Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold329
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: 1169685
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 72846 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:932522 original size:53 final size:53
Alignment explanation
Indices: 932456--932563 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
932446 CAGTTTCAAG
932456 CTTCTGAACGTCTATGTCTAATCTTAAGTTCATCTTCTCTTCCTCCATTTGTT
1 CTTCTGAACGTCTATGTCTAATCTTAAGTTCATCTTCTCTTCCTCCATTTGTT
932509 CTTCTGAACGTCTATGTCTAATCTTAAGTTCATCTTCTCTTCCTCCATTTGTT
1 CTTCTGAACGTCTATGTCTAATCTTAAGTTCATCTTCTCTTCCTCCATTTGTT
932562 CT
1 CT
932564 ATCTTCTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.17, C:0.27, G:0.09, T:0.47
Consensus pattern (53 bp):
CTTCTGAACGTCTATGTCTAATCTTAAGTTCATCTTCTCTTCCTCCATTTGTT
Found at i:938715 original size:72 final size:72
Alignment explanation
Indices: 938598--938768 Score: 191
Period size: 72 Copynumber: 2.4 Consensus size: 72
938588 AAAGCGCCGC
* * * * * *
938598 AAAAACCAAAGCCCAACGATGCCGTTTCTG-AGCTTTTGGGGATTTAGCGACGTTTTTAATCAAG
1 AAAAACCTAAGCCAAACGGTGTCGTTTCCGTAG-TTTTGGGGATTTAACGACGTTTTTAATCAAG
938662 CGCCACTA
65 CGCCACTA
* * * * * ** *
938670 ATAATCCTAAGCCAAACGGTGTCGTTTCCGTAGTTTTTGGGATTTAATGGCGTTTTTGGTGAAGC
1 AAAAACCTAAGCCAAACGGTGTCGTTTCCGTAGTTTTGGGGATTTAACGACGTTTTTAATCAAGC
*
938735 GCCGCTA
66 GCCACTA
938742 AAAAACCTAAGCCAAACGGTGTCGTTT
1 AAAAACCTAAGCCAAACGGTGTCGTTT
938769 TCTCAACTTT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 79 0.98
73 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (72 bp):
AAAAACCTAAGCCAAACGGTGTCGTTTCCGTAGTTTTGGGGATTTAACGACGTTTTTAATCAAGC
GCCACTA
Found at i:939597 original size:136 final size:136
Alignment explanation
Indices: 939440--939707 Score: 491
Period size: 136 Copynumber: 2.0 Consensus size: 136
939430 GTTTCAACGC
* *
939440 ATCAAAGTGTTGAGCAAAATCCATCGTTTTATTTTAGGTTTTAGGGTCTAAAATTTAAGATTTAA
1 ATCAAAGTGTTAAGCAAAATCCATCATTTTATTTTAGGTTTTAGGGTCTAAAATTTAAGATTTAA
*
939505 TGTCAATGGTTTAGGGTTTATGGTATACTGTTTATTAATTTGGGTTAAGTGTTTATGTGTTAGAG
66 TGTCAACGGTTTAGGGTTTATGGTATACTGTTTATTAATTTGGGTTAAGTGTTTATGTGTTAGAG
939570 ATGCAT
131 ATGCAT
*
939576 ATCAAAGTGTTAAGCAAAATCCATCATTTTATTTTAGGTTTTAGGGTTTAAAATTTAAGATTTAA
1 ATCAAAGTGTTAAGCAAAATCCATCATTTTATTTTAGGTTTTAGGGTCTAAAATTTAAGATTTAA
*
939641 TGTCTACGGTTTAGGGTTTATGGTATACTGTTTATTAATTTGGGTTAAGTGTTTATGTGTTAGAG
66 TGTCAACGGTTTAGGGTTTATGGTATACTGTTTATTAATTTGGGTTAAGTGTTTATGTGTTAGAG
939706 AT
131 AT
939708 TGAGTTTGGG
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 127 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.44
Consensus pattern (136 bp):
ATCAAAGTGTTAAGCAAAATCCATCATTTTATTTTAGGTTTTAGGGTCTAAAATTTAAGATTTAA
TGTCAACGGTTTAGGGTTTATGGTATACTGTTTATTAATTTGGGTTAAGTGTTTATGTGTTAGAG
ATGCAT
Found at i:939745 original size:21 final size:20
Alignment explanation
Indices: 939707--939756 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
939697 GTGTTAGAGA
939707 TTGAGTTTGGGGTTTAAGGT
1 TTGAGTTTGGGGTTTAAGGT
*
939727 TTGAGTTTAGGGTTTTAAGGT
1 TTGAGTTT-GGGGTTTAAGGT
939748 TT-AGTTTGG
1 TTGAGTTTGG
939757 AAATAGAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 13 0.46
21 13 0.46
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (20 bp):
TTGAGTTTGGGGTTTAAGGT
Found at i:939897 original size:14 final size:13
Alignment explanation
Indices: 939872--939934 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
939862 CAAAAAATAT
939872 GGTTTAGGTTTAC
1 GGTTTAGGTTTAC
939885 GGTTTAGGGTTTAC
1 GGTTTA-GGTTTAC
* *
939899 GATTTATAGTTTA-
1 GGTTTA-GGTTTAC
*
939912 GAGTTTTAGGTTTAG
1 G-G-TTTAGGTTTAC
939927 GGTTTAGG
1 GGTTTAGG
939935 ATATTTAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 13 0.32
14 23 0.56
15 5 0.12
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (13 bp):
GGTTTAGGTTTAC
Found at i:939931 original size:21 final size:20
Alignment explanation
Indices: 939872--939934 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
939862 CAAAAAATAT
939872 GGTTTAGGTTTACGGTTTAG
1 GGTTTAGGTTTACGGTTTAG
* **
939892 GGTTTACGATTTATAGTTTAG
1 GGTTTA-GGTTTACGGTTTAG
* *
939913 AGTTTTAGGTTTAGGGTTTAG
1 -GGTTTAGGTTTACGGTTTAG
939934 G
1 G
939935 ATATTTAGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (20 bp):
GGTTTAGGTTTACGGTTTAG
Found at i:940534 original size:115 final size:115
Alignment explanation
Indices: 940332--940570 Score: 388
Period size: 115 Copynumber: 2.1 Consensus size: 115
940322 GCGCTTCAGA
* * ** *
940332 AAAAACGCCGCTAAAGGTGATATATTACCGGCGTTTTGTGAAGAAACGCCGCAAATTTCCTTTAA
1 AAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATTTCCTTTAA
940397 CTGTAACAAAGACGGTGCCGTTTCGTTGTTTTCTTTTAGTGACGCATTTG
66 CTGTAACAAAGACGGTGCCGTTTCGTTGTTTTCTTTTAGTGACGCATTTG
*
940447 AAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCATAAATTTCCTTTAA
1 AAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATTTCCTTTAA
* * * *
940512 CTGTAACAAAGACGGTGTCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTT
66 CTGTAACAAAGACGGTGCCGTTTCGTTGTTTTCTTTTAGTGACGCATTTG
940562 AAAAACGCC
1 AAAAACGCC
940571 AGAAATATTT
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (115 bp):
AAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATTTCCTTTAA
CTGTAACAAAGACGGTGCCGTTTCGTTGTTTTCTTTTAGTGACGCATTTG
Found at i:940903 original size:261 final size:261
Alignment explanation
Indices: 940439--940958 Score: 934
Period size: 261 Copynumber: 2.0 Consensus size: 261
940429 CTTTTAGTGA
*
940439 CGCATTTGAAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCATAAATT
1 CGCATTTGAAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATT
940504 TCCTTTAACTGTAACAAAGACGGTGTCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTTAAAAACG
66 TCCTTTAACTGTAACAAAGACGGTGTCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTTAAAAACG
*
940569 CCAGAAATATTTATTACGAGCTGAGGAAACGGCGTCGTTTCCTATTTTTATTAGTGGCGCTTTAG
131 CCACAAATATTTATTACGAGCTGAGGAAACGGCGTCGTTTCCTATTTTTATTAGTGGCGCTTTAG
* *
940634 CTAAAGCGCCGCGAAAATGTTTAATGTTATCTTATAACGGTGCCGTTTTGTCCGTGTTATTAGTT
196 CTAAAGCGCCGCAAAAATGTTTAATGTTATCTTATAACGATGCCGTTTTGTCCGTGTTATTAGTT
940699 G
261 G
* *
940700 CGCATTTGAAAAACGCTGCTAAAGGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATT
1 CGCATTTGAAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATT
* *
940765 TCCTTTAACTGTAACGAAGACGGTGTCGTTTTGTTGTTTTCTTTTAGTGGTGCATTTTAAAAACG
66 TCCTTTAACTGTAACAAAGACGGTGTCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTTAAAAACG
940830 CCACAAATATTTATTACGAGCTGAGGAAACGGCG-CTGTTTCCTATTTTTATTAGTGGCGCTTTA
131 CCACAAATATTTATTACGAGCTGAGGAAACGGCGTC-GTTTCCTATTTTTATTAGTGGCGCTTTA
* *
940894 GCTAAAGCGCCGCAAAAATGTTTAATGTTATCTTATAACGATGCCGTTTTTTCTGTGTTATTAGT
195 GCTAAAGCGCCGCAAAAATGTTTAATGTTATCTTATAACGATGCCGTTTTGTCCGTGTTATTAGT
940959 GGCGTTTTTA
Statistics
Matches: 248, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
260 1 0.00
261 247 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (261 bp):
CGCATTTGAAAAACGCCGCTAAAAGTGATATATTACCAGCGTTTTACGAAGAAACGCCACAAATT
TCCTTTAACTGTAACAAAGACGGTGTCGTTTTGTTGTTTTCTTTTAGTGGCGCATTTTAAAAACG
CCACAAATATTTATTACGAGCTGAGGAAACGGCGTCGTTTCCTATTTTTATTAGTGGCGCTTTAG
CTAAAGCGCCGCAAAAATGTTTAATGTTATCTTATAACGATGCCGTTTTGTCCGTGTTATTAGTT
G
Found at i:941063 original size:23 final size:23
Alignment explanation
Indices: 941037--941084 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
941027 TTAGTGGCGC
941037 TTATTGTTAAGCGCCGCAAATGA
1 TTATTGTTAAGCGCCGCAAATGA
*
941060 TTATTGTTAAGCGCTGCAAATGA
1 TTATTGTTAAGCGCCGCAAATGA
941083 TT
1 TT
941085 TCAATTTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (23 bp):
TTATTGTTAAGCGCCGCAAATGA
Found at i:941402 original size:173 final size:169
Alignment explanation
Indices: 941117--941459 Score: 530
Period size: 173 Copynumber: 2.0 Consensus size: 169
941107 TCGTTTTTTT
*
941117 CCCATACATTTTACAGAAACTTAAACCCCTATCGTGACTTATCCCCCAAAATCCCATTCTCCCCC
1 CCCATACATTTAACAGAAACTTAAACCCCTATCGTGACTTATCCCCCAAAATCCCATTCTCCCCC
* *
941182 AAATCCCTAAATTTCCCCTAATCCAAATTTCCCCAAAGCCGACCTCTTGCAACGTTGCCGTTTCC
66 AAATCCCGAAATTTCCCCTAATCCAAATTTCCCCAAACCCGACCTCTTGCAACGTTGCCGTTTCC
*
941247 TCTGGCGCATCACCGTCTCCCTCCGTTGGTCTCCTCTGC
131 TCTGGCGCATCACCGTCTCCCTCCGTCGGTCTCCTCTGC
* *
941286 CCCATACATTTAACCGAAACTTAAACCCCAACTATTGTGACTTAT-CCCCAAAAT-CCATTTCTC
1 CCCATACATTTAACAGAAACTTAAA-CCC--CTATCGTGACTTATCCCCCAAAATCCCA-TTCT-
* *
941349 CCCCCAAA-CATGCGAAATTTCCCCTAATCCACATTTCCCCAAACCCGACCTCTTGCAACGTTGC
61 CCCCCAAATC--CCGAAATTTCCCCTAATCCAAATTTCCCCAAACCCGACCTCTTGCAACGTTGC
941413 CGTTTCCTCTGGCGCATCACCGTCTCCCTCCGTCGGTCTCCTCTGC
124 CGTTTCCTCTGGCGCATCACCGTCTCCCTCCGTCGGTCTCCTCTGC
941459 C
1 C
941460 TCAACAATCG
Statistics
Matches: 159, Mismatches: 8, Indels: 10
0.90 0.05 0.06
Matches are distributed among these distances:
169 23 0.14
170 6 0.04
171 14 0.09
172 21 0.13
173 95 0.60
ACGTcount: A:0.23, C:0.40, G:0.10, T:0.27
Consensus pattern (169 bp):
CCCATACATTTAACAGAAACTTAAACCCCTATCGTGACTTATCCCCCAAAATCCCATTCTCCCCC
AAATCCCGAAATTTCCCCTAATCCAAATTTCCCCAAACCCGACCTCTTGCAACGTTGCCGTTTCC
TCTGGCGCATCACCGTCTCCCTCCGTCGGTCTCCTCTGC
Found at i:943116 original size:9 final size:9
Alignment explanation
Indices: 943102--943465 Score: 186
Period size: 9 Copynumber: 40.6 Consensus size: 9
943092 TTTAATTTAA
*
943102 TACATAATT
1 TACATAACT
943111 TACATAACT
1 TACATAACT
*
943120 CACATAACT
1 TACATAACT
* *
943129 TACAAAAGT
1 TACATAACT
* *
943138 CACAT-ACA
1 TACATAACT
943146 TACATAACT
1 TACATAACT
*
943155 TA-ATAAAT
1 TACATAACT
*
943163 GGTACATAGCT
1 --TACATAACT
*
943174 TATATAACT
1 TACATAACT
943183 TACATAA--
1 TACATAACT
943190 TACATAACT
1 TACATAACT
* *
943199 TAAATAA-A
1 TACATAACT
943207 TACATAACT
1 TACATAACT
**
943216 TATTTAA--
1 TACATAACT
*
943223 TACATTACT
1 TACATAACT
943232 TACATAATAACT
1 TAC---ATAACT
*
943244 TACATAGCT
1 TACATAACT
*
943253 TATATAACT
1 TACATAACT
943262 TACATAACT
1 TACATAACT
*
943271 TATATAACT
1 TACATAACT
943280 TACAT-AC-
1 TACATAACT
*
943287 TCCATAACT
1 TACATAACT
*
943296 TACATAATT
1 TACATAACT
*
943305 TACTTAA--
1 TACATAACT
943312 TACATAA-T
1 TACATAACT
* *
943320 CAACATATATT
1 -TACATA-ACT
*
943331 ATATCTTAACT
1 -TA-CATAACT
943342 TACATAATAACT
1 TAC---ATAACT
*
943354 TACATAGCT
1 TACATAACT
* *
943363 TATAATAACC
1 TA-CATAACT
943373 TACATAACT
1 TACATAACT
943382 TACATAACT
1 TACATAACT
943391 TACATAA--
1 TACATAACT
943398 TACATAACT
1 TACATAACT
*
943407 TACATATCT
1 TACATAACT
**
943416 TTTAT-ACTAT
1 TACATAAC--T
943426 ATACATAACT
1 -TACATAACT
*
943436 TACATAATT
1 TACATAACT
*
943445 TACTTAA--
1 TACATAACT
943452 TACATAACT
1 TACATAACT
943461 TACAT
1 TACAT
943466 TGAGAAAAAT
Statistics
Matches: 265, Mismatches: 59, Indels: 62
0.69 0.15 0.16
Matches are distributed among these distances:
7 34 0.13
8 21 0.08
9 165 0.62
10 13 0.05
11 11 0.04
12 21 0.08
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:943200 original size:25 final size:25
Alignment explanation
Indices: 943165--943465 Score: 110
Period size: 25 Copynumber: 12.6 Consensus size: 25
943155 TAATAAATGG
* *
943165 TACATAGCTTATATAACTTACATAA
1 TACATAACTTACATAACTTACATAA
* *
943190 TACATAACTTAAATAA-ATACAT-A
1 TACATAACTTACATAACTTACATAA
* * *
943213 -AC-TTATTTA-AT-ACATTACTTACA
1 TACATAACTTACATAAC-TTACATA-A
* *
943236 TA-ATAACTTACATAGCTTATATAA
1 TACATAACTTACATAACTTACATAA
* *
943260 CTTACATAACTTATATAACTTACATAC
1 --TACATAACTTACATAACTTACATAA
* * *
943287 TCCATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
*
943312 TACATAA-TCAACATATA-TT--AT-A
1 TACATAACT-TACATA-ACTTACATAA
* *
943334 T-CTTAACTTACATAA-TAAC-T--
1 TACATAACTTACATAACTTACATAA
* * *
943354 TACATAGCTTATAATAACCTACATAA
1 TACATAACTTA-CATAACTTACATAA
943380 CTTACATAACTTACATAA--TACATAA
1 --TACATAACTTACATAACTTACATAA
* **
943405 CTTACATATCTTTTAT-AC-T--AT-A
1 --TACATAACTTACATAACTTACATAA
* *
943427 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACATAA
943452 TACATAACTTACAT
1 TACATAACTTACAT
943466 TGAGAAAAAT
Statistics
Matches: 204, Mismatches: 42, Indels: 60
0.67 0.14 0.20
Matches are distributed among these distances:
19 1 0.00
20 16 0.08
21 27 0.13
22 11 0.05
23 7 0.03
24 16 0.08
25 90 0.44
26 4 0.02
27 22 0.11
28 10 0.05
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.38
Consensus pattern (25 bp):
TACATAACTTACATAACTTACATAA
Found at i:943261 original size:18 final size:18
Alignment explanation
Indices: 943172--943465 Score: 125
Period size: 16 Copynumber: 16.4 Consensus size: 18
943162 TGGTACATAG
* *
943172 CTTATATAACTTACATAA
1 CTTACATAACTTATATAA
*
943190 --TACATAACTTAAATAA
1 CTTACATAACTTATATAA
* *
943206 -ATACATAACTTATTTAA
1 CTTACATAACTTATATAA
*
943223 --TACATTACTTACATAATAA
1 CTTACATAACTT--AT-ATAA
*
943242 CTTACATAGCTTATATAA
1 CTTACATAACTTATATAA
943260 CTTACATAACTTATATAA
1 CTTACATAACTTATATAA
**
943278 CTTACAT-AC-TCCATAA
1 CTTACATAACTTATATAA
*
943294 CTTACATAATTTACT-TAA
1 CTTACATAACTTA-TATAA
* *
943312 --TACATAA-TCAACATATA
1 CTTACATAACT-TATATA-A
* *
943329 TTATATCTTAACTTACATAATAA
1 CT-TA-CATAACTT--AT-ATAA
*
943352 CTTACATAGCTTATAATAA
1 CTTACATAACTTAT-ATAA
* *
943371 CCTACATAACTTACATAA
1 CTTACATAACTTATATAA
*
943389 CTTACATAA--TACATAA
1 CTTACATAACTTATATAA
* *
943405 CTTACATATCTTTTAT-A
1 CTTACATAACTTATATAA
*
943422 CTATATACATAACTTACATAA
1 C--T-TACATAACTTATATAA
* * *
943443 TTTACTTAA--TACATAA
1 CTTACATAACTTATATAA
943459 CTTACAT
1 CTTACAT
943466 TGAGAAAAAT
Statistics
Matches: 214, Mismatches: 36, Indels: 54
0.70 0.12 0.18
Matches are distributed among these distances:
15 1 0.00
16 72 0.34
17 20 0.09
18 55 0.26
19 25 0.12
20 13 0.06
21 19 0.09
22 3 0.01
23 3 0.01
24 3 0.01
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.38
Consensus pattern (18 bp):
CTTACATAACTTATATAA
Found at i:943369 original size:19 final size:19
Alignment explanation
Indices: 943345--943397 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
943335 CTTAACTTAC
*
943345 ATAATAACTTACATAGCTT
1 ATAATAACTTACATAACTT
*
943364 ATAATAACCTACATAACTT
1 ATAATAACTTACATAACTT
*
943383 A-CATAACTTACATAA
1 ATAATAACTTACATAA
943398 TACATAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATAACTTACATAACTT
Found at i:945486 original size:21 final size:20
Alignment explanation
Indices: 945460--945528 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 20
945450 CAACAACTTA
*
945460 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGC-GCAGCGAGAG
*
945481 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGC-GCAGCGAGAG
*
945502 AAGCAGAGGTCGCAGCAAGAG
1 AAGCAGAGG-CGCAGCGAGAG
945523 AAGCAG
1 AAGCAG
945529 CGATAAAAGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.42, T:0.03
Consensus pattern (20 bp):
AAGCAGAGGCGCAGCGAGAG
Found at i:946031 original size:42 final size:42
Alignment explanation
Indices: 945972--946230 Score: 167
Period size: 42 Copynumber: 5.9 Consensus size: 42
945962 GTTTGTGAAA
945972 TAAGCGCCGCTAAAGAACACTACTTTTAGCGGCGTTTT-TGACC
1 TAAGCGCCGCTAAAGAACA-TACTTTTAGCGGCGTTTTCT-ACC
* * * *
946015 -AAGCGCCGCTATAGAACATTACTTTTAGTGGCATTTTCTTCC
1 TAAGCGCCGCTAAAGAACA-TACTTTTAGCGGCGTTTTCTACC
946057 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTAGCGGCGTTTT-T-CC
1 TAAGCGCCGCTAAAGAACAT-A-C--T-------TTTAGCGGCGTTTTCTACC
* * * *
946108 TAAACGCCGCTAAAGAACATGA-TATTTAACGGCGTTTTTTA-A
1 TAAGCGCCGCTAAAGAACAT-ACT-TTTAGCGGCGTTTTCTACC
* *
946150 TAAGCGCCACTAAAGAACATGA-TCTTTAGCGGCGTTTAT-TTCC
1 TAAGCGCCGCTAAAGAACAT-ACT-TTTAGCGGCGTTT-TCTACC
*
946193 TTAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTT
1 TAAGCGCCGCTAAAGAACAT-ACT-TTTAGCGGCGTTTT
946231 TTTCTGTAAA
Statistics
Matches: 179, Mismatches: 20, Indels: 35
0.76 0.09 0.15
Matches are distributed among these distances:
41 13 0.07
42 72 0.40
43 55 0.31
44 1 0.01
46 1 0.01
47 1 0.01
51 23 0.13
52 1 0.01
53 12 0.07
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATACTTTTAGCGGCGTTTTCTACC
Found at i:946155 original size:136 final size:136
Alignment explanation
Indices: 945976--946229 Score: 354
Period size: 136 Copynumber: 1.9 Consensus size: 136
945966 GTGAAATAAG
* * * * *
945976 CGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTGACCAAGCGCCGCTATAGAACATTA-CTTT
1 CGCCGCTAAAGAACACTACTTTTAACGGCGTTTTTGAACAAGCGCCACTAAAGAACATGATC-TT
*
946040 TAGTGGCATTT-TCTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTAGCGGCGTTT
65 TAGCGGCATTTAT-TTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTAGCGGCGTTT
946104 TTCCTAAA
129 TTCCTAAA
* *
946112 CGCCGCTAAAGAACA-TGA-TATTTAACGGCGTTTTTTAATAAGCGCCACTAAAGAACATGATCT
1 CGCCGCTAAAGAACACT-ACT-TTTAACGGCGTTTTTGAACAAGCGCCACTAAAGAACATGATCT
* *
946175 TTAGCGGCGTTTATTTCCTTAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
64 TTAGCGGCATTTATTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
946230 TTTTCTGTAA
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
135 2 0.02
136 100 0.96
137 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (136 bp):
CGCCGCTAAAGAACACTACTTTTAACGGCGTTTTTGAACAAGCGCCACTAAAGAACATGATCTTT
AGCGGCATTTATTTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTAGCGGCGTTTTT
CCTAAA
Found at i:946165 original size:93 final size:94
Alignment explanation
Indices: 945996--946187 Score: 255
Period size: 93 Copynumber: 2.0 Consensus size: 94
945986 GAACACTACT
* * * ** **
945996 TTTAGCGGCGTTTTTGACCAAGCGCCGCTATAGAACATTACTTTTAGTGGCATTTTCTTCCTAAG
1 TTTAGCGGCGTTTTT-ACCAAACGCCGCTAAAGAACATGACTTTTAACGGCATTTTCTTAATAAG
*
946061 CGCCGCTAAAGAACATGATCTTTAGCGGCG
65 CGCCACTAAAGAACATGATCTTTAGCGGCG
*
946091 TTTAGCGGCGTTTTT-CCTAAACGCCGCTAAAGAACATGA-TATTTAACGGCGTTTT-TTAATAA
1 TTTAGCGGCGTTTTTACC-AAACGCCGCTAAAGAACATGACT-TTTAACGGCATTTTCTTAATAA
946153 GCGCCACTAAAGAACATGATCTTTAGCGGCG
64 GCGCCACTAAAGAACATGATCTTTAGCGGCG
946184 TTTA
1 TTTA
946188 TTTCCTTAGC
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
93 42 0.49
94 29 0.34
95 15 0.17
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (94 bp):
TTTAGCGGCGTTTTTACCAAACGCCGCTAAAGAACATGACTTTTAACGGCATTTTCTTAATAAGC
GCCACTAAAGAACATGATCTTTAGCGGCG
Found at i:958870 original size:22 final size:23
Alignment explanation
Indices: 958840--958912 Score: 107
Period size: 22 Copynumber: 3.3 Consensus size: 23
958830 TAATCCTCTT
958840 TCAAATTTCCTCTCAATTTGCTC
1 TCAAATTTCCTCTCAATTTGCTC
958863 T-AAATTTCCTCTCAATTTGCTC
1 TCAAATTTCCTCTCAATTTGCTC
*
958885 TCAAATTTCTTC-CAAATTT-CTC
1 TCAAATTTCCTCTC-AATTTGCTC
958907 TCAAAT
1 TCAAAT
958913 CCATATTTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
22 32 0.68
23 15 0.32
ACGTcount: A:0.26, C:0.27, G:0.03, T:0.44
Consensus pattern (23 bp):
TCAAATTTCCTCTCAATTTGCTC
Found at i:958911 original size:11 final size:12
Alignment explanation
Indices: 958840--958912 Score: 84
Period size: 11 Copynumber: 6.5 Consensus size: 12
958830 TAATCCTCTT
958840 TCAAATTTCCTC
1 TCAAATTTCCTC
*
958852 TC-AATTTGCTC
1 TCAAATTTCCTC
958863 T-AAATTTCCTC
1 TCAAATTTCCTC
*
958874 TC-AATTTGCTC
1 TCAAATTTCCTC
*
958885 TCAAATTTCTTC
1 TCAAATTTCCTC
958897 -CAAATTT-CTC
1 TCAAATTTCCTC
958907 TCAAAT
1 TCAAAT
958913 CCATATTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
10 2 0.04
11 40 0.78
12 9 0.18
ACGTcount: A:0.26, C:0.27, G:0.03, T:0.44
Consensus pattern (12 bp):
TCAAATTTCCTC
Found at i:960164 original size:7 final size:7
Alignment explanation
Indices: 960152--960176 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
960142 NNNNNNNNNN
960152 TATTTAG
1 TATTTAG
960159 TATTTAG
1 TATTTAG
960166 TATTTAG
1 TATTTAG
960173 TATT
1 TATT
960177 ATGTATATAA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:961320 original size:43 final size:44
Alignment explanation
Indices: 961273--961356 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
961263 TTATTTGTAC
*
961273 AAATATTTTGA-ATATTTTGATATTATTTTATGTAATAAAATAT
1 AAATATTTTGAGATATTTTGATATTATTTGATGTAATAAAATAT
*
961316 AAATATTTTGAGTTATTTTGATATTATTTGATGTAATAAAA
1 AAATATTTTGAGATATTTTGATATTATTTGATGTAATAAAA
961357 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 11 0.29
44 27 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (44 bp):
AAATATTTTGAGATATTTTGATATTATTTGATGTAATAAAATAT
Found at i:962570 original size:30 final size:28
Alignment explanation
Indices: 962536--962591 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
962526 GTGATTAAAT
962536 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
962566 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
962592 TAAGTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:975294 original size:147 final size:147
Alignment explanation
Indices: 975065--975340 Score: 421
Period size: 147 Copynumber: 1.9 Consensus size: 147
975055 CTACTTTTCT
* * *
975065 TCAAAGCTTTATTTCGAAATAGTTGGACAAGATCAAAACTTTGTTTTAAAAAATTTAAAATTTTC
1 TCAAAACTTTATTTCGAAATAGTTGAAAAAGATCAAAACTTTGTTTTAAAAAATTTAAAATTTTC
*
975130 CTTAAAAATGACTAAAAAT-ATTTTTATTTTAAAAATCTAAAATTTCTCTTTTTTTTAAAAAAAT
66 CTTAAAAATGACTAAAAATAATTTTTATTTTAAAAATCTAAAATCTCT-TTTTTTTTAAAAAAAT
975194 CACTATTTTTCTTAAAAA
130 CACTATTTTTCTTAAAAA
* * *
975212 TCAAAACTTTATTTTGAAATAGTTGAAAAAGATCAAAATTTTGTTTT-AAAAATTTAAATTTTTC
1 TCAAAACTTTATTTCGAAATAGTTGAAAAAGATCAAAACTTTGTTTTAAAAAATTTAAAATTTTC
* * *
975276 CTTTAATATGACTAAAAAATAGATTTTTATTTTAAAAATCTAAACTCTCTTTTTTTTTAAAAAAA
66 CTTAAAAATGACT-AAAAATA-ATTTTTATTTTAAAAATCTAAAATCTCTTTTTTTTTAAAAAAA
975341 ATCAATTTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
146 27 0.23
147 48 0.41
148 15 0.13
149 26 0.22
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (147 bp):
TCAAAACTTTATTTCGAAATAGTTGAAAAAGATCAAAACTTTGTTTTAAAAAATTTAAAATTTTC
CTTAAAAATGACTAAAAATAATTTTTATTTTAAAAATCTAAAATCTCTTTTTTTTTAAAAAAATC
ACTATTTTTCTTAAAAA
Found at i:975530 original size:11 final size:11
Alignment explanation
Indices: 975508--975543 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
975498 TGTATATGAC
975508 AAAAAAAAAAG
1 AAAAAAAAAAG
* *
975519 AAGAAGAAAAG
1 AAAAAAAAAAG
975530 AAAAAAAAAAG
1 AAAAAAAAAAG
975541 AAA
1 AAA
975544 CTAGAATGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:979035 original size:51 final size:50
Alignment explanation
Indices: 978959--979401 Score: 613
Period size: 51 Copynumber: 9.2 Consensus size: 50
978949 CTTGCGTATG
978959 ATCACTTAT-CACTTGTCCCTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTT-TCCACTTGT-CCTGATCAGATAAGTGTAGCTGAAGCTATCACTT
* *
979010 ATCACTTTCCACTTGTCACTGATCAGATAAGTGTAGCCGAAGCTATCACTC
1 ATCACTTTCCACTTGTC-CTGATCAGATAAGTGTAGCTGAAGCTATCACTT
979061 ATCACTTTCCAC---T--TGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTTCCACTTGTCCTGATCAGATAAGTGTAGCTGAAGCTATCACTT
* *
979106 ATCACTTTCCACTTGTCACTGATCAGATAAGTGTAGCCGAAGCTATCACTC
1 ATCACTTTCCACTTGTC-CTGATCAGATAAGTGTAGCTGAAGCTATCACTT
979157 ATCACTTTCCAC---T--TGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTTCCACTTGTCCTGATCAGATAAGTGTAGCTGAAGCTATCACTT
* *
979202 ATCACTTTCCACTTGTCACTGATCAGATAAGTGTAGCCGAAGCTATCACTC
1 ATCACTTTCCACTTGTC-CTGATCAGATAAGTGTAGCTGAAGCTATCACTT
979253 ATCACTTTCCAC---T--TGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTTCCACTTGTCCTGATCAGATAAGTGTAGCTGAAGCTATCACTT
* *
979298 ATCACTTTCCACTTGTCACTGATCAGATAAGTGTAGCCGAAGCTATCACTC
1 ATCACTTTCCACTTGTC-CTGATCAGATAAGTGTAGCTGAAGCTATCACTT
979349 ATCACTTTCCAC---T--TGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTTCCACTTGTCCTGATCAGATAAGTGTAGCTGAAGCTATCACTT
979394 ATCACTTT
1 ATCACTTT
979402 GTCACTTGAT
Statistics
Matches: 356, Mismatches: 16, Indels: 46
0.85 0.04 0.11
Matches are distributed among these distances:
45 164 0.46
48 7 0.02
50 2 0.01
51 183 0.51
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (50 bp):
ATCACTTTCCACTTGTCCTGATCAGATAAGTGTAGCTGAAGCTATCACTT
Found at i:979085 original size:45 final size:45
Alignment explanation
Indices: 979029--979415 Score: 522
Period size: 45 Copynumber: 8.2 Consensus size: 45
979019 CACTTGTCAC
979029 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
* *
979074 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACTTGT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCAC---T
979122 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
1 ---TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
* *
979170 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACTTGT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCAC---T
979218 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
1 ---TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
* *
979266 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACTTGT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCAC---T
979314 CACTGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
1 ---TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
* * *
979362 TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACT
1 TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTT-CCACT
979408 TGATCAGA
1 TGATCAGA
979416 AGTACTCAAA
Statistics
Matches: 308, Mismatches: 15, Indels: 37
0.86 0.04 0.10
Matches are distributed among these distances:
45 164 0.53
46 12 0.04
48 6 0.02
51 126 0.41
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (45 bp):
TGATCAGATAAGTGTAGCCGAAGCTATCACTCATCACTTTCCACT
Found at i:979091 original size:96 final size:96
Alignment explanation
Indices: 978959--979401 Score: 854
Period size: 96 Copynumber: 4.6 Consensus size: 96
978949 CTTGCGTATG
*
978959 ATCACTTATCACTTGTCC-C-TGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCAC
1 ATCACTCATCACTT-TCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCAC
979022 TTGTCACTGATCAGATAAGTGTAGCCGAAGCT
65 TTGTCACTGATCAGATAAGTGTAGCCGAAGCT
979054 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACT
1 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACT
979119 TGTCACTGATCAGATAAGTGTAGCCGAAGCT
66 TGTCACTGATCAGATAAGTGTAGCCGAAGCT
979150 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACT
1 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACT
979215 TGTCACTGATCAGATAAGTGTAGCCGAAGCT
66 TGTCACTGATCAGATAAGTGTAGCCGAAGCT
979246 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACT
1 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACT
979311 TGTCACTGATCAGATAAGTGTAGCCGAAGCT
66 TGTCACTGATCAGATAAGTGTAGCCGAAGCT
979342 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTT
1 ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTT
979402 GTCACTTGAT
Statistics
Matches: 345, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
94 3 0.01
95 14 0.04
96 328 0.95
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (96 bp):
ATCACTCATCACTTTCCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCACT
TGTCACTGATCAGATAAGTGTAGCCGAAGCT
Found at i:984933 original size:13 final size:13
Alignment explanation
Indices: 984915--984962 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
984905 TTTTTTATAG
984915 AAAATTTAATTAA
1 AAAATTTAATTAA
*
984928 AAAA-TTAA-TAG
1 AAAATTTAATTAA
984939 AAAATTTAATTAA
1 AAAATTTAATTAA
* *
984952 ATAATATAATT
1 AAAATTTAATT
984963 TCATTTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 6 0.21
12 8 0.28
13 15 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AAAATTTAATTAA
Found at i:984938 original size:24 final size:25
Alignment explanation
Indices: 984911--984961 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
984901 AAATTTTTTT
984911 ATAGAAAATTTAATTAAAAAAT-TA
1 ATAGAAAATTTAATTAAAAAATATA
*
984935 ATAGAAAATTTAATTAAATAATATA
1 ATAGAAAATTTAATTAAAAAATATA
984960 AT
1 AT
984962 TTCATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATAGAAAATTTAATTAAAAAATATA
Found at i:985248 original size:22 final size:22
Alignment explanation
Indices: 985223--985277 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
985213 TTTGCATTAT
985223 TTAATTAAAATTA-AAATTAAAA
1 TTAATTAAAATTATAAA-TAAAA
* *
985245 TTAATCTTAAA-TATAAATAAAT
1 TTAAT-TAAAATTATAAATAAAA
985267 TTAATTAAAAT
1 TTAATTAAAAT
985278 CTCATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.15
22 16 0.59
23 7 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAATTAAAATTATAAATAAAA
Found at i:996734 original size:30 final size:30
Alignment explanation
Indices: 996700--996771 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
996690 TTTAATTATT
996700 TTTGGAGCATGTCTCTTTTTTGAGATAATA
1 TTTGGAGCATGTCTCTTTTTTGAGATAATA
996730 TTTGGAGCATGTCTCTTTTTTGAGATAATA
1 TTTGGAGCATGTCTCTTTTTTGAGATAATA
996760 TTTGGAGCATGT
1 TTTGGAGCATGT
996772 ATGATGCAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (30 bp):
TTTGGAGCATGTCTCTTTTTTGAGATAATA
Found at i:1005624 original size:66 final size:68
Alignment explanation
Indices: 1005479--1005631 Score: 168
Period size: 66 Copynumber: 2.3 Consensus size: 68
1005469 TAGCCAAACA
* * * ** *
1005479 ATGGTCTTACACATGTAATCCTCATGTTTAATGTCTTGGCGAACTCCATATGTTGCCATAGCTGA
1 ATGGTCTTACACATGTAACCCTCATGTTAAATGTCCTGAAGAACTCCATATGTTGCCATAGCCGA
1005544 GAT
66 GAT
* *
1005547 ATAGACTTACACATGTAACCCT-ATGTTAAATGTCCTGAA-AGACTCCAT-TGTTGCCATAGCCG
1 ATGGTCTTACACATGTAACCCTCATGTTAAATGTCCTGAAGA-ACTCCATATGTTGCCATAGCCG
*
1005609 AGCT
65 AGAT
* * *
1005613 GTGGTGTTACACCTGTAAC
1 ATGGTCTTACACATGTAAC
1005632 TTCTTTCGAG
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
66 31 0.44
67 20 0.29
68 19 0.27
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (68 bp):
ATGGTCTTACACATGTAACCCTCATGTTAAATGTCCTGAAGAACTCCATATGTTGCCATAGCCGA
GAT
Found at i:1006817 original size:25 final size:26
Alignment explanation
Indices: 1006764--1006816 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
1006754 TTTGATATAC
*
1006764 TTAAGAGTATTCTTTGAGTTTTCTTT
1 TTAAGAATATTCTTTGAGTTTTCTTT
1006790 TTAAGAAT-TTCTATTGAGTTTTCTTT
1 TTAAGAATATTCT-TTGAGTTTTCTTT
1006816 T
1 T
1006817 AGAAGAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.58
Consensus pattern (26 bp):
TTAAGAATATTCTTTGAGTTTTCTTT
Found at i:1010763 original size:24 final size:25
Alignment explanation
Indices: 1010718--1010764 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1010708 GAGTTAATAA
* *
1010718 AATTTTCTTTGAGTTTTTTTTTAAG
1 AATTTTCTTTAAGTTTTATTTTAAG
1010743 AATTTT-TTTAAGTTTTATTTTA
1 AATTTTCTTTAAGTTTTATTTTA
1010765 GAAGAGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (25 bp):
AATTTTCTTTAAGTTTTATTTTAAG
Found at i:1026778 original size:27 final size:27
Alignment explanation
Indices: 1026734--1026791 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
1026724 CCCTCAGAGG
*
1026734 CCACGCCTCTGGTGTAACCAACTAAAC
1 CCACGCCTCCGGTGTAACCAACTAAAC
* *
1026761 CCACGCCTCCGGTTTAACCCACTAAAC
1 CCACGCCTCCGGTGTAACCAACTAAAC
1026788 CCAC
1 CCAC
1026792 TAAAAATGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.43, G:0.12, T:0.17
Consensus pattern (27 bp):
CCACGCCTCCGGTGTAACCAACTAAAC
Found at i:1027401 original size:14 final size:14
Alignment explanation
Indices: 1027382--1027423 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
1027372 ACATATCAAG
1027382 ATATCAATCTCATC
1 ATATCAATCTCATC
*
1027396 ATATCAATATCATC
1 ATATCAATCTCATC
1027410 ATATCAATCATCAT
1 ATATCAATC-TCAT
1027424 AATAATCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATCAATCTCATC
Found at i:1033459 original size:19 final size:19
Alignment explanation
Indices: 1033435--1033488 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 19
1033425 ATGAATACTC
1033435 ATTAAAATAGTTTTCACCT
1 ATTAAAATAGTTTTCACCT
*
1033454 ATTAAATTATATTTTTCACCT
1 ATTAAA--ATAGTTTTCACCT
1033475 ATTAAAATAGTTTT
1 ATTAAAATAGTTTT
1033489 AACTTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (19 bp):
ATTAAAATAGTTTTCACCT
Found at i:1035325 original size:23 final size:24
Alignment explanation
Indices: 1035299--1035357 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
1035289 TTAACTTGAT
1035299 CGAACATGTTCATGAACAT-TAAA
1 CGAACATGTTCATGAACATATAAA
* *
1035322 CGAACATGTTTATGAACATATAAT
1 CGAACATGTTCATGAACATATAAA
*
1035346 TGAACATGTTCA
1 CGAACATGTTCA
1035358 CGGACAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 18 0.58
24 13 0.42
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (24 bp):
CGAACATGTTCATGAACATATAAA
Found at i:1035595 original size:11 final size:12
Alignment explanation
Indices: 1035579--1035610 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1035569 TTAATAGTAA
1035579 ATAAACAAG-TC
1 ATAAACAAGTTC
1035590 ATAAACAAGTTC
1 ATAAACAAGTTC
1035602 ATAAACAAG
1 ATAAACAAG
1035611 CTTGTTGGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAAACAAGTTC
Found at i:1035940 original size:14 final size:14
Alignment explanation
Indices: 1035923--1035951 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1035913 GGTTCACACC
1035923 TAGGGGTTTGCACA
1 TAGGGGTTTGCACA
1035937 TAGGGGTTTGCACA
1 TAGGGGTTTGCACA
1035951 T
1 T
1035952 GTAGGGTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.34, T:0.31
Consensus pattern (14 bp):
TAGGGGTTTGCACA
Found at i:1036323 original size:44 final size:44
Alignment explanation
Indices: 1036273--1036357 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
1036263 TCGCATGGTA
*
1036273 TAACATATA-GAATCACATATATAAACATTTAGGTTCACATATAT
1 TAACATATATG-ATCACATATATAAACATATAGGTTCACATATAT
* * *
1036317 TAACATATATGGTCACATATATCAACATATAGGTTCTCATA
1 TAACATATATGATCACATATATAAACATATAGGTTCACATA
1036358 CTTTAGAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (44 bp):
TAACATATATGATCACATATATAAACATATAGGTTCACATATAT
Found at i:1036357 original size:22 final size:22
Alignment explanation
Indices: 1036274--1036357 Score: 98
Period size: 22 Copynumber: 3.8 Consensus size: 22
1036264 CGCATGGTAT
**
1036274 AACATATAGAATCACATATATA
1 AACATATAGGTTCACATATATA
* *
1036296 AACATTTAGGTTCACATATATT
1 AACATATAGGTTCACATATATA
*
1036318 AACATATATGG-TCACATATATC
1 AACATATA-GGTTCACATATATA
*
1036340 AACATATAGGTTCTCATA
1 AACATATAGGTTCACATA
1036358 CTTTAGAACT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.04
22 49 0.92
23 2 0.04
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.33
Consensus pattern (22 bp):
AACATATAGGTTCACATATATA
Found at i:1036656 original size:13 final size:14
Alignment explanation
Indices: 1036638--1036668 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1036628 CCTAATCTCT
1036638 TAATTATTCA-ACA
1 TAATTATTCATACA
1036651 TAATTATTCATACA
1 TAATTATTCATACA
1036665 TAAT
1 TAAT
1036669 GATTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATTATTCATACA
Found at i:1041706 original size:63 final size:62
Alignment explanation
Indices: 1041619--1041786 Score: 203
Period size: 63 Copynumber: 2.7 Consensus size: 62
1041609 GTGGCCCTGG
* * * *
1041619 CCCGTGTAACTCTTAAGAACAAACAGTGAGTTACACAGCCTGA-AAACATGCCCGTGTCCCTAA
1 CCCGTGTGACTCTTAAGCACAAACAGTGAGTTACACGGCCTGACAAAC--GCCCATGTCCCTAA
* * *
1041682 CCCGTGTGACTCTTAAGCATAAACAGTGAGTTACACGGCTTGGACAAACGCCCATGTCCCTAG
1 CCCGTGTGACTCTTAAGCACAAACAGTGAGTTACACGGCCT-GACAAACGCCCATGTCCCTAA
* * * *
1041745 CCCGTGTGATTCTAAATCACAAACAGTGAGTTATACGGCCTG
1 CCCGTGTGACTCTTAAGCACAAACAGTGAGTTACACGGCCTG
1041787 TCCCGCGGAC
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
62 1 0.01
63 83 0.92
64 2 0.02
65 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (62 bp):
CCCGTGTGACTCTTAAGCACAAACAGTGAGTTACACGGCCTGACAAACGCCCATGTCCCTAA
Found at i:1050389 original size:23 final size:23
Alignment explanation
Indices: 1050357--1050409 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1050347 AGGCCGGAGA
1050357 TGTG-TGGTAGAGGAAGCTTGAT
1 TGTGCTGGTAGAGGAAGCTTGAT
*
1050379 TGTGCTGGTAGGGGAAGCTTGAT
1 TGTGCTGGTAGAGGAAGCTTGAT
1050402 TGTGCTGG
1 TGTGCTGG
1050410 GATGCTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.17, C:0.08, G:0.43, T:0.32
Consensus pattern (23 bp):
TGTGCTGGTAGAGGAAGCTTGAT
Found at i:1060228 original size:126 final size:124
Alignment explanation
Indices: 1059982--1060249 Score: 274
Period size: 126 Copynumber: 2.1 Consensus size: 124
1059972 TTTAATGCCA
* * *
1059982 TACACGGCTTGGCACACGCCATGTCCTTGGCCCTTGTGACCCTATATCACAAATAGTGAGTTACT
1 TACACGGCCTGGCACACGCCATGTCCTTGGCCCATGTGACCCTAAATCACAAATAGTGAGTTACT
* * *
1060047 CAACCTGGACACAAGCTGGTGTCCCTGGCTCGTGTGACTCTTAAGTATAAACAGTGAGT
66 CAACCTGAACACAAGCTGGTGTCCCTGGCTCGTGTGACTCTTAAATACAAACAGTGAGT
* ** *
1060106 TACACGGCCTGGACACACGTCCGTGTCCTTGGCCCATGTGACTTTAAATCACAAATAGTGTGTTA
1 TACACGGCCTGG-CACACG-CCATGTCCTTGGCCCATGTGACCCTAAATCACAAATAGTGAGTTA
** * * * * *
1060171 CAT-GGCCTGAAGACACG-TATGTGTTCCTGG-TCCGTGTGACT-TTAAATCACAATCAGTGAGT
64 C-TCAACCTGAACACAAGCT-GGTGTCCCTGGCT-CGTGTGACTCTTAAAT-ACAAACAGTGAGT
* * *
1060232 TACATGGCTTAGCACACG
1 TACACGGCCTGGCACACG
1060250 ATTGTGTGAC
Statistics
Matches: 118, Mismatches: 20, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
124 11 0.09
125 19 0.16
126 87 0.74
127 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (124 bp):
TACACGGCCTGGCACACGCCATGTCCTTGGCCCATGTGACCCTAAATCACAAATAGTGAGTTACT
CAACCTGAACACAAGCTGGTGTCCCTGGCTCGTGTGACTCTTAAATACAAACAGTGAGT
Found at i:1060236 original size:63 final size:64
Alignment explanation
Indices: 1060003--1060239 Score: 184
Period size: 63 Copynumber: 3.8 Consensus size: 64
1059993 GCACACGCCA
* ** * ** * * *
1060003 TGTCCTTGGCCCTTGTGACCCTATATCACAAAT-AGTGAGTTAC-TCAACCTGGACACAAGCT-G
1 TGTCCTTGGCCCATGTGACTTTAAATCACAAATCAGTGAGTTACAT-GGCCTGAACACACG-TAC
1060065 G
64 G
* * * * * * * *
1060066 TGTCCCTGGCTCGTGTGACTCTTAAGT-ATAAA-CAGTGAGTTACACGGCCTGGACACACGTCCG
1 TGTCCTTGGCCCATGTGACT-TTAAATCACAAATCAGTGAGTTACATGGCCTGAACACACGTACG
* * *
1060129 TGTCCTTGGCCCATGTGACTTTAAATCACAAAT-AGTGTGTTACATGGCCTGAAGACACGTATG
1 TGTCCTTGGCCCATGTGACTTTAAATCACAAATCAGTGAGTTACATGGCCTGAACACACGTACG
* *
1060192 TGTTCC-TGGTCCGTGTGACTTTAAATCAC-AATCAGTGAGTTACATGGC
1 TG-TCCTTGGCCCATGTGACTTTAAATCACAAATCAGTGAGTTACATGGC
1060240 TTAGCACACG
Statistics
Matches: 139, Mismatches: 27, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
62 9 0.06
63 124 0.89
64 6 0.04
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (64 bp):
TGTCCTTGGCCCATGTGACTTTAAATCACAAATCAGTGAGTTACATGGCCTGAACACACGTACG
Found at i:1063075 original size:50 final size:50
Alignment explanation
Indices: 1063013--1063244 Score: 338
Period size: 50 Copynumber: 4.6 Consensus size: 50
1063003 CAATTTCATA
* ** * * * *
1063013 TCCCAGATATGGTCTTACATGGGAGTTCTCATATCGATGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
***
1063063 TCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
*
1063113 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCAATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
* *
1063163 TCCCAAACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
*
1063213 TCCCAGGCATGGTCTTACATGGGACCTCTCAT
1 TCCCAGACATGGTCTTACATGGGACCTCTCAT
1063245 ATCTATTTCA
Statistics
Matches: 163, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 163 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
Found at i:1065431 original size:18 final size:18
Alignment explanation
Indices: 1065408--1065460 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
1065398 TTCTTTATAT
1065408 ATAAAGAAAAAGGTCAAA
1 ATAAAGAAAAAGGTCAAA
* *
1065426 ATAAAGAAAAAGCTAAAA
1 ATAAAGAAAAAGGTCAAA
1065444 ATAAAGAAAAAGG-CAAA
1 ATAAAGAAAAAGGTCAAA
1065461 TAGTCTGTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 3 0.10
18 28 0.90
ACGTcount: A:0.70, C:0.06, G:0.15, T:0.09
Consensus pattern (18 bp):
ATAAAGAAAAAGGTCAAA
Found at i:1069433 original size:104 final size:104
Alignment explanation
Indices: 1069253--1069694 Score: 562
Period size: 104 Copynumber: 4.3 Consensus size: 104
1069243 GGCCAGTAGT
* * * * * * *
1069253 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAGACTTAAGCTTGTAGCTCCCAGATAAC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTCGTAACTCCCAGACAAC
* *
1069318 TAGCGGACCTACGCTCCCAGCTGATTATTTAAGGTTAGC
66 TAGCGGACCTACACTCCCAGCTGATTATTAAAGGTTAGC
* * *
1069357 AGAGTTAAGCTTGTAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTTGTAACTCCCAGACAAC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTCGTAACTCCCAGACAAC
*
1069422 TAGCGGACCTACACTCCCATCTGATTATT-AAGGTTAGC
66 TAGCGGACCTACACTCCCAGCTGATTATTAAAGGTTAGC
* * * *
1069460 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAGTTAAACTCATAACTCCTAGACAGC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTCGTAACTCCCAGACAAC
** ** * * *
1069525 TAGAAGACCTATGCTCCCAGTTGAGTATTAAAAGTTAGC
66 TAGCGGACCTACACTCCCAGCTGATTATTAAAGGTTAGC
* * * * * *
1069564 AGAGTTAAGCTCGCAACCTCTGGTCTTTTGAGTTAGCAGAGTTAAGCTCGCAACTCCCATACAAC
1 AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTCGTAACTCCCAGACAAC
* * *
1069629 TCGTGGACCTACACTTCCAGCTGATTATTAAAGGTTAGC
66 TAGCGGACCTACACTCCCAGCTGATTATTAAAGGTTAGC
* *
1069668 AGAGTTAAGCTCGCAACCCCCAATCTT
1 AGAGTTAAGCTCGCAACCTCCGATCTT
1069695 ATTTACAAAC
Statistics
Matches: 289, Mismatches: 48, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
103 89 0.31
104 200 0.69
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (104 bp):
AGAGTTAAGCTCGCAACCTCCGATCTTTTGAGTTAGCAAAGTTAAACTCGTAACTCCCAGACAAC
TAGCGGACCTACACTCCCAGCTGATTATTAAAGGTTAGC
Found at i:1069621 original size:207 final size:208
Alignment explanation
Indices: 1069253--1069694 Score: 598
Period size: 207 Copynumber: 2.1 Consensus size: 208
1069243 GGCCAGTAGT
* * ** * *
1069253 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAGACTTAAGCTTGTAGCTCCCAGATAAC
1 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAACTTAAACTCATAACTCCCAGACAAC
** * * * * *
1069318 TAGCGGACCTACGCTCCCAGCTGATTATTTAAGGTTAGCAGAGTTAAGCTTGTAACCTCCGATCT
66 TAGAAGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCGATCT
* * *
1069383 TTTGAGTTAGCAAAGTTAAACTTGTAACTCCCAGACAACTAGCGGACCTACACTCCCATCTGATT
131 TTTGAGTTAGCAAAGTTAAACTCGCAACTCCCAGACAACTAGCGGACCTACACTCCCAGCTGATT
1069448 ATT-AAGGTTAGC
196 ATTAAAGGTTAGC
* * *
1069460 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAAGTTAAACTCATAACTCCTAGACAGC
1 AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAACTTAAACTCATAACTCCCAGACAAC
* * * *
1069525 TAGAAGACCTATGCTCCCAGTTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCTGGTCT
66 TAGAAGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCGATCT
* * * * * *
1069590 TTTGAGTTAGCAGAGTTAAGCTCGCAACTCCCATACAACTCGTGGACCTACACTTCCAGCTGATT
131 TTTGAGTTAGCAAAGTTAAACTCGCAACTCCCAGACAACTAGCGGACCTACACTCCCAGCTGATT
1069655 ATTAAAGGTTAGC
196 ATTAAAGGTTAGC
* *
1069668 AGAGTTAAGCTCGCAACCCCCAATCTT
1 AGAGTTAAGCTCGCAACCTCCTATCTT
1069695 ATTTACAAAC
Statistics
Matches: 203, Mismatches: 31, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
207 169 0.83
208 34 0.17
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (208 bp):
AGAGTTAAGCTCGCAACCTCCTATCTTTTGAGTTAGCAAACTTAAACTCATAACTCCCAGACAAC
TAGAAGACCTACGCTCCCAGCTGAGTATTAAAAGTTAGCAGAGTTAAGCTCGCAACCTCCGATCT
TTTGAGTTAGCAAAGTTAAACTCGCAACTCCCAGACAACTAGCGGACCTACACTCCCAGCTGATT
ATTAAAGGTTAGC
Found at i:1078403 original size:42 final size:42
Alignment explanation
Indices: 1078344--1078425 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1078334 GGAAGTTGAA
*
1078344 AATTCTTTAATCAAAATCTTTGGACTTCAAATAATGCTAGAC
1 AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAGAC
*
1078386 AATTCTTTAAACAAAATCTTTGGACTTCGAATAATGCTAG
1 AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAG
1078426 TATTATGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (42 bp):
AATTCTTTAAACAAAATCTTTGGACTTCAAATAATGCTAGAC
Found at i:1078456 original size:14 final size:14
Alignment explanation
Indices: 1078437--1078481 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
1078427 ATTATGGAAG
1078437 TATGAAAGCTCATC
1 TATGAAAGCTCATC
*
1078451 TATGAAAGCTCATT
1 TATGAAAGCTCATC
*
1078465 TAT-AAAGATCAATC
1 TATGAAAGCTC-ATC
1078479 TAT
1 TAT
1078482 TTGAAATAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (14 bp):
TATGAAAGCTCATC
Found at i:1084448 original size:6 final size:6
Alignment explanation
Indices: 1084429--1084479 Score: 84
Period size: 6 Copynumber: 8.3 Consensus size: 6
1084419 TCTAAATAAA
*
1084429 TTCATT TCTCATT TTCATT TTCATT TTCATT TTCATT TTCATT TCCATT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT
1084478 TT
1 TT
1084480 GAGAAAACCA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 36 0.86
7 6 0.14
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.65
Consensus pattern (6 bp):
TTCATT
Found at i:1087846 original size:20 final size:20
Alignment explanation
Indices: 1087821--1087865 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1087811 TGGGTAGGAT
* *
1087821 TTGTTTTCTGGAAATCTACA
1 TTGTTTTCTGAAAATCCACA
1087841 TTGTTTTCTGAAAATCCACA
1 TTGTTTTCTGAAAATCCACA
1087861 TTGTT
1 TTGTT
1087866 ATTGAAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (20 bp):
TTGTTTTCTGAAAATCCACA
Found at i:1087871 original size:19 final size:20
Alignment explanation
Indices: 1087821--1087873 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1087811 TGGGTAGGAT
* * *
1087821 TTGTTTTCTGGAAATCTACA
1 TTGTTATCTGAAAATCCACA
*
1087841 TTGTTTTCTGAAAATCCACA
1 TTGTTATCTGAAAATCCACA
1087861 TTGTTAT-TGAAAA
1 TTGTTATCTGAAAA
1087874 GCGTTGCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (20 bp):
TTGTTATCTGAAAATCCACA
Found at i:1091900 original size:11 final size:11
Alignment explanation
Indices: 1091884--1091944 Score: 83
Period size: 11 Copynumber: 5.6 Consensus size: 11
1091874 AAATATTTTT
1091884 TATTTTTAAAA
1 TATTTTTAAAA
1091895 TATTTTTAAAA
1 TATTTTTAAAA
1091906 TAATTTTT-AAA
1 T-ATTTTTAAAA
1091917 -A-TTTTAAAA
1 TATTTTTAAAA
1091926 TATTTTTAAAA
1 TATTTTTAAAA
1091937 TACTTTTT
1 TA-TTTTT
1091945 TTTAATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
10 1 0.02
11 25 0.56
12 11 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:1091923 original size:20 final size:19
Alignment explanation
Indices: 1091884--1091937 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 19
1091874 AAATATTTTT
1091884 TATTTTTAAAATATTTTTAAAA
1 TATTTTT-AAA-A-TTTTAAAA
1091906 TAATTTTTAAAATTTTAAAA
1 T-ATTTTTAAAATTTTAAAA
1091926 TATTTTTAAAAT
1 TATTTTTAAAAT
1091938 ACTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.35
20 9 0.29
21 1 0.03
22 4 0.13
23 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTTAAAATTTTAAAA
Found at i:1100749 original size:12 final size:12
Alignment explanation
Indices: 1100732--1100759 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1100722 GGTGTTACTT
1100732 ACTAAGAAAATG
1 ACTAAGAAAATG
1100744 ACTAAGAAAATG
1 ACTAAGAAAATG
1100756 ACTA
1 ACTA
1100760 TGTGTGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (12 bp):
ACTAAGAAAATG
Found at i:1102448 original size:29 final size:30
Alignment explanation
Indices: 1102407--1102474 Score: 120
Period size: 29 Copynumber: 2.3 Consensus size: 30
1102397 TTTTAGTGGT
1102407 TTTTAAAGCATCGCCGTTTTTTGAACCACAA
1 TTTTAAA-CATCGCCGTTTTTTGAACCACAA
1102438 TTTTAAA-ATCGCCGTTTTTTGAACCACAA
1 TTTTAAACATCGCCGTTTTTTGAACCACAA
1102467 TTTTAAAC
1 TTTTAAAC
1102475 CTTTCCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
29 29 0.81
31 7 0.19
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (30 bp):
TTTTAAACATCGCCGTTTTTTGAACCACAA
Found at i:1106439 original size:20 final size:20
Alignment explanation
Indices: 1106414--1106451 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1106404 AAACCAAGAC
1106414 TAATTTT-TATTCTTCATAAT
1 TAATTTTATATT-TTCATAAT
1106434 TAATTTTATATTTTCATA
1 TAATTTTATATTTTCATA
1106452 CAAATTTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTTTATATTTTCATAAT
Found at i:1106806 original size:15 final size:17
Alignment explanation
Indices: 1106788--1106823 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
1106778 TCTCTTCTTC
1106788 TTTTCTTTCT-TTTT-T
1 TTTTCTTTCTCTTTTAT
1106803 TTTTCTTTCTCTTTTAT
1 TTTTCTTTCTCTTTTAT
1106820 TTTT
1 TTTT
1106824 TATTCGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 5 0.26
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTTTCTCTTTTAT
Found at i:1106822 original size:20 final size:20
Alignment explanation
Indices: 1106785--1106824 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1106775 TATTCTCTTC
*
1106785 TTCTTTTCTTTCTTTTTTTT
1 TTCTTTTCTTTCTATTTTTT
1106805 TTCTTTCTCTTT-TATTTTTT
1 TTCTTT-TCTTTCTATTTTTT
1106825 ATTCGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (20 bp):
TTCTTTTCTTTCTATTTTTT
Found at i:1109879 original size:12 final size:12
Alignment explanation
Indices: 1109841--1109944 Score: 104
Period size: 12 Copynumber: 8.2 Consensus size: 12
1109831 TCAAAAGGTG
*
1109841 ATTTCTATTTATT
1 ATTTTTATTT-TT
1109854 ATTTTTTATATTTT
1 A-TTTTTAT-TTTT
1109868 -TTATTTATTTTT
1 ATT-TTTATTTTT
* *
1109880 AAATTTTTTAATCT-
1 --A-TTTTTATTTTT
1109894 ATTTTTATTTTT
1 ATTTTTATTTTT
1109906 ATTTTTATTTTT
1 ATTTTTATTTTT
1109918 ATTTTTATTTTT
1 ATTTTTATTTTT
1109930 ATTTTTATTTTT
1 ATTTTTATTTTT
1109942 ATT
1 ATT
1109945 AATATATGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
11 8 0.10
12 46 0.59
13 6 0.08
14 8 0.10
15 8 0.10
16 2 0.03
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:1109886 original size:18 final size:16
Alignment explanation
Indices: 1109841--1109944 Score: 84
Period size: 18 Copynumber: 5.9 Consensus size: 16
1109831 TCAAAAGGTG
*
1109841 ATTTCTATTTATTATTT
1 ATTTTTATTT-TTATTT
*
1109858 -TTTATATTTTTTATTT
1 ATTTTTA-TTTTTATTT
*
1109874 ATTTTTAAATTTTTTAATCT
1 ATTTTT--A-TTTTT-ATTT
1109894 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTA--TTT
1109912 ATTTTTATTTTTATTTTT
1 ATTTTTATTTTTA--TTT
1109930 ATTTTTATTTTTATT
1 ATTTTTATTTTTATT
1109945 AATATATGTA
Statistics
Matches: 76, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
16 14 0.18
17 12 0.16
18 34 0.45
19 7 0.09
20 9 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTTATTTTTATTT
Found at i:1109904 original size:6 final size:6
Alignment explanation
Indices: 1109893--1109944 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
1109883 TTTTTTAATC
1109893 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
1109941 TATT
1 TATT
1109945 AATATATGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:1110322 original size:17 final size:16
Alignment explanation
Indices: 1110286--1110326 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1110276 TATTTGATAA
*
1110286 ACTAAAAAATTAAGCT
1 ACTAAAAAATTAAGAT
1110302 -CTAAAAAATTAAGTAT
1 ACTAAAAAATTAAG-AT
1110318 ACTAAAAAA
1 ACTAAAAAA
1110327 ATATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (16 bp):
ACTAAAAAATTAAGAT
Found at i:1112990 original size:13 final size:13
Alignment explanation
Indices: 1112948--1112990 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1112938 GGCTGAAAGA
1112948 TTATGAAAATATT
1 TTATGAAAATATT
* *
1112961 TTGTAGAAACTTATT
1 TTAT-GAAA-ATATT
1112976 TTATGAAAATATT
1 TTATGAAAATATT
1112989 TT
1 TT
1112991 TAGCTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 9 0.38
14 8 0.33
15 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (13 bp):
TTATGAAAATATT
Found at i:1124517 original size:32 final size:32
Alignment explanation
Indices: 1124481--1124544 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1124471 TGCAAGGAAA
1124481 CGATGGACTAAGGGTGGAGTTGGCACTTCAAT
1 CGATGGACTAAGGGTGGAGTTGGCACTTCAAT
1124513 CGATGGACTAAGGGTGGAGTTGGCACTTCAAT
1 CGATGGACTAAGGGTGGAGTTGGCACTTCAAT
1124545 TGTTAAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (32 bp):
CGATGGACTAAGGGTGGAGTTGGCACTTCAAT
Found at i:1124698 original size:24 final size:24
Alignment explanation
Indices: 1124670--1124733 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
1124660 CGAATTTGGA
1124670 TTTTAAATATTAACGGG-TATCAGG-
1 TTTTAAATATTAA-GGGCTAT-AGGC
*
1124694 TTTTAAATTTTAAGGGCTATAGGC
1 TTTTAAATATTAAGGGCTATAGGC
1124718 TTTTAAGAGTATTAAG
1 TTTTAA-A-TATTAAG
1124734 TTTTAATGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 6 0.18
24 21 0.62
25 1 0.03
26 6 0.18
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTTAAATATTAAGGGCTATAGGC
Found at i:1133867 original size:35 final size:35
Alignment explanation
Indices: 1133821--1133905 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
1133811 GTATTTTATT
1133821 AATAAAAAATCAAGCTCTGTCAAAAAATAAAATAA
1 AATAAAAAATCAAGCTCTGTCAAAAAATAAAATAA
*
1133856 AATAAAAAATCAAGCTCTGTCAACAAATAAAATAA
1 AATAAAAAATCAAGCTCTGTCAAAAAATAAAATAA
*
1133891 AATAAAAAGTCAAGC
1 AATAAAAAATCAAGC
1133906 AAATTACATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.19
Consensus pattern (35 bp):
AATAAAAAATCAAGCTCTGTCAAAAAATAAAATAA
Done.