Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 132 of 187
Found at i:40003796 original size:86 final size:86
Alignment explanation
Indices: 40003684--40003968 Score: 353
Period size: 86 Copynumber: 3.3 Consensus size: 86
40003674 TTTTAGAAAC
* *
40003684 AAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCTACAAACGCCGCTAAAGACCAATAC
1 AAACGCCGCTAAAGAACATGACCTTTAACGGCGCTTTTCCTACAAACGCTGCTAAAGACCAATAC
*
40003749 CTTTACCGGCGCTTTTCCCAA
66 CTTTAACGGCGCTTTTCCCAA
* * * *
40003770 AAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGACC-ATGA
1 AAACGCCGCTAAAGAACATGACCTTTAACGGCGCTTTTCCTACAAACGCTGCTAAAGACCAAT-A
*
40003834 CCTTTAACGGCGCTTTTCCCAC
65 CCTTTAACGGCGCTTTTCCCAA
** * * *
40003856 AAACGCCGCTAAAGAACATGACCTTTAGA-GGCGCTTTTTGTCACCAACGCTGCTATAGATCAA-
1 AAACGCCGCTAAAGAACATGACCTTTA-ACGGCGCTTTTCCT-ACAAACGCTGCTAAAGACCAAT
* * *
40003919 ACCTTTAGCGGCGCTTCTCGCAA
64 ACCTTTAACGGCGCTTTTCCCAA
* *
40003942 AAACGCCACTAAA-AACATAACCTTTAA
1 AAACGCCGCTAAAGAACATGACCTTTAA
40003969 AAAAATTTAT
Statistics
Matches: 172, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 14 0.08
86 140 0.81
87 16 0.09
88 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGACCTTTAACGGCGCTTTTCCTACAAACGCTGCTAAAGACCAATAC
CTTTAACGGCGCTTTTCCCAA
Found at i:40003925 original size:129 final size:129
Alignment explanation
Indices: 40003682--40003968 Score: 339
Period size: 129 Copynumber: 2.2 Consensus size: 129
40003672 GTTTTTAGAA
* *
40003682 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCTACAAACGCCGCTAAAGACCAAT
1 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGAACAAT
* * *
40003747 ACCTTTACCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTCCC
66 ACCTTTACAGGCGCTTTTCCCAAAAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCC
* * *
40003811 ACAAACGCTGCTAAAGACCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGAAC-AT
1 ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGAACAAT
* ** ** * * * * *
40003875 GACCTTTAGAGGCGCTTTTTGTCACCAACGCTGCTATAGATCA-AACCTTTAGCGGCGCTTCTCG
66 -ACCTTTACAGGCGC-TTTTCCCAAAAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCC
40003939 C
129 C
* *
40003940 AAAAACGCCACTAAA-AACATA-ACCTTTAA
1 ACAAACGCCGCTAAAGAACA-AGACCTTTAA
40003969 AAAAATTTAT
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
128 13 0.10
129 99 0.75
130 20 0.15
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (129 bp):
ACAAACGCCGCTAAAGAACAAGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGAACAAT
ACCTTTACAGGCGCTTTTCCCAAAAACGCCGCTAAAGACCATAACCTTTAGCGGCGCTTTTCCC
Found at i:40008749 original size:7 final size:8
Alignment explanation
Indices: 40008729--40008757 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40008719 CTAACTTGAC
40008729 CCCTAAAT
1 CCCTAAAT
40008737 CCCTAAA-
1 CCCTAAAT
40008744 CCCTAAAT
1 CCCTAAAT
40008752 CCCTAA
1 CCCTAA
40008758 CTCTTAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (8 bp):
CCCTAAAT
Found at i:40008749 original size:15 final size:15
Alignment explanation
Indices: 40008729--40008757 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40008719 CTAACTTGAC
40008729 CCCTAAATCCCTAAA
1 CCCTAAATCCCTAAA
40008744 CCCTAAATCCCTAA
1 CCCTAAATCCCTAA
40008758 CTCTTAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCCCTAAA
Found at i:40008801 original size:27 final size:27
Alignment explanation
Indices: 40008769--40008820 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40008759 TCTTAACTCT
* *
40008769 TAACCCTTAAACCTTAAATCCCAACAC
1 TAACCCCTAAACCTGAAATCCCAACAC
40008796 TAACCCCTAAACCTGAAATCCCAAC
1 TAACCCCTAAACCTGAAATCCCAAC
40008821 CCTTAAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.38, G:0.02, T:0.19
Consensus pattern (27 bp):
TAACCCCTAAACCTGAAATCCCAACAC
Found at i:40009307 original size:41 final size:41
Alignment explanation
Indices: 40009227--40009336 Score: 184
Period size: 41 Copynumber: 2.7 Consensus size: 41
40009217 GTTTTTGCGA
* *
40009227 CGCTTTTTCAAAAACGCCGCTAAAAGGCCAGAGCGTTAGCGG
1 CGCTTCTTCAAAAACGCCGCT-AAAGGCCAGAGCATTAGCGG
*
40009269 CGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGG
1 CGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGG
40009310 CGCTTCTTCAAAAACGCCGCTAAAGGC
1 CGCTTCTTCAAAAACGCCGCTAAAGGC
40009337 TTCAAAAACG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
41 45 0.69
42 20 0.31
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (41 bp):
CGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGG
Found at i:40009340 original size:21 final size:21
Alignment explanation
Indices: 40009315--40009357 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40009305 AGCGGCGCTT
40009315 CTTCAAAAACGCCGCTAAAGG
1 CTTCAAAAACGCCGCTAAAGG
40009336 CTTCAAAAACGCCGCTAAAGG
1 CTTCAAAAACGCCGCTAAAGG
40009357 C
1 C
40009358 CCGAGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (21 bp):
CTTCAAAAACGCCGCTAAAGG
Found at i:40009371 original size:62 final size:62
Alignment explanation
Indices: 40009274--40009398 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
40009264 AGCGGCGCTT
* *
40009274 CTTCAAAAACGCCGCTAAAGGCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
1 CTTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
40009336 CTTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
1 CTTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
40009398 C
1 C
40009399 CCGAGCATTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.31, C:0.30, G:0.22, T:0.17
Consensus pattern (62 bp):
CTTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGG
Found at i:40009413 original size:103 final size:104
Alignment explanation
Indices: 40009233--40009439 Score: 371
Period size: 103 Copynumber: 2.0 Consensus size: 104
40009223 GCGACGCTTT
** *
40009233 TTCAAAAACGCCGCTAAAAGGCCAGAGCGTTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCT
1 TTCAAAAACGCCGCTAAAAGGCCAGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
40009298 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGC
66 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGC
*
40009337 TTCAAAAACGCCGCT-AAAGGCCCGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
1 TTCAAAAACGCCGCTAAAAGGCCAGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
40009401 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGC
66 GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGC
40009440 CCGAGCATTA
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 84 0.85
104 15 0.15
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.17
Consensus pattern (104 bp):
TTCAAAAACGCCGCTAAAAGGCCAGAGAATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGC
Found at i:40009482 original size:41 final size:41
Alignment explanation
Indices: 40009336--40009470 Score: 261
Period size: 41 Copynumber: 3.3 Consensus size: 41
40009326 CCGCTAAAGG
*
40009336 CTTCAAAAACGCCGCTAAAGGCCCGAGAATTAGCGGCGCTT
1 CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTT
40009377 CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTT
1 CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTT
40009418 CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTT
1 CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTT
40009459 CTTCAAAAACGC
1 CTTCAAAAACGC
40009471 TTTTAAAGGC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (41 bp):
CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTT
Found at i:40009488 original size:144 final size:145
Alignment explanation
Indices: 40009227--40009489 Score: 438
Period size: 144 Copynumber: 1.8 Consensus size: 145
40009217 GTTTTTGCGA
* *
40009227 CGCTTTTTCAAAAACGCCGCTAAAAGGCCAGAGCGTTAGCGGCGCTTCTTCAAAAACGCCGCTAA
1 CGCTTCTTCAAAAACGCCGCTAAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
* **
40009292 AGGCCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCTTCAAAAACGCCGCTAAAGG
66 AGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAAAAACGCCGCTAAAGG
40009357 CCCGAGAATTAGCGG
131 CCCGAGAATTAGCGG
*
40009372 CGCTTCTTCAAAAACGCCGCT-AAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
1 CGCTTCTTCAAAAACGCCGCTAAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
***
40009436 AGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCTTTTAAAGGCCCCAAAAAC
66 AGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAAAAAC
40009490 TTAGAAAACG
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
144 89 0.82
145 20 0.18
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (145 bp):
CGCTTCTTCAAAAACGCCGCTAAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
AGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCCAAAAACGCCGCTAAAGG
CCCGAGAATTAGCGG
Found at i:40009567 original size:39 final size:39
Alignment explanation
Indices: 40009518--40009653 Score: 148
Period size: 41 Copynumber: 3.4 Consensus size: 39
40009508 GGGCTTAGGC
* * *
40009518 TTTTT-GCGGCGCTTTTCAAAAAACGCCGCTAATTCTTA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTTA
* *
40009556 TTTTTAGCGGCGTTTTTCAAAAAGCGCAGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCT-TA
** * *
40009596 CCTTTAGCGGCGTTTTTTATAAAAGCGTCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCA-AAAAGCGCCGCTAATGCTT-A
*
40009637 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
40009654 TGTCCAAACG
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
38 5 0.06
39 27 0.34
40 17 0.21
41 31 0.39
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTTA
Found at i:40009669 original size:41 final size:41
Alignment explanation
Indices: 40009530--40009670 Score: 130
Period size: 41 Copynumber: 3.5 Consensus size: 41
40009520 TTTGCGGCGC
* *
40009530 TTTTCAAAAAACGCCGCTAATTCTT-ATTTTTAGCGGCG--T
1 TTTTC-AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTT
* * **
40009569 TTTTCAAAAAGCGCAGCTAATGCTCGACCTTTAGCGGCGTTT
1 TTTTC-AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTT
* *
40009611 TTTAT-AAAAGCGTCGCTAATGCTTGATTTTTAGTGGCGTTT
1 TTT-TCAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTT
*
40009652 TTTGTCCAAA-CGCCGCTAA
1 TTT-TCAAAAGCGCCGCTAA
40009671 AAACGCCGCT
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
39 21 0.26
40 11 0.13
41 42 0.51
42 7 0.09
43 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (41 bp):
TTTTCAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTT
Found at i:40009676 original size:12 final size:12
Alignment explanation
Indices: 40009659--40009684 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40009649 TTTTTTGTCC
40009659 AAACGCCGCTAA
1 AAACGCCGCTAA
40009671 AAACGCCGCTAA
1 AAACGCCGCTAA
40009683 AA
1 AA
40009685 GCTTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:40012231 original size:25 final size:26
Alignment explanation
Indices: 40012197--40012245 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
40012187 TCTTATCCTT
*
40012197 ATTTTACCCCCAGT-AAATTTTGACA
1 ATTTTACCCCCAATAAAATTTTGACA
*
40012222 ATTTTACCCCTAATAAAATTTTGA
1 ATTTTACCCCCAATAAAATTTTGA
40012246 GAAAATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCCAATAAAATTTTGACA
Found at i:40012412 original size:12 final size:12
Alignment explanation
Indices: 40012391--40012420 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40012381 GCAAATGAAT
*
40012391 CATTTCTATTTC
1 CATTTTTATTTC
40012403 CATTTTTATTTC
1 CATTTTTATTTC
40012415 CATTTT
1 CATTTT
40012421 GGAAACCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (12 bp):
CATTTTTATTTC
Found at i:40012791 original size:18 final size:17
Alignment explanation
Indices: 40012768--40012806 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40012758 ATGCATTTTA
40012768 AGTTGTTGGAATAAAGTT
1 AGTTGTT-GAATAAAGTT
* *
40012786 AGTTGTTTAATTAAGTT
1 AGTTGTTGAATAAAGTT
40012803 AGTT
1 AGTT
40012807 AATTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (17 bp):
AGTTGTTGAATAAAGTT
Found at i:40013717 original size:22 final size:20
Alignment explanation
Indices: 40013692--40013731 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40013682 GCTAGGAAAC
*
40013692 TTCAAGGAAGCTTCCAAGGATG
1 TTCAA-GAAACTT-CAAGGATG
40013714 TTCAAGAAACTTCAAGGA
1 TTCAAGAAACTTCAAGGA
40013732 AATTTCCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
TTCAAGAAACTTCAAGGATG
Found at i:40014679 original size:71 final size:71
Alignment explanation
Indices: 40014593--40014747 Score: 168
Period size: 71 Copynumber: 2.2 Consensus size: 71
40014583 TGTAGTTCAA
* * *
40014593 TTTTTTCTTT-TTTTTTTTTGTGCTCTATCATTTGCTTAAATCATCAAAAGAAGGATTTTCAACT
1 TTTTTT-TTTCTTTTTCTTT-TGCACTAACATTTGCTTAAATCATCAAAAGAAGGATTTTCAACT
40014657 TAACAAGC
64 TAACAAGC
* * * * * * *
40014665 TTTTTTTTTCTTTTTCTTTTGCACTAACTTTTGCTTAAGTCGTCTAATGAAGGATTTTTAGCTTA
1 TTTTTTTTTCTTTTTCTTTTGCACTAACATTTGCTTAAATCATCAAAAGAAGGATTTTCAACTTA
**
40014730 ATGAGC
66 ACAAGC
40014736 TTTTTGTTTTCT
1 TTTTT-TTTTCT
40014748 CTAACTTTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
71 49 0.71
72 20 0.29
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (71 bp):
TTTTTTTTTCTTTTTCTTTTGCACTAACATTTGCTTAAATCATCAAAAGAAGGATTTTCAACTTA
ACAAGC
Found at i:40014757 original size:60 final size:61
Alignment explanation
Indices: 40014674--40014807 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 61
40014664 CTTTTTTTTT
* * * * *
40014674 CTTTTTCTTTTGCACTAACTTTTGCTTAAGTCGTCTAATGAAGGATTTTTAGCTTAATGAG
1 CTTTTTCTTTTGCACTAACTTTTGCTTAAGCCATCCAATGAAGGATATTCAGCTTAATGAG
* * * * *
40014735 CTTTTTGTTTT-CTCTAACTTTTGCTTGAGCCATCCAATGAAGTATATTCAGCTTAATTAG
1 CTTTTTCTTTTGCACTAACTTTTGCTTAAGCCATCCAATGAAGGATATTCAGCTTAATGAG
40014795 CTCTTCTTCTTTT
1 CT-TT-TTCTTTT
40014808 CTTTATGCTC
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
60 42 0.70
61 12 0.20
62 6 0.10
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (61 bp):
CTTTTTCTTTTGCACTAACTTTTGCTTAAGCCATCCAATGAAGGATATTCAGCTTAATGAG
Found at i:40017006 original size:23 final size:23
Alignment explanation
Indices: 40016955--40016998 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
40016945 GTTGACATAT
40016955 TAATCAAATTGAGAAAGCGATAA
1 TAATCAAATTGAGAAAGCGATAA
*
40016978 TAATCAGATTGAGAAAGCGAT
1 TAATCAAATTGAGAAAGCGAT
40016999 TGTTATCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (23 bp):
TAATCAAATTGAGAAAGCGATAA
Found at i:40025137 original size:14 final size:13
Alignment explanation
Indices: 40025100--40025141 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
40025090 ACGATTAGTG
40025100 ATTAA-TTAATTA
1 ATTAAGTTAATTA
40025112 TGATTAAGTTAATTA
1 --ATTAAGTTAATTA
40025127 ATTAAGTTTAATTA
1 ATTAAG-TTAATTA
40025141 A
1 A
40025142 AACTAAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.23
14 13 0.50
15 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
ATTAAGTTAATTA
Found at i:40025137 original size:19 final size:18
Alignment explanation
Indices: 40025100--40025141 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
40025090 ACGATTAGTG
*
40025100 ATTAATTAATTATGATTA
1 ATTAATTAATTAAGATTA
*
40025118 AGTTAATTAATTAAGTTTA
1 A-TTAATTAATTAAGATTA
40025137 ATTAA
1 ATTAA
40025142 AACTAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
ATTAATTAATTAAGATTA
Found at i:40037611 original size:22 final size:22
Alignment explanation
Indices: 40037584--40037627 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40037574 TAGCCATATA
* *
40037584 ATAAATTGTTAATATAATAAAT
1 ATAAATTATTAAAATAATAAAT
40037606 ATAAATTATTAAAATAATAAAT
1 ATAAATTATTAAAATAATAAAT
40037628 TATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATAAATTATTAAAATAATAAAT
Found at i:40037627 original size:16 final size:15
Alignment explanation
Indices: 40037602--40037631 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40037592 TTAATATAAT
40037602 AAATATAAATTATTA
1 AAATATAAATTATTA
40037617 AAATAATAAATTATT
1 AAAT-ATAAATTATT
40037632 TAATATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATATAAATTATTA
Found at i:40037663 original size:13 final size:14
Alignment explanation
Indices: 40037647--40037688 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
40037637 TTTCAATTTT
40037647 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
40037660 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
40037675 ATTTTAGATAATAT
1 ATTTTA-ATAATAT
40037689 GATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 9 0.38
16 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:40037749 original size:19 final size:19
Alignment explanation
Indices: 40037722--40037769 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
40037712 TCAATATTAA
*
40037722 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
* *
40037741 TATTATAATTACAAATATT
1 TATTATAATAATAAATATT
40037760 TA--ATAATAAT
1 TATTATAATAAT
40037770 TTTTTTTGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 6 0.25
19 18 0.75
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:40044226 original size:19 final size:19
Alignment explanation
Indices: 40044204--40044248 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
40044194 TACCATTTCG
*
40044204 TTATTATATTACTACTATT
1 TTATTATATAACTACTATT
* * *
40044223 TTATTGTATAACTATTGTT
1 TTATTATATAACTACTATT
40044242 TTATTAT
1 TTATTAT
40044249 TAATTTTACT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (19 bp):
TTATTATATAACTACTATT
Found at i:40060154 original size:28 final size:28
Alignment explanation
Indices: 40060111--40060169 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
40060101 ACTAGGAATA
*
40060111 AAAAAAAATTTAAATTATTAAA-ATTAT
1 AAAAAAAATGTAAATTATTAAATATTAT
* *
40060138 AAAAAAAATGTACAATTTTTAAATATTTT
1 AAAAAAAATGTA-AATTATTAAATATTAT
40060167 AAA
1 AAA
40060170 TTTTATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 11 0.41
28 9 0.33
29 7 0.26
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAAAAAATGTAAATTATTAAATATTAT
Found at i:40060202 original size:11 final size:11
Alignment explanation
Indices: 40060186--40060232 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
40060176 TAAAAATAAT
40060186 AAATAATATTA
1 AAATAATATTA
40060197 AAATAATATT-
1 AAATAATATTA
* *
40060207 GAATAAT-GTA
1 AAATAATATTA
40060217 AACATAATATTA
1 AA-ATAATATTA
40060229 AAAT
1 AAAT
40060233 TTTTATACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
9 1 0.03
10 7 0.24
11 17 0.59
12 4 0.14
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (11 bp):
AAATAATATTA
Found at i:40066952 original size:28 final size:28
Alignment explanation
Indices: 40066920--40066996 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 28
40066910 TTTTTTAGGG
*
40066920 TTTAGGGTTTTGTTTATTTAAAGGAGGT
1 TTTAGGGTTTTGTTTATTTAAAGGAGGA
*
40066948 TTTAGGTTAATGTTTTGTTTATTTAAAGTAGGA
1 TTTAGG-----GTTTTGTTTATTTAAAGGAGGA
*
40066981 TTTAGGGTTTTTTTTA
1 TTTAGGGTTTTGTTTA
40066997 GATTTCTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
28 15 0.37
33 26 0.63
ACGTcount: A:0.22, C:0.00, G:0.23, T:0.55
Consensus pattern (28 bp):
TTTAGGGTTTTGTTTATTTAAAGGAGGA
Found at i:40069581 original size:23 final size:24
Alignment explanation
Indices: 40069524--40069618 Score: 95
Period size: 26 Copynumber: 3.8 Consensus size: 24
40069514 GAGCCATGAT
*
40069524 TGGTAAGCTCATTCCGAGCTGAAGAA
1 TGGTAAGCTCA-TACGAGCTG-AGAA
*
40069550 CGGTAAGCTC-TATCGAGCTGA-AA
1 TGGTAAGCTCATA-CGAGCTGAGAA
* *
40069573 TGGTAAGCTCATAAGAGCTGATATA
1 TGGTAAGCTCATACGAGCTGAGA-A
40069598 TCGGTAAGCTCATACGAGCTG
1 T-GGTAAGCTCATACGAGCTG
40069619 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
23 18 0.31
24 5 0.08
25 9 0.15
26 27 0.46
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (24 bp):
TGGTAAGCTCATACGAGCTGAGAA
Found at i:40069583 original size:49 final size:49
Alignment explanation
Indices: 40069524--40069618 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
40069514 GAGCCATGAT
**
40069524 TGGTAAGCTCATTCCGAGCTGA-AGAACGGTAAGCTC-TATCGAGCTGAAA
1 TGGTAAGCTCA-TAAGAGCTGATAGAACGGTAAGCTCATA-CGAGCTGAAA
* *
40069573 TGGTAAGCTCATAAGAGCTGATATATCGGTAAGCTCATACGAGCTG
1 TGGTAAGCTCATAAGAGCTGATAGAACGGTAAGCTCATACGAGCTG
40069619 TGGTGAGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 8 0.20
49 30 0.75
50 2 0.05
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
TGGTAAGCTCATAAGAGCTGATAGAACGGTAAGCTCATACGAGCTGAAA
Found at i:40070309 original size:43 final size:42
Alignment explanation
Indices: 40070241--40070407 Score: 124
Period size: 43 Copynumber: 3.9 Consensus size: 42
40070231 ATAGCTCATA
* * * *
40070241 CAATGCC-ATATCCCATG-TATAGTCTTACATGTTATCACGTAT
1 CAATGCCAATATCCCA-GACATGGTCTTACACGTAATCAC-TAT
* * * * *
40070283 CAATGCCACTATCCCAGACAAGGTCTTATACGAAATTA-TAT
1 CAATGCCAATATCCCAGACATGGTCTTACACGTAATCACTAT
* * * *
40070324 AATGATGCCAATATACCAGACATGGTCTTACACATAATCACAAT
1 CA--ATGCCAATATCCCAGACATGGTCTTACACGTAATCACTAT
* * *
40070368 ACAATGCCAATGTCCCAGACATGGTCTTACATGTTATCAC
1 -CAATGCCAATATCCCAGACATGGTCTTACACGTAATCAC
40070408 CTCTCAGTAA
Statistics
Matches: 95, Mismatches: 24, Indels: 11
0.73 0.18 0.08
Matches are distributed among these distances:
41 4 0.04
42 8 0.08
43 80 0.84
44 2 0.02
45 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (42 bp):
CAATGCCAATATCCCAGACATGGTCTTACACGTAATCACTAT
Found at i:40074979 original size:13 final size:13
Alignment explanation
Indices: 40074937--40075022 Score: 66
Period size: 13 Copynumber: 6.5 Consensus size: 13
40074927 TCATAGATCT
40074937 ATTTCCATATAATC
1 ATTT-CATATAATC
* * *
40074951 AATTCACATAACC
1 ATTTCATATAATC
* *
40074964 ATTTCATTTATTC
1 ATTTCATATAATC
*
40074977 ATTTTATATAATC
1 ATTTCATATAATC
* *
40074990 ATTTCGTACAA-C
1 ATTTCATATAATC
*
40075002 TATTTCGTATAATC
1 -ATTTCATATAATC
40075016 ATTTCAT
1 ATTTCAT
40075023 TTCACACATT
Statistics
Matches: 54, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
12 1 0.02
13 49 0.91
14 4 0.07
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (13 bp):
ATTTCATATAATC
Found at i:40075259 original size:45 final size:45
Alignment explanation
Indices: 40075198--40075364 Score: 223
Period size: 45 Copynumber: 3.7 Consensus size: 45
40075188 TGTTCACTGA
* * * *
40075198 TGCCATAGCGTCTTTCAACCATGGTCATATTTATTTCCGACATGA-
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCG-CATGAG
40075243 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGGCAT-AG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCC-GCATGAG
* * *
40075288 TGCCATAGTGTCTTTCAACTATGGTTTTATTCATTTCTG-GTGTAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGCATG-AG
40075333 TGCCATAGTGTCTTTCAACTATGGTCTTATTC
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTC
40075365 GTTTTTCAAG
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 106 0.96
46 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.41
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGCATGAG
Found at i:40077883 original size:19 final size:19
Alignment explanation
Indices: 40077846--40077884 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
40077836 AAATATTTAC
* *
40077846 ATAATAATATTTTTTATAT
1 ATAATAATATTCTTCATAT
*
40077865 ATAATACTATTCTTCATAT
1 ATAATAATATTCTTCATAT
40077884 A
1 A
40077885 CGCATAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAATAATATTCTTCATAT
Found at i:40080762 original size:20 final size:20
Alignment explanation
Indices: 40080718--40080762 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40080708 AATTAAAATT
40080718 GGACACAATTAATTAAGTTA
1 GGACACAATTAATTAAGTTA
* * **
40080738 AGACACATTTAATTCGGTTA
1 GGACACAATTAATTAAGTTA
40080758 GGACA
1 GGACA
40080763 AGACATATTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (20 bp):
GGACACAATTAATTAAGTTA
Found at i:40084041 original size:18 final size:17
Alignment explanation
Indices: 40083985--40084041 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
40083975 AACACACTCA
40083985 ATTTTTCACATTCTTTTTC
1 ATTTTTCAC-TTC-TTTTC
*
40084004 -TTTTTCA-TTGTTTTC
1 ATTTTTCACTTCTTTTC
*
40084019 TTTTTTCACTCTCTTTTC
1 ATTTTTCACT-TCTTTTC
40084037 ATTTT
1 ATTTT
40084042 CTTTTACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 5 0.16
16 9 0.28
17 1 0.03
18 17 0.53
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTTTTCACTTCTTTTC
Found at i:40084108 original size:40 final size:41
Alignment explanation
Indices: 40084032--40084109 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40084022 TTTCACTCTC
*
40084032 TTTTCATTTTCTTTTACAATTTTCCCTATTTTTTTTCTCAA
1 TTTTCATTTTCTTTTACAATTTTCACTATTTTTTTTCTCAA
** *
40084073 TTTTC-TTTTCTTTT-TGATTTTCACTCTTTTCTTTTCT
1 TTTTCATTTTCTTTTACAATTTTCACTATTTT-TTTTCT
40084110 TTTCCTCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 12 0.38
40 15 0.47
41 5 0.16
ACGTcount: A:0.12, C:0.19, G:0.01, T:0.68
Consensus pattern (41 bp):
TTTTCATTTTCTTTTACAATTTTCACTATTTTTTTTCTCAA
Found at i:40086541 original size:22 final size:22
Alignment explanation
Indices: 40086509--40086553 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40086499 GGTCGAAGAC
* * *
40086509 GATTTAGGTTTAGGCACGTAAT
1 GATTTAAGTTTAAGCACGAAAT
40086531 GATTTAAGTTTAAGCACGAAAT
1 GATTTAAGTTTAAGCACGAAAT
40086553 G
1 G
40086554 GCTTTTGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (22 bp):
GATTTAAGTTTAAGCACGAAAT
Found at i:40087534 original size:20 final size:20
Alignment explanation
Indices: 40087511--40087555 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
40087501 AATTAAAACT
40087511 AGACACAATTAATTAAGTTA
1 AGACACAATTAATTAAGTTA
* *
40087531 AGACACATTTAATTCAGTTA
1 AGACACAATTAATTAAGTTA
*
40087551 GGACA
1 AGACA
40087556 ATACATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
AGACACAATTAATTAAGTTA
Found at i:40089337 original size:514 final size:514
Alignment explanation
Indices: 40088370--40089395 Score: 1926
Period size: 514 Copynumber: 2.0 Consensus size: 514
40088360 TTTAAAGTTA
*
40088370 CTTATTGCTTCTTATTTTTCATTTTTAACATACCTTTTATAACACCCTGAAATAGGGCCTAGGAG
1 CTTATTGCTTCTTATTTTTCATTTTTAACATACCTTTTATAACACCCTAAAATAGGGCCTAGGAG
40088435 TTTTAGGGGTATTTTAGGAATTTTAACCTATATGAGCTCGAAATTTCATAAGATTAGTACACGAT
66 TTTTAGGGGTATTTTAGGAATTTTAACCTATATGAGCTCGAAATTTCATAAGATTAGTACACGAT
* * * *
40088500 AATGTTTTCAATAATGGTTTTGATAGAGTTAAGTTAATTTTTGGAAACGAGTTTTAAATGTCTTT
131 AATGTTTTCAACAATGGTTTTCATAGAGTTAAGTCAATTTTGGGAAACGAGTTTTAAATGTCTTT
40088565 AATTTTAGAAAAACGAATGGTTTGTAAAAGGGTTAAAGTTGTGAGTCTTTATGAAGCAATTAATC
196 AATTTTAGAAAAACGAATGGTTTGTAAAAGGGTTAAAGTTGTGAGTCTTTATGAAGCAATTAATC
40088630 CAATTTCTCAAAATCAACGTAATAAACCTCCATTCCCAGTTATTTTCACGAATGATTTTTCATAT
261 CAATTTCTCAAAATCAACGTAATAAACCTCCATTCCCAGTTATTTTCACGAATGATTTTTCATAT
40088695 CTCCTTAGTGTTGCTGTCCCTTGCTATTCCTCACTATCTCAATAGATTTTTGACTCCCAAACTAT
326 CTCCTTAGTGTTGCTGTCCCTTGCTATTCCTCACTATCTCAATAGATTTTTGACTCCCAAACTAT
40088760 AATACTTTGAATTTCTATCATTTCCAAGCATTAAACCTCTCTAAATCTTCAAGAAATCACCCAAA
391 AATACTTTGAATTTCTATCATTTCCAAGCATTAAACCTCTCTAAATCTTCAAGAAATCACCCAAA
*
40088825 AATCTCACCAATTTCATGATATTCTCCACTTATGGGTGTAACACCCCTAACCCGTATTG
456 AATCTCACCAATTTCATCATATTCTCCACTTATGGGTGTAACACCCCTAACCCGTATTG
40088884 CTTATTGCTTCTTATTTTTCATTTTTAACATACCTTTTATAACACCCTAAAATAGGGCCTAGGAG
1 CTTATTGCTTCTTATTTTTCATTTTTAACATACCTTTTATAACACCCTAAAATAGGGCCTAGGAG
* *
40088949 TTTTAGGGGTATTTTAGGAATTTTAGCCTATATGAGCTCGAAATTTCATAAGATTGGTACACGAT
66 TTTTAGGGGTATTTTAGGAATTTTAACCTATATGAGCTCGAAATTTCATAAGATTAGTACACGAT
*
40089014 AATGTTTTCGACAATGGTTTTCATAGAGTTAAGTCAATTTTGGGAAACGAGTTTTAAATGTCTTT
131 AATGTTTTCAACAATGGTTTTCATAGAGTTAAGTCAATTTTGGGAAACGAGTTTTAAATGTCTTT
*
40089079 AGTTTTAGAAAAACGAATGGTTTGTAAAAGGGTTAAAGTTGTGAGTCTTTATGAAGCAATTAATC
196 AATTTTAGAAAAACGAATGGTTTGTAAAAGGGTTAAAGTTGTGAGTCTTTATGAAGCAATTAATC
* * *
40089144 CAATTTCTCAAAATCAACGTAATAAACCTCCATTCCTAGTTATTTTCACGAATGCTTTTTCCTAT
261 CAATTTCTCAAAATCAACGTAATAAACCTCCATTCCCAGTTATTTTCACGAATGATTTTTCATAT
*
40089209 CTCCTTAGTGTTGCTGTCCCTTGCTATTCCTCACTATCTCAATTGATTTTTGACTCCCAAACTAT
326 CTCCTTAGTGTTGCTGTCCCTTGCTATTCCTCACTATCTCAATAGATTTTTGACTCCCAAACTAT
40089274 AATACTTTGAATTTCTATCATTTCCAAGCATTAAACCTCTCTAAATCTTCAAGAAATCACCCAAA
391 AATACTTTGAATTTCTATCATTTCCAAGCATTAAACCTCTCTAAATCTTCAAGAAATCACCCAAA
40089339 AATCTCACCAATTTCATCATATTCTCCACTTATGGGTGTAACACCCCTAACCCGTAT
456 AATCTCACCAATTTCATCATATTCTCCACTTATGGGTGTAACACCCCTAACCCGTAT
40089396 CCGATGCCGG
Statistics
Matches: 498, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
514 498 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (514 bp):
CTTATTGCTTCTTATTTTTCATTTTTAACATACCTTTTATAACACCCTAAAATAGGGCCTAGGAG
TTTTAGGGGTATTTTAGGAATTTTAACCTATATGAGCTCGAAATTTCATAAGATTAGTACACGAT
AATGTTTTCAACAATGGTTTTCATAGAGTTAAGTCAATTTTGGGAAACGAGTTTTAAATGTCTTT
AATTTTAGAAAAACGAATGGTTTGTAAAAGGGTTAAAGTTGTGAGTCTTTATGAAGCAATTAATC
CAATTTCTCAAAATCAACGTAATAAACCTCCATTCCCAGTTATTTTCACGAATGATTTTTCATAT
CTCCTTAGTGTTGCTGTCCCTTGCTATTCCTCACTATCTCAATAGATTTTTGACTCCCAAACTAT
AATACTTTGAATTTCTATCATTTCCAAGCATTAAACCTCTCTAAATCTTCAAGAAATCACCCAAA
AATCTCACCAATTTCATCATATTCTCCACTTATGGGTGTAACACCCCTAACCCGTATTG
Found at i:40091800 original size:8 final size:9
Alignment explanation
Indices: 40091773--40091801 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
40091763 TGGAAGCTTG
40091773 ATTTGTTTT
1 ATTTGTTTT
40091782 ATTTGTTTT
1 ATTTGTTTT
40091791 ATTT-TTTT
1 ATTTGTTTT
40091799 ATT
1 ATT
40091802 CATTTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (9 bp):
ATTTGTTTT
Found at i:40098299 original size:101 final size:102
Alignment explanation
Indices: 40098179--40098363 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
40098169 AAAGTGATGG
* **
40098179 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGAATGAT-A-GGTCGTATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTATCGG-ATGATAACGGTCACATGTGTAGT
40098242 ACTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA
* * *
40098280 TCACGTGTGTAGTATTATGTGCAGGCTACTACATGTATCGGATGGTAACGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTATCGGATGATAACGGTCACATGTGTAGTA
40098345 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
40098364 TGAACCGAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTATCGGATGATAACGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA
Found at i:40098301 original size:51 final size:51
Alignment explanation
Indices: 40098179--40098363 Score: 187
Period size: 51 Copynumber: 3.6 Consensus size: 51
40098169 AAAGTGATGG
* * * * *
40098179 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTATCGGA-A-TGATA-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-A-ACGA
** **
40098229 TCGTATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTAACGA
* * *** * *
40098280 TCACGTGTGTAGTATTATGTGCAGGCTACTACATGTATCGGATGGTAACGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTAACGA
40098331 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
40098364 TGAACCGAAC
Statistics
Matches: 108, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
50 36 0.33
51 71 0.66
52 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTAACGA
Found at i:40098423 original size:45 final size:45
Alignment explanation
Indices: 40098367--40098461 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
40098357 TACTATGTGA
* * *
40098367 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTAGGTGCTGAATCC
*
40098412 ACCGGACATCATTGATTAATAAGGTGGTTGCTAGGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTAGGTGCTGAATCC
40098457 ACCGA
1 ACCGA
40098462 GTATCTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTAGGTGCTGAATCC
Found at i:40106078 original size:6 final size:7
Alignment explanation
Indices: 40106063--40106089 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40106053 TAATCGTTAA
40106063 TTTTATT
1 TTTTATT
40106070 TTTTATT
1 TTTTATT
40106077 TTTTATT
1 TTTTATT
40106084 TTTTAT
1 TTTTAT
40106090 AAGTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:40110098 original size:26 final size:25
Alignment explanation
Indices: 40110063--40110118 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
40110053 AAATATGATT
* * * *
40110063 AAATTATTTATTATTATTTTTATTA
1 AAATTATTTAATAATAATCTTATTA
40110088 AAATATATTTAATAATAATCTTATTA
1 AAAT-TATTTAATAATAATCTTATTA
40110114 AAATT
1 AAATT
40110119 TAATAACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATTATTTAATAATAATCTTATTA
Found at i:40110115 original size:61 final size:57
Alignment explanation
Indices: 40109972--40110117 Score: 170
Period size: 61 Copynumber: 2.5 Consensus size: 57
40109962 TTATTAATTC
* *
40109972 ATAT-TTTAATAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAA
1 ATATATTTAATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAA
* * * *
40110029 TTGTATTTAACAATAATTATGTTAAAATATGATTAAATTATTTATTATTATTTTTATTAAA
1 ATATATTTAATAATAATTATATTAAAATATGATTAAATTA--TA-TATTA-TTTTATTAAA
40110090 ATATATTTAATAATAATCT-TATTAAAAT
1 ATATATTTAATAATAAT-TATATTAAAAT
40110118 TTAATAACAA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
57 15 0.21
58 18 0.25
59 2 0.03
60 5 0.07
61 32 0.44
62 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (57 bp):
ATATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAA
Found at i:40110296 original size:12 final size:12
Alignment explanation
Indices: 40110279--40110303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40110269 TTAAACCAAT
40110279 TAATTGAATTAC
1 TAATTGAATTAC
40110291 TAATTGAATTAC
1 TAATTGAATTAC
40110303 T
1 T
40110304 CTAACCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TAATTGAATTAC
Found at i:40110788 original size:18 final size:17
Alignment explanation
Indices: 40110767--40110849 Score: 51
Period size: 18 Copynumber: 4.5 Consensus size: 17
40110757 TTCCTCTCAA
40110767 TAAAATTTTTAAAAAATT
1 TAAAATTTTT-AAAAATT
* * *
40110785 TAAATTAACTTTTGAAAATC
1 T-AA--AATTTTTAAAAATT
40110805 TAAAATATTATT-AAAATT
1 TAAAAT-TT-TTAAAAATT
*
40110823 TAAAATATTTATAAAATT
1 TAAAATTTTTA-AAAATT
40110841 CTAAAATTT
1 -TAAAATTT
40110850 ATATTTTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.04
17 3 0.06
18 20 0.40
19 13 0.26
20 6 0.12
21 6 0.12
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAAATTTTTAAAAATT
Found at i:40110880 original size:18 final size:17
Alignment explanation
Indices: 40110799--40110880 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
40110789 TTAACTTTTG
40110799 AAAA-TCTAAAATATTATT
1 AAAATTCTAAAA-ATTA-T
40110817 AAAATT-TAAAATATTTAT
1 AAAATTCTAAAA-A-TTAT
40110835 AAAATTCT-AAAATT-T
1 AAAATTCTAAAAATTAT
* * *
40110850 ATATTTTTAAAAAGTTAT
1 AAAATTCTAAAAA-TTAT
40110868 AAAATTCTAAAAA
1 AAAATTCTAAAAA
40110881 AAATTTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
15 6 0.12
16 6 0.12
17 3 0.06
18 32 0.62
19 5 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
AAAATTCTAAAAATTAT
Found at i:40110891 original size:20 final size:22
Alignment explanation
Indices: 40110858--40110907 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
40110848 TTATATTTTT
* *
40110858 AAAAAGTTATAAAATTCTA-AA
1 AAAAATTTATAAAATTATATAA
40110879 AAAAATTTA-AAAATTATATAA
1 AAAAATTTATAAAATTATATAA
*
40110900 GAAAATTT
1 AAAAATTT
40110908 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAAATTTATAAAATTATATAA
Found at i:40115868 original size:42 final size:42
Alignment explanation
Indices: 40115809--40115896 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
40115799 GATCAGCCGA
*
40115809 AGAAGTATTGGACTGAGATTGCACCAAATCAACATCTAATGG
1 AGAAGCATTGGACTGAGATTGCACCAAATCAACATCTAATGG
* **
40115851 AGAAGCATTGGACTGAGATTGCACCAAATCAATATCTGGTGG
1 AGAAGCATTGGACTGAGATTGCACCAAATCAACATCTAATGG
40115893 AGAA
1 AGAA
40115897 CCTAGTAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (42 bp):
AGAAGCATTGGACTGAGATTGCACCAAATCAACATCTAATGG
Found at i:40117844 original size:18 final size:18
Alignment explanation
Indices: 40117821--40117855 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40117811 ACCATCAGCT
40117821 GCATAGTAACCTTGACCC
1 GCATAGTAACCTTGACCC
40117839 GCATAGTAACCTTGACC
1 GCATAGTAACCTTGACC
40117856 ATAAGAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (18 bp):
GCATAGTAACCTTGACCC
Found at i:40119967 original size:12 final size:13
Alignment explanation
Indices: 40119942--40119973 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
40119932 AAACCCGAAA
40119942 CCAAAAATTGAAT
1 CCAAAAATTGAAT
40119955 CCAAAAATT-AAT
1 CCAAAAATTGAAT
40119967 CCAAAAA
1 CCAAAAA
40119974 CCAAAAGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.59, C:0.19, G:0.03, T:0.19
Consensus pattern (13 bp):
CCAAAAATTGAAT
Found at i:40134902 original size:21 final size:21
Alignment explanation
Indices: 40134856--40134911 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
40134846 GAATAAATAC
*
40134856 TAAAAATAAAATAAATGAAAG
1 TAAAAATAAAATAAATCAAAG
*
40134877 AAAAAATAAAATAAATCAGAA-
1 TAAAAATAAAATAAATCA-AAG
*
40134898 TAAAAGTAAAATAA
1 TAAAAATAAAATAA
40134912 TAAATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (21 bp):
TAAAAATAAAATAAATCAAAG
Found at i:40134918 original size:7 final size:7
Alignment explanation
Indices: 40134906--40134938 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
40134896 AATAAAAGTA
40134906 AAATAAT
1 AAATAAT
40134913 AAATAAT
1 AAATAAT
40134920 AAATAAT
1 AAATAAT
40134927 AAATAGAT
1 AAATA-AT
40134935 AAAT
1 AAAT
40134939 TGGGTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:40134920 original size:21 final size:20
Alignment explanation
Indices: 40134858--40134922 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
40134848 ATAAATACTA
40134858 AAAATAAAATAAATGAAAGAA-
1 AAAATAAAAT-AAT-AAAGAAT
*
40134879 AAAATAAAATAA-ATCAGAAT
1 AAAATAAAATAATA-AAGAAT
*
40134899 AAAAGTAAAATAATAAATAAT
1 AAAA-TAAAATAATAAAGAAT
40134920 AAA
1 AAA
40134923 TAATAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 6 0.16
21 25 0.68
22 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAATAAAGAAT
Found at i:40154197 original size:22 final size:22
Alignment explanation
Indices: 40154154--40154197 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40154144 ATGCATGCCA
*
40154154 TATGATATATGATATATGTATG
1 TATGATATATGATATAAGTATG
*
40154176 TATGATATTTGAT-TAAGATATG
1 TATGATATATGATATAAG-TATG
40154198 CATATGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (22 bp):
TATGATATATGATATAAGTATG
Found at i:40159240 original size:38 final size:40
Alignment explanation
Indices: 40159189--40159268 Score: 137
Period size: 38 Copynumber: 2.0 Consensus size: 40
40159179 GAGGTGGGGG
*
40159189 GTGTTGGAGTGATTTTAGGAGGAAAATATGGGA-T-TGGA
1 GTGTTGGAGTGATTTTAGAAGGAAAATATGGGACTGTGGA
40159227 GTGTTGGAGTGATTTTAGAAGGAAAATATGGGACTGTGGA
1 GTGTTGGAGTGATTTTAGAAGGAAAATATGGGACTGTGGA
40159267 GT
1 GT
40159269 TATCCTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 32 0.82
39 1 0.03
40 6 0.15
ACGTcount: A:0.29, C:0.01, G:0.39, T:0.31
Consensus pattern (40 bp):
GTGTTGGAGTGATTTTAGAAGGAAAATATGGGACTGTGGA
Found at i:40160802 original size:34 final size:34
Alignment explanation
Indices: 40160764--40160831 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
40160754 CCCTAATGCT
*
40160764 TACTGATACT-AAAATGGGCTTAGGCCTAAACTGA
1 TACTGATACTGAAAA-GGGCTTAGGCCCAAACTGA
40160798 TACTGATACTGAAAAGGGCTTAGGCCCAAACTGA
1 TACTGATACTGAAAAGGGCTTAGGCCCAAACTGA
40160832 GATTATTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 28 0.88
35 4 0.12
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (34 bp):
TACTGATACTGAAAAGGGCTTAGGCCCAAACTGA
Found at i:40171169 original size:16 final size:16
Alignment explanation
Indices: 40171148--40171179 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40171138 GTTTTGTTGC
*
40171148 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
40171164 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
40171180 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:40171462 original size:51 final size:51
Alignment explanation
Indices: 40171397--40171597 Score: 248
Period size: 51 Copynumber: 4.0 Consensus size: 51
40171387 ATTAATGATA
* *
40171397 CCGGTTCACATAGTAGCCTGTACATAGTACTACACATGTGACCATCACTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
* * *
40171448 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTAT
* **
40171499 ACGGTACACATAGTAGCCTGCACATAGTACTACACATGCAACCTATCA-T-T
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTAT
* * *
40171549 CTGGTAGACATAGTACCCTGCACATAGTACTACACATGTGACCATCACT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACT
40171598 TTCACTTTCA
Statistics
Matches: 127, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
49 4 0.03
50 41 0.32
51 79 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
CCGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
Found at i:40171835 original size:16 final size:16
Alignment explanation
Indices: 40171814--40171844 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40171804 AATCCAGTCC
40171814 AAAAATCACATTTTGG
1 AAAAATCACATTTTGG
*
40171830 AAAAATTACATTTTG
1 AAAAATCACATTTTG
40171845 CCCCTAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAATCACATTTTGG
Found at i:40173913 original size:18 final size:18
Alignment explanation
Indices: 40173876--40173915 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40173866 TGAGCCGAGT
*
40173876 TGGGCCATGTGGGCCTCA
1 TGGGCCATGTGGGCCACA
40173894 TGGG-CATGTGGGCCCACA
1 TGGGCCATGTGGG-CCACA
40173912 TGGG
1 TGGG
40173916 TGAACTACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.12, C:0.25, G:0.42, T:0.20
Consensus pattern (18 bp):
TGGGCCATGTGGGCCACA
Found at i:40174206 original size:16 final size:17
Alignment explanation
Indices: 40174180--40174212 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40174170 ATGTTGAGCA
*
40174180 TGATATATACATTATAC
1 TGATATATACATGATAC
40174197 TGAT-TATACATGATAC
1 TGATATATACATGATAC
40174213 CATGACATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (17 bp):
TGATATATACATGATAC
Found at i:40176929 original size:21 final size:20
Alignment explanation
Indices: 40176903--40176944 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40176893 AATATGGACG
* *
40176903 AATTGAGATTGTATAAATTAA
1 AATTGAAATTGTA-AAACTAA
40176924 AATTGAAATTGTAAAACTAA
1 AATTGAAATTGTAAAACTAA
40176944 A
1 A
40176945 CAAAATAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (20 bp):
AATTGAAATTGTAAAACTAA
Found at i:40178389 original size:3 final size:3
Alignment explanation
Indices: 40178381--40178416 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
40178371 ATTACATAGC
*
40178381 AAG AAG AAGG AAA AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AA
40178417 ACAAATAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:40178886 original size:6 final size:6
Alignment explanation
Indices: 40178875--40178925 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
40178865 AACATGCAAG
* * * *
40178875 AAAATA AAAATA AAAAAA TAAAATA AAAA-A TATATA TAAATA AAAATA
1 AAAATA AAAATA AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA
40178923 AAA
1 AAA
40178926 TTGGGTTGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
5 3 0.08
6 29 0.78
7 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:40178894 original size:14 final size:14
Alignment explanation
Indices: 40178875--40178920 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 14
40178865 AACATGCAAG
40178875 AAAATAAAAATAAA
1 AAAATAAAAATAAA
40178889 AAAAT-AAAATAAA
1 AAAATAAAAATAAA
40178902 AAATATATATAAATAAA
1 AAA-ATA-A-AAATAAA
40178919 AA
1 AA
40178921 TAAAATTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.39
14 7 0.25
16 1 0.04
17 9 0.32
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:40187887 original size:15 final size:15
Alignment explanation
Indices: 40187869--40187898 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40187859 TTTATACTTC
40187869 TTATGCCTATAAATA
1 TTATGCCTATAAATA
40187884 TTATGCCTATAAATA
1 TTATGCCTATAAATA
40187899 GAGACTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
TTATGCCTATAAATA
Found at i:40188907 original size:34 final size:33
Alignment explanation
Indices: 40188869--40188967 Score: 86
Period size: 34 Copynumber: 3.2 Consensus size: 33
40188859 TAAACACAAC
*
40188869 AATTTATAACAGAATCCTAAATTACTAATAAATT
1 AATTTATAACA-AATCCTAAATTACTAACAAATT
* * **
40188903 AATTT-T-A-AAA---T-AATTACAAACACAGC
1 AATTTATAACAAATCCTAAATTACTAACAAATT
40188929 AATTTATAACATAATCCTAAATTACTAACAAATT
1 AATTTATAACA-AATCCTAAATTACTAACAAATT
40188963 AATTT
1 AATTT
40188968 TAAAATAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
26 15 0.31
27 2 0.04
28 1 0.02
29 1 0.02
30 4 0.08
31 1 0.02
32 1 0.02
33 2 0.04
34 21 0.44
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (33 bp):
AATTTATAACAAATCCTAAATTACTAACAAATT
Found at i:40188932 original size:60 final size:60
Alignment explanation
Indices: 40188860--40188978 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
40188850 ATACTAAACT
*
40188860 AAACACAACAATTTATAACAGAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACAGAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
* *
40188920 AAACACAGCAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACAGAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
40188979 TAAAAAACAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (60 bp):
AAACACAACAATTTATAACAGAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:40189665 original size:26 final size:23
Alignment explanation
Indices: 40189636--40189701 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
40189626 TATATATTTA
40189636 AATATTTCTAATAAAAATAAAATAAT
1 AATATTT-TAATAAAAAT-AAA-AAT
* * *
40189662 AATATTTTATTTAAAGTAAAAAT
1 AATATTTTAATAAAAATAAAAAT
40189685 AATATTTTAATATAAAA
1 AATATTTTAATA-AAAA
40189702 AAAGTGATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 13 0.39
24 6 0.18
25 7 0.21
26 7 0.21
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AATATTTTAATAAAAATAAAAAT
Found at i:40192750 original size:31 final size:25
Alignment explanation
Indices: 40192691--40192743 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
40192681 ACCAAAATTG
40192691 AAAATTAATTATTGTTATAAAATGA
1 AAAATTAATTATTGTTATAAAATGA
40192716 AAAATTAATTATTGTTATAAAATGA
1 AAAATTAATTATTGTTATAAAATGA
40192741 AAA
1 AAA
40192744 TAAAAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.38
Consensus pattern (25 bp):
AAAATTAATTATTGTTATAAAATGA
Found at i:40203780 original size:35 final size:35
Alignment explanation
Indices: 40203723--40203790 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
40203713 ACATTTAACC
* ** *
40203723 AGCAGCATTAAATTCGGGTGGACACACTTTAGAAA
1 AGCAACATTAAATTCGACTGGACACAATTTAGAAA
40203758 AGCAACATTAAATTCGACTGGACACAATTTAGA
1 AGCAACATTAAATTCGACTGGACACAATTTAGA
40203791 TATCATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (35 bp):
AGCAACATTAAATTCGACTGGACACAATTTAGAAA
Found at i:40207038 original size:18 final size:16
Alignment explanation
Indices: 40207015--40207059 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
40207005 ATGCACTCAA
*
40207015 TTTTTCACTTTTGTTTT
1 TTTTTCACTTTTG-TCT
*
40207032 CTTTTTCACCTTTGTCT
1 -TTTTTCACTTTTGTCT
40207049 TTTTTCACTTT
1 TTTTTCACTTT
40207060 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 2 0.08
18 12 0.50
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTTCACTTTTGTCT
Found at i:40210798 original size:20 final size:20
Alignment explanation
Indices: 40210738--40210799 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
40210728 TACTAATTAG
* * *
40210738 AACATATTTAATAGACTTAA
1 AACATATTTAACACACATAA
* **
40210758 GACATATTAATAACATGCATAA
1 AACATATT--TAACACACATAA
40210780 AACATATTTAACACACATAA
1 AACATATTTAACACACATAA
40210800 TTAAATTTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 17 0.53
22 15 0.47
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (20 bp):
AACATATTTAACACACATAA
Found at i:40211884 original size:17 final size:19
Alignment explanation
Indices: 40211850--40211885 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40211840 ATTATCATTA
40211850 AAAATAAAAAACTCAAATT
1 AAAATAAAAAACTCAAATT
40211869 AAAA-AAAAAACT-AAATT
1 AAAATAAAAAACTCAAATT
40211886 TCTGAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAATAAAAAACTCAAATT
Found at i:40213920 original size:11 final size:10
Alignment explanation
Indices: 40213893--40213933 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
40213883 TCCTTATTTG
40213893 CATAATTAAA
1 CATAATTAAA
40213903 CATAATTAAA
1 CATAATTAAA
*
40213913 CAATAATTAAT
1 C-ATAATTAAA
*
40213924 CATAAATAAA
1 CATAATTAAA
40213934 TGTTAAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (10 bp):
CATAATTAAA
Found at i:40213920 original size:21 final size:21
Alignment explanation
Indices: 40213894--40213933 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40213884 CCTTATTTGC
*
40213894 ATAATTAAACATAATTAAACA
1 ATAATTAAACATAAATAAACA
*
40213915 ATAATTAATCATAAATAAA
1 ATAATTAAACATAAATAAA
40213934 TGTTAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATTAAACATAAATAAACA
Found at i:40219018 original size:24 final size:24
Alignment explanation
Indices: 40218962--40219018 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
40218952 ATCAAAAAAC
*
40218962 TAAAAACATTAAAATAAATATTTT
1 TAAAAAAATTAAAATAAATATTTT
** *
40218986 CCAACAAATTGAAAATAAAT-TTTT
1 TAAAAAAATT-AAAATAAATATTTT
40219010 TAAAAAAAT
1 TAAAAAAAT
40219019 CTTTATACTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAAAATTAAAATAAATATTTT
Found at i:40219586 original size:44 final size:44
Alignment explanation
Indices: 40219520--40219606 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
40219510 GCAAATAAGG
* *
40219520 CATGATTTGTGGGTATGACCTACATCGTCTTGGATATATGAGGC
1 CATGATTTGTGGGTATGACCTACATCGTCTTGGAGATACGAGGC
* *
40219564 CATGATTTGTGGGTATGGCCTACGTCGTCTTGGAGATACGAGG
1 CATGATTTGTGGGTATGACCTACATCGTCTTGGAGATACGAGG
40219607 ATATCATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (44 bp):
CATGATTTGTGGGTATGACCTACATCGTCTTGGAGATACGAGGC
Found at i:40220077 original size:13 final size:13
Alignment explanation
Indices: 40220038--40220090 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
40220028 AGTTCTTCAT
40220038 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
40220051 T-ATTATGGAAAAG
1 TGCTT-TTGAAAAG
*
40220064 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
40220077 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
40220090 T
1 T
40220091 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:40226792 original size:22 final size:22
Alignment explanation
Indices: 40226767--40226813 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
40226757 ATACTATATG
40226767 AAATAAAAATATATT-ATTAAAT
1 AAATAAAAATA-ATTAATTAAAT
*
40226789 AAATTAAAATAATTAATTAAAT
1 AAATAAAAATAATTAATTAAAT
40226811 AAA
1 AAA
40226814 AATAACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATAAAAATAATTAATTAAAT
Found at i:40226818 original size:18 final size:18
Alignment explanation
Indices: 40226782--40226823 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40226772 AAAATATATT
*
40226782 ATTAAATAAATTAAAATA
1 ATTAAATAAATAAAAATA
*
40226800 ATTAATTAAATAAAAATA
1 ATTAAATAAATAAAAATA
*
40226818 ACTAAA
1 ATTAAA
40226824 CACATAATAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATTAAATAAATAAAAATA
Found at i:40231562 original size:24 final size:24
Alignment explanation
Indices: 40231535--40231581 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40231525 CTGGGTCTTG
*
40231535 TTTGTTGGTTTGGGCCCGGGCATA
1 TTTGTTGGCTTGGGCCCGGGCATA
*
40231559 TTTGTTTGCTTGGGCCCGGGCAT
1 TTTGTTGGCTTGGGCCCGGGCAT
40231582 TATTGGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.19, G:0.36, T:0.38
Consensus pattern (24 bp):
TTTGTTGGCTTGGGCCCGGGCATA
Found at i:40232070 original size:50 final size:50
Alignment explanation
Indices: 40231990--40232460 Score: 374
Period size: 50 Copynumber: 9.4 Consensus size: 50
40231980 GGATTAATTT
* * * * * *
40231990 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCATCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACCAGATCCGCCGTCGTAG
** * *** * * *
40232040 CTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCTGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACCAGATCCGCCGTCGTAG
* ** * * *
40232090 CTTCAATCTTTTAAATTGCAATGTCAGGAAAACTAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACCAGATCCGCCGTCGTAG
* * *** * *
40232140 CTTCAATCTATTCCATTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACCAGATCCGCCGTCGTAG
* ** * *
40232190 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACCAGATCCGCCGTCGTAG
* * *** * *
40232240 CTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACCAGATCCGCCGTCGTAG
* ** * *
40232290 CTTCAATCTTTTTTATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACCAGATCCGCCGTCGTAG
* * ** * *
40232340 CTTCAATCTGTTCCACTGCACTG-CTAAGG-AAGTAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACCAGATCCGCCGTCGTAG
* ** * *
40232389 CTTCAATCTTTTTGATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACCAGATCCGCCGTCGTAG
*
40232439 CTTCAATCTGTTCCACTGCACT
1 CTTCAATCTGTTCCATTGCACT
40232461 ACTAAGGAAG
Statistics
Matches: 314, Mismatches: 100, Indels: 14
0.73 0.23 0.03
Matches are distributed among these distances:
49 39 0.12
50 273 0.87
51 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTCCATTGCACTGTCAGGGAAACCAGATCCGCCGTCGTAG
Found at i:40232171 original size:100 final size:100
Alignment explanation
Indices: 40232006--40232477 Score: 768
Period size: 100 Copynumber: 4.7 Consensus size: 100
40231996 TTTGTTCAAC
* * * * * *
40232006 TGCAATGTCGGGGAAACCAGATCCGCCATCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGA
* *
40232070 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * * *
40232106 TGCAATGTCAGGAAAACTAGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
40232171 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
40232206 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
*
40232271 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTTAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
40232306 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
*
40232371 GT-AGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
*
40232405 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTACTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
40232470 GTTAAGAT
66 G-TAAGAT
40232478 TACTGGCTTC
Statistics
Matches: 350, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
99 96 0.27
100 249 0.71
101 5 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
Found at i:40232586 original size:47 final size:44
Alignment explanation
Indices: 40232527--40232725 Score: 133
Period size: 45 Copynumber: 4.4 Consensus size: 44
40232517 AAAATCTGCC
40232527 ATCTTCGATCTACTTCAAGCCAATACATGAAGACAAGATCTGCTTT
1 ATCTTCGATCTACTTC--GCCAATACATGAAGACAAGATCTGCTTT
* *** *
40232573 TTCCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTG--TT
1 AT-CTTCGATCTACTTCGCCA--A-TACATGAAGACAAGATCTGCTTT
*
40232619 ATC-TCTGATCTACTTCGCGCCAGTACATGAAGACAAGATCTGC-TT
1 ATCTTC-GATCTACTT--CGCCAATACATGAAGACAAGATCTGCTTT
** ***
40232664 -TCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTG--TT
1 ATCTTCGATCTACTTCGCCA--A-TACATGAAGACAAGATCTGCTTT
*
40232708 ATCTTCGATCCACTTCGC
1 ATCTTCGATCTACTTCGC
40232726 TACCAGCATA
Statistics
Matches: 120, Mismatches: 20, Indels: 27
0.72 0.12 0.16
Matches are distributed among these distances:
42 5 0.04
44 28 0.23
45 48 0.40
46 4 0.03
47 20 0.17
48 15 0.12
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTTCGATCTACTTCGCCAATACATGAAGACAAGATCTGCTTT
Found at i:40232636 original size:45 final size:45
Alignment explanation
Indices: 40232555--40232757 Score: 214
Period size: 45 Copynumber: 4.5 Consensus size: 45
40232545 GCCAATACAT
* *
40232555 GAAGACAAGATCTGCTTTTTCCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTG--TTAT-CTTCGATCTACTTCGCCACCAGTATAG
* * * *
40232603 GAAGGCAAGATCTGTTATC-TCTGATCTACTTCG-CGCCAGTACAT
1 GAAGACAAGATCTGTTATCTTC-GATCTACTTCGCCACCAGTATAG
** *
40232647 GAAGACAAGATCTGCTT-TCTTCGATCTGTTTCGCCACCAGTATGG
1 GAAGACAAGATCTG-TTATCTTCGATCTACTTCGCCACCAGTATAG
* * *
40232692 GAAGACAAGATCTGTTATCTTCGATCCACTTCGCTACCAGCATAG
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATAG
* *
40232737 AAAGACAGGATCTGTTATCTT
1 GAAGACAAGATCTGTTATCTT
40232758 TCAACCTGCT
Statistics
Matches: 129, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
44 35 0.27
45 78 0.60
46 3 0.02
48 13 0.10
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (45 bp):
GAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATAG
Found at i:40232705 original size:89 final size:91
Alignment explanation
Indices: 40232527--40232725 Score: 296
Period size: 89 Copynumber: 2.2 Consensus size: 91
40232517 AAAATCTGCC
**
40232527 ATCTTCGATCTACTTCAAGCCAATACATGAAGACAAGATCTGCTTTTTCCTTCGATCTACTTCGC
1 ATCTTCGATCTACTTCGCGCCAATACATGAAGACAAGATCTGC-TTTTCCTTCGATCTACTTCGC
*
40232592 CACCAGTATGGGAAGGCAAGATCTGTT
65 CACCAGTATGGGAAGACAAGATCTGTT
* **
40232619 ATC-TCTGATCTACTTCGCGCCAGTACATGAAGACAAGATCTGC-TTT-CTTCGATCTGTTTCGC
1 ATCTTC-GATCTACTTCGCGCCAATACATGAAGACAAGATCTGCTTTTCCTTCGATCTACTTCGC
40232681 CACCAGTATGGGAAGACAAGATCTGTT
65 CACCAGTATGGGAAGACAAGATCTGTT
*
40232708 ATCTTCGATCCACTTCGC
1 ATCTTCGATCTACTTCGC
40232726 TACCAGCATA
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
89 54 0.55
90 5 0.05
91 2 0.02
92 37 0.38
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (91 bp):
ATCTTCGATCTACTTCGCGCCAATACATGAAGACAAGATCTGCTTTTCCTTCGATCTACTTCGCC
ACCAGTATGGGAAGACAAGATCTGTT
Found at i:40234064 original size:47 final size:46
Alignment explanation
Indices: 40233995--40234083 Score: 142
Period size: 47 Copynumber: 1.9 Consensus size: 46
40233985 AGCCTCTCCA
* *
40233995 TTTTTTTTGCTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTTTTT
1 TTTTTTTTGCTCAAGGCGCCCTTTGTAGGCTTTCACCCTGGTTTTT
*
40234041 TTTTTTTTGACTCAAGGCGCCCTTTGTAGGCTTTCACCTTGGT
1 TTTTTTTTG-CTCAAGGCGCCCTTTGTAGGCTTTCACCCTGGT
40234084 CCCACCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 9 0.23
47 30 0.77
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.47
Consensus pattern (46 bp):
TTTTTTTTGCTCAAGGCGCCCTTTGTAGGCTTTCACCCTGGTTTTT
Found at i:40234094 original size:47 final size:46
Alignment explanation
Indices: 40233997--40234095 Score: 108
Period size: 47 Copynumber: 2.1 Consensus size: 46
40233987 CCTCTCCATT
* * ******
40233997 TTTTTTGCTCAAGGCTCCCTTTGTAGGGTTTCACCCTGGTTTTTTT
1 TTTTTTGCTCAAGGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
*
40234043 TTTTTTGACTCAAGGCGCCCTTTGTAGGCTTTCACCTTGGTCCCACC
1 TTTTTTG-CTCAAGGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
40234090 TTTTTT
1 TTTTTT
40234096 AAGCAGAGTA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
46 7 0.16
47 36 0.84
ACGTcount: A:0.10, C:0.25, G:0.18, T:0.46
Consensus pattern (46 bp):
TTTTTTGCTCAAGGCGCCCTTTGTAGGCTTTCACCCTGGTCCCACC
Found at i:40244630 original size:24 final size:24
Alignment explanation
Indices: 40244603--40244649 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40244593 CTGGGTCTTG
*
40244603 TTTGTTGGTTTGGGCCCGGGCATA
1 TTTGTTGGCTTGGGCCCGGGCATA
*
40244627 TTTGTTTGCTTGGGCCCGGGCAT
1 TTTGTTGGCTTGGGCCCGGGCAT
40244650 TATTGGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.19, G:0.36, T:0.38
Consensus pattern (24 bp):
TTTGTTGGCTTGGGCCCGGGCATA
Found at i:40256013 original size:25 final size:24
Alignment explanation
Indices: 40255962--40256012 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
40255952 TTGAATATTA
* *
40255962 TTTAATATTTTTTATTTATGTAAT
1 TTTAATAATTTTTATTTATATAAT
40255986 TTTAATTAATTTTTATTT-TATAAT
1 TTTAA-TAATTTTTATTTATATAAT
40256010 TTT
1 TTT
40256013 TTATAACAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTAATAATTTTTATTTATATAAT
Found at i:40257566 original size:18 final size:18
Alignment explanation
Indices: 40257543--40257579 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40257533 GCCAGGTGCA
*
40257543 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
40257561 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
40257579 T
1 T
40257580 TTTCTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:40258092 original size:62 final size:60
Alignment explanation
Indices: 40257977--40258093 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 60
40257967 TTATACAAAC
* * ***
40257977 TATTTTTATATTGTTTCATTGAATAAAATAAAATTTGTTTTGAATATTTTAATAGTAAAT
1 TATTTTTATATTGTTTCATTGAATAAAATAAAAGTTCTTTTGAATAAGGTAATAGTAAAT
* * *
40258037 TATTTTTATATTTTTTCCTATTTAATAAAATAGAAGTTCTTTTGAATAAGGTAATAG
1 TATTTTTATATTGTTT-C-ATTGAATAAAATAAAAGTTCTTTTGAATAAGGTAATAG
40258094 AATAATGCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 15 0.32
61 1 0.02
62 31 0.66
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.50
Consensus pattern (60 bp):
TATTTTTATATTGTTTCATTGAATAAAATAAAAGTTCTTTTGAATAAGGTAATAGTAAAT
Found at i:40261565 original size:126 final size:126
Alignment explanation
Indices: 40261124--40261644 Score: 751
Period size: 126 Copynumber: 4.1 Consensus size: 126
40261114 GGCCAAACAT
* * *
40261124 GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTCCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* *
40261189 CTGCTTGAAGCGTTTTTGACACTATTTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTC-T
66 CTGCTTGAAGCGTTTTTGACACTA-TTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * *
40261250 GAAACTATTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGCAT
1 G-AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCAT
* * * *
40261315 CCTGTTTGAAGTGTTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATTA-TTTTTCAG
65 CCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * *
40261376 GAACTATTGTAGAAAAAGAGTGTCTACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* *
40261441 CTGCTTGAAGTGTTTTTGAAACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * *
40261502 GAACTACTGTAGAAAAGGAACGTCCACTTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * *
40261567 CTGGTTGAAGCGTTTTTGGCATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTAA
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC-AA
40261629 -AACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
40261645 AATAAAATCC
Statistics
Matches: 357, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
125 116 0.32
126 159 0.45
127 82 0.23
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
Found at i:40261584 original size:251 final size:253
Alignment explanation
Indices: 40261124--40261644 Score: 780
Period size: 251 Copynumber: 2.1 Consensus size: 253
40261114 GGCCAAACAT
40261124 GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTCCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTCCTGACAGTGCATC
* * *
40261189 CTGCTTGAAGCGTTTTTGACACTATTTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTCTGAAA
66 CTGCTTGAAGCGTTTTTGAAACTATTTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGAAA
* * * *
40261254 CTATTGTAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGCATCCTG
131 CTACTGTAGAAAAAGAACGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCCTG
* * * *
40261319 TTTGAAGTGTTTTTGACACTATTTTTTCAGAACTGTCTTCTCAAAATT-ATTTTTC-A
196 GTTGAAGCGTTTTTGACACTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTA
* ** * * * *
40261375 GGAACTATTGTAGAAAAAGAGTGTCTACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGCAT
1 -GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTCCTGACAGTGCAT
*
40261440 CCTGCTTGAAGTGTTTTTGAAACTA-TTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCA-AG
65 CCTGCTTGAAGCGTTTTTGAAACTATTTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGA-
* *
40261503 AACTACTGTAGAAAAGGAACGTCCACTTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCC
129 AACTACTGTAGAAAAAGAACGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCC
* *
40261568 TGGTTGAAGCGTTTTTGGCATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTA
194 TGGTTGAAGCGTTTTTGACACTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTA
*
40261628 AAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
40261645 AATAAAATCC
Statistics
Matches: 241, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
250 1 0.00
251 137 0.57
252 102 0.42
253 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (253 bp):
GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTCCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGAAACTATTTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAGAAA
CTACTGTAGAAAAAGAACGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCCTG
GTTGAAGCGTTTTTGACACTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTA
Found at i:40261756 original size:34 final size:31
Alignment explanation
Indices: 40261704--40261838 Score: 148
Period size: 34 Copynumber: 4.3 Consensus size: 31
40261694 CACAAAATTA
** *
40261704 TTTTAAAAAACTAAACCCTAATTTAATTAATT
1 TTTTAAAACTCTAAAACCTAATTTAATT-ATT
*
40261736 TTCTTAAACACTCTAAACCCTAATTTAATTAATT
1 TT-TTAAA-ACTCTAAAACCTAATTTAATT-ATT
*
40261770 TATTTAAAACTCTAAAATCTAATTTAA-T-TT
1 T-TTTAAAACTCTAAAACCTAATTTAATTATT
* *
40261800 ATTTAAAACCCTAAAACCTAATTTAATTATT
1 TTTTAAAACTCTAAAACCTAATTTAATTATT
40261831 TTTTAAAA
1 TTTTAAAA
40261839 AAAACTCTAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
29 23 0.26
30 3 0.03
31 9 0.10
32 3 0.03
33 22 0.24
34 29 0.32
35 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTAAAACTCTAAAACCTAATTTAATTATT
Found at i:40261800 original size:29 final size:29
Alignment explanation
Indices: 40261764--40261831 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
40261754 CCTAATTTAA
* *
40261764 TTAATTTATTTAAAACTCTAAAATCTAAT
1 TTAATTTATTTAAAACCCTAAAACCTAAT
40261793 TTAATTTATTTAAAACCCTAAAACCTAAT
1 TTAATTTATTTAAAACCCTAAAACCTAAT
40261822 TTAA-TTATTT
1 TTAATTTATTT
40261832 TTTAAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
28 6 0.16
29 31 0.84
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAATTTATTTAAAACCCTAAAACCTAAT
Found at i:40268287 original size:51 final size:51
Alignment explanation
Indices: 40268197--40268309 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 51
40268187 ATAGAAATGG
* *
40268197 TGAAAATGAAGAAATAAGAAATATTTGGAAATGATTATGGTTTTCTCCAAAA
1 TGAAAATGAAGAAAT-AGAAACATTTGGAAATGAATATGGTTTTCTCCAAAA
*
40268249 TGAAAATGGAGAAAT-GAAACCATTTGGAAATGAATATGGTTTTCTCCAAAA
1 TGAAAATGAAGAAATAGAAA-CATTTGGAAATGAATATGGTTTTCTCCAAAA
40268300 TGAAAATGAA
1 TGAAAATGAA
40268310 TATGACCTGG
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
50 4 0.07
51 38 0.68
52 14 0.25
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (51 bp):
TGAAAATGAAGAAATAGAAACATTTGGAAATGAATATGGTTTTCTCCAAAA
Found at i:40269308 original size:9 final size:9
Alignment explanation
Indices: 40269298--40269386 Score: 142
Period size: 9 Copynumber: 9.9 Consensus size: 9
40269288 ATTAAACCAC
*
40269298 TTAACCGAC
1 TTAACCGAT
40269307 TTAACCGAT
1 TTAACCGAT
*
40269316 TAAACCGAT
1 TTAACCGAT
*
40269325 TTAACTGAT
1 TTAACCGAT
40269334 TTAACCGAT
1 TTAACCGAT
*
40269343 TTAACCGAC
1 TTAACCGAT
40269352 TTAACCGAT
1 TTAACCGAT
40269361 TTAACCGAT
1 TTAACCGAT
40269370 TTAACCGAT
1 TTAACCGAT
40269379 TTAACCGA
1 TTAACCGA
40269387 ATTGAATCAC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 73 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (9 bp):
TTAACCGAT
Found at i:40269337 original size:27 final size:27
Alignment explanation
Indices: 40269288--40269386 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
40269278 TTGGTTAAAA
*
40269288 ATTAAACC-ACTTAACCGACTTAACCG
1 ATTAAACCGACTTAACCGATTTAACCG
* *
40269314 ATTAAACCGATTTAACTGATTTAACCG
1 ATTAAACCGACTTAACCGATTTAACCG
*
40269341 ATTTAACCGACTTAACCGATTTAACCG
1 ATTAAACCGACTTAACCGATTTAACCG
* *
40269368 ATTTAACCGATTTAACCGA
1 ATTAAACCGACTTAACCGA
40269387 ATTGAATCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 8 0.12
27 57 0.88
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (27 bp):
ATTAAACCGACTTAACCGATTTAACCG
Found at i:40269438 original size:37 final size:37
Alignment explanation
Indices: 40269388--40269499 Score: 172
Period size: 37 Copynumber: 3.0 Consensus size: 37
40269378 TTTAACCGAA
40269388 TTGAATCACTACATAATTAAAAGA-ATTACATAAATCT
1 TTGAATCACTACATAATTAAAA-ACATTACATAAATCT
* *
40269425 TTGAATCAATACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAATCT
* *
40269462 TTGAATCACTACATAATTAAAAACATTAGATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAATCT
40269499 T
1 T
40269500 GAAATTAACA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 1 0.01
37 69 0.99
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.33
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAATCT
Found at i:40269456 original size:17 final size:17
Alignment explanation
Indices: 40269434--40269494 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
40269424 TTTGAATCAA
40269434 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
40269451 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
40269471 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
*
40269488 TAGATAA
1 TACATAA
40269495 GTCTTGAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 19 0.59
20 13 0.41
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:40273185 original size:51 final size:45
Alignment explanation
Indices: 40273069--40273162 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 45
40273059 ACTTTATTTT
* **
40273069 TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAGTTGGGTTTGGG
1 TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAATTAAGTTTGGG
40273114 TAGACTTTAG-TTTATTGGGTTGGTAAATGGTAATTAAGTTTGGG
1 TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAATTAAGTTTGGG
40273158 TAGAC
1 TAGAC
40273163 AAGGGTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 36 0.78
45 10 0.22
ACGTcount: A:0.22, C:0.03, G:0.32, T:0.43
Consensus pattern (45 bp):
TAGACTTTAGTTTTATTGGGTTGGTAAATGGTAATTAAGTTTGGG
Found at i:40273363 original size:18 final size:18
Alignment explanation
Indices: 40273320--40273355 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40273310 TCGGTTAACC
40273320 GATCGGTTAACTGAATTT
1 GATCGGTTAACTGAATTT
40273338 GATCGGTTAACTGAATTT
1 GATCGGTTAACTGAATTT
40273356 TTTCGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (18 bp):
GATCGGTTAACTGAATTT
Found at i:40274847 original size:97 final size:97
Alignment explanation
Indices: 40274679--40274872 Score: 379
Period size: 97 Copynumber: 2.0 Consensus size: 97
40274669 TAACTCTTCC
40274679 TCATTAAGCTAGAAACTATGGTTCTGGATCTAATTAGAGGTTATTTTATCTCTTAGTAAAGTATT
1 TCATTAAGCTAGAAACTATGGTTCTGGATCTAATTAGAGGTTATTTTATCTCTTAGTAAAGTATT
40274744 ACAACTTTGCATGTTAAGTTCTTATAGCGTGG
66 ACAACTTTGCATGTTAAGTTCTTATAGCGTGG
40274776 TCATTAAGCTAGAAACTATGGTTCTGGATCTAATTAGAGGTTATTTTATCTCTTAGTAAAGTATT
1 TCATTAAGCTAGAAACTATGGTTCTGGATCTAATTAGAGGTTATTTTATCTCTTAGTAAAGTATT
*
40274841 ATAACTTTGCATGTTAAGTTCTTATAGCGTGG
66 ACAACTTTGCATGTTAAGTTCTTATAGCGTGG
40274873 GTCTATATGG
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (97 bp):
TCATTAAGCTAGAAACTATGGTTCTGGATCTAATTAGAGGTTATTTTATCTCTTAGTAAAGTATT
ACAACTTTGCATGTTAAGTTCTTATAGCGTGG
Found at i:40275771 original size:21 final size:21
Alignment explanation
Indices: 40275747--40275789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40275737 TGTATGGTAA
* *
40275747 GATGTGATTGTCCGCCCTTAT
1 GATGTGATTATCCACCCTTAT
*
40275768 GATGTGGTTATCCACCCTTAT
1 GATGTGATTATCCACCCTTAT
40275789 G
1 G
40275790 GTAAGTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (21 bp):
GATGTGATTATCCACCCTTAT
Found at i:40278835 original size:14 final size:14
Alignment explanation
Indices: 40278801--40278828 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40278791 AAAATAACCA
40278801 CTTTTTCTTATTCT
1 CTTTTTCTTATTCT
40278815 CTTTTTCTTATTCT
1 CTTTTTCTTATTCT
40278829 TATTTTCGTT
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:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (14 bp):
CTTTTTCTTATTCT
Found at i:40278849 original size:26 final size:27
Alignment explanation
Indices: 40278819--40278889 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 27
40278809 TATTCTCTTT
40278819 TTCTTATTCTTATTTTCGT-TCACACC
1 TTCTTATTCTTATTTTCGTATCACACC
* * *
40278845 TTCTT-TTCCTATTATCGTATCACTCC
1 TTCTTATTCTTATTTTCGTATCACACC
* *
40278871 TCCTTAGTCTT-TTTT-GTAT
1 TTCTTATTCTTATTTTCGTAT
40278890 AACTTAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
25 15 0.42
26 18 0.50
27 3 0.08
ACGTcount: A:0.14, C:0.25, G:0.06, T:0.55
Consensus pattern (27 bp):
TTCTTATTCTTATTTTCGTATCACACC
Found at i:40282177 original size:54 final size:55
Alignment explanation
Indices: 40282077--40282181 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 55
40282067 GACAACCAAG
* *
40282077 GTGGTGGAGCCATAAAGAATGGCTCTACCAAAATAAAATATCATTTTTTAATAAA
1 GTGGTGGAGCCATAAAGAATGACTCCACCAAAATAAAATATCATTTTTTAATAAA
* ** *
40282132 GTGGTGGCGCCATTTAGAATGACTCCA-CAAAATAAAATATTATTTTTTAA
1 GTGGTGGAGCCATAAAGAATGACTCCACCAAAATAAAATATCATTTTTTAA
40282182 AAATTTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 22 0.50
55 22 0.50
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (55 bp):
GTGGTGGAGCCATAAAGAATGACTCCACCAAAATAAAATATCATTTTTTAATAAA
Found at i:40288609 original size:24 final size:24
Alignment explanation
Indices: 40288573--40288618 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40288563 GACACATTGC
40288573 AGCTCGCAAGAGCATCCCGATAAT
1 AGCTCGCAAGAGCATCCCGATAAT
* * *
40288597 AGCTCTCATGAGCATCTCGATA
1 AGCTCGCAAGAGCATCCCGATA
40288619 TTTGGCTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (24 bp):
AGCTCGCAAGAGCATCCCGATAAT
Found at i:40288853 original size:24 final size:24
Alignment explanation
Indices: 40288783--40288853 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
40288773 AACTAGATCT
*
40288783 TATGAGCTTCCCGATTAATGGCTCT
1 TATGAGCTTCCCG-TTAATGGCTCG
* * *** *
40288808 TAGGA-CTTACTAATATTGGCTCG
1 TATGAGCTTCCCGTTAATGGCTCG
40288831 TATGAGCTTCCCGTTAATGGCTC
1 TATGAGCTTCCCGTTAATGGCTC
40288854 TCCGGAGCTT
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
23 12 0.38
24 16 0.50
25 4 0.12
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (24 bp):
TATGAGCTTCCCGTTAATGGCTCG
Found at i:40288886 original size:25 final size:24
Alignment explanation
Indices: 40288832--40288891 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
40288822 ATTGGCTCGT
* *
40288832 ATGAGCTTCCCGTTAATGGCTCTC
1 ATGAGCTTTCCGTTAATGGCTCAC
** *
40288856 CGGAGCTTTCCGTTTCATGGCTCAC
1 ATGAGCTTTCCG-TTAATGGCTCAC
40288881 ATGAGCTTTCC
1 ATGAGCTTTCC
40288892 ATTTATGTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (24 bp):
ATGAGCTTTCCGTTAATGGCTCAC
Found at i:40291279 original size:26 final size:27
Alignment explanation
Indices: 40291235--40291306 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
40291225 AATTTTCTTG
*
40291235 AAATTTTACCAGGATTAAAATCATC-A
1 AAATTTTACCAGGAGTAAAATCATCAA
* * **
40291261 AAATTTTACCGGGGGTAAAATTGTCAA
1 AAATTTTACCAGGAGTAAAATCATCAA
*
40291288 AAATTTTACTAGG-GTAAAA
1 AAATTTTACCAGGAGTAAAA
40291307 CTAGGATGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 26 0.68
27 12 0.32
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (27 bp):
AAATTTTACCAGGAGTAAAATCATCAA
Done.