Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 2 of 30
Found at i:196358 original size:13 final size:13
Alignment explanation
Indices: 196340--196364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
196330 ATTACTCACA
196340 TGTATCGATACAT
1 TGTATCGATACAT
196353 TGTATCGATACA
1 TGTATCGATACA
196365 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:196501 original size:52 final size:52
Alignment explanation
Indices: 196373--196493 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
196363 CACTGATCTT
*
196373 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
196425 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
196477 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
196494 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:202036 original size:14 final size:14
Alignment explanation
Indices: 202017--202045 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
202007 GCTCCATATT
202017 AAAGCTTTGTATGA
1 AAAGCTTTGTATGA
202031 AAAGCTTTGTATGA
1 AAAGCTTTGTATGA
202045 A
1 A
202046 TGATACGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (14 bp):
AAAGCTTTGTATGA
Found at i:207170 original size:13 final size:13
Alignment explanation
Indices: 207154--207184 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
207144 ACAATTCATC
207154 ATGTATCGATACA
1 ATGTATCGATACA
207167 ATGTATCGATACA
1 ATGTATCGATACA
*
207180 TTGTA
1 ATGTA
207185 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:207175 original size:33 final size:33
Alignment explanation
Indices: 207132--207200 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
207122 CCATTACGAG
*
207132 CAATGCATCGATACAATT-CATCATGTATCGATA
1 CAATGCATCGATAC-ATTGCACCATGTATCGATA
* *
207165 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGCATCGATACATTGCACCATGTATCGATA
207198 CAA
1 CAA
207201 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (33 bp):
CAATGCATCGATACATTGCACCATGTATCGATA
Found at i:207277 original size:19 final size:19
Alignment explanation
Indices: 207229--207284 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
207219 CTGCCAATCT
**
207229 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
207249 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
207268 CATGTTTCGATACAATG
1 CATGTATCGATACAATG
207285 TATGGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:207889 original size:21 final size:22
Alignment explanation
Indices: 207865--207905 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
207855 AAAGAATTTC
*
207865 TCAAA-AATTTCTCTCCCTTAA
1 TCAAAGAATTTCTCCCCCTTAA
*
207886 TCAAAGCATTTCTCCCCCTT
1 TCAAAGAATTTCTCCCCCTT
207906 TGTTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (22 bp):
TCAAAGAATTTCTCCCCCTTAA
Found at i:208545 original size:20 final size:20
Alignment explanation
Indices: 208500--208551 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
208490 GTAGCCAAAC
* **
208500 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
208520 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
208539 TTGTATCGATACA
1 TTGTATCGATACA
208552 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:210784 original size:21 final size:21
Alignment explanation
Indices: 210751--210800 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
210741 TTGCAAGTTG
*
210751 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
210773 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
210794 AAATAAA
1 AAATAAA
210801 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:212617 original size:15 final size:15
Alignment explanation
Indices: 212597--212627 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
212587 TAAAAATGTC
*
212597 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
212612 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
212627 C
1 C
212628 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:214875 original size:20 final size:20
Alignment explanation
Indices: 214832--214877 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
214822 AAATCTTTTG
214832 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
214853 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
214873 CAAAA
1 CAAAA
214878 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:217280 original size:20 final size:20
Alignment explanation
Indices: 217235--217286 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
217225 GTAGCCAAAC
* **
217235 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
217255 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
217274 TTGTATCGATACA
1 TTGTATCGATACA
217287 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:219723 original size:13 final size:13
Alignment explanation
Indices: 219701--219740 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
219691 ATAGTAACCC
*
219701 ATGTATCGATACA
1 ATGTACCGATACA
219714 ATGTACCGATACA
1 ATGTACCGATACA
219727 ATGTACCGATACA
1 ATGTACCGATACA
219740 A
1 A
219741 AGAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (13 bp):
ATGTACCGATACA
Found at i:221421 original size:65 final size:65
Alignment explanation
Indices: 221341--221468 Score: 256
Period size: 65 Copynumber: 2.0 Consensus size: 65
221331 TTTTGACATC
221341 CATTTGATATAATTTAAAATCATAAAAGCATGCAAAGGCTAGCAAAATTCTAATGGCTTCTAATG
1 CATTTGATATAATTTAAAATCATAAAAGCATGCAAAGGCTAGCAAAATTCTAATGGCTTCTAATG
221406 CATTTGATATAATTTAAAATCATAAAAGCATGCAAAGGCTAGCAAAATTCTAATGGCTTCTAA
1 CATTTGATATAATTTAAAATCATAAAAGCATGCAAAGGCTAGCAAAATTCTAATGGCTTCTAA
221469 CCTAGCAACG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (65 bp):
CATTTGATATAATTTAAAATCATAAAAGCATGCAAAGGCTAGCAAAATTCTAATGGCTTCTAATG
Found at i:225175 original size:453 final size:453
Alignment explanation
Indices: 224325--225695 Score: 2708
Period size: 453 Copynumber: 3.0 Consensus size: 453
224315 TTTTTGTTTG
*
224325 AAAA-ATCATGTGTTTGAACTCACTTAATCACAAATCTAGACCTGAAAATTAACTTTACCCCAAG
1 AAAATATCATGTGTTTGAACTCACTTAATCACAAATCCAGACCTGAAAATTAACTTTACCCCAAG
224389 ATTGTGATATTTGCTTGGAAAAAACCTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATG
66 ATTGTGATATTTGCTTGGAAAAAACCTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATG
224454 CTTAACTTAGGGGAGTTTTTTTTGAAAAATCGATTTTCAAATACAAACAAGCATGCATATTGACA
131 CTTAACTTAGGGGAGTTTTTTTTGAAAAATCGATTTTCAAATACAAACAAGCATGCATATTGACA
*
224519 TGAAAAATGTGATAATCATACAATGAACTAATGGATAACATTAAATGAGATGCTGGACATATTAA
196 TGGAAAATGTGATAATCATACAATGAACTAATGGATAACATTAAATGAGATGCTGGACATATTAA
224584 AAATGCATGAAACATAATAAAAAAAATGCATGGTCAAAGGCTACTAGGATGAACATTGCATTTTA
261 AAATGCATGAAACATAATAAAAAAAATGCATGGTCAAAGGCTACTAGGATGAACATTGCATTTTA
224649 GTCACAAAAGATGGCATCAAAACATTAAGACAATCCTAAAACTACCACATTCAAGGCCACATTAA
326 GTCACAAAAGATGGCATCAAAACATTAAGACAATCCTAAAACTACCACATTCAAGGCCACATTAA
224714 TGCATGATGTTCTTAAAAAGGTTATGGAAGCATGATAAGCTCACTAAAATGATGAGAATAACA
391 TGCATGATGTTCTTAAAAAGGTTATGGAAGCATGATAAGCTCACTAAAATGATGAGAATAACA
224777 AAAATATCATGTGTTTGAACTCACTTAATCACAAATCCAGACCTGAAAATTAACTTTACCCCAAG
1 AAAATATCATGTGTTTGAACTCACTTAATCACAAATCCAGACCTGAAAATTAACTTTACCCCAAG
224842 ATTGTGATATTTGCTTGGAAAAAACCTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATG
66 ATTGTGATATTTGCTTGGAAAAAACCTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATG
224907 CTTAACTTAGGGGAGTTTTTTTTGAAAAATCGATTTTCAAATACAAACAAGCATGCATATTGACA
131 CTTAACTTAGGGGAGTTTTTTTTGAAAAATCGATTTTCAAATACAAACAAGCATGCATATTGACA
224972 TGGAAAATGTGATAATCATACAATGAACTAATGGATAACATTAAATGAGATGCTGGACATATTAA
196 TGGAAAATGTGATAATCATACAATGAACTAATGGATAACATTAAATGAGATGCTGGACATATTAA
225037 AAATGCATGAAACATAATAAAAAAAATGCATGGTCAAAGGCTACTAGGATGAACATTGCATTTTA
261 AAATGCATGAAACATAATAAAAAAAATGCATGGTCAAAGGCTACTAGGATGAACATTGCATTTTA
225102 GTCACAAAAGATGGCATCAAAACATTAAGACAATCCTAAAACTACCACATTCAAGGCCACATTAA
326 GTCACAAAAGATGGCATCAAAACATTAAGACAATCCTAAAACTACCACATTCAAGGCCACATTAA
225167 TGCATGATGTTCTTAAAAAGGTTATGGAAGCATGATAAGCTCACTAAAATGATGAGAATAACA
391 TGCATGATGTTCTTAAAAAGGTTATGGAAGCATGATAAGCTCACTAAAATGATGAGAATAACA
225230 AAAATATCATGTGTTTGAACTCACTTAATCACAAATCCAGACCTGAAAATTAACTTTACCCCAAG
1 AAAATATCATGTGTTTGAACTCACTTAATCACAAATCCAGACCTGAAAATTAACTTTACCCCAAG
225295 ATTGTGATATTTGCTTGGAAAAAACCTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATG
66 ATTGTGATATTTGCTTGGAAAAAACCTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATG
225360 CTTAACTTAGGGGAGTTTTTTTTGAAAAATCGATTTTCAAATACAAACAAGCATGCATATTGACA
131 CTTAACTTAGGGGAGTTTTTTTTGAAAAATCGATTTTCAAATACAAACAAGCATGCATATTGACA
225425 TGGAAAATGTGATAATCATACAATGAACTAATGGATAACATTAAATGAGATGCTGGACATATTAA
196 TGGAAAATGTGATAATCATACAATGAACTAATGGATAACATTAAATGAGATGCTGGACATATTAA
*
225490 AAATGCATGAAACATAATAAAAAAAATGCATGGTCAAAGGCTACTAGGATTAACATTGCATTTTA
261 AAATGCATGAAACATAATAAAAAAAATGCATGGTCAAAGGCTACTAGGATGAACATTGCATTTTA
225555 GTCACAAAAGATGGCATCAAAACATTAAGACAATCCTAAAACTACCACATTCAAGGCCACATTAA
326 GTCACAAAAGATGGCATCAAAACATTAAGACAATCCTAAAACTACCACATTCAAGGCCACATTAA
225620 TGCATGATGTTCTTAAAAAGGTTATGGAAGCATGATAAGCTCACTAAAATGATGAGAATAACA
391 TGCATGATGTTCTTAAAAAGGTTATGGAAGCATGATAAGCTCACTAAAATGATGAGAATAACA
225683 AAAATATCATGTG
1 AAAATATCATGTG
225696 AAAGTGAAAA
Statistics
Matches: 915, Mismatches: 3, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
452 4 0.00
453 911 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (453 bp):
AAAATATCATGTGTTTGAACTCACTTAATCACAAATCCAGACCTGAAAATTAACTTTACCCCAAG
ATTGTGATATTTGCTTGGAAAAAACCTTAAGCTTATGTTAATCCTCATTGATTGAGGCTAACATG
CTTAACTTAGGGGAGTTTTTTTTGAAAAATCGATTTTCAAATACAAACAAGCATGCATATTGACA
TGGAAAATGTGATAATCATACAATGAACTAATGGATAACATTAAATGAGATGCTGGACATATTAA
AAATGCATGAAACATAATAAAAAAAATGCATGGTCAAAGGCTACTAGGATGAACATTGCATTTTA
GTCACAAAAGATGGCATCAAAACATTAAGACAATCCTAAAACTACCACATTCAAGGCCACATTAA
TGCATGATGTTCTTAAAAAGGTTATGGAAGCATGATAAGCTCACTAAAATGATGAGAATAACA
Found at i:226461 original size:20 final size:19
Alignment explanation
Indices: 226432--226506 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
226422 TAAAAGACAT
226432 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
226451 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
226472 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
226492 AATGTATCGATACAT
1 AATGTATCGATACAT
226507 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:226489 original size:40 final size:39
Alignment explanation
Indices: 226429--226506 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
226419 AGGTAAAAGA
*
226429 CATAATGTATCGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
226468 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
226507 CTGGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:231874 original size:156 final size:156
Alignment explanation
Indices: 231622--232768 Score: 882
Period size: 156 Copynumber: 7.3 Consensus size: 156
231612 TACGACTTGG
*
231622 TTCTAATAAAAATTATC-AAAATG-TCCCT-AAGATATATCTTCGACATGAAAGTATCCTGATAA
1 TTCTAA-AAAAATTA-CGAAAATGCT-CCTAAAG-TATACCTTCGACATGAAAGTATCCTGATAA
* * * * * * * * *
231684 -TCTAAAGGACTTAAAATTGGTCATAAATGAGATGAGCCTATCCTAAATGTATACTTTTGGCATA
62 CCCTAAAGAACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCATA
** *
231748 AAAGCATCCTGGTGACAAATTAGGACTCGG
127 AAAGCATCCTGGTGACAACCTAGGACTCGA
* * * *
231778 TTCTAAAAAAATTACGAAAATGCTCTTAAAGTATACCTTTGACATGAAAGTATCTTGGTAACCCT
1 TTCTAAAAAAATTACGAAAATGCTCCTAAAGTATACCTTCGACATGAAAGTATCCTGATAACCCT
* **
231843 GAAGAACTTAAAAATGATCATAAATGGGATGAACCTA---TAAATGCATGCCTTTGGTATAAAAG
66 AAAGAACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTT-G-------G
* * *
231905 TATCCCTGTGATAAAAGCATCCTGATGACAACTTAAGACTCGA
123 -----C----ATAAAAGCATCCTGGTGACAACCTAGGACTCGA
** * * * * *
231948 TTCTAAAAGGATTACAAAAATGCCCCTAAAATATACCTTCGACATGAAAGTATCC-AAGTAACTC
1 TTCTAAAAAAATTACGAAAATGCTCCTAAAGTATACCTTCGACATGAAAGTATCCTGA-TAACCC
* * * * * *
232012 T-AAGAGATTTAAAAATGATCATAAATGGGATGAATCTATCTTAAATACACACGTTTAGCATAAA
65 TAAAGA-ACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCATAAA
** * * * *
232076 AGCATATTGATGACAACCTCGGACTTGG
129 AGCATCCTGGTGACAACCTAGGACTCGA
* * * * * ** * * *
232104 TTCTAGAAAAATTATGAAAATGC-CTTTAGGATATATATTCAACATG-AAGATATCCTGGTAACT
1 TTCTAAAAAAATTACGAAAATGCTCCTAAAG-TATACCTTCGACATGAAAG-TATCCTGATAACC
* * * *
232167 CTAAAGAACTTAAAAATGATCACAAATGGGATTAACCTATCCTAAATGCATACCTTTGGCAAAAA
64 CTAAAGAACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCATAAA
232232 AGCAT-CTCGGTGACAACCTCA-GACTCGA
129 AGCATCCT-GGTGACAACCT-AGGACTCGA
* * * * * *
232260 TTTTAAAAAAATTACAAAAATACTCCTAAAATATACCTTCGACATGAAAGTAT-ATCGATAACCT
1 TTCTAAAAAAATTACGAAAATGCTCCTAAAGTATACCTTCGACATGAAAGTATCCT-GATAACCC
* * * *
232324 TAAA-AGACTTAAAAATAATCACAAA-GAGGATAAACCTATCCTAAATGCACGCCTTTGGCATAA
65 TAAAGA-ACTTAAAAATGATCATAAATG-GGATGAACCTATCCTAAATGCACACCTTTGGCATAA
232387 AAGCATTCC-GGTGACAACCTAGGACTCGA
128 AAGCA-TCCTGGTGACAACCTAGGACTCGA
* * * * * * ** * *
232416 TTTTAAAAAAGTTATGAAAATACCCCT-AAGTTATACTTTTTACATAAAAGTATTCTGATAACCC
1 TTCTAAAAAAATTACGAAAATGCTCCTAAAG-TATACCTTCGACATGAAAGTATCCTGATAACCC
* *
232480 TAAAGGACTTTAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCATAAAA
65 TAAAGAACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCATAAAA
*
232545 GCATCCTGGTGACAACCTAAGACTCGA
130 GCATCCTGGTGACAACCTAGGACTCGA
* ** * * ** * *
232572 TTTTAAGCAAATTATGAAAATAACT--TAGGGTATGCCTTCAACATGAAAGTATCAC-GATAACC
1 TTCTAAAAAAATTACGAAAAT-GCTCCTAAAGTATACCTTCGACATGAAAGTATC-CTGATAACC
* * * *
232634 TTAAA-AGACCTAAGAATGATCATAAATGGGATGAACCTATCATAAATGCACACCTTTGGCATAA
64 CTAAAGA-ACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCATAA
* *** *
232698 AAACATCCCCATGACAACCTAGGACTCGG
128 AAGCATCCTGGTGACAACCTAGGACTCGA
* * ** * *
232727 TTTTAAGAAAATTATAAAAATGCCCCT-AAGATATACTTTCGA
1 TTCTAAAAAAATTACGAAAATGCTCCTAAAG-TATACCTTCGA
232769 TAATCCTAAA
Statistics
Matches: 794, Mismatches: 145, Indels: 104
0.76 0.14 0.10
Matches are distributed among these distances:
153 12 0.02
154 3 0.00
155 183 0.23
156 449 0.57
157 15 0.02
158 1 0.00
160 1 0.00
161 1 0.00
165 1 0.00
166 1 0.00
169 4 0.01
170 112 0.14
173 11 0.01
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.27
Consensus pattern (156 bp):
TTCTAAAAAAATTACGAAAATGCTCCTAAAGTATACCTTCGACATGAAAGTATCCTGATAACCCT
AAAGAACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCATAAAAG
CATCCTGGTGACAACCTAGGACTCGA
Found at i:232027 original size:170 final size:170
Alignment explanation
Indices: 231745--232050 Score: 443
Period size: 170 Copynumber: 1.8 Consensus size: 170
231735 TACTTTTGGC
* * * * * * *
231745 ATAAAAGCATCCTGGTGACAAATTAGGACTCGGTTCTAAAAAAATTACGAAAATGCTCTTAAAGT
1 ATAAAAGCATCCTGATGACAAATTAAGACTCGATTCTAAAAAAATTACAAAAATGCCCCTAAAAT
* ***
231810 ATACCTTTGACATGAAAGTATCTTGGTAACCCTGAAGAACTTAAAAATGATCATAAATGGGATGA
66 ATACCTTCGACATGAAAGTATCCAAGTAACCCTGAAGAACTTAAAAATGATCATAAATGGGATGA
231875 ACCTATAAATGCATGCCTTTGGTATAAAAGTATCCCTGTG
131 ACCTATAAATGCATGCCTTTGGTATAAAAGTATCCCTGTG
* **
231915 ATAAAAGCATCCTGATGACAACTTAAGACTCGATTCTAAAAGGATTACAAAAATGCCCCTAAAAT
1 ATAAAAGCATCCTGATGACAAATTAAGACTCGATTCTAAAAAAATTACAAAAATGCCCCTAAAAT
* *
231980 ATACCTTCGACATGAAAGTATCCAAGTAACTCT-AAGAGATTTAAAAATGATCATAAATGGGATG
66 ATACCTTCGACATGAAAGTATCCAAGTAACCCTGAAGA-ACTTAAAAATGATCATAAATGGGATG
*
232044 AATCTAT
130 AACCTAT
232051 CTTAAATACA
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
169 4 0.03
170 114 0.97
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (170 bp):
ATAAAAGCATCCTGATGACAAATTAAGACTCGATTCTAAAAAAATTACAAAAATGCCCCTAAAAT
ATACCTTCGACATGAAAGTATCCAAGTAACCCTGAAGAACTTAAAAATGATCATAAATGGGATGA
ACCTATAAATGCATGCCTTTGGTATAAAAGTATCCCTGTG
Found at i:232497 original size:312 final size:310
Alignment explanation
Indices: 231917--232766 Score: 987
Period size: 312 Copynumber: 2.7 Consensus size: 310
231907 TCCCTGTGAT
* * * ** * *
231917 AAAAGCATCCTGATGACAACTTAAGACTCGATTCTAAAAGGATTACAAAAATGCCCCTAAAATAT
1 AAAAGCATCCTGGTGACAACCTAAGACTCGATTTTAAAAAAATTACAAAAATACTCCTAAAATAT
* * * *
231982 ACCTTCGACATGAAAGTATCCAAGTAA-CTCTAAGAGATTTAAAAATGATCATAAATGGGATGAA
66 ACCTTCGACATGAAAGTATACGA-TAACCT-TAAAAGACTTAAAAATGATCATAAATGGGATGAA
* * * * * * * * *
232046 TCTATCTTAAATACACACGTTTAGCATAAAAGCATAT-TGATGACAACCTCGGACTTGGTTCTAG
129 CCTATCATAAATGCACACCTTTGGCATAAAAGCAT-TCCGATGACAACCTAGGACTCGGTTTTA-
** * * * *
232110 AAAAATTATGAAAATGCCTTTAGGATATA-TATTCAACATGAAGATATCCTGGTAACTCTAAAGA
192 AAAAATTATGAAAATGCCCCTAAGATATACT-TTCAACATAAAGATATCCTGATAACCCTAAAGA
* *
232174 ACTTAAAAATGATCACAAATGGGATTAACCTATCCTAAATGCATACCTTTGGCAA
256 ACTTAAAAATGATCACAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCAA
*
232229 AAAAGCAT-CTCGGTGACAACCTCAGACTCGATTTTAAAAAAATTACAAAAATACTCCTAAAATA
1 AAAAGCATCCT-GGTGACAACCTAAGACTCGATTTTAAAAAAATTACAAAAATACTCCTAAAATA
* * *
232293 TACCTTCGACATGAAAGTATATCGATAACCTTAAAAGACTTAAAAATAATCACAAA-GAGGATAA
65 TACCTTCGACATGAAAGTATA-CGATAACCTTAAAAGACTTAAAAATGATCATAAATG-GGATGA
* * * *
232357 ACCTATCCTAAATGCACGCCTTTGGCATAAAAGCATTCCGGTGACAACCTAGGACTCGATTTTAA
128 ACCTATCATAAATGCACACCTTTGGCATAAAAGCATTCCGATGACAACCTAGGACTCGGTTTTAA
* * ** * *
232422 AAAAGTTATGAAAATACCCCTAAGTTATACTTTTTACATAAA-AGTATTCTGATAACCCTAAAGG
193 AAAA-TTATGAAAATGCCCCTAAGATATACTTTCAACATAAAGA-TATCCTGATAACCCTAAAGA
* * *
232486 ACTTTAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCAT
256 ACTTAAAAATGATCACAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCAA
** ** ***
232541 AAAAGCATCCTGGTGACAACCTAAGACTCGATTTTAAGCAAATTATGAAAATAACT--TAGGGTA
1 AAAAGCATCCTGGTGACAACCTAAGACTCGATTTTAAAAAAATTACAAAAAT-ACTCCTAAAATA
* * * *
232604 TGCCTTCAACATGAAAGTATCACGATAACCTTAAAAGACCTAAGAATGATCATAAATGGGATGAA
65 TACCTTCGACATGAAAGTAT-ACGATAACCTTAAAAGACTTAAAAATGATCATAAATGGGATGAA
* * *
232669 CCTATCATAAATGCACACCTTTGGCATAAAAACATCCCCATGACAACCTAGGACTCGGTTTTAAG
129 CCTATCATAAATGCACACCTTTGGCATAAAAGCATTCCGATGACAACCTAGGACTCGGTTTTAA-
*
232734 AAAATTATAAAAATGCCCCTAAGATATACTTTC
193 AAAATTATGAAAATGCCCCTAAGATATACTTTC
232767 GATAATCCTA
Statistics
Matches: 455, Mismatches: 70, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
311 150 0.33
312 295 0.65
313 10 0.02
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (310 bp):
AAAAGCATCCTGGTGACAACCTAAGACTCGATTTTAAAAAAATTACAAAAATACTCCTAAAATAT
ACCTTCGACATGAAAGTATACGATAACCTTAAAAGACTTAAAAATGATCATAAATGGGATGAACC
TATCATAAATGCACACCTTTGGCATAAAAGCATTCCGATGACAACCTAGGACTCGGTTTTAAAAA
ATTATGAAAATGCCCCTAAGATATACTTTCAACATAAAGATATCCTGATAACCCTAAAGAACTTA
AAAATGATCACAAATGGGATGAACCTATCCTAAATGCACACCTTTGGCAA
Found at i:232747 original size:155 final size:154
Alignment explanation
Indices: 231978--232918 Score: 748
Period size: 156 Copynumber: 6.1 Consensus size: 154
231968 TGCCCCTAAA
* * * *
231978 ATATACCTTCGACATGAAAGTATCCAAGTAA-CTCTAAGAGATTTAAAAATGATCATAAATGGGA
1 ATATACCTTCAACATGAAAGTATCCGA-TAACCT-TAAAAGACTTAAAAATGATCATAAATGGGA
* * * * * *** * * * * *
232042 TGAATCTATCTTAAATACACACGTTTAGCATAAAAGCATATTGATGACAACCTCGGACTTGGTTC
64 TGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAGGACTCGATTT
** *
232107 T-AGAAAAATTATGAAAATGCCTTTAGG
129 TAAG-AAAATTATGAAAATAAC-TTAAG
** * *
232134 ATATATATTCAACATG-AAGATATCCTGGTAA-CTCT-AAAGAACTTAAAAATGATCACAAATGG
1 ATATACCTTCAACATGAAAG-TATCC-GATAACCT-TAAAAG-ACTTAAAAATGATCATAAATGG
* * * *
232196 GATTAACCTATCCTAAATGCATACCTTTGGCAAAAAAGCATCTCGGTGACAACCTCA-GACTCGA
62 GATGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCT-AGGACTCGA
* ** *
232260 TTTTAAAAAAATTACAAAAAT-ACTCCTAAA
126 TTTTAAGAAAATTATGAAAATAACT--TAAG
* * * *
232290 ATATACCTTCGACATGAAAGTATATCGATAACCTTAAAAGACTTAAAAATAATCACAAA-GAGGA
1 ATATACCTTCAACATGAAAGTAT-CCGATAACCTTAAAAGACTTAAAAATGATCATAAATG-GGA
* * *
232354 TAAACCTATCCTAAATGCACGCCTTTGGCATAAAAGCATTCCGGTGACAACCTAGGACTCGATTT
64 TGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAGGACTCGATTT
* *
232419 TAA-AAAAGTTATGAAAATACCCCTAAG
129 TAAGAAAA-TTATGAAAATA-ACTTAAG
* * ** * * * * *
232446 TTATACTTTTTACATAAAAGTATTCTGATAACCCTAAAGGACTTTAAAATGATCATAAATGGGAT
1 ATATACCTTCAACATGAAAGTA-TCCGATAACCTTAAAAGACTTAAAAATGATCATAAATGGGAT
* *
232511 GAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCTGGTGACAACCTAAGACTCGATTTT
65 GAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAGGACTCGATTTT
* *
232576 AAGCAAATTATGAAAATAACTTAGG
130 AAGAAAATTATGAAAATAACTTAAG
* * * *
232601 GTATGCCTTCAACATGAAAGTATCACGATAACCTTAAAAGACCTAAGAATGATCATAAATGGGAT
1 ATATACCTTCAACATGAAAGTATC-CGATAACCTTAAAAGACTTAAAAATGATCATAAATGGGAT
* * ** *
232666 GAACCTATCATAAATGCACACCTTTGGCATAAAAACATCCCCATGACAACCTAGGACTCGGTTTT
65 GAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAGGACTCGATTTT
* ** *
232731 AAGAAAATTATAAAAATGCCCCTAAG
130 AAGAAAATTATGAAAAT-AACTTAAG
* * *
232757 ATATA-CTT--TC--G--A-TA----AT--CC-TAAAAGACTTAAGAATGATCATAAATAGGATG
1 ATATACCTTCAACATGAAAGTATCCGATAACCTTAAAAGACTTAAAAATGATCATAAATGGGATG
* ** * * * * *
232807 AAACTATCCTAAATGCACATTTTTGGCAAAAAAGCATCCCAGCGACAACCAAAGG-CTC-AGTTC
66 AACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACC-TAGGACTCGA-TTT
* * * *
232870 TAAAAAAATTATAAAAATACCTT-TG
129 TAAGAAAATTATGAAAATAACTTAAG
* *
232895 AGTATACCTTCGACATAAAAGTAT
1 A-TATACCTTCAACATGAAAGTAT
232919 TTTAATAATC
Statistics
Matches: 637, Mismatches: 115, Indels: 74
0.77 0.14 0.09
Matches are distributed among these distances:
138 2 0.00
139 7 0.01
140 96 0.15
141 5 0.01
142 1 0.00
143 2 0.00
146 1 0.00
147 2 0.00
148 2 0.00
149 1 0.00
151 1 0.00
153 1 0.00
154 3 0.00
155 143 0.22
156 353 0.55
157 16 0.03
158 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (154 bp):
ATATACCTTCAACATGAAAGTATCCGATAACCTTAAAAGACTTAAAAATGATCATAAATGGGATG
AACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAGGACTCGATTTTA
AGAAAATTATGAAAATAACTTAAG
Found at i:232878 original size:140 final size:140
Alignment explanation
Indices: 232626--232887 Score: 361
Period size: 140 Copynumber: 1.9 Consensus size: 140
232616 GAAAGTATCA
* *
232626 CGATAACCTTAAAAGACCTAAGAATGATCATAAATGGGATGAACCTATCATAAATGCACACCTTT
1 CGATAACCTTAAAAGACCTAAGAATGATCATAAATAGGATGAAACTATCATAAATGCACACCTTT
* * * * *
232691 GGCATAAAAACATCCCCATGACAACCTAGGACTCGGTTTTAAGAAAATTATAAAAATGCCCCTAA
66 GGCATAAAAACATCCCCACGACAACCAAGGACTCAGTTCTAAAAAAATTATAAAAATGCCCCTAA
232756 GATATACTTT
131 GATATACTTT
* * **
232766 CGATAATCC-TAAAAGACTTAAGAATGATCATAAATAGGATGAAACTATCCTAAATGCACATTTT
1 CGATAA-CCTTAAAAGACCTAAGAATGATCATAAATAGGATGAAACTATCATAAATGCACACCTT
232830 TGGCA-AAAAAGCAT-CCCAGCGACAACCAAAGG-CTCAGTTCTAAAAAAATTATAAAAAT
65 TGGCATAAAAA-CATCCCCA-CGACAACC-AAGGACTCAGTTCTAAAAAAATTATAAAAAT
232888 ACCTTTGAGT
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
139 9 0.08
140 93 0.87
141 5 0.05
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (140 bp):
CGATAACCTTAAAAGACCTAAGAATGATCATAAATAGGATGAAACTATCATAAATGCACACCTTT
GGCATAAAAACATCCCCACGACAACCAAGGACTCAGTTCTAAAAAAATTATAAAAATGCCCCTAA
GATATACTTT
Found at i:234475 original size:41 final size:41
Alignment explanation
Indices: 234413--234493 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
234403 TGATGATCAT
234413 GATAAAATAAAATAATAGATAGTTAGAATCAAACTAAATTG
1 GATAAAATAAAATAATAGATAGTTAGAATCAAACTAAATTG
* *
234454 GATAAAATCAAATAATGGATAGTTAGAATCAAACTAAATT
1 GATAAAATAAAATAATAGATAGTTAGAATCAAACTAAATT
234494 AGCTAAGGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.27
Consensus pattern (41 bp):
GATAAAATAAAATAATAGATAGTTAGAATCAAACTAAATTG
Found at i:234485 original size:21 final size:21
Alignment explanation
Indices: 234422--234486 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
234412 TGATAAAATA
*
234422 AAATAATAGATAGTTAGAATC
1 AAATAATGGATAGTTAGAATC
234443 AAACTAAATTGGATA---A-AATC
1 AAA-T-AA-TGGATAGTTAGAATC
234463 AAATAATGGATAGTTAGAATC
1 AAATAATGGATAGTTAGAATC
234484 AAA
1 AAA
234487 CTAAATTAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
17 6 0.17
18 2 0.06
19 1 0.03
20 8 0.22
21 11 0.31
22 1 0.03
23 2 0.06
24 5 0.14
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (21 bp):
AAATAATGGATAGTTAGAATC
Found at i:237512 original size:32 final size:32
Alignment explanation
Indices: 237476--237547 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
237466 TTGTTATTTA
* *
237476 ATTTTGATACATTTATTGAATTGAAACAATTG
1 ATTTTGATACATTTAATGAATTAAAACAATTG
* *
237508 ATTTTGATATATTTAATGAATTAAAACATTTG
1 ATTTTGATACATTTAATGAATTAAAACAATTG
237540 ATTTTGAT
1 ATTTTGAT
237548 TTGAATGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (32 bp):
ATTTTGATACATTTAATGAATTAAAACAATTG
Found at i:243772 original size:20 final size:20
Alignment explanation
Indices: 243725--243772 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
243715 GAAATTTATT
*
243725 AATACATTCACTAATGTATC
1 AATACATTCACTAATGTATA
* * * *
243745 GATGCATTCATTTATGTATA
1 AATACATTCACTAATGTATA
243765 AATACATT
1 AATACATT
243773 TAGGTTCAAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (20 bp):
AATACATTCACTAATGTATA
Found at i:245618 original size:31 final size:31
Alignment explanation
Indices: 245582--245647 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
245572 AGTATCATTT
*
245582 CAATTTAGTTATTAGTTAGTGTTGTTTATAC
1 CAATTTAGGTATTAGTTAGTGTTGTTTATAC
*
245613 CAATTTAGGTATTAGTTAGTGTTGTTTATGC
1 CAATTTAGGTATTAGTTAGTGTTGTTTATAC
245644 CAAT
1 CAAT
245648 ATATAATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (31 bp):
CAATTTAGGTATTAGTTAGTGTTGTTTATAC
Found at i:247393 original size:25 final size:23
Alignment explanation
Indices: 247353--247409 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 23
247343 TATATGAAAG
247353 AAATTACATAATTTATATAAATAA
1 AAATTA-ATAATTTATATAAATAA
*
247377 AAATTAATATATATTATATAATTAA
1 AAATTAATA-AT-TTATATAAATAA
247402 AAATTAAT
1 AAATTAAT
247410 CGGGTTAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 3 0.10
24 8 0.27
25 19 0.63
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTAATAATTTATATAAATAA
Found at i:250888 original size:16 final size:17
Alignment explanation
Indices: 250868--250938 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
250858 TATGATACGG
250868 ATAAAATATAAAAAAAT
1 ATAAAATATAAAAAAAT
*
250885 -TAAAATATAAAATAAT
1 ATAAAATATAAAAAAAT
*
250901 ATAAAAAATAAAATAAAT
1 ATAAAATATAAAA-AAAT
* * *
250919 ATGAAATATATACAAAT
1 ATAAAATATAAAAAAAT
250936 ATA
1 ATA
250939 TCAAAATCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 15 0.34
17 17 0.39
18 12 0.27
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (17 bp):
ATAAAATATAAAAAAAT
Found at i:250899 original size:28 final size:25
Alignment explanation
Indices: 250871--250928 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
250861 GATACGGATA
250871 AAATATAAAAAAATTAAAATATAAAAT
1 AAATATAAAAAAA-TAAAATA-AAAAT
*
250898 -AATAT-AAAAAATAAAATAAATAT
1 AAATATAAAAAAATAAAATAAAAAT
250921 GAAATATA
1 -AAATATA
250929 TACAAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
23 4 0.15
24 7 0.26
25 11 0.41
26 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
AAATATAAAAAAATAAAATAAAAAT
Found at i:250911 original size:17 final size:17
Alignment explanation
Indices: 250868--250928 Score: 79
Period size: 16 Copynumber: 3.6 Consensus size: 17
250858 TATGATACGG
*
250868 ATAAAATATAAAAAAAT
1 ATAAAATATAAAATAAT
250885 -TAAAATATAAAATAAT
1 ATAAAATATAAAATAAT
*
250901 ATAAAAAATAAAATAAAT
1 ATAAAATATAAAAT-AAT
*
250919 ATGAAATATA
1 ATAAAATATA
250929 TACAAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 15 0.39
17 12 0.32
18 11 0.29
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAAAATATAAAATAAT
Found at i:250912 original size:24 final size:23
Alignment explanation
Indices: 250868--250915 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
250858 TATGATACGG
250868 ATAAAATATAAAAAAATTAAAAT
1 ATAAAATATAAAAAAATTAAAAT
250891 ATAAAATAATATAAAAAA-TAAAAT
1 ATAAAAT-ATA-AAAAAATTAAAAT
250915 A
1 A
250916 AATATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.30
24 10 0.43
25 6 0.26
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (23 bp):
ATAAAATATAAAAAAATTAAAAT
Found at i:251669 original size:11 final size:11
Alignment explanation
Indices: 251649--251695 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
251639 TATAAGATTT
251649 TAATACTAAATA
1 TAATA-TAAATA
251661 -AATATTAAATA
1 TAATA-TAAATA
*
251672 TAATATAAATT
1 TAATATAAATA
*
251683 TAATAAAAATA
1 TAATATAAATA
251694 TA
1 TA
251696 TATTTAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 26 0.87
12 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATATAAATA
Found at i:251671 original size:18 final size:17
Alignment explanation
Indices: 251625--251685 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
251615 TAAAAGAAAT
251625 ATTTAAATATTATATATAA
1 ATTTAAATA-TA-ATATAA
*
251644 GATTTTAATACTAA-ATAA
1 -ATTTAAATA-TAATATAA
251662 ATATTAAATATAATATAA
1 AT-TTAAATATAATATAA
251680 ATTTAA
1 ATTTAA
251686 TAAAAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 9 0.25
18 16 0.44
19 1 0.03
20 10 0.28
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTAAATATAATATAA
Found at i:255178 original size:17 final size:17
Alignment explanation
Indices: 255156--255193 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
255146 TTCTTTCATT
255156 TTCTTCTTCTTCCTTCC
1 TTCTTCTTCTTCCTTCC
* *
255173 TTCTTCTTTTTCCTTCT
1 TTCTTCTTCTTCCTTCC
255190 TTCT
1 TTCT
255194 CACCCATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTTCTTCTTCCTTCC
Found at i:257312 original size:166 final size:163
Alignment explanation
Indices: 256975--257440 Score: 517
Period size: 166 Copynumber: 2.8 Consensus size: 163
256965 GAGACTGAAA
* * * *
256975 GGATAAAAGATTTACCTGGGACTAAGCCAACAGGTAAACAAAGGATAAAAAAGTTGACCGGGATT
1 GGATAAAGGATTTACCCGAGACTAGGCC-ACAGGTAAACAAAGGAT-AAAAAGTTGACC-GGATT
* * * * * *
257040 GAACCGACAAGTCAATAAAATATAAAAGAAAGTACTTAGGACCTAGCCGATAGGTGAATAAAGGA
63 GGACCGACAAGTCAACAAAAGATAAAAGAAAGTACTTGGGACCAAGCCGATAGGTGAATGAAGGA
* * *
257105 TAAAAAATTGACTGGGATTAAATCGATAGTCAACGAG
128 T-AAAAATTAACCGGGATTAAATCGATAGTCAACAAG
*
257142 GGATAAAGGATTT-CCCGAGACTGGGCCGACAGGTAAACAAAGGATAAAGAAGTTGACCAGGATT
1 GGATAAAGGATTTACCCGAGACTAGGCC-ACAGGTAAACAAAGGATAAA-AAGTTGACC-GGATT
* * * * * * *
257206 GGGCCAACAAGTTAACAAAAGATAAAAGGAAGAACCTGGGACCAAGCCGATAAAG-GAATGAAGG
63 GGACCGACAAGTCAACAAAAGATAAAAGAAAGTACTTGGGACCAAGCCGAT-AGGTGAATGAAGG
* *
257270 ATAAAAGTTAACCGGGATTAAA-CTGATAAGTCAATAAG
127 ATAAAAATTAACCGGGATTAAATC-GAT-AGTCAACAAG
* * *
257308 GGATAAAGGATTTACCTGGGACTAGGCCAGCAGGTAAACAAAGGATATAAAAGTTGATCGAGATT
1 GGATAAAGGATTTACCCGAGACTAGGCCA-CAGGTAAACAAAGGATA-AAAAGTTGACCG-GATT
* * * *
257373 AGACTGATAAGTCAACAAAAGATAAAA-AAAGTACTTGGGACCAAGCCGACAGGTGAATGAAGGA
63 GGACCGACAAGTCAACAAAAGATAAAAGAAAGTACTTGGGACCAAGCCGATAGGTGAATGAAGGA
257437 TAAA
128 TAAA
257441 GGTTGATTGG
Statistics
Matches: 250, Mismatches: 40, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
164 1 0.00
165 25 0.10
166 147 0.59
167 75 0.30
168 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.25, T:0.18
Consensus pattern (163 bp):
GGATAAAGGATTTACCCGAGACTAGGCCACAGGTAAACAAAGGATAAAAAGTTGACCGGATTGGA
CCGACAAGTCAACAAAAGATAAAAGAAAGTACTTGGGACCAAGCCGATAGGTGAATGAAGGATAA
AAATTAACCGGGATTAAATCGATAGTCAACAAG
Found at i:257436 original size:84 final size:85
Alignment explanation
Indices: 257214--257438 Score: 208
Period size: 84 Copynumber: 2.7 Consensus size: 85
257204 TTGGGCCAAC
* * ** *
257214 AAGTTAACAAAAGATAAAAGGAAGAACCTGGGACCAAGCCGATAAAG-GAATGAAGG--ATAAAA
1 AAGTCAACAAAAGATAAAA-GAAGTACCTGGGACCAAGCCGAGCAGGTGAATGAAGGATATAAAA
*
257276 GTTAACCGGGATTAAACTGAT
65 GTTAACCGAGATTAAACTGAT
* ** * ** * * * **
257297 AAGTCAATAAGGGATAAAGGATTTACCTGGGACTAGGCC-AGCAGGTAAACAAAGGATATAAAAG
1 AAGTCAACAAAAGATAAAAGAAGTACCTGGGACCAAGCCGAGCAGGTGAATGAAGGATATAAAAG
* * *
257361 TTGATCGAGATTAGACTGAT
66 TTAACCGAGATTAAACTGAT
* *
257381 AAGTCAACAAAAGATAAAAAAAGTACTTGGGACCAAGCCGA-CAGGTGAATGAAGGATA
1 AAGTCAACAAAAGATAAAAGAAGTACCTGGGACCAAGCCGAGCAGGTGAATGAAGGATA
257439 AAGGTTGATT
Statistics
Matches: 105, Mismatches: 33, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
81 3 0.03
82 21 0.20
83 14 0.13
84 66 0.63
85 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.17
Consensus pattern (85 bp):
AAGTCAACAAAAGATAAAAGAAGTACCTGGGACCAAGCCGAGCAGGTGAATGAAGGATATAAAAG
TTAACCGAGATTAAACTGAT
Found at i:257497 original size:84 final size:84
Alignment explanation
Indices: 257409--257681 Score: 329
Period size: 84 Copynumber: 3.2 Consensus size: 84
257399 AAAAGTACTT
* ** * * *
257409 GGGACCAAGCCGACAGGTGAATGAAGGATAAAGGTTGATTGGAGACTGAGCTGACAAGTCACCAT
1 GGGACTAAGCCGACAGGT-AAAAAAGGATGAAGGTTGATCGGAGACTGAGCTGACAGGTCACCAT
*
257474 AAGGGTAATGGGCTTA-TTG
65 AAGGGTAATGGGCTTACTAG
* * *
257493 GGGACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGAAGACTGAGCTGACAGGTCACCAT
1 GGGACTAAGCCGACAGGTAAA-AAAGGATGAAGGTTGATCGGAGACTGAGCTGACAGGTCACCAT
*
257558 AAGGGTAATGGGTTTACTAG
65 AAGGGTAATGGGCTTACTAG
* * *
257578 GGG-CTAAGCCGACAGGTAAACAAAAGATGAAGGTTGATCGGAGACTAAGCTGACAGGTCATCAT
1 GGGACTAAGCCGACAGGTAAA-AAAGGATGAAGGTTGATCGGAGACTGAGCTGACAGGTCACCAT
*
257642 AAGGGTAATGGG-TCTAC-CG
65 AAGGGTAATGGGCT-TACTAG
**
257661 GGGACTAAGCTAACAGGTAAA
1 GGGACTAAGCCGACAGGTAAA
257682 CAATAGATTA
Statistics
Matches: 165, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
83 7 0.04
84 153 0.93
85 5 0.03
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.19
Consensus pattern (84 bp):
GGGACTAAGCCGACAGGTAAAAAAGGATGAAGGTTGATCGGAGACTGAGCTGACAGGTCACCATA
AGGGTAATGGGCTTACTAG
Found at i:257633 original size:41 final size:41
Alignment explanation
Indices: 257495--257635 Score: 106
Period size: 41 Copynumber: 3.4 Consensus size: 41
257485 GCTTATTGGG
** * *
257495 GACTAAGCCGACAGGTAAACAATGGATGAAGGTTGACCGAA
1 GACTAAGCCGACAGGTAAACAAAAGATGAAGGTTGATCGGA
* * * * * * * *
257536 GACTGAGCTGACAGGTCACCATAAG-GGTAATGGGTTTACTAGG-
1 GACTAAGCCGACAGGTAAACAAAAGATG-AA--GGTTGA-TCGGA
*
257579 GGCTAAGCCGACAGGTAAACAAAAGATGAAGGTTGATCGGA
1 GACTAAGCCGACAGGTAAACAAAAGATGAAGGTTGATCGGA
*
257620 GACTAAGCTGACAGGT
1 GACTAAGCCGACAGGT
257636 CATCATAAGG
Statistics
Matches: 71, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
40 4 0.06
41 39 0.55
43 26 0.37
44 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (41 bp):
GACTAAGCCGACAGGTAAACAAAAGATGAAGGTTGATCGGA
Found at i:257669 original size:43 final size:42
Alignment explanation
Indices: 257452--257683 Score: 136
Period size: 43 Copynumber: 5.5 Consensus size: 42
257442 GTTGATTGGA
* * * **
257452 GACTGAGCTGACAAGTCACCATAAGGGTAATGGGCTTATTGGG
1 GACTAAGCTGACAGGTCAACATAAGGGTAATGGG-TTACCGGG
* * * * **
257495 GACTAAGCCGACAGGTAAACA-ATGGATGAA--GGTTGACCGAA
1 GACTAAGCTGACAGGTCAACATAAGGGT-AATGGGTT-ACCGGG
* * *
257536 GACTGAGCTGACAGGTCACCATAAGGGTAATGGGTTTACTAGGG
1 GACTAAGCTGACAGGTCAACATAAGGGTAATGGG-TTAC-CGGG
* * * * * *
257580 G-CTAAGCCGACAGGTAAACA-AAAGATGAA--GGTTGATCGGA
1 GACTAAGCTGACAGGTCAACATAAGGGT-AATGGGTT-ACCGGG
*
257620 GACTAAGCTGACAGGTCATCATAAGGGTAATGGGTCTACCGGG
1 GACTAAGCTGACAGGTCAACATAAGGGTAATGGGT-TACCGGG
* *
257663 GACTAAGCTAACAGGTAAACA
1 GACTAAGCTGACAGGTCAACA
257684 ATAGATTAAG
Statistics
Matches: 136, Mismatches: 39, Indels: 28
0.67 0.19 0.14
Matches are distributed among these distances:
40 7 0.05
41 44 0.32
42 16 0.12
43 64 0.47
44 5 0.04
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (42 bp):
GACTAAGCTGACAGGTCAACATAAGGGTAATGGGTTACCGGG
Found at i:257682 original size:84 final size:84
Alignment explanation
Indices: 257439--257696 Score: 349
Period size: 84 Copynumber: 3.1 Consensus size: 84
257429 ATGAAGGATA
* * **
257439 AAGGTTGATTGGAGACTGAGCTGACAAGTCACCATAAGGGTAATGGG-CTTATTGGGGACTAAGC
1 AAGGTTGATCGGAGACTGAGCTGACAGGTCACCATAAGGGTAATGGGTC-TACAGGGGACTAAGC
*
257503 CGACAGGTAAACAATGGATG
65 CGACAGGTAAACAATAGATG
* * *
257523 AAGGTTGACCGAAGACTGAGCTGACAGGTCACCATAAGGGTAATGGGTTTACTAGGGG-CTAAGC
1 AAGGTTGATCGGAGACTGAGCTGACAGGTCACCATAAGGGTAATGGGTCTAC-AGGGGACTAAGC
*
257587 CGACAGGTAAACAAAAGATG
65 CGACAGGTAAACAATAGATG
* * * *
257607 AAGGTTGATCGGAGACTAAGCTGACAGGTCATCATAAGGGTAATGGGTCTACCGGGGACTAAGCT
1 AAGGTTGATCGGAGACTGAGCTGACAGGTCACCATAAGGGTAATGGGTCTACAGGGGACTAAGCC
* *
257672 AACAGGTAAACAATAGATT
66 GACAGGTAAACAATAGATG
257691 AAGGTT
1 AAGGTT
257697 ATTCCCAGGA
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
83 4 0.03
84 144 0.95
85 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.21
Consensus pattern (84 bp):
AAGGTTGATCGGAGACTGAGCTGACAGGTCACCATAAGGGTAATGGGTCTACAGGGGACTAAGCC
GACAGGTAAACAATAGATG
Found at i:258074 original size:43 final size:42
Alignment explanation
Indices: 257929--258720 Score: 236
Period size: 43 Copynumber: 18.6 Consensus size: 42
257919 AAGCCAACGA
* * ** *
257929 GCAGACGATTGATAAAGAAAGTCTCTTGGGACTGAA-CCGATGG
1 GCAGACAATGGATAAAG-AAGTCTCCCGAGACT-AAGCCGATGG
* * * * * * ** *
257972 GTAGACTATGGATGAA-AAGTCTCCTGGGTCTAAGTTGACGG
1 GCAGACAATGGATAAAGAAGTCTCCCGAGACTAAGCCGATGG
* * * * **
258013 GCAAACGATTGATAAAGAAAGTCTCCCGAGACTGAGCCGACCG
1 GCAGACAATGGATAAAG-AAGTCTCCCGAGACTAAGCCGATGG
* * * *
258056 GCAGACTATGGATGAAGAAGTCTCCCAAGTCTAAGCCGATGG
1 GCAGACAATGGATAAAGAAGTCTCCCGAGACTAAGCCGATGG
** * * * *
258098 GCAGACGGTTGATAAAGGAAGTCTCTCAGGGACTAAGCCGATAG
1 GCAGACAATGGATAAA-GAAGTCTC-CCGAGACTAAGCCGATGG
* * * *
258142 GCAAACAATGGATAAAGAAATCTCCCTAGGTCTAAGCCGATGG
1 GCAGACAATGGATAAAGAAGTCTCCCGA-GACTAAGCCGATGG
* ** ** *
258185 GCAAACGGTTCATAACGAAAGTCTCCCGAGACTAA-CCTGACT-G
1 GCAGACAATGGATAAAG-AAGTCTCCCGAGACTAAGCC-GA-TGG
* * * *
258228 GCAAACAATGGATGAAGAAGTCTCCCGAGTCTAAGTCGATGG
1 GCAGACAATGGATAAAGAAGTCTCCCGAGACTAAGCCGATGG
** * *** * * **
258270 GCAGACGGTTGATAAAGGAAGTCTCATAAGACTGAGCTGACAG
1 GCAGACAATGGATAAA-GAAGTCTCCCGAGACTAAGCCGATGG
* * * * * * * *
258313 GCAGACAAAGGATGAAGAAGTCTCCAGTGTCAAAGCTGACGG
1 GCAGACAATGGATAAAGAAGTCTCCCGAGACTAAGCCGATGG
* * * ** * * *
258355 GTAGACGAA-AGATAAAGAAAGTTTTTC-AGGTCAAAGCTGATGG
1 GCAGAC-AATGGATAAAG-AAGTCTCCCGA-GACTAAGCCGATGG
* ** * * * **
258398 GTAGATGATTGATAAAGAAAGTCTCCCAAGACTGAGCCGACAG
1 GCAGACAATGGATAAAG-AAGTCTCCCGAGACTAAGCCGATGG
* * * *
258441 GCAGACTATGGATGAAGAAGTCTCCC-ACGTCTAAGTCGATGG
1 GCAGACAATGGATAAAGAAGTCTCCCGA-GACTAAGCCGATGG
*** * * * * *
258483 GCAGATGGTTGATAAAGGAAGTCTCCCAAGACTAACCCGACGA
1 GCAGACAATGGATAAA-GAAGTCTCCCGAGACTAAGCCGATGG
* * * **
258526 GCAAACAATGGATGAAGAAGTCTCCC-AGGTCTAAGCTAATGG
1 GCAGACAATGGATAAAGAAGTCTCCCGA-GACTAAGCCGATGG
* * ** **
258568 GCAGACAGTTGATAAAGGAAGTCT-TTGAGGACTGAA-CCGACAG
1 GCAGACAATGGATAAA-GAAGTCTCCCGA-GACT-AAGCCGATGG
** * * * * *
258611 GCAGACAATGGATGGAGAAGTCTCTCGAGTCAAAGCTGACGG
1 GCAGACAATGGATAAAGAAGTCTCCCGAGACTAAGCCGATGG
* ** * * * * * * *
258653 GCAGGCAAAAGATGAATGAAGTCTCTCGGGTCAAAGCTGACGG
1 GCAGACAATGGAT-AAAGAAGTCTCCCGAGACTAAGCCGATGG
* * *
258696 GCAGACAAAGGGTGAAGAAGTCTCC
1 GCAGACAATGGATAAAGAAGTCTCC
258721 AAGGTCAAAG
Statistics
Matches: 544, Mismatches: 178, Indels: 55
0.70 0.23 0.07
Matches are distributed among these distances:
40 2 0.00
41 33 0.06
42 187 0.34
43 283 0.52
44 39 0.07
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (42 bp):
GCAGACAATGGATAAAGAAGTCTCCCGAGACTAAGCCGATGG
Found at i:258121 original size:85 final size:85
Alignment explanation
Indices: 257827--258337 Score: 420
Period size: 85 Copynumber: 6.0 Consensus size: 85
257817 AAAAAAGTTT
* * * * * * *
257827 CCAACGTCTAAGTCGATAGGCAGACAATTGATAAA-AGAAGTCTCTTGGGACT--GCGGACGGGC
1 CCAA-GTCTAAGCCGATGGGCAGACGATTGATAAAGA-AAGTCTCCTGAGACTGAGCCGACAGGC
*
257889 AAACAATGGATGGAGAAGTCTC
64 AAACAATGGATGAAGAAGTCTC
** * * * * * * * ** * *
257911 TTAGGTCTAAGCCAACGAGCAGACGATTGATAAAGAAAGTCTCTTGGGACTGAACCGATGGGTAG
1 CCAAGTCTAAGCCGATGGGCAGACGATTGATAAAGAAAGTCTCCTGAGACTGAGCCGACAGGCAA
*
257976 ACTATGGATGAA-AAGTCTC
66 ACAATGGATGAAGAAGTCTC
*** ** * * * * *
257995 CTGGGTCTAAGTTGACGGGCAAACGATTGATAAAGAAAGTCTCCCGAGACTGAGCCGACCGGCAG
1 CCAAGTCTAAGCCGATGGGCAGACGATTGATAAAGAAAGTCTCCTGAGACTGAGCCGACAGGCAA
*
258060 ACTATGGATGAAGAAGTCTC
66 ACAATGGATGAAGAAGTCTC
* * * * * *
258080 CCAAGTCTAAGCCGATGGGCAGACGGTTGATAAAGGAAGTCTCTCAGGGACTAAGCCGATAGGCA
1 CCAAGTCTAAGCCGATGGGCAGACGATTGATAAAGAAAGTCTC-CTGAGACTGAGCCGACAGGCA
* *
258145 AACAATGGATAAAGAAATCTC
65 AACAATGGATGAAGAAGTCTC
* * * * * * * *
258166 CCTAGGTCTAAGCCGATGGGCAAACGGTTCATAACGAAAGTCTCCCGAGACT-AACCTGACTGGC
1 CC-AAGTCTAAGCCGATGGGCAGACGATTGATAAAGAAAGTCTCCTGAGACTGAGCC-GACAGGC
258230 AAACAATGGATGAAGAAGTCTC
64 AAACAATGGATGAAGAAGTCTC
* * * * * * * *
258252 CCGAGTCTAAGTCGATGGGCAGACGGTTGATAAAGGAAGTCTCATAAGACTGAGCTGACAGGCAG
1 CCAAGTCTAAGCCGATGGGCAGACGATTGATAAAGAAAGTCTCCTGAGACTGAGCCGACAGGCAA
*
258317 ACAAAGGATGAAGAAGTCTC
66 ACAATGGATGAAGAAGTCTC
258337 C
1 C
258338 AGTGTCAAAG
Statistics
Matches: 344, Mismatches: 75, Indels: 15
0.79 0.17 0.03
Matches are distributed among these distances:
83 39 0.11
84 72 0.21
85 127 0.37
86 70 0.20
87 36 0.10
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (85 bp):
CCAAGTCTAAGCCGATGGGCAGACGATTGATAAAGAAAGTCTCCTGAGACTGAGCCGACAGGCAA
ACAATGGATGAAGAAGTCTC
Found at i:258242 original size:172 final size:169
Alignment explanation
Indices: 257886--258294 Score: 498
Period size: 172 Copynumber: 2.4 Consensus size: 169
257876 ACTGCGGACG
* ** * * * * * *
257886 GGCAAACAATGGATGGAGAAGTCTCTTAGGTCTAAGCCAACGAGCAGACGATTGATAAAGAAAGT
1 GGCAAACAATGGATGAAGAAGTCTCCCAAGTCTAAGCCGATGGGCAGACGGTTGATAAAGGAAGT
* * * * * * * * **
257951 CTCTTGGGACTGAACCGATGGGTAGACTATGGATGAAAAGTCTCCTGGGTCTAAGTTGACGGGCA
66 CTCTAGGGACTGAACCGATAGGCAAACAATGGATAAAAAATCTCCTAGGTCTAAGCCGACGGGCA
* *
258016 AACGATTGATAAAGAAAGTCTCCCGAGACTGAGCCGACC
131 AACGATTCATAAAGAAAGTCTCCCGAGACTGAACCGACC
* *
258055 GGCAGACTATGGATGAAGAAGTCTCCCAAGTCTAAGCCGATGGGCAGACGGTTGATAAAGGAAGT
1 GGCAAACAATGGATGAAGAAGTCTCCCAAGTCTAAGCCGATGGGCAGACGGTTGATAAAGGAAGT
*
258120 CTCTCAGGGACT-AAGCCGATAGGCAAACAATGGATAAAGAAATCTCCCTAGGTCTAAGCCGATG
66 CTCT-AGGGACTGAA-CCGATAGGCAAACAATGGATAAA-AAATCT-CCTAGGTCTAAGCCGACG
* * *
258184 GGCAAACGGTTCATAACGAAAGTCTCCCGAGACT-AACCTGACT
127 GGCAAACGATTCATAAAGAAAGTCTCCCGAGACTGAACC-GACC
* *
258227 GGCAAACAATGGATGAAGAAGTCTCCCGAGTCTAAGTCGATGGGCAGACGGTTGATAAAGGAAGT
1 GGCAAACAATGGATGAAGAAGTCTCCCAAGTCTAAGCCGATGGGCAGACGGTTGATAAAGGAAGT
258292 CTC
66 CTC
258295 ATAAGACTGA
Statistics
Matches: 204, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
169 60 0.29
170 24 0.12
171 8 0.04
172 112 0.55
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (169 bp):
GGCAAACAATGGATGAAGAAGTCTCCCAAGTCTAAGCCGATGGGCAGACGGTTGATAAAGGAAGT
CTCTAGGGACTGAACCGATAGGCAAACAATGGATAAAAAATCTCCTAGGTCTAAGCCGACGGGCA
AACGATTCATAAAGAAAGTCTCCCGAGACTGAACCGACC
Found at i:258495 original size:85 final size:85
Alignment explanation
Indices: 258388--258656 Score: 312
Period size: 85 Copynumber: 3.2 Consensus size: 85
258378 TTTCAGGTCA
* * * * *
258388 AAGCTGATGGGTAGATGATTGATAAAGAAAGTCTCCCAAGACTGAGCCGACAGGCAGACTATGGA
1 AAGCTGATGGGCAGATGGTTGATAAAGGAAGTCTCCCAAGACTGAACCGACAGGCAGACAATGGA
258453 TGAAGAAGTCTCCCACGTCT
66 TGAAGAAGTCTCCCACGTCT
*
258473 AAG-TCGATGGGCAGATGGTTGATAAAGGAAGTCTCCCAAGACT-AACCCGAC-GAGCAAACAAT
1 AAGCT-GATGGGCAGATGGTTGATAAAGGAAGTCTCCCAAGACTGAA-CCGACAG-GCAGACAAT
*
258535 GGATGAAGAAGTCTCCCAGGTCT
63 GGATGAAGAAGTCTCCCACGTCT
* ** *** *
258558 AAGCTAATGGGCAGACAGTTGATAAAGGAAGTCTTTGAGGACTGAACCGACAGGCAGACAATGGA
1 AAGCTGATGGGCAGATGGTTGATAAAGGAAGTCTCCCAAGACTGAACCGACAGGCAGACAATGGA
* * *
258623 TGGAGAAGTCTCTCGA-GTCA
66 TGAAGAAGTCTC-CCACGTCT
*
258643 AAGCTGACGGGCAG
1 AAGCTGATGGGCAG
258657 GCAAAAGATG
Statistics
Matches: 157, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
84 3 0.02
85 148 0.94
86 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.18
Consensus pattern (85 bp):
AAGCTGATGGGCAGATGGTTGATAAAGGAAGTCTCCCAAGACTGAACCGACAGGCAGACAATGGA
TGAAGAAGTCTCCCACGTCT
Found at i:258497 original size:128 final size:128
Alignment explanation
Indices: 257998--258504 Score: 370
Period size: 128 Copynumber: 4.0 Consensus size: 128
257988 AAGTCTCCTG
* * * * *
257998 GGTCTAAGTTGACGGGCAAACGATTGATAAAGAAAGTCTCCCGAGACTGAGCCGACCGGCAGACT
1 GGTCTAAGCTGATGGGCAGACGATTGATAAAGAAAGTCTCCCAAGACTGAGCCGACAGGCAGACT
* * *
258063 ATGGATGAAGAAGTCTCCCAAGTCTAAGCC-GATGGGCAGACGGTTGATAAAGGAAGTCTCTCA
66 ATGGATGAAGAAGTCTCCC-AGTCTAAGCCTGATGGGCAGACGATTGATAAAGGAAGTTTTTCA
* * * * * * * * * ** *
258126 GGGACTAAGCCGATAGGCAAACAATGGATAAAGAAA-TCTCCCTAGGTCTAAGCCGATGGGCAAA
1 -GGTCTAAGCTGATGGGCAGACGATTGATAAAGAAAGTCTCCC-AAGACTGAGCCGACAGGCAGA
** ** * * * * * *
258190 CGGTTCAT-AACGAAAGTCTCCCGAGACTAA-CCTGACT-GGCAAACAATGGATGAA-GAAG-TC
64 CTATGGATGAA-G-AAGTCTCCC-AGTCTAAGCCTGA-TGGGCAGACGATTGATAAAGGAAGTTT
* *
258250 TCCC
125 TTCA
* * ** *
258254 GAGTCTAAG-TCGATGGGCAGACGGTTGATAAAGGAAGTCTCATAAGACTGAGCTGACAGGCAGA
1 G-GTCTAAGCT-GATGGGCAGACGATTGATAAAGAAAGTCTCCCAAGACTGAGCCGACAGGCAGA
* * * * * ** *
258318 CAAAGGATGAAGAAGTCT-CCAGTGTCAAAG-CTGACGGGTAGACGAAAGATAAAGAAAGTTTTT
64 CTATGGATGAAGAAGTCTCCCA--GTCTAAGCCTGATGGGCAGACGATTGATAAAGGAAGTTTTT
258381 CA
127 CA
* * *
258383 GGTCAAAGCTGATGGGTAGATGATTGATAAAGAAAGTCTCCCAAGACTGAGCCGACAGGCAGACT
1 GGTCTAAGCTGATGGGCAGACGATTGATAAAGAAAGTCTCCCAAGACTGAGCCGACAGGCAGACT
* * *
258448 ATGGATGAAGAAGTCTCCCACGTCTAAGTC-GATGGGCAGATGGTTGATAAAGGAAGT
66 ATGGATGAAGAAGTCTCCCA-GTCTAAGCCTGATGGGCAGACGATTGATAAAGGAAGT
258505 CTCCCAAGAC
Statistics
Matches: 276, Mismatches: 84, Indels: 37
0.70 0.21 0.09
Matches are distributed among these distances:
125 1 0.00
126 2 0.01
127 26 0.09
128 149 0.54
129 68 0.25
130 29 0.11
131 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (128 bp):
GGTCTAAGCTGATGGGCAGACGATTGATAAAGAAAGTCTCCCAAGACTGAGCCGACAGGCAGACT
ATGGATGAAGAAGTCTCCCAGTCTAAGCCTGATGGGCAGACGATTGATAAAGGAAGTTTTTCA
Found at i:258813 original size:48 final size:48
Alignment explanation
Indices: 258757--258863 Score: 160
Period size: 48 Copynumber: 2.2 Consensus size: 48
258747 GGGTGAGGAA
* * *
258757 AGTTTGACCAGGTCCTAACACCAATACAGTTAAATGAGGGATAAAAAG
1 AGTTTGACCAGGCCCTAACACCAATACAGTCAAAAGAGGGATAAAAAG
* * *
258805 AGTTTGACCAAGCCCTAACACCAATACAGTCAAAAGAGGGATGAATAG
1 AGTTTGACCAGGCCCTAACACCAATACAGTCAAAAGAGGGATAAAAAG
258853 AGTTTGACCAG
1 AGTTTGACCAG
258864 ACACAATCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (48 bp):
AGTTTGACCAGGCCCTAACACCAATACAGTCAAAAGAGGGATAAAAAG
Found at i:259238 original size:89 final size:89
Alignment explanation
Indices: 259122--259285 Score: 256
Period size: 89 Copynumber: 1.8 Consensus size: 89
259112 AAGAGAGTGG
*
259122 TATGATTGGGAATGTGTAGGCTACACCTTACCCCAAAGGAAATCAAGCTTAGTGATGCATCAATA
1 TATGATTGGGAATGTGTAGGCTACACCTTACCCCAAAGAAAATCAAGCTTAGTGATGCATCAATA
259187 CCATCTAGTGATTGGATGAAAGGA
66 CCATCTAGTGATTGGATGAAAGGA
* * * * * * *
259211 TATGATTGGGAATGTGTGGGCTGCACCTTGCCCCAAAGAAAATCAGGCTTGGTGGTGCATTAATA
1 TATGATTGGGAATGTGTAGGCTACACCTTACCCCAAAGAAAATCAAGCTTAGTGATGCATCAATA
259276 CCATCTAGTG
66 CCATCTAGTG
259286 GTCGGATAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 67 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (89 bp):
TATGATTGGGAATGTGTAGGCTACACCTTACCCCAAAGAAAATCAAGCTTAGTGATGCATCAATA
CCATCTAGTGATTGGATGAAAGGA
Found at i:265823 original size:8 final size:8
Alignment explanation
Indices: 265810--265835 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
265800 ATTTGATTAA
265810 ATTTTGTG
1 ATTTTGTG
265818 ATTTTGTG
1 ATTTTGTG
265826 ATTTTGTG
1 ATTTTGTG
265834 AT
1 AT
265836 GAATGATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:266075 original size:13 final size:13
Alignment explanation
Indices: 266056--266094 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
266046 ACAGCATTCT
266056 CTGTATCGATACA
1 CTGTATCGATACA
* *
266069 TTGTATCGGTACA
1 CTGTATCGATACA
266082 CTGTATCGATACA
1 CTGTATCGATACA
266095 AGGGGATTAT
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:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:266560 original size:20 final size:21
Alignment explanation
Indices: 266527--266579 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
266517 ACCTCTAGGC
*
266527 AGCACCCACCAGGTCGCGACCG
1 AGCACCC-CCAGGTCGCAACCG
266549 -GCACCCCCAGGTCGCAACCG
1 AGCACCCCCAGGTCGCAACCG
266569 AGCAGCCCCCA
1 AGCA-CCCCCA
266580 CACTAGCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 13 0.46
21 9 0.32
22 6 0.21
ACGTcount: A:0.23, C:0.49, G:0.25, T:0.04
Consensus pattern (21 bp):
AGCACCCCCAGGTCGCAACCG
Found at i:267989 original size:22 final size:21
Alignment explanation
Indices: 267964--268007 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
267954 TGAAATTGTC
*
267964 AAATTATTTTACTAAGGGGGAG
1 AAATT-TTTGACTAAGGGGGAG
*
267986 AAATTTTTGATTAAGGGGGAG
1 AAATTTTTGACTAAGGGGGAG
268007 A
1 A
268008 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (21 bp):
AAATTTTTGACTAAGGGGGAG
Found at i:268549 original size:20 final size:20
Alignment explanation
Indices: 268518--268573 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
268508 GTCAAAACCC
*
268518 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
268538 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
268558 TGCATTGTATCGATAC
1 TGAAATGTATCGATAC
268574 TTGAAAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:268665 original size:13 final size:13
Alignment explanation
Indices: 268647--268671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
268637 ACACACAGTA
268647 TGTATCGATACAT
1 TGTATCGATACAT
268660 TGTATCGATACA
1 TGTATCGATACA
268672 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:268692 original size:33 final size:32
Alignment explanation
Indices: 268627--268694 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
268617 GTAGCCAAAC
** *
268627 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGCATCGATACA
*
268659 TTGTATCGATACACCATAAAATGCATCGATACA
1 TTGTATCGATACA-CACAAAATGCATCGATACA
268692 TTG
1 TTG
268695 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGCATCGATACA
Found at i:274395 original size:156 final size:154
Alignment explanation
Indices: 274141--275520 Score: 1157
Period size: 156 Copynumber: 8.9 Consensus size: 154
274131 TAACTTCAAG
* * * * * * *
274141 AAAAATTACAAAAAAGCCCTTAAGGGATACCTTCAACGTGAAAGTATCTCGGCAACCCTAAAGGA
1 AAAAATTACGAAAATGCCCTTAGGGGATACCTTCGACGTAAAAGTATCCCGG-TACCCTAAAGGA
* * * * *
274206 CCTAAAAAGACTAGAAAAAGGATGAACCTATCCTAAATGCCCATCTTCGGCATAAAAGCAGACCC
65 CTTAAAAAGACTAGAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCC
*
274271 GGTGACGACCTATGAGTTGGTTCTAA
130 GGTGACGACCTAGGAGTTGGTTCT-A
* *
274297 AAAAATTATGAAAATGCCCTTAGGGGATACCTTCGATGTGAAAA-TATCCCGGTACCCTAAAGGA
1 AAAAATTACGAAAATGCCCTTAGGGGATACCTTCGACGT-AAAAGTATCCCGGTACCCTAAAGGA
* * * * * *
274361 CCTAAAAAGACTAGAAATGGTGATGAACCTATCCTAAATGCCCACATTCGGCATAAAAGCAGACA
65 CTTAAAAAGACTAGAAAAGG-GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACC
* * * * * *
274426 CAGTGACAACTTA-GACTCGATTCTA
129 CGGTGACGACCTAGGAGTTGGTTCTA
** * ** * * *
274451 GGAAATTAAGAAAAAACCC-TAAGGGATACCGTCGACATAAAAGTATCCCGGTACCCCTATAA-G
1 AAAAATTACGAAAATGCCCTTAGGGGATACCTTCGACGTAAAAGTATCCCGGTA-CCCTA-AAGG
* * * *
274514 ACTTAAAAAGGA-TAACAGAAAAGAGATGACCCTATCCTAAATGCCCACCTTCAGCATAAAAGCG
64 ACTTAAAAA-GACT---AGAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCG
**
274578 GACCCGGTGACGATTTAGGAGTTGGTTCTA
125 GACCCGGTGACGACCTAGGAGTTGGTTCTA
** * * * * * *
274608 CGAAATTACGAAAATGGCCCTCTA-GGTATACCTTCGATGTAAAAGTA-CTCTGGCAATCCTAAG
1 AAAAATTACGAAAAT-GCCCT-TAGGGGATACCTTCGACGTAAAAGTATC-CCGG-TACCCTAAA
* * * * * *
274671 GGACCTAAAAAGACCAGAAAAAGGGATGAAACTATCCTAAATGCCCACATTCGGCATAAAAGTGG
62 GGACTTAAAAAGACTAG-AAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGG
* *
274736 ACCCGATGACGACCTAGGAGTTGGTT-TT
126 ACCCGGTGACGACCTAGGAGTTGGTTCTA
* * ** ** * * *
274764 GAAAATTACAAAAATGCCCCGAGGGGATACCTTTTACGTTAAAGTATCCTGGTACTCCTAAAAGA
1 AAAAATTACGAAAATGCCCTTAGGGGATACCTTCGACGTAAAAGTATCCCGGTAC-CCTAAAGGA
* * * * * *
274829 CTTAAAAATAACTA-TAAAGGGGTGAACCCATCCTAAATACCCATCTTCGGTATAAAAGCGGACC
65 CTTAAAAA-GACTAGAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACC
* * * * *
274893 CAGTGACAACCTAAGAGTTAGTTC-C
129 CGGTGACGACCTAGGAGTTGGTTCTA
* * * *
274918 AAAAATTACGTAAATGCCCTTAGGAGATACCTTCGACGTTAAAGTATCTCGGTACCCCTAAAGGA
1 AAAAATTACGAAAATGCCCTTAGGGGATACCTTCGACGTAAAAGTATCCCGGTA-CCCTAAAGGA
* ** * *
274983 CTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCAATTTCGACATAAAAACGGACC
65 CTTAAAAA-GACTAGAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACC
* *
275048 CGGTGATGACCTAAGAGTTGGTTCTAA
129 CGGTGACGACCTAGGAGTTGGTTCT-A
* * * * **
275075 AAAAATTATGAAAATACCCTTAGGGGATACCTTCGACGAAAAAGTA-CCCGGCACCCCTAAAAAA
1 AAAAATTACGAAAATGCCCTTAGGGGATACCTTCGACGTAAAAGTATCCCGGTA-CCCTAAAGGA
* * * * * ** * * *
275139 CTTAAAGAGGATTAGAAAATGGATGAACCTATCCTAAATATCTACCTTCAACACAAAAGTGAACC
65 CTTAAA-AAGACTAGAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACC
**
275204 TAGTGACGACCTAGGAGTTGGTTCTA
129 CGGTGACGACCTAGGAGTTGGTTCTA
* * * * * *
275230 AAAAATTATGAAAATGCCCCTACGGGTATACCTTAGACATAAAAGTATCCCGGCAACCCTAAAGG
1 AAAAATTACGAAAATGCCCTTA-GGGGATACCTTCGACGTAAAAGTATCCCGG-TACCCTAAAGG
* * * * * *
275295 ACTTATAAAGATTAGAAAATGGG-TGAACCTATCCTAAATATCTACCTTCAGCATAAAAGTGGAC
64 ACTTAAAAAGACTAGAAAA-GGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
* * *** * * *
275359 CTGATGGTAACCTAGGACTCGGTTCTG
128 CCGGTGACGACCTAGGAGTTGGTTCTA
* * * *
275386 AAAAATTATGAAAATG-CCTCTAAGGGATACCTTTGACGTAAAAGTGTCCCGGTACCCCTAAAGG
1 AAAAATTACGAAAATGCCCT-TAGGGGATACCTTCGACGTAAAAGTATCCCGGTA-CCCTAAAGG
* * * ** * * * *
275450 ACCTGAAAAGGATTTTAAAAAGGATGAACCTATCCTAAATATCTACCTTTGGCATAAAAGCGGAC
64 A-CTTAAAAAGACTAGAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
*
275515 TCGGTG
128 CCGGTG
275521 GTGGTTACCT
Statistics
Matches: 994, Mismatches: 194, Indels: 72
0.79 0.15 0.06
Matches are distributed among these distances:
152 4 0.00
153 25 0.03
154 156 0.16
155 204 0.21
156 404 0.41
157 155 0.16
158 8 0.01
159 35 0.04
160 3 0.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (154 bp):
AAAAATTACGAAAATGCCCTTAGGGGATACCTTCGACGTAAAAGTATCCCGGTACCCTAAAGGAC
TTAAAAAGACTAGAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCCG
GTGACGACCTAGGAGTTGGTTCTA
Found at i:275393 original size:622 final size:621
Alignment explanation
Indices: 274140--275510 Score: 1456
Period size: 622 Copynumber: 2.2 Consensus size: 621
274130 CTAACTTCAA
* * * * * *
274140 GAAAAATTACAAAAAAGCCCTTAAGGGATACCTTCAACGTGAAAGTAT-CTCGGCAACCCTAAAG
1 GAAAAATTACAAAAATGCCCCTAAGGGATACCTTTAACGTAAAAGTATCCT-GG-TACCCTAAAA
* * *
274204 GACCTAAAAAGACTAGAAAAAGGATGAACCTATCCTAAATGCCCATCTTCGGCATAAAAGCAGAC
64 GACCTAAAAAAACTAGAAAAAGGATGAACCCATCCTAAATACCCATCTTCGGCATAAAAGCAGAC
* * * * * * *
274269 CCGGTGACGACCTATGAGTTGGTTCTAAAAAAATTATGAAAATGCCCTTAGGGGATACCTTCGAT
129 CCAGTGACAACCTAAGAGTTAGTTC-AAAAAAATTACGAAAATGCCCTTAGGAGATACCTTCGAC
*
274334 GTGAAAATATCCCGGTACCCTAAAGGACCTAAAAAGACTAGAAATGGTGATGAACCTATCCTAAA
193 GTGAAAATATCCCGGTACCCTAAAGGACCTAAAAAGACTAGAAAAGGTGATGAACCTATCCTAAA
* * * * **
274399 TGCCCACATTCGGCATAAAAGCAGACACAGTGACAACTTAGACTCGATTCTAGGAAATTAAGAAA
258 TACCCACATTCGACATAAAAACAGACACAGTGACAACTAAGACTCGATTCTAAAAAATTAAGAAA
* * *
274464 AAACCCTAAGGGATACCGTCGACATAAAAGTATCCCGGTACCCCTATAAGACTTAAAAAGGATAA
323 AAACCCTAAGGGATACCGTCGACATAAAAGTATCCCGGCACCCCTAAAAAACTTAAAAAGGAT-A
* * * * * * **
274529 CAGAAAAGAGATGACCCTATCCTAAATGCCCACCTTCAGCATAAAAGCGGACCCGGTGACGATTT
387 CAGAAAAGAGATGAACCTATCCTAAATACCCACCTTCAACACAAAAGCGAACCCAGTGACGACCT
** * ** *
274594 AGGAGTTGGTTCTACGAAATTACGAAAATGGCCCTCTAGGTATACCTTCGATGTAAAAGTACTCT
452 AGGAGTTGGTTCTAAAAAATTACGAAAATGGCCCTCTAGGTATACCTTAGACATAAAAGTACTCC
* * * *
274659 GGCAATCCTAAGGGACCTAAAAAGACCAGAAAAAGGGATGAAACTATCCTAAATGCCCACATTCG
517 GGCAACCCTAAAGGACCTAAAAAGACCAGAAAAAGGGATGAAACTATCCTAAATACCCACATTCA
* * * *
274724 GCATAAAAGTGGACCCGATGACGACCTAGGAGTTGGTTTT
582 GCATAAAAGTGGACCCGATGACAACCTAGGACTCGGTTCT
* * * *
274764 G-AAAATTACAAAAATGCCCCGAGGGGATACCTTTTACGTTAAAGTATCCTGGTACTCCTAAAAG
1 GAAAAATTACAAAAATGCCCCTAAGGGATACCTTTAACGTAAAAGTATCCTGGTAC-CCTAAAAG
* * * * * *
274828 ACTTAAAAATAACTA-TAAAGGGGTGAACCCATCCTAAATACCCATCTTCGGTATAAAAGCGGAC
65 ACCTAAAAA-AACTAGAAAAAGGATGAACCCATCCTAAATACCCATCTTCGGCATAAAAGCAGAC
* *
274892 CCAGTGACAACCTAAGAGTTAGTTC-CAAAAATTACGTAAATGCCCTTAGGAGATACCTTCGACG
129 CCAGTGACAACCTAAGAGTTAGTTCAAAAAAATTACGAAAATGCCCTTAGGAGATACCTTCGACG
* * * * *
274956 TTAAAGTATCTCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGG-GATGAACCTATCCTAA
194 TGAAAATATCCCGGTA-CCCTAAAGGACCTAAAAA-GACTAGAAAAGGTGATGAACCTATCCTAA
* * * * * * * * *
275020 ATACCCA-ATTTCGACATAAAAACGGACCCGGTGATGACCTAAGAGTTGGTTCTAAAAAAATTAT
257 ATACCCACA-TTCGACATAAAAACAGACACAGTGA-CAACTAAGACTCGATTCT-AAAAAATTAA
* * * *
275084 GAAAATACCCTTAGGGGATACCTTCGACGA-AAAAGTA-CCCGGCACCCCTAAAAAACTTAAAGA
319 GAAAAAACCC-TAAGGGATACCGTCGAC-ATAAAAGTATCCCGGCACCCCTAAAAAACTTAAAAA
* * * * *
275147 GGAT-TAGAAAATG-GATGAACCTATCCTAAATATCTACCTTCAACACAAAAGTGAACCTAGTGA
382 GGATACAGAAAA-GAGATGAACCTATCCTAAATACCCACCTTCAACACAAAAGCGAACCCAGTGA
*
275210 CGACCTAGGAGTTGGTTCTAAAAAATTATGAAAAT-GCCC-CTACGGGTATACCTTAGACATAAA
446 CGACCTAGGAGTTGGTTCTAAAAAATTACGAAAATGGCCCTCTA--GGTATACCTTAGACATAAA
* * ** * * *
275273 AGTA-TCCCGGCAACCCTAAAGGACTTATAAAGATTAGAAAATGGG-TGAACCTATCCTAAATAT
509 AGTACT-CCGGCAACCCTAAAGGACCTAAAAAGACCAGAAAAAGGGATGAAACTATCCTAAATAC
* * * **
275336 CTACCTTCAGCATAAAAGTGGACCTGATGGTAACCTAGGACTCGGTTCT
573 CCACATTCAGCATAAAAGTGGACCCGATGACAACCTAGGACTCGGTTCT
** * * * * *
275385 GAAAAATTATGAAAATGCCTCTAAGGGATACCTTTGACGTAAAAGTGTCCCGGTACCCCTAAAGG
1 GAAAAATTACAAAAATGCCCCTAAGGGATACCTTTAACGTAAAAGTATCCTGGTA-CCCTAAAAG
** * ** * * * * *
275450 ACCTGAAAAGGATTTTAAAAAGGATGAACCTATCCTAAATATCTACCTTTGGCATAAAAGC
65 ACCT-AAAAAAACTAGAAAAAGGATGAACCCATCCTAAATACCCATCTTCGGCATAAAAGC
275511 GGACTCGGTG
Statistics
Matches: 610, Mismatches: 119, Indels: 37
0.80 0.16 0.05
Matches are distributed among these distances:
620 3 0.00
621 108 0.18
622 244 0.40
623 183 0.30
624 49 0.08
625 22 0.04
626 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (621 bp):
GAAAAATTACAAAAATGCCCCTAAGGGATACCTTTAACGTAAAAGTATCCTGGTACCCTAAAAGA
CCTAAAAAAACTAGAAAAAGGATGAACCCATCCTAAATACCCATCTTCGGCATAAAAGCAGACCC
AGTGACAACCTAAGAGTTAGTTCAAAAAAATTACGAAAATGCCCTTAGGAGATACCTTCGACGTG
AAAATATCCCGGTACCCTAAAGGACCTAAAAAGACTAGAAAAGGTGATGAACCTATCCTAAATAC
CCACATTCGACATAAAAACAGACACAGTGACAACTAAGACTCGATTCTAAAAAATTAAGAAAAAA
CCCTAAGGGATACCGTCGACATAAAAGTATCCCGGCACCCCTAAAAAACTTAAAAAGGATACAGA
AAAGAGATGAACCTATCCTAAATACCCACCTTCAACACAAAAGCGAACCCAGTGACGACCTAGGA
GTTGGTTCTAAAAAATTACGAAAATGGCCCTCTAGGTATACCTTAGACATAAAAGTACTCCGGCA
ACCCTAAAGGACCTAAAAAGACCAGAAAAAGGGATGAAACTATCCTAAATACCCACATTCAGCAT
AAAAGTGGACCCGATGACAACCTAGGACTCGGTTCT
Found at i:276349 original size:129 final size:129
Alignment explanation
Indices: 276201--276434 Score: 337
Period size: 129 Copynumber: 1.8 Consensus size: 129
276191 AATTATTTCT
* *
276201 AAAAAATCATTTCGTACCTTAA-TGCACACCCGAAAA-ATTACGAAAATTTTTTGAAATATTTTA
1 AAAAAATCATTTCGCACCTTAATTG-ACACCCGAAAAGA-TACGAAAAGTTTTTGAAATATTTTA
* *
276264 TACCCCTACGGATACCCATAGGAATATAAAAGACTTGAAAATAATTGATATTCAATTATATTTGG
64 TACCCCTAAGGATACCCATAGGAATATAAAAGACTTAAAAATAATTGATATTCAATTATATTTGG
276329 A
129 A
* *
276330 AAAAAATCATTTCGCACCTTAATTGATACCCGAAAAGATACGAAAAGTTTTTGAAATCTTTTATA
1 AAAAAATCATTTCGCACCTTAATTGACACCCGAAAAGATACGAAAAGTTTTTGAAATATTTTATA
** ** *
276395 CCTTTAAGGATACTTATAGGAATATAAAAGATTTAAAAAT
66 CCCCTAAGGATACCCATAGGAATATAAAAGACTTAAAAAT
276435 GATCAACATT
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
129 89 0.97
130 3 0.03
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (129 bp):
AAAAAATCATTTCGCACCTTAATTGACACCCGAAAAGATACGAAAAGTTTTTGAAATATTTTATA
CCCCTAAGGATACCCATAGGAATATAAAAGACTTAAAAATAATTGATATTCAATTATATTTGGA
Found at i:277165 original size:20 final size:20
Alignment explanation
Indices: 277142--277216 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
277132 AAGTACCCAG
277142 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
277162 ATGTATCGATACATATATGA
1 ATGTATCGATACATTTTTCA
*
277182 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
277202 ATGTATCGATACATT
1 ATGTATCGATACATT
277217 CTATCTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:277250 original size:16 final size:16
Alignment explanation
Indices: 277226--277260 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
277216 TCTATCTTTT
277226 TACCCAGATGTATCAA
1 TACCCAGATGTATCAA
* *
277242 TACCTAGATGTATCGA
1 TACCCAGATGTATCAA
277258 TAC
1 TAC
277261 ATCTAGTTAA
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:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (16 bp):
TACCCAGATGTATCAA
Found at i:282157 original size:17 final size:18
Alignment explanation
Indices: 282137--282171 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
282127 AGAAAATACC
282137 GCATTT-AGGAAAAAAAG
1 GCATTTAAGGAAAAAAAG
282154 GCATTTCAAGGAAAAAAA
1 GCATTT-AAGGAAAAAAA
282172 TCCAAAACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.54, C:0.09, G:0.20, T:0.17
Consensus pattern (18 bp):
GCATTTAAGGAAAAAAAG
Found at i:282192 original size:167 final size:167
Alignment explanation
Indices: 281982--282685 Score: 694
Period size: 167 Copynumber: 4.3 Consensus size: 167
281972 TTTGGGAAAA
* *
281982 AAAAAAAGGAATTTC-A--ATAAAAATTCAAAACGCATGAAAATGAATTTATTTGTTAAAACTGA
1 AAAAAAAGGAATTTCAAGGAAAAAAATCCAAAACGCATGAAAATGAATTTATTT-TTAAAACTGA
* * * * * ** *
282044 ATTAAAATCAAATAGATGATAATATTTTATGACTTTTAAAATTTTAAAACTAAGAAAAATCCCCT
65 ATTAACATGAAATAAATGATAATATTTGATGACTTTTAAAAATCAAAAACTAAGAAAAATCACCT
* *
282109 TAAAAAAATTTATAG-AGTAGAAAATACCGCATTTAGG
130 CAAAAAAATTTATAGAAGTAGAAAATACCGTATTTAGG
* *
282146 AAAAAAAGGCATTTCAAGGAAAAAAATCCAAAACGCATGAAAATGAATTTATTTTTTACAACTGA
1 AAAAAAAGGAATTTCAAGGAAAAAAATCCAAAACGCATGAAAATGAATTTA-TTTTTAAAACTGA
*
282211 ATTAACATGAAATAAATGATAATATTTGATGACTTTTAAAAATCAAAAACTGAGAAAAAT-ACCT
65 ATTAACATGAAATAAATGATAATATTTGATGACTTTTAAAAATCAAAAACTAAGAAAAATCACC-
* *
282275 TC-AAAAAATTT-TACGAAATAGAAAATACTGTATTTAGG
129 TCAAAAAAATTTATA-GAAGTAGAAAATACCGTATTTAGG
** * * * *
282313 -AAAAGGGGAATTTCAAGG-AAAAAATCTAAAACTCATGAATATGATTTTATTTTATAAAACTGG
1 AAAAAAAGGAATTTCAAGGAAAAAAATCCAAAACGCATGAAAATGAATTTATTTT-TAAAACT-G
* * * *
282376 AATTAACATGAAATAAATGATAATATTTTATGACTTTTAAAAATCAAAAACTGAGAAAAATCTCA
64 AATTAACATGAAATAAATGATAATATTTGATGACTTTTAAAAATCAAAAACTAAGAAAAATCACC
*
282441 TCGAAAAAATTTAT-GAAGTAGAAAATACCGTATTTCA--
129 TCAAAAAAATTTATAGAAGTAGAAAATACCGTATTT-AGG
* * ** * ** *
282478 AAAAAAGAGGGATTTCAA-GAAAAAAATTCAAAAATCATGTAAATGAATGAATTTTTGAAAAAAT
1 AAAAAA-AGGAATTTCAAGGAAAAAAATCCAAAACGCATGAAAATGAATTTATTTTT--AAAACT
* * * * *
282542 GAATTAATAT--AA-AAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCAC
63 GAATTAACATGAAATAAATGATAATATTTGATGACTTTTAAAAATCAAAAACTAAGAAAAATCAC
* * * *
282604 CACAAAAAAATTCAT-GGAGTAGAAAACT-CTGTATTTTA-G
128 CTCAAAAAAATTTATAGAAGTAGAAAA-TACCGTA-TTTAGG
* * * **
282643 -AAAAAAGAAAATTTCAA-GAAAAAATTCAAAAACTAATGAAAAT
1 AAAAAAAG-GAATTTCAAGGAAAAAAATCCAAAACGCATGAAAAT
282686 AAAAGAATTC
Statistics
Matches: 454, Mismatches: 64, Indels: 44
0.81 0.11 0.08
Matches are distributed among these distances:
163 2 0.00
164 119 0.26
165 42 0.09
166 115 0.25
167 167 0.37
168 9 0.02
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (167 bp):
AAAAAAAGGAATTTCAAGGAAAAAAATCCAAAACGCATGAAAATGAATTTATTTTTAAAACTGAA
TTAACATGAAATAAATGATAATATTTGATGACTTTTAAAAATCAAAAACTAAGAAAAATCACCTC
AAAAAAATTTATAGAAGTAGAAAATACCGTATTTAGG
Found at i:282450 original size:333 final size:327
Alignment explanation
Indices: 281989--282673 Score: 799
Period size: 333 Copynumber: 2.1 Consensus size: 327
281979 AAAAAAAAAA
* *
281989 GGAATTTCAATAAAAATTCAAAACGCATGAAAATGAATTTATTTGTTAAAACTGAATTAAAATCA
1 GGAATTTCAAGAAAAAATCAAAACGCATGAAAATGAATTTATTTGTTAAAACTGAATTAAAATCA
* * ** * *
282054 AATAGATGATAATATTTTATGACTTTTAAAATTTTAAAACTAAGAAAAATCCCCTTAAAAAAATT
66 AATAAATGATAATATTTTATGACTTTTAAAAATCAAAAACTAAGAAAAATCCCATCAAAAAAATT
*
282119 TAT-AGAGTAGAAAATACCGCATTT-AGGAAAAAA-AGGCATTTCAAGGAAAAAAATCCAAAACG
131 TATGA-AGTAGAAAATACCGCATTTCA--AAAAAAGAGGCATTTCAA-GAAAAAAATCCAAAAAG
** * * * * *
282181 CATGAAAATGAATTTATTTTT-TACAACTGAATTAACATGAAATAAATGATAATATTTGATGACT
192 CATGAAAATGAATGAATTTTTGAAAAAATGAATTAACAT--AA-AAATAATAATATTTGATGAAT
**
282245 TTTAAAAATCAAAAACTGAGAAAAATACCTTCAAAAAATTTTACGAAATAGAAAATACTGTATTT
254 TTTAAAAATCAAAAACCAAGAAAAATACCTTCAAAAAATTTTACGAAATAGAAAATACTGTATTT
282310 AGGAAAAGG
319 AGGAAAAGG
* * * *
282319 GGAATTTCAAGGAAAAAATCTAAAACTCATGAATATGATTTTATTT-TATAAAACTGGAATTAAC
1 GGAATTTCAA-GAAAAAATC-AAAACGCATGAAAATGAATTTATTTGT-TAAAACT-GAATTAAA
* * * *
282383 ATGAAATAAATGATAATATTTTATGACTTTTAAAAATCAAAAACTGAGAAAAATCTCATCGAAAA
62 ATCAAATAAATGATAATATTTTATGACTTTTAAAAATCAAAAACTAAGAAAAATCCCATCAAAAA
* * * *
282448 AATTTATGAAGTAGAAAATACCGTATTTCAAAAAAAGAGGGATTTCAAGAAAAAAATTCAAAAAT
127 AATTTATGAAGTAGAAAATACCGCATTTCAAAAAAAGAGGCATTTCAAGAAAAAAATCCAAAAAG
* *
282513 CATGTAAATGAATGAATTTTTGAAAAAATGAATTAATATAAAAATAATAATATTTGATGAATTTT
192 CATGAAAATGAATGAATTTTTGAAAAAATGAATTAACATAAAAATAATAATATTTGATGAATTTT
* * * * * * *
282578 AAAAATTAAAAACCAAGAAAAATCACC-ACAAAAAAATTCATGGAGTAGAAAACT-CTGTATTTT
257 AAAAATCAAAAACCAAGAAAAAT-ACCTTCAAAAAATTTTACGAAATAGAAAA-TACTGTA-TTT
* *
282641 AGAAAAAAG
319 AGGAAAAGG
**
282650 AAAATTTCAAGAAAAAATTCAAAA
1 GGAATTTCAAGAAAAAA-TCAAAA
282674 ACTAATGAAA
Statistics
Matches: 300, Mismatches: 43, Indels: 24
0.82 0.12 0.07
Matches are distributed among these distances:
330 87 0.29
331 34 0.11
332 67 0.22
333 110 0.37
334 2 0.01
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (327 bp):
GGAATTTCAAGAAAAAATCAAAACGCATGAAAATGAATTTATTTGTTAAAACTGAATTAAAATCA
AATAAATGATAATATTTTATGACTTTTAAAAATCAAAAACTAAGAAAAATCCCATCAAAAAAATT
TATGAAGTAGAAAATACCGCATTTCAAAAAAAGAGGCATTTCAAGAAAAAAATCCAAAAAGCATG
AAAATGAATGAATTTTTGAAAAAATGAATTAACATAAAAATAATAATATTTGATGAATTTTAAAA
ATCAAAAACCAAGAAAAATACCTTCAAAAAATTTTACGAAATAGAAAATACTGTATTTAGGAAAA
GG
Found at i:292524 original size:97 final size:96
Alignment explanation
Indices: 292373--292651 Score: 351
Period size: 97 Copynumber: 2.9 Consensus size: 96
292363 TTATTCATTA
* * * *
292373 GGGATACTCTAACCCCATTATTCCAAGGGGATGCTCCAACCCTTTTTTTAAACTCGTCAAGGTTT
1 GGGATACTCTAACCCCATTATTCGAA-GGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTT
* *
292438 AAATCTTATTTTTGCTTAAATTATTATCATCG
65 AAATCTTATTTTTGCCTAAATTATCATCATCG
* *
292470 GGGATATTTTAACCCCATTATTCGGAAGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTT
1 GGGATACTCTAACCCCATTATTC-GAAGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTT
* *
292535 AAATCATACTTTTGCCTAAATTATCATCATCG
65 AAATCTTATTTTTGCCTAAATTATCATCATCG
* * * * ** ** *
292567 GGGATACTCCAACCCTATTCTTTCGAGGGGATACTCCAACCCCGTTTTTAAACTTATCAAAATTT
1 GGGATACTCTAACCCCATT-ATTCGAAGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTT
*
292632 AAATCTTATTTTTTCCTAAA
65 AAATCTTATTTTTGCCTAAA
292652 CGGTCATCGT
Statistics
Matches: 156, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
97 151 0.97
98 5 0.03
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (96 bp):
GGGATACTCTAACCCCATTATTCGAAGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTTA
AATCTTATTTTTGCCTAAATTATCATCATCG
Found at i:292659 original size:97 final size:97
Alignment explanation
Indices: 292373--292683 Score: 336
Period size: 97 Copynumber: 3.2 Consensus size: 97
292363 TTATTCATTA
* * * * * * *
292373 GGGATACTCTAACCCCATTATTCCAAGGGGATGCTCCAACCCTTTTTTTAAACTCGTCAAGGTTT
1 GGGATACTCCAACCCCATTCTTTCGAGGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTT
* *
292438 AAATCTTATTTTTGCTTAAATTATTATCATCG
66 AAATCTTATTTTTGCCTAAATTATCATCATCG
* ** * *
292470 GGGATATTTTAACCCCATT-ATTCGGAAGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATT
1 GGGATACTCCAACCCCATTCTTTC-GAGGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATT
* *
292534 TAAATCATACTTTTGCCTAAATTATCATCATCG
65 TAAATCTTATTTTTGCCTAAATTATCATCATCG
* ** ** *
292567 GGGATACTCCAACCCTATTCTTTCGAGGGGATACTCCAACCCCGTTTTTAAACTTATCAAAATTT
1 GGGATACTCCAACCCCATTCTTTCGAGGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTT
* *** * *
292632 AAATCTTATTTTTTCCTAAACGGTCATCGTCA
66 AAATCTTATTTTTGCCTAAATTATCATCATCG
* *
292664 GGGACACTCCAACCCTATTC
1 GGGATACTCCAACCCCATTC
292684 CTCTAAGGAC
Statistics
Matches: 179, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
96 2 0.01
97 174 0.97
98 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (97 bp):
GGGATACTCCAACCCCATTCTTTCGAGGGGATACTCCAACCCTATTTTTAAACTCGTCAAGATTT
AAATCTTATTTTTGCCTAAATTATCATCATCG
Found at i:294989 original size:21 final size:20
Alignment explanation
Indices: 294964--295011 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
294954 GCATAAAATG
294964 TGTTTTGAAAGTGATAAGGAAA
1 TGTTTTGAAAG-GAT-AGGAAA
* *
294986 -GTTTAGAATGGATAGGAAA
1 TGTTTTGAAAGGATAGGAAA
295005 TGTTTTG
1 TGTTTTG
295012 TAAAATTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.27
20 8 0.36
21 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (20 bp):
TGTTTTGAAAGGATAGGAAA
Found at i:299143 original size:18 final size:18
Alignment explanation
Indices: 299116--299166 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
299106 CATAGGCTTG
*
299116 TTTTTT-AACTAAGAAAT
1 TTTTTTAAACTAAAAAAT
299133 TTTTTTAAACTAAAAAAT
1 TTTTTTAAACTAAAAAAT
* *
299151 TATTTTCAAACCAAAA
1 T-TTTTTAAACTAAAA
299167 GAAATGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 6 0.21
18 11 0.38
19 12 0.41
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTTTTAAACTAAAAAAT
Found at i:300727 original size:22 final size:23
Alignment explanation
Indices: 300682--300730 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
300672 TTAATTAAAT
300682 TAAATTAAATTAAATATTACTTA
1 TAAATTAAATTAAATATTACTTA
* *
300705 TAAATTAAA-TAAATTTTATTTA
1 TAAATTAAATTAAATATTACTTA
300727 TAAA
1 TAAA
300731 AAAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAATTAAATTAAATATTACTTA
Found at i:300767 original size:20 final size:20
Alignment explanation
Indices: 300731--300768 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
300721 TATTTATAAA
*
300731 AAAATTTATAATGATAATTT
1 AAAATTTATAATAATAATTT
300751 AAAATTT-TAATAAATAAT
1 AAAATTTATAAT-AATAAT
300769 AATGATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATTTATAATAATAATTT
Found at i:300813 original size:15 final size:16
Alignment explanation
Indices: 300793--300822 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
300783 TTAATTTAAA
300793 ATAATTTT-TATATTC
1 ATAATTTTATATATTC
300808 ATAATTTTATATATT
1 ATAATTTTATATATT
300823 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATAATTTTATATATTC
Found at i:300843 original size:3 final size:3
Alignment explanation
Indices: 300835--300865 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
300825 ATATTATAGG
300835 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
300866 AGATTGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:301052 original size:30 final size:30
Alignment explanation
Indices: 301002--301071 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
300992 AAATTGGTAA
* *
301002 TTTATT-TATT-TAAATATATTTTATATAT
1 TTTATTATATTATAAATATATTTAAAATAT
*
301030 TTTATTATATTATAATTATATTTAAAATAT
1 TTTATTATATTATAAATATATTTAAAATAT
301060 TTTA-TAT-TTATA
1 TTTATTATATTATA
301072 TAAATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 11 0.30
29 7 0.19
30 19 0.51
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTATTATATTATAAATATATTTAAAATAT
Found at i:301141 original size:33 final size:35
Alignment explanation
Indices: 301104--301205 Score: 95
Period size: 39 Copynumber: 2.9 Consensus size: 35
301094 TTATATTATT
*
301104 TAAATTTTAA-AATATTTATATATTTATAT-ATAA
1 TAAATTTTAATAATATTTATATATTTATATAAAAA
*
301137 TAAATTTTTATATTAAAATTTATTATTATTTA-ATAAAAA
1 TAAA-TTTTA-A-TAATATTTA-TA-TATTTATATAAAAA
*
301176 TAAA-TTTAATAATATTTTATATAATTATAT
1 TAAATTTTAATAATA-TTTATATATTTATAT
301206 GAATATAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
33 4 0.07
34 10 0.18
35 9 0.16
36 5 0.09
37 11 0.20
38 4 0.07
39 13 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (35 bp):
TAAATTTTAATAATATTTATATATTTATATAAAAA
Found at i:301245 original size:113 final size:113
Alignment explanation
Indices: 301121--301338 Score: 248
Period size: 113 Copynumber: 1.9 Consensus size: 113
301111 TAAAATATTT
* * * * *
301121 ATATATTTATATATAAT-AAATTTTTATATTAAAATTTATT-AT-TATTTAATAAAAATAAATTT
1 ATATAATTATAT-TAATAAAATTTATATAATAAAATTTATTAATATATTAAATAAAAATAAATAT
*
301183 AATAATATTTT-ATATAATTATATGAATATAAT-AAATATAAAATGTGATATA
65 AA-AATATTTTAATATAATTA-A--AATAAAATAAAATATAAAATGTGATATA
** * * *
301234 ATATAATTATATTTTTAAAATTTATATAATATAATTTATTAATATATTAAATTAATATAAATATA
1 ATATAATTATATTAATAAAATTTATATAATAAAATTTATTAATATATTAAATAAAAATAAATATA
301299 AAATATTTTAAATATAATTAAAATAAAATAAAATATAAAA
66 AAATATTTT-AATATAATTAAAATAAAATAAAATATAAAA
301339 ATATGATGCT
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
112 2 0.02
113 38 0.43
114 20 0.23
115 19 0.22
116 9 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (113 bp):
ATATAATTATATTAATAAAATTTATATAATAAAATTTATTAATATATTAAATAAAAATAAATATA
AAATATTTTAATATAATTAAAATAAAATAAAATATAAAATGTGATATA
Found at i:301266 original size:28 final size:28
Alignment explanation
Indices: 301220--301273 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
301210 ATAATAAATA
301220 TAAAATGTGATATAATATAATTATATTTT
1 TAAAATGTGATATAATATAATT-TATTTT
*
301249 TAAAAT-TTATATAATATAATTTATT
1 TAAAATGTGATATAATATAATTTATT
301274 AATATATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 14 0.58
29 6 0.25
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TAAAATGTGATATAATATAATTTATTTT
Found at i:301278 original size:13 final size:14
Alignment explanation
Indices: 301194--301298 Score: 62
Period size: 14 Copynumber: 7.8 Consensus size: 14
301184 ATAATATTTT
*
301194 ATATAATTATATGA
1 ATATAATTATATTA
*
301208 ATATAA-TA-AAT-
1 ATATAATTATATTA
*
301219 ATAAAATGTGATA-TA
1 ATATAAT-T-ATATTA
*
301234 ATATAATTATATTT
1 ATATAATTATATTA
* *
301248 TTAAAATT-TATATA
1 ATATAATTATAT-TA
301262 ATATAATT-TATTA
1 ATATAATTATATTA
*
301275 ATAT-ATTAAATTA
1 ATATAATTATATTA
*
301288 ATATAAATATA
1 ATATAATTATA
301299 AAATATTTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
11 5 0.07
12 4 0.06
13 23 0.33
14 30 0.43
15 7 0.10
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATATAATTATATTA
Found at i:301303 original size:26 final size:25
Alignment explanation
Indices: 301274--301328 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
301264 ATAATTTATT
301274 AATATATTAAAT-TAATATAAATATAA
1 AATATATTAAATATAAT-TAAA-ATAA
*
301300 AATATTTTAAATATAATTAAAATAA
1 AATATATTAAATATAATTAAAATAA
301325 AATA
1 AATA
301329 AAATATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.30
26 15 0.56
27 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATATTAAATATAATTAAAATAA
Found at i:314114 original size:22 final size:22
Alignment explanation
Indices: 314075--314117 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
314065 CTGCAAAAAG
314075 CTTGAATCAATTACAATCTAAT
1 CTTGAATCAATTACAATCTAAT
*
314097 CTTGATATCAATT-TAATCTAA
1 CTTGA-ATCAATTACAATCTAA
314118 AATCTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (22 bp):
CTTGAATCAATTACAATCTAAT
Found at i:315124 original size:16 final size:16
Alignment explanation
Indices: 315105--315201 Score: 99
Period size: 16 Copynumber: 6.0 Consensus size: 16
315095 ATTATGTCCG
315105 AAATAATTTAAACTTA
1 AAATAATTTAAACTTA
* *
315121 AAATAATCTCAACTTA
1 AAATAATTTAAACTTA
*
315137 AAATTATTTAAACTTA
1 AAATAATTTAAACTTA
315153 AAA-AATATGTAAACTTA
1 AAATAAT-T-TAAACTTA
* *
315170 AAATAA-CTAAATTTA
1 AAATAATTTAAACTTA
*
315185 AAATAAATTCAAACTTA
1 AAAT-AATTTAAACTTA
315202 CAAAAACCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
15 13 0.20
16 33 0.51
17 17 0.26
18 2 0.03
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (16 bp):
AAATAATTTAAACTTA
Found at i:315165 original size:17 final size:17
Alignment explanation
Indices: 315113--315172 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
315103 CGAAATAATT
*
315113 TAAACTTAAAATA-ATC
1 TAAACTTAAAAAATATC
* * *
315129 TCAACTT-AAAATTATT
1 TAAACTTAAAAAATATC
*
315145 TAAACTTAAAAAATATG
1 TAAACTTAAAAAATATC
315162 TAAACTTAAAA
1 TAAACTTAAAA
315173 TAACTAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
15 3 0.09
16 14 0.40
17 18 0.51
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAACTTAAAAAATATC
Found at i:315169 original size:49 final size:50
Alignment explanation
Indices: 315113--315207 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 50
315103 CGAAATAATT
* * *
315113 TAAACTTAAAATAATCTCAACTTAAAAT-TATTTAAACTTA-AAAAATATG
1 TAAACTTAAAATAA-CTAAACTTAAAATAAATTCAAACTTACAAAAATATG
*
315162 TAAACTTAAAATAACTAAATTTAAAATAAATTCAAACTTACAAAAA
1 TAAACTTAAAATAACTAAACTTAAAATAAATTCAAACTTACAAAAA
315208 CCTTAATCTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 11 0.28
49 24 0.60
50 5 0.12
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (50 bp):
TAAACTTAAAATAACTAAACTTAAAATAAATTCAAACTTACAAAAATATG
Found at i:315174 original size:15 final size:15
Alignment explanation
Indices: 315113--315189 Score: 73
Period size: 15 Copynumber: 4.9 Consensus size: 15
315103 CGAAATAATT
315113 TAAACTTAAAATAATC
1 TAAACTTAAAAT-ATC
* *
315129 TCAACTTAAAATTATT
1 TAAACTTAAAA-TATC
*
315145 TAAACTTAAAAAATATG
1 TAAACTT--AAAATATC
*
315162 TAAACTTAAAATAAC
1 TAAACTTAAAATATC
*
315177 TAAATTTAAAATA
1 TAAACTTAAAATA
315190 AATTCAAACT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
15 18 0.35
16 18 0.35
17 11 0.22
18 4 0.08
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (15 bp):
TAAACTTAAAATATC
Found at i:315659 original size:6 final size:6
Alignment explanation
Indices: 315600--315660 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
315590 GTGTTATATC
* * * *
315600 ATATTT ATATTC ATATTA ATTTTT ATA-TT ATAATT ATATTT AT-TTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
*
315646 AT-TAT ATATTT ATAT
1 ATATTT ATATTT ATAT
315661 AAATTTTAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
5 14 0.31
6 31 0.69
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (6 bp):
ATATTT
Found at i:315666 original size:22 final size:22
Alignment explanation
Indices: 315601--315668 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
315591 TGTTATATCA
*
315601 TATT-TATATTCATATTAATTT
1 TATTATATATTTATATTAATTT
* *
315622 T-TATATTATAATTATATTTATTT
1 TAT-TA-TATATTTATATTAATTT
*
315645 TATTATATATTTATATAAATTT
1 TATTATATATTTATATTAATTT
315667 TA
1 TA
315669 ATAAATTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.03
21 2 0.05
22 16 0.43
23 17 0.46
24 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATATATTTATATTAATTT
Found at i:319263 original size:11 final size:11
Alignment explanation
Indices: 319247--319294 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
319237 TTGGGCAAAT
319247 AGAGAAAAAAG
1 AGAGAAAAAAG
319258 AGAGAAAAAAAG
1 AGAG-AAAAAAG
* *
319270 AAAGAAAAAAAAA
1 --AGAGAAAAAAG
319283 AGAGAAAAAAG
1 AGAGAAAAAAG
319294 A
1 A
319295 AAAATTAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 14 0.47
12 7 0.23
13 6 0.20
14 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AGAGAAAAAAG
Found at i:319265 original size:9 final size:9
Alignment explanation
Indices: 319247--319298 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
319237 TTGGGCAAAT
319247 AGAGAAAAA
1 AGAGAAAAA
319256 AGAGAGAAAA
1 AGAGA-AAAA
*
319266 AAAGAAAGAA
1 AGAGAAA-AA
319276 A-A-AAAAA
1 AGAGAAAAA
319283 AGAGAAAAA
1 AGAGAAAAA
319292 AGA-AAAA
1 AGAGAAAA
319299 TTAAGGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
7 3 0.08
8 8 0.21
9 16 0.42
10 11 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AGAGAAAAA
Found at i:319268 original size:12 final size:12
Alignment explanation
Indices: 319247--319292 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
319237 TTGGGCAAAT
319247 AGAG-AAAAAAG
1 AGAGAAAAAAAG
319258 AGAGAAAAAAAG
1 AGAGAAAAAAAG
* *
319270 AAAGAAAAAAAAA
1 AGAG-AAAAAAAG
319283 AGAGAAAAAA
1 AGAGAAAAAA
319293 GAAAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 4 0.13
12 16 0.53
13 10 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AGAGAAAAAAAG
Found at i:319282 original size:15 final size:13
Alignment explanation
Indices: 319251--319297 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
319241 GCAAATAGAG
*
319251 AAAAAAGAGAGAA
1 AAAAAAAAGAGAA
*
319264 AAAAAGAA-AGAA
1 AAAAAAAAGAGAA
319276 AAAAAAAAGAGAA
1 AAAAAAAAGAGAA
319289 AAAAGAAAA
1 AAAA-AAAA
319298 ATTAAGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.38
13 14 0.48
14 4 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:323174 original size:13 final size:13
Alignment explanation
Indices: 323158--323196 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
323148 ATTAATTAAG
323158 TTAAATTTTAATT
1 TTAAATTTTAATT
*
323171 TTAAATTTTATTTT
1 TTAAATTTTA-ATT
323185 TTAAA-TTTAATT
1 TTAAATTTTAATT
323197 ATAATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 14 0.61
14 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAAATTTTAATT
Found at i:323505 original size:2 final size:2
Alignment explanation
Indices: 323493--323532 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
323483 ACGGATTTGG
*
323493 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
323533 GGGACTCGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:327701 original size:118 final size:118
Alignment explanation
Indices: 327493--327730 Score: 467
Period size: 118 Copynumber: 2.0 Consensus size: 118
327483 AGACCAGGCA
*
327493 TCCATATTCTGGGCAGGCTTCAAGGAGAAGAACCATGTTTGGATGTCGTATGCAGCTTAACACTT
1 TCCATATTCTGGGCAGGCTCCAAGGAGAAGAACCATGTTTGGATGTCGTATGCAGCTTAACACTT
327558 CAACCTACACGAGTTGCCAAAATATACGTATCGAGTAAGTTTCTGTAGGTATT
66 CAACCTACACGAGTTGCCAAAATATACGTATCGAGTAAGTTTCTGTAGGTATT
327611 TCCATATTCTGGGCAGGCTCCAAGGAGAAGAACCATGTTTGGATGTCGTATGCAGCTTAACACTT
1 TCCATATTCTGGGCAGGCTCCAAGGAGAAGAACCATGTTTGGATGTCGTATGCAGCTTAACACTT
327676 CAACCTACACGAGTTGCCAAAATATACGTATCGAGTAAGTTTCTGTAGGTATT
66 CAACCTACACGAGTTGCCAAAATATACGTATCGAGTAAGTTTCTGTAGGTATT
327729 TC
1 TC
327731 AGCAGTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (118 bp):
TCCATATTCTGGGCAGGCTCCAAGGAGAAGAACCATGTTTGGATGTCGTATGCAGCTTAACACTT
CAACCTACACGAGTTGCCAAAATATACGTATCGAGTAAGTTTCTGTAGGTATT
Found at i:329638 original size:6 final size:6
Alignment explanation
Indices: 329627--329653 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
329617 GAATGCTACA
329627 GGGTTG GGGTTG GGGTTG GGGTTG GGG
1 GGGTTG GGGTTG GGGTTG GGGTTG GGG
329654 CTGCAGCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.70, T:0.30
Consensus pattern (6 bp):
GGGTTG
Found at i:333502 original size:52 final size:51
Alignment explanation
Indices: 333424--333572 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
333414 CGAAATATGA
333424 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* * *
333476 AAATTTGCCTGCGTGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
333528 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
333573 ATGTATTGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:333663 original size:33 final size:33
Alignment explanation
Indices: 333626--333692 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
333616 AGTAGCTTGA
333626 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
333659 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
333692 A
1 A
333693 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:333666 original size:13 final size:13
Alignment explanation
Indices: 333648--333672 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
333638 CAAAAAAATA
333648 TGTATCGATACAT
1 TGTATCGATACAT
333661 TGTATCGATACA
1 TGTATCGATACA
333673 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:337241 original size:10 final size:10
Alignment explanation
Indices: 337226--337339 Score: 65
Period size: 10 Copynumber: 11.4 Consensus size: 10
337216 CTTCCACATT
337226 ATTCTAGAAC
1 ATTCTAGAAC
337236 ATTCTAGAATC
1 ATTCTAGAA-C
*
337247 -TTCTAGAGC
1 ATTCTAGAAC
* * * * *
337256 CTCCCACAAT
1 ATTCTAGAAC
337266 ATTCTAGAAC
1 ATTCTAGAAC
337276 ATTCTAGAATC
1 ATTCTAGAA-C
* *
337287 -TTCCAGAGC
1 ATTCTAGAAC
* * *
337296 CTTCCACG-AT
1 ATTCTA-GAAC
337306 ATTCTAGAAC
1 ATTCTAGAAC
337316 ATT-TCAGAAC
1 ATTCT-AGAAC
337326 ATTCTAGAAC
1 ATTCTAGAAC
337336 ATTC
1 ATTC
337340 CAAAGTGTTC
Statistics
Matches: 78, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.05
10 70 0.90
11 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:337251 original size:40 final size:39
Alignment explanation
Indices: 337207--337341 Score: 166
Period size: 40 Copynumber: 3.4 Consensus size: 39
337197 CTCCATAAAG
337207 TTCTAGAACCTTCCACATTATTCTAGAACATTCTAGAATC
1 TTCTAGAACCTTCCACA-TATTCTAGAACATTCTAGAATC
* *
337247 TTCTAGAGCCTCCCACAATATTCTAGAACATTCTAGAATC
1 TTCTAGAACCTTCCAC-ATATTCTAGAACATTCTAGAATC
* *
337287 TTCCAGAGCCTTCCACGATATTCTAGAACATT-TCAGAA-C
1 TTCTAGAACCTTCCAC-ATATTCTAGAACATTCT-AGAATC
*
337326 ATTCTAGAACATTCCA
1 -TTCTAGAACCTTCCA
337342 AAGTGTTCTA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
39 2 0.02
40 81 0.96
41 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (39 bp):
TTCTAGAACCTTCCACATATTCTAGAACATTCTAGAATC
Found at i:341400 original size:20 final size:20
Alignment explanation
Indices: 341377--341511 Score: 99
Period size: 20 Copynumber: 6.8 Consensus size: 20
341367 CTCCATAAAG
*
341377 TTCTAGAACCTTCCACATTA
1 TTCTAGAACCTTCCACAATA
** * * *
341397 TTCTAGAATGTTCTAGAATC
1 TTCTAGAACCTTCCACAATA
* *
341417 TTCTAGAGCCTCCCACAATA
1 TTCTAGAACCTTCCACAATA
* * * *
341437 TTCTAGAACATTCTAGAATC
1 TTCTAGAACCTTCCACAATA
* *
341457 TTCTAGAGCCTTCCACGATA
1 TTCTAGAACCTTCCACAATA
* * * *
341477 TTCTAGAACATTTCAGAACA
1 TTCTAGAACCTTCCACAATA
*
341497 TTCTAGAACATTCCA
1 TTCTAGAACCTTCCA
341512 AAGTGTTCTA
Statistics
Matches: 83, Mismatches: 32, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (20 bp):
TTCTAGAACCTTCCACAATA
Found at i:341412 original size:10 final size:10
Alignment explanation
Indices: 341397--341463 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
341387 TTCCACATTA
*
341397 TTCTAGAATG
1 TTCTAGAATC
341407 TTCTAGAATC
1 TTCTAGAATC
**
341417 TTCTAGAGCC
1 TTCTAGAATC
* * * *
341427 TCCCACAATA
1 TTCTAGAATC
341437 TTCTAGAA-C
1 TTCTAGAATC
341446 ATTCTAGAATC
1 -TTCTAGAATC
341457 TTCTAGA
1 TTCTAGA
341464 GCCTTCCACG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
10 41 0.98
11 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (10 bp):
TTCTAGAATC
Found at i:341421 original size:40 final size:39
Alignment explanation
Indices: 341377--341488 Score: 161
Period size: 40 Copynumber: 2.8 Consensus size: 39
341367 CTCCATAAAG
* **
341377 TTCTAGAACCTTCCACATTATTCTAGAATGTTCTAGAATC
1 TTCTAGAGCCTTCCACA-TATTCTAGAACATTCTAGAATC
*
341417 TTCTAGAGCCTCCCACAATATTCTAGAACATTCTAGAATC
1 TTCTAGAGCCTTCCAC-ATATTCTAGAACATTCTAGAATC
341457 TTCTAGAGCCTTCCACGATATTCTAGAACATT
1 TTCTAGAGCCTTCCAC-ATATTCTAGAACATT
341489 TCAGAACATT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 64 0.98
41 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (39 bp):
TTCTAGAGCCTTCCACATATTCTAGAACATTCTAGAATC
Found at i:341501 original size:40 final size:40
Alignment explanation
Indices: 341377--341503 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
341367 CTCCATAAAG
*
341377 TTCTAGAACCTTCCACATTATTCTAG-A-ATGTTCTAGAATC
1 TTCTAGAGCCTTCCACA-TATTCTAGAACAT-TTCTAGAATC
*
341417 TTCTAGAGCCTCCCACAATATTCTAGAACA-TTCTAGAATC
1 TTCTAGAGCCTTCCAC-ATATTCTAGAACATTTCTAGAATC
341457 TTCTAGAGCCTTCCACGATATTCTAGAACATTTC-AGAA-C
1 TTCTAGAGCCTTCCAC-ATATTCTAGAACATTTCTAGAATC
341496 ATTCTAGA
1 -TTCTAGA
341504 ACATTCCAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
39 1 0.01
40 71 0.91
41 5 0.06
42 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.33
Consensus pattern (40 bp):
TTCTAGAGCCTTCCACATATTCTAGAACATTTCTAGAATC
Found at i:341509 original size:10 final size:10
Alignment explanation
Indices: 341436--341509 Score: 64
Period size: 10 Copynumber: 7.4 Consensus size: 10
341426 CTCCCACAAT
341436 ATTCTAGAAC
1 ATTCTAGAAC
341446 ATTCTAGAATC
1 ATTCTAGAA-C
*
341457 -TTCTAGAGC
1 ATTCTAGAAC
* * *
341466 CTTCCACG-AT
1 ATTCTA-GAAC
341476 ATTCTAGAAC
1 ATTCTAGAAC
341486 ATT-TCAGAAC
1 ATTCT-AGAAC
341496 ATTCTAGAAC
1 ATTCTAGAAC
341506 ATTC
1 ATTC
341510 CAAAGTGTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.06
10 45 0.88
11 3 0.06
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (10 bp):
ATTCTAGAAC
Found at i:343314 original size:165 final size:165
Alignment explanation
Indices: 342900--343468 Score: 606
Period size: 165 Copynumber: 3.5 Consensus size: 165
342890 AATTACAAGA
* * *
342900 TTTTTTTCTCCGTAAA-ATTTTTCG-GGAGGATTTTTCATGG-TTTTAATTTTTAAAATTCATCA
1 TTTTTTACTCCATAAATATTTTTCGAGGA-GATTTTTCTTGGTTTTTAATTTTTAAAATTCATCA
* * * *
342962 AATATTATTATTTATTTCATGTTAAATTAGTTTTAAAAAATTCATTCATTTTCATT-AGTTTTTG
65 AATATTATTATTTA-TTCATATTAAATTAG-TTTGAAAAATTCATTAATTTTC-TTGAATTTTTG
* * * * *
343026 AATTTTTTCCTTAAAATTCTCTTTTTTTTGAAAAATAGAG
127 AA-TTTTTCTTTAAAATTCTCCTATTTTCGAAAAATGGAG
*
343066 TTTTTTACTCCATAAATA-TTTTCAAGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
1 TTTTTTACTCCATAAATATTTTTCGAGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
* * ** * *
343130 ATATGATTATTTAATTCATATTAAATCAGTTTGCAAAAATTCACAAATCTTCTTGAATTTTTTAA
66 ATATTATTATTT-ATTCATATTAAATTAGTTTG-AAAAATTCATTAATTTTCTTGAATTTTTGAA
* * *
343195 TTTTTCTTTGAAATTCTCCTATTTTCGAAATACGGAG
129 TTTTTCTTTAAAATTCTCCTATTTTCGAAAAATGGAG
* * *
343232 TTTTCTACTTCATAAATATTTTTCGAGG-GA-TTTTCTTGGTTTTTAATTTTTAAAATTCATCCA
1 TTTTTTACTCCATAAATATTTTTCGAGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
* * * * * *
343295 ATGTTATCATTTGATTCATATTAAATTAGTTTTGAAAAATTAATTTATTTTCATG-AGTTTTGAA
66 ATATTATTATTT-ATTCATATTAAATTAG-TTTGAAAAATTCATTAATTTTCTTGAATTTTTGAA
* * * *
343359 TATTTTCTTCAAAATTTTCCTATTTTCGAAAAATGAAA
129 T-TTTTCTTTAAAATTCTCCTATTTTCGAAAAATGGAG
* *
343397 TTTTTTACTCCGTAAATATTTTT-GGGGAGA-TTTT-TTGAGTTTTTAATTTTTAAAATTCAT--
1 TTTTTTACTCCATAAATATTTTTCGAGGAGATTTTTCTTG-GTTTTTAATTTTTAAAATTCATCA
*
343457 AATATTGTTATT
65 AATATTATTATT
343469 AAACTTCCAT
Statistics
Matches: 339, Mismatches: 53, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
163 9 0.03
164 14 0.04
165 148 0.44
166 86 0.25
167 81 0.24
168 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (165 bp):
TTTTTTACTCCATAAATATTTTTCGAGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAA
ATATTATTATTTATTCATATTAAATTAGTTTGAAAAATTCATTAATTTTCTTGAATTTTTGAATT
TTTCTTTAAAATTCTCCTATTTTCGAAAAATGGAG
Found at i:343969 original size:21 final size:20
Alignment explanation
Indices: 343932--343978 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
343922 GGAGAGTGAA
* *
343932 AGAAAAATAGAAAAAAAGAG
1 AGAAAAAAAGAAAAAAAAAG
343952 AGAAAAAAAGAAAGAAAAAAG
1 AGAAAAAAAGAAA-AAAAAAG
343973 AGAAAA
1 AGAAAA
343979 CTAAGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AGAAAAAAAGAAAAAAAAAG
Found at i:343976 original size:13 final size:12
Alignment explanation
Indices: 343940--343977 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
343930 AAAGAAAAAT
*
343940 AGAAAAAAAGAG
1 AGAAAAAAAGAA
343952 AGAAAAAAAGAA
1 AGAAAAAAAGAA
343964 AGAAAAAAGAGAA
1 AGAAAAAA-AGAA
343977 A
1 A
343978 ACTAAGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAA
Found at i:346232 original size:156 final size:154
Alignment explanation
Indices: 345733--346233 Score: 476
Period size: 156 Copynumber: 3.2 Consensus size: 154
345723 TTCATGTCGG
* * ***
345733 AGGTATACCCATAAGGGCATTTTCATAATTTTTTAGAATTGAGTCCTAGGTTGTCACCGGGTCTG
1 AGGTAT-CCCCTAGGGGCATTTTCATAATTTTTTAGAAACAAGTCCTAGGTTGTCACCGGGTCTG
* * * * * *
345798 CTTTTACGCCAAAGGTGAGTATTTAGGATAGGTTCAT-CC-TTTCTATGATCC-TTTTAAATCTT
65 CTTTTATGTC-AAGGTGGGTATTTAGGATAGGTTCATCCCATTTTTA-AATCCTTTTTAAGTCTT
* *
345860 TTAGGGGTACTAGGTACTTTTATGTCAA
128 TTAGGGGTA-TAGGTACTTCTACGTCAA
* * ** * **
345888 AAGTATCCCCATA-GGGTATTTTTGTAACTTTTTAGATCCAAGTCCTAGGTTGTCACCGGGTCTG
1 AGGTATCCCC-TAGGGGCATTTTCATAATTTTTTAGAAACAAGTCCTAGGTTGTCACCGGGTCTG
* * *
345952 -TTTTATTGTCGAATGTGGGTATTTAGGATAGGTTCATCCCATTTTGT-AATCCTTTGTAAGTCG
65 CTTTTA-TGTC-AAGGTGGGTATTTAGGATAGGTTCATCCCATTTT-TAAATCCTTTTTAAGTCT
* * * *
346015 TTTAGGGATATCGGGCACTTCTACGTCGA
127 TTTAGGGGTAT-AGGTACTTCTACGTCAA
* ** * * * * * *
346044 AGATAT-CTTTTGAGGGCATTTTGATAATTTTTTAGAAACAAGTCTTATGTTATCACCGGGTCCG
1 AGGTATCCCCTAG-GGGCATTTTCATAATTTTTTAGAAACAAGTCCTAGGTTGTCACCGGGTCTG
346108 CTTTTATGTCATAGGTGGGTATTTAGGATAGGTTCATCCCATTTTTAAAATCCTTTTTAAGTCTT
65 CTTTTATGTCA-AGGTGGGTATTTAGGATAGGTTCATCCCATTTTT-AAATCCTTTTTAAGTCTT
* * *
346173 TTAGGGGTATAAAGTAATTCTACGTTAA
128 TTAGGGGTAT-AGGTACTTCTACGTCAA
*
346201 AGGTATCCCCTAGGGGTATTTTCATAATTTTTT
1 AGGTATCCCCTAGGGGCATTTTCATAATTTTTT
346234 GTGAACTTAG
Statistics
Matches: 274, Mismatches: 58, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
153 5 0.02
154 73 0.27
155 17 0.06
156 112 0.41
157 64 0.23
158 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (154 bp):
AGGTATCCCCTAGGGGCATTTTCATAATTTTTTAGAAACAAGTCCTAGGTTGTCACCGGGTCTGC
TTTTATGTCAAGGTGGGTATTTAGGATAGGTTCATCCCATTTTTAAATCCTTTTTAAGTCTTTTA
GGGGTATAGGTACTTCTACGTCAA
Found at i:347691 original size:13 final size:13
Alignment explanation
Indices: 347673--347697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
347663 CAATTCGTCA
347673 TGTATCGATACAT
1 TGTATCGATACAT
347686 TGTATCGATACA
1 TGTATCGATACA
347698 AATAGTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:347771 original size:19 final size:19
Alignment explanation
Indices: 347728--347783 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
347718 TGCCAGTTTA
347728 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGTCC
347748 ATGTATCGATACAATGAT-C
1 ATGTATCGATACAATG-TCC
* *
347767 ATGTATTGGTACAATGT
1 ATGTATCGATACAATGT
347784 ATCGATACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.03
19 17 0.52
20 15 0.45
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (19 bp):
ATGTATCGATACAATGTCC
Found at i:348426 original size:13 final size:13
Alignment explanation
Indices: 348408--348432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348398 ATCGGTTTAA
348408 AAAAATTTTCTCT
1 AAAAATTTTCTCT
348421 AAAAATTTTCTC
1 AAAAATTTTCTC
348433 CCCCTTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAATTTTCTCT
Found at i:350332 original size:13 final size:13
Alignment explanation
Indices: 350314--350340 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
350304 ATAGTAACCC
350314 ATGTATCGATACA
1 ATGTATCGATACA
350327 ATGTATCGATACA
1 ATGTATCGATACA
350340 A
1 A
350341 AGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:356625 original size:20 final size:20
Alignment explanation
Indices: 356600--356656 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
356590 TTTTACCCAG
*
356600 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
** *
356620 ATGTATCGATACATGCATGA
1 ATGTATCGATACATTTATCA
356640 ATGTATCGATACATTTA
1 ATGTATCGATACATTTA
356657 GTTAAAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:361733 original size:20 final size:20
Alignment explanation
Indices: 361708--361762 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
361698 TTGAAACAAT
* *
361708 TTGTATCAATACATT-TTGTA
1 TTGTATCGATACATTATT-CA
361728 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
361748 TTGTATCGATACATT
1 TTGTATCGATACATT
361763 GTATCGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:361764 original size:13 final size:13
Alignment explanation
Indices: 361746--361775 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
361736 ATACATTATT
361746 CATTGTATCGATA
1 CATTGTATCGATA
361759 CATTGTATCGATA
1 CATTGTATCGATA
361772 CATT
1 CATT
361776 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:361816 original size:20 final size:19
Alignment explanation
Indices: 361791--361864 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
361781 TTTACCCAGA
361791 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
361811 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
361831 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
361851 TGTATCGATACATT
1 TGTATCGATACATT
361865 CAGGCATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:375832 original size:1 final size:1
Alignment explanation
Indices: 375828--375879 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
375818 ATTCTTTTTC
* * * * * *
375828 AAAAAAACAAAAAAACAAAAAAACAAAAAAAAAAAACAAAACAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
375880 GAGAGAAAAT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:375868 original size:8 final size:8
Alignment explanation
Indices: 375827--375863 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
375817 CATTCTTTTT
375827 CAAAAAAA
1 CAAAAAAA
375835 CAAAAAAA
1 CAAAAAAA
375843 CAAAAAAA
1 CAAAAAAA
375851 CAAAAAAA
1 CAAAAAAA
375859 -AAAAA
1 CAAAAA
375864 CAAAACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:375877 original size:16 final size:14
Alignment explanation
Indices: 375828--375879 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 14
375818 ATTCTTTTTC
375828 AAAAAAACAAAAAA
1 AAAAAAACAAAAAA
375842 ACAAAAAA-ACAAAAA
1 A-AAAAAACA-AAAAA
375857 AAAAAAACAAAACAA
1 AAAAAAACAAAA-AA
375872 AGAAAAAA
1 A-AAAAAA
375880 GAGAGAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 11 0.33
15 16 0.48
16 6 0.18
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:377059 original size:55 final size:55
Alignment explanation
Indices: 376899--377061 Score: 218
Period size: 55 Copynumber: 3.0 Consensus size: 55
376889 CTGCCTTTCT
* **
376899 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* * *
376954 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAAAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
* * * * * *
377009 CCTTTCAAAGCCCACTCAAGTTTGTGGCACTTCCCAGTCCTCCAGGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
377062 TGCTCTCTCC
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 94 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
Found at i:377207 original size:149 final size:149
Alignment explanation
Indices: 376931--377223 Score: 435
Period size: 149 Copynumber: 2.0 Consensus size: 149
376921 GGTGGCATTT
*
376931 TTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
* * * *
376996 AAAAAGCAGGACGCCTTTCAAAGCCCACTCAAGTTTGTGGCACTTCCCAGTCCTCCAGGAGCAGG
66 AAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGG
*
377061 ATG-CTCTCTCCTTTCGCCC
131 ACGCCT-TCTCCTTTCGCCC
* * ** *
377080 TTTAGTCCTCAAATAGTAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1 TTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
* * * *
377145 AAAGAGCAGGATGCCTTTTAAAGCCCACACGAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGG
66 AAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGG
377210 ACGCCTTCTCCTTT
131 ACGCCTTCTCCTTT
377224 TAAAGCCCAC
Statistics
Matches: 128, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
149 126 0.98
150 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (149 bp):
TTTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
AAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGG
ACGCCTTCTCCTTTCGCCC
Found at i:377256 original size:61 final size:60
Alignment explanation
Indices: 377103--377346 Score: 320
Period size: 61 Copynumber: 4.1 Consensus size: 60
377093 TAGTAGGATG
** *
377103 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA-----TG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTT
* *
377158 CCTTTTAAAGCCCACACGAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGGACG-CTTTT
*
377219 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTT
* * **
377279 TCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG-CTTTT
377341 CCTTTT
1 CCTTTT
377347 CTTCTTTGTC
Statistics
Matches: 166, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
54 2 0.01
55 48 0.29
60 9 0.05
61 94 0.57
62 13 0.08
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (60 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTT
Done.