Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 18
Found at i:3099006 original size:17 final size:17
Alignment explanation
Indices: 3098981--3099014 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3098971 CTTTATCCTA
*
3098981 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
3098998 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
3099015 TCATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:3103176 original size:29 final size:31
Alignment explanation
Indices: 3103121--3103180 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
3103111 GAATTTAAGG
* *
3103121 CAAAATGGTTTTTGTACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3103152 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3103181 TTCATTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:3103344 original size:21 final size:21
Alignment explanation
Indices: 3103320--3103361 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3103310 ATTTGAATAT
**
3103320 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
3103341 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
3103362 CCATTCTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:3106132 original size:31 final size:31
Alignment explanation
Indices: 3106065--3106124 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3106055 GAATTTAAGG
*
3106065 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3106096 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3106125 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:3106216 original size:19 final size:19
Alignment explanation
Indices: 3106189--3106237 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
3106179 AATGTTTTTA
*
3106189 TGAATAGTAATTTACTA-TT
1 TGAACAGTAA-TTACTATTT
3106208 TGAACAGTACATTACTATTT
1 TGAACAGTA-ATTACTATTT
*
3106228 TAAACAGTAA
1 TGAACAGTAA
3106238 CCCGAGGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
TGAACAGTAATTACTATTT
Found at i:3106368 original size:21 final size:21
Alignment explanation
Indices: 3106342--3106383 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3106332 ATTTGAATAT
*
3106342 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTATCGATTCCC
3106363 TATGAAGAGGTATCGATTCCC
1 TATGAAGAGGTATCGATTCCC
3106384 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (21 bp):
TATGAAGAGGTATCGATTCCC
Found at i:3106445 original size:21 final size:21
Alignment explanation
Indices: 3106412--3106451 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3106402 TTTTTGCAGA
*
3106412 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
3106434 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
3106452 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:3109450 original size:85 final size:85
Alignment explanation
Indices: 3109298--3109492 Score: 239
Period size: 85 Copynumber: 2.3 Consensus size: 85
3109288 TTCTCTTGGA
** * * *
3109298 AGTGTTGATCCAACTCCTTCTGTGATTCGTAATTCGCGGGTGACACTGGATCAACTCCTTATATG
1 AGTGTTGATCCAACTCCTTCTGTGAAGCGTAATTCACGGGTGACACTGGATCAACTCATTACATG
*
3109363 ATGGAATCAAGCGTAGTGTT
66 ATGGAATAAAGCGTAGTGTT
* * * * *
3109383 AGTGTTGATTCAACTCCTTCTGTGAAGGGTAATTCATGGGTGACGCT-GATCTAACTCATTACGT
1 AGTGTTGATCCAACTCCTTCTGTGAAGCGTAATTCACGGGTGACACTGGATC-AACTCATTACAT
*
3109447 GATGGAATAAAGTGTAGTGTT
65 GATGGAATAAAGCGTAGTGTT
* * *
3109468 TGTGTTTATCCAACTCCTTATGTGA
1 AGTGTTGATCCAACTCCTTCTGTGA
3109493 TGGATGAACT
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 4 0.04
85 89 0.96
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (85 bp):
AGTGTTGATCCAACTCCTTCTGTGAAGCGTAATTCACGGGTGACACTGGATCAACTCATTACATG
ATGGAATAAAGCGTAGTGTT
Found at i:3109738 original size:79 final size:79
Alignment explanation
Indices: 3109570--3109759 Score: 220
Period size: 79 Copynumber: 2.4 Consensus size: 79
3109560 TCAATCGATC
* * ** * * *
3109570 AAATGTTAAGAAAGTTCTTCTCATTAGGACTTTTTCTATTAGGAATGATGATCGAACTCTTTCCG
1 AAATGTTGAGCAAGTTCTTCTCATTAAAACTTCTTCTATTAGGAATGATGATCCAACTCCTTCCG
* * *
3109635 CGATGGAATTGAGA
66 CGAGGGAATTCAAA
* * * *
3109649 AAATATTGAGCAAGTTCTTCTCATTATAAACTTCTTCTCTTGGGAATGTTGATCCAACTCCTTCC
1 AAATGTTGAGCAAGTTCTTCTCATTA-AAACTTCTTCTATTAGGAATGATGATCCAACTCCTTCC
*
3109714 GTGAGGGAA-TCAAA
65 GCGAGGGAATTCAAA
3109728 AAATGTTGAGCAAGTTCTTCTCATTACAAACT
1 AAATGTTGAGCAAGTTCTTCTCATTA-AAACT
3109760 CTCCTTCAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 56 0.60
80 37 0.40
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (79 bp):
AAATGTTGAGCAAGTTCTTCTCATTAAAACTTCTTCTATTAGGAATGATGATCCAACTCCTTCCG
CGAGGGAATTCAAA
Found at i:3120312 original size:94 final size:95
Alignment explanation
Indices: 3120148--3120367 Score: 293
Period size: 94 Copynumber: 2.3 Consensus size: 95
3120138 TCGATGAGGT
* * *
3120148 AGTATCGATACCATGGTAAGAGTGTCGATACCAGTAAACATTGAATCTAATTTCGGTATCGATAC
1 AGTATCGATACCATGGTAAGAGTATCGATACCAGTAAACATCGAAGCTAATTTCGGTATCGATAC
* **
3120213 CTGAAGGGGGTATCGGTGTCATAGTATAGA
66 CTGAAGGGGGTATCAGTACCATAGTATAGA
* * *
3120243 AGTATCGATACCATGGTAAGGGTATC-ATACCA-TGCAACATCGAAGCTAATTTCGGTATTGATA
1 AGTATCGATACCATGGTAAGAGTATCGATACCAGT-AAACATCGAAGCTAATTTCGGTATCGATA
*
3120306 CTTGAAGGGGGTATCAGTACCATAGTATAGA
65 CCTGAAGGGGGTATCAGTACCATAGTATAGA
* *
3120337 AGTATCGATACCAGGGT-AGTATTATCGATAC
1 AGTATCGATACCATGGTAAG-AGTATCGATAC
3120368 TATTGAGCAT
Statistics
Matches: 109, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
93 3 0.03
94 78 0.72
95 28 0.26
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.28
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGAGTATCGATACCAGTAAACATCGAAGCTAATTTCGGTATCGATAC
CTGAAGGGGGTATCAGTACCATAGTATAGA
Found at i:3122292 original size:90 final size:90
Alignment explanation
Indices: 3122138--3122310 Score: 274
Period size: 90 Copynumber: 1.9 Consensus size: 90
3122128 GGGAAATGAT
* * *
3122138 GCTTGGCCGAATAGGGAGATAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGTACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
3122203 GGGCTGTTCACATGCAAAATACATG
66 GGGCTGGTCACATGCAAAATACATG
* * *
3122228 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
3122293 GGGCTGGTCATATGCAAA
66 GGGCTGGTCACATGCAAA
3122311 GCACATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (90 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGCTGGTCACATGCAAAATACATG
Found at i:3125262 original size:20 final size:20
Alignment explanation
Indices: 3125213--3125256 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3125203 AAAGTTTTCT
*
3125213 CTTTTATTTTACTTTTCAAG
1 CTTTCATTTTACTTTTCAAG
* *
3125233 TTTTCATTTTTCTTTTCAAG
1 CTTTCATTTTACTTTTCAAG
3125253 CTTT
1 CTTT
3125257 GTTTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.64
Consensus pattern (20 bp):
CTTTCATTTTACTTTTCAAG
Found at i:3132167 original size:85 final size:86
Alignment explanation
Indices: 3132056--3132218 Score: 283
Period size: 85 Copynumber: 1.9 Consensus size: 86
3132046 CAGCCCATGA
* *
3132056 AAATCTAGAGTGCCATCGAAGGGGTCAGTCATACATTGTCCCT-CCGAAGAGACGATGCATGGGT
1 AAATCCAGAGTGCCACCGAAGGGGTCAGTCATACATTGTCCCTCCCGAAGAGACGATGCATGGGT
3132120 ATTTACAATTTTTGCCCACGG
66 ATTTACAATTTTTGCCCACGG
*
3132141 AAATCCAGAGTGCCACCGAAGGGGTCAGTCATACATTGTCCCTCCCGAAGAGATGATGCATGGGT
1 AAATCCAGAGTGCCACCGAAGGGGTCAGTCATACATTGTCCCTCCCGAAGAGACGATGCATGGGT
*
3132206 ATTTGCAATTTTT
66 ATTTACAATTTTT
3132219 CGATGACGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 41 0.56
86 32 0.44
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (86 bp):
AAATCCAGAGTGCCACCGAAGGGGTCAGTCATACATTGTCCCTCCCGAAGAGACGATGCATGGGT
ATTTACAATTTTTGCCCACGG
Found at i:3133563 original size:110 final size:116
Alignment explanation
Indices: 3133356--3133581 Score: 383
Period size: 110 Copynumber: 2.0 Consensus size: 116
3133346 TTGTTGAAAA
3133356 TTTTTGGAATGTTATGCTTGTTTGGGAACACATATGATTGTTTATGTAAGGATGTTCTTGAAAGT
1 TTTTTGGAATGTTATGCTTGTTTGGGAACACA-ATGATTGTTTATGTAAGGATGTTCTTGAAAG-
3133421 GAATAGCATGAATTGTGATTAAGTTGGTATTTTTGTGATATTCCATGATTTTGC
64 G-ATAGCATGAATTGTGATTAAGTTGGTATTTTTGTGATATTCCATGATTTTGC
3133475 TTTTTGGAATGTTATGCTTGTTTGGGAACAC-AT-A-TGTTTATGTAAGGATGTTCTTGAAA-G-
1 TTTTTGGAATGTTATGCTTGTTTGGGAACACAATGATTGTTTATGTAAGGATGTTCTTGAAAGGA
3133535 T-GCATGAATTGTGATTAAGTTGGTATTTTTGTGATATTCCATGATTT
66 TAGCATGAATTGTGATTAAGTTGGTATTTTTGTGATATTCCATGATTT
3133582 GCTGGTTGAA
Statistics
Matches: 107, Mismatches: 0, Indels: 9
0.92 0.00 0.08
Matches are distributed among these distances:
110 46 0.43
111 1 0.01
113 1 0.01
115 25 0.23
116 1 0.01
117 2 0.02
119 31 0.29
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (116 bp):
TTTTTGGAATGTTATGCTTGTTTGGGAACACAATGATTGTTTATGTAAGGATGTTCTTGAAAGGA
TAGCATGAATTGTGATTAAGTTGGTATTTTTGTGATATTCCATGATTTTGC
Found at i:3135091 original size:21 final size:20
Alignment explanation
Indices: 3135062--3135101 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3135052 AAGCTTTCTC
3135062 TTTTATTTTACTTTTCAAGT
1 TTTTATTTTACTTTTCAAGT
*
3135082 TTTTCATTTTTCTTTTCAAG
1 TTTT-ATTTTACTTTTCAAG
3135102 CTTTGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTATTTTACTTTTCAAGT
Found at i:3144058 original size:17 final size:17
Alignment explanation
Indices: 3144016--3144072 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
3144006 AGCCAATTCT
3144016 AGTATCGGTACTCAAAG
1 AGTATCGGTACTCAAAG
3144033 AGT-TCGGTACTCAAAG
1 AGTATCGGTACTCAAAG
3144049 AGTATCGGTACTCAAAG
1 AGTATCGGTACTCAAAG
3144066 AGTATCG
1 AGTATCG
3144073 CTACCCTAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.41
17 23 0.59
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (17 bp):
AGTATCGGTACTCAAAG
Found at i:3145335 original size:77 final size:79
Alignment explanation
Indices: 3145246--3145404 Score: 207
Period size: 77 Copynumber: 2.0 Consensus size: 79
3145236 TTTGAATTAA
* * * * *
3145246 TTAAACTCTTATTTAATTAATTCAAATTAAATATCCAT-TAAAGACTTATATTTC-GAATTGCAC
1 TTAAACTCTTATTTAATTAATCCAAATTAAATATCCATAAAAAGAATTATA-ATCAAAATTGCAC
3145309 TC-TTTAATGTTTAT
65 TCTTTTAATGTTTAT
* * * *
3145323 TTAATCTCTTATTTAATTACTCCAAATTAAATATCCATAAAAAGAATTGTAATCAAAATTGCATT
1 TTAAACTCTTATTTAATTAATCCAAATTAAATATCCATAAAAAGAATTATAATCAAAATTGCACT
3145388 CTTTTAATGTTTAT
66 CTTTTAATGTTTAT
3145402 TTA
1 TTA
3145405 CTATATTTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
77 37 0.53
78 18 0.26
79 15 0.21
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.45
Consensus pattern (79 bp):
TTAAACTCTTATTTAATTAATCCAAATTAAATATCCATAAAAAGAATTATAATCAAAATTGCACT
CTTTTAATGTTTAT
Found at i:3153146 original size:19 final size:20
Alignment explanation
Indices: 3153122--3153169 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3153112 AACGATTTTC
*
3153122 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3153141 TTTTGAAAGCTAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3153161 TTTTGAAAA
1 TTTTGAAAA
3153170 ATGATTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3154313 original size:21 final size:22
Alignment explanation
Indices: 3154287--3154332 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3154277 CAACAGTTGG
3154287 TAACAATTGATATCATTTT-AT
1 TAACAATTGATATCATTTTCAT
* *
3154308 TAACAATTGGTATCTTTTTCAT
1 TAACAATTGATATCATTTTCAT
3154330 TAA
1 TAA
3154333 ACATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (22 bp):
TAACAATTGATATCATTTTCAT
Found at i:3160171 original size:14 final size:14
Alignment explanation
Indices: 3160143--3160175 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3160133 ATTCTATCCT
3160143 CCAAACCCAAATAC
1 CCAAACCCAAATAC
3160157 CGCAAACCC-AATAC
1 C-CAAACCCAAATAC
3160171 CCAAA
1 CCAAA
3160176 ATCACTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 7 0.39
15 7 0.39
ACGTcount: A:0.48, C:0.42, G:0.03, T:0.06
Consensus pattern (14 bp):
CCAAACCCAAATAC
Found at i:3167840 original size:17 final size:18
Alignment explanation
Indices: 3167811--3167844 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3167801 TTGGTTATTA
3167811 TTTATTCTAAAAAAGATT
1 TTTATTCTAAAAAAGATT
3167829 TTTATT-TAAAAAAGAT
1 TTTATTCTAAAAAAGAT
3167845 ATCTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTATTCTAAAAAAGATT
Found at i:3168394 original size:20 final size:20
Alignment explanation
Indices: 3168355--3168394 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3168345 TTCAATAGAT
* *
3168355 AAAATTCTTTTAAAATAAAA
1 AAAATTATTTTAAAAGAAAA
*
3168375 AAAATTATTTTATAAGAAAA
1 AAAATTATTTTAAAAGAAAA
3168395 GGACAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAATTATTTTAAAAGAAAA
Found at i:3169508 original size:22 final size:21
Alignment explanation
Indices: 3169411--3169497 Score: 65
Period size: 20 Copynumber: 4.3 Consensus size: 21
3169401 ATAACCAACG
*
3169411 AATTCGCAACGCG-ATTT-CA
1 AATTCGCAACACGAATTTCCA
* *
3169430 AATTCGCAATACGAA-CTCCA
1 AATTCGCAACACGAATTTCCA
* *** *
3169450 ATTTTATAACAC-AGTTTCCA
1 AATTCGCAACACGAATTTCCA
3169470 AATTCGCAACACGAATTTCTCA
1 AATTCGCAACACGAATTTC-CA
3169492 AATTCG
1 AATTCG
3169498 TAATTCGAAT
Statistics
Matches: 48, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
19 13 0.27
20 22 0.46
21 5 0.10
22 8 0.17
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (21 bp):
AATTCGCAACACGAATTTCCA
Found at i:3169719 original size:49 final size:50
Alignment explanation
Indices: 3169658--3169752 Score: 156
Period size: 49 Copynumber: 1.9 Consensus size: 50
3169648 AGAGTTGTGT
*
3169658 ATTTTTTCTACCGTGTTTACCTACATCGGTAATTGAATT-CGAAATGCGG
1 ATTTTTTATACCGTGTTTACCTACATCGGTAATTGAATTACGAAATGCGG
* *
3169707 ATTTTTTATACCGTGTTTACCTATATCGGTAATTGAGTTACGAAAT
1 ATTTTTTATACCGTGTTTACCTACATCGGTAATTGAATTACGAAAT
3169753 TGACGAATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 36 0.86
50 6 0.14
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (50 bp):
ATTTTTTATACCGTGTTTACCTACATCGGTAATTGAATTACGAAATGCGG
Found at i:3169772 original size:22 final size:23
Alignment explanation
Indices: 3169742--3169812 Score: 103
Period size: 22 Copynumber: 3.2 Consensus size: 23
3169732 TCGGTAATTG
*
3169742 AGTTACGAAATTGACGAATTCGA
1 AGTTGCGAAATTGACGAATTCGA
*
3169765 A-TTGCGAAATTGGCGAATTC-A
1 AGTTGCGAAATTGACGAATTCGA
3169786 AGTTGCGAAATTGACGAATTCG-
1 AGTTGCGAAATTGACGAATTCGA
3169808 AGTTG
1 AGTTG
3169813 TGGATTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 2 0.05
22 40 0.93
23 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (23 bp):
AGTTGCGAAATTGACGAATTCGA
Found at i:3170524 original size:2 final size:2
Alignment explanation
Indices: 3170502--3170544 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
3170492 AATTTGGTGA
*
3170502 AT AT -T AT AT TT AT AT -T 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
3170542 AT A
1 AT A
3170545 GAGTAGGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3172512 original size:3 final size:3
Alignment explanation
Indices: 3172411--3172494 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
3172401 ATATGTTTTG
3172411 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3172459 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3172495 GGTTTACCTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3173632 original size:15 final size:15
Alignment explanation
Indices: 3173612--3173640 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3173602 TCGTGTACAT
3173612 ATGTTTCATATAATA
1 ATGTTTCATATAATA
3173627 ATGTTTCATATAAT
1 ATGTTTCATATAAT
3173641 TTTTTATAAA
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:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
ATGTTTCATATAATA
Found at i:3178742 original size:22 final size:23
Alignment explanation
Indices: 3178710--3178776 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
3178700 CTAAACTATC
*
3178710 GAAAACATGTCA-AAAGGCATAA
1 GAAAACGTGTCACAAAGGCATAA
3178732 GAAAACGTGTCACAAAGGCATAA
1 GAAAACGTGTCACAAAGGCATAA
* *
3178755 GAAAACGTGTCATAAAGACATA
1 GAAAACGTGTCACAAAGGCATA
3178777 TTTAAACGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 11 0.27
23 30 0.73
ACGTcount: A:0.51, C:0.15, G:0.19, T:0.15
Consensus pattern (23 bp):
GAAAACGTGTCACAAAGGCATAA
Found at i:3179674 original size:156 final size:158
Alignment explanation
Indices: 3179452--3179740 Score: 431
Period size: 157 Copynumber: 1.8 Consensus size: 158
3179442 CAATTCATCA
* * * * * *
3179452 TTTATTTTAAGTTCGTTTTTTACCAAATTTAAATTACATGCTCCTAAACCATTATAGAATATATA
1 TTTATTTTAAGTTCGTATTTTACCAAATTTAAATCACATGCTCCTAAACCATCAAAAAATACATA
3179517 TGTACTTTCAATTCCAC-TTTTGATAAAAAAATTTCTATTTTTCAATTTAGTCCCTCAAATTTTT
66 TGTACTTTCAATTCCACTTTTTGATAAAAAAATTTCTATTTTTCAATTTAGTCCCTCAAATTTTT
3179581 ATAATGTTTTTATTTCTTCAATTACTAC
131 ATAATGTTTTTATTTCTTCAATTACTAC
*
3179609 TTTATTTTAAGTAT-G-ATTTTACCAAATTTGAATCACATGCTCCTAAACCATCAAAAAATACAT
1 TTTATTTTAAGT-TCGTATTTTACCAAATTTAAATCACATGCTCCTAAACCATCAAAAAATACAT
* * * * * *
3179672 ATGTATTTTGAATTCCTCTTTTTGATAACAAATTTTCTATTTTTCAATTTAGTCCCTCAATTTTT
65 ATGTACTTTCAATTCCACTTTTTGATAAAAAAATTTCTATTTTTCAATTTAGTCCCTCAAATTTT
3179737 TATA
130 TATA
3179741 TTTTCCTTAT
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
156 56 0.48
157 60 0.51
158 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.47
Consensus pattern (158 bp):
TTTATTTTAAGTTCGTATTTTACCAAATTTAAATCACATGCTCCTAAACCATCAAAAAATACATA
TGTACTTTCAATTCCACTTTTTGATAAAAAAATTTCTATTTTTCAATTTAGTCCCTCAAATTTTT
ATAATGTTTTTATTTCTTCAATTACTAC
Found at i:3179795 original size:140 final size:139
Alignment explanation
Indices: 3179625--3179889 Score: 388
Period size: 140 Copynumber: 1.9 Consensus size: 139
3179615 TTAAGTATGA
* * *
3179625 TTTTACCAAATTTGAATCACATGCTCCTAAACCATCAAAAAATACATATGTATTTTGAATTCCTC
1 TTTTACCAAATTTGAATCACATGCTCCTAAACCATCAAAAAACACATATGTACTTTCAATTCCTC
* *
3179690 TTTTTGATAACAAATTTTCTATTTTTCAATTTAGTCCCTCAATTTTTTATATTTTCCTTATCTTA
66 TTTTTGATAA-AAATTTTCTATTTTTCAAGTTAGTCCCTCAATTTTTTATAATTTCCTTATCTTA
3179755 AGTATGTTTT
130 AGTATGTTTT
* * ** *
3179765 TTTTACCAAATTTGAA-CTATATGTTCCTAAACCATCGTACAACACATATGTACTTTCAATTCCT
1 TTTTACCAAATTTGAATC-ACATGCTCCTAAACCATCAAAAAACACATATGTACTTTCAATTCCT
***
3179829 CTTTTTGATAATTTTTTTCTATTTTTCAAGTTAGTCCCTCAATTTTTTATAATTTCCTTAT
65 CTTTTTGATAAAAATTTTCTATTTTTCAAGTTAGTCCCTCAATTTTTTATAATTTCCTTAT
3179890 TTCTTCACTC
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
139 46 0.41
140 65 0.59
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.48
Consensus pattern (139 bp):
TTTTACCAAATTTGAATCACATGCTCCTAAACCATCAAAAAACACATATGTACTTTCAATTCCTC
TTTTTGATAAAAATTTTCTATTTTTCAAGTTAGTCCCTCAATTTTTTATAATTTCCTTATCTTAA
GTATGTTTT
Found at i:3180866 original size:22 final size:22
Alignment explanation
Indices: 3180838--3180881 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3180828 AATTTTAATG
*
3180838 ATTTTTCGTAAATGTTTGTTCA
1 ATTTTTCATAAATGTTTGTTCA
3180860 ATTTTTCATAAATGTTTGTTCA
1 ATTTTTCATAAATGTTTGTTCA
3180882 TCATAATGAA
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:0.09, G:0.11, T:0.55
Consensus pattern (22 bp):
ATTTTTCATAAATGTTTGTTCA
Found at i:3181882 original size:22 final size:21
Alignment explanation
Indices: 3181857--3181897 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3181847 TTAAAAATTA
3181857 TAAATGAAATACCGATACTCAT
1 TAAA-GAAATACCGATACTCAT
* *
3181879 TAAAGGAGTACCGATACTC
1 TAAAGAAATACCGATACTC
3181898 CCTGTCCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (21 bp):
TAAAGAAATACCGATACTCAT
Found at i:3185954 original size:51 final size:52
Alignment explanation
Indices: 3185878--3186000 Score: 203
Period size: 51 Copynumber: 2.4 Consensus size: 52
3185868 TATAGTAGAT
*
3185878 TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTT-TATCTTGC
1 TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTTCGATCTTGC
* *
3185929 TTGGGATATCTCGGCGTCTTCAGGGTTGAATCAGATTTTTTTTCGGTCTTGC
1 TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTTCGATCTTGC
*
3185981 TTGGGATCTCTCGGCGTCTT
1 TTGGGATATCTCGGCGTCTT
3186001 TAAGGTGTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 42 0.63
52 25 0.37
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.42
Consensus pattern (52 bp):
TTGGGATATCTCGGCGTCTTCAGGGTTGAACCAGATTTTTTTTCGATCTTGC
Found at i:3186483 original size:13 final size:13
Alignment explanation
Indices: 3186467--3186526 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
3186457 TAACTGTAAA
3186467 AAATAAAATAATT
1 AAATAAAATAATT
3186480 AAATAAAATAATT
1 AAATAAAATAATT
* *
3186493 AAATAATACAA-T
1 AAATAAAATAATT
*
3186505 -AATTAAATAATT
1 AAATAAAATAATT
3186517 AAATAAAATA
1 AAATAAAATA
3186527 CTAACAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 7 0.18
12 2 0.05
13 30 0.77
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:3186485 original size:8 final size:8
Alignment explanation
Indices: 3186472--3186522 Score: 65
Period size: 8 Copynumber: 6.8 Consensus size: 8
3186462 GTAAAAAATA
3186472 AAATAATT
1 AAATAATT
3186480 AAAT-A--
1 AAATAATT
3186485 AAATAATT
1 AAATAATT
3186493 AAATAA-T
1 AAATAATT
3186500 ACAATAATT
1 A-AATAATT
3186509 AAATAATT
1 AAATAATT
3186517 AAATAA
1 AAATAA
3186523 AATACTAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 3 0.08
8 28 0.74
9 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATAATT
Found at i:3186500 original size:16 final size:16
Alignment explanation
Indices: 3186463--3186522 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
3186453 TTTATAACTG
*
3186463 TAAAAAATAAAATAAT
1 TAAATAATAAAATAAT
3186479 T--A-AATAAAATAAT
1 TAAATAATAAAATAAT
*
3186492 TAAATAATACAATAAT
1 TAAATAATAAAATAAT
*
3186508 TAAATAATTAAATAA
1 TAAATAATAAAATAA
3186523 AATACTAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.32
14 1 0.03
15 1 0.03
16 24 0.63
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATAATAAAATAAT
Found at i:3186536 original size:24 final size:24
Alignment explanation
Indices: 3186484--3186537 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3186474 ATAATTAAAT
* *
3186484 AAAATAATTAAATAATACAATAAT
1 AAAATAATTAAATAAAACAATAAC
* * *
3186508 TAAATAATTAAATAAAATACTAAC
1 AAAATAATTAAATAAAACAATAAC
3186532 AAAATA
1 AAAATA
3186538 TGATTAATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (24 bp):
AAAATAATTAAATAAAACAATAAC
Found at i:3188503 original size:101 final size:96
Alignment explanation
Indices: 3188345--3188568 Score: 234
Period size: 101 Copynumber: 2.2 Consensus size: 96
3188335 CATTCATAAT
* **
3188345 TCAATTATGAATTATTAGTATAGATACTAAAGCTCAGGCCTAATTGTCAGTTTCAAATGCG-GCA
1 TCAATTATGAATTA-T-G-A-ACATACTAAAGCTCAGGCCTAATTGTCAGCATCAAATGCGAG-A
* *
3188409 AACCATTCACTAAGTAAAACAACCAGTTTCATGAAAA
61 AACCATTCACCAA-TAAAACAACCAGTTCCATGAAAA
* * *
3188446 TCAATTATGAATTATGAATATACTAAAGCTCAGGCCAAATTAATTGTCGGCATCAAATTCGAGAA
1 TCAATTATGAATTATGAACATACTAAAGCTCAGGCC----TAATTGTCAGCATCAAATGCGAGAA
* **
3188511 ACCATTCACCAATAAATCAACCAGTTCCATGAATT
62 ACCATTCACCAATAAAACAACCAGTTCCATGAAAA
* *
3188546 TCAATTATGTATAATGAACATAC
1 TCAATTATGAATTATGAACATAC
3188569 CAAAATTAAG
Statistics
Matches: 105, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
97 18 0.17
98 1 0.01
99 1 0.01
100 40 0.38
101 44 0.42
102 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (96 bp):
TCAATTATGAATTATGAACATACTAAAGCTCAGGCCTAATTGTCAGCATCAAATGCGAGAAACCA
TTCACCAATAAAACAACCAGTTCCATGAAAA
Found at i:3188563 original size:100 final size:97
Alignment explanation
Indices: 3188368--3188568 Score: 235
Period size: 100 Copynumber: 2.0 Consensus size: 97
3188358 ATTAGTATAG
** *
3188368 ATACTAAAGCTCAGGCCTAATTGTCAGTTTCAAATGCGGCAAACCATTCACTAAGTAAAACAACC
1 ATACTAAAGCTCAGGCCTAATTGTCAGCATCAAATGCGGCAAACCATTCACCAAGTAAAACAACC
* * *
3188433 AGTTTCATGAAAATCAATTATGAATTATGAAT
66 AGTTCCATGAAAATCAATTATGAATAATGAAC
* * *
3188465 ATACTAAAGCTCAGGCCAAATTAATTGTCGGCATCAAATTCGAG-AAACCATTCACCAA-TAAAT
1 ATACTAAAGCTCAGGCC----TAATTGTCAGCATCAAATGCG-GCAAACCATTCACCAAGTAAAA
** *
3188528 CAACCAGTTCCATGAATTTCAATTATGTATAATGAAC
61 CAACCAGTTCCATGAAAATCAATTATGAATAATGAAC
3188565 ATAC
1 ATAC
3188569 CAAAATTAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
97 17 0.20
100 39 0.45
101 30 0.34
102 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (97 bp):
ATACTAAAGCTCAGGCCTAATTGTCAGCATCAAATGCGGCAAACCATTCACCAAGTAAAACAACC
AGTTCCATGAAAATCAATTATGAATAATGAAC
Found at i:3190366 original size:51 final size:51
Alignment explanation
Indices: 3190300--3190399 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
3190290 ATGTTTACAC
* *
3190300 TTATATAGGATTATATCAATTTAAACTATAATAAAATTA-AAAAAATATTA
1 TTATATAGAATTATATCAATTTAAACTATAATAAAACTATAAAAAATATTA
*
3190350 TTATATATGAATTATATCAATTTAAATTATAATAAAACTATAAAAAATAT
1 TTATATA-GAATTATATCAATTTAAACTATAATAAAACTATAAAAAATAT
3190400 AAATAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 7 0.16
51 29 0.64
52 9 0.20
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (51 bp):
TTATATAGAATTATATCAATTTAAACTATAATAAAACTATAAAAAATATTA
Found at i:3190398 original size:15 final size:14
Alignment explanation
Indices: 3190388--3190430 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 14
3190378 ATAATAAAAC
3190388 TATAAAAAATATAA
1 TATAAAAAATATAA
3190402 -ATAAAAAATATAA
1 TATAAAAAATATAA
3190415 TTATAATAAAAATATA
1 -TAT-A-AAAAATATA
3190431 TTTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.52
15 2 0.08
16 1 0.04
17 9 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TATAAAAAATATAA
Found at i:3201349 original size:25 final size:25
Alignment explanation
Indices: 3201321--3201370 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3201311 CTACAACTGA
*
3201321 ACTTAATTTATTTACCTTTCAAAGT
1 ACTTAATTTAATTACCTTTCAAAGT
3201346 ACTTAATTTAATTACCTTTCAAAGT
1 ACTTAATTTAATTACCTTTCAAAGT
3201371 TCAATCTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.46
Consensus pattern (25 bp):
ACTTAATTTAATTACCTTTCAAAGT
Found at i:3206453 original size:21 final size:21
Alignment explanation
Indices: 3206429--3206482 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
3206419 TTGGAAGGGT
*
3206429 AGTATCGATACTCATTCGTAG
1 AGTATCGATACTCAATCGTAG
* *
3206450 AGTATCAATAC-CAATGGTAG
1 AGTATCGATACTCAATCGTAG
* *
3206470 ATTATAGATACTC
1 AGTATCGATACTC
3206483 CCCATAGAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTCAATCGTAG
Found at i:3207674 original size:45 final size:45
Alignment explanation
Indices: 3207595--3207716 Score: 140
Period size: 45 Copynumber: 2.7 Consensus size: 45
3207585 TACTTTTATA
* *
3207595 CCGATAATGCACCCATATGCA-T-TTCAGCTATGGCACCCTTTCATG
1 CCGATAATGCACCCATATGCATTATTC--TTTTGGCACCCTTTCATG
* *
3207640 CCGATAATGCACCCATATGCATTATTCTTTTGGCATCCTTTGATG
1 CCGATAATGCACCCATATGCATTATTCTTTTGGCACCCTTTCATG
* * **
3207685 CCAATAATTCACCCATATATATTATTCTTTTG
1 CCGATAATGCACCCATATGCATTATTCTTTTG
3207717 TTCTTTCATT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
45 63 0.94
46 1 0.01
47 3 0.04
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (45 bp):
CCGATAATGCACCCATATGCATTATTCTTTTGGCACCCTTTCATG
Found at i:3208036 original size:32 final size:31
Alignment explanation
Indices: 3207968--3208036 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
3207958 TTGGTATTCA
* ** *
3207968 GGTCAGATTTTTATTAAAAAATTTCGGGATC
1 GGTCGGATTTTTATTAAAAAAAATCAGGATC
* *
3207999 GGTCGGATTTTTTTTAAAAAAAATCAGGTTC
1 GGTCGGATTTTTATTAAAAAAAATCAGGATC
3208030 GAGTCGG
1 G-GTCGG
3208037 GTCGGGTCGG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.36
Consensus pattern (31 bp):
GGTCGGATTTTTATTAAAAAAAATCAGGATC
Found at i:3208122 original size:16 final size:18
Alignment explanation
Indices: 3208090--3208122 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
3208080 GTTTAGGGTG
3208090 AAAAATACCCACCGACCC
1 AAAAATACCCACCGACCC
3208108 AAAAA-ACCC-CCGACC
1 AAAAATACCCACCGACC
3208123 TGACCCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.45, C:0.45, G:0.06, T:0.03
Consensus pattern (18 bp):
AAAAATACCCACCGACCC
Found at i:3208144 original size:25 final size:26
Alignment explanation
Indices: 3208104--3208160 Score: 98
Period size: 25 Copynumber: 2.2 Consensus size: 26
3208094 ATACCCACCG
*
3208104 ACCCAAAAAACCCCCGACCTGACCCA
1 ACCCAAAAAACACCCGACCTGACCCA
3208130 ACCCAAAAAA-ACCCGACCTGACCCA
1 ACCCAAAAAACACCCGACCTGACCCA
3208155 ACCCAA
1 ACCCAA
3208161 CTTGACCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.42, C:0.47, G:0.07, T:0.04
Consensus pattern (26 bp):
ACCCAAAAAACACCCGACCTGACCCA
Found at i:3208233 original size:32 final size:33
Alignment explanation
Indices: 3208176--3208237 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
3208166 CCCATGGCCA
* *
3208176 TCCCTTGTTCTCTTGTTCAGGTCGGGTGGAGGT
1 TCCCTTGTTCTCTGGGTCAGGTCGGGTGGAGGT
3208209 TCCCTTGTTCT-TGGGTCAGGTCGGGTGGA
1 TCCCTTGTTCTCTGGGTCAGGTCGGGTGGA
3208238 CCAAAAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.06, C:0.21, G:0.35, T:0.37
Consensus pattern (33 bp):
TCCCTTGTTCTCTGGGTCAGGTCGGGTGGAGGT
Found at i:3209123 original size:20 final size:20
Alignment explanation
Indices: 3209085--3209121 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3209075 TGTTTTAAAA
*
3209085 TGGTATCGATACCTTCCCTT
1 TGGTATCGATACCTCCCCTT
3209105 TGGTATCGATA-CTCCCC
1 TGGTATCGATACCTCCCC
3209122 CTCCAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACCTCCCCTT
Found at i:3213404 original size:21 final size:20
Alignment explanation
Indices: 3213380--3213432 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
3213370 TTGGAAGGGT
3213380 AGTATCGATACTAATTCGTAG
1 AGTATCGATACTAATT-GTAG
* *
3213401 AGTATCAATACCAATTGTAG
1 AGTATCGATACTAATTGTAG
* *
3213421 ATTATAGATACT
1 AGTATCGATACT
3213433 CCCCATAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTAATTGTAG
Found at i:3214606 original size:45 final size:45
Alignment explanation
Indices: 3214499--3214753 Score: 311
Period size: 45 Copynumber: 5.6 Consensus size: 45
3214489 ATTCATGTTT
* * * * *
3214499 ATAATGCA-CCATTATGCATT-TTCAATTATAGCATACTTTTATTCCG
1 ATAATGCACCCA-TATGCATTATTC--TTTTGGCATCCTTTCATGCCG
** * *
3214545 ATAATGCACCTGTATGCATT-TTAGC-TATGGCACCCTTTCATGCCG
1 ATAATGCACCCATATGCATTATT--CTTTTGGCATCCTTTCATGCCG
*
3214590 ATAATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCG
*
3214635 ATAATGCACCCATATGCATTATTCTTTTGGCATTCTTTCATGCCG
1 ATAATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCG
* *
3214680 ATAATGCACCCATATGCATTATTCTTTTGGCATCATTTCATGCCA
1 ATAATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCG
*
3214725 ATAATGCACCCATATGTATTATTCTTTTG
1 ATAATGCACCCATATGCATTATTCTTTTG
3214754 TTCTTTCGTT
Statistics
Matches: 186, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
44 1 0.01
45 163 0.88
46 20 0.11
47 1 0.01
48 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCG
Found at i:3215571 original size:16 final size:15
Alignment explanation
Indices: 3215535--3215571 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
3215525 GGTTTCAGAT
3215535 TCAGATTCCAATTCC
1 TCAGATTCCAATTCC
3215550 TACAGATTCCAATTCGC
1 T-CAGATTCCAATTC-C
3215567 TCAGA
1 TCAGA
3215572 AACATTCCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 17 0.85
17 2 0.10
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (15 bp):
TCAGATTCCAATTCC
Found at i:3216110 original size:20 final size:20
Alignment explanation
Indices: 3216072--3216108 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3216062 TGTTTTAAAA
*
3216072 TGGTATCGATACCTTCCCTT
1 TGGTATCGATACCTCCCCTT
3216092 TGGTATCGATA-CTCCCC
1 TGGTATCGATACCTCCCC
3216109 CTCCAATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.35
Consensus pattern (20 bp):
TGGTATCGATACCTCCCCTT
Found at i:3218251 original size:29 final size:30
Alignment explanation
Indices: 3218182--3218240 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3218172 CAATTTAAGG
3218182 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
3218212 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3218241 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:3218388 original size:20 final size:19
Alignment explanation
Indices: 3218363--3218452 Score: 64
Period size: 20 Copynumber: 4.8 Consensus size: 19
3218353 CACCTGCACT
3218363 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATC-TGC
*
3218383 AATGCATCCATGCA-CT-C
1 AATGCATCGATGCATCTGC
* *
3218400 AA-ACATCGAATGCA-CT-T
1 AATGCATCG-ATGCATCTGC
*
3218417 AGTGCATCGATGCATCCTGC
1 AATGCATCGATGCAT-CTGC
* *
3218437 CATGCATCCATGCATC
1 AATGCATCGATGCATC
3218453 CATGCAGGCT
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
16 4 0.07
17 16 0.29
18 6 0.11
19 4 0.07
20 25 0.45
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (19 bp):
AATGCATCGATGCATCTGC
Found at i:3218850 original size:34 final size:32
Alignment explanation
Indices: 3218811--3218880 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3218801 TTTTGTAAAG
* *
3218811 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3218845 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
3218877 GGGA
1 GGGA
3218881 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (32 bp):
GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3219762 original size:19 final size:20
Alignment explanation
Indices: 3219738--3219785 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3219728 AATGATTTTC
*
3219738 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3219757 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3219777 TTTTGAAAA
1 TTTTGAAAA
3219786 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3220309 original size:29 final size:30
Alignment explanation
Indices: 3220240--3220298 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3220230 CAATTTAAGG
3220240 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
*
3220270 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3220299 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:3220406 original size:13 final size:13
Alignment explanation
Indices: 3220388--3220425 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3220378 AGTGCATCCA
* *
3220388 TGCATCCCTGTAG
1 TGCATCCATGCAG
3220401 TGCATCCATGCAG
1 TGCATCCATGCAG
3220414 TGCATCCATGCA
1 TGCATCCATGCA
3220426 CCTGTACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:3220912 original size:34 final size:32
Alignment explanation
Indices: 3220873--3220942 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3220863 TTTTGTAAAG
* *
3220873 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3220907 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3220939 GGGA
1 GGGA
3220943 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3224888 original size:32 final size:31
Alignment explanation
Indices: 3224819--3224879 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
3224809 AACATGGAAA
3224819 AAATAAAA--AAATCAAATTAAAAAATAAATG
1 AAATAAAAGGAAATCAAATTAAAAAATAAA-G
*
3224849 AAATAAAAGGAAATTAAATTAATAAAATAAA
1 AAATAAAAGGAAATCAAATTAA-AAAATAAA
3224880 AATGTAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
32 11 0.41
33 8 0.30
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (31 bp):
AAATAAAAGGAAATCAAATTAAAAAATAAAG
Found at i:3229978 original size:19 final size:20
Alignment explanation
Indices: 3229954--3230004 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3229944 AATTGAATTA
*
3229954 GTATCGATACTAA-AGTGAG
1 GTATCGATACTAAGAGTAAG
*
3229973 GTATCGATACCAAGAGTAAG
1 GTATCGATACTAAGAGTAAG
3229993 GTATCGATACTA
1 GTATCGATACTA
3230005 TTATTAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (20 bp):
GTATCGATACTAAGAGTAAG
Found at i:3230673 original size:23 final size:22
Alignment explanation
Indices: 3230643--3230738 Score: 97
Period size: 23 Copynumber: 4.3 Consensus size: 22
3230633 GTCGAGGGTT
** *
3230643 CTATGTGGTATTTCAGGACAAAC
1 CTATGTGGTCCTTC-GGACAAAA
3230666 CTATGTGGTCCTTCGAGACAAAA
1 CTATGTGGTCCTTCG-GACAAAA
*
3230689 CTATGTGGTCCTTGGGGACAAAA
1 CTATGTGGTCCTT-CGGACAAAA
*
3230712 CTATGTGGTCATTCGAGA-AAAA
1 CTATGTGGTCCTTCG-GACAAAA
3230734 -TATGT
1 CTATGT
3230739 TGCACTTCGG
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.08
22 6 0.09
23 52 0.81
24 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGACAAAA
Found at i:3230696 original size:46 final size:45
Alignment explanation
Indices: 3230643--3230738 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 45
3230633 GTCGAGGGTT
* * *
3230643 CTATGTGGTATTTCAGGACAAACCTATGTGGTCCTTCGAGACAAAA
1 CTATGTGGTACTTCAGGACAAAACTATGTGGTCATTCGAGA-AAAA
* **
3230689 CTATGTGGTCCTTGGGGACAAAACTATGTGGTCATTCGAGAAAAA
1 CTATGTGGTACTTCAGGACAAAACTATGTGGTCATTCGAGAAAAA
3230734 -TATGT
1 CTATGT
3230739 TGCACTTCGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
44 5 0.11
45 4 0.09
46 35 0.80
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (45 bp):
CTATGTGGTACTTCAGGACAAAACTATGTGGTCATTCGAGAAAAA
Found at i:3230737 original size:21 final size:23
Alignment explanation
Indices: 3230659--3230738 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
3230649 GGTATTTCAG
*
3230659 GACAAACCTATGTGGTCCTTCGA
1 GACAAAACTATGTGGTCCTTCGA
* *
3230682 GACAAAACTATGTGGTCCTTGGG
1 GACAAAACTATGTGGTCCTTCGA
*
3230705 GACAAAACTATGTGGTCATTCGA
1 GACAAAACTATGTGGTCCTTCGA
3230728 GA-AAAA-TATGT
1 GACAAAACTATGT
3230739 TGCACTTCGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.10
22 4 0.08
23 42 0.82
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (23 bp):
GACAAAACTATGTGGTCCTTCGA
Found at i:3233432 original size:23 final size:22
Alignment explanation
Indices: 3233401--3233449 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
3233391 CTAGTATAAA
3233401 TGCACGAAGTGCCACGTAGAAT
1 TGCACGAAGTGCCACGTAGAAT
*
3233423 TGCACCGAAGTGCCGCGTAGAAT
1 TGCA-CGAAGTGCCACGTAGAAT
3233446 TGCA
1 TGCA
3233450 TCAAAGTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (22 bp):
TGCACGAAGTGCCACGTAGAAT
Found at i:3233456 original size:23 final size:23
Alignment explanation
Indices: 3233407--3233456 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3233397 TAAATGCACG
*
3233407 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCA
* *
3233430 AAGTGCCGCGTAGAATTGCATCA
1 AAGTGCCACGTAGAATTGCACCA
3233453 AAGT
1 AAGT
3233457 ACTATATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCA
Found at i:3244600 original size:22 final size:19
Alignment explanation
Indices: 3244574--3244630 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
3244564 ATAGGGCAGA
3244574 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCC---AAG
* *
3244596 GGGAACCGATTCCCTCCAAG
1 GGGAATCGATACCC-CCAAG
*
3244616 GGGAATTGATACCCC
1 GGGAATCGATACCCC
3244631 ATGAGGGTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
22 12 0.41
23 2 0.07
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (19 bp):
GGGAATCGATACCCCCAAG
Found at i:3248823 original size:21 final size:21
Alignment explanation
Indices: 3248799--3248854 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
3248789 TATTTGAGAG
*
3248799 TGCATTGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
3248820 TGCATCGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
*
3248841 TGCATCGATGCACA
1 TGCATCGATACACA
3248855 CAACCCAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACATTGAAGA
Found at i:3258767 original size:13 final size:12
Alignment explanation
Indices: 3258749--3258788 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
3258739 CAGGGAAGAA
3258749 TTATATTAAATTT
1 TTATATT-AATTT
3258762 TTATA-TAATTT
1 TTATATTAATTT
3258773 TTATATT--TTT
1 TTATATTAATTT
3258783 TTATAT
1 TTATAT
3258789 ATTTTAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.35
11 10 0.38
12 2 0.08
13 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATATTAATTT
Found at i:3258771 original size:21 final size:19
Alignment explanation
Indices: 3258754--3258793 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3258744 AAGAATTATA
3258754 TTAAATTTTTATATAATTT
1 TTAAATTTTTATATAATTT
* *
3258773 TTATATTTTTTTATATATTT
1 TTAAATTTTTATATA-ATTT
3258793 T
1 T
3258794 AGTAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTAAATTTTTATATAATTT
Found at i:3258773 original size:11 final size:10
Alignment explanation
Indices: 3258758--3258793 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3258748 ATTATATTAA
3258758 ATTTTTATAT
1 ATTTTTATAT
3258768 AATTTTTATAT
1 -ATTTTTATAT
*
3258779 TTTTTTATAT
1 ATTTTTATAT
3258789 ATTTT
1 ATTTT
3258794 AGTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:3260994 original size:31 final size:30
Alignment explanation
Indices: 3260959--3261042 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
3260949 ATGTGGAGGG
* * *
3260959 AGATGCTGACGTGGCATGTCCATATCATAGT
1 AGATGCTGACGTGGCATGTCCACAT-AGACT
* *
3260990 AGATGATGATGTGGCA-GATCCACATAGACT
1 AGATGCTGACGTGGCATG-TCCACATAGACT
* *
3261020 AAATGCTGACGTGGCATATCCAC
1 AGATGCTGACGTGGCATGTCCAC
3261043 GTGTGATGTC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 22 0.52
31 20 0.48
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (30 bp):
AGATGCTGACGTGGCATGTCCACATAGACT
Found at i:3261390 original size:19 final size:19
Alignment explanation
Indices: 3261368--3261429 Score: 92
Period size: 19 Copynumber: 3.4 Consensus size: 19
3261358 TTATTTGAGT
3261368 AAATTTAAATTCATATTTA
1 AAATTTAAATTCATATTTA
3261387 AAATTTAAATTCATATTTA
1 AAATTTAAATTCATATTTA
* *
3261406 AAATTTTAATT-A-ATTTT
1 AAATTTAAATTCATATTTA
3261423 AAATTTA
1 AAATTTA
3261430 TAAACTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.25
18 1 0.03
19 29 0.73
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTAAATTCATATTTA
Found at i:3262917 original size:19 final size:18
Alignment explanation
Indices: 3262877--3262918 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3262867 TTTAAGTTTA
*
3262877 TAAA-TTTAAAATTAATT
1 TAAATTTTAAAATGAATT
*
3262894 AAAATTTTAAATATGAATT
1 TAAATTTTAAA-ATGAATT
3262913 TAAATT
1 TAAATT
3262919 GACTCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 6 0.30
19 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAATGAATT
Found at i:3268501 original size:15 final size:15
Alignment explanation
Indices: 3268481--3268510 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3268471 GAGATCCAAG
3268481 GCAATGTGGAGTGGC
1 GCAATGTGGAGTGGC
3268496 GCAATGTGGAGTGGC
1 GCAATGTGGAGTGGC
3268511 CCAACCAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.47, T:0.20
Consensus pattern (15 bp):
GCAATGTGGAGTGGC
Found at i:3270462 original size:13 final size:14
Alignment explanation
Indices: 3270439--3270468 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3270429 TTCCCATTAC
3270439 AGACGTGCATATGA
1 AGACGTGCATATGA
3270453 AGAC-TGCATATGA
1 AGACGTGCATATGA
3270466 AGA
1 AGA
3270469 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:3272751 original size:205 final size:203
Alignment explanation
Indices: 3272364--3272771 Score: 782
Period size: 205 Copynumber: 2.0 Consensus size: 203
3272354 GGATTACCAC
3272364 CTCAGAGGACTCATGATCATGCTATTCCTCTAAAGCCTAATGCTACACCTGTTAATCTGAGACCT
1 CTCAGAGGACTCATGATCATGCTATTCCTCTAAAGCCTAATGCTACACCTGTTAATCTGAGACCT
3272429 ACAGGTTTCCTCATAATCAGAAGATGAGGTAGAAAAACAGATTGCCATATGCTTTCTTCTTCTGT
66 ACAGGTTTCCTCATAATCAGAAGATGAGGTAGAAAAACAGATTGCCATATGCTTTCTTCTTCTGT
3272494 TATTCAGCCTAGCAAAAGTCCTTTTGCATCACCCTGCCTTCTTATTAAAAAAATGAT-GCACTTG
131 TATTCAGCCTAGCAAAAGTCCTTTTGCATCACCCTGCCTTCTTATTAAAAAAATGATGGCACTTG
3272558 GAGATTTT
196 GAGATTTT
3272566 CTCAGAGGACTCATGATCATGCTATTCCTCTAAAGCCTAATGCTACACCTGTTAATCTGAGACCC
1 CTCAGAGGACTCATGATCATGCTATTCCTCTAAAGCCTAATGCTACACCTGTTAATCTGAGA-CC
3272631 TACAGGTTTCCTCATAATCAGAAGATTGAGGTAGAAAAACAGATTGCCAGTATGCTTTCTTCTTC
65 TACAGGTTTCCTCATAATCAGAAGA-TGAGGTAGAAAAACAGATTGCCA-TATGCTTTCTTCTTC
3272696 TGTTATTCAGCCTAGCAAAAGTCCTTTTGCATCACCCTGCCTTCTTATTAAAAAAATGATGGCAC
128 TGTTATTCAGCCTAGCAAAAGTCCTTTTGCATCACCCTGCCTTCTTATTAAAAAAATGATGGCAC
3272761 TTGGAGATTTT
193 TTGGAGATTTT
3272772 GTGTGGATTG
Statistics
Matches: 202, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
202 62 0.31
203 27 0.13
204 23 0.11
205 75 0.37
206 15 0.07
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (203 bp):
CTCAGAGGACTCATGATCATGCTATTCCTCTAAAGCCTAATGCTACACCTGTTAATCTGAGACCT
ACAGGTTTCCTCATAATCAGAAGATGAGGTAGAAAAACAGATTGCCATATGCTTTCTTCTTCTGT
TATTCAGCCTAGCAAAAGTCCTTTTGCATCACCCTGCCTTCTTATTAAAAAAATGATGGCACTTG
GAGATTTT
Found at i:3275582 original size:5 final size:5
Alignment explanation
Indices: 3275572--3275597 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3275562 TTGCAATTTC
3275572 TCCTT TCCTT TCCTT TCCTT TCCTT T
1 TCCTT TCCTT TCCTT TCCTT TCCTT T
3275598 TCTAGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCCTT
Found at i:3284213 original size:154 final size:156
Alignment explanation
Indices: 3284024--3284421 Score: 588
Period size: 154 Copynumber: 2.5 Consensus size: 156
3284014 TGGCCTTGCT
* * *
3284024 CCTGGAGATGACCTGCTTGCCAACCCTTCTGTTCAAGCAGATGTGAAGCTATCTTTGACTTCTGA
1 CCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAAGCAGATGTGAAGCTATCTTTGACATCAGA
*
3284089 GTCAGAGATCAGTAATAACAGAAGGAATATGGAGAAACGAGAATCAG-GCTGAGGATCCGCCGAT
66 GTCAGAGATCAGTAATAACAGAAGGAATATGGAGAAACGAGAATCAGCACTGAGGATCCGCCGAT
* *
3284153 GCCAACTGAAAAGCCTACTGTTCTTG
131 GCCAACCGAAAAGCCTACGGTTCTTG
* * * * *
3284179 -CTGGAGATGACCTCCTTGCCAACCATTCTGTTCAACCAGATGTGAAGCCATCTTTGACGTCCGA
1 CCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAAGCAGATGTGAAGCTATCTTTGACATCAGA
* *
3284243 GTCCGAGATCAGTAATAACAGAAGGATTATGGAGAAACGAGAATCAGTCACTGAGGATCCGCCGA
66 GTCAGAGATCAGTAATAACAGAAGGAATATGGAGAAACGAGAATCAG-CACTGAGGATCCGCCGA
3284308 TGCCAACCGAAAAGCCTACGGTTCTTG
130 TGCCAACCGAAAAGCCTACGGTTCTTG
3284335 CTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTC-AGCCAGATGTGAAGCTATCTTTGACATC
1 --CCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAAG-CAGATGTGAAGCTATCTTTGACATC
**
3284399 AGAGTCCA-AGATCCCTAATAACA
63 AGAGT-CAGAGATCAGTAATAACA
3284422 AAAGTAAATT
Statistics
Matches: 217, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
154 103 0.47
156 40 0.18
158 1 0.00
159 72 0.33
160 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (156 bp):
CCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAAGCAGATGTGAAGCTATCTTTGACATCAGA
GTCAGAGATCAGTAATAACAGAAGGAATATGGAGAAACGAGAATCAGCACTGAGGATCCGCCGAT
GCCAACCGAAAAGCCTACGGTTCTTG
Found at i:3284391 original size:159 final size:159
Alignment explanation
Indices: 3284007--3284928 Score: 759
Period size: 159 Copynumber: 5.8 Consensus size: 159
3283997 CCGGCAGAGG
** * *
3284007 AGCCTACTGGCCTTGCTCCTGGAGATGACCTGCTTGCCAACCCTTCTGTTCAAGCAGATGTGAAG
1 AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATGTGAAG
* * * * *
3284072 CTATCTTTGACTTCTGAGT-CAGAGATCAGTAATAACAGAAGGAATATGGAGAAACGAGAATCAG
66 CTATCTTTGACGTCCGAGTCCA-AGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATCAG
* *
3284136 G--CTGAGGATCCGCCGATGCCAACTGAAA
130 GCACTGAGGAGCCACCGATGCCAACTGAAA
*
3284164 AGCCTACTGTTCTTG---CTGGAGATGACCTCCTTGCCAACCATTCTGTTCAACCAGATGTGAAG
1 AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATGTGAAG
* * * * * * *
3284226 CCATCTTTGACGTCCGAGTCCGAGATCAGTAATAACAGAAGGATTATGGAGAAACGAGAATCAGT
66 CTATCTTTGACGTCCGAGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATCAGG
* * *
3284291 CACTGAGGATCCGCCGATGCCAACCGAAA
131 CACTGAGGAGCCACCGATGCCAACTGAAA
* *
3284320 AGCCTACGGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAGCCAGATGTGAAG
1 AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATGTGAAG
* * * * * *
3284385 CTATCTTTGACATCAGAGTCCAAGATCCCTAATAACAAAAGTAA-ATTGGGGAAACAAAAATCAG
66 CTATCTTTGACGTCCGAGTCCAAGATCACTAATAACAAAAGGAATA-TGGAGAAACGAAAATCAG
** * **
3284449 GCACAAATGAGCCATTGATG-CAGACTGAAA
130 GCACTGAGGAGCCACCGATGCCA-ACTGAAA
* * * * * * *
3284479 AACCTACTGTTATTTCTCCAGGAGATGACCTCCCTGCAAACCCTTCTGTTCAACCGGATGTGAAG
1 AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATGTGAAG
* * ** * * * * * * * *
3284544 GTACCTTCAATGTCCAAGTCCAAGATCCCTAAAAATAAAAGGAAGAGATGGGGAGACGAAAATCA
66 CTATCTTTGACGTCCGAGTCCAAGATCACTAATAACAAAAGG-A-ATATGGAGAAACGAAAATCA
* * *
3284609 GGCACTGAGGAGCCACTGTTGCCAACTAAAA
129 GGCACTGAGGAGCCACCGATGCCAACTGAAA
* ** * *
3284640 AGCCTACTG---TTGCTCCAGGAGATGACCTCCCAGCAAACCCTTCTGTTCAACCAGATGCGAAG
1 AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATGTGAAG
* * * ** * *
3284702 CTATCTTCT--CTGT-CGAAATCCAAGGTCCCTAATAACAAAAGGAA-GCGGGGGAAC-AAAAGT
66 CTATCTT-TGAC-GTCCG-AGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAA-T
* ** * * * * **
3284762 CGGGCACCAAAGAGCCGCCAATGCCTACCAAAA
127 CAGGCACTGAGGAGCCACCGATGCCAACTGAAA
* * * * * * * *
3284795 AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCCTGCAAACCCTTTTGCTCAAGCAGACGCAGAT
1 AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATG-TGAA
* * * * * * *
3284860 G-TATCTTCCTCA-G-CCAAGTCCAAGGTC-CTAATTACAAAAGGAAGAGGGGGAAACGAAAATC
65 GCTATCTT--TGACGTCCGAGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATC
3284921 AGGCACTG
128 AGGCACTG
3284929 GCTGGTGGAG
Statistics
Matches: 630, Mismatches: 109, Indels: 51
0.80 0.14 0.06
Matches are distributed among these distances:
154 105 0.17
155 40 0.06
156 41 0.07
157 30 0.05
158 153 0.24
159 211 0.33
160 1 0.00
161 46 0.07
162 3 0.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.21
Consensus pattern (159 bp):
AGCCTACTGTTCTTGCTCCTGGAGATGACCTCCTTGCCAACCCTTCTGTTCAACCAGATGTGAAG
CTATCTTTGACGTCCGAGTCCAAGATCACTAATAACAAAAGGAATATGGAGAAACGAAAATCAGG
CACTGAGGAGCCACCGATGCCAACTGAAA
Found at i:3292683 original size:16 final size:16
Alignment explanation
Indices: 3292662--3292693 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3292652 ATAATAACAT
3292662 TTATTATTTATTATTA
1 TTATTATTTATTATTA
3292678 TTATTATTTATTATTA
1 TTATTATTTATTATTA
3292694 AAAGATTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATTTATTATTA
Found at i:3297464 original size:30 final size:30
Alignment explanation
Indices: 3297407--3297465 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3297397 TCAAAATTTA
** *
3297407 TTCGGTTCGGTTAATATTTTCAAAAAAAAG
1 TTCGGTTCGGTTAATAGGTTAAAAAAAAAG
3297437 TTCGGTTCGGTTAAT-GGTTAAAGAAAAAA
1 TTCGGTTCGGTTAATAGGTTAAA-AAAAAA
3297466 ATTCAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (30 bp):
TTCGGTTCGGTTAATAGGTTAAAAAAAAAG
Found at i:3297959 original size:120 final size:120
Alignment explanation
Indices: 3297746--3297985 Score: 471
Period size: 120 Copynumber: 2.0 Consensus size: 120
3297736 GGGTTGTGAA
*
3297746 ACTTATGTAAAACCTCAGATGTCTACAAAGCTCGAACCTAAATCTCATAAGTGTATATTTGTTGG
1 ACTTATGTAAAACATCAGATGTCTACAAAGCTCGAACCTAAATCTCATAAGTGTATATTTGTTGG
3297811 ATATCCTAAAAAAACTAAGGGATACTATTTCTTCAACCCAAACGAGAACAAAGTG
66 ATATCCTAAAAAAACTAAGGGATACTATTTCTTCAACCCAAACGAGAACAAAGTG
3297866 ACTTATGTAAAACATCAGATGTCTACAAAGCTCGAACCTAAATCTCATAAGTGTATATTTGTTGG
1 ACTTATGTAAAACATCAGATGTCTACAAAGCTCGAACCTAAATCTCATAAGTGTATATTTGTTGG
3297931 ATATCCTAAAAAAACTAAGGGATACTATTTCTTCAACCCAAACGAGAACAAAGTG
66 ATATCCTAAAAAAACTAAGGGATACTATTTCTTCAACCCAAACGAGAACAAAGTG
3297986 TTTGTTTCTC
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (120 bp):
ACTTATGTAAAACATCAGATGTCTACAAAGCTCGAACCTAAATCTCATAAGTGTATATTTGTTGG
ATATCCTAAAAAAACTAAGGGATACTATTTCTTCAACCCAAACGAGAACAAAGTG
Found at i:3299879 original size:64 final size:65
Alignment explanation
Indices: 3299725--3299880 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
3299715 ATAAGACCTA
* * * * * * * *
3299725 GTGCATCGATACACTAATTACATTCGATGTTTCAAAAGAGCTAGGAGTGTATCGATGCATGGTCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAAAGCTAAGAGTGCATCGATGCATAGTCT
* *
3299790 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAATC-AAGAGTGCATCGATGTATAGT-
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAA-AAAAGCTAAGAGTGCATCGATGCATAGTC
3299853 T
65 T
3299854 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
3299881 AATAGGGTGT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 28 0.35
65 48 0.60
66 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAAAGCTAAGAGTGCATCGATGCATAGTCT
Found at i:3300524 original size:2 final size:2
Alignment explanation
Indices: 3300517--3300560 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3300507 ACCAAAACCA
3300517 AT AT AT AT AT AT AT AT AT AT -T 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
3300558 AT A
1 AT A
3300561 AAATCATCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3302040 original size:13 final size:13
Alignment explanation
Indices: 3302021--3302059 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3302011 CCTAATGGGC
3302021 AATGTTTGAAAAT
1 AATGTTTGAAAAT
* *
3302034 TATGTTTGAAAAC
1 AATGTTTGAAAAT
3302047 AATGTTTGAAAAT
1 AATGTTTGAAAAT
3302060 CAATATAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (13 bp):
AATGTTTGAAAAT
Found at i:3302611 original size:44 final size:44
Alignment explanation
Indices: 3302506--3302612 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
3302496 CGATGCACAA
* *
3302506 CATAGTGTATCGATGCACATTCAAGGCATGCATCAGTGCACCTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCAGTACACCTT
* ** *
3302550 CATAGTGTATCGATGCATATTCAAGGGATGCATTGGTACACTTT
1 CATAGTGTATCGATGCATATTCAAGGCATGCATCAGTACACCTT
3302594 CATAGTGTATCGATGCATA
1 CATAGTGTATCGATGCATA
3302613 GTGCACAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (44 bp):
CATAGTGTATCGATGCATATTCAAGGCATGCATCAGTACACCTT
Found at i:3309153 original size:23 final size:23
Alignment explanation
Indices: 3309123--3309183 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
3309113 CTCGTATAAA
3309123 TGCACCGAAGTGCCACGCAGAAT
1 TGCACCGAAGTGCCACGCAGAAT
* *
3309146 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGCAGAAT
*
3309169 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3309184 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGCAGAAT
Found at i:3309914 original size:19 final size:19
Alignment explanation
Indices: 3309890--3309937 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3309880 ATTTAAGGGG
*
3309890 GTGCATCGATGCACTACTT
1 GTGCATCGATGCACTACAT
*
3309909 GTGCATCGATGCACTTCAT
1 GTGCATCGATGCACTACAT
3309928 GTGCATCGAT
1 GTGCATCGAT
3309938 ACACCTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCACTACAT
Found at i:3312078 original size:16 final size:16
Alignment explanation
Indices: 3312057--3312090 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3312047 CTCAAAATCC
3312057 TTACTTTC-CTTATTCT
1 TTACTTTCTC-TATTCT
3312073 TTACTTTCTCTATTCT
1 TTACTTTCTCTATTCT
3312089 TT
1 TT
3312091 TCAAACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (16 bp):
TTACTTTCTCTATTCT
Found at i:3316021 original size:23 final size:23
Alignment explanation
Indices: 3316003--3316063 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
3315993 CTCATATAAA
3316003 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
3316026 TGCACCGAAGTGCCTCGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
3316049 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3316064 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:3316073 original size:23 final size:23
Alignment explanation
Indices: 3315995--3316067 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
3315985 CACCACTGCT
3315995 CATATA-AA-TGCACCGAAGTGC
1 CATATAGAATTGCACCGAAGTGC
*
3316016 CACATAGAATTGCACCGAAGTGC
1 CATATAGAATTGCACCGAAGTGC
* *
3316039 C-TCGTAGAATTGCACCGTAGTGC
1 CAT-ATAGAATTGCACCGAAGTGC
3316062 CATATA
1 CATATA
3316068 AGATTGTCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
23 35 0.81
24 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (23 bp):
CATATAGAATTGCACCGAAGTGC
Found at i:3317765 original size:19 final size:19
Alignment explanation
Indices: 3317741--3317789 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3317731 AAGACCTAGC
*
3317741 GCATCGGTACATTTGGGGT
1 GCATCGGTACAGTTGGGGT
3317760 GCATCGGTACAGTTGGGGT
1 GCATCGGTACAGTTGGGGT
*
3317779 GCATCAGTACA
1 GCATCGGTACA
3317790 CTAATTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (19 bp):
GCATCGGTACAGTTGGGGT
Found at i:3318273 original size:65 final size:64
Alignment explanation
Indices: 3318154--3318364 Score: 223
Period size: 65 Copynumber: 3.3 Consensus size: 64
3318144 TTTTTCAGAG
* * * * *
3318154 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCAAATGC
1 TGATGCATCGATGCACTAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
3318216 ATT
62 ATT
* * *
3318219 TCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACTAACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
3318283 T
64 T
* * * * *
3318284 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACTAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
3318348 TGATGCATCGATGCACT
1 TGATGCATCGATGCACT
3318365 CTTAGTGCAC
Statistics
Matches: 123, Mismatches: 17, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 46 0.37
65 71 0.58
66 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACTAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:3318363 original size:17 final size:19
Alignment explanation
Indices: 3318335--3318383 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3318325 TATTTTGAAA
3318335 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3318353 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3318372 CACCGATGCACT
1 CATCGATGCACT
3318384 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3336240 original size:25 final size:25
Alignment explanation
Indices: 3336205--3336260 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3336195 ATTTCATGAT
*
3336205 TGGACGCAAGTAGTGATGTTATACAA
1 TGGA-GCAAGTAGTGATGTTATAAAA
* *
3336231 TGGAGCAAGTGGTGATGTTTTAAAA
1 TGGAGCAAGTAGTGATGTTATAAAA
3336256 TGGAG
1 TGGAG
3336261 TCAACGCACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.29
Consensus pattern (25 bp):
TGGAGCAAGTAGTGATGTTATAAAA
Found at i:3351975 original size:29 final size:29
Alignment explanation
Indices: 3351920--3352001 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
3351910 GAAATTTTAG
* *
3351920 TTAGTGGTCAAAATGTAAGTTTTGAAAA-T
1 TTAGTGGTCAAAGTATAA-TTTTGAAAAGT
3351949 TTAGTGGTCAAAGTATAATTTTGGAAAAGT
1 TTAGTGGTCAAAGTATAATTTT-GAAAAGT
*
3351979 TTAG-GGACTAAAGTGATAATTTT
1 TTAGTGGTC-AAAGT-ATAATTTT
3352002 TCCAAAATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.09
29 24 0.52
30 10 0.22
31 8 0.17
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (29 bp):
TTAGTGGTCAAAGTATAATTTTGAAAAGT
Found at i:3356510 original size:73 final size:73
Alignment explanation
Indices: 3356410--3356579 Score: 225
Period size: 73 Copynumber: 2.3 Consensus size: 73
3356400 TAAGATCGGT
* * *
3356410 AGTTAAAATATC-AGTACTTATGCTATGATATTCAATACATTTAAATTTGAAAAAGTTGAAAAAA
1 AGTTAAAATATCGA-TACTTATGCTATGACATTCAATACATTTAAATTTGAAAAAATCGAAAAAA
*
3356474 GTAATTGAA
65 GTAATCGAA
* * * ** *
3356483 AGTTAAAATATCGATATTTATGCTATGACGTTCAATACATTTACATTTGAAAAAATCGATGAAGG
1 AGTTAAAATATCGATACTTATGCTATGACATTCAATACATTTAAATTTGAAAAAATCGAAAAAAG
3356548 TAATCGAA
66 TAATCGAA
*
3356556 AGTTAAAATATGGATACTTATGCT
1 AGTTAAAATATCGATACTTATGCT
3356580 CTAATGTTTG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 83 0.99
74 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (73 bp):
AGTTAAAATATCGATACTTATGCTATGACATTCAATACATTTAAATTTGAAAAAATCGAAAAAAG
TAATCGAA
Found at i:3357166 original size:297 final size:297
Alignment explanation
Indices: 3356632--3357225 Score: 1152
Period size: 297 Copynumber: 2.0 Consensus size: 297
3356622 AAAATATTTA
*
3356632 ATGTTGAGGAGTCAAGTTTGTTAGAGATCATTATTCCAATATCAATTCTAGAAGACCAACTAGTA
1 ATGTTGAGGAGTCAAGTTTGTTAGAGATCATTATGCCAATATCAATTCTAGAAGACCAACTAGTA
3356697 TTTTCCATTTCAAGAGGTGCATAACTTTTAGAACTAATATTGGCATAAGGACTTAAAGAAAATGA
66 TTTTCCATTTCAAGAGGTGCATAACTTTTAGAACTAATATTGGCATAAGGACTTAAAGAAAATGA
*
3356762 CACCTGAGTAGAGAAGACCAATAACCCATTTGGTTGTTTGAGTTTCTTTTGTAAAAGAATTCTGG
131 CACCTGAGTAGAGAAGACCAATAACCCATTTGGTTGTTTGAGTTTCTTTTGCAAAAGAATTCTGG
3356827 TACCAATACCGATATTATAACATTGTAAAAGACACTCAAAACATCAGATGAGATATTGGATGATA
196 TACCAATACCGATATTATAACATTGTAAAAGACACTCAAAACATCAGATGAGATATTGGATGATA
3356892 AAAGAAAAAGACTGAAAAGGAATTATGCCTTATAAAG
261 AAAGAAAAAGACTGAAAAGGAATTATGCCTTATAAAG
3356929 ATGTTGAGGAGTCAAGTTTGTTAGAGATCATTATGCCAATATCAATTCTAGAAGACCAACTAGTA
1 ATGTTGAGGAGTCAAGTTTGTTAGAGATCATTATGCCAATATCAATTCTAGAAGACCAACTAGTA
*
3356994 TTTTCCATTTCAAGAGGTGCATAACTTTTAGCACTAATATTGGCATAAGGACTTAAAGAAAATGA
66 TTTTCCATTTCAAGAGGTGCATAACTTTTAGAACTAATATTGGCATAAGGACTTAAAGAAAATGA
3357059 CACCTGAGTAGAGAAGACCAATAACCCATTTGGTTGTTTGAGTTTCTTTTGCAAAAGAATTCTGG
131 CACCTGAGTAGAGAAGACCAATAACCCATTTGGTTGTTTGAGTTTCTTTTGCAAAAGAATTCTGG
3357124 TACCAATACCGATATTATAACATTGTAAAAGACACTCAAAACATCAGATGAGATATTGGATGATA
196 TACCAATACCGATATTATAACATTGTAAAAGACACTCAAAACATCAGATGAGATATTGGATGATA
*
3357189 AAAGAAAAAGACTGAAAATGAATTATGCCTTATAAAG
261 AAAGAAAAAGACTGAAAAGGAATTATGCCTTATAAAG
3357226 GCATCCTCTA
Statistics
Matches: 293, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
297 293 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (297 bp):
ATGTTGAGGAGTCAAGTTTGTTAGAGATCATTATGCCAATATCAATTCTAGAAGACCAACTAGTA
TTTTCCATTTCAAGAGGTGCATAACTTTTAGAACTAATATTGGCATAAGGACTTAAAGAAAATGA
CACCTGAGTAGAGAAGACCAATAACCCATTTGGTTGTTTGAGTTTCTTTTGCAAAAGAATTCTGG
TACCAATACCGATATTATAACATTGTAAAAGACACTCAAAACATCAGATGAGATATTGGATGATA
AAAGAAAAAGACTGAAAAGGAATTATGCCTTATAAAG
Found at i:3358859 original size:61 final size:61
Alignment explanation
Indices: 3358764--3358885 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
3358754 ATAGGGCCTG
3358764 TTGTTTAAGAATCATGCATAAAAACAACATTCAGAACCAAACTCATGGATGCATCAACATC
1 TTGTTTAAGAATCATGCATAAAAACAACATTCAGAACCAAACTCATGGATGCATCAACATC
* *
3358825 TTGTTTAAGAATCATGCGTAAAAACAACATTCAGAACCAAGCTCATGGATGCATCAACATC
1 TTGTTTAAGAATCATGCATAAAAACAACATTCAGAACCAAACTCATGGATGCATCAACATC
3358886 AGACACCCTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (61 bp):
TTGTTTAAGAATCATGCATAAAAACAACATTCAGAACCAAACTCATGGATGCATCAACATC
Found at i:3359168 original size:7 final size:6
Alignment explanation
Indices: 3359124--3359179 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
3359114 AAAAATGTAC
* * *
3359124 AATAAA AA-GAA AATAAA AGTAAA ATTTCAAA AATAAA AATAAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA A-AT-AAA AATAAA AAT-AAA AATAAA
3359174 AATAAA
1 AATAAA
3359180 TCATCATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 4 0.10
6 25 0.61
7 8 0.20
8 4 0.10
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:3359170 original size:13 final size:13
Alignment explanation
Indices: 3359152--3359179 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3359142 GTAAAATTTC
3359152 AAAAATAAAAATA
1 AAAAATAAAAATA
3359165 AAAAATAAAAATA
1 AAAAATAAAAATA
3359178 AA
1 AA
3359180 TCATCATAAA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:3359175 original size:20 final size:19
Alignment explanation
Indices: 3359133--3359179 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3359123 CAATAAAAAG
* **
3359133 AAAATAAAAGTAAAATTTCA
1 AAAATAAAAATAAAAAAT-A
3359153 AAAATAAAAATAAAAAATA
1 AAAATAAAAATAAAAAATA
3359172 AAAATAAA
1 AAAATAAA
3359180 TCATCATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAATAAAAATAAAAAATA
Found at i:3361871 original size:37 final size:37
Alignment explanation
Indices: 3361798--3361872 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
3361788 GTTGGAAAAT
* *
3361798 ATTTATATATATTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATATTCTTTAAAAAATTGAAAATCATAAA
* * *
3361835 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATATTCTTTAAAAAATTGAAAATCATAAA
3361872 A
1 A
3361873 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATATTCTTTAAAAAATTGAAAATCATAAA
Found at i:3372318 original size:3 final size:3
Alignment explanation
Indices: 3372310--3372346 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
3372300 CTACAAAAAA
3372310 TAT TAT TAT TAT TAT TAT TAT TAT T-T TCAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
3372347 ATACAATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 25 0.81
4 2 0.06
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3372470 original size:18 final size:18
Alignment explanation
Indices: 3372447--3372487 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3372437 TTCAACCCAG
3372447 AGCCCAACACTAATTACA
1 AGCCCAACACTAATTACA
*
3372465 AGCCCAACAGTAATTACA
1 AGCCCAACACTAATTACA
3372483 AGCCC
1 AGCCC
3372488 TTATACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (18 bp):
AGCCCAACACTAATTACA
Found at i:3377388 original size:24 final size:23
Alignment explanation
Indices: 3377358--3377446 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 23
3377348 AGATCCAATC
*
3377358 AAAACAAGAGAAAAGAAGAAAAGG
1 AAAACAA-AGAAAAGAAGAAAAGA
* *
3377382 AAAACAAAGAGCAAAGAGAAAAAAATA
1 AAAAC-AA-AG-AAA-AGAAGAAAAGA
3377409 AGAAACAAAGGAAAA-AAGCAAAAGA
1 A-AAACAAA-GAAAAGAAG-AAAAGA
3377434 AAAACAAAGAAAA
1 AAAACAAAGAAAA
3377447 AAAATGAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
23 5 0.09
24 14 0.26
25 12 0.22
26 7 0.13
27 12 0.22
28 4 0.07
ACGTcount: A:0.74, C:0.07, G:0.18, T:0.01
Consensus pattern (23 bp):
AAAACAAAGAAAAGAAGAAAAGA
Found at i:3377390 original size:18 final size:18
Alignment explanation
Indices: 3377368--3377413 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3377358 AAAACAAGAG
3377368 AAAAGAAGAAAAG-GAAA
1 AAAAGAAGAAAAGAGAAA
*
3377385 ACAAAG-AGCAAAGAGAAA
1 A-AAAGAAGAAAAGAGAAA
*
3377403 AAAATAAGAAA
1 AAAAGAAGAAA
3377414 CAAAGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAAAAGAGAAA
Found at i:3377448 original size:25 final size:24
Alignment explanation
Indices: 3377358--3377459 Score: 66
Period size: 25 Copynumber: 4.0 Consensus size: 24
3377348 AGATCCAATC
* *
3377358 AAAACAAGAGAAAAGAA-GAAAAGG
1 AAAACAA-AGAAAAAAATGAAAAGA
* *
3377382 AAAACAAAGAGCAAAGAGAA-AAAAATA
1 AAAACAAAGA--AAA-A-AATGAAAAGA
*
3377409 AGAAACAAAGGAAAAAA-GCAAAAGA
1 A-AAACAAAGAAAAAAATG-AAAAGA
3377434 AAAACAAAGAAAAAAAATGAAAAGA
1 AAAACAAAG-AAAAAAATGAAAAGA
3377459 A
1 A
3377460 GTACATGCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
23 3 0.05
24 17 0.27
25 23 0.37
26 4 0.06
27 7 0.11
28 8 0.13
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.02
Consensus pattern (24 bp):
AAAACAAAGAAAAAAATGAAAAGA
Found at i:3378335 original size:24 final size:23
Alignment explanation
Indices: 3378280--3378336 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
3378270 TCGGAAGGAG
* *
3378280 TAATATTTCTCAAAATCTTTGAT
1 TAATATTTTTCAAAATCTTTAAT
* *
3378303 TAAGCATTTTTTAAAACTCTTTAAT
1 TAA-TATTTTTCAAAA-TCTTTAAT
3378328 TAATATTTT
1 TAATATTTT
3378337 AGACTTTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.11
24 14 0.52
25 10 0.37
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATATTTTTCAAAATCTTTAAT
Found at i:3378988 original size:63 final size:63
Alignment explanation
Indices: 3378850--3378991 Score: 182
Period size: 63 Copynumber: 2.3 Consensus size: 63
3378840 CATGAGATTG
* * *
3378850 TTTCCCTTGAAAC-AAGTTTTGTCTCTATTGAGATAGTTTCTTTTGAAAAAATCTTTGAGTATG
1 TTTCCCTTGAAACAAAGTTTTGTCTC-ATTGAGATAGTTTCTTTAGAAAAAACCTTTGAGTATA
* * *
3378913 TTT-CTTTGGAAACAAAGTTTTGTCTC-TTGAGATAGTTTCTTGTAGAAAAAACCTTTGCGTCTA
1 TTTCCCTT-GAAACAAAGTTTTGTCTCATTGAGATAGTTTCTT-TAGAAAAAACCTTTGAGTATA
3378976 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
3378992 ACAAACAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
62 18 0.26
63 35 0.51
64 15 0.22
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (63 bp):
TTTCCCTTGAAACAAAGTTTTGTCTCATTGAGATAGTTTCTTTAGAAAAAACCTTTGAGTATA
Found at i:3379029 original size:28 final size:30
Alignment explanation
Indices: 3378994--3379060 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
3378984 GAAACAAAAC
3378994 AAACAAAATA-TTTGAGTATGTTTCTCTTG
1 AAACAAAATACTTTGAGTATGTTTCTCTTG
*
3379023 AAA-AAAATATCTTTGAGTCTGTTTCTCTTG
1 AAACAAAATA-CTTTGAGTATGTTTCTCTTG
3379053 AAACAAAA
1 AAACAAAA
3379061 CCATCTTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.18
29 3 0.09
30 21 0.62
31 4 0.12
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (30 bp):
AAACAAAATACTTTGAGTATGTTTCTCTTG
Found at i:3379040 original size:30 final size:32
Alignment explanation
Indices: 3379004--3379069 Score: 100
Period size: 30 Copynumber: 2.1 Consensus size: 32
3378994 AAACAAAATA
*
3379004 TTTGAGTATGTTTCTCTTGAAA-AAAA-TATC
1 TTTGAGTATGTTTCTCTTGAAACAAAACCATC
*
3379034 TTTGAGTCTGTTTCTCTTGAAACAAAACCATC
1 TTTGAGTATGTTTCTCTTGAAACAAAACCATC
3379066 TTTG
1 TTTG
3379070 GGTCGTTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 21 0.66
31 4 0.12
32 7 0.22
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (32 bp):
TTTGAGTATGTTTCTCTTGAAACAAAACCATC
Found at i:3379237 original size:40 final size:40
Alignment explanation
Indices: 3379176--3379323 Score: 107
Period size: 40 Copynumber: 3.6 Consensus size: 40
3379166 TGGTCTACCG
** *
3379176 TCCTCATCGTGTAAGAACCGTGTCATCCTCTGACCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCTCTGACCAGACC
* * * * * ***
3379216 TCCTCATCACGTAGGAGCCGTGTCAACCTTATATAACCTGTTG
1 TCCTCATCACGTAGGAACCGTGTCATCC---TCTGACCAGACC
* * * *
3379259 TCCTTATCACGTAGGAACTGTGTCATCCCCCGACCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCTCTGACCAGACC
** *
3379299 TCCTCATTGCGTAGGATCCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
3379324 ACTTGATAAT
Statistics
Matches: 77, Mismatches: 28, Indels: 6
0.69 0.25 0.05
Matches are distributed among these distances:
40 47 0.61
43 30 0.39
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCTCTGACCAGACC
Found at i:3379476 original size:131 final size:131
Alignment explanation
Indices: 3379266--3379562 Score: 447
Period size: 131 Copynumber: 2.3 Consensus size: 131
3379256 TTGTCCTTAT
* ** *
3379266 CACGTAGGAACTGTGTCATCCCCCGACCAGACCTCCTCATTGCGTAGGATCCGTGTCAACTTGAT
1 CACGTAGGAACCGTGTCATCCCCCGACCAGACCT-CTCATCACGTAGGATCCGTGTCAACCTGAT
*
3379331 AATCAGTCATCCTCATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGTC-TATCGTCCT
65 AACCAGTCATCCTCATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGG-CATATCGTCCT
3379395 CAA
129 CAA
*
3379398 CACGTAGGAACCGTGTCATCCCCCAACCAGACCTCTCATCACGTAGGAGT-CGTGTCAACCTGAT
1 CACGTAGGAACCGTGTCATCCCCCGACCAGACCTCTCATCACGTAGGA-TCCGTGTCAACCTGAT
* *
3379462 AACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCATGTCGTCCTC
65 AACCAGTCATCCTCATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCATATCGTCCTC
*
3379527 AT
130 AA
* *
3379529 CACGTAGGAA-CGTGTGATCCACCGACCAGACCTC
1 CACGTAGGAACCGTGTCATCCCCCGACCAGACCTC
3379563 ACATAAAACC
Statistics
Matches: 151, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
130 22 0.15
131 96 0.64
132 33 0.22
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (131 bp):
CACGTAGGAACCGTGTCATCCCCCGACCAGACCTCTCATCACGTAGGATCCGTGTCAACCTGATA
ACCAGTCATCCTCATCGCGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCATATCGTCCTCA
A
Found at i:3379493 original size:41 final size:40
Alignment explanation
Indices: 3379388--3379493 Score: 106
Period size: 39 Copynumber: 2.6 Consensus size: 40
3379378 AGATGGTCTA
* * *
3379388 TCGTCCTCAACACGTAGGAACCGTGTCATCCCCCAACCAG
1 TCGTCCTCATCACGTAGGAACCGTGTCAACCCACAACCAG
* * ** * *
3379428 ACCT-CTCATCACGTAGGAGTCGTGTCAACCTGATAACCAG
1 TCGTCCTCATCACGTAGGAACCGTGTCAACC-CACAACCAG
*
3379468 TCGTCCTCATCGCGTAGGAACCGTGT
1 TCGTCCTCATCACGTAGGAACCGTGT
3379494 TATCACCCTT
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
39 22 0.44
40 10 0.20
41 18 0.36
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGTCCTCATCACGTAGGAACCGTGTCAACCCACAACCAG
Found at i:3379769 original size:211 final size:212
Alignment explanation
Indices: 3379355--3379769 Score: 493
Period size: 211 Copynumber: 2.0 Consensus size: 212
3379345 ATCGCGTAGG
* *
3379355 AACCGTGTTATCACCCTTCCTAAAGATGGTCTATCGTCCTCAACACGTAGGAACCGTGTCATCCC
1 AACCGTGTTATCA--CTCCCTAAAGATGGTCTATCATCCTCAACACGTAGGAACCGTGTCATCCC
* *
3379420 CCAACCAGACCTCTCATCACGTAGGAGTCGTGTCAACCTGATAACCAGTCGTCCTCATCGCGTAG
64 CCAACCAGACCTCTCATCACGTAGGAGTCGTGTCAACCTGATAACCAGCCGTCCTCATCGCATAG
* ** * ***
3379485 GAACCGTGTTATCACCCTTCCTAAAGATGGCATGTCGTCCTCATCACGTAGGAACGTGTGATCCA
129 GAACCGTGTTATCACCCTTCCTAAAGATGCCATAACGTCCTCATAACGTAGGAACGTACCATCCA
3379550 CCGACCAGACCTCACATAA
194 CCGACCAGACCTCACATAA
* * * *
3379569 AACCGTGTTATCA-TCCCTAAATATGG-C-ATCATCCTCATCACGTAGGAACTGTGTCATCCCTC
1 AACCGTGTTATCACTCCCTAAAGATGGTCTATCATCCTCAACACGTAGGAACCGTGTCATCCCCC
* * * *
3379631 GACCAGACCTCCTCATTACGTAGGAG-C-TGTTCACCCCTAGATAATCAGCCGTCCTCATCGCAT
66 AACCAGACCT-CTCATCACGTAGGAGTCGTG-TCA-ACCT-GATAACCAGCCGTCCTCATCGCAT
* * * *
3379694 AGGAACCGTGTTATCACCCTTCCTAAATATGACCATAAC-TCTTCATAACGTATGATCCGTACCA
127 AGGAACCGTGTTATCACCCTTCCTAAAGATG-CCATAACGTCCTCATAACGTAGGA-ACGTACCA
*
3379758 TCCA-TGACCAGA
190 TCCACCGACCAGA
3379770 TATCCTCATC
Statistics
Matches: 171, Mismatches: 24, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
208 2 0.01
209 44 0.26
210 18 0.11
211 82 0.48
212 12 0.07
214 13 0.08
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (212 bp):
AACCGTGTTATCACTCCCTAAAGATGGTCTATCATCCTCAACACGTAGGAACCGTGTCATCCCCC
AACCAGACCTCTCATCACGTAGGAGTCGTGTCAACCTGATAACCAGCCGTCCTCATCGCATAGGA
ACCGTGTTATCACCCTTCCTAAAGATGCCATAACGTCCTCATAACGTAGGAACGTACCATCCACC
GACCAGACCTCACATAA
Found at i:3381647 original size:18 final size:21
Alignment explanation
Indices: 3381609--3381647 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3381599 ATTTTTAGTG
3381609 TTTGTAATATGATTGTTATTT
1 TTTGTAATATGATTGTTATTT
3381630 TTTGTAA-AT-ATT-TTATTT
1 TTTGTAATATGATTGTTATTT
3381648 GTATATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 2 0.11
21 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (21 bp):
TTTGTAATATGATTGTTATTT
Done.