Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 15 of 168
Found at i:4139329 original size:3 final size:3
Alignment explanation
Indices: 4139321--4139360 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4139311 AGATAGTGGG
4139321 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4139361 GGGTAAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4139923 original size:24 final size:24
Alignment explanation
Indices: 4139896--4139942 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
4139886 AGAAGAAAGT
*
4139896 TTAAAGAACATAAAAGAAAAAAAA
1 TTAAAGAACATAAAACAAAAAAAA
** *
4139920 TTAAATTACTTAAAACAAAAAAA
1 TTAAAGAACATAAAACAAAAAAA
4139943 TATGGGGATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.19
Consensus pattern (24 bp):
TTAAAGAACATAAAACAAAAAAAA
Found at i:4140140 original size:31 final size:29
Alignment explanation
Indices: 4140079--4140142 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
4140069 ATAACGTAAA
* *
4140079 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACTAAAACGTAACAGTTCAAACAAAAG
4140108 TGACTAAAACGTAACCTAAGTT-AAACAAAAG
1 TGACTAAAACGTAA-C--AGTTCAAACAAAAG
4140139 TGAC
1 TGAC
4140143 CATGGGTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
31 12 0.40
32 3 0.10
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.22
Consensus pattern (29 bp):
TGACTAAAACGTAACAGTTCAAACAAAAG
Found at i:4140163 original size:3 final size:3
Alignment explanation
Indices: 4140155--4140210 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
4140145 TGGGTGTAGC
4140155 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4140203 TTA TTA TT
1 TTA TTA TT
4140211 TCCTTTTGAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4142624 original size:19 final size:20
Alignment explanation
Indices: 4142600--4142637 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4142590 TAATAAACAT
4142600 TAAAAAA-TTATTTTAAAAA
1 TAAAAAATTTATTTTAAAAA
4142619 TAAAAAATTTATTTTAAAA
1 TAAAAAATTTATTTTAAAA
4142638 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAAATTTATTTTAAAAA
Found at i:4156408 original size:19 final size:19
Alignment explanation
Indices: 4156379--4156467 Score: 60
Period size: 20 Copynumber: 4.8 Consensus size: 19
4156369 TCTCTCAACA
*
4156379 AAAATTACAAAATAATTAT
1 AAAATTTCAAAATAATTAT
* **
4156398 TAAATTTCAAAATTTTTAT
1 AAAATTTCAAAATAATTAT
4156417 AAAAGTTTCAAAAT--TTAT
1 AAAA-TTTCAAAATAATTAT
* * *
4156435 --ATTTTTAAAAAAATTAT
1 AAAATTTCAAAATAATTAT
*
4156452 AAAAATTTAAAAATAA
1 -AAAATTTCAAAATAA
4156468 ATCTAAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
15 7 0.13
16 1 0.02
17 4 0.08
18 4 0.08
19 18 0.34
20 19 0.36
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (19 bp):
AAAATTTCAAAATAATTAT
Found at i:4156446 original size:26 final size:27
Alignment explanation
Indices: 4156409--4156460 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
4156399 AAATTTCAAA
* * *
4156409 ATTTTTATAAAAGTT-TCAAAATTTAT
1 ATTTTTAAAAAAATTATAAAAATTTAT
4156435 ATTTTTAAAAAAATTATAAAAATTTA
1 ATTTTTAAAAAAATTATAAAAATTTA
4156461 AAAATAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
ATTTTTAAAAAAATTATAAAAATTTAT
Found at i:4156474 original size:20 final size:19
Alignment explanation
Indices: 4156438--4156477 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
4156428 AATTTATATT
*
4156438 TTTAAAAAAATTATAAAAA
1 TTTAAAAAAAATATAAAAA
*
4156457 TTTAAAAATAAATCTAAAAA
1 TTTAAAAA-AAATATAAAAA
4156477 T
1 T
4156478 AAATAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TTTAAAAAAAATATAAAAA
Found at i:4161259 original size:52 final size:50
Alignment explanation
Indices: 4161182--4161309 Score: 145
Period size: 51 Copynumber: 2.5 Consensus size: 50
4161172 TTTTTCTCGT
*
4161182 ATTAATTTAAATTAATTAAGAGATAAATATTAAA-AATTTATATTATCATTA
1 ATTAA-TTAAATTAATTAAGAGATAAATATCAAATAA-TTATATTATCATTA
* * * * *
4161233 ATTAAAATTAAAATAATTAAGTGAT-AATATCAAATGATTATTTTATCTTTA
1 ATT--AATTAAATTAATTAAGAGATAAATATCAAATAATTATATTATCATTA
4161284 ATTAATTAAATTAA-TAAGAGATAAAT
1 ATTAATTAAATTAATTAAGAGATAAAT
4161310 GAAAAACAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
48 7 0.11
49 13 0.20
51 26 0.40
52 17 0.26
53 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (50 bp):
ATTAATTAAATTAATTAAGAGATAAATATCAAATAATTATATTATCATTA
Found at i:4171790 original size:179 final size:180
Alignment explanation
Indices: 4171449--4171797 Score: 461
Period size: 179 Copynumber: 1.9 Consensus size: 180
4171439 GCACTCTCGT
* * * * *
4171449 AATAAAAATAAGTAATATTATTCAAAGATATTTTAAATTAATATTATTTGAGGGTATTTTTGTTT
1 AATAAAAATAAGTAATATTATTCAAAGATATTTTAAAGTAATATTAGTGGAGGGTATTTTCGTCT
* * *
4171514 TTTCACTTTAAAAAATCAAAAGAAATTATGGGAATGCCCTTCCGTAATAAAAATAAGTAAAATTA
66 TTTCACTTTAAAAAATCAAAAGAAATTATGAGAATACCCTTCCATAATAAAAATAAGTAAAATTA
* *
4171579 TTCGAGGATATTTTAATCTTTTTACATAAAAAAT-AATAAGCCTTTCTGC
131 TTCGAAGATATTTTAATCTTTTCACATAAAAAATCAATAAGCCTTTCTGC
* * ** * *
4171628 AATAAAAATAATTAATATTGTTTGAGGATATTTTAAAGTAATATTAGTGGATGGTATTTTCGTCT
1 AATAAAAATAAGTAATATTATTCAAAGATATTTTAAAGTAATATTAGTGGAGGGTATTTTCGTCT
* * * *
4171693 TTTCACTTTACAATAATC-AAATAAATTATGAG-ATACCCTTCTATAATAAAAATAAGTAATATT
66 TTTCACTTTA-AAAAATCAAAAGAAATTATGAGAATACCCTTCCATAATAAAAATAAGTAAAATT
* *
4171756 ATTCGAAGATATTTTAATCTTTTCGCTGTAAAAAATCAATAA
130 ATTCGAAGATATTTTAATCTTTTCAC-ATAAAAAATCAATAA
4171798 AAATATACAT
Statistics
Matches: 145, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
178 50 0.34
179 84 0.58
180 11 0.08
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39
Consensus pattern (180 bp):
AATAAAAATAAGTAATATTATTCAAAGATATTTTAAAGTAATATTAGTGGAGGGTATTTTCGTCT
TTTCACTTTAAAAAATCAAAAGAAATTATGAGAATACCCTTCCATAATAAAAATAAGTAAAATTA
TTCGAAGATATTTTAATCTTTTCACATAAAAAATCAATAAGCCTTTCTGC
Found at i:4178640 original size:8 final size:8
Alignment explanation
Indices: 4178622--4178660 Score: 69
Period size: 8 Copynumber: 4.8 Consensus size: 8
4178612 CAGAATAAAA
4178622 AAAAGTTAT
1 AAAA-TTAT
4178631 AAAATTAT
1 AAAATTAT
4178639 AAAATTAT
1 AAAATTAT
4178647 AAAATTAT
1 AAAATTAT
4178655 AAAATT
1 AAAATT
4178661 TTATTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 26 0.87
9 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
AAAATTAT
Found at i:4180266 original size:24 final size:24
Alignment explanation
Indices: 4180237--4180298 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
4180227 GAATTCAGAT
*
4180237 GAGGATGGTATTGACGGTTCTAAG
1 GAGGATGGAATTGACGGTTCTAAG
*
4180261 GAGGATGGCATTGACGGTTCTAAG
1 GAGGATGGAATTGACGGTTCTAAG
4180285 GAGGATGGAATTGA
1 GAGGATGGAATTGA
4180299 TAGAACTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.08, G:0.39, T:0.26
Consensus pattern (24 bp):
GAGGATGGAATTGACGGTTCTAAG
Found at i:4185054 original size:36 final size:36
Alignment explanation
Indices: 4185006--4185079 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
4184996 CATATAGCAG
* *
4185006 TTCTACCAAGTATGCTATTATCAATGATGGGGGAAA
1 TTCTACCAAGTATGCTATAATCAATAATGGGGGAAA
*
4185042 TTCTACCTAGTATGCTATAATCAATAATGGGGGAAA
1 TTCTACCAAGTATGCTATAATCAATAATGGGGGAAA
4185078 TT
1 TT
4185080 TTTTGTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (36 bp):
TTCTACCAAGTATGCTATAATCAATAATGGGGGAAA
Found at i:4193163 original size:15 final size:16
Alignment explanation
Indices: 4193128--4193166 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
4193118 TATTATGAAT
*
4193128 ATATTTTTTTAAGTTT
1 ATATTTTTTTAAGTTC
*
4193144 TTATTTTTTTAA-TTC
1 ATATTTTTTTAAGTTC
4193159 ATATTTTT
1 ATATTTTT
4193167 AATTAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (16 bp):
ATATTTTTTTAAGTTC
Found at i:4194379 original size:22 final size:20
Alignment explanation
Indices: 4194354--4194401 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
4194344 ATTTTCATAT
4194354 ATATTATTATATTACTTATAAA
1 ATATTATTATATTA--TATAAA
* *
4194376 ATATTATTATTTTATGTAAA
1 ATATTATTATATTATATAAA
4194396 ATATTA
1 ATATTA
4194402 AATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
22 13 0.54
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATTATTATATTATATAAA
Found at i:4194499 original size:22 final size:22
Alignment explanation
Indices: 4194454--4194499 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
4194444 CAAAACAGGT
* * * *
4194454 CTTTAGCGGCGTTTTTTTAGGC
1 CTTTAGCGACGCTTTTTAACGC
4194476 CTTTAGCGACGCTTTTTAACGC
1 CTTTAGCGACGCTTTTTAACGC
4194498 CT
1 CT
4194500 AAATGTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (22 bp):
CTTTAGCGACGCTTTTTAACGC
Found at i:4194688 original size:41 final size:41
Alignment explanation
Indices: 4194596--4194770 Score: 251
Period size: 42 Copynumber: 4.2 Consensus size: 41
4194586 ACGTAAAAAA
* *
4194596 CGCCGCTAAAGAACATGGGCTTTAGCGGCATTTTTTATTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTTT-CTAAG
* *
4194638 CGCCGCTAAAGAACATGGTTTTTAGCGGCGTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTCTAAG
* * *
4194679 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTC-TAAG
4194721 CGCCGCTAAAGAACATGGTCTTTAGCGGCAATTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC-ATTTTTTCTAAG
*
4194763 CGCTGCTA
1 CGCCGCTA
4194771 TTTTGGGGAT
Statistics
Matches: 120, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
41 38 0.32
42 75 0.62
43 7 0.06
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTCTAAG
Found at i:4194745 original size:83 final size:84
Alignment explanation
Indices: 4194596--4194770 Score: 271
Period size: 83 Copynumber: 2.1 Consensus size: 84
4194586 ACGTAAAAAA
*
4194596 CGCCGCTAAAGAACATGGGCTTTAGCGGCATTTTTTATTAAGCGCCGCTAAAGAACATGGTTTTT
1 CGCCGCTAAAGAACATGGGCTTTAGCGGCATTTTTTATTAAGCGCCGCTAAAGAACATGGTCTTT
*
4194661 AGCGGC-GTTTTTTCTAAG
66 AGCGGCAATTTTTTCTAAG
* ** * *
4194679 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTTAAGCGCCGCTAAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGGGCTTTAGCGGCATTTTTTATTAAGCGCCGCTAAAGAACATGGTCTTT
4194744 AGCGGCAATTTTTTCTAAG
66 AGCGGCAATTTTTTCTAAG
*
4194763 CGCTGCTA
1 CGCCGCTA
4194771 TTTTGGGGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
83 65 0.79
84 17 0.21
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGGGCTTTAGCGGCATTTTTTATTAAGCGCCGCTAAAGAACATGGTCTTT
AGCGGCAATTTTTTCTAAG
Found at i:4198174 original size:9 final size:9
Alignment explanation
Indices: 4198160--4198187 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4198150 TGAATGAAGG
4198160 AAAATTTTA
1 AAAATTTTA
4198169 AAAATTTTA
1 AAAATTTTA
4198178 AAAATTTTA
1 AAAATTTTA
4198187 A
1 A
4198188 TTAACACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAATTTTA
Found at i:4200659 original size:9 final size:9
Alignment explanation
Indices: 4200645--4200687 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
4200635 TTATGTATTA
4200645 TGTAAGTAC
1 TGTAAGTAC
4200654 TGTAAGTAC
1 TGTAAGTAC
*
4200663 TGTAAGTAA
1 TGTAAGTAC
4200672 TGTAAGTTA-
1 TGTAAG-TAC
4200681 TGTAAGT
1 TGTAAGT
4200688 TACTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 1 0.03
9 29 0.91
10 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (9 bp):
TGTAAGTAC
Found at i:4200668 original size:18 final size:18
Alignment explanation
Indices: 4200642--4201095 Score: 305
Period size: 18 Copynumber: 25.2 Consensus size: 18
4200632 GTATTATGTA
*
4200642 TTATGTAAGTACTGTAAG
1 TTATGTAAGTAATGTAAG
4200660 -TACTGTAAGTAATGTAAG
1 TTA-TGTAAGTAATGTAAG
* *
4200678 TTATGTAAGTTACT-TAAT
1 TTATGTAAG-TAATGTAAG
* *
4200696 TTATGTAAGTTACT-TAAT
1 TTATGTAAG-TAATGTAAG
*
4200714 TTATGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* *
4200732 TTACT-TAATTTATGTAAG
1 TTA-TGTAAGTAATGTAAG
* *
4200750 TTATGTAAG-ATATTTAAT
1 TTATGTAAGTA-ATGTAAG
*
4200768 TTATGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* * *
4200786 TTATTTAATTTATGTAAG
1 TTATGTAAGTAATGTAAG
* * *
4200804 TTATGTAAGTTATTTAAT
1 TTATGTAAGTAATGTAAG
*
4200822 TTATGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* * * *
4200840 ATAT-TTAGTTTATGTAAT
1 TTATGTAAG-TAATGTAAG
*
4200858 TTATGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* * **
4200876 TTATTTAATTTTTGTAAG
1 TTATGTAAGTAATGTAAG
* *
4200894 TTATGTAAGTTACT-TAAT
1 TTATGTAAG-TAATGTAAG
*
4200912 TTATGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* * *
4200930 TTATGTAAGTTATTTAAT
1 TTATGTAAGTAATGTAAG
*
4200948 TTATGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* * * *
4200966 ATAT-TTAGTTTATGTAAT
1 TTATGTAAG-TAATGTAAG
* * *
4200984 TTATGTAAGTTATTTAAT
1 TTATGTAAGTAATGTAAG
* *
4201002 TTTTGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* *
4201020 TTACT-TAATTTATGTAAG
1 TTA-TGTAAGTAATGTAAG
*
4201038 TTATGTAAGTTATGTAAG
1 TTATGTAAGTAATGTAAG
* * **
4201056 TTATTTAATTTTTGTAAG
1 TTATGTAAGTAATGTAAG
*
4201074 TTATGTAATTAATGTAAG
1 TTATGTAAGTAATGTAAG
4201092 TTAT
1 TTAT
4201096 TTAATTTGTG
Statistics
Matches: 359, Mismatches: 61, Indels: 32
0.79 0.13 0.07
Matches are distributed among these distances:
17 14 0.04
18 330 0.92
19 15 0.04
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATGTAAGTAATGTAAG
Found at i:4200674 original size:27 final size:27
Alignment explanation
Indices: 4200642--4201095 Score: 332
Period size: 27 Copynumber: 16.1 Consensus size: 27
4200632 GTATTATGTA
4200642 TTATGTAAG-TACTGTAA-GTACTGTAAG
1 TTATGTAAGTTACT-TAATGTA-TGTAAG
* *
4200669 TAATGTAAGTTA-TGTAAGT-TACT-TAAT
1 TTATGTAAGTTACT-TAA-TGTA-TGTAAG
*
4200696 TTATGTAAGTTACTTAATTTATGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
*
4200723 TTATGTAAGTTACTTAATTTATGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
* * *
4200750 TTATGTAAGATATTTAATTTATGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
* *
4200777 TTATGTAAGTTATTTAATTTATGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
* *
4200804 TTATGTAAGTTATTTAATTTATGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
* *
4200831 TTATGTAAGATATTTAGTTTATGTAATTTATGTAAG
1 TTATGTAAG----TTA----CT-TAATGTATGTAAG
* * *
4200867 TTATGTAAGTTATTTAATTTTTGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
4200894 TTATGTAAGTTACTTAATTTATGTAAGTTATGTAAG
1 TTATGTAAGTTACTT-A---A--T--G-TATGTAAG
* *
4200930 TTATGTAAGTTATTTAATTTATGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
* * * * *
4200957 TTATGTAAGATATTTAGTTTATGTAAT
1 TTATGTAAGTTACTTAATGTATGTAAG
* * *
4200984 TTATGTAAGTTATTTAATTTTTGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
*
4201011 TTATGTAAGTTACTTAATTTATGTAAG
1 TTATGTAAGTTACTTAATGTATGTAAG
* *
4201038 TTATGTAAGTTA-TGTAA-GTTATTTAAT
1 TTATGTAAGTTACT-TAATG-TATGTAAG
*
4201065 TTTTGTAAGTTA-TGTAAT-TAATGTAAG
1 TTATGTAAGTTACT-TAATGT-ATGTAAG
4201092 TTAT
1 TTAT
4201096 TTAATTTGTG
Statistics
Matches: 368, Mismatches: 31, Indels: 56
0.81 0.07 0.12
Matches are distributed among these distances:
26 4 0.01
27 300 0.82
28 9 0.02
30 1 0.00
31 4 0.01
32 4 0.01
33 1 0.00
35 2 0.01
36 43 0.12
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (27 bp):
TTATGTAAGTTACTTAATGTATGTAAG
Found at i:4200704 original size:54 final size:54
Alignment explanation
Indices: 4200642--4201095 Score: 431
Period size: 54 Copynumber: 8.2 Consensus size: 54
4200632 GTATTATGTA
*
4200642 TTATGTAAG-TACTGTAAG-TACTGTAAGTAATGTAAGTTATGTAAGTTACTTAAT
1 TTATGTAAGTTA-TGTAAGTTA-TGTAAGTTATGTAAGTTATGTAAGTTACTTAAT
* * *
4200696 TTATGTAAGTTACT-TAATTTATGTAAGTTATGTAAGTTACT-TAATTTA-TGTAAG
1 TTATGTAAGTTA-TGTAAGTTATGTAAGTTATGTAAGTTA-TGTAAGTTACT-TAAT
* * * * * *
4200750 TTATGTAAGATATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTA-TGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTACT-TAAT
* * * *
4200804 TTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATAT-TTAGTTTA-TGTAAT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG-TTACT-TAAT
* * *
4200858 TTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAAT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTACTTAAT
* * *
4200912 TTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATTTAGT
1 TTATGTAAGTTATGTAAGTTATGTAAG---------TTATGTAAGTTATGTAAGTTACTTAAT
* * * *
4200975 TTATGTAATTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAAT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTACTTAAT
* * *
4201029 TTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTA-TGTAAT
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTACT-TAAT
*
4201083 TAATGTAAGTTAT
1 TTATGTAAGTTAT
4201096 TTAATTTGTG
Statistics
Matches: 343, Mismatches: 38, Indels: 38
0.82 0.09 0.09
Matches are distributed among these distances:
53 6 0.02
54 279 0.81
55 11 0.03
63 47 0.14
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (54 bp):
TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTACTTAAT
Found at i:4201060 original size:63 final size:62
Alignment explanation
Indices: 4200663--4201081 Score: 518
Period size: 63 Copynumber: 6.8 Consensus size: 62
4200653 CTGTAAGTAC
* * * * *
4200663 TGTAAGTAATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTACT-TAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTA-TGTAAGTTAT-TAATTTA
* * * * * *
4200726 TGTAAGTTACT-TAATTTATGTAAGTTATGTAAGATATT-TAATTTATGTAAGTTATGTAAGTTA
1 TGTAAGTTA-TGTAAGTTATGTAAGTTATTTAA-TTTTTGTAAGTTATGTAAGTTAT-TAATTTA
* * * * *
4200789 TTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGATATTTAGTTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTA-TTAATTTA
*
4200852 TGTAATTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTA-TTAATTTA
*
4200915 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAG--A-T-ATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTATTAATTTA
*
4200973 -GT---TTATGTAATTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTA-TTAATTTA
4201032 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAA
1 TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAA
4201082 TTAATGTAAG
Statistics
Matches: 311, Mismatches: 30, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
54 43 0.14
56 1 0.00
57 2 0.01
58 6 0.02
59 6 0.02
60 2 0.01
61 1 0.00
62 4 0.01
63 242 0.78
64 4 0.01
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.50
Consensus pattern (62 bp):
TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTATTAATTTA
Found at i:4201093 original size:36 final size:36
Alignment explanation
Indices: 4200671--4201102 Score: 451
Period size: 36 Copynumber: 12.0 Consensus size: 36
4200661 ACTGTAAGTA
* * *
4200671 ATGTAAGTTATGTAAGTTACT-TAATTTATGTAAGTT
1 ATGTAAGTTATGTAAGTTA-TGTAAGTTATTTAATTT
* *
4200707 ACT-TAATTTATGTAAGTTATGTAAGTTACTTAATTT
1 A-TGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
* * * * *
4200743 ATGTAAGTTATGTAAGATATTTAATTTATGTAAGTT
1 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
* * * *
4200779 ATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTT
1 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
* * * *
4200815 ATTTAATTTATGTAAGTTATGTAAGATATTTAGTTT
1 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
*
4200851 ATGTAATTTATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
* * * *
4200887 TTGTAAGTTATGTAAGTTACT-TAATTTATGTAAGTT
1 ATGTAAGTTATGTAAGTTA-TGTAAGTTATTTAATTT
* * * *
4200923 ATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTT
1 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
* * * * *
4200959 ATGTAAGATAT-TTAGTTTATGTAATTTATGTAAGTT
1 ATGTAAGTTATGTAAG-TTATGTAAGTTATTTAATTT
* * * *
4200995 ATTTAATTTTTGTAAGTTATGTAAGTTACTTAATTT
1 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
4201031 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
*
4201067 TTGTAAGTTATGTAA-TTAATGTAAGTTATTTAATTT
1 ATGTAAGTTATGTAAGTT-ATGTAAGTTATTTAATTT
4201103 GTGAACCCTA
Statistics
Matches: 337, Mismatches: 51, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
35 8 0.02
36 324 0.96
37 5 0.01
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (36 bp):
ATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTT
Found at i:4204693 original size:13 final size:13
Alignment explanation
Indices: 4204677--4204701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4204667 TTTAGATTAA
4204677 ATTTTTAAAATAT
1 ATTTTTAAAATAT
4204690 ATTTTTAAAATA
1 ATTTTTAAAATA
4204702 CTAATTACTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTTAAAATAT
Found at i:4205573 original size:21 final size:20
Alignment explanation
Indices: 4205549--4205633 Score: 53
Period size: 21 Copynumber: 4.0 Consensus size: 20
4205539 ACTAGTTAAT
4205549 CTAAACTGTAAACCATAAACC
1 CTAAACT-TAAACCATAAACC
* * *
4205570 CTAAAATCATAAACCCTTAACAC
1 CT-AAA-CTTAAACCATAAAC-C
* * *
4205593 ATAACCTTAAACCTTAAACC
1 CTAAACTTAAACCATAAACC
* *
4205613 CCAACCTTTAAACCATAAACC
1 CTAAAC-TTAAACCATAAACC
4205634 ATAGACCAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 5 0.10
21 26 0.53
22 15 0.31
23 3 0.06
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (20 bp):
CTAAACTTAAACCATAAACC
Found at i:4205574 original size:14 final size:14
Alignment explanation
Indices: 4205557--4205636 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
4205547 ATCTAAACTG
4205557 TAAACCATAAACCC
1 TAAACCATAAACCC
*
4205571 TAAAATCATAAACCC
1 T-AAACCATAAACCC
* *
4205586 TTAACACAT-AACCT
1 TAAAC-CATAAACCC
*
4205600 TAAACCTTAAACCC
1 TAAACCATAAACCC
* * *
4205614 -CAACCTTTAAACCA
1 TAAACC-ATAAACCC
4205628 TAAACCATA
1 TAAACCATA
4205637 GACCAAATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
13 6 0.12
14 24 0.48
15 20 0.40
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:4205904 original size:115 final size:114
Alignment explanation
Indices: 4205706--4206231 Score: 409
Period size: 115 Copynumber: 4.6 Consensus size: 114
4205696 ACCAAAACTT
* * * *
4205706 TGCGTTTTGGTTAAGATATTTTCCGGCGCTTCTCAAAAAGCGCCGTTAATACTATGCTTTAGCAG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* * * **
4205771 CGATT-TCTCGTGGACGCCACTAATTCCATTATACATCAAGACTTAAACGC
66 CG-TTCCCTCATTG-CGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * *
4205821 TGCGTTTTTGTTAATATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATATGCTTTAGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* * * * * * *
4205886 CGTTCCCTCATAAGCGCCACTAAGTCTAATATACCTCATGA-AAAAACTC
66 CGTTCCCTCAT-TGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * * * **** * *
4205935 TGCGTTTTGGTGAGCATATTTTGTGGCGCTTTTTGCCAAGCGCCGCTAATACTATGATTTCGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* *** * ** * *
4206000 CATTTTTTAATATGCGCCACTAATAAC-TGTATACATCAAGACAAAAATGT
66 CGTTCCCTCAT-TGCGCCACTAATTCCAT-TATACATCAAGACAAAAACGC
* * * * ** * * *
4206050 TGCGTTTTGGTTACCAAATGTTGCGGCACTTCTCTGAAAGCGCCACTAATAGTATGCCTTAGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* * * * * *
4206115 CGTGTTCCCT--TTGCGCCACTAATTCTAGTATACCTGAAGAC-CAAACTC
66 C--GTTCCCTCATTGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * * * *
4206163 TGCGTTTTGGTTCAGATATTTTACGACGCTTCTCACAAAA-CGCCGCTAATATTATGCTTTAGCG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCA-AAAAGCGCCGCTAATACTATGCTTTAGCG
4206227 GCGTT
65 GCGTT
4206232 TTCCATTAAA
Statistics
Matches: 314, Mismatches: 89, Indels: 20
0.74 0.21 0.05
Matches are distributed among these distances:
111 3 0.01
113 52 0.17
114 112 0.36
115 143 0.46
116 1 0.00
117 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (114 bp):
TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
CGTTCCCTCATTGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
Found at i:4222006 original size:205 final size:205
Alignment explanation
Indices: 4221654--4222068 Score: 812
Period size: 205 Copynumber: 2.0 Consensus size: 205
4221644 GTCAATACTA
4221654 GAATTTCAAAACCTTAAACACAAAGTTTTGTAGGACTATCTTTGAATAGGTGTTGTGGAGGTGCT
1 GAATTTCAAAACCTTAAACACAAAGTTTTGTAGGACTATCTTTGAATAGGTGTTGTGGAGGTGCT
4221719 TTAGCCTTTTCTACACGTAACTATACTCTTGAATCCAGATTTGATTATGAGATCGTTCCTTAGTT
66 TTAGCCTTTTCTACACGTAACTATACTCTTGAATCCAGATTTGATTATGAGATCGTTCCTTAGTT
4221784 TTAAGATTTTCCCTTACATTTGTCTTAGGATTAGCCTTAGAACTTTGGGTGATAGGTGACTAGTC
131 TTAAGATTTTCCCTTACATTTGTCTTAGGATTAGCCTTAGAACTTTGGGTGATAGGTGACTAGTC
4221849 GACAAAACCC
196 GACAAAACCC
*
4221859 GAATTTCAAAACCTTAAACACAAAGTTTTGTAGGACTATCTTTGAATAGGTGTTGTGGGGGTGCT
1 GAATTTCAAAACCTTAAACACAAAGTTTTGTAGGACTATCTTTGAATAGGTGTTGTGGAGGTGCT
4221924 TTAGCCTTTTCTACACGTAACTATACTCTTGAATCCAGATTTGATTATGAGATCGTTCCTTAGTT
66 TTAGCCTTTTCTACACGTAACTATACTCTTGAATCCAGATTTGATTATGAGATCGTTCCTTAGTT
*
4221989 TTAAGATTTTCCCTTACATTTGTCTTAGGATTAGCCTTAGAACTTTGGGTGATTGGTGACTAGTC
131 TTAAGATTTTCCCTTACATTTGTCTTAGGATTAGCCTTAGAACTTTGGGTGATAGGTGACTAGTC
4222054 GACAAAACCC
196 GACAAAACCC
4222064 GAATT
1 GAATT
4222069 GATTAATGAC
Statistics
Matches: 208, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
205 208 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (205 bp):
GAATTTCAAAACCTTAAACACAAAGTTTTGTAGGACTATCTTTGAATAGGTGTTGTGGAGGTGCT
TTAGCCTTTTCTACACGTAACTATACTCTTGAATCCAGATTTGATTATGAGATCGTTCCTTAGTT
TTAAGATTTTCCCTTACATTTGTCTTAGGATTAGCCTTAGAACTTTGGGTGATAGGTGACTAGTC
GACAAAACCC
Found at i:4226741 original size:11 final size:11
Alignment explanation
Indices: 4226725--4226773 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
4226715 AGACAACCCA
4226725 ATTTTATTTTT
1 ATTTTATTTTT
*
4226736 ATTTTA-TGTT
1 ATTTTATTTTT
4226746 ATTTATATATTTT
1 ATTT-TAT-TTTT
4226759 -TTTTATTTTT
1 ATTTTATTTTT
4226769 ATTTT
1 ATTTT
4226774 CTTGCATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 11 0.34
11 15 0.47
12 3 0.09
13 3 0.09
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:4227855 original size:11 final size:12
Alignment explanation
Indices: 4227840--4227881 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
4227830 TTCTTAAGTA
4227840 AAAAAGAAAAA-
1 AAAAAGAAAAAG
4227851 AAAAAGAAGAAAAG
1 AAAAAG-A-AAAAG
4227865 AAAAAGAAAAAG
1 AAAAAGAAAAAG
4227877 AAAAA
1 AAAAA
4227882 ATATTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 11 0.39
13 5 0.18
14 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:4229381 original size:21 final size:21
Alignment explanation
Indices: 4229355--4229402 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
4229345 CTCCAAAACA
4229355 AGGGAAAATGGGTTACATTTT
1 AGGGAAAATGGGTTACATTTT
4229376 AGGGAAAATGGGTTACATTTT
1 AGGGAAAATGGGTTACATTTT
4229397 AGGGAA
1 AGGGAA
4229403 CATGTCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.29
Consensus pattern (21 bp):
AGGGAAAATGGGTTACATTTT
Found at i:4229412 original size:21 final size:21
Alignment explanation
Indices: 4229355--4229412 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
4229345 CTCCAAAACA
*
4229355 AGGGAAAATGGGTTACATTTT
1 AGGGAAAATGGCTTACATTTT
*
4229376 AGGGAAAATGGGTTACATTTT
1 AGGGAAAATGGCTTACATTTT
* *
4229397 AGGGAACATGTCTTAC
1 AGGGAAAATGGCTTAC
4229413 CCTTTCAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.31
Consensus pattern (21 bp):
AGGGAAAATGGCTTACATTTT
Found at i:4229852 original size:34 final size:35
Alignment explanation
Indices: 4229794--4229860 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
4229784 CAAACACCAG
4229794 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
4229829 AAAATATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
4229861 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:4230160 original size:62 final size:62
Alignment explanation
Indices: 4230063--4230188 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
4230053 CGTGTGCATC
4230063 CTGGAAACAACTCTATATGCTTGATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCT
1 CTGGAAACAACTCTATATGCTTGATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCT
4230125 CTGGAAACAACTCTATATGCTTGATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCT
1 CTGGAAACAACTCTATATGCTTGATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCT
4230187 CT
1 CT
4230189 CCTAAGTATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.40
Consensus pattern (62 bp):
CTGGAAACAACTCTATATGCTTGATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCT
Found at i:4230254 original size:66 final size:66
Alignment explanation
Indices: 4230148--4230280 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
4230138 TATATGCTTG
4230148 ATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCTCTCCTAAGTATAGAAACATGAATTTA
1 ATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCTCTCCTAAGTATAGAAACATGAATTTA
4230213 A
66 A
*
4230214 ATTTTGGCTCGTTTTTCGCTCCTTTCGCTCCCAATTGCTCTCCTAAGTATAGAAACATGAATTTA
1 ATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCTCTCCTAAGTATAGAAACATGAATTTA
4230279 A
66 A
4230280 A
1 A
4230281 GGATCAGGAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (66 bp):
ATTTTGGCTCGTTTTTCGCTCCTTTCACTCCCAATTGCTCTCCTAAGTATAGAAACATGAATTTA
A
Found at i:4230752 original size:66 final size:66
Alignment explanation
Indices: 4230671--4230799 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
4230661 GTTGTAATTG
* *
4230671 TCCTAGACATTAAACTATTAGGATTGGTCTCCTATGAATGGATCATGTCATCTATTTTAGATTTT
1 TCCTAGACATTAAACTACTAGGATTGGTCTCCCATGAATGGATCATGTCATCTATTTTAGATTTT
4230736 T
66 T
4230737 TCCTAGACATTAAACTACTAGGATTGGTCTCCCATGAATGGATCATGTCATCTATTTTAGATT
1 TCCTAGACATTAAACTACTAGGATTGGTCTCCCATGAATGGATCATGTCATCTATTTTAGATT
4230800 CTTCATCACC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.40
Consensus pattern (66 bp):
TCCTAGACATTAAACTACTAGGATTGGTCTCCCATGAATGGATCATGTCATCTATTTTAGATTTT
T
Found at i:4233138 original size:23 final size:23
Alignment explanation
Indices: 4233108--4233153 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4233098 ATAGTGTAAT
4233108 CAAATTGATTCCTACGTTAAGCA
1 CAAATTGATTCCTACGTTAAGCA
4233131 CAAATTGATTCCTACGTTAAGCA
1 CAAATTGATTCCTACGTTAAGCA
4233154 TTGGATCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (23 bp):
CAAATTGATTCCTACGTTAAGCA
Found at i:4236116 original size:94 final size:96
Alignment explanation
Indices: 4235983--4236209 Score: 298
Period size: 94 Copynumber: 2.4 Consensus size: 96
4235973 TCCTGTTTAT
* * * * *
4235983 GGTTTTTAAATAAAAAATCAATTAAATTAGGGTTTAGGGTTTCTTGAGTAATTTAATTAAAATTT
1 GGTTTTTAAGT-AAAAATCAAATAAATTAGGGTTTAGGGTTACTTCAGTAAATTAATTAAAA-TT
**
4236048 TTTTAAAAATTAGA-TTAGGGTTTA-GTGTTAA
64 TTAAAAAAATTAGATTTAGGGTTTAGGTGTTAA
* *
4236079 GGTTTTTAAG-GAAAATCAAATAAATTAGGGTTTAGGGTTACTTCAGTAAATTAATTATAATTTT
1 GGTTTTTAAGTAAAAATCAAATAAATTAGGGTTTAGGGTTACTTCAGTAAATTAATTAAAATTTT
* *
4236143 AAAAAAATTAGATTTAGGGTTTAGGGTTTTAG
66 AAAAAAATTAGATTTAGGGTTTA-GGTGTTAA
4236175 GGTTTTTAAGTAAAAACTCAAATAAATTAGGGTTT
1 GGTTTTTAAGTAAAAA-TCAAATAAATTAGGGTTT
4236210 GGGGATTAGG
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
93 14 0.12
94 54 0.47
96 24 0.21
97 4 0.04
98 18 0.16
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (96 bp):
GGTTTTTAAGTAAAAATCAAATAAATTAGGGTTTAGGGTTACTTCAGTAAATTAATTAAAATTTT
AAAAAAATTAGATTTAGGGTTTAGGTGTTAA
Found at i:4236236 original size:105 final size:94
Alignment explanation
Indices: 4235913--4236209 Score: 287
Period size: 94 Copynumber: 3.1 Consensus size: 94
4235903 TAAATAAGGG
* * * * * * * *
4235913 ATTAGGGTTTAGGGTTTCTCAATTAAATTAATTATAAAATTTT--CAAAATTGGATTA-AGTTTC
1 ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTA-AAATTTTTAAAAAAATTAGATTAGGGTTTA
* * * *
4235975 CTGTTTATGGTTTTTAAATAAAAAATCAATTAA
65 GTG-TTAAGGTTTTT-AA-GAAAAATCAAATAA
* * * **
4236008 ATTAGGGTTTAGGGTTTCTTGAGTAATTTAATTAAAATTTTTTTAAAAATTAGATTAGGGTTTAG
1 ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTAAAATTTTTAAAAAAATTAGATTAGGGTTTAG
*
4236073 TGTTAAGGTTTTTAAGGAAAATCAAATAA
66 TGTTAAGGTTTTTAAGAAAAATCAAATAA
* *
4236102 ATTAGGGTTTAGGGTTACTTCAGTAAATTAATTATAA-TTTTAAAAAAATTAGATTTAGGGTTTA
1 ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTAAAATTTTTAAAAAAATTAGA-TTAGGGTTTA
* *
4236166 GGGTTTTAGGGTTTTTAAGTAAAAACTCAAATAA
65 --GTGTTAAGGTTTTTAAG-AAAAA-TCAAATAA
4236200 ATTAGGGTTT
1 ATTAGGGTTT
4236210 GGGGATTAGG
Statistics
Matches: 171, Mismatches: 23, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
93 14 0.08
94 61 0.36
95 32 0.19
96 36 0.21
97 10 0.06
98 18 0.11
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (94 bp):
ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTAAAATTTTTAAAAAAATTAGATTAGGGTTTAG
TGTTAAGGTTTTTAAGAAAAATCAAATAA
Found at i:4236473 original size:126 final size:126
Alignment explanation
Indices: 4236248--4236666 Score: 678
Period size: 126 Copynumber: 3.3 Consensus size: 126
4236238 TTGTTAATTT
* *
4236248 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGAC
1 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGAAGAC
*
4236313 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGTAAAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
* *
4236374 AAAGAAGCTCTCACGTGGACGCACTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGAAGAC
4236439 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
* * *
4236500 AAAGAAACTCCCACGTAGACGCACTTTTGCTACAGTAGCTCCTT-AAAAAATAATTTCGAGCAGA
1 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCT-CTTGAAAAAATAATTTCGAGAAGA
* * * * *
4236564 CGTTTATGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAACGAAAGTACTA
65 CGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
***
4236626 AAAGAAGCTCCCACGTGGACGTGTTTTTGCTACAGTAGCTC
1 AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTC
4236667 ATGTTTGGCC
Statistics
Matches: 273, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
125 1 0.00
126 269 0.99
127 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCACTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGAAGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAGCAAAAGTACTG
Found at i:4237706 original size:21 final size:22
Alignment explanation
Indices: 4237676--4237716 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4237666 GCGGCTGTTG
*
4237676 TGGTTGCTCCAGT-GGGGATTC
1 TGGTTCCTCCAGTAGGGGATTC
*
4237697 TGGTTCCTCCGGTAGGGGAT
1 TGGTTCCTCCAGTAGGGGAT
4237717 CTAGTTGTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.10, C:0.20, G:0.39, T:0.32
Consensus pattern (22 bp):
TGGTTCCTCCAGTAGGGGATTC
Found at i:4238124 original size:30 final size:30
Alignment explanation
Indices: 4238090--4238156 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
4238080 GTGCTATTGC
4238090 TGGGCCTGGTGATTGTATGGGCGCT-GATGA
1 TGGGCCTGGTGATTGTATGGGC-CTCGATGA
* * *
4238120 TGGGCCGGGTGATTGTTTGGGCCTCGTTGA
1 TGGGCCTGGTGATTGTATGGGCCTCGATGA
4238150 TGGGCCT
1 TGGGCCT
4238157 ACATCGTCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.09, C:0.16, G:0.43, T:0.31
Consensus pattern (30 bp):
TGGGCCTGGTGATTGTATGGGCCTCGATGA
Found at i:4239444 original size:16 final size:16
Alignment explanation
Indices: 4239409--4239442 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4239399 TACATCATCC
4239409 AAACAAATAAAATATA
1 AAACAAATAAAATATA
*
4239425 AAACGAATAAAAT-TA
1 AAACAAATAAAATATA
4239440 AAA
1 AAA
4239443 ACATTCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (16 bp):
AAACAAATAAAATATA
Found at i:4239573 original size:34 final size:34
Alignment explanation
Indices: 4239535--4239641 Score: 159
Period size: 34 Copynumber: 3.2 Consensus size: 34
4239525 ATTAAAATAT
4239535 ATGTGTATATGTATATGTACTTACAAAGGTAAAA
1 ATGTGTATATGTATATGTACTTACAAAGGTAAAA
*
4239569 ATGTGTACATAGATATAT-TA--TA-AAAGGTAAAA
1 ATGTGTATAT-G-TATATGTACTTACAAAGGTAAAA
4239601 ATGTGTATATGTATATGTACTTACAAAGGTAAAA
1 ATGTGTATATGTATATGTACTTACAAAGGTAAAA
4239635 ATGTGTA
1 ATGTGTA
4239642 CATAGATATA
Statistics
Matches: 65, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
30 5 0.08
31 3 0.05
32 19 0.29
33 4 0.06
34 26 0.40
35 3 0.05
36 5 0.08
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.35
Consensus pattern (34 bp):
ATGTGTATATGTATATGTACTTACAAAGGTAAAA
Found at i:4239597 original size:32 final size:33
Alignment explanation
Indices: 4239559--4239658 Score: 134
Period size: 34 Copynumber: 3.0 Consensus size: 33
4239549 ATGTACTTAC
4239559 AAAGGTAAAAATGTGTACATAGATATAT-TATA
1 AAAGGTAAAAATGTGTACATAGATATATATATA
* *
4239591 AAAGGTAAAAATGTGTATAT-G-TATATGTACTTA
1 AAAGGTAAAAATGTGTACATAGATATATATA--TA
4239624 CAAAGGTAAAAATGTGTACATAGATATATATATA
1 -AAAGGTAAAAATGTGTACATAGATATATATATA
4239658 A
1 A
4239659 TACACATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
30 5 0.08
31 3 0.05
32 19 0.32
33 3 0.05
34 21 0.36
35 1 0.02
36 7 0.12
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (33 bp):
AAAGGTAAAAATGTGTACATAGATATATATATA
Found at i:4239854 original size:3 final size:3
Alignment explanation
Indices: 4239848--4239890 Score: 68
Period size: 3 Copynumber: 13.7 Consensus size: 3
4239838 AAGTAAAGAC
4239848 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AACT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T -AAT AAT AA
4239891 AATTGCCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 34 0.89
4 2 0.05
5 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4241674 original size:95 final size:95
Alignment explanation
Indices: 4241511--4242361 Score: 1369
Period size: 95 Copynumber: 9.0 Consensus size: 95
4241501 AATATCTGAA
*
4241511 ATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTA-CTGGCTTCAATGTACTCCACTGT
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATC-GGCTTCAATGTACTCCACTGT
* *
4241575 AGTCACAGGAAGGTAAAATCTGCCATCTTCG
65 AGTCACAGGGAGGTAAAATCTGCCATCTTTG
* * * *
4241606 ATCTTCAATCTATTCCACCGCCAACCAGGAAGATAGAATTATCGGCTTCAATGTACTCCATTGTA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
4241671 GTCACAGGGAGGTAAAATCTGCCATC----
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
* *
4241697 -T-TT-AATCTATTCCACTGCCAACCAGGGAGATAGAATTATCAGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
* * *
4241759 GTTACAGGGAGGTAAAATCTACCAT-TTTT
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
*
4241788 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCGATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
4241853 GTCACAGGGAGGTAAAATTTGCCATCTTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
* *
4241883 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCGATGTACTCTACTGTA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
4241948 GTCACAGGGAGGTAAAATCTGCCATATTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
4241978 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
* * *
4242043 GTTACAGGAAGGTAAAATCTGCCATCTTTA
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
*
4242073 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTATA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
*
4242138 GTTACAGGGAGGTAAAATCTGCCATCTTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
* * *
4242168 ATCTTCAATCTATTCCACTGCCAACTAGGGAGATAGAATTATCGACTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
* * *
4242233 GTTACAGAGAGGTAAAATCTGCCATATTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
*
4242263 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGTTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
4242328 GTCACAGGGAGGTAAAATCTGCCATCTTTG
66 GTCACAGGGAGGTAAAATCTGCCATCTTTG
4242358 ATCT
1 ATCT
4242362 GCCCCGCTGT
Statistics
Matches: 705, Mismatches: 42, Indels: 18
0.92 0.05 0.02
Matches are distributed among these distances:
88 78 0.11
89 2 0.00
90 1 0.00
92 1 0.00
93 2 0.00
94 78 0.11
95 542 0.77
96 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTA
GTCACAGGGAGGTAAAATCTGCCATCTTTG
Found at i:4241756 original size:43 final size:43
Alignment explanation
Indices: 4241608--4241756 Score: 120
Period size: 43 Copynumber: 3.4 Consensus size: 43
4241598 CATCTTCGAT
* * * *
4241608 CTTCAATCTATTCCACCGCCAACCAGGAAGATAGAATTATCGG
1 CTTCAATCTACTCCACTGCCAACCAGGGAGATAGAATTATCAG
* * * * * * ** *
4241651 CTTCAATGTACTCCATTG-TAGTCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGCCA-AC-CAGGGAGATAGAAT-TATCAG
* *
4241696 CTTTAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCAG
1 CTTCAATCTACTCCACTGCCAACCAGGGAGATAGAATTATCAG
*
4241739 CTTCAATGTACTCCACTG
1 CTTCAATCTACTCCACTG
4241757 TAGTTACAGG
Statistics
Matches: 75, Mismatches: 27, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
42 1 0.01
43 33 0.44
44 23 0.31
45 17 0.23
46 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (43 bp):
CTTCAATCTACTCCACTGCCAACCAGGGAGATAGAATTATCAG
Found at i:4241849 original size:43 final size:43
Alignment explanation
Indices: 4241790--4242325 Score: 161
Period size: 43 Copynumber: 11.4 Consensus size: 43
4241780 CCATTTTTAT
* *
4241790 CTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGG
1 CTTCAATGTACTCCACTGCTAACCAGGGAGATAGAATTATCGG
* * * * *
4241833 CTTCGATGTACTCCACTG-TAGTCACAGGGAGGTAAAATTTGCCATCTTTGAT
1 CTTCAATGTACTCCACTGCTA-AC-CAGGGAGATAGAA-TT---ATC---G-G
* *
4241885 CTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGG
1 CTTCAATGTACTCCACTGCTAACCAGGGAGATAGAATTATCGG
* * * * * * *
4241928 CTTCGATGTACTCTACTG-TAGTCACAGGGAGGTAAAATCTGCCATATTTGAT
1 CTTCAATGTACTCCACTGCTA-AC-CAGGGAGATAGAA--T----TA-TCG-G
* *
4241980 CTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGG
1 CTTCAATGTACTCCACTGCTAACCAGGGAGATAGAATTATCGG
* * * **
4242023 CTTCAATGTACTCCACTG-TAGTTA-CAGGAAGGTAAAATCTGCCATCTTTAAT
1 CTTCAATGTACTCCACTGCTA---ACCAGGGAGATAGAAT-T---ATC----GG
* *
4242075 CTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGG
1 CTTCAATGTACTCCACTGCTAACCAGGGAGATAGAATTATCGG
* * * *
4242118 CTTCAATGTACTCCACTATAG-TTA-CAGGGAGGTAAAATCTGCCATCTTTGAT
1 CTTCAATGTACTCCAC--T-GCTAACCAGGGAGATAGAAT-T---ATC---G-G
* * * * *
4242170 CTTCAATCTATTCCACTGCCAACTAGGGAGATAGAATTATCGA
1 CTTCAATGTACTCCACTGCTAACCAGGGAGATAGAATTATCGG
* * * * *
4242213 CTTCAATGTACTCCACTG-TAGTTA-CAGAGAGGTAAAATCTGCCATATTTGAT
1 CTTCAATGTACTCCACTGCTA---ACCAGGGAGATAGAA--T----TA-TCG-G
* *
4242265 CTTCAATCTATTCCACTGCTAACCAGGGAGATAGAATTATCGG
1 CTTCAATGTACTCCACTGCTAACCAGGGAGATAGAATTATCGG
*
4242308 TTTCAATGTACTCCACTG
1 CTTCAATGTACTCCACTG
4242326 TAGTCACAGG
Statistics
Matches: 353, Mismatches: 79, Indels: 122
0.64 0.14 0.22
Matches are distributed among these distances:
42 7 0.02
43 92 0.26
44 60 0.17
45 13 0.04
46 3 0.01
47 9 0.03
48 9 0.03
49 3 0.01
50 12 0.03
51 60 0.17
52 77 0.22
53 8 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTCAATGTACTCCACTGCTAACCAGGGAGATAGAATTATCGG
Found at i:4242475 original size:88 final size:88
Alignment explanation
Indices: 4242366--4242656 Score: 501
Period size: 88 Copynumber: 3.3 Consensus size: 88
4242356 TGATCTGCCC
** *
4242366 CGCTGTCAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCA
1 CGCTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCA
*
4242431 AGGTTTGTGTCTTCGACCTACTT
66 AGGTTTGTGTCTTCGACCTGCTT
*
4242454 CGCTGCCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCA
1 CGCTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCA
4242519 AGGTTTGTGTCTTCGACCTGCTT
66 AGGTTTGTGTCTTCGACCTGCTT
* *
4242542 CGCTATCAATACAGGAAGGCAAGATCTATTATCTTCAACCAGCTCCACCACAACCGAGAGAGGCA
1 CGCTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCA
* *
4242607 AGATTTGCGTCTTCGACCTGCTT
66 AGGTTTGTGTCTTCGACCTGCTT
4242630 CGCTGTCAATACAGGAAGGCAAGATCT
1 CGCTGTCAATACAGGAAGGCAAGATCT
4242657 GTAACTTCAT
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 192 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (88 bp):
CGCTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCA
AGGTTTGTGTCTTCGACCTGCTT
Found at i:4242650 original size:44 final size:44
Alignment explanation
Indices: 4242372--4242654 Score: 171
Period size: 44 Copynumber: 6.4 Consensus size: 44
4242362 GCCCCGCTGT
* * *
4242372 CAATACAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTA-
1 CAATACAGGAAGGCAAGATTTG-TGTCTTCAACCAGCTTCGCTAC
* * * *
4242416 C-A-ACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTA-CTTCGCTGC
1 CAATACAG-GA-AGGCAAGATTTGTGTCTTCAACC-AGCTTCGCTAC
4242460 CAATACAGGAAGGCAAGATCTAT-TGTCTTCAACCAGC-TC-C-AC
1 CAATACAGGAAGGCAAGAT-T-TGTGTCTTCAACCAGCTTCGCTAC
* * * * *
4242502 CACA-ACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTAT
1 CA-ATACAG-GA-AGGCAAGATTTGTGTCTTCAACCAGCTTCGCTAC
*
4242548 CAATACAGGAAGGCAAGATCTAT-TATCTTCAACCAGC-TC-C-AC
1 CAATACAGGAAGGCAAGAT-T-TGTGTCTTCAACCAGCTTCGCTAC
* * * * **
4242590 CACA-ACCGAGAGAGGCAAGATTTGCGTCTTCGACCTGCTTCGCTGT
1 CA-ATACAG-GA-AGGCAAGATTTGTGTCTTCAACCAGCTTCGCTAC
4242636 CAATACAGGAAGGCAAGAT
1 CAATACAGGAAGGCAAGAT
4242655 CTGTAACTTC
Statistics
Matches: 182, Mismatches: 30, Indels: 54
0.68 0.11 0.20
Matches are distributed among these distances:
42 17 0.09
43 50 0.27
44 64 0.35
45 35 0.19
46 16 0.09
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (44 bp):
CAATACAGGAAGGCAAGATTTGTGTCTTCAACCAGCTTCGCTAC
Found at i:4243921 original size:23 final size:22
Alignment explanation
Indices: 4243882--4243931 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
4243872 TCACCTTGGC
* *
4243882 CTTTCCTTTTTTCCTTTCTTTT
1 CTTTTCTTCTTTCCTTTCTTTT
*
4243904 CTTTTCTTCTTTCTCTTTGTTTT
1 CTTTTCTTCTTTC-CTTTCTTTT
*
4243927 TTTTT
1 CTTTT
4243932 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (22 bp):
CTTTTCTTCTTTCCTTTCTTTT
Found at i:4248948 original size:19 final size:21
Alignment explanation
Indices: 4248923--4248970 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
4248913 TATATATATT
*
4248923 AATATATATA-AGA-AAAGAA
1 AATATATATAGAGATAAAAAA
*
4248942 CATATATATAGAGATAAAAAA
1 AATATATATAGAGATAAAAAA
4248963 AATATATA
1 AATATATA
4248971 ATACACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 12 0.50
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (21 bp):
AATATATATAGAGATAAAAAA
Found at i:4248951 original size:2 final size:2
Alignment explanation
Indices: 4248898--4248932 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
4248888 AGATAAGATA
4248898 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4248933 AGAAAAGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4250451 original size:7 final size:7
Alignment explanation
Indices: 4250439--4250463 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4250429 TATTAGTTAT
4250439 ATACATA
1 ATACATA
4250446 ATACATA
1 ATACATA
4250453 ATACATA
1 ATACATA
4250460 ATAC
1 ATAC
4250464 TAAATACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:4251657 original size:11 final size:11
Alignment explanation
Indices: 4251643--4251688 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
4251633 TTTTTTAAAT
4251643 AGGAATTTGAG
1 AGGAATTTGAG
4251654 AGGAATTTGAG
1 AGGAATTTGAG
4251665 A-GAATATT-AG
1 AGGAAT-TTGAG
*
4251675 AGAGAAATTGAG
1 AG-GAATTTGAG
4251687 AG
1 AG
4251689 AAATGATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.23
11 16 0.53
12 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:4251687 original size:10 final size:10
Alignment explanation
Indices: 4251649--4251692 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
4251639 AAATAGGAAT
*
4251649 TTGAGAGGAAT
1 TTGAGA-GAAA
4251660 TTGAGAGAATA
1 TTGAGAGAA-A
4251671 TTAGAGAGAAA
1 TT-GAGAGAAA
4251682 TTGAGAGAAA
1 TTGAGAGAAA
4251692 T
1 T
4251693 GATTTAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 12 0.40
11 11 0.37
12 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:4260556 original size:5 final size:5
Alignment explanation
Indices: 4260546--4260579 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
4260536 TGTACCCATG
4260546 TATTA TATTA TATTA TATTA TATTA TATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATT
4260580 TCACATGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:4262126 original size:16 final size:16
Alignment explanation
Indices: 4262105--4262139 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
4262095 ATGGCTGCTA
4262105 CAATGTTTACATCTAT
1 CAATGTTTACATCTAT
4262121 CAATGTTTACATCTAT
1 CAATGTTTACATCTAT
4262137 CAA
1 CAA
4262140 AACATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (16 bp):
CAATGTTTACATCTAT
Found at i:4269326 original size:12 final size:12
Alignment explanation
Indices: 4269309--4269335 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4269299 TAAAAAAAAT
4269309 AAAATATATAAC
1 AAAATATATAAC
4269321 AAAATATATAAC
1 AAAATATATAAC
4269333 AAA
1 AAA
4269336 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATATATAAC
Found at i:4270378 original size:21 final size:20
Alignment explanation
Indices: 4270339--4270380 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4270329 TTTATAGATA
*
4270339 CCTCTATTTCTGTTGAAAAT
1 CCTCTATTTCTGTTAAAAAT
*
4270359 CCTCTATTTTCTTTTAAAAAT
1 CCTCTA-TTTCTGTTAAAAAT
4270380 C
1 C
4270381 AACAGTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (20 bp):
CCTCTATTTCTGTTAAAAAT
Found at i:4271950 original size:7 final size:7
Alignment explanation
Indices: 4271940--4271967 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
4271930 GAAAAAAAGT
4271940 AAAAATA
1 AAAAATA
4271947 AAAAATA
1 AAAAATA
4271954 AAAAATA
1 AAAAATA
4271961 AAAAATA
1 AAAAATA
4271968 TGGACGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:4278052 original size:38 final size:37
Alignment explanation
Indices: 4278001--4278075 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
4277991 TTTTTAAATA
4278001 TTTTATTTTGAATTGCATT-AAT-TAATATAAAATAGTATT
1 TTTTATTTTGAATT--ATTGAATATAAT-TAAAATA-TATT
4278040 TTTTA-TTTGAATTATTGAATATAATTAAAATATATT
1 TTTTATTTTGAATTATTGAATATAATTAAAATATATT
4278076 AACTTACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
36 7 0.21
37 10 0.29
38 12 0.35
39 5 0.15
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (37 bp):
TTTTATTTTGAATTATTGAATATAATTAAAATATATT
Found at i:4284380 original size:25 final size:25
Alignment explanation
Indices: 4284346--4284395 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4284336 TGGTTTTATA
4284346 TGTTAATGACATACTGATTGTCAAT
1 TGTTAATGACATACTGATTGTCAAT
4284371 TGTTAATGACATACTGATTGTCAAT
1 TGTTAATGACATACTGATTGTCAAT
4284396 AATAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (25 bp):
TGTTAATGACATACTGATTGTCAAT
Found at i:4285404 original size:11 final size:11
Alignment explanation
Indices: 4285388--4285428 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4285378 TATTGGTCAA
*
4285388 TCTTCCTCTAG
1 TCTTCCTCGAG
4285399 TCTTCCTCGAG
1 TCTTCCTCGAG
*
4285410 TCTTCTTCGAG
1 TCTTCCTCGAG
*
4285421 TCTCCCTC
1 TCTTCCTC
4285429 ACATGTCGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.07, C:0.39, G:0.12, T:0.41
Consensus pattern (11 bp):
TCTTCCTCGAG
Found at i:4286831 original size:7 final size:7
Alignment explanation
Indices: 4286819--4287000 Score: 139
Period size: 7 Copynumber: 26.0 Consensus size: 7
4286809 TAAAAAAATT
4286819 AATTGAG
1 AATTGAG
4286826 AATTGAG
1 AATTGAG
*
4286833 AATTAAG
1 AATTGAG
4286840 AATTGAG
1 AATTGAG
*
4286847 GATTGAG
1 AATTGAG
*
4286854 GATTGAG
1 AATTGAG
* *
4286861 GATCGAG
1 AATTGAG
4286868 AATTGAG
1 AATTGAG
4286875 AATTGAG
1 AATTGAG
* *
4286882 AAATGAA
1 AATTGAG
4286889 AATTGAG
1 AATTGAG
* *
4286896 GATCGAG
1 AATTGAG
*
4286903 AATTTAG
1 AATTGAG
* *
4286910 GATTAAG
1 AATTGAG
*
4286917 GATTGAG
1 AATTGAG
*
4286924 AAATGAG
1 AATTGAG
4286931 AATTGAG
1 AATTGAG
* *
4286938 AAATGAA
1 AATTGAG
4286945 AATTGAG
1 AATTGAG
*
4286952 GATTGAG
1 AATTGAG
*
4286959 AATTTAG
1 AATTGAG
* *
4286966 GATTAAG
1 AATTGAG
*
4286973 GATTGAG
1 AATTGAG
* *
4286980 TATTGGG
1 AATTGAG
*
4286987 TATTGAG
1 AATTGAG
*
4286994 TATTGAG
1 AATTGAG
4287001 TTGAGAAGAA
Statistics
Matches: 141, Mismatches: 34, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 141 1.00
ACGTcount: A:0.40, C:0.01, G:0.30, T:0.29
Consensus pattern (7 bp):
AATTGAG
Found at i:4286919 original size:56 final size:56
Alignment explanation
Indices: 4286819--4286993 Score: 233
Period size: 56 Copynumber: 3.1 Consensus size: 56
4286809 TAAAAAAATT
* * * * * * * *
4286819 AATTGAGAATTGAGAATTAAGAATTGAGGATTGAGGATTGAGGATCGAGAATTGAG
1 AATTGAGAAATGAAAATTGAGGATTGAGAATTTAGGATTAAGGATTGAGAATTGAG
* *
4286875 AATTGAGAAATGAAAATTGAGGATCGAGAATTTAGGATTAAGGATTGAGAAATGAG
1 AATTGAGAAATGAAAATTGAGGATTGAGAATTTAGGATTAAGGATTGAGAATTGAG
* *
4286931 AATTGAGAAATGAAAATTGAGGATTGAGAATTTAGGATTAAGGATTGAGTATTGGG
1 AATTGAGAAATGAAAATTGAGGATTGAGAATTTAGGATTAAGGATTGAGAATTGAG
*
4286987 TATTGAG
1 AATTGAG
4286994 TATTGAGTTG
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 104 1.00
ACGTcount: A:0.41, C:0.01, G:0.30, T:0.28
Consensus pattern (56 bp):
AATTGAGAAATGAAAATTGAGGATTGAGAATTTAGGATTAAGGATTGAGAATTGAG
Found at i:4297177 original size:1 final size:1
Alignment explanation
Indices: 4297171--4297195 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4297161 TTGTAATTCC
4297171 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
4297196 CAATGTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4297393 original size:21 final size:21
Alignment explanation
Indices: 4297369--4297411 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4297359 ATTTTATTAC
4297369 TTTTAAATATTATTTG-ATAAA
1 TTTTAAA-ATTATTTGTATAAA
*
4297390 TTTTCAAATTATTTGTATAAA
1 TTTTAAAATTATTTGTATAAA
4297411 T
1 T
4297412 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTAAAATTATTTGTATAAA
Found at i:4297751 original size:15 final size:14
Alignment explanation
Indices: 4297726--4297755 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
4297716 AACAATTATT
4297726 TAAAATATAAAAAA
1 TAAAATATAAAAAA
4297740 TAAAACTATAAAAAA
1 TAAAA-TATAAAAAA
4297755 T
1 T
4297756 TATAAACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATATAAAAAA
Found at i:4299774 original size:22 final size:22
Alignment explanation
Indices: 4299746--4299787 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
4299736 GTAATATAAC
4299746 TTAGTTAAAATTTTCTATTAGT
1 TTAGTTAAAATTTTCTATTAGT
4299768 TTAGTTAAAATTTTCTATTA
1 TTAGTTAAAATTTTCTATTA
4299788 ATCATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (22 bp):
TTAGTTAAAATTTTCTATTAGT
Found at i:4303065 original size:22 final size:22
Alignment explanation
Indices: 4303018--4303065 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
4303008 TAAATTATAT
*
4303018 TAAACTAATTCTAAATCCAAAT
1 TAAACTAATTCTAAATCCAAAC
4303040 TAAACTATACTTCT-AAT-CAAAC
1 TAAACTA-A-TTCTAAATCCAAAC
4303062 TAAA
1 TAAA
4303066 ATTTGAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 15 0.65
23 4 0.17
24 4 0.17
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAACTAATTCTAAATCCAAAC
Found at i:4305971 original size:3 final size:3
Alignment explanation
Indices: 4305965--4306027 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
4305955 GTAGTAGTTG
* * * * * *
4305965 TAA TAA TAA CAA TAA TAA TAA TGA TAA TAA CAA CAA TGA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
4306013 TAG TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA
4306028 ATTAATATTA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:4306557 original size:12 final size:12
Alignment explanation
Indices: 4306535--4306568 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
4306525 CTATTTCAGA
4306535 ATAAAAAAAAGG
1 ATAAAAAAAAGG
4306547 A-AAAGAAAAAGG
1 ATAAA-AAAAAGG
4306559 ATAAAAAAAA
1 ATAAAAAAAA
4306569 CCCTAAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (12 bp):
ATAAAAAAAAGG
Found at i:4307644 original size:50 final size:50
Alignment explanation
Indices: 4307577--4308524 Score: 707
Period size: 50 Copynumber: 19.1 Consensus size: 50
4307567 TAACTTCAAT
* * * * *
4307577 CTGCAACG-CCGGAGAAGTAAGATTCATTGTTGTAGCTTTAACCTGCTTCA
1 CTGCAACGTCAGG-GAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* ** *
4307627 CTGCAACATCAGGGAAGTAAGATTTGCTGTTGTAGCTTCAATCTGTTTTA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
** * ** ** * * *
4307677 CTATAACGTTAGACAAGTAAGATTCGTTGTTGTAGCTTTAATCTATTTAA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
** * * * * *
4307727 CTGCAATTTCGGGGAAGCAAG-----CTGTTGTAACTTTAATCTGTTCCA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* ** * *
4307772 CTGC-ACTGCCAGGGAAGTAAGATTCGTTGTTGTAGCTTCAATCTATTTAA
1 CTGCAAC-GTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * * *
4307822 CTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAACCTGTTCCA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * * *
4307872 CTGCACCGCCAGGGAAGTAAGATTCATTGTTGTAGCTTCAATCTATTTAA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * * * ** *
4307922 CTGCAATGTCGGGGCAGCAAGACTT-GCTGTTGTAGCTTCAATCCATTCCA
1 CTGCAACGTCAGGGAAGTAAGA-TTCACTGTTGTAGCTTCAATCTGTTTCA
* * * * * * * *
4307972 CTAC-ACCTCCAGGGAAGTAAGATTCGCTATAGTACCTTCAATCTATTTAA
1 CTGCAACGT-CAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * *
4308022 CTGCAATGTCAGGGAAGCAAGATTCACTGTGGTAGCTTCAATCTGTTCCA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * * * *
4308072 CTGCACCGCCAGGAAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * *
4308122 CTGTAATGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATTTGTTCCA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * *
4308172 CTGC-ACTGCCAGGGAAGTAAGATTCATTGTTGTAGCTTCAATCTATTTAA
1 CTGCAAC-GTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* ** * * * * *
4308222 CTGCAATGTTGGGGAAGCAAGATTCGCTATTTTAGCTTCAATCTGTTCCA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * * *
4308272 CTAC-ACTGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAA
1 CTGCAAC-GTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * * * * *
4308322 CTGTAATGTC-GGGTAAGCAAGATTCGCTATTGTAGCTTCAATCTGTTCCA
1 CTGCAACGTCAGGG-AAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
** * * ** * *
4308372 CTATATCGCCAGGGAAGTAAGATTTGCTGTTGTAGCTTCAATCTATTTAA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
* * *
4308422 CTGTAATGTCAGGGAAGTAAGATTCACTGTTATAGCTTCAATCTGTTGT-A
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTT-TCA
* * ** * * * * *
4308472 CTACACCACCAGGGAAGGAAGATTCGCTATTGTAGCTTCAATCTATTCCA
1 CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
4308522 CTG
1 CTG
4308525 TAATGCCAAA
Statistics
Matches: 688, Mismatches: 190, Indels: 40
0.75 0.21 0.04
Matches are distributed among these distances:
44 1 0.00
45 33 0.05
49 9 0.01
50 631 0.92
51 14 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (50 bp):
CTGCAACGTCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTTCA
Found at i:4307904 original size:100 final size:100
Alignment explanation
Indices: 4307590--4308518 Score: 1141
Period size: 100 Copynumber: 9.3 Consensus size: 100
4307580 CAACGCCGGA
** * * ** * ** * * **
4307590 GAAGTAAGATTCATTGTTGTAGCTTTAACCTGCTTCACTGCAACATCAGGGAAGTAAGATTTGCT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
** * * ** *
4307655 GTTGTAGCTTCAATCTGTTTTACTATAACGTTAGA
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
* * * *
4307690 CAAGTAAGATTCGTTGTTGTAGCTTTAATCTATTTAACTGCAATTTCGGGGAAGCAAG-----CT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
* * * *
4307750 GTTGTAACTTTAATCTGTTCCACTGCACTGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
*
4307785 GAAGTAAGATTCGTTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
* *
4307850 GTTGTAGCTTCAACCTGTTCCACTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
** * *
4307885 GAAGTAAGATTCATTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGCAGCAAGACTT-GC
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGA-TTCAC
** *
4307949 TGTTGTAGCTTCAATCCATTCCACTACACCTCCAGG
65 TGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
* * * *
4307985 GAAGTAAGATTCGCTATAGTACCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCACT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
* *
4308050 GTGGTAGCTTCAATCTGTTCCACTGCACCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
* * * *
4308085 AAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGTAATGTCAGGGAAGTAAGATTCACT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
* * *
4308150 GTTGTAGCTTCAATTTGTTCCACTGCACTGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
** * *
4308185 GAAGTAAGATTCATTGTTGTAGCTTCAATCTATTTAACTGCAATGTTGGGGAAGCAAGATTCGCT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
* * *
4308250 ATTTTAGCTTCAATCTGTTCCACTACACTGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
* * *
4308285 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGTAATGTCGGGTAAGCAAGATTCGCT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
* * *
4308350 ATTGTAGCTTCAATCTGTTCCACTATATCGCCAGG
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
* * * *
4308385 GAAGTAAGATTTGCTGTTGTAGCTTCAATCTATTTAACTGTAATGTCAGGGAAGTAAGATTCACT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
* ** *
4308450 GTTATAGCTTCAATCTGTTGTACTACACCACCAGG
66 GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
* *
4308485 GAAGGAAGATTCGCTATTGTAGCTTCAATCTATT
1 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATT
4308519 CCACTGTAAT
Statistics
Matches: 728, Mismatches: 94, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
95 81 0.11
99 2 0.00
100 643 0.88
101 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (100 bp):
GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGATTCACT
GTTGTAGCTTCAATCTGTTCCACTACACCGCCAGG
Found at i:4308810 original size:88 final size:88
Alignment explanation
Indices: 4308690--4309120 Score: 497
Period size: 88 Copynumber: 4.9 Consensus size: 88
4308680 AGTAGTGGTG
* ** * *
4308690 TCTTCGGTCTACTTTTCTGCCAATACAGGAAGACTAGATCTGCTATTTTTAACCTACTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
4308755 TGCTCAGGGAGACAAGGCTAATA
66 TGCTCAGGGAGATAAGGCTAAGA
* * * * *
4308778 TCCTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTACTAGTTTCAACCTACTCCACTAC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* * * * *
4308843 TACTCAGGAAGATAAGGTTGAGG
66 TGCTCAGGGAGATAAGGCTAAGA
** * * ** * **
4308866 TCTTCGATCTACTTCATTGCTAATACAGGAAGACAAGATCTGTTATCTTT-AGTCTGCTCGGCTG
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-TTTCAACCTACTCCACTG
*
4308930 CTACTCAGGGAGATAAGGCT-AGTA
65 CTGCTCAGGGAGATAAGGCTAAG-A
* * *
4308954 TCTTCGATCTATTTCGCTGCCAATATAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACCGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
4309019 TGCTCAGGGAGATAAGGCTGAGG
66 TGCTCAGGGAGATAAGGCTAAGA
* * * *
4309042 TCTTCGATCTTCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATTTTCAACTTATTCCACTGC
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
*
4309107 TGCTCAAGGAGATA
66 TGCTCAGGGAGATA
4309121 GGATTTATGG
Statistics
Matches: 283, Mismatches: 56, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
87 5 0.02
88 273 0.96
89 5 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTGC
TGCTCAGGGAGATAAGGCTAAGA
Found at i:4310394 original size:22 final size:21
Alignment explanation
Indices: 4310369--4310419 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
4310359 TTACCCTCTC
*
4310369 CATTTTTACTTTTTCCA-TTTTT
1 CATTTTT-CGTTTT-CATTTTTT
4310391 CATTTTTCGTTTTCATTTTTTT
1 CATTTTTCGTTTTCA-TTTTTT
4310413 CATTTTT
1 CATTTTT
4310420 TATGACTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 5 0.19
22 19 0.73
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.71
Consensus pattern (21 bp):
CATTTTTCGTTTTCATTTTTT
Found at i:4311359 original size:15 final size:14
Alignment explanation
Indices: 4311326--4311375 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
4311316 CTTTTTTATC
* *
4311326 ATTTTTTTATTTTT
1 ATTTTTTGATTTTG
4311340 ATTTTTTGATTTTG
1 ATTTTTTGATTTTG
* *
4311354 ACTTTTTAGATTTAG
1 A-TTTTTTGATTTTG
4311369 ATTTTTT
1 ATTTTTT
4311376 AAATTGTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.72
Consensus pattern (14 bp):
ATTTTTTGATTTTG
Found at i:4315102 original size:3 final size:3
Alignment explanation
Indices: 4315096--4315193 Score: 61
Period size: 3 Copynumber: 32.7 Consensus size: 3
4315086 TTGATAAAAA
* * * * * ** *
4315096 AAT AAT ACT AAT AAT AAT AAT AGT AGT AGT AGT TGT AAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
4315144 AAT AAT AAT GAT AAT AAC AAC AAT GAT AGT AAT AAT AGT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4315192 AA
1 AA
4315194 ATTAATATTA
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4319986 original size:30 final size:30
Alignment explanation
Indices: 4319952--4320021 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
4319942 TGGCCCTTAA
*
4319952 GATCCGCGCGC-GACCCGACCCGCTATAGGG
1 GATCCGCGCGCAG-CCCGACCCGCTACAGGG
* *
4319982 GATCCGAGCGCAGCCCGACCCGCTCCAGGG
1 GATCCGCGCGCAGCCCGACCCGCTACAGGG
4320012 GATCCGCGCG
1 GATCCGCGCG
4320022 TTTCTGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.16, C:0.41, G:0.34, T:0.09
Consensus pattern (30 bp):
GATCCGCGCGCAGCCCGACCCGCTACAGGG
Found at i:4326983 original size:19 final size:19
Alignment explanation
Indices: 4326959--4326996 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4326949 AAGAGATAGT
4326959 ATATTTGTTGTTGTTGATA
1 ATATTTGTTGTTGTTGATA
4326978 ATATTTGTTGTTGTTGATA
1 ATATTTGTTGTTGTTGATA
4326997 GGTTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (19 bp):
ATATTTGTTGTTGTTGATA
Found at i:4339133 original size:24 final size:24
Alignment explanation
Indices: 4339101--4339158 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
4339091 ATGTCCCAAA
4339101 ATTACAGTGGACTT-AACCTTAAAG
1 ATTACAGTGGA-TTGAACCTTAAAG
* *
4339125 ATTACAGTGGATTGAACTTTGAAG
1 ATTACAGTGGATTGAACCTTAAAG
4339149 ATTACAGTGG
1 ATTACAGTGG
4339159 GGGCAATCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (24 bp):
ATTACAGTGGATTGAACCTTAAAG
Found at i:4339612 original size:44 final size:42
Alignment explanation
Indices: 4339474--4340002 Score: 231
Period size: 43 Copynumber: 12.5 Consensus size: 42
4339464 TCTTATCAAG
* * *
4339474 TCTTATCTCGCTAAGCAGTAGTGGAGCA-GACAGAAGAAATCA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGA-TGAAG--ATCAGA
* * * * * * *
4339517 TCTTATGTTCCTAAGCAGTAGTGAAGCAGAATTAAGCCACCA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAG--ATCAGA
* * * * *
4339560 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGCTGAAGATTGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGA-T-CAGA
* * *
4339604 TCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCG--CATCAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGAT-GAAGATCAGA
* * *
4339644 TCTTATCTCCCTAAGCAGTAGTGGAGCA-GATCG--CATCAGG
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGAT-GAAGATCAGA
* *
4339684 TCTTATCTCCCTAAGCAGTAGTGGAGT-GGACAGAAGAAACCA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGA-TGAAG--ATCAGA
* * * * *
4339727 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGA-T-CAGA
* * *
4339771 TCTTATCTCCCTAAGCAGTAGTGGAGCA-AATCG--CATCA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGAT-GAAGATCAGA
* * *
4339810 GTCTTATCTCCCTAAGCAGTAGTGGAGCA-GACAGAAGAAACTA-A
1 -TCTTATCTCCCTAAGCAGTAGTGGAGTAGGA-TGAAG-ATC-AGA
* * *
4339854 TCTTATTTCCCTAAGCAGTAGTGGAGCA-GATCG--CATCA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGAT-GAAGATCAGA
* * ** *
4339893 GTCTTATCTCCCTAAGTAGTAGTGGAGCA-GACAAAAGAAACCA-A
1 -TCTTATCTCCCTAAGCAGTAGTGGAGTAGGA-TGAAG--ATCAGA
* * * * *
4339937 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATCGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGATC--AGA
*
4339981 TCTTATCTCTCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGT
4340003 AGAGCAGATC
Statistics
Matches: 373, Mismatches: 80, Indels: 65
0.72 0.15 0.13
Matches are distributed among these distances:
39 3 0.01
40 130 0.35
41 6 0.02
42 2 0.01
43 148 0.40
44 84 0.23
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (42 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAGATCAGA
Found at i:4339658 original size:40 final size:40
Alignment explanation
Indices: 4339603--4339923 Score: 313
Period size: 40 Copynumber: 7.8 Consensus size: 40
4339593 AAGATTGTAG
4339603 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
*
4339643 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
* * * * *
4339683 GTCTTATCTCCCTAAGCAGTAGTGGAGTGGACAGA-AGAAACCA
1 ATCTTATCTCCCTAAGCAGTAGTGGA---G-CAGATCGCATCAA
* * * * * * * * *
4339726 ATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG--CA-T-CAA
*
4339770 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGCATCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
* * * *
4339810 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAAGAAACTA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----GCATCAA
*
4339853 ATCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
* *
4339893 GTCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
4339924 CAAAAGAAAC
Statistics
Matches: 225, Mismatches: 42, Indels: 28
0.76 0.14 0.09
Matches are distributed among these distances:
39 3 0.01
40 128 0.57
41 1 0.00
42 2 0.01
43 59 0.26
44 32 0.14
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (40 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
Found at i:4339858 original size:210 final size:207
Alignment explanation
Indices: 4339604--4340028 Score: 672
Period size: 210 Copynumber: 2.0 Consensus size: 207
4339594 AGATTGTAGA
* *
4339604 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAATCTTATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAACAAATCTTATCTCCCTAAGCAGTAGTGGA
* ** *
4339669 GCAGATCGCATCAGGTCTTATCTCCCTAAGCAGTAGTGGAGTGGACAGAAGAAACCAATCCTATC
66 GCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAATCCTATC
* * *
4339734 TCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCA
131 TCCCTGAGCAGCAGTGGAGTAGGTTGAAAATCGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCA
4339799 AATCGCATCAAG
196 AATCGCATCAAG
* *
4339811 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAAGAAACTAATCTTATTTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----GAAACAAATCTTATCTCCCTAAGCAGTAG
*
4339875 TGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTGGAGCAGACAAAAGAAACCAATCC
62 TGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAATCC
*
4339940 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATCGTAGATCTTATCTCTCTAAGCAGTAGTAG
127 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATCGTAGATCTTATCTCCCTAAGCAGTAGTAG
* *
4340005 AGCAGATCGCATCCAG
192 AGCAAATCGCATCAAG
4340021 TCTTATCT
1 TCTTATCT
4340029 TCCTGAAGTT
Statistics
Matches: 199, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
206 1 0.01
207 30 0.15
210 168 0.84
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (207 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAACAAATCTTATCTCCCTAAGCAGTAGTGGA
GCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACCAATCCTATC
TCCCTGAGCAGCAGTGGAGTAGGTTGAAAATCGTAGATCTTATCTCCCTAAGCAGTAGTAGAGCA
AATCGCATCAAG
Found at i:4339903 original size:167 final size:167
Alignment explanation
Indices: 4339468--4339919 Score: 580
Period size: 167 Copynumber: 2.7 Consensus size: 167
4339458 AAGTCATCTT
*
4339468 ATCAAGTCTTATCTCGCTAAGCAGTAGTGGAGCAGACAGAAGAAA-TCAATCTTATGTT-CCTAA
1 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAACT-AATCTTAT-TTCCCTAA
* *
4339531 GCAGTAGTGAAGCAGAATTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGCTGAAG
64 GCAGTAGTGGAGCAG-A-T-AGACACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGCTGAAG
*
4339596 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGC
126 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGC
* * * * *
4339638 ATCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----GCATC-AGGTCTTATCTCCCTAA
1 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAAGAAACTA-ATCTTATTTCCCTAA
* *
4339698 GCAGTAGTGGAGTGGACAGA-AGAAACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAA
64 GCAGTAGTGGA---G-CAGATAGACACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGCTGAA
4339762 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGC
125 GATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGC
4339805 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAACTAATCTTATTTCCCTAAGC
1 ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAACTAATCTTATTTCCCTAAGC
* * * * * *
4339870 AGTAGTGGAGCAGATCG-CATCAAGTCTTATCTCCCTAAGTAGTAGTGGAG
66 AGTAGTGGAGCAGATAGACACCAA-TCCTATCTCCCTGAGCAGCAGTGGAG
4339920 CAGACAAAAG
Statistics
Matches: 244, Mismatches: 23, Indels: 33
0.81 0.08 0.11
Matches are distributed among these distances:
166 11 0.05
167 165 0.68
170 63 0.26
171 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (167 bp):
ATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAACTAATCTTATTTCCCTAAGC
AGTAGTGGAGCAGATAGACACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGCTGAAGATTGT
AGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGC
Found at i:4340011 original size:127 final size:125
Alignment explanation
Indices: 4339474--4340028 Score: 468
Period size: 127 Copynumber: 4.4 Consensus size: 125
4339464 TCTTATCAAG
* * * *
4339474 TCTTATCTCGCTAAGCAGTAGTGGAGCAGA-CAGAAGAAATCAA-TCTTATGTTCCTAAGCAGTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----G-CATCAAGTCTTATCTCCCTAAGCAGTA
* * * * ***
4339537 GTGAAGCAGA-ATTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGCTGAAGATTGT
61 GTGGAGCAGACA-AAAG-CACCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGCAGAAGAAACT
4339601 AGA
124 A-A
*
4339604 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAATCTTATCTCCCTAAGCAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
* * * * *
4339669 GCAGATC----GCATCAGGTCTTATCTCCCTAAGCAGTAGTGGAGT-GGACAGAAGAAACCAA
66 GCAGA-CAAAAGCACCA-ATCCTATCTCCCTAAGCAGCAGTGGAGTAGG-CAGAAGAAACTAA
* * * * * * * **
4339727 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG--CA-TCAAG-TCTTATCTCCCTAAGCAGTAG
** * * * * *
4339792 TGGAGC--A-AATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAACTAA
62 TGGAGCAGACAAAAGCACCAA-TCCTATCTCCCTAAGCAGCAGTGGAGTAGGCAGAAGAAACTAA
* *
4339854 TCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTGGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
* * ** *
4339919 GCAGACAAAAGAAACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAA-AATCGTAGA
66 GCAGACAAAAG-CACCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGCAGAAGAAAC-TA-A
* * *
4339981 TCTTATCTCTCTAAGCAGTAGTAGAGCAGATCGCATCCAGTCTTATCT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCT
4340029 TCCTGAAGTT
Statistics
Matches: 347, Mismatches: 56, Indels: 47
0.77 0.12 0.10
Matches are distributed among these distances:
123 60 0.17
124 35 0.10
125 7 0.02
126 40 0.12
127 174 0.50
128 1 0.00
130 29 0.08
131 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (125 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGA
GCAGACAAAAGCACCAATCCTATCTCCCTAAGCAGCAGTGGAGTAGGCAGAAGAAACTAA
Found at i:4340026 original size:40 final size:40
Alignment explanation
Indices: 4339604--4340028 Score: 300
Period size: 40 Copynumber: 10.2 Consensus size: 40
4339594 AGATTGTAGA
* *
4339604 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCCAG
4339644 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCAT-CAGG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCCA-G
* * * *
4339684 TCTTATCTCCCTAAGCAGTAGTGGAGTGGACAGA-AGAAACCAA
1 TCTTATCTCCCTAAGCAGTAGTGGA---G-CAGATCGCATCCAG
* * * * * * * **
4339727 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG--CA-TCCAG
* *
4339770 ATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCCAG
* * * *
4339811 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAGAAGAAACTAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----GCATCCAG
* *
4339854 TCTTATTTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCCAG
* * * *
4339894 TCTTATCTCCCTAAGTAGTAGTGGAGCAGA-CAAAAGAAACCAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC----GCATCCAG
* * * * * * * *
4339937 TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATCGTAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG--CATC-CAG
* *
4339980 ATCTTATCTCTCTAAGCAGTAGTAGAGCAGATCGCATCCAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCCAG
4340021 TCTTATCT
1 TCTTATCT
4340029 TCCTGAAGTT
Statistics
Matches: 297, Mismatches: 63, Indels: 50
0.72 0.15 0.12
Matches are distributed among these distances:
39 5 0.02
40 133 0.45
41 5 0.02
42 8 0.03
43 88 0.30
44 58 0.20
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCCAG
Found at i:4343814 original size:21 final size:21
Alignment explanation
Indices: 4343788--4343830 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4343778 TTAAATATAA
4343788 GACTAAGACCTAAGGAGATTT
1 GACTAAGACCTAAGGAGATTT
** *
4343809 GACTAAGTGCTAGGGAGATTT
1 GACTAAGACCTAAGGAGATTT
4343830 G
1 G
4343831 CTAGCTTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.26
Consensus pattern (21 bp):
GACTAAGACCTAAGGAGATTT
Found at i:4345900 original size:185 final size:184
Alignment explanation
Indices: 4345436--4345918 Score: 646
Period size: 184 Copynumber: 2.6 Consensus size: 184
4345426 ATTCATATAT
* * * ** * *
4345436 GAATCCAATTCAGCAA-TGAATATCGATATACCCAACAATTCAACAATGTATAACCATTCACGAA
1 GAAT-CAATTCAGCAACT-TATATCCATATACCAAACAATTCGGCAATATATAACCATACACGAA
* ** * * * * * *
4345500 TCAAGTTCGGCAATATATAATTATACACAAATCAAATTTGGCATCCTATATTCATAAACAATTCA
64 TGAAGTTCGATAATGTATAATCAAATACAAATCAAATTTGGCATCCTATATACATAAAAAATTCA
* * * * *
4345565 ATATCAACAATATATAACCAAGTATGAATTAATTTCAGCAATGTACAACCCTGTAC
129 ATATCAACAATATATAACCAAGTATCAATTAATTTCAGCAAGGTAAAACCATCTAC
*
4345621 GAATCAATTCAGCAACTTATATCCATATACCAAACAATTCGGCAATATATAACCATACATGAATG
1 GAATCAATTCAGCAACTTATATCCATATACCAAACAATTCGGCAATATATAACCATACACGAATG
*
4345686 AAGTTCGATAATGTATAATCAAATACAAATCTAATTTGGCATCCTATATACATAAAAAATTCAAT
66 AAGTTCGATAATGTATAATCAAATACAAATCAAATTTGGCATCCTATATACATAAAAAATTCAAT
* * *
4345751 ATCGACAATATATGACCATGTA-CAATTTAATTTCAGCAAGGTAAAACCATCTAC
131 ATCAACAATATATAACCAAGTATCAA-TTAATTTCAGCAAGGTAAAACCATCTAC
*
4345805 GAATCAATTCAGCAACTTTTATCCCATATACCAAACAATTCGGCAATATATAACCATACACGAAT
1 GAATCAATTCAGCAACTTATAT-CCATATACCAAACAATTCGGCAATATATAACCATACACGAAT
* * *
4345870 GAAGTTCAATAATGTATAATCAAATACAAATCCAATTCGGCATCCTATA
65 GAAGTTCGATAATGTATAATCAAATACAAATCAAATTTGGCATCCTATA
4345919 CAATTCAATA
Statistics
Matches: 264, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
183 2 0.01
184 170 0.64
185 92 0.35
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (184 bp):
GAATCAATTCAGCAACTTATATCCATATACCAAACAATTCGGCAATATATAACCATACACGAATG
AAGTTCGATAATGTATAATCAAATACAAATCAAATTTGGCATCCTATATACATAAAAAATTCAAT
ATCAACAATATATAACCAAGTATCAATTAATTTCAGCAAGGTAAAACCATCTAC
Found at i:4350308 original size:12 final size:12
Alignment explanation
Indices: 4350287--4350320 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4350277 TACCAACAAC
*
4350287 AATAATAAATAGT
1 AATAA-AAATAAT
4350300 AATAAAAATAAT
1 AATAAAAATAAT
4350312 AATAAAAAT
1 AATAAAAAT
4350321 TAATTAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:4359664 original size:186 final size:186
Alignment explanation
Indices: 4359350--4359724 Score: 651
Period size: 186 Copynumber: 2.0 Consensus size: 186
4359340 CGTCCGTGGA
* * *
4359350 TACCTCGTGCGCTCATCGTAGAATTCGTAGCTTATCTGTGTTACCAATTTTATGAATCAGTTACA
1 TACCTCGTGCACTCATCATAGAATTCGTAGCTTATCCGTGTTACCAATTTTATGAATCAGTTACA
4359415 ATTTCGATATCTATTAGTAGACATTTTATGCAAAACAATATCAGATGTTTAAAGTTTGTTATCAC
66 ATTTCGATATCTATTAGTAGACATTTTATGCAAAACAATATCAGATGTTTAAAGTTTGTTATCAC
*
4359480 GAATCGCAGTCTTACTACAGTTTTTAGTTTCTCTACTATTTTCAGTATACACTATC
131 GAATCGCAGTCTTACTACAATTTTTAGTTTCTCTACTATTTTCAGTATACACTATC
* * *
4359536 TACCTCGTGCACTCATCATAGAATTTGTAGCTTATCCGTGTTATCAGTTTTATGAATCAGTTACA
1 TACCTCGTGCACTCATCATAGAATTCGTAGCTTATCCGTGTTACCAATTTTATGAATCAGTTACA
* * * *
4359601 GTTTCGATATCTATTAGTAGATATTTTATGCAAAACAGTATCAGATGTTTAGAGTTTGTTATCAC
66 ATTTCGATATCTATTAGTAGACATTTTATGCAAAACAATATCAGATGTTTAAAGTTTGTTATCAC
4359666 GAATCGCAGTCTTACTACAATTTTTAGTTTCTCTACTATTTTCAGTATACACTATC
131 GAATCGCAGTCTTACTACAATTTTTAGTTTCTCTACTATTTTCAGTATACACTATC
4359722 TAC
1 TAC
4359725 AGTGTTCTTA
Statistics
Matches: 178, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
186 178 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (186 bp):
TACCTCGTGCACTCATCATAGAATTCGTAGCTTATCCGTGTTACCAATTTTATGAATCAGTTACA
ATTTCGATATCTATTAGTAGACATTTTATGCAAAACAATATCAGATGTTTAAAGTTTGTTATCAC
GAATCGCAGTCTTACTACAATTTTTAGTTTCTCTACTATTTTCAGTATACACTATC
Found at i:4363592 original size:21 final size:22
Alignment explanation
Indices: 4363541--4363592 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 22
4363531 TTTTAACCAA
*
4363541 ATTAGTTCTTGAACACTAAATT
1 ATTAATTCTTGAACACTAAATT
4363563 -TTAATTTCTT-AAC-CTAAAATT
1 ATTAA-TTCTTGAACACT-AAATT
4363584 ATTAATTCT
1 ATTAATTCT
4363593 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 2 0.08
21 15 0.58
22 9 0.35
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTAATTCTTGAACACTAAATT
Found at i:4369572 original size:23 final size:22
Alignment explanation
Indices: 4369508--4369609 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
4369498 TCACCCACCG
* *
4369508 AATAGAACCAAACATAACCTCCA
1 AATACAACCAAACATACCCT-CA
* * **
4369531 AACACATCC-AATTTACCCTCAA
1 AATACAACCAAACATACCCTC-A
* *
4369553 AATATAACCAAACATACCCTCC
1 AATACAACCAAACATACCCTCA
* * *
4369575 AACACAACCAAATATAGCCTCCA
1 AATACAACCAAACATACCCT-CA
4369598 AATACAACCAAA
1 AATACAACCAAA
4369610 TATTCCATCC
Statistics
Matches: 58, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
21 1 0.02
22 30 0.52
23 27 0.47
ACGTcount: A:0.49, C:0.33, G:0.02, T:0.16
Consensus pattern (22 bp):
AATACAACCAAACATACCCTCA
Found at i:4369601 original size:45 final size:46
Alignment explanation
Indices: 4369508--4369659 Score: 157
Period size: 45 Copynumber: 3.4 Consensus size: 46
4369498 TCACCCACCG
* * * * * *
4369508 AATAGAACCAAACATAACCTCCAAACACATCC-AATTTACCCTCAA
1 AATACAACCAAACATACCCTCCAAACACAACCAAATATAGCCTCCA
*
4369553 AATATAACCAAACATACCCTCC-AACACAACCAAATATAGCCTCCA
1 AATACAACCAAACATACCCTCCAAACACAACCAAATATAGCCTCCA
* * * * *
4369598 AATACAACCAAATATTCCATCCAAACACAACCAGATATAGCCTCCC
1 AATACAACCAAACATACCCTCCAAACACAACCAAATATAGCCTCCA
* *
4369644 AACAC-ACCAAATATAC
1 AATACAACCAAACATAC
4369660 AACATAATAT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 8 0.09
45 58 0.64
46 25 0.27
ACGTcount: A:0.47, C:0.34, G:0.03, T:0.16
Consensus pattern (46 bp):
AATACAACCAAACATACCCTCCAAACACAACCAAATATAGCCTCCA
Found at i:4369610 original size:23 final size:23
Alignment explanation
Indices: 4369513--4369659 Score: 138
Period size: 23 Copynumber: 6.5 Consensus size: 23
4369503 CACCGAATAG
* *
4369513 AACCAAACATAACCTCCAAACAC
1 AACCAAATATACCCTCCAAACAC
* * * * *
4369536 ATCC-AATTTACCCTCAAAATAT
1 AACCAAATATACCCTCCAAACAC
*
4369558 AACCAAACATACCCTCC-AACAC
1 AACCAAATATACCCTCCAAACAC
* *
4369580 AACCAAATATAGCCTCCAAATAC
1 AACCAAATATACCCTCCAAACAC
* *
4369603 AACCAAATATTCCATCCAAACAC
1 AACCAAATATACCCTCCAAACAC
* * *
4369626 AACCAGATATAGCCTCCCAACAC
1 AACCAAATATACCCTCCAAACAC
4369649 -ACCAAATATAC
1 AACCAAATATAC
4369660 AACATAATAT
Statistics
Matches: 95, Mismatches: 27, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
22 42 0.44
23 53 0.56
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.16
Consensus pattern (23 bp):
AACCAAATATACCCTCCAAACAC
Found at i:4370962 original size:38 final size:38
Alignment explanation
Indices: 4370910--4370985 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
4370900 AATTTAGGAG
*
4370910 AATGAAAAACTACCAAAATGCCCCTGTACTTTGTCATT
1 AATGAAAAACTACCAAAATGCCCCTATACTTTGTCATT
*
4370948 AATGAAAAATTACCAAAATGCCCCTATACTTTGTCATT
1 AATGAAAAACTACCAAAATGCCCCTATACTTTGTCATT
4370986 TCTGCAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.30
Consensus pattern (38 bp):
AATGAAAAACTACCAAAATGCCCCTATACTTTGTCATT
Found at i:4371190 original size:29 final size:29
Alignment explanation
Indices: 4371148--4371459 Score: 154
Period size: 29 Copynumber: 10.7 Consensus size: 29
4371138 TATCGATGAT
* *
4371148 TATCGAACATGAAAAGGGATGGCTTCGGC
1 TATCGAATATGAAAAGGGATGGCTTCGAC
* ** * *
4371177 TATCGATTATGAAAAGGGATAACTTCAAT
1 TATCGAATATGAAAAGGGATGGCTTCGAC
*** ** *
4371206 TATCGAATATGAAAAAGGGATAAATTAAAA
1 TATCGAATATG-AAAAGGGATGGCTTCGAC
*
4371236 TATCGAATATGAAAAGGGA-GAGCTTCGAT
1 TATCGAATATGAAAAGGGATG-GCTTCGAC
* * *
4371265 TATCGATTTTGAAAAGGGATGG-TGACGAC
1 TATCGAATATGAAAAGGGATGGCT-TCGAC
* * *
4371294 CATC-AACAATGAAAAGGGATGG-TGACGAC
1 TATCGAA-TATGAAAAGGGATGGCT-TCGAC
* * * *
4371323 CATCGAATATGAAAAGGGATAGCTTTGGC
1 TATCGAATATGAAAAGGGATGGCTTCGAC
** *
4371352 TATCGCTTATGAAAAGGGATGG-TGAT-GAT
1 TATCGAATATGAAAAGGGATGGCT--TCGAC
* * *
4371381 TATC-AACTATGAAATGGGATGG-TGACAAC
1 TATCGAA-TATGAAAAGGGATGGCT-TCGAC
* * * *
4371410 CATCGATTAATGAAAAGGGATGGTTTTGAC
1 TATCGAAT-ATGAAAAGGGATGGCTTCGAC
* *
4371440 CATCGAGTATGAAAAGGGAT
1 TATCGAATATGAAAAGGGAT
4371460 AGTTACGACC
Statistics
Matches: 219, Mismatches: 50, Indels: 28
0.74 0.17 0.09
Matches are distributed among these distances:
28 3 0.01
29 161 0.74
30 54 0.25
31 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (29 bp):
TATCGAATATGAAAAGGGATGGCTTCGAC
Found at i:4371347 original size:87 final size:87
Alignment explanation
Indices: 4371237--4371471 Score: 290
Period size: 87 Copynumber: 2.7 Consensus size: 87
4371227 AAATTAAAAT
* * * *
4371237 ATCGAATATGAAAAGGGAGAGCTTCGATTATCGATTTTGAAAAGGGATGGTGACGACCATCAACA
1 ATCGAATATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAGGGATGGTGACGACCATCAACA
*
4371302 ATGAAAAGGGATGGTGACGACC
66 ATGAAAAGGGATGGTGACAACC
* * * ** *
4371324 ATCGAATATGAAAAGGGATAGCTTTGGCTATCGCTTATGAAAAGGGATGGTGATGATTATCAACT
1 ATCGAATATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAGGGATGGTGACGACCATCAACA
*
4371389 ATGAAATGGGATGGTGACAACC
66 ATGAAAAGGGATGGTGACAACC
* * * * * * *
4371411 ATCGATTAATGAAAAGGGATGGTTTTGACCATCGAGTATGAAAAGGGATAGTTACGACCAT
1 ATCGAAT-ATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAGGGATGGTGACGACCAT
4371472 TTTTTAGCAC
Statistics
Matches: 123, Mismatches: 24, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
87 81 0.66
88 42 0.34
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (87 bp):
ATCGAATATGAAAAGGGATAGCTTTGACTATCGATTATGAAAAGGGATGGTGACGACCATCAACA
ATGAAAAGGGATGGTGACAACC
Found at i:4371469 original size:29 final size:29
Alignment explanation
Indices: 4371266--4371471 Score: 171
Period size: 29 Copynumber: 7.1 Consensus size: 29
4371256 AGCTTCGATT
*
4371266 ATCGATTTTGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* **
4371295 ATCAACAATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
* * ** * *
4371324 ATCGAATATGAAAAGGGATAGCT-TTGGCT
1 ATCGATTATGAAAAGGGAT-GGTGACGACC
* * **
4371353 ATCGCTTATGAAAAGGGATGGTGATGATT
1 ATCGATTATGAAAAGGGATGGTGACGACC
* * * *
4371382 ATCAACTATGAAATGGGATGGTGACAACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
***
4371411 ATCGATTAATGAAAAGGGATGGTTTTGACC
1 ATCGATT-ATGAAAAGGGATGGTGACGACC
* * *
4371441 ATCGAGTATGAAAAGGGATAGTTACGACC
1 ATCGATTATGAAAAGGGATGGTGACGACC
4371470 AT
1 AT
4371472 TTTTTAGCAC
Statistics
Matches: 137, Mismatches: 37, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
28 2 0.01
29 110 0.80
30 25 0.18
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATGGTGACGACC
Found at i:4384200 original size:27 final size:26
Alignment explanation
Indices: 4384149--4384208 Score: 57
Period size: 27 Copynumber: 2.2 Consensus size: 26
4384139 GTAATGGGCC
* *
4384149 TAAAATGACCAAAATATCCCTGAAGGG
1 TAAAATGACC-AAATACCCCCGAAGGG
* *
4384176 TAAAATGACCAACATACTCTCGAAGGG
1 TAAAATGACCAA-ATACCCCCGAAGGG
*
4384203 TGAAAT
1 TAAAAT
4384209 ACCCTCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (26 bp):
TAAAATGACCAAATACCCCCGAAGGG
Found at i:4384233 original size:27 final size:27
Alignment explanation
Indices: 4384203--4384455 Score: 287
Period size: 27 Copynumber: 9.4 Consensus size: 27
4384193 TCTCGAAGGG
* *
4384203 TGAAATACCCTCAAAGGCTAAAATGAC
1 TGAAATACCCCCAAAGGGTAAAATGAC
*
4384230 TGAAATACCCCCGAAGGGTAAAATGA-
1 TGAAATACCCCCAAAGGGTAAAATGAC
4384256 TCGAAATACCCCCGAAA-GGTAAAATGAC
1 T-GAAATACCCCC-AAAGGGTAAAATGAC
* * *
4384284 TAAAATACCCTCGAAGGGTAAAATGAC
1 TGAAATACCCCCAAAGGGTAAAATGAC
* * *
4384311 TAAAATACCCCAAAATGGTAAAATGAC
1 TGAAATACCCCCAAAGGGTAAAATGAC
* * * *
4384338 TGAAATAGCCCAAAATGGTAAAATGAT
1 TGAAATACCCCCAAAGGGTAAAATGAC
*
4384365 TGAAATACCCTCAAAGGGTAAAATGAC
1 TGAAATACCCCCAAAGGGTAAAATGAC
*
4384392 TGAAATACCCCCAAAGGGTAAAATGAA
1 TGAAATACCCCCAAAGGGTAAAATGAC
* * *
4384419 TGAAATA-CCCCGAAGAGTAAAATAAC
1 TGAAATACCCCCAAAGGGTAAAATGAC
**
4384445 TGTTATACCCC
1 TGAAATACCCC
4384456 TAGGAGTTGA
Statistics
Matches: 194, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
26 23 0.12
27 168 0.87
28 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (27 bp):
TGAAATACCCCCAAAGGGTAAAATGAC
Found at i:4384343 original size:81 final size:79
Alignment explanation
Indices: 4384205--4384441 Score: 323
Period size: 81 Copynumber: 2.9 Consensus size: 79
4384195 TCGAAGGGTG
* *
4384205 AAATACCCTCAAAGGCTAAAATGACTGAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCCG
1 AAATACCCTCAAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAATGAT-GAAATA-CCCCG
4384270 AAAGGTAAAATGACTA
64 AAAGGTAAAATGACTA
* * * * * *
4384286 AAATACCCTCGAAGGGTAAAATGACTAAAATACCCCAAAATGGTAAAATGACTGAAATAGCCCAA
1 AAATACCCTCAAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAATGA-TGAAATACCCCGA
* *
4384351 AATGGTAAAATGATTG
65 AA-GGTAAAATGACTA
4384367 AAATACCCTCAAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAATGAATGAAATACCCCG-
1 AAATACCCTCAAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAATG-ATGAAATACCCCGA
4384431 AAGAGTAAAAT
65 AAG-GTAAAAT
4384442 AACTGTTATA
Statistics
Matches: 136, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
79 1 0.01
80 15 0.11
81 118 0.87
82 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.17
Consensus pattern (79 bp):
AAATACCCTCAAAGGGTAAAATGACTGAAATACCCCCAAAGGGTAAAATGATGAAATACCCCGAA
AGGTAAAATGACTA
Found at i:4391603 original size:20 final size:20
Alignment explanation
Indices: 4391555--4391604 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4391545 GTTTATGTTG
* *
4391555 AGTAAATGAAATGGAAAGTA
1 AGTAAATGGAATGGAAAGAA
4391575 AGTAAATGGAAT-GATAAGAA
1 AGTAAATGGAATGGA-AAGAA
4391595 AGTAAATGGA
1 AGTAAATGGA
4391605 GTGGTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (20 bp):
AGTAAATGGAATGGAAAGAA
Found at i:4397263 original size:28 final size:28
Alignment explanation
Indices: 4397231--4397286 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4397221 GTGCTTAATC
* *
4397231 ACATAAGTTAACAATATAATCACATGAT
1 ACATAACTTAACAATATAACCACATGAT
*
4397259 ACATAACTTAACAATATCACCACATGAT
1 ACATAACTTAACAATATAACCACATGAT
4397287 TAGATAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (28 bp):
ACATAACTTAACAATATAACCACATGAT
Found at i:4397504 original size:58 final size:58
Alignment explanation
Indices: 4397426--4397536 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 58
4397416 TGCTACAAGG
*
4397426 TGGTCAAAACCATCCCTTTTCATA-TTCGATGGTCATCACCATCCCTTTTCATATTTGA
1 TGGTCAAAACCATCCATTTTCATAGTT-GATGGTCATCACCATCCCTTTTCATATTTGA
* *
4397484 TGGTTAAAACCATCCATTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATA
1 TGGTCAAAACCATCCATTTTCATAGTTGATGGTCATCACCATCCCTTTTCATA
4397537 GTCAATAGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
58 47 0.96
59 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (58 bp):
TGGTCAAAACCATCCATTTTCATAGTTGATGGTCATCACCATCCCTTTTCATATTTGA
Found at i:4397537 original size:29 final size:29
Alignment explanation
Indices: 4397434--4397538 Score: 140
Period size: 29 Copynumber: 3.6 Consensus size: 29
4397424 GGTGGTCAAA
4397434 ACCATCCCTTTTCATA-TTCGATGGTCATC
1 ACCATCCCTTTTCATAGTT-GATGGTCATC
* * **
4397463 ACCATCCCTTTTCATATTTGATGGTTAAA
1 ACCATCCCTTTTCATAGTTGATGGTCATC
* *
4397492 ACCATCCATTTTCATAGTTGATGGTCGTC
1 ACCATCCCTTTTCATAGTTGATGGTCATC
4397521 ACCATCCCTTTTCATAGT
1 ACCATCCCTTTTCATAGT
4397539 CAATAGTCGA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 63 0.97
30 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (29 bp):
ACCATCCCTTTTCATAGTTGATGGTCATC
Found at i:4397547 original size:29 final size:29
Alignment explanation
Indices: 4397426--4397565 Score: 136
Period size: 29 Copynumber: 4.8 Consensus size: 29
4397416 TGCTACAAGG
*
4397426 TGGTCAAAACCATCCCTTTTCATATTCGA
1 TGGTCAAAACCATCCCTTTTCATAGTCGA
** * *
4397455 TGGTCATCACCATCCCTTTTCATATTTGA
1 TGGTCAAAACCATCCCTTTTCATAGTCGA
* * *
4397484 TGGTTAAAACCATCCATTTTCATAGTTGA
1 TGGTCAAAACCATCCCTTTTCATAGTCGA
*** *
4397513 TGGTCGTCACCATCCCTTTTCATAGTCAA
1 TGGTCAAAACCATCCCTTTTCATAGTCGA
* * * *
4397542 TAGTCGAAACTATCCTTTTTCATA
1 TGGTCAAAACCATCCCTTTTCATA
4397566 TTCGTTGGGC
Statistics
Matches: 91, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 91 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (29 bp):
TGGTCAAAACCATCCCTTTTCATAGTCGA
Found at i:4397562 original size:58 final size:58
Alignment explanation
Indices: 4397428--4397569 Score: 178
Period size: 58 Copynumber: 2.4 Consensus size: 58
4397418 CTACAAGGTG
* * ** *
4397428 GTCAAAACCATCCCTTTTCATATTCGATGGTCATCACCATCCCTTTTCATATTTGATG
1 GTCAAAACCATCCATTTTCATATTCGATGGTCATCACCATCCCTTTTCATAGTCAATA
* *
4397486 GTTAAAACCATCCATTTTCATAGTT-GATGGTCGTCACCATCCCTTTTCATAGTCAATA
1 GTCAAAACCATCCATTTTCATA-TTCGATGGTCATCACCATCCCTTTTCATAGTCAATA
* * *
4397544 GTCGAAACTATCCTTTTTCATATTCG
1 GTCAAAACCATCCATTTTCATATTCG
4397570 TTGGGCATTG
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
57 2 0.03
58 67 0.94
59 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.38
Consensus pattern (58 bp):
GTCAAAACCATCCATTTTCATATTCGATGGTCATCACCATCCCTTTTCATAGTCAATA
Found at i:4404258 original size:29 final size:29
Alignment explanation
Indices: 4404178--4404262 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
4404168 GTGTGCTAAA
* *
4404178 CGATAGTTGAAACCATCCCTTTTCAAATT
1 CGATGGTTGAAACCATCCCTTTTCATATT
* **
4404207 CAATGGTTGTCACCATCCCTTTTCATATT
1 CGATGGTTGAAACCATCCCTTTTCATATT
* *
4404236 CGATGGTTGAAACCGTCCATTTTCATA
1 CGATGGTTGAAACCATCCCTTTTCATA
4404263 GTTCACACCA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (29 bp):
CGATGGTTGAAACCATCCCTTTTCATATT
Found at i:4405659 original size:15 final size:18
Alignment explanation
Indices: 4405639--4405679 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4405629 TTCAAGCTAG
4405639 TTTTTTTCT-T-T-TTAT
1 TTTTTTTCTGTGTATTAT
*
4405654 TTTTTTTTTGTGTATTAT
1 TTTTTTTCTGTGTATTAT
4405672 TTTTTTTC
1 TTTTTTTC
4405680 AATCTCTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 1 0.05
17 1 0.05
18 11 0.52
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (18 bp):
TTTTTTTCTGTGTATTAT
Found at i:4406933 original size:30 final size:30
Alignment explanation
Indices: 4406899--4406962 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
4406889 CCGTGTGTCT
4406899 AGGCTATGTACAACACACAACCATGTCACC
1 AGGCTATGTACAACACACAACCATGTCACC
* *
4406929 AGGCTATGTACACCACACAACCATGTCGCC
1 AGGCTATGTACAACACACAACCATGTCACC
4406959 AGGC
1 AGGC
4406963 CGTGTGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.34, G:0.17, T:0.16
Consensus pattern (30 bp):
AGGCTATGTACAACACACAACCATGTCACC
Found at i:4408066 original size:18 final size:18
Alignment explanation
Indices: 4408039--4408080 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
4408029 CTAATTGAAC
*
4408039 ATTT-TATAAGATATTAG
1 ATTTATATAAGACATTAG
4408056 ATTTATATAAGACATTAG
1 ATTTATATAAGACATTAG
4408074 ATTTATA
1 ATTTATA
4408081 CTAGGACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (18 bp):
ATTTATATAAGACATTAG
Found at i:4409495 original size:143 final size:143
Alignment explanation
Indices: 4409237--4409516 Score: 454
Period size: 143 Copynumber: 2.0 Consensus size: 143
4409227 TTCCAGAATT
* * *
4409237 GTTCTTGAGTTTCTTTTAGAAGAGTTTTAACAATCTTTTATATTATGAGGTCATCTTCAAACATT
1 GTTCTTGAGTTTCTTTTAGAAGAGTTTTAAAAATCTTTTAGATTATGAGGTCATCTTCAAAAATT
* * *
4409302 TTCTTGCAAAGGTTTCTATCTTAGAGGGGAAATTAGAGCCACTTGAAGGGGGTTGTGGATTTTTC
66 TTCTTGCAAAGGTTTCTATCTTAGAGGGGAAATTAAAACCACTTGAAGGGGGTTGTGGATTCTTC
*
4409367 GTGTTTCGTTCCA
131 GCGTTTCGTTCCA
*
4409380 GTTCTTGAGTTTCTTTTAGAAGAGTTTTAAAAATCTTTTAGATTATGGGGTCATCTTCAAAAATT
1 GTTCTTGAGTTTCTTTTAGAAGAGTTTTAAAAATCTTTTAGATTATGAGGTCATCTTCAAAAATT
* *
4409445 TTGTTGCCAAA-GTTTCTATCTTGGAGGGGAAATTAAAACCACTTGAAGGGGGTTGTGGATTCTT
66 TTCTTG-CAAAGGTTTCTATCTTAGAGGGGAAATTAAAACCACTTGAAGGGGGTTGTGGATTCTT
4409509 CGCGTTTC
130 CGCGTTTC
4409517 CAAGGCTTCT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
143 122 0.97
144 4 0.03
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (143 bp):
GTTCTTGAGTTTCTTTTAGAAGAGTTTTAAAAATCTTTTAGATTATGAGGTCATCTTCAAAAATT
TTCTTGCAAAGGTTTCTATCTTAGAGGGGAAATTAAAACCACTTGAAGGGGGTTGTGGATTCTTC
GCGTTTCGTTCCA
Found at i:4411329 original size:17 final size:17
Alignment explanation
Indices: 4411307--4411347 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4411297 TAGTACACGA
4411307 GGCAATTAAGATTGAGC
1 GGCAATTAAGATTGAGC
*
4411324 GGCAATTGAGATTGAGC
1 GGCAATTAAGATTGAGC
*
4411341 AGCAATT
1 GGCAATT
4411348 TCAACAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.24
Consensus pattern (17 bp):
GGCAATTAAGATTGAGC
Found at i:4412341 original size:20 final size:20
Alignment explanation
Indices: 4412316--4412368 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4412306 TTTTATAGGT
*
4412316 TTATTTCCTCTTGCAACAAA
1 TTATTTCATCTTGCAACAAA
*
4412336 TTATTTTATCTTGCAACAAA
1 TTATTTCATCTTGCAACAAA
*
4412356 AT-TTTCTATCTTG
1 TTATTTC-ATCTTG
4412369 ACCTTTAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (20 bp):
TTATTTCATCTTGCAACAAA
Found at i:4427785 original size:27 final size:27
Alignment explanation
Indices: 4427747--4428013 Score: 374
Period size: 27 Copynumber: 9.9 Consensus size: 27
4427737 CCATAATAGT
* * *
4427747 TAATTTTGCCCATTGGGGGTATTTCGA
1 TAATTTTACCCATCGAGGGTATTTCGA
4427774 TAATTTTACCCATCGAGGGTATTTCGA
1 TAATTTTACCCATCGAGGGTATTTCGA
* *
4427801 TAATTTTACCCATCGAGAGTTTTTCGA
1 TAATTTTACCCATCGAGGGTATTTCGA
4427828 TAATTTTACCCATCGAGGGTATTTCGA
1 TAATTTTACCCATCGAGGGTATTTCGA
* * * * *
4427855 TAATATTACCCATTGGGGGTATTTTGG
1 TAATTTTACCCATCGAGGGTATTTCGA
* *
4427882 TAATTTTACCCATCGAAGGTATTTCGG
1 TAATTTTACCCATCGAGGGTATTTCGA
4427909 TAATTTTACCCATCGAGGGTATTTCGA
1 TAATTTTACCCATCGAGGGTATTTCGA
* *
4427936 TAATTTTACCTATCGAGGGTATTTAGA
1 TAATTTTACCCATCGAGGGTATTTCGA
*
4427963 TAATTTTACCCATAGAGGGTATTTC-A
1 TAATTTTACCCATCGAGGGTATTTCGA
*
4427989 GTAATTTTACCCATCGAGGATATTT
1 -TAATTTTACCCATCGAGGGTATTT
4428014 TGGTACAGTT
Statistics
Matches: 213, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
26 1 0.00
27 212 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (27 bp):
TAATTTTACCCATCGAGGGTATTTCGA
Done.