Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold211
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: 2193984
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 112243 characters in sequence are not A, C, G, or T
File 1 of 6
Found at i:695 original size:31 final size:31
Alignment explanation
Indices: 657--720 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
647 AGGTACTTAG
657 AACAACTCTTGACAATCAAATTGCTTCTTCA
1 AACAACTCTTGACAATCAAATTGCTTCTTCA
688 AACAACTCTTGACAATCAAATTGCTTCTTCA
1 AACAACTCTTGACAATCAAATTGCTTCTTCA
719 AA
1 AA
721 TAAATGTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (31 bp):
AACAACTCTTGACAATCAAATTGCTTCTTCA
Found at i:2336 original size:147 final size:146
Alignment explanation
Indices: 2037--2311 Score: 388
Period size: 147 Copynumber: 1.9 Consensus size: 146
2027 CTCTCCATCA
*
2037 ATTTCTAGAATATAACAGGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAATT
1 ATTTCTAGAATATAACAAGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAATT
* * **
2102 TCCATAAGATAACAAAAAAAAACTAAAACTAAAACCCACTTCTCAATAATAGATCTGCAAAATTC
66 TCCAGAAGATAACAAAAAAAAACTAAAACTAAAACCCACTTCTCAATAATAAATCTGCAAAATGA
* * * * *
2167 TCTTCTACTCTCCATC
131 TCTTCGACACGCAAGC
* *
2183 AATTTCTAGAATATAACAAGAAAGAATAAAAATTCATTTCTCAACAGTTTCAACTCTCAATCAAT
1 -ATTTCTAGAATATAACAAGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAAT
* * * *
2248 TTCCAGAAGATAATAAAAAAAAACCTAAAACTAAAGCCCATTTCTCAATAATAAATCTGTAAAA
65 TTCCAGAAGATAACAAAAAAAAA-CTAAAACTAAAACCCACTTCTCAATAATAAATCTGCAAAA
2312 CGTGATTTGG
Statistics
Matches: 118, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
147 82 0.69
148 36 0.31
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.28
Consensus pattern (146 bp):
ATTTCTAGAATATAACAAGAAAAAATAAAAATTCATTTATCAACAGTTTCAACTCTCAATCAATT
TCCAGAAGATAACAAAAAAAAACTAAAACTAAAACCCACTTCTCAATAATAAATCTGCAAAATGA
TCTTCGACACGCAAGC
Found at i:4230 original size:19 final size:19
Alignment explanation
Indices: 4206--4259 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
4196 AATCACATCT
*
4206 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
4225 TCTAAGATTGCATATCATC
1 TCTAAGATTGCATATCATA
*
4244 CCTAAGATTGCATATC
1 TCTAAGATTGCATATC
4260 CTCGAAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:4269 original size:17 final size:18
Alignment explanation
Indices: 4228--4269 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
4218 TATCATATCT
*
4228 AAGATTGCATATCATCCCT
1 AAGATTGCATATCA-CCCG
*
4247 AAGATTGCATATC-CTCG
1 AAGATTGCATATCACCCG
4264 AAGATT
1 AAGATT
4270 ATGTTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (18 bp):
AAGATTGCATATCACCCG
Found at i:4458 original size:15 final size:14
Alignment explanation
Indices: 4423--4462 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
4413 ATTAGGTGGG
4423 TTTTAAATA-AA--
1 TTTTAAATATAATT
4434 TTTTAAATATAATT
1 TTTTAAATATAATT
4448 TTTTAAAATATAATT
1 TTTT-AAATATAATT
4463 ACATGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
14 4 0.16
15 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTTAAATATAATT
Found at i:5162 original size:14 final size:15
Alignment explanation
Indices: 5143--5180 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5133 TAATATTTTT
*
5143 TTATAAACTA-AAAA
1 TTATAAAATACAAAA
5157 TTATAAAATATCAAAA
1 TTATAAAATA-CAAAA
5173 TTATAAAA
1 TTATAAAA
5181 AAAACTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
16 12 0.57
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
TTATAAAATACAAAA
Found at i:5552 original size:99 final size:100
Alignment explanation
Indices: 5403--5604 Score: 397
Period size: 99 Copynumber: 2.0 Consensus size: 100
5393 ATTGACAATC
5403 TTTCTCTTCCAAACGTCACTTCTTTAGTCTACTACACAAGCAAATTCTTCTTCTTTTTTGCTTTG
1 TTTCTCTTCCAAACGTCACTTCTTTAGTCTACTACACAAGCAAATTCTTCTTCTTTTTTGCTTTG
5468 TCGTAAGTTTAAATTTTTTAAA-TTAAAATTTAAT
66 TCGTAAGTTTAAATTTTTTAAATTTAAAATTTAAT
5502 TTTCTCTTCCAAACGTCACTTCTTTAGTCTACTACACAAGCAAATTCTTCTTCTTTTTTGCTTTG
1 TTTCTCTTCCAAACGTCACTTCTTTAGTCTACTACACAAGCAAATTCTTCTTCTTTTTTGCTTTG
5567 TCGTAAGTTTAAATTTTTTAAATTTAAAATTTAAT
66 TCGTAAGTTTAAATTTTTTAAATTTAAAATTTAAT
5602 TTT
1 TTT
5605 TATATTTTAA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 87 0.85
100 15 0.15
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (100 bp):
TTTCTCTTCCAAACGTCACTTCTTTAGTCTACTACACAAGCAAATTCTTCTTCTTTTTTGCTTTG
TCGTAAGTTTAAATTTTTTAAATTTAAAATTTAAT
Found at i:7429 original size:2 final size:2
Alignment explanation
Indices: 7422--7451 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7412 GCAAAACATC
7422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7452 CCTCCAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19381 original size:20 final size:20
Alignment explanation
Indices: 19356--19395 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19346 CGTAAAATGA
*
19356 TTTCTGGAAAATGGTTTACT
1 TTTCTGGAAAATGATTTACT
*
19376 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
19396 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:19411 original size:14 final size:15
Alignment explanation
Indices: 19335--19411 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
19325 GATTGCCAGT
* *
19335 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
19349 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
19363 AAAATGGTTTACTTTTCTGT
1 AAAAT-G---A-TTTTCTGG
*
19383 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
19398 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
19412 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
19 1 0.02
20 11 0.22
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:39446 original size:16 final size:18
Alignment explanation
Indices: 39418--39455 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
39408 CTAAATAATA
39418 AAATATAATAATTA-TTT
1 AAATATAATAATTACTTT
39435 AAATAT-ATAATTACTTT
1 AAATATAATAATTACTTT
39452 AAAT
1 AAAT
39456 TCTTAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATAATAATTACTTT
Found at i:39957 original size:33 final size:33
Alignment explanation
Indices: 39916--39982 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
39906 TTTTTAAATT
39916 TAAATTTAATTATAAAAGTATATAAAATATCAA
1 TAAATTTAATTATAAAAGTATATAAAATATCAA
39949 TAAATTTAATTATAAAAGTATATAAAATATCAA
1 TAAATTTAATTATAAAAGTATATAAAATATCAA
39982 T
1 T
39983 TGCAAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (33 bp):
TAAATTTAATTATAAAAGTATATAAAATATCAA
Found at i:40243 original size:15 final size:15
Alignment explanation
Indices: 40223--40257 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
40213 GTCAGTCTCG
40223 GGTTCAGATTTTTTA
1 GGTTCAGATTTTTTA
*
40238 GGTTCAGGTTTTTTA
1 GGTTCAGATTTTTTA
*
40253 AGTTC
1 GGTTC
40258 GAGTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.09, G:0.23, T:0.51
Consensus pattern (15 bp):
GGTTCAGATTTTTTA
Found at i:40281 original size:15 final size:15
Alignment explanation
Indices: 40231--40281 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
40221 CGGGTTCAGA
* *
40231 TTTTTTAGGTTCAGG
1 TTTTTTAAGTTCGGG
*
40246 TTTTTTAAGTTCGAG
1 TTTTTTAAGTTCGGG
*
40261 TCTTTTTGAGTTCGGG
1 T-TTTTTAAGTTCGGG
40277 TTTTT
1 TTTTT
40282 GACTTTTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.12, C:0.08, G:0.24, T:0.57
Consensus pattern (15 bp):
TTTTTTAAGTTCGGG
Found at i:49581 original size:51 final size:52
Alignment explanation
Indices: 49523--49799 Score: 321
Period size: 51 Copynumber: 5.2 Consensus size: 52
49513 AGGTTATTTT
* *
49523 CATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGA-TTCCATTTCTC
1 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
* *
49574 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGA-TTCTATTTCTA
1 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
49625 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTTCCATTTCTC
1 CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
*
49676 CATTTTCACTTTCATTTTGAAGAAAACCATAATCA-TTCCAAATGATTTGCCATTTCTC
1 CA---T---TTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTT-CCATTTCTC
* * *
49734 TATTTTCACTTTTATTTTGAAGAAAACCATCATCA-TTCCAAATGATTTCCCATTTCTC
1 CATTTT--C----ATTTTGGAGAAAACCATAATCATTTCCAAATGATTT-CCATTTCTC
49792 CATTTTCA
1 CATTTTCA
49800 CCATTTCTTT
Statistics
Matches: 200, Mismatches: 11, Indels: 29
0.83 0.05 0.12
Matches are distributed among these distances:
50 1 0.00
51 96 0.48
52 4 0.02
54 2 0.01
55 1 0.00
56 9 0.05
57 29 0.14
58 58 0.29
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (52 bp):
CATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGATTTCCATTTCTC
Found at i:49751 original size:58 final size:57
Alignment explanation
Indices: 49627--49800 Score: 269
Period size: 58 Copynumber: 3.0 Consensus size: 57
49617 TATTTCTACA
*
49627 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAAT-ATTTCCATTTCTCCATTTTCAC
1 TTTT-ATTTTGAAGAAAACCATAATCA-TTCCAAATGATTTCCATTTCTCCATTTTCAC
* *
49685 TTTCATTTTGAAGAAAACCATAATCATTCCAAATGATTTGCCATTTCTCTATTTTCAC
1 TTTTATTTTGAAGAAAACCATAATCATTCCAAATGATTT-CCATTTCTCCATTTTCAC
*
49743 TTTTATTTTGAAGAAAACCATCATCATTCCAAATGATTTCCCATTTCTCCATTTTCAC
1 TTTTATTTTGAAGAAAACCATAATCATTCCAAATGATTT-CCATTTCTCCATTTTCAC
49801 CATTTCTTTT
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
56 8 0.07
57 25 0.23
58 74 0.69
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (57 bp):
TTTTATTTTGAAGAAAACCATAATCATTCCAAATGATTTCCATTTCTCCATTTTCAC
Found at i:51305 original size:32 final size:31
Alignment explanation
Indices: 51269--51355 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 31
51259 TACTTATTAC
* *
51269 ATACTGAAACTATAGATTGTGAAATTTCTTAT
1 ATACTGAAACTATAGATTGTGAAATTT-ATAA
* * *
51301 ATACTAAAACTTTAGATTGAGAAA-TTATAA
1 ATACTGAAACTATAGATTGTGAAATTTATAA
*
51331 ATTA-TGAAACTATAGATAGTGAAAT
1 A-TACTGAAACTATAGATTGTGAAAT
51356 CGTGACTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
30 19 0.43
31 4 0.09
32 21 0.48
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (31 bp):
ATACTGAAACTATAGATTGTGAAATTTATAA
Found at i:57746 original size:63 final size:63
Alignment explanation
Indices: 57665--57857 Score: 242
Period size: 63 Copynumber: 3.1 Consensus size: 63
57655 TAGTTTGGCT
* * * *
57665 ACAACATTATTGAGTGGCTTGACCACAACGTGCAGCTTGTATGTGATATTCAGTGGCTTGACC
1 ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
* * * *
57728 ACAACGTTATTGAGTGGCTTGACCACTATGTGCAACTTGTCTACGATATTAAGTGGCTTGACC
1 ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
* * * * * * * *
57791 ACAACTTTATTTAGTGGTTTGACTACAATGAGCAACTTCTCTGCAATATACAGTGGCTTGACC
1 ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
57854 ACAA
1 ACAA
57858 TGTGGAGTGT
Statistics
Matches: 111, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 111 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (63 bp):
ACAACATTATTGAGTGGCTTGACCACAATGTGCAACTTGTCTGCGATATTCAGTGGCTTGACC
Found at i:60676 original size:644 final size:644
Alignment explanation
Indices: 59442--60696 Score: 2126
Period size: 644 Copynumber: 1.9 Consensus size: 644
59432 AATTGTTAAC
59442 CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
1 CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
* *
59507 TTTGTTTTGAATCAACTTACCATCCAAAGCCCCCTTTTTACTCATGATCCACTTTTTACTCCTTT
66 TTTGTTTTGAATCAACTTACAATCCAAAGCCCCCTTTTTACTCATGATCCACTTTTTACTCCCTT
*
59572 TGTCCCTAAACATACCATCTTTTCACCTTTGACTACCCATGGCCGGTCATAGCACCCCAAAAACC
131 TGTCCCTAAACATACCATCTTTTCACCTTTGACTACACATGGCCGGTCATAGCACCCCAAAAACC
* *
59637 CTACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTTT
196 CCACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTCT
* * * *
59702 GCACAAGATTTTCAGCTTTTTCTTCTTTATTTTTCCACCTTTGAAGCCGTATTTCTTCATTCTTC
261 CCACAAGATTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCTC
59767 TTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGCA
326 TTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGCA
* * *
59832 CTGCCGCCGCACCATTGCCATCGGCCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCTTT
391 CAGCCGCCGCACCACTGCCATCGACCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCTTT
* *
59897 CCAAAAATCATCTCCGTAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTTGTATT
456 CCAAAAATCATCTCCATAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTCGTATT
* *
59962 ATTTTATCTAAACTCTTCTATTTTGCGTTTATAGTGTTCAATCCTCCACTTTAATCGGCTTTTCG
521 ATTTTATCTAAACTCTTCTATTTTGCATTTATAGTGTCCAATCCTCCACTTTAATCGGCTTTTCG
60027 GGATTTATCGT-TGAGCCTTTTTCCTCCGTTTTATCGTAGGTATGAAGGACTACTATTCA
586 GGATTTATCGTCT-AGCCTTTTTCCTCCGTTTTATCGTAGGTATGAAGGACTACTATTCA
* *
60086 CATTTTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCTTTTCCT
1 CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
60151 TTTGTTTTGAATCAACTTACAATCCAAAG-CCCCTATTTTACTCATGATCCACTTTTTACTCCCT
66 TTTGTTTTGAATCAACTTACAATCCAAAGCCCCCT-TTTTACTCATGATCCACTTTTTACTCCCT
* * *
60215 TTGTCTCTAAACATGCCATCTTTTCACCTTTGACTACACATGGCCGGTCCTAGCACCCCAAAAAC
130 TTGTCCCTAAACATACCATCTTTTCACCTTTGACTACACATGGCCGGTCATAGCACCCCAAAAAC
*
60280 CCCACTTTTCATTTTATTTTTCTAGTTTTTCTCTCCTCTCCTCTCTTTACCGTCCACCACCCTTC
195 CCCACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTC
*
60345 TCCACAAGTTTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCT
260 TCCACAAGATTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCT
*
60410 CTTCCACTCCACCACCACACACGGCAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGC
325 CTTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGC
** *
60475 ACAGCCGCCGTGCCACCT-CCATCGACCACTGTTGATTTTCACCATTTTTCTTCTTTTCTCCTCT
390 ACAGCCGCCGCACCA-CTGCCATCGACCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCT
* *
60539 TTCCAAAAATCATCTCCATAAATTCTTGAATTTTATTTTTAAATATTAAAATATCAACTTTCGTA
454 TTCCAAAAATCATCTCCATAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTCGTA
* *
60604 TTATTTTCTCTAAACTCTTCTATTTTGCATTTATAGTG-CCGACTCCTCCACTTTAATCGAAG-T
519 TTATTTTATCTAAACTCTTCTATTTTGCATTTATAGTGTCC-AATCCTCCACTTTAATCG--GCT
*
60667 TTT-GGGATTTATTGTCTAGCCTTTTTCCTC
581 TTTCGGGATTTATCGTCTAGCCTTTTTCCTC
60697 TATTTTGTAA
Statistics
Matches: 573, Mismatches: 32, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
643 6 0.01
644 560 0.98
645 6 0.01
646 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (644 bp):
CATTCTAGAAGGTCAACCCTCATTATTGTCCAAGCTTTTCCATAAAAGGGGGAGATTCCTTTCCT
TTTGTTTTGAATCAACTTACAATCCAAAGCCCCCTTTTTACTCATGATCCACTTTTTACTCCCTT
TGTCCCTAAACATACCATCTTTTCACCTTTGACTACACATGGCCGGTCATAGCACCCCAAAAACC
CCACTTTTCATTTTATTTTTCTAGTTTTTCACTCCTCTCCTCTCTTTACCGTCCACCACCCTTCT
CCACAAGATTTTCAGCTTTTTCTTCTTTATTTTACCACCTTTGAAGCCATATTTCTTCATTCCTC
TTCCACTCCACCACCACACACGACAATCGCACCACCACCTTACCTCCATCATCGTCGTTGTCGCA
CAGCCGCCGCACCACTGCCATCGACCACTGTTGATTTTCACCATTTTTCTTATTTTCTCCTCTTT
CCAAAAATCATCTCCATAAATTCTTGAATTTGATTTTTAAATATTAAAATATCAAATTTCGTATT
ATTTTATCTAAACTCTTCTATTTTGCATTTATAGTGTCCAATCCTCCACTTTAATCGGCTTTTCG
GGATTTATCGTCTAGCCTTTTTCCTCCGTTTTATCGTAGGTATGAAGGACTACTATTCA
Found at i:73448 original size:25 final size:25
Alignment explanation
Indices: 73420--73478 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
73410 AGCTCGTATA
*
73420 AGCTTATCGATACTCAGCTCGCACG
1 AGCTTACCGATACTCAGCTCGCACG
* **
73445 AGCTTACCGTTTTTCAGCTCGCACG
1 AGCTTACCGATACTCAGCTCGCACG
73470 AGCTTACCG
1 AGCTTACCG
73479 TTTTTTAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.32, G:0.20, T:0.27
Consensus pattern (25 bp):
AGCTTACCGATACTCAGCTCGCACG
Found at i:73479 original size:25 final size:25
Alignment explanation
Indices: 73433--73483 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
73423 TTATCGATAC
73433 TCAGCTCGCACGAGCTTACCGTTTT
1 TCAGCTCGCACGAGCTTACCGTTTT
73458 TCAGCTCGCACGAGCTTACCGTTTT
1 TCAGCTCGCACGAGCTTACCGTTTT
73483 T
1 T
73484 TAGCATACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (25 bp):
TCAGCTCGCACGAGCTTACCGTTTT
Found at i:83179 original size:23 final size:23
Alignment explanation
Indices: 83124--83183 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
83114 ATACCAGTAG
*
83124 AGTACTCCTG--ACTTGTACTTC
1 AGTACTCCTGTTACTTGAACTTC
* *
83145 GGTACTCTTGTTACTTGAACTTC
1 AGTACTCCTGTTACTTGAACTTC
*
83168 AGTGCTCCTGTT-CTTG
1 AGTACTCCTGTTACTTG
83184 GCACAACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 8 0.26
22 4 0.13
23 19 0.61
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (23 bp):
AGTACTCCTGTTACTTGAACTTC
Found at i:85826 original size:16 final size:18
Alignment explanation
Indices: 85795--85828 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
85785 CAGCCTCCAT
85795 GGAGAAAGGAAAGAAAAG
1 GGAGAAAGGAAAGAAAAG
85813 GGAGAAA-G-AAGAAAAG
1 GGAGAAAGGAAAGAAAAG
85829 AAAGTAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
GGAGAAAGGAAAGAAAAG
Found at i:90844 original size:6 final size:6
Alignment explanation
Indices: 90833--90862 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
90823 TTACTAACTT
*
90833 TTTTTC TTTTTC CTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
90863 AATTTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:90868 original size:18 final size:18
Alignment explanation
Indices: 90833--90868 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
90823 TTACTAACTT
**
90833 TTTTTCTTTTTCCTTTTC
1 TTTTTCTTTTTCAATTTC
90851 TTTTTCTTTTTCAATTTC
1 TTTTTCTTTTTCAATTTC
90869 AATATATGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCTTTTTCAATTTC
Found at i:105283 original size:40 final size:40
Alignment explanation
Indices: 105228--105307 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
105218 TTAGAATAAG
105228 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
1 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
105268 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
1 TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
105308 ACCGTTGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (40 bp):
TGTACCATTCGAATTTCAACATTAGTGAAACTTCTCCTCT
Found at i:107727 original size:96 final size:93
Alignment explanation
Indices: 107584--107755 Score: 308
Period size: 96 Copynumber: 1.8 Consensus size: 93
107574 CTTATTACCC
*
107584 AAAAAATATGAAAGTAACAAAAAAAATAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAAAAA
1 AAAAAATATGAAAGTAACAAAAAAAAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAAAAA
107649 GCTCATTAAGTAACAAAAAAATATGTTA
66 GCTCATTAAGTAACAAAAAAATATGTTA
107677 AAAAAATATGAAAGTAACAAAAAAAACAAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAA
1 AAAAAATATGAAAGTAAC--AAAAAA-AAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAA
107742 AAAGCTCATTAAGT
63 AAAGCTCATTAAGT
107756 GCATCGAAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
93 18 0.24
95 6 0.08
96 51 0.68
ACGTcount: A:0.56, C:0.10, G:0.09, T:0.25
Consensus pattern (93 bp):
AAAAAATATGAAAGTAACAAAAAAAAAAAAAACTATGTTAAAAACTCTATTTTTCTCGAGAAAAA
GCTCATTAAGTAACAAAAAAATATGTTA
Found at i:109539 original size:16 final size:15
Alignment explanation
Indices: 109514--109543 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
109504 ATTAATTTAA
109514 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
109529 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
109544 ATGAAATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:110861 original size:15 final size:15
Alignment explanation
Indices: 110841--110869 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
110831 TAGCTAGTTA
110841 AATTATGCAAAATTT
1 AATTATGCAAAATTT
110856 AATTATGCAAAATT
1 AATTATGCAAAATT
110870 CAATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
AATTATGCAAAATTT
Found at i:118073 original size:61 final size:61
Alignment explanation
Indices: 117978--118095 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 61
117968 ACATTAATAA
* *
117978 TAAATTAATAAAATATTATATAGATAAATATTAAATTTAA-TTCCATATCTCATATTAGTAT
1 TAAATTAATAAAATACTATATAGATAAATATTAAATTTAACTT-AATATCTCATATTAGTAT
*
118039 TAAATTAATAAAATACTATCTAGATAAATATTAAATTTAACTTAATATCTCATATTA
1 TAAATTAATAAAATACTATATAGATAAATATTAAATTTAACTTAATATCTCATATTA
118096 ATATCTAGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
61 51 0.96
62 2 0.04
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (61 bp):
TAAATTAATAAAATACTATATAGATAAATATTAAATTTAACTTAATATCTCATATTAGTAT
Found at i:126255 original size:14 final size:13
Alignment explanation
Indices: 126238--126289 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 13
126228 TTTCTTATTC
126238 TTTTTTCTTTCGAA
1 TTTTTT-TTTCGAA
*
126252 TTTTTTTTTCAAAA
1 TTTTTTTTTC-GAA
126266 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
126279 CTTCTTTTTTT
1 -TT-TTTTTTT
126290 TTTACGTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 6 0.18
14 20 0.61
15 7 0.21
ACGTcount: A:0.15, C:0.12, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:138418 original size:8 final size:8
Alignment explanation
Indices: 138405--138441 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
138395 TGCTTAAAAA
138405 TATTAAAT
1 TATTAAAT
138413 TATTAAAT
1 TATTAAAT
138421 TATTAAAT
1 TATTAAAT
138429 TATTAAAT
1 TATTAAAT
138437 T-TTAA
1 TATTAA
138442 TAGTATAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 4 0.14
8 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
TATTAAAT
Found at i:140124 original size:32 final size:31
Alignment explanation
Indices: 140077--140147 Score: 106
Period size: 32 Copynumber: 2.3 Consensus size: 31
140067 AAATTACTCT
* * *
140077 TCCCCTAACTTATTACAAGTTGTTATTTTTC
1 TCCCCTAACTCATTACAAGTTATTATTTCTC
140108 TCCCACTAACTCATTACAAGTTATTATTTCTC
1 TCCC-CTAACTCATTACAAGTTATTATTTCTC
140140 TCCCCTAA
1 TCCCCTAA
140148 TGTCGGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 8 0.22
32 28 0.78
ACGTcount: A:0.25, C:0.28, G:0.04, T:0.42
Consensus pattern (31 bp):
TCCCCTAACTCATTACAAGTTATTATTTCTC
Found at i:143678 original size:17 final size:16
Alignment explanation
Indices: 143656--143689 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
143646 ATTATATAAT
143656 TAATGATAATTAAATTA
1 TAATGAT-ATTAAATTA
*
143673 TAATGATATTATATTA
1 TAATGATATTAAATTA
143689 T
1 T
143690 TAAATAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATATTAAATTA
Found at i:144045 original size:19 final size:20
Alignment explanation
Indices: 144007--144045 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
143997 AAGTAGGAAC
*
144007 GAAACAGAGAAAGGAGAGAA
1 GAAACAGAGAAAGGAAAGAA
*
144027 GAAACAGAG-CAGGAAAGAA
1 GAAACAGAGAAAGGAAAGAA
144046 AAAGGATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.59, C:0.08, G:0.33, T:0.00
Consensus pattern (20 bp):
GAAACAGAGAAAGGAAAGAA
Found at i:144850 original size:40 final size:41
Alignment explanation
Indices: 144766--144850 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 41
144756 AATTATAGAA
* * * *
144766 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTAAAAT
*
144807 TACTGAATATTG-TTATGTGTACT-ACATTGAACTGTAAAAT
1 TACTGAATATTGTTTATGAGTACTGA-ATTGAACTGTAAAAT
144847 TACT
1 TACT
144851 AAAGTAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 1 0.03
40 25 0.66
41 12 0.32
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTGTAAAAT
Found at i:145125 original size:45 final size:45
Alignment explanation
Indices: 145057--145157 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
145047 GCCGACTACT
* * * *
145057 GTTACTGTTACCGAATTGACACTTTGTATGTTGAATACTGTTACC
1 GTTACTGTTACAGAATTCACACTTTGTATATTGAATACTATTACC
* * *
145102 GTTACTGTTACAG-ATTCAGCACTTTGTGTATTGAATATTATTACT
1 GTTACTGTTACAGAATTCA-CACTTTGTATATTGAATACTATTACC
*
145147 GTTCCTGTTAC
1 GTTACTGTTAC
145158 TGCTACCGTT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGAATTCACACTTTGTATATTGAATACTATTACC
Found at i:149357 original size:7 final size:7
Alignment explanation
Indices: 149339--149374 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
149329 ATACAATACA
149339 ATTTCTCC
1 ATTTC-CC
149347 ATTTCCC
1 ATTTCCC
149354 ATTTCCC
1 ATTTCCC
149361 ATTTCCC
1 ATTTCCC
149368 ATTTCCC
1 ATTTCCC
149375 CTCTTCCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.14, C:0.42, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTCCC
Found at i:150580 original size:40 final size:40
Alignment explanation
Indices: 150531--150653 Score: 110
Period size: 40 Copynumber: 3.0 Consensus size: 40
150521 TTAAATTTTA
*
150531 ATTAGACATTGGTTATTATTAAATTTATATAAATATTATC
1 ATTACACATTGGTTATTATTAAATTTATATAAATATTATC
* * * * *
150571 ATCT-CACATT-ATAATATATGTAACTTTAAATTAAAT-TT-TA
1 AT-TACACATTGGTTAT-TAT-TAAATTTATA-TAAATATTATC
*
150611 ATTAGACATTGGTTATTATTAAATTTATATAAAATATTATC
1 ATTACACATTGGTTATTATTAAATTTATAT-AAATATTATC
150652 AT
1 AT
150654 ACTATAAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
38 1 0.02
39 16 0.26
40 23 0.37
41 17 0.27
42 5 0.08
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (40 bp):
ATTACACATTGGTTATTATTAAATTTATATAAATATTATC
Found at i:150589 original size:80 final size:81
Alignment explanation
Indices: 150492--150653 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 81
150482 CAGTATCAAC
150492 TCTCACATTATAATATATGTAACTTTAAATTAAATTTTAATTAGACATTGGTTATTATTAAATTT
1 TCTCACATTATAATATATGTAACTTTAAATTAAATTTTAATTAGACATTGGTTATTATTAAATTT
150557 ATAT-AAATATTATCA
66 ATATAAAATATTATCA
150572 TCTCACATTATAATATATGTAACTTTAAATTAAATTTTAATTAGACATTGGTTATTATTAAATTT
1 TCTCACATTATAATATATGTAACTTTAAATTAAATTTTAATTAGACATTGGTTATTATTAAATTT
150637 ATATAAAATATTATCA
66 ATATAAAATATTATCA
150653 T
1 T
150654 ACTATAAAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 69 0.85
81 12 0.15
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (81 bp):
TCTCACATTATAATATATGTAACTTTAAATTAAATTTTAATTAGACATTGGTTATTATTAAATTT
ATATAAAATATTATCA
Found at i:153428 original size:9 final size:9
Alignment explanation
Indices: 153416--153513 Score: 52
Period size: 10 Copynumber: 10.0 Consensus size: 9
153406 CAAAAAATCA
153416 TTAAAAATT
1 TTAAAAATT
*
153425 TTAAAACTTAT
1 TTAAAA-AT-T
153436 TTAAAAATT
1 TTAAAAATT
* *
153445 TATAGAATTT
1 T-TAAAAATT
153455 TGTAAAAATT
1 T-TAAAAATT
* *
153465 CTAAAAATA
1 TTAAAAATT
* *
153474 ATAATAATT
1 TTAAAAATT
*
153483 TTGAATGAATT
1 TT-AA-AAATT
153494 ATTAAAAATT
1 -TTAAAAATT
153504 TTACAAAATT
1 TTA-AAAATT
153514 ACAAAAAAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
9 25 0.37
10 27 0.40
11 13 0.19
12 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (9 bp):
TTAAAAATT
Found at i:153574 original size:32 final size:31
Alignment explanation
Indices: 153493--153575 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
153483 TTGAATGAAT
153493 TATTAAAAATT-TTACAAAATTACAAAAAAAC
1 TATTAAAAATTATTA-AAAATTACAAAAAAAC
* *
153524 TATTCAATAA-TAGT-AAAATTACAAAAAGAAAC
1 TATT-AAAAATTATTAAAAATTAC-AAAA-AAAC
153556 TA-TAAAAATTATTAAAAATT
1 TATTAAAAATTATTAAAAATT
153576 GAAAAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
30 12 0.29
31 13 0.31
32 17 0.40
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (31 bp):
TATTAAAAATTATTAAAAATTACAAAAAAAC
Found at i:154373 original size:17 final size:17
Alignment explanation
Indices: 154325--154363 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
154315 GAAAGAAGAT
* *
154325 ATTTCGTTTAAGTTTTA
1 ATTTTGTTTAATTTTTA
154342 ATTTTGTTTAATTTTTA
1 ATTTTGTTTAATTTTTA
154359 ATTTT
1 ATTTT
154364 TTATGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (17 bp):
ATTTTGTTTAATTTTTA
Found at i:155713 original size:140 final size:140
Alignment explanation
Indices: 155503--155930 Score: 624
Period size: 140 Copynumber: 3.1 Consensus size: 140
155493 ATCATAAGAC
** * * * *
155503 GACACTTTTGGGGTGACACTTTCCTAAGTGTTGGGATAAACTTGCCGACATATGCTTTGGTCAAG
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAAC
* *
155568 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAATAGTTGGCTTTGTTCG
66 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTTCA
*
155633 ACACTATGCC
131 ACACTATGCT
* * *
155643 GATACTTTTGGGCCGACACTTTCCTAAGTGTTGGTATAGATTTGCCGACATACGCTTTGGCCAAC
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAAC
* ****
155708 CCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGCCAACTTTG-TCT
66 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTTC-
*
155772 AACATTATGCT
130 AACACTATGCT
**
155783 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTTGACATACGCTTTGGCCAAC
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAAC
* * * *
155848 TCTTTGTATAAGGGTTGGGATATGCATGCCTAGGGTAACGCTTAAATAAGAGTTGGCTGTGTCCA
66 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTTCA
155913 ACACTATGCT
131 ACACTATGCT
155923 GACACTTT
1 GACACTTT
155931 CCTAAGTGTT
Statistics
Matches: 253, Mismatches: 33, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
139 2 0.01
140 250 0.99
141 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (140 bp):
GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGGCCAAC
TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTTGGCTTTGTTCA
ACACTATGCT
Found at i:159954 original size:120 final size:120
Alignment explanation
Indices: 159824--160114 Score: 573
Period size: 120 Copynumber: 2.4 Consensus size: 120
159814 ACGTGGGGGG
*
159824 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
159889 ATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTA
159944 AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
160009 ATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTA
160064 AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATA
1 AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATA
160115 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 170 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (120 bp):
AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
ATATTATGATTTTAGTAAATTCATATAAGAATATTTCATACTAAGAATTTTATTA
Found at i:159994 original size:26 final size:28
Alignment explanation
Indices: 159934--160114 Score: 102
Period size: 28 Copynumber: 6.2 Consensus size: 28
159924 TCATACTAAG
* * *
159934 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
159962 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
* *
159988 AATTATATTTTATAGTATTATATATTATGATTT
1 AATTATA-TTTA-A-TA--ATATATTATTATTA
* * * * * *
160021 TAGTAAATTCATATAAGAATATT-TCATACTAA
1 AATTATATTTA-ATAA-TATATTAT--TA-TTA
* * *
160053 GAATTTTATTAAATTATATATTATTATTA
1 -AATTATATTTAATAATATATTATTATTA
160082 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
160108 AATTATA
1 AATTATA
160115 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 24, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
26 20 0.17
27 16 0.14
28 29 0.25
29 6 0.05
30 7 0.06
31 11 0.09
32 15 0.13
33 12 0.10
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:160105 original size:61 final size:59
Alignment explanation
Indices: 159823--160110 Score: 242
Period size: 61 Copynumber: 4.8 Consensus size: 59
159813 AACGTGGGGG
* * * *
159823 GAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATA
1 GAATTATATATTATTATTAAATTATATTTAATAATAATTATTTCAAATAAAATTTTATA
* * ** * * * * *
159882 GTATTATATATTATGATTTTAGTAAATTCATATAAGAA-TATTTCATACTAAGAATTTTATTA
1 GAATTATATATTATTATTAAATTATATTTA-ATAATAATTATTTCA-AATAA-AATTTTA-TA
* * *
159944 -AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATA
1 GAATTATATATTATTATTAAATTATATTTAATAATAATTATTTCAAATAAAATTTTATA
* * ** * * * * *
160002 GTATTATATATTATGATTTTAGTAAATTCATATAAGAA-TATTTCATACTAAGAATTTTATTA
1 GAATTATATATTATTATTAAATTATATTTA-ATAATAATTATTTCA-AATAA-AATTTTA-TA
*
160064 -AATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAAT
1 GAATTATATATTATTATTAAATTATATTTAATAATAATTATTTCAAAT
160111 TATANNNNNN
Statistics
Matches: 171, Mismatches: 47, Indels: 21
0.72 0.20 0.09
Matches are distributed among these distances:
58 2 0.01
59 62 0.36
60 35 0.20
61 68 0.40
62 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (59 bp):
GAATTATATATTATTATTAAATTATATTTAATAATAATTATTTCAAATAAAATTTTATA
Found at i:163136 original size:41 final size:41
Alignment explanation
Indices: 163079--163237 Score: 223
Period size: 41 Copynumber: 3.9 Consensus size: 41
163069 AAATAAGATG
163079 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
163120 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
* * * *
163161 CTTCAGACTTTATGTCTAGCAGGCTT-AGTGCCGGTGAAATG
1 TTTCAGACTTTACGTCTAGCAGGCTTGA-TGCCGGTGAATTA
* * *
163202 TATCAGACCTTATGTCTAGCAGGCTTTG-TGCCGGTG
1 TTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGTG
163238 GAATGTATCG
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
40 1 0.01
41 105 0.97
42 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (41 bp):
TTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:163243 original size:41 final size:41
Alignment explanation
Indices: 163076--163278 Score: 211
Period size: 41 Copynumber: 5.0 Consensus size: 41
163066 TGAAAATAAG
* *
163076 ATGTTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGT-GA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGGA
*
163116 AT-TATTTCAGACTTTACGTCTAGCAGGC-TTGATGCCGGT-GA
1 ATGTA--TCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGGA
* *
163157 AT-TACTTCAGACTTTATGTCTAGCAGGCTTAGTGCCGGTGAA
1 ATGTA--TCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
*
163199 ATGTATCAGACCTTATGTCTAGCAGGCTTTGTGCCGGTGGA
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
* * * * *
163240 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTG
163279 TTTTATACAA
Statistics
Matches: 144, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 2 0.01
41 134 0.93
42 5 0.03
43 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (41 bp):
ATGTATCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGGA
Found at i:165207 original size:125 final size:123
Alignment explanation
Indices: 165017--165361 Score: 564
Period size: 125 Copynumber: 2.8 Consensus size: 123
165007 CGAGTTGATG
** *
165017 TTTCTGAGTAAATAGTATAAAATCGCTTTTAGTAAGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAG-CAGATGCTATTTGAGAAGAATTTGTGAAATCG
165082 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTTTTGACT
65 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAAT-AATTTTTTTTGACT
*
165142 TTTCTTACCAAATAGTATAAAATCGCTTTTAGCATGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAGCA-GATGCTATTTGAGAAGAATTTGTGAAATCG
* * *
165207 CGGCCTCGTAGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATATTTTTTTTTTACT
65 CGGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
*
165266 TTTCTGACCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAG-ATGCTATTTGAGAAGAATTTGTGAAATCG
* *
165331 CGGCCTCGTGGGCGTGCTTTTGCTACAGTAG
65 CGGCCTCGTGGACGCGCTTTTGCTACAGTAG
165362 CATGTTTGGG
Statistics
Matches: 206, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
123 1 0.00
124 102 0.50
125 103 0.50
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (123 bp):
TTTCTGACCAAATAGTATAAAATCGCTTTTAGCAGATGCTATTTGAGAAGAATTTGTGAAATCGC
GGCCTCGTGGACGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACT
Found at i:167755 original size:114 final size:114
Alignment explanation
Indices: 167573--168444 Score: 1394
Period size: 114 Copynumber: 7.6 Consensus size: 114
167563 GTCGAAAAAC
* * *
167573 GCCGCTAAATCACACCATTAGCGGCGCATTATACAAAGCACCGCAAAAAATCTTAACCAAAACTC
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
167638 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAAGATAAAT
66 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAAGATAAAT
*
167687 GTCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
167752 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAAGATAAAT
66 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAAGATAAAT
*
167801 GTCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
167866 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAAGATAAAT
66 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAAGATAAAT
*
167915 GTCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
* *
167980 ATCGTTTTGGGTTGAGGTATTTTATATTTAGTGGCGC-TTAAGGATAAAT
66 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAA-GATAAAT
* * * *
168029 GCCGCTAAAGCACACCATTAGCAGCGCATCATACAAAGCGCCGCCAAAAATCTTAACCGAAACGC
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
* * *
168094 ATCATTTTGGGTTGAGGTATATTAGAATTAGTGGCGC-TTACGGATAAAT
66 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTA-AGATAAAT
** * *
168143 GCCATTAAAGCACACCATTAGCAGCGCATTATTCAAAGCGCCGCAAAAAATCTTAACCAAAACGC
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
* *
168208 ATCGTTTTGGGTTGAGGTATTTTATATTTAGTGGCGC-TTAAGGATAAAT
66 ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAA-GATAAAT
* *
168257 GCCGCTAAAGCACACCATTAGCGGCACATTATACAAAGCGCCGCAAAAAATCATAACCAAAACGC
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
* * * *
168322 ATCGTTTTTGGTTGAGGTATTTTTAGAATTAGTAGCGCTAT-AG-TAAAAC
66 ATCGTTTTGGGTTGAGGTA-TTTTAGAATTAGTGGCGCTTTAAGAT-AAAT
* *
168371 GCCGCTAAAGTACATCATTAGCGGCGCATTATACAAAGCGCCGCAAACAAATCTTAACCAAAACG
1 GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAA-AAATCTTAACCAAAACG
168436 CATCGTTTT
65 CATCGTTTT
168445 AAACCGAAAC
Statistics
Matches: 708, Mismatches: 43, Indels: 13
0.93 0.06 0.02
Matches are distributed among these distances:
113 5 0.01
114 661 0.93
115 41 0.06
116 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (114 bp):
GCCGCTAAAGCACACCATTAGCGGCGCATTATACAAAGCGCCGCAAAAAATCTTAACCAAAACGC
ATCGTTTTGGGTTGAGGTATTTTAGAATTAGTGGCGCTTTAAGATAAAT
Found at i:168924 original size:21 final size:21
Alignment explanation
Indices: 168860--168924 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
168850 GGGCCATGGT
*
168860 TTAAGGGTT-GGGGTTTAATG
1 TTAAGGGTTAGGGGTTTAAGG
*
168880 -TATAGGTGTTACGGG-TTAATGG
1 TTA-AGG-GTTAGGGGTTTAA-GG
*
168902 TTAAGGGTTAGGGGTTTAGGG
1 TTAAGGGTTAGGGGTTTAAGG
168923 TT
1 TT
168925 TATAGTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 18 0.51
22 10 0.29
23 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.40, T:0.38
Consensus pattern (21 bp):
TTAAGGGTTAGGGGTTTAAGG
Found at i:169133 original size:21 final size:21
Alignment explanation
Indices: 169109--169152 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
169099 AAGGGTACTT
* *
169109 GGTTTA-ATGGTTTGAGTTTAA
1 GGTTTAGA-GGTTGGAGATTAA
169130 GGTTTAGAGGTTGGAGATTAA
1 GGTTTAGAGGTTGGAGATTAA
169151 GG
1 GG
169153 GATAGGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (21 bp):
GGTTTAGAGGTTGGAGATTAA
Found at i:169292 original size:22 final size:23
Alignment explanation
Indices: 169249--169305 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
169239 TTGGGGCTAA
* *
169249 GGTTTAGGGTTTAAGTGTTAAAG
1 GGTTTAAGGTTTAAGAGTTAAAG
* *
169272 GGTTTAAGGTTTCAGAG-TAAAT
1 GGTTTAAGGTTTAAGAGTTAAAG
169294 GGTTTAAGGTTT
1 GGTTTAAGGTTT
169306 TTTGGTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40
Consensus pattern (23 bp):
GGTTTAAGGTTTAAGAGTTAAAG
Found at i:170153 original size:190 final size:190
Alignment explanation
Indices: 169815--170193 Score: 598
Period size: 190 Copynumber: 2.0 Consensus size: 190
169805 TGTAAATCCC
* ** *
169815 TAGACCTTTCACCTTTTCAACGACGATTTCCCCTCTTCTCGGTCGAATATCGCTTCTCGTCTGGG
1 TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGG
* *
169880 CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTTAACTCCGTATATGGCTGTTCATTT
66 CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTTAACTACGTATATGGCTATTCATTT
* *
169945 TTATGTTCGATTTTTTCTTTCTGTAATGCCCACTTTGTTTTTCCTTTCTCTTTAAATTCA
131 TTATGTTCGATTTTTTCTTTCTCTAATGCCCACTTTGTTTTTCCTTTCGCTTTAAATTCA
* *
170005 TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTTTCGATCGAATATTGCTTCTCGTCTGGG
1 TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGG
* *
170070 CTGACTGGTAAAAATCTTTCCAAATCCCTAATTTCTTCGTTGAA-TACGTATATGGCTATTCATT
66 CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTT-AACTACGTATATGGCTATTCATT
* * * *
170134 TTTCTGTTTGATTTTTTCTTTCTCTAATGCTCGCTTTGTTTTTCCTTTCGCTTTAAATTC
130 TTTATGTTCGATTTTTTCTTTCTCTAATGCCCACTTTGTTTTTCCTTTCGCTTTAAATTC
170194 TGTGTTGCTT
Statistics
Matches: 172, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
190 170 0.99
191 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43
Consensus pattern (190 bp):
TAGACCATTCACCCCTTCAACGACGATTTCCCCTCTTCTCGATCGAATATCGCTTCTCGTCTGGG
CTGACTGGTAAAAAACTTTCCAAATCCCTAATTTCTCCGTTAACTACGTATATGGCTATTCATTT
TTATGTTCGATTTTTTCTTTCTCTAATGCCCACTTTGTTTTTCCTTTCGCTTTAAATTCA
Found at i:179309 original size:21 final size:21
Alignment explanation
Indices: 179283--179351 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
179273 CAACAACTTA
* *
179283 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
* * *
179304 AAGCAGAGGTTACAGAGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
179325 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
179346 AAGCAG
1 AAGCAG
179352 CGAGAGAAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:179351 original size:12 final size:12
Alignment explanation
Indices: 179336--179375 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
179326 AGCAGAGGCT
179336 GCAGCGAGAGAA
1 GCAGCGAGAGAA
179348 GCAGCGAGAGAA
1 GCAGCGAGAGAA
* *
179360 ACAGCGATAGAA
1 GCAGCGAGAGAA
179372 GCAG
1 GCAG
179376 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.17, G:0.38, T:0.03
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:180295 original size:42 final size:42
Alignment explanation
Indices: 180248--180414 Score: 235
Period size: 43 Copynumber: 3.9 Consensus size: 42
180238 TCTTTAGCGG
*
180248 AAGCGCCGCTAAAGAACATGATCATTAGGGGCGTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTCCT
* * *
180290 AAGCGCTGCTAAAGAACATGATCATTAACGGCATTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGC-GTTTTTTCCT
* *
180333 AAGCGCTGCTAAAGAACATGATCATTAGCGACGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCG-TTTTTTCCT
* * *
180376 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCGTTTTTT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTT
180415 TTCTGTAAGC
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
42 35 0.32
43 76 0.68
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTCCT
Found at i:180342 original size:43 final size:42
Alignment explanation
Indices: 180248--180434 Score: 230
Period size: 43 Copynumber: 4.3 Consensus size: 42
180238 TCTTTAGCGG
* *
180248 AAGCGCCGCTAAAGAACATGATCATTAGGGGCGTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCTTTTTTTCCT
* *
180290 AAGCGCTGCTAAAGAACATGATCATTAACGGCATTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGC-TTTTTTTCCT
* *
180333 AAGCGCTGCTAAAGAACATGATCATTAGCGACGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGC-TTTTTTTCCT
* * * *
180376 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCGTTTTTTTTCTGT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGC--TTTTTTTC-CT
*
180421 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
180435 TTAGCGACGT
Statistics
Matches: 127, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
42 29 0.23
43 76 0.60
44 8 0.06
45 14 0.11
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCATTAGCGGCTTTTTTTCCT
Found at i:180413 original size:85 final size:85
Alignment explanation
Indices: 180248--180414 Score: 239
Period size: 85 Copynumber: 2.0 Consensus size: 85
180238 TCTTTAGCGG
* * * *
180248 AAGCGCCGCTAAAGAACATGATCATTAGGGGCGTTTTTTCCTAAGCGCTGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCATTAGCGACGTTTTTTCCTAAGCGCCGCTAAAGAACATGACC
*
180313 ATTAACGGCATTTTTTTCCT
66 ATTAACGGCAGTTTTTTCCT
*
180333 AAGCGCTGCTAAAGAACATGATCATTAGCGACGTTTTTTTCCTAAGCGCCGCTAAAGAACATGAC
1 AAGCGCCGCTAAAGAACATGATCATTAGCGACG-TTTTTTCCTAAGCGCCGCTAAAGAACATGAC
*
180398 CTTTAGA-GGC-GTTTTTT
65 CATTA-ACGGCAGTTTTTT
180415 TTCTGTAAGC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
85 36 0.49
86 36 0.49
87 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGATCATTAGCGACGTTTTTTCCTAAGCGCCGCTAAAGAACATGACC
ATTAACGGCAGTTTTTTCCT
Found at i:182822 original size:9 final size:9
Alignment explanation
Indices: 182808--182835 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
182798 AGTTGATTCA
182808 AATAACTCG
1 AATAACTCG
182817 AATAACTCG
1 AATAACTCG
182826 AATAACTCG
1 AATAACTCG
182835 A
1 A
182836 TTCGTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (9 bp):
AATAACTCG
Found at i:184300 original size:13 final size:12
Alignment explanation
Indices: 184280--184311 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
184270 TCACCAACTT
184280 ATATGTTAGTCC
1 ATATGTTAGTCC
184292 ATGATGTTAGTCC
1 AT-ATGTTAGTCC
184305 ATATGTT
1 ATATGTT
184312 CAAAATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (12 bp):
ATATGTTAGTCC
Found at i:185659 original size:70 final size:71
Alignment explanation
Indices: 185510--185709 Score: 201
Period size: 70 Copynumber: 2.8 Consensus size: 71
185500 CCTTAGACGT
* * * * *
185510 GTCTATTCCAACCTTTTAAAGGTTGTCTTAGACGGGTCTATCCTAACCTTTTTAAATGTTGTTTT
1 GTCTATCCCAACCTTTTTAAGGTTGTATTAGAC-GGACTATCCTAACCTTTTTAAAGGTTGTTTT
*
185575 AGATAAG
65 AGACAAG
* * * *
185582 GTATATCCCAACCTTTTTAAGGTTGTATTAGA-TGACTATCTTGACCTTTTTAAAGGTTGCTTTT
1 GTCTATCCCAACCTTTTTAAGGTTGTATTAGACGGACTATCCTAACCTTTTTAAAGGTTG-TTTT
185646 -GACAAG
65 AGACAAG
* * * *
185652 GTCTATCCCAACTTTTTTAGGGTTGCT-TTAGACGGGTCTATTCC-AACCTTTTTTAAGG
1 GTCTATCCCAACCTTTTTAAGGTTG-TATTAGAC-GGACTA-TCCTAACCTTTTTAAAGG
185710 GTTACCTTAG
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
70 54 0.51
71 5 0.05
72 44 0.42
73 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.41
Consensus pattern (71 bp):
GTCTATCCCAACCTTTTTAAGGTTGTATTAGACGGACTATCCTAACCTTTTTAAAGGTTGTTTTA
GACAAG
Found at i:185704 original size:35 final size:34
Alignment explanation
Indices: 185502--185709 Score: 136
Period size: 36 Copynumber: 5.9 Consensus size: 34
185492 AAAAATTACC
* *
185502 TTAGACGTGTCTATTCCAACCTTTTAAAGGTTGT
1 TTAGACGGGTCTATTCCAACCTTTTTAAGGTTGT
*
185536 CTTAGACGGGTCTA-TCCTAACCTTTTTAAATGTTGTT
1 -TTAGACGGGTCTATTCC-AACCTTTTT-AAGGTTG-T
** * *
185573 TTAGATAAGGTATATCCCAACCTTTTTAAGGTTGT
1 TTAGA-CGGGTCTATTCCAACCTTTTTAAGGTTGT
* * **
185608 ATTAGA--TGACTA-TCTTGACCTTTTTAAAGGTTGCT
1 -TTAGACGGGTCTATTC-CAACCTTTTT-AAGGTTG-T
* * * * *
185643 TTTGACAAGGTCTATCCCAACTTTTTTAGGGTTGCT
1 TTAGAC-GGGTCTATTCCAACCTTTTTAAGGTTG-T
185679 TTAGACGGGTCTATTCCAACCTTTTTTAAGG
1 TTAGACGGGTCTATTCCAACC-TTTTTAAGG
185710 GTTACCTTAG
Statistics
Matches: 132, Mismatches: 27, Indels: 27
0.71 0.15 0.15
Matches are distributed among these distances:
32 1 0.01
33 11 0.08
34 14 0.11
35 34 0.26
36 43 0.33
37 26 0.20
38 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (34 bp):
TTAGACGGGTCTATTCCAACCTTTTTAAGGTTGT
Found at i:185720 original size:37 final size:35
Alignment explanation
Indices: 185651--185721 Score: 97
Period size: 37 Copynumber: 2.0 Consensus size: 35
185641 CTTTTGACAA
* *
185651 GGTCTATCCCAACTTTTTTAGGGTTGCTTTAGACG
1 GGTCTATCCCAACTTTTTTAGGGTTACCTTAGACG
*
185686 GGTCTATTCCAACCTTTTTTAAGGGTTACCTTAGAC
1 GGTCTATCCCAA-CTTTTTT-AGGGTTACCTTAGAC
185722 AATGTCTAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 11 0.35
36 7 0.23
37 13 0.42
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (35 bp):
GGTCTATCCCAACTTTTTTAGGGTTACCTTAGACG
Found at i:187207 original size:47 final size:47
Alignment explanation
Indices: 187153--187247 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
187143 TTTTTATTTT
187153 TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
1 TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
* * * * **
187200 TTATAGATGGCAGTCTTATTTTTGGAGAAGTGTCGTCGGTGGAAATC
1 TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
187247 T
1 T
187248 CAAGTTGCGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (47 bp):
TTATAGATGACAATCTTAGTTTTGGAGAAGTGTCATCAATGGAAATC
Found at i:191883 original size:19 final size:20
Alignment explanation
Indices: 191834--191883 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
191824 TTAATAAAAA
*
191834 TTATAAAAAAATCAAAATAAT
1 TTAT-AAAAATTCAAAATAAT
*
191855 TT-TTAAAATTCAAAAT-AT
1 TTATAAAAATTCAAAATAAT
191873 TTATAAAAATT
1 TTATAAAAATT
191884 TTAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 4 0.16
19 18 0.72
20 1 0.04
21 2 0.08
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
TTATAAAAATTCAAAATAAT
Found at i:195358 original size:4 final size:4
Alignment explanation
Indices: 195343--195394 Score: 95
Period size: 4 Copynumber: 13.0 Consensus size: 4
195333 TTCAAAACAC
*
195343 CATA CGTA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
195391 CATA
1 CATA
195395 AAAAAACTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:206440 original size:15 final size:15
Alignment explanation
Indices: 206420--206472 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
206410 GTAAGATATA
206420 ATTTTTTCTTATCGT
1 ATTTTTTCTTATCGT
* *
206435 ATTTTTAT-TCATACAT
1 ATTTTT-TCTTAT-CGT
206451 AATTTTTTCTTATCGT
1 -ATTTTTTCTTATCGT
206467 ATTTTT
1 ATTTTT
206473 ATTCATACCG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 15 0.50
16 6 0.20
17 9 0.30
ACGTcount: A:0.21, C:0.11, G:0.04, T:0.64
Consensus pattern (15 bp):
ATTTTTTCTTATCGT
Found at i:206458 original size:32 final size:32
Alignment explanation
Indices: 206417--206480 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
206407 ACTGTAAGAT
206417 ATAATTTTTTCTTATCGTATTTTTATTCATAC
1 ATAATTTTTTCTTATCGTATTTTTATTCATAC
206449 ATAATTTTTTCTTATCGTATTTTTATTCATAC
1 ATAATTTTTTCTTATCGTATTTTTATTCATAC
206481 CGTCTGGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (32 bp):
ATAATTTTTTCTTATCGTATTTTTATTCATAC
Found at i:212940 original size:45 final size:45
Alignment explanation
Indices: 212870--213042 Score: 149
Period size: 45 Copynumber: 3.8 Consensus size: 45
212860 TCGGCTTGAA
* *
212870 GAAAATGAATAAGACTATAGTTGAAAGACACTATGGCACTATA-C
1 GAAAATGAATAAGACCATAGATGAAAGACACTATGGCACTATATC
* * * * *
212914 TGGAACTGAATAAGTCCATAGATGAAAGAAACTATGGCATTATATC
1 -GAAAATGAATAAGACCATAGATGAAAGACACTATGGCACTATATC
* *
212960 GAAAATGAGTAAGACCATA-ACTGAAAGACGCTATGGCA-TA-AT-
1 GAAAATGAATAAGACCATAGA-TGAAAGACACTATGGCACTATATC
* * * *
213002 GATTATAATGAGTAAGACCATAGCTAAAAGACATTATGGCA
1 GA--A-AATGAATAAGACCATAGATGAAAGACACTATGGCA
213043 TCACAATTCT
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 4 0.04
45 96 0.91
46 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (45 bp):
GAAAATGAATAAGACCATAGATGAAAGACACTATGGCACTATATC
Found at i:213023 original size:90 final size:90
Alignment explanation
Indices: 212924--213174 Score: 220
Period size: 90 Copynumber: 2.8 Consensus size: 90
212914 TGGAACTGAA
* * * * *
212924 TAAGTCCATAGATGAAAGAAACTATGGCATTA-TA-TCGAAAATGAGTAAGACCATAACTGAAAG
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATTC--AAACGAGTAAGACCATAACTGAAAG
* * *
212987 ACGCTATGGCATAATGATTATAATGAG
64 ACGCTATGACATAATGACTATAACGAG
* * * * *
213014 TAAGACCATAGCTAAAAGACATTATGGCATCACAATTCTAACGAGTAAGACCATAGCTGAAAGAC
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATTCAAACGAGTAAGACCATAACTGAAAGAC
* * *
213079 GTTATGACATCATGACTGTAACGAG
66 GCTATGACATAATGACTATAACGAG
* * * *** * * *
213104 TAAGGCCATAGCTAGAAGACGTTATGTCATCATAATTCTAACGAGTAAGACCATAGA-TGAAAGA
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATTCAAACGAGTAAGACCATA-ACTGAAAGA
*
213168 TGCTATG
65 CGCTATG
213175 GTATCATGAA
Statistics
Matches: 134, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
90 131 0.98
91 1 0.01
92 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (90 bp):
TAAGACCATAGATAAAAGAAACTATGGCATCACAATTCAAACGAGTAAGACCATAACTGAAAGAC
GCTATGACATAATGACTATAACGAG
Found at i:213043 original size:45 final size:45
Alignment explanation
Indices: 212966--213202 Score: 242
Period size: 45 Copynumber: 5.3 Consensus size: 45
212956 TATCGAAAAT
* * * * * * *
212966 GAGTAAGACCATAACTGAAAGACGCTATGGCATAATGATTATAAT
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* *
213011 GAGTAAGACCATAGCTAAAAGACATTATGGCATCACAATTCTAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* * * * *
213056 GAGTAAGACCATAGCTGAAAGACGTTATGACATCATGACTGTAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* * *
213101 GAGTAAGGCCATAGCTAGAAGACGTTATGTCATCATAATTCTAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
* * * * * *
213146 GAGTAAGACCATAGATGAAAGATGCTATGGTATCATGAA-TCAAAC
1 GAGTAAGACCATAGCTAAAAGACGTTATGGCATCAT-AATTCTAAC
*
213191 GAATAAGACCAT
1 GAGTAAGACCAT
213203 GGTTGGAAGA
Statistics
Matches: 158, Mismatches: 33, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
45 156 0.99
46 2 0.01
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (45 bp):
GAGTAAGACCATAGCTAAAAGACGTTATGGCATCATAATTCTAAC
Found at i:213181 original size:90 final size:90
Alignment explanation
Indices: 212966--213202 Score: 298
Period size: 90 Copynumber: 2.6 Consensus size: 90
212956 TATCGAAAAT
* * *
212966 GAGTAAGACCATA-ACTGAAAGACGCTATGGCATAATGATTATAATGAGTAAGACCATAGCTAAA
1 GAGTAAGACCATAGA-TGAAAGACGCTATGGCATCATGACTATAACGAGTAAGACCATAGCTAAA
213030 AGACATTATGGCATCACAATTCTAAC
65 AGACATTATGGCATCACAATTCTAAC
* * * * * *
213056 GAGTAAGACCATAGCTGAAAGACGTTATGACATCATGACTGTAACGAGTAAGGCCATAGCTAGAA
1 GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGACTATAACGAGTAAGACCATAGCTAAAA
* * *
213121 GACGTTATGTCATCATAATTCTAAC
66 GACATTATGGCATCACAATTCTAAC
* * * *
213146 GAGTAAGACCATAGATGAAAGATGCTATGGTATCATGAATCA-AACGAATAAGACCAT
1 GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGACT-ATAACGAGTAAGACCAT
213203 GGTTGGAAGA
Statistics
Matches: 124, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
90 124 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (90 bp):
GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGACTATAACGAGTAAGACCATAGCTAAAA
GACATTATGGCATCACAATTCTAAC
Found at i:219960 original size:4 final size:4
Alignment explanation
Indices: 219953--219978 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
219943 AAATGCATGC
219953 ATGA ATGA ATGA ATGA ATGA ATGA AT
1 ATGA ATGA ATGA ATGA ATGA ATGA AT
219979 TGCCATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
ATGA
Found at i:232034 original size:46 final size:46
Alignment explanation
Indices: 231927--232141 Score: 265
Period size: 45 Copynumber: 4.7 Consensus size: 46
231917 TGAATCAAAG
* * *
231927 AAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGGAAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTG-AAAAT
* *
231974 GAATAAGACCATGGTTGAAAGACACTATGGCAACACGA-TGAAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTG-AAAAT
* * * * * *
232020 GAATAAGACCATGGTAGAAAGACATTATGGCATCAAGA-AGAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTGAAAAT
* *
232065 AAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACT-AGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTGAAAAT
*
232110 AAATAAGACCATGGTTGAAAGACACCATGGCA
1 AAATAAGACCATGGTTGAAAGACACTATGGCA
232142 CACTTTGATC
Statistics
Matches: 153, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
45 75 0.49
46 42 0.27
47 36 0.24
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (46 bp):
AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACTGAAAAT
Found at i:233931 original size:12 final size:12
Alignment explanation
Indices: 233914--233943 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
233904 TCAGGCAGTT
233914 ACACGGCCTAGC
1 ACACGGCCTAGC
*
233926 ACACGGCCTGGC
1 ACACGGCCTAGC
233938 ACACGG
1 ACACGG
233944 GCGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:241518 original size:16 final size:16
Alignment explanation
Indices: 241485--241514 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
241475 GATTTTCTGA
241485 TTGTTTTTTCTTTTCT
1 TTGTTTTTTCTTTTCT
241501 TTGTTTTTT-TTTTC
1 TTGTTTTTTCTTTTC
241515 CTTTTTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (16 bp):
TTGTTTTTTCTTTTCT
Found at i:249571 original size:31 final size:32
Alignment explanation
Indices: 249510--249574 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
249500 TTTTAATCTC
249510 AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
1 AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
*
249542 AAAGTTAAAAACAGTGGGAGCT-AAAGCAAAT
1 AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
249573 AA
1 AA
249575 TTCCTTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.15
Consensus pattern (32 bp):
AAAGTTAAAAACAATGGGAGCTAAAAGCAAAT
Found at i:251778 original size:23 final size:23
Alignment explanation
Indices: 251733--251779 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
251723 TCAGAGTAAT
**
251733 TTAATCTCTATCAATTTTGAGAG
1 TTAATCTCTATCAATTTCAAGAG
251756 TTAATCTCTATCAATTTCAAGAG
1 TTAATCTCTATCAATTTCAAGAG
251779 T
1 T
251780 GAGAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (23 bp):
TTAATCTCTATCAATTTCAAGAG
Found at i:251972 original size:51 final size:51
Alignment explanation
Indices: 251870--251988 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
251860 GCCCTCAAAG
* * *
251870 TTTACATATTCTGTCAATTTGGTCTTGATTTAACAAATTTAGCCAATAACA
1 TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGCCAATAACA
* * * **
251921 TTTACACATTTTATCAATTTGGTCCTGATTTAATATATTTAGCTTGA-AACA
1 TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGC-CAATAACA
251972 TTTACACATTCTATCAA
1 TTTACACATTCTATCAA
251989 CATTTACACA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 57 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (51 bp):
TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGCCAATAACA
Found at i:266022 original size:27 final size:27
Alignment explanation
Indices: 265981--266102 Score: 133
Period size: 27 Copynumber: 4.5 Consensus size: 27
265971 ACACGCTAGA
*
265981 AAAAGAAAGCCTTTGTGCTGATCTATC
1 AAAAGAAAGCCTTTGTGCTGATCTATG
* *
266008 AAAAGAAAGCTTTTGTGGTGATCTATG
1 AAAAGAAAGCCTTTGTGCTGATCTATG
* *
266035 AAAA-AGAAGCATTTATGGCT-ATCTATG
1 AAAAGA-AAGCCTTTGT-GCTGATCTATG
*
266062 AAAAGAAAGCCTTTGTGGC-AATCTATG
1 AAAAGAAAGCCTTTGT-GCTGATCTATG
*
266089 AAAAGAATGCCTTT
1 AAAAGAAAGCCTTT
266103 ATGGTGCACT
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
26 1 0.01
27 78 0.95
28 3 0.04
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (27 bp):
AAAAGAAAGCCTTTGTGCTGATCTATG
Found at i:266066 original size:54 final size:55
Alignment explanation
Indices: 265979--266106 Score: 163
Period size: 54 Copynumber: 2.3 Consensus size: 55
265969 GAACACGCTA
* * **
265979 GAAAAAGAAAGCCTTTGT-GCTGATCTATCAAAAGAAAGCTTTTGTGGTGATCTAT
1 GAAAAAG-AAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTTGTGGCAATCTAT
* *
266034 GAAAAAGAAGCATTTATGGCT-ATCTATGAAAAGAAAGCCTTTGTGGCAATCTAT
1 GAAAAAGAAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTTGTGGCAATCTAT
266088 G-AAAAGAATGCCTTTATGG
1 GAAAAAGAA-GCCTTTATGG
266107 TGCACTCTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
53 7 0.11
54 47 0.73
55 10 0.16
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (55 bp):
GAAAAAGAAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTTGTGGCAATCTAT
Found at i:269997 original size:40 final size:39
Alignment explanation
Indices: 269939--270061 Score: 156
Period size: 40 Copynumber: 3.1 Consensus size: 39
269929 AGCTCGCATG
* * *
269939 GGGAGCTTTCACTAATACACATCTTATCCCTAAGCTTACA
1 GGGAGC-TTCACTGATACACAACTTATCCATAAGCTTACA
* * *
269979 GGAGAGCTTCACTGATACACAGCTTATCTATAAGCTCACA
1 GG-GAGCTTCACTGATACACAACTTATCCATAAGCTTACA
*
270019 TGGGAGTTTCACTGATACACAACTTATCCATAAGCTTACA
1 -GGGAGCTTCACTGATACACAACTTATCCATAAGCTTACA
270059 GGG
1 GGG
270062 GAAATTTTCC
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 3 0.04
40 63 0.88
41 6 0.08
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (39 bp):
GGGAGCTTCACTGATACACAACTTATCCATAAGCTTACA
Found at i:270076 original size:40 final size:39
Alignment explanation
Indices: 269953--270081 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 39
269943 GCTTTCACTA
* * * **
269953 ATACACATCTTATCCCTAAGCTTACAGGAG-AGCTTCACTG
1 ATACACAACTTATCCATAAGCTTACAGGGGAATTTTC-C-G
* * * * *
269993 ATACACAGCTTATCTATAAGCTCACATGGG-AGTTTCACTG
1 ATACACAACTTATCCATAAGCTTACAGGGGAATTTTC-C-G
270033 ATACACAACTTATCCATAAGCTTACAGGGGAAATTTTCCG
1 ATACACAACTTATCCATAAGCTTACAGGGG-AATTTTCCG
270073 ATACACAAC
1 ATACACAAC
270082 GTATAAAATC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
40 69 0.92
41 1 0.01
42 5 0.07
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (39 bp):
ATACACAACTTATCCATAAGCTTACAGGGGAATTTTCCG
Found at i:270076 original size:80 final size:82
Alignment explanation
Indices: 269929--270079 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 82
269919 CTATCACTTC
* * * ** *
269929 AGCTCGCATGGGGAGCTTTCACTAATACACATCTTATCCCTAAGCTTACAGGAGAGCTTCACTGA
1 AGCTCACATGGGGAGCTTTCACTAATACACAACTTATCCATAAGCTTACAGGAGAAATTCACCGA
269994 TACACAGCTTATCTATA
66 TACACAGCTTATCTATA
* * **
270011 AGCTCACAT-GGGAG-TTTCACTGATACACAACTTATCCATAAGCTTACAGGGGAAATTTTCCGA
1 AGCTCACATGGGGAGCTTTCACTAATACACAACTTATCCATAAGCTTACAGGAGAAATTCACCGA
270074 TACACA
66 TACACA
270080 ACGTATAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 46 0.78
81 5 0.08
82 8 0.14
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (82 bp):
AGCTCACATGGGGAGCTTTCACTAATACACAACTTATCCATAAGCTTACAGGAGAAATTCACCGA
TACACAGCTTATCTATA
Found at i:275730 original size:50 final size:50
Alignment explanation
Indices: 275543--275784 Score: 170
Period size: 50 Copynumber: 4.7 Consensus size: 50
275533 GATAATAACA
* * ** *
275543 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTT-AT-T-GTAC
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCG--G
* * * * * *
275592 TACCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATATCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTT-TCATCTCGG
* * * * *
275642 TGCCCATGCCATGTTCTAGACATGGTCTTAC-GGAGGACCTTTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATG-GGACCTTTCATCTCGG
* * * * *
275692 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTTAATGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTTTCAT---C-T--CGG
275748 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
275785 TCTCATTCCC
Statistics
Matches: 154, Mismatches: 26, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
48 3 0.02
49 35 0.23
50 73 0.47
51 4 0.03
52 1 0.01
53 1 0.01
54 1 0.01
56 36 0.23
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCGG
Found at i:275759 original size:56 final size:54
Alignment explanation
Indices: 275692--275800 Score: 164
Period size: 56 Copynumber: 2.0 Consensus size: 54
275682 TTCATCTCGG
275692 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTTAATGA
1 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGA--TCTCATAACCTTAATGA
* * **
275748 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCATTCCCTTAATG
1 TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGATCTCATAACCTTAATG
275801 TCATGACATT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 14 0.29
56 35 0.71
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (54 bp):
TGCCAACGTCATGTCCCAAACATGGTCTTACATGGGATCTCATAACCTTAATGA
Found at i:283936 original size:3 final size:3
Alignment explanation
Indices: 283928--283970 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
283918 ACTGCTGTCT
283928 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
283971 ATCTTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:290670 original size:44 final size:45
Alignment explanation
Indices: 290561--290716 Score: 154
Period size: 45 Copynumber: 3.5 Consensus size: 45
290551 ACTCGATGCG
* * ** * *
290561 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACTTA-CTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGGTCAGCTTCA
* * * * *
290606 ATCCGCTCCACTACAACTTCAGGGAGATAGGATT-TTCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTCAGCTTCA
* * *
290650 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTCAGCTTCA
*
290695 ATCTGCCCCACTGCAACTTCAG
1 ATCTGCTCCACTGCAACTTCAG
290717 TTGGGATAAG
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
43 1 0.01
44 35 0.39
45 54 0.60
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (45 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTCAGCTTCA
Found at i:290713 original size:45 final size:43
Alignment explanation
Indices: 290561--290909 Score: 183
Period size: 44 Copynumber: 8.0 Consensus size: 43
290551 ACTCGATGCG
* * * *
290561 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACTTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-CTCACTTCA
* * * * *
290606 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTTTCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTC-ACTTCA
* * *
290650 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-CTCA-CTTCA
* * *
290695 ATCTGCCCCACTGCAACTTCAGTTGG-GATAAGACCTGCTTACTT-A
1 ATCTGCTCCACTGCAACTTCAG--GGAGATAAGA--TTCTCACTTCA
* * * * * * * * *
290740 GTCTTCTCCACTGTAACTTTAGGGAAATAAGA-CCTGACGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCACTTCA
* ** * * * * *
290781 GTCCACTCTACTGCAACTTCAGAGAGATAAGATCCATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-TCACTTCA
* * * *
290825 ATTCT-CTCCACTACAACTTCAGGGAGATAGGATTATTGACTTCA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-CTCACTTCA
* *
290869 ATTTGCTCCACTACAA-TCTCAGGGAGATAAGATT-T-ACTTCA
1 ATCTGCTCCACTGCAACT-TCAGGGAGATAAGATTCTCACTTCA
290910 CCGACCTGTT
Statistics
Matches: 235, Mismatches: 54, Indels: 34
0.73 0.17 0.11
Matches are distributed among these distances:
41 36 0.15
42 3 0.01
43 10 0.04
44 98 0.42
45 73 0.31
46 10 0.04
47 4 0.02
48 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCACTTCA
Found at i:301518 original size:16 final size:16
Alignment explanation
Indices: 301494--301542 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
301484 TTCGCTGTAT
301494 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
301510 TGGATTAGAGGCGTAA
1 TGGAATAGAGGCGTAA
301526 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
301542 T
1 T
301543 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:301573 original size:45 final size:44
Alignment explanation
Indices: 301522--301611 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
301512 GATTAGAGGC
301522 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGC-AATC-ATGTGTTTGGTTGAAT
*
301567 GTAATGGAATAGAGGCGTAATAGCAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAAT
301611 G
1 G
301612 GAATAGAGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.42
45 24 0.56
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAAT
Found at i:301626 original size:39 final size:42
Alignment explanation
Indices: 301522--301630 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 42
301512 GATTAGAGGC
301522 GTAATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGC-AATCAATTGTTTGGTT--AT
*
301567 GTAATGGAATAGAGGCGTAATAGCAATC-TTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGCAATCAAT-TGTTTGGTTAT
*
301607 G-AATGGAATAGAGGTGTAATAGCA
1 GTAATGGAATAGAGGCGTAATAGCA
301631 TAATGGAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
39 22 0.36
40 2 0.03
43 2 0.03
44 11 0.18
45 24 0.39
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.30
Consensus pattern (42 bp):
GTAATGGAATAGAGGCGTAATAGCAATCAATTGTTTGGTTAT
Found at i:301793 original size:16 final size:16
Alignment explanation
Indices: 301756--301797 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
301746 TTAATCATAT
*
301756 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
301772 TT-AAATATATTATAA
1 TTAAAATATATTATAA
301787 TTAAAATATAT
1 TTAAAATATAT
301798 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:301804 original size:14 final size:15
Alignment explanation
Indices: 301765--301806 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
301755 TTTAAACATA
*
301765 ATTATTATTAAATAT
1 ATTATAATTAAATAT
301780 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
301794 A-TATAATTTAATA
1 ATTATAATTAAATA
301807 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:302018 original size:24 final size:25
Alignment explanation
Indices: 301972--302019 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
301962 TATGAATTTG
301972 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
301998 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
302020 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:302023 original size:92 final size:92
Alignment explanation
Indices: 301927--302155 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
301917 TGATTTAATA
* * *
301927 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
301989 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
302019 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
302084 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
302109 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
302156 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:311748 original size:16 final size:17
Alignment explanation
Indices: 311710--311748 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
311700 AAAAAATTAT
*
311710 AAATAAAATATTCAAAA
1 AAATAAAACATTCAAAA
*
311727 ATATAAAACATT-AAAA
1 AAATAAAACATTCAAAA
311743 AAATAA
1 AAATAA
311749 TCAATCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAACATTCAAAA
Found at i:316876 original size:16 final size:16
Alignment explanation
Indices: 316866--316896 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
316856 ATTGGGCTTG
316866 AATATTTTTGGGCTCC
1 AATATTTTTGGGCTCC
*
316882 AATTTTTTTGGGCTC
1 AATATTTTTGGGCTC
316897 AAAATTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.48
Consensus pattern (16 bp):
AATATTTTTGGGCTCC
Found at i:318573 original size:17 final size:17
Alignment explanation
Indices: 318551--318583 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
318541 AATAAAAAGC
318551 TATAAAATTTTTAATAT
1 TATAAAATTTTTAATAT
*
318568 TATAAACTTTTTAATA
1 TATAAAATTTTTAATA
318584 AAAATTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAAATTTTTAATAT
Found at i:319012 original size:11 final size:11
Alignment explanation
Indices: 318993--319062 Score: 59
Period size: 11 Copynumber: 6.4 Consensus size: 11
318983 TATCGAAACC
*
318993 ATAACAACAAA
1 ATAATAACAAA
* *
319004 ATAAAAACAAT
1 ATAATAACAAA
**
319015 ATAATAGTAAA
1 ATAATAACAAA
319026 ATAATAACAAA
1 ATAATAACAAA
* * **
319037 ACAACAATGAA
1 ATAATAACAAA
319048 ATAATAACAAA
1 ATAATAACAAA
319059 ATAA
1 ATAA
319063 CAACGAAAAA
Statistics
Matches: 43, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (11 bp):
ATAATAACAAA
Found at i:319018 original size:22 final size:22
Alignment explanation
Indices: 318993--319071 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
318983 TATCGAAACC
* *
318993 ATAACAACAAAATAAAAACAAT
1 ATAACAACAAAATAATAACAAA
* **
319015 ATAATAGTAAAATAATAACAAA
1 ATAACAACAAAATAATAACAAA
* **
319037 ACAACAATGAAATAATAACAAA
1 ATAACAACAAAATAATAACAAA
319059 ATAACAACGAAAA
1 ATAACAAC-AAAA
319072 AGTTAATTCG
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 41 0.93
23 3 0.07
ACGTcount: A:0.70, C:0.11, G:0.04, T:0.15
Consensus pattern (22 bp):
ATAACAACAAAATAATAACAAA
Found at i:319515 original size:35 final size:31
Alignment explanation
Indices: 319435--319503 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
319425 TTCCTTCGCA
*
319435 CAAACAGCATGACAGAAACTAACAAAGCAAG
1 CAAACAGCATGACAGAAACCAACAAAGCAAG
319466 CAAACAGCATGACAGAAACCAACAAAGCAAG
1 CAAACAGCATGACAGAAACCAACAAAGCAAG
319497 CAAACAG
1 CAAACAG
319504 GCAACTGGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.55, C:0.25, G:0.16, T:0.04
Consensus pattern (31 bp):
CAAACAGCATGACAGAAACCAACAAAGCAAG
Found at i:321304 original size:70 final size:67
Alignment explanation
Indices: 321185--321314 Score: 179
Period size: 70 Copynumber: 1.9 Consensus size: 67
321175 AACAATATAA
* **
321185 TGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAATAAAGTAGTTTTGCCTTTTAACTT
1 TGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAATAAAGTAGTTTTGCCTTTTAACTT
321250 AC
66 AC
***
321252 TGGTTTTGACTTTTAACTTTAAAAAAGATAAACATTTATCAAAATGGCGTAGTTTTGCCTTTT
1 TGGTTTTGACTTTTAAC-TT-AAAAAG-TAAACATTTATCAAAATAAAGTAGTTTTGCCTTTT
321315 CTTATTCGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
67 16 0.30
68 2 0.04
69 4 0.07
70 32 0.59
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (67 bp):
TGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAATAAAGTAGTTTTGCCTTTTAACTT
AC
Found at i:326140 original size:26 final size:26
Alignment explanation
Indices: 326111--326165 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
326101 TTTCAGTAAA
326111 GAACAATCATCAAAACTGTTTCCATT
1 GAACAATCATCAAAACTGTTTCCATT
326137 GAACAATCATCAAAACTGTTTCCATT
1 GAACAATCATCAAAACTGTTTCCATT
326163 GAA
1 GAA
326166 ATCTGAACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (26 bp):
GAACAATCATCAAAACTGTTTCCATT
Found at i:332503 original size:20 final size:19
Alignment explanation
Indices: 332461--332503 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
332451 ATTGAACTTG
*
332461 AAAATTGGACCTAAGATCC
1 AAAATTGGACCTAAGACCC
*
332480 AAAATTGGACCTGAGAACCC
1 AAAATTGGACCTAAG-ACCC
332500 AAAA
1 AAAA
332504 CCAAGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATTGGACCTAAGACCC
Found at i:332889 original size:61 final size:58
Alignment explanation
Indices: 332823--332955 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 58
332813 TCCAAAAATA
* * * *
332823 ATATTATTTTAATAGTTTTAATATTAAATTAAATTTAATATTTATCTTGTATATAAGTATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTG-ATA-AA-TATT
* *
332884 CTATTAATTTAATAGATTTAATATAAAATTTAATCTAATATTTATCTTGATAAATATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
332942 ATATTAATTTAATA
1 ATATTAATTTAATA
332956 TTAAAGTGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 17 0.26
59 2 0.03
60 3 0.05
61 43 0.66
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
Found at i:333394 original size:25 final size:26
Alignment explanation
Indices: 333353--333404 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
333343 AAAAAATTAA
* *
333353 CTTTGGTTTTCTTAAA-CTTATTTTC
1 CTTTGGTTTTCTCAAACCTGATTTTC
333378 CTTTGTGTTTT-TCAAACCTGATTTTC
1 CTTTG-GTTTTCTCAAACCTGATTTTC
333404 C
1 C
333405 AACAGCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (26 bp):
CTTTGGTTTTCTCAAACCTGATTTTC
Found at i:344376 original size:22 final size:22
Alignment explanation
Indices: 344351--344394 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
344341 ATTGCACTCA
*
344351 AATT-ATTAATATATTGAATTTT
1 AATTAATT-ATATAATGAATTTT
*
344373 AATTAATTTTATAATGAATTTT
1 AATTAATTATATAATGAATTTT
344395 CATAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTAATTATATAATGAATTTT
Found at i:344402 original size:22 final size:22
Alignment explanation
Indices: 344360--344404 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
344350 AAATTATTAA
* *
344360 TATATTGAATTTTAATTAATTT
1 TATAATGAATTTTAATAAATTT
*
344382 TATAATGAATTTTCATAAATTT
1 TATAATGAATTTTAATAAATTT
344404 T
1 T
344405 GATTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TATAATGAATTTTAATAAATTT
Found at i:347494 original size:45 final size:45
Alignment explanation
Indices: 347443--347528 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
347433 TGTGAACCGA
* * *
347443 ACATCATAAATTAGTAAGGTGGTTGCTATGTGCTGATTCCATCGG
1 ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCATCGG
** *
347488 ACATCATTGATTAATAAGGTGGTTACTGTGTGCTGAATCCA
1 ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCA
347529 CCGAGTATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCATCGG
Found at i:356863 original size:45 final size:45
Alignment explanation
Indices: 356799--356887 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
356789 AACAGATACT
* * *
356799 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
356844 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
1 CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
356888 TTGGTTCACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (45 bp):
CGGTGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:356956 original size:51 final size:50
Alignment explanation
Indices: 356898--357084 Score: 187
Period size: 51 Copynumber: 3.7 Consensus size: 50
356888 TTGGTTCACA
* * *
356898 CAGTAGCCTGCACATAGTAATACACATGTGACCATTACCATTCGATACACG
1 CAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGGTACACG
* * * * * *
356949 CAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCA
1 CAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATTCGGTACACG
* * * * * * *
357000 TAGTACCCTACACATAGTACTACAGATGCGACC-TATCATTCCGGTACACG
1 CAGTAGCCTGCACATAGTACTACACACGTGACCATACCATT-CGGTACACG
*
357050 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CAGTAGCCTGCACATAGTACTACACACGTGACCAT
357085 CATTTTCACT
Statistics
Matches: 106, Mismatches: 27, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
49 3 0.03
50 36 0.34
51 65 0.61
52 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (50 bp):
CAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGGTACACG
Found at i:359253 original size:24 final size:26
Alignment explanation
Indices: 359211--359263 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
359201 TTCTCCTAAA
*
359211 TTTCAAATTTATTGCATTATTTAAT-T
1 TTTCAAATTTATTGAATTA-TTAATAT
359237 TTTC-AATTTATT-AATTATTAATAT
1 TTTCAAATTTATTGAATTATTAATAT
359261 TTT
1 TTT
359264 ATGAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 8 0.32
25 8 0.32
26 4 0.16
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCAAATTTATTGAATTATTAATAT
Found at i:359262 original size:25 final size:26
Alignment explanation
Indices: 359211--359263 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
359201 TTCTCCTAAA
* *
359211 TTTCAAATTTATTGCATTATTTAATT
1 TTTCAAATTTATTGAATTATTAAATT
359237 TTTC-AATTTATT-AATTATTAATATT
1 TTTCAAATTTATTGAATTATTAA-ATT
359262 TT
1 TT
359264 ATGAAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCAAATTTATTGAATTATTAAATT
Found at i:364695 original size:28 final size:27
Alignment explanation
Indices: 364654--364718 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
364644 AATACGAAAG
* *
364654 AAAAGAAATTATATATTAAA-ATAAATTT
1 AAAATAAATAATATA-TAAATA-AAATTT
364682 AAAATAAATAATATATAAATGAAAATTT
1 AAAATAAATAATATATAAAT-AAAATTT
*
364710 GAAATAAAT
1 AAAATAAAT
364719 TAAAACTACG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.12
28 27 0.84
29 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAATAAATAATATATAAATAAAATTT
Found at i:365073 original size:3 final size:3
Alignment explanation
Indices: 365065--365124 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
365055 AACTAATATA
* * * * * *
365065 AAT AAT AAT ACT AAT AGT TAT AAT AAC ATT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
365113 AAT GAA- AAT AAT
1 AAT -AAT AAT AAT
365125 TGAGTAATTA
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:365102 original size:15 final size:15
Alignment explanation
Indices: 365065--365115 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
365055 AACTAATATA
365065 AATAATAAT-ACTAAT
1 AATAATAATAAC-AAT
* * *
365080 AGTTATAATAACATT
1 AATAATAATAACAAT
365095 AATAATAATAACAAT
1 AATAATAATAACAAT
365110 AATAAT
1 AATAAT
365116 GAAAATAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 27 0.93
16 2 0.07
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:365774 original size:5 final size:6
Alignment explanation
Indices: 365762--365786 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
365752 AAAACCAAAC
365762 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
365787 GATGAAACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Done.