Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168147.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_389, 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: 29382
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Found at i:382 original size:179 final size:181
Alignment explanation
Indices: 135--530 Score: 550
Period size: 180 Copynumber: 2.2 Consensus size: 181
125 TAAAATGTCC
* * *
135 CTTTTGTTTTGTCATAAACCAACTGTTTCTATTCATAAAAAGTTTTTTTGAAATAAAATAATACT
1 CTTTTGTTTTGTCATAAAACAA-TATTTCTATTCATAAAAAGTTTTTTTGAAATAAAATAACACT
* *
200 AATTTATTAACATTCCAAAAATTAATAAG-TAGAGATTTTAAAAATAAATCTGTTTACCGAGCAA
65 AATTTATTAACATTCCAAAAATTAATAAGTTAGAGATTTAAAAAATAAATCTGTTTACCGAACAA
* * *
264 GTTCAAATAGTTATGA-TTATTGGAA-TAATTATTTATTTCAAATCATTATGAT
130 GTTCAAATAGTCAT-ATTTATTGGAACT-ATTATCTATTTCAAATCATAATGAT
* *
316 CTTTTGTTTTGTAATAAAACAATATTTCTATTCAT-ACAA-TTTTATTTGAAATAAAATAACACT
1 CTTTTGTTTTGTCATAAAACAATATTTCTATTCATAAAAAGTTTT-TTTGAAATAAAATAACACT
* * * *
379 AATTTATTAATATTCTAAAAATTAATAAGTTTGAGATTTAAAAAATAAATTTGTTTACCGAACAA
65 AATTTATTAACATTCCAAAAATTAATAAGTTAGAGATTTAAAAAATAAATCTGTTTACCGAACAA
* *
444 GTTTAAATAGTCATATTTATTTGAACTATTATCTATTTCAAATCATAATGAT
130 GTTCAAATAGTCATATTTATTGGAACTATTATCTATTTCAAATCATAATGAT
* * *
496 ATTTTGTTTTGTCGTAAAACAATATTTCTGTTCAT
1 CTTTTGTTTTGTCATAAAACAATATTTCTATTCAT
531 GTACAATTAT
Statistics
Matches: 191, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
178 4 0.02
179 49 0.26
180 117 0.61
181 21 0.11
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (181 bp):
CTTTTGTTTTGTCATAAAACAATATTTCTATTCATAAAAAGTTTTTTTGAAATAAAATAACACTA
ATTTATTAACATTCCAAAAATTAATAAGTTAGAGATTTAAAAAATAAATCTGTTTACCGAACAAG
TTCAAATAGTCATATTTATTGGAACTATTATCTATTTCAAATCATAATGAT
Found at i:1608 original size:16 final size:16
Alignment explanation
Indices: 1570--1614 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1560 TATCTAATTT
*
1570 ATATAATTAAGTTCATTA
1 ATATTATTAA-TT-ATTA
1588 ATATTATTAATTATTA
1 ATATTATTAATTATTA
*
1604 TTATTATTAAT
1 ATATTATTAAT
1615 AAAATAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 14 0.56
17 2 0.08
18 9 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATTATTAATTATTA
Found at i:1983 original size:19 final size:19
Alignment explanation
Indices: 1961--1998 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1951 CGTTATTTTA
1961 TAAAAAATAAATTATTAAT
1 TAAAAAATAAATTATTAAT
* *
1980 TAAAATATTAATTATTAAT
1 TAAAAAATAAATTATTAAT
1999 ATTTCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAAAATAAATTATTAAT
Found at i:2484 original size:3 final size:3
Alignment explanation
Indices: 2469--2499 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2459 ATTAAACTAT
*
2469 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2500 TAATCAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5722 original size:134 final size:132
Alignment explanation
Indices: 5513--5777 Score: 338
Period size: 133 Copynumber: 2.0 Consensus size: 132
5503 AATGGACTTG
* * *
5513 ACTATTTGAATTTGTTTGGTAAACAATTTTTTTTTAAATCTCCAACTTATTAATTTTTGGAATAT
1 ACTATTTGAACTGGTTTGGTAAACAATTTTTTTTTAAATCT---ACTTACTAATTTTTGGAATAT
* * * * *
5578 TAATTGATTAGTATTATTTT-ATTTCGAATAAACTTGTATGAATAGAAACATATGTTTTATGACA
63 TAATTAATTAGTATTATTTTAATAT-G-ATAAACTTGTATGAACACAAAAATATGTTTTATGACA
5642 AAACCTA
126 AAACCTA
5649 ACTATTTGAACTGGTTTGGTAAACATATTTATTTTTTAAATCT-CTTACTAATTTTTGGAATATT
1 ACTATTTGAACTGGTTTGGTAAACA-ATTT-TTTTTTAAATCTACTTACTAATTTTTGGAATATT
* * *
5713 -ATTAAATTAGTATTATTTTAATATGATAAGCTTGTATGAACACAAAAATTTGTTTTATGCCAAA
64 AATT-AATTAGTATTATTTTAATATGATAAACTTGTATGAACACAAAAATATGTTTTATGACAAA
5777 A
128 A
5778 TAAAAATCAT
Statistics
Matches: 114, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
133 37 0.32
134 35 0.31
135 3 0.03
136 23 0.20
137 4 0.04
138 12 0.11
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (132 bp):
ACTATTTGAACTGGTTTGGTAAACAATTTTTTTTTAAATCTACTTACTAATTTTTGGAATATTAA
TTAATTAGTATTATTTTAATATGATAAACTTGTATGAACACAAAAATATGTTTTATGACAAAACC
TA
Found at i:6206 original size:181 final size:179
Alignment explanation
Indices: 5915--6886 Score: 709
Period size: 181 Copynumber: 5.5 Consensus size: 179
5905 AAAATTTTAC
* * * * * * *
5915 ATGAACAGAAACAATTGTTTTATAACAACATAAAAGGTCATAACAATTTAAAATAAATAATTGTT
1 ATGAATAGAAACAATTGTTTTATGACAAAACAAAAGATCATAACTATTTGAAATAAATAATTGTT
* * * * * * * * * ** * *
5980 CAAATGGA-CATGACTATTTGAACTTGTTTGATGAGCAGGTTTATTTTTTAAATCTCCTACCTAC
66 C-AA-GAATCATAACTATTTAAACTTATTCGGTAAACAGATTTATTTTTTAAATCTTTTACTTAT
* * *
6044 TAATTTTTAGAGTATTAATCAATTAGTATTATTTTATTCCAAATAAACTTGT
129 TAATTTTT-GAATATTAATAAATTAGTATTATTTTATTCCGAATAAACTTGT
* *
6096 ATGAATAGAAACAATTCTTTTAGGACAAAACAAAAGATCATAACTATTTGAAATAAATAATTGTT
1 ATGAATAGAAACAATTGTTTTATGACAAAACAAAAGATCATAACTATTTGAAATAAATAATTGTT
* * * * * * *
6161 CAAGCAATCATGACGATTTAAACTAACTCGGTAAACAGATTTATTTTTAAAATTTTTTACTCATT
66 CAAG-AATCATAACTATTTAAACTTATTCGGTAAACAGATTTATTTTTTAAATCTTTTACTTATT
* * * * *
6226 AATTTTTGGAATATTAAGAAATTAGTATTGTTTTATTTCGAATACATTTGT
130 AATTTTT-GAATATTAATAAATTAGTATTATTTTATTCCGAATAAACTTGT
* * * * **
6277 ATGAATAGAATCAATTGGTTTATGACAAAATAAAGGATCATAACTATTTGAAATCGATAATTGTT
1 ATGAATAGAAACAATTGTTTTATGACAAAACAAAAGATCATAACTATTTGAAATAAATAATTGTT
* * ** * * ** *
6342 CAAAAAGTCATAACTATTTAAA-TGTGTTTAGAAAATATTTTTAGTTTTTAAAT-TTTTACTTAT
66 CAAGAA-TCATAACTATTTAAACT-TATTCGGTAAACAGATTTATTTTTTAAATCTTTTACTTAT
** * *
6405 TAATTTTTGAAATATTAATAAATTTA-TATTATTTTATTCAAAATCAGCTTGT
129 TAATTTTTG-AATATTAATAAA-TTAGTATTATTTTATTCCGAATAAACTTGT
* * * * *
6457 TTGAATAGAAATAATTATTTTATGACAAAA-AAAATG-TCATAACGATTTGAAATAAATAATAGT
1 ATGAATAGAAACAATTGTTTTATGACAAAACAAAA-GATCATAACTATTTGAAATAAATAATTGT
* * * * ** * ***
6520 TCAAATGGA-CATGATTATTTAAACTTGTTCGGTAAATTG-TTTTTTTTTTAAATCTCCAACTTA
65 TC-AA-GAATCATAACTATTTAAACTTATTCGGTAAACAGATTTATTTTTTAAATCTTTTACTTA
6583 TTAATTTTTAGAATA-T--T--A--A-T-TTA--TT-TT--GAATAAACTTGT
128 TTAATTTTT-GAATATTAATAAATTAGTATTATTTTATTCCGAATAAACTTGT
*
6622 ATGAATAGAAAC-ATATGTTTTATGACAAAACAAAAGATCATAA-TGATTTGAAATAAATAAATG
1 ATGAATAGAAACAAT-TGTTTTATGACAAAACAAAAGATCATAACT-ATTTGAAATAAATAATTG
* * * * * * * *
6685 TTTAA-ATAGTTATAATTATTTGAACTCATTCGGTAAACAAATTTAGTTTTTAAATCTTTTGCTT
64 TTCAAGA-A-TCATAACTATTTAAACTTATTCGGTAAACAGATTTATTTTTTAAATCTTTTACTT
* * ** * *
6749 ATTAATTTTTAAAATTTTAATAAATTAGTATTATTTTATTTTGAATAAATTTTT
127 ATTAATTTTT-GAATATTAATAAATTAGTATTATTTTATTCCGAATAAACTTGT
* * * * * * * * * *
6803 ATGCACAAAAACAATTGGTTTATGACAAAACAAAAGGTAATATCGATTAGAAATAGATAATTGTT
1 ATGAATAGAAACAATTGTTTTATGACAAAACAAAAGATCATAACTATTTGAAATAAATAATTGTT
*
6868 -AAAATAGTCATAACTATTT
66 CAAGA-A-TCATAACTATTT
6887 GTATATGTTT
Statistics
Matches: 620, Mismatches: 134, Indels: 74
0.75 0.16 0.09
Matches are distributed among these distances:
164 3 0.00
165 36 0.06
166 50 0.08
167 33 0.05
168 3 0.00
170 4 0.01
171 2 0.00
172 1 0.00
174 2 0.00
175 1 0.00
176 4 0.01
178 15 0.02
179 72 0.12
180 84 0.14
181 308 0.50
182 2 0.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (179 bp):
ATGAATAGAAACAATTGTTTTATGACAAAACAAAAGATCATAACTATTTGAAATAAATAATTGTT
CAAGAATCATAACTATTTAAACTTATTCGGTAAACAGATTTATTTTTTAAATCTTTTACTTATTA
ATTTTTGAATATTAATAAATTAGTATTATTTTATTCCGAATAAACTTGT
Found at i:7126 original size:13 final size:13
Alignment explanation
Indices: 7110--7227 Score: 61
Period size: 13 Copynumber: 9.2 Consensus size: 13
7100 TTACAAATAA
7110 ATATAATATAATT
1 ATATAATATAATT
7123 ATATAA-A-AATT
1 ATATAATATAATT
**
7134 ATATGACA-ATTGTT
1 ATAT-A-ATATAATT
* *
7148 ATCTAATGTAATT
1 ATATAATATAATT
*
7161 ATA-ATATTTAATT
1 ATATA-ATATAATT
7174 ATAGTAATA-AATT
1 ATA-TAATATAATT
**
7187 ATATTCTATAATTT
1 ATATAATATAA-TT
* *
7201 AAATATTATAATT
1 ATATAATATAATT
7214 -TATAATA-AATT
1 ATATAATATAATT
7225 ATA
1 ATA
7228 AATGTATAAT
Statistics
Matches: 79, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
11 12 0.15
12 14 0.18
13 35 0.44
14 17 0.22
15 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:7243 original size:41 final size:38
Alignment explanation
Indices: 7156--7239 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
7146 TTATCTAATG
*
7156 TAATTATAATATT-TAATTATAGTAATAAATTATATTCTA
1 TAATT-TAATATTATAATT-TAGTAATAAATTATAATCTA
*
7195 TAATTTAAATATTATAATTTA-TAATAAATTATAAATGTA
1 TAATTT-AATATTATAATTTAGTAATAAATTAT-AATCTA
7234 TAATTT
1 TAATTT
7240 TTAATAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
38 12 0.30
39 23 0.57
40 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (38 bp):
TAATTTAATATTATAATTTAGTAATAAATTATAATCTA
Found at i:7352 original size:22 final size:22
Alignment explanation
Indices: 7326--7375 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
7316 TTATAATTTG
* *
7326 TAATTAGTACA-AATTAGTTAAT
1 TAATTAATACATAAATA-TTAAT
*
7348 TAATTAATATATAAATATTAAT
1 TAATTAATACATAAATATTAAT
7370 TAATTA
1 TAATTA
7376 TAGTATTAAT
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:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
TAATTAATACATAAATATTAAT
Found at i:7367 original size:18 final size:17
Alignment explanation
Indices: 7346--7389 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
7336 AAATTAGTTA
7346 ATTAATTAATATATAAAT
1 ATTAATTAATATAT-AAT
*
7364 ATTAATTAAT-TATAGT
1 ATTAATTAATATATAAT
7380 ATTAA-TAATA
1 ATTAATTAATA
7390 ATTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 3 0.12
18 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTAATTAATATATAAT
Found at i:7386 original size:22 final size:21
Alignment explanation
Indices: 7343--7397 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
7333 TACAAATTAG
7343 TTAATTAATTAATATATAAATA
1 TTAATTAATT-ATATATAAATA
*
7365 TTAATTAATTATAGTATTAATA
1 TTAATTAATTATA-TATAAATA
* *
7387 ATAATTTATTA
1 TTAATTAATTA
7398 ATTCAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
TTAATTAATTATATATAAATA
Found at i:8146 original size:19 final size:19
Alignment explanation
Indices: 8131--8168 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
8121 TATTAATTTT
* *
8131 TAATATTTATAATAATTAA
1 TAATATTAAAAATAATTAA
8150 TAATATTAAAAATAATTAA
1 TAATATTAAAAATAATTAA
8169 ATGGTAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATATTAAAAATAATTAA
Found at i:8892 original size:180 final size:181
Alignment explanation
Indices: 8482--8894 Score: 426
Period size: 183 Copynumber: 2.3 Consensus size: 181
8472 AATCTTTTAA
* * * * * * *
8482 TCATAATAATTTTAAATAGATAATTGTTCAAATAATCATAACTATTTGAACTTGTTTAGTAGACA
1 TCATAATAATTTAAAATAGACAATTGTTCAAACAATCGT-ACTATTTAAACTTGATTAGTAAACA
* * * * * *
8547 GATTTATTTTTTCAAATCTCTTACTTATTAATTTTTAGAATGTTAATAAATTAGTATTTTTTTTA
65 AATTAACTTTTTCAAATCACTTACTTATTAATTTTTAGAATATTAATAAATTAGTATTTATTTTA
** * *
8612 TTTTGAATAATTTTGCATGAACAGAAAGAAGTGTTTTATGAAAAAACAAAAGG
130 TTTTGAATAAGCTTG-ATAAACAGAAACAAGTGTTTTATGAAAAAACAAAAGG
* **** * * *
8665 TCATAACAATTTGGTGTAGAGAATTGTTCAAATGGACAT-G-ACTATTTAAAC-TGATTCGATAA
1 TCATAATAATTTAAAATAGACAATTGTTCAAA--CA-ATCGTACTATTTAAACTTGATTAG-TAA
* *
8727 ACAAATTAACTTTTT-AAATCACTTAGTTATTAATTTTTGGAATATTAATAAATTAGT-TTTATT
62 ACAAATTAACTTTTTCAAATCACTTACTTATTAATTTTTAGAATATTAATAAATTAGTATTTATT
* *
8790 TTATTTTGAATAAGCTTG-TAAACTA-AAACAATTGTTTTATGACAAAACAAAAAGG
127 TTATTTTGAATAAGCTTGATAAAC-AGAAACAAGTGTTTTATGAAAAAAC-AAAAGG
*
8845 TCATAATGATTTAAAATAGACAATTGTTCAAACAATCGTAGCTATTTAAA
1 TCATAATAATTTAAAATAGACAATTGTTCAAACAATCGTA-CTATTTAAA
8895 TTTGTTAATA
Statistics
Matches: 187, Mismatches: 34, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
177 2 0.01
178 2 0.01
179 25 0.13
180 41 0.22
181 21 0.11
182 43 0.23
183 50 0.27
185 1 0.01
186 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.40
Consensus pattern (181 bp):
TCATAATAATTTAAAATAGACAATTGTTCAAACAATCGTACTATTTAAACTTGATTAGTAAACAA
ATTAACTTTTTCAAATCACTTACTTATTAATTTTTAGAATATTAATAAATTAGTATTTATTTTAT
TTTGAATAAGCTTGATAAACAGAAACAAGTGTTTTATGAAAAAACAAAAGG
Found at i:9166 original size:12 final size:12
Alignment explanation
Indices: 9149--9174 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9139 AAATAATAAA
9149 AATTAAATATTT
1 AATTAAATATTT
9161 AATTAAATATTT
1 AATTAAATATTT
9173 AA
1 AA
9175 ATTTAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATTAAATATTT
Found at i:9417 original size:181 final size:182
Alignment explanation
Indices: 9182--10122 Score: 692
Period size: 181 Copynumber: 5.1 Consensus size: 182
9172 TAAATTTAAG
* * * * * * *
9182 TATTAACATTCAAAAAATTAATAAGCAAAAGATATGAAAAAATAAATTTGTTTACCGATCAAGTT
1 TATTAATATTCCAAAAATTAATAAGCAAGAGATTTAAAAAAATAAATTTGTTTACCGAACAAATT
* * * *
9247 TAAATAGTTATGACTATTTGAACAATTATTTATTTAAAATTATTATGA-GTATTTGTTTTGACA-
66 CAAATAGTTATGACTATTTGAACAATTATCTATTTAAAATCATTATGACCT-TTTGTTTTGACAT
*
9310 AAAACAAATTGTTTCAGTTCATAAAAGCTTA-TCTAAAATAAAATTATACTAATT
130 AAAA-AAATTGTTTCAGTTCATAAAAGCTTATTC-AAAATAAAATAATACTAATT
* * * *
9364 TCTTAATATTTCAAAAATTAATAAGCAAGAG-TTTAAAAAAATTAATTTGTTTACTGAACAAATT
1 TATTAATATTCCAAAAATTAATAAGCAAGAGATTTAAAAAAATAAATTTGTTTACCGAACAAATT
*
9428 CAAATAGTTATGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTGTCATA
66 CAAATAGTTATGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTGACATA
* * *
9493 AAATAATTGTTTCAGTTCATACAAGCTTATTCAAAATAAAATAATAGTAATT
131 AAAAAATTGTTTCAGTTCATAAAAGCTTATTCAAAATAAAATAATACTAATT
* * * * * ** *
9545 TATTAATATTCCAAAAATTAATAAGTAAGTGATTT-AAAAAAT-GATTCTCTTTATCGAATTAGT
1 TATTAATATTCCAAAAATTAATAAGCAAGAGATTTAAAAAAATAAATT-TGTTTACCGAACAAAT
* * * * * * *
9608 TCAAATAATTATGGCTATTTCAATAATTATCTATTTGAAATCAATATTACCTTTTG-TTTGATCA
65 TCAAATAGTTATGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTGA-CA
* * ** * *
9672 TATAACAATTGTTT-TTTATCATACAAGC---TTCAGAATAAAATAATACTAATT
129 TAAAAAAATTGTTTCAGT-TCATAAAAGCTTATTCAAAATAAAATAATACTAATT
* * ** * * * * * ***
9723 TATTAATCTTTCAAAAGCTAATAAGTAAGAAATTT-AAAAAATAAATTTATTTATCAAACCTGTT
1 TATTAATATTCCAAAAATTAATAAGCAAGAGATTTAAAAAAATAAATTTGTTTACCGAACAAATT
* * * * * * * *
9787 TAAATAGTTATGATTATTTAAACAAATGTATAGTTTAAATCAGTTATTTAAAAAATAAACCTTTT
66 CAAATAGTTATGACTATTTGAACAATTATCTA-TTTAAA--A-TCA-TT-----AT-GACCTTTT
* * ** * *
9852 -TTGTTCTATCATAAAACAATT-ACTCATGTTCATACAAGCTTATTCGAAATAAAATAATACTAA
120 GTT-TT-GA-CATAAAAAAATTGTTTCA-GTTCATAAAAGCTTATTCAAAATAAAATAATACTAA
*
9915 TC
181 TT
* * ** * * * * * *
9917 TAATAATACTCTGAAAATTAATAA-CTAGGAGATTT-AAAAAATAAATTTTTTTGCTGAACCAGT
1 TATTAATATTCCAAAAATTAATAAGC-AAGAGATTTAAAAAAATAAATTTGTTTACCGAACAAAT
* * * * * ***
9980 TTAAATAGTTAAGACTATATGAACAATTATCTATTTTAAATCGTTATGACCTTTTGTTTTTTTAT
65 TCAAATAGTTATGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTGACAT
* * * **** * *
10045 AAAACAATTTTTTCAATTCAGGCTAGCTTATTCAGAATAAAATAA-AATGAATT
130 AAAAAAATTGTTTCAGTTCATAAAAGCTTATTCAAAATAAAATAATACT-AATT
*
10098 TATTAATATTTCAAAAATTAATAAG
1 TATTAATATTCCAAAAATTAATAAG
10123 AGATTTAACA
Statistics
Matches: 603, Mismatches: 124, Indels: 64
0.76 0.16 0.08
Matches are distributed among these distances:
178 92 0.15
179 8 0.01
180 10 0.02
181 300 0.50
182 42 0.07
183 10 0.02
184 4 0.01
188 2 0.00
189 10 0.02
190 4 0.01
191 24 0.04
192 1 0.00
193 5 0.01
194 91 0.15
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (182 bp):
TATTAATATTCCAAAAATTAATAAGCAAGAGATTTAAAAAAATAAATTTGTTTACCGAACAAATT
CAAATAGTTATGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTTGTTTTGACATA
AAAAAATTGTTTCAGTTCATAAAAGCTTATTCAAAATAAAATAATACTAATT
Found at i:9643 original size:16 final size:17
Alignment explanation
Indices: 9611--9643 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9601 AATTAGTTCA
9611 AATAATTATGGCTATTTC
1 AATAATTAT-GCTATTTC
9629 AATAATTAT-CTATTT
1 AATAATTATGCTATTT
9644 GAAATCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (17 bp):
AATAATTATGCTATTTC
Found at i:10506 original size:25 final size:26
Alignment explanation
Indices: 10478--10535 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
10468 TTTATATAGT
*
10478 ATAAATT-TAAATAATTAATATTATA
1 ATAAATTATAAATAATTAATAATATA
* *
10503 AT-AATTATAAATTATTACTAATATA
1 ATAAATTATAAATAATTAATAATATA
10528 AT-AATTAT
1 ATAAATTAT
10536 GTTTATTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATAAATTATAAATAATTAATAATATA
Found at i:10619 original size:92 final size:89
Alignment explanation
Indices: 10455--10625 Score: 195
Period size: 91 Copynumber: 1.9 Consensus size: 89
10445 ATTTAAAATA
* * *
10455 TTAAAATAATAATTTTATATAGTATAAATTTAAATAATTAATATTATAATAATTATAAATTATTA
1 TTAAAATAATAATTTTATATAGTATAAATTTAAATAATTAATATTAAAATAATAATAAA-TACTA
*
10520 CTAATATAATAATTATGTTTATTAGT
65 ATAATATAA-AATTATGTTTATTAGT
* * *
10546 TTAAAATAATTATTTTATTATATTATAAA-TTATAATAAATAATTAGTTTAAAATAATAATAAA-
1 TTAAAATAATAATTTTA-TATAGTATAAATTTA-AATAATTAA-TA--TTAAAATAATAATAAAT
10609 ACTAAT-ATATAAAATTA
61 ACTAATAATATAAAATTA
10626 CATAAAAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
91 24 0.35
92 24 0.35
93 6 0.09
95 14 0.21
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (89 bp):
TTAAAATAATAATTTTATATAGTATAAATTTAAATAATTAATATTAAAATAATAATAAATACTAA
TAATATAAAATTATGTTTATTAGT
Found at i:10716 original size:16 final size:16
Alignment explanation
Indices: 10695--10729 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10685 CAATAAATTA
* *
10695 TTATATTAGTTATAAT
1 TTATATTAATAATAAT
10711 TTATATTAATAATAAT
1 TTATATTAATAATAAT
10727 TTA
1 TTA
10730 AACAATAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTATATTAATAATAAT
Found at i:11155 original size:181 final size:179
Alignment explanation
Indices: 10864--11920 Score: 765
Period size: 181 Copynumber: 5.9 Consensus size: 179
10854 TTTTATTCAA
* * * * * * * **
10864 AATAAGCTTGTATGAATAGAAAAAATCATTTTATGACATAGCAAAAGGTTATAGTGATTTTCAAT
1 AATAAGCTTATATGAATAGAAATAATTATTTTATGACAAAACAAAAGGTCATAATGATTTGAAAT
* * * * * * * *
10929 AAATAATTGTTCCAATAATTATAATTATTTAAACTTGTTCAGTAAACAGATTCATTTTTTAAATC
66 AGATAATTATTCAAATAGTCATAACTATTT-AACTAGTTCAGTAAACAGATTTATTTTTTAAATC
* * *
10994 TCTTAATTATTAATTTTTAAAATATTAATAACTTAATACTATTTTATTTCG
130 TCTTACTTATTAATTTTTAAAATATTAATAA-TTAGTATTATTTTATTTCG
* * * * *
11045 AATAAGCTTATATGAATTGAAATAATTTTTTTATGATAGAAGAAAAGGTCATAATGATTTGAAAT
1 AATAAGCTTATATGAATAGAAATAATTATTTTATGACAAAACAAAAGGTCATAATGATTTGAAAT
* * * * *
11110 AGATAACTATTCAAATAGTCATGATTGTTTAATCTAGTTCAGTAAAC--A--TA---TTT-AATT
66 AGATAATTATTCAAATAGTCATAACTATTTAA-CTAGTTCAGTAAACAGATTTATTTTTTAAATC
* * * * * *
11167 TTTTACTTATTAATTATCAAAATATTAATAAATTTGTATTATTTTAATCCG
130 TCTTACTTATTAATTTTTAAAATATTAAT-AATTAGTATTATTTTATTTCG
* * * * * *
11218 AATAAGCTTGA-ATAAATAGAAACT-ATTATCTTATAATAGAACAAAAAGTCATAATGATTTGAA
1 AATAAGCTT-ATATGAATAGAAA-TAATTATTTTATGACAAAACAAAAGGTCATAATGATTTGAA
* * * * * * * * *
11281 ATAAATAATTGCTT-AAATTGTCCTAA-T-TTGAACCAATT-TGATAAATAGATTTATTTTTTAA
64 ATAGATAATT-ATTCAAATAGTCATAACTATTTAACTAGTTCAG-TAAACAGATTTATTTTTTAA
* * *
11342 A-AT-TT--TTATTAATTCTTGAAATATTAATAGATTAGTATTATTTTATTTCG
127 ATCTCTTACTTATTAATTTTTAAAATATTAATA-ATTAGTATTATTTTATTTCG
* * * *
11392 AACAAACTTATATGAACA-AAA-ACATTAGTTTTATGACAAAACAAAAGGTCATAATAATTTGAA
1 AATAAGCTTATATGAATAGAAATA-ATTA-TTTTATGACAAAACAAAAGGTCATAATGATTTGAA
* * * ** * *
11455 ATAGATAATTGTTCAAATAGTCATAATTAATTGAACCGGTT-AGGTAAACATAATTATTTTTTAA
64 ATAGATAATTATTCAAATAGTCATAACT-ATTTAACTAGTTCA-GTAAACAGATTTATTTTTTAA
* * * * *
11519 TTCTCTTACTTATTAATTTTTGAAATTTTAATAAATTTA-TTTTATTTTA-TTCT
127 ATCTCTTACTTATTAATTTTTAAAATATTAAT-AA-TTAGTATTATTTTATTTCG
* * *
11572 ATATAAGC-TAGTATGAATTGAAA-ATATTGTTTTATGACAAAACAAAAGGTTATAATGATTTGA
1 A-ATAAGCTTA-TATGAATAGAAATA-ATTATTTTATGACAAAACAAAAGGTCATAATGATTTGA
* * ** * *
11635 AATAGATAATTATTTATATAGTTTTAACTATTTGAACTAGTTCGGCAAACA-ATTTTATTTTTTA
63 AATAGATAATTATTCAAATAGTCATAACTATTT-AACTAGTTCAGTAAACAGA-TTTATTTTTTA
* * * * * *
11699 AATCTCTTAGTTATTAATTTTCATAATATTATTAGATTAGTTTTATTTTATTTCA
126 AATCTCTTACTTATTAATTTTTAAAATATTAATA-ATTAGTATTATTTTATTTCG
* * * * *
11754 AATAAGCTTGTATGAACAAAAATAATTATTTTATGACAAAACAAAAGGTTATAAT-ATTTTGAAG
1 AATAAGCTTATATGAATAGAAATAATTATTTTATGACAAAACAAAAGGTCATAATGA-TTTGAAA
* * * ** * * * *
11818 TATAAAACTGCTCTAATAGTCATAACTATTTGAATTGGTT-TGTAAACAGATTTATTTTTTAAA-
65 TAGATAATTATTCAAATAGTCATAACTATTT-AACTAGTTCAGTAAACAGATTTATTTTTTAAAT
* *
11881 -TC-T-CTTATTAATTTTTGAAAGATTAATAAATTAGTATTAT
129 CTCTTACTTATTAATTTTTAAAATATTAAT-AATTAGTATTAT
11921 ATAATATATA
Statistics
Matches: 693, Mismatches: 139, Indels: 93
0.75 0.15 0.10
Matches are distributed among these distances:
169 1 0.00
170 8 0.01
171 4 0.01
172 2 0.00
173 122 0.18
174 108 0.16
175 1 0.00
176 30 0.04
177 33 0.05
178 6 0.01
179 3 0.00
180 36 0.05
181 322 0.46
182 17 0.02
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (179 bp):
AATAAGCTTATATGAATAGAAATAATTATTTTATGACAAAACAAAAGGTCATAATGATTTGAAAT
AGATAATTATTCAAATAGTCATAACTATTTAACTAGTTCAGTAAACAGATTTATTTTTTAAATCT
CTTACTTATTAATTTTTAAAATATTAATAATTAGTATTATTTTATTTCG
Found at i:11504 original size:347 final size:349
Alignment explanation
Indices: 10982--11878 Score: 846
Period size: 347 Copynumber: 2.5 Consensus size: 349
10972 AAACAGATTC
* * *
10982 ATTTTTTAAATCTCTTAATTATTAATTTTTAAAATATTAATA-ACTTAATACTATTTTATTTCGA
1 ATTTTTTAAATATCTT-ATTATTAA-TTTTAAAATATTAATAGA-TTAGTATTATTTTATTTCGA
* * * * * * *
11046 ATAAGCTTATATGAATTGAAATAATTTTTTTATGATAGAAGAAAAGGTCATAATGATTTGAAATA
63 ATAAGCTTATATGAA--CAAAAAATTATTTTATGACAAAACAAAAGGTCATAATAATTTGAAATA
* * * * *
11111 GATAACTATTCAAATAGTCATGATT-GTTTAATCTAGTTCAGTAAACATATTTAATTTTTTACTT
126 GATAACTGTTCAAATAGTCATAATTAATTGAA-CTGGTT-AGTAAACATATTTAATTTTTTACTT
* *
11175 ATTAATTATCAAAATATTAATAAATTTGTATTATTTTAATCCGA-ATAAGCTTGAATAAATAGAA
189 ATTAATTATCAAAATATTAATAAATTTATATTATTTT-ATCCGATATAAGCTAGAATAAATAGAA
* * * *
11239 ACTATTATCTTATAATAGAACAAAAAGTCATAATGATTTGAAATAAATAATTGCTTA-A-A-TTG
253 AATATTATCTTATAACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTACTTATATAGTTG
* * * *
11301 T-CCTAATTTGAACCAATTTGATAAATAGA-TTT
318 TAACT-ATTTGAACCAATTCGACAAACA-ATTTT
* *
11333 ATTTTTTAAA-AT-TT-TTATTAATTCTTGAAATATTAATAGATTAGTATTATTTTATTTCGAAC
1 ATTTTTTAAATATCTTATTATTAATT-TTAAAATATTAATAGATTAGTATTATTTTATTTCGAAT
*
11395 AAACTTATATGAACAAAAACATTAGTTTTATGACAAAACAAAAGGTCATAATAATTTGAAATAGA
65 AAGCTTATATGAACAAAAA-ATTA-TTTTATGACAAAACAAAAGGTCATAATAATTTGAAATAGA
* * *
11460 TAATTGTTCAAATAGTCATAATTAATTGAACCGGTTAGGTAAACATAATTATTTTTTAATTCTCT
128 TAACTGTTCAAATAGTCATAATTAATTGAACTGGTTA-GTAAAC---A-TA---TTTAATT-TTT
* ** * * * * * *
11525 TACTTATTAATTTTTGAAATTTTAATAAATTTATTTTATTTTATTCTATATAAGCTAGTATGAAT
184 TACTTATTAATTATCAAAATATTAATAAATTTATATTATTTTATCCGATATAAGCTAGAATAAAT
* * * * * * * *
11590 TGAAAATATTGTTTTATGACAAAACAAAAGGTTATAATGATTTGAAATAGATAATTATTTATATA
249 AGAAAATATTATCTTATAACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTACTTATATA
* * * *
11655 GTTTTAACTATTTGAACTAGTTCGGCAAACAATTTT
314 GTTGTAACTATTTGAACCAATTCGACAAACAATTTT
* * * * *
11691 ATTTTTTAAATCTCTTAGTTATTAATTTTCATAATATTATTAGATTAGTTTTATTTTATTTCAAA
1 ATTTTTTAAATATCTTA-TTATTAATTTT-AAAATATTAATAGATTAGTATTATTTTATTTCGAA
* * * * *
11756 TAAGCTTGTATGAACAAAAATAATTATTTTATGACAAAACAAAAGGTTATAATATTTTGAAGTAT
64 TAAGCTTATATGAAC-AAAA-AATTATTTTATGACAAAACAAAAGGTCATAATAATTTGAAATAG
* * * * * * * *
11821 AAAACTGCTCTAATAGTCATAACTATTTGAATTGGTTTGTAAACAGATTT-ATTTTTTA
127 ATAACTGTTCAAATAGTCATAATTAATTGAACTGGTTAGTAAACATATTTAATTTTTTA
11879 AATCTCTTAT
Statistics
Matches: 443, Mismatches: 76, Indels: 53
0.77 0.13 0.09
Matches are distributed among these distances:
345 4 0.01
346 6 0.01
347 117 0.26
348 5 0.01
349 2 0.00
350 2 0.00
351 12 0.03
352 4 0.01
353 3 0.01
354 14 0.03
355 100 0.23
356 1 0.00
357 3 0.01
358 33 0.07
359 3 0.01
360 2 0.00
361 8 0.02
362 115 0.26
363 8 0.02
364 1 0.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (349 bp):
ATTTTTTAAATATCTTATTATTAATTTTAAAATATTAATAGATTAGTATTATTTTATTTCGAATA
AGCTTATATGAACAAAAAATTATTTTATGACAAAACAAAAGGTCATAATAATTTGAAATAGATAA
CTGTTCAAATAGTCATAATTAATTGAACTGGTTAGTAAACATATTTAATTTTTTACTTATTAATT
ATCAAAATATTAATAAATTTATATTATTTTATCCGATATAAGCTAGAATAAATAGAAAATATTAT
CTTATAACAAAACAAAAAGTCATAATGATTTGAAATAAATAATTACTTATATAGTTGTAACTATT
TGAACCAATTCGACAAACAATTTT
Found at i:11968 original size:32 final size:35
Alignment explanation
Indices: 11917--11982 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 35
11907 TAAATTAGTA
*
11917 TTATATAATATATAATAAT-ATTAATTTTACTATC
1 TTATATAATATATAATAATAATAAATTTTACTATC
*
11951 TTATA-AATAT-TATTAATAATAAATTTTACTAT
1 TTATATAATATATAATAATAATAAATTTTACTAT
11983 TAATACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 18 0.62
34 5 0.17
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (35 bp):
TTATATAATATATAATAATAATAAATTTTACTATC
Found at i:11986 original size:16 final size:16
Alignment explanation
Indices: 11939--11987 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
11929 TAATAATATT
*
11939 AATTTTACTATCTTATA
1 AATTTTACTAT-TAATA
* * *
11956 AATATTATTAATAATA
1 AATTTTACTATTAATA
11972 AATTTTACTATTAATA
1 AATTTTACTATTAATA
11988 CTAAAATTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTTACTATTAATA
Found at i:12128 original size:13 final size:14
Alignment explanation
Indices: 12109--12148 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
12099 TGTTTTGAAA
12109 ATAATTAATTAATT
1 ATAATTAATTAATT
12123 -TAATTAA-TAATT
1 ATAATTAATTAATT
12135 ATAA-TAATTAATT
1 ATAATTAATTAATT
12148 A
1 A
12149 ATAACAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTAATTAATT
Found at i:12133 original size:20 final size:20
Alignment explanation
Indices: 12108--12152 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
12098 TTGTTTTGAA
*
12108 AATAATTA-ATTAATTTAATT
1 AATAATTATAATAA-TTAATT
12128 AATAATTATAATAATTAATT
1 AATAATTATAATAATTAATT
12148 AATAA
1 AATAA
12153 CAAAAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATAATTATAATAATTAATT
Found at i:12329 original size:11 final size:11
Alignment explanation
Indices: 12306--12348 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
12296 ACAATTTTAA
12306 AATATTATTATT
1 AATATT-TTATT
12318 AATATTTTATT
1 AATATTTTATT
*
12329 AATTGTTTATATT
1 AA-TATTT-TATT
12342 AATATTT
1 AATATTT
12349 AAATAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.26
12 14 0.52
13 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
AATATTTTATT
Found at i:12615 original size:25 final size:24
Alignment explanation
Indices: 12574--12623 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
12564 ATTCAATTAA
12574 ATATTTTTAATAATTATTATTAAAT
1 ATATTTTTAATAATTA-TATTAAAT
* * *
12599 ATATTTTTACTAGTTATATTTAAT
1 ATATTTTTAATAATTATATTAAAT
12623 A
1 A
12624 CTATAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATTTTTAATAATTATATTAAAT
Found at i:12691 original size:16 final size:16
Alignment explanation
Indices: 12660--12705 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
12650 TAAATCTAAT
12660 TTATTTATATAATTAAAA
1 TTATTTA-A-AATTAAAA
12678 TTATTTAAAATTAAAA
1 TTATTTAAAATTAAAA
12694 TTATTTAAAATT
1 TTATTTAAAATT
12706 TTTGTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
17 1 0.04
18 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTTAAAATTAAAA
Found at i:12808 original size:13 final size:14
Alignment explanation
Indices: 12779--12810 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12769 AATAATTTAA
12779 TAAATTATATAATT
1 TAAATTATATAATT
12793 TAAATTATAT-ATT
1 TAAATTATATAATT
12806 TAAAT
1 TAAAT
12811 CATAAGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATTATATAATT
Found at i:13058 original size:17 final size:17
Alignment explanation
Indices: 13036--13070 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13026 CCATTTATGA
13036 AATATTAGA-TAATTAAT
1 AATATTA-ATTAATTAAT
13053 AATATTAATTAATTAAT
1 AATATTAATTAATTAAT
13070 A
1 A
13071 TTTTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AATATTAATTAATTAAT
Found at i:13080 original size:25 final size:25
Alignment explanation
Indices: 13052--13101 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
13042 AGATAATTAA
13052 TAATATTAATTAA-TTAATATTTTAT
1 TAAT-TTAATTAATTTAATATTTTAT
*
13077 TAATTTTATTAATTTAATATTTTAT
1 TAATTTAATTAATTTAATATTTTAT
13102 CATTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TAATTTAATTAATTTAATATTTTAT
Found at i:14074 original size:181 final size:179
Alignment explanation
Indices: 13401--14074 Score: 637
Period size: 181 Copynumber: 3.7 Consensus size: 179
13391 TTAATTATTT
* * * * *
13401 TAATACCAATTTATCAATATTTTGAAAATTAATAATTAAGAGATTTAAAAAAATGAATTTGTTTA
1 TAATACTAATTTATTAATATTATGAAAATTAATAAGTAAGAGATTT-AAAAAATAAATTTGTTTA
* * * * * *
13466 CTAGAAAAGTTTAAATAATTATGAC-ATTTGAACAATTAT-TTTTTTGAAATCAGTATAACCTTT
65 CCA-ACAAGTTCAAATAGTTATGACTATTTGAACAATTATCTATTTT-AAATCATTATAACCTTT
* *
13529 TGTTTTATCATAAAATAAAATTTTT-TGTTCATACAAGCTTCTTTCAAATAAAA
128 TGTTTTGTCAT-AAA-AAAATTTTTCTGTTCATACAAGCTTATTTCAAATAAAA
* * *
13582 TAATA-TAAATTTATTAATATTAAGACAATTAATAAGTAAAAGATTTAAAAAATAAATTTGTTTA
1 TAATACT-AATTTATTAATATTATGAAAATTAATAAGTAAGAGATTTAAAAAATAAATTTGTTTA
* * * * ** * *
13646 TCGAATAAGTTCAAACT-GTTATGACTATTTGAATAATTATTTA-TTTAAATTGTTATGACTTTT
65 -CCAACAAGTTCAAA-TAGTTATGACTATTTGAACAATTATCTATTTTAAATCATTATAACCTTT
* * * * *
13709 TGTTTTGGCATAAAATAGTTATTTCTGTTCATACAAGGTTA-TTCAAATTAAAG
128 TGTTTTGTCATAAAAAAATT-TTTCTGTTCATACAAGCTTATTTCAAA-TAAAA
* * * *
13762 TAATATTAATTTATTAAT-TTTTGACAATTAATAAGT-AGAAGATTTAAAAAATAAATATGTTTA
1 TAATACTAATTTATTAATATTATGAAAATTAATAAGTAAG-AGATTTAAAAAATAAATTTGTTTA
* ** * * * * **
13825 CCGAACAAGTTGAAATAGCCATGACAATTTGAATAATTAACTATTTCAAATCATTATGCCCTTTT
65 CC-AACAAGTTCAAATAGTTATGACTATTTGAACAATTATCTATTTTAAATCATTATAACC-TTT
* * * * * *
13890 TGTTTTGTAATAAAACAATTGTTTCAGTTCAAATAAGCTTATTTGAAATAAAA
128 TGTTTTGTCATAAAAAAATT-TTTCTGTTCATACAAGCTTATTTCAAATAAAA
* * * * *
13943 TAATACTAATTTATTAATATTATGAAAATTAATGAGTAAGAGAATTAAAAAATGAATCTGTTTGC
1 TAATACTAATTTATTAATATTATGAAAATTAATAAGTAAGAGATTTAAAAAATAAATTTGTTTAC
* * * *
14008 CAACCATGTTCAAATAGTTATGACTATCTAAACAATTATCTATTTTAAAACATTATAACCTTTTG
66 CAA-CAAGTTCAAATAGTTATGACTATTTGAACAATTATCTATTTTAAATCATTATAACCTTTTG
14073 TT
130 TT
14075 AATGATTCAA
Statistics
Matches: 400, Mismatches: 75, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
178 7 0.02
179 82 0.20
180 100 0.25
181 123 0.31
182 86 0.22
183 2 0.00
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (179 bp):
TAATACTAATTTATTAATATTATGAAAATTAATAAGTAAGAGATTTAAAAAATAAATTTGTTTAC
CAACAAGTTCAAATAGTTATGACTATTTGAACAATTATCTATTTTAAATCATTATAACCTTTTGT
TTTGTCATAAAAAAATTTTTCTGTTCATACAAGCTTATTTCAAATAAAA
Found at i:15500 original size:19 final size:19
Alignment explanation
Indices: 15476--15512 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15466 AATTTATTTT
15476 TTAAAT-TTAATTTAAATAA
1 TTAAATATTAA-TTAAATAA
15495 TTAAATATTAATTAAATA
1 TTAAATATTAATTAAATA
15513 TATGACTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATATTAATTAAATAA
Found at i:15942 original size:180 final size:174
Alignment explanation
Indices: 15598--16356 Score: 526
Period size: 181 Copynumber: 4.2 Consensus size: 174
15588 ACAAACAATG
* * * ** ** *
15598 AATTTATTAATATTTTGAAAATTAAGAAGTAAGAA-ATTTAAAAAGTAAAATTGTTTACTAAACC
1 AATTTATTAATATTCTG-AAA-TAATAAGTAA-AAGATTTAAAAAAT-AAATAATTTA-TCGACA
* * * * *
15662 AGTTCAATTATTTATAACTATTTGAACAATTATTTATTTCAAATTATTATGACCA-TTTGTATTG
61 AGTTCAAATAATTATAACTATTTGAATAATTATTTATTTCAAATCATTATGA-CATTTTGTTTTG
* * * * *
15726 TCATAAAATAATTATTTCTATTTGTACAGTCTTATTTGAAATAAAGTAATACT
125 TCACAAAACAATTGTTTCTA-TTATACA-ACTTATTTGAAATAAA-TAATACT
* * * * *** *
15779 AATTTATCAATATTTTGAAATTAATAAGTAATAGATTTAAAAAATGAATCAATTGGCCTGACCAG
1 AATTTATTAATATTCTGAAA-TAATAAGTAAAAGATTTAAAAAATAAAT-AATTTATC-GACAAG
* * * * *
15844 TGCAAATAGTTATGACTGTTTGAATAATTATTTATTTCAAATCATTATGACATTTTGTTTTATCA
63 TTCAAATAATTATAACTATTTGAATAATTATTTATTTCAAATCATTATGACATTTTGTTTTGTCA
* *
15909 CAAAACAATTGTTTCTGTCTATACTAACTTATTTGAAATAATATAATTCT
128 CAAAACAATTGTTTCTAT-TATAC-AACTTATTTGAAATAA-ATAATACT
* * *
15959 ATTTTATTAATATTCT-AAA-AATTAA-TAAGAGATTTAAAAAATAAATATGTTTATCGAACAAG
1 AATTTATTAATATTCTGAAATAA-TAAGTAAAAGATTTAAAAAATAAATA-ATTTATCG-ACAAG
* * * ** * *
16021 TACAAATAATTATAACTATTTGAATAATTATCTATTTCTAATCGCTATAACCTTTTGTTTTGTC-
63 TTCAAATAATTATAACTATTTGAATAATTATTTATTTCAAATCATTATGACATTTTGTTTTGTCA
* * * *
16085 CTAAAACAAAAT-TTTCTATTCATACAAGCTTATTTCAAATAAAATTATACA
128 C-AAAAC-AATTGTTTCTATT-ATACAA-CTTATTTGAAAT-AAATAATACT
* * * *
16136 AATTTATTAATATTCAGACAACTAATAAGTAAAAGATTTAAAAAATAAATTTATTTATCAAATAA
1 AATTTATTAATATTCTGA-AA-TAATAAGTAAAAGATTTAAAAAATAAA-TAATTTATC-GACAA
* * * ** * *
16201 GTTTAAATAATTATGACTATTTGAATAATTATTTATTTCTAATTGTTATGACTTTTTGTTTTCTC
62 GTTCAAATAATTATAACTATTTGAATAATTATTTATTTCAAATCATTATGACATTTTGTTTTGTC
** * * * * * * * *
16266 ATGACACAATTGTTTTTCTTCATTA-AAGCCTATTCGGATTAAAATAATATT
127 ACAAAACAATTGTTTCTATT-A-TACAA-CTTATTTGAAAT-AAATAATACT
* * *
16317 AATTTATTAATATTTTAAAAATTAATAAGTATAAGATTTA
1 AATTTATTAATATTCT-GAAA-TAATAAGTAAAAGATTTA
16357 TTAATTTTTA
Statistics
Matches: 462, Mismatches: 90, Indels: 52
0.76 0.15 0.09
Matches are distributed among these distances:
176 6 0.01
177 126 0.27
178 9 0.02
179 12 0.03
180 139 0.30
181 166 0.36
182 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (174 bp):
AATTTATTAATATTCTGAAATAATAAGTAAAAGATTTAAAAAATAAATAATTTATCGACAAGTTC
AAATAATTATAACTATTTGAATAATTATTTATTTCAAATCATTATGACATTTTGTTTTGTCACAA
AACAATTGTTTCTATTATACAACTTATTTGAAATAAATAATACT
Found at i:16057 original size:16 final size:17
Alignment explanation
Indices: 16025--16057 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16015 AACAAGTACA
16025 AATAATTATAACTATTTG
1 AATAATTAT-ACTATTTG
16043 AATAATTAT-CTATTT
1 AATAATTATACTATTT
16058 CTAATCGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AATAATTATACTATTTG
Found at i:16231 original size:181 final size:177
Alignment explanation
Indices: 15756--16262 Score: 468
Period size: 177 Copynumber: 2.8 Consensus size: 177
15746 TTTGTACAGT
* * * * * * *
15756 CTTATTTGAAATAAAGTAATACTAATTTATCAATATTTTGAAATTAATAAGTAATAGATTTAAAA
1 CTTATTTCAAATAAAATAATACAAATTTATTAATATTCT-AAA-AAATAA-TAAAAGATTTAAAA
* *** ** * * * * *
15821 AATGAATCA-ATTGGCCTGACCAGTGCAAATAGTTATGACTGTTTGAATAATTATTTATTTCAAA
63 AATAAAT-ATATTTATCAAACAAGTACAAATAATTATGACTATTTGAATAATTATTTATTTCTAA
* *
15885 TCATTATGACATTTTGTTTTATCACAAAACAATTGTTTCTGTCTATACTAA
127 TCGTTATGACATTTTGTTTTATCACAAAACAAATGTTTCTGTCTATACTAA
* * * * * * *
15936 CTTATTTGAAATAATATAATTCTATTTTATTAATATTCTAAAAATTAATAAGAGATTTAAAAAAT
1 CTTATTTCAAATAAAATAATACAAATTTATTAATATTCTAAAAAATAATAAAAGATTTAAAAAAT
* * * * *
16001 AAATATGTTTATCGAACAAGTACAAATAATTATAACTATTTGAATAATTATCTATTTCTAATCGC
66 AAATATATTTATCAAACAAGTACAAATAATTATGACTATTTGAATAATTATTTATTTCTAATCGT
* * * *
16066 TATAACCTTTTGTTTTGTC-CTAAAACAAAAT-TTTCTAT-TCATAC-AA
131 TATGACATTTTGTTTTATCAC-AAAAC-AAATGTTTCTGTCT-ATACTAA
*
16112 GCTTATTTCAAATAAAATTATACAAATTTATTAATATTC-AGACAACTAATAAGTAAAAGATTTA
1 -CTTATTTCAAATAAAATAATACAAATTTATTAATATTCTA-A-AA--AATAA-TAAAAGATTTA
* * **
16176 AAAAATAAATTTATTTATCAAATAAGTTTAAATAATTATGACTATTTGAATAATTATTTATTTCT
60 AAAAATAAATATATTTATCAAACAAGTACAAATAATTATGACTATTTGAATAATTATTTATTTCT
* *
16241 AATTGTTATGACTTTTTGTTTT
125 AATCGTTATGACATTTTGTTTT
16263 CTCATGACAC
Statistics
Matches: 267, Mismatches: 50, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
176 6 0.02
177 127 0.48
178 9 0.03
179 3 0.01
180 37 0.14
181 85 0.32
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (177 bp):
CTTATTTCAAATAAAATAATACAAATTTATTAATATTCTAAAAAATAATAAAAGATTTAAAAAAT
AAATATATTTATCAAACAAGTACAAATAATTATGACTATTTGAATAATTATTTATTTCTAATCGT
TATGACATTTTGTTTTATCACAAAACAAATGTTTCTGTCTATACTAA
Found at i:16864 original size:21 final size:22
Alignment explanation
Indices: 16830--16870 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16820 TTAATCAATT
* *
16830 ATATATAATTATAATTAATAAA
1 ATATATAATAATAACTAATAAA
16852 ATAT-TAATAATAACTAATA
1 ATATATAATAATAACTAATA
16871 GTCTAATATA
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:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATATAATAATAACTAATAAA
Found at i:17245 original size:22 final size:21
Alignment explanation
Indices: 17217--17284 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
17207 ATTTTATATG
17217 TATTATATAAATATTAAGTAAT
1 TATTATATAAATATTAA-TAAT
* *
17239 TATTATATAATTTATTTATAAT
1 TATTATATAA-ATATTAATAAT
* * *
17261 T-TAATATAAATATAAATATT
1 TATTATATAAATATTAATAAT
17281 TATT
1 TATT
17285 TGAACAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
20 8 0.22
21 8 0.22
22 15 0.42
23 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TATTATATAAATATTAATAAT
Found at i:17478 original size:16 final size:17
Alignment explanation
Indices: 17446--17478 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17436 AATTAGTTCA
17446 AATAATTATGGCTATTTC
1 AATAATTAT-GCTATTTC
17464 AATAATTAT-CTATTT
1 AATAATTATGCTATTT
17479 GAAATCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (17 bp):
AATAATTATGCTATTTC
Found at i:18148 original size:13 final size:13
Alignment explanation
Indices: 18130--18171 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18120 ATCTATTAAT
18130 TAATTAAAATCAA
1 TAATTAAAATCAA
*
18143 TAATTAAAAT-ATT
1 TAATTAAAATCA-A
18156 TAAATTAAAATCAA
1 T-AATTAAAATCAA
18170 TA
1 TA
18172 TTCAGATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.50
14 10 0.42
15 1 0.04
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAAATCAA
Found at i:18191 original size:27 final size:28
Alignment explanation
Indices: 18124--18191 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
18114 TTAAATATCT
18124 ATTAATTAATTAAAATCAATAATTAAAATA
1 ATTAA-TAA-TAAAATCAATAATTAAAATA
* * * *
18154 TTTAA-ATTAAAATCAAT-ATTCAGATA
1 ATTAATAATAAAATCAATAATTAAAATA
18180 ATTAATAATAAA
1 ATTAATAATAAA
18192 TTATAAGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 11 0.35
27 15 0.48
28 1 0.03
30 4 0.13
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (28 bp):
ATTAATAATAAAATCAATAATTAAAATA
Found at i:18211 original size:26 final size:27
Alignment explanation
Indices: 18177--18232 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
18167 CAATATTCAG
*
18177 ATAATTAATAA-TAAATTATAAGTATTT
1 ATAATTAATAATTAAATTA-AAATATTT
*
18204 ATAA-TAATAATTTAATTAAAATATTT
1 ATAATTAATAATTAAATTAAAATATTT
18230 ATA
1 ATA
18233 TTTTAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
ATAATTAATAATTAAATTAAAATATTT
Found at i:18535 original size:14 final size:13
Alignment explanation
Indices: 18515--18586 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
18505 AGTCATTTTT
18515 ATTAATATTAATA
1 ATTAATATTAATA
*
18528 ATTCAATATTATTA
1 ATT-AATATTAATA
*
18542 TTTAA-ATATAATA
1 ATTAATAT-TAATA
*
18555 A-TAATATTAAAA
1 ATTAATATTAATA
18567 TATTAAT-TTAAATA
1 -ATTAATATT-AATA
18581 ATTAAT
1 ATTAAT
18587 TTTTAATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
12 9 0.19
13 20 0.43
14 18 0.38
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTAATATTAATA
Found at i:20090 original size:19 final size:18
Alignment explanation
Indices: 20032--20100 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 18
20022 AACAAAAGGT
*
20032 TATAATAATTTGAAATA-
1 TATAATTATTTGAAATAG
* *
20049 TATAATTGTTT-AAGTAG
1 TATAATTATTTGAAATAG
*
20066 TAATAATTATTTGAACTAG
1 T-ATAATTATTTGAAATAG
20085 TCATAATTATTT-AAAT
1 T-ATAATTATTTGAAAT
20101 TGGTTTGGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 4 0.10
17 10 0.24
18 12 0.29
19 16 0.38
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (18 bp):
TATAATTATTTGAAATAG
Found at i:20726 original size:23 final size:23
Alignment explanation
Indices: 20695--20742 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20685 ATTAATTTTT
*
20695 TAAATATTAATATAA-TATTATTA
1 TAAAGATT-ATATAATTATTATTA
*
20718 TAAAGATTATATAATTGTTATTA
1 TAAAGATTATATAATTATTATTA
20741 TA
1 TA
20743 TTAGTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
TAAAGATTATATAATTATTATTA
Found at i:21662 original size:22 final size:21
Alignment explanation
Indices: 21625--21669 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
21615 TGTTTTATAA
21625 AAATATTGTTATTCATATATT
1 AAATATTGTTATTCATATATT
*
21646 AAATATTTTATATTCATATATT
1 AAATATTGT-TATTCATATATT
21668 AA
1 AA
21670 GTAAAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATATTGTTATTCATATATT
Found at i:21903 original size:35 final size:35
Alignment explanation
Indices: 21838--21905 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
21828 AATATAAAAC
*
21838 AATAAATATTTAATATTATTTTACAAATAATATAT
1 AATAAATATTTAATATTATTTGACAAATAATATAT
*
21873 AATATATATTT-ATA-TATTTGACTAATATAATAT
1 AATAAATATTTAATATTATTTGAC-AA-ATAATAT
21906 TATTTTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 7 0.24
34 5 0.17
35 17 0.59
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (35 bp):
AATAAATATTTAATATTATTTGACAAATAATATAT
Found at i:21917 original size:27 final size:28
Alignment explanation
Indices: 21869--21930 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
21859 TACAAATAAT
21869 ATATAATATATATTTATATATTTGACTA
1 ATATAATATATATTTATATATTTGACTA
*
21897 ATATAATAT-TATTT-TACTATTTGATTA
1 ATATAATATATATTTATA-TATTTGACTA
21924 AT-TAATA
1 ATATAATA
21931 ATTGTTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.22
27 16 0.50
28 9 0.28
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
ATATAATATATATTTATATATTTGACTA
Found at i:22025 original size:18 final size:18
Alignment explanation
Indices: 22002--22054 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
21992 TTAATTTGTC
22002 ATTAATTTTATAATATTA
1 ATTAATTTTATAATATTA
* *
22020 ATTAATTATAAAATATT-
1 ATTAATTTTATAATATTA
*
22037 A-TAATACTTATAATATTA
1 ATTAAT-TTTATAATATTA
22055 TAATTAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 15 0.54
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAATTTTATAATATTA
Found at i:22053 original size:17 final size:17
Alignment explanation
Indices: 22009--22058 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
21999 GTCATTAATT
*
22009 TTATAATATTA-ATTAA
1 TTATAATATTATAATAA
*
22025 TTATAAAATATTATAATAC
1 TTAT--AATATTATAATAA
22044 TTATAATATTATAAT
1 TTATAATATTATAAT
22059 TAATATGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 4 0.14
17 11 0.38
18 7 0.24
19 7 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATAATATTATAATAA
Found at i:22088 original size:40 final size:35
Alignment explanation
Indices: 22004--22089 Score: 86
Period size: 40 Copynumber: 2.3 Consensus size: 35
21994 AATTTGTCAT
22004 TAAT-TTTATAATATTAATTAATTATAAAATATTA
1 TAATATTTATAATATTAATTAATTATAAAATATTA
* *
22038 TAATACTTATAATATTATAATTAATATGATTAAATTATTA
1 TAATATTTATAATA-T-TAATTAAT-T-A-TAAAATATTA
22078 -AATTATTTATAA
1 TAA-TATTTATAA
22090 ATTTAAAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
34 4 0.10
35 8 0.19
36 1 0.02
37 8 0.19
38 1 0.02
39 3 0.07
40 17 0.40
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
TAATATTTATAATATTAATTAATTATAAAATATTA
Found at i:22473 original size:17 final size:17
Alignment explanation
Indices: 22441--22483 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
22431 TTATATTAAT
* *
22441 AATAATTATTATTATTA
1 AATAATTATAAATATTA
22458 AATAATTATAAATATTA
1 AATAATTATAAATATTA
*
22475 TAT-ATTATA
1 AATAATTATA
22484 CTTATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATTATAAATATTA
Found at i:22534 original size:26 final size:26
Alignment explanation
Indices: 22485--22542 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
22475 TATATTATAC
*
22485 TTATATTTATAATATAAATTAATAAA
1 TTATATTTATAATATAAATAAATAAA
* *
22511 TTATATTTATTAA-ATATATAAATAGA
1 TTATATTTA-TAATATAAATAAATAAA
22537 TT-TATT
1 TTATATT
22543 ATACAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.14
26 21 0.75
27 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTATATTTATAATATAAATAAATAAA
Found at i:22582 original size:61 final size:64
Alignment explanation
Indices: 22440--22582 Score: 149
Period size: 61 Copynumber: 2.3 Consensus size: 64
22430 GTTATATTAA
*
22440 TAAT-AATTATTA-TTATTAAATAATTATAAATATTATATATTATACTTATATTTATAATATAAA
1 TAATAAATTA-TAGTTATTAAATAATTATAAATATGATATATTATAC-TATATTTATAATATAAA
22503 T
64 T
* *
22504 TAATAAATTATATTTATTAAAT-A-TATAAATA-GATTTATTATAC-A-ATTTATCAAATATAAA
1 TAATAAATTATAGTTATTAAATAATTATAAATATGATATATTATACTATATTTAT--AATATAAA
22564 T
64 T
*
22565 T-ATAAGATTTTAGTTATT
1 TAATAA-ATTATAGTTATT
22583 GCTTATATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
59 6 0.09
60 5 0.07
61 20 0.29
62 10 0.14
63 8 0.11
64 7 0.10
65 14 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (64 bp):
TAATAAATTATAGTTATTAAATAATTATAAATATGATATATTATACTATATTTATAATATAAAT
Found at i:23043 original size:36 final size:34
Alignment explanation
Indices: 22981--23049 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 34
22971 TTAAATATTA
22981 ATTATTAATGATAAACTATATTATTATCTTAATT
1 ATTATTAATGATAAACTATATTATTATCTTAATT
* *
23015 ATTATTAATTATAACATTATTATTATTATCTTAAT
1 ATTATTAATGATAA-ACTA-TATTATTATCTTAAT
23050 AATAACAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 13 0.42
35 3 0.10
36 15 0.48
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (34 bp):
ATTATTAATGATAAACTATATTATTATCTTAATT
Found at i:24829 original size:23 final size:23
Alignment explanation
Indices: 24812--24857 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
24802 CTAATATATT
24812 AACATTCTAAAAATTAATAAGTTG
1 AACATT-TAAAAATTAATAAGTTG
* *
24836 AAGATTTAAAAATTAATTAGTT
1 AACATTTAAAAATTAATAAGTT
24858 TACCAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (23 bp):
AACATTTAAAAATTAATAAGTTG
Found at i:24932 original size:180 final size:179
Alignment explanation
Indices: 24572--24947 Score: 411
Period size: 180 Copynumber: 2.1 Consensus size: 179
24562 TTGTTTTATC
** * *
24572 ATAAACCAATTGTTTCTCTTCAAACAAGCTTATTTGGAATAAAATAATTCTAATTAATTAATATT
1 ATAAA-CAATTGTTTCGATTCAAACAAGCTTATTTGGAATAAAATAATACTAATTAATTAACATT
* * *** * * *
24637 CCAAAATTAATAAGTAAAAGATTTAAAAAAATAAATTTATTTACCGAGTGATTTTAAATAGTTAT
65 CAAAAATTAATAAGTAAAAGATTT-AAAAAATAAATTTATTTACCAAACCAGTTCAAATAGTCAT
** * **
24702 GATTGTTTGAACAATTATTTATTTCAAATCGTTATAATCTTTTGTTTTGTT
129 GATCATTTGAACAATTATCTATTTCAAATCGTTATAATCTTTAATTTTGTT
* * *
24753 ATAAAATAATTGTTTCGATTCATACAAGTTTATTTGGAATAAAATAATACTAA-TATATTAACAT
1 AT-AAACAATTGTTTCGATTCAAACAAGCTTATTTGGAATAAAATAATACTAATTA-ATTAACAT
** *
24817 TCTAAAAATTAATAAGTTGAAGATTT-AAAAATTAA-TTAGTTTACCAAACCAGTTCAAATAGTC
64 TC-AAAAATTAATAAGTAAAAGATTTAAAAAATAAATTTA-TTTACCAAACCAGTTCAAATAGTC
* *
24880 ATG-TCCATTTGAACTATTATCTATTTCAAATTGTTATACAT-TTTAATTTTGTT
127 ATGAT-CATTTGAACAATTATCTATTTCAAATCGTTATA-ATCTTTAATTTTGTT
*
24933 GTAAACAATTGTTTC
1 ATAAACAATTGTTTC
24948 TTATCGATCA
Statistics
Matches: 162, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
179 16 0.10
180 69 0.43
181 54 0.33
182 23 0.14
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.42
Consensus pattern (179 bp):
ATAAACAATTGTTTCGATTCAAACAAGCTTATTTGGAATAAAATAATACTAATTAATTAACATTC
AAAAATTAATAAGTAAAAGATTTAAAAAATAAATTTATTTACCAAACCAGTTCAAATAGTCATGA
TCATTTGAACAATTATCTATTTCAAATCGTTATAATCTTTAATTTTGTT
Found at i:25712 original size:17 final size:17
Alignment explanation
Indices: 25670--25722 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
25660 AAATAATTGT
25670 TATAATTAA--ATAATAA
1 TATAATTAATTATAAT-A
*
25686 TCTAATTTAATTATAATA
1 TATAA-TTAATTATAATA
*
25704 TATAATTAATTAAAATA
1 TATAATTAATTATAATA
25721 TA
1 TA
25723 ATACAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 4 0.13
17 17 0.55
18 5 0.16
19 5 0.16
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAATTAATTATAATA
Found at i:25713 original size:22 final size:22
Alignment explanation
Indices: 25672--25725 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
25662 ATAATTGTTA
25672 TAATTA-AATAATAATCTAATT
1 TAATTATAATAATAATCTAATT
25693 TAATTATAATATATAAT-TAATT
1 TAATTATAATA-ATAATCTAATT
* *
25715 AAAATATAATA
1 TAATTATAATA
25726 CAAATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 18 0.62
23 5 0.17
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTATAATAATAATCTAATT
Found at i:25818 original size:13 final size:13
Alignment explanation
Indices: 25802--25826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25792 AATACAAATA
25802 AATCTAATTATTT
1 AATCTAATTATTT
25815 AATCTAATTATT
1 AATCTAATTATT
25827 AAATAAATTA
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:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AATCTAATTATTT
Found at i:26022 original size:14 final size:14
Alignment explanation
Indices: 25999--26035 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
25989 TTGTCCAAAA
25999 TAAA-AATAATTAT
1 TAAATAATAATTAT
*
26012 TTAATAATAATTAT
1 TAAATAATAATTAT
26026 TAAAT-ATAAT
1 TAAATAATAAT
26036 AAAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATAATAATTAT
Found at i:26229 original size:18 final size:18
Alignment explanation
Indices: 26181--26230 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
26171 TATTAAAGAT
26181 ATTATTTATATATAATTTA
1 ATTATTTATAT-TAATTTA
**
26200 A-TAAATATTATTAATTTA
1 ATTATTTA-TATTAATTTA
26218 ATTATTTATATTA
1 ATTATTTATATTA
26231 TATATAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTTATATTAATTTA
Found at i:26250 original size:35 final size:37
Alignment explanation
Indices: 26181--26256 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
26171 TATTAAAGAT
*
26181 ATTATTTATATATAATTTAATAAATATTATTAATTTA
1 ATTATTTATATATAATATAATAAATATTATTAATTTA
* *
26218 ATTATTTATAT-TATATATAATATA-ATTA-TAATTTG
1 ATTATTTATATATA-ATATAATAAATATTATTAATTTA
26253 ATTA
1 ATTA
26257 ATAATAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 10 0.29
36 6 0.17
37 19 0.54
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (37 bp):
ATTATTTATATATAATATAATAAATATTATTAATTTA
Found at i:26856 original size:14 final size:15
Alignment explanation
Indices: 26815--26929 Score: 55
Period size: 14 Copynumber: 7.5 Consensus size: 15
26805 ATGTAATAAT
26815 TTAATAA-ATTATTA
1 TTAATAATATTATTA
26829 -TAATTAA-A-TATTA
1 TTAA-TAATATTATTA
26842 TTAATAATATT-TTA
1 TTAATAATATTATTA
* *
26856 TGAATCATATTAATTA
1 TTAATAATATT-ATTA
26872 TT-ATAATATGTAATTA
1 TTAATAATAT-T-ATTA
** *
26888 -TAATTGTATATAATA
1 TTAATAATAT-TATTA
26903 TTATATAATAATTATTTA
1 TTA-ATAAT-ATTA-TTA
26921 TTATATAAT
1 TTA-ATAAT
26930 TTAATTGGAC
Statistics
Matches: 78, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
13 11 0.14
14 20 0.26
15 11 0.14
16 18 0.23
17 5 0.06
18 13 0.17
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATAATATTATTA
Found at i:27028 original size:13 final size:12
Alignment explanation
Indices: 26982--27033 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
26972 ATTGTTTGAC
26982 AATAATAGTTAAT
1 AATAATA-TTAAT
26995 AA-AATATTAAT
1 AATAATATTAAT
27006 AATAACTATTAACT
1 AATAA-TATTAA-T
*
27020 ACTAATATT-AT
1 AATAATATTAAT
27031 AAT
1 AAT
27034 TAATTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 10 0.29
12 7 0.21
13 12 0.35
14 5 0.15
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:27074 original size:6 final size:6
Alignment explanation
Indices: 27026--27158 Score: 57
Period size: 6 Copynumber: 22.2 Consensus size: 6
27016 AACTACTAAT
* * *
27026 ATTATA ATTA-A TTTATA AGTTATA ATTAAA ATTAT- TTGCTATA ATTAT-
1 ATTATA ATTATA ATTATA A-TTATA ATTATA ATTATA AT--TATA ATTATA
* * * *
27074 ATTTTA ATTTTA ATT-TA ATTATTA A-TAGTA ATTA-A GTTATTTT ATTATA
1 ATTATA ATTATA ATTATA ATTA-TA ATTA-TA ATTATA ATTA--TA ATTATA
* *
27123 AGTTATA ATAATA ATT-TA A-TATT ATTATA ATTATA A
1 A-TTATA ATTATA ATTATA ATTATA ATTATA ATTATA A
27159 AATATTGAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
4 1 0.01
5 23 0.24
6 48 0.50
7 20 0.21
8 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (6 bp):
ATTATA
Found at i:28313 original size:13 final size:12
Alignment explanation
Indices: 28282--28322 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
28272 ATATTTGGAT
*
28282 AATATTATTATA
1 AATATTAATATA
28294 AATATTAATATA
1 AATATTAATATA
28306 ATATATTAATAATA
1 A-ATATTAAT-ATA
28320 AAT
1 AAT
28323 TTATTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.46
13 10 0.38
14 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATATTAATATA
Found at i:28330 original size:25 final size:25
Alignment explanation
Indices: 28283--28330 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
28273 TATTTGGATA
*
28283 ATATTATTATAAATATTAATATAAT
1 ATATTATAATAAATATTAATATAAT
*
28308 ATATTAATAATAAAT-TTATTATA
1 ATATT-ATAATAAATATTAATATA
28331 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATATTATAATAAATATTAATATAAT
Found at i:28487 original size:16 final size:16
Alignment explanation
Indices: 28446--28493 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
28436 TCCAATCTTC
28446 AATTGTTAAAAT-TTAA
1 AATTG-TAAAATATTAA
*
28462 AATATTTAAAATATTAA
1 AAT-TGTAAAATATTAA
28479 AATTGTAAAA-ATTAA
1 AATTGTAAAATATTAA
28494 TCAAAGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.18
16 15 0.54
17 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (16 bp):
AATTGTAAAATATTAA
Done.