Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold130
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: 730134
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:2971 original size:19 final size:19
Alignment explanation
Indices: 2927--2982 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
2917 CTGGCAGTTT
**
2927 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
2947 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
2966 CATGTATGGATACAATG
1 CATGTATCGATACAATG
2983 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:10748 original size:28 final size:28
Alignment explanation
Indices: 10705--11367 Score: 758
Period size: 28 Copynumber: 23.3 Consensus size: 28
10695 TCGTTGAAGT
* *
10705 GCTTTCAAAGGATGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
10733 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
10761 GCTTTGAAAGGGTGCCACTGACTTG-GG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
10788 GCTTTGAAAGGATGCCACTAACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
*
10816 GCTTTGAAAGGGTGCCACTGACTTATGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
** *
10844 GCTTTGAAAGAATACCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
10872 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
10900 GCTTTGAAAGGATGCCACTGACTTATGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
10928 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
** * *
10956 GCTTTGAAAAAAGTGCCATTGACTTGTGA
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
10985 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * *
11013 GCTTTGAAGAGAGTTGCCATTGACTCGTGTAG
1 GCTTTGAA-AG-GGTGCCACTGACT--TGTGG
**
11045 GCTTTGAAAAGAATGCCACTGACTTGTGG
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
11074 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* ** **
11102 GCTTTGGAAAGAGTTGCCACCAACTCATGG
1 GCTTT-GAAAG-GGTGCCACTGACTTGTGG
* *
11132 GCTTTGAAAGGATGCCACTGACTTGTAG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
**
11160 GCTTTGAAAGAATGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * * *
11188 GCTTTGGAAAGAGTTGCCAC-CAATTCATGG
1 GCTTT-GAAAG-GGTGCCACTGACTT-GTGG
*
11218 GCTTTGAAAGGGGGCCA-TCGACTTGTGG
1 GCTTTGAAAGGGTGCCACT-GACTTGTGG
* * **
11246 GCTTTGGAAAGAGTTGCTA-TCGACTAATGG
1 GCTTT-GAAAG-GGTGCCACT-GACTTGTGG
* *
11276 GCTTTGAAAGGATGCCACTAACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
11304 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * * * *
11332 GTTTTGAAAGAGTGCCAATAACTTGTAG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
*
11360 GTTTTGAA
1 GCTTTGAA
11368 GAGATGAACG
Statistics
Matches: 543, Mismatches: 75, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
27 25 0.05
28 360 0.66
29 73 0.13
30 61 0.11
31 10 0.02
32 12 0.02
33 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
GCTTTGAAAGGGTGCCACTGACTTGTGG
Found at i:11189 original size:86 final size:85
Alignment explanation
Indices: 10705--11367 Score: 773
Period size: 86 Copynumber: 7.8 Consensus size: 85
10695 TCGTTGAAGT
*
10705 GCTTTCAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
1 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
* *
10770 G-GGTGCCACTGACTTG-GG
66 GAGTTGCCACTGACTCGTGG
* *
10788 GCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTGAAA
1 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
* * *
10853 GA-ATACCACTGACTTGTGG
66 GAGTTGCCACTGACTCGTGG
* * *
10872 GCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAA
1 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
* *
10937 G-GGTGCCACTGACTTGTGG
66 GAGTTGCCACTGACTCGTGG
** * *
10956 GCTTTGAAAAAAGTGCCATTGACTTGTGAGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
1 GCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
*
11021 GAGAGTTGCCATTGACTCGTGTAG
65 -AGAGTTGCCACTGACTCGTG--G
*
11045 GCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGA
1 GCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-GA
** *
11110 AAGAGTTGCCACCAACTCATGG
64 AAGAGTTGCCACTGACTCGTGG
* **
11132 GCTTTGAAAGGATGCCACTGACTTGTAGGCTTTGAAAGAATGCCACTGACTTGTGGGCTTTGGAA
1 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-GAA
** * *
11197 AGAGTTGCCACCAATTCATGG
65 AGAGTTGCCACTGACTCGTGG
** * * **
11218 GCTTTGAAAGGGGGCCA-TCGACTTGTGGGCTTTGGAAAGAGTTGCTA-TCGACTAATGGGCTTT
1 GCTTTGAAAGGATGCCACT-GACTTGTGGGCTTT-GAAAG-GGTGCCACT-GACTTGTGGGCTTT
* * *
11281 GAAAG-GATGCCACTAACTTGTGG
62 GAAAGAGTTGCCACTGACTCGTGG
* * * * * * *
11304 GCTTTGAAAGGGTGCCACTGACTTGTGGGTTTTGAAAGAGTGCCAATAACTTGTAGGTTTTGAA
1 GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
11368 GAGATGAACG
Statistics
Matches: 509, Mismatches: 55, Indels: 31
0.86 0.09 0.05
Matches are distributed among these distances:
83 75 0.15
84 105 0.21
85 55 0.11
86 147 0.29
87 33 0.06
88 16 0.03
89 70 0.14
90 8 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (85 bp):
GCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
GAGTTGCCACTGACTCGTGG
Found at i:15115 original size:207 final size:208
Alignment explanation
Indices: 14743--15130 Score: 566
Period size: 207 Copynumber: 1.9 Consensus size: 208
14733 ATTAGGTCGC
* * *
14743 ATTATACTCAAGAAACCAATTAAATGGACAAAATACACTAAAATGGAACCATTTTTGGGAATGTG
1 ATTATACTCAAGAAACCAATTAAATGGACAAAATACACTAAAATGGAACCATCTTTAGGAATGGG
* ** * *
14808 TTTCTTTCTTACAAAGAATGACATTTGGACACCCATAGGGATATCCTATTGCTTAAATGGAAACT
66 TTTCTTTCTTACAAAGAAGGACATTTGGACACCCATAGGGATATCAAATTGCTTAAAAGAAAACT
14873 TTGACTAGACTTGAAAATGGATTTTAGGCATGAGATTTTTGCCTGAACCAAGGGAGTATCTAAAA
131 TTGACTAGACTTGAAAATGGATTTTAGGCATGAGATTTTTGCCTGAACCAAGGGAGTATCTAAAA
14938 ACCATGGAAAAAG
196 ACCATGGAAAAAG
* * *
14951 ATTATTCTCAAGAAACCAATTAAATGGACAAAATGCATTAAAATGGAACCATCTTTAGGAATGGG
1 ATTATACTCAAGAAACCAATTAAATGGACAAAATACACTAAAATGGAACCATCTTTAGGAATGGG
* ***
15016 TTT-TTTCTTACAAAGAGGGACATTTGGACATTGATAGGGATATCGAAATTG-TTAAAAGAAAAC
66 TTTCTTTCTTACAAAGAAGGACATTTGGACACCCATAGGGATATC-AAATTGCTTAAAAGAAAAC
* * * *
15079 TTTGATTGGACTTGAAAATGGATTTT-GGATATGAGATTTTTGCTTGAACCAA
130 TTTGACTAGACTTGAAAATGGATTTTAGG-CATGAGATTTTTGCCTGAACCAA
15131 ATGAGCATTT
Statistics
Matches: 159, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
206 2 0.01
207 91 0.57
208 66 0.42
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (208 bp):
ATTATACTCAAGAAACCAATTAAATGGACAAAATACACTAAAATGGAACCATCTTTAGGAATGGG
TTTCTTTCTTACAAAGAAGGACATTTGGACACCCATAGGGATATCAAATTGCTTAAAAGAAAACT
TTGACTAGACTTGAAAATGGATTTTAGGCATGAGATTTTTGCCTGAACCAAGGGAGTATCTAAAA
ACCATGGAAAAAG
Found at i:19699 original size:21 final size:23
Alignment explanation
Indices: 19665--19712 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
19655 CTTTTTATAT
19665 CACT-ATTTTCTTTTTC-TTGTG
1 CACTCATTTTCTTTTTCATTGTG
*
19686 CACTCATTTT-TTTTTCATTTTG
1 CACTCATTTTCTTTTTCATTGTG
19708 CACTC
1 CACTC
19713 TTTAACTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.12, C:0.23, G:0.06, T:0.58
Consensus pattern (23 bp):
CACTCATTTTCTTTTTCATTGTG
Found at i:23102 original size:20 final size:20
Alignment explanation
Indices: 23079--23139 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
23069 AAAATACTTA
23079 AAATATATTTAATAAAATAT
1 AAATATATTTAATAAAATAT
*
23099 AAATATACTTAATAAAATAT
1 AAATATATTTAATAAAATAT
*
23119 AACTATATTTAATAAAATAT
1 AAATATATTTAATAAAATAT
23139 A
1 A
23140 TTTAAAACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTTAATAAAATAT
Found at i:24194 original size:78 final size:77
Alignment explanation
Indices: 23941--24206 Score: 241
Period size: 78 Copynumber: 3.5 Consensus size: 77
23931 TTAGATATCC
* * * * * * * *
23941 TAAGGACTAAGTTTT-AGGTAGTATTACCTAAATACCCCTAACAGACATGTTTCGACACGAAGGT
1 TAAGGACTTAGTTTTAAAGTAGTATTACTTAAATAACCCTAATAGACATGTTTCAACA-TAAAGT
*
24005 TCCTATATGATCT
65 TCCCATATGATCT
** * * * * *
24018 TAAAAACTCAATTTTAAAGTATTATTTCTTAAATAACCCTAATAGACATG-TTCAACATGAAGAT
1 TAAGGACTTAGTTTTAAAGTAGTATTACTTAAATAACCCTAATAGACATGTTTCAACATAAAG-T
* *
24082 T-CCATAAGATCC
65 TCCCATATGATCT
* * * * **
24094 TAAGGACTTAGTCTTAAGGTAGTATTACTTAGATAGCTTTAATAGACATGTTTCAACATAAAAGT
1 TAAGGACTTAGTTTTAAAGTAGTATTACTTAAATAACCCTAATAGACATGTTTCAACAT-AAAGT
*
24159 TCCCACATGATCT
65 TCCCATATGATCT
* *
24172 TAAGGACTTAGTTTTAAAGTAGTATTGCCTAAATA
1 TAAGGACTTAGTTTTAAAGTAGTATTACTTAAATA
24207 CCACTAACGA
Statistics
Matches: 146, Mismatches: 38, Indels: 9
0.76 0.20 0.05
Matches are distributed among these distances:
76 48 0.33
77 29 0.20
78 69 0.47
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (77 bp):
TAAGGACTTAGTTTTAAAGTAGTATTACTTAAATAACCCTAATAGACATGTTTCAACATAAAGTT
CCCATATGATCT
Found at i:24529 original size:58 final size:55
Alignment explanation
Indices: 24390--24530 Score: 169
Period size: 56 Copynumber: 2.5 Consensus size: 55
24380 TGCCTAAAAT
** *
24390 AGACC-TAAAATATATGAAATGCATAAATGGTCCTATATCATGGCAAATTACTAA
1 AGACCTTAAAATCCATGAAATGCATAAATGGTCCGATATCATGGCAAATTACTAA
* * *
24444 AGACCTTAAAATGCATGAAATTTCATAAATTGTCACGA-ATCATGGCAAATTACTATA
1 AGACCTTAAAATCCATGAAA-TGCATAAATGGTC-CGATATCATGGCAAATTACTA-A
24501 ATGACCTTAAAATCCATGAAATGACATAAA
1 A-GACCTTAAAATCCATGAAATG-CATAAA
24531 GGTTTTTAAG
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
54 5 0.07
55 12 0.16
56 28 0.38
57 5 0.07
58 24 0.32
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (55 bp):
AGACCTTAAAATCCATGAAATGCATAAATGGTCCGATATCATGGCAAATTACTAA
Found at i:24604 original size:110 final size:110
Alignment explanation
Indices: 24480--24694 Score: 367
Period size: 110 Copynumber: 2.0 Consensus size: 110
24470 AAATTGTCAC
* * * * *
24480 GAATCATGGCAAATTACTATAATGACCTTAAAATCCATGAAATGACATAAAGGTTTTTAAGTTAT
1 GAATCATGGAAAATTACTAGAATGACCCTAAAATCCATGAAATGACATAAAGATTTCTAAGTTAT
*
24545 GAAAAATGACATTATAGTGCTTGAAATGACATAAAAGTCCTTTTT
66 GAAAAATGACATTATAGTGCATGAAATGACATAAAAGTCCTTTTT
24590 GAATCATGGAAAATTACTAGAATGACCCTAAAATCCATGAAATGACATAAAGATTTCTAAGTTAT
1 GAATCATGGAAAATTACTAGAATGACCCTAAAATCCATGAAATGACATAAAGATTTCTAAGTTAT
*
24655 GAAAAATGTCATTATAGTGCATGAAATGACATAAAAGTCC
66 GAAAAATGACATTATAGTGCATGAAATGACATAAAAGTCC
24695 CTAAGTCATG
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 98 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (110 bp):
GAATCATGGAAAATTACTAGAATGACCCTAAAATCCATGAAATGACATAAAGATTTCTAAGTTAT
GAAAAATGACATTATAGTGCATGAAATGACATAAAAGTCCTTTTT
Found at i:24704 original size:27 final size:26
Alignment explanation
Indices: 24674--24766 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 26
24664 CATTATAGTG
24674 CATGAAATGACATAAAAGTCCCTAAGT
1 CATGAAATGACATAAAA-TCCCTAAGT
* * *
24701 CATGGAAT-AAATAAAATACCACTAAAAT
1 CATGAAATGACATAAAAT-CC-CT-AAGT
24729 GCATGAAATGACATAAAAATCCC-AAGT
1 -CATGAAATGACAT-AAAATCCCTAAGT
*
24756 TATGGAAATGA
1 CAT-GAAATGA
24767 TTGAAATGGC
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
25 1 0.02
26 11 0.21
27 19 0.37
28 3 0.06
29 8 0.15
30 5 0.10
31 5 0.10
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (26 bp):
CATGAAATGACATAAAATCCCTAAGT
Found at i:25367 original size:9 final size:9
Alignment explanation
Indices: 25350--25413 Score: 67
Period size: 9 Copynumber: 7.0 Consensus size: 9
25340 AGAAAACAAC
25350 CTTTTTTTT
1 CTTTTTTTT
25359 CTTTCTTTTT
1 CTTT-TTTTT
25369 CTTTTTTTT
1 CTTTTTTTT
*
25378 CTTTTATTTA
1 CTTTT-TTTT
* *
25388 CCTTTTCTT
1 CTTTTTTTT
*
25397 -TTTTTTTC
1 CTTTTTTTT
25405 CTTTTTTTT
1 CTTTTTTTT
25414 TGCTCTTTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 5 0.11
9 23 0.52
10 16 0.36
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:25393 original size:16 final size:16
Alignment explanation
Indices: 25374--25413 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
25364 TTTTTCTTTT
25374 TTTTCTTTTATTTACC
1 TTTTCTTTTATTTACC
* *
25390 TTTTCTTTTTTTTTCC
1 TTTTCTTTTATTTACC
25406 TTTT-TTTT
1 TTTTCTTTT
25414 TGCTCTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTATTTACC
Found at i:26844 original size:34 final size:35
Alignment explanation
Indices: 26806--26871 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
26796 CCTTACAACA
* * *
26806 CTATCTTTTA-GAAGGCTAAGATAGAACCTCTTCC
1 CTATCTTTTACAAAAGCTAAGATAAAACCTCTTCC
26840 CTATCTTTTACAAAAGCTAAGATAAAACCTCT
1 CTATCTTTTACAAAAGCTAAGATAAAACCTCT
26872 CAATCACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (35 bp):
CTATCTTTTACAAAAGCTAAGATAAAACCTCTTCC
Found at i:27429 original size:13 final size:13
Alignment explanation
Indices: 27411--27468 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
27401 TACAAAGAAC
27411 ATGTATCGATACA
1 ATGTATCGATACA
27424 ATGTATCGATACCAAGCAA
1 ATGTATCGAT----A-C-A
27443 TATGTATCGATACA
1 -ATGTATCGATACA
27457 ATGTATCGATAC
1 ATGTATCGATAC
27469 CAATTAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.58
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 10 0.26
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:27453 original size:33 final size:32
Alignment explanation
Indices: 27393--27489 Score: 140
Period size: 33 Copynumber: 3.0 Consensus size: 32
27383 CATTTTACGG
* *
27393 TGTATCGATACAAAGAACATGTATCGATACAA
1 TGTATCGATACCAAGAATATGTATCGATACAA
27425 TGTATCGATACCAAGCAATATGTATCGATACAA
1 TGTATCGATACCAAG-AATATGTATCGATACAA
* *
27458 TGTATCGATACCAATTAATGTGTATCGATACA
1 TGTATCGATACCAA-GAATATGTATCGATACA
27490 TTCAAGGGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 14 0.24
33 45 0.76
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACCAAGAATATGTATCGATACAA
Found at i:27593 original size:20 final size:22
Alignment explanation
Indices: 27568--27610 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
27558 TACTCTGAAA
27568 TAATTT-TAG-TTGAAAAACAT
1 TAATTTATAGTTTGAAAAACAT
*
27588 TAATTTATTGTTTGAAAAACAT
1 TAATTTATAGTTTGAAAAACAT
27610 T
1 T
27611 TAAACTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 2 0.10
22 12 0.60
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TAATTTATAGTTTGAAAAACAT
Found at i:35660 original size:35 final size:34
Alignment explanation
Indices: 35606--35671 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
35596 CCTTACAACA
* *
35606 CTATCTTTTCGAAGGCTAAGATTGAACCTCTTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTTCC
35640 CTATCTTTTACAAAGGCTAAGATAGAACCTCT
1 CTATCTTTT-CAAAGGCTAAGATAGAACCTCT
35672 CAATCACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (34 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTTCC
Found at i:37210 original size:13 final size:13
Alignment explanation
Indices: 37192--37217 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37182 CAATTTTTTG
37192 TGTATCGATACAT
1 TGTATCGATACAT
37205 TGTATCGATACAT
1 TGTATCGATACAT
37218 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:37229 original size:32 final size:33
Alignment explanation
Indices: 37172--37235 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
37162 TACAAGCCAA
**
37172 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
37205 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
37236 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:38224 original size:37 final size:36
Alignment explanation
Indices: 38165--38388 Score: 147
Period size: 37 Copynumber: 6.2 Consensus size: 36
38155 TTATGAAAAG
* *
38165 TTTGAAAAATTTCCTAATAAAATATACTCATGAGAGGC
1 TTTG-AAATTTTCTTAATAAAATAT-CTCATGAGAGGC
* * * *
38203 TTTGAAATTTTATTGATAAAATAT-TCTTGA-A-GT
1 TTTGAAATTTTCTTAATAAAATATCTCATGAGAGGC
** * * *
38236 TTTGAGAA-TAACTT--TGAAGTATAT-TCAAGAGAGAC
1 TTTGA-AATTTTCTTAAT-AA-AATATCTCATGAGAGGC
*
38271 TTTGGAATTTTCTTAATAAAATATCTTCATGAGAGGC
1 TTTGAAATTTTCTTAATAAAATATC-TCATGAGAGGC
* * * * *
38308 TATGAAACTTTCTTAATAAGATATCCTCATAAGAGGT
1 TTTGAAATTTTCTTAATAAAATAT-CTCATGAGAGGC
* * *
38345 TTTGAAAATTTCTTGATAAAATATCTTCATGAGAGGT
1 TTTGAAATTTTCTTAATAAAATATC-TCATGAGAGGC
38382 TTTGAAA
1 TTTGAAA
38389 GTCATTTTGA
Statistics
Matches: 143, Mismatches: 31, Indels: 25
0.72 0.16 0.13
Matches are distributed among these distances:
31 1 0.01
32 2 0.01
33 17 0.12
34 6 0.04
35 17 0.12
36 3 0.02
37 92 0.64
38 5 0.03
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (36 bp):
TTTGAAATTTTCTTAATAAAATATCTCATGAGAGGC
Found at i:39431 original size:20 final size:20
Alignment explanation
Indices: 39408--39480 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
39398 ACAATTCAAA
39408 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
39428 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
39449 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
39469 GTATCGATACAT
1 GTATCGATACAT
39481 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:39452 original size:21 final size:21
Alignment explanation
Indices: 39426--39501 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
39416 ACATGTTGCA
39426 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
39447 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
39467 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
39488 TTGTATCGATACAT
1 ATGTATCGATACAT
39502 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:39459 original size:41 final size:41
Alignment explanation
Indices: 39408--39501 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
39398 ACAATTCAAA
*
39408 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
39449 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
39490 GTATCGATACAT
1 GTATCGATACAT
39502 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:39558 original size:13 final size:13
Alignment explanation
Indices: 39540--39565 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39530 TACAGCAAGT
39540 ATGTATCGATACA
1 ATGTATCGATACA
39553 ATGTATCGATACA
1 ATGTATCGATACA
39566 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:44931 original size:1 final size:1
Alignment explanation
Indices: 44925--44992 Score: 73
Period size: 1 Copynumber: 68.0 Consensus size: 1
44915 AAATCTTCAC
* * ** * * *
44925 TTTTTTTTTTGTTTTTTTTTTTCTGGTTTTTTTTCTTTTTTTTTTGTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44990 TTT
1 TTT
44993 CCAATTGCCA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:44954 original size:25 final size:24
Alignment explanation
Indices: 44925--44992 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 24
44915 AAATCTTCAC
*
44925 TTTTTTTTTTGTTTTTTTTTTTCTGG
1 TTTTTTTTTT-TTTTTTTTGTT-TGG
*
44951 TTTTTTTTCTTTTTTTTTTGTTTTG
1 TTTTTTTT-TTTTTTTTTTGTTTGG
44976 TTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
44993 CCAATTGCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 9 0.23
25 10 0.26
26 18 0.46
27 2 0.05
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTGTTTGG
Found at i:44963 original size:24 final size:24
Alignment explanation
Indices: 44926--44992 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 24
44916 AATCTTCACT
*
44926 TTTTTTTTTGTTTTTTTTTTTCTGG
1 TTTTTTTTT-TTTTTTTTTGTCTGG
* *
44951 TTTTTTTTCTTTTTTTTTTGTTTTG
1 TTTTTTTT-TTTTTTTTTTGTCTGG
44976 TTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
44993 CCAATTGCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.24
25 28 0.74
26 1 0.03
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (24 bp):
TTTTTTTTTTTTTTTTTTGTCTGG
Found at i:53979 original size:15 final size:15
Alignment explanation
Indices: 53959--53989 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53949 TAAAAATGTC
*
53959 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
53974 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
53989 C
1 C
53990 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:56078 original size:20 final size:21
Alignment explanation
Indices: 55999--56077 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
55989 AATGTCCAAA
*
55999 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
56019 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
56044 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
56064 TTGTATCGATACAT
1 ATGTATCGATACAT
56078 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:56082 original size:13 final size:13
Alignment explanation
Indices: 56064--56102 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
56054 ACATTTTTCT
56064 TTGTATCGATACA
1 TTGTATCGATACA
56077 TTGTATCGATACA
1 TTGTATCGATACA
*
56090 CTGTATCGATACA
1 TTGTATCGATACA
56103 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:58566 original size:20 final size:20
Alignment explanation
Indices: 58543--58615 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
58533 ACAATTCAAA
58543 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
58563 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
58584 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
58604 GTATCGATACAT
1 GTATCGATACAT
58616 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:58587 original size:21 final size:21
Alignment explanation
Indices: 58561--58636 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
58551 ACATGTTGCA
58561 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
58582 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
58602 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
58623 TTGTATCGATACAT
1 ATGTATCGATACAT
58637 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:58594 original size:41 final size:41
Alignment explanation
Indices: 58543--58636 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
58533 ACAATTCAAA
*
58543 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
58584 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
58625 GTATCGATACAT
1 GTATCGATACAT
58637 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:58693 original size:13 final size:13
Alignment explanation
Indices: 58675--58700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58665 TACAGCAAGT
58675 ATGTATCGATACA
1 ATGTATCGATACA
58688 ATGTATCGATACA
1 ATGTATCGATACA
58701 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:59580 original size:25 final size:25
Alignment explanation
Indices: 59532--59583 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
59522 ATACCTAATT
**
59532 AAAGCATTAAAATATTAGTTTTAAA
1 AAAGCATTAAAATATTAGACTTAAA
59557 AAAGCATTAAAATATT-GAACTTAAA
1 AAAGCATTAAAATATTAG-ACTTAAA
59582 AA
1 AA
59584 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAGCATTAAAATATTAGACTTAAA
Found at i:60745 original size:56 final size:57
Alignment explanation
Indices: 60649--60764 Score: 225
Period size: 56 Copynumber: 2.1 Consensus size: 57
60639 GCTAAAAGGG
60649 TTTTAGTAGAGGGCTTCCAAAAGCCAAGAAAGAAAAGAGGATTTGGGCATTTAATGT
1 TTTTAGTAGAGGGCTTCCAAAAGCCAAGAAAGAAAAGAGGATTTGGGCATTTAATGT
60706 TTTTAGTAGAGGGCTTCCAAAAGCCAAG-AAGAAAAGAGGATTTGGGCATTTAATGT
1 TTTTAGTAGAGGGCTTCCAAAAGCCAAGAAAGAAAAGAGGATTTGGGCATTTAATGT
60762 TTT
1 TTT
60765 AGGGTTTTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 31 0.53
57 28 0.47
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.28
Consensus pattern (57 bp):
TTTTAGTAGAGGGCTTCCAAAAGCCAAGAAAGAAAAGAGGATTTGGGCATTTAATGT
Found at i:61598 original size:13 final size:13
Alignment explanation
Indices: 61580--61604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61570 CATTATGCTT
61580 TGTATCGATACAA
1 TGTATCGATACAA
61593 TGTATCGATACA
1 TGTATCGATACA
61605 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:61679 original size:20 final size:19
Alignment explanation
Indices: 61654--61707 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
61644 CTACCACTGT
61654 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGTG-A-A
*
61674 TTGTATTGATACATGTTGAA
1 TTGTATCGATACATG-TGAA
61694 TTGTATCGATACAT
1 TTGTATCGATACAT
61708 TGCTTCCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGTGAA
Found at i:67968 original size:21 final size:22
Alignment explanation
Indices: 67944--67993 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
67934 ATTAAATCTT
* *
67944 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
67965 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
67987 --TCAAAAT
1 CTTCAAAAT
67994 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:72429 original size:48 final size:48
Alignment explanation
Indices: 72343--72438 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
72333 TATTCCTAGA
* * *
72343 TAACCACCGACAATGAAGAGATATATCATGATCGAACCT-TCTTTGCAT
1 TAACCACCAACAATGAAGAGATATATCACGATCAAACCTCT-TTTGCAT
* *
72391 TAACCCCCAACAATGAAGAGATATATCCCGATCAAACCTCTTTTGCAT
1 TAACCACCAACAATGAAGAGATATATCACGATCAAACCTCTTTTGCAT
72439 GCCTTGTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (48 bp):
TAACCACCAACAATGAAGAGATATATCACGATCAAACCTCTTTTGCAT
Found at i:74517 original size:119 final size:122
Alignment explanation
Indices: 74305--74542 Score: 299
Period size: 119 Copynumber: 2.0 Consensus size: 122
74295 CTTGACCTTT
* *
74305 AGAAGGAAAATACCTTAACTTCAATATCGAGGCTCGACCTATTTAAAAGAAATTCAATTTAAAAG
1 AGAAGGAAAATACCTTAACTTCAATATCCAAGCTCGACCTATTTAAAAGAAATT-AATTTAAAAG
*
74370 AAAATATCTCGACTACAATTCTAAGGCTCAACCCATTTTTAAA-AATAAGTTCAAATTA
65 AAAATATCTCAACTACAATTCTAAGGCTCAACCCA-TTTTAAATAATAAGTTCAAATTA
* * *
74428 AGAA-GAAAATACCTTGACTTCAATA-CCAAGCTTGACCTGTTTAAAA-AAATT-ATTTAAAAAG
1 AGAAGGAAAATACCTTAACTTCAATATCCAAGCTCGACCTATTTAAAAGAAATTAATTT-AAAAG
* * * * *
74489 AAAATATCTTAACTTCAATAT-TGAGGCTCAATCCATTTTAAATAATGAGTTCAA
65 AAAATATCTCAACTACAAT-TCTAAGGCTCAACCCATTTTAAATAATAAGTTCAA
74543 CCTAAAAATA
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
118 11 0.11
119 43 0.43
120 6 0.06
121 17 0.17
122 20 0.20
123 4 0.04
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.30
Consensus pattern (122 bp):
AGAAGGAAAATACCTTAACTTCAATATCCAAGCTCGACCTATTTAAAAGAAATTAATTTAAAAGA
AAATATCTCAACTACAATTCTAAGGCTCAACCCATTTTAAATAATAAGTTCAAATTA
Found at i:75263 original size:34 final size:35
Alignment explanation
Indices: 75193--75266 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
75183 TTGGTGTTTG
** *
75193 TGAAAGAATAAGCACAAAGGAATACAAATGAGCTT
1 TGAAAGAATAAAAACAAAGGAATACAAAAGAGCTT
* **
75228 TGAAAGAATAAAAATAAA-GAATACAAAAGTTCTT
1 TGAAAGAATAAAAACAAAGGAATACAAAAGAGCTT
75262 TGAAA
1 TGAAA
75267 TGTAGAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.20
Consensus pattern (35 bp):
TGAAAGAATAAAAACAAAGGAATACAAAAGAGCTT
Found at i:76520 original size:20 final size:20
Alignment explanation
Indices: 76482--76520 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
76472 CAATAAACAA
* *
76482 GCATTCATGTGGAATATATT
1 GCATTCATGTAGAAAATATT
76502 GCATTCATGTAGAAAATAT
1 GCATTCATGTAGAAAATAT
76521 CAAGACAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (20 bp):
GCATTCATGTAGAAAATATT
Found at i:78252 original size:33 final size:33
Alignment explanation
Indices: 78215--78280 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
78205 AATAGTACCT
*
78215 ATATATTGATACGAAGAAC-TCAGTATCGATACA
1 ATATATTGATACGAAGAACGT-AGCATCGATACA
*
78248 ATATATTGATACTAAGAACGTAGCATCGATACA
1 ATATATTGATACGAAGAACGTAGCATCGATACA
78281 TTTGGATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
ATATATTGATACGAAGAACGTAGCATCGATACA
Found at i:81334 original size:3 final size:3
Alignment explanation
Indices: 81316--81353 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
81306 AACCATCAAA
* *
81316 GAT GAT GAA GAA GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
81354 AGTTGACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:81815 original size:15 final size:16
Alignment explanation
Indices: 81775--81816 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
81765 GGAAAAAAAT
*
81775 AAATGAAAAATTGTTGA
1 AAATG-AAAATTCTTGA
81792 AAATG-AAATTCTTGA
1 AAATGAAAATTCTTGA
81807 AAA-GAAAATT
1 AAATGAAAATT
81817 GTCGAGCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 1 0.04
15 17 0.74
17 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (16 bp):
AAATGAAAATTCTTGA
Found at i:86770 original size:133 final size:131
Alignment explanation
Indices: 86521--86855 Score: 451
Period size: 133 Copynumber: 2.5 Consensus size: 131
86511 AACACGGCTG
* *
86521 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAA-AAAATCAGGGTTAGAGTATCCCCGATTG
1 GAGTATCCCCGATTATGAAAAATCGGTGTTCTAAAATAAAATCGGGGTTAGAGTATCCCCGATTG
* * ** *
86585 TG-AAAAAATTGATGCTTTTGAAATAAGGCCGGGGTTAGAGTATCCTTGTGAAAATAACGGGGTT
66 TGAAAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTAGAGTATCCTCGTGAAAATAACGGGGTT
86649 A
131 A
*
86650 GAGTATCCCCGATTATGAAAAATCGGTGTTCTAAAAAATAAAATCGGGGTTAGAGTATCCTCGAT
1 GAGTATCCCCGATTATGAAAAATCGGTGTTCT--AAAATAAAATCGGGGTTAGAGTATCCCCGAT
*
86715 TGTGAAAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTGGAGTAT-CTCCGTGAAAATAACGGG
64 TGTGAAAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTAGAGTATCCT-CGTGAAAATAACGGG
*
86779 GTTG
128 GTTA
* * * * * * * *
86783 GAGTATCCCCGATTGTGAGAAATTGGTGTTATGGAACTAAAATCGGAGTTGGAGTATCCCCGATT
1 GAGTATCCCCGATTATGAAAAATCGGTGTTCT-AAAATAAAATCGGGGTTAGAGTATCCCCGATT
86848 GTGAAAAA
65 GTGAAAAA
86856 TTGATATTTT
Statistics
Matches: 181, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
129 31 0.17
131 4 0.02
132 65 0.36
133 81 0.45
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (131 bp):
GAGTATCCCCGATTATGAAAAATCGGTGTTCTAAAATAAAATCGGGGTTAGAGTATCCCCGATTG
TGAAAAAAATCGATGCTTTAGAAATAAGGCCAAGGTTAGAGTATCCTCGTGAAAATAACGGGGTT
A
Found at i:86846 original size:51 final size:50
Alignment explanation
Indices: 86777--86894 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 50
86767 GAAAATAACG
* * * * *
86777 GGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTATGGAACTAAAATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGATATTATAGAAATAAAATC
*
86827 GGAGTTGGAGTATCCCCGATTGTGAAAAATTGATATTTTAGAAATAAAATC
1 GG-GTTGGAGTATCCCCGATTGTGAAAAATTGATATTATAGAAATAAAATC
*
86878 GGGATTAGAGTATCCCC
1 GGG-TTGGAGTATCCCC
86895 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 3 0.05
51 56 0.95
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTGATATTATAGAAATAAAATC
Found at i:87028 original size:28 final size:28
Alignment explanation
Indices: 86987--87059 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
86977 ATATAAAGCT
*
86987 GGGGTTGGACTATCCCCTCGA-AAATAAC
1 GGGGTTGGAGTATCCCC-CGAGAAATAAC
*
87015 GGGGTTGGAGTAT-CCCCGATGAAATGAC
1 GGGGTTGGAGTATCCCCCGA-GAAATAAC
*
87043 GGGATTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
87060 AATTGTGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 30 0.77
29 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCCGAGAAATAAC
Found at i:99037 original size:1 final size:1
Alignment explanation
Indices: 99031--99086 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
99021 ATTCTCTTCT
* * * * * *
99031 AAAAAAAAAACAAAAACAAAAAAAAAAACAAAAAAAAAAACAAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
99087 GAGAGAAAAG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:99051 original size:12 final size:12
Alignment explanation
Indices: 99031--99075 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
99021 ATTCTCTTCT
*
99031 AAAAA-AAAAAC
1 AAAAACAAAAAA
99042 AAAAACAAAAAA
1 AAAAACAAAAAA
99054 AAAAACAAAAAA
1 AAAAACAAAAAA
99066 AAAAACAAAA
1 AAAAACAAAA
99076 CAAAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 5 0.16
12 27 0.84
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:99054 original size:18 final size:17
Alignment explanation
Indices: 99031--99086 Score: 85
Period size: 18 Copynumber: 3.2 Consensus size: 17
99021 ATTCTCTTCT
99031 AAAAAAAAAACAAAAACA
1 AAAAAAAAAACAAAAA-A
99049 AAAAAAAAAACAAAAAA
1 AAAAAAAAAACAAAAAA
*
99066 AAAAACAAAACAAAGAAA
1 AAAAAAAAAACAAA-AAA
99084 AAA
1 AAA
99087 GAGAGAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 14 0.39
18 22 0.61
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAA
Found at i:100349 original size:60 final size:60
Alignment explanation
Indices: 100182--100411 Score: 251
Period size: 60 Copynumber: 3.9 Consensus size: 60
100172 GAGAATGACG
* * * *
100182 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAATCCTCAAA-AAGCAGG--A-CGT-T
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAA-CAGGACACCTTCT
* * *
100239 --TTTTAAAGCCCACACGAGTTGGTGGCACCCTTCAGTCCTCAAAGACCAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAACAGGACACCTTCT
* * * *
100298 TCTTTTAAAGCCCACATAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAGGACACCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAACAGGACACCTTCT
*
100358 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTTAGTCCTCAAAGAGCAGGAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC--AGTCCTCAAAGAACAGGAC
100412 GCTCTCTCAT
Statistics
Matches: 146, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
55 41 0.28
56 2 0.01
57 1 0.01
58 2 0.01
59 5 0.03
60 54 0.37
61 41 0.28
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (60 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAACAGGACACCTTCT
Found at i:100551 original size:215 final size:214
Alignment explanation
Indices: 100239--100628 Score: 543
Period size: 215 Copynumber: 1.8 Consensus size: 214
100229 GCAGGACGTT
* * * *
100239 TTTTAAAGCCCACACGAGTTGGTGGCACCCTTCAGTCCTCAAAGACCAGGACACCTTTTTCTTTT
1 TTTTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAGACCAGGACACCTTCTCCTTTT
*
100304 AAAGCCCACATAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAGGACACCTTCTCCTTTT-AAAG
66 AAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAGGA-ACCTT-TCCTTTTCAAAG
*
100368 CCCACACAAGTTGGTGGCA-CTTCTTAGTCCTCAAAGAGCAGGACGCTCTCTCATTTCGCCTTTT
129 CCCACACAAGTTGGTGGCACCTT-TCAGTCCTCAAAGAGCAGGACGCTCTCTCATTTCGCCTTTT
100432 TGTCCTCAAAGAGCGGGATGCC
193 TGTCCTCAAAGAGCGGGATGCC
* * ** *
100454 TTTTAAAGCCCAGACAAGCTGGTGGCA-CCTTCAGTCTTCAAAGAGTAGGACGCCTTCTCCTTTT
1 TTTTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAGACCAGGACACCTTCTCCTTTT
* * * * ** *
100518 AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAG
66 AAAGCCCACACAAGCTAGTGGCAC-CTTCAGTCCTCAAAGAACAGGAACCTTTCCTTTT-CAAAG
*
100583 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGGGCAGGACGC
129 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC
100629 CTTTTATTTT
Statistics
Matches: 152, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
213 6 0.04
214 55 0.36
215 88 0.58
216 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (214 bp):
TTTTAAAGCCCACACAAGCTGGTGGCACCCTTCAGTCCTCAAAGACCAGGACACCTTCTCCTTTT
AAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAGGAACCTTTCCTTTTCAAAGCC
CACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCTCTCTCATTTCGCCTTTTTGT
CCTCAAAGAGCGGGATGCC
Found at i:100583 original size:61 final size:61
Alignment explanation
Indices: 100454--100809 Score: 438
Period size: 61 Copynumber: 5.9 Consensus size: 61
100444 GCGGGATGCC
* * * * * *
100454 TTTT-AAAGCCCAGACAAGCTGGTGGCAC-CTTCAGTCTTCAAAGAGTAGGACGCCTTCTCC
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTT-TCT
*
100514 TTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATG-CTTTCT
1 TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
* *
100573 TTTTGCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGGGCAGGACGCCTTT-T
1 TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
** * * *
100634 ATTTTCAAAGCCCACATGAGTTGGTGGCACTGTTCAGTCCTCAAAGAGCAAGATG-CTTTCT
1 -TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
* * * * *
100695 TTTTGCAAAGCCCATACGAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCAGGACGCCTTT-T
1 TTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
*
100756 CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
1 -TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
100810 ACACTTCCTT
Statistics
Matches: 258, Mismatches: 29, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
59 6 0.02
60 37 0.14
61 199 0.77
62 16 0.06
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (61 bp):
TTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCT
Found at i:100634 original size:270 final size:266
Alignment explanation
Indices: 100088--100683 Score: 657
Period size: 270 Copynumber: 2.2 Consensus size: 266
100078 GATGCATGTT
* *
100088 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-TAGTCTTCAAAGAGCAGGACGCTCTCTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTTAGTCCTCAAAGAGCAGGACGCTCTCTCAT
* * *
100152 TTCACCCTTTAGTCCTCAAAGAGAATGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
65 TTCACCCTTTAGTCCTCAAAGAGAAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACTCTTC
*
100217 AATCCTCAAAAAGCAGGACGTTTTTTAAAGCCCACACGAGTTGGTGGCACCCTTCAGTCCTCAAA
130 AATCCTCAAAAAGCAGGACGTTTTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAA
* *
100282 GACCAGGACACCTTTTTCTTTTAAAGCCCACATAAGCTAGTGGCACCTTCAGTCCTCAAAGAACA
195 GACCAGGACACCTTTTTCTTTCAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAACA
*
100347 GGACACCTTCT
260 GGA-A-C--CG
100358 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGACGCTCTCTCATT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGACGCTCTCTCATT
* * * ** * * *
100423 TCGCCTTTTTGTCCTCAAAGAGCGGGATGCCTTTTAAAGCCCAGACAAGCTGGTGGCAC-CTTCA
66 TCACCCTTTAGTCCTCAAAGAGAAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACTCTTCA
* * * * **
100487 GTCTTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCC
131 ATCCTCAAAAAGCAGGACG---T-T--TTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCC
* ** * *
100552 TCAAAGAGCAGGA-TGCTTTCTT-TTTGCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
190 TCAAAGACCAGGACACCTTT-TTCTTT-CAAAGCCCACACAAGCTAGTGGCACC-TTCAGTCCTC
**
100615 AAAGGGCAGG-A-CG
252 AAAGAACAGGAACCG
** *
100628 CCTTTTATTTTCAAAGCCCACATGAGTTGGTGGCACTGT-TCAGTCCTCAAAGAGCA
1 CC-----TTTT-AAAGCCCACACAAGTTGGTGGCACT-TCTTAGTCCTCAAAGAGCA
100684 AGATGCTTTC
Statistics
Matches: 276, Mismatches: 33, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
269 23 0.08
270 110 0.40
272 1 0.00
273 1 0.00
274 8 0.03
275 75 0.27
276 57 0.21
277 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (266 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGACGCTCTCTCATT
TCACCCTTTAGTCCTCAAAGAGAAGGACGCCTTTCAAAGCCCACACAAGCTGGTGGCACTCTTCA
ATCCTCAAAAAGCAGGACGTTTTTTAAAGCCCACACAAGTTGGTGGCACCCTTCAGTCCTCAAAG
ACCAGGACACCTTTTTCTTTCAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAACAG
GAACCG
Found at i:100644 original size:122 final size:122
Alignment explanation
Indices: 100458--100808 Score: 553
Period size: 122 Copynumber: 2.9 Consensus size: 122
100448 GATGCCTTTT
* * * * * *
100458 AAAGCCCAGACAAGCTGGTGGCACC-TTCAGTCTTCAAAGAGTAGGACGCCTTCTCCTTTT-AAA
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGGGCAGGACGCCTT-TTCTTTTCAAA
*
100521 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGC
65 GCCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGC
*
100579 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGGGCAGGACGCCTTTTATTTTCAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGGGCAGGACGCCTTTTCTTTTCAAAG
* * *
100644 CCCACATGAGTTGGTGGCACTGTTCAGTCCTCAAAGAGCAAGATGCTTTCTTTTTGC
66 CCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGC
* * *
100701 AAAGCCCATACGAGTTGGTGGCACCTTCCAGTCCTCAAAGGGCAGGACGCCTTTTCTTTTCAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGGGCAGGACGCCTTTTCTTTTCAAAG
100766 CCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
66 CCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
100809 CACACTTCCT
Statistics
Matches: 210, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
121 28 0.13
122 182 0.87
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (122 bp):
AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGGGCAGGACGCCTTTTCTTTTCAAAG
CCCACACGAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGC
Found at i:101416 original size:51 final size:51
Alignment explanation
Indices: 101361--101527 Score: 176
Period size: 51 Copynumber: 3.3 Consensus size: 51
101351 CTACCGCAAC
* *
101361 CGGGGATACTCCAATCCCGGTTTCATCTCCACAATATCAATTTTTTTTAAT
1 CGGGGATACTCCAATCCCGGTTTCATCTCCACAACATCAATTTTTCTTAAT
* * * * * * * ** ** *
101412 CGGGGATACTCCAA-CTCTGATTTTATTTCTA-AAGCATCGATCTACCACAAC
1 CGGGGATACTCCAATC-CCGGTTTCATCTCCACAA-CATCAATTTTTCTTAAT
101463 CGGGGATACTCCAATCCCGGTTTCATCTCCACAACATCAATTTTTCTTAAT
1 CGGGGATACTCCAATCCCGGTTTCATCTCCACAACATCAATTTTTCTTAAT
101514 CGGGGATACTCCAA
1 CGGGGATACTCCAA
101528 CTCTGATTTT
Statistics
Matches: 86, Mismatches: 26, Indels: 8
0.72 0.22 0.07
Matches are distributed among these distances:
50 3 0.03
51 80 0.93
52 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.32
Consensus pattern (51 bp):
CGGGGATACTCCAATCCCGGTTTCATCTCCACAACATCAATTTTTCTTAAT
Found at i:101555 original size:51 final size:51
Alignment explanation
Indices: 101409--101578 Score: 146
Period size: 51 Copynumber: 3.3 Consensus size: 51
101399 AATTTTTTTT
* * * **
101409 AATCGGGGATACTCCAACTCTGATTTTA-TTTCTAAAGCATCGATCTACCAC
1 AATCGGGGATACTCCAACTCTGATTTTATTTTC-AAAACATCAATTTTTCAC
* * * * * * * **
101460 AACCGGGGATACTCCAA-TCCCGGTTTCATCTCCACAACATCAATTTTTCTT
1 AATCGGGGATACTCCAACT-CTGATTTTATTTTCAAAACATCAATTTTTCAC
* * *
101511 AATCGGGGATACTCCAACTCTGATTTTATTTTCAAAATACCAATTTCTCAC
1 AATCGGGGATACTCCAACTCTGATTTTATTTTCAAAACATCAATTTTTCAC
*
101562 AATTGGGGATACTCCAA
1 AATCGGGGATACTCCAA
101579 TCCCGTCATT
Statistics
Matches: 89, Mismatches: 27, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
50 1 0.01
51 85 0.96
52 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCTGATTTTATTTTCAAAACATCAATTTTTCAC
Found at i:101583 original size:102 final size:102
Alignment explanation
Indices: 101295--101541 Score: 440
Period size: 102 Copynumber: 2.4 Consensus size: 102
101285 GTTAAATTTC
** * *
101295 TCAATTTTTCTTAATCGAAGATACTCCAACTCCGATTTTATTTCTAAAGCATCGATCTACCGCAA
1 TCAATTTTTCTTAATCGGGGATACTCCAACTCTGATTTTATTTCTAAAGCATCGATCTACCACAA
*
101360 CCGGGGATACTCCAATCCCGGTTTCATCTCCACAATA
66 CCGGGGATACTCCAATCCCGGTTTCATCTCCACAACA
*
101397 TCAATTTTTTTTAATCGGGGATACTCCAACTCTGATTTTATTTCTAAAGCATCGATCTACCACAA
1 TCAATTTTTCTTAATCGGGGATACTCCAACTCTGATTTTATTTCTAAAGCATCGATCTACCACAA
101462 CCGGGGATACTCCAATCCCGGTTTCATCTCCACAACA
66 CCGGGGATACTCCAATCCCGGTTTCATCTCCACAACA
101499 TCAATTTTTCTTAATCGGGGATACTCCAACTCTGATTTTATTT
1 TCAATTTTTCTTAATCGGGGATACTCCAACTCTGATTTTATTT
101542 TCAAAATACC
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 138 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (102 bp):
TCAATTTTTCTTAATCGGGGATACTCCAACTCTGATTTTATTTCTAAAGCATCGATCTACCACAA
CCGGGGATACTCCAATCCCGGTTTCATCTCCACAACA
Found at i:101598 original size:28 final size:27
Alignment explanation
Indices: 101566--101639 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
101556 TCTCACAATT
*
101566 GGGGATACTCCAATCCCGTCA-TTTCA
1 GGGGATACTCCAACCCCGTCATTTTCA
*
101592 TCGGGGATACTCCAACCCCGTTATTTTCGA
1 --GGGGATACTCCAACCCCGTCATTTTC-A
101622 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
101640 GCTTTATATC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 37 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTCATTTTCA
Found at i:101775 original size:108 final size:108
Alignment explanation
Indices: 101515--101794 Score: 298
Period size: 108 Copynumber: 2.6 Consensus size: 108
101505 TTTCTTAATC
* ** * *
101515 GGGGATACTCCAACTCTGATTTTATTT-TCAAAATACCAATTTCTCACAAT-TGGGGATACTCCA
1 GGGGATACTCCAACCCTGATTTTATTTCT-AAAATATTAATTTTTCACAATCGGGGGATACTCCA
* * *
101578 ATCCCGTCATTTCATCGGGGATACTCCAACCCCGTTATTTTCGA
65 ACCCCGTCATTTCATCAGGGATACTCCAACCCCGTTATTTCCGA
* ** * * * * * * **
101622 GGGGATACTCCAACCCCGGCTTTATATCCAAAATATTTATCTTTCATAATCGGGGGGTACTTTAA
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAATATTAATTTTTCACAATCGGGGGATACTCCAA
* * *
101687 CCCCGTTATGTT-ATCAGGGATACTCCCATCCCGTTATTTCCGA
66 CCCCGTCAT-TTCATCAGGGATACTCCAACCCCGTTATTTCCGA
**
101730 GGGGATACTCCAACCCTGATTTTATTTCTAAAATATTAATTTTTCACAATC-AAGGATACTCCAA
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAATATTAATTTTTCACAATCGGGGGATACTCCAA
101794 C
66 C
101795 TCCGATTTAG
Statistics
Matches: 135, Mismatches: 35, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
107 46 0.34
108 87 0.64
109 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (108 bp):
GGGGATACTCCAACCCTGATTTTATTTCTAAAATATTAATTTTTCACAATCGGGGGATACTCCAA
CCCCGTCATTTCATCAGGGATACTCCAACCCCGTTATTTCCGA
Found at i:103020 original size:132 final size:129
Alignment explanation
Indices: 102791--103196 Score: 516
Period size: 132 Copynumber: 3.1 Consensus size: 129
102781 ACAACAGGGC
* *
102791 TGGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAA-AAAATTGGGATTAGAGTATCCCCGAT
1 TGGAGTATCCCCGATTATTGAAAATCGGTGTTCTAAAATAAAATCGGG-TTAGAGTATCCCCGAT
102855 TGTGAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGT
65 TGTGAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGT
* * *
102920 TAGAGTATCCCCGATTATTGAAAATCGATGTTCTAAAAAATAAAATCAGGGTTAAAGTATCCCCG
1 TGGAGTATCCCCGATTATTGAAAATCGGTGTTCT--AAAATAAAATC-GGGTTAGAGTATCCCCG
* *
102985 ATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCCCTGTGAAAATAACGGG
63 ATTGTGAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGG
103050 GT
128 GT
* * * * * *
103052 TGGAGTATCCCCGATT-GTGAGAAATTGGTGTTTTGGAACTAAAATCGGAGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTATTGA-AAATCGGTGTTCT-AAAATAAAATCGG-GTTAGAGTATCCCCG
* * * **
103116 ATTATGAAAAATTGGTAT--TTTAGAAATAAAATCGGGGTTGGAGTATCCCC-TCGAAAATAACG
63 ATTGTGAAAAAATCG-ATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGT-GAAAATAACG
*
103178 GGAT
126 GGGT
*
103182 GGGAGTATCCCCGAT
1 TGGAGTATCCCCGAT
103197 GACATAACGG
Statistics
Matches: 243, Mismatches: 26, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
129 32 0.13
130 57 0.23
131 41 0.17
132 110 0.45
133 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (129 bp):
TGGAGTATCCCCGATTATTGAAAATCGGTGTTCTAAAATAAAATCGGGTTAGAGTATCCCCGATT
GTGAAAAAATCGATGCTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGTGAAAATAACGGGGT
Found at i:103117 original size:51 final size:51
Alignment explanation
Indices: 103050--103165 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
103040 AAATAACGGG
* * * * *
103050 GTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAACTAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAAATCGGA
*
103101 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAAATCGGA
103152 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
103166 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTAGAAATAAAATCGGA
Found at i:105788 original size:20 final size:20
Alignment explanation
Indices: 105763--105819 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
105753 AAAATGCCTG
*
105763 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
*
105783 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
105803 AATGTATCGATACAATG
1 AATGTATCGATACAATG
105820 CATTGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 1 0.03
20 33 0.97
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:105839 original size:33 final size:33
Alignment explanation
Indices: 105791--105854 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
105781 AAAATGTATC
105791 GATACAATGAGCAATGTATCGATACAATGCATT
1 GATACAATGAGCAATGTATCGATACAATGCATT
* *
105824 GATATAATGATCAATGTATCGATACAATGCA
1 GATACAATGAGCAATGTATCGATACAATGCA
105855 AAATGTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (33 bp):
GATACAATGAGCAATGTATCGATACAATGCATT
Found at i:105847 original size:20 final size:19
Alignment explanation
Indices: 105795--105869 Score: 63
Period size: 20 Copynumber: 4.1 Consensus size: 19
105785 TGTATCGATA
105795 CAATGAGCAATGTATCGATA
1 CAATGA-CAATGTATCGATA
105815 CAATG-C-A--T-T-GATA
1 CAATGACAATGTATCGATA
*
105828 TAATGATCAATGTATCGATA
1 CAATGA-CAATGTATCGATA
*
105848 CAATGCAAAATGTATCGATA
1 CAATG-ACAATGTATCGATA
105868 CA
1 CA
105870 TCTGGGTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
13 8 0.18
14 1 0.02
15 2 0.05
16 1 0.02
17 1 0.02
18 2 0.05
19 1 0.02
20 27 0.61
21 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (19 bp):
CAATGACAATGTATCGATA
Found at i:105926 original size:13 final size:13
Alignment explanation
Indices: 105908--105933 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
105898 AAAAAGATCG
105908 ATGTATCGATACA
1 ATGTATCGATACA
105921 ATGTATCGATACA
1 ATGTATCGATACA
105934 TTTCCTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:109852 original size:32 final size:32
Alignment explanation
Indices: 109811--110405 Score: 618
Period size: 32 Copynumber: 18.6 Consensus size: 32
109801 TAGTGCTAAG
109811 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
109843 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
109875 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
*
109907 GGTTGCCACCGACTTGTGTGGGCTTTAGAA-AG
1 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* *
109939 GGTTGCCACCAACTTGTGTGGGCTTTAAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
*
109971 GGTTGCCACCGACTTGTGTGGGCTTTAGAA-AG
1 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* *
110003 GGTTGCCACCAACTTGTGTGGGCTTTAAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
* * * *
110035 GGTTGCCACCGACTTATGTAGACTTTAGAA-AG
1 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* * * *
110067 GGTCGCCACCAACTTGTGTGGGCTTTAAAAAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
* * *
110099 GGTTGCCACCGATTTATGTGGGCTTTAGAA-AG
1 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* * *
110131 GGTCGCCACCAACTTATGTGGGCTTT--AGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
* * *
110161 TGAGTTGACACCGATTTGTGTGGGCTTTAGAA-AG
1 -G-GTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* *
110195 GGTCGCCACCAACTTGTGTGGGCTTTGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
* * *
110227 GGTTGCCACCAACTTGTGTTGGCTTTAGAA-AG
1 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* * * * *
110259 GGTCGCCAACAACTTATGTGGGCTTTAGAA-AG
1 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* * * *
110291 GGTCGCCACCAACTTATGTGGGCTTTAGAA-AG
1 GGTTGCCACCGACTTGTGTGGGCTTT-GAAGAA
* * * *
110323 GGTCGCCACCAACTTTTGTGGGTTTTGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
* * *
110355 GGTCT-CTACCGACTTGTATGGGTTTTGAAGAA
1 GGT-TGCCACCGACTTGTGTGGGCTTTGAAGAA
110387 GGTTGCCACCGACTTGTGT
1 GGTTGCCACCGACTTGTGT
110406 AGGTTTTTGA
Statistics
Matches: 483, Mismatches: 62, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.00
30 1 0.00
31 14 0.03
32 452 0.94
33 13 0.03
34 1 0.00
35 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (32 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGAAGAA
Found at i:109912 original size:64 final size:64
Alignment explanation
Indices: 109808--110405 Score: 785
Period size: 64 Copynumber: 9.3 Consensus size: 64
109798 TCTTAGTGCT
* *
109808 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTT-GA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * *
109871 AGAAGGTTGCCACCGACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
1 A-AGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* *
109936 AAGGGTTGCCACCAACTTGTGTGGGCTTTAAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * * * *
110000 AAGGGTTGCCACCAACTTGTGTGGGCTTTAAAGAAGGTTGCCACCGACTTATGTAGACTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * * *
110064 AAGGGTCGCCACCAACTTGTGTGGGCTTTAAAAAAGGTTGCCACCGATTTATGTGGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * *
110128 AAGGGTCGCCACCAACTTATGTGGGCTTT--AGAATGAGTTGACACCGATTTGTGTGGGCTTTAG
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAA-G-GTTGCCACCGACTTGTGTGGGCTTTAG
110191 A
64 A
* *
110192 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAACTTGTGTTGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * * * * *
110256 AAGGGTCGCCAACAACTTATGTGGGCTTTAGAA-AGGGTCGCCACCAACTTATGTGGGCTTTAGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTT-GAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
* * * * *
110320 AAGGGTCGCCACCAACTTTTGTGGGTTTTGAAGAAGGTCT-CTACCGACTTGTATGGG-TTTTGA
1 AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGT-TGCCACCGACTTGTGTGGGCTTTAGA
* * *
110383 AGAAGGTTGCCACCGACTTGTGT
1 A-AGGGTCGCCACCAACTTGTGT
110406 AGGTTTTTGA
Statistics
Matches: 484, Mismatches: 41, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
62 3 0.01
63 11 0.02
64 459 0.95
65 7 0.01
66 4 0.01
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (64 bp):
AAGGGTCGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGA
Found at i:110885 original size:27 final size:27
Alignment explanation
Indices: 110845--110902 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
110835 CTTTGAAAAG
* * *
110845 AAAAAGGTGTCACAGAGTTGTGGGCTT
1 AAAAAGATGCCACAGAGTTGTGGACTT
110872 AAAAAGATGCCACAGAGTTGTGGACTT
1 AAAAAGATGCCACAGAGTTGTGGACTT
110899 AAAA
1 AAAA
110903 GGGGAAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (27 bp):
AAAAAGATGCCACAGAGTTGTGGACTT
Found at i:110898 original size:129 final size:125
Alignment explanation
Indices: 110593--110992 Score: 344
Period size: 127 Copynumber: 3.2 Consensus size: 125
110583 TATATACAGC
* * * * *
110593 AAGTGCCACTA-A-TTGTGGACTTCAAAAAGATGCCACTGACTTGTGAACTTCGAAGAGGGAAAA
1 AAGTGCCAC-AGAGTTGTGGGCTT-AAAAAGATGCCACAGAATTGTGGACTT--AAAAGGGAAAA
* *
110656 GGTGCCACGATGTTGTGGACTTAAAAGAAAAAGGATGCTACGGAGTTATGGACTTAAAAGGAAA
62 GGTGCCACGAAGTTATGGACTTAAAAGAAAAAGGATGCTACGGAGTTATGGACTTAAAAGGAAA
** * * * * * * * *
110720 AAGTGCCACAGAGTTGCAGGCTTAAAAGGGTTCAACACAACTGTAGACTTAAAAGGTGAAAGGGT
1 AAGTGCCACAGAGTTGTGGGCTTAAAAAGATGCCACAGAATTGTGGACTTAAAAGG-GAAAAGGT
** * * * * *
110785 GCCACGAAGTTATGGACTTAAAAGGTGAATGGGTGCTAGGGAGTTGTGGGCTTTGAAAA-GAAA
65 GCCACGAAGTTATGGACTTAAAA-GAAAAAGGATGCTACGGAGTTATGGAC-TT-AAAAGGAAA
* * * *
110848 AAGGTGTCACAGAGTTGTGGGCTTAAAAAGATGCCACAGAGTTGTGGACTTAAAAGGG-GAAGAT
1 AA-GTGCCACAGAGTTGTGGGCTTAAAAAGATGCCACAGAATTGTGGACTTAAAAGGGAAAAGGT
* * * * *
110912 GCCA-TAGGGTTATGGACTTAAAAGGAAAA-GACGCCACGGAGTTATGGACTTAAAAGGTAAA
65 GCCACGA-AGTTATGGACTTAAAAGAAAAAGGATGCTACGGAGTTATGGACTTAAAAGG-AAA
*
110973 AGGGTGCCACAGAGTTGTGG
1 A-AGTGCCACAGAGTTGTGG
110993 CTTTGGAAAA
Statistics
Matches: 211, Mismatches: 51, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
123 4 0.02
124 3 0.01
125 39 0.18
126 33 0.16
127 69 0.33
128 16 0.08
129 47 0.22
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.21
Consensus pattern (125 bp):
AAGTGCCACAGAGTTGTGGGCTTAAAAAGATGCCACAGAATTGTGGACTTAAAAGGGAAAAGGTG
CCACGAAGTTATGGACTTAAAAGAAAAAGGATGCTACGGAGTTATGGACTTAAAAGGAAA
Found at i:110988 original size:34 final size:32
Alignment explanation
Indices: 110650--111073 Score: 178
Period size: 32 Copynumber: 13.2 Consensus size: 32
110640 CTTCGAAGAG
*
110650 GGAAAAGGTGCCAC-GATGTTGTGGACTTAAAA
1 GGAAAAGGTGCCACAGA-GTTATGGACTTAAAA
* * *
110682 GAAAAAGGATGCTACGGAGTTATGGACTTAAAA
1 GGAAAAGG-TGCCACAGAGTTATGGACTTAAAA
*
110715 GGAAAAAGTGCCACAGAGTTGCA-GG-CTTAAAA
1 GGAAAAGGTGCCACAGAGTT--ATGGACTTAAAA
* * * ** * *
110747 -G----GGTTCAACACAACTGTAGACTTAAAA
1 GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
*
110774 GGTGAAAGGGTGCCAC-GAAGTTATGGACTTAAAA
1 -G-GAAAAGGTGCCACAG-AGTTATGGACTTAAAA
** * ** * *
110808 GGTGAATGGGTGCTAGGGAGTTGTGGGCTTTGAAAA
1 -G-GAAAAGGTGCCACAGAGTTATGGAC-TT-AAAA
* * * *
110844 GAAAAAGGTGTCACAGAGTTGTGGGCTT---A
1 GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
* *
110873 --AAAAGATGCCACAGAGTTGTGGACTTAAAA
1 GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
** * * *
110903 GGGGAAGATGCCATAGGGTTATGGACTTAAAA
1 GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
** *
110935 GGAAAAGACGCCACGGAGTTATGGACTTAAAA
1 GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
*
110967 GGTAAAAGGGTGCCACAGAGTTGTGG-CTTTGGAAAA
1 GG-AAAA-GGTGCCACAGAGTTATGGAC-TT--AAAA
* ** *
111003 -AAAAAGGTGCCATGGAGTTGTGGACTTAAAA
1 GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
** * ** * *
111034 GGGGAAGATGCCATGGTGTTGTGGACTTAAAA
1 GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
111066 GGAAAAGG
1 GGAAAAGG
111074 ATTCCACTAA
Statistics
Matches: 300, Mismatches: 63, Indels: 58
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.00
27 38 0.13
29 1 0.00
30 2 0.01
31 5 0.02
32 108 0.36
33 52 0.17
34 81 0.27
35 4 0.01
36 8 0.03
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (32 bp):
GGAAAAGGTGCCACAGAGTTATGGACTTAAAA
Found at i:111113 original size:30 final size:29
Alignment explanation
Indices: 111066--111124 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
111056 GGACTTAAAA
*
111066 GGAAAAGGATTCCACTAAGTCGTGGACTT
1 GGAAAAGGATGCCACTAAGTCGTGGACTT
111095 GGAAAAGAGATGCCACTAAGTCGTGGACTT
1 GGAAAAG-GATGCCACTAAGTCGTGGACTT
111125 TTGGAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (29 bp):
GGAAAAGGATGCCACTAAGTCGTGGACTT
Found at i:116504 original size:13 final size:13
Alignment explanation
Indices: 116486--116511 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116476 CAATTTTTTG
116486 TGTATCGATACAT
1 TGTATCGATACAT
116499 TGTATCGATACAT
1 TGTATCGATACAT
116512 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:118888 original size:21 final size:21
Alignment explanation
Indices: 118864--118910 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
118854 TTTGATGCTG
118864 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
118884 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
118905 ATTTTG
1 ATTTTG
118911 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:119049 original size:13 final size:13
Alignment explanation
Indices: 119031--119069 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
119021 ATAATCACCC
*
119031 TGTATCGATACAG
1 TGTATCGATACAA
119044 TGTATCGATACAA
1 TGTATCGATACAA
119057 TGTATCGATACAA
1 TGTATCGATACAA
119070 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:119080 original size:20 final size:20
Alignment explanation
Indices: 119055--119133 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
119045 GTATCGATAC
119055 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
119075 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
119100 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
119120 CATGTATCGATACA
1 AATGTATCGATACA
119134 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:121168 original size:15 final size:15
Alignment explanation
Indices: 121148--121178 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
121138 ATTTCGTTTG
*
121148 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
121163 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
121178 G
1 G
121179 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:123012 original size:21 final size:21
Alignment explanation
Indices: 122983--123027 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
122973 AAGTTTTCAT
*
122983 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
123003 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
123025 TTT
1 TTT
123028 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:125263 original size:13 final size:13
Alignment explanation
Indices: 125245--125270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
125235 CAATTTTTTG
125245 TGTATCGATACAT
1 TGTATCGATACAT
125258 TGTATCGATACAT
1 TGTATCGATACAT
125271 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:127244 original size:27 final size:27
Alignment explanation
Indices: 127169--127234 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
127159 AAAAATGAAG
* *
127169 TTGGAGTATCCCCTCGAAATAATGGGA
1 TTGGAGTATCCCCTTGGAATAATGGGA
*
127196 TTGGAGTATCCCCTTGGAATAATGGGG
1 TTGGAGTATCCCCTTGGAATAATGGGA
127223 TTGGAGTATCCC
1 TTGGAGTATCCC
127235 TAATGAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (27 bp):
TTGGAGTATCCCCTTGGAATAATGGGA
Found at i:130806 original size:13 final size:13
Alignment explanation
Indices: 130788--130812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
130778 ACAAAACTTA
130788 TGTATCGATACAC
1 TGTATCGATACAC
130801 TGTATCGATACA
1 TGTATCGATACA
130813 AATTGTAAAA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:133568 original size:20 final size:22
Alignment explanation
Indices: 133530--133569 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
133520 TTTGGAAACA
*
133530 AAAAAGAGGAAAGATATTTTTG
1 AAAAAGAGGAAAGAAATTTTTG
133552 AAAAAG-GG-AAGAAATTTT
1 AAAAAGAGGAAAGAAATTTT
133570 ATTAAGTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.25
Consensus pattern (22 bp):
AAAAAGAGGAAAGAAATTTTTG
Found at i:138687 original size:3 final size:3
Alignment explanation
Indices: 138679--138713 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
138669 CAAGTCAACT
*
138679 TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
138714 TTTGATGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:138714 original size:9 final size:9
Alignment explanation
Indices: 138677--138715 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
138667 TCCAAGTCAA
138677 CTTCATCAT
1 CTTCATCAT
*
138686 CATCATCAT
1 CTTCATCAT
*
138695 CATCATCAT
1 CTTCATCAT
138704 CTTCATCAT
1 CTTCATCAT
138713 CTT
1 CTT
138716 TGATGGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (9 bp):
CTTCATCAT
Found at i:139552 original size:20 final size:20
Alignment explanation
Indices: 139527--139600 Score: 114
Period size: 20 Copynumber: 3.7 Consensus size: 20
139517 GTTAGAAGCA
*
139527 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
139547 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
139567 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
*
139587 ATGTATCAATACAA
1 ATGTATCGATACAA
139601 ATAGTGGTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 50 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:140572 original size:13 final size:13
Alignment explanation
Indices: 140554--140579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
140544 CATTTTGGGA
140554 TGTATCGATACAT
1 TGTATCGATACAT
140567 TGTATCGATACAT
1 TGTATCGATACAT
140580 CTTATGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:140576 original size:33 final size:32
Alignment explanation
Indices: 140534--140597 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
140524 TACAAGCCAA
* *
140534 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTAGG-TGTATCGATACAT
*
140567 TGTATCGATACATCTTATGTGTATCGATACA
1 TGTATCGATACATCTTAGGTGTATCGATACA
140598 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTAGGTGTATCGATACAT
Found at i:140697 original size:13 final size:13
Alignment explanation
Indices: 140679--140703 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140669 ACATTTGGTC
140679 ATGTATCGATACA
1 ATGTATCGATACA
140692 ATGTATCGATAC
1 ATGTATCGATAC
140704 TGTGCAATAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:142727 original size:21 final size:21
Alignment explanation
Indices: 142696--142740 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
142686 GCTGTGAGTG
* *
142696 TGGGGGTTGCCCGGTTGCGACC
1 TGGGGGTTG-CCGATCGCGACC
142718 TGGGGG-TGCCGATCGCGACC
1 TGGGGGTTGCCGATCGCGACC
142738 TGG
1 TGG
142741 TGAGTGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.07, C:0.27, G:0.47, T:0.20
Consensus pattern (21 bp):
TGGGGGTTGCCGATCGCGACC
Found at i:151251 original size:34 final size:35
Alignment explanation
Indices: 151181--151254 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
151171 CTGGTGTTTG
* *
151181 TGAAAGAATAAGCAAAAAGGAATACAAATGAGCTT
1 TGAAAAAATAAGCAAAAAGGAATACAAAAGAGCTT
**
151216 TGAAAAAATAA-CAACAAA-GAATACAAAAGCTCTT
1 TGAAAAAATAAGCAA-AAAGGAATACAAAAGAGCTT
151250 TGAAA
1 TGAAA
151255 TGTAGAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 21 0.62
35 13 0.38
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.18
Consensus pattern (35 bp):
TGAAAAAATAAGCAAAAAGGAATACAAAAGAGCTT
Found at i:154245 original size:21 final size:21
Alignment explanation
Indices: 154196--154239 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
154186 AAGGGTGATA
* * *
154196 AGGAAACATGAATTTTGCTAG
1 AGGAAATAGGAATTTTGCCAG
154217 AGGAAATAGGAATTTTGCCAG
1 AGGAAATAGGAATTTTGCCAG
154238 AG
1 AG
154240 TTAATACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (21 bp):
AGGAAATAGGAATTTTGCCAG
Found at i:158210 original size:29 final size:29
Alignment explanation
Indices: 158168--158223 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
158158 CATCCAAAGC
158168 ATTTTATATATTTCTTTTCATT-TTTTCAT
1 ATTTTATATATTTC-TTTCATTCTTTTCAT
158197 ATTTTCATAT-TTTCTTTCATTCTTTTC
1 ATTTT-ATATATTTCTTTCATTCTTTTC
158224 TTTCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 7 0.28
29 14 0.56
30 4 0.16
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (29 bp):
ATTTTATATATTTCTTTCATTCTTTTCAT
Found at i:158228 original size:9 final size:9
Alignment explanation
Indices: 158207--158270 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
158197 ATTTTCATAT
158207 TTTC-TTTC
1 TTTCTTTTC
*
158215 ATTCTTTTC
1 TTTCTTTTC
*
158224 TTTCTTTTT
1 TTTCTTTTC
*
158233 TTTCTTTTT
1 TTTCTTTTC
158242 TTTCCTTTTC
1 TTT-CTTTTC
158252 TTT-TTCTT-
1 TTTCTT-TTC
158260 TTT-TTTTC
1 TTTCTTTTC
158268 TTT
1 TTT
158271 TTCACTCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
7 2 0.04
8 13 0.27
9 25 0.52
10 8 0.17
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:158240 original size:8 final size:8
Alignment explanation
Indices: 158182--158272 Score: 60
Period size: 8 Copynumber: 11.2 Consensus size: 8
158172 TATATATTTC
*
158182 TTTTCATT
1 TTTTCTTT
* *
158190 TTTTCATA
1 TTTTCTTT
* *
158198 TTTTCATA
1 TTTTCTTT
158206 TTTTCTTT
1 TTTTCTTT
**
158214 CATTCTTT
1 TTTTCTTT
158222 TCTTTCTTTT
1 T-TTTC-TTT
158232 TTTTCTTT
1 TTTTCTTT
**
158240 TTTT-TCC
1 TTTTCTTT
158247 TTTTCTTT
1 TTTTCTTT
158255 TTCTT-TTT
1 TT-TTCTTT
158263 TTTTCTTT
1 TTTTCTTT
158271 TT
1 TT
158273 CACTCTTTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
7 7 0.10
8 47 0.70
9 9 0.13
10 4 0.06
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCTTT
Found at i:158241 original size:10 final size:10
Alignment explanation
Indices: 158219--158272 Score: 74
Period size: 10 Copynumber: 5.4 Consensus size: 10
158209 TCTTTCATTC
*
158219 TTTTCTTTC-
1 TTTTTTTTCT
158228 TTTTTTTTCT
1 TTTTTTTTCT
*
158238 TTTTTTTCCT
1 TTTTTTTTCT
158248 TTTCTTTTTCT
1 TTT-TTTTTCT
158259 TTTTTTTTCT
1 TTTTTTTTCT
158269 TTTT
1 TTTT
158273 CACTCTTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.20
10 23 0.57
11 9 0.22
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:158243 original size:21 final size:21
Alignment explanation
Indices: 158219--158270 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
158209 TCTTTCATTC
*
158219 TTTTCTTTCTTTTTTTTCTTTT
1 TTTTCTTTCTTTTTCTT-TTTT
158241 TTTTCCTTTTCTTTTTC-TTTTT
1 TTTT-C-TTTCTTTTTCTTTTTT
158263 TTTTCTTT
1 TTTTCTTT
158271 TTCACTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
22 12 0.44
23 2 0.07
24 9 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTCTTTCTTTTTCTTTTTT
Found at i:158250 original size:6 final size:5
Alignment explanation
Indices: 158216--158271 Score: 64
Period size: 5 Copynumber: 11.4 Consensus size: 5
158206 TTTTCTTTCA
*
158216 TTCTT TTC-T TTCTT TT-TT TTCTT TT-TT TTCCTT TTCTTT TTCTT TTTTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT-CTT TTC-TT TTCTT TTCTT
158265 TTCTT TT
1 TTCTT TT
158272 TCACTCTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 12 0.27
5 23 0.52
6 9 0.20
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTCTT
Found at i:158271 original size:9 final size:9
Alignment explanation
Indices: 158216--158272 Score: 69
Period size: 9 Copynumber: 5.9 Consensus size: 9
158206 TTTTCTTTCA
*
158216 TTCTTTTCT
1 TTCTTTTTT
158225 TTCTTTTTT
1 TTCTTTTTT
158234 TTCTTTTTT
1 TTCTTTTTT
158243 TTCCTTTTCTTT
1 TT-C-TTT-TTT
158255 TTCTTTTTTT
1 TTC-TTTTTT
158265 TTCTTTTT
1 TTCTTTTT
158273 CACTCTTTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
9 24 0.55
10 7 0.16
11 8 0.18
12 5 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:158271 original size:21 final size:21
Alignment explanation
Indices: 158206--158271 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
158196 TATTTTCATA
*
158206 TTTTCTTTCATTC-TTTTCTTTC
1 TTTTCTTT--TTCTTTTTTTTTC
*
158228 TTTT--TTTTCTTTTTTTTCC
1 TTTTCTTTTTCTTTTTTTTTC
158247 TTTTCTTTTTCTTTTTTTTTC
1 TTTTCTTTTTCTTTTTTTTTC
158268 TTTT
1 TTTT
158272 TCACTCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 18 0.47
22 4 0.11
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTTCTTTTTTTTTC
Found at i:158272 original size:6 final size:6
Alignment explanation
Indices: 158224--158273 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
158214 CATTCTTTTC
* *
158224 TTTCTT TTT-TT TCTTTTT TTTCCT TTTCTT TTTC-T TTT-TT TTTCTT
1 TTTCTT TTTCTT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
158270 TTTC
1 TTTC
158274 ACTCTTTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
5 11 0.30
6 23 0.62
7 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:158281 original size:31 final size:31
Alignment explanation
Indices: 158206--158282 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 31
158196 TATTTTCATA
* *
158206 TTTTCTTTCATTCTTTTCTTTCTTTTTTTTC
1 TTTTTTTTCACTCTTTTCTTTCTTTTTTTTC
158237 TTTTTTTT--C-CTTTTCTTT-TTCTTTTTT-
1 TTTTTTTTCACTCTTTTCTTTCTT-TTTTTTC
158264 TTTCTTTTTCACTCTTTTC
1 TTT-TTTTTCACTCTTTTC
158283 CCATCATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 5 0.13
28 20 0.51
30 1 0.03
31 13 0.33
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTTTTCACTCTTTTCTTTCTTTTTTTTC
Found at i:161766 original size:23 final size:25
Alignment explanation
Indices: 161731--161782 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
161721 AAATCAAAAA
**
161731 TTTTAAATATTAATTTAATT-AATT
1 TTTTAAATATTAATAAAATTAAATT
161755 TTTTAAAT-TTAATAAAATTAAATT
1 TTTTAAATATTAATAAAATTAAATT
161779 TTTT
1 TTTT
161783 TTATATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTAAATATTAATAAAATTAAATT
Found at i:163680 original size:155 final size:157
Alignment explanation
Indices: 163313--164163 Score: 546
Period size: 155 Copynumber: 5.5 Consensus size: 157
163303 GAACTTATCA
** ** * * * *
163313 TAAACACACACCTTTAATATAAAAATGACCTAGTGATTACGTAAGACTCAG-TTTAGGAAAATTA
1 TAAACACACACCTTTAGCATAAAAGCGACCTAGTGACTACCTAGGACTTAGTTTTAGGAAAATTA
** ** ** * *
163377 CCAAAAATG-CTTTTGGGGTATACCTTTAATGTGAAAGTAT-CTCAGTAA-CTGTAAAAGATAC-
66 CC-AAAATGAC-CCTAAGGTATACCTTTAACATTAAAGTATCCT-AGTAACCT-TAAAAGACACG
* ** * *
163438 AAAAAAATTATAAAAGAAGGGTGAAACTATC-C
127 AAAAAGAGCAT-AAAGAA-AGTGAACCTATCTC
* * * * * * * * * * *
163470 TAAATATATACCTTTGGCATAAAAACAACCCACTAACTACCTATGATTTAGTTTTAGGAAAATTA
1 TAAACACACACCTTTAGCATAAAAGCGACCTAGTGACTACCTAGGACTTAGTTTTAGGAAAATTA
* * *
163535 CCAAAATGACTCTAAGGTATACCTTTAACATTAAAGTATCCTAATAACCTTAAAAGATACGAATA
66 CCAAAATGACCCTAAGGTATACCTTTAACATTAAAGTATCCTAGTAACCTTAAAAGACACGAA-A
** *
163600 TGGAGC-T-AAGAGAGTGAACCTATCTC
130 AAGAGCATAAAGAAAGTGAACCTATCTC
* *
163626 -AAACACACACCTTTAGCATAAAAGCGACCTAGTGATTACCTAGGACTCAGTTTTAGGAAAATTA
1 TAAACACACACCTTTAGCATAAAAGCGACCTAGTGACTACCTAGGACTTAGTTTTAGGAAAATTA
** * * * * * *
163690 CCAAAAATG-CCCTTGGGATATA-TTTTCA-ATGTGAAAGTATCTTGGTAACCGTAAAAGACA-T
66 CC-AAAATGACCCTAAGG-TATACCTTTAACAT-T-AAAGTATCCTAGTAACCTTAAAAGACACG
* * * *
163751 AAAAAGATCATAAAAAAAAAGGTGAATCTCTC-C
127 AAAAAGAGCAT--AAAGAAA-GTGAACCTATCTC
** * * * * * *
163784 TAAACACACATATTTGGCATAAAAACAACCCATTGACTACCTAGGATTTAGTTTTAGGAAAATTA
1 TAAACACACACCTTTAGCATAAAAGCGACCTAGTGACTACCTAGGACTTAGTTTTAGGAAAATTA
* * * * * * *
163849 TCAAAATGA---TAAGGTATACCATTAACATGAAAGTATCTTAGTAACCCTAAAGGATACGAAAA
66 CCAAAATGACCCTAAGGTATACCTTTAACATTAAAGTATCCTAGTAACCTTAAAAGACACGAAAA
*
163911 TGAAGC-T-AAGAAAGTGAACCTATCT-
131 AG-AGCATAAAGAAAGTGAACCTATCTC
* * * *
163936 TAAACACATACCTTT-GACATAAAAGCGACCCAAG-GACTACCTAGGACTTAATTCTAGGAAAAT
1 TAAACACACACCTTTAG-CATAAAAGCGA-CCTAGTGACTACCTAGGACTTAGTTTTAGGAAAAT
* * * * * *
163999 TATCAAAATGCCCCTAAGTTAGACCTTTAATA-TGAAGTATCCTAGTAACCTTAAAAGACAC-AA
64 TACCAAAATGACCCTAAGGTATACCTTTAACATTAAAGTATCCTAGTAACCTTAAAAGACACGAA
* ** * *
164062 AAAGATCATAAAATGAGGGTGAAACTA-CCC
129 AAAGAGCAT-AAA-GAAAGTGAACCTATCTC
* * * * * *
164092 TAAATACACACTTTTAGCATAAAAGCGACCTAATGACTACTTAGGATTTAGTTTTAGAAAAATTA
1 TAAACACACACCTTTAGCATAAAAGCGACCTAGTGACTACCTAGGACTTAGTTTTAGGAAAATTA
*
164157 CTAAAAT
66 CCAAAAT
164164 ATTTCTATGG
Statistics
Matches: 531, Mismatches: 128, Indels: 71
0.73 0.18 0.10
Matches are distributed among these distances:
151 1 0.00
152 68 0.13
153 14 0.03
154 29 0.05
155 123 0.23
156 113 0.21
157 83 0.16
158 34 0.06
159 66 0.12
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (157 bp):
TAAACACACACCTTTAGCATAAAAGCGACCTAGTGACTACCTAGGACTTAGTTTTAGGAAAATTA
CCAAAATGACCCTAAGGTATACCTTTAACATTAAAGTATCCTAGTAACCTTAAAAGACACGAAAA
AGAGCATAAAGAAAGTGAACCTATCTC
Found at i:163959 original size:311 final size:308
Alignment explanation
Indices: 163253--164222 Score: 1002
Period size: 311 Copynumber: 3.1 Consensus size: 308
163243 ACTTTCGATG
** * * * * * *
163253 TGAAAGTATCTCGGTAACCTTAAAGAACACCAAAATGAAGCTAGGAGAA-TGAACTTATCATAAA
1 TGAAAGTATCTTAGTAACCCTAAAGGACACGAAAATGAAGCTAAGA-AAGTGAACCTATCTTAAA
* ** * *
163317 CACACACCTTTAATATAAAAATGACCTAGTGATTACGTAAGACTCAG-TTTAGGAAAATTACCAA
65 CACACACCTTT-ACATAAAAGCGACCTAGTGATTACCTAGGACTCAGTTTTAGGAAAATTACCAA
** * * * * *
163381 AAATGCTTTTGGGGTATACCTTTAATGTGAAAGTATCTCAGTAACTGTAAAAGATACAAAAAAAT
129 AAATGCCCTTGGGATATACCTTTAATGTGAAAGTATCTTAGTAACCGTAAAAGACACAAAAAGAT
* * * * * * * *
163446 TATAAAAGAAGGGTGAAACTATCCTAAATATATACCTTTGGCATAAAAACAACCCACTAACTACC
194 CATAAAAAAAGGGTGAAACTCTCCTAAATACACA-TTTTGGCATAAAAACAACCCAATGACTACC
* * *
163511 TATGATTTAGTTTTAGGAAAATTACCAAAATGACTCTAAGGTATACCTTTAACA
258 TAGGATTTAGTTTTAGGAAAATTATCAAAATGA---TAAGGTATACCATTAACA
* * * * * * * * * *
163565 TTAAAGTATCCTAATAACCTTAAAAGATACGAATATGGAGCTAAGAGAGTGAACCTATCTCAAAC
1 TGAAAGTATCTTAGTAACCCTAAAGGACACGAAAATGAAGCTAAGAAAGTGAACCTATCTTAAAC
163630 ACACACCTTTAGCATAAAAGCGACCTAGTGATTACCTAGGACTCAGTTTTAGGAAAATTACCAAA
66 ACACACCTTTA-CATAAAAGCGACCTAGTGATTACCTAGGACTCAGTTTTAGGAAAATTACCAAA
* * *
163695 AATGCCCTTGGGATATA-TTTTCAATGTGAAAGTATCTTGGTAACCGTAAAAGACATAAAAAGAT
130 AATGCCCTTGGGATATACCTTT-AATGTGAAAGTATCTTAGTAACCGTAAAAGACACAAAAAGAT
* * * *
163759 CATAAAAAAAAAGGTGAATCTCTCCTAAACACACATATTTGGCATAAAAACAACCCATTGACTAC
194 CAT-AAAAAAAGGGTGAAACTCTCCTAAATACACAT-TTTGGCATAAAAACAACCCAATGACTAC
163824 CTAGGATTTAGTTTTAGGAAAATTATCAAAATGATAAGGTATACCATTAACA
257 CTAGGATTTAGTTTTAGGAAAATTATCAAAATGATAAGGTATACCATTAACA
*
163876 TGAAAGTATCTTAGTAACCCTAAAGGATACGAAAATGAAGCTAAGAAAGTGAACCTATCTTAAAC
1 TGAAAGTATCTTAGTAACCCTAAAGGACACGAAAATGAAGCTAAGAAAGTGAACCTATCTTAAAC
* * * * * * *
163941 ACATACCTTTGACATAAAAGCGACCCAAG-GACTACCTAGGACTTAATTCTAGGAAAATTATC-A
66 ACACACCTTT-ACATAAAAGCGA-CCTAGTGATTACCTAGGACTCAGTTTTAGGAAAATTACCAA
* ** * * * * *
164004 AAATGCCCCTAAGTTAGACCTTTAATATG-AAGTATCCTAGTAACCTTAAAAGACACAAAAAGAT
129 AAATGCCCTTGGGATATACCTTTAATGTGAAAGTATCTTAGTAACCGTAAAAGACACAAAAAGAT
** * * * *
164068 CATAAAATGAGGGTGAAACTAC-CCTAAATACACACTTTTAGCATAAAAGCGACCTAATGACTAC
194 CATAAAAAAAGGGTGAAACT-CTCCTAAATACACA-TTTTGGCATAAAAACAACCCAATGACTAC
* * * ** * * **
164132 TTAGGATTTAGTTTTAGAAAAATTACTAAAATATTTCTATGGTATACCATCAATG
257 CTAGGATTTAGTTTTAGGAAAATTA-TCAAA-A-TGATAAGGTATACCATTAACA
*
164187 TGAAAGTAT-TTCGGTAACCCTAAAGGACACGAAAAT
1 TGAAAGTATCTT-AGTAACCCTAAAGGACACGAAAAT
164223 AAAAAGTAAT
Statistics
Matches: 550, Mismatches: 93, Indels: 31
0.82 0.14 0.05
Matches are distributed among these distances:
308 70 0.13
309 40 0.07
310 22 0.04
311 172 0.31
312 94 0.17
313 70 0.13
314 82 0.15
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (308 bp):
TGAAAGTATCTTAGTAACCCTAAAGGACACGAAAATGAAGCTAAGAAAGTGAACCTATCTTAAAC
ACACACCTTTACATAAAAGCGACCTAGTGATTACCTAGGACTCAGTTTTAGGAAAATTACCAAAA
ATGCCCTTGGGATATACCTTTAATGTGAAAGTATCTTAGTAACCGTAAAAGACACAAAAAGATCA
TAAAAAAAGGGTGAAACTCTCCTAAATACACATTTTGGCATAAAAACAACCCAATGACTACCTAG
GATTTAGTTTTAGGAAAATTATCAAAATGATAAGGTATACCATTAACA
Found at i:165519 original size:20 final size:20
Alignment explanation
Indices: 165483--165520 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
165473 TTTAGTGTTG
*
165483 TTTTTTCTTCTTGGAAGCCA
1 TTTTTTCTTCATGGAAGCCA
165503 TTTTTTCTCTCAT-GAAGC
1 TTTTTTCT-TCATGGAAGC
165521 ATCCTCCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTTTTCTTCATGGAAGCCA
Found at i:165849 original size:26 final size:29
Alignment explanation
Indices: 165811--165870 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 29
165801 ATTCACAATC
*
165811 AAAATAAATTTAAAA-TAATAA-ATAAAT
1 AAAAGAAATTTAAAATTAATAACATAAAT
*
165838 AAAAGAAA-TTAAAATTATTAATCATAAAT
1 AAAAGAAATTTAAAATTAATAA-CATAAAT
165867 AAAA
1 AAAA
165871 TTTTGGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.21
27 12 0.43
29 10 0.36
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAAGAAATTTAAAATTAATAACATAAAT
Found at i:167304 original size:64 final size:64
Alignment explanation
Indices: 167096--167576 Score: 252
Period size: 64 Copynumber: 7.5 Consensus size: 64
167086 TCTAGAAGGC
** * * * * * * * *
167096 TAACTAGGGGCAAAAATGATTCAGTCAAGCAAAGATGACTAGGACGTAACCTAAGTCTAGAGGGT
1 TAACTA-GGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATGTAACCTAGGTCTAAAGGGT
* * * * * * * **
167161 TGACCAAGGTAAAACTGATACAGTCAAGCAAGGATAACC-AG-TGCATAACCTAGGTCTAAAGAA
1 TAACTAGGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATG--TAACCTAGGTCTAAAGGG
*
167224 A
64 T
* * *** * * * * *
167225 TGATTAGGATGAAACCGATACAATTAAACAAGGATGACCAAGATGTAACTTAGGTCCAGAGGGT
1 TAACTAGGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATGTAACCTAGGTCTAAAGGGT
* * * * * *
167289 TAACTAGGGCAAAACCAAT-GAGTTAAGCAAGGATAACCAAGATGTAACCTAAGTCTAAAGGGT
1 TAACTAGGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATGTAACCTAGGTCTAAAGGGT
* * * ** * ** * **
167352 TGACCAAGGTGAAATCGATACAGTCAAACAAGGATGATTAGGATGTAACCTAGGTCTAAAGTAT
1 TAACTAGGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATGTAACCTAGGTCTAAAGGGT
* * * * * * * * *
167416 TAACTAGGGCAAAACTGATATAGTCAAGCAAAGATGACGAAGATGTAA-TTGAGATTTAGAGGGT
1 TAACTAGGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATGTAACCT-AGGTCTAAAGGGT
* ** * ** * * * *
167480 TGA-TGAGGGCAAAACTAATACAGTCAATCAAAAATGACTAGGATGTAACCTAGGTCTAGAGTGT
1 TAACT-AGGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATGTAACCTAGGTCTAAAGGGT
* * * *
167544 TGACTAAGGCAAAGCTGATACAGTCAAACAAGG
1 TAACTAGGGCAAAACCGATACAGTCAAACAAGG
167577 TAGATTGAGA
Statistics
Matches: 308, Mismatches: 99, Indels: 19
0.72 0.23 0.04
Matches are distributed among these distances:
62 1 0.00
63 51 0.17
64 246 0.80
65 8 0.03
66 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (64 bp):
TAACTAGGGCAAAACCGATACAGTCAAACAAGGATGACCAAGATGTAACCTAGGTCTAAAGGGT
Found at i:167479 original size:191 final size:191
Alignment explanation
Indices: 167117--167576 Score: 444
Period size: 191 Copynumber: 2.4 Consensus size: 191
167107 AAAAATGATT
* * * * *
167117 CAGTCAAGCAAAGATGACTAGGACGTAACCTAAGTCTAGAGGGTTGACCAAGGTAAAACTGATAC
1 CAGTCAAGCAAAAATAACCAAGATGTAACCTAAGTCTAGAGGGTTGACCAAGGTAAAACTGATAC
* * * **
167182 AGTCAAGCAAGGATAACCAGTGCATAACCTAGGTCTAAAGAAATGATTAGGATGAAACCGATACA
66 AGTCAAACAAGGATAACCAGTG-ATAACCTAGGTCTAAAGAAATAACTAGGACAAAACCGATACA
* * *
167247 ATTAAACAAGGATGACCAAGATGTAACTTAGGTCCAGAGGGTTAACT-AGGGCAAAACCAAT-
130 ATCAAACAAAGATGACCAAGATGTAACTTAGATCCAGAGGGTTAA-TGAGGGCAAAACCAATA
* * ** * *
167308 GAGTTAAGCAAGGATAACCAAGATGTAACCTAAGTCTAAAGGGTTGACCAAGGTGAAA-TCGATA
1 CAGTCAAGCAAAAATAACCAAGATGTAACCTAAGTCTAGAGGGTTGACCAAGGTAAAACT-GATA
* ** * * * *
167372 CAGTCAAACAAGGATGATTAG-GATGTAACCTAGGTCTAAAGTATTAACTAGGGCAAAACTGATA
65 CAGTCAAACAAGGATAACCAGTGA--TAACCTAGGTCTAAAGAAATAACTAGGACAAAACCGATA
* * * * ** * *
167436 TAGTCAAGCAAAGATGACGAAGATGTAA-TTGAGATTTAGAGGGTTGATGAGGGCAAAACTAATA
128 CAATCAAACAAAGATGACCAAGATGTAACTT-AGATCCAGAGGGTTAATGAGGGCAAAACCAATA
* * * * * * * * *
167500 CAGTCAATCAAAAATGACTAGGATGTAACCTAGGTCTAGAGTGTTGACTAAGGCAAAGCTGATAC
1 CAGTCAAGCAAAAATAACCAAGATGTAACCTAAGTCTAGAGGGTTGACCAAGGTAAAACTGATAC
167565 AGTCAAACAAGG
66 AGTCAAACAAGG
167577 TAGATTGAGA
Statistics
Matches: 215, Mismatches: 47, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
189 1 0.00
190 5 0.02
191 148 0.69
192 60 0.28
193 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (191 bp):
CAGTCAAGCAAAAATAACCAAGATGTAACCTAAGTCTAGAGGGTTGACCAAGGTAAAACTGATAC
AGTCAAACAAGGATAACCAGTGATAACCTAGGTCTAAAGAAATAACTAGGACAAAACCGATACAA
TCAAACAAAGATGACCAAGATGTAACTTAGATCCAGAGGGTTAATGAGGGCAAAACCAATA
Found at i:167819 original size:40 final size:40
Alignment explanation
Indices: 167584--167807 Score: 217
Period size: 40 Copynumber: 5.6 Consensus size: 40
167574 AGGTAGATTG
* * * *
167584 AGATGAAACCGATAAGTCAACGAATGGAAATAGTTGACCA
1 AGATGAAACCTACAAGTCAACAAATGGAAAGAGTTGACCA
* *
167624 AGATGAAA-CTGATAAGTCAACAAATGGAATGAGTTGACCA
1 AGATGAAACCT-ACAAGTCAACAAATGGAAAGAGTTGACCA
* * * *
167664 AGATGAAATCTATAAGTCAA-TAATGAGAAA-AGTTGACCG
1 AGATGAAACCTACAAGTCAACAAATG-GAAAGAGTTGACCA
** * *
167703 AGACAAAACTTACAAGTCAACGAAGA-GGAAAG-GTTGACTA
1 AGATGAAACCTACAAGTCAAC-AA-ATGGAAAGAGTTGACCA
* *
167743 AGATGAAACCTACAAGTCAACTAATGGGAAA-AGTTGATCA
1 AGATGAAACCTACAAGTCAACAAAT-GGAAAGAGTTGACCA
167783 AGATGAAACCTACAAGTCAACAAAT
1 AGATGAAACCTACAAGTCAACAAAT
167808 AAAACGAGTT
Statistics
Matches: 152, Mismatches: 22, Indels: 20
0.78 0.11 0.10
Matches are distributed among these distances:
38 1 0.01
39 29 0.19
40 117 0.77
41 4 0.03
42 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (40 bp):
AGATGAAACCTACAAGTCAACAAATGGAAAGAGTTGACCA
Found at i:167828 original size:16 final size:16
Alignment explanation
Indices: 167804--167835 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
167794 ACAAGTCAAC
167804 AAATAAAACGAGTTGA
1 AAATAAAACGAGTTGA
*
167820 AAATTAAACGAGTTGA
1 AAATAAAACGAGTTGA
167836 CTAAGATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (16 bp):
AAATAAAACGAGTTGA
Found at i:168076 original size:40 final size:39
Alignment explanation
Indices: 167998--168113 Score: 101
Period size: 40 Copynumber: 2.9 Consensus size: 39
167988 GTCAAATAAG
* * *
167998 ATAAAAAAGTTGA-CTGAGATGAAA-CTGAGAAGTCAACAA
1 ATAAAAAAGTTGACCAG-GATGAAACCT-ACAAGTTAACAA
168037 ATAAAAAGAGTTGACCAGGATGAAACCTACAAGTTAACAA
1 ATAAAAA-AGTTGACCAGGATGAAACCTACAAGTTAACAA
* * * * **
168077 TTGAGAAAAGTTAACCAAGACAAAACCTACAAGTTAA
1 AT-AAAAAAGTTGACCAGGATGAAACCTACAAGTTAA
168114 TGAATAGGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
39 7 0.11
40 49 0.77
41 8 0.12
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.18
Consensus pattern (39 bp):
ATAAAAAAGTTGACCAGGATGAAACCTACAAGTTAACAA
Found at i:168125 original size:40 final size:40
Alignment explanation
Indices: 168059--168189 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
168049 GACCAGGATG
* *
168059 AAACCTACAAGTTAA-CAATTGAGAAAAGTTAACCAAGACA
1 AAACCTACAAGTTAATGAATAG-GAAAAGTTAACCAAGACA
* *
168099 AAACCTACAAGTTAATGAATAGGAAAAGTTGATCGAA-ACA
1 AAACCTACAAGTTAATGAATAGGAAAAGTT-AACCAAGACA
* * * *
168139 GAACCTACAAGTTAATGAATGGGAAGAGTTGACCAAGACA
1 AAACCTACAAGTTAATGAATAGGAAAAGTTAACCAAGACA
*
168179 AAA-TTACAAGT
1 AAACCTACAAGT
168190 CAATAGATAA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
39 10 0.13
40 58 0.76
41 8 0.11
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (40 bp):
AAACCTACAAGTTAATGAATAGGAAAAGTTAACCAAGACA
Found at i:168554 original size:66 final size:66
Alignment explanation
Indices: 168440--168573 Score: 164
Period size: 66 Copynumber: 2.0 Consensus size: 66
168430 AATTAATGAG
* * * ** *
168440 AAAGTTGATGGAGATGAAACCTATAAGTCAATGAAAGGTAAAAAAGTTGAC-TGGCACAAAACCT
1 AAAGTTAATCGAGATAAAACCTATAAGTCAACAAAAGGTAAAAAAGTTGACAAGG-ACAAAACCT
168504 AC
65 AC
* *
168506 AAAGTTAATCGAGATAAAACCTATAAGTCAACAAAAGAG-AGAAGAGTTGACAAGGACAAAACCT
1 AAAGTTAATCGAGATAAAACCTATAAGTCAACAAAAG-GTAAAAAAGTTGACAAGGACAAAACCT
168570 AC
65 AC
168572 AA
1 AA
168574 GTCATCAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 55 0.95
67 3 0.05
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.17
Consensus pattern (66 bp):
AAAGTTAATCGAGATAAAACCTATAAGTCAACAAAAGGTAAAAAAGTTGACAAGGACAAAACCTA
C
Found at i:168646 original size:39 final size:40
Alignment explanation
Indices: 168521--168667 Score: 190
Period size: 39 Copynumber: 3.6 Consensus size: 40
168511 TAATCGAGAT
* *
168521 AAAACCTATAAGTCAACAAAAGAGAGAAGAGTTGA-CAAGGAC
1 AAAACCTACAAGTCAACAAAAG-G-GAAGAGTTAACCAA-GAC
* * *
168563 AAAACCTACAAGTCATCAAATGGGAAGAATTAACCAAGAC
1 AAAACCTACAAGTCAACAAAAGGGAAGAGTTAACCAAGAC
*
168603 AAAACCTACAAGTCAACAAATGGG-AGAGTTAACCAAGAC
1 AAAACCTACAAGTCAACAAAAGGGAAGAGTTAACCAAGAC
*
168642 AAAACCTCCAAGTCAACAAAAGGGAA
1 AAAACCTACAAGTCAACAAAAGGGAA
168668 AATTTGGTTG
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
39 36 0.38
40 35 0.37
41 4 0.04
42 19 0.20
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.12
Consensus pattern (40 bp):
AAAACCTACAAGTCAACAAAAGGGAAGAGTTAACCAAGAC
Found at i:168655 original size:79 final size:81
Alignment explanation
Indices: 168521--168671 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 81
168511 TAATCGAGAT
* * * *
168521 AAAACCTATAAGTCAACAAAAGAGAGAAGAGTTGACAAGGACAAAACCTACAAGTCATCAAATGG
1 AAAACCTACAAGTCAACAAAAGAGAGAAGAGTTAACAAGGACAAAACCTACAAGTCAACAAAAGG
168586 GAAGAATTAACCAAGAC
66 GAA-AATTAACCAAGAC
* *
168603 AAAACCTACAAGTCAACAAATG-G-G-AGAGTTAACCAA-GACAAAACCTCCAAGTCAACAAAAG
1 AAAACCTACAAGTCAACAAAAGAGAGAAGAGTTAA-CAAGGACAAAACCTACAAGTCAACAAAAG
168664 GGAAAATT
65 GGAAAATT
168672 TGGTTGGGAC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 4 0.06
79 33 0.53
80 4 0.06
81 1 0.02
82 20 0.32
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (81 bp):
AAAACCTACAAGTCAACAAAAGAGAGAAGAGTTAACAAGGACAAAACCTACAAGTCAACAAAAGG
GAAAATTAACCAAGAC
Found at i:168780 original size:40 final size:40
Alignment explanation
Indices: 168521--168792 Score: 217
Period size: 40 Copynumber: 6.8 Consensus size: 40
168511 TAATCGAGAT
* *
168521 AAAACCTATAAGTCAACAAAAGAGAGAAGAGTTGAC-AAGGAC
1 AAAACCTACAAGTCAACAAATG-G-GAAGAGTTGACTAA-GAC
* * * *
168563 AAAACCTACAAGTCATCAAATGGGAAGAATTAACCAAGAC
1 AAAACCTACAAGTCAACAAATGGGAAGAGTTGACTAAGAC
* *
168603 AAAACCTACAAGTCAACAAATGGG-AGAGTTAACCAAGAC
1 AAAACCTACAAGTCAACAAATGGGAAGAGTTGACTAAGAC
* * * * ** **
168642 AAAACCTCCAAGTCAACAAAAGGGAAAATTTGGTTGGGAC
1 AAAACCTACAAGTCAACAAATGGGAAGAGTTGACTAAGAC
* * * *
168682 AAAACTTATAAG-CTAAAAAATGGGAAAAGTTGACTAAGAC
1 AAAACCTACAAGTC-AACAAATGGGAAGAGTTGACTAAGAC
* * * * * *
168722 AACACCTACAAATTAACAAGTGGGATGAGTTGACTAGGAC
1 AAAACCTACAAGTCAACAAATGGGAAGAGTTGACTAAGAC
* * * *
168762 AAAACCTATAAGGCAACAAATGAGAGGAGTT
1 AAAACCTACAAGTCAACAAATGGGAAGAGTT
168793 TATCGAGATA
Statistics
Matches: 181, Mismatches: 45, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
39 37 0.20
40 122 0.67
41 3 0.02
42 19 0.10
ACGTcount: A:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (40 bp):
AAAACCTACAAGTCAACAAATGGGAAGAGTTGACTAAGAC
Found at i:168783 original size:80 final size:79
Alignment explanation
Indices: 168521--168828 Score: 235
Period size: 80 Copynumber: 3.8 Consensus size: 79
168511 TAATCGAGAT
* * *
168521 AAAACCTATAAGTCAACAAAAGAGAGAAGAGTTGACAAGGACAAAACCTACAAGTCATCAAATGG
1 AAAACCTATAAGGCAACAAATG-G-GAAGAGTTGACAA-GACAAAACCTACAAGTCAACAAATGG
* * *
168586 GAAGAATTAACCAAGAC
63 GAAGAATTGACTAGGAC
* * * * *
168603 AAAACCTACAAGTCAACAAATGGG-AGAGTTAACCAAGACAAAACCTCCAAGTCAACAAAAGGGA
1 AAAACCTATAAGGCAACAAATGGGAAGAGTTGA-CAAGACAAAACCTACAAGTCAACAAATGGGA
** *
168667 A-AATTTGGTTGGGAC
65 AGAA-TTGACTAGGAC
* * * * * * *
168682 AAAACTTATAA-GCTAAAAAATGGGAAAAGTTGACTAAGACAACACCTACAAATTAACAAGTGGG
1 AAAACCTATAAGGC-AACAAATGGGAAGAGTTGAC-AAGACAAAACCTACAAGTCAACAAATGGG
* *
168746 ATGAGTTGACTAGGAC
64 AAGAATTGACTAGGAC
* * * * * * * **
168762 AAAACCTATAAGGCAACAAATGAGAGGAGTTTATCGAGATAAAACCTATAAGCCAATGAATGGGA
1 AAAACCTATAAGGCAACAAATGGGAAGAGTTGA-CAAGACAAAACCTACAAGTCAACAAATGGGA
168827 AG
65 AG
168829 GGTTAACCAA
Statistics
Matches: 172, Mismatches: 46, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
78 3 0.02
79 57 0.33
80 87 0.51
81 5 0.03
82 20 0.12
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (79 bp):
AAAACCTATAAGGCAACAAATGGGAAGAGTTGACAAGACAAAACCTACAAGTCAACAAATGGGAA
GAATTGACTAGGAC
Found at i:171145 original size:96 final size:97
Alignment explanation
Indices: 171010--171245 Score: 287
Period size: 96 Copynumber: 2.4 Consensus size: 97
171000 TGAAAAATGA
* * * *
171010 GGTTGGAGTATCTCCTCGAAGGAATGGGGTTAGAATGTCCCCGACGATGGCAATTTAGGTGAAAA
1 GGTTGGAGTATCTCCTCGAAAGAATAGGGTTAGAATGTCCCCAACGATGACAATTTAGGTGAAAA
171075 TAAGATTT-AATCTTGACAAGTTTAAAAACGG
66 TAAGATTTAAATCTTGACAAGTTTAAAAACGG
* * * * *
171106 GGTTGGAGTATC-CTCTCGAAAGAATAGGGTTGGAGTGTCCCCAATGATGACACTTTGGGTGAAA
1 GGTTGGAGTATCTC-CTCGAAAGAATAGGGTTAGAATGTCCCCAACGATGACAATTTAGGTGAAA
*
171170 ATAAGATTTAAATCTTGACAAGTTTAAAAACGA
65 ATAAGATTTAAATCTTGACAAGTTTAAAAACGG
* * * ** * * *
171203 GATTAGAGTATTTCCTTAAAAGAATGGGGTTAGAGTATCCCCA
1 GGTTGGAGTATCTCCTCGAAAGAATAGGGTTAGAATGTCCCCA
171246 TGAATAAAAT
Statistics
Matches: 119, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
95 1 0.01
96 62 0.52
97 55 0.46
98 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (97 bp):
GGTTGGAGTATCTCCTCGAAAGAATAGGGTTAGAATGTCCCCAACGATGACAATTTAGGTGAAAA
TAAGATTTAAATCTTGACAAGTTTAAAAACGG
Done.