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 42 of 143
Found at i:13187962 original size:16 final size:16
Alignment explanation
Indices: 13187917--13187966 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
13187907 TAAACCTAGC
13187917 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
13187933 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
13187947 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
13187963 TAAT
1 TAAT
13187967 ATCCCTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:13188033 original size:30 final size:30
Alignment explanation
Indices: 13187999--13188093 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
13187989 AAATGGTACA
*
13187999 AAATAAATATTTATTTTGTACCATTTTGGT
1 AAATAAATATATATTTTGTACCATTTTGGT
* * **
13188029 AAAT-AATGGTGTA--CGGATACCATTTTGGT
1 AAATAAAT-ATATATTTTG-TACCATTTTGGT
* * *
13188058 ATATAAATATATATTTTGTACTATTTTAGT
1 AAATAAATATATATTTTGTACCATTTTGGT
13188088 AAATAA
1 AAATAA
13188094 CTCATTTTGG
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
28 1 0.02
29 21 0.44
30 25 0.52
31 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACCATTTTGGT
Found at i:13189997 original size:21 final size:21
Alignment explanation
Indices: 13189956--13189999 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13189946 GAGCCACCGT
*
13189956 AATACTCTACTCTTCTCGGGC
1 AATACTCTACTCCTCTCGGGC
13189977 AATACTCTACTCCTC-CAGGGC
1 AATACTCTACTCCTCTC-GGGC
13189998 AA
1 AA
13190000 ATGGACCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (21 bp):
AATACTCTACTCCTCTCGGGC
Found at i:13190236 original size:7 final size:7
Alignment explanation
Indices: 13190220--13190265 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
13190210 TTCACAACAT
*
13190220 TAAACCC
1 TAAACTC
*
13190227 TAAAATC
1 TAAACTC
*
13190234 TAAAATC
1 TAAACTC
*
13190241 TAAACCC
1 TAAACTC
13190248 TAAACTC
1 TAAACTC
13190255 TAAACTC
1 TAAACTC
13190262 TAAA
1 TAAA
13190266 TCGTAAACCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAACTC
Found at i:13190244 original size:21 final size:21
Alignment explanation
Indices: 13190220--13190265 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
13190210 TTCACAACAT
13190220 TAAACCCTAAAATCTAAAATC
1 TAAACCCTAAAATCTAAAATC
* *
13190241 TAAACCCTAAACTCTAAACTC
1 TAAACCCTAAAATCTAAAATC
13190262 TAAA
1 TAAA
13190266 TCGTAAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAAATCTAAAATC
Found at i:13190272 original size:14 final size:13
Alignment explanation
Indices: 13190236--13190274 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
13190226 CTAAAATCTA
13190236 AAATCTAAACCCT
1 AAATCTAAACCCT
*
13190249 AAACTCTAAACTCT
1 AAA-TCTAAACCCT
13190263 AAATCGTAAACC
1 AAATC-TAAACC
13190275 TTATACCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.46, C:0.28, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATCTAAACCCT
Found at i:13195897 original size:24 final size:24
Alignment explanation
Indices: 13195845--13195897 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
13195835 TACTAAAAAT
* *
13195845 ATTATTAAATTATATATTATTATT
1 ATTATTAAATTATATATTATAATA
*
13195869 TTTATTAAATTATAT-TTAATAATA
1 ATTATTAAATTATATATT-ATAATA
13195893 ATTAT
1 ATTAT
13195898 ATTAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTATTAAATTATATATTATAATA
Found at i:13195924 original size:61 final size:62
Alignment explanation
Indices: 13195827--13195945 Score: 186
Period size: 61 Copynumber: 1.9 Consensus size: 62
13195817 TTAATATAAA
* * *
13195827 AATAATTATACTAAAAATATTATTAAATTATATATTATTATTTTTATTAAATTATATTTAAT
1 AATAATTATACTAAAAATATGATTAAATCATATATTATCATTTTTATTAAATTATATTTAAT
* *
13195889 AATAATTATA-TTAAAATATGATTAAATCATTTATTATCATTTTTATTAAATTATATT
1 AATAATTATACTAAAAATATGATTAAATCATATATTATCATTTTTATTAAATTATATT
13195946 AACAACAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
61 42 0.81
62 10 0.19
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (62 bp):
AATAATTATACTAAAAATATGATTAAATCATATATTATCATTTTTATTAAATTATATTTAAT
Found at i:13196141 original size:16 final size:16
Alignment explanation
Indices: 13196122--13196157 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13196112 ATTTTATCCT
*
13196122 ATTACAACTCTATTCC
1 ATTACAACCCTATTCC
*
13196138 ATTACAACCCTATTCT
1 ATTACAACCCTATTCC
13196154 ATTA
1 ATTA
13196158 GAGCACTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAACCCTATTCC
Found at i:13196466 original size:44 final size:44
Alignment explanation
Indices: 13196403--13196489 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
13196393 CTTCCATTTC
13196403 CTTTTGTGGTTTCCCGAGTCCTACGGCCCTTAGAAGGCAGACAA
1 CTTTTGTGGTTTCCCGAGTCCTACGGCCCTTAGAAGGCAGACAA
13196447 CTTTTGTGGTTTCCCGAGTCCTACGGCCCTTAGAAGGCAGACA
1 CTTTTGTGGTTTCCCGAGTCCTACGGCCCTTAGAAGGCAGACA
13196490 GGGCAATCGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (44 bp):
CTTTTGTGGTTTCCCGAGTCCTACGGCCCTTAGAAGGCAGACAA
Found at i:13200123 original size:14 final size:14
Alignment explanation
Indices: 13200106--13200136 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13200096 TAAAAACTTA
*
13200106 ATAAACAAAATAAT
1 ATAAACAAAAAAAT
13200120 ATAAACAAAAAAAT
1 ATAAACAAAAAAAT
13200134 ATA
1 ATA
13200137 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (14 bp):
ATAAACAAAAAAAT
Found at i:13200478 original size:20 final size:20
Alignment explanation
Indices: 13200453--13200490 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13200443 ACAAACAACT
*
13200453 TTAATTTTTAATTATTATAA
1 TTAATTTTTAAATATTATAA
13200473 TTAATTTTTAAATATTAT
1 TTAATTTTTAAATATTAT
13200491 TTAATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTTTTAAATATTATAA
Found at i:13200760 original size:13 final size:13
Alignment explanation
Indices: 13200715--13200760 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
13200705 ATTAACGTAA
*
13200715 AAAATAT-TATTT
1 AAAATATATAATT
13200727 AAAATA-ATAATT
1 AAAATATATAATT
13200739 AATAA-ATATAATT
1 AA-AATATATAATT
13200752 AAAATATAT
1 AAAATATAT
13200761 CAATCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 15 0.52
13 14 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAATATATAATT
Found at i:13201251 original size:7 final size:7
Alignment explanation
Indices: 13201239--13201271 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
13201229 TTCGTTATAA
*
13201239 AAAATTT
1 AAAATTC
13201246 AAAATTC
1 AAAATTC
13201253 AAAATTC
1 AAAATTC
13201260 AAAATTC
1 AAAATTC
13201267 AAAAT
1 AAAAT
13201272 ACAATTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTC
Found at i:13202480 original size:35 final size:34
Alignment explanation
Indices: 13202436--13202555 Score: 136
Period size: 34 Copynumber: 3.5 Consensus size: 34
13202426 TTATATACTA
*
13202436 TATCTCAACCTTTTTAATGTTGCCTTAGACGTATC
1 TATCCCAACCTTTTTAATGTTGCCTTAGACG-ATC
* *
13202471 TATCCCAACC-TTTTATTGTTGCCTTAGACGAGTA
1 TATCCCAACCTTTTTAATGTTGCCTTAGACGA-TC
*** *
13202505 TATCCCAACCTTTTTCGGGTTGCTTTAGACGGATC
1 TATCCCAACCTTTTTAATGTTGCCTTAGAC-GATC
13202540 TAT-CCAACCTTTTTAA
1 TATCCCAACCTTTTTAA
13202556 AGCAACATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
33 1 0.01
34 41 0.57
35 28 0.39
36 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (34 bp):
TATCCCAACCTTTTTAATGTTGCCTTAGACGATC
Found at i:13204191 original size:21 final size:21
Alignment explanation
Indices: 13204167--13204216 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
13204157 CCTATGACAG
* *
13204167 TTCTACCGATACAAGTAAAGC
1 TTCTACCGAAACAAATAAAGC
* *
13204188 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATAAAGC
13204209 TTCTACCG
1 TTCTACCG
13204217 GAACTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (21 bp):
TTCTACCGAAACAAATAAAGC
Found at i:13204311 original size:24 final size:22
Alignment explanation
Indices: 13204279--13204336 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
13204269 ATAAGTACAT
13204279 AAACTACCGATACTT-TTATAGGC
1 AAACTACCGATACTTATTAT--GC
*
13204302 AAAACTACCGGTACTTATTATGC
1 -AAACTACCGATACTTATTATGC
13204325 -AACTACCGATAC
1 AAACTACCGATAC
13204337 AACTCAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 11 0.35
23 2 0.06
24 14 0.45
25 4 0.13
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (22 bp):
AAACTACCGATACTTATTATGC
Found at i:13205132 original size:94 final size:94
Alignment explanation
Indices: 13204971--13205158 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 94
13204961 CCAGTACTCG
* * *
13204971 ATGCTGCTCACACGAGCTGTCGAGGACTCGCAATGTATGCGGTACCCCAGCTATCGATACGGTGC
1 ATGCTGCTCACACGAGCTGTCGAGCACTCGCAACGTATGCGGTACCCCAACTATCGATACGGTGC
13205036 TTGTCTGTACTATAAACTGTTCCCTAACA
66 TTGTCTGTACTATAAACTGTTCCCTAACA
*
13205065 ATGCTGCTCACACGAGCTGTCGAGCACTCGTAACGTATGCGGTACCCCAACTATCGATACGGTGC
1 ATGCTGCTCACACGAGCTGTCGAGCACTCGCAACGTATGCGGTACCCCAACTATCGATACGGTGC
13205130 TTGTCTGTACTATAAACTGTTCCCTAACA
66 TTGTCTGTACTATAAACTGTTCCCTAACA
13205159 CTCACACGAG
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (94 bp):
ATGCTGCTCACACGAGCTGTCGAGCACTCGCAACGTATGCGGTACCCCAACTATCGATACGGTGC
TTGTCTGTACTATAAACTGTTCCCTAACA
Found at i:13209848 original size:24 final size:25
Alignment explanation
Indices: 13209813--13209860 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
13209803 AAAAATTTAA
13209813 AAAATAAATTCATGCTAATATTGCT
1 AAAATAAATTCATGCTAATATTGCT
13209838 AAAA-AAATTCATGCTAATATTGC
1 AAAATAAATTCATGCTAATATTGC
13209861 CTTACCTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (25 bp):
AAAATAAATTCATGCTAATATTGCT
Found at i:13211023 original size:21 final size:21
Alignment explanation
Indices: 13210995--13211048 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
13210985 TGGGAAGGTT
13210995 CTACCGATACAAGTATGACTA
1 CTACCGATACAAGTATGACTA
* * * *
13211016 CTATCGATACAATTATTACTT
1 CTACCGATACAAGTATGACTA
13211037 CTACCGATACAA
1 CTACCGATACAA
13211049 CAAACTCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (21 bp):
CTACCGATACAAGTATGACTA
Found at i:13211969 original size:94 final size:94
Alignment explanation
Indices: 13211803--13212122 Score: 423
Period size: 94 Copynumber: 3.4 Consensus size: 94
13211793 AAAATTGCCT
*
13211803 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGATGAGGACTCACAACATATGCAGTACCTC
1 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGATGAGGACTCGCAACATATGCAGTACCTC
*
13211868 AGCAATCGATACGGTATCTGTACATATAA
66 AGTAATCGATACGGTATCTGTACATATAA
* * *
13211897 -TGGTTACTAGTATACGATGCTGCTCACACTAAGCTGATGACGACTCGCAACATATGAAGTACCT
1 CT-GTTACCAGTATACGATGCTGCTCACACTAAGCTGATGAGGACTCGCAACATATGCAGTACCT
* *
13211961 CAGTAATCGATACAGTATCTATACATATAA
65 CAGTAATCGATACGGTATCTGTACATATAA
* * ** *
13211991 CTGTTACCAGTATATGATGCTGCTCACACTAAGCTAACAAGGACTCGCAACATATGCGGTACCTC
1 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGATGAGGACTCGCAACATATGCAGTACCTC
* * *
13212056 AGTCATCGATATGGTATCTGTACATAGAA
66 AGTAATCGATACGGTATCTGTACATATAA
* * * * *
13212085 TTGTT-CC-CTA-ACAATGCTGCTCACACTGAGCTAATGAG
1 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGATGAG
13212123 AATATGCAAA
Statistics
Matches: 197, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
91 23 0.12
92 2 0.01
93 3 0.02
94 168 0.85
95 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (94 bp):
CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGATGAGGACTCGCAACATATGCAGTACCTC
AGTAATCGATACGGTATCTGTACATATAA
Found at i:13213934 original size:15 final size:16
Alignment explanation
Indices: 13213909--13213941 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13213899 TTTAAAAACT
13213909 TATTATAAAAAATTTC
1 TATTATAAAAAATTTC
*
13213925 TATTATAAAAATTTTC
1 TATTATAAAAAATTTC
13213941 T
1 T
13213942 CGTCGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTATAAAAAATTTC
Found at i:13217096 original size:94 final size:92
Alignment explanation
Indices: 13216919--13217237 Score: 342
Period size: 94 Copynumber: 3.4 Consensus size: 92
13216909 AAAATTGTCT
* * * *
13216919 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTAATGAGGACTCACAACATATGCGGTACCTC
1 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGCAACATATGC-GTACCTT
* * *
13216984 AGCAATCAATATGGTATCTGTACATATAA
65 AGC-ATCGATACGATATCTGTACATATAA
* *
13217013 CTGTTACCAGTATACGATGCTACTCACACTAAGTTGACGAGGACTCGCAACATATGCAGTACCTT
1 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGCAACATATGC-GTACCTT
* *
13217078 AGTCATCGATACAATATCTATACATATAA
65 AG-CATCGATACGATATCTGTACATATAA
* * * * *
13217107 CTGTTACCAGTATACGATGTTGCGCATACTAAGCTGACGTGGACTCGCAACATATGCGATATCTC
1 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGCAACATATGCG-TACCT-
*
13217172 T-GCCATCGATTCGATATCTGTACATATAA
64 TAG-CATCGATACGATATCTGTACATATAA
* * * * *
13217201 -TGAT-CC-CTA-ACGATGATTCTCACACTAAGATGACGAG
1 CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAG
13217238 AATAAGAAAA
Statistics
Matches: 191, Mismatches: 31, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
90 22 0.12
91 2 0.01
92 2 0.01
93 4 0.02
94 159 0.83
95 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (92 bp):
CTGTTACCAGTATACGATGCTGCTCACACTAAGCTGACGAGGACTCGCAACATATGCGTACCTTA
GCATCGATACGATATCTGTACATATAA
Found at i:13222352 original size:322 final size:322
Alignment explanation
Indices: 13221759--13222709 Score: 1652
Period size: 322 Copynumber: 3.0 Consensus size: 322
13221749 CCAGCTACTT
13221759 TTTGAATCTCTCCCATGCCTCGTACGAGGACTCATCATTCAATTGTTGAAAAGTAGTGATCTCGA
1 TTTGAATCTCTCCCATGCCTCGTACGAGGACTCATCATTCAATTGTTGAAAAGTAGTGATCTCGA
13221824 TTTGCAACATAGCATTTTTGCTAGGTGGGAAATACTTTACCAGAAAGCG-TTCTGTTAATTCTTG
66 TTTGCAACATAGCATTTTTGCTAGGTGGGAAATACTTTACCAGAAAGCGTTTC-GTTAATTCTTG
* * *
13221888 CCATGTAGAGATTGAATTTAGCAGCAATGAATTAAGCCATGTTAGTGCTCTATCTCACAACGAGT
130 CCATGTAGAGATTGAATTTAGCGGCAATGAATTAAGCCATGCTCGTGCTCTATCTCACAACGAGT
13221953 ATGAAAATAATTTCAATCTCAATGCGTCTTCAATTACACCAACCATCTTAAAGGAATCGCTCACC
195 ATGAAAATAATTTCAATCTCAATGCGTCTTCAATTACACCAACCATCTTAAAGGAATCGCTCACC
* * *
13222018 TCCATGAATAATCGAAGGTGGAGATGTGGATCTTCCATGGGCATTCCACTTATGAAGTAACTC
260 TCCATGAATAATCGAAGGTGAAGATGTAGATCTTCCGTGGGCATTCCACTTATGAAGTAACTC
*
13222081 TTTGAATCTCTCCCATGCCTCATACGAGGACTCATCATTCAATTGTTGAAAAGTAGTGATCTCGA
1 TTTGAATCTCTCCCATGCCTCGTACGAGGACTCATCATTCAATTGTTGAAAAGTAGTGATCTCGA
* *
13222146 TTTGCAACATAGCATTTTTGCTAGGTGGGAAATATTTTACCAGAAAGCGTTTCATTAATTCTTGC
66 TTTGCAACATAGCATTTTTGCTAGGTGGGAAATACTTTACCAGAAAGCGTTTCGTTAATTCTTGC
13222211 CATGTAGAGATTGAATTTAGCGGCAATGAATTAAGCCATGCTCGTGCTCTATCTCACAACGAGTA
131 CATGTAGAGATTGAATTTAGCGGCAATGAATTAAGCCATGCTCGTGCTCTATCTCACAACGAGTA
**
13222276 TGAAAATAATTTCAATCTCAATGTTTCTTCAATTACACCAACCATCTTAAAGGAATCGCTCACCT
196 TGAAAATAATTTCAATCTCAATGCGTCTTCAATTACACCAACCATCTTAAAGGAATCGCTCACCT
* * *
13222341 TCATCAATAATCAAAGGTGAAGATGTAGATCTTCCGTGGGCATTCCACTTATGAAGTAACTC
261 CCATGAATAATCGAAGGTGAAGATGTAGATCTTCCGTGGGCATTCCACTTATGAAGTAACTC
* *
13222403 TTTGAATCTCTCTCATGCCTCGTACGAGGACTCATCATTCAATTGTTGAAAAGTAGTGATCTTGA
1 TTTGAATCTCTCCCATGCCTCGTACGAGGACTCATCATTCAATTGTTGAAAAGTAGTGATCTCGA
** * * *
13222468 TTCACAACATAACATTTTTGCTAGGTGGGAAATACTTTACCAAAAAGCGTTCCGTTAATTCTTGC
66 TTTGCAACATAGCATTTTTGCTAGGTGGGAAATACTTTACCAGAAAGCGTTTCGTTAATTCTTGC
*
13222533 CATGTAGAGATTGAATTTAGCGGTAATGAATTAAGCCATGCTCGTGCTCTATCTCACAACGAGTA
131 CATGTAGAGATTGAATTTAGCGGCAATGAATTAAGCCATGCTCGTGCTCTATCTCACAACGAGTA
* * *
13222598 TGAAAACAATTTCAATCTCAATGCGTCTTCAATTACACCAACTATCTTAAAGGAGTCGCTCACCT
196 TGAAAATAATTTCAATCTCAATGCGTCTTCAATTACACCAACCATCTTAAAGGAATCGCTCACCT
*
13222663 CCATGAATAATCGAAGGTGAAGATGTAGATCTTCCGTGAGCATTCCA
261 CCATGAATAATCGAAGGTGAAGATGTAGATCTTCCGTGGGCATTCCA
13222710 AGTGGAATTG
Statistics
Matches: 594, Mismatches: 34, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
322 591 0.99
323 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (322 bp):
TTTGAATCTCTCCCATGCCTCGTACGAGGACTCATCATTCAATTGTTGAAAAGTAGTGATCTCGA
TTTGCAACATAGCATTTTTGCTAGGTGGGAAATACTTTACCAGAAAGCGTTTCGTTAATTCTTGC
CATGTAGAGATTGAATTTAGCGGCAATGAATTAAGCCATGCTCGTGCTCTATCTCACAACGAGTA
TGAAAATAATTTCAATCTCAATGCGTCTTCAATTACACCAACCATCTTAAAGGAATCGCTCACCT
CCATGAATAATCGAAGGTGAAGATGTAGATCTTCCGTGGGCATTCCACTTATGAAGTAACTC
Found at i:13224332 original size:23 final size:23
Alignment explanation
Indices: 13224305--13224354 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
13224295 AAGGAAAAGG
13224305 ATAAAAAAATT-TAAAATAGAAGA
1 ATAAAAAAATTCTAAAATAGAA-A
* * *
13224328 ATAAACAGATTCTAAAATTGAAA
1 ATAAAAAAATTCTAAAATAGAAA
13224351 ATAA
1 ATAA
13224355 TACTTGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (23 bp):
ATAAAAAAATTCTAAAATAGAAA
Found at i:13225013 original size:30 final size:30
Alignment explanation
Indices: 13224979--13225155 Score: 134
Period size: 30 Copynumber: 5.9 Consensus size: 30
13224969 TTGACCCCTA
* * *
13224979 AACTTTCCAAAAGTTATGTTTTAACCCTCG
1 AACTTTCTAAAAATTATGTTTTGACCCTCG
*
13225009 AACTTTCTAAAAATTATGTTTTGACCCCCG
1 AACTTTCTAAAAATTATGTTTTGACCCTCG
*
13225039 AACTTTCTAAAAATT-TGAATTTGACCCTCG
1 AACTTTCTAAAAATTATG-TTTTGACCCTCG
** *
13225069 AAC-TTCATAAAAATTCA-AATTTGACCCTCA
1 AACTTTC-TAAAAATT-ATGTTTTGACCCTCG
* *
13225099 AACTTT-TCAAAAATT-TGACTTTGGCTCCT-G
1 AACTTTCT-AAAAATTATG-TTTTGAC-CCTCG
* *
13225129 AACTTTC-CAAAATTTTGTTTTTGACCC
1 AACTTTCTAAAAATTATG-TTTTGACCC
13225156 CATTTTTCCT
Statistics
Matches: 120, Mismatches: 16, Indels: 23
0.75 0.10 0.14
Matches are distributed among these distances:
29 14 0.12
30 101 0.84
31 5 0.04
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (30 bp):
AACTTTCTAAAAATTATGTTTTGACCCTCG
Found at i:13225066 original size:60 final size:60
Alignment explanation
Indices: 13224968--13225156 Score: 165
Period size: 60 Copynumber: 3.1 Consensus size: 60
13224958 GAAATTGTTA
* * * * *
13224968 TTTGACCCCTAAACTTTCCAAAAGTTATG-TTTTAACCCTCGAACTTTCTAAAAATTATGT
1 TTTGACCCCCAAACTTTTCAAAAATT-TGAATTTGACCCTCGAACTTTCTAAAAATTATGT
* **
13225028 TTTGACCCCCGAAC-TTTCTAAAAATTTGAATTTGACCCTCGAAC-TTCATAAAAATTCA-AA
1 TTTGACCCCCAAACTTTTC-AAAAATTTGAATTTGACCCTCGAACTTTC-TAAAAATT-ATGT
* * * * *
13225088 TTTGACCCTCAAACTTTTCAAAAATTTGACTTTGGCTCCT-GAACTTTC-CAAAATTTTGTT
1 TTTGACCCCCAAACTTTTCAAAAATTTGAATTTGAC-CCTCGAACTTTCTAAAAATTATG-T
13225148 TTTGACCCC
1 TTTGACCCC
13225157 ATTTTTCCTT
Statistics
Matches: 103, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
59 14 0.14
60 78 0.76
61 11 0.11
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (60 bp):
TTTGACCCCCAAACTTTTCAAAAATTTGAATTTGACCCTCGAACTTTCTAAAAATTATGT
Found at i:13229541 original size:15 final size:16
Alignment explanation
Indices: 13229513--13229545 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13229503 ACATGTTATC
*
13229513 AAAAGAGGTCAAAAGA
1 AAAAGAGGTAAAAAGA
13229529 AAAAGAGG-AAAAAGA
1 AAAAGAGGTAAAAAGA
13229544 AA
1 AA
13229546 GAAATAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.70, C:0.03, G:0.24, T:0.03
Consensus pattern (16 bp):
AAAAGAGGTAAAAAGA
Found at i:13229593 original size:11 final size:10
Alignment explanation
Indices: 13229524--13229592 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 10
13229514 AAAGAGGTCA
13229524 AAAGAAAAAG
1 AAAGAAAAAG
*
13229534 -AGGAAAAAG
1 AAAGAAAAAG
13229543 AAAGAAATAAAG
1 AAAG-AA-AAAG
*
13229555 AAAGAAAGAGG
1 AAAGAAA-AAG
*
13229566 AAGGAAAAA-
1 AAAGAAAAAG
13229575 AAAGAAAGAA-
1 AAAGAAA-AAG
13229585 AAAGAAAA
1 AAAGAAAA
13229593 GGGTCGAGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
9 15 0.31
10 13 0.27
11 12 0.25
12 8 0.17
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.01
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:13230555 original size:18 final size:18
Alignment explanation
Indices: 13230534--13230590 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
13230524 AAACGAGAGA
13230534 GAAAAAAGAAAAGAAAAG
1 GAAAAAAGAAAAGAAAAG
*
13230552 G---AAA-CAAA-AAAAG
1 GAAAAAAGAAAAGAAAAG
13230565 GAAAAAAGAAGAAGAAAA-
1 GAAAAAAGAA-AAGAAAAG
13230583 GAAAAAAG
1 GAAAAAAG
13230591 GAGAGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
13 6 0.19
14 3 0.10
15 3 0.10
16 3 0.10
17 1 0.03
18 11 0.35
19 4 0.13
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAAAAGAAAAG
Found at i:13230581 original size:26 final size:26
Alignment explanation
Indices: 13230542--13230592 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
13230532 GAGAAAAAAG
13230542 AAAAGAAAAGGAAACA-AAAAAAGGAA
1 AAAAGAAAAGGAAA-AGAAAAAAGGAA
13230568 AAAAGAAGAA-GAAAAGAAAAAAGGA
1 AAAAGAA-AAGGAAAAGAAAAAAGGA
13230593 GAGGTCAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 1 0.04
26 20 0.87
27 2 0.09
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (26 bp):
AAAAGAAAAGGAAAAGAAAAAAGGAA
Found at i:13231718 original size:49 final size:49
Alignment explanation
Indices: 13231438--13231723 Score: 206
Period size: 49 Copynumber: 5.9 Consensus size: 49
13231428 TCTAAAGACA
* * **
13231438 TGAAGGGAAAGATTGAGGTCGTAAC-GATGAATCTCGTACCCTAG-GAATG
1 TGAAGGGAAAGATTGAGGCCGCAACAG-TGAATCTTATACCCTAGAG-ATG
* * *
13231487 TGAAGGGAAAGATTGAGGCCGTAACAGTGAATCTTGTACCTTAGAGATG
1 TGAAGGGAAAGATTGAGGCCGCAACAGTGAATCTTATACCCTAGAGATG
* * * * *
13231536 TGAAAGGAAATG-TTGAGGCCGCAACAGTGAACCTTATACCTTAGAAATA
1 TGAAGGGAAA-GATTGAGGCCGCAACAGTGAATCTTATACCCTAGAGATG
* * ** * * * * *
13231585 AGAA-AGCCAGATTGAAGCTGCAA-TGACGAATCTTGA-ACCCTAAAGATG
1 TGAAGGGAAAGATTGAGGCCGCAACAG-TGAATCTT-ATACCCTAGAGATG
* * * ** * * *
13231633 TGAAAGGAAAGGTCGAGGCCTTAACGGCGAACCTTATACCCTAGAGATG
1 TGAAGGGAAAGATTGAGGCCGCAACAGTGAATCTTATACCCTAGAGATG
* *
13231682 TGAAGGGAAAGATTAAGGCCGCAATAGTGAATCTTATACCCT
1 TGAAGGGAAAGATTGAGGCCGCAACAGTGAATCTTATACCCT
13231724 GAAGATAAAG
Statistics
Matches: 183, Mismatches: 45, Indels: 18
0.74 0.18 0.07
Matches are distributed among these distances:
47 2 0.01
48 30 0.16
49 147 0.80
50 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (49 bp):
TGAAGGGAAAGATTGAGGCCGCAACAGTGAATCTTATACCCTAGAGATG
Found at i:13232098 original size:123 final size:123
Alignment explanation
Indices: 13231950--13232970 Score: 1123
Period size: 123 Copynumber: 8.2 Consensus size: 123
13231940 TACAGTGGGT
** *
13231950 TGGATCAAAACAAATGAAAAGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAATCAATGA
1 TGGATCAAAAC-AATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGA
* * * *
13232015 AGC-AGAGCTCAATGTAAGTGAAACTTCAAACTCCATATTCCTGATGAGATACATAGAAG
65 AGCGA-AGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
* * * * * *
13232074 TGGATTAAAACAATGAAGTGGTCATCTTCTTGATGAGATATATAGAGAGGTGGACCAAATTAA-C
1 TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAG--ATACAGAGAAGTGGACCAAATCAATG
* * * * * *
13232138 AAGCGGAGCTCAATGTGGGTGAAATTTCGAACCCTATCTTCCTGAAGAGATACAGAGAAG
64 AAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
* * *** * * * *
13232198 TGAATCAAAACAGTGAAACAGTTATCTTCCTGAGGAGATATAGAGAAGTGGACCAAATCAACGAA
1 TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAA
* *
13232263 GCGAAGCTCAATGTGAGTGAAACTTCGAACCCCATCTTCTTGATGAGATACAG-GAAG
66 GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
** * * *
13232320 TGGATCAAAACAATGAAGCAGTCATCTTCCTAATGAGATAAAGAGAAGTCGACCAAATCAATGAA
1 TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAA
* * * * * * * *
13232385 GCGGAGCTCAATGTGGGTGAAACTTCAAACCCCATATTCCTAATTAGATACAAAAAAA
66 GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
* * * * ** * * * *
13232443 TAGATTAAAACAATTAAATCATTATCTTCCTGATGAGATACAAAGAAGTGGACCAAATTAACGAA
1 TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAA
* ** ** *
13232508 GCGAAGCTCAATGTGAGTGAAATTTTGAACCCCATCTTTTTGATGAGATACAGAGAAT
66 GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
* ** * * * *
13232566 TGGATTAAAACAATGAAGTGACCATCTTCCTAATGAGATAAAAAGAAGTGGACCAAAATAAAATA
1 TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACC-AAAT----CA
* *
13232631 ATGAAGCGAAGCTCAATTTGAGTGAAACTTCAAACCCCCATCTTCC-GAATGAGATACATAGAAG
61 ATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAA-CCCCATCTTCCTG-ATGAGATACAGAGAAG
* * * * *
13232695 TGGGTCAAAACAATGAAGTGGTCATCTTCTTGATGAGGTACAGAGAATTGGACCAAATCAACGAA
1 TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAA
* * * * *
13232760 GCGAAGCTTAGTGTGAGTGAAACTTCAAACCCAATCTTCCTAATGAGATACAGAGCAG
66 GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
* * * *
13232818 TGGGTCAAAACAATGAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAATGAA
1 TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAA
* * *
13232883 GTGAAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAG
66 GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
* * *
13232941 TGGGTCAAAATAATGAAGTAGTCATCTTCC
1 TGGATCAAAACAATGAAGTGGTCATCTTCC
13232971 AAATAATGAA
Statistics
Matches: 751, Mismatches: 133, Indels: 27
0.82 0.15 0.03
Matches are distributed among these distances:
122 127 0.17
123 377 0.50
124 122 0.16
125 22 0.03
128 36 0.05
129 67 0.09
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (123 bp):
TGGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAA
GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
Found at i:13232789 original size:375 final size:369
Alignment explanation
Indices: 13231950--13232970 Score: 1210
Period size: 375 Copynumber: 2.8 Consensus size: 369
13231940 TACAGTGGGT
* *
13231950 TGGATCAAAACAAATGAAAAGGTCATCTTCCTGATGAGATATAGAGAAGTGGACCAAATCAATGA
1 TGGATCAAAAC-AATGAAGAGGTCATCTTCCTGATGAGATAAAGAGAAGTGGACCAAATCAATGA
* * * *
13232015 AGC-AGAGCTCAATGTAAGTGAAACTTCAAACTCCATATTCCTGATGAGATACATAGAAGTGGAT
65 AGCGA-AGCTCAATGTGAGTGAAACTTCAAACCCCATATTCCTAATGAGATACAAAGAAGTGGAT
* *
13232079 TAAAACAATGAAGTGGTCATCTTCTTGATGAGATATATAGAGAGGTGGACCAAATTAAC-AAGCG
129 TAAAACAATGAAGTGGTCATCTTCTTGATGAGATACA-A-AGAAGTGGACCAAATTAACGAAGCG
* * * * * *
13232143 GAGCTCAATGTGGGTGAAATTTCGAACCCTATCTTCCTGAAGAGATACAGAGAAGTGAATCAAAA
192 AAGCTCAATGTGAGTGAAATTTCGAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAA
* * ** * * *
13232208 CAGTGAA-ACAGTTATCTTCCTGAGGAGATATAGAGAAGTGGACCAAATCAACGAAGCGAAGCTC
257 CAATGAAGTCAGCCATCTTCCTAAGGAGATAAAAAGAAGTGGACCAAATCAACGAAGCGAAGCTC
* * *
13232272 AATGTGAGTGAAACTTCGAACCCCATCTTCTTGATGAGATACAGGAAG
322 AATGTGAGTGAAACTTCAAACCCCATCTTCTCGATGAGATACAAGAAG
* *
13232320 TGGATCAAAACAATGAAGCA-GTCATCTTCCTAATGAGATAAAGAGAAGTCGACCAAATCAATGA
1 TGGATCAAAACAATGAAG-AGGTCATCTTCCTGATGAGATAAAGAGAAGTGGACCAAATCAATGA
* * * * * *
13232384 AGCGGAGCTCAATGTGGGTGAAACTTCAAACCCCATATTCCTAATTAGATACAAAAAAATAGATT
65 AGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCCTAATGAGATACAAAGAAGTGGATT
* * ** * *
13232449 AAAACAATTAAATCATTATCTTCCTGATGAGATACAAAGAAGTGGACCAAATTAACGAAGCGAAG
130 AAAACAATGAAGTGGTCATCTTCTTGATGAGATACAAAGAAGTGGACCAAATTAACGAAGCGAAG
* * * *
13232514 CTCAATGTGAGTGAAATTTTGAACCCCATCTTTTTGATGAGATACAGAGAATTGGATTAAAACAA
195 CTCAATGTGAGTGAAATTTCGAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAA
* * * *
13232579 TGAAGTGA-CCATCTTCCTAATGAGATAAAAAGAAGTGGACCAAAATAAAATAATGAAGCGAAGC
260 TGAAGTCAGCCATCTTCCTAAGGAGATAAAAAGAAGTGGACC-AAAT----CAACGAAGCGAAGC
*
13232643 TCAATTTGAGTGAAACTTCAAACCCCCATCTTC-CGAATGAGATACATAGAAG
320 TCAATGTGAGTGAAACTTCAAA-CCCCATCTTCTCG-ATGAGATACA-AGAAG
* * * * * * *
13232695 TGGGTCAAAACAATGAAGTGGTCATCTTCTTGATGAGGTACAGAGAATTGGACCAAATCAACGAA
1 TGGATCAAAACAATGAAGAGGTCATCTTCCTGATGAGATAAAGAGAAGTGGACCAAATCAATGAA
* * * * * * * *
13232760 GCGAAGCTTAGTGTGAGTGAAACTTCAAACCCAATCTTCCTAATGAGATACAGAGCAGTGGGTCA
66 GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCCTAATGAGATACAAAGAAGTGGATTA
* * ** * *
13232825 AAACAATGAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGTGAAGC
131 AAACAATGAAGTGGTCATCTTCTTGATGAGATACAAAGAAGTGGACCAAATTAACGAAGCGAAGC
* * * * *
13232890 TCAATGCGAGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAGTGGGTCAAAATAAT
196 TCAATGTGAGTGAAATTTCGAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAT
*
13232955 GAAGT-AGTCATCTTCC
261 GAAGTCAGCCATCTTCC
13232971 AAATAATGAA
Statistics
Matches: 545, Mismatches: 92, Indels: 23
0.83 0.14 0.03
Matches are distributed among these distances:
367 18 0.03
368 94 0.17
369 135 0.25
370 12 0.02
373 33 0.06
374 21 0.04
375 232 0.43
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (369 bp):
TGGATCAAAACAATGAAGAGGTCATCTTCCTGATGAGATAAAGAGAAGTGGACCAAATCAATGAA
GCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCCTAATGAGATACAAAGAAGTGGATTA
AAACAATGAAGTGGTCATCTTCTTGATGAGATACAAAGAAGTGGACCAAATTAACGAAGCGAAGC
TCAATGTGAGTGAAATTTCGAACCCCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAAT
GAAGTCAGCCATCTTCCTAAGGAGATAAAAAGAAGTGGACCAAATCAACGAAGCGAAGCTCAATG
TGAGTGAAACTTCAAACCCCATCTTCTCGATGAGATACAAGAAG
Found at i:13232875 original size:48 final size:48
Alignment explanation
Indices: 13232793--13232885 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
13232783 TTCAAACCCA
* * **
13232793 ATCTTCCTAATGAGATACAGAGCAGTGGGTCAAAACAATGAAGTGGTC
1 ATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGTGGTC
* *
13232841 ATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGTG
1 ATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGTG
13232886 AAGCTCAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.23
Consensus pattern (48 bp):
ATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGTGGTC
Found at i:13233026 original size:98 final size:98
Alignment explanation
Indices: 13232877--13233068 Score: 330
Period size: 98 Copynumber: 2.0 Consensus size: 98
13232867 AGACCAAAAC
* * *
13232877 AATGAAGTGAAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAGT
1 AATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAACCCCATATTCTTGATGAGATACAGAAAAGT
13232942 GGGTCAAAATAATGAAGTAGTCATCTTCCAAAT
66 GGGTCAAAATAATGAAGTAGTCATCTTCCAAAT
*
13232975 AATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCTTGATGAGATACAGAAAAGT
1 AATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAACCCCATATTCTTGATGAGATACAGAAAAGT
* *
13233040 GGGTTAAAATAATGAAGTGGTCATCTTCC
66 GGGTCAAAATAATGAAGTAGTCATCTTCC
13233069 TGATGAGATA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (98 bp):
AATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAACCCCATATTCTTGATGAGATACAGAAAAGT
GGGTCAAAATAATGAAGTAGTCATCTTCCAAAT
Found at i:13233163 original size:221 final size:222
Alignment explanation
Indices: 13232747--13233929 Score: 843
Period size: 246 Copynumber: 5.0 Consensus size: 222
13232737 GAGAATTGGA
* * *
13232747 CCAAATCAACGAAGCGAAGCTTAGTGTGAGTGAAACTTCAAACCCAATCTTCCTAATGAGATACA
1 CCAAATCAACGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCAATATTCCTAATGAGATACA
** * *
13232812 GAGCAGTGGGTCAAAACAATGAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAAC
66 GAAAAGTGGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAAC
* * * *
13232877 AATGAAGTGAAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAGT
131 AATGAAATGAAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATAAGATACAAAGAAGT
* *
13232942 GGGTCAAAATAATGAAGTAGTCATCTT
196 GGGTCAAAACAATGAAGCAGTCATCTT
* * * *
13232969 CCAAAT-AATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCTTGATGAGATACA
1 CCAAATCAACGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCAATATTCCTAATGAGATACA
* *
13233033 GAAAAGTGGGTTAAAATAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAAC
66 GAAAAGTGGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAAC
** * * * *
13233098 AATGAAATGAATTTCAATGTGAGTGAAACTTCAAACCCTATTTTCCTGATAAGATATAAAGAAGT
131 AATGAAATGAAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATAAGATACAAAGAAGT
13233163 GGGTCAAAACAATGAAGCAGTCATCTT
196 GGGTCAAAACAATGAAGCAGTCATCTT
* *
13233190 CCTGATGAGATACAAAAGAGTGGATCAAATCAACAAAGCGAAGCTCAATGTGAGTTAAACTTCAA
1 -C----------C---A-A----ATC-A----ACGAAGCGAAGCTCAATGTGAGTGAAACTTCAA
* * * * *
13233255 ACCCCATCTTCTTAATGAGATACAGAGAAGTGGGTCAAAACAATAAAGTGGTCATCTTCCT-ATT
42 ACCCAATATTCCTAATGAGATACAGAAAAGTGGGTCAAAACAATGAAGTGGTCATCTTCCTGA-T
* *** * ** * * *
13233319 GGGATATTGAGAAGTGGACCAAGTCAACGAAGT-AGAGCTCAATGTGAGTGAAACTTCAAACCCC
106 GAGATACAAAGAAGTAGACCAAAACAATGAAATGA-AGCTCAATGCGAGTGAAACTTCAAACCCC
* * * * **
13233383 ATCTTCCTGATGAGATA-AAGAGAAGTCGGTCAAAATAAGGAAGTGGTCATCTT
170 ATCTTCCTGATAAGATACAA-AGAAGTGGGTCAAAACAATGAAGCAGTCATCTT
* **
13233436 CCTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGCGATGCTCAATACGAGTGAAACTTCAA
1 -C----------C--A-AA-T----C--AAC---GAAGCGAAGCTCAATGTGAGTGAAACTTCAA
** ** * * * * *
13233501 ACCCCGTCCTCCTGATGAGATACAAAAAAGTGGGTCAAAATAATGAAGTGGTCATCTTCTTGATA
42 ACCCAATATTCCTAATGAGATACAGAAAAGTGGGTCAAAACAATGAAGTGGTCATCTTCCTGATG
* * * *
13233566 AGATATAAAGAAGTAGACCAAATCAATGAAATGGAGCTCAATGTGAGTGAAACTTCAAACCCCAT
107 AGATACAAAGAAGTAGACCAAAACAATGAAATGAAGCTCAATGCGAGTGAAACTTCAAACCCCAT
* * * * **
13233631 CTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAAGTGGTCATCTT
172 CTTCCTGATAAGATACAAAGAAGTGGGTCAAAACAATGAAGCAGTCATCTT
* *
13233682 CCTGATGAGATATAGAGAAGTAGACCAAAAC-AATGAAGCAAAGCTCAATGCGAGTGAAACTTCA
1 CC-------------A-AA-T----C--AACGAA-G---CGAAGCTCAATGTGAGTGAAACTTCA
* * * * * *
13233746 AACCCCATCTTCTTGATGAGATATAGAGAAA-TGGGTAAAAACAATGAAGTGGTCATCTTCCTGA
41 AACCCAATATTCCTAATGAGATACAGA-AAAGTGGGTCAAAACAATGAAGTGGTCATCTTCCTGA
* *
13233810 TGAGATACAGAGAAGTAGACCAAAACAAT-AAAGCGAAGCTCAATGC-ATGTGAAACTTCAAACC
105 TGAGATACAAAGAAGTAGACCAAAACAATGAAA-TGAAGCTCAATGCGA-GTGAAACTTCAAACC
* * **
13233873 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATGAAGTGGTCATCTT
168 CCATCTTCCTGATAAGATACAAAGAAGTGGGTCAAAACAATGAAGCAGTCATCTT
13233928 CC
1 CC
13233930 TGATGAGATA
Statistics
Matches: 800, Mismatches: 103, Indels: 92
0.80 0.10 0.09
Matches are distributed among these distances:
221 190 0.24
222 7 0.01
232 1 0.00
235 2 0.00
236 1 0.00
240 2 0.00
241 1 0.00
242 4 0.00
243 3 0.00
245 13 0.02
246 569 0.71
247 7 0.01
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (222 bp):
CCAAATCAACGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCAATATTCCTAATGAGATACA
GAAAAGTGGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAAC
AATGAAATGAAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCCTGATAAGATACAAAGAAGT
GGGTCAAAACAATGAAGCAGTCATCTT
Found at i:13233194 original size:123 final size:123
Alignment explanation
Indices: 13232975--13234149 Score: 1464
Period size: 123 Copynumber: 9.6 Consensus size: 123
13232965 TCTTCCAAAT
* * * *
13232975 AATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCCCATATTCTTGATGAGATACAGAAAAGT
1 AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
* * *
13233040 GGGTTAAAATAATGAAGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAAC
66 GGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
* ** * * * * *
13233098 AATGAAATGAATTTCAATGTGAGTGAAACTTCAAACCCTATTTTCCTGATAAGATATAAAGAAGT
1 AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
** * * * *
13233163 GGGTCAAAACAATGAAGCAGTCATCTTCCTGATGAGATACA-AAAGAGTGGATCAAATC
66 GGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGA-AGTAGACCAAAAC
* * * *
13233221 AA-CAAAGCGAAGCTCAATGTGAGTTAAACTTCAAACCCCATCTTCTTAATGAGATACAGAGAAG
1 AATGAAA-CGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAG
* * ** * **
13233285 TGGGTCAAAACAATAAAGTGGTCATCTTCCT-ATTGGGATATTGAGAAGTGGACCAAGTC
65 TGGGTCAAAACAATGAAGTGGTCATCTTCCTGA-TGAGATACAGAGAAGTAGACCAAAAC
* *
13233344 AACG-AA-GTAGAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATAAAGAGAA
1 AATGAAACG-A-AGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAA
* * *
13233407 GTCGGTCAAAATAAGGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
64 GTGGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
* * ** * * * *
13233467 AATGAAGCGATGCTCAATACGAGTGAAACTTCAAACCCCGTCCTCCTGATGAGATACAAAAAAGT
1 AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
* * * * * *
13233532 GGGTCAAAATAATGAAGTGGTCATCTTCTTGATAAGATATAAAGAAGTAGACCAAATC
66 GGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
* * *
13233590 AATGAAATGGAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTAATGAGATACAGAGAAGT
1 AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
* *
13233655 GGATCAAAACAATGAAGTGGTCATCTTCCTGATGAGATATAGAGAAGTAGACCAAAAC
66 GGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
* * * * * *
13233713 AATGAAGCAAAGCTCAATGCGAGTGAAACTTCAAACCCCATCTTCTTGATGAGATATAGAGAAAT
1 AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
*
13233778 GGGTAAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
66 GGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
*
13233836 AAT-AAAGCGAAGCTCAATG-CATGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAA
1 AATGAAA-CGAAGCTCAATGTGA-GTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAA
* *
13233899 GTGGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATATAGAGAAGTAGCCCAAAAC
64 GTGGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
* ** ** ** * *
13233959 AATGAAGCGAAAATCAATACGAGTGAAACTTCAAACCTTATCTTCTTAATGAGATACAGAGAAGT
1 AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
* *
13234024 AGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGACAAGTAGACCAAAAC
66 GGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
* * * ** * * * *
13234082 AATGAAGCAAAGCTAAATACGAGTGAAACTTAAAACTCCATCTTTCTGATGAGATACAAAGAAGT
1 AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
13234147 GGG
66 GGG
13234150 CTAAATAAGT
Statistics
Matches: 902, Mismatches: 136, Indels: 28
0.85 0.13 0.03
Matches are distributed among these distances:
121 1 0.00
122 10 0.01
123 882 0.98
124 8 0.01
125 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (123 bp):
AATGAAACGAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGT
GGGTCAAAACAATGAAGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAAC
Found at i:13233684 original size:48 final size:48
Alignment explanation
Indices: 13233628--13233719 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
13233618 CTTCAAACCC
* *
13233628 CATCTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAAGTGGT
1 CATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGTGGT
* *
13233676 CATCTTCCTGATGAGATATAGAGAAGTAGACCAAAACAATGAAG
1 CATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAG
13233720 CAAAGCTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (48 bp):
CATCTTCCTAATGAGATACAGAGAAGTAGACCAAAACAATGAAGTGGT
Found at i:13233945 original size:48 final size:48
Alignment explanation
Indices: 13233874--13233965 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
13233864 CTTCAAACCC
* **
13233874 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAACAATGAAGTGGT
1 CATCTTCCTGATGAGATACAGAGAAGTAGCCCAAAACAATGAAGTGGT
*
13233922 CATCTTCCTGATGAGATATAGAGAAGTAGCCCAAAACAATGAAG
1 CATCTTCCTGATGAGATACAGAGAAGTAGCCCAAAACAATGAAG
13233966 CGAAAATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAGAAGTAGCCCAAAACAATGAAGTGGT
Found at i:13234280 original size:46 final size:46
Alignment explanation
Indices: 13234222--13234321 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 46
13234212 TCATTCAGTC
* *
13234222 TTTTACCCTTAAGTCAAGAGGGGCAAATTGAAGCCATCATCCAATA
1 TTTTACCCTTAAGTCAAGAAGGGCAAATTGAAGCCACCATCCAATA
* * * *
13234268 TTTTACCTTTAAGTCAAGAAGGGCAGATTGAAGTCACCATCCAATC
1 TTTTACCCTTAAGTCAAGAAGGGCAAATTGAAGCCACCATCCAATA
*
13234314 TTCTACCC
1 TTTTACCC
13234322 CGATCATAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (46 bp):
TTTTACCCTTAAGTCAAGAAGGGCAAATTGAAGCCACCATCCAATA
Found at i:13235287 original size:3 final size:3
Alignment explanation
Indices: 13235279--13235308 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
13235269 TGTTTATTCG
13235279 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
13235309 ATTGTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13235297 original size:14 final size:14
Alignment explanation
Indices: 13235280--13235311 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
13235270 GTTTATTCGT
13235280 TATTATTATTATTA
1 TATTATTATTATTA
13235294 TATTATTATTATTA
1 TATTATTATTATTA
13235308 TATT
1 TATT
13235312 GTGAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:13236382 original size:30 final size:29
Alignment explanation
Indices: 13236229--13236385 Score: 161
Period size: 30 Copynumber: 5.2 Consensus size: 29
13236219 AAAATTATTA
* *
13236229 TTTGACCCCCAAACTTTCAAAAACTTATGT
1 TTTGACCCCTAAACTTTCAAAAA-TTTTGT
* **
13236259 TTTAACCCCTAAACTTTCTAAAAATTAAGT
1 TTTGACCCCTAAACTTTC-AAAAATTTTGT
* * * *
13236289 TTTAACCCTTAAACTTTCTAAAAATTTAGA
1 TTTGACCCCTAAACTTTC-AAAAATTTTGT
* *
13236319 TTTGACCCTTAAACTTTCCAAAATTTTGAT
1 TTTGACCCCTAAACTTTCAAAAATTTTG-T
*
13236349 TTTGGCCCCTAAACTTTCAAAAATTTTGTT
1 TTTGACCCCTAAACTTTCAAAAATTTTG-T
13236379 TTTGACC
1 TTTGACC
13236386 TCGTTTTTCC
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 8 0.07
30 97 0.88
31 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTGACCCCTAAACTTTCAAAAATTTTGT
Found at i:13238660 original size:18 final size:18
Alignment explanation
Indices: 13238634--13238668 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
13238624 TTGTCGTCCA
*
13238634 ATGTGCATGAAATAATTC
1 ATGTCCATGAAATAATTC
13238652 ATGTCCATGAAATAATT
1 ATGTCCATGAAATAATT
13238669 TATATCATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (18 bp):
ATGTCCATGAAATAATTC
Found at i:13239940 original size:23 final size:23
Alignment explanation
Indices: 13239921--13240356 Score: 559
Period size: 23 Copynumber: 19.0 Consensus size: 23
13239911 TCCATTTACA
13239921 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
13239944 CATAAATCACAATAACATTTAAG
1 CATAAATCACATTAATATTTAAG
13239967 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
13239990 TACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
13240013 TATAAATCACATTAATATTTAAA
1 CATAAATCACATTAATATTTAAG
* *
13240036 CACAAATCATATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
13240059 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * * *
13240082 CACAAATCTCGTTAATATTTAAT
1 CATAAATCACATTAATATTTAAG
*
13240105 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
13240128 CATAAATAACATTAACT-TTTAAG
1 CATAAATCACATTAA-TATTTAAG
* *
13240151 CATAAATCATATTAACATTTAAG
1 CATAAATCACATTAATATTTAAG
13240174 CATAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * * *
13240197 AACAAATTACATTGATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
13240220 CATAAATCACGTTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
13240243 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
13240266 CACAGATCGCATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
13240289 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * * *
13240312 CATAAACCATATTAACATTTAAA
1 CATAAATCACATTAATATTTAAG
* *
13240335 CATAGATCACAGTAATATTTAA
1 CATAAATCACATTAATATTTAA
13240357 CACATTTAAT
Statistics
Matches: 360, Mismatches: 51, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
23 359 1.00
24 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.33
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:13240788 original size:36 final size:36
Alignment explanation
Indices: 13240748--13241001 Score: 346
Period size: 36 Copynumber: 7.1 Consensus size: 36
13240738 TTAGCACAAT
* *
13240748 ATATTCACTGTCACATGGAATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
13240784 ATATTTATTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
*
13240820 ATATTTACTGTCACATGGCATGAATAATATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
13240856 ATATTAACTGTCACATGACATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * *
13240892 ATATTTACTGTCTCATGGCATGAATAATATACACAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
13240928 ATATTAACTGTCACATGACATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * * * * *
13240964 ATATTTATTGCCTCATGTCATGGATAACATACTCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
13241000 AT
1 AT
13241002 GTTCACTTTC
Statistics
Matches: 191, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 191 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATACCCAC
Found at i:13246233 original size:17 final size:17
Alignment explanation
Indices: 13246211--13246249 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
13246201 AGGTGGAGAA
* *
13246211 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
13246228 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
13246245 CTTGT
1 CTTGT
13246250 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:13246296 original size:41 final size:41
Alignment explanation
Indices: 13246239--13246334 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
13246229 TTGTTCGTAG
* *
13246239 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTAACT
*
13246280 AGAATTCTTGTTAAGGTGGAGATTGTTAGGATTGGGTAACT
1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTAACT
13246321 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
13246335 AATAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.28, C:0.06, G:0.29, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTAACT
Found at i:13250059 original size:13 final size:14
Alignment explanation
Indices: 13250021--13250059 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
13250011 TCTTGGGATA
*
13250021 ATTTTTAATAATATT
1 ATTTTTAGT-ATATT
13250036 ATTTTTAGTATATT
1 ATTTTTAGTATATT
13250050 ATTTTT-GTAT
1 ATTTTTAGTAT
13250060 TTTAAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 11 0.48
15 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (14 bp):
ATTTTTAGTATATT
Found at i:13250498 original size:16 final size:17
Alignment explanation
Indices: 13250459--13250499 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
13250449 ACAAAAATTC
*
13250459 ATTTATTT-TTAATAAT
1 ATTTATTTATGAATAAT
13250475 ATTT-TTTATGAAT-AT
1 ATTTATTTATGAATAAT
13250490 ATTTATTTAT
1 ATTTATTTAT
13250500 ATTTTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTATTTATGAATAAT
Found at i:13264127 original size:39 final size:40
Alignment explanation
Indices: 13264050--13264129 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 40
13264040 GATTAATTTA
13264050 AAATCCATATTTAGGTAGCATGAAAAAAATTAAAGTAAATT
1 AAATCCATATTTAGGTAGCAT-AAAAAAATTAAAGTAAATT
13264091 AAATCCATATTTAGGTAGCAT-AAAAAATTAAAGTAAATT
1 AAATCCATATTTAGGTAGCATAAAAAAATTAAAGTAAATT
13264130 TATTTTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 18 0.46
41 21 0.54
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.30
Consensus pattern (40 bp):
AAATCCATATTTAGGTAGCATAAAAAAATTAAAGTAAATT
Found at i:13267621 original size:29 final size:28
Alignment explanation
Indices: 13267560--13267623 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
13267550 ACAAAGATAG
* *
13267560 CCACAAAGGCTTTCCTGTTTAGAGTTTA
1 CCACAAAGGCTTTCCTGTTTAGAGATCA
*
13267588 CCACAAAGTCTTTCCT-TTAATAGAGATCA
1 CCACAAAGGCTTTCCTGTT--TAGAGATCA
13267617 CCACAAA
1 CCACAAA
13267624 TGTGTGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 15 0.48
29 14 0.45
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (28 bp):
CCACAAAGGCTTTCCTGTTTAGAGATCA
Found at i:13267690 original size:28 final size:29
Alignment explanation
Indices: 13267659--13267713 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
13267649 CAAAGACAAT
*
13267659 CCTTT-GAGAGGTTCA-CTATAAAGGCTTA
1 CCTTTCGAGAGGTT-AGCCATAAAGGCTTA
*
13267687 CCTTTCTAGAGGTTAGCCATAAAGGCT
1 CCTTTCGAGAGGTTAGCCATAAAGGCT
13267714 GTCTTAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (29 bp):
CCTTTCGAGAGGTTAGCCATAAAGGCTTA
Found at i:13284816 original size:12 final size:12
Alignment explanation
Indices: 13284799--13284823 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13284789 TCAATCTCCA
13284799 CAGGATCTTCTT
1 CAGGATCTTCTT
13284811 CAGGATCTTCTT
1 CAGGATCTTCTT
13284823 C
1 C
13284824 TTCTTCTTCA
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:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (12 bp):
CAGGATCTTCTT
Found at i:13291007 original size:166 final size:165
Alignment explanation
Indices: 13290635--13291100 Score: 692
Period size: 166 Copynumber: 2.8 Consensus size: 165
13290625 GGTGGAGGAT
* * *
13290635 TTCTAACTTGAACTGGCTACTTCATTTTTTGTGGAACTTTTACATCTAAAGAAGTTGTTATATCA
1 TTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTTTACATCTAAAGAAGTTGTTAGATCA
* * *
13290700 TCAGACTTGACTGGTTTTGAAGTCTCTTTCTCAACATTCATCGGTTTTGTTTCTGGTGAAA----
66 TCAGACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCACCGGTTTTATTTCTGGTGAAACTGT
*
13290761 -CTGGTTCTGGTTCTAGTTCTGACAAAGTTGGAGT
131 TCTGGTTCTGGTTCTAGTTCTGACAAAGTTGGAGC
* * *
13290795 TTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTCTACATCTAAAAAAGTTGTAAGATCA
1 TTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTTTACATCTAAAGAAGTTGTTAGATCA
* * * * *
13290860 TCATACTTGACTTTTTTTGAAGTCTCTTTCTCAATATTCACCGGTTCTATTTCTGATGAAACTCG
66 TCAGACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCACCGGTTTTATTTCTGGTGAAACT-G
13290925 TTCTGGTTCTGGTTCTAGTTCT-AGCAAAGTTGGAGC
130 TTCTGGTTCTGGTTCTAGTTCTGA-CAAAGTTGGAGC
* *
13290961 TTCTAACTAGAACTGGCTGTTTCATTTTTTGTGGCACTTTTACATCTAAAGAAGTTGTTAGATCA
1 TTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTTTACATCTAAAGAAGTTGTTAGATCA
* *
13291026 TCAGACTTGACTTGTTTTAAAGTCTCTTTCTCAACATTCACTGGTTTTATTTCTGGTGAAACTAG
66 TCAGACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCACCGGTTTTATTTCTGGTGAAACT-G
13291091 TTCTGGTTCT
130 TTCTGGTTCT
13291101 AGCAAAGTTG
Statistics
Matches: 271, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
160 112 0.41
165 1 0.00
166 158 0.58
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (165 bp):
TTCTAACTTGAACTGGCTGCTTCATTTTTTGTGGCACTTTTACATCTAAAGAAGTTGTTAGATCA
TCAGACTTGACTTGTTTTGAAGTCTCTTTCTCAACATTCACCGGTTTTATTTCTGGTGAAACTGT
TCTGGTTCTGGTTCTAGTTCTGACAAAGTTGGAGC
Found at i:13294625 original size:15 final size:15
Alignment explanation
Indices: 13294582--13294619 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
13294572 GGTGAATGAT
*
13294582 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
13294595 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
13294610 ATTAATCTAA
1 ATTAATCTAA
13294620 GTTAAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:13299029 original size:21 final size:21
Alignment explanation
Indices: 13299003--13299054 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
13298993 TGAGACATTA
13299003 CTACCGATACAAGT-ATGACTT
1 CTACCGATACAAGTCATG-CTT
* * *
13299024 CTACCGAAATATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
13299045 CTACCGATAC
1 CTACCGATAC
13299055 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:13303646 original size:14 final size:15
Alignment explanation
Indices: 13303627--13303655 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13303617 GCCATTTTTA
13303627 ATTTTTATTT-TAAT
1 ATTTTTATTTGTAAT
13303641 ATTTTTATTTGTAAT
1 ATTTTTATTTGTAAT
13303656 TTAATTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATTTTTATTTGTAAT
Found at i:13303650 original size:20 final size:20
Alignment explanation
Indices: 13303620--13303669 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
13303610 TAATTTAGCC
* *
13303620 ATTTTTAATTTTTATTTTAAT
1 ATTTTT-ATTTGTAATTTAAT
13303641 ATTTTTATTTGTAATTTAAT
1 ATTTTTATTTGTAATTTAAT
13303661 -TTTTCTATT
1 ATTTT-TATT
13303670 ATAATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 16 0.62
21 6 0.23
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTTATTTGTAATTTAAT
Found at i:13308740 original size:30 final size:30
Alignment explanation
Indices: 13308706--13308774 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
13308696 ACACGGGCAC
* * *
13308706 ACGATCGTGTGGCTGAACACGAACCCTTAA
1 ACGATCGTGTGGCCGAACACAAACCCTCAA
13308736 ACGATCGTGTGGCCGAACACAAACCCTCAA
1 ACGATCGTGTGGCCGAACACAAACCCTCAA
*
13308766 ACAATCGTG
1 ACGATCGTG
13308775 CCTCTAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (30 bp):
ACGATCGTGTGGCCGAACACAAACCCTCAA
Found at i:13309424 original size:35 final size:34
Alignment explanation
Indices: 13309384--13309462 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 34
13309374 TGATTTTTGT
* *
13309384 TTATTATTTTATTATTTACTTTTTGTTTTCTTGA-A
1 TTATTATTTTATTA-TTA-TTGTTATTTTCTTGATA
*
13309419 TTATTATTATTATTATTATTGTTATTTTGTTGATA
1 TTATTATT-TTATTATTATTGTTATTTTCTTGATA
13309454 TTATTATTT
1 TTATTATTT
13309463 AATACTCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 13 0.33
35 20 0.51
36 6 0.15
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (34 bp):
TTATTATTTTATTATTATTGTTATTTTCTTGATA
Found at i:13315116 original size:18 final size:17
Alignment explanation
Indices: 13315090--13315143 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
13315080 AGTTTTTCAA
*
13315090 ATTTTTATGATTTTTTT
1 ATTTTTATGATTTTTAT
13315107 ATTTTATATGAATTTTTAT
1 ATTTT-TATG-ATTTTTAT
13315126 ATCTTTT-TAGATTTTTAT
1 AT-TTTTAT-GATTTTTAT
13315144 GAAGTACACA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.16
18 13 0.41
19 11 0.34
20 3 0.09
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (17 bp):
ATTTTTATGATTTTTAT
Found at i:13315144 original size:28 final size:28
Alignment explanation
Indices: 13315089--13315146 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
13315079 TAGTTTTTCA
*
13315089 AATTTTTATGATTTTTTTATTTTATATG
1 AATTTTTATGATTTTTTGATTTTATATG
13315117 AATTTTTAT-ATCTTTTTAGATTTT-TATG
1 AATTTTTATGAT-TTTTT-GATTTTATATG
13315145 AA
1 AA
13315147 GTACACATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 20 0.74
29 5 0.19
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.64
Consensus pattern (28 bp):
AATTTTTATGATTTTTTGATTTTATATG
Found at i:13335093 original size:41 final size:41
Alignment explanation
Indices: 13334975--13335128 Score: 177
Period size: 41 Copynumber: 3.7 Consensus size: 41
13334965 AATCACTTGA
*
13334975 TATATAAATGGAAGACTCATGTCTC-GAGATGAGCGTGAGAT
1 TATATAAATGGAAGACTCATGTCTCGGA-ATGAGCATGAGAT
* * **
13335016 TATGTATAAATGGAAGACTCGTGACTTAGAATGAGCATGAGAT
1 TA--TATAAATGGAAGACTCATGTCTCGGAATGAGCATGAGAT
* * * *
13335059 TATATTAAGGGAAGACTCATGTCTCGGAAGGAGCATGAGAC
1 TATATAAATGGAAGACTCATGTCTCGGAATGAGCATGAGAT
13335100 TATATTAAA-GGAAGACTCATGTCTCGGAA
1 TATA-TAAATGGAAGACTCATGTCTCGGAA
13335129 AGAGTGTGAG
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
41 57 0.59
42 3 0.03
43 34 0.35
44 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (41 bp):
TATATAAATGGAAGACTCATGTCTCGGAATGAGCATGAGAT
Found at i:13335139 original size:41 final size:41
Alignment explanation
Indices: 13334974--13335168 Score: 176
Period size: 41 Copynumber: 4.6 Consensus size: 41
13334964 GAATCACTTG
* *
13334974 ATATATAAATGGAAGACTCATGTCTC-GAGATGAGCGTGAGATT
1 ATAT-TAAA-GGAAGACTCATGTCTCGGA-ATGAGCATGAGACT
* * * ** *
13335017 ATGTATAAATGGAAGACTCGTGACTTAGAATGAGCATGAGATT
1 ATAT-TAAA-GGAAGACTCATGTCTCGGAATGAGCATGAGACT
* *
13335060 ATATTAAGGGAAGACTCATGTCTCGGAAGGAGCATGAGACT
1 ATATTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGACT
* **
13335101 ATATTAAAGGAAGACTCATGTCTCGGAAAGAGTGTGAGACT
1 ATATTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGACT
* * * *
13335142 ATGTTTAATGGAAGACTTATGGCTCGG
1 AT-ATTAAAGGAAGACTCATGTCTCGG
13335169 TGTAGCATAA
Statistics
Matches: 129, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 66 0.51
42 23 0.18
43 38 0.29
44 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (41 bp):
ATATTAAAGGAAGACTCATGTCTCGGAATGAGCATGAGACT
Found at i:13335847 original size:21 final size:21
Alignment explanation
Indices: 13335821--13335868 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13335811 TCTAGTGTTG
13335821 GTAGAAG-CATGACTTGTATCA
1 GTAGAAGTCAT-ACTTGTATCA
* *
13335842 GTAGAAGTTATACTTGTGTCA
1 GTAGAAGTCATACTTGTATCA
13335863 GTAGAA
1 GTAGAA
13335869 CTGGTACAAG
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:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (21 bp):
GTAGAAGTCATACTTGTATCA
Found at i:13339891 original size:3 final size:3
Alignment explanation
Indices: 13339883--13339947 Score: 50
Period size: 3 Copynumber: 22.7 Consensus size: 3
13339873 TGGCACAAAA
* *
13339883 TCT TCT TCT TCT TCT TTT TCCT TC- TCT TC- TCT TCCT TCC TCT TC-
1 TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT T-CT TCT TCT TCT
*
13339927 TCT T-T TC- TCT TCT TCC TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC
13339948 AACACCTGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
2 10 0.20
3 34 0.69
4 5 0.10
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:13362900 original size:6 final size:6
Alignment explanation
Indices: 13362889--13362932 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
13362879 TTTATAGCAA
13362889 TTTTTC TTTTTC TTTTCTC TTTTTC TCTTTT- TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTT-TC TTTTTC T-TTTTC TTTTTC TTTTTC T
13362933 CATTCACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 4 0.11
6 21 0.60
7 10 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:13394462 original size:11 final size:12
Alignment explanation
Indices: 13394437--13394465 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
13394427 TTTTTACTAT
13394437 AATATTATAAAA
1 AATATTATAAAA
13394449 AATATTAT-AAA
1 AATATTATAAAA
13394460 AATATT
1 AATATT
13394466 TTTAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATTATAAAA
Found at i:13407137 original size:20 final size:22
Alignment explanation
Indices: 13407112--13407153 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
13407102 TAAGAATTTT
*
13407112 TTAAATAG-TTTTAAA-CAAAA
1 TTAAATAGATTTGAAAGCAAAA
13407132 TTAAATAGATTTGAAAGCAAAA
1 TTAAATAGATTTGAAAGCAAAA
13407154 AAGAAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.31
Consensus pattern (22 bp):
TTAAATAGATTTGAAAGCAAAA
Found at i:13407806 original size:59 final size:59
Alignment explanation
Indices: 13407693--13407840 Score: 156
Period size: 59 Copynumber: 2.5 Consensus size: 59
13407683 TCATATTTTG
* * * *
13407693 ACCCCCAAACTTTTCCAAAATTACATTTTAACCCTCAAGCTTTTCCAAAATTACACTTTA
1 ACCCCTAAACTTTTCAAAAATTACATTTTAACACTCAAACTTTT-CAAAATTACACTTTA
* * * * * *
13407753 ACCTC-GAGCTTTTCAAAAATTACATTTTGACACTCAAACTTTGT-AAAATTTACATTTTT
1 ACCCCTAAACTTTTCAAAAATTACATTTTAACACTCAAACTTT-TCAAAA-TTACACTTTA
*
13407812 ACCCCTAAACTTCTCAAAAATTACATTTT
1 ACCCCTAAACTTTTCAAAAATTACATTTT
13407841 TGCCCTTGAA
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
58 4 0.06
59 43 0.60
60 25 0.35
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.36
Consensus pattern (59 bp):
ACCCCTAAACTTTTCAAAAATTACATTTTAACACTCAAACTTTTCAAAATTACACTTTA
Found at i:13407832 original size:89 final size:89
Alignment explanation
Indices: 13407673--13407836 Score: 199
Period size: 89 Copynumber: 1.8 Consensus size: 89
13407663 GTCCCTAAAC
* * * *
13407673 TTTCTAAAAATCATATTTTGACCCCCAAACTTTTCCAAAATTACATTTTAACCCTCAAGCTTTTC
1 TTTCTAAAAATCACATTTTGACACCCAAACTTTT-CAAAATTACATTTTAACCCTCAAACTTCTC
*
13407738 CAAAATTACACTTTAACCTCGAGCT
65 AAAAATTACACTTTAACCTCGAGCT
* * *
13407763 TTTC-AAAAATTACATTTTGACACTCAAACTTTGT-AAAATTTACATTTTTACCC-CTAAACTTC
1 TTTCTAAAAATCACATTTTGACACCCAAACTTT-TCAAAA-TTACATTTTAACCCTC-AAACTTC
13407825 TCAAAAATTACA
63 TCAAAAATTACA
13407837 TTTTTGCCCT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
88 5 0.08
89 53 0.84
90 5 0.08
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.37
Consensus pattern (89 bp):
TTTCTAAAAATCACATTTTGACACCCAAACTTTTCAAAATTACATTTTAACCCTCAAACTTCTCA
AAAATTACACTTTAACCTCGAGCT
Found at i:13407841 original size:30 final size:30
Alignment explanation
Indices: 13407665--13407933 Score: 124
Period size: 30 Copynumber: 9.1 Consensus size: 30
13407655 CCCAGAAGGT
* * *
13407665 CCCTAAACTT-TCTAAAAATCATATTTTGAC
1 CCCTAAACTTCTC-AAAAATTACATTTTTAC
* * * *
13407695 CCCCAAACTTTTCCAAAATTACA-TTTTAA
1 CCCTAAACTTCTCAAAAATTACATTTTTAC
* * * * *
13407724 CCCTCAAGCTTTTCCAAAATTACACTTTAAC
1 CCCT-AAACTTCTCAAAAATTACATTTTTAC
* * * * *
13407755 CTC-GAGCTTTTCAAAAATTACATTTTGA-
1 CCCTAAACTTCTCAAAAATTACATTTTTAC
* * *
13407783 CACTCAAACTT-TGTAAAATTTACATTTTTAC
1 CCCT-AAACTTCT-CAAAAATTACATTTTTAC
*
13407814 CCCTAAACTTCTCAAAAATTACATTTTTGC
1 CCCTAAACTTCTCAAAAATTACATTTTTAC
* * * * *
13407844 CCTTGAACATCTCAAAAATTACATCTTTGC
1 CCCTAAACTTCTCAAAAATTACATTTTTAC
** * * *
13407874 CCCCGAACTTC-CAGAAATCACCA-TTTTGC
1 CCCTAAACTTCTCAAAAATTA-CATTTTTAC
* *
13407903 CCCTAAGCATC-CAAAAATTACCA-TTTTAC
1 CCCTAAACTTCTCAAAAATTA-CATTTTTAC
13407932 CC
1 CC
13407934 TCAACTTTTA
Statistics
Matches: 188, Mismatches: 42, Indels: 19
0.76 0.17 0.08
Matches are distributed among these distances:
28 2 0.01
29 65 0.35
30 109 0.58
31 12 0.06
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (30 bp):
CCCTAAACTTCTCAAAAATTACATTTTTAC
Found at i:13416642 original size:99 final size:99
Alignment explanation
Indices: 13416457--13417080 Score: 457
Period size: 99 Copynumber: 6.3 Consensus size: 99
13416447 CAAGTTTGAC
* ** * ** * * *
13416457 AGGGAA-GATTGAGGCCGCAACGGAAAATCTAATACCCT-GGAGATATGAAGGGAAAGGTTGAGG
1 AGGGAAGGATTGAGGCCGCAATGGCGAACCTGGTACCCTAGAAGATGTGATGGGAAAGGTTGAGG
* * *
13416520 CTGTAAC-AGCGAACCCAATACCATGAAGAGATGA
66 CCGCAACGA-CGAACCCGATACCATGAAGAGATGA
* * * * *
13416554 AGGGAAGGATTGAGGCCGCGATGGTGAACCTGGTACCCTAGAAGATGCGATGGGAAATGTTAAGG
1 AGGGAAGGATTGAGGCCGCAATGGCGAACCTGGTACCCTAGAAGATGTGATGGGAAAGGTTGAGG
*** *
13416619 CCGCAACGGTAAACCCGATACCATGAAGATATGA
66 CCGCAACGACGAACCCGATACCATGAAGAGATGA
* * *
13416653 AGGGAAAGATTGAGGTCGCAATGGCGAACCTGGTA-CCTAAGAAGATGTGATGGGAAAGGCTGAG
1 AGGGAAGGATTGAGGCCGCAATGGCGAACCTGGTACCCT-AGAAGATGTGATGGGAAAGGTTGAG
* * *
13416717 GCCGCAACGACGAA-CCTAGTACGATGAAGATG-CGA
65 GCCGCAACGACGAACCCGA-TACCATGAAGA-GATGA
* ** * * * * *
13416752 AGGGAAGGATTAAGGCCGTGACGGCGAATCC-GATACCTTAAAAGATGTGATAGGAAAGGTTGAG
1 AGGGAAGGATTGAGGCCGCAATGGCGAA-CCTGGTACCCTAGAAGATGTGATGGGAAAGGTTGAG
* * * * *
13416816 GCCCCAACGACGAACTCGGTACCATGAAGATACGA
65 GCCGCAACGACGAACCCGATACCATGAAGAGATGA
* * * *
13416851 AGAGAAAGG-TTGAGGTCGCAATGGCAAACCTGGTA-CCTAAAAAGATGTGATGGGAAAGGTTGA
1 AG-GGAAGGATTGAGGCCGCAATGGCGAACCTGGTACCCT-AGAAGATGTGATGGGAAAGGTTGA
* ** * *
13416914 GGTCGCAACGGTGAACCCGGTACCTAAGAAGATG-TGA
64 GGCCGCAACGACGAACCCGATACC-ATGAAGA-GATGA
* * ** * *
13416951 AGGGAAAGG-TAGAGGCCGCAACGGCGAACCCAGTACCTTAGAAGATGCGATGGG-AAGGATTGA
1 AGGG-AAGGATTGAGGCCGCAATGGCGAACCTGGTACCCTAGAAGATGTGATGGGAAAGG-TTGA
* * * * * *
13417014 GGTCACAA-TAGCGAATCCGATACCATGAATATATGA
64 GGCCGCAACGA-CGAACCCGATACCATGAAGAGATGA
* **
13417050 ATGGAAAGG-TTGAGGGTGCAATGGCGAACCT
1 A-GGGAAGGATTGAGGCCGCAATGGCGAACCT
13417081 AACACCTTAG
Statistics
Matches: 411, Mismatches: 95, Indels: 40
0.75 0.17 0.07
Matches are distributed among these distances:
97 6 0.01
98 35 0.09
99 288 0.70
100 80 0.19
101 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.17
Consensus pattern (99 bp):
AGGGAAGGATTGAGGCCGCAATGGCGAACCTGGTACCCTAGAAGATGTGATGGGAAAGGTTGAGG
CCGCAACGACGAACCCGATACCATGAAGAGATGA
Found at i:13416830 original size:149 final size:150
Alignment explanation
Indices: 13416595--13417006 Score: 370
Period size: 149 Copynumber: 2.8 Consensus size: 150
13416585 GGTACCCTAG
* * ** * *
13416595 AAGATGCGATGGGAAATGTTAAGGCCGCAACGGTAAACCCGATACC-ATGAAGATATGAAGGGAA
1 AAGATGCGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGATACCTAAGAAGATGTGAAGGGAA
* * * * * * *
13416659 AGATTGAGGTCGCAATGGCGAACCTGGTACCTAAGAAGATGTGATGGGAAAGGCTGAGGCCGCAA
66 AGGTAGAGGCCCCAACGACGAACCTGGTACCTAAGAAGATGCGATGGGAAAGGCTGAGGCCGCAA
* **
13416724 CGACGAACCTAGTA-CGATG
131 CGACAAACCTAGTACCGAAA
** *
13416743 AAGATGCGAAGGG-AAGGATTAAGGCCGTGACGGCGAATCCGATACCTTAA-AAGATGTGATA-G
1 AAGATGCGAAGGGAAAGG-TTAAGGCCGCAACGGCGAACCCGATACC-TAAGAAGATGTGA-AGG
* * * * * * *
13416805 GAAAGGTTGAGGCCCCAACGACGAA-CTCGGTACC-ATGAAGATACGAAGAGAAAGGTTGAGGTC
63 GAAAGGTAGAGGCCCCAACGACGAACCT-GGTACCTAAGAAGATGCGATGGGAAAGGCTGAGGCC
* * * *
13416868 GCAATGGCAAACCTGGTACCTAAA
127 GCAACGACAAACCTAGTACCGAAA
* * * * * *
13416892 AAGATGTGATGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAA
1 AAGATGCGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGATACCTAAGAAGATGTGAAGGGAA
* * ** *
13416957 AGGTAGAGGCCGCAACGGCGAACCCAGTACCTTAGAAGATGCGATGGGAA
66 AGGTAGAGGCCCCAACGACGAACCTGGTACCTAAGAAGATGCGATGGGAA
13417007 GGATTGAGGT
Statistics
Matches: 206, Mismatches: 47, Indels: 20
0.75 0.17 0.07
Matches are distributed among these distances:
147 3 0.01
148 77 0.37
149 106 0.51
150 20 0.10
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.16
Consensus pattern (150 bp):
AAGATGCGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCGATACCTAAGAAGATGTGAAGGGAA
AGGTAGAGGCCCCAACGACGAACCTGGTACCTAAGAAGATGCGATGGGAAAGGCTGAGGCCGCAA
CGACAAACCTAGTACCGAAA
Found at i:13416846 original size:198 final size:197
Alignment explanation
Indices: 13416497--13417080 Score: 576
Period size: 198 Copynumber: 2.9 Consensus size: 197
13416487 AATACCCTGG
* * * * * *
13416497 AGATATGAAGGGAAAGGTTGAGGCTGTAAC-AGCGAACCCAATACCATGAAG-AGAT--GAAGGG
1 AGATGTGATGGGAAAGGCTGAGGCCGCAACGA-CGAACCCAGTACC--GAAGAAGATGCGAAGGG
* * * * * * * *
13416558 AAGGATTGAGGCCGCGATGGTGAACCTGGTACCCTAGAAGATGCGATGGGAAATGTTAAGGCCGC
63 AAGGATTAAGGCCGCGACGGCGAACC-GATACCTTAGAAGATGCGAT-GGAAAGGTTGAGGCCAC
*** * *
13416623 AACGGTAAACCCGATACCATGAAGATATGAAGGGAAAGATTGAGGTCGCAATGGCGAACCTGGTA
126 AACGACGAACTCGATACCATGAAGATATGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCTGGTA
*
13416688 CCTAAGA
191 CCTAAAA
* *
13416695 AGATGTGATGGGAAAGGCTGAGGCCGCAACGACGAACCTAGTA-CGATGAAGATGCGAAGGGAAG
1 AGATGTGATGGGAAAGGCTGAGGCCGCAACGACGAACCCAGTACCGAAGAAGATGCGAAGGGAAG
* * * *
13416759 GATTAAGGCCGTGACGGCGAATCCGATACCTTAAAAGATGTGATAGGAAAGGTTGAGGCCCCAAC
66 GATTAAGGCCGCGACGGCGAA-CCGATACCTTAGAAGATGCGAT-GGAAAGGTTGAGGCCACAAC
* * * *
13416824 GACGAACTCGGTACCATGAAGATACGAAGAGAAAGGTTGAGGTCGCAATGGCAAACCTGGTACCT
129 GACGAACTCGATACCATGAAGATATGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCTGGTACCT
13416889 AAAA
194 AAAA
* * ** * * *
13416893 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCTAAGAAGATGTGAAGGGAAA
1 AGATGTGATGGGAAAGGCTGAGGCCGCAACGACGAACCCAGTACCGAAGAAGATGCGAAGGG-AA
* * * *
13416958 GG--TAGAGGCCGCAACGGCGAACCCAGTACCTTAGAAGATGCGATGGGAAGGATTGAGGTCACA
65 GGATTA-AGGCCGCGACGGCGAACCGA-TACCTTAGAAGATGCGATGGAAAGG-TTGAGGCCACA
* * *
13417021 A-TAGCGAA-TCCGATACCATGAATATATGAATGGAAAGGTTGAGGGT-GCAATGGCGAACCT
127 ACGA-CGAACT-CGATACCATGAAGATATGAAGGGAAAGGTTGA-GGTCGCAATGGCGAACCT
13417081 AACACCTTAG
Statistics
Matches: 319, Mismatches: 54, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
195 3 0.01
196 4 0.01
197 1 0.00
198 202 0.63
199 102 0.32
200 7 0.02
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.17
Consensus pattern (197 bp):
AGATGTGATGGGAAAGGCTGAGGCCGCAACGACGAACCCAGTACCGAAGAAGATGCGAAGGGAAG
GATTAAGGCCGCGACGGCGAACCGATACCTTAGAAGATGCGATGGAAAGGTTGAGGCCACAACGA
CGAACTCGATACCATGAAGATATGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCTGGTACCTAA
AA
Found at i:13417028 original size:50 final size:50
Alignment explanation
Indices: 13416497--13417079 Score: 348
Period size: 50 Copynumber: 11.8 Consensus size: 50
13416487 AATACCCTGG
* * * * ** *
13416497 AGATATGAAGGGAAAGGTTGAGG-CTGTAACAGCGAACCCAATACC-ATGA
1 AGATGTGATGGGAAAGGTTGAGGTC-GCAACGGCGAACCCGGTACCTAAGA
* * * * * *
13416546 AGA-GATGAAGGG-AAGGATTGAGGCCGCGATGGTGAACCTGGTACCCT-AGA
1 AGATG-TGATGGGAAAGG-TTGAGGTCGCAACGGCGAACCCGGTA-CCTAAGA
* * * * ** * *
13416596 AGATGCGATGGGAAATGTTAAGGCCGCAACGGTAAACCCGATACC-ATGA
1 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
* * * * *
13416645 AGATATGAAGGGAAAGATTGAGGTCGCAATGGCGAACCTGGTACCTAAGA
1 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
* * * ** * *
13416695 AGATGTGATGGGAAAGGCTGAGGCCGCAACGACGAACCTAGTA-CGATGA
1 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
* * * * ** * *
13416744 AGATGCGAAGGG-AAGGATTAAGGCCGTGACGGCGAATCCGATACCTTAA-A
1 AGATGTGATGGGAAAGG-TTGAGGTCGCAACGGCGAACCCGGTACC-TAAGA
* * * * * *
13416794 AGATGTGATAGGAAAGGTTGAGGCCCCAACGACGAACTCGGTACC-ATGA
1 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
** * * * * * *
13416843 AGATACGAAGAGAAAGGTTGAGGTCGCAATGGCAAACCTGGTACCTAAAA
1 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
*
13416893 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGTGAACCCGGTACCTAAGA
1 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
* * * * *
13416943 AGATGTGAAGGGAAAGGTAGAGGCCGCAACGGCGAACCCAGTACCTTAGA
1 AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
* * ** * * *
13416993 AGATGCGATGGG-AAGGATTGAGGTCACAATAGCGAATCCGATACC-ATGA
1 AGATGTGATGGGAAAGG-TTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
* * *
13417042 ATATATGAAT-GGAAAGGTTGAGGGT-GCAATGGCGAACC
1 AGATGTG-ATGGGAAAGGTTGA-GGTCGCAACGGCGAACC
13417080 TAACACCTTA
Statistics
Matches: 400, Mismatches: 115, Indels: 38
0.72 0.21 0.07
Matches are distributed among these distances:
48 9 0.02
49 154 0.38
50 228 0.57
51 9 0.02
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.16
Consensus pattern (50 bp):
AGATGTGATGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTAAGA
Found at i:13417559 original size:17 final size:17
Alignment explanation
Indices: 13417539--13417595 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
13417529 TAAACCCAAT
13417539 TTTTAATTCTTAATTTA
1 TTTTAATTCTTAATTTA
*
13417556 TTTTAAGTT-TAAATTTA
1 TTTTAA-TTCTTAATTTA
*
13417573 TTTTAA-ACTTAAATTTA
1 TTTTAATTCTT-AATTTA
13417590 TTTTAA
1 TTTTAA
13417596 ATTTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 31 0.91
18 2 0.06
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTTAATTCTTAATTTA
Found at i:13417596 original size:17 final size:17
Alignment explanation
Indices: 13417550--13417602 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
13417540 TTTAATTCTT
*
13417550 AATTTATTTTAAGTTTA
1 AATTTATTTTAAATTTA
*
13417567 AATTTATTTTAAACTTA
1 AATTTATTTTAAATTTA
13417584 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
13417601 AA
1 AA
13417603 ATTTGAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:13419412 original size:29 final size:29
Alignment explanation
Indices: 13419322--13419433 Score: 129
Period size: 30 Copynumber: 3.8 Consensus size: 29
13419312 TTTATCCCCC
* *
13419322 AAACTTTTCTAAAATTACATTTTGACCCTC
1 AAACTTATC-AAAATTACATTTTGACCCTT
*
13419352 AAACTTTTCCAAAATTACATTTTGACCCTT
1 AAACTTAT-CAAAATTACATTTTGACCCTT
*
13419382 AAACTTCA-CAAAATTTACATTTT-ACCTTT
1 AAACTT-ATCAAAA-TTACATTTTGACCCTT
13419411 AAACTTATCAAAAATTACATTTT
1 AAACTTATC-AAAATTACATTTT
13419434 TGCCCCGAAC
Statistics
Matches: 74, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
28 1 0.01
29 26 0.35
30 46 0.62
31 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (29 bp):
AAACTTATCAAAATTACATTTTGACCCTT
Found at i:13419521 original size:58 final size:54
Alignment explanation
Indices: 13419332--13419523 Score: 177
Period size: 58 Copynumber: 3.3 Consensus size: 54
13419322 AAACTTTTCT
* *
13419332 AAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTGACCCTTAAACTTCACA
1 AAAATTACATTTT-A-CCTCAAACTTAT-CAAAATTACATTTTG-CCC-TGAACTTC-CA
* * * *
13419392 AAATTTACATTTTACCTTTAAACTTATCAAAAATTACATTTTTGCCCCGAACTCCCA
1 AAAATTACATTTTACC-TCAAACTTATC-AAAATTACA-TTTTGCCCTGAACTTCCA
* * *
13419449 AAAATCACATTTTTATCCTCGAACTTCTCAAAATTACATCTTTGCCCGTGAACTTCCA
1 AAAATTACA-TTTTA-CCTCAAACTTATCAAAATTACAT-TTTGCCC-TGAACTTCCA
13419507 AAAATTACCATTTTACC
1 AAAATTA-CATTTTACC
13419524 CATGAGCATC
Statistics
Matches: 110, Mismatches: 14, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
56 1 0.01
57 27 0.25
58 40 0.36
59 25 0.23
60 17 0.15
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (54 bp):
AAAATTACATTTTACCTCAAACTTATCAAAATTACATTTTGCCCTGAACTTCCA
Found at i:13419540 original size:58 final size:56
Alignment explanation
Indices: 13419332--13419577 Score: 174
Period size: 58 Copynumber: 4.2 Consensus size: 56
13419322 AAACTTTTCT
* * * * * *
13419332 AAAATTACATTTTGACCCTCAAACTTTTCCAAAATTACATTTTGACCCTTAAACTTCACA
1 AAAATCACATTTT-ACCCTCGAACATCTCAAAAATTACATTTTG-CCC-TGAACTTC-CA
* * * ** * * * *
13419392 AAATTTACATTTTACCTTTAAACTTATCAAAAATTACATTTTTGCCCCGAACTCCCA
1 AAAATCACATTTTACCCTCGAACATCTCAAAAATTACA-TTTTGCCCTGAACTTCCA
* *
13419449 AAAATCACATTTTTATCCTCGAACTTCTC-AAAATTACATCTTTGCCCGTGAACTTCCA
1 AAAATCACA-TTTTACCCTCGAACATCTCAAAAATTACAT-TTTGCCC-TGAACTTCCA
* * * *
13419507 AAAATTACCATTTTACCCAT-GAGCATC-CAAAAATCACCATTTTGCCCTCGAATTTCCA
1 AAAATCA-CATTTTACCC-TCGAACATCTCAAAAATTA-CATTTTGCCCT-GAACTTCCA
13419565 AAAATCACATTTT
1 AAAATCACATTTT
13419578 CGACCCTCAA
Statistics
Matches: 153, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
56 1 0.01
57 33 0.22
58 72 0.47
59 30 0.20
60 17 0.11
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (56 bp):
AAAATCACATTTTACCCTCGAACATCTCAAAAATTACATTTTGCCCTGAACTTCCA
Found at i:13419564 original size:29 final size:28
Alignment explanation
Indices: 13419332--13419577 Score: 133
Period size: 29 Copynumber: 8.5 Consensus size: 28
13419322 AAACTTTTCT
* *
13419332 AAAATTACATTTTGACCCTCAAACTTTTCC-
1 AAAATCACATTTTG-CCCTCGAAC--TTCCA
* **
13419362 AAAATTACATTTTGACCCTTAAACTTCACA
1 AAAATCACATTTTG-CCCTCGAACTTC-CA
* * * * ** *
13419392 AAATTTACATTTTACCTTTAAACTTATCA
1 AAAATCACATTTTGCCCTCGAACTT-CCA
* *
13419421 AAAATTACATTTTTGCCC-CGAACTCCCA
1 AAAATCACA-TTTTGCCCTCGAACTTCCA
**
13419449 AAAATCACATTTTTATCCTCGAACTTCTC-
1 AAAATCACA-TTTTGCCCTCGAACTTC-CA
*
13419478 AAAATTACATCTTTGCCCGT-GAACTTCCA
1 AAAATCACAT-TTTGCCC-TCGAACTTCCA
* * * *
13419507 AAAATTACCATTTTACCCAT-GAGCATCCA
1 AAAATCA-CATTTTGCCC-TCGAACTTCCA
*
13419536 AAAATCACCATTTTGCCCTCGAATTTCCA
1 AAAATCA-CATTTTGCCCTCGAACTTCCA
13419565 AAAATCACATTTT
1 AAAATCACATTTT
13419578 CGACCCTCAA
Statistics
Matches: 177, Mismatches: 28, Indels: 24
0.77 0.12 0.10
Matches are distributed among these distances:
28 29 0.16
29 102 0.58
30 46 0.26
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAATCACATTTTGCCCTCGAACTTCCA
Found at i:13419593 original size:30 final size:29
Alignment explanation
Indices: 13419431--13419597 Score: 98
Period size: 29 Copynumber: 5.8 Consensus size: 29
13419421 AAAATTACAT
* *
13419431 TTTTGCCC-CGAACTCCCAAAAATCA-CA
1 TTTTGCCCTCGAATTTCCAAAAATCACCA
** * *
13419458 TTTTTATCCTCGAACTTCTC-AAAATTA-CA
1 -TTTTGCCCTCGAATTTC-CAAAAATCACCA
* *
13419487 TCTTTGCCCGT-GAACTTCCAAAAATTACCA
1 T-TTTGCCC-TCGAATTTCCAAAAATCACCA
* ***
13419517 TTTTACCCAT-GAGCATCCAAAAATCACCA
1 TTTTGCCC-TCGAATTTCCAAAAATCACCA
13419546 TTTTGCCCTCGAATTTCCAAAAATCA-CA
1 TTTTGCCCTCGAATTTCCAAAAATCACCA
13419574 TTTTCGACCCTC-AATTTTCCAAAA
1 TTTT-G-CCCTCGAA-TTTCCAAAA
13419598 GTTTGACTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
28 15 0.13
29 80 0.70
30 19 0.17
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.31
Consensus pattern (29 bp):
TTTTGCCCTCGAATTTCCAAAAATCACCA
Found at i:13424137 original size:15 final size:16
Alignment explanation
Indices: 13424114--13424147 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
13424104 ATTAGGGATC
*
13424114 AATTGCATTT-ATTTT
1 AATTACATTTAATTTT
13424129 AATTACATTTAATTTT
1 AATTACATTTAATTTT
13424145 AAT
1 AAT
13424148 CATCACTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
AATTACATTTAATTTT
Found at i:13427960 original size:29 final size:26
Alignment explanation
Indices: 13427928--13427981 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
13427918 ATTGTCATAA
*
13427928 TTACTATAATTATATTACTATTTTATTTC
1 TTACCATAATTAT-TT--TATTTTATTTC
*
13427957 TTACCATGATTATTTTATTTTATTT
1 TTACCATAATTATTTTATTTTATTT
13427982 TATTGTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
28 2 0.09
29 11 0.48
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (26 bp):
TTACCATAATTATTTTATTTTATTTC
Found at i:13436988 original size:112 final size:112
Alignment explanation
Indices: 13436791--13437016 Score: 434
Period size: 112 Copynumber: 2.0 Consensus size: 112
13436781 TTGGGAAAAT
*
13436791 GACAAAGACCTACAAAGATTGGCTTGAGAAGTTACCACTTTCTCTCTACGCCTATAGAACGTCTG
1 GACAAAGACCTACAAAGATTGGCTTGAGAAGTTACCACTTGCTCTCTACGCCTATAGAACGTCTG
13436856 TCAGAACTTCTATTGGGGTAACAACGTTCTCATTAGTATATGGAATG
66 TCAGAACTTCTATTGGGGTAACAACGTTCTCATTAGTATATGGAATG
13436903 GACAAAGACCTACAAAGATTGGCTTGAGAAGTTACCACTTGCTCTCTACGCCTATAGAACGTCTG
1 GACAAAGACCTACAAAGATTGGCTTGAGAAGTTACCACTTGCTCTCTACGCCTATAGAACGTCTG
*
13436968 TCAGAACTTCTATTGGGGTAACACCGTTCTCATTAGTATATGGAATG
66 TCAGAACTTCTATTGGGGTAACAACGTTCTCATTAGTATATGGAATG
13437015 GA
1 GA
13437017 GATAGTTCTG
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (112 bp):
GACAAAGACCTACAAAGATTGGCTTGAGAAGTTACCACTTGCTCTCTACGCCTATAGAACGTCTG
TCAGAACTTCTATTGGGGTAACAACGTTCTCATTAGTATATGGAATG
Found at i:13438542 original size:49 final size:48
Alignment explanation
Indices: 13438489--13439122 Score: 299
Period size: 49 Copynumber: 12.8 Consensus size: 48
13438479 AGTTGAAGAG
* * *
13438489 GGAAAGATTAAAGTGGCAACGACGAATCTTATACCCTAAAATAGAAAAA
1 GGAAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAATA-AAAAA
* * *
13438538 GGAAAGATTAAAATTGCAACGGCGAATCTTACACCTCAAAAATAAAAAA
1 GGAAAGATTAAAGTCGCAACGGCGAATCTTACACC-CTAAAATAAAAAA
* * * * **
13438587 -GAAAGATTAAAGCCACAACGACGAATCTTACACCCCAAAACCAAAAA
1 GGAAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAATAAAAAA
* * * * * * *
13438634 GGAAAAGATTAAAGTTGTAATGGCAAATCTTACACCCTAAAATTGAACAG
1 GG-AAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAA-TAAAAAA
* ** * * *
13438684 GGAAAGATTAAAGCCATAATGGCGAATCTTACACTCTAAAATCAAAAAG
1 GGAAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAAT-AAAAAA
* ** * * * *
13438733 GGAAAGATTAAAGCCAAAATGGTGAATCTTACACCCTAAAACCAAAAAG
1 GGAAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAA-TAAAAAA
* * * *** *
13438782 GGAAAAGATTAAAGCCGTAATGATAAATCTTACACCTTAAAATCAAAAAA
1 GG-AAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAAT-AAAAAA
* *** * * ***
13438832 GGGAAAGATTAAAG-CTGTAACGATAAATCTTACACTCTAAAACCAAAGTG
1 -GGAAAGATTAAAGTC-GCAACGGCGAATCTTACACCCTAAAA-TAAAAAA
* * * * * * *
13438882 GGAAAGATTAAAGCCACAATGACTAATCTTACACCCT-AAATCAAAGA
1 GGAAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAATAAAAAA
* * *** *
13438929 GGTATAGATTAAAGCCAG-AACGATAAATCTTACACCCTAAAAAACTAAAAA
1 GG-AAAGATTAAAGTC-GCAACGGCGAATCTTACACCCTAAAATA--AAAAA
* * ** ** * * * *
13438980 GAGACATATTAAAGTCATAACGATGAATCTTACTCCCTAAAACTGAAGAG
1 G-GAAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAA-TAAAAAA
** * * *
13439030 GGGCAGATTAAAGACGTAACGGC-AAGTCTTACACCCCTAAAAAACTAAATAA
1 GGAAAGATTAAAGTCGCAACGGCGAA-TCTTACA-CCCT--AAAA-TAAAAAA
** *
13439082 GGACAA-ATTAAAGTTTCAACGGTGAATCTTACACCTCTAAA
1 GGA-AAGATTAAAGTCGCAACGGCGAATCTTACACC-CTAAA
13439123 GTTGAAGAGA
Statistics
Matches: 462, Mismatches: 96, Indels: 53
0.76 0.16 0.09
Matches are distributed among these distances:
47 14 0.03
48 65 0.14
49 206 0.45
50 100 0.22
51 41 0.09
52 33 0.07
53 3 0.01
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (48 bp):
GGAAAGATTAAAGTCGCAACGGCGAATCTTACACCCTAAAATAAAAAA
Found at i:13438713 original size:98 final size:98
Alignment explanation
Indices: 13438487--13439071 Score: 444
Period size: 97 Copynumber: 5.9 Consensus size: 98
13438477 AAAGTTGAAG
*** * * * * *
13438487 AGGGAAAGATTAAAGTGGCAACGACGAATCTTATACCCTAAAA-TAGAAAAAGGAAAGATTAAAA
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCA-AAAAGGGAAAGATTAAAG
* * * **
13438551 TTGCAACGGCGAATCTTACA-CCTCAAAAATAAAA
65 CTGTAACGGCAAATCTTACACCCT-AAAACCAAAA
* * * * *
13438585 A-AGAAAGATTAAAGCCACAACGACGAATCTTACACCCCAAAACCAAAAAGGAAAAGATTAAAGT
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGC
* *** *
13438649 TGTAATGGCAAATCTTACACCCTAAAATTGAAC
66 TGTAACGGCAAATCTTACACCCTAAAACCAAAA
* * * *
13438682 AGGGAAAGATTAAAGCCATAATGGCGAATCTTACACTCTAAAATCAAAAAGGGAAAGATTAAAGC
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGC
*** * **
13438747 CAAAATGGTGAATCTTACACCCTAAAACCAAAA
66 TGTAACGGCAAATCTTACACCCTAAAACCAAAA
** ** * *
13438780 AGGGAAAAGATTAAAGCCGTAATGATAAATCTTACACCTTAAAATCAAAAAAGGGAAAGATTAAA
1 AGGG-AAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAA-CCAAAAAGGGAAAGATTAAA
** * *
13438845 GCTGTAACGATAAATCTTACACTCTAAAACCAAAG
64 GCTGTAACGGCAAATCTTACACCCTAAAACCAAAA
* * * * * *
13438880 TGGGAAAGATTAAAGCCACAATGACTAATCTTACACCCT-AAATCAAAGAGGTATAGATTAAAGC
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAG-
* ** *
13438944 CAG-AACGATAAATCTTACACCCTAAAAAACTAAAA
65 CTGTAACGGCAAATCTTACACCCT--AAAACCAAAA
* * * * * * * * ** * **
13438979 AGAGACATATTAAAGTCATAACGATGAATCTTACTCCCTAAAACTGAAGAGGGGCAGATTAAAGA
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAG-
*
13439044 C-GTAACGGCAAGTCTTACACCCCTAAAA
65 CTGTAACGGCAAATCTTACA-CCCTAAAA
13439072 AACTAAATAA
Statistics
Matches: 391, Mismatches: 85, Indels: 21
0.79 0.17 0.04
Matches are distributed among these distances:
97 110 0.28
98 92 0.24
99 105 0.27
100 80 0.20
101 4 0.01
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (98 bp):
AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGC
TGTAACGGCAAATCTTACACCCTAAAACCAAAA
Found at i:13438811 original size:50 final size:49
Alignment explanation
Indices: 13438562--13439022 Score: 365
Period size: 49 Copynumber: 9.4 Consensus size: 49
13438552 TGCAACGGCG
** * ** * **
13438562 AATCTTACA-CCTCAAAAATAAAAA-AGAAAGATTAAAGCCACAACGACG
1 AATCTTACACCCT-AAAACCAAAAAGGGAAAGATTAAAGCCGTAATGATA
* * ** **
13438610 AATCTTACACCCCAAAACCAAAAAGGAAAAGATTAAAGTTGTAATGGCA
1 AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCGTAATGATA
*** * * ***
13438659 AATCTTACACCCTAAAATTGAACAGGGAAAGATTAAAGCCATAATGGCG
1 AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCGTAATGATA
* * ** * *
13438708 AATCTTACACTCTAAAATCAAAAAGGGAAAGATTAAAGCCAAAATGGTG
1 AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCGTAATGATA
13438757 AATCTTACACCCTAAAACCAAAAAGGGAAAAGATTAAAGCCGTAATGATA
1 AATCTTACACCCTAAAACCAAAAAGGG-AAAGATTAAAGCCGTAATGATA
* * * *
13438807 AATCTTACACCTTAAAATCAAAAAAGGGAAAGATTAAAGCTGTAACGATA
1 AATCTTACACCCTAAAA-CCAAAAAGGGAAAGATTAAAGCCGTAATGATA
* ** **
13438857 AATCTTACACTCTAAAACCAAAGTGGGAAAGATTAAAGCCACAATGACT-
1 AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCGTAATGA-TA
* * * * *
13438906 AATCTTACACCCT-AAATCAAAGAGGTATAGATTAAAGCCAG-AACGATA
1 AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCC-GTAATGATA
* * * * * * * *
13438954 AATCTTACACCCTAAAAAACTAAAAAGAGACATATTAAAGTCATAACGATG
1 AATCTTACACCCT--AAAACCAAAAAGGGAAAGATTAAAGCCGTAATGATA
*
13439005 AATCTTACTCCCTAAAAC
1 AATCTTACACCCTAAAAC
13439023 TGAAGAGGGG
Statistics
Matches: 337, Mismatches: 65, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
47 1 0.00
48 57 0.17
49 164 0.49
50 70 0.21
51 45 0.13
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.20
Consensus pattern (49 bp):
AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCGTAATGATA
Found at i:13438823 original size:99 final size:97
Alignment explanation
Indices: 13438562--13439021 Score: 404
Period size: 99 Copynumber: 4.7 Consensus size: 97
13438552 TGCAACGGCG
** * * * * *
13438562 AATCTTACA-CCTCAAAAATAAAAA-AGAAAGATTAAAGCCACAACGACGAATCTTACACCCCAA
1 AATCTTACACCCT-AAAACCAAAAAGGGAAAGATTAAAGCCATAATGA-TAATCTTACACCCTAA
* * *** * **
13438625 AACCAAAAAGGAAAAGATTAAAGTTGTAATGGCA
64 AATCAAAAAGGGAAAGATTAAAGCCATAACGATA
*** * ** *
13438659 AATCTTACACCCTAAAATTGAACAGGGAAAGATTAAAGCCATAATGGCGAATCTTACACTCTAAA
1 AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCATAAT-GATAATCTTACACCCTAAA
* * * *
13438724 ATCAAAAAGGGAAAGATTAAAGCCAAAATGGTG
65 ATCAAAAAGGGAAAGATTAAAGCCATAACGATA
* *
13438757 AATCTTACACCCTAAAACCAAAAAGGGAAAAGATTAAAGCCGTAATGATAAATCTTACACCTTAA
1 AATCTTACACCCTAAAACCAAAAAGGG-AAAGATTAAAGCCATAATGAT-AATCTTACACCCTAA
**
13438822 AATCAAAAAAGGGAAAGATTAAAGCTGTAACGATA
64 AATC-AAAAAGGGAAAGATTAAAGCCATAACGATA
* ** *
13438857 AATCTTACACTCTAAAACCAAAGTGGGAAAGATTAAAGCCACAATGACTAATCTTACACCCT-AA
1 AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCATAATGA-TAATCTTACACCCTAAA
* * * *
13438921 ATCAAAGAGGTATAGATTAAAGCCAGAACGATA
65 ATCAAAAAGGGAAAGATTAAAGCCATAACGATA
* * * * * * *
13438954 AATCTTACACCCTAAAAAACTAAAAAGAGACATATTAAAGTCATAACGATGAATCTTACTCCCTA
1 AATCTTACACCCT--AAAACCAAAAAGGGAAAGATTAAAGCCATAATGAT-AATCTTACACCCTA
13439019 AAA
63 AAA
13439022 CTGAAGAGGG
Statistics
Matches: 297, Mismatches: 55, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
97 53 0.18
98 90 0.30
99 102 0.34
100 52 0.18
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.20
Consensus pattern (97 bp):
AATCTTACACCCTAAAACCAAAAAGGGAAAGATTAAAGCCATAATGATAATCTTACACCCTAAAA
TCAAAAAGGGAAAGATTAAAGCCATAACGATA
Found at i:13438993 original size:198 final size:197
Alignment explanation
Indices: 13438487--13439071 Score: 536
Period size: 198 Copynumber: 3.0 Consensus size: 197
13438477 AAAGTTGAAG
*** * * * *
13438487 AGGGAAAGATTAAAGTGGCAACGACGAATCTTATACCCTAAAAT-AGAAAAAGGAAAGATTAAAA
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAATCA-AAAAGGGAAAGATTAAAG
**** *** * *
13438551 TTGCAACGGCGAATCTTACA-CCTCAAAAA-TAAAAA-AGAAAGATTAAAGCCACAACGACGAAT
65 CCAAAACGATAAATCTTACACCCT-AAAAACTAAAAAGAGAAAGATTAAAGCCATAACGATGAAT
* * * * * **
13438613 CTTACACCCCAAAACCAAAAAGGAAAAGATTAAAGTTGTAATGGCAAATCTTACACCCTAAAATT
129 CTTACACCCTAAAACAAAAAAGGAAAAGATTAAAGCTGTAACGACAAATCTTACACCCTAAAACC
*
13438678 GAAC
194 AAAC
* * *
13438682 AGGGAAAGATTAAAGCCATAATGGCGAATCTTACACTCTAAAATCAAAAAGGGAAAGATTAAAGC
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAATCAAAAAGGGAAAGATTAAAGC
* * * * * * * *
13438747 CAAAATGGTGAATCTTACACCCT-AAAACCAAAAAGGGAAAAGATTAAAGCCGTAATGATAAATC
66 CAAAACGATAAATCTTACACCCTAAAAACTAAAAAGAG-AAAGATTAAAGCCATAACGATGAATC
* * * *
13438811 TTACACCTTAAAATCAAAAAAGGGAAAGATTAAAGCTGTAACGATAAATCTTACACTCTAAAACC
130 TTACACCCTAAAA-CAAAAAAGGAAAAGATTAAAGCTGTAACGACAAATCTTACACCCTAAAACC
*
13438876 AAAG
194 AAAC
* * * * *
13438880 TGGGAAAGATTAAAGCCACAATGACTAATCTTACACCCT-AAATCAAAGAGGTATAGATTAAAGC
1 AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAATCAAAAAGGGAAAGATTAAAGC
* * * *
13438944 CAGAACGATAAATCTTACACCCTAAAAAACTAAAAAGAGACATATTAAAGTCATAACGATGAATC
66 CAAAACGATAAATCTTACACCCT-AAAAACTAAAAAGAGAAAGATTAAAGCCATAACGATGAATC
* ** * *** * *
13439009 TTACTCCCTAAAACTGAAGAGGGGCAGATTAAAGAC-GTAACGGCAAGTCTTACACCCCTAAAA
130 TTACACCCTAAAACAAAAAAGGAAAAGATTAAAG-CTGTAACGACAAATCTTACA-CCCTAAAA
13439072 AACTAAATAA
Statistics
Matches: 313, Mismatches: 67, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
194 4 0.01
195 71 0.23
196 5 0.02
197 104 0.33
198 117 0.37
199 12 0.04
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (197 bp):
AGGGAAAGATTAAAGCCACAATGACGAATCTTACACCCTAAAATCAAAAAGGGAAAGATTAAAGC
CAAAACGATAAATCTTACACCCTAAAAACTAAAAAGAGAAAGATTAAAGCCATAACGATGAATCT
TACACCCTAAAACAAAAAAGGAAAAGATTAAAGCTGTAACGACAAATCTTACACCCTAAAACCAA
AC
Found at i:13439038 original size:148 final size:149
Alignment explanation
Indices: 13438587--13439042 Score: 408
Period size: 148 Copynumber: 3.1 Consensus size: 149
13438577 AAATAAAAAA
* * * **
13438587 GAAAGATTAAAGCCACAACGAC-GAATCTTACACCCCAAAACCAAAAA-GGAAAAGATTAAAGTT
1 GAAAGATTAAAGCCAAAATG-CTGAATCTTACACCCTAAAACCAAAAAGGGAAAAGATTAAAGCC
* ** *** * * * * ***
13438650 GTAATGGCAAATCTTACACCCT--AAAATTGAACAGGGAAAGATTAAAGCCATAATGGCGAATCT
65 GTAACGATAAATCTTACA-CCTAAAAAACAAAAAAGAGAAAGATTAAAGCTATAACGATAAATCT
* * *
13438713 TACACTCTAAAATCAAAAAGG
129 TACACCCTAAAACCAAAGAGG
*
13438734 GAAAGATTAAAGCCAAAATGGTGAATCTTACACCCTAAAACCAAAAAGGGAAAAGATTAAAGCCG
1 GAAAGATTAAAGCCAAAATGCTGAATCTTACACCCTAAAACCAAAAAGGGAAAAGATTAAAGCCG
* * * * *
13438799 TAATGATAAATCTTACACCTTAAAATCAAAAAAGGGAAAGATTAAAGCTGTAACGATAAATCTTA
66 TAACGATAAATCTTACACCTAAAAAACAAAAAAGAGAAAGATTAAAGCTATAACGATAAATCTTA
* *
13438864 CACTCTAAAACCAAAGTGG
131 CACCCTAAAACCAAAGAGG
* * * * *
13438883 GAAAGATTAAAGCCACAATGACT-AATCTTACACCCT-AAATCAAAGA-GGTATAGATTAAAGCC
1 GAAAGATTAAAGCCAAAATG-CTGAATCTTACACCCTAAAACCAAAAAGGGAAAAGATTAAAGCC
* * * *
13438945 AG-AACGATAAATCTTACACCCTAAAAAACTAAAAAGAGACATATTAAAG-TCATAACGATGAAT
65 -GTAACGATAAATCTTACA-CCTAAAAAACAAAAAAGAGAAAGATTAAAGCT-ATAACGATAAAT
* **
13439008 CTTACTCCCTAAAACTGAAGAGG
127 CTTACACCCTAAAACCAAAGAGG
**
13439031 GGCAGATTAAAG
1 GAAAGATTAAAG
13439043 ACGTAACGGC
Statistics
Matches: 257, Mismatches: 44, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
147 75 0.29
148 101 0.39
149 80 0.31
150 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (149 bp):
GAAAGATTAAAGCCAAAATGCTGAATCTTACACCCTAAAACCAAAAAGGGAAAAGATTAAAGCCG
TAACGATAAATCTTACACCTAAAAAACAAAAAAGAGAAAGATTAAAGCTATAACGATAAATCTTA
CACCCTAAAACCAAAGAGG
Found at i:13440732 original size:38 final size:37
Alignment explanation
Indices: 13440664--13440736 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 37
13440654 TTACTCGTTA
13440664 TTTATTTATTTGGGATATATTTTTACTTTATATTTAAT
1 TTTATTTATTTGGGATATATTTTTACTTTAT-TTTAAT
* *
13440702 TTTATTTATTATTGG-TATTTTATTTA-TTTATTTTA
1 TTTATTTATT-TGGGATATATT-TTTACTTTATTTTA
13440737 TCAATTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 4 0.13
38 20 0.65
39 7 0.23
ACGTcount: A:0.25, C:0.01, G:0.07, T:0.67
Consensus pattern (37 bp):
TTTATTTATTTGGGATATATTTTTACTTTATTTTAAT
Found at i:13441000 original size:26 final size:25
Alignment explanation
Indices: 13440971--13441038 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 25
13440961 TAATTAATTA
*
13440971 ATATTATTGTTATTATTACTATGATT
1 ATATTATT-TTATTATTACCATGATT
13440997 ATATTACTATTTTATTTATTACCATGATT
1 ATA-T--TATTTTA-TTATTACCATGATT
*
13441026 ATGTTATTTTATT
1 ATATTATTTTATT
13441039 TAATTGTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 2 0.06
26 10 0.28
27 1 0.03
28 4 0.11
29 19 0.53
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (25 bp):
ATATTATTTTATTATTACCATGATT
Found at i:13447104 original size:20 final size:21
Alignment explanation
Indices: 13447076--13447123 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
13447066 ATACACATGA
*
13447076 TTGTTTTTTGTTTT-TTCTAT
1 TTGTCTTTTGTTTTCTTCTAT
13447096 TTGTCTTTTGTTTTGCTTCTAT
1 TTGTCTTTTGTTTT-CTTCTAT
13447118 TT-TCTT
1 TTGTCTT
13447124 CTTTGATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 13 0.52
21 4 0.16
22 8 0.32
ACGTcount: A:0.04, C:0.10, G:0.10, T:0.75
Consensus pattern (21 bp):
TTGTCTTTTGTTTTCTTCTAT
Found at i:13447298 original size:17 final size:17
Alignment explanation
Indices: 13447278--13447320 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
13447268 AGCAGATTAA
* *
13447278 GGTTTTTGTTTATTTAG
1 GGTTTTTGGTCATTTAG
*
13447295 GGTTTTAGGTCATTTAG
1 GGTTTTTGGTCATTTAG
*
13447312 GCTTTTTGG
1 GGTTTTTGG
13447321 GTGTTTGGGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.12, C:0.05, G:0.28, T:0.56
Consensus pattern (17 bp):
GGTTTTTGGTCATTTAG
Found at i:13447747 original size:39 final size:39
Alignment explanation
Indices: 13447695--13447788 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 39
13447685 CTGGATGGGG
*
13447695 TAAAAGA-CTGGATGGCTTCAATATGCAC-TCTAGTTAGG-
1 TAAAAGATC-GGATGGCTTCAATATAC-CTTCTAGTTAGGC
* * *
13447733 TAAAAAGATCGGATGATCTTCAATCTACCTTCTGGTTAGGC
1 T-AAAAGATCGGATG-GCTTCAATATACCTTCTAGTTAGGC
13447774 TAAAAGATCGGATGG
1 TAAAAGATCGGATGG
13447789 TCCTCAATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
38 1 0.02
39 12 0.26
40 32 0.70
41 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (39 bp):
TAAAAGATCGGATGGCTTCAATATACCTTCTAGTTAGGC
Found at i:13447818 original size:40 final size:40
Alignment explanation
Indices: 13447738--13448266 Score: 369
Period size: 40 Copynumber: 13.0 Consensus size: 40
13447728 TTAGGTAAAA
* * * * * *
13447738 AGATCGGATGATCTTCAATCTACCTTC-TGGTTAGGCTAAA
1 AGATCGGATGGTCTTCAATCTGCC-CCATGGTTGGGGTAAG
* * * * *
13447778 AGATCGGATGGTCCTCAATCTACCCCACGGTTGGGATAAA
1 AGATCGGATGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * * * * *
13447818 AGATTGGACGATCTTTAATCTGCCCCATGATTGGGGTAAT
1 AGATCGGATGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * ** *
13447858 AGATCAGAGGGTCTTCAATCTGCCTAATGGTTGGGGGAAG
1 AGATCGGATGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * ** * *
13447898 AGATCGGATGGTCTTCAATTTGCGCTTTAGTTAGGGTAAG
1 AGATCGGATGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
*
13447938 AGATCGGATGGTCTTCAATCTGCCTCATGGTTGGGGTAAG
1 AGATCGGATGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * *
13447978 AGATCGGAGGGTCTTCAATCTACCCCATGGTTGGGTTAAG
1 AGATCGGATGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * * *
13448018 AGATTGAATGGTGTCTTCAATCTGCCTCGTGGTTGGGGTAAG
1 AGATCGGAT-G-GTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * * * * *
13448060 AGATTGGATGGTGTTTTCAATTTGCCCTATGGTTAGGGTGAG
1 AGATCGGAT-G-GTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * * * *
13448102 AGATCGAATGGTCATT-GATTTGCCCCGTGGTTTGGGTAAG
1 AGATCGGATGGTC-TTCAATCTGCCCCATGGTTGGGGTAAG
* ** * * * *
13448142 AGATCGAATAATATCTTCTATCTGCCTCGTGGTTGAGGTAAG
1 AGATCGGAT--GGTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * * *
13448184 AGATCGAATGGTGTCTTCAATCTACACCATGGTTGGGGTAAA
1 AGATCGGAT-G-GTCTTCAATCTGCCCCATGGTTGGGGTAAG
* * * * *
13448226 AGATCGAATGGTGTATTTAATTTGCCCCGTGGTTGGGGTAA
1 AGATCGGAT-G-GTCTTCAATCTGCCCCATGGTTGGGGTAA
13448267 TCGAATCTGC
Statistics
Matches: 388, Mismatches: 93, Indels: 14
0.78 0.19 0.03
Matches are distributed among these distances:
39 1 0.00
40 227 0.59
41 6 0.02
42 154 0.40
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (40 bp):
AGATCGGATGGTCTTCAATCTGCCCCATGGTTGGGGTAAG
Found at i:13448008 original size:120 final size:123
Alignment explanation
Indices: 13447829--13448231 Score: 361
Period size: 124 Copynumber: 3.3 Consensus size: 123
13447819 GATTGGACGA
* * * * * *
13447829 TCTTTAATCTGCCCCATGATTGGGGTAATAGATCAGAGGGTCTTCAATCTGCCTAATGGTTGGGG
1 TCTTCAATCTG-CCCATGGTTGGGGTAAGAGATCGGAGGGTCTTCAATCTACCCAATGGTTGGGG
* * *
13447894 GAAGAGATCGGAT-G-GTCTTCAATTTGCGCT-TTAGTTAGGGTAAGAGATCGGAT-G-G
65 GAAGAGATCGAATGGTGTCTTCAATCTGC-CTCGTAGTTAGGGTAAGAGATCGGATGGTG
* *
13447949 TCTTCAATCTGCCTCATGGTTGGGGTAAGAGATCGGAGGGTCTTCAATCTACCCCATGGTTGGGT
1 TCTTCAATCTGCC-CATGGTTGGGGTAAGAGATCGGAGGGTCTTCAATCTACCCAATGGTTGGGG
* * * * *
13448014 TAAGAGATTGAATGGTGTCTTCAATCTGCCTCGTGGTTGGGGTAAGAGATTGGATGGTG
65 GAAGAGATCGAATGGTGTCTTCAATCTGCCTCGTAGTTAGGGTAAGAGATCGGATGGTG
* * * * * * * * * ** *
13448073 TTTTCAATTTGCCCTATGGTTAGGGTGAGAGATCGAATGGTCATT-GATTTGCCCCGTGGTTTGG
1 TCTTCAATCTGCCC-ATGGTTGGGGTAAGAGATCGGAGGGTC-TTCAATCTACCCAATGGTTGGG
* ** * * * *
13448137 GTAAGAGATCGAATAATATCTTCTATCTGCCTCGTGGTT-GAGGTAAGAGATCGAATGGTG
64 GGAAGAGATCGAATGGTGTCTTCAATCTGCCTCGTAGTTAG-GGTAAGAGATCGGATGGTG
* *
13448197 TCTTCAATCTACACCATGGTTGGGGTAAAAGATCG
1 TCTTCAATCTGC-CCATGGTTGGGGTAAGAGATCG
13448232 AATGGTGTAT
Statistics
Matches: 232, Mismatches: 41, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
119 2 0.01
120 64 0.28
121 3 0.01
122 31 0.13
123 3 0.01
124 125 0.54
125 4 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (123 bp):
TCTTCAATCTGCCCATGGTTGGGGTAAGAGATCGGAGGGTCTTCAATCTACCCAATGGTTGGGGG
AAGAGATCGAATGGTGTCTTCAATCTGCCTCGTAGTTAGGGTAAGAGATCGGATGGTG
Found at i:13448142 original size:124 final size:124
Alignment explanation
Indices: 13447931--13448266 Score: 378
Period size: 124 Copynumber: 2.7 Consensus size: 124
13447921 GCTTTAGTTA
* *
13447931 GGGTAAGAGATCGGAT-G-GTCTTCAATCTG-CCTCATGGTTGGGGTAAGAGATCGGAGGGTC-T
1 GGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCT-ATGGTTGGGGTAAGAGATCGAATGGTCAT
* * * * ** *
13447992 TCAATCTACCCCATGG-TTGGGTTAAGAGATTGAATGGTGTCTTCAATCTGCCTCGTGGTTG
65 T-AATTTGCCCCGTGGTTTGGG-TAAGAGATCGAATAATATCTTCAATCTGCCTCGTGGTTG
* * * * *
13448053 GGGTAAGAGATTGGATGGTGTTTTCAATTTGCCCTATGGTTAGGGTGAGAGATCGAATGGTCATT
1 GGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCTATGGTTGGGGTAAGAGATCGAATGGTCATT
* *
13448118 GATTTGCCCCGTGGTTTGGGTAAGAGATCGAATAATATCTTCTATCTGCCTCGTGGTTG
66 AATTTGCCCCGTGGTTTGGGTAAGAGATCGAATAATATCTTCAATCTGCCTCGTGGTTG
* * * * *
13448177 AGGTAAGAGATCGAATGGTGTCTTCAATCTACACC-ATGGTTGGGGTAAAAGATCGAATGGTGTA
1 GGGTAAGAGATCGGATGGTGTCTTCAATCTGC-CCTATGGTTGGGGTAAGAGATCGAATGGT-CA
*
13448241 TTTAATTTGCCCCGTGGTTGGGGTAA
64 -TTAATTTGCCCCGTGGTTTGGGTAA
13448267 TCGAATCTGC
Statistics
Matches: 178, Mismatches: 28, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
122 15 0.08
123 1 0.01
124 126 0.71
125 13 0.07
126 23 0.13
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.32
Consensus pattern (124 bp):
GGGTAAGAGATCGGATGGTGTCTTCAATCTGCCCTATGGTTGGGGTAAGAGATCGAATGGTCATT
AATTTGCCCCGTGGTTTGGGTAAGAGATCGAATAATATCTTCAATCTGCCTCGTGGTTG
Found at i:13460220 original size:5 final size:6
Alignment explanation
Indices: 13460205--13460236 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
13460195 ATTTATTATT
13460205 TTTTTC TTTTTC TTTTTC TTTCTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC T
13460237 CATTTTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:13460230 original size:13 final size:12
Alignment explanation
Indices: 13460205--13460236 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
13460195 ATTTATTATT
13460205 TTTTTCTTTTTC
1 TTTTTCTTTTTC
13460217 TTTTTCTTTCTTC
1 TTTTTCTTT-TTC
13460230 TTTTTCT
1 TTTTTCT
13460237 CATTTTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:13460855 original size:17 final size:17
Alignment explanation
Indices: 13460832--13460878 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
13460822 AAACTAAAAT
13460832 GAATGCAATGAAAATTAA
1 GAATGCAATGAAAA-TAA
13460850 -AATGCAA-GAACAATAA
1 GAATGCAATGAA-AATAA
13460866 GAATGC-ATGAAAA
1 GAATGCAATGAAAA
13460879 CTAACTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 9 0.35
17 17 0.65
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (17 bp):
GAATGCAATGAAAATAA
Found at i:13461308 original size:12 final size:12
Alignment explanation
Indices: 13461291--13461324 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13461281 AACAGGTTCT
*
13461291 TCTTCTTCTTTC
1 TCTTCTTCATTC
13461303 TCTTCTTCATTC
1 TCTTCTTCATTC
*
13461315 TCTTCCTCAT
1 TCTTCTTCAT
13461325 CTTGATCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTTCTTCATTC
Found at i:13475032 original size:15 final size:14
Alignment explanation
Indices: 13475012--13475059 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
13475002 GGCAATGCTT
13475012 TCTTTTTCTTCCTTC
1 TCTTTTTCTT-CTTC
13475027 TCTTTTTCCTT-TTC
1 TCTTTTT-CTTCTTC
*
13475041 TTCTTTATCTTCTTC
1 -TCTTTTTCTTCTTC
13475056 TCTT
1 TCTT
13475060 GCTCCTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.34
15 16 0.55
16 3 0.10
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (14 bp):
TCTTTTTCTTCTTC
Found at i:13475051 original size:21 final size:21
Alignment explanation
Indices: 13475010--13475051 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13475000 GGGGCAATGC
* *
13475010 TTTCTTTTTCTTCCTTCTCTT
1 TTTCCTTTTCTTCCTTATCTT
*
13475031 TTTCCTTTTCTTCTTTATCTT
1 TTTCCTTTTCTTCCTTATCTT
13475052 CTTCTCTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTCCTTTTCTTCCTTATCTT
Found at i:13476703 original size:23 final size:23
Alignment explanation
Indices: 13476673--13476726 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
13476663 AATAAATTAC
13476673 GTCGACAAGTTAGGTTGTCATGT
1 GTCGACAAGTTAGGTTGTCATGT
13476696 GTCGACAAGTTAGGTTGTCATGT
1 GTCGACAAGTTAGGTTGTCATGT
13476719 GTCGACAA
1 GTCGACAA
13476727 AGAGGCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (23 bp):
GTCGACAAGTTAGGTTGTCATGT
Found at i:13479199 original size:30 final size:30
Alignment explanation
Indices: 13479165--13479294 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 30
13479155 AAAATCATTT
*
13479165 TTTGACCCCCAAAGTTTTCAAAAATTTAAA
1 TTTGACCCCCAAAGTTTTCAAAAATTCAAA
* ** *
13479195 TTTGACCGCTGAATTTTTCAAAAAATTCAAA
1 TTTGACCCCCAAAGTTTTC-AAAAATTCAAA
* *
13479226 TTTCACCCTCAAA-TTTTCCAAAAATTCAAA
1 TTTGACCCCCAAAGTTTT-CAAAAATTCAAA
* * **
13479256 TTTAACCCCTAAAGTTTTCAAAAATAAAAA
1 TTTGACCCCCAAAGTTTTCAAAAATTCAAA
*
13479286 ATTGACCCC
1 TTTGACCCC
13479295 ATTTTAATGT
Statistics
Matches: 80, Mismatches: 17, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
30 57 0.71
31 23 0.29
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (30 bp):
TTTGACCCCCAAAGTTTTCAAAAATTCAAA
Found at i:13479227 original size:31 final size:30
Alignment explanation
Indices: 13479179--13479279 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 30
13479169 ACCCCCAAAG
* * * *
13479179 TTTTC-AAAAATTTAAATTTGACCGCTGAAT
1 TTTTCAAAAAATTCAAATTTAACC-CTAAAA
* *
13479209 TTTTCAAAAAATTCAAATTTCACCCTCAAA
1 TTTTCAAAAAATTCAAATTTAACCCTAAAA
* *
13479239 TTTTCCAAAAATTCAAATTTAACCCCTAAAG
1 TTTTCAAAAAATTCAAATTTAA-CCCTAAAA
13479270 TTTTCAAAAA
1 TTTTCAAAAA
13479280 TAAAAAATTG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
30 29 0.48
31 31 0.52
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.36
Consensus pattern (30 bp):
TTTTCAAAAAATTCAAATTTAACCCTAAAA
Found at i:13479288 original size:61 final size:61
Alignment explanation
Indices: 13479169--13479294 Score: 139
Period size: 61 Copynumber: 2.1 Consensus size: 61
13479159 TCATTTTTTG
* * * * * **
13479169 ACCCCCAAAGTTTTCAAAAATTTAAATTTGACCGCTGAATTTTTCAAAAAATTCAAATTTC
1 ACCCCCAAAGTTTTCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAAATAAAAATTTC
* * *
13479230 ACCCTCAAA-TTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTC-AAAAATAAAAAATTG
1 ACCCCCAAAGTTTT-CAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAAATAAAAATTTC
13479290 ACCCC
1 ACCCC
13479295 ATTTTAATGT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
60 19 0.36
61 34 0.64
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.31
Consensus pattern (61 bp):
ACCCCCAAAGTTTTCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAAATAAAAATTTC
Found at i:13491004 original size:50 final size:50
Alignment explanation
Indices: 13490933--13491059 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 50
13490923 ATCTTTTACC
* * * *
13490933 CCTAAAGCTAT-GAAGGTGCAGATTGAAACCGCAATGGCAAATCTCATACA
1 CCTAAAGCTGTAG-AGGGGCAGATTGAAACCGCAATGACAAATATCATACA
* * * *
13490983 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGTAATGACAAATATCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAATGACAAATATCATACA
* **
13491033 CCTAAAGTTGTAGAGGGATAGATTGAA
1 CCTAAAGCTGTAGAGGGGCAGATTGAA
13491060 GTCACAAGGA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 63 0.98
51 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAACCGCAATGACAAATATCATACA
Found at i:13491285 original size:79 final size:78
Alignment explanation
Indices: 13491115--13491326 Score: 241
Period size: 79 Copynumber: 2.7 Consensus size: 78
13491105 GTTACAACCA
* *
13491115 CCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGTCAATCCAATCTCTTACCCCAACCATGGGG
1 CCAATCTTTTACCCTAACCAGAGGGCAGATTGAAG-CAATCCAATCTTTTACCCCAACCATGGGG
*
13491180 CAGATTGAAATAAT
65 CAGATTGAAACAAT
* * *
13491194 CCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGCAATCCAATCTTTTACCCTAACTA-GAGGG
1 CCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCAATCCAATCTTTTACCCCAACCATG-GGG
* * *
13491258 TAGGTTGAAGACCAT
65 CAGATTGAA-ACAAT
* * * *
13491273 -CAGATCTCTTACCCCT-ACCATAGGGCAGATTGAAACAATTCAATCTTTTACCCC
1 CCA-ATCTTTTA-CCCTAACCAGAGGGCAGATTGAAGCAATCCAATCTTTTACCCC
13491327 TAAAGTTATA
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
77 1 0.01
78 33 0.29
79 76 0.67
80 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (78 bp):
CCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGCAATCCAATCTTTTACCCCAACCATGGGGC
AGATTGAAACAAT
Found at i:13491328 original size:39 final size:39
Alignment explanation
Indices: 13491115--13491325 Score: 230
Period size: 39 Copynumber: 5.4 Consensus size: 39
13491105 GTTACAACCA
* *
13491115 CCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGTCAAT
1 CCAATCTTTTACCCTAACCAGAGGGCAGATTGAA-ACAAT
* * *
13491155 CCAATCTCTTACCCCAACCATG-GGGCAGATTGAAATAAT
1 CCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAACAAT
* *
13491194 CCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGCAAT
1 CCAATCTTTTACCCTAACCAGAGGGCAGATTGAAACAAT
* * * *
13491233 CCAATCTTTTACCCTAACTAGAGGGTAGGTTGAAGACCAT
1 CCAATCTTTTACCCTAACCAGAGGGCAGATTGAA-ACAAT
* *
13491273 -CAGATCTCTTACCCCT-ACCATAGGGCAGATTGAAACAAT
1 CCA-ATCTTTTA-CCCTAACCAGAGGGCAGATTGAAACAAT
*
13491312 TCAATCTTTTACCC
1 CCAATCTTTTACCC
13491326 CTAAAGTTAT
Statistics
Matches: 142, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 4 0.03
39 78 0.55
40 55 0.39
41 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (39 bp):
CCAATCTTTTACCCTAACCAGAGGGCAGATTGAAACAAT
Found at i:13492848 original size:25 final size:26
Alignment explanation
Indices: 13492799--13492852 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
13492789 TTTTAAAATT
*
13492799 AAAGAATGGGTTTTGTCTTTTAATGG
1 AAAGAATGAGTTTTGTCTTTTAATGG
13492825 AAAGAATGAGTTATT-T-TTTTAATGG
1 AAAGAATGAGTT-TTGTCTTTTAATGG
13492850 AAA
1 AAA
13492853 TAATCAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 12 0.46
26 12 0.46
27 2 0.08
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (26 bp):
AAAGAATGAGTTTTGTCTTTTAATGG
Found at i:13492864 original size:25 final size:25
Alignment explanation
Indices: 13492816--13492866 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
13492806 GGGTTTTGTC
* **
13492816 TTTTAATGGAAAGAATGAGTTATTT
1 TTTTAATGGAAAGAATCAAATATTT
*
13492841 TTTTAATGGAAATAATCAAATATTT
1 TTTTAATGGAAAGAATCAAATATTT
13492866 T
1 T
13492867 ATTTGTTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (25 bp):
TTTTAATGGAAAGAATCAAATATTT
Found at i:13493274 original size:30 final size:30
Alignment explanation
Indices: 13493151--13493274 Score: 146
Period size: 30 Copynumber: 4.1 Consensus size: 30
13493141 ATTTTTTGAC
13493151 CCCT-AAAGTTTT-CAAAAATTCAAATTTAA
1 CCCTCAAA-TTTTCCAAAAATTCAAATTTAA
* *
13493180 CCCCCAAATTTTCCAAAAAATTCAAATTTCA
1 CCCTCAAATTTTCC-AAAAATTCAAATTTAA
*
13493211 CCCTCAAATTTTCCAAAAATTCAAAGTTAA
1 CCCTCAAATTTTCCAAAAATTCAAATTTAA
* * *
13493241 CCCTTAAAGTTTT-CAAAAATTAAAATTTGA
1 CCCTCAAA-TTTTCCAAAAATTCAAATTTAA
13493271 CCCT
1 CCCT
13493275 GTTTTAATGT
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
29 7 0.09
30 43 0.52
31 32 0.39
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (30 bp):
CCCTCAAATTTTCCAAAAATTCAAATTTAA
Found at i:13494979 original size:24 final size:24
Alignment explanation
Indices: 13494951--13495000 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
13494941 AGAAATAATC
*
13494951 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
13494975 TTTCAATTAAACTCTTTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
13494999 TT
1 TT
13495001 AGAGTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:13495010 original size:24 final size:24
Alignment explanation
Indices: 13494959--13495014 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
13494949 TCTTTCAGTT
* * *
13494959 AAACTCTATTTATTTGTTTCAATT
1 AAACTCTTTTTATTTGTTACAATA
* *
13494983 AAACTCTTTTTATTTGTTAGAGTA
1 AAACTCTTTTTATTTGTTACAATA
13495007 AAACTCTT
1 AAACTCTT
13495015 ATTAGTCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (24 bp):
AAACTCTTTTTATTTGTTACAATA
Done.