Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold62
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: 1452230
ACGTcount: A:0.24, C:0.12, G:0.13, T:0.24
Warning! 388291 characters in sequence are not A, C, G, or T
File 7 of 7
Found at i:1340395 original size:79 final size:79
Alignment explanation
Indices: 1340307--1340650 Score: 374
Period size: 79 Copynumber: 4.4 Consensus size: 79
1340297 ATAAAAATGG
* * * * * * * **
1340307 GGTTAGAGTATCCCCAATGGTGAAAAGTTGATATTTTGGAAGCAAAATTAGGGTTGGAGTATCTT
1 GGTTGGAGTATCCCCGATGGTGAAAAATTGATGTTGTAGAAACAAAATTAGGGTTGGAGTATCCC
* *
1340372 TTCGGAAATAACAA
66 CTCGAAAATAACAA
* * *
1340386 GGTTGGAGTATCCCCGATGGTGAAAAATT-AGTGTTGTAGAAATAAAATCAAGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATTGA-TGTTGTAGAAACAAAATTAGGGTTGGAGTATCC
* *
1340450 TCTCGAAAATAACAG
65 CCTCGAAAATAACAA
* * * *
1340465 GGTTGGAATATCCCCGATGGTGGAAAATTGATGTTGTAAAAACAAAA-TCGAGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATTGATGTTGTAGAAACAAAATTAG-GGTTGGAGTATCC
1340529 CCTC-AGAAATAACAA
65 CCTCGA-AAATAACAA
* * * *
1340544 GGTTGGAGTATCCCCGATAGTGAAAAATTGGTGCTT-TAGAAACATAACT-GGAGTTGGAGTATC
1 GGTTGGAGTATCCCCGATGGTGAAAAATTGATG-TTGTAGAAACAAAATTAGG-GTTGGAGTATC
1340607 CCCTCGAAAATAACAA
64 CCCTCGAAAATAACAA
* *
1340623 GGTTGGAGTATCCTCGATGGTGGAAAAT
1 GGTTGGAGTATCCCCGATGGTGAAAAAT
1340651 CGATATGTTA
Statistics
Matches: 225, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
78 3 0.01
79 217 0.96
80 5 0.02
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATGGTGAAAAATTGATGTTGTAGAAACAAAATTAGGGTTGGAGTATCCC
CTCGAAAATAACAA
Found at i:1340540 original size:158 final size:158
Alignment explanation
Indices: 1340358--1340650 Score: 428
Period size: 158 Copynumber: 1.9 Consensus size: 158
1340348 GCAAAATTAG
*** * *
1340358 GGTTGGAGTATCTTTTCGGAAATAACAAGGTTGGAGTATCCCCGATGGTGAAAAATTAGTG-TTG
1 GGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATAGTGAAAAATTAGTGCTT-
* * *
1340422 TAGAAATAAAATCAAG-GTTGGAGTATCCTCTCGAAAATAACAGGGTTGGAATATCCCCGATGGT
65 TAGAAACAAAA-CAAGAGTTGGAGTATCCCCTCGAAAATAACAAGGTTGGAATATCCCCGATGGT
1340486 GGAAAATTGATGTTGTAAAAACAAAATCGA
129 GGAAAATTGATGTTGTAAAAACAAAATCGA
*
1340516 GGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATAGTGAAAAATTGGTGCTTT
1 GGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATAGTGAAAAATTAGTGCTTT
* ** * *
1340581 AGAAACATAACTGGAGTTGGAGTATCCCCTCGAAAATAACAAGGTTGGAGTATCCTCGATGGTGG
66 AGAAACAAAACAAGAGTTGGAGTATCCCCTCGAAAATAACAAGGTTGGAATATCCCCGATGGTGG
1340646 AAAAT
131 AAAAT
1340651 CGATATGTTA
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
157 2 0.02
158 115 0.97
159 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (158 bp):
GGTTGGAGTATCCCCTCAGAAATAACAAGGTTGGAGTATCCCCGATAGTGAAAAATTAGTGCTTT
AGAAACAAAACAAGAGTTGGAGTATCCCCTCGAAAATAACAAGGTTGGAATATCCCCGATGGTGG
AAAATTGATGTTGTAAAAACAAAATCGA
Found at i:1341128 original size:29 final size:29
Alignment explanation
Indices: 1341082--1341147 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
1341072 TTGAACTTTG
*
1341082 AAAAATCAACTCGGACACATTTAGTATCA
1 AAAAATCAACTCGAACACATTTAGTATCA
*
1341111 AAAAATCAAC-CTGAACACATTTGGTATCA
1 AAAAATCAACTC-GAACACATTTAGTATCA
1341140 AAAAATCA
1 AAAAATCA
1341148 CAAATGATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (29 bp):
AAAAATCAACTCGAACACATTTAGTATCA
Found at i:1342237 original size:1 final size:1
Alignment explanation
Indices: 1342231--1342269 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
1342221 AAAGTGTTTG
***
1342231 AAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1342270 TTTAAATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.92, C:0.00, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:1342256 original size:22 final size:22
Alignment explanation
Indices: 1342228--1342269 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1342218 GATAAAGTGT
1342228 TTGAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAA
1342250 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
1342270 TTTAAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (22 bp):
TTGAAAAAAAAAAAAAAAAAAA
Found at i:1342258 original size:20 final size:20
Alignment explanation
Indices: 1342233--1342271 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1342223 AGTGTTTGAA
1342233 AAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAATTG
1342253 AAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAATT
1342272 TAAATGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAATTG
Found at i:1342298 original size:21 final size:21
Alignment explanation
Indices: 1342274--1342372 Score: 189
Period size: 21 Copynumber: 4.7 Consensus size: 21
1342264 AAAAAATTTA
1342274 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1342295 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1342316 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1342337 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1342358 AATGTATCGATACAT
1 AATGTATCGATACAT
1342373 CCTACAAATG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1342383 original size:42 final size:42
Alignment explanation
Indices: 1342274--1342392 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 42
1342264 AAAAAATTTA
** *
1342274 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTAG
1 AATGTATCGATACATTCCTAAAATGTATCGATACATTTGTAG
** * *
1342316 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTCCTAAAATGTATCGATACATTTGTAG
1342358 AATGTATCGATACA-TCCTACAAATGTATCGATACA
1 AATGTATCGATACATTCCTA-AAATGTATCGATACA
1342393 GGGTCCCAAC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 3 0.04
42 69 0.96
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (42 bp):
AATGTATCGATACATTCCTAAAATGTATCGATACATTTGTAG
Found at i:1342383 original size:63 final size:63
Alignment explanation
Indices: 1342274--1342392 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 63
1342264 AAAAAATTTA
** *
1342274 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTAGAATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAGAATGTATCGATACATTCCTAAAATGTATCGATACATTTGTAG
*
1342337 AATGTATCGATACATTTGTGGAATGTATCGATACA-TCCTACAAATGTATCGATACA
1 AATGTATCGATACATTTGTAGAATGTATCGATACATTCCTA-AAATGTATCGATACA
1342393 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (63 bp):
AATGTATCGATACATTTGTAGAATGTATCGATACATTCCTAAAATGTATCGATACATTTGTAG
Found at i:1342452 original size:19 final size:19
Alignment explanation
Indices: 1342428--1342495 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1342418 AATTCAACAA
1342428 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1342447 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1342462 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1342479 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1342496 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1342467 original size:13 final size:13
Alignment explanation
Indices: 1342449--1342473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1342439 ACATAAGTTT
1342449 TGTATCGATACAA
1 TGTATCGATACAA
1342462 TGTATCGATACA
1 TGTATCGATACA
1342474 TAAGTATTGT
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:1342471 original size:32 final size:32
Alignment explanation
Indices: 1342430--1342492 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1342420 TTCAACAATT
*
1342430 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1342462 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1342493 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1342553 original size:13 final size:13
Alignment explanation
Indices: 1342535--1342560 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1342525 CATTTTTCTG
1342535 TGTATCGATACAT
1 TGTATCGATACAT
1342548 TGTATCGATACAT
1 TGTATCGATACAT
1342561 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1342557 original size:33 final size:33
Alignment explanation
Indices: 1342515--1342581 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1342505 GCCAAGGAAA
***
1342515 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1342548 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1342581 T
1 T
1342582 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1345107 original size:28 final size:27
Alignment explanation
Indices: 1345040--1345112 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1345030 CTTCACAATC
* *
1345040 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1345067 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1345095 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1345113 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1345157 original size:51 final size:51
Alignment explanation
Indices: 1345095--1345265 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1345085 TTATTTCTGA
* * *
1345095 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1345146 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
1345199 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1345251 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1345266 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1345284 original size:28 final size:28
Alignment explanation
Indices: 1345248--1345329 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1345238 ATTTTTCACA
*
1345248 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1345276 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
1345304 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1345330 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1357734 original size:8 final size:8
Alignment explanation
Indices: 1357721--1357780 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
1357711 CCTTCTCTTC
1357721 AAAAAAGA
1 AAAAAAGA
1357729 AAAAAA-A
1 AAAAAAGA
* *
1357736 ACAAAACA
1 AAAAAAGA
*
1357744 AAAAAACA
1 AAAAAAGA
1357752 AAACAAAGA
1 AAA-AAAGA
*
1357761 AAAAGAGA
1 AAAAAAGA
* *
1357769 GAAAAGGA
1 AAAAAAGA
1357777 AAAA
1 AAAA
1357781 CCTACTTAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
7 6 0.14
8 29 0.69
9 7 0.17
ACGTcount: A:0.82, C:0.07, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1357748 original size:13 final size:13
Alignment explanation
Indices: 1357730--1357763 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
1357720 CAAAAAAGAA
1357730 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1357743 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1357756 AAAGAAAA
1 AAA-AAAA
1357764 AGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:1357764 original size:18 final size:17
Alignment explanation
Indices: 1357720--1357764 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
1357710 ACCTTCTCTT
1357720 CAAAAAAGAAAAA-AAAA
1 CAAAAAA-AAAAACAAAA
1357737 CAAAACAAAAAAACAAAA
1 CAAAA-AAAAAAACAAAA
1357755 CAAAGAAAAA
1 CAAA-AAAAA
1357765 GAGAGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 10 0.40
18 14 0.56
19 1 0.04
ACGTcount: A:0.84, C:0.11, G:0.04, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAACAAAA
Found at i:1358832 original size:55 final size:55
Alignment explanation
Indices: 1358746--1359114 Score: 535
Period size: 55 Copynumber: 6.6 Consensus size: 55
1358736 TCCGCTTTTT
*
1358746 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*
1358801 AATCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* ***
1358856 AGTCCTCAAAGAGCAAGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
1358911 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*** *
1358966 AGTCCTCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
*
1359027 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1359082 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCC
1359115 TCCAGTCCTC
Statistics
Matches: 284, Mismatches: 22, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
54 5 0.02
55 225 0.79
56 4 0.01
57 1 0.00
59 1 0.00
60 3 0.01
61 45 0.16
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:1359025 original size:28 final size:28
Alignment explanation
Indices: 1358992--1359080 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
1358982 GATGCTTTTT
1358992 ATTTTCAAAGCCCACACAAGTTGGTGGC
1 ATTTTCAAAGCCCACACAAGTTGGTGGC
* * * * **
1359020 ATTTTC-CAGTCCTCA-AAG-AGCAGGAC
1 ATTTTCAAAGCCCACACAAGTTGGTGG-C
1359046 ACCTTTT-AAAGCCCACACAAGTTGGTGGC
1 A--TTTTCAAAGCCCACACAAGTTGGTGGC
1359075 ATTTTC
1 ATTTTC
1359081 CAGTCCTCAA
Statistics
Matches: 42, Mismatches: 12, Indels: 14
0.62 0.18 0.21
Matches are distributed among these distances:
25 3 0.07
26 5 0.12
27 10 0.24
28 16 0.38
29 5 0.12
30 3 0.07
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (28 bp):
ATTTTCAAAGCCCACACAAGTTGGTGGC
Found at i:1359126 original size:36 final size:36
Alignment explanation
Indices: 1359079--1359150 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
1359069 GGTGGCATTT
1359079 TCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCC
1 TCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCC
*
1359115 TCCAGTCCTCAACGAGCAGGACACCTCTTAAAGCCC
1 TCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCC
1359151 ACACAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 32 0.94
37 2 0.06
ACGTcount: A:0.29, C:0.38, G:0.17, T:0.17
Consensus pattern (36 bp):
TCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCC
Found at i:1359151 original size:91 final size:91
Alignment explanation
Indices: 1359024--1359205 Score: 296
Period size: 91 Copynumber: 2.0 Consensus size: 91
1359014 GGTGGCATTT
* * *
1359024 TCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCT
1 TCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCC
1359088 CAAAGAGCAGGACACCT-TTCAAAGCCC
65 CAAAGAGCAGGACACCTCTT-AAAGCCC
*
1359115 TCCAGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCC
1 TCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCC
1359180 AAAGAGCAGGACACCTCTTAAAGCCC
66 AAAGAGCAGGACACCTCTTAAAGCCC
1359206 ACACAAGTTG
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
91 80 0.94
92 5 0.06
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (91 bp):
TCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCC
AAAGAGCAGGACACCTCTTAAAGCCC
Found at i:1359201 original size:55 final size:56
Alignment explanation
Indices: 1359117--1359575 Score: 661
Period size: 55 Copynumber: 8.3 Consensus size: 56
1359107 CAAAGCCCTC
*
1359117 CAGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
1359172 CAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1359227 CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGT
1 CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTT-T
1359281 CCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 -CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* *
1359337 CAGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1 CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1359391 CCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 -CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * *
1359447 CATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACGAGTGGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * * *
1359502 CAGTCCTCAAAGAGCAGGACGCCT-TTCAAGGCCCACACGAGTTAGTGGCACTTTT
1 CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * *
1359557 TACTCCTCAATGAGCAGGA
1 CAGTCCTCAAAGAGCAGGA
1359576 TACAATTTAT
Statistics
Matches: 370, Mismatches: 22, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
53 2 0.01
54 12 0.03
55 344 0.93
56 10 0.03
57 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.20
Consensus pattern (56 bp):
CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:1359224 original size:29 final size:29
Alignment explanation
Indices: 1359136--1359224 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
1359126 ACGAGCAGGA
1359136 CACCTCTTAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* * **
1359165 CACCT-TT-CAGTCCC-CA-AAG-AGCAGG
1 CACCTCTTAAAG-CCCACACAAGTTGGTGG
1359190 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
1359220 CACCT
1 CACCT
1359225 TTCAGTCCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:1359250 original size:26 final size:26
Alignment explanation
Indices: 1359165--1359254 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
1359155 AAGTTGGTGG
*
1359165 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
1359191 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
1359220 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
1359246 CACCTTTCA
1 CACCTTTCA
1359255 AAGCCCACAC
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:1360101 original size:1 final size:1
Alignment explanation
Indices: 1360095--1360135 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
1360085 AAAGTGTTTG
***
1360095 AAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1360136 TTTAAATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:1360115 original size:18 final size:18
Alignment explanation
Indices: 1360092--1360127 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1360082 GATAAAGTGT
1360092 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
1360110 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
1360128 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (18 bp):
TTGAAAAAAAAAAAAAAA
Found at i:1360164 original size:21 final size:21
Alignment explanation
Indices: 1360140--1360217 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
1360130 AAAAAATTTA
*
1360140 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTGG
1360161 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
1360182 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTGG
1360203 AATGTATCGATACAT
1 AATGTATCGATACAT
1360218 CCTACAAATG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTGG
Found at i:1360228 original size:42 final size:42
Alignment explanation
Indices: 1360139--1360237 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
1360129 AAAAAAATTT
* **
1360139 AAATGTATCGATACATTTGTAGAATGTATCGATACATTTGTG
1 AAATGTATCGATACATTTGTAGAATGTATCGATACATCTGAC
* *
1360181 GAATGTATCGATACATTTGTGGAATGTATCGATACATCCT-AC
1 AAATGTATCGATACATTTGTAGAATGTATCGATACAT-CTGAC
1360223 AAATGTATCGATACA
1 AAATGTATCGATACA
1360238 GGGTCCCAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (42 bp):
AAATGTATCGATACATTTGTAGAATGTATCGATACATCTGAC
Found at i:1360297 original size:19 final size:19
Alignment explanation
Indices: 1360273--1360340 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1360263 AATTCAACAA
1360273 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1360292 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1360307 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1360324 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1360341 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1360312 original size:13 final size:13
Alignment explanation
Indices: 1360294--1360318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1360284 ACATAAGTTT
1360294 TGTATCGATACAA
1 TGTATCGATACAA
1360307 TGTATCGATACA
1 TGTATCGATACA
1360319 TAAGTATTGT
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:1360316 original size:32 final size:32
Alignment explanation
Indices: 1360275--1360337 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1360265 TTCAACAATT
*
1360275 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1360307 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1360338 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1360398 original size:13 final size:13
Alignment explanation
Indices: 1360380--1360405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1360370 CATTTTTCTG
1360380 TGTATCGATACAT
1 TGTATCGATACAT
1360393 TGTATCGATACAT
1 TGTATCGATACAT
1360406 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1360402 original size:33 final size:33
Alignment explanation
Indices: 1360360--1360426 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1360350 GCCAAGGAAA
***
1360360 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1360393 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1360426 T
1 T
1360427 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1362954 original size:28 final size:27
Alignment explanation
Indices: 1362887--1362959 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1362877 CTTCACAATC
* *
1362887 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1362914 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1362942 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1362960 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1363004 original size:51 final size:51
Alignment explanation
Indices: 1362942--1363112 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1362932 TTATTTCTGA
* * *
1362942 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1362993 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
1363046 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1363098 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1363113 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1363131 original size:28 final size:28
Alignment explanation
Indices: 1363095--1363176 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1363085 ATTTTTCACA
*
1363095 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1363123 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
1363151 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1363177 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1365200 original size:20 final size:20
Alignment explanation
Indices: 1365175--1365219 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1365165 AAAATCCCAG
1365175 AATATACTGATACAATGATA
1 AATATACTGATACAATGATA
* *
1365195 AATATATTGATACAATTATA
1 AATATACTGATACAATGATA
1365215 AATAT
1 AATAT
1365220 GTATCGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
AATATACTGATACAATGATA
Found at i:1365245 original size:20 final size:20
Alignment explanation
Indices: 1365217--1365257 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1365207 CAATTATAAA
*
1365217 TATGTATCGATACATTTCCT
1 TATGCATCGATACATTTCCT
1365237 TATGCATCGATACATTTCCT
1 TATGCATCGATACATTTCCT
1365257 T
1 T
1365258 GGCGGTATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (20 bp):
TATGCATCGATACATTTCCT
Found at i:1369830 original size:97 final size:97
Alignment explanation
Indices: 1369647--1369831 Score: 239
Period size: 97 Copynumber: 1.9 Consensus size: 97
1369637 TCCAACCCTA
* *
1369647 TTTTTAAACTTTCCAAGATTTAAATCATGTTTTTGCTCAAATTATCATCGCCGGGAATACTCAAA
1 TTTTTAAACTTTCCAAGATTTAAATCATATTTTCGCTCAAATTATCATCGCCGGGAATACTCAAA
* * ** *
1369712 TCCTATTCTTTTGAGGGGATACTTTAATTCCG
66 CCCCATTCTTTCAAGGAGATACTTTAATTCCG
** * *
1369744 TTTTTAAACTTAT-CAAGATTTAAATTTTATTTTCGC-CTAAATTATCATCGCCGGGGATACTCC
1 TTTTTAAACTT-TCCAAGATTTAAATCATATTTTCGCTC-AAATTATCATCGCCGGGAATACTCA
1369807 AACCCCATTCTTTCAAGGAGATACT
64 AACCCCATTCTTTCAAGGAGATACT
1369832 CAAGCCTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
96 1 0.01
97 73 0.97
98 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (97 bp):
TTTTTAAACTTTCCAAGATTTAAATCATATTTTCGCTCAAATTATCATCGCCGGGAATACTCAAA
CCCCATTCTTTCAAGGAGATACTTTAATTCCG
Found at i:1369845 original size:97 final size:94
Alignment explanation
Indices: 1369605--1369844 Score: 234
Period size: 97 Copynumber: 2.5 Consensus size: 94
1369595 CATTTATTGA
* *
1369605 GGATACTCGAACTCCATTCTTTCGAGGGATACTCCAACCCTATTTTTAAACTTTCCAAGATTTAA
1 GGATACTCAAACCCCATTCTTTCGAGGGATACT-CAA-CCTATTTTTAAACTTTCCAAGATTTAA
* *
1369670 ATCATGTTTTTGCTCAAATTATCATCGCCGG
64 ATCATATTTTCGCTCAAATTATCATCGCCGG
* * * * * *
1369701 GAATACTCAAATCCTATTCTTTTGAGGGGATACTTTAATTCC-GTTTTTAAACTTAT-CAAGATT
1 GGATACTCAAACCCCATTCTTTCGA-GGGATAC-TCAA--CCTATTTTTAAACTT-TCCAAGATT
**
1369764 TAAATTTTATTTTCGC-CTAAATTATCATCGCCGG
61 TAAATCATATTTTCGCTC-AAATTATCATCGCCGG
* * *
1369798 GGATACTCCAACCCCATTCTTTCAAGGAGATACTCAAGCCTTTTTTT
1 GGATACTCAAACCCCATTCTTTCGAGG-GATACTCAA-CCTATTTTT
1369845 TCAACCAAAG
Statistics
Matches: 115, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
95 2 0.02
96 30 0.26
97 79 0.69
98 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (94 bp):
GGATACTCAAACCCCATTCTTTCGAGGGATACTCAACCTATTTTTAAACTTTCCAAGATTTAAAT
CATATTTTCGCTCAAATTATCATCGCCGG
Found at i:1372426 original size:31 final size:31
Alignment explanation
Indices: 1372390--1372721 Score: 161
Period size: 31 Copynumber: 11.0 Consensus size: 31
1372380 ACATCAATCA
*
1372390 AAGATCCTTCATGGAGGAATATTTTCTTTTT
1 AAGATCCTTAATGGAGGAATATTTTCTTTTT
* **
1372421 AAGATCTTTAATGGAGGAATGGTTTCTTTTT
1 AAGATCCTTAATGGAGGAATATTTTCTTTTT
* * * * *
1372452 AAGAACCTTAGTAGAGGAATTTTTTTTTATTTT
1 AAGATCCTTAATGGAGGAA-TATTTTCT-TTTT
* * * *
1372485 AAGATTC-TAAGTGAAGGATTATTTCCTTTTT
1 AAGATCCTTAA-TGGAGGAATATTTTCTTTTT
* ** * * *
1372516 AAGATCGTTGGTGAAGGCAT-TGTTCCTTTTT
1 AAGATCCTTAATGGAGGAATAT-TTTCTTTTT
* * * *
1372547 AAGACCCTTAATGTAGGGATATGTT-TTTTT
1 AAGATCCTTAATGGAGGAATATTTTCTTTTT
* * * *
1372577 AAAATCC-T-CT-GTGGAATATTTT-ATTTT
1 AAGATCCTTAATGGAGGAATATTTTCTTTTT
* * * * *
1372604 AAGAT-CTCCAATCGAAGAATATTTTATTCTGT
1 AAGATCCT-TAATGGAGGAATATTTTCTT-TTT
* *
1372636 --GACCCTTAATGGAGGAATGTTTTCTTTTT
1 AAGATCCTTAATGGAGGAATATTTTCTTTTT
*
1372665 ATGA-CCTTAATGGAGG-AT-TTTT-TTTTT
1 AAGATCCTTAATGGAGGAATATTTTCTTTTT
** * *
1372692 AAGATCCTTGGTGGAGGAAAATTTCCTTTT
1 AAGATCCTTAATGGAGGAATATTTTCTTTT
1372722 AAAAGTAGAT
Statistics
Matches: 221, Mismatches: 61, Indels: 38
0.69 0.19 0.12
Matches are distributed among these distances:
26 1 0.00
27 24 0.11
28 15 0.07
29 7 0.03
30 53 0.24
31 91 0.41
32 16 0.07
33 14 0.06
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (31 bp):
AAGATCCTTAATGGAGGAATATTTTCTTTTT
Found at i:1372673 original size:30 final size:29
Alignment explanation
Indices: 1372639--1372710 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
1372629 ATTCTGTGAC
*
1372639 CCTTAATGGAGGAATGTTTTCTTTTTATGA-
1 CCTTAATGGAGGAAT-TTTT-TTTTTAAGAT
1372669 CCTTAATGGAGG-ATTTTTTTTTTAAGAT
1 CCTTAATGGAGGAATTTTTTTTTTAAGAT
**
1372697 CCTTGGTGGAGGAA
1 CCTTAATGGAGGAA
1372711 AATTTCCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 14 0.38
29 3 0.08
30 12 0.32
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.43
Consensus pattern (29 bp):
CCTTAATGGAGGAATTTTTTTTTTAAGAT
Found at i:1376766 original size:19 final size:19
Alignment explanation
Indices: 1376742--1376804 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
1376732 AAACAGTAAC
1376742 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
1376761 TGTATCAATAC--AA----
1 TGTATCGATACATAAGTGT
1376774 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
1376793 TGTATCGATACA
1 TGTATCGATACA
1376805 ATGTATCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:1376783 original size:32 final size:32
Alignment explanation
Indices: 1376742--1376811 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
1376732 AAACAGTAAC
1376742 TGTATCGATACATAAGTGTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
*
1376774 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
1376806 TGTATC
1 TGTATC
1376812 ACTACAAAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCAATACAA
Found at i:1376874 original size:13 final size:13
Alignment explanation
Indices: 1376856--1376881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1376846 CATCACTCAA
1376856 TGTATCGATACAT
1 TGTATCGATACAT
1376869 TGTATCGATACAT
1 TGTATCGATACAT
1376882 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1379099 original size:24 final size:25
Alignment explanation
Indices: 1379072--1379120 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
1379062 TCAAAATTTT
1379072 ATTCATC-GGGGACACTCCAACCTC
1 ATTCATCAGGGGACACTCCAACCTC
*
1379096 ATTCCTCTGAGGGGACACTCCAACC
1 ATTCATC--AGGGGACACTCCAACC
1379121 CCGTTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
27 15 0.71
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.20
Consensus pattern (25 bp):
ATTCATCAGGGGACACTCCAACCTC
Found at i:1384109 original size:13 final size:13
Alignment explanation
Indices: 1384091--1384118 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1384081 ACACAAAGAT
1384091 CAATGTATCGATA
1 CAATGTATCGATA
1384104 CAATGTATCGATA
1 CAATGTATCGATA
1384117 CA
1 CA
1384119 TTTCCTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1384174 original size:19 final size:18
Alignment explanation
Indices: 1384150--1384209 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
1384140 AGCCATACAT
1384150 TGTATCGATGCAACACTTA
1 TGTATCGAT-CAACACTTA
1384169 TGTATCGAT--ACA--T-
1 TGTATCGATCAACACTTA
*
1384182 TGTATCGATCCAAAACTTA
1 TGTATCGAT-CAACACTTA
1384201 TGTATCGAT
1 TGTATCGAT
1384210 ACATTTACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
16 5 0.15
18 1 0.03
19 18 0.53
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (18 bp):
TGTATCGATCAACACTTA
Found at i:1384185 original size:32 final size:32
Alignment explanation
Indices: 1384144--1384214 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1384134 CTTTGTAGCC
* *
1384144 ATACATTGTATCGATGCAACACTTATGTATCG
1 ATACATTGTATCGATCCAAAACTTATGTATCG
1384176 ATACATTGTATCGATCCAAAACTTATGTATCG
1 ATACATTGTATCGATCCAAAACTTATGTATCG
1384208 ATACATT
1 ATACATT
1384215 TACTGTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
ATACATTGTATCGATCCAAAACTTATGTATCG
Found at i:1385312 original size:13 final size:13
Alignment explanation
Indices: 1385294--1385320 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1385284 AGAATTCTTT
1385294 ATGTATCGATACA
1 ATGTATCGATACA
1385307 ATGTATCGATACA
1 ATGTATCGATACA
1385320 A
1 A
1385321 GGTCCCATGT
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:1387354 original size:20 final size:20
Alignment explanation
Indices: 1387331--1387403 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1387321 ACAATTCAAA
1387331 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1387351 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1387372 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1387392 GTATCGATACAT
1 GTATCGATACAT
1387404 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1387375 original size:21 final size:21
Alignment explanation
Indices: 1387349--1387424 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1387339 ACATGTTGCA
1387349 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1387370 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1387390 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1387411 TTGTATCGATACAT
1 ATGTATCGATACAT
1387425 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1387382 original size:41 final size:41
Alignment explanation
Indices: 1387331--1387424 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1387321 ACAATTCAAA
*
1387331 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1387372 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1387413 GTATCGATACAT
1 GTATCGATACAT
1387425 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1387481 original size:13 final size:13
Alignment explanation
Indices: 1387463--1387488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1387453 TACAGCAAGT
1387463 ATGTATCGATACA
1 ATGTATCGATACA
1387476 ATGTATCGATACA
1 ATGTATCGATACA
1387489 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1391571 original size:15 final size:15
Alignment explanation
Indices: 1391551--1391581 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1391541 TAAAAATGTC
*
1391551 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1391566 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1391581 C
1 C
1391582 TAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1393677 original size:20 final size:21
Alignment explanation
Indices: 1393598--1393676 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1393588 AATGTCCAAA
*
1393598 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
1393618 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
1393643 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
1393663 TTGTATCGATACAT
1 ATGTATCGATACAT
1393677 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:1393681 original size:13 final size:13
Alignment explanation
Indices: 1393663--1393701 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1393653 ACATTTTTCT
1393663 TTGTATCGATACA
1 TTGTATCGATACA
1393676 TTGTATCGATACA
1 TTGTATCGATACA
*
1393689 CTGTATCGATACA
1 TTGTATCGATACA
1393702 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1395516 original size:21 final size:21
Alignment explanation
Indices: 1395490--1395531 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1395480 AAATAAATTT
*
1395490 TTGTTGTGATTTACTTGATTA
1 TTGTTGTGAATTACTTGATTA
1395511 TTGTTGTGAATTACTTGATTA
1 TTGTTGTGAATTACTTGATTA
1395532 AGGGGGAGAT
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:0.21, C:0.05, G:0.19, T:0.55
Consensus pattern (21 bp):
TTGTTGTGAATTACTTGATTA
Found at i:1396189 original size:20 final size:20
Alignment explanation
Indices: 1396166--1396238 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1396156 ACAATTCAAA
1396166 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1396186 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1396207 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1396227 GTATCGATACAT
1 GTATCGATACAT
1396239 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1396210 original size:21 final size:21
Alignment explanation
Indices: 1396184--1396259 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1396174 ACATGTTGCA
1396184 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1396205 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1396225 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1396246 TTGTATCGATACAT
1 ATGTATCGATACAT
1396260 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1396217 original size:41 final size:41
Alignment explanation
Indices: 1396166--1396259 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1396156 ACAATTCAAA
*
1396166 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1396207 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1396248 GTATCGATACAT
1 GTATCGATACAT
1396260 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1396316 original size:13 final size:13
Alignment explanation
Indices: 1396298--1396323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1396288 TACAGCAAGT
1396298 ATGTATCGATACA
1 ATGTATCGATACA
1396311 ATGTATCGATACA
1 ATGTATCGATACA
1396324 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1398743 original size:2 final size:2
Alignment explanation
Indices: 1398736--1398767 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1398726 AACTTGTTTC
1398736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1398768 GTTCTTTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1399652 original size:19 final size:20
Alignment explanation
Indices: 1399620--1399659 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1399610 TTACTACTTA
1399620 TTTAACATTAAAAA-TATTT
1 TTTAACATTAAAAATTATTT
* *
1399639 TTTAATATTTAAAATTATTT
1 TTTAACATTAAAAATTATTT
1399659 T
1 T
1399660 ATTTCATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAACATTAAAAATTATTT
Found at i:1401285 original size:16 final size:16
Alignment explanation
Indices: 1401261--1401340 Score: 90
Period size: 16 Copynumber: 5.0 Consensus size: 16
1401251 TTTGAATTAT
*
1401261 TTTCGGGTTCGGGTCA
1 TTTCAGGTTCGGGTCA
*
1401277 TTTCAGGTTCGGGTTA
1 TTTCAGGTTCGGGTCA
* *
1401293 TTTCAAGTTCGGATCA
1 TTTCAGGTTCGGGTCA
**
1401309 TTTCAGGTTTAGGTCA
1 TTTCAGGTTCGGGTCA
1401325 TTTC-GGATTCGGGTCA
1 TTTCAGG-TTCGGGTCA
1401341 ATCGAGTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 2 0.04
16 50 0.96
ACGTcount: A:0.15, C:0.16, G:0.29, T:0.40
Consensus pattern (16 bp):
TTTCAGGTTCGGGTCA
Found at i:1401414 original size:53 final size:53
Alignment explanation
Indices: 1401311--1401434 Score: 126
Period size: 53 Copynumber: 2.3 Consensus size: 53
1401301 TCGGATCATT
** * *
1401311 TCAGGTTTAGGTCATTTCGGATTCGGGTCAATCGAGTTTAATACTTGGGTTAA
1 TCAGGTTTAAATCATTTCGGATTCGAGTCAATCGAGTTTAACACTTGGGTTAA
* *
1401364 TCAGGTTTAAATCA-TTCTGGATTCGAGTCAATTGGGTTTAACA-TTCGGGTTAAA
1 TCAGGTTTAAATCATTTC-GGATTCGAGTCAATCGAGTTTAACACTT-GGGTT-AA
* * *
1401418 TCGGGTTCAAGTCATTT
1 TCAGGTTTAAATCATTT
1401435 TAGGTTTAGA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
52 5 0.09
53 38 0.66
54 13 0.22
55 2 0.03
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (53 bp):
TCAGGTTTAAATCATTTCGGATTCGAGTCAATCGAGTTTAACACTTGGGTTAA
Found at i:1405042 original size:2 final size:2
Alignment explanation
Indices: 1405035--1405078 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1405025 TTCAAAATTG
* * *
1405035 TA TA TA TA T- TA TA TA TA TA TA TA TG TA TG TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1405076 TA T
1 TA T
1405079 GTATGTCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1408663 original size:21 final size:20
Alignment explanation
Indices: 1408629--1408669 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1408619 AAGGTGCTGG
*
1408629 ACATACTCTAAATGCATGAA
1 ACATACTCAAAATGCATGAA
1408649 ACATAGCTCAAAATGCATGAA
1 ACATA-CTCAAAATGCATGAA
1408670 TCATGGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (20 bp):
ACATACTCAAAATGCATGAA
Found at i:1409611 original size:13 final size:13
Alignment explanation
Indices: 1409593--1409620 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1409583 ATACAAAGAT
1409593 CAATGTATCGATA
1 CAATGTATCGATA
1409606 CAATGTATCGATA
1 CAATGTATCGATA
1409619 CA
1 CA
1409621 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1409617 original size:33 final size:33
Alignment explanation
Indices: 1409575--1409640 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1409565 AAAATTCCAG
1409575 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
1409608 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
1409641 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:1412850 original size:31 final size:31
Alignment explanation
Indices: 1412790--1412847 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1412780 TAACTAGTAT
*
1412790 ATTCTAAAATTTAAAGTATAAGGGTAAATTC
1 ATTCTAAAATTTAAAGTATAAGGATAAATTC
* *
1412821 ATTCTAGAATTTAAA-TATAATGATAAA
1 ATTCTAAAATTTAAAGTATAAGGATAAA
1412848 ATTACATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.36
Consensus pattern (31 bp):
ATTCTAAAATTTAAAGTATAAGGATAAATTC
Found at i:1413299 original size:2 final size:2
Alignment explanation
Indices: 1413292--1413322 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1413282 AGGAGAATCA
*
1413292 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1413323 CCCATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1414413 original size:22 final size:22
Alignment explanation
Indices: 1414371--1414413 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1414361 AAAGCATATC
**
1414371 AAACCTTATCAGATTTTTGGTT
1 AAACCTTATCAGATTAGTGGTT
1414393 AAACCTTATCAGATTAGTGGT
1 AAACCTTATCAGATTAGTGGT
1414414 CTTGACATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (22 bp):
AAACCTTATCAGATTAGTGGTT
Found at i:1414746 original size:21 final size:21
Alignment explanation
Indices: 1414721--1414762 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1414711 CAACTCTATG
1414721 GGGGAAATTTGAGAATGATTT
1 GGGGAAATTTGAGAATGATTT
1414742 GGGGAAATTTGAGAATGATTT
1 GGGGAAATTTGAGAATGATTT
1414763 TTTCGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
GGGGAAATTTGAGAATGATTT
Found at i:1415906 original size:20 final size:20
Alignment explanation
Indices: 1415883--1415956 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1415873 ACAATTCAAA
1415883 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1415903 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1415924 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1415944 GTATCGATACATG
1 GTATCGATACATG
1415957 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1415927 original size:21 final size:21
Alignment explanation
Indices: 1415901--1415976 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1415891 ACATGTTGCA
1415901 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1415922 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1415942 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1415963 ATGTATCGATACAT
1 ATGTATCGATACAT
1415977 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1415934 original size:41 final size:41
Alignment explanation
Indices: 1415883--1415976 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1415873 ACAATTCAAA
1415883 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1415924 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1415965 GTATCGATACAT
1 GTATCGATACAT
1415977 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1416033 original size:13 final size:13
Alignment explanation
Indices: 1416015--1416040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1416005 TACAGCAAGT
1416015 ATGTATCGATACA
1 ATGTATCGATACA
1416028 ATGTATCGATACA
1 ATGTATCGATACA
1416041 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1416562 original size:34 final size:35
Alignment explanation
Indices: 1416499--1416565 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1416489 CTAAGTGATT
1416499 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1416535 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1416566 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1419670 original size:13 final size:13
Alignment explanation
Indices: 1419652--1419676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1419642 TTTTCCAGAT
1419652 TGTATCGATACAA
1 TGTATCGATACAA
1419665 TGTATCGATACA
1 TGTATCGATACA
1419677 TTGCTTCAGT
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:1419981 original size:12 final size:12
Alignment explanation
Indices: 1419964--1419990 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1419954 ATTTGTTTGA
1419964 TTTGTGTGCTGG
1 TTTGTGTGCTGG
1419976 TTTGTGTGCTGG
1 TTTGTGTGCTGG
1419988 TTT
1 TTT
1419991 CATTCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.37, T:0.56
Consensus pattern (12 bp):
TTTGTGTGCTGG
Found at i:1421472 original size:20 final size:20
Alignment explanation
Indices: 1421449--1421522 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1421439 ACAATTCAAA
1421449 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1421469 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1421490 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1421510 GTATCGATACATG
1 GTATCGATACATG
1421523 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1421493 original size:21 final size:21
Alignment explanation
Indices: 1421467--1421542 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1421457 ACATGTTGCA
1421467 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1421488 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1421508 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1421529 ATGTATCGATACAT
1 ATGTATCGATACAT
1421543 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1421500 original size:41 final size:41
Alignment explanation
Indices: 1421449--1421542 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1421439 ACAATTCAAA
1421449 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1421490 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1421531 GTATCGATACAT
1 GTATCGATACAT
1421543 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1421599 original size:13 final size:13
Alignment explanation
Indices: 1421581--1421606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1421571 TACAGCAAGT
1421581 ATGTATCGATACA
1 ATGTATCGATACA
1421594 ATGTATCGATACA
1 ATGTATCGATACA
1421607 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1422128 original size:34 final size:35
Alignment explanation
Indices: 1422065--1422131 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1422055 CTAAGTGATT
1422065 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1422101 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1422132 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1426206 original size:128 final size:126
Alignment explanation
Indices: 1426030--1426365 Score: 407
Period size: 128 Copynumber: 2.7 Consensus size: 126
1426020 AATTAATAAA
1426030 ATTTTAATTTAAAATTTTTTATTTTA-AAAAATATAATAATTAATATTTTAATTTGTTAATGTAA
1 ATTTT-ATTT-AAATTTTTTATTTTATAAAAATATAATAATTAATATTTTAATTTGTTAATGT-A
* * *
1426094 ATTTTTTAAACTTAATTAAATAGTTTTT-ATTTTATT-AAAAATTATAATAAAAAA-CTTTTTTT
63 ATTTTTTAAACTTAATTAAATAATTTTTAATTTTATTAAAAAATAATAATAAAAAATC-CTTTTT
*
1426156 ATTTTTATGTTAAATTTTTTTATTTTATAAAAATATAATAATTAATATTTTAATTTGTTAATATA
1 A-TTTTAT-TTAAA-TTTTTTATTTTATAAAAATATAATAATTAATATTTTAATTTGTTAATGTA
*
1426221 ATTTTTTAAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATAATAATAATAAATCCTTT
63 ATTTTTT-AAACTTAATTAAATA--ATTTTTAATTTTATTAAAAAATAATAATAAAAAATCCTTT
1426286 TT
125 TT
*
1426288 A----ATTT-AATTTTTTATTTT-T---AA-A-AATAATTAATATTTTAATTTATTAATGTAA-T
1 ATTTTATTTAAATTTTTTATTTTATAAAAATATAATAATTAATATTTTAATTTGTTAATGTAATT
*
1426341 TTTTAAAGTTAATTAAATAATTTTT
66 TTTTAAACTTAATTAAATAATTTTT
1426366 TATTAAAAAT
Statistics
Matches: 192, Mismatches: 8, Indels: 32
0.83 0.03 0.14
Matches are distributed among these distances:
114 6 0.03
116 14 0.07
117 5 0.03
118 28 0.15
119 1 0.01
120 2 0.01
123 1 0.01
124 11 0.06
125 2 0.01
126 8 0.04
127 28 0.15
128 50 0.26
130 5 0.03
131 8 0.04
132 22 0.11
133 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (126 bp):
ATTTTATTTAAATTTTTTATTTTATAAAAATATAATAATTAATATTTTAATTTGTTAATGTAATT
TTTTAAACTTAATTAAATAATTTTTAATTTTATTAAAAAATAATAATAAAAAATCCTTTTT
Found at i:1426227 original size:53 final size:55
Alignment explanation
Indices: 1426117--1426227 Score: 124
Period size: 52 Copynumber: 2.1 Consensus size: 55
1426107 AATTAAATAG
* * *
1426117 TTTTTATTTTATTAAAAATTATAATAAAAAACTTTTTTTATTTTTATGTTAAATT
1 TTTTTATTTTATTAAAAATTATAATAAAAAACTATTTTAATTTTTATGATAAATT
**
1426172 TTTTTATTTTA-TAAAAA-TATAATAATTAA-TATTTTAATTTGTTA--ATATAATT
1 TTTTTATTTTATTAAAAATTATAATAAAAAACTATTTTAATTT-TTATGATA-AATT
1426224 TTTT
1 TTTT
1426228 AAAACTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
51 2 0.04
52 17 0.35
53 13 0.27
54 6 0.12
55 11 0.22
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (55 bp):
TTTTTATTTTATTAAAAATTATAATAAAAAACTATTTTAATTTTTATGATAAATT
Found at i:1426567 original size:23 final size:23
Alignment explanation
Indices: 1426505--1426575 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
1426495 TTTAAATTCA
*
1426505 TATATAATAATAAA-AAATAAATTT
1 TATA-AATAA-AAATAAATTAATTT
* ** *
1426529 CATAAATTGAATTAAATTAATTT
1 TATAAATAAAAATAAATTAATTT
1426552 TATAAATAAAAATAAATTAGATTT
1 TATAAATAAAAATAAATTA-ATTT
1426576 AAAAAAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
22 2 0.06
23 27 0.75
24 7 0.19
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (23 bp):
TATAAATAAAAATAAATTAATTT
Found at i:1426613 original size:23 final size:22
Alignment explanation
Indices: 1426538--1426617 Score: 69
Period size: 23 Copynumber: 3.7 Consensus size: 22
1426528 TCATAAATTG
1426538 AATTAAATT-AATTTTATAAATAA
1 AATTAAATTAAATTTT-TAAA-AA
* * *
1426561 AAATAAATTAGA-TTTAAAAAA
1 AATTAAATTAAATTTTTAAAAA
*
1426582 AATT--TTTAAATTATTTAAAAA
1 AATTAAATTAAATT-TTTAAAAA
1426603 AATTAAATTAAATTT
1 AATTAAATTAAATTT
1426618 GTATAATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
19 4 0.09
20 1 0.02
21 16 0.36
22 4 0.09
23 18 0.41
24 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
AATTAAATTAAATTTTTAAAAA
Found at i:1427166 original size:14 final size:14
Alignment explanation
Indices: 1427147--1427193 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
1427137 TATATTCATA
1427147 AAAAAATCTATTTT
1 AAAAAATCTATTTT
1427161 AAAAAA--TATTTT
1 AAAAAATCTATTTT
1427173 ATTAAAAATCTATTTAT
1 A--AAAAATCTATTT-T
1427190 AAAA
1 AAAA
1427194 TTAATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.25
14 11 0.39
15 3 0.11
16 5 0.18
17 2 0.07
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAAAATCTATTTT
Found at i:1427169 original size:28 final size:29
Alignment explanation
Indices: 1427138--1427193 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
1427128 ATTTCTTAAT
1427138 ATATTCATA-AAAAAATCTATTT-TAAAAA
1 ATATT-ATATAAAAAATCTATTTATAAAAA
* *
1427166 ATATTTTATTAAAAATCTATTTATAAAA
1 ATATTATATAAAAAATCTATTTATAAAA
1427194 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 17 0.71
29 5 0.21
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (29 bp):
ATATTATATAAAAAATCTATTTATAAAAA
Found at i:1428221 original size:9 final size:9
Alignment explanation
Indices: 1428209--1428241 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
1428199 AAAAAATCAC
1428209 AAAAAATTT
1 AAAAAATTT
1428218 AAAAAATTT
1 AAAAAATTT
1428227 AAAAAATTT
1 AAAAAATTT
1428236 AAAAAA
1 AAAAAA
1428242 AAACACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAAATTT
Found at i:1428221 original size:18 final size:18
Alignment explanation
Indices: 1428198--1428241 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1428188 AAAATAAAAA
1428198 TAAAAAATCACAAAAAATT
1 TAAAAAAT-ACAAAAAATT
**
1428217 TAAAAAATTTAAAAAATT
1 TAAAAAATACAAAAAATT
1428235 TAAAAAA
1 TAAAAAA
1428242 AAACACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAAATACAAAAAATT
Found at i:1428339 original size:13 final size:13
Alignment explanation
Indices: 1428321--1428347 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1428311 AACGAATCTG
1428321 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1428334 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
1428347 A
1 A
1428348 GAAAGAGACC
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:1429289 original size:25 final size:24
Alignment explanation
Indices: 1429232--1429294 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
1429222 ATAAAATATA
*
1429232 TATATTT-TTTATTATTTTATAAT
1 TATATTTATTTATTATTTAATAAT
*
1429255 TATATATTATTTATTATTTAATGTAT
1 TATAT-TTATTTATTATTTAAT-AAT
1429281 TATATTTATTTATT
1 TATATTTATTTATT
1429295 TACTTGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 5 0.14
24 2 0.06
25 21 0.60
26 7 0.20
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATATTTATTTATTATTTAATAAT
Found at i:1431480 original size:31 final size:32
Alignment explanation
Indices: 1431413--1431492 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 32
1431403 ATCTTTATGC
* *
1431413 CAAAACATGAATTTAGT-TCTTATACTAATGT
1 CAAAATATAAATTTAGTCTCTTATACTAATGT
* * *
1431444 CAAAATATTAATTTAGTCT-TTATACTTATTT
1 CAAAATATAAATTTAGTCTCTTATACTAATGT
*
1431475 TAAAATATAAATTTAGTC
1 CAAAATATAAATTTAGTC
1431493 CCACTACAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 41 0.98
32 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (32 bp):
CAAAATATAAATTTAGTCTCTTATACTAATGT
Found at i:1431700 original size:24 final size:25
Alignment explanation
Indices: 1431677--1431723 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
1431667 TCTACTAATA
1431677 ATTTATGATTAA-AATA-TAAAAAT
1 ATTTATGATTAATAATATTAAAAAT
* *
1431700 ATTTGTGTTTAATAATATTAAAAA
1 ATTTATGATTAATAATATTAAAAA
1431724 AATATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 4 0.20
25 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (25 bp):
ATTTATGATTAATAATATTAAAAAT
Found at i:1431969 original size:20 final size:20
Alignment explanation
Indices: 1431944--1431987 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1431934 AAAAATAAAT
1431944 TATAAACATATTAA-AATTTA
1 TATAAACATA-TAATAATTTA
* *
1431964 TATAAATATATAATATTTTA
1 TATAAACATATAATAATTTA
1431984 TATA
1 TATA
1431988 CGATTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAACATATAATAATTTA
Found at i:1432789 original size:31 final size:31
Alignment explanation
Indices: 1432746--1432815 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1432736 CACTTTACTT
* *
1432746 TTTTTAAT-AAATTTTACCATTAAATTTTGA
1 TTTTTAATAAAATTTTACCATTAAACTTTAA
*
1432776 TTTTTAATAAAATTTTACCATTCAACTTTAA
1 TTTTTAATAAAATTTTACCATTAAACTTTAA
*
1432807 TTTTAAATA
1 TTTTTAATA
1432816 GTTTAACGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (31 bp):
TTTTTAATAAAATTTTACCATTAAACTTTAA
Found at i:1433291 original size:54 final size:54
Alignment explanation
Indices: 1433221--1433374 Score: 137
Period size: 54 Copynumber: 2.8 Consensus size: 54
1433211 AATATTAATC
* * * *
1433221 AAAATAAAATACATATAATGACTAATTTCAATATCTACCGATAATTCAGTGGCA
1 AAAATAAAGTATATATAATGACTAATTTCAATATCTACCGATAATCCAATGGCA
** * * * *
1433275 AAAATAAAGTATATATAGGGACAAATTTTAATATCTACCAATAATCCAATGGTA
1 AAAATAAAGTATATATAATGACTAATTTCAATATCTACCGATAATCCAATGGCA
* * * * * *
1433329 GACATAAAAGTGTATATATATTGACTAATTTGAACATCCACCGATA
1 AAAAT-AAA--GTATATATAATGACTAATTTCAATATCTACCGATA
1433375 TAATCTGATG
Statistics
Matches: 78, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
54 47 0.60
55 3 0.04
57 28 0.36
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (54 bp):
AAAATAAAGTATATATAATGACTAATTTCAATATCTACCGATAATCCAATGGCA
Found at i:1435227 original size:20 final size:20
Alignment explanation
Indices: 1435202--1435249 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1435192 TTTCTCATGT
1435202 TTTCATGCCCTACTTAGGAC
1 TTTCATGCCCTACTTAGGAC
*
1435222 TTTCATGCCGTACTTAGGAC
1 TTTCATGCCCTACTTAGGAC
1435242 TTTCATGC
1 TTTCATGC
1435250 ATTATTGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.38
Consensus pattern (20 bp):
TTTCATGCCCTACTTAGGAC
Found at i:1440352 original size:24 final size:23
Alignment explanation
Indices: 1440308--1440354 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1440298 AAAATAAAAT
*
1440308 AAATTAATTATAAAATGAATTTA
1 AAATTAATTATAAAATAAATTTA
1440331 AAATTAAATTA-AAAATCAAATTTA
1 AAATT-AATTATAAAAT-AAATTTA
1440355 TTTTATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATTAATTATAAAATAAATTTA
Found at i:1440707 original size:28 final size:27
Alignment explanation
Indices: 1440655--1440710 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
1440645 GTAAATTAGG
1440655 AAAATTCATCTATAAAAATTCTAATTA
1 AAAATTCATCTATAAAAATTCTAATTA
* *
1440682 AAAATTTCATGTATGAAATATT-TAATTA
1 AAAA-TTCATCTAT-AAAAATTCTAATTA
1440710 A
1 A
1440711 GACCATAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 15 0.60
29 6 0.24
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (27 bp):
AAAATTCATCTATAAAAATTCTAATTA
Found at i:1442964 original size:94 final size:94
Alignment explanation
Indices: 1442795--1443138 Score: 209
Period size: 95 Copynumber: 3.6 Consensus size: 94
1442785 ATCGTTAGTA
** * * *
1442795 AAAAAGATTGACTAGGTTATAACCATGATAGTCAAATAAGAAGACTGAGGCAAAACCTATTAGTC
1 AAAAAGATTGACTAGGACAAAACCATGATAGTCAAAGAAGAAGACTGAGGCAAAACCTATCAGTC
*
1442860 GAAAAAATGACCAGATAAAACCTTCAATG
66 CAAAAAATGACCAGATAAAACCTTCAATG
* * * *
1442889 AAAAAGATTGACTAGGACAAAACCATTATAGTTAAAGAAGACA-ACT-AGGGCGAAACTTATCAG
1 AAAAAGATTGACTAGGACAAAACCATGATAGTCAAAGAAGA-AGACTGA-GGCAAAACCTATCAG
** * *
1442952 -CCAAAAATATGACCAAGGCAAAAACTTCAGTCG
64 TCCAAAAA-ATGACC-AGATAAAACCTTCAAT-G
* *** ** * * * * ** *
1442985 AAAAA-ATCGACTAGGGTGAAATTATGATAATCAAAAAAGACGAAT-AGGGTGAAACCTATTAGT
1 AAAAAGATTGACTAGGACAAAACCATGATAGTCAAAGAAGAAGACTGA-GGCAAAACCTATCAGT
** * *
1443048 --AAAAAAT-ACAACAAAGGCAAAACCTTCAGTT
65 CCAAAAAATGAC--C--AGATAAAACCTTCAATG
* * * * * *
1443079 AGAAAGATTGACTAAGACAAAACCATGATGGTCAAAGAAGATGACTAAGGGAAAACCTAT
1 AAAAAGATTGACTAGGACAAAACCATGATAGTCAAAGAAGAAGACTGAGGCAAAACCTAT
1443139 TAATTGAAAA
Statistics
Matches: 192, Mismatches: 46, Indels: 23
0.74 0.18 0.09
Matches are distributed among these distances:
92 2 0.01
93 9 0.05
94 66 0.34
95 108 0.56
96 7 0.04
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (94 bp):
AAAAAGATTGACTAGGACAAAACCATGATAGTCAAAGAAGAAGACTGAGGCAAAACCTATCAGTC
CAAAAAATGACCAGATAAAACCTTCAATG
Found at i:1443241 original size:31 final size:32
Alignment explanation
Indices: 1443206--1443284 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 32
1443196 CTTTAAGGCA
* *
1443206 AAACCTATTAGTTGAAAAGA-TGACCAGGGTT
1 AAACCTATTAGTTGAAAAGATTGACCAAGGTG
** *
1443237 AAACCT-TTAGTAAAAAAGATTGACTAAGGTG
1 AAACCTATTAGTTGAAAAGATTGACCAAGGTG
*
1443268 AAACCATAATAGTTGAA
1 AAACC-TATTAGTTGAA
1443285 GAAAATGATC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 11 0.30
31 19 0.51
32 1 0.03
33 6 0.16
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (32 bp):
AAACCTATTAGTTGAAAAGATTGACCAAGGTG
Found at i:1447459 original size:19 final size:18
Alignment explanation
Indices: 1447433--1447533 Score: 87
Period size: 19 Copynumber: 6.0 Consensus size: 18
1447423 AATTTCAGCG
1447433 ATTTGTATCGATACATAA
1 ATTTGTATCGATACATAA
1447451 ATGTTGTATCGATAC---A
1 AT-TTGTATCGATACATAA
1447467 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
1447483 GTATTGTATCGATAC---A
1 AT-TTGTATCGATACATAA
1447499 A--TGTATCGATACATAA
1 ATTTGTATCGATACATAA
*
1447515 GTATTGTATCGATACATAA
1 AT-TTGTATCGATACATAA
1447534 TTACTGCCAA
Statistics
Matches: 67, Mismatches: 3, Indels: 25
0.71 0.03 0.26
Matches are distributed among these distances:
13 22 0.33
16 5 0.07
18 2 0.03
19 38 0.57
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTTGTATCGATACATAA
Found at i:1447472 original size:32 final size:32
Alignment explanation
Indices: 1447436--1447530 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
1447426 TTCAGCGATT
* *
1447436 TGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1447468 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1447500 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1447531 TAATTACTGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1447473 original size:13 final size:13
Alignment explanation
Indices: 1447455--1447511 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1447445 ACATAAATGT
1447455 TGTATCGATACAA
1 TGTATCGATACAA
1447468 TGTATCGATACATAAGTA
1 TGTATCGATAC---A--A
1447486 TTGTATCGATACAA
1 -TGTATCGATACAA
1447500 TGTATCGATACA
1 TGTATCGATACA
1447512 TAAGTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1447612 original size:34 final size:33
Alignment explanation
Indices: 1447549--1447615 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1447539 GCCAAGGGAA
*
1447549 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
* *
1447582 TGTATTGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
1447616 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:1447812 original size:10 final size:10
Alignment explanation
Indices: 1447797--1447837 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
1447787 GTGGGGACCT
1447797 TTTTCGATAA
1 TTTTCGATAA
1447807 TTTTCGATAA
1 TTTTCGATAA
*
1447817 TTTTCGACAA
1 TTTTCGATAA
*
1447827 TTTTCGCTAA
1 TTTTCGATAA
1447837 T
1 T
1447838 AGGCCTAGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.49
Consensus pattern (10 bp):
TTTTCGATAA
Found at i:1447908 original size:52 final size:52
Alignment explanation
Indices: 1447843--1448034 Score: 249
Period size: 52 Copynumber: 3.6 Consensus size: 52
1447833 CTAATAGGCC
1447843 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATA
* * *
1447895 TAACTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATG
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATA
* * * *
1447947 TAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATA
1 TAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CATCTTTAAGTCCAATA
* * * * *
1448002 TCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 TAGCTGGCCTTGAATCAGCATATTGGCACCTTT
1448035 ATCACTTTTC
Statistics
Matches: 120, Mismatches: 17, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
52 74 0.62
53 5 0.04
54 6 0.05
55 35 0.29
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (52 bp):
TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATA
Found at i:1448026 original size:107 final size:104
Alignment explanation
Indices: 1447843--1448034 Score: 267
Period size: 107 Copynumber: 1.8 Consensus size: 104
1447833 CTAATAGGCC
* * * * *
1447843 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATATAACTGGCCTTGA
1 TAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAGCTTTAAGCCCAATATAACTGGCCGTGA
*
1447908 ATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATG
66 ATCAACATATTGGCACCTTTTCCATCTTTAAGTTCAATG
***
1447947 TAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCG
1 TAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAGCTTTAAGCCCAATATAACTGGCCG
*
1448012 TGAATCAACATATTGGCATCTTT
63 TGAATCAACATATTGGCACCTTT
1448035 ATCACTTTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
104 26 0.35
105 2 0.03
106 5 0.07
107 42 0.56
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (104 bp):
TAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAGCTTTAAGCCCAATATAACTGGCCGTGA
ATCAACATATTGGCACCTTTTCCATCTTTAAGTTCAATG
Found at i:1452040 original size:52 final size:51
Alignment explanation
Indices: 1451962--1452109 Score: 224
Period size: 51 Copynumber: 2.9 Consensus size: 51
1451952 CGAAATATGA
1451962 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
** *
1452014 AAATTTGCCTGCATGTATCGATACATTTTTAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
* **
1452065 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1452110 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 46 0.53
52 40 0.47
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1452116 original size:13 final size:13
Alignment explanation
Indices: 1452098--1452122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1452088 CAAAGATCAG
1452098 TGTATCGATACAA
1 TGTATCGATACAA
1452111 TGTATCGATACA
1 TGTATCGATACA
1452123 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1452205 original size:13 final size:13
Alignment explanation
Indices: 1452187--1452211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1452177 AAAAAAAATA
1452187 TGTATCGATACAT
1 TGTATCGATACAT
1452200 TGTATCGATACA
1 TGTATCGATACA
1452212 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
Done.