Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, whole genome shotgun sequence
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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 38
Found at i:3228916 original size:13 final size:14
Alignment explanation
Indices: 3228898--3228931 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3228888 ATAATAAATC
*
3228898 ATTTTATTAT-TTT
1 ATTTTATCATATTT
3228911 ATTTTATCATATTT
1 ATTTTATCATATTT
3228925 ATTTTAT
1 ATTTTAT
3228932 AAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTATCATATTT
Found at i:3236147 original size:18 final size:17
Alignment explanation
Indices: 3236124--3236157 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3236114 CAGTCTGTTT
3236124 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
3236142 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
3236158 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:3236218 original size:21 final size:22
Alignment explanation
Indices: 3236194--3236241 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
3236184 TGCCTCACTA
*
3236194 ATTT-ATACTTAGTGCGTGATG
1 ATTTCATACTTAGCGCGTGATG
*
3236215 ATTTTCATGCTTAGCGCGTGATG
1 A-TTTCATACTTAGCGCGTGATG
3236238 ATTT
1 ATTT
3236242 TCATGCGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 6 0.26
23 16 0.70
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (22 bp):
ATTTCATACTTAGCGCGTGATG
Found at i:3236227 original size:23 final size:23
Alignment explanation
Indices: 3236201--3236247 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3236191 CTAATTTATA
*
3236201 CTTAGTGCGTGATGATTTTCATG
1 CTTAGCGCGTGATGATTTTCATG
3236224 CTTAGCGCGTGATGATTTTCATG
1 CTTAGCGCGTGATGATTTTCATG
3236247 C
1 C
3236248 GTAGGTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (23 bp):
CTTAGCGCGTGATGATTTTCATG
Found at i:3243739 original size:17 final size:18
Alignment explanation
Indices: 3243705--3243743 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
3243695 TCCAGTCTGT
3243705 TTTATTTTAATGATTTTA
1 TTTATTTTAATGATTTTA
*
3243723 TTTATTTTGAT-ATTTTA
1 TTTATTTTAATGATTTTA
3243740 TTTA
1 TTTA
3243744 ATTATTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTATTTTAATGATTTTA
Found at i:3243816 original size:23 final size:23
Alignment explanation
Indices: 3243781--3243834 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
3243771 TCACTAAGTT
*
3243781 ATACTTAGCGCGTGATGATTTTC
1 ATACGTAGCGCGTGATGATTTTC
*
3243804 ATGCGTAGCGCGTGATGATTTTC
1 ATACGTAGCGCGTGATGATTTTC
3243827 ATACGTAG
1 ATACGTAG
3243835 GTTCTAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (23 bp):
ATACGTAGCGCGTGATGATTTTC
Found at i:3248761 original size:29 final size:30
Alignment explanation
Indices: 3248729--3248799 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
3248719 AAATTTGACC
* *
3248729 AGTGACTGAAATAT-AAGTTTAAAAAGTTT
1 AGTGACTGAAATATAAACTTTAAAAAGTGT
* *
3248758 AGTGGCT-AAAGTATAAACTTTGAAAAGTGT
1 AGTGACTGAAA-TATAAACTTTAAAAAGTGT
*
3248788 AGGGACTGAAAT
1 AGTGACTGAAAT
3248800 TTGTAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.09
29 9 0.27
30 18 0.55
31 3 0.09
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.30
Consensus pattern (30 bp):
AGTGACTGAAATATAAACTTTAAAAAGTGT
Found at i:3251314 original size:18 final size:17
Alignment explanation
Indices: 3251291--3251324 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3251281 CAGTCTGTTT
3251291 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
3251309 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
3251325 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:3251400 original size:23 final size:23
Alignment explanation
Indices: 3251370--3251418 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
3251360 AAGTTATACT
3251370 TAGCGCGTGATGATTTTCATGCG
1 TAGCGCGTGATGATTTTCATGCG
3251393 TAGCGCGTGATGATTTTCATGCG
1 TAGCGCGTGATGATTTTCATGCG
3251416 TAG
1 TAG
3251419 GTTCTAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (23 bp):
TAGCGCGTGATGATTTTCATGCG
Found at i:3261977 original size:21 final size:22
Alignment explanation
Indices: 3261931--3261979 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3261921 ATAATTTATA
3261931 CATAT-TATATAAATATAAGTT
1 CATATATATATAAATATAAGTT
* *
3261952 -GTATATATTTAAATATAA-TT
1 CATATATATATAAATATAAGTT
3261972 CATATATA
1 CATATATA
3261980 AACTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
CATATATATATAAATATAAGTT
Found at i:3261981 original size:65 final size:64
Alignment explanation
Indices: 3261912--3262059 Score: 166
Period size: 61 Copynumber: 2.3 Consensus size: 64
3261902 GTTGATATCA
3261912 ATAAACTATATAATTTATACATATTATATAAA-TATA-AGTTGTATATATTTAAAT-ATAATTCA
1 ATAAACTATATAATTTATACATATTA-ATAAACTATATAGTT-TATATA--TAAATAATAATTCA
3261974 TAT
62 TAT
* *
3261977 ATAAACTATATAA-TT-T--ATATTAATAAACTATATAGTTTATATATAATTCAATAGTTCATAT
1 ATAAACTATATAATTTATACATATTAATAAACTATATAGTTTATATATAAAT-AATAATTCATAT
* *
3262038 ATAAACTCTATAGTTTATACAT
1 ATAAACTATATAATTTATACAT
3262060 GGTATATATA
Statistics
Matches: 71, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
59 4 0.06
60 5 0.07
61 37 0.52
62 6 0.08
63 2 0.03
64 2 0.03
65 15 0.21
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (64 bp):
ATAAACTATATAATTTATACATATTAATAAACTATATAGTTTATATATAAATAATAATTCATAT
Found at i:3262005 original size:22 final size:22
Alignment explanation
Indices: 3261964--3262023 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
3261954 ATATATTTAA
*
3261964 ATATAATTCATA-T-ATAAACT
1 ATATAATTTATATTAATAAACT
3261984 ATATAATTTATATTAATAAACT
1 ATATAATTTATATTAATAAACT
*
3262006 ATATAGTTTATATATAAT
1 ATATAATTTATAT-TAAT
3262024 TCAATAGTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 11 0.31
21 1 0.03
22 19 0.54
23 4 0.11
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATAATTTATATTAATAAACT
Found at i:3262052 original size:20 final size:20
Alignment explanation
Indices: 3261964--3262052 Score: 83
Period size: 20 Copynumber: 4.4 Consensus size: 20
3261954 ATATATTTAA
*
3261964 ATATAATTCATATATAAACT
1 ATATAGTTCATATATAAACT
* *
3261984 ATATAATTTATATTAATAAACT
1 ATATAGTTCATA-T-ATAAACT
* *
3262006 ATATAGTTTATATAT-AATT
1 ATATAGTTCATATATAAACT
3262025 CA-ATAGTTCATATATAAACT
1 -ATATAGTTCATATATAAACT
*
3262045 CTATAGTT
1 ATATAGTT
3262053 TATACATGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.26
20 23 0.40
21 2 0.03
22 18 0.31
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
ATATAGTTCATATATAAACT
Found at i:3262069 original size:2 final size:2
Alignment explanation
Indices: 3262062--3262167 Score: 74
Period size: 2 Copynumber: 51.0 Consensus size: 2
3262052 TTATACATGG
* *
3262062 TA TA TA TA GTT TA TA TA TA TA TA TA TA TA TA TA CTA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * *
3262105 TA TA T- TA -A TA AA CTA TA TA AA CTA TA TA TA TA -A TT TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
3262146 TA CTT TA TA TA TA TA CTA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA
3262168 GTTTATATTA
Statistics
Matches: 82, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
1 3 0.04
2 70 0.85
3 9 0.11
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3262099 original size:13 final size:13
Alignment explanation
Indices: 3262062--3262167 Score: 78
Period size: 13 Copynumber: 8.2 Consensus size: 13
3262052 TTATACATGG
* *
3262062 TATATATAGTTTA
1 TATATATACTATA
3262075 TATATATA-TATA
1 TATATATACTATA
3262087 TATATATACTATA
1 TATATATACTATA
* *
3262100 TAGTTTATATTAATAAA
1 TA---TATA-TACTATA
*
3262117 CTATATAAACTATA
1 -TATATATACTATA
3262131 TATATA-A-T-T-
1 TATATATACTATA
*
3262140 TATATATACTTTA
1 TATATATACTATA
3262153 TATATATACTATA
1 TATATATACTATA
3262166 TA
1 TA
3262168 GTTTATATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
11 2 0.03
12 13 0.17
13 34 0.45
14 4 0.05
15 4 0.05
16 4 0.05
17 5 0.07
18 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (13 bp):
TATATATACTATA
Found at i:3262119 original size:22 final size:22
Alignment explanation
Indices: 3262094--3262187 Score: 86
Period size: 22 Copynumber: 4.3 Consensus size: 22
3262084 ATATATATAT
*
3262094 ACTATATAGTTTATATTAATAA
1 ACTATATACTTTATATTAATAA
* **
3262116 ACTATATAAACTATATATATAATTT
1 ACTATAT--ACTTTATAT-TAATAA
*
3262141 A-TATATACTTTATA-T-ATAT
1 ACTATATACTTTATATTAATAA
*
3262160 ACTATATAGTTTATATTAATAA
1 ACTATATACTTTATATTAATAA
3262182 ACTATA
1 ACTATA
3262188 CATATTATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
19 4 0.07
20 13 0.22
21 1 0.02
22 23 0.40
24 12 0.21
25 5 0.09
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (22 bp):
ACTATATACTTTATATTAATAA
Found at i:3262168 original size:66 final size:66
Alignment explanation
Indices: 3262062--3262187 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
3262052 TTATACATGG
*
3262062 TATATATAGTTTATATATATATATATATATATACTATATAGTTTATATTAATAAACTATATAAAC
1 TATATATAATTTATATATATATATATATATA-ACTATATAGTTTATATTAATAAACTATATAAAC
3262127 TA
65 TA
*
3262129 TATATATAATTTATATATACTTTATATATAT-ACTATATAGTTTATATTAATAAACTATA
1 TATATATAATTTATATATA-TATATATATATAACTATATAGTTTATATTAATAAACTATA
3262188 CATATTATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 28 0.50
67 18 0.32
68 10 0.18
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (66 bp):
TATATATAATTTATATATATATATATATATAACTATATAGTTTATATTAATAAACTATATAAACT
A
Found at i:3264687 original size:2 final size:2
Alignment explanation
Indices: 3264680--3264745 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3264670 GATAATGATA
3264680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3264722 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
3264746 CTTTTTAAGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3266157 original size:60 final size:60
Alignment explanation
Indices: 3266093--3266208 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
3266083 CACAAACGAG
*
3266093 TCCCTTAATTATAGAGTGTTGCTTTATTGAAT-CCTCCGACTATTAAAAGTTACAAATTGC
1 TCCCTTAACTATAGAGTGTTGCTTTATTGAATCCCT-CGACTATTAAAAGTTACAAATTGC
* * * * *
3266153 TCCCTTGACTATAGGGTGTTTCTTTATTGAGTCCCTTGACTATTAAAAGTTACAAA
1 TCCCTTAACTATAGAGTGTTGCTTTATTGAATCCCTCGACTATTAAAAGTTACAAA
3266209 ATGATCAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 46 0.94
61 3 0.06
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (60 bp):
TCCCTTAACTATAGAGTGTTGCTTTATTGAATCCCTCGACTATTAAAAGTTACAAATTGC
Found at i:3266702 original size:31 final size:31
Alignment explanation
Indices: 3266664--3266724 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3266654 ATCGAGTTTG
3266664 TGTTAATATGTGTGTTCAACAGGTAAATTTA
1 TGTTAATATGTGTGTTCAACAGGTAAATTTA
*
3266695 TGTTAATATGTGTGTTCAATAGGTAAATTT
1 TGTTAATATGTGTGTTCAACAGGTAAATTT
3266725 GTGTATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (31 bp):
TGTTAATATGTGTGTTCAACAGGTAAATTTA
Found at i:3270410 original size:86 final size:86
Alignment explanation
Indices: 3270264--3270592 Score: 433
Period size: 86 Copynumber: 3.8 Consensus size: 86
3270254 GTTAGCGGCG
* * * * *
3270264 CAAATGCCGCTATTGAATGTGTATTTAGCGGCTTTTGTCTTTACAAACGCTGCTAATGATTGTTT
1 CAAATGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGATTGTGT
***
3270329 ATTTAGCGGCGTTTGTAAATA
66 ATTTAGCGGCGTTTGTCTTTA
* * * * *
3270350 CAAATGCTGTTATTGACTGTGTATTTAGCGGCATTTATCTTTATAAACGCCGCTATTGATTGTGT
1 CAAATGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGATTGTGT
*
3270415 ATTTAGCAGCGTTTGTCTTTA
66 ATTTAGCGGCGTTTGTCTTTA
* * *
3270436 CAAATGCTGCTATTGACTGTGTATTTAGCGGCGTTTGTATTTACAAACTCCGCTATTGATTGTGT
1 CAAATGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGATTGTGT
* * *
3270501 ATGTAGCGACGTTTGTCTTTT
66 ATTTAGCGGCGTTTGTCTTTA
* * * * *
3270522 CAAATGCCACTATTGACTGTGAATTTAGTGGCGTTTTTCTTTACAAACGCCGCTATTGACTGTGT
1 CAAATGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGATTGTGT
3270587 ATTTAG
66 ATTTAG
3270593 TGACATTTGT
Statistics
Matches: 211, Mismatches: 32, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 211 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (86 bp):
CAAATGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGATTGTGT
ATTTAGCGGCGTTTGTCTTTA
Found at i:3270602 original size:129 final size:131
Alignment explanation
Indices: 3270264--3270616 Score: 421
Period size: 129 Copynumber: 2.7 Consensus size: 131
3270254 GTTAGCGGCG
* * *
3270264 CAAATGCCGCTATTGAATGTGTATTTAGCGGC-TTTTGTCTTTACAAACGCTGCTAATGATTGTT
1 CAAATGCCGCTATTGAATGTGTATTTAGCGGCGTTTT-TCTTTACAAACGCTGCTATTGACTGTG
* * * * *
3270328 TATTTAGCGGCGTTTGTAAATACAAA-TGCTGTTATTGACTGTGTATTTAGCGGCATTTATCTTT
65 TATTTAGCGGCGTTTGTAATTACAAACTGCCGCTATTGACTGTGTATGTAGCGACATTTATCTTT
3270392 AT
130 AT
* * * * *
3270394 -AAACGCCGCTATTGATTGTGTATTTAGCAGCGTTTGTCTTTACAAATGCTGCTATTGACTGTGT
1 CAAATGCCGCTATTGAATGTGTATTTAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGT
* * * *
3270458 ATTTAGCGGCGTTTGTATTTACAAACT-CCGCTATTGATTGTGTATGTAGCGACGTTTGTCTTT-
66 ATTTAGCGGCGTTTGTAATTACAAACTGCCGCTATTGACTGTGTATGTAGCGACATTTATCTTTA
3270521 T
131 T
* * * * *
3270522 CAAATGCCACTATTGACTGTGAATTTAGTGGCGTTTTTCTTTACAAACGCCGCTATTGACTGTGT
1 CAAATGCCGCTATTGAATGTGTATTTAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGT
* * * *
3270587 ATTTAGTGACATTTGTAATTAAAAAC-GCCG
66 ATTTAGCGGCGTTTGTAATTACAAACTGCCG
3270617 TAAATAATCC
Statistics
Matches: 188, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
128 1 0.01
129 183 0.97
130 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (131 bp):
CAAATGCCGCTATTGAATGTGTATTTAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGT
ATTTAGCGGCGTTTGTAATTACAAACTGCCGCTATTGACTGTGTATGTAGCGACATTTATCTTTA
T
Found at i:3270616 original size:43 final size:43
Alignment explanation
Indices: 3270264--3270592 Score: 379
Period size: 43 Copynumber: 7.7 Consensus size: 43
3270254 GTTAGCGGCG
* * *
3270264 CAAATGCCGCTATTGAATGTGTATTTAGCGGCTTTTGTCTTTA
1 CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
* * * * ***
3270307 CAAACGCTGCTAATGATTGTTTATTTAGCGGCGTTTGTAAATA
1 CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
* * * * *
3270350 CAAATGCTGTTATTGACTGTGTATTTAGCGGCATTTATCTTTA
1 CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
* * *
3270393 TAAACGCCGCTATTGATTGTGTATTTAGCAGCGTTTGTCTTTA
1 CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
* * *
3270436 CAAATGCTGCTATTGACTGTGTATTTAGCGGCGTTTGTATTTA
1 CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
* * * * *
3270479 CAAACTCCGCTATTGATTGTGTATGTAGCGACGTTTGTCTTTT
1 CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
* * * * *
3270522 CAAATGCCACTATTGACTGTGAATTTAGTGGCGTTTTTCTTTA
1 CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
3270565 CAAACGCCGCTATTGACTGTGTATTTAG
1 CAAACGCCGCTATTGACTGTGTATTTAG
3270593 TGACATTTGT
Statistics
Matches: 232, Mismatches: 54, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 232 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (43 bp):
CAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTA
Found at i:3270724 original size:15 final size:15
Alignment explanation
Indices: 3270704--3270732 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3270694 CATAAAACTG
3270704 AACTATACACATTAA
1 AACTATACACATTAA
3270719 AACTATACACATTA
1 AACTATACACATTA
3270733 GTTCACCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
AACTATACACATTAA
Found at i:3276415 original size:13 final size:13
Alignment explanation
Indices: 3276397--3276425 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3276387 CCACCGTACT
3276397 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
3276410 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
3276423 CCG
1 CCG
3276426 TGAACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:3277147 original size:3 final size:3
Alignment explanation
Indices: 3277139--3277222 Score: 132
Period size: 3 Copynumber: 27.3 Consensus size: 3
3277129 TTATTTATTA
* *
3277139 AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
3277186 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3277223 TAAATAACAT
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
3 69 0.92
4 6 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:3277727 original size:113 final size:113
Alignment explanation
Indices: 3277453--3278122 Score: 913
Period size: 113 Copynumber: 6.0 Consensus size: 113
3277443 TAGAGTCATT
* ** * * *
3277453 CAAAAGGTTGAATAAGCTCTTCTTATTATGAA---CTTATT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
**** * * * * **
3277514 TTATGAACTTTCTCTGTAAAGGTTGATCCATTAAGTGATGAATTCAAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
* * *
3277562 CAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAATTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
*** * * * * **
3277626 TTATGAACTCTTTCTGGAAAAGCTAATCCATCAAATGATGAATTCAAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
* *
3277674 CAAAAGGTTGAACAAATTCTTCTCATTATGAACATCTTCTTCATTCTTCAGATGAATTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
*
3277739 TTGTGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
*
3277787 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
*
3277852 TTGTGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
* *
3277900 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
*
3277965 TTATGAACTCGAACTAGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
3278013 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAA-TTCTTCTC
** * *
3278077 ATTATGAACTCGAACT-GACACTGTTGATCCATTAAATGATGGATTT
65 ATTATGAACTCGAACTGGA-AAAGTTGATCCATCAAGTGATGGATTT
3278123 AAATCTTTGC
Statistics
Matches: 514, Mismatches: 40, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
108 24 0.05
109 5 0.01
111 5 0.01
112 69 0.13
113 411 0.80
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
TTATGAACTCGAACTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
Found at i:3279201 original size:83 final size:83
Alignment explanation
Indices: 3279057--3279607 Score: 897
Period size: 83 Copynumber: 6.6 Consensus size: 83
3279047 GGTTTCATAT
* * *
3279057 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAGGATGCTATGATCACATTCATCTTTCAAA
1 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
3279122 TTCAATGATTGGTTTTAC
66 TTCAATGATTGATTTTAC
** *
3279140 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATATTACGAGCACATTCATCTTTCAAA
1 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
3279205 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
*
3279223 CAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
3279288 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
* * * *
3279306 CAAATCAGATCAGATAACTCAAAGAACACTTCCCGAAGATGCTATGAGCACATTCCTCTTCCACA
1 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
3279371 TTCAATGATTGATTTTAC
66 TTCAATGATTGATTTTAC
* *
3279389 CAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGCACATT-ATTCTTCCAA
1 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCA-TCTTTCAA
* * *
3279453 ATTCAATAACTGGTTTTAC
65 ATTCAATGATTGATTTTAC
* * *
3279472 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGATGATGCTATGATCACATTCATCTTTCAAA
1 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
*
3279537 TTCAATGATTGGTTTTAC
66 TTCAATGATTGATTTTAC
3279555 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
3279608 GGCATTTGTT
Statistics
Matches: 433, Mismatches: 33, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
83 432 1.00
84 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
CAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
TTCAATGATTGATTTTAC
Found at i:3280329 original size:13 final size:13
Alignment explanation
Indices: 3280311--3280338 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3280301 CATGTATTTA
3280311 AAAGTATTAACAT
1 AAAGTATTAACAT
3280324 AAAGTATTAACAT
1 AAAGTATTAACAT
3280337 AA
1 AA
3280339 GATGGTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAGTATTAACAT
Found at i:3286464 original size:13 final size:13
Alignment explanation
Indices: 3286446--3286474 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3286436 CCACCGTACT
3286446 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
3286459 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
3286472 CCG
1 CCG
3286475 TTCACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:3287192 original size:3 final size:3
Alignment explanation
Indices: 3287184--3287290 Score: 90
Period size: 3 Copynumber: 35.3 Consensus size: 3
3287174 TTATTTATTA
*
3287184 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * * * * * * *
3287231 AAT TAT TAT TAT TAT TAT TAT -AT AAT TAT AAT AAT AAT AAT TAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3287278 AAT AAC AAT AAT A
1 AAT AAT AAT AAT A
3287291 TAAATAACAT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.02
3 84 0.91
4 6 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:3297214 original size:14 final size:14
Alignment explanation
Indices: 3297195--3297237 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
3297185 AAGGTTAGCT
3297195 AAATTAAAAAGAAA
1 AAATTAAAAAGAAA
3297209 AAATTAAAATTA-AAA
1 AAATTAAAA--AGAAA
*
3297224 AAATTAAAATGAAA
1 AAATTAAAAAGAAA
3297238 TGAAAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 12 0.48
15 12 0.48
16 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (14 bp):
AAATTAAAAAGAAA
Found at i:3298690 original size:18 final size:18
Alignment explanation
Indices: 3298653--3298690 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3298643 CATAATATGC
*
3298653 AATATAAATATATTATAT
1 AATATAAATATATTAAAT
3298671 AATATAAATA-ATTCAAAT
1 AATATAAATATATT-AAAT
3298689 AA
1 AA
3298691 GCAATATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATAAATATATTAAAT
Found at i:3301519 original size:33 final size:31
Alignment explanation
Indices: 3301435--3301536 Score: 159
Period size: 31 Copynumber: 3.2 Consensus size: 31
3301425 TATACTAGGC
3301435 CCGACAAGTTTGGAAAATATATATATTAGTA
1 CCGACAAGTTTGGAAAATATATATATTAGTA
3301466 CCGACAAGTTTGGAAAATATATATATTAGTA
1 CCGACAAGTTTGGAAAATATATATATTAGTA
** *
3301497 CCGACAAGTTTATAAAATATATATATATTAGTC
1 CCGACAAGTTT-GGAAA-ATATATATATTAGTA
3301530 CCGACAA
1 CCGACAA
3301537 AATCCATCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
31 42 0.64
32 3 0.05
33 21 0.32
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (31 bp):
CCGACAAGTTTGGAAAATATATATATTAGTA
Found at i:3305180 original size:22 final size:22
Alignment explanation
Indices: 3305066--3305180 Score: 115
Period size: 22 Copynumber: 5.1 Consensus size: 22
3305056 AATGTCGTCA
3305066 GATAGCTAAAGTGCCTTAGCATT
1 GATA-CTAAAGTGCCTTAGCATT
* *
3305089 GGTACTAAAGTGCCTTGGCATT
1 GATACTAAAGTGCCTTAGCATT
*
3305111 GAATACTAAAGTGCCTTAGCACT
1 G-ATACTAAAGTGCCTTAGCATT
* * *** *
3305134 AATA-TAGAACTATATTAGCACT
1 GATACTA-AAGTGCCTTAGCATT
3305156 GATACTAAAGTGCCTTAGCATT
1 GATACTAAAGTGCCTTAGCATT
3305178 GAT
1 GAT
3305181 TGGATTATAT
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
21 2 0.03
22 48 0.66
23 23 0.32
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (22 bp):
GATACTAAAGTGCCTTAGCATT
Found at i:3318766 original size:13 final size:14
Alignment explanation
Indices: 3318748--3318776 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3318738 AGTAATCTCT
3318748 AATTAACTC-GTAA
1 AATTAACTCAGTAA
3318761 AATTAACTCAGTAA
1 AATTAACTCAGTAA
3318775 AA
1 AA
3318777 AGTTTTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (14 bp):
AATTAACTCAGTAA
Found at i:3320496 original size:16 final size:16
Alignment explanation
Indices: 3320472--3320509 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3320462 ACGGTGGAGG
* *
3320472 GGGGGAGGGAAGGGAA
1 GGGGAAGGGAAAGGAA
3320488 GGGGAAGGGAAAGGAA
1 GGGGAAGGGAAAGGAA
3320504 GGGGAA
1 GGGGAA
3320510 AGAGGTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (16 bp):
GGGGAAGGGAAAGGAA
Found at i:3330441 original size:2 final size:2
Alignment explanation
Indices: 3330434--3330470 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3330424 AATGATAAAA
3330434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3330471 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3330599 original size:110 final size:109
Alignment explanation
Indices: 3330370--3330580 Score: 338
Period size: 110 Copynumber: 2.0 Consensus size: 109
3330360 TAATAAACAC
*
3330370 ATAATTATATTGGTGTAAGAATATTTTTATATTTTCAAAGAAATAAAAAATAAAAATGATAAAAA
1 ATAATTATATTAGTGTAAGAATATTTTTATATTTTCAAAGAAATAAAAAATAAAAATGAT-AAAA
* * *
3330435 TATATATATATATATATATATATATATATATATATACACACACAC
65 TATATATATATATATATATATAAATATATATATATACAAACACAA
3330480 ATAATTATATTAGTGTAAGAATATTTTTATATTTTCAAAGAAATAAAAAATAAAAATGAT-AAAT
1 ATAATTATATTAGTGTAAGAATATTTTTATATTTTCAAAGAAATAAAAAATAAAAATGATAAAAT
* *
3330544 ATATATATATATATATAT-TAAAT-TATTTGTATACAAA
66 ATATATATATATATATATATAAATATATATATATACAAA
3330581 TTTTATTAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
106 11 0.11
107 4 0.04
108 22 0.23
110 59 0.61
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (109 bp):
ATAATTATATTAGTGTAAGAATATTTTTATATTTTCAAAGAAATAAAAAATAAAAATGATAAAAT
ATATATATATATATATATATAAATATATATATATACAAACACAA
Found at i:3330800 original size:32 final size:31
Alignment explanation
Indices: 3330742--3330805 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
3330732 CTTAACCGTT
* *
3330742 AATCATTAATTTTAACGGTTCAATTAACTAA
1 AATCATTAATATTAACGATTCAATTAACTAA
* * *
3330773 AATCATTTAATATTAATGATTCGATTAATTAA
1 AATCA-TTAATATTAACGATTCAATTAACTAA
3330805 A
1 A
3330806 CTATTAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (31 bp):
AATCATTAATATTAACGATTCAATTAACTAA
Found at i:3341010 original size:15 final size:16
Alignment explanation
Indices: 3340981--3341015 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3340971 AGAGATATGC
3340981 ATTTTTTTAATTTTTG
1 ATTTTTTTAATTTTTG
*
3340997 ATTTTTTTTA-TTTTG
1 ATTTTTTTAATTTTTG
3341012 ATTT
1 ATTT
3341016 ATATTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (16 bp):
ATTTTTTTAATTTTTG
Found at i:3341589 original size:13 final size:13
Alignment explanation
Indices: 3341571--3341595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3341561 AAGGGAGTTT
3341571 ATCAATATCGATG
1 ATCAATATCGATG
3341584 ATCAATATCGAT
1 ATCAATATCGAT
3341596 AATGAAGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
ATCAATATCGATG
Found at i:3346106 original size:37 final size:36
Alignment explanation
Indices: 3346051--3346169 Score: 148
Period size: 37 Copynumber: 3.2 Consensus size: 36
3346041 GGGGCAAATC
*
3346051 TAAGTCTTCACCAAAGAGTAGTGAATCAAATCCATTT
1 TAAGCCTTCACCAAAGAGTAGTGAA-CAAATCCATTT
* * * *
3346088 TGAGCCTTCACCAAAGAGTAGTGAAGAAAACCATCT
1 TAAGCCTTCACCAAAGAGTAGTGAACAAATCCATTT
* * *
3346124 TAAGCCTTCACCAAAGAGTAATGAAGCATATCCTTTT
1 TAAGCCTTCACCAAAGAGTAGTGAA-CAAATCCATTT
3346161 TAAGCCTTC
1 TAAGCCTTC
3346170 TCGGAAGAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
36 31 0.45
37 38 0.55
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (36 bp):
TAAGCCTTCACCAAAGAGTAGTGAACAAATCCATTT
Found at i:3346137 original size:36 final size:36
Alignment explanation
Indices: 3346051--3346149 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 36
3346041 GGGGCAAATC
* * * *
3346051 TAAGTCTTCACCAAAGAGTAGTGAATCAAATCCATTT
1 TAAGCCTTCACCAAAGAGTAGTGAA-GAAAACCATCT
*
3346088 TGAGCCTTCACCAAAGAGTAGTGAAGAAAACCATCT
1 TAAGCCTTCACCAAAGAGTAGTGAAGAAAACCATCT
*
3346124 TAAGCCTTCACCAAAGAGTAATGAAG
1 TAAGCCTTCACCAAAGAGTAGTGAAG
3346150 CATATCCTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
36 32 0.58
37 23 0.42
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (36 bp):
TAAGCCTTCACCAAAGAGTAGTGAAGAAAACCATCT
Found at i:3346618 original size:54 final size:54
Alignment explanation
Indices: 3346556--3346842 Score: 486
Period size: 54 Copynumber: 5.3 Consensus size: 54
3346546 GTAGTAAAGC
3346556 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
3346610 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAACGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
3346664 ATAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
3346718 AGAAGAAGATGTTTGTGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * * *
3346772 AGAAGAAGATGTTCGAGTTCCATATTCCCTAAAGAAAGAGGGAGAGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
3346826 AG-AGAATATGTTCGAGT
1 AGAAGAAGATGTTCGAGT
3346843 CTTATACTCT
Statistics
Matches: 220, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
53 14 0.06
54 206 0.94
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:3346919 original size:55 final size:55
Alignment explanation
Indices: 3346834--3346961 Score: 229
Period size: 55 Copynumber: 2.3 Consensus size: 55
3346824 TAAGAGAATA
* *
3346834 TGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGCAGACACGATTATTGAAGAT
1 TGTTCGAGTCTTATACTCTCTAAAGAAATATGGAGCAGACACGATTATTGAAGAT
*
3346889 TGTTCGAGTCTTATACTCTCTAAAGAAATATGGAGCAGACACGTTTATTGAAGAT
1 TGTTCGAGTCTTATACTCTCTAAAGAAATATGGAGCAGACACGATTATTGAAGAT
3346944 TGTTCGAGTCTTATACTC
1 TGTTCGAGTCTTATACTC
3346962 CCTGAAGGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (55 bp):
TGTTCGAGTCTTATACTCTCTAAAGAAATATGGAGCAGACACGATTATTGAAGAT
Found at i:3346995 original size:55 final size:54
Alignment explanation
Indices: 3346834--3346999 Score: 201
Period size: 55 Copynumber: 3.0 Consensus size: 54
3346824 TAAGAGAATA
* **
3346834 TGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGCAGACACGATTATTGAAGAT
1 TGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGAAGACATTA-TATTGAAGAT
* * *
3346889 TGTTCGAGTCTTATACTCTCTAAAGAAATATGGAGCAGACACGTT-TATTGAAGAT
1 TGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGAAGACA--TTATATTGAAGAT
* *
3346944 TGTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGAAGAC-TTATCATTTGAAGAT
1 TGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGAAGACATTAT-A-TTGAAGAT
3346999 T
1 T
3347000 TTTCAAGTTT
Statistics
Matches: 97, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 1 0.01
55 93 0.96
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (54 bp):
TGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGAAGACATTATATTGAAGAT
Found at i:3349748 original size:35 final size:35
Alignment explanation
Indices: 3349702--3349779 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
3349692 TACCAGTTGA
3349702 AGGTCAAGGATGTTGATATAGCCAAGACAGTGTTT
1 AGGTCAAGGATGTTGATATAGCCAAGACAGTGTTT
*
3349737 AGGTCAAGGATGTTGATATAGCCAAGACGGTGTTT
1 AGGTCAAGGATGTTGATATAGCCAAGACAGTGTTT
*
3349772 AGGACAAG
1 AGGTCAAG
3349780 ATATGGCATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.26
Consensus pattern (35 bp):
AGGTCAAGGATGTTGATATAGCCAAGACAGTGTTT
Found at i:3355480 original size:2 final size:2
Alignment explanation
Indices: 3355475--3355511 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3355465 TTTTTAACTA
3355475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3355512 AAACTATCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3358852 original size:132 final size:132
Alignment explanation
Indices: 3358622--3359397 Score: 1049
Period size: 132 Copynumber: 5.9 Consensus size: 132
3358612 GATCCCATTT
* * * * * *
3358622 CTTCTATGATGGATTTGATCGAAATAAAAATGTCAATCCGCTTCATTTTGTGATGGAATCGAACG
1 CTTCTGTGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACG
* * * * *
3358687 AAATATCGGTGCTGGTATACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTAATGCTGATCCAAC
66 AGATGTCGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAAC
*
3358752 TT
131 TC
* *
3358754 CTTCTGTGATGGATTTGAGCAAAATAAAAATGTCAATCCACCTCATTCTGTGATGGAATCGAACG
1 CTTCTGTGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACG
* * *
3358819 AGATGCCGGTGCTGATCTACCTCCTTCTATGATAGAATCGAGTAAAAAGTTGATGCTGATCCAAC
66 AGATGTCGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAAC
3358884 TC
131 TC
* * * * * *
3358886 CTCCTGTGATGGATTTGAGCGAGAT-AAAATGCCGATCCACCTCCTTCTATGATGGAATTGAAC-
1 CTTCTGTGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACG
* *
3358949 -GATGTCGGTGTTGATCTACCTTCTTCTGTGATAGAATCGAGCAAAAAGTTGATG-TCGATCCAA
66 AGATGTCGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCT-GATCCAA
3359012 CTC
130 CTC
* * *
3359015 CTTCTGTGATGGATTTGAGTGAAATAAAATTGTCGATCCACCTCATTCTGTGATGGAATCGAACA
1 CTTCTGTGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACG
* * * * * * *
3359080 AGATATCGGTGTTGATATACCTCATTCTGTGATAGAATCAAGCAAAAAAGTTTAT-ATCGATCCA
66 AGATGTCGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGC-AAAAAGTTGATGCT-GATCCA
3359144 ACTC
129 ACTC
* * *
3359148 CTTCTGTGATGGATTTGAGGGAAATAAAAATGCCGATCCACCTCATTCTGTGATGGAATCGAACA
1 CTTCTGTGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACG
* *
3359213 AAATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAAC
66 AGATGTCGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAAC
3359278 TC
131 TC
* * * *
3359280 CTTCTGTGATGGATTTCAGCGAAATGAAAATGTCGATCCACCTCCTTCTATGATGGAATCGAACG
1 CTTCTGTGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACG
* * * * *
3359345 AGATGTCGGTGTTGATCTACCTCCTTCTATGATAGAGTCGAGAAAAAAATTGA
66 AGATGTCGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGA
3359398 ACAATCTCTT
Statistics
Matches: 569, Mismatches: 68, Indels: 14
0.87 0.10 0.02
Matches are distributed among these distances:
128 1 0.00
129 81 0.14
130 33 0.06
131 33 0.06
132 300 0.53
133 121 0.21
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (132 bp):
CTTCTGTGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACG
AGATGTCGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAAC
TC
Found at i:3358881 original size:88 final size:88
Alignment explanation
Indices: 3358705--3359397 Score: 311
Period size: 88 Copynumber: 7.9 Consensus size: 88
3358695 GTGCTGGTAT
* * * * ** * * * *
3358705 ACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTAATGCTGATCCAACTTCTTCTGTGATGGATTT
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGAATC
** *
3358770 GAGCAAAATAA--AAATG-TCAATCC
66 GAG-AAAA-AAGTTGATGCT-GATCC
* * * * * * *
3358793 ACCTCATTCTGTGATGGAATCGAACGAGATGCCGGTGCTGATCTACCTCCTTCTATGATAGAATC
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGAATC
*
3358858 GAGTAAAAAGTTGATGCTGATCC
66 GAGAAAAAAGTTGATGCTGATCC
* * * * *** * *
3358881 AACTCCTCCTGTGATGGATTTGAGCGAGAT-AAAATGCCGATCCACCTCCTTCTATGATGGAAT-
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGAATC
* ** * * * * *
3358944 -TGAACGATGTCGGTGTTGATCT
66 GAGAAAAAAGTTGATGCTGATCC
* * * * * * * *
3358966 ACCTTCTTCTGTGATAGAATCGAGCAAAAAGTTGATG-TCGATCCAACTCCTTCTGTGATGGATT
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCT-GATCCACCTCCTTCTGTGATGGAAT
* *
3359030 TGAGTGAAATAAAATTG-T-C-GATCC
65 CGA--GAAA-AAAGTTGATGCTGATCC
* * * * * * ** * *
3359054 ACCTCATTCTGTGATGGAATCGAACAAGATATCGGTGTTGATATACCTCATTCTGTGATAGAATC
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGAATC
* * *
3359119 AAGCAAAAAAGTTTAT-ATCGATCC
66 GAG-AAAAAAGTTGATGCT-GATCC
* * * * * **** * *
3359143 AACTCCTTCTGTGATGGATTTGAGGGAAATAAAAATGCCGATCCACCTCATTCTGTGATGGAATC
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGAATC
* * *
3359208 GA-ACAAAATGTTGGTGCTGATCT
66 GAGA-AAAAAGTTGATGCTGATCC
* * * * * * *
3359231 ACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTCTGTGATGGATTT
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGA-AT
* *
3359296 CAGCGAAATGAAA-ATG-T-C-GATCC
65 C-GAGAAA--AAAGTTGATGCTGATCC
* * * * * * * *
3359319 ACCTCCTTCTATGATGGAATCGAACGAGATGTCGGTGTTGATCTACCTCCTTCTATGATAGAGTC
1 ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGAATC
*
3359384 GAGAAAAAAATTGA
66 GAGAAAAAAGTTGA
3359398 ACAATCTCTT
Statistics
Matches: 436, Mismatches: 145, Indels: 50
0.69 0.23 0.08
Matches are distributed among these distances:
84 3 0.01
85 36 0.08
86 38 0.09
87 36 0.08
88 247 0.57
89 60 0.14
90 8 0.02
91 6 0.01
92 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (88 bp):
ACCTCCTTCTGTGATGGAATCGAGCGAGATGTCGATGCTGATCCACCTCCTTCTGTGATGGAATC
GAGAAAAAAGTTGATGCTGATCC
Found at i:3359367 original size:44 final size:44
Alignment explanation
Indices: 3358670--3359377 Score: 281
Period size: 44 Copynumber: 16.1 Consensus size: 44
3358660 CGCTTCATTT
* * * * * **
3358670 TGTGATGGAATCGAACGAAATATCGGTGCTGGTATACCTCCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * * * *
3358714 TGTGATAGAATCGAGCAAAAAGTTAATGCTGATCCAACTTCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * **** * *
3358758 TGTGATGGATTTGAGCAAAATAAAAATG-TCAATCCACCTCATTC
1 TGTGATGGAATCGAACAAAATGTTGATGCT-GATCCACCTCCTTC
* * ** * *
3358802 TGTGATGGAATCGAACGAGATGCCGGTGCTGATCTACCTCCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * ** * * *
3358846 TATGATAGAATCGAGTAAAAAGTTGATGCTGATCCAACTCCTCC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * * * *** *
3358890 TGTGATGGATTTGAGCGAGAT-AAAATGCCGATCCACCTCCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * * * * * *
3358933 TATGATGGAATTGAAC--GATGTCGGTGTTGATCTACCTTCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * *
3358975 TGTGATAGAATCGAGCAAAAAGTTGATG-TCGATCCAACTCCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCT-GATCCACCTCCTTC
* * ** *
3359019 TGTGATGGATTTGAGTGA-AATAAAATTG-T-C-GATCCACCTCATTC
1 TGTGATGGAATCGA---ACAA-AATGTTGATGCTGATCCACCTCCTTC
* * * * * ** *
3359063 TGTGATGGAATCGAACAAGATATCGGTGTTGATATACCTCATTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * * *
3359107 TGTGATAGAATC-AAGCAAAAAAGTTTAT-ATCGATCCAACTCCTTC
1 TGTGATGGAATCGAA-C-AAAATGTTGATGCT-GATCCACCTCCTTC
* * *** **** * *
3359152 TGTGATGGATTTGAGGGAAATAAAAATGCCGATCCACCTCATTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* *
3359196 TGTGATGGAATCGAACAAAATGTTGGTGCTGATCTACCTCCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * *
3359240 TGTGATAGAATCGAGCAAAAAGTTGATGCTGATCCAACTCCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
* * * ***
3359284 TGTGATGGATTTC-AGCGAAATGAAAATG-TCGATCCACCTCCTTC
1 TGTGATGGA-ATCGAACAAAATGTTGATGCT-GATCCACCTCCTTC
* * * * * * *
3359328 TATGATGGAATCGAACGAGATGTCGGTGTTGATCTACCTCCTTC
1 TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
*
3359372 TATGAT
1 TGTGAT
3359378 AGAGTCGAGA
Statistics
Matches: 476, Mismatches: 164, Indels: 48
0.69 0.24 0.07
Matches are distributed among these distances:
41 8 0.02
42 29 0.06
43 36 0.08
44 365 0.77
45 28 0.06
46 4 0.01
47 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
TGTGATGGAATCGAACAAAATGTTGATGCTGATCCACCTCCTTC
Found at i:3359816 original size:70 final size:72
Alignment explanation
Indices: 3359711--3359847 Score: 170
Period size: 70 Copynumber: 1.9 Consensus size: 72
3359701 AGAGAAGCTC
* ** * *
3359711 TCTCGAGTGAGATAAATTTTATTTCGAGGGTAAACT-TCTCA-AGTGACGAAGTTGGGTTTAAGA
1 TCTCGAGTGAGATAAAATTTATTTAAAGGGAAAACTGTCTCAGAGAGACGAAGTTGGGTTTAAGA
3359774 AAAACCA
66 AAAACCA
* * * *
3359781 TCTCGAGTTAGATAAAATTTGTTTAAAGGGAAAACTGTCTCATGCGAGACGAAGTTGGTTTTAAG
1 TCTCGAGTGAGATAAAATTTATTTAAAGGGAAAACTGTCTCA-GAGAGACGAAGTTGGGTTTAAG
3359846 AA
65 AA
3359848 TAAAAAACCA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
70 30 0.55
71 5 0.09
73 20 0.36
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (72 bp):
TCTCGAGTGAGATAAAATTTATTTAAAGGGAAAACTGTCTCAGAGAGACGAAGTTGGGTTTAAGA
AAAACCA
Found at i:3359993 original size:66 final size:66
Alignment explanation
Indices: 3359912--3360058 Score: 158
Period size: 66 Copynumber: 2.2 Consensus size: 66
3359902 AAAGTTTTTT
* ** *
3359912 TGTTTCAA-GAGAAACTGTCTCCACGGAGACAAAA-TTCATTTCAAGGGAAA-CGATCTCAAAGA
1 TGTTTCAAGGA-AAACTGTCTCAAAAGAGACAAAACTT-ATTTCAAGAGAAATCG-TCTCAAAGA
3359974 T-TAG
63 TGT-G
* *
3359978 TGTTTCAAGGAAAACTGTCTCAAAAGAGACAAAACTTGTTTCAAGAGAAATTGTCTCAAAGATGT
1 TGTTTCAAGGAAAACTGTCTCAAAAGAGACAAAACTTATTTCAAGAGAAATCGTCTCAAAGATGT
*
3360043 T
66 G
*
3360044 TGTTTCAAGAAAAAC
1 TGTTTCAAGGAAAAC
3360059 ATATTCAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
66 63 0.91
67 6 0.09
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGGAAAACTGTCTCAAAAGAGACAAAACTTATTTCAAGAGAAATCGTCTCAAAGATGT
G
Found at i:3360082 original size:31 final size:30
Alignment explanation
Indices: 3360013--3360097 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
3360003 GAGACAAAAC
* * *
3360013 TTGTTTCAAGAGAAATTGTCTCAAAGATGT
1 TTGTTTCAAGAAAAACTATCTCAAAGATGT
*
3360043 TTGTTTCAAGAAAAACATAT-TCAAAGATTT
1 TTGTTTCAAGAAAAAC-TATCTCAAAGATGT
*
3360073 TGTGTTTCAAGAGAAACTATCTCAA
1 T-TGTTTCAAGAAAAACTATCTCAA
3360098 GCGAGACAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 27 0.57
31 20 0.43
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (30 bp):
TTGTTTCAAGAAAAACTATCTCAAAGATGT
Found at i:3360115 original size:36 final size:36
Alignment explanation
Indices: 3360075--3360233 Score: 221
Period size: 36 Copynumber: 4.4 Consensus size: 36
3360065 AAAGATTTTG
* * *
3360075 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
*
3360111 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
* * *
3360147 CGTTTCAAGGGAAACTGTTTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
*
3360183 CGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-T
*
3360219 TGTTTCAAAAGAAAC
1 TGTTTCAAGAGAAAC
3360234 AGACTCATGC
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 5 0.04
36 107 0.96
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
Found at i:3360155 original size:21 final size:20
Alignment explanation
Indices: 3360122--3360194 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
3360112 GTTTCAAGGG
*
3360122 AAACTGTCTCAAGAGAGACA
1 AAACTGTTTCAAGAGAGACA
3360142 AAACTCGTTTCAAG-G-G---
1 AAACT-GTTTCAAGAGAGACA
3360158 AAACTGTTTCAAGAGAGACA
1 AAACTGTTTCAAGAGAGACA
3360178 AAACTCGTTTCAAGAGA
1 AAACT-GTTTCAAGAGA
3360195 AACTGTCTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
15 8 0.18
16 6 0.13
17 1 0.02
19 1 0.02
20 11 0.24
21 18 0.40
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (20 bp):
AAACTGTTTCAAGAGAGACA
Found at i:3360168 original size:15 final size:15
Alignment explanation
Indices: 3360111--3360170 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 15
3360101 AGACAAAATT
3360111 TGTTTCAAGGGAAAC
1 TGTTTCAAGGGAAAC
*
3360126 TGTCTCAAGAGAGACAAAAC
1 TGTTTCAAG-G-G---AAAC
3360146 TCGTTTCAAGGGAAAC
1 T-GTTTCAAGGGAAAC
3360162 TGTTTCAAG
1 TGTTTCAAG
3360171 AGAGACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
15 16 0.43
16 6 0.16
17 1 0.03
19 1 0.03
20 6 0.16
21 7 0.19
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (15 bp):
TGTTTCAAGGGAAAC
Found at i:3360487 original size:42 final size:42
Alignment explanation
Indices: 3360408--3360513 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
3360398 GTCTTATGGT
* *
3360408 TGGCCCGAATGACTTA-TCATCTTGCTCGAAAGTCTTACAAA
1 TGGCCCGAATGACTTACTCATCATGCTCGAAAGACTTACAAA
* * * **
3360449 TGGCCCAAAGGACTTACACATCATGCTCGAAAGACTTACTGA
1 TGGCCCGAATGACTTACTCATCATGCTCGAAAGACTTACAAA
3360491 TGGCCCGAATGACTTACTCATCA
1 TGGCCCGAATGACTTACTCATCA
3360514 AGAAACTCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 14 0.26
42 40 0.74
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
TGGCCCGAATGACTTACTCATCATGCTCGAAAGACTTACAAA
Found at i:3360594 original size:43 final size:43
Alignment explanation
Indices: 3360547--3360628 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
3360537 AATTTCTTAG
* *
3360547 TTGTCATCAAAGAACCCCTACATATCATGTTGGTTCCTCAAGC
1 TTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTCAAGC
*
3360590 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTC
1 TTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTC
3360629 GAGTGAGGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (43 bp):
TTGTCATCAAAGAACCCCTACATATCACGTTGGTCCCTCAAGC
Found at i:3360819 original size:42 final size:42
Alignment explanation
Indices: 3360720--3360819 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
3360710 TGGATGGCTG
* **
3360720 GAAGGACTTA-TCATCTTGCTTGAAAGACTTACAGATGACCC
1 GAAGGACTTACTCATCATGCTCAAAAGACTTACAGATGACCC
* * * *
3360761 GAAGGATTTACGCATCATGCTCAAAAGACTTACTGATGGCCC
1 GAAGGACTTACTCATCATGCTCAAAAGACTTACAGATGACCC
**
3360803 GAATTACTTACTCATCA
1 GAAGGACTTACTCATCA
3360820 AGAAACCCTT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
41 9 0.19
42 38 0.81
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (42 bp):
GAAGGACTTACTCATCATGCTCAAAAGACTTACAGATGACCC
Found at i:3360909 original size:39 final size:39
Alignment explanation
Indices: 3360852--3360999 Score: 224
Period size: 39 Copynumber: 3.8 Consensus size: 39
3360842 TAGTTTCTTT
* * * *
3360852 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCAAGATA
1 AAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACA
**
3360891 AAATCTTCTGTTTTGAGGGAAACTATCTCAAGCGAGACA
1 AAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACA
* *
3360930 AAATCTTCTGTTTCAAGGGAAACTATCTCCAGTGAGACA
1 AAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACA
3360969 AAATCTTCTGTTTCAAGGGAAACTATCTCAA
1 AAATCTTCTGTTTCAAGGGAAACTATCTCAA
3361000 TACAACCAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 100 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (39 bp):
AAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACA
Found at i:3362431 original size:14 final size:15
Alignment explanation
Indices: 3362411--3362447 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
3362401 GCAAATGCAA
*
3362411 AGATGCAAAAATGGG
1 AGATGCAAAAATGCG
3362426 AG-TGC-AAAATGCG
1 AGATGCAAAAATGCG
3362439 AGATGCAAA
1 AGATGCAAA
3362448 TGCAAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.46, C:0.11, G:0.30, T:0.14
Consensus pattern (15 bp):
AGATGCAAAAATGCG
Found at i:3364223 original size:14 final size:15
Alignment explanation
Indices: 3364206--3364242 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3364196 AGTTTAAGAA
3364206 ATTCGAGTT-AAGTT
1 ATTCGAGTTCAAGTT
*
3364220 ATTCGA-TTCGAGTT
1 ATTCGAGTTCAAGTT
3364234 ATTCGAGTT
1 ATTCGAGTT
3364243 TGTATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 16 0.80
15 2 0.10
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (15 bp):
ATTCGAGTTCAAGTT
Found at i:3364989 original size:14 final size:14
Alignment explanation
Indices: 3364970--3364997 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3364960 TTGAGTTGAT
3364970 TCGAATAACTCAAA
1 TCGAATAACTCAAA
3364984 TCGAATAACTCAAA
1 TCGAATAACTCAAA
3364998 ATTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
TCGAATAACTCAAA
Found at i:3373516 original size:2 final size:2
Alignment explanation
Indices: 3373509--3373539 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3373499 GTTTAAATTG
3373509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3373540 AGTGTGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3377217 original size:27 final size:27
Alignment explanation
Indices: 3377187--3377263 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 27
3377177 AAAATAAAAA
3377187 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
* *
3377214 AATAAAATATATTT-AA-TAAGTTGAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
3377239 ATTAAATAATATTTTTTAAAGTTAA
1 AAT-AA-AATA-TTTTTAAA-TTAA
3377264 TATATATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.25
26 4 0.10
27 17 0.43
28 4 0.10
29 2 0.05
31 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
AATAAAATATTTTTAAATTAAGTTAAT
Found at i:3381299 original size:16 final size:16
Alignment explanation
Indices: 3381278--3381314 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
3381268 TACTAACTTA
3381278 TATTAGTTTTGCCTTC
1 TATTAGTTTTGCCTTC
3381294 TATTAGTTTTGCCTTC
1 TATTAGTTTTGCCTTC
3381310 TATTA
1 TATTA
3381315 TATATGTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (16 bp):
TATTAGTTTTGCCTTC
Found at i:3385782 original size:20 final size:20
Alignment explanation
Indices: 3385730--3385776 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3385720 AATTCAAGTA
*
3385730 GAGGCAGGGGTGGACCAAGG
1 GAGGCGGGGGTGGACCAAGG
3385750 GAGGCGGGGGTGGACCAAGG
1 GAGGCGGGGGTGGACCAAGG
3385770 GAGGCGG
1 GAGGCGG
3385777 TTGTGGGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.60, T:0.04
Consensus pattern (20 bp):
GAGGCGGGGGTGGACCAAGG
Found at i:3387026 original size:24 final size:24
Alignment explanation
Indices: 3386999--3387046 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
3386989 GGCTCGATTT
3386999 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
*
3387023 TCTTCCAACAGTCATACCTTTTAA
1 TCTTCCAACAGTCAGACCTTTTAA
3387047 ATTCCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (24 bp):
TCTTCCAACAGTCAGACCTTTTAA
Found at i:3387621 original size:20 final size:20
Alignment explanation
Indices: 3387561--3387623 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
3387551 ACTTGTTATT
3387561 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
** *
3387582 TTGTTTATCTATAATATGTTTAA
1 TTG-TTA--GGTAATCTGTTTAA
3387605 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
3387624 GAATTTAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 10 0.30
21 4 0.12
22 5 0.15
23 14 0.42
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:3393619 original size:20 final size:20
Alignment explanation
Indices: 3393583--3393620 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3393573 ATCCTATTCC
**
3393583 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3393603 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3393621 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3393664 original size:21 final size:21
Alignment explanation
Indices: 3393638--3393678 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3393628 AAACGCACCC
3393638 TTAGGGTGCATCGGTACACTT
1 TTAGGGTGCATCGGTACACTT
3393659 TTAGGGTGCATCGGTACACT
1 TTAGGGTGCATCGGTACACT
3393679 AATTACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (21 bp):
TTAGGGTGCATCGGTACACTT
Found at i:3393742 original size:19 final size:19
Alignment explanation
Indices: 3393710--3393755 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3393700 AGAGCCAAGA
*
3393710 GTGCATCGATGCATGGTCT
1 GTGCATCGACGCATGGTCT
* *
3393729 GTGTATCGACGCATGGTTT
1 GTGCATCGACGCATGGTCT
3393748 GTGCATCG
1 GTGCATCG
3393756 GTACATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (19 bp):
GTGCATCGACGCATGGTCT
Found at i:3393805 original size:84 final size:84
Alignment explanation
Indices: 3393664--3393820 Score: 237
Period size: 84 Copynumber: 1.9 Consensus size: 84
3393654 CACTTTTAGG
*
3393664 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACTAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGTCT
*
3393729 GTGTATCGACGCATGGTTT
66 GTGCATCGACGCATGGTTT
* **
3393748 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAA-ATTCAAGAGTGCATCGATGCATGGT
1 GTGCATCGGTACACT-AAATACATTCGATGTTTCAA-AAGAGCCAAGAGTGCATCGATGCATGGT
3393811 CTGTGCATCG
64 CTGTGCATCG
3393821 GTACACAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 1 0.02
84 63 0.95
85 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (84 bp):
GTGCATCGGTACACTAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGTCT
GTGCATCGACGCATGGTTT
Found at i:3394192 original size:12 final size:13
Alignment explanation
Indices: 3394170--3394203 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3394160 TAAGATTTTC
3394170 TTTGAAAATCA-TT
1 TTTG-AAATCAGTT
3394183 TTTGAAATCAGTT
1 TTTGAAATCAGTT
3394196 TTTGAAAT
1 TTTGAAAT
3394204 TACTTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (13 bp):
TTTGAAATCAGTT
Found at i:3395975 original size:13 final size:13
Alignment explanation
Indices: 3395956--3395994 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3395946 CTAATGGGCA
3395956 AAATTTTGAAAAC
1 AAATTTTGAAAAC
*
3395969 TAATTTTGATAAAC
1 AAATTTTGA-AAAC
*
3395983 AAAGTTTGAAAA
1 AAATTTTGAAAA
3395995 ATCAATATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (13 bp):
AAATTTTGAAAAC
Found at i:3397176 original size:22 final size:22
Alignment explanation
Indices: 3397144--3397187 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3397134 GTGCACAACA
3397144 GCTACCAGCTGAAATGTATTCC
1 GCTACCAGCTGAAATGTATTCC
*
3397166 GCTACCGGCTGAAATGTATTCC
1 GCTACCAGCTGAAATGTATTCC
3397188 ACTTCAATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (22 bp):
GCTACCAGCTGAAATGTATTCC
Found at i:3402370 original size:19 final size:19
Alignment explanation
Indices: 3402346--3402399 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
3402336 GTAAGACTTA
*
3402346 GTGCATCTGTACACTAGGG
1 GTGCATCGGTACACTAGGG
3402365 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
3402384 GTGCATCGGTACACTA
1 GTGCATCGGTACACTA
3402400 ATTACATTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.24
Consensus pattern (19 bp):
GTGCATCGGTACACTAGGG
Found at i:3402473 original size:65 final size:65
Alignment explanation
Indices: 3402385--3402540 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
3402375 ACACTAGGGG
* * *
3402385 TGCATCGGTACACT-AATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTC
1 TGCATCGGTACA-TAAAATGCATTCGATGTTTCAATAA-AGCCAAGAGTGCATCGATGCATGGTC
3402448 TA
64 TA
** *
3402450 TGCATCGGTACATAAAATGCATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGGTCTG
1 TGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGTCTA
*
3402515 TGCATCGGTACACAAAATGCATTCGA
1 TGCATCGGTACATAAAATGCATTCGA
3402541 AATAGGGTGT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
64 1 0.01
65 79 0.96
66 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (65 bp):
TGCATCGGTACATAAAATGCATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGTCTA
Found at i:3403048 original size:43 final size:43
Alignment explanation
Indices: 3402984--3403104 Score: 215
Period size: 43 Copynumber: 2.8 Consensus size: 43
3402974 CCTGATTCAG
*
3402984 TGTCAAATACTCACACCTGATTTCGTGTAATATAAGATGCTTA
1 TGTCAAACACTCACACCTGATTTCGTGTAATATAAGATGCTTA
*
3403027 TGTCAAACACTCACACTTGATTTCGTGTAATATAAGATGCTTA
1 TGTCAAACACTCACACCTGATTTCGTGTAATATAAGATGCTTA
*
3403070 TGTCAAACACTCACACCTGATTCCGTGTAATATAA
1 TGTCAAACACTCACACCTGATTTCGTGTAATATAA
3403105 CATGAATTAG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (43 bp):
TGTCAAACACTCACACCTGATTTCGTGTAATATAAGATGCTTA
Found at i:3405277 original size:24 final size:24
Alignment explanation
Indices: 3405245--3405302 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
3405235 TAATTATATT
3405245 ATTATTATTATTATAATAATAATA
1 ATTATTATTATTATAATAATAATA
* * *
3405269 ATTATTATTATTTTATTATTAATA
1 ATTATTATTATTATAATAATAATA
*
3405293 AATATTATTA
1 ATTATTATTA
3405303 CATATTACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTATTATTATTATAATAATAATA
Found at i:3405291 original size:21 final size:21
Alignment explanation
Indices: 3405232--3405302 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
3405222 TTCATTTGAA
3405232 TATTAATTATATTATT-ATTAT
1 TATT-ATTATATTATTAATTAT
* * *
3405253 TATTATAATAATAATAATTAT
1 TATTATTATATTATTAATTAT
* * *
3405274 TATTATTTTATTATTAATAAA
1 TATTATTATATTATTAATTAT
3405295 TATTATTA
1 TATTATTA
3405303 CATATTACAG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 8 0.21
21 31 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATTATATTATTAATTAT
Found at i:3405302 original size:3 final size:3
Alignment explanation
Indices: 3405232--3405289 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
3405222 TTCATTTGAA
* * * *
3405232 TAT TAAT TA- TAT TAT TAT TAT TAT TAT AAT AAT AAT AAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3405277 TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TA
3405290 ATAAATATTA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:3406991 original size:23 final size:23
Alignment explanation
Indices: 3406965--3407008 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3406955 TATTTCTAAA
*
3406965 TAAATAAATATCTTATTTATATT
1 TAAATAAATATATTATTTATATT
* *
3406988 TAAATTAATATATTTTTTATA
1 TAAATAAATATATTATTTATA
3407009 AAATAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAATAAATATATTATTTATATT
Found at i:3407470 original size:6 final size:7
Alignment explanation
Indices: 3407449--3407473 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3407439 TGTCTCTATT
3407449 AATTAAA
1 AATTAAA
3407456 AATTAAA
1 AATTAAA
3407463 AATTAAA
1 AATTAAA
3407470 AATT
1 AATT
3407474 CATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:3407551 original size:26 final size:27
Alignment explanation
Indices: 3407499--3407556 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
3407489 TAATTCTTTC
*
3407499 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
3407527 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
3407553 TTTT
1 TTTT
3407557 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:3417663 original size:11 final size:11
Alignment explanation
Indices: 3417649--3417673 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3417639 TTGAAAAAAT
3417649 AAAAAAATAAA
1 AAAAAAATAAA
3417660 AAAAAAATAAA
1 AAAAAAATAAA
3417671 AAA
1 AAA
3417674 TGAGGGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:3418052 original size:18 final size:18
Alignment explanation
Indices: 3418031--3418068 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3418021 ATTTATTATT
* *
3418031 TTTTTGAGATTTAATTTA
1 TTTTTGAAATTCAATTTA
3418049 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
3418067 TT
1 TT
3418069 CTTTTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:3419408 original size:113 final size:111
Alignment explanation
Indices: 3419213--3419755 Score: 698
Period size: 113 Copynumber: 4.9 Consensus size: 111
3419203 GATTCGAATC
* * *
3419213 CATCATTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGGACTCATCTGAAGGAGGAA
1 CATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
3419278 GAAGAAATTCATAATGAGAAGAATTCGTTCGAACCTTTTGTTTGAATT
66 GAAGAAGTTCATAATGAGAAGAATT-GTTC-AACCTTTTGTTTCAATT
* * *
3419326 CATCATTCGATGGATCAACGTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAA
1 CATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
3419391 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG-TTCAAAT
66 GAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTGTTTCAATT
* * * *
3419437 C--CATAACAATGGATCAACATTTCC-GAG-TGTTCATAATGAGAAGAACTCATCTGAATAAGGA
1 CATCAT-TCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
3419498 AGAGGAAGTTCATAATGAGAAGAGATTGTTCAACCTTTTG-CTCAAAT
65 AGAAGAAGTTCATAATGAGAAGA-ATTGTTCAACCTTTTGTTTCAATT
*
3419545 CTATCACTT-GATGGATCAA-TTTTCCAGAGAAAGTTCATAAT--GAAGAACTCATCTGAAG-AG
1 C-ATCA-TTCGATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* *
3419605 GAAGAAGAAGTTCATAAT--GAAGACTTGTTCAACCTTTTGCTTCAATT
63 GAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTGTTTCAATT
* *
3419652 CATCACTCGATGGATCAGCATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACA-TTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
3419717 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT
65 AGAAGAAGTTCATAATGAGAAGA-ATTGTTCAACCTTTT
3419756 TCATGACTCT
Statistics
Matches: 380, Mismatches: 30, Indels: 40
0.84 0.07 0.09
Matches are distributed among these distances:
105 1 0.00
106 28 0.07
107 22 0.06
108 82 0.22
109 48 0.13
110 64 0.17
111 8 0.02
112 24 0.06
113 101 0.27
114 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (111 bp):
CATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTGTTTCAATT
Found at i:3419770 original size:113 final size:112
Alignment explanation
Indices: 3419222--3419890 Score: 661
Period size: 113 Copynumber: 6.0 Consensus size: 112
3419212 CCATCATTCA
* * *
3419222 ATGGATCAACA-TTTCCAGAGAAGTTCATAATGAGAAGGACTCATCTGAAGGAGGAAGAAGAAAT
1 ATGGATCAACATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * *
3419286 TCATAATGAGAAGA-ATTCGTTCGAACCTTTTGT-TTGAAT-TCATCATTCG
66 TCATAATGAGAAGAGCTT-GTTC-AACCTTTT-TCAT-AATCT-ATCACTCG
* * * *
3419335 ATGGATCAAC-GTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAAT
1 ATGGATCAACATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** * * *
3419399 TCATAATGAGAAGAATTTGTTCAACCTTTTGTTCA-AATCCAT-A-ACA
66 TCATAATGAGAAGAGCTTGTTCAACC-TTT-TTCATAATCTATCACTCG
* * *
3419445 ATGGATCAACA-TTTCC-GAG-TGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAGGAAGT
1 ATGGATCAACATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
3419507 TCATAATGAGAAGAGATTGTTCAACCTTTTGCTCA-AATCTATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTT--TCATAATCTATCACTCG
3419555 ATGGATC-A-ATTTTCCAGAGAAAGTTCATAAT--GAAGAACTCATCTGAAG-AGGAAGAAGAAG
1 ATGGATCAACATTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
3419615 TTCATAAT--GAAGA-CTTGTTCAACCTTTTGCTTCAAT-TCATCACTCG
65 TTCATAATGAGAAGAGCTTGTTCAACCTTTTTCAT-AATCT-ATCACTCG
*
3419661 ATGGATCAGCATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* **
3419726 TCATAATGAGAAGAGCTTGTTCAACCTTTTTCATGACTCTATCACAGAAGGAG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTTCAT-AATCTATCAC-----TCG
* *
3419779 ATAGATCAACACCAATTTTTTCCAGAGAAAGTTCATAAT---AAG-ACTCATCTGAAGAAGCAAG
1 ATGGATC-A-A-C-A--TTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
3419840 AAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTCTTGT-ATAATCTATCAC
59 AAGAAGTTCATAATGAGAAGAGCTTGTTCAACCT-TTTTCATAATCTATCAC
3419891 AAAAGGATAG
Statistics
Matches: 476, Mismatches: 40, Indels: 73
0.81 0.07 0.12
Matches are distributed among these distances:
104 1 0.00
105 1 0.00
106 32 0.07
107 19 0.04
108 82 0.17
109 46 0.10
110 62 0.13
111 1 0.00
112 23 0.05
113 105 0.22
114 4 0.01
118 7 0.01
119 1 0.00
120 9 0.02
121 55 0.12
122 7 0.01
124 10 0.02
125 11 0.02
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (112 bp):
ATGGATCAACATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAGCTTGTTCAACCTTTTTCATAATCTATCACTCG
Found at i:3419970 original size:121 final size:124
Alignment explanation
Indices: 3419670--3419953 Score: 374
Period size: 121 Copynumber: 2.4 Consensus size: 124
3419660 GATGGATCAG
*
3419670 CATTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 CATTTTCCAGAGAAAGTTCATAATGAG-AGAACTCATCTGAAGAAGCAAGAAGAAGTTCATAATG
* * *
3419734 AGAAGAGCTTGTTCAACCTTTTTCATGACTCTATCACAGAAGGAGATAGATCAACACCAA
65 AGAAGAGCTTGTTCAACCTTTGTCATGAATCTATCACAGAAAGAGATAGATCAACACCAA
**
3419794 TTTTTTCCAGAGAAAGTTCATAAT-A-AG-ACTCATCTGAAGAAGCAAGAAGAAGTTCATAATGA
1 CATTTTCCAGAGAAAGTTCATAATGAGAGAACTCATCTGAAGAAGCAAGAAGAAGTTCATAATGA
* * *
3419856 GAAGAGCTTGTTCAACCTCTTGT-AT-AATCTATCACA-AAAG-GATAGATTAGCATCAA
66 GAAGAGCTTGTTCAACCT-TTGTCATGAATCTATCACAGAAAGAGATAGATCAACACCAA
*
3419912 CATTTT-CAGA-AATA-TTTATAATGAGAGAACTCATCTGAAGAA
1 CATTTTCCAGAGAA-AGTTCATAATGAGAGAACTCATCTGAAGAA
3419954 TAAGGAGAAC
Statistics
Matches: 142, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
116 9 0.06
117 6 0.04
118 19 0.13
119 17 0.12
120 10 0.07
121 54 0.38
122 5 0.04
124 11 0.08
125 11 0.08
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (124 bp):
CATTTTCCAGAGAAAGTTCATAATGAGAGAACTCATCTGAAGAAGCAAGAAGAAGTTCATAATGA
GAAGAGCTTGTTCAACCTTTGTCATGAATCTATCACAGAAAGAGATAGATCAACACCAA
Found at i:3420271 original size:3 final size:3
Alignment explanation
Indices: 3420226--3420256 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3420216 ATAATAATAA
3420226 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3420257 ATAATAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3427021 original size:39 final size:39
Alignment explanation
Indices: 3426962--3427085 Score: 221
Period size: 39 Copynumber: 3.2 Consensus size: 39
3426952 ACATCAAATG
*
3426962 AAAAGCTACATTTACATCTCTTGGAAGCATAGACTCTCAT
1 AAAA-CTACATTTACATCTCTTGGAAGTATAGACTCTCAT
3427002 AAAACTACATTTACATCTCTTGGAAGTATAGACTCTCAT
1 AAAACTACATTTACATCTCTTGGAAGTATAGACTCTCAT
*
3427041 AAAATTACATTTACATCTCTTGGAAGTATAGACTCTCAT
1 AAAACTACATTTACATCTCTTGGAAGTATAGACTCTCAT
3427080 AAAACT
1 AAAACT
3427086 GGAAAAAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 77 0.95
40 4 0.05
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.32
Consensus pattern (39 bp):
AAAACTACATTTACATCTCTTGGAAGTATAGACTCTCAT
Found at i:3430669 original size:124 final size:119
Alignment explanation
Indices: 3430503--3430728 Score: 319
Period size: 124 Copynumber: 1.9 Consensus size: 119
3430493 CTTTTACTAC
* * * *
3430503 TCGACCTTGTGGTGACTCAATCCAAGGTAAGATCCACATTATTATGGTTCGGACTCTGCTAACTA
1 TCGACCTTGTGGTGACCCAATCCAAGGTAAGATCCACATTATTATAGTTCAGACTATGCTAACTA
* *
3430568 CTATTTTTTTTATTTTTTTATTATATTTTATTTTTATATATTTGTTTGCATTATTCGAT
66 CTAATTATTTTA--TTTTTA-TAT-TTTTATTTTTAT-TATTTGTTTGCATTATTCGAT
* *
3430627 TCGACCTTGTGGTGACCCGATCCAAGGTAAGATTCA-ATTTATTATAGTTCAGACTATGCTAACT
1 TCGACCTTGTGGTGACCCAATCCAAGGTAAGATCCACA-TTATTATAGTTCAGACTATGCTAACT
3430691 ACTAATTATTTTATTTTTATATTTTTATTTTTATTATT
65 ACTAATTATTTTATTTTTATATTTTTATTTTTATTATT
3430729 CGATTCGACC
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
119 4 0.04
120 12 0.13
121 3 0.03
122 6 0.06
123 1 0.01
124 67 0.72
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.48
Consensus pattern (119 bp):
TCGACCTTGTGGTGACCCAATCCAAGGTAAGATCCACATTATTATAGTTCAGACTATGCTAACTA
CTAATTATTTTATTTTTATATTTTTATTTTTATTATTTGTTTGCATTATTCGAT
Found at i:3431535 original size:22 final size:22
Alignment explanation
Indices: 3431488--3431537 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3431478 AAACTTTATT
* * *
3431488 TTTTATATATATAAATCATCAT
1 TTTTATATATAAAAATCATAAA
3431510 TTTTATATATAGAAAAT-ATAAA
1 TTTTATATATA-AAAATCATAAA
3431532 TTTTAT
1 TTTTAT
3431538 TGTAAGGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTATATATAAAAATCATAAA
Found at i:3446189 original size:72 final size:70
Alignment explanation
Indices: 3446082--3446245 Score: 211
Period size: 72 Copynumber: 2.3 Consensus size: 70
3446072 CGTCTCATTC
*
3446082 GAGACAATTTTTCTTGAAACAAAATTAATCTCACTTGAGATTGTTTCCTCTAAAAACAAATTTCG
1 GAGACAA-TTTTCTTGAAACAAAATTAATCACACTTGAGATTGTTTCCTCTAAAAACAAA-TT-G
* *
3446147 TCTTGTTT
63 TCTCGCTT
* * * * * *
3446155 TAGATAATTTTCTTGAAACAAAATTGATCACACTTGAGATTGTTTTCTCTAGAAATAAATTGTCT
1 GAGACAATTTTCTTGAAACAAAATTAATCACACTTGAGATTGTTTCCTCTAAAAACAAATTGTCT
3446220 CGCTT
66 CGCTT
3446225 GAGACAATTTCTCTTGAAACA
1 GAGACAATTT-TCTTGAAACA
3446246 TAAACCTTTG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
70 15 0.19
71 12 0.15
72 47 0.59
73 5 0.06
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (70 bp):
GAGACAATTTTCTTGAAACAAAATTAATCACACTTGAGATTGTTTCCTCTAAAAACAAATTGTCT
CGCTT
Found at i:3446201 original size:35 final size:35
Alignment explanation
Indices: 3446090--3446228 Score: 95
Period size: 35 Copynumber: 3.9 Consensus size: 35
3446080 TCGAGACAAT
*
3446090 TTTTCTTGAAACAAAATTAATCTCACTTGAGATTG
1 TTTTCTTGAAACAAAATTGATCTCACTTGAGATTG
** * *** * **
3446125 TTTCCTCTAAAAACAAATTTCG-TCTTGTTTTAGATAA
1 TTT--TCTTGAAACAAAATT-GATCTCACTTGAGATTG
*
3446162 TTTTCTTGAAACAAAATTGATCACACTTGAGATTG
1 TTTTCTTGAAACAAAATTGATCTCACTTGAGATTG
* *
3446197 TTTTCTCTAGAAA-TAAATTG-TCTCGCTTGAGA
1 TTTTCT-T-GAAACAAAATTGATCTCACTTGAGA
3446229 CAATTTCTCT
Statistics
Matches: 75, Mismatches: 23, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
34 1 0.01
35 39 0.52
36 7 0.09
37 28 0.37
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (35 bp):
TTTTCTTGAAACAAAATTGATCTCACTTGAGATTG
Found at i:3446293 original size:67 final size:67
Alignment explanation
Indices: 3446216--3446378 Score: 218
Period size: 67 Copynumber: 2.4 Consensus size: 67
3446206 GAAATAAATT
* * * * *
3446216 GTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCTTTGAGACTGTTTCTCTCGAAACAAAGTT
1 GTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCGTTCACACTGTTTCTCCCGAAACAAAATT
3446281 TC
66 TC
* * *
3446283 GTCTCGCTTGAGACAGTTTCTCTTGAAACATAAATCGTTCACATTGTTTCTCCCGAAACAAAATT
1 GTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCGTTCACACTGTTTCTCCCGAAACAAAATT
3446348 TC
66 TC
* * *
3446350 GTCTTGCTTGAGAAAATTTTTCCTTGAAA
1 GTCTCGCTTGAGACAATTTCT-CTTGAAA
3446379 TTCAAATTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
67 76 0.92
68 7 0.08
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (67 bp):
GTCTCGCTTGAGACAATTTCTCTTGAAACATAAACCGTTCACACTGTTTCTCCCGAAACAAAATT
TC
Found at i:3450280 original size:2 final size:2
Alignment explanation
Indices: 3450273--3450308 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3450263 TCTATTAATT
3450273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3450309 AGATATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3450589 original size:13 final size:14
Alignment explanation
Indices: 3450571--3450601 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3450561 TTATTTTTCT
3450571 TAAAAGT-AATTTA
1 TAAAAGTAAATTTA
3450584 TAAAAGTAAATTTA
1 TAAAAGTAAATTTA
3450598 TAAA
1 TAAA
3450602 TAGGATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
TAAAAGTAAATTTA
Found at i:3452204 original size:3 final size:3
Alignment explanation
Indices: 3452196--3452300 Score: 98
Period size: 3 Copynumber: 36.7 Consensus size: 3
3452186 AAATTTTTAT
*
3452196 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA -AA TAA TAA TAA CAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
3452241 TAAA TAA -AA TAA TGA TAA TTA -AA TAA TAA TAA CAA T-A TAAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
3452285 -AA TAA TGA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
3452301 TAAAAAACAA
Statistics
Matches: 83, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
2 13 0.16
3 66 0.80
4 4 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3452217 original size:14 final size:14
Alignment explanation
Indices: 3452198--3452303 Score: 99
Period size: 14 Copynumber: 7.3 Consensus size: 14
3452188 ATTTTTATTA
3452198 ATAATAATAATAAT
1 ATAATAATAATAAT
*
3452212 ATAATAATAATAAA
1 ATAATAATAATAAT
*
3452226 ATAATAATAACAAT
1 ATAATAATAATAAT
3452240 ATAAATAA-AATAAT
1 AT-AATAATAATAAT
3452254 GATAATTAAATAATAAT
1 -ATAA-T-AATAATAAT
* *
3452271 AACAAT-ATAAATAAA
1 -ATAATAAT-AATAAT
*
3452286 ATAATGATAATAAT
1 ATAATAATAATAAT
3452300 ATAA
1 ATAA
3452304 AAAACAAATG
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 49 0.64
15 15 0.20
16 3 0.04
17 9 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:3452259 original size:37 final size:37
Alignment explanation
Indices: 3452206--3452310 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
3452196 TAATAATAAT
* *
3452206 AATAATATAATAATAATAAAATAATAATAACAATATA
1 AATAAAATAATGATAATAAAATAATAATAACAATATA
*
3452243 AATAAAATAATGATAATTAAATAATAATAACAATATA
1 AATAAAATAATGATAATAAAATAATAATAACAATATA
*
3452280 AATAAAATAATGATAATAATATAA-AA-AACAA
1 AATAAAATAATGATAATAAAATAATAATAACAA
3452311 ATGGATAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 5 0.08
36 2 0.03
37 56 0.89
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.28
Consensus pattern (37 bp):
AATAAAATAATGATAATAAAATAATAATAACAATATA
Found at i:3452318 original size:23 final size:23
Alignment explanation
Indices: 3452261--3452304 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3452251 AATGATAATT
*
3452261 AAATAATAATAACAATATAAATA
1 AAATAATGATAACAATATAAATA
*
3452284 AAATAATGATAATAATATAAA
1 AAATAATGATAACAATATAAA
3452305 AAACAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAATGATAACAATATAAATA
Found at i:3452832 original size:18 final size:18
Alignment explanation
Indices: 3452774--3452832 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
3452764 TTGAACAAGC
3452774 TCTTCTCATTATGAACTTAT
1 TCTTCTCATTATGAAC-T-T
* *
3452794 TCTTCCTCTTTA-GATA-GT
1 TCTT-CTCATTATGA-ACTT
3452812 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
3452830 TCT
1 TCT
3452833 CTGGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
17 7 0.23
18 11 0.35
20 6 0.19
21 7 0.23
ACGTcount: A:0.20, C:0.22, G:0.07, T:0.51
Consensus pattern (18 bp):
TCTTCTCATTATGAACTT
Found at i:3452886 original size:122 final size:123
Alignment explanation
Indices: 3452632--3453092 Score: 660
Period size: 123 Copynumber: 3.7 Consensus size: 123
3452622 GAATTAAGGC
*
3452632 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCTTCTTCTTCTTCAGATGAGTTCTTCT
1 AAGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCTTC--CTTCTTCAGATGAGTTCTTCT
* * * * * * *
3452697 CATTATGAACACTTCTGGAAATA-TTGATGATGATCTATCTCCTTCCGTGATAGAGTCATGCAA
61 CATTATGAACTCTTCTGGAAA-AGTTGATGATGATTTATCTCTTTCTGGGATAGAATCAAGCAA
* * *
3452760 AAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCC-TCTTTAGAT-AGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
3452823 TGAACTTTCTCTGGAAAAGTTGATGTTGATTTATCTCTTTCTGGGATAGAATCAAGCAA
66 TGAACTCT-TCTGGAAAAGTTGATGATGATTTATCTCTTTCTGGGATAGAATCAAGCAA
* *
3452882 AAGGTTGAACAAATTCTTCACATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
3452947 TGAACTCTTCTGGAAAAGTTGAT-ACTAATTTATCTCTTTCTGGGATAGAATCAAGCAA
66 TGAACTCTTCTGGAAAAGTTGATGA-TGATTTATCTCTTTCTGGGATAGAATCAAGCAA
*
3453005 AACGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
3453070 TGAACTCTTTTGGAAAAGTTGAT
66 TGAACTCTTCTGGAAAAGTTGAT
3453093 CCATTGAGTA
Statistics
Matches: 303, Mismatches: 25, Indels: 15
0.88 0.07 0.04
Matches are distributed among these distances:
121 21 0.07
122 85 0.28
123 140 0.46
124 21 0.07
125 9 0.03
128 27 0.09
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTTCTGGAAAAGTTGATGATGATTTATCTCTTTCTGGGATAGAATCAAGCAA
Found at i:3455632 original size:18 final size:18
Alignment explanation
Indices: 3455598--3455632 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3455588 GTGAAAGAAT
*
3455598 AAATTCAATTTCGAAAAC
1 AAATTCAATTTCAAAAAC
*
3455616 AAATTGAATTTCAAAAA
1 AAATTCAATTTCAAAAA
3455633 GATAATCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATTCAATTTCAAAAAC
Found at i:3456019 original size:15 final size:14
Alignment explanation
Indices: 3455970--3456021 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
3455960 TTGAACCTCC
*
3455970 TTTTTT-ATATATT
1 TTTTTTCATTTATT
*
3455983 TTTTTATCATTTTTT
1 TTTTT-TCATTTATT
3455998 TTCTTTTCATTTCATT
1 TT-TTTTCATTT-ATT
3456014 TTTTTTCA
1 TTTTTTCA
3456022 AGCGTAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 5 0.16
14 1 0.03
15 19 0.59
16 7 0.22
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTTCATTTATT
Found at i:3466707 original size:13 final size:12
Alignment explanation
Indices: 3466689--3466733 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
3466679 AAAATAAAAT
3466689 AAAAATATTAATA
1 AAAAATATT-ATA
*
3466702 AAAAATAATATA
1 AAAAATATTATA
*
3466714 TATAAATATTATA
1 -AAAAATATTATA
3466727 AAAAATA
1 AAAAATA
3466734 ATAAGTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAAATATTATA
Found at i:3466742 original size:25 final size:25
Alignment explanation
Indices: 3466679--3466742 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
3466669 TTAATACTTG
*
3466679 AAAATAA-AATAAAAATATTAATAA
1 AAAATAATAATATAAATATTAATAA
3466703 AAAATAATATATATAAATATT-ATAA
1 AAAATAATA-ATATAAATATTAATAA
3466728 AAAATAATAAGTATA
1 AAAATAATAA-TATA
3466743 TATAAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 8 0.22
25 18 0.50
26 10 0.28
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAATAATAATATAAATATTAATAA
Found at i:3467268 original size:2 final size:2
Alignment explanation
Indices: 3467263--3467288 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3467253 TATATTAATT
3467263 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3467289 AATAAGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3467947 original size:5 final size:5
Alignment explanation
Indices: 3467937--3467964 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3467927 TTTGAACATC
3467937 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
3467965 ACATGCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:3469211 original size:3 final size:3
Alignment explanation
Indices: 3469203--3469245 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3469193 AATTTTTTAT
*
3469203 TAA TAA TAA TAA TAA TAA T-A TAAA TAA -AA TAA TGA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA
3469246 TAAAAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3469235 original size:23 final size:22
Alignment explanation
Indices: 3469207--3469254 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
3469197 TTTTATTAAT
3469207 AATAATAATAATAATATAAATAA
1 AATAATAATAATAATATAAA-AA
*
3469230 AATAATGATAATAATATAAAAA
1 AATAATAATAATAATATAAAAA
3469252 AAT
1 AAT
3469255 GGATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AATAATAATAATAATATAAAAA
Found at i:3473174 original size:83 final size:83
Alignment explanation
Indices: 3473021--3473209 Score: 270
Period size: 83 Copynumber: 2.3 Consensus size: 83
3473011 AAAGACAGCT
* * *
3473021 AGACGTCCTCATCACGTAGGAACAATGTCATCTACCGACCAGATCTCCTCAACGCGTAGGAGCAG
1 AGACTTCCTCATCACGTAGGAACAATGTCATCCACCGACCAAATCTCCTCAACGCGTAGGAGCAG
*
3473086 CGTCATCCTTAGGCAATC
66 CGTCATCCTTAGGAAATC
* * * * *
3473104 AGACTTCCTTATCACGTAGGAACAATGTCGTCCACCGATCAAATCTCCTTAATGCGTAGGAGCAG
1 AGACTTCCTCATCACGTAGGAACAATGTCATCCACCGACCAAATCTCCTCAACGCGTAGGAGCAG
* *
3473169 TGTCATTCTTAGGAAATC
66 CGTCATCCTTAGGAAATC
*
3473187 AGACTTCCTCATCACATAGGAAC
1 AGACTTCCTCATCACGTAGGAAC
3473210 CGTGTTTTCT
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (83 bp):
AGACTTCCTCATCACGTAGGAACAATGTCATCCACCGACCAAATCTCCTCAACGCGTAGGAGCAG
CGTCATCCTTAGGAAATC
Found at i:3473378 original size:138 final size:138
Alignment explanation
Indices: 3473121--3473506 Score: 413
Period size: 138 Copynumber: 2.8 Consensus size: 138
3473111 CTTATCACGT
* * * * ** * * *
3473121 AGGAACAATGTCGTCCACCGATCAAATCTCCTTAATGCGTAGGAGCAGTGTCATTCTTAGGA-AA
1 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCAAAGGAACAGTGTCATCCTCA-GACAA
* *
3473185 TCAGACTTCCTCATCACATAGGAACCGTGTTTTCTCCAATTATCCTTAAAGATGGCTAGACGTGC
65 TCAGACTTCCTCATCACATAGGAACCGTGTTGTCTCCAATTATCCTTAAAGATGGCTAGACGTCC
* * *
3473250 TCATCATGT
130 TAACCATGA
* * *
3473259 ATGAACAAAT-TCGTCCACCGACCAGATTTCCTCAACGCAAAGGAATAGTGTCATCCTCA-AGCA
1 AGGAAC-AATGTCGTCCACCGACCAGATCTCCTCAACGCAAAGGAACAGTGTCATCCTCAGA-CA
* * * *
3473322 ATCAGACTTCCTCATCACGTAGGAACTGTGTTGTCTCCAAATTTAT-TTTAAA-ATGGCTAGACT
64 ATCAGACTTCCTCATCACATAGGAACCGTGTTGTCTCC-AA-TTATCCTTAAAGATGGCTAGACG
3473385 TCCTAACCATGA
127 TCCTAACCATGA
* * *
3473397 AGGAACAATGTCGTCTACCGACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAGACAAT
1 AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCAAAGGAACAGTGTCATCCTCAGACAAT
* * * * * *
3473462 AAGACTTCCTCAACGCAAAGGAACCGTATTATCTCCAAATTATCC
66 CAGACTTCCTCATCACATAGGAACCGTGTTGTCTCC-AATTATCC
3473507 AAATTGACCT
Statistics
Matches: 204, Mismatches: 36, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
136 1 0.00
137 7 0.03
138 181 0.89
139 11 0.05
140 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (138 bp):
AGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCAAAGGAACAGTGTCATCCTCAGACAAT
CAGACTTCCTCATCACATAGGAACCGTGTTGTCTCCAATTATCCTTAAAGATGGCTAGACGTCCT
AACCATGA
Found at i:3473737 original size:122 final size:122
Alignment explanation
Indices: 3473502--3473912 Score: 448
Period size: 122 Copynumber: 3.4 Consensus size: 122
3473492 ATCTCCAAAT
* * * ** *
3473502 TATCCAAATTGACCTC-ACTTCCTCAACGGGAATTAATAATGTCATCTTCAACAAACAATTTATC
1 TATCCAGATTGACC-CGATTTCCTCAACGAGAAGGAACAATGTCATCTTCAACAAACAATTTATC
* * *
3473566 TTAAAGCGACCATATCTCTTCAACATGGATGAGCAGAGTCGTCTTCAACACCAAATTA
65 TAAAAGCGACCAGATCTCTTCAACATGGATGAGCAGAGTCATCTTCAACACCAAATTA
* * * ** ** *
3473624 TTTCCAGATTAACCCGATTTCCTCAACGAGAATGAACAACATCATCTTCAGTAAACAATTTACCT
1 TATCCAGATTGACCCGATTTCCTCAACGAGAAGGAACAATGTCATCTTCAACAAACAATTTATCT
* * * * *
3473689 GAAAGTGACCAGATCTCTTCAACACGAATGAGTAGAGTCATCTTCAACACCAAATTA
66 AAAAGCGACCAGATCTCTTCAACATGGATGAGCAGAGTCATCTTCAACACCAAATTA
* * * * *
3473746 TCTCCAGATTGACCCGATTTCTTCAACAATAAGGAACAATGTCATCTTTAACAAACAATTTATCT
1 TATCCAGATTGACCCGATTTCCTCAACGAGAAGGAACAATGTCATCTTCAACAAACAATTTATCT
* ** * *
3473811 AAAAACGTTCAGATCTCTTCAACATGGATGAGCA-ACGTCATATTCAACACCAAGTTA
66 AAAAGCGACCAGATCTCTTCAACATGGATGAGCAGA-GTCATCTTCAACACCAAATTA
* * ** * *
3473868 TATCCATATTGACTCGAAGTCCTCAACGTGAAGGAACATTGTCAT
1 TATCCAGATTGACCCGATTTCCTCAACGAGAAGGAACAATGTCAT
3473913 ATCTGAATCA
Statistics
Matches: 236, Mismatches: 51, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
121 2 0.01
122 234 0.99
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (122 bp):
TATCCAGATTGACCCGATTTCCTCAACGAGAAGGAACAATGTCATCTTCAACAAACAATTTATCT
AAAAGCGACCAGATCTCTTCAACATGGATGAGCAGAGTCATCTTCAACACCAAATTA
Found at i:3473759 original size:61 final size:60
Alignment explanation
Indices: 3473573--3473773 Score: 156
Period size: 61 Copynumber: 3.3 Consensus size: 60
3473563 ATCTTAAAGC
* * * *
3473573 GACCATATCTCTTCAACATGGATGAGCAGAGTCGTCTTCAACACCAAATTATTTCCAGATT
1 GACCAGATCTCTTCAACA-GAATGAGCAGAGTCATCTTCAACACCAAATTATCTCCAGATT
* * * * * * * * * * * *
3473634 AACCCGATTTCCTCAACGAGAATGAACA-ACATCATCTTCAGTA-AACAATTTACCT-GAAAGT
1 GACCAGATCTCTTCAAC-AGAATGAGCAGA-GTCATCTTCA--ACACCAAATTATCTCCAGATT
*
3473695 GACCAGATCTCTTCAACACGAATGAGTAGAGTCATCTTCAACACCAAATTATCTCCAGATT
1 GACCAGATCTCTTCAACA-GAATGAGCAGAGTCATCTTCAACACCAAATTATCTCCAGATT
* *
3473756 GACCCGATTTCTTCAACA
1 GACCAGATCTCTTCAACA
3473774 ATAAGGAACA
Statistics
Matches: 101, Mismatches: 31, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
59 1 0.01
60 11 0.11
61 78 0.77
62 10 0.10
63 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (60 bp):
GACCAGATCTCTTCAACAGAATGAGCAGAGTCATCTTCAACACCAAATTATCTCCAGATT
Found at i:3475163 original size:5 final size:5
Alignment explanation
Indices: 3475153--3475185 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3475143 ACCACTAACT
3475153 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3475186 TATATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Done.