Indices: 62519298--62519333 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
62519288 TTTTTTGTAA
62519298 AATTTA-ATTTTAATATAT
1 AATTTATATTTTAA-ATAT
62519316 AATTTATATTTTAAATAT
1 AATTTATATTTTAAATAT
62519334 TATTAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTATATTTTAAATAT
Found at i:62520526 original size:22 final size:23
Alignment explanation
Indices: 62520501--62520543 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
62520491 CTACTTGTAC
62520501 CGTAGTGCCAC-AACACTTGCAA
1 CGTAGTGCCACTAACACTTGCAA
*
62520523 CGTAGTGCCACTATCACTTGC
1 CGTAGTGCCACTAACACTTGC
62520544 GCATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.23
Consensus pattern (23 bp):
CGTAGTGCCACTAACACTTGCAA
Found at i:62520624 original size:2 final size:2
Alignment explanation
Indices: 62520617--62520647 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62520607 AGGTATTTAA
62520617 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 A
62520648 ATTTCACTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62524629 original size:20 final size:20
Alignment explanation
Indices: 62524606--62524665 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 20
62524596 AAATTAAGAG
62524606 TTATTAATTTAATATATTAT
1 TTATTAATTTAATATATTAT
*
62524626 TTATTTATTT--T-TATTAT
1 TTATTAATTTAATATATTAT
* *
62524643 TTTTTACATATAATTATATTAT
1 TTATTA-ATTTAA-TATATTAT
62524665 T
1 T
62524666 GAGTTATCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
17 10 0.32
18 4 0.13
20 9 0.29
21 1 0.03
22 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTAATTTAATATATTAT
Found at i:62528290 original size:18 final size:18
Alignment explanation
Indices: 62528256--62528289 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
62528246 TAACAAATTA
62528256 TTTTATAAATTTATATAT
1 TTTTATAAATTTATATAT
62528274 TTTTAT-AA-TTATATAT
1 TTTTATAAATTTATATAT
62528290 AATATTCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATAAATTTATATAT
Found at i:62535051 original size:15 final size:16
Alignment explanation
Indices: 62535023--62535052 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62535013 TAAATTTATC
62535023 TTTTTTTTATAGATAT
1 TTTTTTTTATAGATAT
62535039 TTTTTTTTA-AGATA
1 TTTTTTTTATAGATA
62535053 GTAGAGTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTTTTTTATAGATAT
Found at i:62555398 original size:31 final size:32
Alignment explanation
Indices: 62555328--62555399 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
62555318 CTAATATGGA
*
62555328 TAATTTTTTAAAATATTTTTTTTATAATTTGT
1 TAATTTTTTAAAATATTTTTCTTATAATTTGT
**
62555360 TGTTTTTTTAAAATATTTTTCTTA-AATTT-T
1 TAATTTTTTAAAATATTTTTCTTATAATTTGT
*
62555390 TAAATTTTTA
1 TAATTTTTTA
62555400 TGAATTATAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 8 0.24
31 5 0.15
32 21 0.62
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (32 bp):
TAATTTTTTAAAATATTTTTCTTATAATTTGT
Found at i:62559487 original size:28 final size:28
Alignment explanation
Indices: 62559447--62559525 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
62559437 GCAATCAAAT
* *
62559447 ATGGCACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
62559475 ATGGCACTTAGTGTGC-AAGATATTGAGA
1 ATGGCACTTAGTGTGCGAA-ATATTGAGA
*
62559503 ATGGCATTTAGTGTGCGAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
62559526 CGAATGATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 2 0.04
28 42 0.91
29 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:62561123 original size:5 final size:5
Alignment explanation
Indices: 62561096--62561132 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
62561086 TTGTGTGTTC
62561096 TTTA- TTTAT TTT-T TTTAAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTAT TTT
62561133 TTCAAAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.27
5 18 0.60
6 4 0.13
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:62562314 original size:12 final size:12
Alignment explanation
Indices: 62562297--62562334 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
62562287 ATCAAAGAAA
62562297 AATAAAATAAAT
1 AATAAAATAAAT
62562309 AATAAAATAAAT
1 AATAAAATAAAT
62562321 AATAAAATAAAT
1 AATAAAATAAAT
62562333 AA
1 AA
62562335 CAATAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:62564457 original size:26 final size:24
Alignment explanation
Indices: 62564427--62564475 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
62564417 AATAAAAAAT
*
62564427 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
62564453 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
62564476 TAGAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:62566546 original size:27 final size:26
Alignment explanation
Indices: 62566476--62566588 Score: 138
Period size: 27 Copynumber: 4.3 Consensus size: 26
62566466 AGCATGGCTG
* *
62566476 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
62566502 CCAG-ATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
62566528 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
62566555 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
62566582 CCAGAAC
1 CCAGAAC
62566589 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
25 8 0.11
26 18 0.24
27 48 0.63
28 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:62566557 original size:53 final size:53
Alignment explanation
Indices: 62566476--62566588 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 53
62566466 AGCATGGCTG
*
62566476 CCAGAACAGATAATGTGACAGAGTCACCAGAT-AGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
* * * *
62566528 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
62566582 CCAGAAC
1 CCAGAAC
62566589 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 12 0.22
53 18 0.33
54 24 0.44
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (53 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:62568245 original size:26 final size:25
Alignment explanation
Indices: 62568222--62568366 Score: 236
Period size: 26 Copynumber: 5.6 Consensus size: 25
62568212 CATAACATCA
*
62568222 TACCTAACCATTATCATGAAACATT
1 TACCTAACCATTATCATGGAACATT
62568247 TACCTAACCCATTATCATGGAACATT
1 TACCTAA-CCATTATCATGGAACATT
*
62568273 TACCTAACCATTATCATGAAACATT
1 TACCTAACCATTATCATGGAACATT
62568298 TACCTAACCCATTATCATGGAACATT
1 TACCTAA-CCATTATCATGGAACATT
62568324 TACCTAACCTATTATCATGGAACATT
1 TACCTAACC-ATTATCATGGAACATT
62568350 TACCTAACCTATTATCA
1 TACCTAACC-ATTATCA
62568367 ATTTGTATCA
Statistics
Matches: 114, Mismatches: 3, Indels: 5
0.93 0.02 0.04
Matches are distributed among these distances:
25 33 0.29
26 81 0.71
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (25 bp):
TACCTAACCATTATCATGGAACATT
Found at i:62568292 original size:51 final size:51
Alignment explanation
Indices: 62568222--62568366 Score: 263
Period size: 51 Copynumber: 2.8 Consensus size: 51
62568212 CATAACATCA
62568222 TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATT
1 TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATT
62568273 TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATT
1 TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATT
* *
62568324 TACCTAACCTATTATCATGGAACATTTACCTAACCTATTATCA
1 TACCTAACC-ATTATCATGAAACATTTACCTAACCCATTATCA
62568367 ATTTGTATCA
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
51 60 0.66
52 31 0.34
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (51 bp):
TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATT
Found at i:62568314 original size:77 final size:77
Alignment explanation
Indices: 62568222--62568366 Score: 256
Period size: 77 Copynumber: 1.9 Consensus size: 77
62568212 CATAACATCA
62568222 TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACC-ATTA
1 TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTATTA
62568286 TCATGAAACATT
66 TCATGAAACATT
* *
62568298 TACCTAACCCATTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCTATT
1 TACCTAA-CCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTATT
62568363 ATCA
65 ATCA
62568367 ATTTGTATCA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
76 7 0.11
77 51 0.78
78 7 0.11
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (77 bp):
TACCTAACCATTATCATGAAACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTATTA
TCATGAAACATT
Found at i:62571229 original size:10 final size:10
Alignment explanation
Indices: 62571202--62571231 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
62571192 ACAGACAGAT
62571202 AATTCAGAAA
1 AATTCAGAAA
62571212 ATATTCAGAAA
1 A-ATTCAGAAA
62571223 AATTCAGAA
1 AATTCAGAA
62571232 TACTTACAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (10 bp):
AATTCAGAAA
Found at i:62572339 original size:27 final size:26
Alignment explanation
Indices: 62572302--62572416 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
62572292 AGCATGGCTG
* *
62572302 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
62572328 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
62572356 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
62572383 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
62572410 CCAGAAC
1 CCAGAAC
62572417 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:62572361 original size:54 final size:54
Alignment explanation
Indices: 62572302--62572416 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
62572292 AGCATGGCTG
*
62572302 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
62572356 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
62572410 CCAGAAC
1 CCAGAAC
62572417 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:62574061 original size:26 final size:26
Alignment explanation
Indices: 62574025--62574134 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
62574015 CATGAAATTC
62574025 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
62574051 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
62574077 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
62574103 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
62574129 TTATCA
1 TTATCA
62574135 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:62578168 original size:27 final size:26
Alignment explanation
Indices: 62578075--62578167 Score: 123
Period size: 27 Copynumber: 3.5 Consensus size: 26
62578065 AGCATGGCTG
* *
62578075 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
62578101 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
62578129 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
*
62578156 CCAGATCAGATA
1 CCAGAACAGATA
62578168 TTTGTAGTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.08
27 37 0.63
28 17 0.29
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:62578181 original size:27 final size:27
Alignment explanation
Indices: 62578075--62578189 Score: 110
Period size: 27 Copynumber: 4.3 Consensus size: 27
62578065 AGCATGGCTG
*
62578075 CCAGAACAGATA-ATGT-GACAGAGTCA
1 CCAGAACAGATATATGTAG-CAGAGCCA
* *
62578101 CCAGATATAGATA-ATCGTGGCAGAGCCA
1 CCAGA-ACAGATATAT-GTAGCAGAGCCA
*
62578129 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTAGCAGAGCCA
* * * *
62578156 CCAGATCAGATATTTGTAGTATAGCCA
1 CCAGAACAGATATATGTAGCAGAGCCA
62578183 CCAGAAC
1 CCAGAAC
62578190 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
26 5 0.07
27 54 0.71
28 16 0.21
29 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATATATGTAGCAGAGCCA
Found at i:62578182 original size:54 final size:54
Alignment explanation
Indices: 62578075--62578189 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 54
62578065 AGCATGGCTG
* * *
62578075 CCAGAACAGATAATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTAGCAGAGCCA
* * * * *
62578129 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTAGTATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTAGCAGAGCCA
62578183 CCAGAAC
1 CCAGAAC
62578190 GCTTCCTCCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTAGCAGAGCCA
Found at i:62579826 original size:26 final size:26
Alignment explanation
Indices: 62579790--62579977 Score: 313
Period size: 26 Copynumber: 7.2 Consensus size: 26
62579780 CATGAAATTC
*
62579790 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
62579816 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
62579842 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
62579868 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
62579894 TTATTATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
62579920 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
62579946 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
62579972 TTATCA
1 TTATCA
62579978 ATTTGTATAA
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 154 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:62585360 original size:16 final size:16
Alignment explanation
Indices: 62585336--62585372 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
62585326 AATGAGCACT
*
62585336 TTCAGACTTATCACGC
1 TTCAAACTTATCACGC
62585352 TTCAAACTTATCACGC
1 TTCAAACTTATCACGC
62585368 TTCAA
1 TTCAA
62585373 CCTTTCTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (16 bp):
TTCAAACTTATCACGC
Found at i:62598640 original size:23 final size:23
Alignment explanation
Indices: 62598558--62598644 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
62598548 CCTGATCAGT
*
62598558 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
62598580 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
62598600 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
62598623 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
62598645 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:62601985 original size:71 final size:69
Alignment explanation
Indices: 62601791--62602054 Score: 323
Period size: 71 Copynumber: 3.7 Consensus size: 69
62601781 GAGTTAAGCC
* *
62601791 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
62601856 GAGGTAT
63 GAGGTAT
* * ** * *
62601863 TTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTAATTTTTGT-TTTAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGGGGCACGCTG
62601927 AGGTAT
64 AGGTAT
*
62601933 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
1 TTTTAATTTTTGTTTT--AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
62601998 AGGTAT
64 AGGTAT
* * ** * *
62602004 TTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
62602055 TTTAATTTTT
Statistics
Matches: 166, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
69 35 0.21
70 56 0.34
71 59 0.36
72 16 0.10
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTTTAATTTTTGTTTTAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAG
GTAT
Found at i:62602099 original size:122 final size:124
Alignment explanation
Indices: 62601933--62602179 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 124
62601923 GTTGAGGTAT
62601933 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
* *
62601998 AGGTATTTT-TA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC
66 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
* * *
62602054 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACT
* * * *
62602119 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 GAGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
62602179 T
1 T
62602180 CAGGTCACGC
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
121 12 0.11
122 59 0.52
123 1 0.01
124 13 0.12
125 28 0.25
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (124 bp):
TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTG
AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:62602140 original size:263 final size:257
Alignment explanation
Indices: 62601624--62602216 Score: 1033
Period size: 263 Copynumber: 2.3 Consensus size: 257
62601614 TTTCAAGGAA
*
62601624 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTGTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
*
62601689 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTTAGT
62601754 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
131 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
62601819 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
196 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
62601881 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
*
62601946 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACACTGAGGTATTTTTAGT
66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTA---TT--T
62602011 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA
126 TTA-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA
62602076 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
190 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT
62602141 TTT
255 TTT
* * * * * *
62602144 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT
1 AA--TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
62602209 GTTTTCAA
64 GTTTTCAA
62602217 TTTACGTTGT
Statistics
Matches: 319, Mismatches: 9, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
257 119 0.37
260 2 0.01
262 4 0.01
263 131 0.41
265 63 0.20
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (257 bp):
AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTTAGT
TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT
CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT
Found at i:62602175 original size:72 final size:71
Alignment explanation
Indices: 62602054--62602494 Score: 290
Period size: 72 Copynumber: 6.1 Consensus size: 71
62602044 GAGTTAAGCC
* *
62602054 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTGTTTTT-AAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
62602118 TGAGGTA
65 TGAGGTA
* * *
62602125 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAATTTTTGT-TTTTAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC
62602190 TGAGGTA
65 TGAGGTA
* * * * * * * ** * *** *
62602197 TTTTCAATTTCTG-TTTTCAATT-TACGT--TGTT-CAAGA-ATCAACTCATATTGCGAGAGGTA
1 TTTTCAATTTTTGTTTTTAAATTCAAC-TCATATTGCGAGAGGTGAGTTGAGCCT-CG-G-GGCA
* * ***
62602256 GGTTGA-ACC
62 CGCTGAGGTA
** * * * *
62602265 TTTT-AATTTCTACTTTTTCAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTTCAATTT-TTGTTTTT-AAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
62602329 CTGAGGTA
64 CTGAGGTA
* * ** * *
62602337 ATTTCAATTTCTGTTGTCAAAAAAATT-AACTCATATTACTAGAGGTGAGTTGAGCCTCGGGGCA
1 TTTTCAATTTTTGTT-T---TTAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCA
62602401 CGCTGAGGTA
62 CGCTGAGGTA
* * * * **
62602411 TTTTCAATTTTTATGTTTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACAC
1 TTTTCAATTTTTGT-TTTTAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GGCAC
*
62602476 GCCGAGGTA
63 GCTGAGGTA
62602485 TTTTCAATTT
1 TTTTCAATTT
62602495 CCGTTTTTCA
Statistics
Matches: 269, Mismatches: 77, Indels: 45
0.69 0.20 0.12
Matches are distributed among these distances:
66 5 0.02
67 10 0.04
68 8 0.03
69 12 0.04
70 12 0.04
71 16 0.06
72 105 0.39
73 16 0.06
74 80 0.30
75 5 0.02
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (71 bp):
TTTTCAATTTTTGTTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT
GAGGTA
Found at i:62602477 original size:74 final size:74
Alignment explanation
Indices: 62602284--62602495 Score: 236
Period size: 74 Copynumber: 2.9 Consensus size: 74
62602274 CTACTTTTTC
* *
62602284 AAAA-TCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
62602348 TGTTGTCAAA
66 TGTTGT-AAA
* * * *
62602358 AAAATT-AACTCATATTACTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTT-
1 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
**
62602421 T-TATGT-TT
66 TGT-TGTAAA
* * * * *
62602429 TAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATT
1 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTTCAATT
62602494 TC
64 TC
62602496 CGTTTTTCAA
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
71 4 0.03
72 30 0.26
73 4 0.03
74 76 0.66
75 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (74 bp):
AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTGTAAA
Found at i:62602626 original size:74 final size:75
Alignment explanation
Indices: 62602520--62602662 Score: 225
Period size: 74 Copynumber: 1.9 Consensus size: 75
62602510 TGTCTTTCAA
* *
62602520 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAAT
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCACACGCCGAGGTAATTTCAAT
62602584 TTCTGTTGTC
66 TTCTGTTGTC
* * *
62602594 AAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-CACACGCCGAGGTAATTTCAA
62602659 TTTC
65 TTTC
62602663 CGTTTTTCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 40 0.65
76 22 0.35
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (75 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGCACACGCCGAGGTAATTTCAAT
TTCTGTTGTC
Found at i:62602658 original size:167 final size:167
Alignment explanation
Indices: 62602355--62602998 Score: 919
Period size: 165 Copynumber: 3.9 Consensus size: 167
62602345 TTCTGTTGTC
* * * * * *
62602355 AAAAAAATTAACTCATATTACTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*** *
62602420 T-T-TATGT-TTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAG
66 TCTGT-TGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAG
*
62602482 GTATTTTCAATTTCCGTTTTTCAATTTTTGTCTTTCAA
130 GTATTTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAA
62602520 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* *
62602585 TCTGTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGG
66 TCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGG
62602650 TATTTTCAATTTCCGTTTTTCAATTTTTGCCTTTC--
131 TATTTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAA
62602685 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* ** * *
62602750 TCTGTTGTCAAAAAAGTCAACTCGTATTGCGAGAGGTTAGTTGAGCCTCAGATCACACGTCGAGG
66 TCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGG
* *
62602815 TATTTTCAATTTCCATTTTTCAATTTCTGCCTTTCAAAA
131 TATTTTCAATTTCCGTTTTTCAATTTTTGCCTTTC--AA
*
62602854 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* * *** * * **
62602919 TCTGTTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCAAG--ACACGTTGAGG
66 TCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGG
*
62602980 TATTTTCAATTTCTGTTTT
131 TATTTTCAATTTCCGTTTT
62602999 CAAAAAATCA
Statistics
Matches: 438, Mismatches: 34, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
165 244 0.56
166 4 0.01
167 118 0.27
169 72 0.16
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (167 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
TCTGTTGTCAAAAAATTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGG
TATTTTCAATTTCCGTTTTTCAATTTTTGCCTTTCAA
Found at i:62602792 original size:74 final size:76
Alignment explanation
Indices: 62602683--62602827 Score: 215
Period size: 74 Copynumber: 1.9 Consensus size: 76
62602673 TTTTTGCCTT
*
62602683 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACG-CTGAGGTAATTT
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTC-GAGGTAATTT
62602745 CAATTTCTGTTG
65 CAATTTCTGTTG
* * * *
62602757 TCAAAAAAGTCAACTCGTATTGCGAGAGGTTAGTTGAGCCTCAGATCACACGTCGAGGTATTTTC
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC
62602822 AATTTC
66 AATTTC
62602828 CATTTTTCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
74 41 0.65
76 21 0.33
77 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (76 bp):
TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC
AATTTCTGTTG
Found at i:62602960 original size:332 final size:327
Alignment explanation
Indices: 62602353--62602998 Score: 927
Period size: 332 Copynumber: 2.0 Consensus size: 327
62602343 ATTTCTGTTG
* * * * *
62602353 TCAAAAAAATTAACTCATATTACTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
1 TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
*** ** *
62602418 TTTTTATGTTTTAATTTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGG
66 TTTTTATGTAAAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGATCACACGCCGAGG
* * *
62602483 TATTTTCAATTTCCGTTTTTCAATTTTTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGT
131 TATTTTCAATTTCCATTTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGT
*
62602548 GAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATT
196 GAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTC-AAAAAATCAACTCATATT
*** * *
62602613 GCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTTT
260 GCGAGAAACGAGTTGAACCTCAAG--ACACGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTTT
62602678 GCCTT
323 GCCTT
*
62602683 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
1 TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
** *
62602748 TTTCTGT-TGTCAAAAAAGTCAACTCGTATTGCGAGAGGTTAGTTGAGCCTCAGATCACACGTCG
66 TTT-T-TATGT-AAAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGATCACACGCCG
62602812 AGGTATTTTCAATTTCCATTTTTCAATTTCTGCCTTTCAAAAAAAAAAATCAACTCATATTGCGA
128 AGGTATTTTCAATTTCCATTTTTCAATTTCTGCCTTTC--AAAAAAAAATCAACTCATATTGCGA
* * *
62602877 GAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTTC-AAAATTCAACTCA
191 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATCAACTCA
* ** *
62602941 TATTGCGAGAAATGAGTTGAACCTCAAGACACGTTGAGGTATTTTCAATTTCTGTTTT
256 TATTGCGAGAAACGAGTTGAACCTCAAGACACGCCGAGGTATTTTCAATTTCCGTTTT
62602999 CAAAAAATCA
Statistics
Matches: 280, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
330 89 0.32
331 4 0.01
332 113 0.40
334 74 0.26
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (327 bp):
TCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
TTTTTATGTAAAAAAGTCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGATCACACGCCGAGG
TATTTTCAATTTCCATTTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGT
GAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATCAACTCATATTG
CGAGAAACGAGTTGAACCTCAAGACACGCCGAGGTATTTTCAATTTCCGTTTTTCAATTTTTGCC
TT
Found at i:62603145 original size:79 final size:76
Alignment explanation
Indices: 62602854--62603361 Score: 411
Period size: 72 Copynumber: 6.5 Consensus size: 76
62602844 CCTTTCAAAA
** *
62602854 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTAATTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
62602917 TTTCTGTTTTC
66 TTTCTATTTTC
* ** * * *
62602928 --AAAATTCAACTCATATTGCGAGAAATGAGTTGAACCTCA-A-GACACGTTGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
62602989 TTTCTGTTTTC
66 TTTCTATTTTC
* * ** * ** *
62603000 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
62603064 TTTCTATCTTTC
66 TTTCTAT-TTTC
* * *
62603076 AAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTA--TTTTC
*
62603141 AATTTATATTTTTC
64 AATTTCTA-TTTTC
* * * * *
62603155 AAAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCT-GAGGTATTTTCA
**
62603219 AAATCTATTTTTC
65 ATTTCTA-TTTTC
* ** * **
62603232 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
* *
62603297 GCTATTTTCAATTTCTGTTTTTTTTTC
55 GGTATTTTCAATTTC-----TATTTTC
62603324 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
62603362 TTTTTAATTT
Statistics
Matches: 352, Mismatches: 53, Indels: 50
0.77 0.12 0.11
Matches are distributed among these distances:
72 64 0.18
73 32 0.09
75 22 0.06
76 4 0.01
77 62 0.18
78 3 0.01
79 64 0.18
80 1 0.00
81 5 0.01
82 29 0.08
88 57 0.16
89 1 0.00
91 2 0.01
92 5 0.01
93 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (76 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
TTTCTATTTTC
Found at i:62603379 original size:30 final size:30
Alignment explanation
Indices: 62603343--62603404 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
62603333 CAACTCATAT
62603343 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
62603373 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
62603403 TG
1 TG
62603405 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:62603505 original size:254 final size:244
Alignment explanation
Indices: 62602994--62603533 Score: 658
Period size: 254 Copynumber: 2.2 Consensus size: 244
62602984 TTCAATTTCT
* * *
62602994 GTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
62603059 TTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCTTCAGATCACA
66 TTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCTTCAGATCACA
* *
62603124 CACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCATATTGCGAGATGTGAGTTG
131 CACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* ** * * * **
62603189 AGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTATTTTTCAAATTCT
195 AACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
* *
62603239 GTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
* * * *
62603303 TTCAATTTCTGTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA
66 TTCAATTTC----TATCTTTCAAAAAAA-TCAACTCATATTGCGAAAGGTGAGTTGAGC--TTCA
* * * * * *
62603368 -ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGC
124 GA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGC
* *
62603430 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAA
182 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
*
62603493 G-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGGTGAGC
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
62603534 TGAGCTATTT
Statistics
Matches: 251, Mismatches: 29, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
244 62 0.25
245 6 0.02
248 13 0.05
249 29 0.12
250 1 0.00
251 3 0.01
252 2 0.01
253 5 0.02
254 107 0.43
255 5 0.02
256 13 0.05
257 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (244 bp):
GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
TTCAATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCTTCAGATCACA
CACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
ACCTCCAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAATTAA
Found at i:62604221 original size:16 final size:16
Alignment explanation
Indices: 62604202--62604237 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
62604192 AACCTAACCC
*
62604202 AAAAAAAAA-ACAAAG
1 AAAAAAAAAGAAAAAG
62604217 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
62604233 AAAAA
1 AAAAA
62604238 CCTACCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:62604247 original size:16 final size:17
Alignment explanation
Indices: 62604228--62604268 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 17
62604218 AAAAAAAAGA
62604228 AAAAGAAAAACCT-A-CC
1 AAAA-AAAAACCTAACCC
62604244 -AAAAAAAACCTAACCC
1 AAAAAAAAACCTAACCC
62604260 AAAAAAAAA
1 AAAAAAAAA
62604269 AAAGAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 2 0.09
17 8 0.36
ACGTcount: A:0.71, C:0.22, G:0.02, T:0.05
Consensus pattern (17 bp):
AAAAAAAAACCTAACCC
Found at i:62604250 original size:14 final size:16
Alignment explanation
Indices: 62604233--62604267 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
62604223 AAAGAAAAAG
62604233 AAAAACCT-A-CCAAA
1 AAAAACCTAACCCAAA
62604247 AAAAACCTAACCCAAA
1 AAAAACCTAACCCAAA
62604263 AAAAA
1 AAAAA
62604268 AAAAGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 1 0.05
16 10 0.53
ACGTcount: A:0.69, C:0.26, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAACCTAACCCAAA
Found at i:62604864 original size:2 final size:2
Alignment explanation
Indices: 62604859--62604887 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62604849 TAAATACTAT
62604859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62604888 TTTTTTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62604867 original size:39 final size:39
Alignment explanation
Indices: 62604795--62604869 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
62604785 TTTATATATA
* * *
62604795 TTATGTATATATTTTTTAATGCCATTAGTTATATATTTC
1 TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
*
62604834 TTATGTATATATTCTTAAATACTATTA-TATATATAT
1 TTATGTATATATTCTTAAATACCATTAGT-TATATAT
62604870 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (39 bp):
TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
Done.