Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 109 of 163
Found at i:35021929 original size:11 final size:11
Alignment explanation
Indices: 35021915--35021968 Score: 90
Period size: 11 Copynumber: 4.9 Consensus size: 11
35021905 TTTAAATAGA
35021915 AATTTGAGAGG
1 AATTTGAGAGG
35021926 AATTTGAGAGG
1 AATTTGAGAGG
* *
35021937 AAATTAAGAGG
1 AATTTGAGAGG
35021948 AATTTGAGAGG
1 AATTTGAGAGG
35021959 AATTTGAGAG
1 AATTTGAGAG
35021969 AATATTAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.26
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:35021988 original size:33 final size:33
Alignment explanation
Indices: 35021912--35021990 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
35021902 TCTTTTAAAT
*
35021912 AGAAATTTGAGAGGAATTTGAGAGGAAATTAAG
1 AGAAAATTGAGAGGAATTTGAGAGGAAATTAAG
* *
35021945 AGGAATTTGAGAGGAATTTGAGA-GAATATT-AG
1 AGAAAATTGAGAGGAATTTGAGAGGAA-ATTAAG
35021977 AGAAAAATTGAGAG
1 AG-AAAATTGAGAG
35021991 AAAGGATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
32 7 0.17
33 34 0.83
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.24
Consensus pattern (33 bp):
AGAAAATTGAGAGGAATTTGAGAGGAAATTAAG
Found at i:35021989 original size:10 final size:11
Alignment explanation
Indices: 35021912--35021993 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 11
35021902 TCTTTTAAAT
*
35021912 AGAAATTTGAG
1 AGAAAATTGAG
* *
35021923 AGGAATTTGAG
1 AGAAAATTGAG
* *
35021934 AGGAAATTAAG
1 AGAAAATTGAG
* *
35021945 AGGAATTTGAG
1 AGAAAATTGAG
* *
35021956 AGGAATTTGAG
1 AGAAAATTGAG
*
35021967 AGAATATT-AG
1 AGAAAATTGAG
35021977 AGAAAAATTGAG
1 AG-AAAATTGAG
35021989 AGAAA
1 AGAAA
35021994 GGATTTAGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
10 4 0.07
11 52 0.87
12 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (11 bp):
AGAAAATTGAG
Found at i:35027463 original size:17 final size:18
Alignment explanation
Indices: 35027441--35027475 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
35027431 TAAATTATTT
35027441 AAATTAAAAATA-AAATA
1 AAATTAAAAATATAAATA
35027458 AAATTAAAAATATAAATA
1 AAATTAAAAATATAAATA
35027476 CAAAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATTAAAAATATAAATA
Found at i:35027976 original size:7 final size:7
Alignment explanation
Indices: 35027948--35027993 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
35027938 ATTTTTTATT
35027948 CTTTTTC
1 CTTTTTC
35027955 C-TTTTC
1 CTTTTTC
*
35027961 TTTTCTTC
1 CTTT-TTC
35027969 CTTTTTC
1 CTTTTTC
35027976 CTTTTTC
1 CTTTTTC
*
35027983 CTTTTTT
1 CTTTTTC
35027990 CTTT
1 CTTT
35027994 CCTTTCTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 5 0.15
7 23 0.68
8 6 0.18
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
CTTTTTC
Found at i:35027990 original size:30 final size:28
Alignment explanation
Indices: 35027949--35028005 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
35027939 TTTTTTATTC
*
35027949 TTTTTCCTTTTCTTTTCTTCCTTTTTCC
1 TTTTTCCTTTTCTTTCCTTCCTTTTTCC
*
35027977 TTTTTCCTTTTTTCTTTCCTTTCTTTTTC
1 TTTTTCC--TTTTCTTTCCTTCCTTTTTC
35028006 TTCTTCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
30 18 0.72
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTTTCCTTTTCTTTCCTTCCTTTTTCC
Found at i:35028005 original size:6 final size:6
Alignment explanation
Indices: 35027946--35028037 Score: 62
Period size: 6 Copynumber: 14.8 Consensus size: 6
35027936 AAATTTTTTA
* * *
35027946 TTCTTT TTCCTT TTCTTTT CTTCCTTT TTCCTTT TTCCTTT TT-TCT TTC-CT
1 TTCTTT TTCTTT TTC-TTT -TT-CTTT TT-CTTT TT-CTTT TTCTTT TTCTTT
* * * *
35027997 TTCTTT TTCTTC TTCTTC TTCTTC TTCTTT TTCTTC TTCTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
35028038 CAAAAGCCTA
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
5 9 0.12
6 41 0.55
7 18 0.24
8 5 0.07
9 1 0.01
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (6 bp):
TTCTTT
Found at i:35028011 original size:3 final size:3
Alignment explanation
Indices: 35027997--35028038 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
35027987 TTTCTTTCCT
* *
35027997 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
35028039 AAAAGCCTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:35028015 original size:15 final size:15
Alignment explanation
Indices: 35027940--35028038 Score: 69
Period size: 15 Copynumber: 6.6 Consensus size: 15
35027930 CTGTTAAAAT
* *
35027940 TTTTTATTCTTTTTC
1 TTTTTCTTCTTCTTC
*
35027955 CTTTTCTT-TTCTTCC
1 TTTTTCTTCTTCTT-C
* *
35027970 TTTTTCCTTTTTCCT-
1 TTTTT-CTTCTTCTTC
*
35027985 TTTTTCTT-TCCTTTC
1 TTTTTCTTCTTC-TTC
35028000 TTTTTCTTCTTCTTC
1 TTTTTCTTCTTCTTC
* *
35028015 TTCTTCTTCTTTTTC
1 TTTTTCTTCTTCTTC
*
35028030 TTCTTCTTC
1 TTTTTCTTC
35028039 AAAAGCCTAG
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
13 2 0.03
14 8 0.12
15 49 0.72
16 5 0.07
17 4 0.06
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTCTTCTTCTTC
Found at i:35028030 original size:12 final size:12
Alignment explanation
Indices: 35027946--35028037 Score: 75
Period size: 12 Copynumber: 7.4 Consensus size: 12
35027936 AAATTTTTTA
35027946 TTCTTTTTCCTT-
1 TTCTTTTT-CTTC
35027958 TTC-TTTTCTTC
1 TTCTTTTTCTTC
*
35027969 --CTTTTTCCTTT
1 TTCTTTTT-CTTC
35027980 TTCCTTTTTTCTTTCC
1 TT-C-TTTTTC-TT-C
35027996 TTTCTTTTTCTTC
1 -TTCTTTTTCTTC
*
35028009 TTCTTCTTCTTC
1 TTCTTTTTCTTC
35028021 TTCTTTTTCTTC
1 TTCTTTTTCTTC
35028033 TTCTT
1 TTCTT
35028038 CAAAAGCCTA
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
9 1 0.02
10 7 0.11
11 7 0.11
12 30 0.45
13 1 0.02
14 4 0.06
15 13 0.20
16 1 0.02
17 2 0.03
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:35028436 original size:30 final size:30
Alignment explanation
Indices: 35028402--35028517 Score: 87
Period size: 30 Copynumber: 3.9 Consensus size: 30
35028392 TAATTTCCAA
35028402 AAAGTTCAAGGGTTAAAATGAAATTTTAAG
1 AAAGTTCAAGGGTTAAAATGAAATTTTAAG
* * * * *
35028432 AAAGTTTAAAGGTTAAAATGTACTTTTGA-
1 AAAGTTCAAGGGTTAAAATGAAATTTTAAG
** *
35028461 AAAGTT-AAGGGGTCCAAAT-ATAATTTTAGG
1 AAAGTTCAA-GGGTTAAAATGA-AATTTTAAG
* *
35028491 CAAGTTC-AGAGGTTAAAATGTAATTTT
1 AAAGTTCAAG-GGTTAAAATGAAATTTT
35028518 GAAAAATAAA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
28 2 0.03
29 19 0.30
30 43 0.67
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (30 bp):
AAAGTTCAAGGGTTAAAATGAAATTTTAAG
Found at i:35042607 original size:13 final size:13
Alignment explanation
Indices: 35042589--35042616 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35042579 GCATTGAACT
35042589 TAGACATGCATAA
1 TAGACATGCATAA
35042602 TAGACATGCATAA
1 TAGACATGCATAA
35042615 TA
1 TA
35042617 ACCAATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (13 bp):
TAGACATGCATAA
Found at i:35046024 original size:24 final size:25
Alignment explanation
Indices: 35045997--35046048 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
35045987 ACCTAAACTA
*
35045997 AGTTTATTGTTTAGGTCTACTC-TC
1 AGTTTATTGTTCAGGTCTACTCTTC
35046021 AGTTTATTGTTCAGGTCTACTCTTC
1 AGTTTATTGTTCAGGTCTACTCTTC
35046046 AGT
1 AGT
35046049 ATTTAGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (25 bp):
AGTTTATTGTTCAGGTCTACTCTTC
Found at i:35050616 original size:55 final size:55
Alignment explanation
Indices: 35050557--35050717 Score: 144
Period size: 47 Copynumber: 3.1 Consensus size: 55
35050547 AATTTTTATC
35050557 ATTTTTGAGAGTATCCAAAATTTAATTTTATCATTACTAATTTAAAATTTTATAA
1 ATTTTTGAGAGTATCCAAAATTTAATTTTATCATTACTAATTTAAAATTTTATAA
** ** * * ** * * *
35050612 A-TTTT-CCA-T-T-TTAGA-TAAATTTTAAGGATTA--AA-TCAAATTTTTAT-C
1 ATTTTTGAGAGTATCCAAAATTTAATTTT-ATCATTACTAATTTAAAATTTTATAA
35050658 ATTTTTGAGAGTATCCAAAATTTAATTTTATCATTACTAATTTAAAATTTTATAA
1 ATTTTTGAGAGTATCCAAAATTTAATTTTATCATTACTAATTTAAAATTTTATAA
35050713 ATTTT
1 ATTTT
35050718 CCATTTTAGA
Statistics
Matches: 73, Mismatches: 22, Indels: 22
0.62 0.19 0.19
Matches are distributed among these distances:
46 1 0.01
47 14 0.19
48 3 0.04
49 8 0.11
50 8 0.11
51 8 0.11
52 8 0.11
53 3 0.04
54 14 0.19
55 6 0.08
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (55 bp):
ATTTTTGAGAGTATCCAAAATTTAATTTTATCATTACTAATTTAAAATTTTATAA
Found at i:35050641 original size:101 final size:102
Alignment explanation
Indices: 35050524--35050727 Score: 401
Period size: 101 Copynumber: 2.0 Consensus size: 102
35050514 CTATATCTTT
35050524 ATAAATTTTAAAGGATTAAATCAAATTTTTATCATTTTTGAGAGTATCCAAAATTTAATTTTATC
1 ATAAATTTTAAAGGATTAAATCAAATTTTTATCATTTTTGAGAGTATCCAAAATTTAATTTTATC
35050589 ATTACTAATTTAAAATTTTATAAATTTTCCATTTTAG
66 ATTACTAATTTAAAATTTTATAAATTTTCCATTTTAG
35050626 ATAAATTTT-AAGGATTAAATCAAATTTTTATCATTTTTGAGAGTATCCAAAATTTAATTTTATC
1 ATAAATTTTAAAGGATTAAATCAAATTTTTATCATTTTTGAGAGTATCCAAAATTTAATTTTATC
35050690 ATTACTAATTTAAAATTTTATAAATTTTCCATTTTAG
66 ATTACTAATTTAAAATTTTATAAATTTTCCATTTTAG
35050727 A
1 A
35050728 ACTTAGTGGA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 93 0.91
102 9 0.09
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (102 bp):
ATAAATTTTAAAGGATTAAATCAAATTTTTATCATTTTTGAGAGTATCCAAAATTTAATTTTATC
ATTACTAATTTAAAATTTTATAAATTTTCCATTTTAG
Found at i:35051139 original size:23 final size:25
Alignment explanation
Indices: 35051091--35051144 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
35051081 GTTTTAAAAC
*
35051091 TAATTTAAAATATTGTTTTATGTAT
1 TAATTTAAAATATTATTTTATGTAT
35051116 TAATTT-AAAT-TTATTTTAAT-TAT
1 TAATTTAAAATATTATTTT-ATGTAT
35051139 TAATTT
1 TAATTT
35051145 CTTTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 15 0.56
24 6 0.22
25 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TAATTTAAAATATTATTTTATGTAT
Found at i:35066492 original size:26 final size:24
Alignment explanation
Indices: 35066444--35066493 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
35066434 ATTTTATATA
**
35066444 TTGAAATTTTTTATAATGTATTTT
1 TTGAAATTTTTTATAATAAATTTT
35066468 TTGAAATTTTATCTATAATAAATTTT
1 TTGAAATTTT-T-TATAATAAATTTT
35066494 AGAGAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 1 0.05
26 11 0.50
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TTGAAATTTTTTATAATAAATTTT
Found at i:35067393 original size:86 final size:87
Alignment explanation
Indices: 35067248--35067411 Score: 276
Period size: 86 Copynumber: 1.9 Consensus size: 87
35067238 ATTAAGGTTC
* *
35067248 CATTGGACGAAATGATATAAATGGAATCGGGAATTTGAAATTGGATGAAATGAACTTGGT-CTCA
1 CATTGGACGAAATGATATAAATGAAATCGAGAATTTGAAATTGGATGAAATGAACTTGGTCCTCA
*
35067312 AATTGAAATGTTACTGAAAGAA
66 AATTAAAATGTTACTGAAAGAA
* *
35067334 CATTGGACGAAATGGTATAAATGAAATTGAGAATTTGAAATTGGATGAAATGAACTTGGTCCTCA
1 CATTGGACGAAATGATATAAATGAAATCGAGAATTTGAAATTGGATGAAATGAACTTGGTCCTCA
35067399 AATTAAAATGTTA
66 AATTAAAATGTTA
35067412 TTAAGAATTT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
86 56 0.78
87 16 0.22
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (87 bp):
CATTGGACGAAATGATATAAATGAAATCGAGAATTTGAAATTGGATGAAATGAACTTGGTCCTCA
AATTAAAATGTTACTGAAAGAA
Found at i:35090746 original size:31 final size:31
Alignment explanation
Indices: 35090704--35090762 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
35090694 GATTATACAC
* *
35090704 ATGAAATTTTAATTACAATTCAAGTGTATAA
1 ATGAAACTTTAATTACAATTCAACTGTATAA
**
35090735 ATGAAACTTTAATTTTAATTCAACTGTA
1 ATGAAACTTTAATTACAATTCAACTGTA
35090763 CATATTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (31 bp):
ATGAAACTTTAATTACAATTCAACTGTATAA
Found at i:35091992 original size:17 final size:17
Alignment explanation
Indices: 35091965--35092008 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
35091955 ACTAACAAAT
35091965 AATTC-AAAAAT-TATAA
1 AATTCAAAAAATGTA-AA
*
35091981 AATTTAAAAAATGTAAA
1 AATTCAAAAAATGTAAA
35091998 AATTCAAAAAA
1 AATTCAAAAAA
35092009 ATTAGCATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.17
17 18 0.75
18 2 0.08
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (17 bp):
AATTCAAAAAATGTAAA
Found at i:35113260 original size:94 final size:94
Alignment explanation
Indices: 35113099--35113285 Score: 293
Period size: 94 Copynumber: 2.0 Consensus size: 94
35113089 GCTTGAGTTC
* * * *
35113099 AATCCTCTTGTCTTCCTTACTTTCATACAAAGACTCGAACTATTTGGAATCCATGATGCGAAGTC
1 AATCCTCTCGTCTTCCTTACTTTCATACAAAGACTCGAACTATTTGGAATCAATGATGCAAAATC
* *
35113164 TCACTTCCTTTCTCAAAATAAACTTGAAT
66 TCACTTCCTTTCTCAAAACAAAATTGAAT
* * *
35113193 AATCCTCTCGTCTTCCTTACTTTCATACAAAGATTCGAACTATTTGGGATTAATGATGCAAAATC
1 AATCCTCTCGTCTTCCTTACTTTCATACAAAGACTCGAACTATTTGGAATCAATGATGCAAAATC
35113258 TCACTTCCTTTCTCAAAACAAAATTGAA
66 TCACTTCCTTTCTCAAAACAAAATTGAA
35113286 CAATAAAAGG
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.35
Consensus pattern (94 bp):
AATCCTCTCGTCTTCCTTACTTTCATACAAAGACTCGAACTATTTGGAATCAATGATGCAAAATC
TCACTTCCTTTCTCAAAACAAAATTGAAT
Found at i:35118538 original size:27 final size:27
Alignment explanation
Indices: 35118500--35118554 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
35118490 TATGAGGAGA
35118500 AGTTTTGAGTTAAATTGCGGAATTGAC
1 AGTTTTGAGTTAAATTGCGGAATTGAC
35118527 AGTTTTGAGTTAAATTGCGGAATTGAC
1 AGTTTTGAGTTAAATTGCGGAATTGAC
35118554 A
1 A
35118555 AACTCCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (27 bp):
AGTTTTGAGTTAAATTGCGGAATTGAC
Found at i:35118566 original size:27 final size:27
Alignment explanation
Indices: 35118509--35118566 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
35118499 AAGTTTTGAG
*** ** *
35118509 TTAAATTGCGGAATTGACAGTTTTGAG
1 TTAAATTGCGGAATTGACAAACTCCAA
35118536 TTAAATTGCGGAATTGACAAACTCCAA
1 TTAAATTGCGGAATTGACAAACTCCAA
35118563 TTAA
1 TTAA
35118567 TCGAATTCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (27 bp):
TTAAATTGCGGAATTGACAAACTCCAA
Found at i:35125224 original size:67 final size:67
Alignment explanation
Indices: 35125116--35125571 Score: 698
Period size: 67 Copynumber: 6.8 Consensus size: 67
35125106 CAATTGTAAT
* * * *
35125116 AGTAATTAAATGTATGTGTTTAATTGAATTGATTATTTGTATATAATTTGAGAAAGTATGTGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
35125181 TG
66 TG
*
35125183 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTACGCGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
35125248 TG
66 TG
* *
35125250 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATGTGATTTGAGAAAGTATGTGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
35125315 TG
66 TG
*
35125317 AGTAATTAAATGTATGTATTTAATTGAATGGATTATATGTATATGATTTGAGAAAGTATGCGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
35125382 TG
66 TG
* * * * * *
35125384 AGTATTTAAATGTATGTA-TTAATTAAATCGATTATATATATGTGATTTGAGAAAGTATTCGAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
35125448 TG
66 TG
* * * * *
35125450 AGTATTTAAATGTATGTATTTAATTAAATCGATTATATGTATATGATTTGAGAAGGTATGCAAAT
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
35125515 TG
66 TG
* * * *
35125517 AGTATTTAAATGTATGTATTTAATTGAATAGATTATATATATGTGATTTGAGAAA
1 AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAA
35125572 TTGAATTATT
Statistics
Matches: 361, Mismatches: 27, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
66 61 0.17
67 300 0.83
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (67 bp):
AGTAATTAAATGTATGTATTTAATTGAATTGATTATATGTATATGATTTGAGAAAGTATGCGAAT
TG
Found at i:35125770 original size:22 final size:22
Alignment explanation
Indices: 35125719--35125794 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 22
35125709 GACTCACCAT
*
35125719 AGCTCGTATGGGCTTACCGATATTTC
1 AGCTCGTATGGGCTTA-C--T-GTTC
35125745 AGCTCGTATGGGCTTACTGTTC
1 AGCTCGTATGGGCTTACTGTTC
* *
35125767 AGCTCAT-TAGAGCTTACTGTTTC
1 AGCTCGTAT-GGGCTTACTG-TTC
35125790 AGCTC
1 AGCTC
35125795 AATAGAGCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.02
22 18 0.40
23 9 0.20
25 1 0.02
26 16 0.36
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (22 bp):
AGCTCGTATGGGCTTACTGTTC
Found at i:35125794 original size:23 final size:23
Alignment explanation
Indices: 35125756--35125820 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
35125746 GCTCGTATGG
*
35125756 GCTTACTG-TTCAGCTCATTAGA
1 GCTTACTGTTTCAGCTCAATAGA
35125778 GCTTACTGTTTCAGCTCAATAGA
1 GCTTACTGTTTCAGCTCAATAGA
*
35125801 GCCTACTGTTTATCAGCTCA
1 GCTTACTG-TT-TCAGCTCA
35125821 GGAGTTTATC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 8 0.21
23 20 0.53
24 2 0.05
25 8 0.21
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (23 bp):
GCTTACTGTTTCAGCTCAATAGA
Found at i:35132612 original size:16 final size:16
Alignment explanation
Indices: 35132591--35132627 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
35132581 TGCTGTTAGG
*
35132591 GATTGTGGTCTCTCGA
1 GATTGTGGTCCCTCGA
35132607 GATTGTGGTCCCTCGA
1 GATTGTGGTCCCTCGA
35132623 GATTG
1 GATTG
35132628 GTTTGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.32, T:0.35
Consensus pattern (16 bp):
GATTGTGGTCCCTCGA
Found at i:35135820 original size:62 final size:63
Alignment explanation
Indices: 35135723--35135848 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 63
35135713 ACTTTTGTAG
35135723 TGGTGAGGGTTATATAAGTTATTTACACTATTATTT-AAAGTTTGACTGAATTGGTATCACCT
1 TGGTGAGGGTTATATAAGTTATTTACACTATTATTTAAAAGTTTGACTGAATTGGTATCACCT
* * * *
35135785 TGGTGAGGGTTATATAATTTATTTATACTATTATTTAAAATTTTGATTGAATTGGTATCACCT
1 TGGTGAGGGTTATATAAGTTATTTACACTATTATTTAAAAGTTTGACTGAATTGGTATCACCT
35135848 T
1 T
35135849 TTACTCAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
62 34 0.58
63 25 0.42
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.45
Consensus pattern (63 bp):
TGGTGAGGGTTATATAAGTTATTTACACTATTATTTAAAAGTTTGACTGAATTGGTATCACCT
Found at i:35136313 original size:21 final size:21
Alignment explanation
Indices: 35136289--35136333 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
35136279 AAAACCTATT
*
35136289 AAAATTAGAAAAA-AATTTATA
1 AAAATCAGAAAAAGAA-TTATA
*
35136310 AAAATCATAAAAAGAATTATA
1 AAAATCAGAAAAAGAATTATA
35136331 AAA
1 AAA
35136334 TGCATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAATCAGAAAAAGAATTATA
Found at i:35136339 original size:21 final size:21
Alignment explanation
Indices: 35136297--35136344 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
35136287 TTAAAATTAG
35136297 AAAAAAATTTATAAAAATCAT
1 AAAAAAATTTATAAAAATCAT
35136318 AAAAAGAA-TTAT-AAAATGCAT
1 AAAAA-AATTTATAAAAAT-CAT
35136339 AAAAAA
1 AAAAAA
35136345 GCCCTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.24
21 17 0.68
22 2 0.08
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAAAAATTTATAAAAATCAT
Found at i:35136605 original size:11 final size:11
Alignment explanation
Indices: 35136597--35136637 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
35136587 AAAATTTTAC
35136597 AATTTTTTTCT
1 AATTTTTTTCT
* *
35136608 ATATTATTTTAT
1 A-ATTTTTTTCT
35136620 AATTTTTTTCT
1 AATTTTTTTCT
35136631 AATTTTT
1 AATTTTT
35136638 AATAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (11 bp):
AATTTTTTTCT
Found at i:35138065 original size:21 final size:21
Alignment explanation
Indices: 35138041--35138085 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
35138031 AAAACCTATT
*
35138041 AAAATTAGAAAAA-AATTTATA
1 AAAATCAGAAAAAGAA-TTATA
*
35138062 AAAATCATAAAAAGAATTATA
1 AAAATCAGAAAAAGAATTATA
35138083 AAA
1 AAA
35138086 TGCATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAATCAGAAAAAGAATTATA
Found at i:35138091 original size:21 final size:21
Alignment explanation
Indices: 35138049--35138096 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
35138039 TTAAAATTAG
35138049 AAAAAAATTTATAAAAATCAT
1 AAAAAAATTTATAAAAATCAT
35138070 AAAAAGAA-TTAT-AAAATGCAT
1 AAAAA-AATTTATAAAAAT-CAT
35138091 AAAAAA
1 AAAAAA
35138097 GCCCTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.24
21 17 0.68
22 2 0.08
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAAAAATTTATAAAAATCAT
Found at i:35140172 original size:12 final size:12
Alignment explanation
Indices: 35140155--35140179 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35140145 GGTGTTCATT
35140155 CGGTTAACCGAC
1 CGGTTAACCGAC
35140167 CGGTTAACCGAC
1 CGGTTAACCGAC
35140179 C
1 C
35140180 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:35142622 original size:12 final size:12
Alignment explanation
Indices: 35142605--35142629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35142595 GGTGTTCATT
35142605 CGGTTAACCGAC
1 CGGTTAACCGAC
35142617 CGGTTAACCGAC
1 CGGTTAACCGAC
35142629 C
1 C
35142630 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:35142773 original size:9 final size:9
Alignment explanation
Indices: 35142759--35142834 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
35142749 TTTGGTTAAA
35142759 AATTAACCG
1 AATTAACCG
**
35142768 AATTAACTA
1 AATTAACCG
35142777 AATTAACCG
1 AATTAACCG
*
35142786 AATTACCCG
1 AATTAACCG
35142795 AATTAACCG
1 AATTAACCG
35142804 AATTAACCG
1 AATTAACCG
*
35142813 AATTACCCG
1 AATTAACCG
*
35142822 AATTAACCT
1 AATTAACCG
35142831 AATT
1 AATT
35142835 CATTCATACA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:35144190 original size:27 final size:23
Alignment explanation
Indices: 35144160--35144214 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 23
35144150 AAATTAGCGC
35144160 GCTTATCGTATTATTTCGCACTTTGGT
1 GCTTATCG--TTATTT-GCACTTT-GT
35144187 GCTTATCGTTATTTGCACTTTGT
1 GCTTATCGTTATTTGCACTTTGT
35144210 GCTTA
1 GCTTA
35144215 GTGATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.25
24 7 0.25
25 6 0.21
27 8 0.29
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.49
Consensus pattern (23 bp):
GCTTATCGTTATTTGCACTTTGT
Found at i:35149091 original size:3 final size:3
Alignment explanation
Indices: 35149080--35149114 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
35149070 GGTTGAGGAG
* *
35149080 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA AAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
35149115 GCAACAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35155740 original size:3 final size:3
Alignment explanation
Indices: 35155732--35155766 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35155722 TAGAAAAAGT
35155732 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35155767 TAAATCAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35155891 original size:18 final size:18
Alignment explanation
Indices: 35155868--35155922 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
35155858 ATCGTCATCT
35155868 AATCATAAAAAACATAAA
1 AATCATAAAAAACATAAA
*
35155886 AATCATAAAAAA-A-GAA
1 AATCATAAAAAACATAAA
*
35155902 AAT-ATACAAAACAATAAA
1 AATCATAAAAAAC-ATAAA
35155920 AAT
1 AAT
35155923 ATGATTTCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 2 0.06
18 17 0.55
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (18 bp):
AATCATAAAAAACATAAA
Found at i:35155923 original size:18 final size:17
Alignment explanation
Indices: 35155875--35155924 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
35155865 TCTAATCATA
35155875 AAAAAC-ATAAAAATCAT
1 AAAAACAATAAAAAT-AT
*
35155892 AAAAA-AA-GAAAATAT
1 AAAAACAATAAAAATAT
35155907 ACAAAACAATAAAAATAT
1 A-AAAACAATAAAAATAT
35155925 GATTTCTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.11
16 9 0.33
17 8 0.30
18 7 0.26
ACGTcount: A:0.74, C:0.08, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAACAATAAAAATAT
Found at i:35156142 original size:12 final size:12
Alignment explanation
Indices: 35156125--35156150 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35156115 ATTCTGAATT
35156125 AACTTTAGAAAC
1 AACTTTAGAAAC
35156137 AACTTTAGAAAC
1 AACTTTAGAAAC
35156149 AA
1 AA
35156151 ATCTAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AACTTTAGAAAC
Found at i:35160690 original size:13 final size:13
Alignment explanation
Indices: 35160672--35160697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35160662 CATAAACCCT
35160672 CGAATTAACCCAA
1 CGAATTAACCCAA
35160685 CGAATTAACCCAA
1 CGAATTAACCCAA
35160698 TGAGGGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (13 bp):
CGAATTAACCCAA
Found at i:35167722 original size:44 final size:44
Alignment explanation
Indices: 35167673--35167798 Score: 112
Period size: 44 Copynumber: 3.1 Consensus size: 44
35167663 TTAAAGACTT
35167673 TTTTTAATGTATTTTCAATATATTGAGAAACATTTATTTTAATA
1 TTTTTAATGTATTTTCAATATATTGAGAAACATTTATTTTAATA
* * ** * *
35167717 TTTTTAGTGTA-TTT-AATGTATT-ATTAA-A--GA--CT--T-
1 TTTTTAATGTATTTTCAATATATTGAGAAACATTTATTTTAATA
35167750 TTTTTAATGTATTTTCAATATATTGAGAAACATTTTATTTTAATA
1 TTTTTAATGTATTTTCAATATATTGAGAAACA-TTTATTTTAATA
35167795 TTTT
1 TTTT
35167799 AAGGGATTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 23
0.62 0.13 0.25
Matches are distributed among these distances:
33 10 0.17
34 4 0.07
35 7 0.12
36 4 0.07
37 1 0.02
38 1 0.02
40 2 0.03
41 3 0.05
42 8 0.14
43 3 0.05
44 11 0.19
45 4 0.07
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (44 bp):
TTTTTAATGTATTTTCAATATATTGAGAAACATTTATTTTAATA
Found at i:35167750 original size:77 final size:77
Alignment explanation
Indices: 35167661--35167817 Score: 280
Period size: 77 Copynumber: 2.0 Consensus size: 77
35167651 TAGTTATATA
*
35167661 TATTAAAGACTTTTTTTAATGTATTTTCAATATATTGAGAAACA-TTTATTTTAATATTTTTAGT
1 TATTAAAGACTTTTTTTAATGTATTTTCAATATATTGAGAAACATTTTATTTTAATATTTTAAG-
*
35167725 GTATTTAATGTAT
65 GGATTTAATGTAT
35167738 TATTAAAGACTTTTTTTAATGTATTTTCAATATATTGAGAAACATTTTATTTTAATATTTTAAGG
1 TATTAAAGACTTTTTTTAATGTATTTTCAATATATTGAGAAACATTTTATTTTAATATTTTAAGG
35167803 GATTTAATGTAT
66 GATTTAATGTAT
35167815 TAT
1 TAT
35167818 ATTTTTTTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
77 59 0.77
78 18 0.23
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (77 bp):
TATTAAAGACTTTTTTTAATGTATTTTCAATATATTGAGAAACATTTTATTTTAATATTTTAAGG
GATTTAATGTAT
Found at i:35171866 original size:44 final size:41
Alignment explanation
Indices: 35171817--35172189 Score: 259
Period size: 44 Copynumber: 8.7 Consensus size: 41
35171807 ATCTGCTCTT
* * *
35171817 CTGCAACTTCAGAGAGATAAGACCTATCATTTTAATCCGCTTCA
1 CTGCAACTTCAGGGAGATAAGA--T-TGATTTTAATCTGCTTCA
* * * *
35171861 CTGCAACTTCAGGAAGATATGATTGGTTTCTTCAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATT-GATT-TT-AATCTGCTTCA
* * *
35171905 CTGCAACTTCAGGGAGATAAGATTGGA-TGTGATTTGC-TCTA
1 CTGCAACTTCAGGGAGATAAGATT-GATTTTAATCTGCTTC-A
** *
35171946 CTGCAACTTCAGAAAGATAAGATCTGTGATTTTAATCCGCTTCA
1 CTGCAACTTCAGGGAGATAAGA--T-TGATTTTAATCTGCTTCA
* * * *
35171990 CTGCAACTTCAGGGAGATAGGATTAGTTTCTTCAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATT-GATT-TT-AATCTGCTTCA
* * *
35172034 CTGCAACTTCAGGGAGATAAGATTGGA-TGTGATCTAC-TCTA
1 CTGCAACTTCAGGGAGATAAGATT-GATTTTAATCTGCTTC-A
* * * *
35172075 CTGCAACTTTAGAGAGATAAGATCTGTGATTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGA--T-TGATTTTAATCTGCTTCA
* * * * *
35172119 CTGCAACTTCAGGGAGATAGGATAGTTTCTTCAGTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATTGATT-TT-AATCTGCTTCA
35172162 CTGCAACTTCAGGGAGATAAGACTTGAT
1 CTGCAACTTCAGGGAGATAAGA-TTGAT
35172190 ATGATCTACT
Statistics
Matches: 256, Mismatches: 52, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
40 2 0.01
41 56 0.22
42 12 0.05
43 42 0.16
44 141 0.55
45 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
CTGCAACTTCAGGGAGATAAGATTGATTTTAATCTGCTTCA
Found at i:35172031 original size:129 final size:129
Alignment explanation
Indices: 35171801--35172228 Score: 671
Period size: 129 Copynumber: 3.3 Consensus size: 129
35171791 CATAAAGTCT
* * * * *
35171801 GATGTGATCTGCTCTTCTGCAACTTCAGAGAGATAAGACCTATCATTTTAATCCGCTTCACTGCA
1 GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTTCACTGCA
* * * *
35171866 ACTTCAGGAAGATATGATTGGTTTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG
66 ACTTCAGGGAGATAGGATTAGTTTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTG
* * *
35171930 GATGTGATTTGCTCTACTGCAACTTCAGAAAGATAAGATCTGTGATTTTAATCCGCTTCACTGCA
1 GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTTCACTGCA
35171995 ACTTCAGGGAGATAGGATTAGTTTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTG
66 ACTTCAGGGAGATAGGATTAGTTTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTG
* *
35172059 GATGTGATCTACTCTACTGCAACTTTAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCA
1 GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTTCACTGCA
35172124 ACTTCAGGGAGATAGGA-TAGTTTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-
66 ACTTCAGGGAGATAGGATTAGTTTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG
* * * *
35172187 GATATGATCTACTCTACTGCAACTTCAAAGATATAATATCTG
1 GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTG
35172229 CAATGTATAG
Statistics
Matches: 278, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
128 80 0.29
129 198 0.71
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (129 bp):
GATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTTCACTGCA
ACTTCAGGGAGATAGGATTAGTTTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTG
Found at i:35172396 original size:50 final size:50
Alignment explanation
Indices: 35172342--35172596 Score: 154
Period size: 50 Copynumber: 5.1 Consensus size: 50
35172332 TTGCGGTTTC
* *
35172342 AATCTTTTAAATTGCAATATCGGGGAAGCAAGATTTGCCGTCCTAGCTTT
1 AATCTTTTAAATTGCAATATCGGGGAAGTAAGATTCGCCGTCCTAGCTTT
** ** * ** * * ** * * *
35172392 AATCTGCTCCATTGCACTGCCAGAGAAGTAAGATTCGTCATTGC-GGCTTC
1 AATCTTTTAAATTGCAATATCGGGGAAGTAAGATTCG-CCGTCCTAGCTTT
* * * *
35172442 AATCTTTTAAATTGCAAAATCGGGGAAGCAAGATTCACCGTCGTAGCTTT
1 AATCTTTTAAATTGCAATATCGGGGAAGTAAGATTCGCCGTCCTAGCTTT
** ** * * * ** * * * *
35172492 AATCTGCTCCACTGTACTGCCAGGGAAGTAAGATTCGCCGTTGC-GGCTTC
1 AATCTTTTAAATTGCAATATCGGGGAAGTAAGATTCGCCG-TCCTAGCTTT
* * *
35172542 AATATTTTTAATTGCAATATCGGGGAAGTAAGATTCGCCGTCGTAGCTTT
1 AATCTTTTAAATTGCAATATCGGGGAAGTAAGATTCGCCGTCCTAGCTTT
35172592 AATCT
1 AATCT
35172597 GCTCCACTGC
Statistics
Matches: 134, Mismatches: 67, Indels: 8
0.64 0.32 0.04
Matches are distributed among these distances:
49 3 0.02
50 127 0.95
51 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (50 bp):
AATCTTTTAAATTGCAATATCGGGGAAGTAAGATTCGCCGTCCTAGCTTT
Found at i:35172446 original size:100 final size:99
Alignment explanation
Indices: 35172238--35173153 Score: 1039
Period size: 100 Copynumber: 9.2 Consensus size: 99
35172228 GCAATGTATA
* * * *
35172238 GCTTCAATCTTTTTAAACTGCAATGTCGGGGAAACAA-ATTCGCTGTTGTAGCTTCAATCTGTTC
1 GCTTCAATC-TTTT-AATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTC
* * * *
35172302 CACTACACTGCC-GGGAAGTAAGATTCGTCATTGCG
64 CACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTG
* * * ** *
35172337 GTTTCAATCTTTTAAATTGCAATATCGGGGAAGCAAGATTTGCCGTCCTAGCTTTAATCTGCTCC
1 GCTTCAATCTTTT-AATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCC
* * * * * *
35172402 ATTGCACTGCCAGAGAAGTAAGATTCGTCATTGCG
65 ACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTG
** * * *
35172437 GCTTCAATCTTTTAAATTGCAAAATCGGGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCC
1 GCTTCAATCTTTT-AATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCC
* * *
35172502 ACTGTACTGCCAGGGAAGTAAGATTCGCCGTTGCG
65 ACTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTG
* * * * *
35172537 GCTTCAATATTTTTAATTGCAATATCGGGGAAGTAAGATTCGCCGTCGTAGCTTTAATCTGCTCC
1 GCTTCAAT-CTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCC
* * *
35172602 ACTGCACCGCTTGGGAAAATAAGATTCGCCGTTGTG
65 ACTGCACTGCCTGGG-AAGTAAGATTCGCCGTTGTG
* * *
35172638 GCTTCAATCTTTCAATTGCAATGTCGGGGAAGCAAGATTCACCATTGTAGCTTTAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCA
* * * *
35172703 TTGCACTACCTGGGAAAGTAAGATTTGTCGTTGTG
66 CTGCACTGCCTGGG-AAGTAAGATTCGCCGTTGTG
* * *
35172738 GCTTCAATATTTTAATTGCAATGTCGGGGAAGCGAGATTCGTCGTTGTAGCTTTAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCA
** *
35172803 CTGCACCACCTGGGAAAGTAAGATTTGCCGTTGTG
66 CTGCACTGCCTGGG-AAGTAAGATTCGCCGTTGTG
* * * * *
35172838 GTTTCAAT-TTTTAATTGCAATGTCGGGGAAGCGAGATTCACCATTGTAGCTTCAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCA
* * *
35172902 CTGCACCGCCTGGGAAAGTAAGATTTGCCATTGTG
66 CTGCACTGCCTGGG-AAGTAAGATTCGCCGTTGTG
** * *
35172937 GCTTCAATCTTTTAATTGCAATGTCGAAGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCA
*
35173002 CTACA-TCGCCTGGGAAGGTAAGATTCGCCGTTGTG
66 CTGCACT-GCCTGGGAA-GTAAGATTCGCCGTTGTG
* ** * *
35173037 GCCTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGATTCGCCGTTGTGGCTTCAATCTGTTCCA
1 GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCA
* * * * *
35173102 TTGCACCGCCTAGGAGATTAAGATTCGCCATTGTG
66 CTGCACTGCCTGGGA-AGTAAGATTCGCCGTTGTG
*
35173137 GCTTCAATATTTTAATT
1 GCTTCAATCTTTTAATT
35173154 ACAAACTATG
Statistics
Matches: 720, Mismatches: 88, Indels: 17
0.87 0.11 0.02
Matches are distributed among these distances:
98 24 0.03
99 133 0.18
100 532 0.74
101 31 0.04
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (99 bp):
GCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGTTCCA
CTGCACTGCCTGGGAAGTAAGATTCGCCGTTGTG
Found at i:35172618 original size:50 final size:50
Alignment explanation
Indices: 35172464--35172647 Score: 127
Period size: 50 Copynumber: 3.7 Consensus size: 50
35172454 TGCAAAATCG
* * * * * *
35172464 GGGAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCA
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACAGCTA
* ** * ** ** * ** *
35172514 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATATTTTTAATTGCA-ATATCG
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACAGCT-A
* * *
35172564 GGGAAGTAAGATTCGCCGTCGTAGCTTTAATCTGCTCCACTGCACCGCTT
1 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACAGCTA
* * *
35172614 GGGAAAATAAGATTCGCCGTTGTGGCTTCAATCT
1 GGG-AAGTAAGATTCGCCGTCGTAGCTTCAATCT
35172648 TTCAATTGCA
Statistics
Matches: 95, Mismatches: 36, Indels: 5
0.70 0.26 0.04
Matches are distributed among these distances:
50 68 0.72
51 27 0.28
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTGCTCCACTGCACAGCTA
Found at i:35172959 original size:299 final size:298
Alignment explanation
Indices: 35172238--35173153 Score: 1113
Period size: 299 Copynumber: 3.1 Consensus size: 298
35172228 GCAATGTATA
* * * *
35172238 GCTTCAATCTTTTTAAACTGCAATGTCGGGGAAACAAATTCGCTGTTGTAGCTTCAATCTGTTCC
1 GCTTCAA--TTTTT-AATTGCAATGTCGGGGAAGCAGATTCGCCGTTGTAGCTTCAATCTGTTCC
* * * * * *
35172303 ACTACACTGCC-GGG-AAGTAAGATTCGTCATTGCGGTTTCAATCTTTTAAATTGCAATATCGGG
63 ACTGCACCGCCTGGGAAAGTAAGATTCGCCATTGTGGCTTCAATCTTTT-AATTGCAATGTCGGG
** ** * * *
35172366 GAAGCAAGATTTGCCGTCCTAGCTTTAATCTGCTCCATTGCACTGCCAGAG-AAGTAAGATTCGT
127 GAAGCAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCACTGCCTGGGAAAGTAAGATTCGT
* * ** * * *
35172430 CATTGCGGCTTCAATCTTTTAAATTGCAAAATCGGGGAAGCAAGATTCACCGTCGTAGCTTTAAT
192 CGTTGTGGCTTCAATCTTTT-AATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTTAAT
* * * * *
35172495 CTGCTCCACTGTACTGCCAGGG-AAGTAAGATTCGCCGTTGCG
256 CTGTTCCACTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTG
* * * * *
35172537 GCTTCAATATTTTTAATTGCAATATCGGGGAAGTAAGATTCGCCGTCGTAGCTTTAATCTGCTCC
1 GCTTC-A-ATTTTTAATTGCAATGTCGGGGAAG-CAGATTCGCCGTTGTAGCTTCAATCTGTTCC
* * * *
35172602 ACTGCACCGCTTGGGAAAATAAGATTCGCCGTTGTGGCTTCAATCTTTCAATTGCAATGTCGGGG
63 ACTGCACCGCCTGGGAAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTAATTGCAATGTCGGGG
* * *
35172667 AAGCAAGATTCACCATTGTAGCTTTAATCTGTTCCATTGCACTACCTGGGAAAGTAAGATTTGTC
128 AAGCAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCACTGCCTGGGAAAGTAAGATTCGTC
* *
35172732 GTTGTGGCTTCAATATTTTAATTGCAATGTCGGGGAAGCGAGATTCGTCGTTGTAGCTTTAATCT
193 GTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTTAATCT
* *
35172797 GTTCCACTGCACCACCTGGGAAAGTAAGATTTGCCGTTGTG
258 GTTCCACTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTG
* * *
35172838 GTTTCAATTTTTAATTGCAATGTCGGGGAAGCGAGATTCACCATTGTAGCTTCAATCTGTTCCAC
1 GCTTCAATTTTTAATTGCAATGTCGGGGAAGC-AGATTCGCCGTTGTAGCTTCAATCTGTTCCAC
* **
35172903 TGCACCGCCTGGGAAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTAATTGCAATGTCGAAGAA
65 TGCACCGCCTGGGAAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAA
* * * * *
35172968 GCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTACA-TCGCCTGGGAAGGTAAGATTCGCCG
130 GCAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCACT-GCCTGGGAAAGTAAGATTCGTCG
* * * *
35173032 TTGTGGCCTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGATTCGCCGTTGTGGCTTCAATCTG
194 TTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTTAATCTG
* * * * *
35173097 TTCCATTGCACCGCCTAGGAGATTAAGATTCGCCATTGTG
259 TTCCACTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTG
35173137 GCTTCAATATTTTAATT
1 GCTTCAAT-TTTTAATT
35173154 ACAAACTATG
Statistics
Matches: 525, Mismatches: 82, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
298 17 0.03
299 305 0.58
300 124 0.24
301 79 0.15
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (298 bp):
GCTTCAATTTTTAATTGCAATGTCGGGGAAGCAGATTCGCCGTTGTAGCTTCAATCTGTTCCACT
GCACCGCCTGGGAAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAG
CAAGATTCACCGTTGTAGCTTTAATCTGTTCCATTGCACTGCCTGGGAAAGTAAGATTCGTCGTT
GTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGCGAGATTCGCCGTTGTAGCTTTAATCTGTT
CCACTGCACCGCCTGGGAAAGTAAGATTCGCCGTTGTG
Found at i:35177124 original size:19 final size:19
Alignment explanation
Indices: 35177077--35177128 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
35177067 CCTTTTGTGA
*
35177077 AAATCTAATGCAAATGATG
1 AAATGTAATGCAAATGATG
* *
35177096 CACTGTAATGCAAATGCATG
1 AAATGTAATGCAAATG-ATG
35177116 AAATG-AATGCAAA
1 AAATGTAATGCAAA
35177129 AAGAAATAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.23
Consensus pattern (19 bp):
AAATGTAATGCAAATGATG
Found at i:35180243 original size:11 final size:11
Alignment explanation
Indices: 35180229--35180268 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
35180219 TCTTATGTAG
35180229 AAAATAAAATA
1 AAAATAAAATA
35180240 AAAATAAAAT-
1 AAAATAAAATA
*
35180250 AAAATGAAATA
1 AAAATAAAATA
*
35180261 AACATAAA
1 AAAATAAA
35180269 CGCAAATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:35180250 original size:16 final size:15
Alignment explanation
Indices: 35180229--35180268 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
35180219 TCTTATGTAG
35180229 AAAATAAAATAAAAAT
1 AAAATAAAAT-AAAAT
*
35180245 AAAATAAAATGAAAT
1 AAAATAAAATAAAAT
35180260 AAACATAAA
1 AAA-ATAAA
35180269 CGCAAATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:35180269 original size:6 final size:5
Alignment explanation
Indices: 35180229--35180268 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
35180219 TCTTATGTAG
*
35180229 AAAAT AAAAT AAAAAT AAAAT AAAAT GAAAT AAACAT AAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAA-AT AAA
35180269 CGCAAATCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 21 0.68
6 10 0.32
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:35181810 original size:38 final size:38
Alignment explanation
Indices: 35181756--35181847 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
35181746 GGTATCCATT
** * *
35181756 CGATAACGTGCCAGATTGCTTATAAGAGCTATTCCAAC
1 CGATAACACGCCAGATTGCTCATAAGAGATATTCCAAC
* *
35181794 CGATAACACGCTAGATTGCTCATAAGAGATATTTCAAC
1 CGATAACACGCCAGATTGCTCATAAGAGATATTCCAAC
*
35181832 CGATAATACGCCAGAT
1 CGATAACACGCCAGAT
35181848 GCACATAGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (38 bp):
CGATAACACGCCAGATTGCTCATAAGAGATATTCCAAC
Found at i:35181968 original size:92 final size:92
Alignment explanation
Indices: 35181793--35182083 Score: 318
Period size: 92 Copynumber: 3.2 Consensus size: 92
35181783 GCTATTCCAA
* * * * * *
35181793 CCGATAACACGCTAGATTGCTCATAAGAGATATTTCAACCGATAATACGCCAGATGCACATAGTG
1 CCGATAACATGCCAAATTGCTCATAAGAGTTATTTCAACCGATAACACGCTAGATGCACATAGTG
* * * *
35181858 CAAAGCACGTAGGTTAAATATTCTTCC
66 CAAAACCCTTAGGCTAAATATTCTTCC
* * * *
35181885 CCGATAACATGCCAAATTGCTAATAAGAGTTATTTCAATCAATAACACGTTAGATGCACATAGTG
1 CCGATAACATGCCAAATTGCTCATAAGAGTTATTTCAACCGATAACACGCTAGATGCACATAGTG
* *
35181950 TAAAACCCTTAGGCTAAATGTTC-TCC
66 CAAAACCCTTAGGCTAAATATTCTTCC
* * * * * *
35181976 TCCTATAA-ATGCCAAATTGTTCATAAAAGTTATTACAACCGATAACACGCTAGATACGCATAGT
1 -CCGATAACATGCCAAATTGCTCATAAGAGTTATTTCAACCGATAACACGCTAGATGCACATAGT
* *
35182040 ACAAAA-CCTGTAGGCTAAATATTCTCCC
65 GCAAAACCCT-TAGGCTAAATATTCTTCC
*
35182068 CCGATAACCTGCCAAA
1 CCGATAACATGCCAAA
35182084 ATCTCTGAAA
Statistics
Matches: 163, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
90 3 0.02
91 73 0.45
92 87 0.53
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (92 bp):
CCGATAACATGCCAAATTGCTCATAAGAGTTATTTCAACCGATAACACGCTAGATGCACATAGTG
CAAAACCCTTAGGCTAAATATTCTTCC
Found at i:35182095 original size:91 final size:89
Alignment explanation
Indices: 35181823--35182095 Score: 257
Period size: 91 Copynumber: 3.0 Consensus size: 89
35181813 TCATAAGAGA
* * * * *
35181823 TATTTCAACCGATAATACGCCAGATGCACATAGTGCAAAGCAC-GTAGGTTAAATATTCTTCCCC
1 TATTTCAACCGATAACACGCTAGATGCACATAGTGCAAAAC-CTGTAGGCTAAATATTCTCCCCC
35181887 GATAACATGCC-AAATTGCTAATAAGAGT
65 GATAACATGCCAAAATT-CT-A-AA-AGT
* * * * * *
35181915 TATTTCAATCAATAACACGTTAGATGCACATAGTGTAAAACCCT-TAGGCTAAATGTTCTCCTCC
1 TATTTCAACCGATAACACGCTAGATGCACATAGTGCAAAA-CCTGTAGGCTAAATATTCTCCCCC
* *
35181979 TATAA-ATGCCAAATTGTTCATAAAAGT
65 GATAACATGCCAAA--ATTC-TAAAAGT
* * * *
35182006 TATTACAACCGATAACACGCTAGATACGCATAGTACAAAACCTGTAGGCTAAATATTCTCCCCCG
1 TATTTCAACCGATAACACGCTAGATGCACATAGTGCAAAACCTGTAGGCTAAATATTCTCCCCCG
*
35182071 ATAACCTGCCAAAATCTCTGAAAAG
66 ATAACATGCCAAAAT-TCT-AAAAG
35182096 ATTAAATTGG
Statistics
Matches: 145, Mismatches: 26, Indels: 21
0.76 0.14 0.11
Matches are distributed among these distances:
90 5 0.03
91 69 0.48
92 65 0.45
93 3 0.02
94 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (89 bp):
TATTTCAACCGATAACACGCTAGATGCACATAGTGCAAAACCTGTAGGCTAAATATTCTCCCCCG
ATAACATGCCAAAATTCTAAAAGT
Found at i:35182751 original size:26 final size:26
Alignment explanation
Indices: 35182722--35182774 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
35182712 CCTATAATAC
35182722 TTAACACATTAATTTTCATAGTTAAA
1 TTAACACATTAATTTTCATAGTTAAA
35182748 TTAACACATTAATTTTCATAGTTAAA
1 TTAACACATTAATTTTCATAGTTAAA
35182774 T
1 T
35182775 GAAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (26 bp):
TTAACACATTAATTTTCATAGTTAAA
Found at i:35184867 original size:20 final size:21
Alignment explanation
Indices: 35184805--35184851 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
35184795 TTTGTTGTAA
*
35184805 AATGAGTCTTAGTTTATTTTT
1 AATGTGTCTTAGTTTATTTTT
35184826 AATGTGTCTTAGTTTATTTTT
1 AATGTGTCTTAGTTTATTTTT
35184847 AATGT
1 AATGT
35184852 TTTTAGGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.04, G:0.15, T:0.57
Consensus pattern (21 bp):
AATGTGTCTTAGTTTATTTTT
Found at i:35193469 original size:27 final size:27
Alignment explanation
Indices: 35193431--35193482 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
35193421 AGACACACGA
*
35193431 CTGTGTGTGGCACGACTGTGTGACATC
1 CTGTGTGTGGCACGACCGTGTGACATC
*
35193458 CTGTGTGTGGCATGACCGTGTGACA
1 CTGTGTGTGGCACGACCGTGTGACA
35193483 ACCCATGTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (27 bp):
CTGTGTGTGGCACGACCGTGTGACATC
Found at i:35196843 original size:31 final size:31
Alignment explanation
Indices: 35196804--35196877 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
35196794 AAGAGTTACA
**
35196804 ATTT-AGTCATTGAACTATTTGAAAGTTTTC
1 ATTTAAGTCATTGAACTATTCAAAAGTTTTC
* *
35196834 ATTTAAGTCACTGAACTATTCAAAAGTTTTT
1 ATTTAAGTCATTGAACTATTCAAAAGTTTTC
35196865 ATTTAAGTCATTG
1 ATTTAAGTCATTG
35196878 GTATGTTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 4 0.11
31 34 0.89
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTAAGTCATTGAACTATTCAAAAGTTTTC
Found at i:35198113 original size:2 final size:2
Alignment explanation
Indices: 35198108--35198135 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35198098 ATAAATATGC
35198108 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
35198136 GGTTTCTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35204590 original size:19 final size:20
Alignment explanation
Indices: 35204566--35204603 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
35204556 ATTGTTAAAG
35204566 AATATA-GTGTATA-GTTGTA
1 AATATATGT-TATAGGTTGTA
35204585 AATATATGTTATAGGTTGT
1 AATATATGTTATAGGTTGT
35204604 TTTTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (20 bp):
AATATATGTTATAGGTTGTA
Found at i:35208730 original size:13 final size:13
Alignment explanation
Indices: 35208712--35208736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35208702 TTGGTTATAT
35208712 GTGTGAAAATTTC
1 GTGTGAAAATTTC
35208725 GTGTGAAAATTT
1 GTGTGAAAATTT
35208737 AATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:35210026 original size:2 final size:2
Alignment explanation
Indices: 35209984--35210008 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35209974 AGTATAAGAA
35209984 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
35210009 ATGACTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35210256 original size:41 final size:42
Alignment explanation
Indices: 35210107--35210267 Score: 207
Period size: 42 Copynumber: 3.8 Consensus size: 42
35210097 ATTGGAATAT
* *
35210107 AATTGATTTTCAGGCTTAATGCCTAGTAGGCTTGATGCCGGTG
1 AATT-ATTTTCAGACTTAATGCCTAGCAGGCTTGATGCCGGTG
* * * *
35210150 AATTATTTTTAGGCTTAATGCCTAGCAAGCTTGATACCGGTG
1 AATTATTTTCAGACTTAATGCCTAGCAGGCTTGATGCCGGTG
* *
35210192 AATTATTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTG
1 AATTATTTTCAGACTTAATGCCTAGCAGGCTTGATGCCGGTG
* * *
35210234 AATTA-CTTCAGACTTTATGTCTAGCAGGCTTGAT
1 AATTATTTTCAGACTTAATGCCTAGCAGGCTTGAT
35210268 ATGAGTTGAA
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 28 0.26
42 75 0.70
43 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (42 bp):
AATTATTTTCAGACTTAATGCCTAGCAGGCTTGATGCCGGTG
Found at i:35210415 original size:42 final size:42
Alignment explanation
Indices: 35210340--35210507 Score: 185
Period size: 42 Copynumber: 4.0 Consensus size: 42
35210330 ATTGGAATAT
* * *
35210340 AATTGATTTTTAGGCTTAATGCATAGTAGGCTTGATGCCAGTG
1 AATT-ATTTTTAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG
* * *
35210383 AACTATTTTTAGGCTTAATGCCTAGCAAGCTTGATGTCGGTG
1 AATTATTTTTAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG
* * * *
35210425 AATTATCTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTG
1 AATTATTTTTAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG
* * * * *
35210467 AATTA-TTTCAGACTTATTGTCTAGCAGGCTTCATGCCGGTG
1 AATTATTTTTAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG
35210508 TACTTCAGTA
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 31 0.29
42 73 0.68
43 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (42 bp):
AATTATTTTTAGGCTTAATGCCTAGCAGGCTTGATGCCGGTG
Found at i:35210444 original size:233 final size:233
Alignment explanation
Indices: 35210037--35210497 Score: 791
Period size: 233 Copynumber: 2.0 Consensus size: 233
35210027 TGAGTTTGAC
* *
35210037 GAGTTGAATTTATTGGTGTGAACTATTGTTAGCTTATTCGAATGTATGTTGGTTATGAATATTGG
1 GAGTTGAATTTAATGGTGTGAACTATTGTTAGCTTATTCGAATGTATGTTGGTAATGAATATTGG
* * *
35210102 AATATAATTGATTTTCAGGCTTAATGCCTAGTAGGCTTGATGCCGGTGAATTATTTTTAGGCTTA
66 AATATAATTGATTTTCAGGCTTAATGCATAGTAGGCTTGATGCCAGTGAACTATTTTTAGGCTTA
35210167 ATGCCTAGCAAGCTTGATACCGGTGAATTATTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGG
131 ATGCCTAGCAAGCTTGATACCGGTGAATTATTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGG
35210232 TGAATTACTTCAGACTT-TATGTCTAGCAGGCTTGATAT
196 TGAATTACTTCAGACTTAT-TGTCTAGCAGGCTTGATAT
* *
35210270 GAGTTGAATTTAATGGTGTGAACTATTGTTAGGTTATTCGAATGTATGTTGGTAATGTATATTGG
1 GAGTTGAATTTAATGGTGTGAACTATTGTTAGCTTATTCGAATGTATGTTGGTAATGAATATTGG
*
35210335 AATATAATTGATTTTTAGGCTTAATGCATAGTAGGCTTGATGCCAGTGAACTATTTTTAGGCTTA
66 AATATAATTGATTTTCAGGCTTAATGCATAGTAGGCTTGATGCCAGTGAACTATTTTTAGGCTTA
**
35210400 ATGCCTAGCAAGCTTGATGTCGGTGAATTATCTTT-AGACTTTATGTCTAGCAGGCTTGATGCCG
131 ATGCCTAGCAAGCTTGATACCGGTGAATTAT-TTTCAGACTTTATGTCTAGCAGGCTTGATGCCG
*
35210464 GTGAATTATTTCAGACTTATTGTCTAGCAGGCTT
195 GTGAATTACTTCAGACTTATTGTCTAGCAGGCTT
35210498 CATGCCGGTG
Statistics
Matches: 215, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
233 211 0.98
234 4 0.02
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.39
Consensus pattern (233 bp):
GAGTTGAATTTAATGGTGTGAACTATTGTTAGCTTATTCGAATGTATGTTGGTAATGAATATTGG
AATATAATTGATTTTCAGGCTTAATGCATAGTAGGCTTGATGCCAGTGAACTATTTTTAGGCTTA
ATGCCTAGCAAGCTTGATACCGGTGAATTATTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGG
TGAATTACTTCAGACTTATTGTCTAGCAGGCTTGATAT
Found at i:35212763 original size:11 final size:13
Alignment explanation
Indices: 35212747--35212780 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
35212737 ATTTTACGGA
35212747 AAAAATTTCG-T-
1 AAAAATTTCGTTC
35212758 AAAAATTTCGTTC
1 AAAAATTTCGTTC
35212771 AAAAATTTCG
1 AAAAATTTCG
35212781 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:35221479 original size:42 final size:42
Alignment explanation
Indices: 35221415--35221623 Score: 269
Period size: 42 Copynumber: 5.0 Consensus size: 42
35221405 ATTGGAATAT
* * *
35221415 AATTGATTTTCAGGCTTAATGCCTAGTAGGCTTGATGCCGGTG
1 AATT-ATTTTCAGACTTAATGTCTAGCAGGCTTGATGCCGGTG
* * * * *
35221458 AATTATTTTTAGGCTTAATGCCTAGCAAGCTTGATACCGGTG
1 AATTATTTTCAGACTTAATGTCTAGCAGGCTTGATGCCGGTG
*
35221500 AATTATTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTG
1 AATTATTTTCAGACTTAATGTCTAGCAGGCTTGATGCCGGTG
* * *
35221542 AATTA-CTTCAGACTTTATGTCTAGCAGGCTTGATGCTGGTG
1 AATTATTTTCAGACTTAATGTCTAGCAGGCTTGATGCCGGTG
* *
35221583 AATTA-TTTCAGACTTATTGTCTAGCAGGCTTCATGCCGGTG
1 AATTATTTTCAGACTTAATGTCTAGCAGGCTTGATGCCGGTG
35221624 TACTTCAGTA
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 70 0.47
42 75 0.50
43 4 0.03
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (42 bp):
AATTATTTTCAGACTTAATGTCTAGCAGGCTTGATGCCGGTG
Found at i:35236992 original size:30 final size:30
Alignment explanation
Indices: 35236948--35237010 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
35236938 ACTTAACAAG
35236948 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
35236978 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
35237008 CAA
1 CAA
35237011 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:35240643 original size:7 final size:8
Alignment explanation
Indices: 35240627--35240652 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
35240617 TTAAGATACA
35240627 TTTTATTT
1 TTTTATTT
35240635 TTTTATTT
1 TTTTATTT
35240643 TTTTATTT
1 TTTTATTT
35240651 TT
1 TT
35240653 CCCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:35244362 original size:16 final size:16
Alignment explanation
Indices: 35244319--35244362 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
35244309 TTTGTTTTAT
*
35244319 TTAATCTTTTAACTTAA
1 TTAATCTTTT-ACTAAA
*
35244336 TTAATCATTTACTAAA
1 TTAATCTTTTACTAAA
*
35244352 TTAACCTTTTA
1 TTAATCTTTTA
35244363 AAAACTATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATCTTTTACTAAA
Found at i:35250331 original size:19 final size:18
Alignment explanation
Indices: 35250288--35250331 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35250278 AAAAAAGTTC
*
35250288 TGAAATTGAATAATGATT
1 TGAAAATGAATAATGATT
* *
35250306 TGTAAATGAATAATGTTT
1 TGAAAATGAATAATGATT
35250324 TGGAAAAT
1 T-GAAAAT
35250332 AACGACATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (18 bp):
TGAAAATGAATAATGATT
Found at i:35252501 original size:22 final size:22
Alignment explanation
Indices: 35252450--35252509 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
35252440 GACATTGGCG
35252450 GGCT-ATGTCTCGAGACAAACA
1 GGCTAATGTCTCGAGACAAACA
* * *
35252471 GAC-ATATGTCTCGAGACATATA
1 GGCTA-ATGTCTCGAGACAAACA
*
35252493 GGCTAATGTCTCTAGAC
1 GGCTAATGTCTCGAGAC
35252510 TTGCAACCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (22 bp):
GGCTAATGTCTCGAGACAAACA
Found at i:35252829 original size:65 final size:65
Alignment explanation
Indices: 35252723--35252853 Score: 190
Period size: 65 Copynumber: 2.0 Consensus size: 65
35252713 TATAAAAAAA
* * *
35252723 TTTATCTTAAATATTGTTATATCAAAAGCTTGAGACATCAAAATTAACTCGTATAATTGATACCT
1 TTTATCTTAAATATTGTTATATCAAAAGCTTGAGACATCAAAATTAACACGAATAATTAATACCT
* * ** *
35252788 TTTATCTTAAATGTTGTTATATCAAAAGTTTGAGATTTCAAAATTAACACGAATAGTTAATACCT
1 TTTATCTTAAATATTGTTATATCAAAAGCTTGAGACATCAAAATTAACACGAATAATTAATACCT
35252853 T
1 T
35252854 CAATTAATTG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (65 bp):
TTTATCTTAAATATTGTTATATCAAAAGCTTGAGACATCAAAATTAACACGAATAATTAATACCT
Found at i:35257778 original size:60 final size:60
Alignment explanation
Indices: 35257641--35257778 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 60
35257631 CAAAAAATTG
* * ** *
35257641 ATTTGTTGAATTTTTTAAAATTAAAACTAAGTCGATAAATTTTATAAATTTTGAGGGCTAA
1 ATTTGTTGAATTTTTT-AAATTAAAACTAAATCGACAAATTTTATAAACATTGAGAGCTAA
* * * *
35257702 ATTTATT-AATTTTTTTAAATTCAAATTAAAAT-GACAAATTTTGTAAACATTGAGAGCTAA
1 ATTTGTTGAA-TTTTTTAAATTAAAACT-AAATCGACAAATTTTATAAACATTGAGAGCTAA
*
35257762 ATTTGTTGAATGTTTTA
1 ATTTGTTGAATTTTTTA
35257779 TATTTAGAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
60 46 0.73
61 17 0.27
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (60 bp):
ATTTGTTGAATTTTTTAAATTAAAACTAAATCGACAAATTTTATAAACATTGAGAGCTAA
Found at i:35258703 original size:3 final size:3
Alignment explanation
Indices: 35258695--35258741 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
35258685 GAAAAGGGGT
*
35258695 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35258742 GGAAACTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35263579 original size:19 final size:20
Alignment explanation
Indices: 35263552--35263591 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
35263542 AAATTTATAT
*
35263552 TTTTAAAAAAAATTTAAAAA
1 TTTTAAAAAAAATTAAAAAA
*
35263572 TTTT-AAAAATATTAAAAAA
1 TTTTAAAAAAAATTAAAAAA
35263591 T
1 T
35263592 CTAAAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTTAAAAAAAATTAAAAAA
Found at i:35263596 original size:9 final size:9
Alignment explanation
Indices: 35263558--35263622 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
35263548 ATATTTTTAA
35263558 AAAAAATTT
1 AAAAAATTT
35263567 -AAAAATTT
1 AAAAAATTT
*
35263575 TAAAAATATT
1 AAAAAAT-TT
*
35263585 AAAAAATCT
1 AAAAAATTT
*
35263594 AAAGAATATAT
1 AAA-AA-ATTT
**
35263605 AAAAAATAA
1 AAAAAATTT
35263614 AAAAAATTT
1 AAAAAATTT
35263623 CTAAAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 8 0.17
9 20 0.43
10 12 0.26
11 6 0.13
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAAATTT
Found at i:35263601 original size:19 final size:18
Alignment explanation
Indices: 35263559--35263611 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
35263549 TATTTTTAAA
* *
35263559 AAAAAT-TTAAAAATTTT
1 AAAAATATTAAAAAATCT
35263576 AAAAATATTAAAAAATCT
1 AAAAATATTAAAAAATCT
35263594 AAAGAATATATAAAAAAT
1 AAA-AATAT-TAAAAAAT
35263612 AAAAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 5 0.16
20 8 0.26
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATATTAAAAAATCT
Found at i:35264153 original size:21 final size:20
Alignment explanation
Indices: 35264123--35264163 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
35264113 TGAGATTCAA
*
35264123 AAGCACTTTTCAACCCAAAC
1 AAGCACTTTTCAAACCAAAC
35264143 AAGCAGCTTTTCAAACCAAAC
1 AAGCA-CTTTTCAAACCAAAC
35264164 CTGATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.41, C:0.32, G:0.07, T:0.20
Consensus pattern (20 bp):
AAGCACTTTTCAAACCAAAC
Found at i:35267120 original size:54 final size:54
Alignment explanation
Indices: 35267057--35267165 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
35267047 GCCAAGGTCT
* *
35267057 ATGTATCTGTACAAATATCAAGTCTTTTACGGGTTTGGTGTCACAAGTTAGTTG
1 ATGTATCTGTACAAATATCAAGTATTTTACCGGTTTGGTGTCACAAGTTAGTTG
* *
35267111 ATGTATCTGTACAAATATCAAGTATTTTGCCGGTTTGGTGTCACAATTTAGTTG
1 ATGTATCTGTACAAATATCAAGTATTTTACCGGTTTGGTGTCACAAGTTAGTTG
35267165 A
1 A
35267166 CATCAATCTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (54 bp):
ATGTATCTGTACAAATATCAAGTATTTTACCGGTTTGGTGTCACAAGTTAGTTG
Found at i:35269216 original size:3 final size:3
Alignment explanation
Indices: 35269210--35269254 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
35269200 AAAAACGGTG
*
35269210 ATA ATA ATA ATA ATA ATAA ATA ATA GTA ATA GATTA ATA ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -A-TA ATA ATA ATA
35269255 TTACCGAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 30 0.81
4 5 0.14
5 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35270071 original size:27 final size:27
Alignment explanation
Indices: 35270020--35270072 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
35270010 ATTTTTCTCC
*
35270020 TATTTTTCTTTTTTGTTGCTAGTTTGT
1 TATTTTTCTTTTTTCTTGCTAGTTTGT
*
35270047 TATTTTTCTTTTTCTCTTTCT-GTTTG
1 TATTTTTCTTTTT-TCTTGCTAGTTTG
35270073 CTGCTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (27 bp):
TATTTTTCTTTTTTCTTGCTAGTTTGT
Found at i:35270792 original size:44 final size:43
Alignment explanation
Indices: 35270737--35271058 Score: 201
Period size: 44 Copynumber: 7.5 Consensus size: 43
35270727 GATCTACTTT
**
35270737 ACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCC
1 ACTGCAACTTCAGAGAGATAAGATCTG-GATTTTAATCTGCTCC
* * * * **
35270781 ACTGCACCTTCAGGGAGATAGGAT-TGGTTTCTTCTGTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCTGGATT-TT-AATCTGCTCC
*** * *
35270825 ACTGCAACTTCAGAGAGATAAGA-CTGGA-TGCGATTTGCTCT
1 ACTGCAACTTCAGAGAGATAAGATCTGGATTTTAATCTGCTCC
* * **
35270866 ACTGCAACTTCAGAGAGAGAAGATCTGTGGTTTTAATCCACTCC
1 ACTGCAACTTCAGAGAGATAAGATCTG-GATTTTAATCTGCTCC
* * * * * **
35270910 ACTACACCTTCAGGGAGATAGGAT-TGGTTTCTTCTGTCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCTGGATT-TT-AATCTGCTCC
*** *
35270954 ACTGCAACTTCACG-GAGATAAGA-CTGGA-TACGATCTGCTCT
1 ACTGCAACTTCA-GAGAGATAAGATCTGGATTTTAATCTGCTCC
* * *
35270995 ACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAAT-TCACTCC
1 ACTGCAACTTCAGAGAGATAAGATCTG-GATTTTAATCT-GCTCC
* * *
35271039 ACTGCACCTCCAGGGAGATA
1 ACTGCAACTTCAGAGAGATA
35271059 GGATTGGTTT
Statistics
Matches: 206, Mismatches: 57, Indels: 30
0.70 0.19 0.10
Matches are distributed among these distances:
40 1 0.00
41 55 0.27
42 12 0.06
43 13 0.06
44 124 0.60
45 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (43 bp):
ACTGCAACTTCAGAGAGATAAGATCTGGATTTTAATCTGCTCC
Found at i:35270837 original size:129 final size:129
Alignment explanation
Indices: 35270681--35271071 Score: 622
Period size: 129 Copynumber: 3.0 Consensus size: 129
35270671 AAATCCGCCA
* * * * * *
35270681 TCTTCAGTCTGCCCCTCTGCAACTTCAGGGGGATAAGACCT-GATGCGATCTACTTTACTGCAAC
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTGGATGCGATCTGCTCTACTGCAAC
*
35270745 TTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCACCTTCAGGGAGATAGGATTGGTT
65 TTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCACCTTCAGGGAGATAGGATTGGTT
* *
35270810 TCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCGATTTGCTCTACTGCAACT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
* *
35270875 TCAGAGAGAGAAGATCTGTGGTTTTAATCCACTCCACTACACCTTCAGGGAGATAGGATTGGTT
66 TCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCACCTTCAGGGAGATAGGATTGGTT
* * *
35270939 TCTTCTGTCTGCTCCACTGCAACTTCACGGAGATAAGACTGGATACGATCTGCTCTACTGTAACT
1 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
* *
35271004 TCAGAGAGATAAGATCTGTGGTTTTAATTCACTCCACTGCACCTCCAGGGAGATAGGATTGGTT
66 TCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCACCTTCAGGGAGATAGGATTGGTT
35271068 TCTT
1 TCTT
35271072 GTAGCTTCTC
Statistics
Matches: 241, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
128 2 0.01
129 239 0.99
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (129 bp):
TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACT
TCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGCACCTTCAGGGAGATAGGATTGGTT
Found at i:35271479 original size:44 final size:44
Alignment explanation
Indices: 35271408--35271698 Score: 182
Period size: 44 Copynumber: 6.7 Consensus size: 44
35271398 ACCTGATGCG
* * * *
35271408 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTTCA
* * * ** * * *
35271452 ATCCGCTCCACTGTAATTTCAGGGAGATAGGATAGTGT-CTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTTCA
* * ***
35271495 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTATTTCA
*** *
35271539 ATCTGCTCCACTGTAACCTT-AGGGAGATAAGATCTAAAATTCTTCG
1 ATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATCTTTTA-T-TTCA
* * * * * *
35271585 TTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-TTGA-TGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTTCA
* * * * * *
35271626 ATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTTCA
*
35271670 ATCCGCTCCACTGCT-ACTTCAGGGAGATA
1 ATCTGCTCCACTG-TAACTTCAGGGAGATA
35271699 GGATTATCAG
Statistics
Matches: 187, Mismatches: 49, Indels: 22
0.72 0.19 0.09
Matches are distributed among these distances:
41 30 0.16
42 2 0.01
43 33 0.18
44 87 0.47
45 5 0.03
46 30 0.16
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTTCA
Found at i:35271569 original size:218 final size:217
Alignment explanation
Indices: 35271174--35271702 Score: 665
Period size: 218 Copynumber: 2.4 Consensus size: 217
35271164 CAACTTTTAA
* * * * * * * * * *
35271174 AGATAAG-TCTGATGAGATCTGCTCTACTGCAACTTTAGAGGGATGAGATCCATCATTTTGATCC
1 AGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
* * * * * * *
35271238 GCTCCACTGCAACTTCAGGGAAATAAGATTTCTTGCTTCTATCTGCTCCGCTGTAATCTTAGAGA
66 GCTCCACTGTAACTTCAGGGAGATAGGATGTCGTGCTTCGATCTGCTCCGCTGTAATCTCAGAGA
* * * *
35271303 AATAAGATTGGTATCCTCGATCTGCTCCATTACTGCTTAGGGAGATAAGACCTGAAATTCTTCGG
131 AATAAGATTGCTAGCCTCAATCTGCTCCATTAC-GCTTAGGGAGATAAGACCTAAAATTCTTCGG
35271368 TCTACTCCACTGTAACCTCAGAG
195 TCTACTCCACTGTAACCTCAGAG
*
35271391 AGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCC
1 AGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
* *
35271456 GCTCCACTGTAATTTCAGGGAGATAGGATAGT-GT-CTTCGATCTGCTCCGCTGTAATCTCAGGG
66 GCTCCACTGTAACTTCAGGGAGATAGGAT-GTCGTGCTTCGATCTGCTCCGCTGTAATCTCAGAG
* * * *
35271519 AGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAAC-CTTAGGGAGATAAGATCTAAAATTCT
130 AAATAAGAT-TGCTAGCCTCAATCTGCTCCA-T-T-ACGCTTAGGGAGATAAGACCTAAAATTCT
* *
35271582 TCGTTCTACTCCACTGTAACCTCAGGG
191 TCGGTCTACTCCACTGTAACCTCAGAG
* *
35271609 AGATAAGACTTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 AGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
35271674 GCTCCACTGCT-ACTTCAGGGAGATAGGAT
66 GCTCCACTG-TAACTTCAGGGAGATAGGAT
35271703 TATCAGCTTC
Statistics
Matches: 271, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
217 55 0.20
218 211 0.78
219 3 0.01
220 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (217 bp):
AGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
GCTCCACTGTAACTTCAGGGAGATAGGATGTCGTGCTTCGATCTGCTCCGCTGTAATCTCAGAGA
AATAAGATTGCTAGCCTCAATCTGCTCCATTACGCTTAGGGAGATAAGACCTAAAATTCTTCGGT
CTACTCCACTGTAACCTCAGAG
Found at i:35271913 original size:131 final size:131
Alignment explanation
Indices: 35271708--35271965 Score: 351
Period size: 131 Copynumber: 2.0 Consensus size: 131
35271698 AGGATTATCA
* * *
35271708 GCTTCAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTTGCCGCTTAGATCTGTTTCCCTACTC
1 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGCTTAGATCTGCTTCCCTACTC
* * * *
35271773 CTGGGGGGAGATAAGATCCGTAATCTT-CAACCTA-TCCCACTGCTGACCAGGGAGATATGACTA
66 CTGGAGGGAGACAAGATCCGTAAT-TTCCAACCTACT-CCACTGCTGACCAGGGACATAGGACTA
35271836 GTG
129 GTG
* * *
35271839 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTTCGCTACT
1 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCG-CTTAGATCTGCTTCCCTACT
* * *
35271904 GCT-TAGGGAGACAAGATCTGTAATTTCCAACCTACTCCACTGCTGACCAGGGACATAGGACT
65 CCTGGAGGGAGACAAGATCCGTAATTTCCAACCTACTCCACTGCTGACCAGGGACATAGGACT
35271966 TGTGATTTCA
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
130 2 0.02
131 90 0.81
132 19 0.17
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (131 bp):
GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGCTTAGATCTGCTTCCCTACTC
CTGGAGGGAGACAAGATCCGTAATTTCCAACCTACTCCACTGCTGACCAGGGACATAGGACTAGT
G
Found at i:35278876 original size:17 final size:17
Alignment explanation
Indices: 35278854--35278898 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
35278844 AAAACGGTGA
35278854 TAATAATAATAATAAAT
1 TAATAATAATAATAAAT
* *
35278871 TAATAATACTAATAGAT
1 TAATAATAATAATAAAT
35278888 TAATAATAATA
1 TAATAATAATA
35278899 TTACCGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATAATAATAATAAAT
Found at i:35278878 original size:20 final size:20
Alignment explanation
Indices: 35278853--35278898 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
35278843 AAAAACGGTG
35278853 ATAATAATAATA-ATAAATTA
1 ATAATAATAATAGATAAA-TA
* *
35278873 ATAATACTAATAGATTAATA
1 ATAATAATAATAGATAAATA
35278893 ATAATA
1 ATAATA
35278899 TTACCGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAATAATAATAGATAAATA
Found at i:35282193 original size:124 final size:125
Alignment explanation
Indices: 35281972--35282230 Score: 502
Period size: 124 Copynumber: 2.1 Consensus size: 125
35281962 TGGAACTCGT
*
35281972 CATCTTAATTTATGCATCAAAGAAAATGATAAATTAAGCTTCTAAATAAACATGACATGATATCA
1 CATCTTAGTTTATGCATCAAAGAAAATGATAAATTAAGCTTCTAAATAAACATGACATGATATCA
35282037 ACTAAGCCTATGAATTCAACTGAAATCATATTAACCCAATTTTAATTTGTTGTGAAAGGG
66 ACTAAGCCTATGAATTCAACTGAAATCATATTAACCCAATTTTAATTTGTTGTGAAAGGG
35282097 CATCTTAGTTTATGCATC-AAGAAAATGATAAATTAAGCTTCTAAATAAACATGACATGATATCA
1 CATCTTAGTTTATGCATCAAAGAAAATGATAAATTAAGCTTCTAAATAAACATGACATGATATCA
35282161 ACTAAGCCTATGAATTCAACTGAAATCATATTAACCCAATTTTAATTTGTTGTGAAAGGG
66 ACTAAGCCTATGAATTCAACTGAAATCATATTAACCCAATTTTAATTTGTTGTGAAAGGG
35282221 CATCTTAGTT
1 CATCTTAGTT
35282231 GTCTGAACTT
Statistics
Matches: 133, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
124 116 0.87
125 17 0.13
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (125 bp):
CATCTTAGTTTATGCATCAAAGAAAATGATAAATTAAGCTTCTAAATAAACATGACATGATATCA
ACTAAGCCTATGAATTCAACTGAAATCATATTAACCCAATTTTAATTTGTTGTGAAAGGG
Found at i:35285427 original size:11 final size:11
Alignment explanation
Indices: 35285411--35285470 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
35285401 TCTGTCGTTG
*
35285411 TTTTGCTACCA
1 TTTTGCTACTA
*
35285422 TTTTGCTGCTA
1 TTTTGCTACTA
*
35285433 TTTTGTTA-TCA
1 TTTTGCTACT-A
*
35285444 TTTTGCTATTA
1 TTTTGCTACTA
*
35285455 TATTGCTACTA
1 TTTTGCTACTA
35285466 TTTTG
1 TTTTG
35285471 TTGTTATTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 1 0.03
11 37 0.95
12 1 0.03
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.57
Consensus pattern (11 bp):
TTTTGCTACTA
Found at i:35285437 original size:22 final size:22
Alignment explanation
Indices: 35285411--35285470 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
35285401 TCTGTCGTTG
*
35285411 TTTTGCTACCATTTTGCTGCTA
1 TTTTGCTACCATTTTGCTACTA
* * *
35285433 TTTTGTTATCATTTTGCTATTA
1 TTTTGCTACCATTTTGCTACTA
* *
35285455 TATTGCTACTATTTTG
1 TTTTGCTACCATTTTG
35285471 TTGTTATTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTGCTACCATTTTGCTACTA
Found at i:35321617 original size:4 final size:4
Alignment explanation
Indices: 35321608--35321635 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
35321598 CTTTTTCACA
35321608 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
35321636 GTAGGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:35322189 original size:22 final size:22
Alignment explanation
Indices: 35322164--35322206 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35322154 GATTTTAGGG
*
35322164 AAATAT-CACTTTCTCATTTGAA
1 AAATATCCACTTACTC-TTTGAA
35322186 AAATATCCACTTACTCTTTGA
1 AAATATCCACTTACTCTTTGA
35322207 GATTTAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (22 bp):
AAATATCCACTTACTCTTTGAA
Found at i:35323497 original size:38 final size:38
Alignment explanation
Indices: 35323393--35323504 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
35323383 AAGCTATGAA
*
35323393 CAATTCAACACTAGTAGTAAACATGCTTAACATGTATT
1 CAATTCAACACTAGCAGTAAACATGCTTAACATGTATT
* * * *
35323431 CAATTCAACA-TTGCCAATCAACATGCTTATCATGTATT
1 CAATTCAACACTAG-CAGTAAACATGCTTAACATGTATT
* ** *
35323469 CAATTTAACACTAGCAGTTGACACGCTTAACATGTA
1 CAATTCAACACTAGCAGTAAACATGCTTAACATGTA
35323505 CTCACTAGGT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
37 2 0.03
38 56 0.93
39 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (38 bp):
CAATTCAACACTAGCAGTAAACATGCTTAACATGTATT
Found at i:35325629 original size:165 final size:165
Alignment explanation
Indices: 35325334--35325659 Score: 535
Period size: 165 Copynumber: 2.0 Consensus size: 165
35325324 CTAACTCCGC
* *
35325334 AACACATCACTCTTGATTGTGGACGAGCCACCACTAGTTTGCAGATAAACTGCCACTTTGTAAAG
1 AACACATCACTCTGGATTGTGGACGAGCCACCACTAGTTTGCAGATAAACTACCACTTTGTAAAG
* * *
35325399 AAAAACGTGGGTAAACCACTAGTATATTAGATAAAATCATTTGCAGTTCCTGCCACTTATTGTGA
66 AAAAACGTAGGTAAACCACTAGTATATTAGATAAAATCATTTGCAGTTACTACCACTTATTGTGA
* *
35325464 GTGCACAATATGGTTTCAGGTTAACCAAACTATCT
131 GTGCACAACATGGTTTCAGGTTAAACAAACTATCT
* * *
35325499 AACATATCAGTCTGGATTGTGGACGAGCCACCACTGGTTTGCAGATAAACTACCACTTTGTAAAG
1 AACACATCACTCTGGATTGTGGACGAGCCACCACTAGTTTGCAGATAAACTACCACTTTGTAAAG
* *
35325564 AAAAACGTAGGTAAACCACTAGTATATTAGATAAAATCATTTTCAGTTACTACCACTTGTTGTGA
66 AAAAACGTAGGTAAACCACTAGTATATTAGATAAAATCATTTGCAGTTACTACCACTTATTGTGA
*
35325629 GTGCACGACATGGTTTCAGGTTAAACAAACT
131 GTGCACAACATGGTTTCAGGTTAAACAAACT
35325660 GCTATTGGGT
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
165 148 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (165 bp):
AACACATCACTCTGGATTGTGGACGAGCCACCACTAGTTTGCAGATAAACTACCACTTTGTAAAG
AAAAACGTAGGTAAACCACTAGTATATTAGATAAAATCATTTGCAGTTACTACCACTTATTGTGA
GTGCACAACATGGTTTCAGGTTAAACAAACTATCT
Found at i:35325754 original size:85 final size:86
Alignment explanation
Indices: 35325602--35325765 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 86
35325592 AGATAAAATC
* * * * * *
35325602 ATTTTCAGTTACTACCACTTGTTGTGAGTGCACGACATGGTTTCAGGTTAAACAAACTGCTATTG
1 ATTTACAGTTACTACCACTTGTTGTGAGTGCACAACATGATTTCAGATTAAACAAACTGCCACTG
35325667 GGTTTT-TGGACGAGCCACAT
66 GGTTTTGTGGACGAGCCACAT
**
35325687 ATTTACAGTTACTGGCACTTGTTGTGAGTGCACAACAT-ATTTGCAGATTAAACAAACTGCCACT
1 ATTTACAGTTACTACCACTTGTTGTGAGTGCACAACATGATTT-CAGATTAAACAAACTGCCACT
35325751 GGGTTTTGTGGACGA
65 GGGTTTTGTGGACGA
35325766 ACCGCTACTT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 3 0.04
85 59 0.86
86 7 0.10
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (86 bp):
ATTTACAGTTACTACCACTTGTTGTGAGTGCACAACATGATTTCAGATTAAACAAACTGCCACTG
GGTTTTGTGGACGAGCCACAT
Found at i:35330479 original size:38 final size:38
Alignment explanation
Indices: 35330375--35330486 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
35330365 AAGCTATGAA
*
35330375 CAATTCAACACTAGTAGTAAACATGCTTAACATGTATT
1 CAATTCAACACTAGCAGTAAACATGCTTAACATGTATT
* * * *
35330413 CAATTCAACA-TTGCCAATCAACATGCTTATCATGTATT
1 CAATTCAACACTAG-CAGTAAACATGCTTAACATGTATT
* ** *
35330451 CAATTTAACACTAGCAGTTGACACGCTTAACATGTA
1 CAATTCAACACTAGCAGTAAACATGCTTAACATGTA
35330487 CTCACTAGGT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
37 2 0.03
38 56 0.93
39 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (38 bp):
CAATTCAACACTAGCAGTAAACATGCTTAACATGTATT
Found at i:35332734 original size:23 final size:23
Alignment explanation
Indices: 35332708--35332754 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
35332698 AGTATTTTAA
* * *
35332708 TTTTAGAACATATATTTTATTTT
1 TTTTAGAACAAAAATTTAATTTT
35332731 TTTTAGAACAAAAATTTAATTTT
1 TTTTAGAACAAAAATTTAATTTT
35332754 T
1 T
35332755 AAAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTTAGAACAAAAATTTAATTTT
Found at i:35332748 original size:22 final size:23
Alignment explanation
Indices: 35332708--35332754 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
35332698 AGTATTTTAA
* * *
35332708 TTTTAGAACATATATTTTATTTT
1 TTTTAGAACATAAAATTTAATTT
35332731 TTTTAGAACA-AAAATTTAATTT
1 TTTTAGAACATAAAATTTAATTT
35332753 TT
1 TT
35332755 AAAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTTAGAACATAAAATTTAATTT
Found at i:35332903 original size:45 final size:46
Alignment explanation
Indices: 35332843--35332932 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
35332833 TTGGCTTACT
* *
35332843 TAATATTTAATTAAATTATATAATATTTATTATGAATTATTTATAC
1 TAATATTTAAATAAATTACATAATATTTATTATGAATTATTTATAC
* *
35332889 TAAT-TTTAAATAAATTACATATTATTTATTATTAATTATTTATA
1 TAATATTTAAATAAATTACATAATATTTATTATGAATTATTTATA
35332933 AGTGGCCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 36 0.90
46 4 0.10
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (46 bp):
TAATATTTAAATAAATTACATAATATTTATTATGAATTATTTATAC
Found at i:35333503 original size:37 final size:36
Alignment explanation
Indices: 35333453--35333525 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
35333443 TTTTAATTAC
*
35333453 AAAATAATAAAAATTTAATTCAT-TTAGAATTATATT
1 AAAATAATAAAAATTAAATTCATATTA-AATTATATT
*
35333489 AAAATAATATAAAATTAAATTCTTATTAAATTATATT
1 AAAATAATA-AAAATTAAATTCATATTAAATTATATT
35333526 TTATTTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 9 0.27
37 21 0.64
38 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (36 bp):
AAAATAATAAAAATTAAATTCATATTAAATTATATT
Found at i:35344579 original size:43 final size:43
Alignment explanation
Indices: 35344532--35344624 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 43
35344522 CATCCATAGT
* *
35344532 CTTACACGGAA-TCACATATCGATGTCAATGTCCCAGACATGGA
1 CTTACACGGAAGTCACATATCGAT-ACAATATCCCAGACATGGA
* * * *
35344575 CTTACAC-GAAGTCTCATATCGATACCATATCCCAGATATGGT
1 CTTACACGGAAGTCACATATCGATACAATATCCCAGACATGGA
35344617 CTTACACG
1 CTTACACG
35344625 TAATATCCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 24 0.57
43 18 0.43
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
CTTACACGGAAGTCACATATCGATACAATATCCCAGACATGGA
Found at i:35344621 original size:42 final size:42
Alignment explanation
Indices: 35344505--35344624 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 42
35344495 TGTAATCTCG
* * ** *
35344505 TATCGATGCCAATAGCCCATCCATAGTCTTACACGGAATCACA
1 TATCGATGACAATATCCCAGACATGGTCTTACAC-GAATCACA
* * * *
35344548 TATCGATGTCAATGTCCCAGACATGGACTTACACGAAGTCTCA
1 TATCGATGACAATATCCCAGACATGGTCTTACACGAA-TCACA
* *
35344591 TATCGAT-ACCATATCCCAGATATGGTCTTACACG
1 TATCGATGACAATATCCCAGACATGGTCTTACACG
35344625 TAATATCCAA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
42 25 0.40
43 38 0.60
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (42 bp):
TATCGATGACAATATCCCAGACATGGTCTTACACGAATCACA
Found at i:35344639 original size:26 final size:26
Alignment explanation
Indices: 35344601--35344654 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
35344591 TATCGATACC
*
35344601 ATATCCCAGATATGGTCTTACACGTA
1 ATATCCAAGATATGGTCTTACACGTA
*
35344627 ATATCCAATATATGGTCTTACACGTA
1 ATATCCAAGATATGGTCTTACACGTA
35344653 AT
1 AT
35344655 CTCGATAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (26 bp):
ATATCCAAGATATGGTCTTACACGTA
Found at i:35359167 original size:20 final size:19
Alignment explanation
Indices: 35359129--35359167 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
35359119 TTTCATTCCT
**
35359129 TTTCATTCTTTTTTTTTTC
1 TTTCATTCTTTTTCCTTTC
35359148 TTTCTATTCTTTTTCCTTTC
1 TTTC-ATTCTTTTTCCTTTC
35359168 CTTTTCCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTCATTCTTTTTCCTTTC
Found at i:35359172 original size:29 final size:29
Alignment explanation
Indices: 35359114--35359172 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
35359104 CCTTATTTTC
**
35359114 TTTTCTTTCATTCCTTTTCATTCTTTTTT
1 TTTTCTTTCATTCCTTTTCATTCTCCTTT
* *
35359143 TTTTCTTTCTATTCTTTTTCCTT-TCCTTT
1 TTTTCTTTC-ATTCCTTTTCATTCTCCTTT
35359172 T
1 T
35359173 CCTTATCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTCTTTCATTCCTTTTCATTCTCCTTT
Found at i:35361950 original size:36 final size:36
Alignment explanation
Indices: 35361903--35361974 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
35361893 CTTGAAGGAT
35361903 TTTGATTAGGGATGATTAGAGAAAGGGGGAGTAATA
1 TTTGATTAGGGATGATTAGAGAAAGGGGGAGTAATA
35361939 TTTGATTAGGGATGATTAGAGAAAGGGGGAGTAATA
1 TTTGATTAGGGATGATTAGAGAAAGGGGGAGTAATA
35361975 ATATGCTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (36 bp):
TTTGATTAGGGATGATTAGAGAAAGGGGGAGTAATA
Found at i:35367800 original size:20 final size:20
Alignment explanation
Indices: 35367775--35367816 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
35367765 ATGAATTCTT
35367775 TTAATGCTTTTATTCAAAGG
1 TTAATGCTTTTATTCAAAGG
35367795 TTAATGCTTTTATTCAAAGG
1 TTAATGCTTTTATTCAAAGG
35367815 TT
1 TT
35367817 GATGGCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (20 bp):
TTAATGCTTTTATTCAAAGG
Found at i:35377393 original size:37 final size:38
Alignment explanation
Indices: 35377310--35377404 Score: 97
Period size: 37 Copynumber: 2.5 Consensus size: 38
35377300 AAATTAAATT
* * *
35377310 TAATATTAAGATGATCACTTTAATATTAAATTAATAAAA
1 TAATATTAAGATAATTA-TTAAATATTAAATTAATAAAA
* *
35377349 TACTATTAAGATAATTATTAAAT-TTAATTTAATAATAA
1 TAATATTAAGATAATTATTAAATATTAAATTAATAA-AA
*
35377387 -AATATTAAAATAA-TATTA
1 TAATATTAAGATAATTATTA
35377405 TTTTTGGAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
36 5 0.10
37 22 0.46
38 7 0.15
39 14 0.29
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (38 bp):
TAATATTAAGATAATTATTAAATATTAAATTAATAAAA
Found at i:35380934 original size:17 final size:16
Alignment explanation
Indices: 35380903--35380943 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
35380893 TCGATATTTT
35380903 TAAATATATTTAATATA
1 TAAA-ATATTTAATATA
35380920 TAAAATATTTAAATATA
1 TAAAATATTT-AATATA
*
35380937 TCAAATA
1 TAAAATA
35380944 AATTAGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATTTAATATA
Found at i:35380942 original size:9 final size:9
Alignment explanation
Indices: 35380902--35380948 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
35380892 ATCGATATTT
35380902 TTAAATATA
1 TTAAATATA
*
35380911 TTTAATATA
1 TTAAATATA
*
35380920 TAAAATAT-
1 TTAAATATA
35380928 TTAAATATA
1 TTAAATATA
* *
35380937 TCAAATAAA
1 TTAAATATA
35380946 TTA
1 TTA
35380949 GATTAAATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (9 bp):
TTAAATATA
Found at i:35389644 original size:19 final size:17
Alignment explanation
Indices: 35389610--35389647 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
35389600 ATATATATCA
35389610 TCTTTATTATTTTAATT
1 TCTTTATTATTTTAATT
35389627 TCTTATATTATGTTTAATT
1 TCTT-TATTAT-TTTAATT
35389646 TC
1 TC
35389648 ATAATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (17 bp):
TCTTTATTATTTTAATT
Found at i:35389654 original size:18 final size:18
Alignment explanation
Indices: 35389614--35389659 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
35389604 ATATCATCTT
*
35389614 TATTATTTTAATTTCTTA
1 TATTATTTTAATTTCATA
35389632 TATTATGTTTAATTTCATA
1 TATTAT-TTTAATTTCATA
*
35389651 -ATTAATTTA
1 TATTATTTTA
35389660 TTGTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTATTTTAATTTCATA
Found at i:35395414 original size:14 final size:14
Alignment explanation
Indices: 35395397--35395424 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35395387 CTCATATTTC
35395397 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
35395411 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
35395425 GATTTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:35395415 original size:19 final size:22
Alignment explanation
Indices: 35395377--35395421 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
35395367 TACGGTACGC
35395377 TTCTTTTCTTCTCATATTTCTT
1 TTCTTTTCTTCTCATATTTCTT
35395399 TTCTTTTC-TC-CAT-TTTCTT
1 TTCTTTTCTTCTCATATTTCTT
35395418 TTCT
1 TTCT
35395422 CCAGATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 2 0.09
22 8 0.35
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (22 bp):
TTCTTTTCTTCTCATATTTCTT
Done.