Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 10 of 27
Found at i:1414726 original size:21 final size:20
Alignment explanation
Indices: 1414700--1414754 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
1414690 ATCAATACAT
*
1414700 TGTATCGATACATTACCCAGA
1 TGTATCGATACATTACACA-A
**
1414721 TGTATCGATACATTTTACAA
1 TGTATCGATACATTACACAA
1414741 TGTATCGATACATT
1 TGTATCGATACATT
1414755 CAGGCATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTACACAA
Found at i:1414745 original size:20 final size:20
Alignment explanation
Indices: 1414606--1414754 Score: 95
Period size: 20 Copynumber: 7.8 Consensus size: 20
1414596 GTTTACCCTG
*
1414606 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTTACA
* *
1414626 TTATATCGATACATTGCTTAC-
1 ATGTATCGATACATT--TTACA
*
1414647 -TGTATCGATACATTTTGCA
1 ATGTATCGATACATTTTACA
*
1414666 TTGTATCGATACATTGCTTAC-
1 ATGTATCGATACATT--TTACA
1414687 -TGTATC---A-A---TACA
1 ATGTATCGATACATTTTACA
* ***
1414699 TTGTATCGATACATTACCCA
1 ATGTATCGATACATTTTACA
1414719 GATGTATCGATACATTTTACA
1 -ATGTATCGATACATTTTACA
1414740 ATGTATCGATACATT
1 ATGTATCGATACATT
1414755 CAGGCATTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
11 3 0.03
13 6 0.06
16 2 0.02
17 2 0.02
18 3 0.03
20 63 0.62
21 16 0.16
22 6 0.06
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTACA
Found at i:1417118 original size:51 final size:51
Alignment explanation
Indices: 1417063--1417191 Score: 134
Period size: 51 Copynumber: 2.5 Consensus size: 51
1417053 TCCCGGTTCC
*
1417063 ATTTCCAAAACATCAATTTTTCTTAATC-AGGGATAATCCAACTCCAATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGA-GGATAATCCAACTCCAATTTT
* * * ** ** ** *
1417114 ATTTCTAAAGCATCGATTTACCGCAATCGAGGATGCTCCAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGAGGATAATCCAACTCCAATTTT
*
1417165 ATTTCCAAAACACCAATTTTTCATAAT
1 ATTTCCAAAACATCAATTTTTCATAAT
1417192 TGGGGATACT
Statistics
Matches: 59, Mismatches: 18, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
51 58 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCATAATCGAGGATAATCCAACTCCAATTTT
Found at i:1417226 original size:28 final size:28
Alignment explanation
Indices: 1417193--1417266 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
1417183 TTTCATAATT
* *
1417193 GGGGATACTCTAACCCCGTTATTTCAT-C
1 GGGGATACTCCAACCCCGTTATTTC-TGA
1417221 GGGGATACTCCAACCCCGTTATTTCTGA
1 GGGGATACTCCAACCCCGTTATTTCTGA
1417249 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1417267 ACTTTATGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCTGA
Found at i:1417381 original size:108 final size:108
Alignment explanation
Indices: 1417181--1417421 Score: 286
Period size: 108 Copynumber: 2.2 Consensus size: 108
1417171 AAAACACCAA
* * * * *
1417181 TTTTTCATAATTGGGGATACTCTAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTATTTC
1 TTTTTCATAATCGGGGATACTCCAACCCCATTATGTCATCGGAGATACTCCAACCCCGTTATTTC
* *
1417246 TGAGGGGATACTCCAACCCCGACTTTATGTCTAACATATTGAT
66 CGAGGGAATACTCCAACCCCGACTTTATGTCTAACATATTGAT
* * * *
1417289 TTTTTCATAATCGGGGGTACTCCGACCCCATTATGTCATCGGAGATACTCCAATCTCGTTATTTC
1 TTTTTCATAATCGGGGATACTCCAACCCCATTATGTCATCGGAGATACTCCAACCCCGTTATTTC
** * * * ** *
1417354 CGAGGGAATACTCCAACCTTGATTTTATTTCTAAAATA-CCAA
66 CGAGGGAATACTCCAACCCCGACTTTATGTCTAACATATTGAT
* *
1417396 TTTTTCACAATCCGGGATACTCCAAC
1 TTTTTCATAATCGGGGATACTCCAAC
1417422 TTCGATTTTA
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
107 23 0.21
108 87 0.79
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (108 bp):
TTTTTCATAATCGGGGATACTCCAACCCCATTATGTCATCGGAGATACTCCAACCCCGTTATTTC
CGAGGGAATACTCCAACCCCGACTTTATGTCTAACATATTGAT
Found at i:1417417 original size:51 final size:52
Alignment explanation
Indices: 1417361--1417473 Score: 176
Period size: 51 Copynumber: 2.2 Consensus size: 52
1417351 TTCCGAGGGA
* * *
1417361 ATACTCCAACCTT-GATTTTATTTCTAAAATACCAATTTTTCACAATCCGGG
1 ATACTCCAACCTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCCGGG
*
1417412 ATACTCCAA-CTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
1 ATACTCCAACCTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCCGGG
1417463 ATACTCCAACC
1 ATACTCCAACC
1417474 CTGTTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
50 3 0.05
51 52 0.93
52 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACTCCAACCTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCCGGG
Found at i:1417497 original size:79 final size:77
Alignment explanation
Indices: 1417409--1417707 Score: 319
Period size: 79 Copynumber: 3.8 Consensus size: 77
1417399 TTCACAATCC
**
1417409 GGGATACTCCAACTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTT-TCACAATCGGGGATACTCCAACC
*
1417474 CTGTTATTATCATG
65 CCGTTATTATCA-G
*** * * * * *
1417488 GGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCGATTTTTTACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACA-CCAATTTTCACAATCGGGGATACTCCAACC
* *
1417553 CCGTTATTTTTAAG
65 CCGTTA-TTATCAG
* * * * *
1417567 GGGATACTCCATCCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATGCTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTC-ACAATCGGGGATACTCCAACC
* *
1417632 CCATTATTTTCGAG
65 CCGTTATTATC-AG
* * * *
1417646 GGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCCATAATCGGGGATGCTCCA
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTT-CACAATCGGGGATACTCCA
1417708 CCCTTGTTGT
Statistics
Matches: 184, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
78 10 0.05
79 164 0.89
80 10 0.05
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (77 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCACAATCGGGGATACTCCAACCC
CGTTATTATCAG
Found at i:1417697 original size:158 final size:158
Alignment explanation
Indices: 1417409--1417707 Score: 361
Period size: 158 Copynumber: 1.9 Consensus size: 158
1417399 TTCACAATCC
** *
1417409 GGGATACTCCAACTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATCAGGGATACTCCAACC
** ** * * * **
1417474 CTGTTATTATCATGGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCGATTTTTTACAATCG
66 CCATTATTATCATGGGGATACTCCAACCCCAACCTTATTTCTAAAACACCAATTTTCCACAATCG
1417539 GGGATACTCCAACCCCGTTATTTTTAAG
131 GGGATACTCCAACCCCGTTATTTTTAAG
* * * *
1417567 GGGATACTCCATCCCCGATTTTATTTTCAAAACACCAATTT-TCTATAATCAGGGATGCTCCAAC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTC-ACAATCAGGGATACTCCAAC
* ** *
1417631 CCCATTATTTTCGA-GGGGATACTCCAACCCCAATTTTATTT-TCAAAACACCAATTTTCCATAA
65 CCCATTATTATC-ATGGGGATACTCCAACCCCAACCTTATTTCT-AAAACACCAATTTTCCACAA
*
1417694 TCGGGGATGCTCCA
128 TCGGGGATACTCCA
1417708 CCCTTGTTGT
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
157 3 0.03
158 113 0.97
159 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (158 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCTCACAATCAGGGATACTCCAACC
CCATTATTATCATGGGGATACTCCAACCCCAACCTTATTTCTAAAACACCAATTTTCCACAATCG
GGGATACTCCAACCCCGTTATTTTTAAG
Found at i:1422360 original size:20 final size:19
Alignment explanation
Indices: 1422315--1422366 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1422305 CTGCTAGTTT
* *
1422315 CATGTATCGTTACAATGAA
1 CATGTATCGATACAAAGAA
1422334 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAAAG-AA
* *
1422354 TATGTATCAATAC
1 CATGTATCGATAC
1422367 TTCTCGGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:1427834 original size:20 final size:20
Alignment explanation
Indices: 1427763--1427837 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1427753 GTAAAAAAAC
*
1427763 AATGTATCAATACATTGAAA
1 AATGTATCGATACATTGAAA
* * *
1427783 AATATATCGATACATTTATA
1 AATGTATCGATACATTGAAA
*
1427803 TATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* *
1427823 AATGCATTGATACAT
1 AATGTATCGATACAT
1427838 CAGGGTTAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1432338 original size:13 final size:13
Alignment explanation
Indices: 1432320--1432345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1432310 TTTGGCTGAT
1432320 AATGTGGTTGAAA
1 AATGTGGTTGAAA
1432333 AATGTGGTTGAAA
1 AATGTGGTTGAAA
1432346 GCAAAAGCCC
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:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
AATGTGGTTGAAA
Found at i:1435623 original size:20 final size:19
Alignment explanation
Indices: 1435578--1435631 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1435568 ACATTATGCT
**
1435578 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
*
1435597 CTGTATCGATACATGCACAA
1 TTGTATCGATACATGCAC-A
*
1435617 TTGTATCGATGCATG
1 TTGTATCGATACATG
1435632 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:1441881 original size:13 final size:13
Alignment explanation
Indices: 1441849--1441887 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1441839 ACAATATTCT
*
1441849 TTGTATCGATATA
1 TTGTATCGATACA
* *
1441862 TTATATCAATACA
1 TTGTATCGATACA
1441875 TTGTATCGATACA
1 TTGTATCGATACA
1441888 AGGGTTACTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1442010 original size:21 final size:22
Alignment explanation
Indices: 1441986--1442035 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1441976 ATCAAATCTT
* *
1441986 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTAATTTTTCA
1442007 CTTCAAAATACTTAATTTTTCA
1 CTTCAAAATACTTAATTTTTCA
1442029 --TCAAAAT
1 CTTCAAAAT
1442036 TATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTAATTTTTCA
Found at i:1443756 original size:20 final size:19
Alignment explanation
Indices: 1443731--1443779 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1443721 TTTTGAAAAT
*
1443731 AAATTTTTATCAAGGGGGAA
1 AAATTTTTATCAA-AGGGAA
1443751 AAATTTTTTATCAAAGGGAA
1 AAA-TTTTTATCAAAGGGAA
*
1443771 AATTTTTTA
1 AAATTTTTA
1443780 ACGAGAGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 10 0.38
21 10 0.38
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (19 bp):
AAATTTTTATCAAAGGGAA
Found at i:1443760 original size:21 final size:19
Alignment explanation
Indices: 1443734--1443779 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
1443724 TGAAAATAAA
*
1443734 TTTTTATCAAGGGGGAAAAAT
1 TTTTTATCAA-AGGG-AAAAT
1443755 TTTTTATCAAAGGGAAAAT
1 TTTTTATCAAAGGGAAAAT
1443774 TTTTTA
1 TTTTTA
1443780 ACGAGAGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.46
20 3 0.12
21 10 0.42
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (19 bp):
TTTTTATCAAAGGGAAAAT
Found at i:1448859 original size:154 final size:154
Alignment explanation
Indices: 1448660--1449092 Score: 407
Period size: 154 Copynumber: 2.8 Consensus size: 154
1448650 ACTGGATAAT
* * * *
1448660 CCTAAAGGAAC-TAAAAAGGATT-ATAGATGGGACAAACCTATCCTAAATACCCACTTTTGGCAT
1 CCTAAAGG-ACTTAAAAAGGATTAACAAATGGGATAAACCTATCCTAAATACCCACCTTTGGCAT
* * * *
1448723 AAAAGTGCACCCGGTGACAACCTAAGACTCAGTTCTAAAAAATTATCAAATACCCCTAAGGAAAT
65 AAAAGAGAACCCGGTGACAACCTAAGACTTAGTTCTAAAAAATTATCAAATACCCCTAAGGAAAC
* * *
1448788 CTTTGACATAGAAGT-GCTCAATACC
130 CTTTGACATAAAAGTACCT-AACACC
* *
1448813 CCTAAAGGACTTAAAAAGGATTAACAAATGGGATGAACCTATCCTAAATGCCCACCTTTGGCATT
1 CCTAAAGGACTTAAAAAGGATTAACAAATGGGATAAACCTATCCTAAATACCCACCTTTGGCA-T
* * * * * * * *
1448878 AAAACA-AACGCGGTGACAACCTAGGACTTGGTTTTAGAAAATTA-CAAAAATACCCTTAGGGGA
65 AAAAGAGAACCCGGTGACAACCTAAGACTTAGTTCTAAAAAATTATC--AAATACCCCTA-AGGA
* **
1448941 TACCTTTGACATAAAAGTACCTGGCACC
127 AACCTTTGACATAAAAGTACCTAACACC
* * * * *
1448969 TCTACAA-GACTTAAAAA-GATCATAGAAA--GGATTAACCTATCCTAAATACCCACCTTTGACA
1 CCTA-AAGGACTTAAAAAGGATTA-ACAAATGGGATAAACCTATCCTAAATACCCACCTTTGGCA
* * * * * *
1449030 TAAAAGAGGACCCGGCGACAACCAAAAACTTAGTTCTAAAAAATTATAAAAAAGCCCCTAAGG
64 TAAAAGAGAACCCGGTGACAACCTAAGACTTAGTTCTAAAAAATTATCAAATA-CCCCTAAGG
1449093 GTTACTTTCG
Statistics
Matches: 224, Mismatches: 44, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
152 2 0.01
153 32 0.14
154 129 0.58
155 19 0.08
156 38 0.17
157 4 0.02
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (154 bp):
CCTAAAGGACTTAAAAAGGATTAACAAATGGGATAAACCTATCCTAAATACCCACCTTTGGCATA
AAAGAGAACCCGGTGACAACCTAAGACTTAGTTCTAAAAAATTATCAAATACCCCTAAGGAAACC
TTTGACATAAAAGTACCTAACACC
Found at i:1450497 original size:16 final size:16
Alignment explanation
Indices: 1450476--1450508 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1450466 AGTTACTATA
1450476 TGGTTGCTTGGTTTTG
1 TGGTTGCTTGGTTTTG
1450492 TGGTTGCTTGGTTTTG
1 TGGTTGCTTGGTTTTG
1450508 T
1 T
1450509 AGCTACTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.36, T:0.58
Consensus pattern (16 bp):
TGGTTGCTTGGTTTTG
Found at i:1451008 original size:7 final size:7
Alignment explanation
Indices: 1450996--1451028 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1450986 ATATATCTAT
1450996 TTTTTTC
1 TTTTTTC
1451003 TTTTTTC
1 TTTTTTC
1451010 TTTTTT-
1 TTTTTTC
*
1451016 TTTTTAC
1 TTTTTTC
1451023 TTTTTT
1 TTTTTT
1451029 GATTGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:1451019 original size:13 final size:14
Alignment explanation
Indices: 1450996--1451028 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1450986 ATATATCTAT
*
1450996 TTTTTTCTTTTTTC
1 TTTTTTCTTTTTAC
1451010 TTTTTT-TTTTTAC
1 TTTTTTCTTTTTAC
1451023 TTTTTT
1 TTTTTT
1451029 GATTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTCTTTTTAC
Found at i:1451707 original size:165 final size:165
Alignment explanation
Indices: 1451501--1451834 Score: 402
Period size: 165 Copynumber: 2.0 Consensus size: 165
1451491 ATTTCTTAAA
* *
1451501 AAAAAAAGGACTTTAAAGAAAAAAATTCAAAACTCATGAAAATGAATTAATTTTTTGAAACCAAT
1 AAAAAAAGGACTTTAAAGAAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTTAAAACCAAT
* ** * * **
1451566 TTAATATGAATCAAATGATGATA-TTGATGAATTTTAAAAATTGAAAACCAA-GAAAATCCTCTT
66 TTAATATGAATCAAATAACAATATTTGATGAATTTTAAAAATTAAAAACCAACAAAAATCCTCCC
* * * * *
1451629 AAAAAAATTTATGGAGTAGAAAATACCTTATTTTG
131 AAAAAAATTTACGGAGAACAAAATACCGTAATTTG
* * * * * * *
1451664 AAAAAAGGGACTTTCAAGGAAACAAATTCAAAAATTTATGAAAATGAATGACTTTTTTAAAACTA
1 AAAAAAAGGACTTT-AAAGAAAAAAATTC-AAAACTCATGAAAATGAATGAATTTTTTAAAACCA
* * *
1451729 ATTTAATATGAGTTAAATAACAATATTTGATGAATTTTAAAAATTAAAAACTAACAAAAATCCTC
64 ATTTAATATGAATCAAATAACAATATTTGATGAATTTTAAAAATTAAAAACCAACAAAAATCCTC
* *
1451794 CCGAAAAAATTTACGGAGAACAAAATCCCGTAATTTG
129 CCAAAAAAATTTACGGAGAACAAAATACCGTAATTTG
1451831 AAAA
1 AAAA
1451835 TAGGAAGAAT
Statistics
Matches: 141, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
163 13 0.09
164 12 0.09
165 49 0.35
166 26 0.18
167 41 0.29
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (165 bp):
AAAAAAAGGACTTTAAAGAAAAAAATTCAAAACTCATGAAAATGAATGAATTTTTTAAAACCAAT
TTAATATGAATCAAATAACAATATTTGATGAATTTTAAAAATTAAAAACCAACAAAAATCCTCCC
AAAAAAATTTACGGAGAACAAAATACCGTAATTTG
Found at i:1452986 original size:18 final size:19
Alignment explanation
Indices: 1452941--1452978 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1452931 AAAACAAAGA
*
1452941 ATAACAAAAGCAAAAAAAC
1 ATAAAAAAAGCAAAAAAAC
1452960 ATAAAAAAAG-AAAAAAAC
1 ATAAAAAAAGCAAAAAAAC
1452978 A
1 A
1452979 AATGAAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.79, C:0.11, G:0.05, T:0.05
Consensus pattern (19 bp):
ATAAAAAAAGCAAAAAAAC
Found at i:1454673 original size:84 final size:83
Alignment explanation
Indices: 1454447--1454723 Score: 240
Period size: 85 Copynumber: 3.3 Consensus size: 83
1454437 GTAACCTGTT
*
1454447 AGCTCAGTCTCCGGTCAACCTTCATCTCATTGTTTACCTATAAGCTCAATCCCCAAG-AAACCCA
1 AGCTCAGTCTCCGGTCAACCTTCATCTCATTGTTTACCTAT-AGCTCAGT-CCC-AGTAAACCCA
1454511 TTACACTTATGGTGACTTGTC
63 TTACACTTATGGTGACTTGTC
* * * ** * * * *
1454532 AACTTAGCCTTTGGTCAACATTCATC-CTTTGTTTACCTATTGACTCAGTCCTTAGTAAACCTC-
1 AGCTCAGTCTCCGGTCAACCTTCATCTCATTGTTTACCTATAG-CTCAGTCC-CAGTAAACC-CA
1454595 TTACA-TCTATGGTGACTTGTC
63 TTACACT-TATGGTGACTTGTC
** * * *
1454616 AGCTCAGTCTCCATTCAACCTTCATCTCCTTGTTTACCTGTCAGCTTAGTCCCAGTAAACCCACT
1 AGCTCAGTCTCCGGTCAACCTTCATCTCATTGTTTACCTAT-AGCTCAGTCCCAGTAAACCCA-T
* ** *
1454681 TAC-CTTTTTGGTGACCGGAC
64 TACAC-TTATGGTGACTTGTC
* *
1454701 AGCTTAGTCTCCGGTCCACCTTC
1 AGCTCAGTCTCCGGTCAACCTTC
1454724 CCTATTGGCT
Statistics
Matches: 150, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
83 7 0.05
84 68 0.45
85 73 0.49
86 2 0.01
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (83 bp):
AGCTCAGTCTCCGGTCAACCTTCATCTCATTGTTTACCTATAGCTCAGTCCCAGTAAACCCATTA
CACTTATGGTGACTTGTC
Found at i:1454934 original size:86 final size:84
Alignment explanation
Indices: 1454786--1454945 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 84
1454776 CAATCTCCGA
* * *
1454786 TCAACCTTCCTCCTTTGTTTACCTGTTGGTTCAATCCCCGATAAACCTCTTACACCTATGGTGAC
1 TCAACCTTCCTCCTTTATTTACCTGTCGGCTCAATCCCCGATAAACCTCTTACACCTATGGTGAC
1454851 TTGTCAACTCATTCTCTAG
66 TTGTCAACTCATTCTCTAG
* * * *
1454870 TCAACCTTCATCTCC-TTATTTATCTGTCGGCTCAGTCCCCGATAAGCCTCCTTAC-CCTTTTGG
1 TCAACCTTC--CTCCTTTATTTACCTGTCGGCTCAATCCCCGATAAACCT-CTTACACC-TATGG
1454933 TGACTTGTCAACT
62 TGACTTGTCAACT
1454946 TAGTTTATGA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 9 0.14
85 30 0.46
86 26 0.40
ACGTcount: A:0.19, C:0.32, G:0.12, T:0.37
Consensus pattern (84 bp):
TCAACCTTCCTCCTTTATTTACCTGTCGGCTCAATCCCCGATAAACCTCTTACACCTATGGTGAC
TTGTCAACTCATTCTCTAG
Found at i:1454960 original size:86 final size:84
Alignment explanation
Indices: 1454784--1454962 Score: 195
Period size: 86 Copynumber: 2.1 Consensus size: 84
1454774 CTCAATCTCC
* * *
1454784 GATCAACCTTCCTCCTTTGTTTACCTGTTGGTTCAATCCCCGATAAACCTCTTACACCTATGGTG
1 GATCAACCTTCCTCCTTTATTTACCTGTCGGCTCAATCCCCGATAAACCTCTTACACCTATGGTG
*
1454849 ACTTGTCAACTCATTCTCT
66 ACTTGTCAACTCATTCTAT
* * * *
1454868 -AGTCAACCTTCATCTCC-TTATTTATCTGTCGGCTCAGTCCCCGATAAGCCTCCTTAC-CCTTT
1 GA-TCAACCTTC--CTCCTTTATTTACCTGTCGGCTCAATCCCCGATAAACCT-CTTACACC-TA
*
1454930 TGGTGACTTGTCAACTTAGTT-TAT
61 TGGTGACTTGTCAACTCA-TTCTAT
1454954 GATCAACCT
1 GATCAACCT
1454963 CTATCTCATT
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
83 1 0.01
84 9 0.11
85 30 0.38
86 36 0.46
87 3 0.04
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (84 bp):
GATCAACCTTCCTCCTTTATTTACCTGTCGGCTCAATCCCCGATAAACCTCTTACACCTATGGTG
ACTTGTCAACTCATTCTAT
Found at i:1455590 original size:8 final size:8
Alignment explanation
Indices: 1455576--1455614 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1455566 TTATTGAGTT
1455576 ATTAAAAA
1 ATTAAAAA
1455584 A-T-AAAA
1 ATTAAAAA
1455590 ATT-AAAA
1 ATTAAAAA
1455597 ATTAAAAA
1 ATTAAAAA
1455605 ATTAAAAA
1 ATTAAAAA
1455613 AT
1 AT
1455615 ATATAATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 5 0.17
7 9 0.31
8 15 0.52
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
ATTAAAAA
Found at i:1455591 original size:6 final size:7
Alignment explanation
Indices: 1455576--1455612 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
1455566 TTATTGAGTT
1455576 ATTAAAA
1 ATTAAAA
*
1455583 AATAAAA
1 ATTAAAA
1455590 ATTAAAA
1 ATTAAAA
1455597 ATTAAAAA
1 ATT-AAAA
1455605 ATTAAAA
1 ATTAAAA
1455612 A
1 A
1455613 ATATATAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
ATTAAAA
Found at i:1455655 original size:22 final size:22
Alignment explanation
Indices: 1455583--1455656 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
1455573 GTTATTAAAA
* * *
1455583 AATAAAAAT-TAAAAATTAAAA
1 AATAAAAATATAATAATCAAAT
1455604 AATTAAAAA-ATATATAATCATAATT
1 AA-TAAAAATATA-ATAATCA-AA-T
1455629 AAATAAAAATATAATAATCAAAT
1 -AATAAAAATATAATAATCAAAT
1455652 AATAA
1 AATAA
1455657 TTAAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
21 2 0.05
22 13 0.30
23 6 0.14
24 4 0.09
25 13 0.30
26 5 0.12
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAAAAATATAATAATCAAAT
Found at i:1455662 original size:25 final size:26
Alignment explanation
Indices: 1455602--1455664 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
1455592 TAAAAATTAA
1455602 AAAATTAAAAAATATATAATCATAAT
1 AAAATTAAAAAATATATAATCATAAT
*
1455628 TAAA-T-AAAAATATAATAATCA-AAT
1 AAAATTAAAAAATAT-ATAATCATAAT
1455652 AATAATTAAAAAA
1 AA-AATTAAAAAA
1455665 AAGAAAGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
24 12 0.39
25 10 0.32
26 4 0.13
27 5 0.16
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAATTAAAAAATATATAATCATAAT
Found at i:1455971 original size:72 final size:72
Alignment explanation
Indices: 1455863--1456008 Score: 202
Period size: 72 Copynumber: 2.0 Consensus size: 72
1455853 CAAAGTCAAC
* *
1455863 ATGAAATTAAAGCAACGAAGCTACTAAACAAAAAGAAGAAACGCATGAAAGAAAAAGCAATTAAG
1 ATGAAATTAAAGCAACGAAGCCACTAAACAAAAAGAAAAAACGCATGAAAGAAAAAGCAATTAAG
* *
1455928 TTGCAAA
66 CTACAAA
* ** * * *
1455935 ATGAAATTAAAGTAATTAAGCCACTGAACAAGAAGAAAAAATGCATGAAAGAAAAAGCAATTAAG
1 ATGAAATTAAAGCAACGAAGCCACTAAACAAAAAGAAAAAACGCATGAAAGAAAAAGCAATTAAG
1456000 CTACAAA
66 CTACAAA
1456007 AT
1 AT
1456009 TAAGCTACTG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.16
Consensus pattern (72 bp):
ATGAAATTAAAGCAACGAAGCCACTAAACAAAAAGAAAAAACGCATGAAAGAAAAAGCAATTAAG
CTACAAA
Found at i:1456013 original size:58 final size:57
Alignment explanation
Indices: 1455948--1456065 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 57
1455938 AAATTAAAGT
* *
1455948 AATTAAGCCACTGAACAAGAAGAAA-AAATGCATGAAAGAAAAAGCAATTAAGCTACAA
1 AATTAAGCCACTGAACAAGAA-AAAGAAACGCATGAAAGAAAAA-CAATTAAACTACAA
* * *
1456006 AATTAAGCTACTGAACAAGAAAAAGAAACGCATGAAAGAAAAATAATTAAACTGCAA
1 AATTAAGCCACTGAACAAGAAAAAGAAACGCATGAAAGAAAAACAATTAAACTACAA
1456063 AAT
1 AAT
1456066 AAAAAACAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 17 0.31
58 37 0.69
ACGTcount: A:0.58, C:0.13, G:0.14, T:0.15
Consensus pattern (57 bp):
AATTAAGCCACTGAACAAGAAAAAGAAACGCATGAAAGAAAAACAATTAAACTACAA
Found at i:1456124 original size:125 final size:129
Alignment explanation
Indices: 1455880--1456124 Score: 322
Period size: 125 Copynumber: 1.9 Consensus size: 129
1455870 TAAAGCAACG
**
1455880 AAGCTACTAAACAAAAAGAAGAAACGCATGAAAGAAAAAGCAATTAAGTTGCAAAATGAAATTAA
1 AAGCTACTAAACAAAAAGAAGAAACGCATGAAAGAAAAAGCAATTAAACTGCAAAATGAAA-TAA
* * * *
1455945 AGTAATTAAGCCACTGAACAAGAAGAAAAAATGCATGAAAGAAAAAGCAATTAAGCTACAAAATT
65 AGCAATTAAGCCACTGAACAAGAAGAAAAAACGCAAGAAAAAAAAAGCAATTAAGCTACAAAATT
* *
1456010 AAGCTACTGAACAAGAAA-AAGAAACGCATGAAAGAAAAA-TAATTAAACTGCAAAAT-AAA-AA
1 AAGCTACTAAACAA-AAAGAAGAAACGCATGAAAGAAAAAGCAATTAAACTGCAAAATGAAATAA
** *
1456071 A-CAATTAAGTTGA-TGAACAAGAAGAAGAAACGCAAGAAAAAAAAAGCAATTAAG
65 AGCAATTAAG-CCACTGAACAAGAAGAAAAAACGCAAGAAAAAAAAAGCAATTAAG
1456125 TAGTAGTAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
125 44 0.43
126 4 0.04
128 3 0.03
129 14 0.14
130 34 0.33
131 3 0.03
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.15
Consensus pattern (129 bp):
AAGCTACTAAACAAAAAGAAGAAACGCATGAAAGAAAAAGCAATTAAACTGCAAAATGAAATAAA
GCAATTAAGCCACTGAACAAGAAGAAAAAACGCAAGAAAAAAAAAGCAATTAAGCTACAAAATT
Found at i:1456177 original size:22 final size:23
Alignment explanation
Indices: 1456132--1456179 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1456122 AAGTAGTAGT
* *
1456132 AAATGAAAGAAATCGATAATAGC
1 AAATGAAAGAAATCGACAACAGC
*
1456155 AAATGAAA-AAATCGACAGCAGC
1 AAATGAAAGAAATCGACAACAGC
1456177 AAA
1 AAA
1456180 GGAAGAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.58, C:0.12, G:0.17, T:0.12
Consensus pattern (23 bp):
AAATGAAAGAAATCGACAACAGC
Found at i:1461625 original size:41 final size:41
Alignment explanation
Indices: 1461568--1461678 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
1461558 TCATAGAGTG
* *
1461568 TGCCCATGCCTTATCAAACAAGAGTTTC-GAGTTTCTTAATA
1 TGCCCACGCCTTATCAAACAAGAGTTTCTG-GTTTCTTAACA
*
1461609 TGCCCACGCCTTATCAAATAAGAGTTTCTGGTTTCTTAACA
1 TGCCCACGCCTTATCAAACAAGAGTTTCTGGTTTCTTAACA
*
1461650 TGCCCACGTCTTATCAAACAAGAGTTTCT
1 TGCCCACGCCTTATCAAACAAGAGTTTCT
1461679 AATTTAAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 63 0.98
42 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (41 bp):
TGCCCACGCCTTATCAAACAAGAGTTTCTGGTTTCTTAACA
Found at i:1463128 original size:13 final size:13
Alignment explanation
Indices: 1463110--1463135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1463100 CATTTTGGGA
1463110 TGTATCGATACAT
1 TGTATCGATACAT
1463123 TGTATCGATACAT
1 TGTATCGATACAT
1463136 CTTGTGTGTA
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:1463134 original size:33 final size:32
Alignment explanation
Indices: 1463090--1463153 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1463080 TACAAGCCAA
*
1463090 TGTATCCATACATTTTGGGATGTATCGATACAT
1 TGTATCCATACATCTTGGG-TGTATCGATACAT
* *
1463123 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCCATACATCTTGGGTGTATCGATACA
1463154 AACAATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCCATACATCTTGGGTGTATCGATACAT
Found at i:1463902 original size:20 final size:20
Alignment explanation
Indices: 1463877--1463914 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1463867 TTTAATCACA
1463877 AGTTTCTTTCTCCCCCTTCT
1 AGTTTCTTTCTCCCCCTTCT
1463897 AGTTTCTTTCTCCCCCTT
1 AGTTTCTTTCTCCCCCTT
1463915 AATCATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.39, G:0.05, T:0.50
Consensus pattern (20 bp):
AGTTTCTTTCTCCCCCTTCT
Found at i:1467577 original size:13 final size:13
Alignment explanation
Indices: 1467559--1467584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1467549 CATTTTGGGA
1467559 TGTATCGATACAT
1 TGTATCGATACAT
1467572 TGTATCGATACAT
1 TGTATCGATACAT
1467585 CTTGTGTGTA
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:1467581 original size:33 final size:32
Alignment explanation
Indices: 1467539--1467602 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1467529 TACAAGCCAA
*
1467539 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
1467572 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
1467603 AACAATTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:1467702 original size:13 final size:13
Alignment explanation
Indices: 1467684--1467708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1467674 ACATTTGGTC
1467684 ATGTATCGATACA
1 ATGTATCGATACA
1467697 ATGTATCGATAC
1 ATGTATCGATAC
1467709 TTTGCAATAT
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):
ATGTATCGATACA
Found at i:1467708 original size:33 final size:31
Alignment explanation
Indices: 1467662--1467729 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
1467652 TACATTCTTA
*
1467662 ACAAGTATCGATACATTTG-GTCATGTATCGAT
1 ACAAGTATCGATAC-TTTGAAT-ATGTATCGAT
1467694 ACAATGTATCGATACTTTGCAATATGTATCGAT
1 ACAA-GTATCGATACTTTG-AATATGTATCGAT
1467727 ACA
1 ACA
1467730 TTTGAAGGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
32 8 0.25
33 23 0.72
34 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (31 bp):
ACAAGTATCGATACTTTGAATATGTATCGAT
Found at i:1467722 original size:20 final size:19
Alignment explanation
Indices: 1467697--1467751 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1467687 TATCGATACA
*
1467697 ATGTATCGATACTTTGCAAT
1 ATGTATCGATACTTTG-AAG
1467717 ATGTATCGATACATTTGAAG
1 ATGTATCGATAC-TTTGAAG
*
1467737 GTGTATCGATACTTT
1 ATGTATCGATACTTT
1467752 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.09
20 25 0.78
21 4 0.12
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACTTTGAAG
Found at i:1476949 original size:21 final size:20
Alignment explanation
Indices: 1476917--1476968 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1476907 TTTTACAATT
1476917 TGTATC-ATACAAACAGTAAA
1 TGTATCGATACAAA-AGTAAA
*
1476937 TGTATCGATACAAAAGTGAA
1 TGTATCGATACAAAAGTAAA
1476957 TGTATCGATACA
1 TGTATCGATACA
1476969 TGCCTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:1477082 original size:20 final size:22
Alignment explanation
Indices: 1477037--1477092 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
1477027 CATAAGTAAA
**
1477037 TGTATCGATACATGCTCACAAT
1 TGTATCGATACATTATCACAAT
1477059 TGTATCGATACATTATC-C-AT
1 TGTATCGATACATTATCACAAT
*
1477079 TGTATTGATACATT
1 TGTATCGATACATT
1477093 TTAGGTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 15 0.48
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (22 bp):
TGTATCGATACATTATCACAAT
Found at i:1485947 original size:42 final size:42
Alignment explanation
Indices: 1485885--1486440 Score: 303
Period size: 42 Copynumber: 13.3 Consensus size: 42
1485875 AACCTTTTTA
* * *
1485885 TTTT-ACCCTTTGTCTACCTGTCCGCTTTGACCTAAGAGACT
1 TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGACT
** *
1485926 TTTTCACCCTTTGTTTGCCTGTCAG-TTTGACCTGGGAAACT
1 TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGACT
** * ** * *
1485967 TTTTTTCCTTTTGTTTGCCCATCGGCTTTGACCTAGGAGACT
1 TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGACT
* * * * * *
1486009 TTTTTACCCTTTGTTTGCCCGTTAGTTTTGACCCAGGAGACTT
1 TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGAC-T
* * *
1486052 CTTTTC-CCTTTTGTCTGCCTGTCAGCTTTGACCTAGGAGACT
1 -TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGACT
*
1486094 TCTTT-ACCCTTTGTTTGCCCT-TCAGTTTTGA-CTAAGGAGACT
1 T-TTTCACCCTTTGTTTG-CCTGTCAGCTTTGACCTAA-GAGACT
* * * *
1486136 TCTTT-TCCCTTTGTCTACCTGTCAGC-TTGACCCAAGAGACT
1 T-TTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGACT
* * * * ** * * **
1486177 TTTTTACCCTTTATCTACCCATTAGCTTT-ATCTCGGGAGACT
1 TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCT-AAGAGACT
* * ** *
1486219 TCTTCACTCTTTGTTTGCCCATCAGCTTTGA-CTCAAGACACT
1 TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCT-AAGAGACT
* * * * *
1486261 TTTTTACCTTTTGTCTGCCTGTTAGCTTTGACCTTAGAGACT
1 TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGACT
* * * ** * *
1486303 TCTTCATCTTTTGTCTT-CCCATCGGCTTTGACGTAAGAGACT
1 TTTTCACCCTTTGT-TTGCCTGTCAGCTTTGACCTAAGAGACT
* * * * * * * *
1486345 TCTACATCCTTTGTCTGCTTAT-TGACTTTGACCT-TGAAGACT
1 TTTTCACCCTTTGTTTGCCTGTCAG-CTTTGACCTAAG-AGACT
* * * **
1486387 TTTTTATCCTTTGTCTT-CCCGTCAGCTTTGACCTGGGAGACT
1 TTTTCACCCTTTGT-TTGCCTGTCAGCTTTGACCTAAGAGACT
1486429 TTTTCACCCTTT
1 TTTTCACCCTTT
1486441 TTCTACCTAT
Statistics
Matches: 398, Mismatches: 95, Indels: 43
0.74 0.18 0.08
Matches are distributed among these distances:
40 3 0.01
41 75 0.19
42 276 0.69
43 40 0.10
44 4 0.01
ACGTcount: A:0.15, C:0.26, G:0.16, T:0.42
Consensus pattern (42 bp):
TTTTCACCCTTTGTTTGCCTGTCAGCTTTGACCTAAGAGACT
Found at i:1486100 original size:85 final size:84
Alignment explanation
Indices: 1485885--1486306 Score: 372
Period size: 83 Copynumber: 5.0 Consensus size: 84
1485875 AACCTTTTTA
* * * *
1485885 TTTTACCCTTTGTCTACCTGTCCGCTTTGACCTAAGAGACTTTTTCACCCTTTGTTTGCCTGTCA
1 TTTT-CCCTTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTTACCCTTTGTTTGCCCGTTA
** * *
1485950 G-TTTGACCTGGGAAACTTT
65 GTTTTGACCAAGGAGACTTC
* * * ** * *
1485969 TTTTCCTTTTGTTTGCCCATCGGCTTTGACCTAGGAGACTTTTTTACCCTTTGTTTGCCCGTTAG
1 TTTTCCCTTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTTACCCTTTGTTTGCCCGTTAG
*
1486034 TTTTGACCCAGGAGACTTC
66 TTTTGACCAAGGAGACTTC
* * *
1486053 TTTTCCCTTTTGTCTGCCTGTCAGCTTTGACCTAGGAGACTTCTTTACCCTTTGTTTGCCC-TTC
1 TTTTCCC-TTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTTACCCTTTGTTTGCCCGTT-
*
1486117 AGTTTTGACTAAGGAGACTTC
64 AGTTTTGACCAAGGAGACTTC
* * * * *
1486138 TTTTCCCTTTGTCTACCTGTCAGC-TTGACCCAAGAGACTTTTTTACCCTTTATCTACCCATTAG
1 TTTTCCCTTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTTACCCTTTGTTTGCCCGTTAG
* *
1486202 CTTT-ATCTC-GGGAGACTTC
66 TTTTGA-C-CAAGGAGACTTC
** * * * ** * * * *
1486221 TTCACTCTTTGTTTGCCCATCAGCTTTGA-CTCAAGACACTTTTTTACCTTTTGTCTGCCTGTTA
1 TTTTCCCTTTGTCTACCTGTCAGCTTTGACCT-AAGAGACTTTTTTACCCTTTGTTTGCCCGTTA
* *
1486285 GCTTTGACCTTA-GAGACTTC
65 GTTTTGACC-AAGGAGACTTC
1486305 TT
1 TT
1486307 CATCTTTTGT
Statistics
Matches: 280, Mismatches: 47, Indels: 22
0.80 0.13 0.06
Matches are distributed among these distances:
82 1 0.00
83 114 0.41
84 90 0.32
85 75 0.27
ACGTcount: A:0.15, C:0.26, G:0.16, T:0.42
Consensus pattern (84 bp):
TTTTCCCTTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTTACCCTTTGTTTGCCCGTTAG
TTTTGACCAAGGAGACTTC
Found at i:1486177 original size:168 final size:168
Alignment explanation
Indices: 1485885--1486440 Score: 425
Period size: 168 Copynumber: 3.3 Consensus size: 168
1485875 AACCTTTTTA
*
1485885 TTTTACCCTTTGTCTACCTGTCCGCTTTGACCTAAGAGACTTTTTCACCCTTTGTTTGCCTGTCA
1 TTTTACCCTTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTCACCCTTTGTTTGCCTGTCA
* * * * * * * *
1485950 GTTTGACCTGGGAAACTTTTTTTCCTTTTGTTTGCCCATCGGCTTTGACCTAGGAGACTTTTTTA
66 GTTTGACCTAGGAAACTTCTTTTCCCTTTGTCTACCCATCAGCTTTGACCCAAGAGACTTTTTTA
1486015 CCCTTTGTTTGCCCGTTAGTTTTGACCCAGGAGACTTC
131 CCCTTTGTTTGCCCGTTAGTTTTGACCCAGGAGACTTC
* *
1486053 TTTT-CCCTTTTGTCTGCCTGTCAGCTTTGACCTAGGAGACTTCTTT-ACCCTTTGTTTGCCCT-
1 TTTTACCC-TTTGTCTACCTGTCAGCTTTGACCTAAGAGACTT-TTTCACCCTTTGTTTG-CCTG
* **
1486115 TCAGTTTTGA-CTAAGGAGACTTCTTTTCCCTTTGTCTACCTGTCAGC-TTGACCCAAGAGACTT
63 TCAG-TTTGACCT-AGGAAACTTCTTTTCCCTTTGTCTACCCATCAGCTTTGACCCAAGAGACTT
* * * * * * *
1486178 TTTTACCCTTTATCTACCCATTAGCTTT-ATCTCGGGAGACTTC
126 TTTTACCCTTTGTTTGCCCGTTAGTTTTGA-CCCAGGAGACTTC
* * * * ** * * * * *
1486221 -TTCACTCTTTGTTTGCCCATCAGCTTTGA-CTCAAGACACTTTTTTACCTTTTGTCTGCCTGTT
1 TTTTACCCTTTGTCTACCTGTCAGCTTTGACCT-AAGAGACTTTTTCACCCTTTGTTTGCCTGTC
* * * * * ** *
1486284 AGCTTTGACCTTA-GAGACTTCTTCAT-CTTTTGTCTTCCCATCGGCTTTGACGTAAGAGACTTC
65 AG-TTTGACC-TAGGAAACTTCTT-TTCCCTTTGTCTACCCATCAGCTTTGACCCAAGAGACTTT
** * * *** * ** *
1486347 TACATCCTTTGTCTGCTTATT-GACTTTGACCTTGAAGACTT-
127 TTTACCCTTTGTTTGCCCGTTAG-TTTTGACCCAGGAGACTTC
* * * **
1486388 TTTTATCCTTTGTCTTCCCGTCAGCTTTGACCTGGGAGACTTTTTCACCCTTT
1 TTTTACCCTTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTCACCCTTT
1486441 TTCTACCTAT
Statistics
Matches: 307, Mismatches: 63, Indels: 36
0.76 0.16 0.09
Matches are distributed among these distances:
166 8 0.03
167 75 0.24
168 184 0.60
169 40 0.13
ACGTcount: A:0.15, C:0.26, G:0.16, T:0.42
Consensus pattern (168 bp):
TTTTACCCTTTGTCTACCTGTCAGCTTTGACCTAAGAGACTTTTTCACCCTTTGTTTGCCTGTCA
GTTTGACCTAGGAAACTTCTTTTCCCTTTGTCTACCCATCAGCTTTGACCCAAGAGACTTTTTTA
CCCTTTGTTTGCCCGTTAGTTTTGACCCAGGAGACTTC
Found at i:1486357 original size:126 final size:127
Alignment explanation
Indices: 1485885--1486978 Score: 382
Period size: 126 Copynumber: 8.7 Consensus size: 127
1485875 AACCTTTTTA
* * * * * * * **
1485885 TTTTACCCTTTGTCTACCTGTCCGCTTTGACCTAAGAGACTTTTTCACCCTTTGTTTGCCTGTCA
1 TTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTAAGAGACTTCTTCACCTTTTGTCTACCCATCA
** * *** * *
1485950 G-TTTGA-CCTGGGAAACTT-TTTTTCCTTTTGTTTGCCCATCGGCTTTGAC-CTAGGAGACTT
66 GCTTTGACCCTAAGAGACTTCTACATCC-TTTGTTTGCCCATCAGCTTTGACTC-AAGAGACTT
* * * * * * **
1486010 TTTTACCCTTTGTTTGCCCGTTAGTTTTGACCCAGGAGACTTCTTTTC-CCTTTTGTCTGCCTGT
1 TTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTAAGAGACTTC--TTCACCTTTTGTCTACCCAT
* ** * * *
1486074 CAGCTTTGA-CCTAGGAGACTTCTTTACCCTTTGTTTGCCCTTCAGTTTTGACT-AAGGAGACTT
64 CAGCTTTGACCCTAAGAGACTTCTACATCCTTTGTTTGCCCATCAGCTTTGACTCAA-GAGACTT
* * * * * * * *
1486137 CTTTT-CCCTTTGTCTACCTGTCAGC-TTGACCCAAGAGACTTTTTTACCCTTTATCTACCCATT
1 -TTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTAAGAGACTTCTTCACCTTTTGTCTACCCATC
* ** * *
1486200 AGCTTT-A-TCTCGGGAGACTTCTTCA-CTCTTTGTTTGCCCATCAGCTTTGACTCAAGACACTT
65 AGCTTTGACCCT-AAGAGACTTCTACATC-CTTTGTTTGCCCATCAGCTTTGACTCAAGAGACTT
* * * * * * *
1486262 TTTTACCTTTTGTCTGCCTGTTAGCTTTGACCTTAGAGACTTCTTCATCTTTTGTCTTCCCATCG
1 TTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTAAGAGACTTCTTCACCTTTTGTCTACCCATCA
* * ** * **
1486327 GCTTTGA-CGTAAGAGACTTCTACATCCTTTGTCTGCTTAT-TGACTTTGAC-CTTGAAGACTT
66 GCTTTGACCCTAAGAGACTTCTACATCCTTTGTTTGCCCATCAG-CTTTGACTCAAG-AGACTT
* * ** * *
1486388 TTTTATCCTTTGTCTTCCCGTCAGCTTTGACCTGGGAGACTTTTTCACCCTTTT-TCTACCTATC
1 TTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTAAGAGACTTCTTCA-CCTTTTGTCTACCCATC
* * * * * * * * **
1486452 GGCTTTAACCCT-AGAGACTTCTACATTCTTTGTCTGCCAACCAGTTTTGACCCGGGAGACTT
65 AGCTTTGACCCTAAGAGACTTCTACATCCTTTGTTTGCCCATCAGCTTTGACTCAAGAGACTT
* * * * ** ** * * * * * * *
1486514 CTTCACCTTTTGTCTACCTATTGGCTTTG-TCTCAAGAAACCTT-TTTACCCTTTGTTTGCCCGT
1 TTTTACCCTTTGTCTGCCCGTCAGCTTTGACCT-AAGAGA-CTTCTTCACCTTTTGTCTACCCAT
** * * * ** * * ** *
1486577 CAAATTT-AACC-AGAGAGATTTATTTATCCTTTATTTGCCCGTCAAATTTAAC-CAGAGAGACT
64 CAGCTTTGACCCTA-AGAGACTTCTACATCCTTTGTTTGCCCATCAGCTTTGACTCA-AGAGACT
1486639 T
127 T
* * * * * * * * ** **
1486640 ATTTATCCTTTATTTGCCCGTCAACTTGGACTCGGAAG-G-CTTTCAT-ATATTTTGTCTACCTG
1 TTTTACCCTTTGTCTGCCCGTCAGCTTTGAC-C-TAAGAGAC-TTCTTCACCTTTTGTCTACCCA
* * * * * * *
1486702 TCAGCTTTGATCCGAA-AGACTT-TTCTATCCTTTGTCTT-CCTATCGGCTTTGACTCGAGGGAC
63 TCAGCTTTGACCCTAAGAGACTTCTAC-ATCCTTTGT-TTGCCCATCAGCTTTGACTCAAGAGAC
1486764 TT
126 TT
* * *** * * * *
1486766 TTTTACCTTTTGTCTACTTATTAGCTTTGACCCT-TGAGACTTCTTTACCTTTTGTCTACCCATT
1 TTTTACCCTTTGTCTGCCCGTCAGCTTTGA-CCTAAGAGACTTCTTCACCTTTTGTCTACCCATC
* * * ** * * * * * * *
1486830 GGCTTTAACCCTAA-AGACATCTTTACCCTTTATCTGCTCATTAGCTATGACCCGAA-AGACTT
65 AGCTTTGACCCTAAGAGACTTCTACATCCTTTGTTTGCCCATCAGCTTTGACTC-AAGAGACTT
* * * ** * * ** *
1486892 TTCT-CCCTTTTGTCTGCCCGTAAGCTTTGACTTGGGAGATTTCTTTACCCCTTGTCTACCCGTC
1 TTTTACCC-TTTGTCTGCCCGTCAGCTTTGACCTAAGAGACTTCTTCACCTTTTGTCTACCCATC
*
1486956 AGCTTTGACCC-GAGAGACTTCTA
65 AGCTTTGACCCTAAGAGACTTCTA
1486979 TACTCTTTAT
Statistics
Matches: 706, Mismatches: 216, Indels: 93
0.70 0.21 0.09
Matches are distributed among these distances:
124 11 0.02
125 137 0.19
126 456 0.65
127 88 0.12
128 14 0.02
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (127 bp):
TTTTACCCTTTGTCTGCCCGTCAGCTTTGACCTAAGAGACTTCTTCACCTTTTGTCTACCCATCA
GCTTTGACCCTAAGAGACTTCTACATCCTTTGTTTGCCCATCAGCTTTGACTCAAGAGACTT
Found at i:1487257 original size:42 final size:41
Alignment explanation
Indices: 1485886--1487280 Score: 274
Period size: 42 Copynumber: 33.2 Consensus size: 41
1485876 ACCTTTTTAT
* * * *
1485886 TTTACCCTTTGTCTACCTGTCCGCTTTGACCTAAGAGACTT-
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCTAGGAGACTTC
* * * * *
1485927 TTTCACCCTTTGTTTGCCTGTCAG-TTTGACCTGGGAAACTTT
1 TTT-ACCCTTTGTCTGCCAGT-AGCTTTGACCTAGGAGACTTC
* * * * *
1485969 TTTTCCTTTTGTTTGCCCA-TCGGCTTTGACCTAGGAGACTTT
1 TTTACCCTTTGTCTG-CCAGT-AGCTTTGACCTAGGAGACTTC
* * * *
1486011 TTTACCCTTTGTTTGCCCGTTAGTTTTGACCCAGGAGACTTC
1 TTTACCCTTTGTCTGCCAG-TAGCTTTGACCTAGGAGACTTC
* *
1486053 TTTTCCCTTTTGTCTGCCTGTCAGCTTTGACCTAGGAGACTTC
1 TTTACCC-TTTGTCTGCCAGT-AGCTTTGACCTAGGAGACTTC
* ** *
1486096 TTTACCCTTTGTTTGCCCTTCAGTTTTGA-CTAAGGAGACTTC
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCT-AGGAGACTTC
* * * * * *
1486138 TTTTCCCTTTGTCTACCTGTCAGC-TTGACCCAAGAGACTTT
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCTAGGAGACTTC
* * * * *
1486179 TTTACCCTTTATCTACCCATTAGCTTT-ATCTCGGGAGACTTC
1 TTTACCCTTTGTCT-GCCAGTAGCTTTGACCT-AGGAGACTTC
* * * * * *
1486221 TTCACTCTTTGTTTGCCCA-TCAGCTTTGA-CTCAAGACACTTT
1 TTTACCCTTTGTCTG-CCAGT-AGCTTTGACCT-AGGAGACTTC
* *
1486263 TTTACCTTTTGTCTGCCTGTTAGCTTTGACCTTA-GAGACTTC
1 TTTACCCTTTGTCTGCCAG-TAGCTTTGACC-TAGGAGACTTC
* * * * * * *
1486305 TTCATCTTTTGTCTTCCCA-TCGGCTTTGACGTAAGAGACTTC
1 TTTACCCTTTGTC-TGCCAGT-AGCTTTGACCTAGGAGACTTC
** * * * * * *
1486347 TACATCCTTTGTCTGCTTA-TTGACTTTGACCTTGAAGACTTT
1 TTTACCCTTTGTCTGC-CAGTAG-CTTTGACCTAGGAGACTTC
* * * *
1486389 TTTATCCTTTGTCTTCCCGTCAGCTTTGACCTGGGAGACTT-
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCTAGGAGACTTC
* * * *
1486430 TTTCACCCTTTTTCTACCTA-TCGGCTTTAACCCTA-GAGACTTC
1 TTT-ACCCTTTGTCTGCC-AGT-AGCTTTGA-CCTAGGAGACTTC
** ** ** * **
1486473 TACATTCTTTGTCTGCCAACCAGTTTTGACCCGGGAGACTTC
1 TTTACCCTTTGTCTGCC-AGTAGCTTTGACCTAGGAGACTTC
* * * * * * * *
1486515 TTCACCTTTTGTCTACCTATTGGCTTTG-TCTCAAGAAACCTT-
1 TTTACCCTTTGTCTGCC-AGTAGCTTTGACCT-AGGAGA-CTTC
* * ** * * *
1486557 TTTACCCTTTGTTTGCCCGTCAAATTTAACC-AGAGAGATTTA
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCTAG-GAGACTTC
* * * * ** * *
1486599 TTTATCCTTTATTTGCCCGTCAAATTTAACC-AGAGAGACTTA
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCTAG-GAGACTTC
* * * * * * * *
1486641 TTTATCCTTTATTTGCCCGTCAACTTGGA-CTCGGAAGGCTTTC
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCTAGG-AGAC-TTC
* * * * * *
1486684 ATATA--TTTTGTCTACCTGTCAGCTTTGATCCGA-AAGACTT-
1 -TTTACCCTTTGTCTGCCAGT-AGCTTTGA-CCTAGGAGACTTC
* * * * *
1486724 TTCTATCCTTTGTCTTCCTA-TCGGCTTTGACTCGAGG-GACTTT
1 TT-TACCCTTTGTCTGCC-AGT-AGCTTTGAC-CTAGGAGACTTC
* * * * *
1486767 TTTACCTTTTGTCTACTTATTAGCTTTGACCCT-TGAGACTTC
1 TTTACCCTTTGTCTGC-CAGTAGCTTTGA-CCTAGGAGACTTC
* * * * * * *
1486809 TTTACCTTTTGTCTACCCATTGGCTTTAACCCTA-AAGACATC
1 TTTACCCTTTGTCT-GCCAGTAGCTTTGA-CCTAGGAGACTTC
* * * * *
1486851 TTTACCCTTTATCTGCTCATTAGCTATGACC-CGAAAGACTT-
1 TTTACCCTTTGTCTGC-CAGTAGCTTTGACCTAG-GAGACTTC
* * * *
1486892 TTCT-CCCTTTTGTCTGCCCGTAAGCTTTGACTTGGGAGATTTC
1 TT-TACCC-TTTGTCTGCCAGT-AGCTTTGACCTAGGAGACTTC
* * * *
1486935 TTTACCCCTTGTCTACCCGTCAGCTTTGACC-CGAGAGACTTC
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGACCTAG-GAGACTTC
* * * * * * * *
1486977 TATACTCTTTATCTACCAATCGACTTTGACCTCA-AAAACTT-
1 TTTACCCTTTGTCTGCCAGTAG-CTTTGACCT-AGGAGACTTC
** * * * * *
1487018 TTATATTCTTTGTCTGCCAATCGACTCT-AACTCGGGAGACTTC
1 TT-TACCCTTTGTCTGCCAGTAG-CTTTGACCT-AGGAGACTTC
** * * *
1487061 TTTACCCTTTGTCTGCTTGTCACCTTTGACACT-GTAGACTTT
1 TTTACCCTTTGTCTGCCAGT-AGCTTTGAC-CTAGGAGACTTC
* * * *
1487103 TTTATCCTTTGTCTTCCCA-TCGACTTTGACTTAGGAGACTTC
1 TTTACCCTTTGTC-TGCCAGTAG-CTTTGACCTAGGAGACTTC
* * * * * *
1487145 TATATCCTTTGTCTGCCCGTTGGCTTTGACCCT-GGAGATTTT
1 TTTACCCTTTGTCTGCCAG-TAGCTTTGA-CCTAGGAGACTTC
* * *
1487187 TTTATCTTTTGTCTTCTC-GTCAGCTTTGACCTAGGAGACTTC
1 TTTACCCTTTGTCTGC-CAGT-AGCTTTGACCTAGGAGACTTC
* * * *
1487229 TTTACCCTTTGTCTGCCAGCTAGTTTTGACCCAGGACATTTC
1 TTTACCCTTTGTCTGCCAG-TAGCTTTGACCTAGGAGACTTC
*
1487271 TTCACCCTTT
1 TTTACCCTTT
1487281 ATCTACCCAG
Statistics
Matches: 1006, Mismatches: 260, Indels: 175
0.70 0.18 0.12
Matches are distributed among these distances:
39 1 0.00
40 2 0.00
41 114 0.11
42 806 0.80
43 76 0.08
44 7 0.01
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (41 bp):
TTTACCCTTTGTCTGCCAGTAGCTTTGACCTAGGAGACTTC
Found at i:1487463 original size:84 final size:84
Alignment explanation
Indices: 1487375--1487548 Score: 183
Period size: 84 Copynumber: 2.1 Consensus size: 84
1487365 TTTTACTTGG
* * *
1487375 GAGACTTATCTATCC-TTTGTTTGCCCGTTGACTTTAACCTAGGAGACTTCTTTATCC-TTTGTC
1 GAGACTTATCTA-CCTTTTGTCTACCCGTTGACTTTAACCTAGGAGACTTCTTT-CCCTTTTGTC
*
1487438 TTCCCATC-AGCTTTGACCCAA
64 TACCCATCTA-CTTTGACCCAA
* * ** * * * *
1487459 GAGACTTTTTTACCTTTTGTCTACTTGTTGGCTTTAACTTTGTAGACTTCTTTCCCTTTTGTCTA
1 GAGACTTATCTACCTTTTGTCTACCCGTTGACTTTAACCTAGGAGACTTCTTTCCCTTTTGTCTA
*
1487524 CCCATCTACTTTGACCTAA
66 CCCATCTACTTTGACCCAA
1487543 GAGACT
1 GAGACT
1487549 ATTTTACCCT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
83 4 0.05
84 69 0.93
85 1 0.01
ACGTcount: A:0.18, C:0.25, G:0.14, T:0.43
Consensus pattern (84 bp):
GAGACTTATCTACCTTTTGTCTACCCGTTGACTTTAACCTAGGAGACTTCTTTCCCTTTTGTCTA
CCCATCTACTTTGACCCAA
Found at i:1487604 original size:126 final size:126
Alignment explanation
Indices: 1487369--1487652 Score: 281
Period size: 126 Copynumber: 2.3 Consensus size: 126
1487359 ATCAGTTTTT
* * * * * * * *
1487369 ACTTGGGAGACTTATCTATCCTTTGTTTGCCCGT-TGACTTTAACCTAGGAGACTTCTTTATCCT
1 ACTTGGGAGACTTCTTTACCCTTTGTCTACCCATCT-ACTTTAACCTAAGAGACTTCTTTACCCT
* * * * ***
1487433 TTGTCTTCCCATCAGCTTTGACCCAAGAGACTTTTTTACCTTTTGTCTACTTGTTGGCTTTA
65 TTATCTGCCCATCAGCTTTGACCCAAGAGACTTCTATACCTTTTGTCTACCAATTGGCTTTA
* * *
1487495 ACTTTGTAGACTTCTTT-CCCTTTTGTCTACCCATCTACTTTGACCTAAGAGACTAT-TTTACCC
1 ACTTGGGAGACTTCTTTACCC-TTTGTCTACCCATCTACTTTAACCTAAGAGACT-TCTTTACCC
* * * * *
1487558 TTTATCTGCCGATC-GACTTTGACCCAGGAGACTTCTATA-CTCTTTGTTTGCCAATTGGCTTTG
64 TTTATCTGCCCATCAG-CTTTGACCCAAGAGACTTCTATACCT-TTTGTCTACCAATTGGCTTTA
1487621 ACTTGGGAGACTTCTTTACCCTTTGTCTACCC
1 ACTTGGGAGACTTCTTTACCCTTTGTCTACCC
1487653 GCCAACTTTA
Statistics
Matches: 127, Mismatches: 25, Indels: 12
0.77 0.15 0.07
Matches are distributed among these distances:
125 5 0.04
126 117 0.92
127 5 0.04
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (126 bp):
ACTTGGGAGACTTCTTTACCCTTTGTCTACCCATCTACTTTAACCTAAGAGACTTCTTTACCCTT
TATCTGCCCATCAGCTTTGACCCAAGAGACTTCTATACCTTTTGTCTACCAATTGGCTTTA
Found at i:1487870 original size:42 final size:41
Alignment explanation
Indices: 1487406--1488188 Score: 282
Period size: 42 Copynumber: 18.8 Consensus size: 41
1487396 TGCCCGTTGA
* * ** *
1487406 CTTTAACCTAGGAGACTTCTTTATCC-TTTGTCTTCCCATCAG
1 CTTTGACCT-GGAGACTTCTTTA-CCTTTTGTCTACCTGTCGG
** * * *
1487448 CTTTGACCCAAGAGACTTTTTTACCTTTTGTCTACTTGTTGG
1 CTTTGA-CCTGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
* * * * ** **
1487490 CTTTAACTTTGTAGACTTCTTTCCCTTTTGTCTACCCATCTA
1 CTTTGAC-CTGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
* * * * *
1487532 CTTTGACCTAAGAGACTAT-TTTACCCTTTATCTGCC-GATCGA
1 CTTTGACCT-GGAGACT-TCTTTACCTTTTGTCTACCTG-TCGG
* * * * ** *
1487574 CTTTGACCCAGGAGACTTCTATA-CTCTTTGTTTGCCAATTGG
1 CTTTGA-CCTGGAGACTTCTTTACCT-TTTGTCTACCTGTCGG
* * * * **
1487616 CTTTGACTTGGGAGACTTCTTTACCCTTTGTCTACCCGCCAA
1 CTTTGACCT-GGAGACTTCTTTACCTTTTGTCTACCTGTCGG
* * * * * * * ** *
1487658 CTTTAACTTGGGAGATTTCTATA-TTCTTTGTTTGCCCATCGA
1 CTTTGACCT-GGAGACTTCTTTACCT-TTTGTCTACCTGTCGG
* * * * * *
1487700 CTTTGATTCAGGAGACTT-TTTCACCCTTTATCTGCCCGTCGG
1 CTTTGA-CCTGGAGACTTCTTT-ACCTTTTGTCTACCTGTCGG
* * **
1487742 CTTTGACTCTAGAGACTTCTTT--GTTTTGTCT-GTTGTCGG
1 CTTTGAC-CTGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
** * ** * **
1487781 CTTTGACCCAAGAGACTTCTTTATC-TTTGT-TTTCTCATCAA
1 CTTTGA-CCTGGAGACTTCTTTACCTTTTGTCTACCT-GTCGG
*
1487822 CTTTGACTTGGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
1 CTTTGACCT-GGAGACTTCTTTACCTTTTGTCTACCTGTCGG
* * * * * *
1487864 TTTTGACCTAGGAAAATTCTTCACCTTTTGTTTGCCTGTCGG
1 CTTTGACCT-GGAGACTTCTTTACCTTTTGTCTACCTGTCGG
* * * * *
1487906 CTTT-AACTCGGTGACTTTTTTACCTTTTGTCTATCTGTCAG
1 CTTTGACCT-GGAGACTTCTTTACCTTTTGTCTACCTGTCGG
** * * * **
1487947 CTTTGACCTTAAAGACTTTTTTACCTTTTCT-TTCCTGTTTG
1 CTTTGACC-TGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
* * * *
1487988 CTTTGACTCGGGAAACTTCTTCACCTTTTGTTTACCTGTCGG
1 CTTTGAC-CTGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
* * * *
1488030 CTTTGACCCTGGAGACTTGTTTTCCTTTTGTCTATCTGTCGT
1 CTTTGA-CCTGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
** * * * *
1488072 CTTTGACCTTAAAGACTTCTATA-TTCTTTGTCTACCCGTCGA
1 CTTTGACC-TGGAGACTTCTTTACCT-TTTGTCTACCTGTCGG
* * *
1488114 CTTTGACCTGAGAGACTTCTTTACCCTTTGTCTATCC-ATCAG
1 CTTTGACCTG-GAGACTTCTTTACCTTTTGTCTA-CCTGTCGG
* * *
1488156 TTTTGACCTAAGAGACTTCTTTACCCTTTGTCT
1 CTTTGACCT-GGAGACTTCTTTACCTTTTGTCT
1488189 GCTCATCAAC
Statistics
Matches: 537, Mismatches: 167, Indels: 74
0.69 0.21 0.10
Matches are distributed among these distances:
39 25 0.05
40 14 0.03
41 92 0.17
42 390 0.73
43 16 0.03
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.43
Consensus pattern (41 bp):
CTTTGACCTGGAGACTTCTTTACCTTTTGTCTACCTGTCGG
Found at i:1487963 original size:125 final size:127
Alignment explanation
Indices: 1487834--1488122 Score: 358
Period size: 125 Copynumber: 2.3 Consensus size: 127
1487824 TTGACTTGGG
* *
1487834 AGACTTCTTTACCTTTTGTCTACCTGTCGGTTTTGACCT-AGGAAAATTCTTCACCTTTTGTTTG
1 AGACTTCTTTACCTTTTGTCTACCTGTCGGCTTTGACCTCAGGAAAATTCTTCACCTTTTGTTTA
* *
1487898 CCTGTCGGCTTTAACTC-GGTGACTT-TTTTACCTTTTGTCTATCTGTCAG-CTTTGACCTTAA
66 CCTGTCGGCTTTAACCCTGGAGACTTGTTTT-CCTTTTGTCTATCTGTC-GTCTTTGACCTTAA
* * * ** * *
1487959 AGACTTTTTTACCTTTTCT-TTCCTGTTTGCTTTGA-CTCGGGAAACTTCTTCACCTTTTGTTTA
1 AGACTTCTTTACCTTTTGTCTACCTGTCGGCTTTGACCTCAGGAAAATTCTTCACCTTTTGTTTA
*
1488022 CCTGTCGGCTTTGACCCTGGAGACTTGTTTTCCTTTTGTCTATCTGTCGTCTTTGACCTTAA
66 CCTGTCGGCTTTAACCCTGGAGACTTGTTTTCCTTTTGTCTATCTGTCGTCTTTGACCTTAA
* * * *
1488084 AGACTTCTATA-TTCTTTGTCTACCCGTCGACTTTGACCT
1 AGACTTCTTTACCT-TTTGTCTACCTGTCGGCTTTGACCT
1488123 GAGAGACTTC
Statistics
Matches: 136, Mismatches: 21, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
123 2 0.01
124 51 0.38
125 66 0.49
126 15 0.11
127 2 0.01
ACGTcount: A:0.15, C:0.24, G:0.16, T:0.45
Consensus pattern (127 bp):
AGACTTCTTTACCTTTTGTCTACCTGTCGGCTTTGACCTCAGGAAAATTCTTCACCTTTTGTTTA
CCTGTCGGCTTTAACCCTGGAGACTTGTTTTCCTTTTGTCTATCTGTCGTCTTTGACCTTAA
Found at i:1488046 original size:83 final size:83
Alignment explanation
Indices: 1487710--1488058 Score: 241
Period size: 83 Copynumber: 4.2 Consensus size: 83
1487700 CTTTGATTCA
* * * * * ** *
1487710 GGAGACTTTTTCACCCTTTATCTGCCCGTCGGCTTTGACTCTAGAGACTTCTTT--GTTTTGTCT
1 GGAGACTTTTTTACCTTTTCTTTGCCTGTCGGCTTTGACTCGGGA-ACTTCTTTACCTTTTGTCT
** *
1487773 -GTTGTCGGCTTTGACCCA
65 ACCTGTCGGCTTTGACCCT
* * * * ** *
1487791 AGAGACTTCTTTATCTTTGT-TTT--CTCATCAACTTTGACTTGGGAGACTTCTTTACCTTTTGT
1 GGAGACTTTTTTACCTTT-TCTTTGCCT-GTCGGCTTTGACTCGGGA-ACTTCTTTACCTTTTGT
*
1487853 CTACCTGTCGGTTTTGA-CCT
63 CTACCTGTCGGCTTTGACCCT
* * * * * * *
1487873 AGGAAAATTCTTCACCTTTTGTTTGCCTGTCGGCTTTAACTCGGTG-ACTTTTTTACCTTTTGTC
1 -GGAGACTTTTTTACCTTTTCTTTGCCTGTCGGCTTTGACTCGG-GAACTTCTTTACCTTTTGTC
* * *
1487937 TATCTGTCAGCTTTGACCTT
64 TACCTGTCGGCTTTGACCCT
** ** * *
1487957 AAAGACTTTTTTACCTTTTCTTT-CCTGTTTGCTTTGACTCGGGAAACTTCTTCACCTTTTGTTT
1 GGAGACTTTTTTACCTTTTCTTTGCCTGTCGGCTTTGACTCGGG-AACTTCTTTACCTTTTGTCT
1488021 ACCTGTCGGCTTTGACCCT
65 ACCTGTCGGCTTTGACCCT
1488040 GGAGACTTGTTTT-CCTTTT
1 GGAGACTT-TTTTACCTTTT
1488059 GTCTATCTGT
Statistics
Matches: 203, Mismatches: 51, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
79 1 0.00
80 21 0.10
81 16 0.08
82 28 0.14
83 117 0.58
84 17 0.08
85 3 0.01
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (83 bp):
GGAGACTTTTTTACCTTTTCTTTGCCTGTCGGCTTTGACTCGGGAACTTCTTTACCTTTTGTCTA
CCTGTCGGCTTTGACCCT
Found at i:1488795 original size:22 final size:24
Alignment explanation
Indices: 1488751--1488795 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1488741 AAAAAAATAA
*
1488751 AAATAAAAAATATATCATCATAATT
1 AAATAAAAAATATA-CATAATAATT
1488776 AAAT-AAAAATATA-ATAATAA
1 AAATAAAAAATATACATAATAA
1488796 ACTAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
24 9 0.47
25 4 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAAAAATATACATAATAATT
Found at i:1489102 original size:72 final size:72
Alignment explanation
Indices: 1489013--1489154 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 72
1489003 GTCAACATAA
* * * * *
1489013 AATTAAAGCAAATAAGCTGCTGAACAATAAAAAGAAATGCATGAAAGAAAAAGCAATTAAGTTGC
1 AATTAAAACAAATAAGCTGCTGAACAAGAAAAAGAAACGCATGAAAGAAAAAGCAATTAAGCTAC
1489078 AAAATGC
66 AAAATGC
* *
1489085 AATTAAAACAATTAAGCTGCTGAACAAGAAGAAGAAACGCATGAAAGAAAAAGCAATTAAGCTAC
1 AATTAAAACAAATAAGCTGCTGAACAAGAAAAAGAAACGCATGAAAGAAAAAGCAATTAAGCTAC
1489150 AAAAT
66 AAAAT
1489155 TAAGCTACTG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.17
Consensus pattern (72 bp):
AATTAAAACAAATAAGCTGCTGAACAAGAAAAAGAAACGCATGAAAGAAAAAGCAATTAAGCTAC
AAAATGC
Found at i:1489159 original size:58 final size:57
Alignment explanation
Indices: 1489094--1489211 Score: 209
Period size: 58 Copynumber: 2.1 Consensus size: 57
1489084 CAATTAAAAC
*
1489094 AATTAAGCTGCTGAACAAGAAGAAGAAACGCATGAAAGAAAAAGCAATTAAGCTACAA
1 AATTAAGCTACTGAACAAGAAGAAGAAACGCATGAAAG-AAAAGCAATTAAGCTACAA
*
1489152 AATTAAGCTACTGAACAAGAAGAAGAAACGCATGAAAGAAAAGCAATTAAGCTGCAA
1 AATTAAGCTACTGAACAAGAAGAAGAAACGCATGAAAGAAAAGCAATTAAGCTACAA
1489209 AAT
1 AAT
1489212 GAAGAAGCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 21 0.36
58 37 0.64
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (57 bp):
AATTAAGCTACTGAACAAGAAGAAGAAACGCATGAAAGAAAAGCAATTAAGCTACAA
Found at i:1492535 original size:11 final size:11
Alignment explanation
Indices: 1492519--1492553 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1492509 TGTAAGAAAA
1492519 TGATGAATATT
1 TGATGAATATT
*
1492530 TGATGAGTATT
1 TGATGAATATT
1492541 TGATGAA-ATT
1 TGATGAATATT
1492551 TGA
1 TGA
1492554 AGTGGATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (11 bp):
TGATGAATATT
Found at i:1492553 original size:21 final size:21
Alignment explanation
Indices: 1492519--1492576 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1492509 TGTAAGAAAA
*
1492519 TGATGAATATTTGATGAGTATT
1 TGATGAA-ATTTGATGAGGATT
* *
1492541 TGATGAAATTTGAAGTGGATT
1 TGATGAAATTTGATGAGGATT
*
1492562 GGATG-AATTTGATGA
1 TGATGAAATTTGATGA
1492577 TTGAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 8 0.27
21 15 0.50
22 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.40
Consensus pattern (21 bp):
TGATGAAATTTGATGAGGATT
Found at i:1494330 original size:24 final size:24
Alignment explanation
Indices: 1494303--1494352 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1494293 AAGCTAGTAG
* *
1494303 TATTTTAATGGCTTCTAACCTAGC
1 TATTCTAATGGCTTATAACCTAGC
1494327 TATTCTAATGGCTTATAACCTAGC
1 TATTCTAATGGCTTATAACCTAGC
1494351 TA
1 TA
1494353 CGGGGGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (24 bp):
TATTCTAATGGCTTATAACCTAGC
Found at i:1495531 original size:13 final size:13
Alignment explanation
Indices: 1495513--1495538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1495503 TACAAAGCAA
1495513 ATTGTATCGATAC
1 ATTGTATCGATAC
1495526 ATTGTATCGATAC
1 ATTGTATCGATAC
1495539 TTAGCAATTT
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):
ATTGTATCGATAC
Found at i:1495538 original size:33 final size:33
Alignment explanation
Indices: 1495495--1495561 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1495485 CATTTTATGG
*
1495495 TGTATTGATACAAAGCAAATTGTATCGATACAT
1 TGTATCGATACAAAGCAAATTGTATCGATACAT
** *
1495528 TGTATCGATACTTAGCAATTTGTATCGATACAT
1 TGTATCGATACAAAGCAAATTGTATCGATACAT
1495561 T
1 T
1495562 TAGGTGTGTA
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:0.34, C:0.13, G:0.15, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAAAGCAAATTGTATCGATACAT
Found at i:1496602 original size:13 final size:13
Alignment explanation
Indices: 1496584--1496613 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1496574 ACAATTCTTC
1496584 ATGTATTGATACA
1 ATGTATTGATACA
1496597 ATGTATTGATACA
1 ATGTATTGATACA
1496610 ATGT
1 ATGT
1496614 CCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:1496609 original size:33 final size:33
Alignment explanation
Indices: 1496563--1496629 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1496553 CATTGGGCAT
* *
1496563 AATGTATCAATACAAT-TCTTCATGTATTGATAC
1 AATGTATCAATACAATGTC-CCATGTATCGATAC
**
1496596 AATGTATTGATACAATGTCCCATGTATCGATAC
1 AATGTATCAATACAATGTCCCATGTATCGATAC
1496629 A
1 A
1496630 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (33 bp):
AATGTATCAATACAATGTCCCATGTATCGATAC
Found at i:1499305 original size:13 final size:13
Alignment explanation
Indices: 1499283--1499319 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1499273 ATAGTAACCT
1499283 TGTATCGATACAA
1 TGTATCGATACAA
*
1499296 TGTATTGATACAA
1 TGTATCGATACAA
*
1499309 TGTATCAATAC
1 TGTATCGATAC
1499320 TTAGAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1505489 original size:20 final size:20
Alignment explanation
Indices: 1505464--1505516 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1505454 GTTGGGCATA
*
1505464 ATGTATCGATACAAT-TCTTC
1 ATGTATCGATACAATGTC-CC
*
1505484 ATGTATCGATATAATGTCCC
1 ATGTATCGATACAATGTCCC
1505504 ATGTATCGATACA
1 ATGTATCGATACA
1505517 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCC
Found at i:1505589 original size:19 final size:20
Alignment explanation
Indices: 1505546--1505595 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1505536 TGCCAGTTTC
*
1505546 ATGTATCGATACAATTGAGT
1 ATGTATCGATACAATTGAGA
*
1505566 GTGTATCGATACAA-TGAGA
1 ATGTATCGATACAATTGAGA
1505585 ATGTATCGATA
1 ATGTATCGATA
1505596 TATTGTATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTGAGA
Found at i:1507149 original size:13 final size:13
Alignment explanation
Indices: 1507131--1507155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1507121 CATATTGCTT
1507131 TGTATCGATACAC
1 TGTATCGATACAC
1507144 TGTATCGATACA
1 TGTATCGATACA
1507156 TAGCAAATTA
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1514963 original size:21 final size:22
Alignment explanation
Indices: 1514937--1514978 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1514927 TTTCCAAGGG
*
1514937 AAATTTTT-ATTAAGGGGGAGA
1 AAATTTTTAATTAAAGGGGAGA
1514958 AAATTTTTAATTAAAGGGGAG
1 AAATTTTTAATTAAAGGGGAG
1514979 TTATATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.33
Consensus pattern (22 bp):
AAATTTTTAATTAAAGGGGAGA
Found at i:1515631 original size:20 final size:21
Alignment explanation
Indices: 1515601--1515658 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
1515591 AAGGTCAAAA
1515601 CCCTAGAAAGTATCGATACAAG
1 CCCT-GAAAGTATCGATACAAG
*
1515623 -CCTGAAAGTATCAATACAAG
1 CCCTGAAAGTATCGATACAAG
*
1515643 CCCTG-AAGTATTGATA
1 CCCTGAAAGTATCGATA
1515659 TATATTGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (21 bp):
CCCTGAAAGTATCGATACAAG
Found at i:1515802 original size:13 final size:13
Alignment explanation
Indices: 1515784--1515808 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1515774 CATGGGACAT
1515784 TGTATCGATACAA
1 TGTATCGATACAA
1515797 TGTATCGATACA
1 TGTATCGATACA
1515809 TTGTGCCCAA
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:1519267 original size:89 final size:89
Alignment explanation
Indices: 1519097--1519266 Score: 261
Period size: 88 Copynumber: 1.9 Consensus size: 89
1519087 TTTTTTCATG
* *
1519097 AGTTTTGAATTTTTTCTTTGAAATTTTTCTATTTCTAAAAAATCGAGTTTTTTATTCCATAAATA
1 AGTTTTGAATTTTTCCTTTGAAATTTTTCTATTTCTAAAAAATCGAGTTTTCTATTCCATAAATA
** ***
1519162 TTTTTGGGGGGATTTTTCTTGATT
66 TTTTCAGAACGATTTTTCTTGATT
*
1519186 AGTTTTGAATTTTTCCTTTGAAATTTTT-TATTTCTGAAAAATCGAGTTTTCTATTCCATAAATA
1 AGTTTTGAATTTTTCCTTTGAAATTTTTCTATTTCTAAAAAATCGAGTTTTCTATTCCATAAATA
1519250 TTTTCAGAACGATTTTT
66 TTTTCAGAACGATTTTT
1519267 TTTTATTTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 46 0.63
89 27 0.37
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.52
Consensus pattern (89 bp):
AGTTTTGAATTTTTCCTTTGAAATTTTTCTATTTCTAAAAAATCGAGTTTTCTATTCCATAAATA
TTTTCAGAACGATTTTTCTTGATT
Found at i:1519666 original size:12 final size:10
Alignment explanation
Indices: 1519648--1519715 Score: 84
Period size: 10 Copynumber: 6.5 Consensus size: 10
1519638 GAACTCAGCA
1519648 AAAAAAAAGAG
1 AAAAAAAA-AG
1519659 AGAAAAAAAAG
1 A-AAAAAAAAG
1519670 AAAGAAAAAAAG
1 -AA-AAAAAAAG
1519682 AAAAAAAAAG
1 AAAAAAAAAG
1519692 AAAAAAAAAG
1 AAAAAAAAAG
*
1519702 -AGAAAAAAG
1 AAAAAAAAAG
1519711 AAAAA
1 AAAAA
1519716 CTAGAAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
9 8 0.16
10 21 0.41
11 6 0.12
12 16 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1519666 original size:13 final size:11
Alignment explanation
Indices: 1519647--1519714 Score: 84
Period size: 12 Copynumber: 5.9 Consensus size: 11
1519637 GGAACTCAGC
1519647 AAAAAAAAAGAG
1 AAAAAAAAA-AG
*
1519659 AGAAAAAAAAG
1 AAAAAAAAAAG
1519670 AAAGAAAAAAAG
1 AAA-AAAAAAAG
1519682 -AAAAAAAAAG
1 AAAAAAAAAAG
1519692 AAAAAAAAAGAG
1 AAAAAAAAA-AG
1519704 AAAAAAGAAAA
1 AAAAAA-AAAA
1519715 ACTAGAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
10 8 0.16
11 14 0.28
12 25 0.50
13 3 0.06
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1519685 original size:18 final size:18
Alignment explanation
Indices: 1519647--1519715 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
1519637 GGAACTCAGC
* *
1519647 AAAAAAAAAGAGAGAAA-
1 AAAAAAAAAGAAAAAAAG
*
1519664 AAAAAGAAAGAAAAAAAG
1 AAAAAAAAAGAAAAAAAG
1519682 AAAAAAAAAGAAAAAAA-
1 AAAAAAAAAGAAAAAAAG
1519699 AAGAGAAAAAAGAAAAA
1 AA-A-AAAAAAGAAAAA
1519716 CTAGAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
17 16 0.36
18 17 0.38
19 12 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAAG
Found at i:1519724 original size:28 final size:27
Alignment explanation
Indices: 1519647--1519715 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 27
1519637 GGAACTCAGC
1519647 AAAAAAAAAGAGAGAAAAAAAAGAAAGAAA
1 AAAAAAAAAGA-A-AAAAAAAA-AAAGAAA
1519677 AAAAGAAAAA-AAAAGAAAAAAAAAGAGAA
1 AAAA-AAAAAGAAAA-AAAAAAAAAGA-AA
1519706 AAAAGAAAAA
1 AAAA-AAAAA
1519716 CTAGAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
28 7 0.19
29 19 0.53
30 5 0.14
31 5 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAAAAAAAAAGAAA
Found at i:1523390 original size:42 final size:42
Alignment explanation
Indices: 1523190--1523646 Score: 193
Period size: 42 Copynumber: 10.8 Consensus size: 42
1523180 TTCCCAAAAT
* ** * * *
1523190 TGAGCCGACGAGCTTACAAAAAGATGAAGAAGTCTCCCGAGCC
1 TGAGTCGACGAGCAGAC-AAAAGATGAAGAAGTCTCTCGGGTC
* * * * * * * *
1523233 TGAGCCAATGGGTAGAC-AAAGTATAAACAAGTCTCTCAGGTC
1 TGAGTCGACGAGCAGACAAAAG-ATGAAGAAGTCTCTCGGGTC
** * * * *
1523275 CAAGCCGACAAGCAGACAAAA-A-GACGAAGTTTCTCAGGGT-
1 TGAGTCGACGAGCAGACAAAAGATGAAGAAGTCTCTC-GGGTC
* ** * * * *
1523315 TGAGCCGATAAGTAGACAAAGGAT-ATAGGAGTCTCTCGAGTC
1 TGAGTCGACGAGCAGACAAAAGATGA-AGAAGTCTCTCGGGTC
* * *
1523357 TGAGTCGACGAGCAGACAAAAGATAAAGAAGTCTCTTGGGCC
1 TGAGTCGACGAGCAGACAAAAGATGAAGAAGTCTCTCGGGTC
* * * * * * *
1523399 TGA-ACTGAC-AGACAGACATAAGATTAAAAAGTCCCTTGGGCC
1 TGAGTC-GACGAG-CAGACAAAAGATGAAGAAGTCTCTCGGGTC
* *
1523441 TAAGTCGA-TAGGCAGACAAAAGAATGAAGAAGTCTC-CTGGGTC
1 TGAGTCGACGA-GCAGACAAAAG-ATGAAGAAGTCTCTC-GGGTC
* * *
1523484 TAAGTTGACCG-GCAGACAAAAAGATGAAGAAGTCTCTTGGGTC
1 TGAGTCGA-CGAGCAGAC-AAAAGATGAAGAAGTCTCTCGGGTC
* * * *
1523527 TGAG-CTGATGGGTAGACAAAAGATGAAGAAGTCT-TATGGGTC
1 TGAGTC-GACGAGCAGACAAAAGATGAAGAAGTCTCT-CGGGTC
* * * * * **
1523569 TGAGCCGATGGGTAGACAAAAGATGAAGAAGTCTCCCAAGTC
1 TGAGTCGACGAGCAGACAAAAGATGAAGAAGTCTCTCGGGTC
* *
1523611 TGAG-CTGACGAGTAGATAAAAAGATGAAGAAGTCTC
1 TGAGTC-GACGAGCAGA-CAAAAGATGAAGAAGTCTC
1523647 CCGAGTCTAA
Statistics
Matches: 319, Mismatches: 69, Indels: 52
0.73 0.16 0.12
Matches are distributed among these distances:
40 25 0.08
41 18 0.06
42 180 0.56
43 91 0.29
44 5 0.02
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (42 bp):
TGAGTCGACGAGCAGACAAAAGATGAAGAAGTCTCTCGGGTC
Found at i:1523487 original size:43 final size:42
Alignment explanation
Indices: 1523368--1523604 Score: 201
Period size: 42 Copynumber: 5.6 Consensus size: 42
1523358 GAGTCGACGA
* * * * *
1523368 GCAGACAAAAGATAAAGAAGTCTCTTGGGCCTGAACT-GACAG
1 GCAGACAAAAGATGAAGAAGTCTCCTGGGTCT-AAGTCGATAG
* * * * *
1523410 ACAGACATAAGATTAAAAAGTC-CCTTGGGCCTAAGTCGATAG
1 GCAGACAAAAGATGAAGAAGTCTCC-TGGGTCTAAGTCGATAG
* **
1523452 GCAGACAAAAGAATGAAGAAGTCTCCTGGGTCTAAGTTGACCG
1 GCAGACAAAAG-ATGAAGAAGTCTCCTGGGTCTAAGTCGATAG
* * *
1523495 GCAGACAAAAAGATGAAGAAGTCTCTTGGGTCTGAG-CTGATGG
1 GCAGAC-AAAAGATGAAGAAGTCTCCTGGGTCTAAGTC-GATAG
* ** * * *
1523538 GTAGACAAAAGATGAAGAAGTCTTATGGGTCTGAGCCGATGG
1 GCAGACAAAAGATGAAGAAGTCTCCTGGGTCTAAGTCGATAG
*
1523580 GTAGACAAAAGATGAAGAAGTCTCC
1 GCAGACAAAAGATGAAGAAGTCTCC
1523605 CAAGTCTGAG
Statistics
Matches: 163, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.02
42 93 0.57
43 59 0.36
44 7 0.04
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.19
Consensus pattern (42 bp):
GCAGACAAAAGATGAAGAAGTCTCCTGGGTCTAAGTCGATAG
Found at i:1523558 original size:85 final size:84
Alignment explanation
Indices: 1523370--1523658 Score: 249
Period size: 85 Copynumber: 3.4 Consensus size: 84
1523360 GTCGACGAGC
* * * * * * * *
1523370 AGACAAAAGATAAAGAAGTCTCTTGGGCCTGAA-CTGACAGACAGACATAAGATTAAAAAGTCCC
1 AGACAAAAGATGAAGAAGTCTCCTGGGTCT-AAGCTGACAGGCAGACAAAAGATGAAGAAGTCTC
* * * *
1523434 TTGGGCCTAAG-TCGATAGGC
65 TTGGGTCTGAGCT-GATGGGT
* *
1523454 AGACAAAAGAATGAAGAAGTCTCCTGGGTCTAAGTTGACCGGCAGACAAAAAGATGAAGAAGTCT
1 AGACAAAAG-ATGAAGAAGTCTCCTGGGTCTAAGCTGACAGGCAGAC-AAAAGATGAAGAAGTCT
1523519 CTTGGGTCTGAGCTGATGGGT
64 CTTGGGTCTGAGCTGATGGGT
** * * ** * *
1523540 AGACAAAAGATGAAGAAGTCTTATGGGTCTGAGCCGATGGGTAGACAAAAGATGAAGAAGTCTCC
1 AGACAAAAGATGAAGAAGTCTCCTGGGTCTAAGCTGACAGGCAGACAAAAGATGAAGAAGTCTCT
*** * *
1523605 CAAGTCTGAGCTGACGAGT
66 TGGGTCTGAGCTGATGGGT
* * *
1523624 AGATAAAAAGATGAAGAAGTCTCCCGAGTCTAAGC
1 AGA-CAAAAGATGAAGAAGTCTCCTGGGTCTAAGC
1523659 CGATGGCAGA
Statistics
Matches: 166, Mismatches: 34, Indels: 9
0.79 0.16 0.04
Matches are distributed among these distances:
84 46 0.28
85 82 0.49
86 37 0.22
87 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (84 bp):
AGACAAAAGATGAAGAAGTCTCCTGGGTCTAAGCTGACAGGCAGACAAAAGATGAAGAAGTCTCT
TGGGTCTGAGCTGATGGGT
Found at i:1523908 original size:88 final size:88
Alignment explanation
Indices: 1523754--1524007 Score: 305
Period size: 88 Copynumber: 2.9 Consensus size: 88
1523744 TGCAAATTAT
* * *
1523754 TTGACCAAGGTGGTAACCATACGCCAAATCAGAATGAAAAGAATCTGACTAGGGTGGTAACTATA
1 TTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAGGGTGGTAACCATA
1523819 CGTCAAACATAAAAAAAAAAAAC
66 CGTCAAACATAAAAAAAAAAAAC
* * * * * *
1523842 TTGACCAGAGG-GGTAACTATACATCAAATCAAAATGAAAAAAATCTAACTAAGATGGTAACCAT
1 TTGACCA-AGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAGGGTGGTAACCAT
* * ** * ***
1523906 ACGTCAGATAGGAAAGAGGCAAAC
65 ACGTCAAACATAAAAAAAAAAAAC
* * *
1523930 TTGACCAAGGTGGTAACCATATGTCAAATCATAATGAAAAGAATCTGATTAGGGTGGTAACCATA
1 TTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAGGGTGGTAACCATA
1523995 CGTCAAAC-TAAAA
66 CGTCAAACATAAAA
1524008 TGAGAAGAGT
Statistics
Matches: 134, Mismatches: 30, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
87 6 0.04
88 125 0.93
89 3 0.02
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (88 bp):
TTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAGGGTGGTAACCATA
CGTCAAACATAAAAAAAAAAAAC
Found at i:1524010 original size:44 final size:44
Alignment explanation
Indices: 1523762--1524026 Score: 186
Period size: 44 Copynumber: 6.0 Consensus size: 44
1523752 ATTTGACCAA
* *
1523762 GGTGGTAACCATACGCCAAATCAGAATGAAAAGAATCTGACTAG
1 GGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAG
* * * * *
1523806 GGTGGTAACTATACGTCAAA-CATAAA-AAAAAAAAACTTGACCAG
1 GGTGGTAACCATACGTCAAATCA-AAATGAAAAGAATC-TGACTAG
* * * * *
1523850 AGG-GGTAACTATACATCAAATCAAAATGAAAAAAATCTAACTAA
1 -GGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAG
* * * * * *
1523894 GATGGTAACCATACGTCAGAT-AGGAAA-G--AGGCAAACTTGACCAA
1 GGTGGTAACCATACGTCAAATCA--AAATGAAAAG-AATC-TGACTAG
* * *
1523938 GGTGGTAACCATATGTCAAATCATAATGAAAAGAATCTGATTAG
1 GGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAG
* * *
1523982 GGTGGTAACCATACGTCAAA-CTAAAATGAGAAGAGTTTGACTAG
1 GGTGGTAACCATACGTCAAATC-AAAATGAAAAGAATCTGACTAG
1524026 G
1 G
1524027 TCCTAACACC
Statistics
Matches: 169, Mismatches: 37, Indels: 30
0.72 0.16 0.13
Matches are distributed among these distances:
42 1 0.01
43 17 0.10
44 130 0.77
45 19 0.11
46 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.20
Consensus pattern (44 bp):
GGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAG
Found at i:1524067 original size:48 final size:48
Alignment explanation
Indices: 1524007--1524241 Score: 319
Period size: 48 Copynumber: 4.9 Consensus size: 48
1523997 TCAAACTAAA
* * * *
1524007 ATGAGAAGAGTTTGACTAGGTCCTAACACCAATATAGTCAAATAAGGG
1 ATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAATAAGGG
* * *
1524055 ATAAAAAGAGTTTGACTAGGCCCTAAAACCAATACAATCAAATGAGGG
1 ATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAATAAGGG
* * *
1524103 ATGAAAAGAGTTTGACTAGGCCCTAGCACCAATACAATCAAACAAGGC
1 ATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAATAAGGG
* * *
1524151 ATGAAAAGAGTTT-AATGAGGTCCTAACACTAATACAATCAAATAAGGG
1 ATGAAAAGAGTTTGACT-AGGCCCTAACACCAATACAATCAAATAAGGG
* *
1524199 ATGAGAAGAGTTTGACTAGGCCCTAACACTAATACAATCAAAT
1 ATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAAT
1524242 GAGGAGGGTC
Statistics
Matches: 163, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
47 2 0.01
48 159 0.98
49 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (48 bp):
ATGAAAAGAGTTTGACTAGGCCCTAACACCAATACAATCAAATAAGGG
Found at i:1524288 original size:30 final size:30
Alignment explanation
Indices: 1524252--1524360 Score: 105
Period size: 30 Copynumber: 3.6 Consensus size: 30
1524242 GAGGAGGGTC
1524252 TTGACCGAATATAGTCAAGAGTGGTAAAAT
1 TTGACCGAATATAGTCAAGAGTGGTAAAAT
* *
1524282 TTGACCGAATATAGTCAA-A-TGAGGAAAGAC
1 TTGACCGAATATAGTCAAGAGTG-GTAAA-AT
* * * * *
1524312 TTGACTGAATACAGTCAAGTAGGGGTGATAT
1 TTGACCGAATATAGTCAAG-AGTGGTAAAAT
*
1524343 TTGACCAAATATAGTCAA
1 TTGACCGAATATAGTCAA
1524361 ATAAGGATTA
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
28 2 0.03
29 5 0.08
30 35 0.56
31 16 0.26
32 3 0.05
33 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (30 bp):
TTGACCGAATATAGTCAAGAGTGGTAAAAT
Found at i:1524315 original size:60 final size:59
Alignment explanation
Indices: 1524251--1524603 Score: 253
Period size: 60 Copynumber: 5.8 Consensus size: 59
1524241 TGAGGAGGGT
* * * *
1524251 CTTGACCGAATATAGTCAAGAGTGGTAAAATTTGACCGAATATAGTCAAATGAGGAAAGA
1 CTTGACCAAATACAGTCAAGAG-GGTGAAATTTGACCGAATATAGTCAAATAAGGAAAGA
** * * * *
1524311 CTTGACTGAATACAGTCAAGTAGGGGTGATATTTGACCAAATATAGTCAAATAAGGATTA-T
1 CTTGACCAAATACAGTCAAG-A-GGGTGAAATTTGACCGAATATAGTCAAATAAGGA-AAGA
* * * * * * * *
1524372 TTTCACCGAATACAGTTAAGAAGAGTGAGATTTGACTGAGTATAGTCAAATAAGGAAAGA
1 CTTGACCAAATACAGTCAAG-AGGGTGAAATTTGACCGAATATAGTCAAATAAGGAAAGA
* * * * ** *
1524432 CTTGACTAAATATAGTCAAGCGAGGGTGAAATTTGA-TGAAATACAGTCAAATAAGGATTGT
1 CTTGACCAAATACAGTCAA--GAGGGTGAAATTTGACCG-AATATAGTCAAATAAGGAAAGA
* * * ** * *
1524493 CTTGACCAAATACAATTAAGGAGGGTGAGATTTGATTGAGTA-CGATCAAATAAGGAAAGA
1 CTTGACCAAATACAGTCAA-GAGGGTGAAATTTGACCGAATATAG-TCAAATAAGGAAAGA
* * * * *
1524553 TTTGACCAAATACAGTTAAGAGGGGTAAAATTTGACCGAGTACAGTCAAAT
1 CTTGACCAAATACAGTCAAGA-GGGTGAAATTTGACCGAATATAGTCAAAT
1524604 GATGATGGAA
Statistics
Matches: 231, Mismatches: 51, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
59 4 0.02
60 130 0.56
61 94 0.41
62 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (59 bp):
CTTGACCAAATACAGTCAAGAGGGTGAAATTTGACCGAATATAGTCAAATAAGGAAAGA
Found at i:1524450 original size:121 final size:120
Alignment explanation
Indices: 1524280--1524603 Score: 389
Period size: 121 Copynumber: 2.7 Consensus size: 120
1524270 GAGTGGTAAA
* * * * *
1524280 ATTTGACCGAATATAGTCAAATGAGGAAAGACTTGACTGAATACAGTCAAGTAGGGGTGATATTT
1 ATTTGACTGAGTATAGTCAAATAAGGAAAGACTTGACTAAATACAGTCAAG-AGGGGTGAAATTT
* * * *
1524345 GACCAAATATAGTCAAATAAGGATTATTTTCACCGAATACAGTTAAGAAGAGTGAG
65 GACCAAATACAGTCAAATAAGGATTATCTTCACCAAATACAATTAAGAAGAGTGAG
* *
1524401 ATTTGACTGAGTATAGTCAAATAAGGAAAGACTTGACTAAATATAGTCAAGCGAGGGTGAAATTT
1 ATTTGACTGAGTATAGTCAAATAAGGAAAGACTTGACTAAATACAGTCAAGAG-GGGTGAAATTT
** * * * *
1524466 GATGAAATACAGTCAAATAAGGATTGTCTTGACCAAATACAATTAAGGAGGGTGAG
65 GACCAAATACAGTCAAATAAGGATTATCTTCACCAAATACAATTAAGAAGAGTGAG
* * * * * *
1524522 ATTTGATTGAGTA-CGATCAAATAAGGAAAGATTTGACCAAATACAGTTAAGAGGGGTAAAATTT
1 ATTTGACTGAGTATAG-TCAAATAAGGAAAGACTTGACTAAATACAGTCAAGAGGGGTGAAATTT
* *
1524586 GACCGAGTACAGTCAAAT
65 GACCAAATACAGTCAAAT
1524604 GATGATGGAA
Statistics
Matches: 172, Mismatches: 29, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
120 26 0.15
121 146 0.85
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (120 bp):
ATTTGACTGAGTATAGTCAAATAAGGAAAGACTTGACTAAATACAGTCAAGAGGGGTGAAATTTG
ACCAAATACAGTCAAATAAGGATTATCTTCACCAAATACAATTAAGAAGAGTGAG
Found at i:1525584 original size:88 final size:88
Alignment explanation
Indices: 1525411--1525584 Score: 190
Period size: 88 Copynumber: 2.0 Consensus size: 88
1525401 GCAGATATGT
* * * * * *
1525411 GTGAAACAATGCAAATGCAAGCATTAATAAAGTGGCTAATACCTATGAAATGACGTAAATACCAA
1 GTGAAACAATGCAAATGCAAGCATCAATAAAATAGCAAATACCTATGAAATGACGCAAATACAAA
* *
1525476 TGTCATCTCAAATTCAAATGTAG
66 TGTCATCTAAAATGCAAATGTAG
* * * *
1525499 GTGAAACAATGCAAATGCAAGGATCAATAAAATAGCAAATGCAC-ATGAAATGATGCAAATGCAA
1 GTGAAACAATGCAAATGCAAGCATCAATAAAATAGCAAATAC-CTATGAAATGACGCAAATACAA
* *
1525563 ATGTTAT-TAAAACTGCGAATGT
65 ATGTCATCTAAAA-TGCAAATGT
1525585 GCATGAAGTG
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
87 4 0.06
88 65 0.93
89 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (88 bp):
GTGAAACAATGCAAATGCAAGCATCAATAAAATAGCAAATACCTATGAAATGACGCAAATACAAA
TGTCATCTAAAATGCAAATGTAG
Found at i:1526957 original size:22 final size:22
Alignment explanation
Indices: 1526932--1526978 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1526922 TATTTCATAC
1526932 TTTTTCTATT-TCATACTTTTTT
1 TTTTTCT-TTCTCATACTTTTTT
* *
1526954 TTTTTCTTTCTCTTTCTTTTTT
1 TTTTTCTTTCTCATACTTTTTT
1526976 TTT
1 TTT
1526979 GGTTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTTCTCATACTTTTTT
Found at i:1526959 original size:16 final size:16
Alignment explanation
Indices: 1526916--1526952 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1526906 CTATCTGCAT
1526916 TTTTTCTATTTCATAC
1 TTTTTCTATTTCATAC
1526932 TTTTTCTATTTCATAC
1 TTTTTCTATTTCATAC
1526948 TTTTT
1 TTTTT
1526953 TTTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTCTATTTCATAC
Found at i:1526988 original size:21 final size:21
Alignment explanation
Indices: 1526949--1526988 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1526939 ATTTCATACT
*
1526949 TTTTTTTTTTCTTTCTCTTTC
1 TTTTTTTTTGCTTTCTCTTTC
* *
1526970 TTTTTTTTTGGTTTTTCTT
1 TTTTTTTTTGCTTTCTCTT
1526989 ATTTAGAGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTTTTTTTGCTTTCTCTTTC
Found at i:1529252 original size:14 final size:14
Alignment explanation
Indices: 1529233--1529260 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1529223 GTTAACACGT
1529233 GATCAATTTTAGGC
1 GATCAATTTTAGGC
1529247 GATCAATTTTAGGC
1 GATCAATTTTAGGC
1529261 TTGACTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
GATCAATTTTAGGC
Found at i:1545114 original size:51 final size:48
Alignment explanation
Indices: 1545031--1545143 Score: 147
Period size: 51 Copynumber: 2.3 Consensus size: 48
1545021 AATTAACTAG
**
1545031 ATGTATCGATACATTTTAATGTATCGATACATCTAGGTAAAAAA-ATAGA
1 ATGTATCGATACATTAAAATGTATCGATACATCTAGGTAAAAAACAT--A
* *
1545080 ATGTATCGATACATTGAAAAATGTATTGATACATCTGGGTAAAAAACATA
1 ATGTATCGATACATT--AAAATGTATCGATACATCTAGGTAAAAAACATA
1545130 ATGTATCGATACAT
1 ATGTATCGATACAT
1545144 GTACTGTTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
49 15 0.26
50 15 0.26
51 25 0.44
52 2 0.04
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (48 bp):
ATGTATCGATACATTAAAATGTATCGATACATCTAGGTAAAAAACATA
Found at i:1545530 original size:13 final size:13
Alignment explanation
Indices: 1545512--1545537 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1545502 TACTGCACCC
1545512 CATTTTTTATTTT
1 CATTTTTTATTTT
1545525 CATTTTTTATTTT
1 CATTTTTTATTTT
1545538 TTTCAACCTC
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:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (13 bp):
CATTTTTTATTTT
Found at i:1551227 original size:157 final size:154
Alignment explanation
Indices: 1550994--1551302 Score: 381
Period size: 157 Copynumber: 2.0 Consensus size: 154
1550984 TGAGAACCGT
* * *
1550994 GGTTGAAGTATCCCTTCGGAGATGGTAGGGTTGGAGTATCCCAGAGATAAAGAATTCAATGTTTT
1 GGTTGAAGTATCCCTTCGAAGATGG-AGGGTTAGAGTATCCCAAAGATAAAGAATTCAATGTTTT
* * * *
1551059 GGAAGTAAAAACGGGGTTGGAGTATCCCCTCGGAGATTGT-GGAGTTAGAGTATCCCCAAAGATG
65 GGAAGTAAAAACAGGGTTGGAGTATCCCCTCAGAAATAGTGGGA-TTAGAGTAT--CC-AAGA-G
*
1551123 AAGAATTTGGTATTGTGGAAGTAAAAATAA
125 AAGAATTTGATATTGTGGAAGTAAAAATAA
* * * *
1551153 GGTTGGAGTATTCCTTCGAATATGG-GGGTTAGAGTTTCCCAAAGATGAAA-AATTCAATGTTTT
1 GGTTGAAGTATCCCTTCGAAGATGGAGGGTTAGAGTATCCCAAAGAT-AAAGAATTCAATGTTTT
* ** * *
1551216 GGAAGTAAAAACAGGGTTGTAGTATCCTTTCAGAAATAGTGGGATTAGAGTATCCTAGAGATGAA
65 GGAAGTAAAAACAGGGTTGGAGTATCCCCTCAGAAATAGTGGGATTAGAGTATCCAAGAGAAGAA
1551281 TTTGATATTGTGGAAGTAAAAA
130 TTTGATATTGTGGAAGTAAAAA
1551303 ATGGAGTTAG
Statistics
Matches: 131, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
153 26 0.20
154 3 0.02
155 2 0.02
157 73 0.56
158 6 0.05
159 21 0.16
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (154 bp):
GGTTGAAGTATCCCTTCGAAGATGGAGGGTTAGAGTATCCCAAAGATAAAGAATTCAATGTTTTG
GAAGTAAAAACAGGGTTGGAGTATCCCCTCAGAAATAGTGGGATTAGAGTATCCAAGAGAAGAAT
TTGATATTGTGGAAGTAAAAATAA
Found at i:1551408 original size:128 final size:132
Alignment explanation
Indices: 1551178--1551452 Score: 332
Period size: 128 Copynumber: 2.1 Consensus size: 132
1551168 TCGAATATGG
* * *
1551178 GGGTTAGAGTTTCCCAAAGATGAAAAATTCAATGTTTTGGAAGTAAAAACAGGGTTGTAGTATCC
1 GGGTTAGAGTATCCCAAAGATGAAAAATTCAATGTTTTGGAAGTAAAAACAGAGTTGGAGTATCC
* * * *
1551243 TTTCAGAAATAGTGGGATTAGAGTATCCTAGAGATG-A-A-TTT-GATATTGTGGAAGT-AAAAA
66 CTTCAGAAATAGTGGGATTAGAGTATCCCAAAAATGAAGAGTTTAG-TATTGTGGAAGTAAAAAA
1551303 AT-
130 ATC
* **
1551305 GGAGTTAGAGTATCCCAAAGATTAAAAATTTGAT-TTTTCGGAAGTAAAAACAGAGTTGGAGTAT
1 GG-GTTAGAGTATCCCAAAGATGAAAAATTCAATGTTTT-GGAAGTAAAAACAGAGTTGGAGTAT
* * *
1551369 CCCTTCAGAGAT-GATGGGGTTGGAGTATCCCAAAAATGAAGAGTTTAGTATTGTGGAAGTAAAA
64 CCCTTCAGAAATAG-TGGGATTAGAGTATCCCAAAAATGAAGAGTTTAGTATTGTGGAAGTAAAA
1551433 AAATC
128 AAATC
*
1551438 GGGTTGGAGTATCCC
1 GGGTTAGAGTATCCC
1551453 CTTGGAGATG
Statistics
Matches: 125, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
127 7 0.06
128 79 0.63
129 1 0.01
130 1 0.01
131 15 0.12
132 20 0.16
133 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.25, T:0.29
Consensus pattern (132 bp):
GGGTTAGAGTATCCCAAAGATGAAAAATTCAATGTTTTGGAAGTAAAAACAGAGTTGGAGTATCC
CTTCAGAAATAGTGGGATTAGAGTATCCCAAAAATGAAGAGTTTAGTATTGTGGAAGTAAAAAAA
TC
Found at i:1551549 original size:79 final size:78
Alignment explanation
Indices: 1551303--1551620 Score: 248
Period size: 79 Copynumber: 4.0 Consensus size: 78
1551293 GAAGTAAAAA
* * * * * * * *
1551303 ATGGAGTTAGAGTATCCCAAAGATTAAAAATTTGATTTTTCGGAAGTAAAAACAGAGTTGGAGTA
1 ATGGGGTTGGAGTATCCTAAAAATGAAAAATTTGATATTACGGAAGTAAAAAC-GGGTTGGAGTA
*
1551368 TCCCTTCAGAGATG
65 TCCCCTCAGAGATG
* * * **
1551382 ATGGGGTTGGAGTATCCCAAAAATGAAGAGTTT-AGTATTGTGGAAGTAAAAAAATCGGGTTGGA
1 ATGGGGTTGGAGTATCCTAAAAATGAAAAATTTGA-TATTACGGAAGT--AAAAA-CGGGTTGGA
**
1551446 GTATCCCCTTGGAGATG
62 GTATCCCCTCAGAGATG
* ** * *
1551463 ATAGGGTTCTAGTATCCTTAAAAATGAAAAATTTGACATTACGGAAGTAAAAACGGGTTGGAGCA
1 ATGGGGTTGGAGTATCC-TAAAAATGAAAAATTTGATATTACGGAAGTAAAAACGGGTTGGAGTA
*
1551528 TCCCCTCCGAGAT-
65 TCCCCTCAGAGATG
* * * * ** * *
1551541 AGTGGGGTTGGAGTGTCCCTAAAGATGAAAAATTCGATGTTTTGGAAGTAGAAACGAGGTTGGAA
1 A-TGGGGTTGGAGTAT-CCTAAAAATGAAAAATTTGATATTACGGAAGTAAAAACG-GGTTGGAG
*
1551606 TAT-TCCT-AGAGATG
63 TATCCCCTCAGAGATG
1551620 A
1 A
1551621 AAAAATCAGT
Statistics
Matches: 189, Mismatches: 40, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
78 7 0.04
79 102 0.54
80 16 0.08
81 40 0.21
82 23 0.12
83 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (78 bp):
ATGGGGTTGGAGTATCCTAAAAATGAAAAATTTGATATTACGGAAGTAAAAACGGGTTGGAGTAT
CCCCTCAGAGATG
Found at i:1557701 original size:10 final size:10
Alignment explanation
Indices: 1557686--1557731 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
1557676 TTCTACAGTT
*
1557686 GTTAATAGTA
1 GTTAATAGTG
1557696 GTTAATAGTG
1 GTTAATAGTG
*
1557706 GTTAAGAGTG
1 GTTAATAGTG
* *
1557716 GTTAATGGAG
1 GTTAATAGTG
1557726 GTTAAT
1 GTTAAT
1557732 TAGTTAGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (10 bp):
GTTAATAGTG
Found at i:1558526 original size:7 final size:7
Alignment explanation
Indices: 1558514--1558539 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1558504 AAATAAACCA
1558514 AACACTG
1 AACACTG
1558521 AACACTG
1 AACACTG
1558528 AACACTG
1 AACACTG
1558535 AACAC
1 AACAC
1558540 CAAACAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.31, G:0.12, T:0.12
Consensus pattern (7 bp):
AACACTG
Found at i:1558545 original size:14 final size:14
Alignment explanation
Indices: 1558510--1558545 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1558500 TATTAAATAA
1558510 ACCAAACACTGAAC
1 ACCAAACACTGAAC
**
1558524 ACTGAACACTGAAC
1 ACCAAACACTGAAC
1558538 ACCAAACA
1 ACCAAACA
1558546 ATAGTATGTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.33, G:0.08, T:0.08
Consensus pattern (14 bp):
ACCAAACACTGAAC
Found at i:1558949 original size:26 final size:29
Alignment explanation
Indices: 1558888--1558951 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 29
1558878 AAATTTATTT
*
1558888 AATTTAAACAAACGAACAAGAAGACATCCA
1 AATTTAAACAAACAAACAAGAAGACA-CCA
* *
1558918 ATTTTAAACAAACAAACACG-A-ACA-CA
1 AATTTAAACAAACAAACAAGAAGACACCA
1558944 AATTTAAA
1 AATTTAAA
1558952 ATTCTTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 9 0.30
28 3 0.10
29 1 0.03
30 17 0.57
ACGTcount: A:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (29 bp):
AATTTAAACAAACAAACAAGAAGACACCA
Found at i:1563665 original size:21 final size:20
Alignment explanation
Indices: 1563635--1563673 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1563625 CACATTTTTG
1563635 TCTAAATGTATAGATACATT
1 TCTAAATGTATAGATACATT
*
1563655 TCTAGAATGTATCGATACA
1 TCTA-AATGTATAGATACA
1563674 AGGTCCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATAGATACATT
Found at i:1563932 original size:234 final size:233
Alignment explanation
Indices: 1563521--1563952 Score: 643
Period size: 234 Copynumber: 1.8 Consensus size: 233
1563511 GCTCCCGACG
* * * * * *
1563521 AAAATGGTTTTTTAGATTAACATGACTTTTTGTTAAGCCTGAATTCATTTCCTATCGTCCTTAGT
1 AAAATGGTTTTTTAGATTAACATAACTTTTTGTTAAGCCCGAATTCATTCCCCATCGTCCCTAAT
* *
1563586 CGAGATAGAGTGTTTAGAAGGCAAAAAGGATGAAAAAATCACATTTTTGTCTAAATGTATAGATA
66 CAAGATAGAGTGTTTAGAAGGCAAAAAGGATGAAAAAATCACATTTTTGTCCAAATGTATAGATA
* *
1563651 CATTTCTAGAATGTATCGATACAAGGTCCCAACGATCAAACATTTTGAATTTCAACAATTTGTAT
131 CATTTCTAAAATGTATCGATACAAGGTCCCAACGATCAAAAATTTTGAATTTCAACAATTTGTAT
1563716 CGAATCAATTTCCCATCAATTTCCCAACGATCAAACTT
196 CGAATCAATTTCCCATCAATTTCCCAACGATCAAACTT
***
1563754 AAAATGGTTTTTTAGATTTTTATAACTTTTTGATTAAGCCCGAA-TCAATTCCCCATCGTCCCTA
1 AAAATGGTTTTTTAGATTAACATAACTTTTTG-TTAAGCCCGAATTC-ATTCCCCATCGTCCCTA
* * * *
1563818 ATCAAGATAGGGTGTTTCGAAGGCAAAAAGGATGAAAAAATTACATTTTTGTCCAAATGTATCGA
64 ATCAAGATAGAGTGTTTAGAAGGCAAAAAGGATGAAAAAATCACATTTTTGTCCAAATGTATAGA
* **
1563883 TACATTGT-TAAAATGTATCGATACAAGGTCCCAACGGTCAAAAATTTTGAATTTCAATGATTTG
129 TACATT-TCTAAAATGTATCGATACAAGGTCCCAACGATCAAAAATTTTGAATTTCAACAATTTG
1563947 TATCGA
193 TATCGA
1563953 TACATAAAAT
Statistics
Matches: 176, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
233 30 0.17
234 145 0.82
235 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (233 bp):
AAAATGGTTTTTTAGATTAACATAACTTTTTGTTAAGCCCGAATTCATTCCCCATCGTCCCTAAT
CAAGATAGAGTGTTTAGAAGGCAAAAAGGATGAAAAAATCACATTTTTGTCCAAATGTATAGATA
CATTTCTAAAATGTATCGATACAAGGTCCCAACGATCAAAAATTTTGAATTTCAACAATTTGTAT
CGAATCAATTTCCCATCAATTTCCCAACGATCAAACTT
Found at i:1563983 original size:13 final size:13
Alignment explanation
Indices: 1563965--1563989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1563955 CATAAAATGT
1563965 TGTATCGATACAA
1 TGTATCGATACAA
1563978 TGTATCGATACA
1 TGTATCGATACA
1563990 TATTTTTTTT
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:1564071 original size:13 final size:13
Alignment explanation
Indices: 1564053--1564077 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1564043 ATTACTCAAA
1564053 TGTATCGATACAT
1 TGTATCGATACAT
1564066 TGTATCGATACA
1 TGTATCGATACA
1564078 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1564142 original size:52 final size:52
Alignment explanation
Indices: 1564086--1564205 Score: 222
Period size: 52 Copynumber: 2.3 Consensus size: 52
1564076 CACTGATCTT
*
1564086 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1564138 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1564190 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1564206 AACAACTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1568206 original size:43 final size:43
Alignment explanation
Indices: 1567955--1568418 Score: 290
Period size: 48 Copynumber: 10.1 Consensus size: 43
1567945 CTTAAGAATG
* * * *
1567955 TTAAAGATGCCAATATGCTGATTCAAGGCCAACAATATCGGA-
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
1567997 TTCAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTC
1 TT----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * **
1568046 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCTAGTGATATCAGAC
1 -T-----TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
1568095 -T---CGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
1568134 TTAAAGACAAGGTGCTAATTTGCTAATTCAAGGCCAGCGATATTGGAG
1 TT----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
1568182 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
1568225 TTAAAGACAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACC
1 TT----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-C
* * * *
1568274 GAAGATGGTAAAGGTGTCAATATGCTAATTTAAGGCTAGCGATATTGGAC
1 -----T--TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
1568324 TTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCAACATTGGAC
1 TT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
1568373 TTAAAAGTGCCAATATGTTGATTCAAGGCCAACGATATTGGAC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1568416 TTA
1 TTA
1568419 GATGAAGATG
Statistics
Matches: 332, Mismatches: 49, Indels: 81
0.72 0.11 0.18
Matches are distributed among these distances:
39 30 0.09
40 1 0.00
42 3 0.01
43 72 0.22
44 4 0.01
45 2 0.01
46 2 0.01
47 2 0.01
48 106 0.32
49 67 0.20
50 2 0.01
51 37 0.11
52 1 0.00
54 1 0.00
55 1 0.00
56 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (43 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
Found at i:1568217 original size:91 final size:92
Alignment explanation
Indices: 1568006--1568418 Score: 442
Period size: 91 Copynumber: 4.5 Consensus size: 92
1567996 ATTCAAGATG
* *
1568006 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGGTGCCAATATGCT
* * * *
1568071 GATTCAAGGCTAGTGATA-T-CAG--A
66 AATTCAAGGCCAGCGATATTGGAGTTA
*** * * * *
1568094 CTCGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTTAAAGA-CAAGGTGCTAATTTGCT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGGTGCCAATATGCT
1568158 AATTCAAGGCCAGCGATATTGGAGTTA
66 AATTCAAGGCCAGCGATATTGGAGTTA
* *
1568185 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGGTGCCAATATGCT
1568249 AATTCAAGGCCAGCGATATTGGACCGAAGATGGTA
66 AATTCAAGGCCAGCGATATT-G---G-AG-T--TA
* * * * * * *
1568284 AAGGTGTCAATATGCTAATTTAAGGCTAGCGATATTGGACTTAAAGATGAAGATGCCAATATGCT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGGTGCCAATATGCT
* * * *
1568349 GATTCAAGGCCAGCAACATTGGACTTA
66 AATTCAAGGCCAGCGATATTGGAGTTA
* * * *
1568376 AAAGTGCCAATATGTTGATTCAAGGCCAACGATATTGGACTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
1568419 GATGAAGATG
Statistics
Matches: 272, Mismatches: 40, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
87 29 0.11
88 42 0.15
89 2 0.01
91 78 0.29
92 39 0.14
94 1 0.00
95 2 0.01
96 3 0.01
97 1 0.00
99 43 0.16
100 32 0.12
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (92 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGGTGCCAATATGCT
AATTCAAGGCCAGCGATATTGGAGTTA
Found at i:1568329 original size:99 final size:100
Alignment explanation
Indices: 1568183--1568372 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 100
1568173 ATATTGGAGT
* * * *
1568183 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATG
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGATGCCAATATG
* *
1568247 CTAATTCAAGGCCAGCGATATTGGACCGAAGATGG
66 CTAATTCAAGGCCAGCAACATTGGACCGAAGATGG
* * * * *
1568282 TAAAGGTGTCAATATGCTAATTTAAGGCTAGCGATATTGGACTTAAAGATGAAGATGCCAATATG
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGATGCCAATATG
*
1568347 CTGATTCAAGGCCAGCAACATTGGAC
66 CTAATTCAAGGCCAGCAACATTGGAC
1568373 TTAAAAGTGC
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
99 42 0.54
100 36 0.46
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (100 bp):
TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATCAAGATGCCAATATG
CTAATTCAAGGCCAGCAACATTGGACCGAAGATGG
Found at i:1568428 original size:148 final size:141
Alignment explanation
Indices: 1568097--1568415 Score: 359
Period size: 143 Copynumber: 2.3 Consensus size: 141
1568087 TATCAGACTC
* * * ** *
1568097 GTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGACTTAA-A--G-ACAAGGTG-CTAATTTGC
1 GTGCCAATATGCTAATTCAAGGCCAACGATATTGGACCGAAGATGGTA-AAGGTGTC-AATATGC
* * *
1568157 TAATTCAAGGCCAGCGATATTGGAGTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG
64 TAATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCAACATTG
*
1568222 GTCTTAAAGACAAG
129 GACTT-AAGACAAG
*
1568236 GTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACCGAAGATGGTAAAGGTGTCAATATGCTA
1 GTGCCAATATGCTAATTCAAGGCCAACGATATTGGACCGAAGATGGTAAAGGTGTCAATATGCTA
* *
1568301 ATTTAAGGCTAGCGATATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCAAC
66 ATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCAAC
1568366 ATTGGACTT-A-A-AA-
125 ATTGGACTTAAGACAAG
* *
1568379 GTGCCAATATGTTGATTCAAGGCCAACGATATTGGAC
1 GTGCCAATATGCTAATTCAAGGCCAACGATATTGGAC
1568416 TTAGATGAAG
Statistics
Matches: 155, Mismatches: 14, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
139 37 0.24
140 1 0.01
142 37 0.24
143 38 0.25
144 3 0.02
145 2 0.01
146 1 0.01
147 1 0.01
148 35 0.23
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (141 bp):
GTGCCAATATGCTAATTCAAGGCCAACGATATTGGACCGAAGATGGTAAAGGTGTCAATATGCTA
ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCAACATTGGA
CTTAAGACAAG
Found at i:1568500 original size:28 final size:28
Alignment explanation
Indices: 1568442--1568687 Score: 238
Period size: 28 Copynumber: 8.6 Consensus size: 28
1568432 CCAACTTGTT
* *
1568442 TGGGCTTTTGAAAGGGTTG-CACCGAATTG
1 TGGGCTTTTGAAA-GG-TGCCACTGACTTG
* *
1568471 TGTGCTTTTG-AAGGTTGCCACTGCCTTG
1 TGGGCTTTTGAAAGG-TGCCACTGACTTG
1568499 TGGGC-TTTG-AAGGTTGCCACTGACTTG
1 TGGGCTTTTGAAAGG-TGCCACTGACTTG
* *
1568526 TGGAC-TTTGAAAAGGTGCCACTAACTTG
1 TGGGCTTTTG-AAAGGTGCCACTGACTTG
*
1568554 TGGGC-TTTGAAAAGGGTGTCACTGACTTG
1 TGGGCTTTTG-AAA-GGTGCCACTGACTTG
*
1568583 TGGGCTTTTGAAAAGGTGCC-CTAACTTG
1 TGGGCTTTTG-AAAGGTGCCACTGACTTG
*
1568611 TGGCCTTTTGAAAAGGTGCCACTGACTTG
1 TGGGCTTTTG-AAAGGTGCCACTGACTTG
1568640 TGGGCTTTTGAAAAAGGGTGCCACTGACTTG
1 TGGGCTTTTG--AAA-GGTGCCACTGACTTG
1568671 TGGGCTTTTCG-AAGGTG
1 TGGGCTTTT-GAAAGGTG
1568688 AGGAATGCCT
Statistics
Matches: 192, Mismatches: 16, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
27 34 0.18
28 67 0.35
29 54 0.28
30 12 0.06
31 24 0.12
32 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.32
Consensus pattern (28 bp):
TGGGCTTTTGAAAGGTGCCACTGACTTG
Found at i:1568581 original size:29 final size:28
Alignment explanation
Indices: 1568481--1568678 Score: 249
Period size: 28 Copynumber: 6.9 Consensus size: 28
1568471 TGTGCTTTTG
*
1568481 AAGGTTGCCACTGCCTTGTGGGCTTTG--
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
*
1568508 AAGGTTGCCACTGACTTGTGGACTTTGAA
1 AAGG-TGCCACTGACTTGTGGGCTTTGAA
*
1568537 AAGGTGCCACTAACTTGTGGGCTTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTGAA
*
1568565 AAGGGTGTCACTGACTTGTGGGCTTTTGAA
1 AA-GGTGCCACTGACTTGTGGGC-TTTGAA
* *
1568595 AAGGTGCC-CTAACTTGTGGCCTTTTGAA
1 AAGGTGCCACTGACTTGTGGGC-TTTGAA
1568623 AAGGTGCCACTGACTTGTGGGCTTTTGAAA
1 AAGGTGCCACTGACTTGTGGGC-TTTG-AA
1568653 AAGGGTGCCACTGACTTGTGGGCTTT
1 AA-GGTGCCACTGACTTGTGGGCTTT
1568679 TCGAAGGTGA
Statistics
Matches: 153, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
27 25 0.16
28 50 0.33
29 43 0.28
30 15 0.10
31 20 0.13
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (28 bp):
AAGGTGCCACTGACTTGTGGGCTTTGAA
Found at i:1568607 original size:57 final size:58
Alignment explanation
Indices: 1568427--1568678 Score: 270
Period size: 57 Copynumber: 4.4 Consensus size: 58
1568417 TAGATGAAGA
* * * *
1568427 TGCCACCAACTTGTTTGGGCTTTTG-AAAGGGTTG-CACCGAATTGTGTGCTTTTG--AAGG
1 TGCCACTAACTTG--TGGGC-TTTGAAAAGGG-TGCCACTGACTTGTGGGCTTTTGAAAAGG
** * *
1568485 TTGCCACTGCCTTGTGGGCTTTG--AAGGTTGCCACTGACTTGTGGAC-TTTGAAAAGG
1 -TGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGG
*
1568541 TGCCACTAACTTGTGGGCTTTGAAAAGGGTGTCACTGACTTGTGGGCTTTTGAAAAGG
1 TGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGG
*
1568599 TGCC-CTAACTTGTGGCCTTTTGAAAA-GGTGCCACTGACTTGTGGGCTTTTGAAAAAGGG
1 TGCCACTAACTTGTGGGC-TTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAAA-GG
*
1568658 TGCCACTGACTTGTGGGCTTT
1 TGCCACTAACTTGTGGGCTTT
1568679 TCGAAGGTGA
Statistics
Matches: 166, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
54 6 0.04
55 35 0.21
56 8 0.05
57 61 0.37
58 26 0.16
59 19 0.11
60 11 0.07
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.33
Consensus pattern (58 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGG
Found at i:1570167 original size:4 final size:4
Alignment explanation
Indices: 1570160--1570212 Score: 55
Period size: 4 Copynumber: 14.8 Consensus size: 4
1570150 TGCTGTTTTT
*
1570160 TTTG TTTG -TT- TTTG TTT- TTTG TTTG TTT- TTTT TTTG TTTG -TT-
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG
1570202 TTTG TTTG TTT
1 TTTG TTTG TTT
1570213 TTTTTGCGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
3 14 0.33
4 28 0.67
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (4 bp):
TTTG
Found at i:1570171 original size:10 final size:10
Alignment explanation
Indices: 1570153--1570218 Score: 82
Period size: 10 Copynumber: 6.6 Consensus size: 10
1570143 CCCTTTTTGC
1570153 TGTTT-TTTT
1 TGTTTGTTTT
1570162 TGTTTGTTTT
1 TGTTTGTTTT
*
1570172 TGTTTTTTGTT
1 TGTTTGTT-TT
*
1570183 TGTTTTTTTTT
1 TG-TTTGTTTT
1570194 TGTTTGTTTT
1 TGTTTGTTTT
1570204 TGTTTGTTTT
1 TGTTTGTTTT
1570214 T-TTTG
1 TGTTTG
1570219 CGAATGACGC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.17
10 29 0.56
11 8 0.15
12 6 0.12
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (10 bp):
TGTTTGTTTT
Found at i:1584348 original size:21 final size:20
Alignment explanation
Indices: 1584322--1584360 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1584312 GTTGGGACCT
1584322 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
*
1584343 TGTATCTATACATTTAGA
1 TGTATCGATACATTTAGA
1584361 CAAAAATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:1585592 original size:16 final size:17
Alignment explanation
Indices: 1585563--1585595 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1585553 CACAAACACT
1585563 AAAATCAATCTTTTAAA
1 AAAATCAATCTTTTAAA
*
1585580 AAAATGAAT-TTTTAAA
1 AAAATCAATCTTTTAAA
1585596 TTTTAAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAATCAATCTTTTAAA
Found at i:1590156 original size:28 final size:28
Alignment explanation
Indices: 1590075--1590156 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1590065 TTTTGGAGAT
*
1590075 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1590103 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1590131 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1590157 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1590262 original size:105 final size:103
Alignment explanation
Indices: 1590113--1590424 Score: 276
Period size: 105 Copynumber: 2.9 Consensus size: 103
1590103 AGTAACGGGG
* * *
1590113 TTGGAGTATCCCCGATGAAAT-AACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTT
1 TTGGAGTATCCTCGA--AAATAAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTT
*
1590177 GGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAGGAGAAA
64 GGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG-G--A
* * * * *
1590220 TTGGTGT-T-GT-GAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTT
1 TTGGAGTATCCTCGAAAAT-AAA-CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTT
* * * * *
1590281 GAAAATAAAGTCAGG-GTTGGAGTATCCCCTCAGAAATAACGGGG
64 GGAAATAAAATC-GGAGTTGGAGTAT-CCC-C-G-ATTAAAGGGA
** * * *
1590325 TTGGAGTATCCTCGATGATTAACGGGGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTT
1 TTGGAGTATCCTCGAAAATAAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATTTT
1590390 TGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
63 TGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
1590425 TAGAAAATTA
Statistics
Matches: 162, Mismatches: 27, Indels: 33
0.73 0.12 0.15
Matches are distributed among these distances:
102 4 0.02
104 27 0.17
105 42 0.26
106 31 0.19
107 16 0.10
108 12 0.07
109 6 0.04
110 24 0.15
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (103 bp):
TTGGAGTATCCTCGAAAATAAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGG
AAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGA
Found at i:1590301 original size:51 final size:50
Alignment explanation
Indices: 1590139--1590309 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 50
1590129 GAAATAACGA
* * *
1590139 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCG
* * * * * *
1590190 GAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 G-GTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATC-G
* * *
1590244 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCAG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATC-G
1590295 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1590310 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 30 0.31
54 12 0.12
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCG
Found at i:1590327 original size:28 final size:28
Alignment explanation
Indices: 1590294--1590364 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
1590284 AATAAAGTCA
1590294 GGGTTGGAGTATCCCCTC-AGAAATAACG
1 GGGTTGGAGTATCCCCTCGAG-AATAACG
*
1590322 GGGTTGGAGTAT--CCTCGATGATTAACG
1 GGGTTGGAGTATCCCCTCGA-GAATAACG
*
1590349 GGGTTGGAGTGTCCCC
1 GGGTTGGAGTATCCCC
1590365 GATTGTGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 4 0.11
27 18 0.49
28 13 0.35
29 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTCGAGAATAACG
Found at i:1592856 original size:13 final size:13
Alignment explanation
Indices: 1592838--1592863 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1592828 ACAAAGATCC
1592838 ATGTATCGATACA
1 ATGTATCGATACA
1592851 ATGTATCGATACA
1 ATGTATCGATACA
1592864 CAGAAAAATG
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
Done.