Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold195
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: 1914327
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.29
Warning! 179916 characters in sequence are not A, C, G, or T
File 9 of 12
Found at i:1186722 original size:32 final size:33
Alignment explanation
Indices: 1186681--1186743 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1186671 CAATTGTGCA
* *
1186681 TGTATCGATACAATG-ATCATGTATCGATACCT
1 TGTATCGATACAAAGCATAATGTATCGATACCT
1186713 TGTATCGATACAAAGCATAATGTATCGATAC
1 TGTATCGATACAAAGCATAATGTATCGATAC
1186744 TTTTGGTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAAAGCATAATGTATCGATACCT
Found at i:1195170 original size:52 final size:52
Alignment explanation
Indices: 1195022--1195150 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1195012 CGAAATATGA
1195022 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
1195074 AAATTTGCCTGTATGCATCGGTACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1195126 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1195151 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1195177 original size:13 final size:13
Alignment explanation
Indices: 1195159--1195183 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1195149 CAAAGATCAG
1195159 TGTATCGATACAA
1 TGTATCGATACAA
1195172 TGTATCGATACA
1 TGTATCGATACA
1195184 TTTGGGTAAT
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:1195273 original size:13 final size:13
Alignment explanation
Indices: 1195255--1195279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1195245 ACAACATTCA
1195255 TGTATCGATACAT
1 TGTATCGATACAT
1195268 TGTATCGATACA
1 TGTATCGATACA
1195280 AATCGTTGAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1196115 original size:105 final size:103
Alignment explanation
Indices: 1195947--1196268 Score: 235
Period size: 105 Copynumber: 3.1 Consensus size: 103
1195937 CCAATACGTT
* * * * * * * *
1195947 GGCCAACGATATTGGGTTTAAAGATGTAAAGAATGTCAATGTGCTGATTCACGGTCAGCGATATT
1 GGCCAACGACATTGGGTTTAAAGATGTAAAGAACGCCAATATACTGATTCAAGGCCAACGATATT
* * *
1196012 AGTCTTGAAGATGAGAAGAAAGC-CAATGTGCTGATTCAA
66 AGACTTAAAGATGA-AA-AAAGCGCAATATGCTGATTCAA
**
1196051 GGCCAACGACATTGGGTTTTAAAGATG-ACGGAGACGCCAATATACTGATTCAAGGCCAACGATA
1 GGCCAACGACATTGGG-TTTAAAGATGTAAAGA-ACGCCAATATACTGATTCAAGGCCAACGATA
* * *
1196115 TTGGACTTAAAGATGACAAAGGCGTCAATATGCTGATTCAA
64 TTAGACTTAAAGATGAAAAAAGCG-CAATATGCTGATTCAA
* * * ** ** * ** * *
1196156 GGCCAGCAATATTGGACTTAAAGATG--AAG-GTGCCAATGTGTTGATTCAAGGCCAGCGACATT
1 GGCCAACGACATTGGGTTTAAAGATGTAAAGAACGCCAATATACTGATTCAAGGCCAACGATATT
* * ***
1196218 GGTCTTAAAGAT-AAAGGTGC-CAATATGCTGATTCAA
66 AGACTTAAAGATGAAAAAAGCGCAATATGCTGATTCAA
* *
1196254 GGCCAGCGATATTGG
1 GGCCAACGACATTGG
1196269 ACTTAAAAGA
Statistics
Matches: 178, Mismatches: 36, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
98 30 0.17
100 4 0.02
101 37 0.21
103 5 0.03
104 28 0.16
105 74 0.42
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (103 bp):
GGCCAACGACATTGGGTTTAAAGATGTAAAGAACGCCAATATACTGATTCAAGGCCAACGATATT
AGACTTAAAGATGAAAAAAGCGCAATATGCTGATTCAA
Found at i:1196151 original size:52 final size:50
Alignment explanation
Indices: 1195947--1196275 Score: 284
Period size: 52 Copynumber: 6.4 Consensus size: 50
1195937 CCAATACGTT
* ** ** * * *
1195947 GGCCAACGATATTGGGTTTAAAGATGTAAAGAATGTCAATGTGCTGATTCAC
1 GGCCAGCGATATTGGACTTAAAGATG-AAAG-GCGCCAATATGCTGATTCAA
* * * * ** *
1195999 GGTCAGCGATATTAGTCTTGAAGATGAGAAGAAAGCCAATGTGCTGATTCAA
1 GGCCAGCGATATTGGACTTAAAGATGA-AAG-GCGCCAATATGCTGATTCAA
* * ** * * *
1196051 GGCCAACGACATTGGGTTTTAAAGATGACGGAGACGCCAATATACTGATTCAA
1 GGCCAGCGATATT-GGACTTAAAGATGA--AAGGCGCCAATATGCTGATTCAA
* *
1196104 GGCCAACGATATTGGACTTAAAGATGACAAAGGCGTCAATATGCTGATTCAA
1 GGCCAGCGATATTGGACTTAAAGATG--AAAGGCGCCAATATGCTGATTCAA
* * * *
1196156 GGCCAGCAATATTGGACTTAAAGATG-AAGGTGCCAATGTGTTGATTCAA
1 GGCCAGCGATATTGGACTTAAAGATGAAAGGCGCCAATATGCTGATTCAA
* * *
1196205 GGCCAGCGACATTGGTCTTAAAGAT-AAAGGTGCCAATATGCTGATTCAA
1 GGCCAGCGATATTGGACTTAAAGATGAAAGGCGCCAATATGCTGATTCAA
1196254 GGCCAGCGATATTGGACTTAAA
1 GGCCAGCGATATTGGACTTAAA
1196276 AGAAGATGCC
Statistics
Matches: 232, Mismatches: 39, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
49 82 0.35
51 1 0.00
52 105 0.45
53 40 0.17
54 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (50 bp):
GGCCAGCGATATTGGACTTAAAGATGAAAGGCGCCAATATGCTGATTCAA
Found at i:1196219 original size:49 final size:49
Alignment explanation
Indices: 1195983--1196275 Score: 271
Period size: 49 Copynumber: 5.8 Consensus size: 49
1195973 TAAAGAATGT
* * * * * * **
1195983 CAATGTGCTGATTCACGGTCAGCGATATTAGTCTTGAAGATGAGAAGAAAGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAG-GCGC
* * * ** *
1196035 CAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACGGAGACGC
1 CAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATGA---AGGCGC
* * *
1196088 CAATATACTGATTCAAGGCCAACGATATTGGACTTAAAGATGACAAAGGCGT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGCGC
* *
1196140 CAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCGC
* * * * * *
1196189 CAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCGC
1196238 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1196276 AGAAGATGCC
Statistics
Matches: 204, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
49 82 0.40
51 2 0.01
52 79 0.39
53 38 0.19
54 2 0.01
55 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCGC
Found at i:1196379 original size:30 final size:30
Alignment explanation
Indices: 1196336--1196566 Score: 245
Period size: 30 Copynumber: 7.8 Consensus size: 30
1196326 TGTGCTTTTG
* *
1196336 AAGGTTGCCACTGACTAATGGGCTTTGGAA
1 AAGGGTGCCACTGACTTATGGGCTTTGGAA
* *
1196366 AAGGGTGCTACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTATGGGCTTTGGAA
* *
1196396 AA-GATGCCACTGACTTATGAGCTTTGGAA
1 AAGGGTGCCACTGACTTATGGGCTTTGGAA
*
1196425 AAGGGTGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTGACTTATGGGCTTTGGAA
* * * **
1196455 AA-GATGCCACTAACTTGTGGGCTTT--TC
1 AAGGGTGCCACTGACTTATGGGCTTTGGAA
* * * *
1196482 TAGGTTGCCACTGACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTATGGGCTTTGGAA
* * *
1196512 AAGGGTGCCACTGGCTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTATGGGCTTTGGAA
* *
1196542 AAAGGTGCCACTGACTTGTGGGCTT
1 AAGGGTGCCACTGACTTATGGGCTT
1196567 AAAAGGAAAA
Statistics
Matches: 172, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.01
28 21 0.12
29 46 0.27
30 104 0.60
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (30 bp):
AAGGGTGCCACTGACTTATGGGCTTTGGAA
Found at i:1196423 original size:59 final size:59
Alignment explanation
Indices: 1196341--1196566 Score: 294
Period size: 59 Copynumber: 3.8 Consensus size: 59
1196331 TTTTGAAGGT
* *
1196341 TGCCACTGACTAATGGGCTTTGGAAAAGGGTGCTACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
*
1196400 TGCCACTGACTTATGAGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
* * *** * * *
1196459 TGCCACTAACTTGTGGGCTTT--TCTAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAA-GA
* * * *
1196517 TGCCACTGGCTTGTGGGCTTTTGAAAAAGGTGCCACTGACTTGTGGGCTT
1 TGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTT
1196567 AAAAGGAAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
57 29 0.20
58 20 0.14
59 74 0.51
60 22 0.15
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (59 bp):
TGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:1196595 original size:34 final size:34
Alignment explanation
Indices: 1196539--1196653 Score: 130
Period size: 35 Copynumber: 3.4 Consensus size: 34
1196529 GTGGGCTTTT
* *
1196539 GAAAAAG-GTGCCACT-GACTTGTGGGCTTAAAAG
1 GAAAAAGAGTGCCA-TGGAGTTGTGGGCTTAAAAA
1196572 GAAAAAGAGTGCCATGGAGTTGTGGGCTTACAAAA
1 GAAAAAGAGTGCCATGGAGTTGTGGGCTTA-AAAA
* * *
1196607 GAAAAGGAGTGCCACGGAGTTGTGGACTTAAAAA
1 GAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAA
1196641 -AGAAAAG-GTGCCA
1 GA-AAAAGAGTGCCA
1196654 CTATGCTGAC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
33 15 0.21
34 27 0.38
35 30 0.42
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.18
Consensus pattern (34 bp):
GAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAA
Found at i:1196618 original size:35 final size:34
Alignment explanation
Indices: 1196546--1196648 Score: 134
Period size: 35 Copynumber: 3.0 Consensus size: 34
1196536 TTTGAAAAAG
* * * *
1196546 GTGCCACTGACTTGTGGGCTTAAAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTAAAAAGAAAAGGA
*
1196580 GTGCCATGGAGTTGTGGGCTTACAAAAGAAAAGGA
1 GTGCCACGGAGTTGTGGGCTTA-AAAAGAAAAGGA
*
1196615 GTGCCACGGAGTTGTGGACTTAAAAAAGAAAAGG
1 GTGCCACGGAGTTGTGGGCTT-AAAAAGAAAAGG
1196649 TGCCACTATG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 19 0.32
35 40 0.67
36 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.19
Consensus pattern (34 bp):
GTGCCACGGAGTTGTGGGCTTAAAAAGAAAAGGA
Found at i:1196762 original size:33 final size:32
Alignment explanation
Indices: 1196687--1196776 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
1196677 TATTGGGCTT
*
1196687 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGA
* *
1196719 AAAGGCGCCACGGAGTTGTGGGCTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAG-A
* * *
1196752 AAAGATGCCACAGACTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
1196777 TTGAAGGTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 28 0.56
33 22 0.44
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (32 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGA
Found at i:1196798 original size:28 final size:28
Alignment explanation
Indices: 1196757--1196843 Score: 104
Period size: 28 Copynumber: 3.0 Consensus size: 28
1196747 AGGAAAAAGA
* *
1196757 TGCCACAGACTTGTGGGCTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGG
*
1196785 TGCCACTGATTTGTGGGC-TTTGAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTG---AAGGG
*
1196815 TGCCATTGACTTGTGGGCTTTTGAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAGGG
1196843 T
1 T
1196844 AAGGAATGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 4 0.08
28 22 0.44
30 20 0.40
31 4 0.08
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTTGAAGGG
Found at i:1198267 original size:1 final size:1
Alignment explanation
Indices: 1198263--1198381 Score: 67
Period size: 1 Copynumber: 119.0 Consensus size: 1
1198253 CTTTTTGTTG
** * * * * * * * * * *
1198263 TTTTTTTTTCCTTCTTTTTTTTGTTTGTTTGTTGTTTTTTTTCTTCTTTTTTTTGTTTGTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
1198328 TTTTTTTTGTTTTGTTTTTTTTTCTTCTTTTTTTTTGTTTGTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1198382 GTTGAGGATG
Statistics
Matches: 82, Mismatches: 36, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (1 bp):
T
Found at i:1198309 original size:32 final size:33
Alignment explanation
Indices: 1198256--1198335 Score: 137
Period size: 32 Copynumber: 2.5 Consensus size: 33
1198246 TCCGGACCTT
1198256 TTTGTTGTTTTTTTTTCCTTCTTTTTTTTGTTTG
1 TTTGTTG-TTTTTTTTCCTTCTTTTTTTTGTTTG
1198290 TTTGTTGTTTTTTTT-CTTCTTTTTTTTGTTTG
1 TTTGTTGTTTTTTTTCCTTCTTTTTTTTGTTTG
1198322 TTTGTT-TTTTTTTT
1 TTTGTTGTTTTTTTT
1198336 GTTTTGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 8 0.17
32 23 0.50
33 8 0.17
34 7 0.15
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (33 bp):
TTTGTTGTTTTTTTTCCTTCTTTTTTTTGTTTG
Found at i:1198337 original size:47 final size:47
Alignment explanation
Indices: 1198278--1198381 Score: 167
Period size: 47 Copynumber: 2.2 Consensus size: 47
1198268 TTTTCCTTCT
1198278 TTTTTTTGTTTG-TTTGTTGTTTTTTTTCTTC-TTTTTTTTGTTTGTTTG
1 TTTTTTT-TTTGTTTTG-T-TTTTTTTTCTTCTTTTTTTTTGTTTGTTTG
1198326 TTTTTTTTTTGTTTTGTTTTTTTTTCTTCTTTTTTTTTGTTTGTTTG
1 TTTTTTTTTTGTTTTGTTTTTTTTTCTTCTTTTTTTTTGTTTGTTTG
1198373 TTTTTTTTT
1 TTTTTTTTT
1198382 GTTGAGGATG
Statistics
Matches: 54, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
46 12 0.22
47 31 0.57
48 11 0.20
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.85
Consensus pattern (47 bp):
TTTTTTTTTTGTTTTGTTTTTTTTTCTTCTTTTTTTTTGTTTGTTTG
Found at i:1198398 original size:47 final size:46
Alignment explanation
Indices: 1198301--1198398 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 46
1198291 TTGTTGTTTT
** * ***
1198301 TTTTCTTCTTTTTTTTGTTTGTTTGTTTTTTTTTTGTTTTGTTTTT
1 TTTTCTTCTTTTTTTTGTTTGTTTGTTTTTTTTTTGTTAGGATGCC
1198347 TTTTCTTCTTTTTTTTTGTTTGTTTG-TTTTTTTTTGTTGAGGATGCC
1 TTTTCTTC-TTTTTTTTGTTTGTTTGTTTTTTTTTTGTT-AGGATGCC
1198394 TTTTC
1 TTTTC
1198399 AAGTTTTTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 20 0.45
47 24 0.55
ACGTcount: A:0.02, C:0.07, G:0.13, T:0.78
Consensus pattern (46 bp):
TTTTCTTCTTTTTTTTGTTTGTTTGTTTTTTTTTTGTTAGGATGCC
Found at i:1215066 original size:20 final size:21
Alignment explanation
Indices: 1215041--1215091 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1215031 ACCCAGAATG
1215041 TATCGATACATTCACT-TAT-A
1 TATCGATACATTCACTGT-TCA
*
1215061 TATCGATACATTTACTGTTCA
1 TATCGATACATTCACTGTTCA
1215082 TATCGATACA
1 TATCGATACA
1215092 AATTATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (21 bp):
TATCGATACATTCACTGTTCA
Found at i:1217957 original size:93 final size:93
Alignment explanation
Indices: 1217882--1218222 Score: 267
Period size: 93 Copynumber: 3.7 Consensus size: 93
1217872 TGTTTTGTAT
* * *
1217882 ATTTTCTTAAACGTTTTAGATCCCACTATCAATAAAAATTTTGTAAAAGTTTTTAAATGCTTCGG
1 ATTTTCTTAAACGTTTTAGATCCCACCATCAACAAAAATTTTGTAAAAGTTCTTAAATGCTTCGG
1217947 ATGCCCCCACCAAAGATTTCTTTCAAAA
66 ATGCCCCCACCAAAGATTTCTTTCAAAA
* * * * *
1217975 ATTTTCTTAAATGTTTTAGATTCCACCATCGACGAAAATTTTGTAAAAGTTCTTAAATGCTTCAG
1 ATTTTCTTAAACGTTTTAGATCCCACCATCAACAAAAATTTTGTAAAAGTTCTTAAATGCTTCGG
* * * * * **
1218040 AT-ACCCTACTAAAGACTTGTTTTGAAA
66 ATGCCCCCACCAAAGATTTCTTTCAAAA
* * * ** ** * * *
1218067 ATTTTCTTCAATGTTTTCGAT-CCACCATGGATGAAACTTTTGTAAAAATAT-TTAAATGCTTTG
1 ATTTTCTTAAACGTTTTAGATCCCACCATCAACAAAAATTTTGTAAAAGT-TCTTAAATGCTTCG
* ** * ** *
1218130 AATGCCCTAATCAAAGGCTTCATTTGAAAA
65 GATGCCCCCACCAAAGATTTC-TTTCAAAA
* * * * * ** *
1218160 TTTTTCTTAAATGTTTCAGATTCCACCATAAATGAAAATTTTGTAAAAGTATC-TAAATACTTC
1 ATTTTCTTAAACGTTTTAGATCCCACCATCAACAAAAATTTTGTAAAAGT-TCTTAAATGCTTC
1218223 AAATGCCTTC
Statistics
Matches: 200, Mismatches: 43, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
91 36 0.18
92 48 0.24
93 82 0.41
94 34 0.17
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (93 bp):
ATTTTCTTAAACGTTTTAGATCCCACCATCAACAAAAATTTTGTAAAAGTTCTTAAATGCTTCGG
ATGCCCCCACCAAAGATTTCTTTCAAAA
Found at i:1223184 original size:16 final size:16
Alignment explanation
Indices: 1223163--1223210 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1223153 TCTTTGTTTA
1223163 TTTTTTCTTTCTTTTC
1 TTTTTTCTTTCTTTTC
*
1223179 TTTTTTCTCTACTTTTC
1 TTTTTTCT-TTCTTTTC
*
1223196 TCTATTTCTTT-TTTT
1 T-TTTTTCTTTCTTTT
1223211 GATCTTGCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.44
17 9 0.33
18 6 0.22
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTCTTTCTTTTC
Found at i:1225335 original size:23 final size:23
Alignment explanation
Indices: 1225308--1225355 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1225298 GTGATGCCAG
1225308 ATAGATTATCTTGGAAACAATGT
1 ATAGATTATCTTGGAAACAATGT
1225331 ATAGATTATCTTGGAAACAATGT
1 ATAGATTATCTTGGAAACAATGT
1225354 AT
1 AT
1225356 CAACAACTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAGATTATCTTGGAAACAATGT
Found at i:1228386 original size:58 final size:58
Alignment explanation
Indices: 1228276--1228395 Score: 136
Period size: 58 Copynumber: 2.1 Consensus size: 58
1228266 CCATCATGAA
* ** *
1228276 AAATGACCCTAACATACATGAAATTGTATAAAAGTCTCTAGATAATTGAAAATAACCT
1 AAATGACCCTAACATACATAAAATTACATAAAAGTCTCTAAATAATTGAAAATAACCT
* * * *
1228334 AAATGACCCTAATATTCATAAAATTACATAAAAGTC-CTTAAATCA-TGAAAAATAGCCT
1 AAATGACCCTAACATACATAAAATTACATAAAAGTCTC-TAAATAATTG-AAAATAACCT
1228392 AAAT
1 AAAT
1228396 AACATCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
57 3 0.06
58 49 0.94
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (58 bp):
AAATGACCCTAACATACATAAAATTACATAAAAGTCTCTAAATAATTGAAAATAACCT
Found at i:1228687 original size:56 final size:57
Alignment explanation
Indices: 1228485--1228836 Score: 226
Period size: 58 Copynumber: 6.1 Consensus size: 57
1228475 CCTGAGTCTC
* ** * * * * *
1228485 TAGATCAAGGTAAATGATTTAAATGAAATCAAAATTTACAAAATTGCATCCAAGTCCC
1 TAGATCACGGTAAATGACCTAAATGACATCAAAATTCATAAAATTACA-CCAAGTCCT
* * * * * * ** *
1228543 TAGTTCATGGAAAATGACTTAAATGACATCAAAATGCAT-TAATTGACATTAAAGTTACT
1 TAGATCACGGTAAATGACCTAAATGACATCAAAATTCATAAAATT-ACA-CCAAG-TCCT
* * * * *
1228602 CA-ATCATGGAAAATGACCTAAATGGCATCAAAATTTATAAAATTACA-CAAGTCCT
1 TAGATCACGGTAAATGACCTAAATGACATCAAAATTCATAAAATTACACCAAGTCCT
* *
1228657 TAGATCACGGTAAATGATCTAGATGACATCAAAATTCATAAAATTACATCCAAGTCCT
1 TAGATCACGGTAAATGACCTAAATGACATCAAAATTCATAAAATTACA-CCAAGTCCT
* ** * * * * * **
1228715 TATATCATAGAAAATGACCTAAATAACATTAAAATGCATAAAATGACATAAAAGTCCTT
1 TAGATCACGGTAAATGACCTAAATGACATCAAAATTCATAAAATTACA-CCAAGTCC-T
* * ** * * *
1228774 TA-AACATGAAAAAATGACCTAAATGGCATCAAAATTCATAAAATTACATCCAAATCCC
1 TAGATCACG-GTAAATGACCTAAATGACATCAAAATTCATAAAATTACA-CCAAGTCCT
1228832 TAGAT
1 TAGAT
1228837 TATTATCATA
Statistics
Matches: 230, Mismatches: 55, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
55 4 0.02
56 42 0.18
57 4 0.02
58 130 0.57
59 50 0.22
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (57 bp):
TAGATCACGGTAAATGACCTAAATGACATCAAAATTCATAAAATTACACCAAGTCCT
Found at i:1228690 original size:172 final size:173
Alignment explanation
Indices: 1228485--1228821 Score: 455
Period size: 172 Copynumber: 2.0 Consensus size: 173
1228475 CCTGAGTCTC
* * *
1228485 TAGATCAAGGTAAATGATTTAAATGAAATCAAAATTTACAAAATTGCATCCAAGTCCCTAGT-TC
1 TAGATCAAGGTAAATGATCTAAATGAAATCAAAATTCACAAAATTACATCCAAGTCCCTA-TATC
* * * * * * * *
1228549 ATGGAAAATGACTTAAATGACATCAAAATGCATTAATTGACATTAAAGTTAC-TCAATCATG-GA
65 ATAGAAAATGACCTAAATAACATCAAAATGCATAAAATGACATAAAAG-TACTTCAAACATGAAA
*
1228612 AAATGACCTAAATGGCATCAAAATTTATAAAATTACACAAGTCCT
129 AAATGACCTAAATGGCATCAAAATTCATAAAATTACACAAGTCCT
* * * * *
1228657 TAGATCACGGTAAATGATCTAGATGACATCAAAATTCATAAAATTACATCCAAGTCCTTATATCA
1 TAGATCAAGGTAAATGATCTAAATGAAATCAAAATTCACAAAATTACATCCAAGTCCCTATATCA
* * *
1228722 TAGAAAATGACCTAAATAACATTAAAATGCATAAAATGACATAAAAGTCCTTTAAACATGAAAAA
66 TAGAAAATGACCTAAATAACATCAAAATGCATAAAATGACATAAAAGTACTTCAAACATGAAAAA
1228787 ATGACCTAAATGGCATCAAAATTCATAAAATTACA
131 ATGACCTAAATGGCATCAAAATTCATAAAATTACA
1228822 TCCAAATCCC
Statistics
Matches: 142, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
171 3 0.02
172 102 0.72
173 37 0.26
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.27
Consensus pattern (173 bp):
TAGATCAAGGTAAATGATCTAAATGAAATCAAAATTCACAAAATTACATCCAAGTCCCTATATCA
TAGAAAATGACCTAAATAACATCAAAATGCATAAAATGACATAAAAGTACTTCAAACATGAAAAA
ATGACCTAAATGGCATCAAAATTCATAAAATTACACAAGTCCT
Found at i:1228722 original size:114 final size:113
Alignment explanation
Indices: 1228504--1228826 Score: 294
Period size: 114 Copynumber: 2.8 Consensus size: 113
1228494 GTAAATGATT
* * * *
1228504 TAAATGAA-ATCAAAATTTACAAAATTGCATCCAAGTCCCTAGTTCATGGAAAATGACTTAAATG
1 TAAAT-AACATCAAAATTTATAAAATTACA--CAAGTCCTTAGATCATGGAAAATGAC-TAAATG
* * ** *
1228568 ACATCAAAATGCAT-TAATTGACATTAAAGTTACTCAATCATGGAAAATGACC
62 ACATCAAAATTCATAAAATT-ACATCCAAGTTACTCAATCATAGAAAATGACC
** * * *
1228620 TAAATGGCATCAAAATTTATAAAATTACACAAGTCCTTAGATCACGGTAAATGATCTAGATGACA
1 TAAATAACATCAAAATTTATAAAATTACACAAGTCCTTAGATCATGGAAAATGA-CTAAATGACA
* *
1228685 TCAAAATTCATAAAATTACATCCAAG-TCCTTATATCATAGAAAATGACC
65 TCAAAATTCATAAAATTACATCCAAGTTACTCA-ATCATAGAAAATGACC
* ** * * * *
1228734 TAAATAACATTAAAATGCATAAAATGACATAAAAGTCCTTTA-AACATGAAAAAATGACCTAAAT
1 TAAATAACATCAAAATTTATAAAATTAC--ACAAGTCC-TTAGATCATG-GAAAATGA-CTAAAT
*
1228798 GGCATCAAAATTCATAAAATTACATCCAA
61 GACATCAAAATTCATAAAATTACATCCAA
1228827 ATCCCTAGAT
Statistics
Matches: 169, Mismatches: 30, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
113 4 0.02
114 83 0.49
115 5 0.03
116 35 0.21
117 42 0.25
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.27
Consensus pattern (113 bp):
TAAATAACATCAAAATTTATAAAATTACACAAGTCCTTAGATCATGGAAAATGACTAAATGACAT
CAAAATTCATAAAATTACATCCAAGTTACTCAATCATAGAAAATGACC
Found at i:1230167 original size:21 final size:21
Alignment explanation
Indices: 1230143--1230201 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1230133 TAATATTCTT
* *
1230143 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
1230164 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
1230185 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
1230202 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:1231275 original size:17 final size:17
Alignment explanation
Indices: 1231253--1231288 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1231243 CCTTTAAGAC
1231253 AAATTTTCGGTCACATG
1 AAATTTTCGGTCACATG
1231270 AAATTTTCGGTCACATG
1 AAATTTTCGGTCACATG
1231287 AA
1 AA
1231289 GATAATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (17 bp):
AAATTTTCGGTCACATG
Found at i:1231759 original size:13 final size:13
Alignment explanation
Indices: 1231741--1231766 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1231731 ACAATCAAAT
1231741 TTATATCGATATA
1 TTATATCGATATA
1231754 TTATATCGATATA
1 TTATATCGATATA
1231767 ATTTTAATGT
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:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTATATCGATATA
Found at i:1234071 original size:97 final size:97
Alignment explanation
Indices: 1233949--1234140 Score: 357
Period size: 97 Copynumber: 2.0 Consensus size: 97
1233939 ACATTTCTTC
* * *
1233949 ATGTATCGATACATTGTACCTTGTATCGATACAAATAGTGATAGGGTAGCTACTGCCAATTTCAT
1 ATGTATCAATACATTGTACCATGTATCGATACAAATAGTGATAGGGTAGCTACTACCAATTTCAT
1234014 GTATCGATACAATTTGTCCATGTATCGATAAA
66 GTATCGATACAATTTGTCCATGTATCGATAAA
1234046 ATGTATCAATACATTGTACCATGTATCGATACAAATAGTGATAGGGTAGCTACTACCAATTTCAT
1 ATGTATCAATACATTGTACCATGTATCGATACAAATAGTGATAGGGTAGCTACTACCAATTTCAT
1234111 GTATCGATACAATTTGTCCATGTATCGATA
66 GTATCGATACAATTTGTCCATGTATCGATA
1234141 CATTGAACAT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (97 bp):
ATGTATCAATACATTGTACCATGTATCGATACAAATAGTGATAGGGTAGCTACTACCAATTTCAT
GTATCGATACAATTTGTCCATGTATCGATAAA
Found at i:1234073 original size:33 final size:35
Alignment explanation
Indices: 1234012--1234081 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
1234002 TGCCAATTTC
*
1234012 ATGTATCGATACAATTTGTCCATGTATCGATA-AA
1 ATGTATCAATACAATTTGTCCATGTATCGATACAA
1234046 ATGTATCAATAC-A-TTGTACCATGTATCGATACAA
1 ATGTATCAATACAATTTGT-CCATGTATCGATACAA
1234080 AT
1 AT
1234082 AGTGATAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 4 0.12
33 14 0.42
34 15 0.45
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (35 bp):
ATGTATCAATACAATTTGTCCATGTATCGATACAA
Found at i:1234134 original size:21 final size:21
Alignment explanation
Indices: 1234108--1234163 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
1234098 CTACCAATTT
**
1234108 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
1234129 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
*
1234148 CATATATCGATACAAT
1 CATGTATCGATACAAT
1234164 ATATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 15 0.50
20 2 0.07
21 13 0.43
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:1234167 original size:13 final size:13
Alignment explanation
Indices: 1234149--1234175 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1234139 TACATTGAAC
1234149 ATATATCGATACA
1 ATATATCGATACA
1234162 ATATATCGATACA
1 ATATATCGATACA
1234175 A
1 A
1234176 GGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
ATATATCGATACA
Found at i:1234734 original size:15 final size:17
Alignment explanation
Indices: 1234714--1234805 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 17
1234704 GTTTTCGTTT
1234714 TTCT-CCCCTTAAA-AA
1 TTCTCCCCCTTAAACAA
1234729 TTCTCCCCCTTAAACAATTA
1 TTCTCCCCCTTAAAC-A--A
*
1234749 TCTTCTCCCCCTTTATGTAAAAA
1 --TTCTCCCCC-TTA---AACAA
1234772 TTCT-CCCCTTAAA-AA
1 TTCTCCCCCTTAAACAA
*
1234787 TTCTTCCCCTTAAACAA
1 TTCTCCCCCTTAAACAA
1234804 TT
1 TT
1234806 ATCTTCTCAA
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
15 10 0.16
16 20 0.32
17 4 0.06
18 1 0.02
19 3 0.05
20 5 0.08
21 4 0.06
22 9 0.14
23 4 0.06
25 1 0.02
26 2 0.03
ACGTcount: A:0.29, C:0.33, G:0.01, T:0.37
Consensus pattern (17 bp):
TTCTCCCCCTTAAACAA
Found at i:1242841 original size:33 final size:33
Alignment explanation
Indices: 1242804--1242867 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
1242794 GTTAAAAGCT
1242804 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
1242837 ATGTATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACATTGTACCATGTATCGATA
1242868 TAAATAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:1242842 original size:13 final size:13
Alignment explanation
Indices: 1242824--1242854 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1242814 ACATTTCTTC
1242824 ATGTATCGATACA
1 ATGTATCGATACA
1242837 ATGTATCGATACA
1 ATGTATCGATACA
*
1242850 TTGTA
1 ATGTA
1242855 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1242961 original size:33 final size:35
Alignment explanation
Indices: 1242900--1242969 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
1242890 TGCCATTTTC
1242900 ATGTATCGATACAATTTGTCCATGTATCGATA-AA
1 ATGTATCGATACAATTTGTCCATGTATCGATACAA
*
1242934 ATGTATTGATAC-A-TTGTACCATGTATCGATACAA
1 ATGTATCGATACAATTTGT-CCATGTATCGATACAA
1242968 AT
1 AT
1242970 AGTGATAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 4 0.12
33 14 0.42
34 15 0.45
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (35 bp):
ATGTATCGATACAATTTGTCCATGTATCGATACAA
Found at i:1242970 original size:97 final size:97
Alignment explanation
Indices: 1242804--1243028 Score: 389
Period size: 97 Copynumber: 2.3 Consensus size: 97
1242794 GTTAAAAGCT
* * *
1242804 ATGTATCGATAC-ATTTCTTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATA
1 ATGTATCGATACAATTTGTCCATGTATCGATAAAATGTATCGATACATTGTACCATGTATCGATA
* *
1242868 TAAATAGTGATAGGGTAGCTACTGCCATTTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
*
1242900 ATGTATCGATACAATTTGTCCATGTATCGATAAAATGTATTGATACATTGTACCATGTATCGATA
1 ATGTATCGATACAATTTGTCCATGTATCGATAAAATGTATCGATACATTGTACCATGTATCGATA
1242965 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
1242997 ATGTATCGATACAATTTGTCCATGTATCGATA
1 ATGTATCGATACAATTTGTCCATGTATCGATA
1243029 CATTGAACAT
Statistics
Matches: 122, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
96 12 0.10
97 110 0.90
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (97 bp):
ATGTATCGATACAATTTGTCCATGTATCGATAAAATGTATCGATACATTGTACCATGTATCGATA
CAAATAGTGATAGGGTAGCTACTGCCAATTTC
Found at i:1243022 original size:21 final size:21
Alignment explanation
Indices: 1242996--1243051 Score: 80
Period size: 19 Copynumber: 2.8 Consensus size: 21
1242986 CTGCCAATTT
**
1242996 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGAA
1243017 CATGTATCGATAC-A-TTGAA
1 CATGTATCGATACAATTTGAA
1243036 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1243052 GTATTGATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGAA
Found at i:1244027 original size:13 final size:13
Alignment explanation
Indices: 1244009--1244033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1243999 TCATTGTTCA
1244009 TGTATCGATACAG
1 TGTATCGATACAG
1244022 TGTATCGATACA
1 TGTATCGATACA
1244034 TTGTGGATAG
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:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1244554 original size:36 final size:35
Alignment explanation
Indices: 1244493--1244560 Score: 100
Period size: 36 Copynumber: 1.9 Consensus size: 35
1244483 CGAAGTGATT
***
1244493 GAGAGGTTCTATCTTAGCTTTTGAAAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCCGTG-AAAAGATAGGGA
1244529 GAGAGGTTCTATCTTAGCCCGTGAAAAGATAG
1 GAGAGGTTCTATCTTAGCCCGTGAAAAGATAG
1244561 AGAGGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCCGTGAAAAGATAGGGA
Found at i:1244585 original size:31 final size:30
Alignment explanation
Indices: 1244528--1244590 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
1244518 AAAGATAGGG
1244528 AGAGAGGTTCTATCTTAGCCCGTGAAAAGAT
1 AGAGAGGTTCTATCTTAGCCCGTG-AAAGAT
* *
1244559 AGAGAGGTTTTTATCTTAG-CCTTGAAAGAT
1 AGAGAGG-TTCTATCTTAGCCCGTGAAAGAT
1244589 AG
1 AG
1244591 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 8 0.28
31 11 0.38
32 10 0.34
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (30 bp):
AGAGAGGTTCTATCTTAGCCCGTGAAAGAT
Found at i:1245365 original size:13 final size:13
Alignment explanation
Indices: 1245340--1245380 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1245330 CCGTTGGACT
1245340 CAATGTATCGATA
1 CAATGTATCGATA
* *
1245353 CACTGTATTGATA
1 CAATGTATCGATA
1245366 CAATGTATCGATA
1 CAATGTATCGATA
1245379 CA
1 CA
1245381 TGAACAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1245436 original size:17 final size:17
Alignment explanation
Indices: 1245381--1245451 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
1245371 TATCGATACA
*
1245381 TGAACAATGATAAACAG
1 TGAACAATGATGAACAG
* *
1245398 T-AATAAATAATG-ACATG
1 TGAA-CAATGATGAACA-G
*
1245415 TGAACAGTTG-TGAACAG
1 TGAACA-ATGATGAACAG
1245432 TGAACAATGATGAACAG
1 TGAACAATGATGAACAG
1245449 TGA
1 TGA
1245452 TGTATCGATA
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
16 7 0.17
17 28 0.68
18 6 0.15
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (17 bp):
TGAACAATGATGAACAG
Found at i:1246058 original size:11 final size:10
Alignment explanation
Indices: 1246025--1246070 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
1246015 CAAACTGATC
1246025 TTTTTC-CTT
1 TTTTTCTCTT
1246034 TTTTTCT-TT
1 TTTTTCTCTT
1246043 GTTTTTCTCATT
1 -TTTTTCTC-TT
1246055 TTTTTCTTCTT
1 TTTTTC-TCTT
1246066 TTTTT
1 TTTTT
1246071 TTTGGGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 8 0.25
10 7 0.22
11 13 0.41
12 4 0.12
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:1249055 original size:15 final size:16
Alignment explanation
Indices: 1249035--1249069 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1249025 ACATCATTTT
1249035 TTTTAAATATTG-ATG
1 TTTTAAATATTGAATG
*
1249050 TTTTAAATTTTGAATG
1 TTTTAAATATTGAATG
1249066 TTTT
1 TTTT
1249070 GGTAAGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTTTAAATATTGAATG
Found at i:1249900 original size:5 final size:5
Alignment explanation
Indices: 1249890--1249914 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1249880 CCTTTTTAGC
1249890 CATAA CATAA CATAA CATAA CATAA
1 CATAA CATAA CATAA CATAA CATAA
1249915 TTAAACATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
CATAA
Found at i:1256029 original size:19 final size:19
Alignment explanation
Indices: 1255983--1256039 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
1255973 CTGCCAGTTT
1255983 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGTC
1256003 CATGTATCGATACAATGAT-
1 CATGTATCGATACAATG-TC
*
1256022 CTTGTATCGATACAATGT
1 CATGTATCGATACAATGT
1256040 ATCGATGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 16 0.46
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
CATGTATCGATACAATGTC
Found at i:1258295 original size:13 final size:13
Alignment explanation
Indices: 1258277--1258301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1258267 ATTACTCAAA
1258277 TGTATCGATACAT
1 TGTATCGATACAT
1258290 TGTATCGATACA
1 TGTATCGATACA
1258302 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1258366 original size:52 final size:52
Alignment explanation
Indices: 1258310--1258418 Score: 200
Period size: 52 Copynumber: 2.1 Consensus size: 52
1258300 CACTGATCTT
*
1258310 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1258362 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1258414 TGTAT
1 TGTAT
1258419 ACATGCAGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1271690 original size:92 final size:91
Alignment explanation
Indices: 1271518--1271841 Score: 328
Period size: 92 Copynumber: 3.5 Consensus size: 91
1271508 TGTTTTCTAT
* * * * *
1271518 ATTTTCTTAAACGTTTTAGATCCCACTATCAATAAAAATTTTGTAAAAGTTTTTAAATGCTTCGG
1 ATTTTCTTAAATGTTTTAGATTCCACCATCAATGAAAATTTTGTAAAAG-TTTTAAATGCTT-TG
* * *
1271583 ATGCCCCCACCAAAGATTTCTTTCAAAA
64 ATGCCCCAATCAAAGACTTCTTTCAAAA
* *
1271611 ATTTTCTTAAATGTTTTAGATTCCACCATCGA-CAAAATTTTGTAAAAGTTCTTAAATGCTTTAG
1 ATTTTCTTAAATGTTTTAGATTCCACCATCAATGAAAATTTTGTAAAAGTT-TTAAATGCTTT-G
* * * * * **
1271675 ATACCTCTATTAAAGACTTGTTTTGAAA
64 ATGCCCCAATCAAAGACTTCTTTCAAAA
* * ** * * *
1271703 ATTTTCTTCAATGTTTTCGA-TCCACCATGGATGAAACTTTTATAAAAATATTTAAATGCTTTGA
1 ATTTTCTTAAATGTTTTAGATTCCACCATCAATGAAAATTTTGTAAAAGT-TTTAAATGCTTTG-
* *
1271767 ATGCCCCAATCAAAGGCTTCATTTGAAAA
64 ATGCCCCAATCAAAGACTTC-TTTCAAAA
*
1271796 TTTTTCTTAAATGTTTTAGATTCCACCATCAATGAAAATTTTGTAA
1 ATTTTCTTAAATGTTTTAGATTCCACCATCAATGAAAATTTTGTAA
1271842 GAGTATCTAA
Statistics
Matches: 187, Mismatches: 37, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
91 13 0.07
92 101 0.54
93 52 0.28
94 21 0.11
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (91 bp):
ATTTTCTTAAATGTTTTAGATTCCACCATCAATGAAAATTTTGTAAAAGTTTTAAATGCTTTGAT
GCCCCAATCAAAGACTTCTTTCAAAA
Found at i:1276834 original size:17 final size:16
Alignment explanation
Indices: 1276804--1276837 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1276794 TCTTTGTTTA
*
1276804 TTTTTTCTTTCTTTTC
1 TTTTTTCTTACTTTTC
1276820 TTTTTTCTCTACTTTTC
1 TTTTTTCT-TACTTTTC
1276837 T
1 T
1276838 CTATTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCTTACTTTTC
Found at i:1281628 original size:19 final size:21
Alignment explanation
Indices: 1281604--1281656 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1281594 AGTGATACAT
1281604 TGTATCGATACAA-TACT-TA
1 TGTATCGATACAATTACTGTA
* *
1281623 TGTATCGATACAATTTCTGTT
1 TGTATCGATACAATTACTGTA
1281644 TGTATCGATACAA
1 TGTATCGATACAA
1281657 ATCATTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (21 bp):
TGTATCGATACAATTACTGTA
Found at i:1285652 original size:58 final size:58
Alignment explanation
Indices: 1285580--1285932 Score: 255
Period size: 58 Copynumber: 6.1 Consensus size: 58
1285570 CTGAGTCTCG
* * * *
1285580 AGATCAAGGTAAATGATTTAAATGACAACAAAATTTACAAAATTACATCCAAGTCCCT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
* * * * ** **
1285638 AGTTCATGGAAAATGATTTAAATGACATCAAAA--TGCATTAATTGACATTAAAGTCATT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACA-AAATT-ACATCCAAGTCCCT
* * * *
1285696 CGATCATGGAAAATGACCTAAATGGCATCAAAATTTATAAAATTACA-CACAAGTCCCT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATC-CAAGTCCCT
* * * * * *
1285754 AGATCATGGTAAATGATCTAGATGACATCAAAATTCATAAAATTACATCTAAGTCCTT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
* * * * * * ** * * ** *
1285812 ATATCATAGAAAATGACCTAAATAATATTAAAATGCATAAAATGACATAAAAGTCCTTT
1 AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCC-CT
* * * * * * *
1285871 A-AACATGAAAAAATGACCTAAATGGCATCAAAATTCATAAAATTACATCCAAATCCCT
1 AGATCATG-GAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
1285929 AGAT
1 AGAT
1285933 TATTATCACA
Statistics
Matches: 230, Mismatches: 56, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
56 3 0.01
57 4 0.02
58 174 0.76
59 47 0.20
60 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (58 bp):
AGATCATGGAAAATGATCTAAATGACATCAAAATTTACAAAATTACATCCAAGTCCCT
Found at i:1285718 original size:116 final size:116
Alignment explanation
Indices: 1285598--1285919 Score: 310
Period size: 116 Copynumber: 2.8 Consensus size: 116
1285588 GTAAATGATT
* *
1285598 TAAATGACAACAAAATTTACAAAATTACATC-CAAGTCCCTAGTTCATGGAAAATGATTTAAATG
1 TAAATGACAACAAAATTTACAAAATTACA-CACAAGTCCCTAGATCATGGAAAATGATCTAAATG
* * *
1285662 ACATCAAAATGCAT-TAATTGACAT-TAAAGTCATTCGATCATGGAAAATGACC
65 ACATCAAAATGCATAAAATT-ACATCT-AAGTCATTAGATCATAGAAAATGACC
* * * * *
1285714 TAAATGGCATCAAAATTTATAAAATTACACACAAGTCCCTAGATCATGGTAAATGATCTAGATGA
1 TAAATGACAACAAAATTTACAAAATTACACACAAGTCCCTAGATCATGGAAAATGATCTAAATGA
* * *
1285779 CATCAAAATTCATAAAATTACATCTAAGTCCTTATATCATAGAAAATGACC
66 CATCAAAATGCATAAAATTACATCTAAGTCATTAGATCATAGAAAATGACC
* * ** ** * * * * * * * *
1285830 TAAATAATATTAAAATGCATAAAATGACATAAAAGTCCTTTA-AACATGAAAAAATGACCTAAAT
1 TAAATGACAACAAAATTTACAAAATTACACACAAGTCC-CTAGATCATG-GAAAATGATCTAAAT
* *
1285894 GGCATCAAAATTCATAAAATTACATC
64 GACATCAAAATGCATAAAATTACATC
1285920 CAAATCCCTA
Statistics
Matches: 172, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
115 1 0.01
116 128 0.74
117 43 0.25
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (116 bp):
TAAATGACAACAAAATTTACAAAATTACACACAAGTCCCTAGATCATGGAAAATGATCTAAATGA
CATCAAAATGCATAAAATTACATCTAAGTCATTAGATCATAGAAAATGACC
Found at i:1285788 original size:174 final size:173
Alignment explanation
Indices: 1285439--1285932 Score: 505
Period size: 174 Copynumber: 2.8 Consensus size: 173
1285429 TGACCCCATT
* ** * *
1285439 ATTCATAAAATTACATAAAAGTCCTTAGATCAT-GAAAAAT-AGCCTAAATGATATCAAAATGCA
1 ATTCACAAAATTACATCCAAGTCCCTATATCATAG-AAAATGA-CCTAAATGATATCAAAATGCA
* * * * ** *
1285502 TGAAATGAC-TTAAAAGTCCGTAGATCATAG-AAATAACCTAAATGGCATCAAAATTCACGAGAT
64 TAAAATGACATT-AAAGTCCTTAGATCATGGAAAATGACCTAAATGGCATCAAAATTCATAAAAT
** * * * *
1285565 TGTACCTGAGTCTCGAGATCAAGGTAAATGATTTAAATGACAACAAA
128 TACACC-AAGTCCCTAGATCAAGGTAAATGATCTAAATGACAACAAA
* * ** *
1285612 ATTTACAAAATTACATCCAAGTCCCTAGT-TCATGGAAAATGATTTAAATGACATCAAAATGCAT
1 ATTCACAAAATTACATCCAAGTCCCTA-TATCATAGAAAATGACCTAAATGATATCAAAATGCAT
* * * * *
1285676 TAATTGACATTAAAGTCATTCGATCATGGAAAATGACCTAAATGGCATCAAAATTTATAAAATTA
65 AAAATGACATTAAAGTCCTTAGATCATGGAAAATGACCTAAATGGCATCAAAATTCATAAAATTA
* * *
1285741 CACACAAGTCCCTAGATCATGGTAAATGATCTAGATGACATCAAA
130 CAC-CAAGTCCCTAGATCAAGGTAAATGATCTAAATGACAACAAA
* * * * *
1285786 ATTCATAAAATTACATCTAAGTCCTTATATCATAGAAAATGACCTAAATAATATTAAAATGCATA
1 ATTCACAAAATTACATCCAAGTCCCTATATCATAGAAAATGACCTAAATGATATCAAAATGCATA
* * *
1285851 AAATGACATAAAAGTCCTTTA-AACATGAAAAAATGACCTAAATGGCATCAAAATTCATAAAATT
66 AAATGACATTAAAGTCC-TTAGATCATG-GAAAATGACCTAAATGGCATCAAAATTCATAAAATT
*
1285915 ACATCCAAATCCCTAGAT
129 ACA-CCAAGTCCCTAGAT
1285933 TATTATCACA
Statistics
Matches: 263, Mismatches: 48, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
173 71 0.27
174 139 0.53
175 52 0.20
176 1 0.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (173 bp):
ATTCACAAAATTACATCCAAGTCCCTATATCATAGAAAATGACCTAAATGATATCAAAATGCATA
AAATGACATTAAAGTCCTTAGATCATGGAAAATGACCTAAATGGCATCAAAATTCATAAAATTAC
ACCAAGTCCCTAGATCAAGGTAAATGATCTAAATGACAACAAA
Found at i:1292003 original size:20 final size:20
Alignment explanation
Indices: 1291974--1292011 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1291964 TAGGCTCAAC
*
1291974 GTATCGATACAATTTACTAT
1 GTATCAATACAATTTACTAT
1291994 GTATCAATACAATTTACT
1 GTATCAATACAATTTACT
1292012 TGGGTAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
GTATCAATACAATTTACTAT
Found at i:1292095 original size:32 final size:33
Alignment explanation
Indices: 1292054--1292117 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1292044 CATTTCATGT
1292054 TGTATCGATACAAAG-AACATGTACCGATACAA
1 TGTATCGATACAAAGCAACATGTACCGATACAA
* * *
1292086 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACAAAGCAACATGTACCGATACA
1292118 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACATGTACCGATACAA
Found at i:1292129 original size:20 final size:21
Alignment explanation
Indices: 1292106--1292144 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1292096 CTAAGCAATA
1292106 TGTATCGATACA-TCTAGGTG
1 TGTATCGATACATTCTAGGTG
1292126 TGTATCGATACATTCTAGG
1 TGTATCGATACATTCTAGG
1292145 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTAGGTG
Found at i:1294844 original size:32 final size:33
Alignment explanation
Indices: 1294783--1294844 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1294773 GACCTAGACG
*
1294783 TATCGATACATATTGCTTTGTATCAATACAATA
1 TATCGATACATATTGCTTAGTATCAATACAATA
*
1294816 TATCGATACATGA-T-CTTAGTATCGATACA
1 TATCGATACAT-ATTGCTTAGTATCAATACA
1294845 CAGCAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 13 0.50
33 12 0.46
34 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (33 bp):
TATCGATACATATTGCTTAGTATCAATACAATA
Found at i:1294928 original size:13 final size:13
Alignment explanation
Indices: 1294910--1294940 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1294900 CAATACATGG
1294910 TACATTGTATCAA
1 TACATTGTATCAA
*
1294923 TACATTGTATCGA
1 TACATTGTATCAA
1294936 TACAT
1 TACAT
1294941 AGTGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTGTATCAA
Found at i:1297108 original size:21 final size:21
Alignment explanation
Indices: 1297055--1297115 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1297045 GATGTGCTTA
* **
1297055 AAAAGAAAAAAAAAGAATTAG
1 AAAAGAAAATAAGTGAATTAG
1297076 AAAAGAAAATAAGTGAATTAG
1 AAAAGAAAATAAGTGAATTAG
* *
1297097 AAAAGAAGATAATTGAATT
1 AAAAGAAAATAAGTGAATT
1297116 GCAAGATGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (21 bp):
AAAAGAAAATAAGTGAATTAG
Found at i:1297156 original size:21 final size:21
Alignment explanation
Indices: 1297130--1297185 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1297120 GATGGTAATA
1297130 AAGAATTAGCTAATGAA-AAC
1 AAGAATTAGCTAATGAAGAAC
*
1297150 AATGAATTGGCTAA-GAAGAAC
1 AA-GAATTAGCTAATGAAGAAC
*
1297171 AAGAACTTACCTAAT
1 AAGAA-TTAGCTAAT
1297186 TCATTTTCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.21
Consensus pattern (21 bp):
AAGAATTAGCTAATGAAGAAC
Found at i:1298283 original size:33 final size:32
Alignment explanation
Indices: 1298237--1298301 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1298227 CACACCCAGA
* * *
1298237 TGTATCGATACATGCTGCTTTGTATTGATACAT
1 TGTATCGACACATG-TGCATTGTATCGATACAT
*
1298270 TGTATCGACACATGTTCATTGTATCGATACAT
1 TGTATCGACACATGTGCATTGTATCGATACAT
1298302 GGACAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGACACATGTGCATTGTATCGATACAT
Found at i:1300641 original size:21 final size:21
Alignment explanation
Indices: 1300617--1300664 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1300607 AAGTAGATAT
*
1300617 TAAAAAATTGGCTAATG-AAAA
1 TAAAAAATTAGCTAA-GAAAAA
*
1300638 TAAAGAATTAGCTAAGAAAAA
1 TAAAAAATTAGCTAAGAAAAA
1300659 TAAAAA
1 TAAAAA
1300665 CTTGCATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.21
Consensus pattern (21 bp):
TAAAAAATTAGCTAAGAAAAA
Found at i:1304583 original size:13 final size:13
Alignment explanation
Indices: 1304565--1304608 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
1304555 ATACAACATT
1304565 CATTGTATCGATA
1 CATTGTATCGATA
1304578 CATTGTATCGATA
1 CATTGTATCGATA
*
1304591 CAATGTATCGATA
1 CATTGTATCGATA
1304604 CATTG
1 CATTG
1304609 GGTACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1309711 original size:52 final size:52
Alignment explanation
Indices: 1309633--1309833 Score: 341
Period size: 52 Copynumber: 3.9 Consensus size: 52
1309623 CGAAATATGA
*
1309633 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
1309685 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
1309737 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
1309789 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
1309834 ATGTATCGAT
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
51 2 0.01
52 141 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:1309840 original size:13 final size:13
Alignment explanation
Indices: 1309822--1309846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1309812 CAAAGATCAG
1309822 TGTATCGATACAA
1 TGTATCGATACAA
1309835 TGTATCGATACA
1 TGTATCGATACA
1309847 TTTAAGTGAT
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:1309926 original size:13 final size:13
Alignment explanation
Indices: 1309908--1309932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1309898 CAAAAAAACA
1309908 TGTATCGATACAT
1 TGTATCGATACAT
1309921 TGTATCGATACA
1 TGTATCGATACA
1309933 ACACTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1310031 original size:21 final size:21
Alignment explanation
Indices: 1309990--1310031 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1309980 GTTGGGACCT
*
1309990 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1310011 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1310032 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1311347 original size:44 final size:45
Alignment explanation
Indices: 1311281--1311372 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 45
1311271 TTAAAGATGG
* * *
1311281 AAAAGGTGCCAATAGGCTGATT-CAAGGCCCAGCT-TATTGGACTT
1 AAAAGGGGCCAATAGGCGGATTCCAAGG-CCAGCTACATTGGACTT
*
1311325 AAAAGGGGCCAAT-GTGCGGATTCCAAGGTCAGCTACATTGGACTT
1 AAAAGGGGCCAATAG-GCGGATTCCAAGGCCAGCTACATTGGACTT
1311370 AAA
1 AAA
1311373 GATGGAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.56
45 17 0.41
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (45 bp):
AAAAGGGGCCAATAGGCGGATTCCAAGGCCAGCTACATTGGACTT
Found at i:1311452 original size:30 final size:29
Alignment explanation
Indices: 1311408--1311858 Score: 196
Period size: 29 Copynumber: 15.3 Consensus size: 29
1311398 GGGCTGTCGA
* *
1311408 AAAGGGTGCCACTGATTTGTGGGGCTTTG-
1 AAAGGTTGCCACTGACTTGT-GGGCTTTGT
1311437 AAAGGTTGCCCACTGACTTGTGGGC-TTGT
1 AAAGGTTG-CCACTGACTTGTGGGCTTTGT
*
1311466 AAAGGTTTGCCACTGACTTGTGGGCTTTCCGA
1 AAAGG-TTGCCACTGACTTGTGGGCTTT--GT
** *
1311498 AAAAATATGCCA-AGACTTGTGGGCTTT-T
1 AAAGGT-TGCCACTGACTTGTGGGCTTTGT
** * *
1311526 GAAAAATAT-CCACTTACTTGTTGGCTTT-T
1 -AAAGGT-TGCCACTGACTTGTGGGCTTTGT
* *
1311555 AAAGGTTTCCACTGACCTTGTGGGCTTGTGAAA
1 AAAGGTTGCCACTGA-CTTGTGGGCTT-TG--T
** *
1311588 AAAAATT-CC-CTGACTTGTGGGCTTTTGA
1 AAAGGTTGCCACTGACTTGTGGGC-TTTGT
* *
1311616 AAAGGGTGCCACTAACATTTACTTGTGGGCTTT-T
1 AAAGGTTG-C-C--AC--TGACTTGTGGGCTTTGT
1311650 -AAGGTTGCCACTGAC-TGT--GCTTT-T
1 AAAGGTTGCCACTGACTTGTGGGCTTTGT
*
1311674 AAAGGTTGCCACTGAATT-TGGGCTTT-T
1 AAAGGTTGCCACTGACTTGTGGGCTTTGT
** *
1311701 CGAAAAATATGCCACTCTGACTTGTGGGCTTTTTGA
1 --AAAGGT-TGCCA--CTGACTTGTGGGC--TTTGT
**
1311737 AAAAATATGCCACTGACTTGTGGGCTTT-T
1 AAAGGT-TGCCACTGACTTGTGGGCTTTGT
1311766 -AAGGTTGCCACTGACTTGT-GGCTTT-T
1 AAAGGTTGCCACTGACTTGTGGGCTTTGT
*
1311792 GAAA--TATGCC-CTGACTTTGGTGGGCTTTTT
1 -AAAGGT-TGCCACTGAC-TT-GTGGGCTTTGT
* *
1311822 GAACAGGGTGCCACTAACTTGTGGGCTTTG-
1 -AA-AGGTTGCCACTGACTTGTGGGCTTTGT
1311852 -AAGGTTG
1 AAAGGTTG
1311859 GCCAACTCTT
Statistics
Matches: 338, Mismatches: 36, Indels: 98
0.72 0.08 0.21
Matches are distributed among these distances:
24 6 0.02
25 15 0.04
26 17 0.05
27 35 0.10
28 29 0.09
29 75 0.22
30 41 0.12
31 33 0.10
32 37 0.11
33 20 0.06
34 13 0.04
35 6 0.02
36 11 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTGT
Found at i:1311522 original size:89 final size:88
Alignment explanation
Indices: 1311424--1311665 Score: 235
Period size: 89 Copynumber: 2.7 Consensus size: 88
1311414 TGCCACTGAT
*
1311424 TTGTGGGGC-TTTGAAAGGTTGCCCACTGACTTGTGGGCTTGTAAAGGTTTGCCACTGACTTGTG
1 TTGT-GGGCTTTTGAAAGGTTGCCCACTTACTTGTGGGCTT-TAAAGGTTTGCCACTGACTTGTG
*
1311488 GGCTT-TCCGAAAAAATATGCCAAGAC
64 GGCTTGT--GAAAAAAAATGCCAAGAC
** *
1311514 TTGTGGGCTTTTGAAAAATAT--CCACTTACTTGTTGGCTTTTAAAGGTTT-CCACTGACCTTGT
1 TTGTGGGCTTTTGAAAGGT-TGCCCACTTACTTGTGGGC-TTTAAAGGTTTGCCACTGA-CTTGT
* **
1311576 GGGCTTGTGAAAAAAAATTCCCTGAC
63 GGGCTTGTGAAAAAAAATGCCAAGAC
* *
1311602 TTGTGGGCTTTTGAAAAGGGTGCCACTAACATTTACTTGTGGGCTTTTAAGG-TTGCCACTGACT
1 TTGTGGGCTTTTG-AAAGGTTGCC-C--AC--TTACTTGTGGGCTTTAAAGGTTTGCCACTGACT
1311666 GTGCTTTTAA
Statistics
Matches: 125, Mismatches: 13, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
88 35 0.28
89 41 0.33
90 16 0.13
91 2 0.02
93 6 0.05
94 14 0.11
95 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (88 bp):
TTGTGGGCTTTTGAAAGGTTGCCCACTTACTTGTGGGCTTTAAAGGTTTGCCACTGACTTGTGGG
CTTGTGAAAAAAAATGCCAAGAC
Found at i:1311739 original size:33 final size:32
Alignment explanation
Indices: 1311680--1311765 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
1311670 TTTTAAAGGT
*
1311680 TGCCACTGAATT-TGGGCTTTTCG-AAAAATA
1 TGCCACTGACTTGTGGGCTTTTCGAAAAAATA
*
1311710 TGCCACTCTGACTTGTGGGCTTTTTGAAAAAATA
1 TGCCA--CTGACTTGTGGGCTTTTCGAAAAAATA
1311744 TGCCACTGACTTGTGGGCTTTT
1 TGCCACTGACTTGTGGGCTTTT
1311766 AAGGTTGCCA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
30 5 0.10
32 23 0.46
33 10 0.20
34 12 0.24
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (32 bp):
TGCCACTGACTTGTGGGCTTTTCGAAAAAATA
Found at i:1311777 original size:91 final size:88
Alignment explanation
Indices: 1311655--1311917 Score: 251
Period size: 91 Copynumber: 3.0 Consensus size: 88
1311645 CTTTTAAGGT
1311655 TGCCACTGAC-TGT--GCTTTTAAAGGTTGCCACTGAATTTGGGCTTTTCGAAAAATATGCCACT
1 TGCCACTGACTTGTGGGCTTTT-AAGGTTGCCACTGAATTTGGGCTTTT-GAAAAATATG-CAC-
*
1311717 CTGACTTGTGGGCTTTTTGAAAAAATA
62 CTGACTTGTGGGCTTTTTGAAAAAAGA
*
1311744 TGCCACTGACTTGTGGGCTTTTAAGGTTGCCACTG-ACTTGTGGCTTTTG--AAATATGC-CCTG
1 TGCCACTGACTTGTGGGCTTTTAAGGTTGCCACTGAATTTG-GGCTTTTGAAAAATATGCACCTG
* * *
1311805 ACTTTGGTGGGCTTTTTG-AACAGGG
65 AC-TT-GTGGGCTTTTTGAAAAAAGA
* * * * *
1311830 TGCCACTAACTTGTGGGCTTTGAAGGTTGGCCAACTCTTGACTTTGGGCTTTTAAAAAAAATGCA
1 TGCCACTGACTTGTGGGCTTTTAAGGTT-GCC-A--C-TGAATTTGGGCTTTTGAAAAATATGCA
1311895 -CTGACTTGTGGGC--TTTGAAAAAA
61 CCTGACTTGTGGGCTTTTTGAAAAAA
1311918 ATTGGCCCCC
Statistics
Matches: 145, Mismatches: 13, Indels: 31
0.77 0.07 0.16
Matches are distributed among these distances:
85 5 0.03
86 32 0.22
87 16 0.11
88 8 0.06
89 14 0.10
90 12 0.08
91 35 0.24
92 11 0.08
93 12 0.08
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (88 bp):
TGCCACTGACTTGTGGGCTTTTAAGGTTGCCACTGAATTTGGGCTTTTGAAAAATATGCACCTGA
CTTGTGGGCTTTTTGAAAAAAGA
Found at i:1311784 original size:59 final size:60
Alignment explanation
Indices: 1311717--1311850 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 60
1311707 ATATGCCACT
*
1311717 CTGACTTGTGGGCTTTTTGAAAAAATATGCCACTGAC-TT-GTGGGC-TTTT-A-AGGTTGCCA
1 CTGACTTGTGGGCTTTTTG---AAATATGCC-CTGACTTTGGTGGGCTTTTTAACAGGGTGCCA
1311776 CTGACTTGT-GGC-TTTTGAAATATGCCCTGACTTTGGTGGGCTTTTTGAACAGGGTGCCA
1 CTGACTTGTGGGCTTTTTGAAATATGCCCTGACTTTGGTGGGCTTTTT-AACAGGGTGCCA
*
1311835 CTAACTTGTGGGCTTT
1 CTGACTTGTGGGCTTT
1311851 GAAGGTTGGC
Statistics
Matches: 65, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
53 5 0.08
54 11 0.17
55 6 0.09
56 4 0.06
57 5 0.08
58 4 0.06
59 25 0.38
60 3 0.05
61 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.37
Consensus pattern (60 bp):
CTGACTTGTGGGCTTTTTGAAATATGCCCTGACTTTGGTGGGCTTTTTAACAGGGTGCCA
Found at i:1311805 original size:26 final size:27
Alignment explanation
Indices: 1311636--1311820 Score: 118
Period size: 27 Copynumber: 6.5 Consensus size: 27
1311626 ACTAACATTT
*
1311636 ACTTGTGGGCTTTTAAGGT-TGCCACTG
1 ACTTGTGGGCTTTTAA-ATATGCCACTG
1311663 AC-TGT--GCTTTTAAAGGT-TGCCACTG
1 ACTTGTGGGCTTTTAAA--TATGCCACTG
*
1311688 AATT-TGGGCTTTTCGAAAAATATGCCACTCTG
1 ACTTGTGGGCTTTT----AAATATGCCA--CTG
1311720 ACTTGTGGGCTTTTTGAAAAAATATGCCACTG
1 ACTTGTGGGC-TTTT----AAATATGCCACTG
*
1311752 ACTTGTGGGCTTTTAAGGT-TGCCACTG
1 ACTTGTGGGCTTTTAA-ATATGCCACTG
1311779 ACTTGT-GGCTTTTGAAATATGCC-CTG
1 ACTTGTGGGCTTTT-AAATATGCCACTG
1311805 ACTTTGGTGGGCTTTT
1 AC-TT-GTGGGCTTTT
1311821 TGAACAGGGT
Statistics
Matches: 131, Mismatches: 7, Indels: 38
0.74 0.04 0.22
Matches are distributed among these distances:
24 8 0.06
25 11 0.08
26 17 0.13
27 32 0.24
28 3 0.02
29 8 0.06
30 5 0.04
31 7 0.05
32 19 0.15
33 5 0.04
34 16 0.12
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (27 bp):
ACTTGTGGGCTTTTAAATATGCCACTG
Found at i:1311824 original size:208 final size:211
Alignment explanation
Indices: 1311424--1311839 Score: 532
Period size: 208 Copynumber: 2.0 Consensus size: 211
1311414 TGCCACTGAT
*
1311424 TTGTGGGGCTTTGAAAGGTTGCCCACTGACTTGTGGGCTTGTAAAGGTTTGCCACTGACTTGTGG
1 TTGTGGGGCTTTGAAAGGTTGCCCACTGACTTGT-GGCTTGTAAAGGTTTGCCACTGAATTGTGG
* *
1311489 GCTTTCCGAAAAAATATGCCAAGACTTGTGGGCTTTTGAAAAATATCCACTTACTTGTTGGCTTT
65 GCTTTCCGAAAAAATATGCCAAGACTTGTGGGCTTTTGAAAAATATCCACTGACTTGTGGGCTTT
* *
1311554 TAAAGGTTTCCACTGACCTTGTGGGCTTGTGAAAAAAAATTCCCTGACTTGTGGGCTTTTGAAAA
130 TAAAGGTTGCCACTGACCTTGTGGGCTTGTG--AAAAAATGCCCTGACTTGTGGGCTTTTGAAAA
1311619 GGGTGCCACTAACATTTAC
193 GGGTGCCACTAACATTTAC
* *
1311638 TTGT-GGGCTTT-TAAGGTTG-CCACTGAC-TGT-GCTTTTAAAGG-TTGCCACTGAATT-TGGG
1 TTGTGGGGCTTTGAAAGGTTGCCCACTGACTTGTGGCTTGTAAAGGTTTGCCACTGAATTGTGGG
* *
1311696 CTTTTCG-AAAAATATGCCACTCTGACTTGTGGGCTTTTTGAAAAAATATGCCACTGACTTGTGG
66 CTTTCCGAAAAAATATGCCA---AGACTTGTGGGC-TTTTG-AAAAATAT-CCACTGACTTGTGG
* *
1311760 GCTTTT-AAGGTTGCCACTGA-CTTGT-GGCTTTTG-AAATATGCCCTGACTTTGGTGGGCTTTT
125 GCTTTTAAAGGTTGCCACTGACCTTGTGGGCTTGTGAAAAAATGCCCTGAC-TT-GTGGGC-TTT
*
1311821 TGAACAGGGTGCCACTAAC
187 TGAAAAGGGTGCCACTAAC
1311840 TTGTGGGCTT
Statistics
Matches: 181, Mismatches: 12, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
205 24 0.13
206 12 0.07
207 18 0.10
208 49 0.27
209 10 0.06
210 24 0.13
211 26 0.14
212 7 0.04
213 7 0.04
214 4 0.02
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (211 bp):
TTGTGGGGCTTTGAAAGGTTGCCCACTGACTTGTGGCTTGTAAAGGTTTGCCACTGAATTGTGGG
CTTTCCGAAAAAATATGCCAAGACTTGTGGGCTTTTGAAAAATATCCACTGACTTGTGGGCTTTT
AAAGGTTGCCACTGACCTTGTGGGCTTGTGAAAAAATGCCCTGACTTGTGGGCTTTTGAAAAGGG
TGCCACTAACATTTAC
Found at i:1311853 original size:116 final size:113
Alignment explanation
Indices: 1311636--1311850 Score: 256
Period size: 116 Copynumber: 1.8 Consensus size: 113
1311626 ACTAACATTT
1311636 ACTTGTGGGCTTTTAAGGTTGCCACTGACTGTGCTTTTAAAGGTTGCCACTGAATTTGGGCTTTT
1 ACTTGTGGGCTTTTAAGGTTGCCACTGACTGTGCTTTTAAA-GTTGCCACTGAATTTGGGCTTTT
* *
1311701 CGAAAAATATGCCACTCTGACTTGTGGGCTTTTTGAAAAAATATGCCACTG
65 CGAAAAAGATGCCAC-CTAACTTGTGGGC-TTTTGAAAAAATATGCCACTG
*
1311752 ACTTGTGGGCTTTTAAGGTTGCCACTGACTTGTGGCTTTTGAAA-TATGCC-CTGACTTTGGTGG
1 ACTTGTGGGCTTTTAAGGTTGCCACTGAC-TGT-GCTTTT-AAAGT-TGCCACTGA-ATT--TGG
* * * *
1311815 GCTTTTTGAACAGGGTGCCA-CTAACTTGTGGGCTTT
59 GCTTTTCGAAAAAGATGCCACCTAACTTGTGGGCTTT
1311851 GAAGGTTGGC
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
116 29 0.34
117 11 0.13
118 24 0.28
119 3 0.04
120 18 0.21
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (113 bp):
ACTTGTGGGCTTTTAAGGTTGCCACTGACTGTGCTTTTAAAGTTGCCACTGAATTTGGGCTTTTC
GAAAAAGATGCCACCTAACTTGTGGGCTTTTGAAAAAATATGCCACTG
Found at i:1498230 original size:20 final size:20
Alignment explanation
Indices: 1498205--1498329 Score: 106
Period size: 20 Copynumber: 5.8 Consensus size: 20
1498195 TTTTTACCTG
*
1498205 AATGTATCGATACATTTTTT
1 AATGTATCGATACATTTTTC
1498225 AATGTATCGATACATTACGTCTTTTACCC
1 AATGTATCGATAC---A--T-TTTT---C
1498254 AAATGTATCGATACATTTTTC
1 -AATGTATCGATACATTTTTC
* * *
1498275 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* *
1498295 AATATATTGATACATTTTTC
1 AATGTATCGATACATTTTTC
1498315 AATGTATCGATACAT
1 AATGTATCGATACAT
1498330 CTAGTTAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
20 58 0.69
21 1 0.01
23 1 0.01
24 4 0.05
25 2 0.02
26 4 0.05
27 1 0.01
30 13 0.15
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1501213 original size:20 final size:20
Alignment explanation
Indices: 1501190--1501262 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1501180 ACAATTCAAA
1501190 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*****
1501210 GTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1501231 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1501251 GTATCGATACAT
1 GTATCGATACAT
1501263 AAAAAAGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1501234 original size:21 final size:21
Alignment explanation
Indices: 1501208--1501283 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1501198 ACATGTTGCA
1501208 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATAAAAAAG
*****
1501229 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATAAAAAAG
1501249 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATAAAAAAG
1501270 ATGTATCGATACAT
1 ATGTATCGATACAT
1501284 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:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATAAAAAAG
Found at i:1501241 original size:41 final size:41
Alignment explanation
Indices: 1501190--1501283 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1501180 ACAATTCAAA
1501190 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1501231 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1501272 GTATCGATACAT
1 GTATCGATACAT
1501284 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1501340 original size:13 final size:13
Alignment explanation
Indices: 1501322--1501347 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1501312 TACAGCAAGT
1501322 ATGTATCGATACA
1 ATGTATCGATACA
1501335 ATGTATCGATACA
1 ATGTATCGATACA
1501348 CAAAAAATTG
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:1505429 original size:15 final size:15
Alignment explanation
Indices: 1505409--1505447 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1505399 TAAAAATTTC
*
1505409 CAAAATGAGGAAACT
1 CAAAATGAAGAAACT
*
1505424 CAAAATGAAGAAGCT
1 CAAAATGAAGAAACT
*
1505439 CCAAATGAA
1 CAAAATGAA
1505448 ATTGATGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAACT
Found at i:1507524 original size:20 final size:21
Alignment explanation
Indices: 1507445--1507523 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1507435 AATGTCCAAA
*
1507445 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
1507465 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
1507490 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
1507510 TTGTATCGATACAT
1 ATGTATCGATACAT
1507524 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:1507528 original size:13 final size:13
Alignment explanation
Indices: 1507510--1507548 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1507500 ACATTTTTCT
1507510 TTGTATCGATACA
1 TTGTATCGATACA
1507523 TTGTATCGATACA
1 TTGTATCGATACA
*
1507536 CTGTATCGATACA
1 TTGTATCGATACA
1507549 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:1510012 original size:20 final size:20
Alignment explanation
Indices: 1509989--1510061 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1509979 ACAATTCAAA
1509989 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
*****
1510009 GTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1510030 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1510050 GTATCGATACAT
1 GTATCGATACAT
1510062 AAAAAAGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1510033 original size:21 final size:21
Alignment explanation
Indices: 1510007--1510082 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1509997 ACATGTTGCA
1510007 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATAAAAAAG
*****
1510028 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATAAAAAAG
1510048 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATAAAAAAG
1510069 ATGTATCGATACAT
1 ATGTATCGATACAT
1510083 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:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATAAAAAAG
Found at i:1510040 original size:41 final size:41
Alignment explanation
Indices: 1509989--1510082 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1509979 ACAATTCAAA
1509989 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1510030 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1510071 GTATCGATACAT
1 GTATCGATACAT
1510083 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1510139 original size:13 final size:13
Alignment explanation
Indices: 1510121--1510146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1510111 TACAGCAAGT
1510121 ATGTATCGATACA
1 ATGTATCGATACA
1510134 ATGTATCGATACA
1 ATGTATCGATACA
1510147 CAAAAAATTG
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:1512346 original size:28 final size:28
Alignment explanation
Indices: 1512306--1512825 Score: 583
Period size: 28 Copynumber: 18.7 Consensus size: 28
1512296 CTAGAACATT
*
1512306 CATCTTTTCAAAGCCCA-AGAGTCAATGG
1 CATCTTTTCAAAGCCCACA-AGTCAGTGG
* *
1512334 CATCTCTTCAAAGCCCATAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
1512362 CATCTTTTCAAAGCCCATAAGTTAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
1512390 CATCCTTTCAAAGCCCACAAGTTAGTAG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
1512418 CATCTTTTCTAAGCCCATAAGTCAATGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
1512446 CACCTTTTCGAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1512474 CACCTTTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
1512502 CATCTTGTCCAAGCTCACAAGTCAGGGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
1512530 AACCTTTTCAAAGCCCATAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
1512558 CATCTTTTCAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1512586 CATCTTTTTAAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
1512614 CATCCGTTT-AAA-CCCTACAAGTTAGTGG
1 CAT-CTTTTCAAAGCCC-ACAAGTCAGTGG
* *
1512642 CATTTTTTCAAAACCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1512670 CATCTTTTCAAAGCCCACAAGTCAGTGA
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1512698 CA-C----C--TGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
1512719 CATCCTTTCAAAAAGCCCACAAGTCAATGG
1 CATCTTTTC--AAAGCCCACAAGTCAGTGG
*
1512749 CATCCTTTCAAAAAGCCCACAAGTCAGTGG
1 CATCTTTTC--AAAGCCCACAAGTCAGTGG
* * * *
1512779 CACCATTTCAAAGCCCACAAGTTAGTGA
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1512807 CATCCTTTCAAAGCCCACA
1 CATCTTTTCAAAGCCCACA
1512826 CAAGTCGGTG
Statistics
Matches: 425, Mismatches: 53, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
21 17 0.04
22 1 0.00
23 1 0.00
26 1 0.00
27 7 0.02
28 339 0.80
29 8 0.02
30 51 0.12
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (28 bp):
CATCTTTTCAAAGCCCACAAGTCAGTGG
Found at i:1512830 original size:30 final size:29
Alignment explanation
Indices: 1512703--1512825 Score: 171
Period size: 30 Copynumber: 4.2 Consensus size: 29
1512693 AGTGACACCT
1512703 GCCCACAAGTCAGTGGCATCCTTTCAAAAA
1 GCCCACAAGTCAGTGGCATCCTTTC-AAAA
*
1512733 GCCCACAAGTCAATGGCATCCTTTCAAAAA
1 GCCCACAAGTCAGTGGCATCCTTTC-AAAA
1512763 GCCCACAAGTCAGTGGCA-CCATTTC-AAA
1 GCCCACAAGTCAGTGGCATCC-TTTCAAAA
* *
1512791 GCCCACAAGTTAGTGACATCCTTTC-AAA
1 GCCCACAAGTCAGTGGCATCCTTTCAAAA
1512819 GCCCACA
1 GCCCACA
1512826 CAAGTCGGTG
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
28 33 0.38
29 4 0.05
30 50 0.57
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.20
Consensus pattern (29 bp):
GCCCACAAGTCAGTGGCATCCTTTCAAAA
Found at i:1512838 original size:58 final size:58
Alignment explanation
Indices: 1512703--1512825 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 58
1512693 AGTGACACCT
*
1512703 GCCCACAAGTCAGTGGCATCCTTTCAAAAAGCCCACAAGTCAATGGCATCCTTTCAAAAA
1 GCCCACAAGTCAGTGGCATCCTTTC-AAAAGCCCACAAGTCAATGACATCCTTTC-AAAA
* *
1512763 GCCCACAAGTCAGTGGCA-CCATTTC-AAAGCCCACAAGTTAGTGACATCCTTTC-AAA
1 GCCCACAAGTCAGTGGCATCC-TTTCAAAAGCCCACAAGTCAATGACATCCTTTCAAAA
1512819 GCCCACA
1 GCCCACA
1512826 CAAGTCGGTG
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
56 10 0.17
58 25 0.42
59 2 0.03
60 22 0.37
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.20
Consensus pattern (58 bp):
GCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGACATCCTTTCAAAA
Found at i:1513546 original size:15 final size:15
Alignment explanation
Indices: 1513523--1513555 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1513513 TTTTTTGATT
1513523 AAAGAGGAGAAATAG
1 AAAGAGGAGAAATAG
*
1513538 AAAGGGGAGAAATAG
1 AAAGAGGAGAAATAG
1513553 AAA
1 AAA
1513556 TTTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (15 bp):
AAAGAGGAGAAATAG
Found at i:1513576 original size:20 final size:22
Alignment explanation
Indices: 1513551--1513593 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1513541 GGGGAGAAAT
1513551 AGAAATT-TTT-ATTAAGAGGG
1 AGAAATTCTTTAATTAAGAGGG
*
1513571 AGAAATTCTTTAATTAAGGGGG
1 AGAAATTCTTTAATTAAGAGGG
1513593 A
1 A
1513594 AAAAATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.33
Consensus pattern (22 bp):
AGAAATTCTTTAATTAAGAGGG
Found at i:1514146 original size:20 final size:20
Alignment explanation
Indices: 1514121--1514170 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
1514111 ACACCCAGAA
1514121 TATCGATACATTATGCT-TTG
1 TATCGATACATTAT-CTATTG
*
1514141 TATCGATACA-TATTTATTG
1 TATCGATACATTATCTATTG
1514160 TATCGATACAT
1 TATCGATACAT
1514171 GCAGAATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 1 0.04
19 16 0.59
20 10 0.37
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (20 bp):
TATCGATACATTATCTATTG
Found at i:1514257 original size:13 final size:13
Alignment explanation
Indices: 1514236--1514321 Score: 70
Period size: 13 Copynumber: 7.5 Consensus size: 13
1514226 CGATACATGG
*
1514236 TACAATGTATCGA
1 TACATTGTATCGA
1514249 TACATTGTATCGA
1 TACATTGTATCGA
*
1514262 TAC-GTG-AT-G-
1 TACATTGTATCGA
1514271 -A-ATTGTATCGA
1 TACATTGTATCGA
1514282 TACATTGTATCGA
1 TACATTGTATCGA
1514295 TACA-TG-AT-G-
1 TACATTGTATCGA
1514304 -A-ATTGTATCGA
1 TACATTGTATCGA
1514315 TACATTG
1 TACATTG
1514322 CTTGTAACGG
Statistics
Matches: 58, Mismatches: 3, Indels: 24
0.68 0.04 0.28
Matches are distributed among these distances:
7 1 0.02
8 6 0.10
9 4 0.07
10 4 0.07
11 4 0.07
12 6 0.10
13 33 0.57
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1514257 original size:33 final size:33
Alignment explanation
Indices: 1514220--1514321 Score: 161
Period size: 33 Copynumber: 3.1 Consensus size: 33
1514210 CTACCACTGT
* *
1514220 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
*
1514253 TTGTATCGATACGTGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
1514286 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
1514319 TTG
1 TTG
1514322 CTTGTAACGG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 63 0.98
34 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:1514318 original size:20 final size:20
Alignment explanation
Indices: 1514252--1514319 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1514242 GTATCGATAC
*
1514252 ATTGTATCGATACGTGATGA
1 ATTGTATCGATACATGATGA
1514272 ATTGTATCGATAC-------
1 ATTGTATCGATACATGATGA
1514285 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
1514305 ATTGTATCGATACAT
1 ATTGTATCGATACAT
1514320 TGCTTGTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.32
20 28 0.68
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:1515094 original size:21 final size:21
Alignment explanation
Indices: 1515065--1515105 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1515055 AAAGGTCAAA
1515065 ACCCTAGAAAGTATTGATACAG
1 ACCCTAG-AAGTATTGATACAG
1515087 ACCC-AGAAGTATTGATACA
1 ACCCTAGAAGTATTGATACA
1515106 TATTGCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 2 0.11
22 4 0.21
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (21 bp):
ACCCTAGAAGTATTGATACAG
Found at i:1515694 original size:23 final size:23
Alignment explanation
Indices: 1515651--1515694 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1515641 GCATTCAAGC
* *
1515651 TTGGGTTATAATCTTTTAAGAAT
1 TTGGGGTATAATCTTTGAAGAAT
1515674 TTGGGGTATAAT-TCTTGAAGA
1 TTGGGGTATAATCT-TTGAAGA
1515695 GATTGAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (23 bp):
TTGGGGTATAATCTTTGAAGAAT
Found at i:1516545 original size:13 final size:13
Alignment explanation
Indices: 1516527--1516551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1516517 ATATTGCTTA
1516527 GTATCGATACATT
1 GTATCGATACATT
1516540 GTATCGATACAT
1 GTATCGATACAT
1516552 GTTCATTGTA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1516708 original size:20 final size:20
Alignment explanation
Indices: 1516683--1516735 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1516673 TTCAAATGCA
1516683 TGTATCGATACATTACGAAT
1 TGTATCGATACATTACGAAT
1516703 TGTATCGATACATTACGAAT
1 TGTATCGATACATTACGAAT
1516723 TGTATCGATACAT
1 TGTATCGATACAT
1516736 AGGAGCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTACGAAT
Found at i:1518258 original size:3 final size:3
Alignment explanation
Indices: 1518250--1518286 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1518240 TCAACTATCA
* *
1518250 ATG ATG ATG AAG ATA ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1518287 AGTTGACTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:1519260 original size:13 final size:13
Alignment explanation
Indices: 1519242--1519266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1519232 ATGTTGCATA
1519242 GTATCGATACATT
1 GTATCGATACATT
1519255 GTATCGATACAT
1 GTATCGATACAT
1519267 GACCAAATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1519362 original size:19 final size:19
Alignment explanation
Indices: 1519338--1519400 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1519328 TAGCCAAACT
1519338 TGTATCGATACACACAGTA
1 TGTATCGATACACACAGTA
1519357 TGTATCGAT----ACA-T-
1 TGTATCGATACACACAGTA
1519370 TGTATCGATACACACAGTA
1 TGTATCGATACACACAGTA
1519389 TGTATCGATACA
1 TGTATCGATACA
1519401 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 3 0.08
17 3 0.08
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (19 bp):
TGTATCGATACACACAGTA
Found at i:1519375 original size:13 final size:13
Alignment explanation
Indices: 1519357--1519413 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1519347 ACACACAGTA
1519357 TGTATCGATACAT
1 TGTATCGATACAT
1519370 TGTATCGATACACACAGT
1 TGTATCGAT----ACA-T
1519388 ATGTATCGATACAT
1 -TGTATCGATACAT
1519402 TGTATCGATACA
1 TGTATCGATACA
1519414 CCATAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
15 3 0.08
17 3 0.08
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1519378 original size:32 final size:32
Alignment explanation
Indices: 1519337--1519436 Score: 164
Period size: 32 Copynumber: 3.1 Consensus size: 32
1519327 GTAGCCAAAC
1519337 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAGTATGTATCGATACA
1519369 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAGTATGTATCGATACA
* **
1519401 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAGTATGTATCGATACA
1519434 TTG
1 TTG
1519437 GCTTGTAACG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 45 0.70
33 19 0.30
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAGTATGTATCGATACA
Found at i:1523518 original size:15 final size:15
Alignment explanation
Indices: 1523500--1523529 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1523490 CCAAATTGAG
1523500 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
1523515 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
1523530 ATTTGATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:1523525 original size:16 final size:16
Alignment explanation
Indices: 1523489--1523529 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1523479 GATAAAAATA
* *
1523489 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
1523505 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
1523520 TCC-AAATGAA
1 TCCAAAATGAA
1523530 ATTTGATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:1525618 original size:13 final size:13
Alignment explanation
Indices: 1525600--1525636 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1525590 AGCATTCTTT
1525600 GTATCGATACATA
1 GTATCGATACATA
*
1525613 GTATCGATACATT
1 GTATCGATACATA
1525626 GTATCGATACA
1 GTATCGATACA
1525637 AGGGGATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACATA
Found at i:1527764 original size:68 final size:69
Alignment explanation
Indices: 1527645--1527781 Score: 179
Period size: 68 Copynumber: 2.0 Consensus size: 69
1527635 ACGGGGTTGG
* ** * *
1527645 AGTATCCCCTTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCCATGATT-GGGAA
1 AGTATCCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-ATTCGGGAA
1527709 ATAAA
65 ATAAA
* * *
1527714 AGTATCCCC-TCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCTGGAAA
1 AGTATCCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTCGGGAAA
1527778 TAAA
66 TAAA
1527782 GCCGGGGTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
67 3 0.05
68 47 0.80
69 9 0.15
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (69 bp):
AGTATCCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTCGGGAAA
TAAA
Found at i:1527793 original size:51 final size:51
Alignment explanation
Indices: 1527733--1527852 Score: 231
Period size: 51 Copynumber: 2.4 Consensus size: 51
1527723 TCGGAAATAA
1527733 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCTGGAAATAAAGC
1527784 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCTGGAAATAAAGC
*
1527835 CAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1527853 TCGGAGGTAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTCTGGAAATAAAGC
Found at i:1527980 original size:53 final size:52
Alignment explanation
Indices: 1527863--1528248 Score: 237
Period size: 51 Copynumber: 7.4 Consensus size: 52
1527853 TCGGAGGTAA
* ** * * * *
1527863 CGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTG-GAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAAGGAAATTTAGTG-TTTTGAGAAATAAAAC
* *
1527915 CGGAGTTGGAGTATCCCCGATTAAAGGAAATTTAGTGTTTTGAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-AAGGAAATTTAGTGTTTTGAGAAATAAAAC
* * *
1527968 CGGGGTTAGAGTATCCCCGATTATGGAAAGTTT-GTGTTTT-AGAAATGAAAC
1 CGGGGTTGGAGTATCCCCGATTAAGGAAA-TTTAGTGTTTTGAGAAATAAAAC
* * * *
1528019 CGGGGTTGGAGTATCCCC-ATTAAGAGAAA-TCAATATTTTG-GAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTAAG-GAAATTTAGTGTTTTGAGAAATAAAAC
* ** * * ***
1528069 CGGGGTTGGAGTATCCCCTCGGAGGTAACGG-GGTTGGAGTATCCCCGATGAAAT--AA-
1 CGGGGTTGGAGTAT-CCC-C-GA-TTAA-GGAAATT-TAGTGT-TTTGA-GAAATAAAAC
* * * * *
1528125 TGAGGTTGGAGTATCCTCGATTGAA--AAA-TTGGTGTTTTTG-GAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATT-AAGGAAATTTAGTG-TTTTGAGAAATAAAAC
* *
1528175 CGGAGTTGGAGTATCCCCGATTAAAGGAAA-TTGGTGTTTTGA-AAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-AAGGAAATTTAGTGTTTTGAGAAATAAAAC
*
1528226 CAGGGTTGGAGTATCCCCGATTA
1 CGGGGTTGGAGTATCCCCGATTA
1528249 TGAGCAATTG
Statistics
Matches: 258, Mismatches: 50, Indels: 54
0.71 0.14 0.15
Matches are distributed among these distances:
47 5 0.02
49 6 0.02
50 55 0.21
51 66 0.26
52 49 0.19
53 44 0.17
54 2 0.01
55 7 0.03
56 17 0.07
57 2 0.01
59 5 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (52 bp):
CGGGGTTGGAGTATCCCCGATTAAGGAAATTTAGTGTTTTGAGAAATAAAAC
Found at i:1528076 original size:50 final size:52
Alignment explanation
Indices: 1527863--1528086 Score: 224
Period size: 52 Copynumber: 4.3 Consensus size: 52
1527853 TCGGAGGTAA
* ** * * *
1527863 CGGGGTTGGAGTATCCTCGATTGTGA-AAAATTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAAGAGAAAGTTAGTG-TTTTGGAAATAAAAC
* * *
1527915 CGGAGTTGGAGTATCCCCGATTAA-AGGAAATTTAGTGTTTTGAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAAGA-GAAAGTTAGTGTTTTG-GAAATAAAAC
* * * * *
1527968 CGGGGTTAGAGTATCCCCGATTATG-GAAAGTTTGTGTTTTAGAAATGAAAC
1 CGGGGTTGGAGTATCCCCGATTAAGAGAAAGTTAGTGTTTTGGAAATAAAAC
* * * *
1528019 CGGGGTTGGAGTATCCCC-ATTAAGAGAAA-TCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTAAGAGAAAGTTAGTGTTTTGGAAATAAAAC
1528069 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1528087 TCGGAGGTAA
Statistics
Matches: 142, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
50 37 0.26
51 30 0.21
52 38 0.27
53 37 0.26
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (52 bp):
CGGGGTTGGAGTATCCCCGATTAAGAGAAAGTTAGTGTTTTGGAAATAAAAC
Found at i:1529244 original size:43 final size:43
Alignment explanation
Indices: 1529197--1529292 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
1529187 TCTCGCTGGA
*
1529197 GCTGCTGTTGCCTGCTGGAGCTGCAATCGCTGCTGGAGTTGCT
1 GCTGCTGTTGCCTGCTGGAGCTGCAATCGCTGCTAGAGTTGCT
* *
1529240 GCTGCTGTTGCGTGCTGGAGCTGCAGTCGCTGCTAGAGTTGCT
1 GCTGCTGTTGCCTGCTGGAGCTGCAATCGCTGCTAGAGTTGCT
1529283 GCTGCTGTTG
1 GCTGCTGTTG
1529293 GAGCTGCTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.08, C:0.24, G:0.36, T:0.31
Consensus pattern (43 bp):
GCTGCTGTTGCCTGCTGGAGCTGCAATCGCTGCTAGAGTTGCT
Found at i:1529334 original size:55 final size:55
Alignment explanation
Indices: 1529240--1529360 Score: 152
Period size: 55 Copynumber: 2.2 Consensus size: 55
1529230 TGGAGTTGCT
* * * * *
1529240 GCTGCTGTTGCGTGCTGGAGCTGCAGTCGCTGCTAGAGTTGCTGCTGCTGTTGGA
1 GCTGCTGTTGCATGCTAGAGCTGCAGCCGCCGCTAGAGTTGCTGCTGCTGCTGGA
** * *
1529295 GCTGCTGTTGCATGCTAGAGCTGTTGCCGCCGCTGGAGTTGGTGCTGCTGCTGGA
1 GCTGCTGTTGCATGCTAGAGCTGCAGCCGCCGCTAGAGTTGCTGCTGCTGCTGGA
*
1529350 GCTGCTTTTGC
1 GCTGCTGTTGC
1529361 GTGTTGGAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.08, C:0.23, G:0.37, T:0.31
Consensus pattern (55 bp):
GCTGCTGTTGCATGCTAGAGCTGCAGCCGCCGCTAGAGTTGCTGCTGCTGCTGGA
Found at i:1529700 original size:26 final size:26
Alignment explanation
Indices: 1529668--1529819 Score: 279
Period size: 26 Copynumber: 5.9 Consensus size: 26
1529658 TCCAATTGCA
1529668 ATTTT-TATTTCCTTTCCCATGCTGC
1 ATTTTCTATTTCCTTTCCCATGCTGC
*
1529693 ATTTTTTATTTCCTTTCCCATGCTGC
1 ATTTTCTATTTCCTTTCCCATGCTGC
1529719 ATTTTCTATTTCCTTTCCCATGCTGC
1 ATTTTCTATTTCCTTTCCCATGCTGC
*
1529745 ATTTTTTATTTCCTTTCCCATGCTGC
1 ATTTTCTATTTCCTTTCCCATGCTGC
1529771 ATTTTCTATTTCCTTTCCCATGCTGC
1 ATTTTCTATTTCCTTTCCCATGCTGC
1529797 ATTTTCTATTTCCTTTCCCATGC
1 ATTTTCTATTTCCTTTCCCATGC
1529820 CGTAAGTTTT
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
25 5 0.04
26 118 0.96
ACGTcount: A:0.12, C:0.29, G:0.07, T:0.52
Consensus pattern (26 bp):
ATTTTCTATTTCCTTTCCCATGCTGC
Found at i:1529881 original size:24 final size:24
Alignment explanation
Indices: 1529839--1529890 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1529829 TCACATTTGC
1529839 TTTTTTT-TTTAATTAATTTATTT
1 TTTTTTTATTTAATTAATTTATTT
*
1529862 TATTTTTTATTT-ATTTATTTATTT
1 T-TTTTTTATTTAATTAATTTATTT
1529886 TTTTT
1 TTTTT
1529891 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 18 0.69
25 3 0.12
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTTTATTTAATTAATTTATTT
Found at i:1529888 original size:20 final size:20
Alignment explanation
Indices: 1529839--1529889 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1529829 TCACATTTGC
1529839 TTTTTTTTTTAATTAATTTA
1 TTTTTTTTTTAATTAATTTA
*
1529859 TTTTATTTTTT-ATTTATTTA
1 TTTT-TTTTTTAATTAATTTA
1529879 TTTATTTTTTT
1 TTT-TTTTTTT
1529890 TATGCATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTTTTAATTAATTTA
Done.