Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 102 of 143
Found at i:31378541 original size:117 final size:117
Alignment explanation
Indices: 31378339--31378551 Score: 322
Period size: 117 Copynumber: 1.8 Consensus size: 117
31378329 CGCCCCGTGA
* **
31378339 TCGGAGTAGGAGATTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGGTCGGATGGTTGCA
1 TCGGAGTAGGAGATTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGTTGCA
31378404 ATCTACCCCAGGCTCAGGGTAAAAGATCAAATGGCTGCAATCTGCCCCTGGC
66 ATCTACCCCAGGCTCAGGGTAAAAGATCAAATGGCTGCAATCTGCCCCTGGC
* *
31378456 TCGGGGTAGGAGATTGGTTGATGATGATCTG-CCTCAGGCTCGGGGTAAAAGATTAAATGGCTT-
1 TCGGAGTAGGAGATTGGTTGATGATGATCTGCCCT-AGGCTCGGGGTAAAAGATCAAATGG-TTG
* * *
31378519 CAATCTACCCCTGGCTCGGGGTAAGAGATCAAA
64 CAATCTACCCCAGGCTCAGGGTAAAAGATCAAA
31378552 ATCTTCATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 3 0.03
117 81 0.94
118 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (117 bp):
TCGGAGTAGGAGATTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGTTGCA
ATCTACCCCAGGCTCAGGGTAAAAGATCAAATGGCTGCAATCTGCCCCTGGC
Found at i:31378865 original size:49 final size:49
Alignment explanation
Indices: 31378811--31378974 Score: 168
Period size: 49 Copynumber: 3.3 Consensus size: 49
31378801 GACTTAAACC
* * * * *
31378811 TTTCCCTTCAAATCTTCGTGGTACTGAATTTACCGTCGCGGCTTAGATA
1 TTTCCCTTCATATCTTCGTGGTACTGAATCTACAGTCACAGCTTAGATA
* * * *
31378860 TTTCCCTTCATGTCTTCGTGGTACTGGATCTGCAGTCACAGCTTAGATC
1 TTTCCCTTCATATCTTCGTGGTACTGAATCTACAGTCACAGCTTAGATA
* ** * ** *
31378909 TTTCCCTTCATATCTTCGTGGTACTGGATCCGCCGTTGCAGCTTAGATC
1 TTTCCCTTCATATCTTCGTGGTACTGAATCTACAGTCACAGCTTAGATA
31378958 TTTCCCTTTC-TATCTTC
1 TTTCCC-TTCATATCTTC
31378975 TGAGGTGCAT
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
49 97 0.97
50 3 0.03
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (49 bp):
TTTCCCTTCATATCTTCGTGGTACTGAATCTACAGTCACAGCTTAGATA
Found at i:31379067 original size:51 final size:51
Alignment explanation
Indices: 31378928--31379116 Score: 188
Period size: 51 Copynumber: 3.7 Consensus size: 51
31378918 ATATCTTCGT
* *
31378928 GGTACTGGATCCGCCGTTGCAG-CTTAGATCTTTCCCTTTCTATC-TTCTGA
1 GGTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTT-TGTCTTTTTGA
* ** * * *
31378978 GGTGCATGG-TCCATCGTTGC-GACTTAGACCTTTCCCTTTTGTCTTTTTGC
1 GGTAC-TGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTTTGTCTTTTTGA
* * * * *
31379028 GGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTTTGTATCTTTGT
1 GGTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTTTGTCTTTTTGA
* * *
31379079 GGTATTGGATCCGCCGTTGCAATCTTGGATCTTTCCCT
1 GGTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCT
31379117 GTCAAACCTG
Statistics
Matches: 113, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
49 7 0.06
50 45 0.40
51 61 0.54
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (51 bp):
GGTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTTTGTCTTTTTGA
Found at i:31379097 original size:101 final size:100
Alignment explanation
Indices: 31378928--31379116 Score: 231
Period size: 101 Copynumber: 1.9 Consensus size: 100
31378918 ATATCTTCGT
*
31378928 GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTTCTATCTTCTGAGGTGCATGGTCCATC
1 GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTTCTATCTTCTGAGGT-CATGGTCCACC
*
31378993 GTTGCGA-CTTAGACCTTTCCCTTTTGTCTTTTTGC
65 GTTGCAATCTTAGACCTTTCCCTTTTGTCTTTTTGC
* * * *
31379028 GGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTTTGTATCTT-TGTGGT-ATTGGATCC
1 GGTACTGGATCCGCCGTTGCAG-CTTAGATCTTTCCC-TTTCTATCTTCTGAGGTCA-TGG-TCC
* * *
31379091 GCCGTTGCAATCTTGGATCTTTCCCT
62 ACCGTTGCAATCTTAGACCTTTCCCT
31379117 GTCAAACCTG
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
99 1 0.01
100 23 0.31
101 29 0.39
102 22 0.29
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (100 bp):
GGTACTGGATCCGCCGTTGCAGCTTAGATCTTTCCCTTTCTATCTTCTGAGGTCATGGTCCACCG
TTGCAATCTTAGACCTTTCCCTTTTGTCTTTTTGC
Found at i:31385618 original size:58 final size:58
Alignment explanation
Indices: 31385511--31385937 Score: 324
Period size: 58 Copynumber: 7.3 Consensus size: 58
31385501 GCCTGGGGGT
* * * * **
31385511 AAAATGG-TAATTTTAGACTTTCGAGGGCAAAATGGTAATTTTGGAAAAAATTAGGGTTA
1 AAAATGGAT-ATTTTGGACATTCGAGGGTAAAATGGTAATTTTTG-AAAGTTTAGGGTTA
* * * ** * * *
31385570 AAAAT-GATATTTTAGACATTCGACGGTAAATTGGTAATTTTTAGAAAAATCA-GGATC
1 AAAATGGATATTTTGGACATTCGAGGGTAAAATGGTAATTTTT-GAAAGTTTAGGGTTA
* * * * * *
31385627 AAAATGGA-ATTTTTGGATATCCGAGGGTAAAATGATAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGATA-TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTAG-GGTTA
*
31385686 AAAATGGA-ATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGTTA
1 AAAATGGATA-TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTAGGGTTA
* *
31385744 AAAATGCAGT-TTTTGGACA-TCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCT-
1 AAAATGGA-TATTTTGGACATTC-GAGGGTAAAATGGTAATTTTTGAAAGTTT-AGGGT-TA
* * * *
31385803 AAAATGGAAATTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAGTTTTA-GGTCA
1 AAAATGGATATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAG-TTTAGGGTTA
* * * *
31385861 AAAATGGA-ATTTTTGGA-AGTT-TAGGGGTAAAAAT-GTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGATA-TTTTGGACA-TTCGA-GGGT-AAAATGGTAATTTTTGAAAG-TTTAGGGTTA
*
31385920 AAAATGTA-ATTTTGGACA
1 AAAATGGATATTTTGGACA
31385938 AGTACGGAGG
Statistics
Matches: 308, Mismatches: 39, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
57 18 0.06
58 163 0.53
59 122 0.40
60 5 0.02
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATGGATATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTAGGGTTA
Found at i:31385748 original size:117 final size:114
Alignment explanation
Indices: 31385569--31385937 Score: 420
Period size: 117 Copynumber: 3.2 Consensus size: 114
31385559 AATTAGGGTT
* * * ** * *
31385569 AAAAAT-GATATTTTAGACATTCGACGGTAAATTGGTAATTTTTAGAAA-AATCAGGATCAAAAT
1 AAAAATGGA-ATTTTGGACATTCGAGGGTAAAATGGTAATTTTT-GAAAGTTTCAGGTTAAAAAT
*
31385632 GGAATTTTTGGATATCCGAGGGTAAAATGATAATTTTTGGAAGTTTCGAGGTC
64 GGAATTTTTGGA-ATCTGAGGGTAAAATG-TAATTTTTGGAAGTTTCGAGGTC
*
31385685 AAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGTTAAAAATG
1 AAAAATGGAA-TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCAGGTTAAAAATG
* * * *
31385750 CAGTTTTTGGACATCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTC
65 GAATTTTTGGA-ATCTGAGGGTAAAAT-GTAATTTTTGGAAGTTTCGAGGTC
* * * * *
31385802 TAAAATGGAAATTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAGTTTTAGGTCAAAAATG
1 AAAAATGG-AATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCAGGTTAAAAATG
* * *
31385867 GAATTTTTGGAAGT-TTAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTC
65 GAATTTTTGGAA-TCTGA-GGGT-AAAATGTAATTTTTGGAAGTTTCGAGGTC
*
31385919 AAAAATGTAATTTTGGACA
1 AAAAATGGAATTTTGGACA
31385938 AGTACGGAGG
Statistics
Matches: 216, Mismatches: 29, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
116 25 0.12
117 183 0.85
118 8 0.04
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (114 bp):
AAAAATGGAATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCAGGTTAAAAATGG
AATTTTTGGAATCTGAGGGTAAAATGTAATTTTTGGAAGTTTCGAGGTC
Found at i:31385935 original size:29 final size:30
Alignment explanation
Indices: 31385655--31385932 Score: 163
Period size: 29 Copynumber: 9.4 Consensus size: 30
31385645 ATCCGAGGGT
* *
31385655 AAAATGATAATTTTTGGAAGTTTCGAGGTCA
1 AAAATG-TAATTTTTGGAAGTTTTGGGGTCA
* *
31385686 AAAATGGAATTTTTGGACA--TTCGAGGGT--
1 AAAATGTAATTTTTGGA-AGTTTTG-GGGTCA
* * *
31385714 AAAATGGTAATTTTTGAAAG-TTTCGGGTTA
1 AAAAT-GTAATTTTTGGAAGTTTTGGGGTCA
* * *
31385744 AAAATGCAGTTTTTGGACA--TCTGAGGGT--
1 AAAATGTAATTTTTGGA-AGTTTTG-GGGTCA
* *** *
31385772 AAAATGGTAATTTTTGAAAGTTTCAAGGTCT
1 AAAAT-GTAATTTTTGGAAGTTTTGGGGTCA
* * **
31385803 AAAATGGAAATTTTGGACA--TCCGAGGGT--
1 AAAATGTAATTTTTGGA-AGTTTTG-GGGTCA
*
31385831 AAAATGGTAATTTTTGGAAGTTTT-AGGTCA
1 AAAAT-GTAATTTTTGGAAGTTTTGGGGTCA
* *
31385861 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
1 AAAATGTAATTTTTGGAAGTTTTGGGGTCA
31385890 AAAATGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGTAATTTTTGGAAGTTTTGGGGTCA
31385920 AAAATGTAATTTT
1 AAAATGTAATTTT
31385933 GGACAAGTAC
Statistics
Matches: 191, Mismatches: 34, Indels: 45
0.71 0.13 0.17
Matches are distributed among these distances:
28 25 0.13
29 94 0.49
30 59 0.31
31 13 0.07
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAGTTTTGGGGTCA
Found at i:31386792 original size:70 final size:68
Alignment explanation
Indices: 31386665--31386798 Score: 187
Period size: 70 Copynumber: 1.9 Consensus size: 68
31386655 ATAAACAATA
* * * *
31386665 TAATGGTTTTGCCTTTTAACTTAAATGGATAAACATTTATCAAAATGATATAATTTTACTTTTTA
1 TAATGGTTTTGACTTTTAACTTAAAAGGATAAACATTTATCAAAACGACATAATTTTACTTTTTA
31386730 ACT
66 ACT
* * *
31386733 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGACGTAGTTTTACTTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAAGGATAAACATTTATCAAAACGACATAATTTTACTTTT
31386798 T
64 T
31386799 CTTATTCGGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 19 0.33
69 3 0.05
70 35 0.61
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (68 bp):
TAATGGTTTTGACTTTTAACTTAAAAGGATAAACATTTATCAAAACGACATAATTTTACTTTTTA
ACT
Found at i:31387657 original size:20 final size:19
Alignment explanation
Indices: 31387632--31387689 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
31387622 TGGACTCTTT
31387632 TTTGTAATTTAGACATTTGA
1 TTTGTAATTTAGACATTT-A
* *
31387652 TTTGTAAATGAG-CATTTA
1 TTTGTAATTTAGACATTTA
* *
31387670 TTTTGTATTTTGGACATTTA
1 -TTTGTAATTTAGACATTTA
31387690 ATTTAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.03
19 13 0.43
20 16 0.53
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.52
Consensus pattern (19 bp):
TTTGTAATTTAGACATTTA
Found at i:31387700 original size:6 final size:6
Alignment explanation
Indices: 31387685--31387771 Score: 60
Period size: 6 Copynumber: 15.2 Consensus size: 6
31387675 TATTTTGGAC
* * *
31387685 ATTT-A ATTTAA ATTTAC TTTTAA ACTTAA ATTTATA A--TAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA
* * *
31387731 ATTTAGA A--TAA ATTTAA ACTTAA A-ATAA ATTTAA TTTTAA A
1 ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
31387772 ACAAATTTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
4 4 0.06
5 12 0.19
6 43 0.68
7 4 0.06
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:31387725 original size:17 final size:17
Alignment explanation
Indices: 31387705--31387782 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
31387695 AATTTACTTT
* *
31387705 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
31387722 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
*
31387739 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
31387756 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
31387773 CAAATTTAAA
1 TAAATTTAAA
31387783 CTCTGTTGGG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:31388458 original size:113 final size:113
Alignment explanation
Indices: 31388269--31388490 Score: 293
Period size: 113 Copynumber: 2.0 Consensus size: 113
31388259 TTTGAAAATT
* * * *
31388269 TTAAAGGAACATACTCGATTATGCAAATTCTACAAAAAAATCACATCCAACACGTTAGGGCGCAA
1 TTAAAGGAACATAATCGATTATGCAAATTCTAC-AAAAAATCACACCCAACACATTAGGGCACAA
** * * *
31388334 TTCTTTGAAGTTTTAACACAAAAGGATATTGCCTCGATTTTAAAAAAAAA
65 TTCTTCAAAGTTTCAACACAAAAGAATATTGCCTC-AATTTAAAAAAAAA
** * *
31388384 TTAAAGGAGGATAATCGATTGTGTAAATTCTAC-AAAAATCACACCCAACACATTAGGGCACAAT
1 TTAAAGGAACATAATCGATTATGCAAATTCTACAAAAAATCACACCCAACACATTAGGGCACAAT
*
31388448 TCTTCAAAGTTTCCACACAAAAGAATATTGCCTCAATTTAAAA
66 TCTTCAAAGTTTCAACACAAAAGAATATTGCCTCAATTTAAAA
31388491 GTATTTATGT
Statistics
Matches: 93, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
112 8 0.09
113 57 0.61
115 28 0.30
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (113 bp):
TTAAAGGAACATAATCGATTATGCAAATTCTACAAAAAATCACACCCAACACATTAGGGCACAAT
TCTTCAAAGTTTCAACACAAAAGAATATTGCCTCAATTTAAAAAAAAA
Found at i:31389312 original size:21 final size:22
Alignment explanation
Indices: 31389264--31389315 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
31389254 AAGGTTTGGA
* *
31389264 TTTTTTTTGTTTCTTTAATCTG
1 TTTTTTTTATTTCTTAAATCTG
**
31389286 CCTTTTTTATTTCTTAAAT-TG
1 TTTTTTTTATTTCTTAAATCTG
31389307 TTTTTTTTA
1 TTTTTTTTA
31389316 CTTAAAAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (22 bp):
TTTTTTTTATTTCTTAAATCTG
Found at i:31390773 original size:98 final size:97
Alignment explanation
Indices: 31390624--31391093 Score: 618
Period size: 98 Copynumber: 4.8 Consensus size: 97
31390614 AGATTTGTCA
* * * * * *
31390624 TTGCGACTTTAATCTTTCCCAGTATGTTTCTGAGGTACAGGGTTCGCCGTTGCGACTTAAATCTT
1 TTGCGGCTTCAATCTTTCCC-TTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTT
* * * *
31390689 TCTCTCCATATCTTCGTGGTACCAGATTCACCA
65 TCCCTCCATATCTTCATGGTACCAGATTCGCCG
**
31390722 TTGCGGCTTTC-ATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAATAT
1 TTGCGGC-TTCAATCTTTCCCTT-ATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCT
* *
31390786 TTCCCTTCATATCTTCATGGTACCAGATTCGTCG
64 TTCCCTCCATATCTTCATGGTACCAGATTCGCCG
* * * *
31390820 TTGCGGCCTCAATCTTTCCCAGTATGTTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTT
1 TTGCGGCTTCAATCTTTCCC-TTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTT
* *
31390885 TCCCTCCATATCTTCGTGGTACCAGATTTGCCG
65 TCCCTCCATATCTTCATGGTACCAGATTCGCCG
* * *** *
31390918 TTACGGCTTCAATCTTTCCCTTCATGTTTTTGAGGTACAAGGTTTACCGTTGTGACTTAAACCTT
1 TTGCGGCTTCAATCTTTCCCTT-ATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTT
*
31390983 TCCCTCCATATCTTCATGGTACCAGATTCGTCG
65 TCCCTCCATATCTTCATGGTACCAGATTCGCCG
* *
31391016 TTGCGGCTTCAATCTTTCCCTTTATGTTTTTGAGGTACAAGGTTTGTCGTTGCGACTTAAACCTT
1 TTGCGGCTTCAATCTTTCCC-TTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTT
31391081 TCCCTCCATATCT
65 TCCCTCCATATCT
31391094 GTAGAATAGA
Statistics
Matches: 327, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
97 4 0.01
98 318 0.97
99 5 0.02
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (97 bp):
TTGCGGCTTCAATCTTTCCCTTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTT
CCCTCCATATCTTCATGGTACCAGATTCGCCG
Found at i:31390977 original size:196 final size:196
Alignment explanation
Indices: 31390634--31391093 Score: 697
Period size: 196 Copynumber: 2.3 Consensus size: 196
31390624 TTGCGACTTT
* * * *
31390634 AATCTTTCCCAGTATGTTTCTGAGGTACAGGGTTCGCCGTTGCGACTTAAATCTTTCTCTCCATA
1 AATCTTTCCCAGTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATA
*
31390699 TCTTCGTGGTACCAGATTCACCATTGCGGCTTTCATCTTTCCCTTCATGTTTCTGAGGTACAAGG
66 TCTTCGTGGTACCAGATTCACCATTACGGCTTTCATCTTTCCCTTCATGTTTCTGAGGTACAAGG
** * *
31390764 TTCGTCGTTGCGACTTAAATATTTCCCTTCATATCTTCATGGTACCAGATTCGTCGTTGCGGCCT
131 TTCACCGTTGCGACTTAAACATTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGGCCT
31390829 C
196 C
* *
31390830 AATCTTTCCCAGTATGTTTCTGAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCTCCATA
1 AATCTTTCCCAGTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATA
** * *
31390895 TCTTCGTGGTACCAGATTTGCCGTTACGGC-TTCAATCTTTCCCTTCATGTTTTTGAGGTACAAG
66 TCTTCGTGGTACCAGATTCACCATTACGGCTTTC-ATCTTTCCCTTCATGTTTCTGAGGTACAAG
* * * *
31390959 GTTTACCGTTGTGACTTAAACCTTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGGCT
130 GTTCACCGTTGCGACTTAAACATTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGGCC
31391024 TC
195 TC
** * *
31391026 AATCTTTCCCTTTATGTTTTTGAGGTACAAGGTTTGTCGTTGCGACTTAAACCTTTCCCTCCATA
1 AATCTTTCCCAGTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATA
31391091 TCT
66 TCT
31391094 GTAGAATAGA
Statistics
Matches: 238, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
195 3 0.01
196 235 0.99
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (196 bp):
AATCTTTCCCAGTATGTTTCTGAGGTACAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCATA
TCTTCGTGGTACCAGATTCACCATTACGGCTTTCATCTTTCCCTTCATGTTTCTGAGGTACAAGG
TTCACCGTTGCGACTTAAACATTTCCCTCCATATCTTCATGGTACCAGATTCGTCGTTGCGGCCT
C
Found at i:31391085 original size:49 final size:49
Alignment explanation
Indices: 31390606--31391085 Score: 302
Period size: 49 Copynumber: 9.8 Consensus size: 49
31390596 ATGTAACTTC
* * * * * * *
31390606 GAGGTAGAAGATTTGTCATTGCGACTTTAATCTTTCCCAGT-ATGTTTCT
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCC-TTCATGTTTTT
* * * * * * *
31390655 GAGGTACAGGGTTCGCCGTTGCGACTTAAATCTTTCTCTCCATATCTTC
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
* * * ** * * ** *
31390704 GTGGTACCAGATTCACCATTGCGGCTTTCATCTTTCCCTTCATGTTTCT
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
* * *
31390753 GAGGTACAAGGTTCGTCGTTGCGACTTAAATATTTCCCTTCAT-ATCTT
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
* * * * * * * *
31390801 CATGGTACCAGATTCGTCGTTGCGGCCTCAATCTTTCCCAGT-ATGTTTCT
1 GA-GGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCC-TTCATGTTTTT
* * * * * * *
31390851 GAGGTATAAGGTTCGTCATTGCGACTTAAACCTTTCCCTCCATATCTTC
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
* * * * * * * *
31390900 GTGGTACCAGATTTGCCGTTACGGCTTCAATCTTTCCCTTCATGTTTTT
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
*** * * * * *
31390949 GAGGTACAAGGTTTACCGTTGTGACTTAAACCTTTCCCTCCAT-ATCTT
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
* * * * * *
31390997 CATGGTACCAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTTATGTTTTT
1 GA-GGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
* *
31391047 GAGGTACAAGGTTTGTCGTTGCGACTTAAACCTTTCCCT
1 GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCT
31391086 CCATATCTGT
Statistics
Matches: 308, Mismatches: 116, Indels: 14
0.70 0.26 0.03
Matches are distributed among these distances:
48 7 0.02
49 293 0.95
50 8 0.03
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (49 bp):
GAGGTACAAGGTTCGTCGTTGCGACTTAAATCTTTCCCTTCATGTTTTT
Found at i:31398532 original size:23 final size:23
Alignment explanation
Indices: 31398489--31398532 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
31398479 AAGCATGAAA
*
31398489 ATGCAATGCAAATGAATGCATGT
1 ATGCAATGCAAATGAAGGCATGT
*
31398512 ATGCAATGTAAGA-GAAGGCAT
1 ATGCAATGCAA-ATGAAGGCAT
31398533 TGATTCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (23 bp):
ATGCAATGCAAATGAAGGCATGT
Found at i:31401950 original size:113 final size:113
Alignment explanation
Indices: 31401799--31402119 Score: 520
Period size: 112 Copynumber: 2.8 Consensus size: 113
31401789 AGGTATATAC
* * * *
31401799 TCGATTATGCAAATTCTCCAAAAAAATCACACCCAACACGTTAGGGCACAATTCTTCAAAGTTTT
1 TCGATTGTGCAAATTCT--ACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTC
* **
31401864 CACACAAAAGGATATTGCCTCGATTTTAAAAAAAAATTAATGGAGGATAA
64 CACACAAAAGAATATTGCCTCGATTTTAAAAAAAAATTAAAAGAGGATAA
*
31401914 TCGATTGTGCAAATTCTACAAAAATCACATCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
1 TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
31401979 CACAAAAGAATATTGCCTCGATTTT-AAAAAAAATTAAAAGAGGATAA
66 CACAAAAGAATATTGCCTCGATTTTAAAAAAAAATTAAAAGAGGATAA
*
31402026 TCAATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
1 TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
*
31402091 CACAAAAGAATATTGCCTC-AATTTAAAAA
66 CACAAAAGAATATTGCCTCGATTTTAAAAA
31402120 TATTTATGTA
Statistics
Matches: 194, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
111 4 0.02
112 106 0.55
113 68 0.35
115 16 0.08
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.26
Consensus pattern (113 bp):
TCGATTGTGCAAATTCTACAAAAATCACACCCAACACGTTAGGGCACAATTCTTCGAAGTTTCCA
CACAAAAGAATATTGCCTCGATTTTAAAAAAAAATTAAAAGAGGATAA
Found at i:31402951 original size:21 final size:22
Alignment explanation
Indices: 31402903--31402954 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
31402893 AAGGTTTGGA
* *
31402903 TTTTTTTTGTTTCTTTAATCTG
1 TTTTTTTTATTTCTTAAATCTG
**
31402925 CCTTTTTTATTTCTTAAATC-G
1 TTTTTTTTATTTCTTAAATCTG
31402946 TTTTTTTTA
1 TTTTTTTTA
31402955 CTTAAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.13, C:0.12, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTTTTTTATTTCTTAAATCTG
Found at i:31410758 original size:193 final size:194
Alignment explanation
Indices: 31410507--31410865 Score: 533
Period size: 193 Copynumber: 1.9 Consensus size: 194
31410497 GTAAAATGTC
*
31410507 CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATTTAAGCATAAATCTCAGCCATCGT
1 CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTAAGCATAAATCTCAGCCATCGT
* *
31410572 AGGGCTTATAATCCATT-TAGGATGCGTATCTCTTTTCT-GACTCACGATGCTGCTCACACGAGC
66 AGGGCTTATAATCCATTCTAGGATGC-TATCTCATTTCTCGACTCACGATGCTACTCACACGAGC
**
31410635 TGTCAAGGACTTGCAACATATGCAGTACCTCAACCATCGATACAGTATCTGTGCATATAACTGAT
130 TGTCAAGGACTCACAACATATGCAGTACCTCAACCATCGATACAGTATCTGTGCATATAACTGAT
* * * *
31410700 CCCTAATGATGTTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAATCTCAGCTATCGT
1 CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTAAGCATAAATCTCAGCCATCGT
* * * * * * *
31410765 AGGGTTTGTAATCCATTCTTGGATTCTTTCTCATTTCTCGATTCACGATGCTACTCACATGAGCT
66 AGGGCTTATAATCCATTCTAGGATGCTATCTCATTTCTCGACTCACGATGCTACTCACACGAGCT
* *
31410830 GTCGAGGACTCATAACATATGCAGTACCTCAACCAT
131 GTCAAGGACTCACAACATATGCAGTACCTCAACCAT
31410866 TGCGTTGGTT
Statistics
Matches: 146, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
193 85 0.58
194 61 0.42
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (194 bp):
CCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTAAGCATAAATCTCAGCCATCGT
AGGGCTTATAATCCATTCTAGGATGCTATCTCATTTCTCGACTCACGATGCTACTCACACGAGCT
GTCAAGGACTCACAACATATGCAGTACCTCAACCATCGATACAGTATCTGTGCATATAACTGAT
Found at i:31414634 original size:21 final size:21
Alignment explanation
Indices: 31414591--31414638 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
31414581 CCTATGATAG
* * *
31414591 TTCTACTGATACAAGTGAAGC
1 TTCTACTGAAACAAATCAAGC
*
31414612 TTCTACTGAAACAAATCATGC
1 TTCTACTGAAACAAATCAAGC
31414633 TTCTAC
1 TTCTAC
31414639 CAGTACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (21 bp):
TTCTACTGAAACAAATCAAGC
Found at i:31421336 original size:15 final size:15
Alignment explanation
Indices: 31421316--31421353 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
31421306 TTGGTGAAAA
31421316 TATTTTAA-TATTTAT
1 TATTTTAATTATTT-T
31421331 TATTTTAATTATTTT
1 TATTTTAATTATTTT
31421346 TATTTTAA
1 TATTTTAA
31421354 AATATTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTAATTATTTT
Found at i:31421359 original size:16 final size:15
Alignment explanation
Indices: 31421316--31421361 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
31421306 TTGGTGAAAA
31421316 TATTTT-AATATTTAT
1 TATTTTAAATATTT-T
*
31421331 TATTTTAATTATTTT
1 TATTTTAAATATTTT
31421346 TATTTTAAAATATTTT
1 TATTTT-AAATATTTT
31421362 AGAAAGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTAAATATTTT
Found at i:31421753 original size:10 final size:10
Alignment explanation
Indices: 31421740--31421768 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
31421730 ATATGAAAAT
31421740 GAAGAAAAGA
1 GAAGAAAAGA
31421750 GAAGAAAAGA
1 GAAGAAAAGA
31421760 GAAGAAAAG
1 GAAGAAAAG
31421769 TGAACAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GAAGAAAAGA
Found at i:31429637 original size:11 final size:11
Alignment explanation
Indices: 31429597--31429651 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
31429587 AGAGTGAATT
31429597 GAGAGAATTGA
1 GAGAGAATTGA
*
31429608 GAAATG-ATTGA
1 GAGA-GAATTGA
31429619 GA-ATGAATTGA
1 GAGA-GAATTGA
*
31429630 GAGAGAATTGT
1 GAGAGAATTGA
*
31429641 GAGTGAATTGA
1 GAGAGAATTGA
31429652 AAAAGTGGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 3 0.08
11 32 0.86
12 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (11 bp):
GAGAGAATTGA
Found at i:31429639 original size:22 final size:22
Alignment explanation
Indices: 31429587--31429651 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
31429577 TAAAAAAATA
*
31429587 AGAGTGAATTGAG-A-GAATTG
1 AGAGAGAATTGAGAATGAATTG
*
31429607 AGAAATG-ATTGAGAATGAATTG
1 AGAGA-GAATTGAGAATGAATTG
* *
31429629 AGAGAGAATTGTGAGTGAATTG
1 AGAGAGAATTGAGAATGAATTG
31429651 A
1 A
31429652 AAAAGTGGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 9 0.25
21 3 0.08
22 24 0.67
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (22 bp):
AGAGAGAATTGAGAATGAATTG
Found at i:31433476 original size:25 final size:23
Alignment explanation
Indices: 31433447--31433510 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 23
31433437 TATACTAATA
31433447 AGAGTTTGACTCAAAACAAATAAAC
1 AGAGTTT-ACT-AAAACAAATAAAC
* * *
31433472 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTT-ACTAAAACAAATAAAC
31433496 AGAGTTTAACTAAAA
1 AGAGTTT-ACTAAAA
31433511 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 24 0.73
25 9 0.27
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (23 bp):
AGAGTTTACTAAAACAAATAAAC
Found at i:31450612 original size:20 final size:19
Alignment explanation
Indices: 31450581--31450629 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
31450571 TAAATAAATC
31450581 ATAAAAATATTACAAA-TTT
1 ATAAAAATATTA-AAAGTTT
31450600 ATAAAAGATATTAAAAGTTT
1 ATAAAA-ATATTAAAAGTTT
31450620 ATAAAAATAT
1 ATAAAAATAT
31450630 ATTAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
ATAAAAATATTAAAAGTTT
Found at i:31455741 original size:30 final size:30
Alignment explanation
Indices: 31455707--31455765 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
31455697 ACTCCAAACA
*
31455707 TTTTTACTTTTCTCTCACAACTTTTACTCT
1 TTTTTACTTTTCTCTCAAAACTTTTACTCT
31455737 TTTTTACTTTTCTCTCAAAACTTTTACTC
1 TTTTTACTTTTCTCTCAAAACTTTTACTC
31455766 CCCTCCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTTTACTTTTCTCTCAAAACTTTTACTCT
Found at i:31459699 original size:13 final size:13
Alignment explanation
Indices: 31459681--31459705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31459671 GTTAGGATCT
31459681 TTTTTGGTTATTA
1 TTTTTGGTTATTA
31459694 TTTTTGGTTATT
1 TTTTTGGTTATT
31459706 CGGTGTTGCT
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:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (13 bp):
TTTTTGGTTATTA
Found at i:31462918 original size:34 final size:34
Alignment explanation
Indices: 31462875--31462943 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
31462865 TTGTCATCTT
*
31462875 ATTCATGGAAGATTGAGAACATTTGATCAACATA
1 ATTCATGGAAGATTGACAACATTTGATCAACATA
*
31462909 ATTCATGGAAGATTGACAGCATTTGATCAACATA
1 ATTCATGGAAGATTGACAACATTTGATCAACATA
31462943 A
1 A
31462944 AATGACCCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (34 bp):
ATTCATGGAAGATTGACAACATTTGATCAACATA
Found at i:31463088 original size:10 final size:9
Alignment explanation
Indices: 31463056--31463130 Score: 69
Period size: 10 Copynumber: 7.8 Consensus size: 9
31463046 ATGAATGACA
31463056 TTTTATAGT
1 TTTTATAGT
31463065 TTTTATTAGAT
1 TTTTA-TAG-T
31463076 TTTTATGAGT
1 TTTTAT-AGT
*
31463086 TTTTATAAT
1 TTTTATAGT
*
31463095 ATTTATAGGT
1 TTTTATA-GT
*
31463105 TTTTATGATT
1 TTTTAT-AGT
*
31463115 TTTTATAAT
1 TTTTATAGT
31463124 TTTTATA
1 TTTTATA
31463131 AATTTATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
9 22 0.40
10 24 0.44
11 9 0.16
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (9 bp):
TTTTATAGT
Found at i:31463126 original size:8 final size:9
Alignment explanation
Indices: 31463056--31463141 Score: 64
Period size: 10 Copynumber: 8.9 Consensus size: 9
31463046 ATGAATGACA
*
31463056 TTTTATAGT
1 TTTTATAAT
31463065 TTTTATTAGAT
1 TTTTA-TA-AT
*
31463076 TTTTATGAGT
1 TTTTAT-AAT
31463086 TTTTATAAT
1 TTTTATAAT
* *
31463095 ATTTATAGGT
1 TTTTATA-AT
*
31463105 TTTTATGATT
1 TTTTAT-AAT
31463115 TTTTATAAT
1 TTTTATAAT
31463124 TTTTATAAAT
1 TTTTAT-AAT
*
31463134 TTATATAA
1 TTTTATAA
31463142 AATTTTAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
9 23 0.37
10 31 0.50
11 8 0.13
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:31463140 original size:19 final size:19
Alignment explanation
Indices: 31463085--31463141 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
31463075 TTTTTATGAG
**
31463085 TTTTTATAATATTTATA-GG
1 TTTTTATAA-ATTTATATAA
* * *
31463104 TTTTTATGATTTTTTATAA
1 TTTTTATAAATTTATATAA
31463123 TTTTTATAAATTTATATAA
1 TTTTTATAAATTTATATAA
31463142 AATTTTAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATAAATTTATATAA
Found at i:31468635 original size:25 final size:24
Alignment explanation
Indices: 31468602--31468648 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
31468592 GGGAGGATTT
31468602 TTATTTTATTTAATATTAATATGA
1 TTATTTTATTTAATATTAATATGA
31468626 TTATATTTATTTAATATTAATAT
1 TTAT-TTTATTTAATATTAATAT
31468649 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTATTTTATTTAATATTAATATGA
Found at i:31474741 original size:13 final size:13
Alignment explanation
Indices: 31474723--31474749 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31474713 TAAGAAAAAA
31474723 ATTAATATTTTTT
1 ATTAATATTTTTT
31474736 ATTAATATTTTTT
1 ATTAATATTTTTT
31474749 A
1 A
31474750 AACACATTTG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTAATATTTTTT
Found at i:31478202 original size:33 final size:33
Alignment explanation
Indices: 31478165--31478233 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
31478155 CCATGGATGG
*
31478165 TTCCATTGAGACTCAATAGTGAGGTTTGGTTTT
1 TTCCACTGAGACTCAATAGTGAGGTTTGGTTTT
31478198 TTCCACTGAGACTCAATAGTGAGGTTTGGTTTT
1 TTCCACTGAGACTCAATAGTGAGGTTTGGTTTT
31478231 TTC
1 TTC
31478234 TTTATATTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.42
Consensus pattern (33 bp):
TTCCACTGAGACTCAATAGTGAGGTTTGGTTTT
Found at i:31484725 original size:20 final size:19
Alignment explanation
Indices: 31484690--31484751 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
31484680 ACATGGTTTT
31484690 TAAAATAATTA-TAAAAATA
1 TAAAA-AATTATTAAAAATA
31484709 TAAAAAATTATTCAAAAATA
1 TAAAAAATTATT-AAAAATA
* *
31484729 TTAAGAATTA-TAAATAAT-
1 TAAAAAATTATTAAA-AATA
31484747 TAAAA
1 TAAAA
31484752 TTAATAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 11 0.31
19 10 0.28
20 15 0.42
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
TAAAAAATTATTAAAAATA
Found at i:31484753 original size:16 final size:17
Alignment explanation
Indices: 31484724--31484760 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
31484714 AATTATTCAA
31484724 AAATATTAAGAATT-AT
1 AAATATTAAGAATTAAT
31484740 AAATAATTAA-AATTAAT
1 AAAT-ATTAAGAATTAAT
31484757 AAAT
1 AAAT
31484761 GTTACTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATTAAGAATTAAT
Found at i:31485066 original size:17 final size:16
Alignment explanation
Indices: 31485035--31485069 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
31485025 ATGGAATGAG
*
31485035 AATAAATATTTAATTA
1 AATAAATAATTAATTA
31485051 AATAAATAAATTAATTA
1 AATAAAT-AATTAATTA
31485068 AA
1 AA
31485070 ATTTTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAATAATTAATTA
Found at i:31485984 original size:10 final size:10
Alignment explanation
Indices: 31485964--31486012 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
31485954 TTAATTTCTA
31485964 AATATATTTTT
1 AATA-ATTTTT
*
31485975 ATTAATTTTT
1 AATAATTTTT
*
31485985 AACAATTTTT
1 AATAATTTTT
* *
31485995 TATAATTCTT
1 AATAATTTTT
31486005 AATAATTT
1 AATAATTT
31486013 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
10 27 0.90
11 3 0.10
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (10 bp):
AATAATTTTT
Found at i:31485994 original size:20 final size:20
Alignment explanation
Indices: 31485970--31486012 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
31485960 TCTAAATATA
*
31485970 TTTTTATTAATTTTTAACAAT
1 TTTTTA-TAATTCTTAACAAT
*
31485991 TTTTTATAATTCTTAATAAT
1 TTTTTATAATTCTTAACAAT
31486011 TT
1 TT
31486013 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTATAATTCTTAACAAT
Found at i:31485995 original size:22 final size:21
Alignment explanation
Indices: 31485953--31486012 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
31485943 TTAAATTAAG
* *
31485953 ATTAATTTCTAAATATATTTTT
1 ATTAATTTTTAAA-ATTTTTTT
31485975 ATTAATTTTTAACAA-TTTTTT
1 ATTAATTTTTAA-AATTTTTTT
*
31485996 A-TAATTCTTAATAATTT
1 ATTAATTTTTAA-AATTT
31486013 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 11 0.34
21 8 0.25
22 12 0.38
23 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTAATTTTTAAAATTTTTTT
Found at i:31487906 original size:19 final size:19
Alignment explanation
Indices: 31487884--31487931 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
31487874 TTTATACAAT
*
31487884 AATAATATTTTAATTTTAG
1 AATAATATTTTAATTTTAA
* *
31487903 AATATGTATTTTATTTTTAA
1 AATA-ATATTTTAATTTTAA
31487923 AAT-ATATTT
1 AATAATATTT
31487932 ATATGATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
AATAATATTTTAATTTTAA
Found at i:31487914 original size:20 final size:20
Alignment explanation
Indices: 31487889--31487927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31487879 ACAATAATAA
*
31487889 TATTTTAATTTTAGAATATG
1 TATTTTAATTTTAAAATATG
*
31487909 TATTTTATTTTTAAAATAT
1 TATTTTAATTTTAAAATAT
31487928 ATTTATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TATTTTAATTTTAAAATATG
Found at i:31488724 original size:17 final size:17
Alignment explanation
Indices: 31488706--31488738 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31488696 ACTGGGATTA
*
31488706 AAAT-AAAATTTTAATT
1 AAATGAAAATATTAATT
31488722 AAATGAAAATATTAATT
1 AAATGAAAATATTAATT
31488739 TAATTACAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATGAAAATATTAATT
Found at i:31489533 original size:19 final size:18
Alignment explanation
Indices: 31489486--31489530 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
31489476 AATAACATAT
31489486 AAATATATTTTAAAAATA
1 AAATATATTTTAAAAATA
31489504 AAATACATATTTT-AAAATA
1 AAAT--ATATTTTAAAAATA
31489523 AAA-ATATT
1 AAATATATT
31489531 ATTATTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.20
18 4 0.16
19 9 0.36
20 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATATATTTTAAAAATA
Found at i:31497697 original size:15 final size:15
Alignment explanation
Indices: 31497660--31497697 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
31497650 TAGTAGGGTA
*
31497660 TATTT-TTAAAATTT
1 TATTTATTAAAATTG
31497674 TATTTTATTAAAATTG
1 TA-TTTATTAAAATTG
31497690 TATTTATT
1 TATTTATT
31497698 TTTAACAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 9 0.43
16 10 0.48
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTTATTAAAATTG
Found at i:31500465 original size:26 final size:26
Alignment explanation
Indices: 31500425--31500476 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
31500415 ATAAATTTGA
*
31500425 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
31500451 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
31500477 TAGTTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:31500631 original size:7 final size:7
Alignment explanation
Indices: 31500621--31500782 Score: 100
Period size: 7 Copynumber: 22.6 Consensus size: 7
31500611 TATTTAGGGT
31500621 TTTAAGG
1 TTTAAGG
*
31500628 TTTAAAG
1 TTTAAGG
31500635 TTTACA-G
1 TTTA-AGG
31500642 TTTAAGAG
1 TTTAAG-G
31500650 TTT-AGTG
1 TTTAAG-G
31500657 TTT-AGTG
1 TTTAAG-G
*
31500664 TTTTAAAG
1 -TTTAAGG
31500672 TTT-AGG
1 TTTAAGG
31500678 ATTTAAGG
1 -TTTAAGG
31500686 TTTAAGG
1 TTTAAGG
* * *
31500693 ATTATGA
1 TTTAAGG
31500700 TTTAAGG
1 TTTAAGG
*
31500707 TTTAATG
1 TTTAAGG
*
31500714 TTTATGG
1 TTTAAGG
31500721 TTGTAAGG
1 TT-TAAGG
* *
31500729 TATATGG
1 TTTAAGG
31500736 -TTAAGGG
1 TTTAA-GG
* *
31500743 TATAGGG
1 TTTAAGG
31500750 TTTTAAGG
1 -TTTAAGG
31500758 TTTAAGG
1 TTTAAGG
31500765 TTTAAGG
1 TTTAAGG
*
31500772 TTTAGGG
1 TTTAAGG
31500779 TTTA
1 TTTA
31500783 GTTTATGCAC
Statistics
Matches: 121, Mismatches: 23, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
6 5 0.04
7 91 0.75
8 24 0.20
9 1 0.01
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (7 bp):
TTTAAGG
Found at i:31500638 original size:22 final size:22
Alignment explanation
Indices: 31500613--31500675 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 22
31500603 TCATTTAGTA
*
31500613 TTTAGGGTTTTAAGGTTTAAAG
1 TTTAGAGTTTTAAGGTTTAAAG
* **
31500635 TTTACAG-TTTAAGAGTTTAGTG
1 TTTAGAGTTTTAAG-GTTTAAAG
* *
31500657 TTTAGTGTTTTAAAGTTTA
1 TTTAGAGTTTTAAGGTTTA
31500676 GGATTTAAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 6 0.19
22 21 0.66
23 5 0.16
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTTAGAGTTTTAAGGTTTAAAG
Found at i:31500781 original size:29 final size:29
Alignment explanation
Indices: 31500641--31500781 Score: 110
Period size: 29 Copynumber: 4.9 Consensus size: 29
31500631 AAAGTTTACA
* *
31500641 GTTTAAGAGTTT-AGTGTTTAGTGTTTTAAA
1 GTTTAAG-GTTTAAG-GTTTAGGGTTTTAAG
* * *
31500671 GTTT-AGGATTTAAGGTTTAAGG-ATTATG
1 GTTTAAGG-TTTAAGGTTTAGGGTTTTAAG
* * * *
31500699 ATTTAAGGTTTAATGTTTATGGTTGTAAG
1 GTTTAAGGTTTAAGGTTTAGGGTTTTAAG
* * *
31500728 GTATATGG-TTAAGGGTATAGGGTTTTAAG
1 GTTTAAGGTTTAA-GGTTTAGGGTTTTAAG
31500757 GTTTAAGGTTTAAGGTTTAGGGTTT
1 GTTTAAGGTTTAAGGTTTAGGGTTT
31500782 AGTTTATGCA
Statistics
Matches: 84, Mismatches: 21, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
28 23 0.27
29 51 0.61
30 10 0.12
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.45
Consensus pattern (29 bp):
GTTTAAGGTTTAAGGTTTAGGGTTTTAAG
Found at i:31501862 original size:43 final size:43
Alignment explanation
Indices: 31501799--31501895 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
31501789 AGCTGCACAA
* * *
31501799 TTAGTAACATGTCACGATATTAATAAGAGTCAAGTAATATAAT
1 TTAGTAACATGCCACCATATTAACAAGAGTCAAGTAATATAAT
*
31501842 TTAGTAACATGCCACCATATTAACACGAGTCAAGTAATATAAT
1 TTAGTAACATGCCACCATATTAACAAGAGTCAAGTAATATAAT
*
31501885 TTAATAACATG
1 TTAGTAACATG
31501896 TCAATGAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (43 bp):
TTAGTAACATGCCACCATATTAACAAGAGTCAAGTAATATAAT
Found at i:31503392 original size:16 final size:17
Alignment explanation
Indices: 31503363--31503399 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
31503353 ATTTATTCAA
31503363 AAATATTAAGAATT-AT
1 AAATATTAAGAATTAAT
31503379 AAATAATTAA-AATTAAT
1 AAAT-ATTAAGAATTAAT
31503396 AAAT
1 AAAT
31503400 GTTACTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATTAAGAATTAAT
Found at i:31506550 original size:19 final size:19
Alignment explanation
Indices: 31506528--31506575 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
31506518 TTTATACAAT
*
31506528 AATAATATTTTAATTTTAG
1 AATAATATTTTAATTTTAA
* *
31506547 AATATGTATTTTATTTTTAA
1 AATA-ATATTTTAATTTTAA
31506567 AAT-ATATTT
1 AATAATATTT
31506576 ATATGATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
AATAATATTTTAATTTTAA
Found at i:31506558 original size:20 final size:20
Alignment explanation
Indices: 31506533--31506571 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31506523 ACAATAATAA
*
31506533 TATTTTAATTTTAGAATATG
1 TATTTTAATTTTAAAATATG
*
31506553 TATTTTATTTTTAAAATAT
1 TATTTTAATTTTAAAATAT
31506572 ATTTATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TATTTTAATTTTAAAATATG
Found at i:31507379 original size:17 final size:17
Alignment explanation
Indices: 31507357--31507389 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31507347 GGATTAAAAT
31507357 AAAATTTTAATTTAATG
1 AAAATTTTAATTTAATG
31507374 AAAATTTTAATTTAAT
1 AAAATTTTAATTTAAT
31507390 TATACCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
AAAATTTTAATTTAATG
Found at i:31508630 original size:6 final size:6
Alignment explanation
Indices: 31508621--31508666 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
31508611 TTTTAGATTT
* *
31508621 ATTTAA ATTTAA ATTT-A TTTTGA ATTTAA ATTT-A A-TTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
31508666 A
1 A
31508667 ATGGTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
4 2 0.06
5 8 0.24
6 24 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:31508632 original size:23 final size:23
Alignment explanation
Indices: 31508606--31508657 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
31508596 TAAGTTTGAA
31508606 TTAATTTTTAGATTT-ATTTAAAT
1 TTAATTTTTA-ATTTAATTTAAAT
* *
31508629 TTAA-ATTTATTTTGAATTTAAAT
1 TTAATTTTTAATTT-AATTTAAAT
31508652 TTAATT
1 TTAATT
31508658 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
21 3 0.13
22 4 0.17
23 16 0.70
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTAATTTTTAATTTAATTTAAAT
Found at i:31508668 original size:17 final size:16
Alignment explanation
Indices: 31508612--31508666 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
31508602 TGAATTAATT
*
31508612 TTTAGATTTATTTAAA
1 TTTAAATTTATTTAAA
*
31508628 TTTAAATTTATTTTGAA
1 TTTAAATTTA-TTTAAA
*
31508645 TTTAAATTTAATTAAA
1 TTTAAATTTATTTAAA
31508661 TTTAAA
1 TTTAAA
31508667 ATGGTTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:31508683 original size:33 final size:33
Alignment explanation
Indices: 31508617--31508688 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
31508607 TAATTTTTAG
* * * * *
31508617 ATTTATTTAAATTTAAATTTATTTTGAATTTAA
1 ATTTAATTAAATTTAAAATGATTTTAAACTTAA
*
31508650 ATTTAATTAAATTTAAAATGGTTTTAAACTTAA
1 ATTTAATTAAATTTAAAATGATTTTAAACTTAA
*
31508683 ACTTAA
1 ATTTAA
31508689 ATTTAAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (33 bp):
ATTTAATTAAATTTAAAATGATTTTAAACTTAA
Found at i:31509507 original size:6 final size:6
Alignment explanation
Indices: 31509498--31509533 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
31509488 ACGTTTTAAA
*
31509498 TAATAA TAATCAT TAATAT TAATAT TAATAT TAATA
1 TAATAT TAAT-AT TAATAT TAATAT TAATAT TAATA
31509534 AATAAAAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAATAT
Found at i:31509901 original size:21 final size:21
Alignment explanation
Indices: 31509855--31509902 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31509845 AGGGGTTTTG
31509855 AAATAAAGAACAAAAAATGAA
1 AAATAAAGAACAAAAAATGAA
*
31509876 GAATAAAGAACAAAAGAA-GAA
1 AAATAAAGAACAAAA-AATGAA
31509897 AAATAA
1 AAATAA
31509903 GAAAGAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.08
Consensus pattern (21 bp):
AAATAAAGAACAAAAAATGAA
Found at i:31510678 original size:60 final size:60
Alignment explanation
Indices: 31510580--31510945 Score: 443
Period size: 60 Copynumber: 6.1 Consensus size: 60
31510570 CCCTAAATTG
* *
31510580 TCCAGAAATTACATTTTGACCCTAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* *
31510641 TCCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* * * * * *
31510701 TCCAAAATTATATTTTAACCTCAAAACTTTACCAAAATTACATTTTAACCTCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
** * * * **
31510761 TCCAAAATTGTATTTCGACCTCAAAACTTTTCCATAATTACATTTTAACCCTGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
** *
31510821 TCCAAAATTACATTTTGACCCTGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* * * * *
31510881 TCTAAAATTATATTTTGACCCCGAAAC--TGCCAAAATTTACCATTTTATTCCCC-AAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAA-TTA-CATTTTA-ACCCCAAAACTTT
31510940 TCCAAA
1 TCCAAA
31510946 TTCTATTTTT
Statistics
Matches: 268, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
58 7 0.03
59 10 0.04
60 243 0.91
61 8 0.03
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (60 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
Found at i:31510902 original size:30 final size:30
Alignment explanation
Indices: 31510580--31510908 Score: 433
Period size: 30 Copynumber: 10.9 Consensus size: 30
31510570 CCCTAAATTG
*
31510580 TCCAGAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
* *
31510611 TCCAAAATTATATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
31510641 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
31510671 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
31510701 TCCAAAATTATATTTTAACCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * * *
31510731 ACCAAAATTACATTTTAACCTCGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
** * *
31510761 TCCAAAATTGTATTTCGACCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * **
31510791 TCCATAATTACATTTTAACCCTGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
**
31510821 TCCAAAATTACATTTTGACCCTGAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
31510851 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
31510881 TCTAAAATTATATTTTGACCCCGAAACT
1 TCCAAAATTACATTTTGACCCCAAAACT
31510909 GCCAAAATTT
Statistics
Matches: 266, Mismatches: 32, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
30 262 0.98
31 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:31510926 original size:30 final size:29
Alignment explanation
Indices: 31510580--31510945 Score: 333
Period size: 30 Copynumber: 12.2 Consensus size: 29
31510570 CCCTAAATTG
**
31510580 TCCAGAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCGAAAC-TT
* * *
31510611 TCCAAAATTATATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAAC-TT
* *
31510641 TCCAAAATTACATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAAC-TT
*
31510671 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAAC-TT
* * * *
31510701 TCCAAAATTATATTTTAACCTCAAAACTT
1 TCCAAAATTACATTTTGACCCCGAAACTT
* *
31510730 TACCAAAATTACATTTTAACCTCGAAACTTT
1 T-CCAAAATTACATTTTGACCCCGAAAC-TT
** * * *
31510761 TCCAAAATTGTATTTCGACCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAAC-TT
* * *
31510791 TCCATAATTACATTTTAACCCTGAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAAC-TT
*
31510821 TCCAAAATTACATTTTGACCCTGAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAAC-TT
*
31510851 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCGAAAC-TT
* *
31510881 TCTAAAATTATATTTTGACCCCGAAAC-T
1 TCCAAAATTACATTTTGACCCCGAAACTT
*
31510909 GCCAAAATTTACCATTTT-ATTCCCC-AAACTT
1 TCCAAAA-TTA-CATTTTGA--CCCCGAAACTT
31510940 TCCAAA
1 TCCAAA
31510946 TTCTATTTTT
Statistics
Matches: 294, Mismatches: 34, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
28 6 0.02
29 7 0.02
30 264 0.90
31 17 0.06
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
TCCAAAATTACATTTTGACCCCGAAACTT
Found at i:31510938 original size:90 final size:88
Alignment explanation
Indices: 31510580--31510945 Score: 466
Period size: 90 Copynumber: 4.1 Consensus size: 88
31510570 CCCTAAATTG
*
31510580 TCCAGAAATTACATTTTGACCCTAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTTCCA
1 TCCA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAAC-TTTCCA
31510645 AAATTACATTTTAACCCCAAAACTTT
64 AAATTACATTTTAACCCC-AAACTTT
*
31510671 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCTCAAAACTTTACCAA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTT-CCAA
*
31510736 AATTACATTTTAACCTCGAAACTTT
65 AATTACATTTTAACC-CCAAACTTT
** * * * * **
31510761 TCCAAAATTGTATTTCGACCTCAAAACTTTTCCATAATTACATTTTAACCCTGAAACTTTTCCAA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAAC-TTTCCAA
* *
31510826 AATTACATTTTGACCCTGAAACTTT
65 AATTACATTTTAACCC-CAAACTTT
* * * *
31510851 TCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAATTATATTTTGACCCCGAAAC-TGCCAAA
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTCCAAA
*
31510915 ATTTACCATTTTATTCCCCAAAC-TT
66 A-TTA-CATTTTA-ACCCCAAACTTT
31510940 TCCAAA
1 TCCAAA
31510946 TTCTATTTTT
Statistics
Matches: 242, Mismatches: 26, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
88 7 0.03
89 15 0.06
90 209 0.86
91 11 0.05
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (88 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTATATTTTAACCCCAAAACTTTCCAAA
ATTACATTTTAACCCCAAACTTT
Found at i:31521173 original size:68 final size:68
Alignment explanation
Indices: 31521084--31521745 Score: 964
Period size: 68 Copynumber: 9.6 Consensus size: 68
31521074 AATTGAAGTA
* *
31521084 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
31521149 GTG
66 GTG
* *
31521152 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGTAACGTCATCCCCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
31521217 GTG
66 GTG
31521220 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
31521285 GTTG
66 G-TG
* * *
31521289 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
*
31521354 GAG
66 GTG
* *
31521357 GATAACACGTCTTCACCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
31521422 GTG
66 GTG
* * * * * *
31521425 GATAATACATCTTTATCTTTGAAATTGAAGTAAGAGCGACGTCACCCCCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
31521490 GTG
66 GTG
*
31521493 GATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
31521558 GTTG
66 G-TG
* * * * * *
31521562 GATAATAAGTCTTCATCTCTGAAATTAAAGTAGGAGTAACATCGTTTCCTATCCTCTTGAAATTG
1 GATAACACGTCTTTATCTCTGAAATTGAAGTA--AG-AGCAACG--T-C-ATCCTCTTGAAATTG
* *
31521627 AAGTAAAACTG
59 AAGT-AGAGTG
* *
31521638 GATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
31521703 GTTG
66 G-TG
* *
31521707 GATAACACGCCTTTATCTCTGAAATTGAAATAAGAGCAA
1 GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
31521746 GATCATTTCC
Statistics
Matches: 536, Mismatches: 47, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
68 316 0.59
69 151 0.28
70 1 0.00
71 3 0.01
72 5 0.01
73 5 0.01
74 3 0.01
75 1 0.00
76 49 0.09
77 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (68 bp):
GATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
GTG
Found at i:31521440 original size:205 final size:205
Alignment explanation
Indices: 31521084--31521745 Score: 979
Period size: 205 Copynumber: 3.2 Consensus size: 205
31521074 AATTGAAGTA
31521084 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGA
1 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGA
* * *
31521149 GTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGTAACGTCATCCCCTTGAAATTGAAGT
66 GTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGT
* *
31521214 AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
131 AGAGTGGATAATACATCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
31521279 AGTAGAGTTG
196 AGTAGAGTTG
*
31521289 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAATGTCATCCCCTTGAAATTGAAGTAGA
1 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGA
* *
31521354 GAGGATAACACGTCTTCACCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGT
66 GTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGT
* * * *
31521419 AGAGTGGATAATACATCTTTATCTTTGAAATTGAAGTAAGAGCGACGTCACCCCCTTGAAATTGA
131 AGAGTGGATAATACATCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
31521484 AGTAGAG-TG
196 AGTAGAGTTG
* * *
31521493 GATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
1 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGA
* * * * *
31521558 GTTGGATAATAAGTCTTCATCTCTGAAATTAAAGTAGGAGTAACATCGTTTCCTATCCTCTTGAA
66 G-TGGATAACACGTCTTCATCTCTGAAATTGAAGTA--AG-AGCAACG--T-C-ATCCTCTTGAA
* *
31521623 ATTGAAGTAAAACTGGAT-AT-CAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCT
123 ATTGAAGT-AGAGTGGATAATAC-A-TCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCT
31521686 CTTGAAATTGAAGTAGAGTTG
185 CTTGAAATTGAAGTAGAGTTG
* * *
31521707 GATAACACGCCTTTATCTCTGAAATTGAAATAAGAGCAA
1 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
31521746 GATCATTTCC
Statistics
Matches: 413, Mismatches: 32, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
204 64 0.15
205 219 0.53
207 2 0.00
208 5 0.01
210 1 0.00
211 2 0.00
212 22 0.05
213 60 0.15
214 38 0.09
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (205 bp):
GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGA
GTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGT
AGAGTGGATAATACATCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
AGTAGAGTTG
Found at i:31521576 original size:273 final size:279
Alignment explanation
Indices: 31521084--31521745 Score: 1050
Period size: 273 Copynumber: 2.4 Consensus size: 279
31521074 AATTGAAGTA
*
31521084 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGA
1 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
* *
31521149 GTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGTAACGTCATCCCCTTGAAATTGAAGT
66 GTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCACCCCCTTGAAATTGAAGT
31521214 AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
131 AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
* * *
31521279 AGTAGAGTTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAG-CA-AT-G-T-C-ATCCCC
196 AGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTAAAGTAAGAGTAACATCGTTCCTATCCCC
*
31521338 TTGAAATTGAAGTAGAGA-G
261 TTGAAATTGAAGTA-AAACG
*
31521357 GATAACACGTCTTCACCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
1 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
* * * *
31521422 GTGGATAATACATCTTTATCTTTGAAATTGAAGTAAGAGCGACGTCACCCCCTTGAAATTGAAGT
66 GTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCACCCCCTTGAAATTGAAGT
*
31521487 AGAGTGGATAACATGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
131 AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
* * *
31521552 AGTAGAGTTGGATAATAAGTCTTCATCTCTGAAATTAAAGTAGGAGTAACATCGTTTCCTATCCT
196 AGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTAAAGTAAGAGTAACATCG-TTCCTATCCC
31521617 CTTGAAATTGAAGTAAAACTG
260 CTTGAAATTGAAGTAAAAC-G
* * *
31521638 GATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
1 GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
* *
31521703 GTTGGATAACACGCCTTTATCTCTGAAATTGAAATAAGAGCAA
66 G-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
31521746 GATCATTTCC
Statistics
Matches: 353, Mismatches: 26, Indels: 11
0.91 0.07 0.03
Matches are distributed among these distances:
273 228 0.65
274 1 0.00
275 2 0.01
276 1 0.00
278 1 0.00
279 3 0.01
280 19 0.05
281 63 0.18
282 35 0.10
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (279 bp):
GATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGA
GTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCACCCCCTTGAAATTGAAGT
AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAACGTCATCCTCTTGAAATTGA
AGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTAAAGTAAGAGTAACATCGTTCCTATCCCC
TTGAAATTGAAGTAAAACG
Found at i:31522113 original size:17 final size:17
Alignment explanation
Indices: 31522081--31522114 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31522071 ACTTGAGATT
*
31522081 TTTGAATTTATATTAAG
1 TTTGAATTAATATTAAG
*
31522098 TTTGAATTAATTTTAAG
1 TTTGAATTAATATTAAG
31522115 ATTTATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTGAATTAATATTAAG
Found at i:31522166 original size:17 final size:16
Alignment explanation
Indices: 31522102--31522164 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
31522092 ATTAAGTTTG
*
31522102 AATTAATTTTAAGATTT
1 AATTAAATTTAA-ATTT
*
31522119 ATTTAAATTTAAATTT
1 AATTAAATTTAAATTT
** *
31522135 GTTTTGAATTTAAATTT
1 -AATTAAATTTAAATTT
31522152 AATTAAATTTAAA
1 AATTAAATTTAAA
31522165 ATGGTTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 14 0.37
17 24 0.63
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (16 bp):
AATTAAATTTAAATTT
Found at i:31522172 original size:33 final size:33
Alignment explanation
Indices: 31522104--31522186 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
31522094 TAAGTTTGAA
* * * *
31522104 TTAATTTTAAGATTTATTTAAATTTAAATTTGTT
1 TTAAATTTAA-ATTTAATTAAATTTAAAATGGTT
*
31522138 TTGAATTTAAATTTAATTAAATTTAAAATGGTT
1 TTAAATTTAAATTTAATTAAATTTAAAATGGTT
* *
31522171 TTAAACTTAAACTTAA
1 TTAAATTTAAATTTAA
31522187 ATTTAAAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 33 0.80
34 8 0.20
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (33 bp):
TTAAATTTAAATTTAATTAAATTTAAAATGGTT
Found at i:31523031 original size:22 final size:22
Alignment explanation
Indices: 31522990--31523031 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31522980 TAACGTTTTA
* *
31522990 AATAATAATAATCATTAATATT
1 AATAATAATAATAATAAATATT
*
31523012 AATATTAATAATAATAAATA
1 AATAATAATAATAATAAATA
31523032 AAAAGGGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AATAATAATAATAATAAATATT
Found at i:31523395 original size:21 final size:21
Alignment explanation
Indices: 31523349--31523396 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31523339 AGGGGTTTTG
31523349 AAATAAAGAACAAAAAATGAA
1 AAATAAAGAACAAAAAATGAA
*
31523370 GAATAAAGAACAAAAGAA-GAA
1 AAATAAAGAACAAAA-AATGAA
31523391 AAATAA
1 AAATAA
31523397 GAAAGAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.08
Consensus pattern (21 bp):
AAATAAAGAACAAAAAATGAA
Found at i:31524113 original size:30 final size:30
Alignment explanation
Indices: 31524078--31524342 Score: 341
Period size: 30 Copynumber: 8.8 Consensus size: 30
31524068 AAATTGTCCA
* ** *
31524078 AAAATTATATTTTGACCATAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
31524108 TAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
** *
31524138 AAAATTACATTTTGACCCTGAAACTTTACC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
31524168 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
31524198 AAAATTATATTTTGACCTCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * * *
31524228 ATAATTACATTTTAACCCCGAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
31524258 AAAATTACATTTTGACCCCGAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
31524288 AAAATTACATTTTGACCCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
31524318 AAAATTATATTTTGACCCCGAAACT
1 AAAATTACATTTTGACCCCAAAACT
31524343 GCCAAAATTT
Statistics
Matches: 204, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 204 1.00
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:31524234 original size:90 final size:90
Alignment explanation
Indices: 31524078--31524342 Score: 377
Period size: 90 Copynumber: 2.9 Consensus size: 90
31524068 AAATTGTCCA
* * ** *
31524078 AAAATTATATTTTGACCATAAAACTTTTCTTAAATTACATTTTAACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
*
31524143 TACATTTTGACCCTGAAACTTTACC
66 TACATTTTGACCCCGAAACTTTACC
* * * *
31524168 AAAATTACATTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCTCAAAACTTTTCCATAAT
1 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
* * *
31524233 TACATTTTAACCCCGAAACTTTTCT
66 TACATTTTGACCCCGAAACTTTACC
** *
31524258 AAAATTACATTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAAT
1 AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
*
31524323 TATATTTTGACCCCGAAACT
66 TACATTTTGACCCCGAAACT
31524343 GCCAAAATTT
Statistics
Matches: 153, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 153 1.00
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (90 bp):
AAAATTACATTTTGACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
TACATTTTGACCCCGAAACTTTACC
Found at i:31524395 original size:90 final size:87
Alignment explanation
Indices: 31524098--31524388 Score: 327
Period size: 90 Copynumber: 3.3 Consensus size: 87
31524088 TTTGACCATA
** * *
31524098 AAACTTTTCTTAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCTGAAACT
1 AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCGAAAC-
*
31524163 TTACCAAAATTACATTTTAACCCTA
65 TTACCAAAATTACATTTT-ACCC-C
* * * *
31524188 AAACTTTTCCAAAATTATATTTTGACCTCAAAACTTTTCCATAATTACATTTTAACCCCGAAACT
1 AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCGAAAC-
* *
31524253 TTTCTAAAATTACATTTTGACCCC
65 TTACCAAAATTACATTTT-ACCCC
* *
31524277 GAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCTAAAATTATATTTTGACCCCGAAAC
1 -AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCGAAAC
*
31524342 -TGCCAAAATTTACCATTTTATTCCCC
65 TTACCAAAA-TTA-CATTTTA--CCCC
* *
31524368 AGAC-TTTCC-AAATTCCATTTT
1 AAACTTTTCCAAAATTACATTTT
31524389 TAGACCCGAT
Statistics
Matches: 174, Mismatches: 22, Indels: 12
0.84 0.11 0.06
Matches are distributed among these distances:
88 17 0.10
89 9 0.05
90 144 0.83
91 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (87 bp):
AAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCGAAACT
TACCAAAATTACATTTTACCCC
Found at i:31535990 original size:51 final size:50
Alignment explanation
Indices: 31535916--31536090 Score: 201
Period size: 51 Copynumber: 3.4 Consensus size: 50
31535906 TTTCATTTAA
* * *
31535916 TACTCACGATAACATATTA-TCATCAGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACA-CTTAGTCATC-GACCTTTAATTCGTCAAGGATTCATT
* * * *
31535967 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAAGATTCATT
1 TACTCACGATGACACTTAGTCATC-GACCTTTAATTCGTCAAGGATTCATT
* * *
31536018 TACTTATGATGACACTTAGTCATCGAACCTTTAATTCG-CAAAGGATTTATT
1 TACTCACGATGACACTTAGTCATCG-ACCTTTAATTCGTC-AAGGATTCATT
31536069 TACTCACGATGACACTTAGTCA
1 TACTCACGATGACACTTAGTCA
31536091 CCGGACTCTT
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 4 0.04
51 100 0.96
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (50 bp):
TACTCACGATGACACTTAGTCATCGACCTTTAATTCGTCAAGGATTCATT
Found at i:31542328 original size:7 final size:7
Alignment explanation
Indices: 31542318--31542401 Score: 71
Period size: 7 Copynumber: 11.6 Consensus size: 7
31542308 TATATTTTTA
*
31542318 TTTAGTG
1 TTTAGAG
31542325 TTTAGAG
1 TTTAGAG
31542332 TTTTA-AGG
1 -TTTAGA-G
*
31542340 TTTAGCG
1 TTTAGAG
31542347 TTTAGAG
1 TTTAGAG
31542354 TTTAAGAG
1 TTT-AGAG
*
31542362 TTTAGTG
1 TTTAGAG
*
31542369 TTTAGGAT
1 TTTA-GAG
*
31542377 TTTAAAG
1 TTTAGAG
31542384 TTTAGAG
1 TTTAGAG
*
31542391 TTTAGGG
1 TTTAGAG
31542398 TTTA
1 TTTA
31542402 AGGATTAGGA
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
7 45 0.73
8 17 0.27
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.48
Consensus pattern (7 bp):
TTTAGAG
Found at i:31542342 original size:15 final size:15
Alignment explanation
Indices: 31542318--31542393 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
31542308 TATATTTTTA
*
31542318 TTTAGTGTTTAGAGT
1 TTTAGAGTTTAGAGT
*
31542333 TTTA-AGGTTTAGCG-
1 TTTAGA-GTTTAGAGT
31542347 TTTAGAGTTTAAGAG-
1 TTTAGAGTTT-AGAGT
*
31542362 TTTAGTGTTTAG-GAT
1 TTTAGAGTTTAGAG-T
*
31542377 TTTAAAGTTTAGAGT
1 TTTAGAGTTTAGAGT
31542392 TT
1 TT
31542394 AGGGTTTAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (15 bp):
TTTAGAGTTTAGAGT
Found at i:31542349 original size:22 final size:21
Alignment explanation
Indices: 31542318--31542409 Score: 96
Period size: 22 Copynumber: 4.2 Consensus size: 21
31542308 TATATTTTTA
31542318 TTTAGTGTTTAGAGTTTTAAGG
1 TTTAGTGTTTAG-GTTTTAAGG
*
31542340 TTTAGCGTTTAGAG-TTTAAGAG
1 TTTAGTGTTTAG-GTTTTAAG-G
*
31542362 TTTAGTGTTTAGGATTTTAAAG
1 TTTAGTGTTTAGG-TTTTAAGG
* *
31542384 TTTAGAGTTTAGGGTTTAAGG
1 TTTAGTGTTTAGGTTTTAAGG
*
31542405 ATTAG
1 TTTAG
31542410 GATTTATGGT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
21 17 0.28
22 38 0.63
23 5 0.08
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.46
Consensus pattern (21 bp):
TTTAGTGTTTAGGTTTTAAGG
Found at i:31542381 original size:44 final size:44
Alignment explanation
Indices: 31542318--31542403 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
31542308 TATATTTTTA
* *
31542318 TTTAGTGTTTAGAGTTTTAAGGTTTAGCGTTTAGAGTTTAAGAG
1 TTTAGTGTTTAGAGTTTTAAAGTTTAGAGTTTAGAGTTTAAGAG
*
31542362 TTTAGTGTTTAG-GATTTTAAAGTTTAGAGTTTAGGGTTTAAG
1 TTTAGTGTTTAGAG-TTTTAAAGTTTAGAGTTTAGAGTTTAAG
31542404 GATTAGGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 1 0.03
44 37 0.97
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.47
Consensus pattern (44 bp):
TTTAGTGTTTAGAGTTTTAAAGTTTAGAGTTTAGAGTTTAAGAG
Found at i:31542446 original size:7 final size:7
Alignment explanation
Indices: 31542333--31542459 Score: 52
Period size: 7 Copynumber: 17.7 Consensus size: 7
31542323 TGTTTAGAGT
31542333 TTTAAGG
1 TTTAAGG
31542340 TTT-AGCG
1 TTTAAG-G
31542347 TTT-AGAG
1 TTTAAG-G
31542354 TTTAAGAG
1 TTTAAG-G
31542362 TTT-AGTG
1 TTTAAG-G
31542369 TTT-AGG
1 TTTAAGG
*
31542375 ATTTTAAAG
1 --TTTAAGG
31542384 TTT-AGAG
1 TTTAAG-G
*
31542391 TTTAGGG
1 TTTAAGG
31542398 TTTAAGG
1 TTTAAGG
*
31542405 ATT-AGG
1 TTTAAGG
*
31542411 ATTTATGG
1 -TTTAAGG
31542419 -TTAAGG
1 TTTAAGG
* *
31542425 CTATAGGG
1 -TTTAAGG
31542433 TTTTAAGG
1 -TTTAAGG
31542441 TTTAAGG
1 TTTAAGG
*
31542448 TTTAGGG
1 TTTAAGG
31542455 TTTAA
1 TTTAA
31542460 TTTATGCACA
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
6 12 0.13
7 56 0.61
8 22 0.24
9 2 0.02
ACGTcount: A:0.27, C:0.02, G:0.28, T:0.43
Consensus pattern (7 bp):
TTTAAGG
Found at i:31542985 original size:6 final size:6
Alignment explanation
Indices: 31542976--31543010 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
31542966 TCATCCGATG
*
31542976 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT GCTCT
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCT
31543011 GGCTCTGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (6 bp):
CCTCTT
Found at i:31543016 original size:18 final size:18
Alignment explanation
Indices: 31542977--31543034 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
31542967 CATCCGATGC
* **
31542977 CTCTTCCTCTTCCTCTTC
1 CTCTTCCTCTTGCTCTGG
31542995 CTCTTCCTCTTGCTCTGG
1 CTCTTCCTCTTGCTCTGG
** *
31543013 CTCTGGCTCTGGCTCTGG
1 CTCTTCCTCTTGCTCTGG
31543031 CTCT
1 CTCT
31543035 AGCTCTAGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.00, C:0.41, G:0.16, T:0.43
Consensus pattern (18 bp):
CTCTTCCTCTTGCTCTGG
Found at i:31543042 original size:6 final size:6
Alignment explanation
Indices: 31543001--31543040 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
31542991 CTTCCTCTTC
* *
31543001 CTCTTG CTCTGG CTCTGG CTCTGG CTCTGG CTCTAG CTCT
1 CTCTGG CTCTGG CTCTGG CTCTGG CTCTGG CTCTGG CTCT
31543041 AGGGCAGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.03, C:0.35, G:0.25, T:0.38
Consensus pattern (6 bp):
CTCTGG
Found at i:31543555 original size:43 final size:43
Alignment explanation
Indices: 31543494--31543590 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
31543484 AACTGCACAA
* * *
31543494 TTAGTAACATGTCACCATATTAATAAGAGTTAATTAATATAAT
1 TTAGTAACATGCCACCATATTAACAAGAGTTAAATAATATAAT
*
31543537 TTAGTAACATGCCACCATATTAACACGAGTTAAATAATATAAT
1 TTAGTAACATGCCACCATATTAACAAGAGTTAAATAATATAAT
*
31543580 TTAATAACATG
1 TTAGTAACATG
31543591 TCAATGAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.34
Consensus pattern (43 bp):
TTAGTAACATGCCACCATATTAACAAGAGTTAAATAATATAAT
Found at i:31545366 original size:21 final size:21
Alignment explanation
Indices: 31545337--31545376 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31545327 TACTTACTAC
*
31545337 TACTTACAAAATGAAATTACT
1 TACTAACAAAATGAAATTACT
*
31545358 TACTAACAAAATTAAATTA
1 TACTAACAAAATGAAATTA
31545377 AATTAAAAAT
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:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (21 bp):
TACTAACAAAATGAAATTACT
Found at i:31545458 original size:25 final size:27
Alignment explanation
Indices: 31545430--31545485 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
31545420 TTACTCAACT
*
31545430 AAATAAAAAAATTAAA-T-AACAAATC
1 AAATAAAAAAATTAAATTAAACAAAAC
31545455 AAAT--AAAAATTAAATTAAACAAAAC
1 AAATAAAAAAATTAAATTAAACAAAAC
31545480 AAATAA
1 AAATAA
31545486 CTTAAAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 15 0.58
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (27 bp):
AAATAAAAAAATTAAATTAAACAAAAC
Found at i:31546543 original size:19 final size:19
Alignment explanation
Indices: 31546521--31546567 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
31546511 TTTATACAAT
31546521 AATAATATTTTAATTTTAA
1 AATAATATTTTAATTTTAA
* *
31546540 AATATGTATTTTATTTTTAA
1 AATA-ATATTTTAATTTTAA
31546560 AAT-ATATT
1 AATAATATT
31546568 ATATGTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATAATATTTTAATTTTAA
Found at i:31546543 original size:22 final size:21
Alignment explanation
Indices: 31546518--31546580 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
31546508 ATTTTTATAC
31546518 AATAATAATATTTTAATTTTAA
1 AATAAT-ATATTTTAATTTTAA
* *
31546540 AAT-ATGTATTTTATTTTTAA
1 AATAATATATTTTAATTTTAA
*
31546560 AATATATTATATGTT-ATTTTA
1 AATA-A-TATATTTTAATTTTA
31546581 CTAATCTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
22 9 0.27
23 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
AATAATATATTTTAATTTTAA
Found at i:31546551 original size:20 final size:20
Alignment explanation
Indices: 31546526--31546564 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31546516 ACAATAATAA
31546526 TATTTTAATTTTAAAATATG
1 TATTTTAATTTTAAAATATG
*
31546546 TATTTTATTTTTAAAATAT
1 TATTTTAATTTTAAAATAT
31546565 ATTATATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATTTTAATTTTAAAATATG
Found at i:31548939 original size:2 final size:2
Alignment explanation
Indices: 31548932--31548983 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
31548922 TGCTCAAGTT
31548932 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31548974 TC TC TC TC TC
1 TC TC TC TC TC
31548984 ACACACACAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31550846 original size:2 final size:2
Alignment explanation
Indices: 31550839--31550894 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
31550829 AGCCTTGTTA
31550839 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
31550881 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
31550895 GCGCTTTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31555714 original size:5 final size:5
Alignment explanation
Indices: 31555704--31555731 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
31555694 AAAAGGCAGG
31555704 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
31555732 CTAAGCATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:31561884 original size:32 final size:32
Alignment explanation
Indices: 31561844--31561904 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
31561834 ATCACCTGAA
* * *
31561844 TAATTAATTATTTTTTTAAAATTTTAAAAAAT
1 TAATTAATTAGTTTTTAAAAAATTTAAAAAAT
31561876 TAATTAATTAGTTTTTAAAAAATTTAAAA
1 TAATTAATTAGTTTTTAAAAAATTTAAAA
31561905 TTAATGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (32 bp):
TAATTAATTAGTTTTTAAAAAATTTAAAAAAT
Found at i:31561906 original size:22 final size:22
Alignment explanation
Indices: 31561865--31561907 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
31561855 TTTTTTAAAA
31561865 TTTTAAAAAATTAATTAATTAGT
1 TTTTAAAAAATTAA-TAATTAGT
31561888 TTTTAAAAAATTTAA-AATTA
1 TTTTAAAAAA-TTAATAATTA
31561908 ATGTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTAAAAAATTAATAATTAGT
Found at i:31574552 original size:24 final size:23
Alignment explanation
Indices: 31574503--31574552 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
31574493 TAAAGTAGGT
* *
31574503 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
31574526 TATAGTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
31574550 TAT
1 TAT
31574553 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:31574617 original size:58 final size:59
Alignment explanation
Indices: 31574526--31574690 Score: 203
Period size: 58 Copynumber: 2.8 Consensus size: 59
31574516 TCTAATATTA
* * * *
31574526 TATAGTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAAT
1 TATA-TATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATATAATTAAAT
*
31574587 TATATATTA-TTTTATTAAATTGTATTTAATAATAATTA-AGTT-AAAATATAATTAAAT
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATA-TTAAAAATATAATTAAAT
* *
31574644 TATTTATTATTTTTATTAAATTATATTTAATAATAATTTTATTAAAA
1 TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAA
31574691 TTTAATAACA
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
57 22 0.24
58 45 0.49
59 12 0.13
60 8 0.09
61 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (59 bp):
TATATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAAT
Found at i:31574901 original size:16 final size:16
Alignment explanation
Indices: 31574860--31574905 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
31574850 ATTACAACCG
* *
31574860 TATTTCGTTAAAGCTC
1 TATTTCATTACAGCTC
31574876 TATTTCATTACAGCTC
1 TATTTCATTACAGCTC
31574892 TA-TTCTATTACAGC
1 TATTTC-ATTACAGC
31574906 GAATCAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (16 bp):
TATTTCATTACAGCTC
Found at i:31586289 original size:16 final size:17
Alignment explanation
Indices: 31586268--31586299 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31586258 TTGGCTCCAC
31586268 TTTATATTT-TATATAG
1 TTTATATTTATATATAG
31586284 TTTATATTTATATATA
1 TTTATATTTATATATA
31586300 AAAATATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTATATTTATATATAG
Found at i:31586486 original size:41 final size:40
Alignment explanation
Indices: 31586440--31586526 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 40
31586430 AAACCCAAAT
* *
31586440 AAAAAAT-GATTAGGATGCCACGTATTAAAAATAAAATTTGA
1 AAAAAATAGATTA-CATG-CACGTATTAAAAATAAAAGTTGA
* * *
31586481 AAAAAATAAGTTTACATGCATGTATTAAAAATAATAGTTGA
1 AAAAAAT-AGATTACATGCACGTATTAAAAATAAAAGTTGA
31586522 AAAAA
1 AAAAA
31586527 TTCTGTATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
41 32 0.82
42 3 0.08
43 4 0.10
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.28
Consensus pattern (40 bp):
AAAAAATAGATTACATGCACGTATTAAAAATAAAAGTTGA
Found at i:31588165 original size:9 final size:9
Alignment explanation
Indices: 31588153--31588204 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
31588143 GAAAAAACTA
31588153 AAAATTATT
1 AAAATTATT
31588162 AAAATTATTT
1 AAAATTA-TT
* *
31588172 AAAAAGTATA
1 -AAAATTATT
31588182 AAAATTATT
1 AAAATTATT
* *
31588191 AAATTTTTT
1 AAAATTATT
31588200 AAAAT
1 AAAAT
31588205 ATTTTTTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
9 25 0.74
10 3 0.09
11 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
AAAATTATT
Found at i:31588174 original size:20 final size:20
Alignment explanation
Indices: 31588151--31588190 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31588141 ATGAAAAAAC
* *
31588151 TAAAAATTATTAAAATTATT
1 TAAAAAGTATAAAAATTATT
31588171 TAAAAAGTATAAAAATTATT
1 TAAAAAGTATAAAAATTATT
31588191 AAATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TAAAAAGTATAAAAATTATT
Found at i:31589646 original size:12 final size:12
Alignment explanation
Indices: 31589625--31589651 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31589615 TGAATATCTA
31589625 TATATATATATT
1 TATATATATATT
31589637 TATATATATATT
1 TATATATATATT
31589649 TAT
1 TAT
31589652 TGATCATTTT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATATATT
Found at i:31593893 original size:16 final size:16
Alignment explanation
Indices: 31593868--31593903 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31593858 TCAGTTAAAG
*
31593868 CCACCTCATGTCATAA
1 CCACCCCATGTCATAA
31593884 CCACCCCATGTCATAA
1 CCACCCCATGTCATAA
31593900 CCAC
1 CCAC
31593904 GACGTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.44, G:0.06, T:0.19
Consensus pattern (16 bp):
CCACCCCATGTCATAA
Found at i:31594210 original size:93 final size:93
Alignment explanation
Indices: 31594042--31594211 Score: 243
Period size: 93 Copynumber: 1.8 Consensus size: 93
31594032 TTTTTGGAAA
* * * * **
31594042 AAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAATAAAAGC
1 AAGTTTGAGAGTCTTTTTGATACATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
*
31594107 AAGAGATTAATTGCTTTTTTTTTTTTTT
66 AAGAAATTAATTGCTTTTTTTTTTTTTT
* *
31594135 AAGTTTGAGAGTTTTTTTGATATATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
1 AAGTTTGAGAGTCTTTTTGATACATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
31594200 -AGAAACTTAATT
66 AAGAAA-TTAATT
31594212 TTTTTTCTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
92 4 0.06
93 63 0.94
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (93 bp):
AAGTTTGAGAGTCTTTTTGATACATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
AAGAAATTAATTGCTTTTTTTTTTTTTT
Found at i:31594228 original size:93 final size:92
Alignment explanation
Indices: 31594042--31594230 Score: 220
Period size: 93 Copynumber: 2.0 Consensus size: 92
31594032 TTTTTGGAAA
* * * * **
31594042 AAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAGTGCAAAATAAAAGC
1 AAGTTTGAGAGTCTTTTTGATACATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
* ***
31594107 AAGAGATTAATTGCTTTTTTTTTTTTTT
66 AAGAAATTAATT-CTTTTTTTAAGTTTT
* *
31594135 AAGTTTGAGAGTTTTTTTGATATATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
1 AAGTTTGAGAGTCTTTTTGATACATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
31594200 -AGAAACTTAATT-TTTTTTCTAAAGTTTT
66 AAGAAA-TTAATTCTTTTTT-T-AAGTTTT
31594228 AAG
1 AAG
31594231 GCTTTTAACA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
91 6 0.07
92 5 0.06
93 70 0.86
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (92 bp):
AAGTTTGAGAGTCTTTTTGATACATTTTAAAAGTTCAAATATCCAAGAGAGTGCAAAATAAAAGC
AAGAAATTAATTCTTTTTTTAAGTTTT
Found at i:31604207 original size:15 final size:15
Alignment explanation
Indices: 31604187--31604216 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31604177 AGGCGGTTAA
31604187 GGGCATTCAAGATTT
1 GGGCATTCAAGATTT
31604202 GGGCATTCAAGATTT
1 GGGCATTCAAGATTT
31604217 TTCCTTGTCG
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:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
GGGCATTCAAGATTT
Found at i:31608649 original size:6 final size:6
Alignment explanation
Indices: 31608640--31608666 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31608630 TTTTAAATTT
31608640 ATATTA ATATTA ATATTA ATATTA ATA
1 ATATTA ATATTA ATATTA ATATTA ATA
31608667 AAAGTGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:31614303 original size:28 final size:28
Alignment explanation
Indices: 31614272--31614325 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
31614262 CATTTATTGT
* *
31614272 ATATTAAATAATTAATATATATTAAACG
1 ATATTAAATAATAAATAAATATTAAACG
*
31614300 ATATTAATTAATAAATAAATATTAAA
1 ATATTAAATAATAAATAAATATTAAA
31614326 TAATGTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
ATATTAAATAATAAATAAATATTAAACG
Found at i:31615578 original size:29 final size:29
Alignment explanation
Indices: 31615475--31615822 Score: 152
Period size: 29 Copynumber: 11.9 Consensus size: 29
31615465 CATGTTTTAA
*
31615475 CCCTCAAACTTTCCAAAAATTATA-TTTTGAC
1 CCCT-AAACTTT-CAAAAATTACATTTTTG-C
* *
31615506 CCCTTAA-TATTCTAAAAAATACA--TTTGAC
1 CCCTAAACT-TTC-AAAAATTACATTTTTG-C
*
31615535 CCCTGAACTTCTCAAAAATTACATTTTTGC
1 CCCTAAACTT-TCAAAAATTACATTTTTGC
* **
31615565 CCCTAAACTTTCAAAAATTACCATATTAAC
1 CCCTAAACTTTCAAAAATTA-CATTTTTGC
* * * *
31615595 CTC-AAAC-ATCTAAAAATTGCATTTTTTTC
1 CCCTAAACTTTC-AAAAATTACA-TTTTTGC
* *
31615624 CCTCT-AACTTCTTAAAAATTACATTTTTAC
1 CC-CTAAACTT-TCAAAAATTACATTTTTGC
* *
31615654 CCTTAAACTTAT-AAAAATTACATCTTTGC
1 CCCTAAACTT-TCAAAAATTACATTTTTGC
* * *
31615683 CGC-GAA-TTTCCAAAAATCACATTTTTG-
1 CCCTAAACTTT-CAAAAATTACATTTTTGC
* * * *
31615710 CCCTCGAACTTCCAAAAATCA-AGTTTTT-A
1 CCCT-AAACTTTCAAAAATTACA-TTTTTGC
* * *
31615739 CCCTAAA-TTTCCCAAAATAACATTTTT-A
1 CCCTAAACTTT-CAAAAATTACATTTTTGC
* * *
31615767 CCCTAAA-TTTCCCAAAATAACATTTTTAC
1 CCCTAAACTTT-CAAAAATTACATTTTTGC
*
31615796 CCCTAAAACTTTCTAAAATTACATTTT
1 CCCT-AAACTTTCAAAAATTACATTTT
31615823 AACCCTAAAA
Statistics
Matches: 253, Mismatches: 38, Indels: 53
0.74 0.11 0.15
Matches are distributed among these distances:
26 1 0.00
27 6 0.02
28 63 0.25
29 93 0.37
30 69 0.27
31 20 0.08
32 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCAAAAATTACATTTTTGC
Found at i:31615782 original size:57 final size:57
Alignment explanation
Indices: 31615687--31615831 Score: 136
Period size: 57 Copynumber: 2.5 Consensus size: 57
31615677 CTTTGCCGCG
* * * *
31615687 AATTTCCAAAAATCACATTTTTGCCCTCGAACTTCCAAAAATCAA-GTTTTTA-CCCT-A
1 AATTTCCAAAAATAACATTTTTACCCT-AAACTTCC-AAAAT-AACATTTTTACCCCTAA
* *
31615744 AATTTCCCAAAATAACATTTTTACCCTAAATTTCCCAAAATAACATTTTTACCCCTAA
1 AATTTCCAAAAATAACATTTTTACCCTAAACTT-CCAAAATAACATTTTTACCCCTAA
* * *
31615802 AACTTT-CTAAAATTACATTTTAACCCTAAA
1 AA-TTTCCAAAAATAACATTTTTACCCTAAA
31615832 ATCTCTAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
55 2 0.03
56 15 0.20
57 30 0.41
58 24 0.32
59 3 0.04
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (57 bp):
AATTTCCAAAAATAACATTTTTACCCTAAACTTCCAAAATAACATTTTTACCCCTAA
Found at i:31615823 original size:29 final size:28
Alignment explanation
Indices: 31615752--31615850 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 28
31615742 TAAATTTCCC
* * * *
31615752 AAAATAACATTTTTACCCT-AAATTTCCC
1 AAAATTACATTTTAACCCTAAAATCT-CT
* * *
31615780 AAAATAACATTTTTACCCCTAAAACTTTCT
1 AAAATTACA-TTTTAACCCTAAAA-TCTCT
31615810 AAAATTACATTTTAACCCTAAAATCTCT
1 AAAATTACATTTTAACCCTAAAATCTCT
31615838 AAAACTT-CATTTT
1 AAAA-TTACATTTT
31615851 TGACACCGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
28 23 0.38
29 23 0.38
30 12 0.20
31 3 0.05
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAATTACATTTTAACCCTAAAATCTCT
Found at i:31615851 original size:29 final size:30
Alignment explanation
Indices: 31615752--31615851 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 30
31615742 TAAATTTCCC
* ** *
31615752 AAAATAACATTTTT-ACCCTAAATTTC-CC
1 AAAATTACATTTTTAACCCTAAAACTCTCT
* * *
31615780 AAAATAACATTTTTACCCCTAAAACTTTCT
1 AAAATTACATTTTTAACCCTAAAACTCTCT
31615810 AAAATTACA-TTTTAACCCTAAAA-TCTCT
1 AAAATTACATTTTTAACCCTAAAACTCTCT
31615838 AAAACTT-CATTTTT
1 AAAA-TTACATTTTT
31615852 GACACCGATT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 24 0.40
29 27 0.45
30 9 0.15
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTTAACCCTAAAACTCTCT
Found at i:31616148 original size:17 final size:17
Alignment explanation
Indices: 31616126--31616159 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31616116 GTAATATTTC
31616126 TTTATTTCGAGTTTTGA
1 TTTATTTCGAGTTTTGA
*
31616143 TTTATTTCGATTTTTGA
1 TTTATTTCGAGTTTTGA
31616160 AAATTCGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.62
Consensus pattern (17 bp):
TTTATTTCGAGTTTTGA
Found at i:31616328 original size:97 final size:97
Alignment explanation
Indices: 31616143--31616317 Score: 244
Period size: 97 Copynumber: 1.8 Consensus size: 97
31616133 CGAGTTTTGA
* *
31616143 TTTATTTCGATTTTTGAAAATTCGTGCCTTAACTTACTAGACGCAATTTTTCTTCAAACCGGGAT
1 TTTATTTCGAGTTTTGAAAATTCGTGCCTTAACTTACTAGACGCAACTTTTCTTCAAACCGGGAT
*
31616208 AATCGAATACCCTTAAATCAAGGTAATATTCC
66 AATCAAATACCCTTAAATCAAGGTAATATTCC
* * * * ** * *
31616240 TTTATTTCGAGTTTTGATAATTTGTGCCTTAATTTACTAGGCGTGACTTTTCTTTAAATCGGGAT
1 TTTATTTCGAGTTTTGAAAATTCGTGCCTTAACTTACTAGACGCAACTTTTCTTCAAACCGGGAT
31616305 AATCAAAT-CCCTT
66 AATCAAATACCCTT
31616318 TTTTTCAAGG
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
96 5 0.07
97 62 0.93
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (97 bp):
TTTATTTCGAGTTTTGAAAATTCGTGCCTTAACTTACTAGACGCAACTTTTCTTCAAACCGGGAT
AATCAAATACCCTTAAATCAAGGTAATATTCC
Found at i:31620717 original size:21 final size:22
Alignment explanation
Indices: 31620688--31620741 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
31620678 GAACTCGGAT
* *
31620688 TTAATGAAAAAAATA-AATAAA
1 TTAAAGAAAAAAAAAGAATAAA
31620709 TTAAAGAAAGAAAAAAGAATAAA
1 TTAAAGAAA-AAAAAAGAATAAA
31620732 --AAAGAAAAAA
1 TTAAAGAAAAAA
31620742 GAAAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 3 0.10
21 15 0.52
22 5 0.17
23 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (22 bp):
TTAAAGAAAAAAAAAGAATAAA
Found at i:31620727 original size:7 final size:7
Alignment explanation
Indices: 31620711--31620801 Score: 69
Period size: 7 Copynumber: 12.6 Consensus size: 7
31620701 TAAATAAATT
31620711 AAAGAAA
1 AAAGAAA
31620718 GAAA-AAA
1 -AAAGAAA
* *
31620725 GAATAAA
1 AAAGAAA
31620732 AAAGAAA
1 AAAGAAA
31620739 AAAGAAAA
1 AAAG-AAA
31620747 AAAGAAAAA
1 AAAG--AAA
31620756 AAAGAGAA
1 AAAGA-AA
*
31620764 AATGAAA
1 AAAGAAA
31620771 AAAG-AA
1 AAAGAAA
*
31620777 AAAGGAA
1 AAAGAAA
*
31620784 ATAGAAA
1 AAAGAAA
*
31620791 ATAGAAA
1 AAAGAAA
31620798 AAAG
1 AAAG
31620802 GGGAAAAAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
6 8 0.11
7 38 0.54
8 16 0.23
9 8 0.11
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Done.