Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold326
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: 1352760
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 2 of 8
Found at i:177467 original size:13 final size:13
Alignment explanation
Indices: 177449--177477 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
177439 AAATAGTACC
177449 CAATGTATCGATA
1 CAATGTATCGATA
177462 CAATGTATCGATA
1 CAATGTATCGATA
177475 CAA
1 CAA
177478 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:180478 original size:79 final size:78
Alignment explanation
Indices: 180356--180580 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 78
180346 TGAGAAATTT
* * * *
180356 AATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAA-AACCGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
* *
180421 GGTTATGAAAAATC
65 GATTACGAAAAATC
* *
180435 GATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGG-TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
* * *
180499 CAATTACGAGAAATT
64 CGATTACGAAAAATC
* * * **
180514 AATATTTTGGAAATAAAGCCGAGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAAAACCG-GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
180579 GA
65 GA
180581 CGAAATAACG
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
78 6 0.05
79 114 0.93
80 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (78 bp):
AATATTTAGGAAATAAAACCGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCG
ATTACGAAAAATC
Found at i:180576 original size:28 final size:28
Alignment explanation
Indices: 180533--180604 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
180523 GAAATAAAGC
* **
180533 CGAGGTTGGAGTATCCCC-TCGGAGGTAA
1 CGAGGTTGGAGTATCCCCGAC-GAAATAA
*
180561 CGGGGTTGGAGTATCCCCGACGAAATAA
1 CGAGGTTGGAGTATCCCCGACGAAATAA
180589 CGAGGTTGGAGTATCC
1 CGAGGTTGGAGTATCC
180605 TTGATTGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.21
Consensus pattern (28 bp):
CGAGGTTGGAGTATCCCCGACGAAATAA
Found at i:180682 original size:52 final size:52
Alignment explanation
Indices: 180626--180977 Score: 223
Period size: 52 Copynumber: 6.7 Consensus size: 52
180616 AATTTAGTGT
* *
180626 TTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
* * ** *
180678 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATT-GTGGAAAATTAGTG
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
* * * *** *
180729 TTTTGGAAATAAAAACAGGGTTGGAGTATCCTCGATT---GTGAGAAATCAATA
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTAAAG-GA-AAATTGGTG
* * * ** *
180780 TTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGGAGGTAACGG--GGTTGGAG
1 TTTTGGAAATAAAATCGGGGTTGGAGTAT-CCC-C-GA-TTAAAGGAAAATTGGTG
* ***** * * ** ** * *
180834 TATCCCCGATGAAATAACGAGGTTGGAGTATCATCGATT-GTGAAAAATTGGTAA
1 TTTTGGAAAT-AAA-ATCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTGGT-G
* *
180888 TTTTGGAAATAAAATCGGAGTTGGAGTATCGCCGATTAAAGGAAAATTGGTG
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
* * *
180940 TTTTGAAAATAAAATTGGGGTTGGAGTATCCCCAATTA
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTA
180978 TGAACAATTG
Statistics
Matches: 220, Mismatches: 65, Indels: 30
0.70 0.21 0.10
Matches are distributed among these distances:
49 1 0.00
50 2 0.01
51 77 0.35
52 88 0.40
53 20 0.09
54 12 0.05
55 5 0.02
56 13 0.06
57 1 0.00
58 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (52 bp):
TTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
Found at i:180742 original size:51 final size:50
Alignment explanation
Indices: 180592--180812 Score: 237
Period size: 51 Copynumber: 4.3 Consensus size: 50
180582 GAAATAACGA
** *
180592 GGTTGGAGTATCCTTGATTGTAAAAATTTAGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAAAA-TTAGTG-TTTTGGAAATAAAATCAG
* * * * *
180644 AGTTGGAGTATCCCCGATTAAAG-GAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAATTAGTGTTTTGGAAATAAAATCAG
*
180696 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTGGAAATAAAAACAG
1 GGTTGGAGTATCCCCGATTGT-GAAAATTAGTGTTTTGGAAATAAAATCAG
* * * * * *
180747 GGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAATTAGTGTTTTGGAAATAAAATCAG
180798 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
180813 TCGGAGGTAA
Statistics
Matches: 142, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 2 0.01
51 80 0.56
52 49 0.35
53 5 0.04
54 4 0.03
55 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTGTGAAAATTAGTGTTTTGGAAATAAAATCAG
Found at i:180851 original size:28 final size:28
Alignment explanation
Indices: 180795--180865 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
180785 GAAATAAAGT
** **
180795 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
180823 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
180851 CGAGGTTGGAGTATC
1 CGGGGTTGGAGTATC
180866 ATCGATTGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:180949 original size:262 final size:262
Alignment explanation
Indices: 180484--180972 Score: 809
Period size: 262 Copynumber: 1.9 Consensus size: 262
180474 GAAAATAACG
*
180484 GGGTTGGAGTATCCCCAATTACGAGAAATTAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCC
* *
180549 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGACGAAATAACGAGGTTGGAGTATCCTTGATTGTA
66 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGACGAAATAACGAGGTTGGAGTATCATCGATTGTA
**
180614 AAAATTTAGTGTTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
131 AAAATTTAGTAATTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
180679 TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTGGAAATAAAAA
196 TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTGGAAATAAAAA
180744 CA
261 CA
* * ** * *
180746 GGGTTGGAGTATCCTCGATTGTGAGAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCC
*
180811 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCATCGATTGTG
66 CCTCGGAGGTAACGGGGTTGGAGTATCCCCGACGAAATAACGAGGTTGGAGTATCATCGATTGT-
* * *
180876 AAAAA-TTGGTAATTTTGGAAATAAAATCGGAGTTGGAGTATCGCCGATTAAAGGAAAATTGGTG
130 AAAAATTTAGTAATTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
**
180940 TTTTGAAAATAAAATTGGGGTTGGAGTATCCCC
195 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCC
180973 AATTATGAAC
Statistics
Matches: 209, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
262 204 0.98
263 5 0.02
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (262 bp):
GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGGAAATAAAGCCGAGGTTGGAGTATCC
CCTCGGAGGTAACGGGGTTGGAGTATCCCCGACGAAATAACGAGGTTGGAGTATCATCGATTGTA
AAAATTTAGTAATTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
TTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTGGAAATAAAAA
CA
Found at i:181453 original size:107 final size:107
Alignment explanation
Indices: 181267--181484 Score: 427
Period size: 107 Copynumber: 2.0 Consensus size: 107
181257 CGAGTAGAAA
181267 AAATCCTTGAACTCGGGTGTATGGCGCTGTTAGCAGAGCTTATGAGGAAAACGGTATATCGAACT
1 AAATCCTTGAACTCGGGTGTATGGCGCTGTTAGCAGAGCTTATGAGGAAAACGGTATATCGAACT
*
181332 TTGAAAAATCACCTCGGAGTCATTTGTTATCAAAAAAATTAC
66 TTGAAAAATCACCTCGGAGTCATTTGTTATAAAAAAAATTAC
181374 AAATCCTTGAACTCGGGTGTATGGCGCTGTTAGCAGAGCTTATGAGGAAAACGGTATATCGAACT
1 AAATCCTTGAACTCGGGTGTATGGCGCTGTTAGCAGAGCTTATGAGGAAAACGGTATATCGAACT
181439 TTGAAAAATCACCTCGGAGTCATTTGTTATAAAAAAAATTAC
66 TTGAAAAATCACCTCGGAGTCATTTGTTATAAAAAAAATTAC
181481 AAAT
1 AAAT
181485 TATACCTTTA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 110 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (107 bp):
AAATCCTTGAACTCGGGTGTATGGCGCTGTTAGCAGAGCTTATGAGGAAAACGGTATATCGAACT
TTGAAAAATCACCTCGGAGTCATTTGTTATAAAAAAAATTAC
Found at i:183465 original size:13 final size:13
Alignment explanation
Indices: 183447--183472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
183437 ACAAAGATCG
183447 ATGTATCGATACA
1 ATGTATCGATACA
183460 ATGTATCGATACA
1 ATGTATCGATACA
183473 TGTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:183549 original size:19 final size:19
Alignment explanation
Indices: 183525--183610 Score: 58
Period size: 19 Copynumber: 4.7 Consensus size: 19
183515 AACGATACAT
183525 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
183544 TGTATCCATAC---A--T-
1 TGTATCGATACAAAACTTA
*
183557 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
* ** *
183576 TGTATCCATACATTTACTGAA
1 TGTATCGATACA-AAACT-TA
183597 TGTATCGATACAAA
1 TGTATCGATACAAA
183611 TTATTGGAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
13 10 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 21 0.42
20 3 0.06
21 12 0.24
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:183560 original size:32 final size:32
Alignment explanation
Indices: 183519--183589 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
183509 CTTCGTAACG
183519 ATACATTGTATCGATACAAAACTTATGTATCC
1 ATACATTGTATCGATACAAAACTTATGTATCC
*
183551 ATACATTGTATCGATACAACACTTATGTATCC
1 ATACATTGTATCGATACAAAACTTATGTATCC
183583 ATACATT
1 ATACATT
183590 TACTGAATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTTATGTATCC
Found at i:184428 original size:26 final size:26
Alignment explanation
Indices: 184399--184486 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
184389 GTGTGGGCTT
184399 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGCGTCCTGCTCTTTGAGGAC
* ** * * *
184425 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGCGTCCTGC-TCTT-TGAGGAC
*
184452 TTTGAAAAGCGTCCTGCTCTTTGAGGAC
1 --TGAAAGGCGTCCTGCTCTTTGAGGAC
184480 TGAAAGG
1 TGAAAGG
184487 TGCCACCAAT
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
25 3 0.07
26 17 0.40
27 5 0.12
28 5 0.12
29 10 0.23
30 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (26 bp):
TGAAAGGCGTCCTGCTCTTTGAGGAC
Found at i:184437 original size:55 final size:56
Alignment explanation
Indices: 184353--185355 Score: 1016
Period size: 55 Copynumber: 17.3 Consensus size: 56
184343 ATAAAGTGTA
* * * *
184353 TCCTGCTCCTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
184408 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA-GCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
* * *
184463 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
* *
184518 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GCG
* * **
184579 TTCTGCTCTTTGAGGACTG-AAGGTGGCACCAACTTGTGTGGGCTTTAAAAGAAAAGATG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAAGGCG
*
184638 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTATGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAAGGCG
* *
184697 -CCTTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAGGTG
1 TCC-TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
* * *
184752 TCCTCCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GCG
* **
184813 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
* * *
184868 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGAGCTTTG-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
* * *
184923 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-----GCG
* * **
184984 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
* * * * * *
185039 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTATGTGGGTTTTGAAAAAAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTG-----AAAAGGCG
* *
185100 TCCTGCTCTTTGAGGATTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGACG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAAGGCG
* *
185159 TTCTACTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAAGGCG
185218 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAAGGCG
* * *
185277 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACGTGTGTGGGCTTTAAAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAAGGCG
185338 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
185356 AAAAAGTGGA
Statistics
Matches: 825, Mismatches: 73, Indels: 94
0.83 0.07 0.09
Matches are distributed among these distances:
54 11 0.01
55 304 0.37
56 29 0.04
58 2 0.00
59 207 0.25
60 103 0.12
61 162 0.20
64 7 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGCG
Found at i:184802 original size:29 final size:29
Alignment explanation
Indices: 184721--184802 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 29
184711 GACTGGAAAA
184721 TGCCACCAACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
* *
184750 TGTCCTCC-TCTT-TG-GGGAC--TGAAAGG
1 TG-CCACCAACTTGTGTGGG-CTTTGAAAGG
184776 TGCCACCAACTTGTGTGGGCTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAA
184803 AGAAAAAGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
25 4 0.10
26 12 0.29
27 6 0.14
28 6 0.14
29 10 0.24
30 4 0.10
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (29 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGG
Found at i:184919 original size:171 final size:170
Alignment explanation
Indices: 184350--185355 Score: 1261
Period size: 171 Copynumber: 5.8 Consensus size: 170
184340 AAAATAAAGT
* * *
184350 GTATCCTGCTCCTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAGGCGTCCTG
1 GTATCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTG
*
184413 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----GAAAAGCGTCCTGCTCTTT
65 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCATCCTGCTCTTT
*
184474 GAGGACTGAAAGGTGCCACCAATTTGTGTGGGCTTTAAGAG
130 GAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAG
* *
184515 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCAT
1 GTATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG-----GCGT
* *
184580 TCTGCTCTTTGAGGACTG-AAGGTGGCACCAACTTGTGTGGGCTTTAAAAGAAAAG-ATGTCCTG
61 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCA--TCCTG
*
184643 CTCTTTGAGGACT-AAAGGTGCCACCAACTTGTATGGGCTTTAAAAGAAAAG
124 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AG
** * *
184694 G-CGCCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGTGTCCTC
1 GTATCC-TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTG
*
184757 CTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
65 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAAGCATCCTGCTCT
184822 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAG
128 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAG
* *
184865 GTATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTTG-AAAGGTGTCCTGC
1 GTATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGC
* *
184929 TCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTT
66 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-AAAAGCATCCTGCTCTT
*
184994 TGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAG
129 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAG
* * * * *
185036 GTATCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTATGTGGGTTTTGAAAAAAAAAAGCAT
1 GTATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-----AAAAGGCGT
* * * *
185101 CCTGCTCTTTGAGGATTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGACGTTCTAC
61 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG-CATCCTGC
185165 TCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAG
125 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AG
** **
185215 GCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTC
1 GTATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----GAAAAGGCGTC
* *
185279 CTGCTCTTTGAGGACTGGAAA-ATGCCACCAACGTGTGTGGGCTTTAAAAGAAAAAGGCATCCTG
62 CTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAA-GCATCCTG
185343 CTCTTTGAGGACT
124 CTCTTTGAGGACT
185356 AAAAAGTGGA
Statistics
Matches: 742, Mismatches: 54, Indels: 76
0.85 0.06 0.09
Matches are distributed among these distances:
165 42 0.06
166 8 0.01
170 26 0.04
171 231 0.31
172 2 0.00
173 17 0.02
174 93 0.13
175 63 0.08
176 64 0.09
177 45 0.06
178 58 0.08
179 91 0.12
180 1 0.00
182 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (170 bp):
GTATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGGCGTCCTGC
TCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGCATCCTGCTCTTTG
AGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAG
Found at i:186341 original size:14 final size:13
Alignment explanation
Indices: 186322--186379 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
186312 AAGCAGATTC
186322 TTCTTTTTTCTTTT
1 TTCTTTTTT-TTTT
186336 TTCTTTGTTTTTTT
1 TTCTTT-TTTTTTT
*
186350 TTGGTTTTTTTTTT
1 TT-CTTTTTTTTTT
*
186364 TGCTTTTGTTTTTT
1 TTCTTTT-TTTTTT
186378 TT
1 TT
186380 AGAAAAGAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 4 0.11
14 27 0.73
15 6 0.16
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:186364 original size:18 final size:18
Alignment explanation
Indices: 186325--186379 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
186315 CAGATTCTTC
186325 TTTTTT-CTTTT-TTCTTT
1 TTTTTTGCTTTTGTT-TTT
*
186342 GTTTTTT--TTTGGTTTTT
1 -TTTTTTGCTTTTGTTTTT
186359 TTTTTTGCTTTTGTTTTT
1 TTTTTTGCTTTTGTTTTT
186377 TTT
1 TTT
186380 AGAAAAGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 20 0.62
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.85
Consensus pattern (18 bp):
TTTTTTGCTTTTGTTTTT
Found at i:195166 original size:79 final size:78
Alignment explanation
Indices: 195063--195266 Score: 266
Period size: 79 Copynumber: 2.6 Consensus size: 78
195053 GATAATAACG
* * * * *
195063 GGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAGTTATGAAAAATCGATGA-T
1 GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTACGAAAAATCAAT-ATT
* **
195127 TAGGAAATAAATTC
65 TAGAAAATAAAGCC
*
195141 GGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTACGAGAAATCAATATT
1 GGG-TTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATT
*
195206 TTGAAAATAAAGCC
65 TAGAAAATAAAGCC
**
195220 AGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCAA
1 -GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAA
195267 CGAAATAATG
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
78 4 0.04
79 104 0.94
80 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTACGAAAAATCAATATTT
AGAAAATAAAGCC
Found at i:195425 original size:51 final size:51
Alignment explanation
Indices: 195278--195497 Score: 230
Period size: 51 Copynumber: 4.3 Consensus size: 51
195268 GAAATAATGA
* * *
195278 GGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATC-G
1 GGTTGGAGTATCCCCAATTGTGAAAAATTAGTG-TTTTGGAAATAAAACCAG
* * * * *
195329 GAGTTGGAGTATCCCCGA-TGAAAGGAAAATTGGTGTTTTGAAAATAAAACCAG
1 G-GTTGGAGTATCCCCAATTG--TGAAAAATTAGTGTTTTGGAAATAAAACCAG
* *
195382 GGTTAGAGTATCCCCAATTGTGAAAAATTAGTGTTTTGGAAATAAAAACAG
1 GGTTGGAGTATCCCCAATTGTGAAAAATTAGTGTTTTGGAAATAAAACCAG
* * * * * * *
195433 GGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGGAGTATCCCCAATTGTGAAAAATTAGTGTTTTGGAAATAAAACCAG
195484 GGTTGGA-TATCCCC
1 GGTTGGAGTATCCCC
195498 TCGAAGGTAA
Statistics
Matches: 142, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
50 7 0.05
51 78 0.55
52 42 0.30
53 15 0.11
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATTGTGAAAAATTAGTGTTTTGGAAATAAAACCAG
Found at i:195545 original size:261 final size:262
Alignment explanation
Indices: 195170--195671 Score: 810
Period size: 261 Copynumber: 1.9 Consensus size: 262
195160 GGAAATAACG
195170 GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTATCC
* * *
195235 CCTCGGAGGTAACGGGGTTGGAGTATCCCCAACGAAATAATGAGGTTGGAGTATCCTCAATTGTG
66 CCTCGAAGGTAACGGGGTTAGAGTATCCCCAACGAAATAACGAGGTTGGAGTATCCTCAATTGTG
*
195300 AAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGA-TGAAAGGAAAATTGGTG
131 AAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTG-AAGGAAAATTGGTG
* *
195364 TTTTGAAAATAAAACCAGGGTTAGAGTATCCCCAATTGTGAAAAATTAGTGTTTTGGAAATAAAA
195 TTTTGAAAAAAAAACCAGGGTTAGAGTATCCCCAATTATGAAAAATTAGTGTTTTGGAAATAAAA
195429 ACA
260 ACA
* ** * *
195432 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGA-TATCC
1 GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTATCC
* *
195496 CCTCGAAGGTAACGGGGTTAGAGTATCCCCAATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
66 CCTCGAAGGTAACGGGGTTAGAGTATCCCCAACGAAATAACGAGGTTGGAGTATCCTCAATTGTG
*
195561 AAAAATTGGTGTTTTTTAAAATAAAATCGGAGTTGGAGTATCCCCGATTGAAGGAAAATTGGTGT
131 AAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTGAAGGAAAATTGGTGT
* * * * *
195626 TTTGAAAAAAAAATCGGGGTTGGAGTATCCCCGATTATGAACAATT
196 TTTGAAAAAAAAACCAGGGTTAGAGTATCCCCAATTATGAAAAATT
195672 GAGAAACTTA
Statistics
Matches: 220, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
261 164 0.75
262 56 0.25
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (262 bp):
GGGTTGGAGTATCCCCAATTACGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTATCC
CCTCGAAGGTAACGGGGTTAGAGTATCCCCAACGAAATAACGAGGTTGGAGTATCCTCAATTGTG
AAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTGAAGGAAAATTGGTGT
TTTGAAAAAAAAACCAGGGTTAGAGTATCCCCAATTATGAAAAATTAGTGTTTTGGAAATAAAAA
CA
Found at i:195598 original size:52 final size:51
Alignment explanation
Indices: 195540--195672 Score: 176
Period size: 52 Copynumber: 2.6 Consensus size: 51
195530 AAATAACGAG
* * *
195540 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTTAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGAAAAAAAAATCGGA
* * *
195592 GTTGGAGTATCCCCGATTGAAGGAAAATTGGTGTTTTGAAAAAAAAATCGGG
1 GTTGGAGTATCCCCGATTG-TGAAAAATTGGTGTTTTGAAAAAAAAATCGGA
* *
195644 GTTGGAGTATCCCCGATTATGAACAATTG
1 GTTGGAGTATCCCCGATTGTGAAAAATTG
195673 AGAAACTTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 7 0.10
52 52 0.74
53 11 0.16
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAAAAAAATCGGA
Found at i:198046 original size:13 final size:13
Alignment explanation
Indices: 198028--198053 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
198018 ACAAAGATCG
198028 ATGTATCGATACA
1 ATGTATCGATACA
198041 ATGTATCGATACA
1 ATGTATCGATACA
198054 TGTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:198064 original size:21 final size:21
Alignment explanation
Indices: 198040--198081 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
198030 GTATCGATAC
198040 AATGTATCGATACATGTCCTT
1 AATGTATCGATACATGTCCTT
*
198061 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATGTCCTT
198082 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATGTCCTT
Found at i:198130 original size:19 final size:19
Alignment explanation
Indices: 198106--198193 Score: 158
Period size: 19 Copynumber: 4.6 Consensus size: 19
198096 AGCGATACAT
198106 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
198125 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
198144 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
* *
198163 CGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
198182 TGTATCGATACA
1 TGTATCGATACA
198194 TTTAATGAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:198642 original size:13 final size:13
Alignment explanation
Indices: 198624--198680 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
198614 ATAAAAATGT
198624 TGTATCGATACAA
1 TGTATCGATACAA
198637 TGTATCGATACATAA
1 TGTATCGATAC--AA
198652 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
198669 TGTATCGATACA
1 TGTATCGATACA
198681 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:198661 original size:19 final size:17
Alignment explanation
Indices: 198600--198699 Score: 72
Period size: 19 Copynumber: 5.9 Consensus size: 17
198590 AATTTCAACG
198600 ATTTGTATCGATACATAAAA
1 ATTTGTATCGATACAT---A
198620 ATGTTGTATCGATAC--A
1 AT-TTGTATCGATACATA
198636 A--TGTATCGATACATA
1 ATTTGTATCGATACATA
198651 AGTGTTGTATCGATAC--A
1 A-T-TTGTATCGATACATA
198668 A--TGTATCGATACATA
1 ATTTGTATCGATACATA
198683 AGTTTTGTATCGATACA
1 A--TTTGTATCGATACA
198700 ATATAAGATA
Statistics
Matches: 67, Mismatches: 0, Indels: 27
0.71 0.00 0.29
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
16 2 0.03
17 2 0.03
19 23 0.34
20 2 0.03
21 12 0.18
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (17 bp):
ATTTGTATCGATACATA
Found at i:198662 original size:32 final size:32
Alignment explanation
Indices: 198603--198701 Score: 162
Period size: 32 Copynumber: 3.0 Consensus size: 32
198593 TTCAACGATT
*
198603 TGTATCGATACATAAAAATGTTGTATCGATACAA
1 TGTATCGATACAT--AAGTGTTGTATCGATACAA
198637 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
198669 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
198701 T
1 T
198702 ATAAGATACT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 50 0.79
34 13 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:198819 original size:52 final size:50
Alignment explanation
Indices: 198755--198903 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 50
198745 ACCAATACAT
* * * *
198755 TGTATCGATACACTGATCTTTGTATCGATACATGCAAGCAAATTTGTCGAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
198807 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
198859 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATTT
198904 TCATATTTCG
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:207008 original size:41 final size:41
Alignment explanation
Indices: 206962--207039 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
206952 AGAATTGTCC
* *
206962 TTGATCTTGAGGAAAGTGAGAAAACATGCATCTAGCAGTTT
1 TTGATCTTGAGAAAAATGAGAAAACATGCATCTAGCAGTTT
*
207003 TTGATCTTGAGAAAAATGAGAAAACATGTATCTAGCA
1 TTGATCTTGAGAAAAATGAGAAAACATGCATCTAGCA
207040 CTTCTAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (41 bp):
TTGATCTTGAGAAAAATGAGAAAACATGCATCTAGCAGTTT
Found at i:211776 original size:19 final size:21
Alignment explanation
Indices: 211730--211783 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
211720 TTTCAACAAT
211730 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAACAGTAA
* *
211751 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAACAGTAA
211770 TTGTATCGATACAA
1 TTGTATCGATACAA
211784 TGTATCACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TTGTATCGATACAAACAGTAA
Found at i:218773 original size:52 final size:52
Alignment explanation
Indices: 218695--218823 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
218685 CGAAATATGA
*
218695 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
*
218747 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGAGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
*
218799 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
218824 ATGTATCGAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGAGC
Found at i:218915 original size:32 final size:33
Alignment explanation
Indices: 218874--218942 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
218864 GGCAGTAGCT
218874 TACATTGTATCGATACAAAAC-TTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
*
218906 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
218939 TACA
1 TACA
218943 AATCGTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
TACATTGTATCGATACAAAACTTTATGTATCGA
Found at i:218916 original size:13 final size:13
Alignment explanation
Indices: 218898--218922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218888 ACAAAACTTA
218898 TGTATCGATACAT
1 TGTATCGATACAT
218911 TGTATCGATACA
1 TGTATCGATACA
218923 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:225875 original size:18 final size:18
Alignment explanation
Indices: 225854--225893 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
225844 TTTTTAAAAA
225854 AAATT-ATTATTTTATTTC
1 AAATTGATTATTTT-TTTC
*
225872 AAATTGTTTATTTTTTTC
1 AAATTGATTATTTTTTTC
225890 AAAT
1 AAAT
225894 CATCATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (18 bp):
AAATTGATTATTTTTTTC
Found at i:227409 original size:17 final size:17
Alignment explanation
Indices: 227387--227420 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
227377 AAATAGTGGT
227387 TAGTTTTTGGGAGAAAA
1 TAGTTTTTGGGAGAAAA
227404 TAGTTTTTGGGAGAAAA
1 TAGTTTTTGGGAGAAAA
227421 CGCCTATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (17 bp):
TAGTTTTTGGGAGAAAA
Found at i:232997 original size:58 final size:58
Alignment explanation
Indices: 232934--233049 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
232924 CGTTAAAAGG
* *
232934 TTTTTTGTTCTAGCAAA-TTAATTTTATCCCTTTTGATTTAGATTTAATGGTAAATTGC
1 TTTTTTGTTCTAG-AAAGTTAATTGTATCCCTTTTGATTTAGATTTAATGGCAAATTGC
232992 TTTTTTGTTCTAGAAAGTTAATTGTATCCCTTTTGATTTAGATTTAATGGCAAATTGC
1 TTTTTTGTTCTAGAAAGTTAATTGTATCCCTTTTGATTTAGATTTAATGGCAAATTGC
233050 ACCACATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
57 3 0.05
58 52 0.95
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (58 bp):
TTTTTTGTTCTAGAAAGTTAATTGTATCCCTTTTGATTTAGATTTAATGGCAAATTGC
Found at i:233136 original size:2 final size:2
Alignment explanation
Indices: 233129--233160 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
233119 ACCCATATAC
*
233129 GT GT GT GT GT GT GT GT GT GG GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
233161 ATGTATCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.53, T:0.47
Consensus pattern (2 bp):
GT
Found at i:233173 original size:2 final size:2
Alignment explanation
Indices: 233168--233194 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
233158 TGTATGTATC
233168 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
233195 TTTGAGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:234186 original size:11 final size:11
Alignment explanation
Indices: 234170--234194 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
234160 GCACTTTGAA
234170 CTACACCCATC
1 CTACACCCATC
234181 CTACACCCATC
1 CTACACCCATC
234192 CTA
1 CTA
234195 ATTTTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.52, G:0.00, T:0.20
Consensus pattern (11 bp):
CTACACCCATC
Found at i:234306 original size:172 final size:172
Alignment explanation
Indices: 234020--234355 Score: 672
Period size: 172 Copynumber: 2.0 Consensus size: 172
234010 TGGGTATGTG
234020 CTAATTTTTAAGAATGGATATGGCTTAGATACATCTTGGGAATGCCTTGGCCAAATTTAACACTG
1 CTAATTTTTAAGAATGGATATGGCTTAGATACATCTTGGGAATGCCTTGGCCAAATTTAACACTG
234085 AAACTCTATGTTTTTATGTCCTATGGCATATTTCCCTTCCCTTTTTTCATCGTCAGCTTGCTTTC
66 AAACTCTATGTTTTTATGTCCTATGGCATATTTCCCTTCCCTTTTTTCATCGTCAGCTTGCTTTC
234150 TTCAAATATTGCACTTTGAACTACACCCATCCTACACCCATC
131 TTCAAATATTGCACTTTGAACTACACCCATCCTACACCCATC
234192 CTAATTTTTAAGAATGGATATGGCTTAGATACATCTTGGGAATGCCTTGGCCAAATTTAACACTG
1 CTAATTTTTAAGAATGGATATGGCTTAGATACATCTTGGGAATGCCTTGGCCAAATTTAACACTG
234257 AAACTCTATGTTTTTATGTCCTATGGCATATTTCCCTTCCCTTTTTTCATCGTCAGCTTGCTTTC
66 AAACTCTATGTTTTTATGTCCTATGGCATATTTCCCTTCCCTTTTTTCATCGTCAGCTTGCTTTC
234322 TTCAAATATTGCACTTTGAACTACACCCATCCTA
131 TTCAAATATTGCACTTTGAACTACACCCATCCTA
234356 TGTGGAGAAG
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 164 1.00
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (172 bp):
CTAATTTTTAAGAATGGATATGGCTTAGATACATCTTGGGAATGCCTTGGCCAAATTTAACACTG
AAACTCTATGTTTTTATGTCCTATGGCATATTTCCCTTCCCTTTTTTCATCGTCAGCTTGCTTTC
TTCAAATATTGCACTTTGAACTACACCCATCCTACACCCATC
Found at i:240334 original size:8 final size:8
Alignment explanation
Indices: 240323--240360 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
240313 ATATCTTCTC
*
240323 TCTTTCTT
1 TCTTTTTT
240331 TCTTTTTT
1 TCTTTTTT
240339 TCTTTTTT
1 TCTTTTTT
240347 TCTTTTTT
1 TCTTTTTT
240355 TCTTTT
1 TCTTTT
240361 ACTCTTCTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TCTTTTTT
Found at i:240366 original size:16 final size:16
Alignment explanation
Indices: 240331--240366 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
240321 TCTCTTTCTT
**
240331 TCTTTTTTTCTTTTTT
1 TCTTTTTTTCTTTTAC
240347 TCTTTTTTTCTTTTAC
1 TCTTTTTTTCTTTTAC
240363 TCTT
1 TCTT
240367 CTGCCAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTTTTTCTTTTAC
Found at i:243463 original size:40 final size:40
Alignment explanation
Indices: 243412--243489 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
243402 AAAAAAATTT
* *
243412 AAACTTGTAACTTTTACCCGAATAAATTTACAAACTTTTA
1 AAACTTGTAACTTTTACCCAAACAAATTTACAAACTTTTA
243452 AAACTTGTAACTTTTACCCAAACAAATTTACAAACTTT
1 AAACTTGTAACTTTTACCCAAACAAATTTACAAACTTT
243490 CCTCGCACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (40 bp):
AAACTTGTAACTTTTACCCAAACAAATTTACAAACTTTTA
Found at i:245646 original size:22 final size:21
Alignment explanation
Indices: 245608--245650 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
245598 GATCTTAAAA
245608 AAAAATAAAAAATTTTACTAAT
1 AAAAATAAAAAATTTTA-TAAT
*
245630 AAAAATAATATAA-TTTATAAT
1 AAAAATAA-AAAATTTTATAAT
245651 TTTTACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 12 0.63
23 3 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATAAAAAATTTTATAAT
Found at i:250702 original size:6 final size:6
Alignment explanation
Indices: 250691--250715 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
250681 AAATTAACAG
250691 GAAGAT GAAGAT GAAGAT GAAGAT G
1 GAAGAT GAAGAT GAAGAT GAAGAT G
250716 CCTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:251088 original size:2 final size:2
Alignment explanation
Indices: 251083--251109 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
251073 TGTGCGTATG
251083 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
251110 CCTATTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:251518 original size:15 final size:16
Alignment explanation
Indices: 251483--251520 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
251473 TATATTTATG
251483 TTATATTT--ATATTT
1 TTATATTTAAATATTT
251497 TTATATTTAAATATTT
1 TTATATTTAAATATTT
251513 TT-TATTTA
1 TTATATTTA
251521 TATAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 6 0.27
16 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTTAAATATTT
Found at i:251570 original size:32 final size:33
Alignment explanation
Indices: 251513--251586 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
251503 TTAAATATTT
251513 TTTAT-TTATATAAAATTTAAAATATTAATA-A
1 TTTATATTATATAAAATTTAAAATATTAATATA
**
251544 TTTATATTATA-AAAATTTTATTATATTAATATA
1 TTTATATTATATAAAA-TTTAAAATATTAATATA
*
251577 TTTTTATTAT
1 TTTATATTAT
251587 TTTTATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 9 0.24
32 18 0.49
33 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTATATTATATAAAATTTAAAATATTAATATA
Found at i:251623 original size:27 final size:26
Alignment explanation
Indices: 251564--251626 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
251554 AAAAATTTTA
251564 TTATATT-AATATATTTTTATTATTT
1 TTATATTAAATATATTTTTATTATTT
251589 TTATATTAAATATATTTTATATTATATT
1 TTATATTAAATATATTTT-TATTAT-TT
251617 TTA-ATTAAAT
1 TTATATTAAAT
251627 TTTCTTGTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
25 7 0.20
26 10 0.29
27 13 0.37
28 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATATTAAATATATTTTTATTATTT
Found at i:251981 original size:27 final size:27
Alignment explanation
Indices: 251890--252078 Score: 101
Period size: 27 Copynumber: 7.1 Consensus size: 27
251880 TATTTAAAAT
*
251890 TTTTAGTTAATTT-TATATTTATA-TAAA
1 TTTTA-TT-ATTTATATATTTATATTATA
* * * **
251917 TTTTAATATATAATTTATTTATAAAAT-
1 TTTTATTAT-TTATATATTTATATTATA
**
251944 TTTTAAAATTTATATATTTATATTATA
1 TTTTATTATTTATATATTTATATTATA
*
251971 TTTTATTATTTA-ATATATCATATT-TA
1 TTTTATTATTTATATAT-TTATATTATA
* * **
251997 TGATTATTTTTTATATAAAT-TATTATA
1 T-TTTATTATTTATATATTTATATTATA
*
252024 TATTTATT-TATATTATATTTATATTATA
1 T-TTTATTATTTA-TATATTTATATTATA
*
252052 TTTTAATTATTT-T-T-TTGATATTATA
1 TTTT-ATTATTTATATATTTATATTATA
252077 TT
1 TT
252079 CGTATCTTAT
Statistics
Matches: 125, Mismatches: 25, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
25 14 0.11
26 30 0.24
27 64 0.51
28 15 0.12
29 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTATTATTTATATATTTATATTATA
Found at i:251994 original size:33 final size:33
Alignment explanation
Indices: 251954--252050 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 33
251944 TTTTAAAATT
251954 TATATATTTATATTATATTTTATTATT-TAATA
1 TATATATTTATATTATATTTTATTATTATAATA
* *
251986 TATCATATTTATGATTATTTTTTATATAAATTATTATA
1 TAT-ATATTTAT-ATTATATTTTAT-T--ATTATAATA
*
252024 TATTTATTTATATTATATTTATATTAT
1 TATATATTTATATTATATTT-TATTAT
252051 ATTTTAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
32 3 0.06
33 8 0.15
34 13 0.24
35 1 0.02
36 9 0.17
37 13 0.24
38 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (33 bp):
TATATATTTATATTATATTTTATTATTATAATA
Found at i:252060 original size:11 final size:12
Alignment explanation
Indices: 251953--252078 Score: 79
Period size: 12 Copynumber: 10.6 Consensus size: 12
251943 TTTTTAAAAT
251953 TTATATATTTATA
1 TTATAT-TTTATA
251966 TTATA-TTT-TA
1 TTATATTTTATA
*
251976 TTAT-TTAATATA
1 TTATATT-TTATA
*
251988 TCATA-TTTATGA
1 TTATATTTTAT-A
*
252000 TTATTTTTTATA
1 TTATATTTTATA
*
252012 -TAAATTATTATA
1 TTATATT-TTATA
*
252024 -TATTTATTTATA
1 TTATAT-TTTATA
252036 TTATA-TTTATA
1 TTATATTTTATA
252047 TTATATTTTA-A
1 TTATATTTTATA
*
252058 TTATTTTTTTGATA
1 TTA-TATTTT-ATA
252072 TTATATT
1 TTATATT
252079 CGTATCTTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
10 7 0.08
11 26 0.30
12 33 0.38
13 18 0.20
14 4 0.05
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:252061 original size:16 final size:15
Alignment explanation
Indices: 251956--252063 Score: 51
Period size: 15 Copynumber: 7.7 Consensus size: 15
251946 TTAAAATTTA
*
251956 TATATTTATATTATAT
1 TATAATTAT-TTATAT
*
251972 T-TTATTATTTA-AT
1 TATAATTATTTATAT
*
251985 ATATCA-TATTTATGAT
1 -TATAATTATTTAT-AT
252001 TAT--TT-TTTATA-
1 TATAATTATTTATAT
252012 TA-AATTA-TTATA-
1 TATAATTATTTATAT
252024 TAT--TTATTTATAT
1 TATAATTATTTATAT
*
252037 TATATTTATATTATAT
1 TATAATTAT-TTATAT
*
252053 TTTAATTATTT
1 TATAATTATTT
252064 TTTTGATATT
Statistics
Matches: 73, Mismatches: 5, Indels: 29
0.68 0.05 0.27
Matches are distributed among these distances:
11 5 0.07
12 15 0.21
13 10 0.14
14 11 0.15
15 16 0.22
16 16 0.22
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (15 bp):
TATAATTATTTATAT
Found at i:252728 original size:18 final size:17
Alignment explanation
Indices: 252691--252738 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
252681 AATTGGTTTA
*
252691 ATTTA-ATTTAAATTAAT
1 ATTTATATTTAAA-AAAT
252708 ATTTAATATTTAAAAAAT
1 ATTT-ATATTTAAAAAAT
*
252726 ATTTTTATTTAAA
1 ATTTATATTTAAA
252739 TTTAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 12 0.44
18 8 0.30
19 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTATATTTAAAAAAT
Found at i:252767 original size:29 final size:30
Alignment explanation
Indices: 252708--252772 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
252698 TTAAATTAAT
* * * *
252708 ATTTAATATTTAAAAAATATTTTTATTTAA
1 ATTTAATATATAAAAAATATATTAATATAA
*
252738 ATTTAAT-TATAAAATATATATTAATATAA
1 ATTTAATATATAAAAAATATATTAATATAA
*
252767 AATTAA
1 ATTTAA
252773 ATTTTTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTTAATATATAAAAAATATATTAATATAA
Found at i:252804 original size:13 final size:13
Alignment explanation
Indices: 252786--252838 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
252776 TTTAATTAAT
252786 TATAAATAATAAA
1 TATAAATAATAAA
252799 TATAAATAATATAA
1 TATAAATAATA-AA
252813 -ATAAATTAATCAAA
1 TATAAA-TAAT-AAA
252827 T-TAAA-AATAAA
1 TATAAATAATAAA
252838 T
1 T
252839 TTAATAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.11
12 3 0.08
13 16 0.44
14 12 0.33
15 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAATAATAAA
Found at i:252975 original size:11 final size:11
Alignment explanation
Indices: 252959--252984 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
252949 GGGCAATGCC
252959 ATTGATTGCAA
1 ATTGATTGCAA
252970 ATTGATTGCAA
1 ATTGATTGCAA
252981 ATTG
1 ATTG
252985 TCATGATGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (11 bp):
ATTGATTGCAA
Found at i:254205 original size:21 final size:20
Alignment explanation
Indices: 254157--254214 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
254147 TATTTATATC
*
254157 ATAAAATATTAA-ATAAAATT
1 ATAAAATA-TAATATAAAATA
254177 ATATAAATATAATATAAAATA
1 ATA-AAATATAATATAAAATA
254198 ATTAAAATATAATATAA
1 A-TAAAATATAATATAA
254215 TATTAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.18
21 26 0.76
22 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAAATATAATATAAAATA
Found at i:254233 original size:26 final size:25
Alignment explanation
Indices: 254151--254233 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
254141 TATCAATATT
* * *
254151 TATATCATAAAATATTAA-ATAAAA
1 TATATAATATAATATTAATATTAAA
*
254175 TTATATAAATATAATATAAAATAATTAAA
1 -TATAT-AATATAATAT-TAAT-ATTAAA
254204 -ATATAATATAATATTAATATTTAAA
1 TATATAATATAATATTAATA-TTAAA
254229 TATAT
1 TATAT
254234 CAAAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
24 1 0.02
25 13 0.28
26 22 0.47
27 6 0.13
29 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TATATAATATAATATTAATATTAAA
Found at i:254313 original size:18 final size:18
Alignment explanation
Indices: 254277--254329 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
254267 AAATTTTTAT
*
254277 AAATATA-AAATATATTA
1 AAATATATAAATATAATA
*
254294 AAAT-TATTATATATAATA
1 AAATATA-TAAATATAATA
254312 AAATATATAAATATAATA
1 AAATATATAAATATAATA
254330 TTAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 2 0.07
17 4 0.13
18 22 0.73
19 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATATAAATATAATA
Found at i:254320 original size:16 final size:16
Alignment explanation
Indices: 254168--254320 Score: 51
Period size: 16 Copynumber: 9.8 Consensus size: 16
254158 TAAAATATTA
254168 AATAAAAT-TATATA-
1 AATAAAATATATATAT
* *
254182 AATATAATATA-AAAT
1 AATAAAATATATATAT
254197 AATTAAAATATA-ATAT
1 AA-TAAAATATATATAT
* * *
254213 AATATTAATATTTAAAT
1 AATA-AAATATATATAT
* *
254230 ATATCAAA-A-ATATAG
1 A-ATAAAATATATATAT
254245 AATATAAAT-TATTCATAT
1 AATA-AAATATA-T-ATAT
* * *
254263 ATTAAAATTTTTATA-
1 AATAAAATATATATAT
254278 AATATAAA-ATATAT-T
1 AATA-AAATATATATAT
*
254293 -A-AAATTATTATATAT
1 AATAAAATA-TATATAT
254308 AATAAAATATATA
1 AATAAAATATATA
254321 AATATAATAT
Statistics
Matches: 99, Mismatches: 21, Indels: 36
0.63 0.13 0.23
Matches are distributed among these distances:
12 2 0.02
13 2 0.02
14 17 0.17
15 21 0.21
16 31 0.31
17 17 0.17
18 9 0.09
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (16 bp):
AATAAAATATATATAT
Found at i:254322 original size:27 final size:28
Alignment explanation
Indices: 254259--254338 Score: 98
Period size: 27 Copynumber: 3.0 Consensus size: 28
254249 TAAATTATTC
* *
254259 ATATATTAAAATTTTTATAAAT-ATAAA
1 ATATATTAAAATTATTATATATAATAAA
254286 ATATATTAAAATTATTATATATAATAAA
1 ATATATTAAAATTATTATATATAATAAA
*
254314 ATATA-T-AAA-TATAATAT-TAATAAA
1 ATATATTAAAATTATTATATATAATAAA
254338 A
1 A
254339 AAATTTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
24 8 0.16
25 7 0.14
26 3 0.06
27 21 0.43
28 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATATTAAAATTATTATATATAATAAA
Found at i:255410 original size:18 final size:18
Alignment explanation
Indices: 255387--255435 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
255377 ATACCAACAT
255387 AAATTATAATATT-TAAAA
1 AAATTAT-ATATTCTAAAA
*
255405 AAATTATTTTATTCTAAAA
1 AAATTA-TATATTCTAAAA
*
255424 AATTTATATATT
1 AAATTATATATT
255436 ATCGTATCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTATATATTCTAAAA
Found at i:255645 original size:8 final size:9
Alignment explanation
Indices: 255620--255644 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
255610 ACACGAAATT
255620 TTTTTTTTA
1 TTTTTTTTA
255629 TTTTTTTTA
1 TTTTTTTTA
255638 TTTTTTT
1 TTTTTTT
255645 AAAGTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:269299 original size:33 final size:33
Alignment explanation
Indices: 269241--269309 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
269231 CCATTACAAG
*
269241 CAATGTATCGATACAATTCATCATGTATCAATA
1 CAATGTATCGATACAATTCACCATGTATCAATA
* *
269274 CAATGTATCGATAC-ATTGTACCATGTATCGATA
1 CAATGTATCGATACAATT-CACCATGTATCAATA
269307 CAA
1 CAA
269310 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATTCACCATGTATCAATA
Found at i:269382 original size:19 final size:19
Alignment explanation
Indices: 269338--269393 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
269328 CTGCCAGTCT
* **
269338 CATGTATTGATACAATTGTC
1 CATGTATCGATACAA-TGAA
269358 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
269377 CATGTATCGATACAATG
1 CATGTATCGATACAATG
269394 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:269396 original size:13 final size:13
Alignment explanation
Indices: 269378--269404 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
269368 TACAATGAAC
269378 ATGTATCGATACA
1 ATGTATCGATACA
269391 ATGTATCGATACA
1 ATGTATCGATACA
269404 A
1 A
269405 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:281328 original size:21 final size:18
Alignment explanation
Indices: 281304--281357 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
281294 TTTCAACAAT
281304 TTGTATCGATACAAACTGTAA
1 TTGTATCGATACAAA--GT-A
*
281325 TTGTATCGATACATAAGTG
1 TTGTATCGATACA-AAGTA
281344 TTGTATCGATACAA
1 TTGTATCGATACAA
281358 TATATCGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 13 0.42
20 2 0.06
21 13 0.42
22 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (18 bp):
TTGTATCGATACAAAGTA
Found at i:282671 original size:43 final size:44
Alignment explanation
Indices: 282605--282695 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 44
282595 TAAATTTAGT
282605 TTTTCAGGTCTGGAATCATGATTAAATCAAGTCCAAAACTCTCA
1 TTTTCAGGTCTGGAATCATGATTAAATCAAGTCCAAAACTCTCA
282649 TTTT-AGGTCTGGAATCATGATTAAATCAAGTCCAAAACTCTCA
1 TTTTCAGGTCTGGAATCATGATTAAATCAAGTCCAAAACTCTCA
282692 TTTT
1 TTTT
282696 TGAACCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 43 0.91
44 4 0.09
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (44 bp):
TTTTCAGGTCTGGAATCATGATTAAATCAAGTCCAAAACTCTCA
Found at i:285300 original size:66 final size:66
Alignment explanation
Indices: 285214--285341 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
285204 CTTAAGTAAT
* * * * *
285214 CCAAGCCTAACCTAACCAAATTTAAATTTAACTAAACC-TAGAATACCTCAATCCTAACCTACCT
1 CCAAGCCTAACCCAAACAAATCTAAACTTAACTAAACCTTAG-ATACCTCAACCCTAACCTACCT
285278 AC
65 AC
* *
285280 CCAAGCCTAGCCCAAACAAATCTAAACTTAACTAAACCTTAGGTACCTCAACCCTAACCTAC
1 CCAAGCCTAACCCAAACAAATCTAAACTTAACTAAACCTTAGATACCTCAACCCTAACCTAC
285342 TTAACCTACC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 51 0.94
67 3 0.06
ACGTcount: A:0.40, C:0.34, G:0.05, T:0.22
Consensus pattern (66 bp):
CCAAGCCTAACCCAAACAAATCTAAACTTAACTAAACCTTAGATACCTCAACCCTAACCTACCTA
C
Found at i:286565 original size:56 final size:55
Alignment explanation
Indices: 286497--286601 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
286487 CATAGGAATC
* * * *
286497 AAAGCCCTCATTAATTGGCATTTGAGTTAAAACCTATCTTAGCTAGCATCTAAATT
1 AAAGCCCTCATTAATTGGCATATGA-TTAAAACCCATATTAACTAGCATCTAAATT
* *
286553 AAAG-CCTACATTAGTTGGCATATGATTAAAGCCCATATTAACTAGCATC
1 AAAGCCCT-CATTAATTGGCATATGATTAAAACCCATATTAACTAGCATC
286602 GAGTCAAAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
55 23 0.55
56 19 0.45
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (55 bp):
AAAGCCCTCATTAATTGGCATATGATTAAAACCCATATTAACTAGCATCTAAATT
Found at i:286640 original size:28 final size:28
Alignment explanation
Indices: 286603--286696 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
286593 ACTAGCATCG
* *
286603 AGTCAAAGCCCGCATTAGTTAACACCTA
1 AGTCAAAGCCCACATTAGTTGACACCTA
* *
286631 AATCAAAGCCCACACTAGTTGACACAC-A
1 AGTCAAAGCCCACATTAGTTGACAC-CTA
* * *
286659 AGTAAAAGCCCACATTAGCTGGCACCTA
1 AGTCAAAGCCCACATTAGTTGACACCTA
286687 AGTCAAAGCC
1 AGTCAAAGCC
286697 TATACTAGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.02
28 52 0.96
29 1 0.02
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (28 bp):
AGTCAAAGCCCACATTAGTTGACACCTA
Found at i:286857 original size:28 final size:28
Alignment explanation
Indices: 286798--286872 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
286788 GTTGGCATCC
* **
286798 AAGTTAAAGCCCACACTAGCTAACTCTT
1 AAGTTAAAGCCCACATTAGCTAACTCAA
*
286826 AAGTCAAAGCCCACATTAGCTAACAT-AA
1 AAGTTAAAGCCCACATTAGCTAAC-TCAA
**
286854 AAGTTAAAATCCACATTAG
1 AAGTTAAAGCCCACATTAG
286873 TTAGTGTCGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.23
Consensus pattern (28 bp):
AAGTTAAAGCCCACATTAGCTAACTCAA
Found at i:290023 original size:52 final size:52
Alignment explanation
Indices: 289953--290093 Score: 228
Period size: 52 Copynumber: 2.7 Consensus size: 52
289943 GAAAATTTAT
289953 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
290005 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
*** *
290057 CTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACA
290094 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:290100 original size:13 final size:13
Alignment explanation
Indices: 290082--290106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290072 CAAAGATTAG
290082 TGTATCGATACAA
1 TGTATCGATACAA
290095 TGTATCGATACA
1 TGTATCGATACA
290107 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:290189 original size:13 final size:13
Alignment explanation
Indices: 290171--290195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
290161 CAAAAAAATA
290171 TGTATCGATACAT
1 TGTATCGATACAT
290184 TGTATCGATACA
1 TGTATCGATACA
290196 ACATTTTACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:291207 original size:52 final size:52
Alignment explanation
Indices: 291075--292287 Score: 1739
Period size: 52 Copynumber: 23.8 Consensus size: 52
291065 GAAAAGTGAT
* * * * * * *
291075 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-A
** * *
291129 AAAGGATGCCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
291182 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
291234 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
291284 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
291335 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
291385 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
291434 -AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
291483 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
291534 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
291584 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
291635 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
291687 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
291737 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* *
291788 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
291840 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
291890 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
291941 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
291991 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
292042 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
292092 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
292143 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
292193 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
292244 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
292288 GAGGGGTTGC
Statistics
Matches: 1042, Mismatches: 92, Indels: 52
0.88 0.08 0.04
Matches are distributed among these distances:
49 445 0.43
50 8 0.01
51 6 0.01
52 538 0.52
53 5 0.00
54 5 0.00
55 35 0.03
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:291326 original size:101 final size:101
Alignment explanation
Indices: 291117--292287 Score: 1949
Period size: 101 Copynumber: 11.5 Consensus size: 101
291107 ATATTGGGCC
** * *
291117 TAAAGATGAGAAAAAGGATGCCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 TAAAGATG-G-AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G-
* * * *
291182 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACT
61 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
*
291224 TAAAGGTGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
291289 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
291325 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
291390 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
* *
291426 TAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
291488 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
291524 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
291589 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
*
291625 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAAAA
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG---AA
* * *
291690 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACT
63 GGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
* * *
291729 TAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAA
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AA
* * * *
291791 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCT
63 GGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
*
291830 TAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
291895 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
*
291931 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
291996 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
*
292032 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
292097 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
*
292133 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGT
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
292198 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
*
292234 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
292288 GAGGGGTTGC
Statistics
Matches: 1021, Mismatches: 33, Indels: 26
0.95 0.03 0.02
Matches are distributed among these distances:
98 95 0.09
99 1 0.00
100 1 0.00
101 776 0.76
102 1 0.00
103 3 0.00
104 130 0.13
105 6 0.01
106 1 0.00
107 7 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (101 bp):
TAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGT
GCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
Found at i:291364 original size:153 final size:153
Alignment explanation
Indices: 291075--292287 Score: 1901
Period size: 153 Copynumber: 7.9 Consensus size: 153
291065 GAAAAGTGAT
* * * * * * *
291075 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGCCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TGCCA
* * * *
291140 ACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCA
60 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCA
*
291205 AGGCCAGCTATATTGGACTTAAAGGTGGA
125 AGGCCAGCTATATTGGACTTAAAGATGGA
291234 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
291299 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
291364 GCTATATTGGACTTAAAGAT-G-
131 GCTATATTGGACTTAAAGATGGA
* * * * *
291385 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * * * *
291449 TGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
*
291511 GCTACATTGGACTTAAAGATGGA
131 GCTATATTGGACTTAAAGATGGA
291534 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
291599 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
* *
291664 GCTATATTGGGCTTAAAGATGAA
131 GCTATATTGGACTTAAAGATGGA
291687 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
291752 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
* *
291817 GCTATATTGGGCTTAAAGATGAA
131 GCTATATTGGACTTAAAGATGGA
291840 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
291905 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
*
291970 GCTATATTGGGCTTAAAGAT-G-
131 GCTATATTGGACTTAAAGATGGA
* * * *
291991 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAATG
* * * * *
292055 TGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGG
63 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGG
*
292117 CCAGCTACATTGGACTTAAAGATGGA
128 CCAGCTATATTGGACTTAAAGATGGA
*
292143 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
292208 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
*
292273 GCTATATTGGGCTTA
131 GCTATATTGGACTTA
292288 GAGGGGTTGC
Statistics
Matches: 979, Mismatches: 60, Indels: 36
0.91 0.06 0.03
Matches are distributed among these distances:
147 45 0.05
148 1 0.00
149 1 0.00
150 311 0.32
151 4 0.00
152 3 0.00
153 567 0.58
154 4 0.00
157 1 0.00
159 42 0.04
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (153 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
GCTATATTGGACTTAAAGATGGA
Found at i:292388 original size:32 final size:33
Alignment explanation
Indices: 292292--292384 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
292282 GGCTTAGAGG
292292 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
292325 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
292358 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
292385 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 27 0.46
34 5 0.08
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:292464 original size:70 final size:70
Alignment explanation
Indices: 292391--292770 Score: 486
Period size: 70 Copynumber: 5.4 Consensus size: 70
292381 TTGGGAAGGA
*
292391 AAAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
292454 AAAAG
66 AAAAG
* *
292459 AAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
*
292524 AAACGG
66 AAA-AG
* * * **
292530 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAATGCCACAAAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
292595 AAAAG
66 AAAAG
* * * * *
292600 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACCGACTTGTGTGGGC
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAG-TGCCACGGA-GT-TGTGGGC
*
292662 TTTAGGAAGGG
63 TTTA--AA-AG
* *
292673 AGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
292736 AAAAG
66 AAAAG
*
292741 AAAAAGGTGCCACGAAGTTGTGGACTTTGA
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGA
292771 GACAAAATGC
Statistics
Matches: 269, Mismatches: 29, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
68 57 0.21
69 7 0.03
70 84 0.31
71 79 0.29
72 5 0.02
73 36 0.13
74 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (70 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
AAAAG
Found at i:292578 original size:141 final size:140
Alignment explanation
Indices: 292358--292770 Score: 566
Period size: 141 Copynumber: 2.9 Consensus size: 140
292348 TTTAGGAAGA
* *
292358 GTTGCCACCGACTTGTGTGGGCTTTGGGAA-GGAAAAAAGATGCCACGGAGTTGTGGACTTAAAA
1 GTTGCCACCGACGTGTGTGGGCTTT-AGAACGG-AAAAAGATGCCACGGAGTTGTGGACTTAAAA
*
292422 GGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT
64 GGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
292487 GAAAAGGGAAAAAG
129 GAAAA--GAAAAAG
* * *
292501 AG-TGCCACGGA-GT-TGTGGGCTTTA-AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
1 -GTTGCCACCGACGTGTGTGGGCTTTAGAACGGAAAAAGATGCCACGGAGTTGTGGAC-TT-AAA
* * ** *
292562 AGGAAAAAAGAATGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTT
63 AGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT
*
292627 TGAAAAGAAGAAG
128 TGAAAAGAAAAAG
* * *
292640 GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAG
1 GTTGCCACCGACGTGTGTGGGCTTTA-GAACGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAG
* *
292705 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGAAGTTGTGGACTTTG
65 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTG
292770 A
130 A
292771 GACAAAATGC
Statistics
Matches: 236, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
138 1 0.00
139 39 0.17
140 5 0.02
141 153 0.65
142 3 0.01
143 34 0.14
144 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (140 bp):
GTTGCCACCGACGTGTGTGGGCTTTAGAACGGAAAAAGATGCCACGGAGTTGTGGACTTAAAAGG
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
AAAGAAAAAG
Found at i:293756 original size:17 final size:16
Alignment explanation
Indices: 293724--293754 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
293714 TTTTCCTCTC
*
293724 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
293740 TTTTGTTTCTTTTTT
1 TTTTGTTTCTTTTTT
293755 TGGAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:301013 original size:52 final size:52
Alignment explanation
Indices: 300943--301083 Score: 228
Period size: 52 Copynumber: 2.7 Consensus size: 52
300933 GAAAATTTAT
300943 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
300995 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
*** *
301047 CTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACA
301084 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:301090 original size:13 final size:13
Alignment explanation
Indices: 301072--301096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301062 CAAAGATTAG
301072 TGTATCGATACAA
1 TGTATCGATACAA
301085 TGTATCGATACA
1 TGTATCGATACA
301097 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:301179 original size:13 final size:13
Alignment explanation
Indices: 301161--301185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301151 CAAAAAAATA
301161 TGTATCGATACAT
1 TGTATCGATACAT
301174 TGTATCGATACA
1 TGTATCGATACA
301186 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:301181 original size:33 final size:33
Alignment explanation
Indices: 301139--301205 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
301129 AGTAGCTTAA
301139 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
301172 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
301205 A
1 A
301206 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:301564 original size:28 final size:28
Alignment explanation
Indices: 301511--301592 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
301501 TGTCTACAGT
* *
301511 TAGCACTTAAGTTAAAGCCTACACTAGAC
1 TAGCACTTAAGTCAAAGCCCACACTAG-C
* * *
301540 -GGCACCTAAGTCAAAGCCCATACTAGC
1 TAGCACTTAAGTCAAAGCCCACACTAGC
*
301567 TAGCACTTAAGTCAAAGTCCACACTA
1 TAGCACTTAAGTCAAAGCCCACACTA
301593 TCTAACTCCT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.21
Consensus pattern (28 bp):
TAGCACTTAAGTCAAAGCCCACACTAGC
Found at i:324971 original size:2 final size:2
Alignment explanation
Indices: 324964--324988 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
324954 CTTGAAACAA
324964 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
324989 ACACATGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:325935 original size:13 final size:13
Alignment explanation
Indices: 325904--325939 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
325894 TAAATTTTTG
325904 ATTATGATAA-AA
1 ATTATGATAAGAA
325916 A-TATGATAAGAA
1 ATTATGATAAGAA
325928 ATTATGATAAGA
1 ATTATGATAAGA
325940 TATAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.36
12 4 0.18
13 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (13 bp):
ATTATGATAAGAA
Found at i:326634 original size:15 final size:15
Alignment explanation
Indices: 326592--326638 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
326582 ATTGTATAAA
*
326592 TAAATTTAATATATT
1 TAAATTTAATATTTT
326607 T--ATTTAAATTATTTT
1 TAAATTT-AA-TATTTT
326622 TAAATTTAATATTTT
1 TAAATTTAATATTTT
326637 TA
1 TA
326639 TCAAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
13 4 0.15
14 2 0.07
15 15 0.56
16 2 0.07
17 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAAATTTAATATTTT
Found at i:326811 original size:49 final size:52
Alignment explanation
Indices: 326720--326817 Score: 123
Period size: 50 Copynumber: 1.9 Consensus size: 52
326710 ATTTGATTGG
* * *
326720 TAAATATATTTTAAATAAATAAGTAGTTTTAATTAATTTTATT-TTAAAATA
1 TAAATATATTTAAAATAAATAAATAGTTTTAAATAATTTTATTATTAAAATA
*
326771 TAAATATA-TTAAAATAAA-AAATATTTTTTAAAT-ATTTTATTATTAAA
1 TAAATATATTTAAAATAAATAAATA-GTTTTAAATAATTTTATTATTAAA
326818 TGTAAGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 12 0.29
50 21 0.51
51 8 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (52 bp):
TAAATATATTTAAAATAAATAAATAGTTTTAAATAATTTTATTATTAAAATA
Found at i:327762 original size:27 final size:27
Alignment explanation
Indices: 327732--327800 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
327722 ATAAAATGAA
*
327732 ATTAAATATTTA-AACTCTTAA-ATTTAT
1 ATTAAATATTTATAA-T-TTAATATATAT
*
327759 ATTAAAAATTATATAATTTAATTATATAT
1 ATTAAATATT-TATAATTTAA-TATATAT
327788 ATTAAATATTTAT
1 ATTAAATATTTAT
327801 TTTATTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
27 13 0.37
28 6 0.17
29 16 0.46
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTAAATATTTATAATTTAATATATAT
Found at i:329283 original size:25 final size:22
Alignment explanation
Indices: 329249--329294 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
329239 TTTTATTATA
329249 TTAATAATTTATATTATATAAATT
1 TTAATAATTTATA-TAT-TAAATT
329273 TTAATATATTTATATATTAAAT
1 TTAATA-ATTTATATATTAAAT
329295 CATATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATAATTTATATATTAAATT
Found at i:330098 original size:19 final size:20
Alignment explanation
Indices: 330070--330107 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
330060 TTTTGCAATT
330070 TTTATATTTTTTAACAAAAA
1 TTTATATTTTTTAACAAAAA
*
330090 TTTAT-TTTTTTAATAAAA
1 TTTATATTTTTTAACAAAA
330108 CTAAGGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATATTTTTTAACAAAAA
Found at i:330463 original size:20 final size:19
Alignment explanation
Indices: 330440--330488 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
330430 TAATATAATA
330440 AATAA-AATATTAATTATTTT
1 AATAATAATATT-ATTA-TTT
330460 AATAATAA-A-TATTATTT
1 AATAATAATATTATTATTT
330477 AATAATAATATT
1 AATAATAATATT
330489 TAATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.42
18 5 0.19
19 2 0.08
20 6 0.23
21 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATAATAATATTATTATTT
Found at i:330485 original size:23 final size:22
Alignment explanation
Indices: 330429--330497 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
330419 ATTATACACG
*
330429 TTAATATAATAAATAAAATATTAA
1 TTAATATAAT-AAT-AAATATTAT
* *
330453 TTATTTTAATAATAAATATTAT
1 TTAATATAATAATAAATATTAT
* *
330475 TTAATAATAATATTTAATATTAT
1 TTAAT-ATAATAATAAATATTAT
330498 AAATTTTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 12 0.32
23 17 0.46
24 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAATATAATAATAAATATTAT
Found at i:330495 original size:20 final size:19
Alignment explanation
Indices: 330440--330495 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
330430 TAATATAATA
330440 AATAA-AATATTAATTATTTT
1 AATAATAATATTAA-TA-TTT
*
330460 AATAATAA-A-TATTATTT
1 AATAATAATATTAATATTT
330477 AATAATAATATTTAATATT
1 AATAATAATA-TTAATATT
330496 ATAAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 11 0.37
18 3 0.10
19 2 0.07
20 12 0.40
21 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATAATATTAATATTT
Found at i:331526 original size:18 final size:19
Alignment explanation
Indices: 331490--331550 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 19
331480 CCTTCTGGTT
* *
331490 AATAATAATTAT-TATAAA
1 AATATTAATTATAAATAAA
331508 AA-ATTAATTATAAATAAAAA
1 AATATTAATTATAAAT--AAA
*
331528 AATATTAATTATTAATAAA
1 AATATTAATTATAAATAAA
331547 AATA
1 AATA
331551 ATGAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.22
18 4 0.11
19 7 0.19
20 5 0.14
21 12 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATTAATTATAAATAAA
Found at i:331534 original size:21 final size:20
Alignment explanation
Indices: 331505--331548 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
331495 TAATTATTAT
331505 AAAAAATTAATTATAAATAA
1 AAAAAATTAATTATAAATAA
*
331525 AAAAATATTAATTATTAATAA
1 AAAAA-ATTAATTATAAATAA
331546 AAA
1 AAA
331549 TAATGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATTAATTATAAATAA
Found at i:335408 original size:21 final size:21
Alignment explanation
Indices: 335384--335426 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
335374 CATAAACTAT
335384 AAGAATTAATATGGATTGTTA
1 AAGAATTAATATGGATTGTTA
335405 AAGAATTAATATGGATTGTTA
1 AAGAATTAATATGGATTGTTA
335426 A
1 A
335427 TATAAGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (21 bp):
AAGAATTAATATGGATTGTTA
Found at i:338100 original size:33 final size:32
Alignment explanation
Indices: 338049--338189 Score: 109
Period size: 33 Copynumber: 4.6 Consensus size: 32
338039 CTTGTTCTAT
* *
338049 TTAGAATGATACAGGTTTGACTCTTTAACTAG
1 TTAGAAGGATACAAGTTTGACTCTTTAACTAG
338081 TTCAGAAGGATACAAGTTTGA--C-----CTA-
1 TT-AGAAGGATACAAGTTTGACTCTTTAACTAG
* * * * *
338106 TTAAAAGGATACAAGTTCGAATCTTTGACTTG
1 TTAGAAGGATACAAGTTTGACTCTTTAACTAG
* *
338138 TTTAGAATGATACAAGTTTGACTCTTTAACTTG
1 -TTAGAAGGATACAAGTTTGACTCTTTAACTAG
*
338171 TTAAGAAAGATACAAGTTT
1 TT-AGAAGGATACAAGTTT
338190 AACTTTTGGC
Statistics
Matches: 87, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
24 16 0.18
25 2 0.02
26 4 0.05
31 3 0.03
32 4 0.05
33 58 0.67
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TTAGAAGGATACAAGTTTGACTCTTTAACTAG
Found at i:338294 original size:32 final size:32
Alignment explanation
Indices: 338234--338294 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
338224 TTCTTTAACT
* ** *
338234 TGTTTAAAAGGATATAAGTTTGATTCTTAGCC
1 TGTTTAAAAGAATATAAGTTCAACTCTTAGCC
*
338266 TGTTTAAAAGAATATAGGTTCAACTCTTA
1 TGTTTAAAAGAATATAAGTTCAACTCTTA
338295 ACTTGTTCAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTTTAAAAGAATATAAGTTCAACTCTTAGCC
Found at i:342369 original size:19 final size:20
Alignment explanation
Indices: 342341--342397 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
342331 TTGTATTGAT
*
342341 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGC
* *
342360 TC-ATTGTATCGATACATAC
1 ACAATTGTATCGATACATGC
342379 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
342398 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGC
Found at i:342465 original size:13 final size:13
Alignment explanation
Indices: 342447--342471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
342437 CATGGCACAT
342447 TGTATCGATACAA
1 TGTATCGATACAA
342460 TGTATCGATACA
1 TGTATCGATACA
342472 TGAATAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:342491 original size:33 final size:33
Alignment explanation
Indices: 342427--342491 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
342417 TACCACTGTT
* * *
342427 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGGAAAATTGTATCAATACAA
*
342460 TGTATCGATACAT-GAATAATTGTATTAATACA
1 TGTATCGATACATGGAA-AATTGTATCAATACA
342492 TTGTCCCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGAAAATTGTATCAATACAA
Found at i:347249 original size:17 final size:16
Alignment explanation
Indices: 347209--347240 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
347199 AAAGGCTTTC
*
347209 AAAATTTTTTAATAGA
1 AAAATGTTTTAATAGA
347225 AAAATGTTTTAATAGA
1 AAAATGTTTTAATAGA
347241 GGAAATGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATGTTTTAATAGA
Found at i:348506 original size:20 final size:20
Alignment explanation
Indices: 348469--348507 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
348459 TGTTGATAAA
*
348469 TTATGTTGTTTTATTAAATC
1 TTATGTTGTTTGATTAAATC
348489 TTAT-TTGTTTGATATAAAT
1 TTATGTTGTTTGAT-TAAAT
348508 TAGGATTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (20 bp):
TTATGTTGTTTGATTAAATC
Found at i:350033 original size:41 final size:41
Alignment explanation
Indices: 349974--350068 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
349964 GGCATTTGAC
* *
349974 AAAAGGGAAGAAATAAAAAGAATTTATTTCTTTGATAGCAAA
1 AAAAGGGAAGAAACAAAAAGAATTTATTTCTTTGATAAC-AA
350016 AAAAGGG-AGAAACAAAAAGAATTTATTTCTTTGATAACAA
1 AAAAGGGAAGAAACAAAAAGAATTTATTTCTTTGATAACAA
350056 AAAAGGGAAGAAA
1 AAAAGGGAAGAAA
350069 ATCTTTTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
40 9 0.18
41 34 0.68
42 7 0.14
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (41 bp):
AAAAGGGAAGAAACAAAAAGAATTTATTTCTTTGATAACAA
Found at i:350137 original size:18 final size:18
Alignment explanation
Indices: 350094--350137 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
350084 AATCTTAATT
* *
350094 ATTTTATTAAGGGGGAGA
1 ATTTTTTTAAGAGGGAGA
*
350112 AATTTTTTAAGAGGGAGA
1 ATTTTTTTAAGAGGGAGA
350130 ATTTTTTT
1 ATTTTTTT
350138 TTCTAATGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (18 bp):
ATTTTTTTAAGAGGGAGA
Found at i:350692 original size:19 final size:19
Alignment explanation
Indices: 350664--350717 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
350654 TTGTATCGAT
* *
350664 ACATTATATCGATACATGT
1 ACATTGTATCGATACATGC
* *
350683 TCATTGTATCGATATATGC
1 ACATTGTATCGATACATGC
350702 ACAATTGTATCGATAC
1 AC-ATTGTATCGATAC
350718 GTAAAACTAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:350792 original size:20 final size:20
Alignment explanation
Indices: 350749--350802 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
350739 CTACCACTGT
* *
350749 TTGTATCGATACATGGTACG
1 TTGTATCGATACATGATACA
350769 TTGTATCGATACATGAATA-A
1 TTGTATCGATACATG-ATACA
*
350789 TTGTATTGATACAT
1 TTGTATCGATACAT
350803 TGTCCCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:364821 original size:11 final size:11
Alignment explanation
Indices: 364791--364824 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
364781 TTCCCCCCAG
364791 AAAATAATTTTT
1 AAAAT-ATTTTT
364803 AAAA-ATTTTT
1 AAAATATTTTT
364813 AAAATATTTTT
1 AAAATATTTTT
364824 A
1 A
364825 GATTGACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 7 0.33
12 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:365442 original size:158 final size:158
Alignment explanation
Indices: 365134--365543 Score: 497
Period size: 158 Copynumber: 2.6 Consensus size: 158
365124 CTCTCAATTA
* * * * *
365134 GGGATACTTCAACCCTATCA-TTTCCAAGGGGATACTCAAACCCTATTTTCATTTCCAAAATATC
1 GGGATACTTCAACCCCATCATTTTCGAA-GGGATACTCAAACCCCATTTTTATTTCCAAAATATT
* * * *
365198 GAATTTTCACCATGGGGGATACTCCAACCCTATCATTTCTGAAGGGATAGTCCAACCCTATTTTT
65 AAATTTTCACCATTGGGGATACTCCAACCCCATCATTTCTGAAGGGATACTCCAACCCTATTTTT
* *
365263 ATTGCCAAAATATCAATTTTTCACCATCG
130 ATTGCCAAAATATAAAATTTTCACCATCG
* * * *
365292 GGGATACTTCAACCCCATCATTTTTGAAGGGATACTCCAACCCCCTTTTTATTTCCTAAATATTA
1 GGGATACTTCAACCCCATCATTTTCGAAGGGATACTCAAACCCCATTTTTATTTCCAAAATATTA
* * * * *
365357 AATTTTCACCATTGGGGATACTCAAACCCCATTATTTTTG-AGGGATACTCTAA-CCTCGTTTTT
66 AATTTTCACCATTGGGGATACTCCAACCCCATCATTTCTGAAGGGATACTCCAACCCT-ATTTTT
* *
365420 ACTT-CTAAAATATTAAAATTTTCACCATTG
130 A-TTGCCAAAATA-TAAAATTTTCACCATCG
* * * *
365450 GGGATACTTCAACCCCATCATTTCCGAAGGGATACTCAAATCCCGTTTTTACTTCCAAAATATTG
1 GGGATACTTCAACCCCATCATTTTCGAAGGGATACTCAAACCCCATTTTTATTTCCAAAATATT-
365515 AAATTTTCACCATTGTGGG-TACTCCAACC
65 AAATTTTCACCATTG-GGGATACTCCAACC
365544 TTATATTCTA
Statistics
Matches: 216, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
156 3 0.01
157 24 0.11
158 157 0.73
159 29 0.13
160 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (158 bp):
GGGATACTTCAACCCCATCATTTTCGAAGGGATACTCAAACCCCATTTTTATTTCCAAAATATTA
AATTTTCACCATTGGGGATACTCCAACCCCATCATTTCTGAAGGGATACTCCAACCCTATTTTTA
TTGCCAAAATATAAAATTTTCACCATCG
Found at i:365519 original size:80 final size:79
Alignment explanation
Indices: 365134--365543 Score: 442
Period size: 79 Copynumber: 5.2 Consensus size: 79
365124 CTCTCAATTA
* * *
365134 GGGATACTTCAACCCTATCATTTC-CAAGGGGATACTCAAACCC-TATTTTCATTTCCAAAATAT
1 GGGATACTTCAACCCCATCATTTCTGAA-GGGATACTCAAACCCGT-TTTT-ACTTCCAAAATAT
* *
365197 CG-AATTTTCACCATGG
63 TGAAATTTTCACCATTG
* * * * *
365213 GGGATACTCCAACCCTATCATTTCTGAAGGGATAGTCCAACCCTATTTTTA-TTGCCAAAATA-T
1 GGGATACTTCAACCCCATCATTTCTGAAGGGATACTCAAACCC-GTTTTTACTT-CCAAAATATT
* * *
365276 CAATTTTTCACCATCG
64 GAAATTTTCACCATTG
* * * * *
365292 GGGATACTTCAACCCCATCATTTTTGAAGGGATACTCCAACCCCCTTTTTATTTCCTAAATATT-
1 GGGATACTTCAACCCCATCATTTCTGAAGGGATACT-CAAACCCGTTTTTACTTCCAAAATATTG
365356 AAATTTTCACCATTG
65 AAATTTTCACCATTG
* * * *
365371 GGGATAC-TCAAACCCCATTATTTTTG-AGGGATACTCTAACCTCGTTTTTACTTCTAAAATATT
1 GGGATACTTC-AACCCCATCATTTCTGAAGGGATACTCAAACC-CGTTTTTACTTCCAAAATATT
*
365434 AAAATTTTCACCATTG
64 GAAATTTTCACCATTG
*
365450 GGGATACTTCAACCCCATCATTTCCGAAGGGATACTCAAATCCCGTTTTTACTTCCAAAATATTG
1 GGGATACTTCAACCCCATCATTTCTGAAGGGATACTCAAA-CCCGTTTTTACTTCCAAAATATTG
365515 AAATTTTCACCATTG
65 AAATTTTCACCATTG
*
365530 TGGG-TACTCCAACC
1 -GGGATACTTCAACC
365544 TTATATTCTA
Statistics
Matches: 284, Mismatches: 32, Indels: 29
0.82 0.09 0.08
Matches are distributed among these distances:
77 4 0.01
78 30 0.11
79 172 0.61
80 72 0.25
81 6 0.02
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (79 bp):
GGGATACTTCAACCCCATCATTTCTGAAGGGATACTCAAACCCGTTTTTACTTCCAAAATATTGA
AATTTTCACCATTG
Found at i:365594 original size:158 final size:152
Alignment explanation
Indices: 365134--365597 Score: 445
Period size: 158 Copynumber: 2.9 Consensus size: 152
365124 CTCTCAATTA
* *
365134 GGGATACTTCAACCCTATCATTTCC-AAGGGGATACTCAAACCCTATTTTCATTTCCAAAATATC
1 GGGATACTTCAACCCCATCATTTCCGAA-GGGATACTCAAACCCT-TTTT-ATTTCCAAAATATT
* * *
365198 G-AATTTTCACCATGGGGGATACTCCAACCCTATCATTTCTGAAGGGATAGTCCAACCCTATTT-
63 GAAATTTTCACCATTGGGGATACTCCAACCTTAT-A-TTCT-AAGGGATACTCCAACCCTATTTC
* * * *
365261 TTATTGCCAAAATATCAATTTTTCACCATCG
125 TT-TTG--AAATTTTAAAATTTTCACCATCG
** * *
365292 GGGATACTTCAACCCCATCATTTTTGAAGGGATACTCCAACCCCCTTTTTATTTCCTAAATATT-
1 GGGATACTTCAACCCCATCATTTCCGAAGGGATACT-CAA-ACCCTTTTTATTTCCAAAATATTG
* * * * *
365356 AAATTTTCACCATTGGGGATACTCAAACCCCATTAT-TTTTGAGGGATACTCTAACCTCGTTTTT
64 AAATTTTCACCATTGGGGATACTCCAA--CC-TTATATTCTAAGGGATACTCCAACC-C-TATTT
* * * *
365420 ACTTCTAAAATATTAAAATTTTCACCATTG
124 -CTTTTGAAATTTTAAAATTTTCACCATCG
*
365450 GGGATACTTCAACCCCATCATTTCCGAAGGGATACTCAAATCCCGTTTTTACTTCCAAAATATTG
1 GGGATACTTCAACCCCATCATTTCCGAAGGGATACTCAAA-CCC-TTTTTATTTCCAAAATATTG
* *
365515 AAATTTTCACCATTGTGGG-TACTCCAACCTTATATTCTAAGGGGACACTCCAGCCCTATTTCTT
64 AAATTTTCACCATTG-GGGATACTCCAACCTTATATTCTAA-GGGATACTCCAACCCTATTTCTT
*
365579 TTGAATATCTTTTAAATTT
127 TTGAA-AT-TTTAAAATTT
365598 CAAACTTTTC
Statistics
Matches: 249, Mismatches: 38, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
155 6 0.02
156 10 0.04
157 34 0.14
158 149 0.60
159 35 0.14
160 10 0.04
161 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (152 bp):
GGGATACTTCAACCCCATCATTTCCGAAGGGATACTCAAACCCTTTTTATTTCCAAAATATTGAA
ATTTTCACCATTGGGGATACTCCAACCTTATATTCTAAGGGATACTCCAACCCTATTTCTTTTGA
AATTTTAAAATTTTCACCATCG
Found at i:365781 original size:23 final size:22
Alignment explanation
Indices: 365750--365798 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
365740 CATCCATCCT
**
365750 TTTTATGTATTTTTGTGCGTTTA
1 TTTTATGTAAATTTGTGCG-TTA
* *
365773 TTTTGTGTAAATTTGTTCGTTA
1 TTTTATGTAAATTTGTGCGTTA
365795 TTTT
1 TTTT
365799 CTTTTTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.14, C:0.04, G:0.16, T:0.65
Consensus pattern (22 bp):
TTTTATGTAAATTTGTGCGTTA
Found at i:368096 original size:9 final size:9
Alignment explanation
Indices: 368082--368106 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
368072 GTATATTGAA
368082 ATATAATTG
1 ATATAATTG
368091 ATATAATTG
1 ATATAATTG
368100 ATATAAT
1 ATATAAT
368107 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATAATTG
Found at i:372330 original size:22 final size:21
Alignment explanation
Indices: 372304--372346 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
372294 CAAATTCAGA
372304 ATATCATATTGTAATCTCTAAT
1 ATATCATATTGTAATC-CTAAT
*
372326 ATATCGTATTGTAATCCTAAT
1 ATATCATATTGTAATCCTAAT
372347 TTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATCATATTGTAATCCTAAT
Found at i:379776 original size:36 final size:36
Alignment explanation
Indices: 379753--379845 Score: 177
Period size: 36 Copynumber: 2.6 Consensus size: 36
379743 CCACATTTTG
*
379753 AGTCTCAAAACCAAGCTAAGTCACTACCACAATCTA
1 AGTCTCAAAACCAGGCTAAGTCACTACCACAATCTA
379789 AGTCTCAAAACCAGGCTAAGTCACTACCACAATCTA
1 AGTCTCAAAACCAGGCTAAGTCACTACCACAATCTA
379825 AGTCTCAAAACCAGGCTAAGT
1 AGTCTCAAAACCAGGCTAAGT
379846 TATTATCTCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (36 bp):
AGTCTCAAAACCAGGCTAAGTCACTACCACAATCTA
Done.