Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 16 of 82
Found at i:5353947 original size:20 final size:19
Alignment explanation
Indices: 5353919--5353956 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5353909 TTTATAAATC
5353919 ATTTTGAAATTGAATAATG
1 ATTTTGAAATTGAATAATG
*
5353938 ATTTTAGAAATTGAGTAAT
1 ATTTT-GAAATTGAATAAT
5353957 TGGAGACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTTTGAAATTGAATAATG
Found at i:5357363 original size:22 final size:22
Alignment explanation
Indices: 5357321--5357363 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5357311 AAAGTTCATA
*
5357321 TGAAAATTATACAAATAAATCT
1 TGAAAATTATACAAAGAAATCT
* *
5357343 TGAAAATTATTCAAAGGAATC
1 TGAAAATTATACAAAGAAATC
5357364 AATCTTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
TGAAAATTATACAAAGAAATCT
Found at i:5360982 original size:7 final size:7
Alignment explanation
Indices: 5360948--5360979 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
5360938 AAAAAGTAAA
5360948 AAAAAAG
1 AAAAAAG
5360955 AAAAAAG
1 AAAAAAG
5360962 AAAAAAG
1 AAAAAAG
5360969 AAAATAAG
1 AAAA-AAG
5360977 AAA
1 AAA
5360980 TAATAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:5371493 original size:52 final size:52
Alignment explanation
Indices: 5371411--5371567 Score: 235
Period size: 52 Copynumber: 3.0 Consensus size: 52
5371401 GCACATGATG
*
5371411 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATATGC
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
* * *
5371463 GTGATAATGGTGTGTTGTGTGAGTGGACACATTGATGATATATGCCATGTGC
1 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
* * *
5371515 GTGATAGTGGTGTGCTT-TGTGATTGCACACACTGATGATGTAGGCCATGTGC
1 GTGATAGTGGTGTG-TTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
5371567 G
1 G
5371568 AGGTGGGAGT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 92 0.98
53 2 0.02
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.33
Consensus pattern (52 bp):
GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
Found at i:5378740 original size:42 final size:42
Alignment explanation
Indices: 5378688--5378853 Score: 188
Period size: 42 Copynumber: 4.0 Consensus size: 42
5378678 ACACATGGCT
* * * * * *
5378688 GGGTCATCATCAGCTTATGCATACCCCCACTCGCATATAGTT
1 GGGTCATCATCGGCTTATGCACACTCCCACTTGCACATAGTC
* *
5378730 GGGTCATCATCGGCTTATGCGCACTCCCACTTGCACATAGCC
1 GGGTCATCATCGGCTTATGCACACTCCCACTTGCACATAGTC
** *
5378772 AAGTCATCATCGGCTTATGCACACTCCTACTTGCACATAGTC
1 GGGTCATCATCGGCTTATGCACACTCCCACTTGCACATAGTC
* * * * *
5378814 GGGTCATCATCGACGTATGCGCACTCCTACTCGCACATAG
1 GGGTCATCATCGGCTTATGCACACTCCCACTTGCACATAG
5378854 CCAGGTCCAT
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 105 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.26
Consensus pattern (42 bp):
GGGTCATCATCGGCTTATGCACACTCCCACTTGCACATAGTC
Found at i:5378790 original size:84 final size:84
Alignment explanation
Indices: 5378690--5378856 Score: 235
Period size: 84 Copynumber: 2.0 Consensus size: 84
5378680 ACATGGCTGG
* * * * *
5378690 GTCATCATCAGCTTATGCATACCCCCACTCGCATATAGTTGGGTCATCATCGGCTTATGCGCACT
1 GTCATCATCAGCTTATGCACACCCCCACTCGCACATAGTCGGGTCATCATCGACGTATGCGCACT
*
5378755 CCCACTTGCACATAGCCAA
66 CCCACTCGCACATAGCCAA
* * * *
5378774 GTCATCATCGGCTTATGCACACTCCTACTTGCACATAGTCGGGTCATCATCGACGTATGCGCACT
1 GTCATCATCAGCTTATGCACACCCCCACTCGCACATAGTCGGGTCATCATCGACGTATGCGCACT
*
5378839 CCTACTCGCACATAGCCA
66 CCCACTCGCACATAGCCA
5378857 GGTCCATATC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (84 bp):
GTCATCATCAGCTTATGCACACCCCCACTCGCACATAGTCGGGTCATCATCGACGTATGCGCACT
CCCACTCGCACATAGCCAA
Found at i:5381454 original size:52 final size:52
Alignment explanation
Indices: 5381377--5381583 Score: 342
Period size: 52 Copynumber: 4.0 Consensus size: 52
5381367 CACATGATGG
** * *
5381377 TGATAGTGGCATGCTATGTGAGTGCACACACTGATGATATATGCCATGTGCG
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCA
* *
5381429 TGATAGTTGTGTGCTGTGTGAGTGCACACTCTGATGATATATGCCATGTGCA
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCA
* *
5381481 TGATAGTGGTGTGTTGTGTGAGTGCACACATTGATGATATATGCCATGTGCA
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCA
5381533 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
1 TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGC
5381584 GAGGTGGGAG
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 143 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (52 bp):
TGATAGTGGTGTGCTGTGTGAGTGCACACACTGATGATATATGCCATGTGCA
Found at i:5381631 original size:35 final size:36
Alignment explanation
Indices: 5381564--5381673 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 36
5381554 GTGCACACAC
* *
5381564 TGATGATATATGCCATGTGCGAG-GTGGGAGTGAACA
1 TGATGATATATGCCTTGTGCG-GTGTGGAAGTGAACA
5381600 TGATGATAT-TGCCTTGTGCGGTGTGGAAGTGAACA
1 TGATGATATATGCCTTGTGCGGTGTGGAAGTGAACA
* * *
5381635 GGATGAT-TCTAG-CTATGTGCGGTGTGGAAGTGCACA
1 TGATGATATAT-GCCT-TGTGCGGTGTGGAAGTGAACA
5381671 TGA
1 TGA
5381674 GCTGCTACAA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
34 2 0.03
35 31 0.48
36 32 0.49
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (36 bp):
TGATGATATATGCCTTGTGCGGTGTGGAAGTGAACA
Found at i:5382630 original size:35 final size:35
Alignment explanation
Indices: 5382532--5382637 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 35
5382522 GCTTAGCCAC
* *
5382532 AACCTTTAACAATGGTTTTTCACGGGATCGACCAA
1 AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
* * * * * *
5382567 AACC--CAA-AGTGGCTTTTCAAAGGCTCAACCAC
1 AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
*
5382599 AACCTTTAACAATGGTTTTTCATGGGATCAACCAA
1 AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
5382634 AACC
1 AACC
5382638 CAAAACTAAC
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
32 22 0.42
33 2 0.04
34 2 0.04
35 27 0.51
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (35 bp):
AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
Found at i:5389949 original size:35 final size:34
Alignment explanation
Indices: 5389910--5390017 Score: 96
Period size: 35 Copynumber: 3.2 Consensus size: 34
5389900 TTACAATGAC
*
5389910 TTTTCACAAGCTCAACCACAACCTATAACAATGGT
1 TTTTCACAAGCTTAACCACAACCT-TAACAATGGT
* * * * * * *
5389945 TTTTCACGAGATTAATCAAAACC-CAA-AGTGGC
1 TTTTCACAAGCTTAACCACAACCTTAACAATGGT
5389977 TTTTCA-AAGGCTTAACCACAACCTTTAACAATGGT
1 TTTTCACAA-GCTTAACCACAACC-TTAACAATGGT
5390012 TTTTCA
1 TTTTCA
5390018 TGGGATCAAC
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
31 1 0.02
32 21 0.39
33 2 0.04
34 2 0.04
35 28 0.52
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (34 bp):
TTTTCACAAGCTTAACCACAACCTTAACAATGGT
Found at i:5389997 original size:67 final size:67
Alignment explanation
Indices: 5389909--5390038 Score: 190
Period size: 67 Copynumber: 1.9 Consensus size: 67
5389899 TTTACAATGA
* *
5389909 CTTTTCACAAGCTCAACCACAACCTATAACAATGGTTTTTCACGAGATTAATCAAAACCCAAAGT
1 CTTTTCACAAGCTCAACCACAACCTATAACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGT
5389974 GG
66 GG
* * * *
5389976 CTTTTCA-AAGGCTTAACCACAACCTTTAACAATGGTTTTTCATGGGATCAACCAAAACCCAAA
1 CTTTTCACAA-GCTCAACCACAACCTATAACAATGGTTTTTCACGAGATCAACCAAAACCCAAA
5390039 ACTAACTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 2 0.04
67 54 0.96
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (67 bp):
CTTTTCACAAGCTCAACCACAACCTATAACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGT
GG
Found at i:5390029 original size:35 final size:34
Alignment explanation
Indices: 5389921--5390034 Score: 79
Period size: 35 Copynumber: 3.4 Consensus size: 34
5389911 TTTCACAAGC
* * *
5389921 TCAACCACAACCTATAACAATGGTTTTTCACGAGA
1 TCAACCAAAACCT-TAACAATGGTTTTTCAAGGGA
* * * * * * *
5389956 TTAATCAAAACC-CAA-AGTGGCTTTTCAAAGGC
1 TCAACCAAAACCTTAACAATGGTTTTTCAAGGGA
* * *
5389988 TTAACCACAACCTTTAACAATGGTTTTTCATGGGA
1 TCAACCAAAACC-TTAACAATGGTTTTTCAAGGGA
5390023 TCAACCAAAACC
1 TCAACCAAAACC
5390035 CAAAACTAAC
Statistics
Matches: 56, Mismatches: 20, Indels: 6
0.68 0.24 0.07
Matches are distributed among these distances:
32 21 0.38
33 2 0.04
34 2 0.04
35 31 0.55
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (34 bp):
TCAACCAAAACCTTAACAATGGTTTTTCAAGGGA
Found at i:5390932 original size:14 final size:15
Alignment explanation
Indices: 5390913--5390944 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5390903 AATGAAAAAT
5390913 AAACAAAAAA-AGAG
1 AAACAAAAAATAGAG
5390927 AAACAAAAAATAGAG
1 AAACAAAAAATAGAG
5390942 AAA
1 AAA
5390945 AGGGGAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.03
Consensus pattern (15 bp):
AAACAAAAAATAGAG
Found at i:5392525 original size:13 final size:13
Alignment explanation
Indices: 5392507--5392569 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
5392497 AAAGTTATTC
5392507 AATAAAAATAATA
1 AATAAAAATAATA
*
5392520 AATAAATAACAATA
1 AATAAA-AATAATA
* *
5392534 GATAAAAA-AA-G
1 AATAAAAATAATA
*
5392545 GATAAAAATAATA
1 AATAAAAATAATA
5392558 AATAAAAATAAT
1 AATAAAAATAAT
5392570 TCAAATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
11 8 0.19
12 4 0.10
13 19 0.45
14 11 0.26
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.21
Consensus pattern (13 bp):
AATAAAAATAATA
Found at i:5392549 original size:21 final size:21
Alignment explanation
Indices: 5392508--5392564 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
5392498 AAGTTATTCA
5392508 ATAAAAATAATAAAT--AA--
1 ATAAAAATAATAAATAAAAGG
*
5392525 ATAACAATAGATAAA-AAAAGG
1 ATAAAAATA-ATAAATAAAAGG
5392546 ATAAAAATAATAAATAAAA
1 ATAAAAATAATAAATAAAA
5392565 ATAATTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 8 0.25
18 5 0.16
19 2 0.06
20 5 0.16
21 12 0.38
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (21 bp):
ATAAAAATAATAAATAAAAGG
Found at i:5398820 original size:28 final size:27
Alignment explanation
Indices: 5398781--5398833 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5398771 ATATCCTGGT
*
5398781 GGTGGAAAATTACAATTTTGCCCTTGA
1 GGTGGAAAATTACAATTTTACCCTTGA
*
5398808 GGTGGCAAAATTACCATTTTACCCTT
1 GGTGG-AAAATTACAATTTTACCCTT
5398834 TTACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCTTGA
Found at i:5398903 original size:20 final size:20
Alignment explanation
Indices: 5398878--5398923 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
5398868 CTTCTAAACC
5398878 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
5398898 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
5398918 TCAAAT
1 TCAAAT
5398924 GGGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:5407589 original size:37 final size:37
Alignment explanation
Indices: 5407515--5407935 Score: 472
Period size: 37 Copynumber: 11.3 Consensus size: 37
5407505 CTTAGTTTTA
* *
5407515 AGGAGTTCATTTTCAAAAGTTTCATTGCCTCAACTTTG
1 AGGAGTTCATTTT-AAAAGTTTCGTTGCCTCAGCTTTG
*
5407553 AGGAGTTCATTTTAAAAATTTCGTTGCCTCAGCTTTG
1 AGGAGTTCATTTTAAAAGTTTCGTTGCCTCAGCTTTG
* ** *
5407590 AGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAATTTTA
1 AGGAGTTCA-TTTTAAAAGTTTCGTTGCCTCAGCTTTG
* * *
5407628 AGGAGTTTATTCTTAAAAATTTCATTGCCTCAGCTTTG
1 AGGAGTTCATT-TTAAAAGTTTCGTTGCCTCAGCTTTG
*
5407666 AGGAGTTCATTTTTAAAAG-TTCGTTGCCTCAGTTTTG
1 AGGAGTTCA-TTTTAAAAGTTTCGTTGCCTCAGCTTTG
* * * ** **
5407703 AGGAGTTCATTTTTAAAGGTCTCATTGCCAAATTTTTG
1 AGGAGTTCA-TTTTAAAAGTTTCGTTGCCTCAGCTTTG
* * *
5407741 AGGAGTTTATTTTAGAAGTTTCGTTGCCTCAACTTTG
1 AGGAGTTCATTTTAAAAGTTTCGTTGCCTCAGCTTTG
** * * * *
5407778 A-GA-TTTTTTTTAAAAGTTTTGTTGTCTTAGATTTG
1 AGGAGTTCATTTTAAAAGTTTCGTTGCCTCAGCTTTG
5407813 AGGAGTTCATTTTAAAAGTCTT-GTTGCCTCAGCTTTG
1 AGGAGTTCATTTTAAAAGT-TTCGTTGCCTCAGCTTTG
*
5407850 AGGAGTTCATTTTTAAAAGTTTTGTTGCCTCAGCTTTG
1 AGGAGTTCA-TTTTAAAAGTTTCGTTGCCTCAGCTTTG
* **
5407888 AGGAGTTCATTTTTAAAGTTTCGTTGCCTCAATTTTG
1 AGGAGTTCATTTTAAAAGTTTCGTTGCCTCAGCTTTG
5407925 AGGAGTTCATT
1 AGGAGTTCATT
5407936 AAAAAAAAAA
Statistics
Matches: 324, Mismatches: 50, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
35 26 0.08
36 4 0.01
37 157 0.48
38 135 0.42
39 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (37 bp):
AGGAGTTCATTTTAAAAGTTTCGTTGCCTCAGCTTTG
Found at i:5407695 original size:75 final size:76
Alignment explanation
Indices: 5407490--5407935 Score: 505
Period size: 75 Copynumber: 6.0 Consensus size: 76
5407480 CAAAAAAGAA
* * * * * *
5407490 AAAAGGTTTCATTACCTTAGTTTTAAGGAGTTCATTTTCAAAAGTTTCATTGCCTCAACTTTGAG
1 AAAA-GTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAG
5407555 GAGTTCA-TTTT
65 GAGTTCATTTTT
* * * * *
5407566 AAAAATTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCGTTGCCTCAATTTTAAGG
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGG
* *
5407631 AGTTTATTCTT
66 AGTTCATTTTT
* **
5407642 AAAAATTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAG-TTCGTTGCCTCAGTTTTGAGG
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGG
5407706 AGTTCATTTTT
66 AGTTCATTTTT
* * ** ** * *
5407717 AAAGGTCTCATTGCCAAATTTTTGAGGAGTTTA-TTTTAGAAGTTTCGTTGCCTCAACTTTGA-G
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGG
*
5407780 A-TT-TTTTTT
66 AGTTCATTTTT
** * * * *
5407789 AAAAGTTTTGTTGTCTTAGATTTGAGGAGTTCA-TTTTAAAAGTCTT-GTTGCCTCAGCTTTGAG
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGT-TTCGTTGCCTCAACTTTGAG
5407852 GAGTTCATTTTT
65 GAGTTCATTTTT
** *
5407864 AAAAGTTTTGTTGCCTCAGCTTTGAGGAGTTCATTTTT-AAAGTTTCGTTGCCTCAATTTTGAGG
1 AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGG
5407928 AGTTCATT
66 AGTTCATT
5407936 AAAAAAAAAA
Statistics
Matches: 313, Mismatches: 49, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
72 52 0.17
73 6 0.02
74 14 0.04
75 188 0.60
76 53 0.17
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (76 bp):
AAAAGTTTCATTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTTTCGTTGCCTCAACTTTGAGG
AGTTCATTTTT
Found at i:5407942 original size:1 final size:1
Alignment explanation
Indices: 5407936--5408018 Score: 67
Period size: 1 Copynumber: 83.0 Consensus size: 1
5407926 GGAGTTCATT
* * * * * * * * * *
5407936 AAAAAAAAAACAAAAACAAAACAAAAAAAAAACAAACAAAAAGAACAAAACAAAACAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
5408001 AAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAA
5408019 CTAAACTTGG
Statistics
Matches: 60, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:5407988 original size:40 final size:38
Alignment explanation
Indices: 5407936--5408024 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 38
5407926 GGAGTTCATT
*
5407936 AAAAAA-AAAACAAAAACAAAACAA-AAAAAAAACAAACA
1 AAAAAACAAAAC-AAAACAAAAAAAGAAAAAAAACAAA-A
5407974 AAAAGAACAAAACAAAACAAAAAAAGAAAAAAAACAAAA
1 AAAA-AACAAAACAAAACAAAAAAAGAAAAAAAACAAAA
*
5408013 AAAAAACTAAAC
1 AAAAAACAAAAC
5408025 TTGGTAAGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
38 11 0.24
39 18 0.39
40 17 0.37
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.01
Consensus pattern (38 bp):
AAAAAACAAAACAAAACAAAAAAAGAAAAAAAACAAAA
Found at i:5408196 original size:15 final size:13
Alignment explanation
Indices: 5408166--5408192 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5408156 AATGAAAAAT
5408166 AAACAAAAAAGAG
1 AAACAAAAAAGAG
5408179 AAACAAAAAAGAG
1 AAACAAAAAAGAG
5408192 A
1 A
5408193 GAAAAGGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAACAAAAAAGAG
Found at i:5410166 original size:21 final size:22
Alignment explanation
Indices: 5410117--5410166 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
5410107 GATAATATGA
* *
5410117 AATAAAAT-GAAAATAATAATT
1 AATAAAATAAAAAATAACAATT
*
5410138 AA-ATAATAAAAAATAACAA-T
1 AATAAAATAAAAAATAACAATT
5410158 AATAAAATA
1 AATAAAATA
5410167 GATAATTGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
AATAAAATAAAAAATAACAATT
Found at i:5410171 original size:9 final size:8
Alignment explanation
Indices: 5410068--5410171 Score: 56
Period size: 8 Copynumber: 13.1 Consensus size: 8
5410058 AACTTAGAAT
5410068 AAATAATA
1 AAATAATA
5410076 AAAT-ATA
1 AAATAATA
** *
5410083 GGAGAATA
1 AAATAATA
*
5410091 AAAAAATA
1 AAATAATA
5410099 AAA-AATA
1 AAATAATA
**
5410106 TGATAATA
1 AAATAATA
**
5410114 TGA-AATA
1 AAATAATA
5410121 AAATGAA-A
1 AAAT-AATA
*
5410129 ATAATAATT
1 A-AATAATA
5410138 AAATAATA
1 AAATAATA
5410146 AAA-AATA
1 AAATAATA
5410153 ACAATAATA
1 A-AATAATA
5410162 AAATAGATA
1 AAATA-ATA
5410171 A
1 A
5410172 TTGCATTAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
7 19 0.25
8 41 0.55
9 15 0.20
ACGTcount: A:0.69, C:0.01, G:0.07, T:0.23
Consensus pattern (8 bp):
AAATAATA
Found at i:5412833 original size:18 final size:19
Alignment explanation
Indices: 5412810--5412847 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5412800 AAGTGAGAAG
5412810 ATTATTTTAT-AATAAAAT
1 ATTATTTTATGAATAAAAT
5412828 ATTATTTTATGAATAAAAT
1 ATTATTTTATGAATAAAAT
5412847 A
1 A
5412848 ATAGTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTATTTTATGAATAAAAT
Found at i:5414653 original size:13 final size:13
Alignment explanation
Indices: 5414632--5414665 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5414622 GAAGAGAGGA
*
5414632 AAGAAAAAAAAAG
1 AAGAGAAAAAAAG
5414645 AAGAGAAAAAAAG
1 AAGAGAAAAAAAG
*
5414658 AAAAGAAA
1 AAGAGAAA
5414666 GGGAGAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAGAGAAAAAAAG
Found at i:5414949 original size:92 final size:92
Alignment explanation
Indices: 5414762--5414948 Score: 270
Period size: 91 Copynumber: 2.0 Consensus size: 92
5414752 AAAGGGTCGA
* * ** * *
5414762 TTTTGAAGGCTGGAAGGAGTAGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTGTCGATTTTTAGG
1 TTTTGAAGGCTGAAAGGAGCAGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTACCCATTTTGAGG
* *
5414827 GTGAGATGAGCAGCTTTAGCTGCTAAT
66 GTGAAATGAGCAACTTTAGCTGCTAAT
*
5414854 TTTTGAAGGCTGAAAGGAGCAGCTTTGGCTGCT-ATTTTTGAGGTTTTGGCTACCCCTTTTGAGG
1 TTTTGAAGGCTGAAAGGAGCAGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTACCCATTTTGAGG
5414918 GTGAAATGAGCAACTTT-GACTGCTAAT
66 GTGAAATGAGCAACTTTAG-CTGCTAAT
5414945 TTTT
1 TTTT
5414949 TTGGCTAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
90 1 0.01
91 53 0.62
92 31 0.36
ACGTcount: A:0.20, C:0.13, G:0.29, T:0.38
Consensus pattern (92 bp):
TTTTGAAGGCTGAAAGGAGCAGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTACCCATTTTGAGG
GTGAAATGAGCAACTTTAGCTGCTAAT
Found at i:5414976 original size:91 final size:92
Alignment explanation
Indices: 5414782--5414989 Score: 244
Period size: 91 Copynumber: 2.3 Consensus size: 92
5414772 TGGAAGGAGT
** * * * *
5414782 AGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTGTCGATTTTTAGGGTGAGATGAGCAGCTTTAGC
1 AGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTACCCATTTTGAGGGTGAAATGAGCAACTTTAGC
* * *
5414847 TGCTAATTTTTGAAGGCTGAAAGGAGC
66 TGCTAATTTTTGAAGGCTAAAAGCAAC
*
5414874 AGCTTTGGCTGCT-ATTTTTGAGGTTTTGGCTACCCCTTTTGAGGGTGAAATGAGCAACTTT-GA
1 AGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTACCCATTTTGAGGGTGAAATGAGCAACTTTAG-
** *
5414937 CTGCTAATTTTT-TTGGCTAAAATCAAC
65 CTGCTAATTTTTGAAGGCTAAAAGCAAC
*
5414964 AGCTTTGAGCTGCTGATTTTTG-GGTT
1 AGCTTTG-GCTGCTAATTTTTGAGGTT
5414990 GAAAGGAGCA
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
90 17 0.17
91 63 0.63
92 20 0.20
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (92 bp):
AGCTTTGGCTGCTAATTTTTGAGGTTTTGGCTACCCATTTTGAGGGTGAAATGAGCAACTTTAGC
TGCTAATTTTTGAAGGCTAAAAGCAAC
Found at i:5416292 original size:2 final size:2
Alignment explanation
Indices: 5416281--5416316 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5416271 TAATGTGTTG
*
5416281 AT AT AT -T AT AT AT AT AT AT AT AG AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5416317 CTATGTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5416431 original size:58 final size:57
Alignment explanation
Indices: 5416340--5416450 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 57
5416330 TATACATTGT
5416340 GTGACAAAATGCAACCATGCATGTGCAGGGTGAGTGTGCACCTACCGGTGATGAANTGC
1 GTGACAAAATGCAACCATGCATGTGCAGGGTGAG-GTGCACCTACCGGTGATGAA-TGC
* * * *
5416399 GTGAC-AAATGCAACCGTGCATGTGCGGGGTGAGGTGCACTTGCCGGTGATGA
1 GTGACAAAATGCAACCATGCATGTGCAGGGTGAGGTGCACCTACCGGTGATGA
5416451 CGGTGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 17 0.35
58 26 0.54
59 5 0.10
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.21
Consensus pattern (57 bp):
GTGACAAAATGCAACCATGCATGTGCAGGGTGAGGTGCACCTACCGGTGATGAATGC
Found at i:5417932 original size:2 final size:2
Alignment explanation
Indices: 5417922--5417952 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5417912 ACATATTTAC
*
5417922 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5417953 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5422425 original size:35 final size:36
Alignment explanation
Indices: 5422345--5422461 Score: 111
Period size: 33 Copynumber: 3.4 Consensus size: 36
5422335 TGGAAAAAAA
* * *
5422345 AAGAGCAGGCTTTTGCTGCC-ATTTTAAGGGG-AA-
1 AAGAGCTGGTTTTTGCTACCAATTTTAAGGGGAAAG
* *
5422378 AAGAGCTAGTTTTTGCTA-TAATTTTAAGGGGAAAG
1 AAGAGCTGGTTTTTGCTACCAATTTTAAGGGGAAAG
* *
5422413 AAGAGCTGG-TTTTGCTACCAATTTTAA-AGGAGAG
1 AAGAGCTGGTTTTTGCTACCAATTTTAAGGGGAAAG
*
5422447 AAAGAGCTGATTTTT
1 -AAGAGCTGGTTTTT
5422462 TAGGAAGAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
33 25 0.37
34 15 0.22
35 24 0.35
36 4 0.06
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (36 bp):
AAGAGCTGGTTTTTGCTACCAATTTTAAGGGGAAAG
Found at i:5422734 original size:17 final size:18
Alignment explanation
Indices: 5422714--5422750 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
5422704 AAGGAGGAAG
5422714 AAAAAAAAAGAAAAG-GA
1 AAAAAAAAAGAAAAGAGA
5422731 AAAAAAAAAGAAAAGAGA
1 AAAAAAAAAGAAAAGAGA
5422749 AA
1 AA
5422751 GAAATGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAGAGA
Found at i:5424862 original size:34 final size:29
Alignment explanation
Indices: 5424796--5424857 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
5424786 CTAGTCTAGA
*
5424796 CACACATAGCATAAGCCACCCATGTGCCT
1 CACACATAGCATAAGCCACCCAGGTGCCT
* *
5424825 CACACATAGCATAGGCCACCCAGGTGGCT
1 CACACATAGCATAAGCCACCCAGGTGCCT
5424854 CACA
1 CACA
5424858 TCACAGCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.37, G:0.18, T:0.15
Consensus pattern (29 bp):
CACACATAGCATAAGCCACCCAGGTGCCT
Found at i:5430256 original size:12 final size:12
Alignment explanation
Indices: 5430239--5430265 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5430229 GAATAATCAA
5430239 ATTAAATAAAAT
1 ATTAAATAAAAT
5430251 ATTAAATAAAAT
1 ATTAAATAAAAT
5430263 ATT
1 ATT
5430266 CCATTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:5431859 original size:25 final size:25
Alignment explanation
Indices: 5431812--5431859 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5431802 GTGATAACAA
*
5431812 AAATAATAAAAATAATAATAAGATG
1 AAATAATAAAAATAATAAAAAGATG
*
5431837 AAATAA-ATAAATAAGTAAAAAGA
1 AAATAATAAAAATAA-TAAAAAGA
5431860 AAGTATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (25 bp):
AAATAATAAAAATAATAAAAAGATG
Found at i:5434123 original size:25 final size:25
Alignment explanation
Indices: 5434069--5434131 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
5434059 TTTTCTTATA
*
5434069 AAATAATATTTATAGAGTTATAAGT
1 AAATAATATTTATAGAGTTAAAAGT
* * *
5434094 GAATAATTTTTATAGCG-TAAAAGCT
1 AAATAATATTTATAGAGTTAAAAG-T
5434119 AAATAA-ATTTATA
1 AAATAATATTTATA
5434132 CATACTGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (25 bp):
AAATAATATTTATAGAGTTAAAAGT
Found at i:5444111 original size:21 final size:21
Alignment explanation
Indices: 5444072--5444112 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5444062 AAGAATGATG
**
5444072 CCATCATTCAAAGTTAAGCAA
1 CCATCATTCAAAGGCAAGCAA
5444093 CCATCATTCAAAGGCAAGCA
1 CCATCATTCAAAGGCAAGCA
5444113 GAATCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (21 bp):
CCATCATTCAAAGGCAAGCAA
Found at i:5445567 original size:24 final size:25
Alignment explanation
Indices: 5445521--5445567 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5445511 TTTTTATTTT
*
5445521 ATTTCTTATTTATACTTCCTCATTA
1 ATTTCTTATTTATACATCCTCATTA
* *
5445546 ATTTCTT-TTTATTCATCTTCAT
1 ATTTCTTATTTATACATCCTCAT
5445568 AGAGTTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTCTTATTTATACATCCTCATTA
Found at i:5448306 original size:79 final size:73
Alignment explanation
Indices: 5448236--5448376 Score: 257
Period size: 73 Copynumber: 1.9 Consensus size: 73
5448226 CATGTAAGTG
*
5448236 ATTTATGATG-TATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
1 ATTTATGAAGTTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
5448300 CTAAGCAT
66 CTAAGCAT
*
5448308 ATTTATGAAGTTCTGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
1 ATTTATGAAGTTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
5448373 CTAA
66 CTAA
5448377 TGTCACAACC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 9 0.14
73 57 0.86
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (73 bp):
ATTTATGAAGTTATGAAATGTATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTATGGG
CTAAGCAT
Found at i:5449110 original size:2 final size:2
Alignment explanation
Indices: 5449103--5449145 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
5449093 ACTTCCCAAG
* *
5449103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5449145 A
1 A
5449146 ACACCACACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5451651 original size:36 final size:36
Alignment explanation
Indices: 5451603--5451741 Score: 145
Period size: 36 Copynumber: 3.6 Consensus size: 36
5451593 ATATTGCCTA
5451603 TGTGCGCGATGTGGGGGAGCACATGATGGCATTAGT
1 TGTGCGCGATGTGGGGGAGCACATGATGGCATTAGT
* * *
5451639 TGTGCGCAATGTGGGGAAGCACACAATGATGATG-ATATTGCCT
1 TGTGCGCGATGTGGGGGAG--CAC-ATGATG--GCAT-TAG--T
*
5451682 ATGTGCGTGATGTGGGGGAGCACATGATGGCATTAGT
1 -TGTGCGCGATGTGGGGGAGCACATGATGGCATTAGT
*
5451719 TGTGCACGATGTGGGGGAGCACA
1 TGTGCGCGATGTGGGGGAGCACA
5451742 CAAACATGAT
Statistics
Matches: 84, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
36 38 0.45
37 1 0.01
38 3 0.04
39 9 0.11
40 4 0.05
41 9 0.11
42 3 0.04
43 1 0.01
44 16 0.19
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.24
Consensus pattern (36 bp):
TGTGCGCGATGTGGGGGAGCACATGATGGCATTAGT
Found at i:5451678 original size:80 final size:80
Alignment explanation
Indices: 5451586--5451757 Score: 290
Period size: 80 Copynumber: 2.1 Consensus size: 80
5451576 TGGGAGTGTG
*
5451586 GATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCACATGATGGCATTAGTTGTGCGCAATGT
1 GATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCACATGATGGCATTAGTTGTGCACAATGT
*
5451651 GGGGAAGCACACAAT
66 GGGGAAGCACACAAA
* *
5451666 GATGATGATATTGCCTATGTGCGTGATGTGGGGGAGCACATGATGGCATTAGTTGTGCACGATGT
1 GATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCACATGATGGCATTAGTTGTGCACAATGT
*
5451731 GGGGGAGCACACAAA
66 GGGGAAGCACACAAA
*
5451746 CATGATGATATT
1 GATGATGATATT
5451758 ACATTGAGCT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 86 1.00
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (80 bp):
GATGATGATATTGCCTATGTGCGCGATGTGGGGGAGCACATGATGGCATTAGTTGTGCACAATGT
GGGGAAGCACACAAA
Found at i:5455892 original size:18 final size:16
Alignment explanation
Indices: 5455869--5455908 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
5455859 CATGGAGGGT
5455869 GAAGAAAACATGGAATG
1 GAAGAAAACATGG-ATG
*
5455886 GAGAGAAAAGATGGATG
1 GA-AGAAAACATGGATG
5455903 GAAGAA
1 GAAGAA
5455909 GAAGCTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 7 0.33
18 10 0.48
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.10
Consensus pattern (16 bp):
GAAGAAAACATGGATG
Found at i:5473688 original size:2 final size:2
Alignment explanation
Indices: 5473676--5473745 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
5473666 GCTTCCATAA
*
5473676 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
5473718 CT CT CT CT CT CT CT CT CT CT TT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5473746 AGCTTCAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:5474391 original size:37 final size:37
Alignment explanation
Indices: 5474342--5474451 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
5474332 TAATGTTGTG
5474342 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
* *
5474379 TGATGATGTTGAAGTGTGTGAGTCGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
* *
5474416 TGATGATGATAGAA-TGTGCGAGTATGGAGTGCACAC
1 TGATGATG-TTGAAGTGTGCGAGTAGGGAGTGCACAC
5474452 GACGATGAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 62 0.94
38 4 0.06
ACGTcount: A:0.27, C:0.11, G:0.36, T:0.25
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:5474734 original size:22 final size:22
Alignment explanation
Indices: 5474703--5474779 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 22
5474693 CCAGCCCTGT
*
5474703 TTCTCGCTGCAACGAAAAAGAA
1 TTCTCACTGCAACGAAAAAGAA
*
5474725 TTCTCACTGCAACG---AGGAA
1 TTCTCACTGCAACGAAAAAGAA
* * * *
5474744 TT-TCACTACAGCGAAAATGGA
1 TTCTCACTGCAACGAAAAAGAA
5474765 TTCTCACTGCAACGA
1 TTCTCACTGCAACGA
5474780 GAAACTCTCG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
21 5 0.12
22 23 0.53
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (22 bp):
TTCTCACTGCAACGAAAAAGAA
Found at i:5475786 original size:43 final size:43
Alignment explanation
Indices: 5475727--5475901 Score: 221
Period size: 43 Copynumber: 4.1 Consensus size: 43
5475717 ATAATGCGAT
* **
5475727 ATCATCA--TCATGTGCACTCCCTAC-TCGCACATAGCCAGGTC
1 ATCATCAGCTCATGTGCACTCCC-ACACCGCACATAGCTGGGTC
* * *
5475768 ATCATCAGCTCATGTGCACTCCCACACCACACATGGTTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
* * * * *
5475811 ATCATCAGTTTATGTGCACTTCCACACTGCACATGGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
5475854 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
5475897 ATCAT
1 ATCAT
5475902 TATCACACAA
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
41 7 0.06
42 2 0.02
43 105 0.92
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (43 bp):
ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
Found at i:5484534 original size:13 final size:13
Alignment explanation
Indices: 5484516--5484540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5484506 NNNNNNNNNG
5484516 ATTTTATAAAATA
1 ATTTTATAAAATA
5484529 ATTTTATAAAAT
1 ATTTTATAAAAT
5484541 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:5490493 original size:73 final size:73
Alignment explanation
Indices: 5490342--5490500 Score: 210
Period size: 73 Copynumber: 2.2 Consensus size: 73
5490332 AAGAAGGATG
* * *
5490342 GTTAGTCGACTAAGAGCCTCCTGCCAAAAATCTAGACTTCAAAACAAAAACAACTTAATCGACTA
1 GTTAGTCGACTAAAAGCCTACTACCAAAAATCTAGACTTCAAAACAAAAACAACTTAATCGACTA
*
5490407 AGAAGAAA
66 AAAAGAAA
* * * * * *
5490415 ATTAGTTGACTAAAAGCTTACTACCAGAAATCTGGACTTCAAAATAAAAACAACTTAATCGACTA
1 GTTAGTCGACTAAAAGCCTACTACCAAAAATCTAGACTTCAAAACAAAAACAACTTAATCGACTA
**
5490480 AAAAGGCA
66 AAAAGAAA
5490488 GTTAGTCGACTAA
1 GTTAGTCGACTAA
5490501 GTGCTCACTG
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (73 bp):
GTTAGTCGACTAAAAGCCTACTACCAAAAATCTAGACTTCAAAACAAAAACAACTTAATCGACTA
AAAAGAAA
Found at i:5491044 original size:11 final size:11
Alignment explanation
Indices: 5491030--5491063 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
5491020 AAGCCATTGT
5491030 AAAGCTTGGTG
1 AAAGCTTGGTG
5491041 AAAGCTTGGTG
1 AAAGCTTGGTG
5491052 AAAGCTT-GTG
1 AAAGCTTGGTG
5491062 AA
1 AA
5491064 TTTCACCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.26
Consensus pattern (11 bp):
AAAGCTTGGTG
Found at i:5491087 original size:17 final size:17
Alignment explanation
Indices: 5491065--5491100 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5491055 GCTTGTGAAT
5491065 TTCACCGTTCATAGTGA
1 TTCACCGTTCATAGTGA
5491082 TTCACCGTTCATAGTGA
1 TTCACCGTTCATAGTGA
5491099 TT
1 TT
5491101 GGTTTGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (17 bp):
TTCACCGTTCATAGTGA
Found at i:5502446 original size:69 final size:69
Alignment explanation
Indices: 5502335--5502493 Score: 300
Period size: 69 Copynumber: 2.3 Consensus size: 69
5502325 GAGCTATACA
* *
5502335 TTTGAATATGAATTTAATTGTCAAGTTTGATCATGGCATATATAGTGAGTTGACATAGTTGAAAT
1 TTTGAATATGCATTTAAATGTCAAGTTTGATCATGGCATATATAGTGAGTTGACATAGTTGAAAT
5502400 TTAT
66 TTAT
5502404 TTTGAATATGCATTTAAATGTCAAGTTTGATCATGGCATATATAGTGAGTTGACATAGTTGAAAT
1 TTTGAATATGCATTTAAATGTCAAGTTTGATCATGGCATATATAGTGAGTTGACATAGTTGAAAT
5502469 TTAT
66 TTAT
5502473 TTTGAATATGCATTTAAATGT
1 TTTGAATATGCATTTAAATGT
5502494 TAACTATGTT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 88 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (69 bp):
TTTGAATATGCATTTAAATGTCAAGTTTGATCATGGCATATATAGTGAGTTGACATAGTTGAAAT
TTAT
Found at i:5503133 original size:27 final size:28
Alignment explanation
Indices: 5503074--5503133 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
5503064 TCTTGCAATG
*
5503074 CTTGCTTCAAAATGACTTGGATGAATAA
1 CTTGCTTCAAAATGACTTGGAAGAATAA
* * *
5503102 C-TGCTTGAAATTGATTTGGAAGAAT-A
1 CTTGCTTCAAAATGACTTGGAAGAATAA
5503128 CTTGCT
1 CTTGCT
5503134 AAAAATGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.07
27 24 0.89
28 1 0.04
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (28 bp):
CTTGCTTCAAAATGACTTGGAAGAATAA
Found at i:5514732 original size:20 final size:21
Alignment explanation
Indices: 5514704--5514742 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5514694 ATATCATTCA
5514704 TATAAATACATATA-AATATT
1 TATAAATACATATATAATATT
*
5514724 TATATATACATATATAATA
1 TATAAATACATATATAATA
5514743 AGCCACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAAATACATATATAATATT
Found at i:5515057 original size:21 final size:23
Alignment explanation
Indices: 5515032--5515076 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5515022 AGAATTTTGG
* *
5515032 AAAAAT-TTTTAAGAATATATAT
1 AAAAATATTTAAAAAATATATAT
5515054 AAAAATATTTAAAAAATATATAT
1 AAAAATATTTAAAAAATATATAT
5515077 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAATATTTAAAAAATATATAT
Found at i:5516421 original size:17 final size:17
Alignment explanation
Indices: 5516391--5516423 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5516381 TTCTTGATAA
5516391 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
5516408 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
5516424 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:5516653 original size:28 final size:28
Alignment explanation
Indices: 5516584--5516647 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
5516574 AATTAAGACC
* *
5516584 AAAAAAAATAT-TTTATCTTGTCTAAATT
1 AAAACAAATATGTTT-TCTTATCTAAATT
* *
5516612 GAGACAAATATGTTTTCTTATCTAAATT
1 AAAACAAATATGTTTTCTTATCTAAATT
5516640 AAAACAAA
1 AAAACAAA
5516648 ACTGTTAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (28 bp):
AAAACAAATATGTTTTCTTATCTAAATT
Found at i:5524203 original size:73 final size:74
Alignment explanation
Indices: 5524018--5524261 Score: 252
Period size: 73 Copynumber: 3.3 Consensus size: 74
5524008 TTAGTTGACC
* * * ** * *
5524018 AAGAAGGATGGTTAGTTGACTAAGAGC-CTACTGCTAGAAATCTAAACTTTAAGACAGAAACAAC
1 AAGAAGGATAGTTAGTCGACTAAGAGCTC-ACTGCTAAAAATCTGGACTTCAAAACAGAAACAAC
5524082 TTAATCGACT
65 TTAATCGACT
* * * *
5524092 AAGAAGGA-AGTTAGTCGACTAAAAGCTTACTACCAAAAATCTGGACTTCAAAACAGAAACAACT
1 AAGAAGGATAGTTAGTCGACTAAGAGCTCACTGCTAAAAATCTGGACTTCAAAACAGAAACAACT
5524156 TAATCGACT
66 TAATCGACT
*
5524165 AAGAAGGA-AGTTAGTCGACTAAGTGCTCACTGCTAAAAA-CTGGGA--TCAGAAGACA-AAGAC
1 AAGAAGGATAGTTAGTCGACTAAGAGCTCACTGCTAAAAATCT-GGACTTCA-AA-ACAGAA-AC
*
5524225 AACTTAGTCGACT
62 AACTTAATCGACT
* *
5524238 AAG-AGCATAGTTAGTCCACTAAGA
1 AAGAAGGATAGTTAGTCGACTAAGA
5524262 TCATTCTATC
Statistics
Matches: 144, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
71 3 0.02
72 9 0.06
73 124 0.86
74 8 0.06
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (74 bp):
AAGAAGGATAGTTAGTCGACTAAGAGCTCACTGCTAAAAATCTGGACTTCAAAACAGAAACAACT
TAATCGACT
Found at i:5526427 original size:25 final size:25
Alignment explanation
Indices: 5526393--5526452 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
5526383 GTGTTCCCAA
5526393 CCACGTATATCAACT-TGTGGCCTAG
1 CCACGTATATCAACTCT-TGGCCTAG
* *
5526418 CCACATATATCAACTCTTGGCCTTG
1 CCACGTATATCAACTCTTGGCCTAG
5526443 CCACGTATAT
1 CCACGTATAT
5526453 ATCACAGACC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (25 bp):
CCACGTATATCAACTCTTGGCCTAG
Found at i:5526873 original size:2 final size:2
Alignment explanation
Indices: 5526861--5526898 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5526851 AATTCTTTAC
*
5526861 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5526899 TCTACACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5528539 original size:84 final size:85
Alignment explanation
Indices: 5528435--5528614 Score: 249
Period size: 84 Copynumber: 2.1 Consensus size: 85
5528425 TCTTTCGTAT
*
5528435 GTTGATG-TGGACCCGACTATGTG-TGAGTAGAAGTGCGCATAAGCCGATGATGACCCAGCTATG
1 GTTGATGAT-GACCCGACTATGTGCT-AGTAGAAGTGCGCATAAGCCGATGATGACCCAGCCATG
* *
5528498 TGCGAGT-AGGAGTGCGCCTAA
64 TGCGAGTGAGGAGTGCACATAA
* *
5528519 GTTGATGATGACCCGGCTATGTGCTAGTAGAAGTGCGCATAAGCCGATGCTGACCCAGCCATGTG
1 GTTGATGATGACCCGACTATGTGCTAGTAGAAGTGCGCATAAGCCGATGATGACCCAGCCATGTG
* *
5528584 CTAGTGGGGAGTGCACATAA
66 CGAGTGAGGAGTGCACATAA
*
5528604 GCTGATGATGA
1 GTTGATGATGA
5528615 TGGGAGACTG
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
84 62 0.73
85 23 0.27
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (85 bp):
GTTGATGATGACCCGACTATGTGCTAGTAGAAGTGCGCATAAGCCGATGATGACCCAGCCATGTG
CGAGTGAGGAGTGCACATAA
Found at i:5528583 original size:42 final size:42
Alignment explanation
Indices: 5528451--5528614 Score: 195
Period size: 42 Copynumber: 3.9 Consensus size: 42
5528441 GTGGACCCGA
5528451 CTATGTG-TGAGTAGAAGTGCGCATAAGCCGATGATGACCCAG
1 CTATGTGCT-AGTAGAAGTGCGCATAAGCCGATGATGACCCAG
* * * ** *
5528493 CTATGTGCGAGTAGGAGTGCGCCTAAGTTGATGATGACCCGG
1 CTATGTGCTAGTAGAAGTGCGCATAAGCCGATGATGACCCAG
*
5528535 CTATGTGCTAGTAGAAGTGCGCATAAGCCGATGCTGACCCAG
1 CTATGTGCTAGTAGAAGTGCGCATAAGCCGATGATGACCCAG
* * * * *
5528577 CCATGTGCTAGTGGGGAGTGCACATAAGCTGATGATGA
1 CTATGTGCTAGT-AGAAGTGCGCATAAGCCGATGATGA
5528615 TGGGAGACTG
Statistics
Matches: 101, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
42 81 0.80
43 20 0.20
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (42 bp):
CTATGTGCTAGTAGAAGTGCGCATAAGCCGATGATGACCCAG
Found at i:5529105 original size:19 final size:19
Alignment explanation
Indices: 5529081--5529117 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5529071 AGGGGTTTGG
5529081 TAAGAAACCCTCGACCAGC
1 TAAGAAACCCTCGACCAGC
*
5529100 TAAGAAACCCTCGGCCAG
1 TAAGAAACCCTCGACCAG
5529118 TTGATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.11
Consensus pattern (19 bp):
TAAGAAACCCTCGACCAGC
Found at i:5535332 original size:19 final size:19
Alignment explanation
Indices: 5535308--5535406 Score: 65
Period size: 19 Copynumber: 5.1 Consensus size: 19
5535298 TGCTCGTGTG
5535308 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
***** *
5535327 CACGATG-GCACTAATTGTG
1 CACGATGTGGGGGGA-TGTA
*
5535346 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* ** *
5535365 CACGATGGTGCTGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
5535386 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
5535405 CA
1 CA
5535407 TGAGCCGAGT
Statistics
Matches: 54, Mismatches: 22, Indels: 8
0.64 0.26 0.10
Matches are distributed among these distances:
18 2 0.04
19 33 0.61
20 8 0.15
21 11 0.20
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:5535355 original size:38 final size:40
Alignment explanation
Indices: 5535304--5535406 Score: 147
Period size: 38 Copynumber: 2.6 Consensus size: 40
5535294 ATAGTGCTCG
5535304 TGTGCACGATGTGGGGGGATGTACACGATGGCACT-AAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAATA
* ** **
5535342 TGTGCACGATGTGGGGGGATGCACACGATGGTGCTGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAATA
5535382 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
5535407 TGAGCCGAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 32 0.56
39 1 0.02
40 24 0.42
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAATA
Found at i:5535671 original size:21 final size:21
Alignment explanation
Indices: 5535632--5535671 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5535622 TCTGTTTTCG
**
5535632 CTGTAGCGAAATTCATTCTCA
1 CTGTAGCGAAAAACATTCTCA
*
5535653 CTGTAGCGAAAAACTTTCT
1 CTGTAGCGAAAAACATTCT
5535672 GTTTTGTCTC
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:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (21 bp):
CTGTAGCGAAAAACATTCTCA
Found at i:5543360 original size:19 final size:19
Alignment explanation
Indices: 5543336--5543434 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
5543326 TGCCCGTGTG
5543336 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
5543355 CACGATG-GCATTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
5543374 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* ** *
5543393 CACGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
5543414 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
5543433 CA
1 CA
5543435 TGAGTCGGGT
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
18 3 0.05
19 33 0.59
20 9 0.16
21 11 0.20
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:5543383 original size:38 final size:40
Alignment explanation
Indices: 5543332--5543434 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 40
5543322 ATAGTGCCCG
**
5543332 TGTGCACGATGTGGGGGGATGTACACGAT-G-GCATTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGGATA
* *
5543370 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
5543410 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
5543435 TGAGTCGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.49
39 3 0.05
40 26 0.46
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
Found at i:5543699 original size:21 final size:21
Alignment explanation
Indices: 5543657--5543699 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5543647 TGCTCTGTTT
**
5543657 TCGCTGCAGCGAAATTCATTC
1 TCGCTGCAGCGAAAAACATTC
*
5543678 TCGCTGCAGCGAAAAACTTTC
1 TCGCTGCAGCGAAAAACATTC
5543699 T
1 T
5543700 ATTTTGTCTC
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:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (21 bp):
TCGCTGCAGCGAAAAACATTC
Found at i:5545213 original size:2 final size:2
Alignment explanation
Indices: 5545204--5545248 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
5545194 ATTGCTTAAG
5545204 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5545245 AT AT
1 AT AT
5545249 CTTAACAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5546192 original size:38 final size:38
Alignment explanation
Indices: 5546149--5546238 Score: 144
Period size: 38 Copynumber: 2.4 Consensus size: 38
5546139 CGCACAAGGA
*
5546149 AATATCATCATCATGTGCTCTCCTTACTCACACATTTC
1 AATATCATCATCATGTGCTCTCCCTACTCACACATTTC
* **
5546187 CATATCATCATCATGTGCTCTCCCTACTTGCACATTTC
1 AATATCATCATCATGTGCTCTCCCTACTCACACATTTC
5546225 AATATCATCATCAT
1 AATATCATCATCAT
5546239 CATCATCATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.27, C:0.31, G:0.06, T:0.37
Consensus pattern (38 bp):
AATATCATCATCATGTGCTCTCCCTACTCACACATTTC
Found at i:5549964 original size:43 final size:43
Alignment explanation
Indices: 5549855--5549979 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
5549845 TCATTCATCA
* * * * * *
5549855 TCATGTGCACTCTCTACTCACACATAGCCAGGTCATCATCGGC
1 TCATGCGCACTCCCTAGTCGCACATAGCCGGGTCATCATCAGC
*
5549898 TTATGCGCACTCCCTAGTCGCACATAGCCGGGTCATCATCAGC
1 TCATGCGCACTCCCTAGTCGCACATAGCCGGGTCATCATCAGC
* * * *
5549941 TCATGTGCACTCCCATA-TTGCACACAGCTGGGTCATCAT
1 TCATGCGCACTCCC-TAGTCGCACATAGCCGGGTCATCAT
5549980 TATCACACAA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
43 67 0.97
44 2 0.03
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (43 bp):
TCATGCGCACTCCCTAGTCGCACATAGCCGGGTCATCATCAGC
Found at i:5555675 original size:42 final size:42
Alignment explanation
Indices: 5555616--5555699 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
5555606 GTATTGATAT
*
5555616 TGACCCGGCTATGTGCGAGTGGGAGTGCATATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
*
5555658 TGACCCTGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
5555700 ATATGAGATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.24
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
Found at i:5555747 original size:2 final size:2
Alignment explanation
Indices: 5555740--5555856 Score: 117
Period size: 2 Copynumber: 58.0 Consensus size: 2
5555730 ATGATAAGTG
5555740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** ** ** ** **
5555782 AT AT AT AT AT AT ANN NN NN NN NN NN AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5555825 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5555857 GGTATATGGT
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5568810 original size:40 final size:38
Alignment explanation
Indices: 5568766--5568868 Score: 120
Period size: 38 Copynumber: 2.7 Consensus size: 38
5568756 CCCCAGCTCA
*
5568766 TGTGCATCCCCCCACATCGTGCACATAGCTGGA-G-TCATCG
1 TGTGCATCCCCCCACATCGTGCACAT--CT-AATGCT-ATCG
* *
5568806 TGTGCATCCCCGCACATCGTGCACATCTAATGCTGTCG
1 TGTGCATCCCCCCACATCGTGCACATCTAATGCTATCG
*
5568844 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
5568869 CACACGATTA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
37 1 0.02
38 29 0.52
39 1 0.02
40 25 0.45
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.23
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACATCTAATGCTATCG
Found at i:5570842 original size:79 final size:79
Alignment explanation
Indices: 5570689--5570976 Score: 305
Period size: 79 Copynumber: 3.6 Consensus size: 79
5570679 TTGTAACATG
* * *
5570689 TATGCCACGAGATGTATGTGTT-AATTATA-TCATGTACATTATGGGCTAAGCATGTAAGTGATT
1 TATGCCATGAGATGTATGTGTTGAA--ATAGTCATATACACTATGGGCTAAGCATGTAAGTGATT
*
5570752 TATGATGTTATGAAATA
64 TAT-AAGTTATGAAATA
* *
5570769 TATGCCATGAGATGTATGTGCTGAAATAGTCATATATACTATGGG-TAAGCATGTAAGTGATTTA
1 TATGCCATGAGATGTATGTGTTGAAATAGTCATATACACTATGGGCTAAGCATGTAAGTGATTTA
* *
5570833 TTAGATTATGAAATG
66 TAAG-TTATGAAATA
** * ** * * * * *
5570848 TACACCATGAGATGCACATGTTGAGATAGTCATGTACACAATGGGCTAAGCATGGATGTGATTTA
1 TATGCCATGAGATGTATGTGTTGAAATAGTCATATACACTATGGGCTAAGCATGTAAGTGATTTA
5570913 TAAGGTTATGAAATA
66 TAA-GTTATGAAATA
* * * *
5570928 TATGCCATG-GATATATGTGTTGAGATAGTCATATAAACTGTGGGCTAAG
1 TATGCCATGAGATGTATGTGTTGAAATAGTCATATACACTATGGGCTAAG
5570977 TATGACGATA
Statistics
Matches: 171, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
78 1 0.01
79 99 0.58
80 68 0.40
81 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (79 bp):
TATGCCATGAGATGTATGTGTTGAAATAGTCATATACACTATGGGCTAAGCATGTAAGTGATTTA
TAAGTTATGAAATA
Found at i:5574056 original size:25 final size:25
Alignment explanation
Indices: 5574022--5574073 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
5574012 TACTAAAAGG
5574022 TAAGGAAAGAAAACTCCTCTGGTTT
1 TAAGGAAAGAAAACTCCTCTGGTTT
5574047 TAAGGAAAGAAAACTCCTCTGGTTT
1 TAAGGAAAGAAAACTCCTCTGGTTT
5574072 TA
1 TA
5574074 CTCTTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (25 bp):
TAAGGAAAGAAAACTCCTCTGGTTT
Found at i:5598812 original size:19 final size:20
Alignment explanation
Indices: 5598783--5598822 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
5598773 TCACTTCTAA
5598783 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
5598803 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
5598822 A
1 A
5598823 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:5608316 original size:21 final size:22
Alignment explanation
Indices: 5608287--5608327 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5608277 TTGGTGCTTT
5608287 ATTTGTCGCTGCAACGAGAATC
1 ATTTGTCGCTGCAACGAGAATC
*
5608309 ATTT-TCGCTGCAGCGAGAA
1 ATTTGTCGCTGCAACGAGAA
5608328 ACTCTTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (22 bp):
ATTTGTCGCTGCAACGAGAATC
Found at i:5610069 original size:44 final size:43
Alignment explanation
Indices: 5609928--5610069 Score: 140
Period size: 44 Copynumber: 3.4 Consensus size: 43
5609918 TGGAATTAGT
*
5609928 TGTGCACGATGTGGGAGTGCACACGATGATGATGATATATGCAA
1 TGTGCACGATGTGGGGGTGCACACGATGATGATGATATATGC-A
* *
5609972 TGTGCACGATGT-GGGG-GAAGCAC-ATGATG--GCAT-TA-G-T
1 TGTGCACGATGTGGGGGTGCA-CACGATGATGATG-ATATATGCA
5610009 TGTGCGA-GATGTGGGGGTGCACACGATGATGATGATATATGCCA
1 TGTGC-ACGATGTGGGGGTGCACACGATGATGATGATATATG-CA
*
5610053 TGTGCACAATGTGGGGG
1 TGTGCACGATGTGGGGG
5610070 GGAGCACATG
Statistics
Matches: 79, Mismatches: 6, Indels: 26
0.71 0.05 0.23
Matches are distributed among these distances:
37 10 0.13
38 8 0.10
39 9 0.11
40 5 0.06
41 5 0.06
42 9 0.11
43 7 0.09
44 26 0.33
ACGTcount: A:0.25, C:0.13, G:0.37, T:0.25
Consensus pattern (43 bp):
TGTGCACGATGTGGGGGTGCACACGATGATGATGATATATGCA
Found at i:5610110 original size:82 final size:81
Alignment explanation
Indices: 5609874--5610119 Score: 393
Period size: 81 Copynumber: 3.0 Consensus size: 81
5609864 AGGGAGTGTG
** * *
5609874 GATGATGATATATGCCATGTGCGGGATGTGGGGGGAGCACATGATGGAATTAGTTGTGCACGATG
1 GATGATGATATATGCCATGTGCACGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCGCGATG
*
5609939 TGGGAGTGCACACGAT
66 TGGGGGTGCACACGAT
* * *
5609955 GATGATGATATATGCAATGTGCACGATGTGGGGGAAGCACATGATGGCATTAGTTGTGCGAGATG
1 GATGATGATATATGCCATGTGCACGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCGCGATG
5610020 TGGGGGTGCACACGAT
66 TGGGGGTGCACACGAT
*
5610036 GATGATGATATATGCCATGTGCACAATGTGGGGGGGAGCACATGATGGCATTAGTTGTGCGCGAT
1 GATGATGATATATGCCATGTGCACGATGT-GGGGGGAGCACATGATGGCATTAGTTGTGCGCGAT
*
5610101 GTGGGGGTGCACATGAT
65 GTGGGGGTGCACACGAT
5610118 GA
1 GA
5610120 CCCCGGCTAT
Statistics
Matches: 151, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
81 100 0.66
82 51 0.34
ACGTcount: A:0.25, C:0.13, G:0.38, T:0.25
Consensus pattern (81 bp):
GATGATGATATATGCCATGTGCACGATGTGGGGGGAGCACATGATGGCATTAGTTGTGCGCGATG
TGGGGGTGCACACGAT
Found at i:5616138 original size:39 final size:39
Alignment explanation
Indices: 5616095--5616217 Score: 94
Period size: 39 Copynumber: 3.2 Consensus size: 39
5616085 GGAAGTGTGG
*
5616095 ATGATGATATATGCCATGTGCGGGATATGGGGGGAGCAC
1 ATGATGATATATGCCATGTGCGCGATATGGGGGGAGCAC
* * * * *
5616134 ATGATGGCAT-TA-G--TTGTGCCCAATCTAGGGGTGCA-CAC
1 ATGAT-G-ATATATGCCATGTGCGCGATAT-GGGG-GGAGCAC
* *
5616172 GATGATGATATATGCCATGTGCGTGATGTGGGGGGAGCAC
1 -ATGATGATATATGCCATGTGCGCGATATGGGGGGAGCAC
5616212 ATGATG
1 ATGATG
5616218 GCATTAGTTG
Statistics
Matches: 62, Mismatches: 12, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
37 10 0.16
38 10 0.16
39 22 0.35
40 10 0.16
41 10 0.16
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.25
Consensus pattern (39 bp):
ATGATGATATATGCCATGTGCGCGATATGGGGGGAGCAC
Found at i:5616231 original size:37 final size:37
Alignment explanation
Indices: 5616111--5616242 Score: 108
Period size: 37 Copynumber: 3.5 Consensus size: 37
5616101 ATATATGCCA
* *
5616111 TGTGCGGGATATGGGGGGAGCACATGATGGCATTAGT
1 TGTGCGTGATGTGGGGGGAGCACATGATGGCATTAGT
*** * * *
5616148 TGTGCCCAATCTAGGGGTGCA-CACGATGAT-G-ATATATGCCA
1 TGTGCGTGATGT-GGGG-GGAGCAC-ATGATGGCAT-TA-G--T
5616189 TGTGCGTGATGTGGGGGGAGCACATGATGGCATTAGT
1 TGTGCGTGATGTGGGGGGAGCACATGATGGCATTAGT
5616226 TGTGCGTGATGTGGGGG
1 TGTGCGTGATGTGGGGG
5616243 TGCACACAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
37 27 0.37
38 10 0.14
39 16 0.22
40 10 0.14
41 10 0.14
ACGTcount: A:0.20, C:0.14, G:0.40, T:0.26
Consensus pattern (37 bp):
TGTGCGTGATGTGGGGGGAGCACATGATGGCATTAGT
Found at i:5616428 original size:19 final size:21
Alignment explanation
Indices: 5616404--5616443 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5616394 ATTGAGAGAA
*
5616404 CTTGA-TTATTGT-CAATGTG
1 CTTGATTTAATGTACAATGTG
5616423 CTTGATTTAATGTACAATGTG
1 CTTGATTTAATGTACAATGTG
5616444 ACATGAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (21 bp):
CTTGATTTAATGTACAATGTG
Found at i:5619279 original size:17 final size:17
Alignment explanation
Indices: 5619259--5619296 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5619249 AATGGAGGAT
5619259 TGCTCCCCCTAAGTGTG
1 TGCTCCCCCTAAGTGTG
* *
5619276 TGCTCCCCTTTAGTGTG
1 TGCTCCCCCTAAGTGTG
5619293 TGCT
1 TGCT
5619297 TATTTTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.08, C:0.32, G:0.24, T:0.37
Consensus pattern (17 bp):
TGCTCCCCCTAAGTGTG
Found at i:5621066 original size:41 final size:41
Alignment explanation
Indices: 5621021--5621121 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
5621011 ATCGTGTGCT
*
5621021 TCCCCCCACATCGTGCACAAGCAATATCATTGC-TT-TATGCA
1 TCCCCCCACATCATGCACAAGCAATATCA-T-CATTGTATGCA
* *
5621062 TCCCCCCACATCATGCACAAGCGATATCATCATTGTGTGCA
1 TCCCCCCACATCATGCACAAGCAATATCATCATTGTATGCA
*
5621103 TCCCCCCTCATCATGCACA
1 TCCCCCCACATCATGCACA
5621122 GCCAATGCCA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
39 1 0.02
40 3 0.06
41 50 0.93
ACGTcount: A:0.26, C:0.38, G:0.12, T:0.25
Consensus pattern (41 bp):
TCCCCCCACATCATGCACAAGCAATATCATCATTGTATGCA
Found at i:5621909 original size:22 final size:22
Alignment explanation
Indices: 5621871--5621914 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5621861 ATTTCCATCA
5621871 AACACTTTCTAAGTTTACATGT
1 AACACTTTCTAAGTTTACATGT
*
5621893 AACACTATTCTCA-TTTACATGT
1 AACACT-TTCTAAGTTTACATGT
5621915 TACCACCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (22 bp):
AACACTTTCTAAGTTTACATGT
Found at i:5632279 original size:22 final size:22
Alignment explanation
Indices: 5632241--5632284 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5632231 ACTTTCATCA
5632241 AACACTTTCTAAGTTTACATGT
1 AACACTTTCTAAGTTTACATGT
*
5632263 AACACTATTCTCA-TTTACATGT
1 AACACT-TTCTAAGTTTACATGT
5632285 TGCCACCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (22 bp):
AACACTTTCTAAGTTTACATGT
Found at i:5641043 original size:25 final size:26
Alignment explanation
Indices: 5641015--5641071 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
5641005 ATGGGCTCTT
5641015 CCCATTTC-TTTCTAATTGGGCCATG
1 CCCATTTCTTTTCTAATTGGGCCATG
* *
5641040 CCCA-TTCTTTTCTTATTGGGTCATG
1 CCCATTTCTTTTCTAATTGGGCCATG
*
5641065 TCCATTT
1 CCCATTT
5641072 ATATGCATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 22 0.81
26 2 0.07
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46
Consensus pattern (26 bp):
CCCATTTCTTTTCTAATTGGGCCATG
Found at i:5641420 original size:33 final size:33
Alignment explanation
Indices: 5641383--5641467 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
5641373 CATATCCACA
5641383 TCAAAATCAGCAGCCAAGCTGCTCTATT-TCTCC
1 TCAAAATCAGCAGCCAAGCTGCTCTATTCTC-CC
* * * *
5641416 TCAAAATTAGTAGCTAAGCTGCTGTATTCTCCC
1 TCAAAATCAGCAGCCAAGCTGCTCTATTCTCCC
*
5641449 TCTAAAAATCAACAGCCAA
1 TC--AAAATCAGCAGCCAA
5641468 AGCTACAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 28 0.68
34 2 0.05
35 11 0.27
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (33 bp):
TCAAAATCAGCAGCCAAGCTGCTCTATTCTCCC
Found at i:5641514 original size:35 final size:34
Alignment explanation
Indices: 5641483--5641587 Score: 138
Period size: 35 Copynumber: 3.0 Consensus size: 34
5641473 CAAAAATTAA
* * *
5641483 CAACTAAAATAGCACCTTTCAACTTTCAAAATCAG
1 CAACCAAAAT-GCACCTTTCAGCCTTCAAAATCAG
* *
5641518 TAACCAACACTGCACCTTTCAGCCTTCAAAATCAG
1 CAACCAA-AATGCACCTTTCAGCCTTCAAAATCAG
5641553 CAACCAAAACTGCACCTTTCAGCCTTCAAAATCAG
1 CAACCAAAA-TGCACCTTTCAGCCTTCAAAATCAG
5641588 TAATTAAAGC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
34 1 0.02
35 58 0.95
36 2 0.03
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (34 bp):
CAACCAAAATGCACCTTTCAGCCTTCAAAATCAG
Found at i:5642412 original size:11 final size:11
Alignment explanation
Indices: 5642392--5642421 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5642382 TTTGGTTAAA
5642392 TATTAATATTT
1 TATTAATATTT
*
5642403 TATTATTATTT
1 TATTAATATTT
5642414 TATTAATA
1 TATTAATA
5642422 AAGTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTAATATTT
Found at i:5658131 original size:19 final size:18
Alignment explanation
Indices: 5658096--5658135 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5658086 CAGACGGAGA
5658096 ATTTTATAATAAGATAAT
1 ATTTTATAATAAGATAAT
5658114 ATTTTATTAATACA-ATAAT
1 ATTTTA-TAATA-AGATAAT
5658133 ATT
1 ATT
5658136 AATATAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 13 0.65
20 1 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTTATAATAAGATAAT
Found at i:5658376 original size:14 final size:14
Alignment explanation
Indices: 5658357--5658386 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5658347 AAGATTAGCT
5658357 TATGCATGTGACAA
1 TATGCATGTGACAA
5658371 TATGCATGTGACAA
1 TATGCATGTGACAA
5658385 TA
1 TA
5658387 CTATTACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (14 bp):
TATGCATGTGACAA
Found at i:5674569 original size:28 final size:28
Alignment explanation
Indices: 5674498--5674576 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
5674488 AATGCAGTGC
* * *
5674498 CTTTTAAAGGTTTAAGCATAACCATTGC
1 CTTTTCAAGGTTCAAGCATAACCATTGA
** *
5674526 CTTTTCAAGGACCAAGCATAATCATT-A
1 CTTTTCAAGGTTCAAGCATAACCATTGA
*
5674553 CTATTTCAAGGTTCAAGCACAACC
1 CT-TTTCAAGGTTCAAGCATAACC
5674577 TTTAAATACT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 2 0.05
28 38 0.95
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (28 bp):
CTTTTCAAGGTTCAAGCATAACCATTGA
Found at i:5675028 original size:20 final size:20
Alignment explanation
Indices: 5674991--5675042 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
5674981 AAATGTGTAG
*
5674991 ATACATTTCTGAAATGTATCC-
1 ATACATTT-TGGAATGTA-CCT
5675012 ATACATTTTGGAATGTACCT
1 ATACATTTTGGAATGTACCT
5675032 ATACATTTTGG
1 ATACATTTTGG
5675043 CCAGAACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 19 0.66
21 8 0.28
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATACATTTTGGAATGTACCT
Found at i:5675210 original size:21 final size:22
Alignment explanation
Indices: 5675186--5675231 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
5675176 AGGGAGTTTT
*
5675186 AAAACTAATTTAAACAAGTT-GA
1 AAAACT-ATTCAAACAAGTTCGA
5675208 AAAACTATTCAAACAAGTTCGA
1 AAAACTATTCAAACAAGTTCGA
5675230 AA
1 AA
5675232 TCATTCAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (22 bp):
AAAACTATTCAAACAAGTTCGA
Found at i:5675259 original size:21 final size:21
Alignment explanation
Indices: 5675233--5675273 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5675223 AGTTCGAAAT
*
5675233 CATTCAAGTAATTTCAAAACC
1 CATTCAAGCAATTTCAAAACC
*
5675254 CATTCAAGCAATTTTAAAAC
1 CATTCAAGCAATTTCAAAAC
5675274 TTTTCACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (21 bp):
CATTCAAGCAATTTCAAAACC
Found at i:5675379 original size:11 final size:11
Alignment explanation
Indices: 5675341--5675399 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 11
5675331 TTCACACCAG
5675341 TTCAAAAACTCA
1 TTCAAAAA-TCA
* *
5675353 TTCAAATAGC-
1 TTCAAAAATCA
5675363 TTCAAAAATCA
1 TTCAAAAATCA
5675374 TTCAAACAA--A
1 TTCAAA-AATCA
*
5675384 TTCAAAGATCA
1 TTCAAAAATCA
5675395 TTCAA
1 TTCAA
5675400 GTAATTTTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
9 1 0.03
10 15 0.39
11 13 0.34
12 9 0.24
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.27
Consensus pattern (11 bp):
TTCAAAAATCA
Found at i:5675387 original size:21 final size:21
Alignment explanation
Indices: 5675341--5675399 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
5675331 TTCACACCAG
* **
5675341 TTCAAAAACTCATTCAAATAGC
1 TTCAAAAA-TCATTCAAACAAA
5675363 TTCAAAAATCATTCAAACAAA
1 TTCAAAAATCATTCAAACAAA
*
5675384 TTCAAAGATCATTCAA
1 TTCAAAAATCATTCAA
5675400 GTAATTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 25 0.76
22 8 0.24
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.27
Consensus pattern (21 bp):
TTCAAAAATCATTCAAACAAA
Found at i:5675537 original size:21 final size:21
Alignment explanation
Indices: 5675479--5675553 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
5675469 ATTAATAAAT
*
5675479 CAAGTTCAAAAAACATATTCAAA
1 CAAGTTCAAAAATC--ATTCAAA
*
5675502 CAACTTCAAAAATCATTCAAA
1 CAAGTTCAAAAATCATTCAAA
**
5675523 CAAGTTCAAGGATCACTT-AAA
1 CAAGTTCAAAAATCA-TTCAAA
*
5675544 CAAGCTCAAA
1 CAAGTTCAAA
5675554 GATTATTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 30 0.68
22 2 0.05
23 12 0.27
ACGTcount: A:0.51, C:0.21, G:0.07, T:0.21
Consensus pattern (21 bp):
CAAGTTCAAAAATCATTCAAA
Found at i:5678213 original size:13 final size:13
Alignment explanation
Indices: 5678195--5678219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5678185 GGAAAATGGG
5678195 ATTTTATAAAATA
1 ATTTTATAAAATA
5678208 ATTTTATAAAAT
1 ATTTTATAAAAT
5678220 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:5681773 original size:28 final size:30
Alignment explanation
Indices: 5681732--5681795 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
5681722 GCATTTTGGC
*
5681732 AATTTTTTAATTTT-T-GGGGCACAAA-TGT
1 AATTTTTCAATTTTATAGGGGCA-AAAGTGT
*
5681760 AATTTTTCACTTTTATAGGGGCAAAAGTGT
1 AATTTTTCAATTTTATAGGGGCAAAAGTGT
5681790 AATTTT
1 AATTTT
5681796 CAAAAATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 12 0.39
29 4 0.13
30 15 0.48
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (30 bp):
AATTTTTCAATTTTATAGGGGCAAAAGTGT
Found at i:5682968 original size:13 final size:13
Alignment explanation
Indices: 5682950--5682974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5682940 GGAAAATGGG
5682950 ATTTTATAAAATA
1 ATTTTATAAAATA
5682963 ATTTTATAAAAT
1 ATTTTATAAAAT
5682975 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:5690996 original size:7 final size:7
Alignment explanation
Indices: 5690973--5691038 Score: 71
Period size: 7 Copynumber: 9.4 Consensus size: 7
5690963 AAGTTTTTTT
5690973 TTTCTTC
1 TTTCTTC
* *
5690980 TTTATCC
1 TTTCTTC
5690987 TTTCTTC
1 TTTCTTC
5690994 TTTCTTC
1 TTTCTTC
*
5691001 TTTCTCC
1 TTTCTTC
5691008 TTTCTTC
1 TTTCTTC
5691015 TTTC-TC
1 TTTCTTC
5691021 TTTTCTTC
1 -TTTCTTC
* *
5691029 CTTCCTC
1 TTTCTTC
5691036 TTT
1 TTT
5691039 TTGCTTCCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
6 2 0.04
7 44 0.92
8 2 0.04
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTCTTC
Found at i:5690999 original size:21 final size:21
Alignment explanation
Indices: 5690973--5691023 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
5690963 AAGTTTTTTT
5690973 TTTCTTCTTTATCCTTTCTTC
1 TTTCTTCTTTATCCTTTCTTC
*
5690994 TTTCTTCTTTCTCCTTTCTTC
1 TTTCTTCTTTATCCTTTCTTC
5691015 TTTC-TCTTT
1 TTTCTTCTTT
5691024 TCTTCCTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCTTCTTTATCCTTTCTTC
Found at i:5691025 original size:21 final size:22
Alignment explanation
Indices: 5690973--5691031 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
5690963 AAGTTTTTTT
*
5690973 TTTCTTCTTT-ATCCTTTCTTC
1 TTTCTTCTTTCTTCCTTTCTTC
5690994 TTTCTTCTTTC-TCCTTTCTTC
1 TTTCTTCTTTCTTCCTTTCTTC
5691015 TTTC-TCTTTTCTTCCTT
1 TTTCTTC-TTTCTTCCTT
5691032 CCTCTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.06
21 28 0.80
22 5 0.14
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTCTTCTTTCTTCCTTTCTTC
Found at i:5693142 original size:18 final size:18
Alignment explanation
Indices: 5693113--5693152 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
5693103 TTTCAATTAT
*
5693113 TAAAACCTAAAATTAAATC
1 TAAAACCTAAAAAT-AATC
5693132 TAAAA-CTAAAAATAATC
1 TAAAACCTAAAAATAATC
5693149 TAAA
1 TAAA
5693153 TTTAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAACCTAAAAATAATC
Found at i:5696223 original size:22 final size:21
Alignment explanation
Indices: 5696179--5696230 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
5696169 AACATAAAGT
* * *
5696179 TTCTCGCTACAGCGAAATTCA
1 TTCTCGCTGCAACGAAATGCA
5696200 TTCTCGCTGCAACGAAAATGCA
1 TTCTCGCTGCAACG-AAATGCA
5696222 TTCTCGCTG
1 TTCTCGCTG
5696231 TAGCAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
TTCTCGCTGCAACGAAATGCA
Found at i:5703403 original size:2 final size:2
Alignment explanation
Indices: 5703396--5703420 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5703386 TGGACGTTCT
5703396 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5703421 CTTTTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5703512 original size:2 final size:2
Alignment explanation
Indices: 5703505--5703529 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5703495 GGTACGGTCT
5703505 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5703530 CTTTTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5703564 original size:109 final size:106
Alignment explanation
Indices: 5703375--5703584 Score: 384
Period size: 109 Copynumber: 2.0 Consensus size: 106
5703365 TTATTACAAT
*
5703375 CTCTCACTAGTTGGACGTTCTAGAGAGAGAGAGAGAGAGAGAGAGACTTTTCACATTTGTTTGGA
1 CTCTCACTAGTTGGACGGTCTAGAGAGAGAGAGAGAGAGAGAGAGACTTTTCACATTTGTTTGGA
5703440 AGCTATTGGAAGAGAATTCAGCTACAAAGAAACCCTNTAATA
66 AGCTATTGGAAGAGAATTCAGCTACAAAGAAACCCT-TAATA
5703482 CTCTCACTAGTTAGGTACGGTCTAGAGAGAGAGAGAGAGAGAGAGAGACTTTTCACATTTGTTTG
1 CTCTCACTAGTT-GG-ACGGTCTAGAGAGAGAGAGAGAGAGAGAGAGACTTTTCACATTTGTTTG
5703547 GAAGCTATTGGAAGAGAATTCAGCTACAAAGAAACCCT
64 GAAGCTATTGGAAGAGAATTCAGCTACAAAGAAACCCT
5703585 AAGGTGAGTG
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
107 12 0.12
108 2 0.02
109 86 0.86
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (106 bp):
CTCTCACTAGTTGGACGGTCTAGAGAGAGAGAGAGAGAGAGAGAGACTTTTCACATTTGTTTGGA
AGCTATTGGAAGAGAATTCAGCTACAAAGAAACCCTTAATA
Found at i:5704495 original size:22 final size:22
Alignment explanation
Indices: 5704446--5704496 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5704436 CTCGCTGTAG
*
5704446 CGAGAAAGCATACTCGCTACAG
1 CGAGAAAGCATACTCGCTACAA
* *
5704468 CAAGAAAGCATACTCGCTGCAA
1 CGAGAAAGCATACTCGCTACAA
*
5704490 TGAGAAA
1 CGAGAAA
5704497 CATTCTGTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (22 bp):
CGAGAAAGCATACTCGCTACAA
Found at i:5710646 original size:37 final size:37
Alignment explanation
Indices: 5710605--5710677 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
5710595 ATAATGTTGT
* ** *
5710605 ATGATGATAATGAGGTGTGCGAGTAGGGAGTGCACAC
1 ATGATGACAATGAAATGTGCGAGTAGCGAGTGCACAC
*
5710642 ATGATGACATTGAAATGTGCGAGTAGCGAGTGCACA
1 ATGATGACAATGAAATGTGCGAGTAGCGAGTGCACA
5710678 TATGGTGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.22
Consensus pattern (37 bp):
ATGATGACAATGAAATGTGCGAGTAGCGAGTGCACAC
Found at i:5710698 original size:37 final size:37
Alignment explanation
Indices: 5710620--5710714 Score: 100
Period size: 37 Copynumber: 2.6 Consensus size: 37
5710610 GATAATGAGG
*
5710620 TGTGCGAGTAGGGAGTGCACACATGATGACATTGAAA
1 TGTGCGAGTAGAGAGTGCACACATGATGACATTGAAA
* * * ** ***
5710657 TGTGCGAGTAGCGAGTGCACATATGGTGGTATTGCCT
1 TGTGCGAGTAGAGAGTGCACACATGATGACATTGAAA
*
5710694 TGTGCGTGTAGAGAGTGCACA
1 TGTGCGAGTAGAGAGTGCACA
5710715 AGAGCTGCAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (37 bp):
TGTGCGAGTAGAGAGTGCACACATGATGACATTGAAA
Found at i:5711022 original size:40 final size:40
Alignment explanation
Indices: 5710964--5711051 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
5710954 CTCGCTGCAA
*
5710964 CGAGAAACATTTTGTTTTGGCCGCCAACAACTCACTGTAG
1 CGAGAAACATTTTCTTTTGGCCGCCAACAACTCACTGTAG
* * *
5711004 CGAGAAACATTTTCTTTTGGCCTCCAGCAACTCGCTGTAG
1 CGAGAAACATTTTCTTTTGGCCGCCAACAACTCACTGTAG
5711044 CGAGAAAC
1 CGAGAAAC
5711052 TCTCAGGTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (40 bp):
CGAGAAACATTTTCTTTTGGCCGCCAACAACTCACTGTAG
Found at i:5712603 original size:20 final size:20
Alignment explanation
Indices: 5712562--5712620 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
5712552 AAGTGAAAAA
5712562 TTTTAGAATAAAATAATA-TT
1 TTTTA-AATAAAATAATATTT
5712582 TTTTAAATAAAATAATATTT
1 TTTTAAATAAAATAATATTT
5712602 TTTTAAATAAAATAATATT
1 TTTTAAATAAAATAATATT
5712621 AAAATATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.32
20 26 0.68
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTTTAAATAAAATAATATTT
Found at i:5713255 original size:14 final size:15
Alignment explanation
Indices: 5713223--5713256 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5713213 CCTCCAAATC
*
5713223 TAAAAACATGAAGTT
1 TAAAAACATGAAGTA
5713238 TAAAAACATG-AGTA
1 TAAAAACATGAAGTA
5713252 TAAAA
1 TAAAA
5713257 CTCAGTGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (15 bp):
TAAAAACATGAAGTA
Found at i:5716854 original size:39 final size:40
Alignment explanation
Indices: 5716768--5716867 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 40
5716758 ATCGGTAATG
* *
5716768 TGCAATGTGGGAGAGCACACG-TCGATGATATATGCCATA
1 TGCAGTGTGGGAGAGCACATGATCGATGATATATGCCATA
* * *
5716807 TGCAGTGTGGGAGAGCACATGAT-GATGATATATGTCGTG
1 TGCAGTGTGGGAGAGCACATGATCGATGATATATGCCATA
** *
5716846 TGTGGTGTGGGAGTGCACATGA
1 TGCAGTGTGGGAGAGCACATGA
5716868 CGGTGATGGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 51 0.98
40 1 0.02
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.26
Consensus pattern (40 bp):
TGCAGTGTGGGAGAGCACATGATCGATGATATATGCCATA
Done.