Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 8 of 259
Found at i:2263506 original size:55 final size:54
Alignment explanation
Indices: 2263419--2263673 Score: 269
Period size: 55 Copynumber: 4.8 Consensus size: 54
2263409 ATTAGGGTTT
* *
2263419 AAGGATACCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * *
2263474 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
2263529 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
*
2263582 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * *
2263631 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
2263674 GTACCTTCGT
Statistics
Matches: 171, Mismatches: 22, Indels: 20
0.80 0.10 0.09
Matches are distributed among these distances:
49 40 0.23
52 7 0.04
53 41 0.24
54 12 0.07
55 67 0.39
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:2263625 original size:108 final size:110
Alignment explanation
Indices: 2263426--2263626 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
2263416 TTTAAGGATA
*
2263426 CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
2263491 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
2263536 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
2263598 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
2263627 TCAAAAGGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATCTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:2274051 original size:23 final size:24
Alignment explanation
Indices: 2274020--2274073 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
2274010 CGACCCATGC
2274020 AAACACAAAACAAACCAA-AAAAAT-
1 AAAC-CAAAACAAA-CAATAAAAATA
*
2274044 AAACC-AAACAAACAATAAACATA
1 AAACCAAAACAAACAATAAAAATA
2274067 AAACCAA
1 AAACCAA
2274074 TAAATTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 12 0.46
23 6 0.23
24 5 0.19
ACGTcount: A:0.72, C:0.22, G:0.00, T:0.06
Consensus pattern (24 bp):
AAACCAAAACAAACAATAAAAATA
Found at i:2274052 original size:22 final size:23
Alignment explanation
Indices: 2274027--2274073 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2274017 TGCAAACACA
2274027 AAACAAACCAA-AAAAAT-AAACC
1 AAACAAA-CAATAAAAATAAAACC
*
2274049 AAACAAACAATAAACATAAAACC
1 AAACAAACAATAAAAATAAAACC
2274072 AA
1 AA
2274074 TAAATTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.55
23 7 0.32
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.06
Consensus pattern (23 bp):
AAACAAACAATAAAAATAAAACC
Found at i:2276679 original size:119 final size:120
Alignment explanation
Indices: 2276497--2276719 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
2276487 TCCTCGTTCA
*
2276497 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* * *
2276562 TTAGTAAC-TCGCACAAATTCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
2276617 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
2276679 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
2276720 CATCATTCAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
118 4 0.04
119 65 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:2276719 original size:40 final size:40
Alignment explanation
Indices: 2276495--2276719 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
2276485 GGTCCTCGTT
* *
2276495 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2276535 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
2276575 CAAATTCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2276615 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
2276654 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
2276695 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2276720 CATCATTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 117 0.72
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:2284548 original size:119 final size:120
Alignment explanation
Indices: 2284366--2284588 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
2284356 TCCTCGTTCA
*
2284366 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
2284431 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
2284486 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
2284548 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
2284589 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:2284588 original size:40 final size:40
Alignment explanation
Indices: 2284364--2284588 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
2284354 GCTCCTCGTT
* *
2284364 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2284404 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2284444 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
2284484 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
2284523 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
2284564 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2284589 CATCATTCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 119 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:2287889 original size:126 final size:127
Alignment explanation
Indices: 2287646--2287890 Score: 323
Period size: 126 Copynumber: 1.9 Consensus size: 127
2287636 TTCACAACTA
* * * * * *
2287646 TTAAGAATCCTTTAAAACGAAGGCAATATTCGATATTTGGTAATTCGTGGAATCGTGCCCTAACG
1 TTAAAAATCCCTTAAAACGAAGGCAATATGCGATATTTGGCAATTCGCGCAATCGTGCCCTAACG
** * * **
2287711 TGTTGGGTTGCAATTTCTCGTTTGCCCAAAGTAATCGAAGGTCCCTTTAAAATTCTATTCTT
66 TGTTGGGTTGCAATTTCTCAATTGCCCAAAGTAATCAAAGATCCCTCCAAAATTCTATTCTT
* *
2287773 TTAAAAATCCCTT-AAACGAAGGCGATGTGCGATATTTGGCAATTCGCGCAATCGTGCCCTAACG
1 TTAAAAATCCCTTAAAACGAAGGCAATATGCGATATTTGGCAATTCGCGCAATCGTGCCCTAACG
* *
2287837 TGTTGGGTTGCAATTTCTCAATTGCTTCAAA-TAATCAAATATCCCTCCAAAATT
66 TGTTGGGTTGCAATTTCTCAATTGC-CCAAAGTAATCAAAGATCCCTCCAAAATT
2287891 TCACTCATGT
Statistics
Matches: 101, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
126 86 0.85
127 15 0.15
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (127 bp):
TTAAAAATCCCTTAAAACGAAGGCAATATGCGATATTTGGCAATTCGCGCAATCGTGCCCTAACG
TGTTGGGTTGCAATTTCTCAATTGCCCAAAGTAATCAAAGATCCCTCCAAAATTCTATTCTT
Found at i:2288279 original size:132 final size:128
Alignment explanation
Indices: 2287786--2288299 Score: 351
Period size: 131 Copynumber: 3.9 Consensus size: 128
2287776 AAAATCCCTT
* * * * * * * * **
2287786 AAACGAAGGCGATGTGCGATATTTGGCAATTCGCGCAATCGTGCCCTAACGTGTTGGGTTGCAAT
1 AAACAAAGGCAATGTTCGATGTTTGGCAATTTG-GGAATAGTGCCCTATCGTACTGGGTTGCAA-
** * * * * * ** * *
2287851 TTCTCAATTGCTTCAAATAATCAAATATCCCTCCAAAATTTCACTCATGTATTCAAAAAAATCCT
64 TTCTCGTTTG-TTAAAACAATCGAATATCTCTTCGGAATTTCACTCATGTTTTC-TAAAAAT-CT
2287916 TTA
126 TTA
* * ** * **
2287919 AAACGAAGGCAGTGTTCGATGTTTTACAATTCGGGAATCA-TGCCCTATCGTACTGGGTTGTGAT
1 AAACAAAGGCAATGTTCGATGTTTGGCAATTTGGGAAT-AGTGCCCTATCGTACTGGGTTGCAAT
* * * * *
2287983 T-TCCATTTGTTCAAAACAATCGAATATTTCTTTCGG-TTTTCATTCATGTTTAT-TAAAAACCT
65 TCT-CGTTTGTT-AAAACAATCGAATATCTC-TTCGGAATTTCACTCATGTTT-TCTAAAAATCT
*
2288045 CTCA
126 -TTA
* * * * * * * * * *
2288049 AAACAAAAGCGATCTTTGATGTCTGGCGATTTGAGAATCGTGCCCTATCGTGCTGGGTTGCGCAT
1 AAACAAAGGCAATGTTCGATGTTTGGCAATTTGGGAATAGTGCCCTATCGTACTGGGTTGC-AAT
* *
2288114 TTTCGTTTGCTTAAAACAATCGAAGGT-TC-CTTCGGAATTTCACTCACGTTTTCTAAAACATCT
65 TCTCGTTTG-TTAAAACAATCGAA--TATCTCTTCGGAATTTCACTCATGTTTTCTAAAA-ATCT
2288177 TTA
126 TTA
* *
2288180 AAACAAAGGAAATGTTCGATGTTTGGCAATTTGGGGAATAGTGCCCTATCATACTGGGTTGCAAT
1 AAACAAAGGCAATGTTCGATGTTTGGCAATTT-GGGAATAGTGCCCTATCGTACTGGGTTGCAAT
* *
2288245 CTCTCGTTTGTTAAAAATAATCGAATATCTCTTCGGGATTTCACTCA--TTTTCTAA
65 -TCTCGTTTGTT-AAAACAATCGAATATCTCTTCGGAATTTCACTCATGTTTTCTAA
2288300 GGTGAGGCAA
Statistics
Matches: 295, Mismatches: 66, Indels: 43
0.73 0.16 0.11
Matches are distributed among these distances:
129 2 0.01
130 70 0.24
131 103 0.35
132 92 0.31
133 28 0.09
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (128 bp):
AAACAAAGGCAATGTTCGATGTTTGGCAATTTGGGAATAGTGCCCTATCGTACTGGGTTGCAATT
CTCGTTTGTTAAAACAATCGAATATCTCTTCGGAATTTCACTCATGTTTTCTAAAAATCTTTA
Found at i:2302633 original size:40 final size:40
Alignment explanation
Indices: 2302452--2302673 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
2302442 TCCTCGTTCA
* * * * *
2302452 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
2302491 AATGCCTTC-GGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2302530 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2302570 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
2302610 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
2302650 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2302674 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
38 24 0.15
39 21 0.13
40 105 0.66
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2302682 original size:41 final size:41
Alignment explanation
Indices: 2302605--2302682 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2302595 TTAGTATCTC
* * *
2302605 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2302646 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2302683 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2310529 original size:40 final size:40
Alignment explanation
Indices: 2310347--2310569 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
2310337 TCCTCGTTCA
* * * * *
2310347 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
2310386 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2310426 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2310466 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
2310506 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
2310546 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2310570 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2310578 original size:41 final size:41
Alignment explanation
Indices: 2310501--2310578 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2310491 TTAGTATCTC
* * *
2310501 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2310542 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2310579 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2314835 original size:95 final size:95
Alignment explanation
Indices: 2314672--2314864 Score: 350
Period size: 95 Copynumber: 2.0 Consensus size: 95
2314662 TACTATGGAA
2314672 ATAAAGGTTGAACAGTAAGAGGGCTTTAAGCACATGGAAAAAATCACAAAAATTAAATATAAAGA
1 ATAAAGGTTGAACAGTAAGAGGGCTTTAAGCACATGGAAAAAATCACAAAAATTAAATATAAAGA
*
2314737 TATTGGTGAGGAAAATTGAAACTAGGACCT
66 TATTGGTAAGGAAAATTGAAACTAGGACCT
* *
2314767 ATAAAGGTTTAACAGTAAGGGGGCTTTAAGCACATGGAAAAAATCACAAAAATTAAATATAAAGA
1 ATAAAGGTTGAACAGTAAGAGGGCTTTAAGCACATGGAAAAAATCACAAAAATTAAATATAAAGA
*
2314832 TATTGGTAAGGAAACTTGAAACTAGGACCT
66 TATTGGTAAGGAAAATTGAAACTAGGACCT
2314862 ATA
1 ATA
2314865 GGATATTAAT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (95 bp):
ATAAAGGTTGAACAGTAAGAGGGCTTTAAGCACATGGAAAAAATCACAAAAATTAAATATAAAGA
TATTGGTAAGGAAAATTGAAACTAGGACCT
Found at i:2315341 original size:16 final size:16
Alignment explanation
Indices: 2315320--2315350 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2315310 TTCACTATTA
*
2315320 TATCTTTTGTATTTTC
1 TATCTTTTATATTTTC
2315336 TATCTTTTATATTTT
1 TATCTTTTATATTTT
2315351 GCATGCATAG
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:0.10, G:0.03, T:0.71
Consensus pattern (16 bp):
TATCTTTTATATTTTC
Found at i:2317005 original size:37 final size:36
Alignment explanation
Indices: 2316955--2317066 Score: 113
Period size: 37 Copynumber: 3.0 Consensus size: 36
2316945 ATTCTAGAAA
* *
2316955 AATATTATTTTAATAGTTTAATATTAAATTAA-ATTT
1 AATATTATCTTAATA-TTTAATATTAATTTAATATTT
* *
2316991 AATACTTATCTTAATAATATT-TTATTAATTTAATATTA
1 AATA-TTATCTTAAT-AT-TTAATATTAATTTAATATTT
2317029 AAGTGATTATCTTAATATTTAAT-TTAATTTAATATTT
1 AA-T-ATTATCTTAATATTTAATATTAATTTAATATTT
2317066 A
1 A
2317067 TCTTGTAGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
36 4 0.06
37 36 0.57
38 11 0.17
39 11 0.17
40 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (36 bp):
AATATTATCTTAATATTTAATATTAATTTAATATTT
Found at i:2317068 original size:68 final size:67
Alignment explanation
Indices: 2316971--2317168 Score: 189
Period size: 62 Copynumber: 3.0 Consensus size: 67
2316961 ATTTTAATAG
* * *
2316971 TTTAATATTAAATTAAATTTAATACTTATCTTAATAATATTTTATTAATTTAATATTAAAGTGAT
1 TTTAATATTAAATTTAATTTAATATTTATCTTAATAATATTATATTAATTTAATATTAAAGTGAT
2317036 TA
66 TA
* * * *
2317038 TCTTAATATTTAATTTAATTTAATATTTATCTTGTAGATAAGCATTCTATT-ATTT--TAAT-AA
1 T-TTAATATTAAATTTAATTTAATATTTATC-T-TA-ATAA-TATTATATTAATTTAATATTAAA
2317099 --G---A
61 GTGATTA
* * *
2317101 TTTAATATTAAATTTAATCTAGTATTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATATTTATCTTAAT-AATATTATATTAATTTAATATTAAAGTGA
2317166 TTA
65 TTA
2317169 AGTTTGATTA
Statistics
Matches: 103, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
59 9 0.09
60 7 0.07
61 1 0.01
62 29 0.28
63 4 0.04
65 1 0.01
66 1 0.01
67 1 0.01
68 29 0.28
69 4 0.04
70 2 0.02
71 8 0.08
72 7 0.07
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (67 bp):
TTTAATATTAAATTTAATTTAATATTTATCTTAATAATATTATATTAATTTAATATTAAAGTGAT
TA
Found at i:2318959 original size:25 final size:25
Alignment explanation
Indices: 2318898--2318961 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
2318888 TATTACCTAC
*
2318898 TAAATAATCACCGGCTCAAGGCCTGA
1 TAAATAA-CACCGGATCAAGGCCTGA
* *
2318924 TAAACAGCACCGGATCAAGGCCTGA
1 TAAATAACACCGGATCAAGGCCTGA
*
2318949 TAGATAACACCGG
1 TAAATAACACCGG
2318962 CACAAAGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.16
Consensus pattern (25 bp):
TAAATAACACCGGATCAAGGCCTGA
Found at i:2318971 original size:25 final size:25
Alignment explanation
Indices: 2318898--2318971 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
2318888 TATTACCTAC
*
2318898 TAAATAATCACCGGCTCAAGGCCTGA
1 TAAATAA-CACCGGCACAAGGCCTGA
* *
2318924 TAAACAGCACCGG-ATCAAGGCCTGA
1 TAAATAACACCGGCA-CAAGGCCTGA
* *
2318949 TAGATAACACCGGCACAAAGCCT
1 TAAATAACACCGGCACAAGGCCT
2318972 ACTAGGCACA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
25 33 0.85
26 6 0.15
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.15
Consensus pattern (25 bp):
TAAATAACACCGGCACAAGGCCTGA
Found at i:2333046 original size:17 final size:18
Alignment explanation
Indices: 2333021--2333054 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2333011 TAATTCTTAA
2333021 AAATAAAAA-GATAAAAG
1 AAATAAAAAGGATAAAAG
*
2333038 AAATTAAAAGGATAAAA
1 AAATAAAAAGGATAAAA
2333055 TTAAGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (18 bp):
AAATAAAAAGGATAAAAG
Found at i:2333116 original size:22 final size:22
Alignment explanation
Indices: 2333069--2333116 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2333059 GTTTTTTTAT
*
2333069 AAAAACCCAAGTTTCTTCCGAT
1 AAAAACCCAAGTTTCTTCCGAC
* *
2333091 AAAAACCTAAGTTAT-TTCCTAC
1 AAAAACCCAAGTT-TCTTCCGAC
2333113 AAAA
1 AAAA
2333117 CCTCAAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (22 bp):
AAAAACCCAAGTTTCTTCCGAC
Found at i:2333163 original size:27 final size:25
Alignment explanation
Indices: 2333133--2333201 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
2333123 GATTTTCTGA
2333133 AAAAAATAAAATAAAATCAATTCTAAT
1 AAAAAATAAAATAAAATCAATT-T-AT
* * *
2333160 AAAAAAGGAAAAGAAAAATTAATTTAT
1 AAAAAA-TAAAA-TAAAATCAATTTAT
2333187 AAAAATATAAAATAA
1 AAAAA-ATAAAATAA
2333202 GTGACCATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
26 2 0.06
27 17 0.50
28 6 0.18
29 9 0.26
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAAAATAAAATAAAATCAATTTAT
Found at i:2333582 original size:16 final size:16
Alignment explanation
Indices: 2333563--2333593 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2333553 CATTTTAGAG
2333563 CATATAAATTTAAAAT
1 CATATAAATTTAAAAT
*
2333579 CATATATATTTAAAA
1 CATATAAATTTAAAA
2333594 AAATTTTAAA
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:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
CATATAAATTTAAAAT
Found at i:2333752 original size:18 final size:19
Alignment explanation
Indices: 2333731--2333766 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2333721 TTTTGAAAAA
*
2333731 ATAAAT-TTTTGAATTTTT
1 ATAAATATTTTAAATTTTT
2333749 ATAAATATTTTAAATTTT
1 ATAAATATTTTAAATTTT
2333767 AAAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
ATAAATATTTTAAATTTTT
Found at i:2333759 original size:19 final size:19
Alignment explanation
Indices: 2333731--2333783 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
2333721 TTTTGAAAAA
2333731 ATAAAT-TTTTGAATTTTT
1 ATAAATATTTTGAATTTTT
*
2333749 ATAAATATTTT-AAATTTT
1 ATAAATATTTTGAATTTTT
*
2333767 AAAAATTATTTTGAATT
1 ATAAA-TATTTTGAATT
2333784 CTTGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 16 0.55
19 10 0.34
20 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
ATAAATATTTTGAATTTTT
Found at i:2352597 original size:15 final size:15
Alignment explanation
Indices: 2352577--2352606 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2352567 AAAGTTTCCT
*
2352577 TTGCCTGCTATTACA
1 TTGCCTGCAATTACA
2352592 TTGCCTGCAATTACA
1 TTGCCTGCAATTACA
2352607 ACAGTTTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (15 bp):
TTGCCTGCAATTACA
Found at i:2353364 original size:21 final size:21
Alignment explanation
Indices: 2353340--2353380 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2353330 TCTTTTAAAA
*
2353340 AGATATAACTATTAAAGTAAG
1 AGATACAACTATTAAAGTAAG
*
2353361 AGATACAACTATTCAAGTAA
1 AGATACAACTATTAAAGTAA
2353381 AGTATCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (21 bp):
AGATACAACTATTAAAGTAAG
Found at i:2354592 original size:30 final size:30
Alignment explanation
Indices: 2354556--2354616 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2354546 ACTATGGGCT
2354556 CCAATGGTCAAACCAAAGAAGCAATCACAC
1 CCAATGGTCAAACCAAAGAAGCAATCACAC
2354586 CCAATGGTCAAACCAAAGAAGCAATCACAC
1 CCAATGGTCAAACCAAAGAAGCAATCACAC
2354616 C
1 C
2354617 AAGCTAGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.31, G:0.13, T:0.10
Consensus pattern (30 bp):
CCAATGGTCAAACCAAAGAAGCAATCACAC
Found at i:2354985 original size:5 final size:5
Alignment explanation
Indices: 2354975--2355002 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2354965 TTGTGTGTTC
2354975 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2355003 CACAAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:2357301 original size:104 final size:105
Alignment explanation
Indices: 2357121--2357376 Score: 444
Period size: 104 Copynumber: 2.4 Consensus size: 105
2357111 TAACCGTTAT
* **
2357121 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
2357186 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
2357225 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
2357290 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
2357330 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCAC
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCAC
2357377 ACAGCAAGCC
Statistics
Matches: 144, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
104 82 0.57
105 61 0.42
106 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:2357753 original size:30 final size:30
Alignment explanation
Indices: 2357719--2357779 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2357709 TCCACCACCC
2357719 AACTTTTGAAAAATTACAATTTTGCCCCCA
1 AACTTTTGAAAAATTACAATTTTGCCCCCA
*** * *
2357749 AACTTTTGCGTAATTACACTTTTGTCCCCA
1 AACTTTTGAAAAATTACAATTTTGCCCCCA
2357779 A
1 A
2357780 GCTCGGAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AACTTTTGAAAAATTACAATTTTGCCCCCA
Found at i:2367067 original size:17 final size:17
Alignment explanation
Indices: 2367011--2367067 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
2367001 CAAAAGAATC
*
2367011 CGCCAAACCATAGA-TCT
1 CGCCAAAACATAGACT-T
*
2367028 CGCCAAAACGTAGACTT
1 CGCCAAAACATAGACTT
** *
2367045 TTCCAAAACATGGACTT
1 CGCCAAAACATAGACTT
2367062 CGCCAA
1 CGCCAA
2367068 TCTGTGCATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
17 30 0.97
18 1 0.03
ACGTcount: A:0.35, C:0.32, G:0.14, T:0.19
Consensus pattern (17 bp):
CGCCAAAACATAGACTT
Found at i:2381298 original size:15 final size:16
Alignment explanation
Indices: 2381269--2381299 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2381259 ATTGCTTACC
2381269 ATATGCAATCAATTTA
1 ATATGCAATCAATTTA
2381285 ATATGCAA-CAATTTA
1 ATATGCAATCAATTTA
2381300 TCATTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
ATATGCAATCAATTTA
Found at i:2386847 original size:27 final size:27
Alignment explanation
Indices: 2386817--2386881 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
2386807 AGCAATCTTG
2386817 TGTTTAATGTCCCAACAGACTATCCCA
1 TGTTTAATGTCCCAACAGACTATCCCA
** *
2386844 TGTTT-ATCGTCCCGGCAGGCTATCCCA
1 TGTTTAAT-GTCCCAACAGACTATCCCA
*
2386871 TGTTTAGTGTC
1 TGTTTAATGTC
2386882 ATGGTAGACT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 2 0.06
27 29 0.91
28 1 0.03
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (27 bp):
TGTTTAATGTCCCAACAGACTATCCCA
Found at i:2386893 original size:27 final size:28
Alignment explanation
Indices: 2386832--2386905 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
2386822 AATGTCCCAA
*
2386832 CAGACTATCCCATGTTTA-TCGTCCCGG
1 CAGACTATCCCATGTTTAGTCGTCACGG
* *
2386859 CAGGCTATCCCATGTTTAGT-GTCATGG
1 CAGACTATCCCATGTTTAGTCGTCACGG
* *
2386886 TAGACTATCCCGTGTTTAGT
1 CAGACTATCCCATGTTTAGT
2386906 ATCTCGATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (28 bp):
CAGACTATCCCATGTTTAGTCGTCACGG
Found at i:2386916 original size:27 final size:27
Alignment explanation
Indices: 2386863--2386919 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2386853 TCCCGGCAGG
* *
2386863 CTATCCCATGTTTAGTGTCATGGTAGA
1 CTATCCCATGTTTAGTATCATGATAGA
*
2386890 CTATCCCGTGTTTAGTATC-TCGATAGA
1 CTATCCCATGTTTAGTATCAT-GATAGA
2386917 CTA
1 CTA
2386920 CCAAAAGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (27 bp):
CTATCCCATGTTTAGTATCATGATAGA
Found at i:2389833 original size:6 final size:6
Alignment explanation
Indices: 2389822--2389849 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2389812 TATTTCTCTT
2389822 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
2389850 GGAGAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:2389843 original size:19 final size:18
Alignment explanation
Indices: 2389808--2389849 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2389798 TTTCAAAATG
*
2389808 ATTTTATTTCTCTTTTTTC
1 ATTTTATTTCTC-ATTTTC
2389827 ATTTTCATTT-TCATTTTC
1 ATTTT-ATTTCTCATTTTC
2389845 ATTTT
1 ATTTT
2389850 GGAGAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 7 0.33
20 4 0.19
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTATTTCTCATTTTC
Found at i:2389876 original size:69 final size:67
Alignment explanation
Indices: 2389759--2389912 Score: 229
Period size: 69 Copynumber: 2.3 Consensus size: 67
2389749 ATTTTTCAAG
* ** *
2389759 TCATTTTCATTTTCA-TTTTTTTGGAGAAAATTACTTTCATTTCAAAATGATTTTATTTCTCTTT
1 TCATTTTCATTTTCATTTTTTTTGGAGAAAATCACTTAAATTTCAAAATGATTTTATTTCTCATT
2389823 TT
66 TT
*
2389825 TCATTTTCATTTTCATTTTCATTTTGGAGAAAATCACTTAAATTTCCAAATGATTTTATTTCTCA
1 TCATTTTCATTTTCATTTT--TTTTGGAGAAAATCACTTAAATTTCAAAATGATTTTATTTCTCA
2389890 TTTT
64 TTTT
*
2389894 TCTTTTTCATTTTCATTTT
1 TCATTTTCATTTTCATTTT
2389913 GGAGAAAACC
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 15 0.19
67 3 0.04
69 61 0.77
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57
Consensus pattern (67 bp):
TCATTTTCATTTTCATTTTTTTTGGAGAAAATCACTTAAATTTCAAAATGATTTTATTTCTCATT
TT
Found at i:2389933 original size:63 final size:67
Alignment explanation
Indices: 2389761--2389943 Score: 195
Period size: 69 Copynumber: 2.8 Consensus size: 67
2389751 TTTTCAAGTC
* * * *
2389761 ATTTTCATTTTCATTTTTTTGGAGAAAATTAC-T-TTCATTTCAAAATGATTTTATTTCTCTTTT
1 ATTTTCATTTTCA---TTTTGGAGAAAATCACATAATCATTTCCAAATGATTTTATTTCTCATTT
2389824 TTCATTTT
63 TTC---TT
*
2389832 CATTTTCATTTTCATTTTGGAGAAAATCACTTAA--ATTTCCAAATGATTTTATTTCTCATTTTT
1 -ATTTTCATTTTCATTTTGGAGAAAATCACATAATCATTTCCAAATGATTTTATTTCTCATTTTT
2389895 C-T
65 CTT
2389897 -TTTTCATTTTCATTTTGGAGAAAA-C-CATAATCATTTCCAAATG-TTTT
1 ATTTTCATTTTCATTTTGGAGAAAATCACATAATCATTTCCAAATGATTTT
2389944 CCATTTTTTT
Statistics
Matches: 102, Mismatches: 5, Indels: 18
0.82 0.04 0.14
Matches are distributed among these distances:
61 4 0.04
62 5 0.05
63 35 0.34
65 1 0.01
69 43 0.42
70 1 0.01
72 13 0.13
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.53
Consensus pattern (67 bp):
ATTTTCATTTTCATTTTGGAGAAAATCACATAATCATTTCCAAATGATTTTATTTCTCATTTTTC
TT
Found at i:2400356 original size:19 final size:17
Alignment explanation
Indices: 2400309--2400360 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 17
2400299 TAATCTTCAA
2400309 TGATATACAATCTTAGAT
1 TGATAT-CAATCTTAGAT
2400327 TGATA-CAATCTTAGAT
1 TGATATCAATCTTAGAT
*
2400343 ATTATATGCAATCTTAGA
1 -TGATAT-CAATCTTAGA
2400361 AGATATGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.37
17 4 0.13
18 5 0.17
19 10 0.33
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TGATATCAATCTTAGAT
Found at i:2400671 original size:17 final size:17
Alignment explanation
Indices: 2400649--2400683 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2400639 TGTTTCCCTA
2400649 AATTTTTT-ATATATTTT
1 AATTTTTTAATA-ATTTT
2400666 AATTTTTTAATAATTTT
1 AATTTTTTAATAATTTT
2400683 A
1 A
2400684 GTATCATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATTTTTTAATAATTTT
Found at i:2406297 original size:11 final size:11
Alignment explanation
Indices: 2406281--2406306 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2406271 TAGAAGAGAC
2406281 GAAACAGGGGA
1 GAAACAGGGGA
2406292 GAAACAGGGGA
1 GAAACAGGGGA
2406303 GAAA
1 GAAA
2406307 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:2406990 original size:18 final size:18
Alignment explanation
Indices: 2406967--2407015 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
2406957 ATGTGAGGTA
*
2406967 AGTATTAATATTAGTATT
1 AGTATTATTATTAGTATT
2406985 AGTATTATTATTAGTATT
1 AGTATTATTATTAGTATT
*
2407003 ATTATTATTATTA
1 AGTATTATTATTA
2407016 TGAGTGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (18 bp):
AGTATTATTATTAGTATT
Found at i:2406995 original size:3 final size:3
Alignment explanation
Indices: 2406969--2407016 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
2406959 GTGAGGTAAG
* * * *
2406969 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2407017 GAGTGGGAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:2407016 original size:12 final size:12
Alignment explanation
Indices: 2406969--2407016 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
2406959 GTGAGGTAAG
* *
2406969 TATTAATATTAG
1 TATTAGTATTAT
2406981 TATTAGTATTAT
1 TATTAGTATTAT
2406993 TATTAGTATTAT
1 TATTAGTATTAT
*
2407005 TATTATTATTAT
1 TATTAGTATTAT
2407017 GAGTGGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:2407210 original size:24 final size:24
Alignment explanation
Indices: 2407156--2407226 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
2407146 TGTGTGAAGT
*
2407156 TGTGAAATAATTATTG-ATTG-AAA
1 TGTGAAA-AATGATTGAATTGAAAA
*
2407179 GGTGGAAAAATGATTGAATTGAAAA
1 TGT-GAAAAATGATTGAATTGAAAA
*
2407204 TGTGAAAATTGTAATTGAATTGA
1 TGTGAAAAATG--ATTGAATTGA
2407227 GAATATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 9 0.23
24 15 0.38
25 5 0.13
26 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.34
Consensus pattern (24 bp):
TGTGAAAAATGATTGAATTGAAAA
Found at i:2413972 original size:11 final size:11
Alignment explanation
Indices: 2413956--2413981 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2413946 TAGAAGAGAC
2413956 GAAACAGGGGA
1 GAAACAGGGGA
2413967 GAAACAGGGGA
1 GAAACAGGGGA
2413978 GAAA
1 GAAA
2413982 GAAGAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:2414670 original size:3 final size:3
Alignment explanation
Indices: 2414644--2414691 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
2414634 GTGAGGTAAG
* * *
2414644 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2414692 GAGTGAGAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2415106 original size:37 final size:39
Alignment explanation
Indices: 2415047--2415142 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
2415037 CGGATAGATT
* * * *
2415047 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
2415084 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
2415123 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
2415143 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:2420719 original size:17 final size:18
Alignment explanation
Indices: 2420697--2420731 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2420687 GATATGATAC
*
2420697 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
2420714 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
2420732 AAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:2421042 original size:19 final size:19
Alignment explanation
Indices: 2421014--2421085 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
2421004 AATCATATCT
2421014 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
2421033 TCTAAAATTG--TATCA-A
1 TCTAAGATTGCATATCATA
2421049 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
2421068 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
2421086 TGAAGATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
16 10 0.21
17 5 0.10
18 5 0.10
19 28 0.58
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:2421093 original size:17 final size:19
Alignment explanation
Indices: 2421017--2421093 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
2421007 CATATCTTCT
*
2421017 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
* *
2421036 AAAATTG--TATCA-ATCT
1 AAGATTGCATATCATATCG
*
2421052 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
2421071 AAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCG
2421088 AAGATT
1 AAGATT
2421094 ATATTTCCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
16 10 0.19
17 11 0.21
18 6 0.12
19 25 0.48
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:2421995 original size:82 final size:82
Alignment explanation
Indices: 2421865--2422017 Score: 272
Period size: 82 Copynumber: 1.9 Consensus size: 82
2421855 ATCTTAAAGG
*
2421865 TTTCTTAATTTCTCCAAGATTGGGTTTCTCTTTCAACACAAGCTCAAGAATTCTATGGGTGGCAT
1 TTTCTTAACTTCTCCAAGATTGGGTTTCTCTTTCAACACAAGCTCAAGAATTCTATGGGTGGCAT
2421930 AAAAAAAAATTTAAACA
66 AAAAAAAAATTTAAACA
*
2421947 TTTCTTAACTTCTCCATGATTGGGTTTCTCTTTCAA-AGCAAGCTCAAGAATTCTATGGGTGGCA
1 TTTCTTAACTTCTCCAAGATTGGGTTTCTCTTTCAACA-CAAGCTCAAGAATTCTATGGGTGGCA
2422011 TAAAAAA
65 TAAAAAA
2422018 TTCAGTGTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
81 1 0.01
82 67 0.99
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (82 bp):
TTTCTTAACTTCTCCAAGATTGGGTTTCTCTTTCAACACAAGCTCAAGAATTCTATGGGTGGCAT
AAAAAAAAATTTAAACA
Found at i:2424854 original size:3 final size:3
Alignment explanation
Indices: 2424846--2424871 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2424836 AAAAGGTCTG
2424846 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
2424872 AATATCTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2427308 original size:131 final size:128
Alignment explanation
Indices: 2427010--2427341 Score: 415
Period size: 130 Copynumber: 2.6 Consensus size: 128
2427000 TTGCCACTAA
* * * *
2427010 CAAGAGTGAAGATTGAATCTTCGAGCTGTTTAACCTTTGATTTT-TATTTTCAGAAAAG-AAAAG
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAGAAAAAG
* * *
2427073 --AGAAGGCCTGCTTGGTCCCTTTACCTAAGAAAATGCTCTTCCTGATTGGTATTCAATCACCAG
66 AAAAAAGGCCTGCTTGGTCCC--TACCTAAGAAAATACTCTTCCTGATTGATATTCAATCACCAG
2427136 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAAGAAAGA
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAG-AAAAGAAA-A
* * * *
2427201 AGAAAAAAGGCCTGCTTGGTGCCC-ATCTAAGAAATTACTCTTGCTGATTGATATTCGATCACCA
64 AGAAAAAAGGCCTGCTTGGT-CCCTACCTAAGAAAATACTCTTCCTGATTGATATTCAATCACCA
2427265 G
128 G
* * * *
2427266 CAAGGTGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGC-TTAGAATTCTCAGGAAAAGAAAA
1 CAA-GAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCA-GAAAAGAAAA
*
2427330 GGAAAAAAGGCC
64 AGAAAAAAGGCC
2427342 ATCTTGTTGT
Statistics
Matches: 181, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
126 41 0.23
127 8 0.04
128 5 0.03
129 14 0.08
130 58 0.32
131 37 0.20
132 15 0.08
133 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (128 bp):
CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAGAAAAAG
AAAAAAGGCCTGCTTGGTCCCTACCTAAGAAAATACTCTTCCTGATTGATATTCAATCACCAG
Found at i:2427377 original size:130 final size:130
Alignment explanation
Indices: 2427010--2427416 Score: 395
Period size: 130 Copynumber: 3.2 Consensus size: 130
2427000 TTGCCACTAA
* * * ** *
2427010 CAAGAGTGAAGATTGAATCTTCGAGCTGTTTAACCTTTGATTT-TTATTTTCAG-AAAAG-AA-A
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAGA
* * * *
2427071 AG--AGAAGGCCTGCTTGGT-CCCTTTACCTAAGAAAATGCTCTTCCTGATTGGTATTCAATCAC
66 AGAAAAAAGGCCTGCTTGGTGCCC---ATCTAAGAAAATGCTCTTGCTGATTGATATTCAATCAC
2427133 CAG
128 CAG
* *
2427136 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTTGTATTATCAGAAAAAGAAAGA
1 CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAGA
* * *
2427201 AGAAAAAAGGCCTGCTTGGTGCCCATCTAAGAAATTACTCTTGCTGATTGATATTCGATCACCAG
66 AGAAAAAAGGCCTGCTTGGTGCCCATCTAAGAAAATGCTCTTGCTGATTGATATTCAATCACCAG
* * *
2427266 CAAGGTGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGC-TTAGAATTCTCAGGAAAAGAAA-
1 CAA-GAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAG
* * * * ** * ** *
2427329 AGGAAAAAAGGCCAT-CTTGTTGTCCGTGCCT-AGAAAATGCTCCAGCTGATTGGTGGTCAACCA
65 AAGAAAAAAGGCC-TGCTTGGTGCCCAT--CTAAGAAAATGCTCTTGCTGATTGATATTCAATCA
*
2427392 CTAG
127 CCAG
* *
2427396 CAAGAGCAAACATTGAATCTT
1 CAAGAGTAAAGATTGAATCTT
2427417 CGAGTAACAA
Statistics
Matches: 236, Mismatches: 34, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
126 40 0.17
127 8 0.03
128 5 0.02
129 38 0.16
130 89 0.38
131 38 0.16
132 15 0.06
133 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (130 bp):
CAAGAGTAAAGATTGAATCTTTGAGCTGTTTAACCTTTGCTTTAGAATTATCAGAAAAAGAAAGA
AGAAAAAAGGCCTGCTTGGTGCCCATCTAAGAAAATGCTCTTGCTGATTGATATTCAATCACCAG
Found at i:2430475 original size:30 final size:32
Alignment explanation
Indices: 2430441--2430511 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
2430431 ACATTTTGAT
2430441 TAATTTTT-AAA-AGTTTAATAAATATTT-TTA
1 TAATTTTTAAAATAGTTTAA-AAATATTTCTTA
*
2430471 TAATTTTTAAAATTATTTTAAAAATATTTCTTA
1 TAATTTTTAAAA-TAGTTTAAAAATATTTCTTA
2430504 TAATTTTT
1 TAATTTTT
2430512 TTAATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 8 0.22
31 3 0.08
32 8 0.22
33 17 0.47
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
TAATTTTTAAAATAGTTTAAAAATATTTCTTA
Found at i:2438653 original size:9 final size:9
Alignment explanation
Indices: 2438639--2438672 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
2438629 GATCAAGCAA
2438639 AATTAAATT
1 AATTAAATT
2438648 AATTAAATT
1 AATTAAATT
*
2438657 AATCAAATT
1 AATTAAATT
2438666 AATTAAA
1 AATTAAA
2438673 ATAAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
AATTAAATT
Found at i:2439170 original size:20 final size:19
Alignment explanation
Indices: 2439123--2439177 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
2439113 AATTTAATAC
**
2439123 TTATCTTAATATTATTGTA
1 TTATCTTAATATTAAAGTA
2439142 TTAAT-TTAATATTAAAGTGA
1 TT-ATCTTAATATTAAAGT-A
2439162 TTATCTTAATATTAAA
1 TTATCTTAATATTAAA
2439178 TTTAATCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (19 bp):
TTATCTTAATATTAAAGTA
Found at i:2439189 original size:68 final size:69
Alignment explanation
Indices: 2439099--2439233 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 69
2439089 TGTAATAAAT
* * * * *
2439099 TTAATATTTAATTTAATTTAATACTTATCTTAAT-ATTATTGTATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATCTTAATAAGTATTATATTAATTTAATAATAAAGTGAT
2439163 TATC
66 TATC
* *
2439167 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATAATAAAGTGAT
1 TTAATATTAAATTTAATCTAATACTTATCTTAATAAGTATTATATTAATTTAATAATAAAGTGAT
2439232 TA
66 TA
2439234 AATTTAATCA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 30 0.51
69 29 0.49
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (69 bp):
TTAATATTAAATTTAATCTAATACTTATCTTAATAAGTATTATATTAATTTAATAATAAAGTGAT
TATC
Found at i:2439394 original size:26 final size:26
Alignment explanation
Indices: 2439365--2439416 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2439355 TTAGAAAATT
*
2439365 TATAAAGATATTTTTCATATTTACAA
1 TATAAAGATATTTTCCATATTTACAA
2439391 TATAAAGATATTTTCCATATTTACAA
1 TATAAAGATATTTTCCATATTTACAA
2439417 CTTGATCCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (26 bp):
TATAAAGATATTTTCCATATTTACAA
Found at i:2441991 original size:26 final size:27
Alignment explanation
Indices: 2441953--2442005 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2441943 TTTTTATTTC
* *
2441953 ATTTTATTTTAA-TAATAAGTTAAAAT
1 ATTTTATTTTAATTAAAAAGTAAAAAT
2441979 ATTTT-TTTCTAATTAAAAAGTAAAAAT
1 ATTTTATTT-TAATTAAAAAGTAAAAAT
2442006 TAATTGTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 3 0.13
26 8 0.35
27 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (27 bp):
ATTTTATTTTAATTAAAAAGTAAAAAT
Found at i:2442904 original size:32 final size:32
Alignment explanation
Indices: 2442868--2442937 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
2442858 ATTTTAGGGA
** *
2442868 GGTGAATGTTCTTATTTATGTGTGTATATTTT
1 GGTGAATGTTCTTATCGATGTGTGCATATTTT
*
2442900 GGTGATTGTTCTTATCGATGTGTGCATATTTT
1 GGTGAATGTTCTTATCGATGTGTGCATATTTT
2442932 GGTGAA
1 GGTGAA
2442938 ATATTAAGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.50
Consensus pattern (32 bp):
GGTGAATGTTCTTATCGATGTGTGCATATTTT
Found at i:2459721 original size:50 final size:50
Alignment explanation
Indices: 2459667--2459768 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
2459657 ATTATAGATG
2459667 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
1 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
2459717 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
1 TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
2459767 TA
1 TA
2459769 AGTTATCTAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (50 bp):
TATGGAATTCATTTCATAATGTATGCCGTGTTTCATAGATATTATATTTT
Found at i:2460651 original size:24 final size:25
Alignment explanation
Indices: 2460618--2460685 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 25
2460608 AAGTCTGTCT
* *
2460618 GGAGAAGATTTAGAAGCTGAA-AAG
1 GGAGAGGATTTAGGAGCTGAATAAG
*
2460642 GGAGAGGATTTAGGAGCT-AATCAG
1 GGAGAGGATTTAGGAGCTGAATAAG
2460666 GGAGAGGATTTAGGAGCTGA
1 GGAGAGGATTTAGGAGCTGA
2460686 TTAGGGTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.05
24 36 0.92
25 1 0.03
ACGTcount: A:0.37, C:0.06, G:0.38, T:0.19
Consensus pattern (25 bp):
GGAGAGGATTTAGGAGCTGAATAAG
Found at i:2462186 original size:29 final size:27
Alignment explanation
Indices: 2462127--2462214 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
2462117 GAAGCGTCCC
*
2462127 GGTGGCTATGCCACAATTATCTGATCT
1 GGTGGCTTTGCCACAATTATCTGATCT
* *
2462154 GGTGGCTTTGCCACATATATATCTGTTTT
1 GGTGGCTTTGCCACA-AT-TATCTGATCT
*
2462183 GGTGG-TTCTGCCACGATTATCTGTATCT
1 GGTGGCTT-TGCCACAATTATCTG-ATCT
2462211 GGTG
1 GGTG
2462215 ACTCTATCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 20 0.39
28 12 0.24
29 19 0.37
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (27 bp):
GGTGGCTTTGCCACAATTATCTGATCT
Found at i:2465091 original size:18 final size:18
Alignment explanation
Indices: 2465068--2465109 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2465058 GTTAAGGACC
2465068 ATTGATGATAGTGACGCT
1 ATTGATGATAGTGACGCT
2465086 ATTGATGATAGTGACGCT
1 ATTGATGATAGTGACGCT
2465104 ATTGAT
1 ATTGAT
2465110 CGTGACCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
ATTGATGATAGTGACGCT
Found at i:2469133 original size:24 final size:24
Alignment explanation
Indices: 2469100--2469173 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
2469090 AAGTCTGTCT
*
2469100 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
2469124 GGAGAGGATTTAGGAACTGATCAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
2469148 GGAGAGAATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
2469172 GG
1 GG
2469174 TGAACTGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.39, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:2470667 original size:29 final size:27
Alignment explanation
Indices: 2470606--2470695 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
2470596 AGGAAGCATC
*
2470606 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTTTGCCACAATTATCTGAT
*
2470633 CTGGTGGCTTTGCCACATATATATCTGTT
1 CTGGTGGCTTTGCCACA-AT-TATCTGAT
* *
2470662 TTGGTGG-TTCTGCCACGATTATCTGTAT
1 CTGGTGGCTT-TGCCACAATTATCTG-AT
2470690 CTGGTG
1 CTGGTG
2470696 ACTCTATCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 22 0.42
28 12 0.23
29 19 0.36
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTTTGCCACAATTATCTGAT
Found at i:2473573 original size:18 final size:18
Alignment explanation
Indices: 2473550--2473591 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2473540 GTTAAGGACC
2473550 ATTGATGATAGTGACGCT
1 ATTGATGATAGTGACGCT
2473568 ATTGATGATAGTGACGCT
1 ATTGATGATAGTGACGCT
2473586 ATTGAT
1 ATTGAT
2473592 CGTGACCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (18 bp):
ATTGATGATAGTGACGCT
Found at i:2477615 original size:24 final size:24
Alignment explanation
Indices: 2477582--2477655 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
2477572 AAGTCTGTCT
*
2477582 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
2477606 GGAGAGGATTTAGGAACTGATCAG
1 GGAGAGGATTTAGGAGCTGATAAG
* *
2477630 GGAGAGAATTTAGGAGCTGATTAG
1 GGAGAGGATTTAGGAGCTGATAAG
2477654 GG
1 GG
2477656 TGAACTGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.39, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGCTGATAAG
Found at i:2479129 original size:27 final size:27
Alignment explanation
Indices: 2479089--2479202 Score: 106
Period size: 27 Copynumber: 4.1 Consensus size: 27
2479079 AGGAAGCATC
*
2479089 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTTTGCCACAATTATCTGAT
* *
2479116 CTGGTGGCTTTGCCACATATATATATGTT
1 CTGGTGGCTTTGCCACA-AT-TATCTGAT
*
2479145 CTGGTGG-TTCTGCCACGATTATCTGTAT
1 CTGGTGGCTT-TGCCACAATTATCTG-AT
* * * *
2479173 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTTTGCCACAATTATCTGAT
2479199 CTGG
1 CTGG
2479203 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
26 5 0.07
27 29 0.40
28 18 0.25
29 20 0.28
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTTTGCCACAATTATCTGAT
Found at i:2483409 original size:18 final size:19
Alignment explanation
Indices: 2483386--2483427 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
2483376 ATGTGACCCC
2483386 TGTTTTCCC-AAATTTTCA
1 TGTTTTCCCAAAATTTTCA
2483404 TGTTTTCCCAAAATTTTCA
1 TGTTTTCCCAAAATTTTCA
2483423 TGTTT
1 TGTTT
2483428 GTTTCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.52
Consensus pattern (19 bp):
TGTTTTCCCAAAATTTTCA
Found at i:2483990 original size:38 final size:38
Alignment explanation
Indices: 2483866--2483976 Score: 152
Period size: 38 Copynumber: 2.9 Consensus size: 38
2483856 ACAAAATTTG
* * *
2483866 CATGTTTACTGTTAATAATAAATTTG-GTACGTGTTAAA
1 CATGTCTACTGTTAATAATGAA-TTGAGTACATGTTAAA
* *
2483904 CATGTCTACTGTTAATGATGAATTGAGTAGATGTTAAA
1 CATGTCTACTGTTAATAATGAATTGAGTACATGTTAAA
*
2483942 CATGTCTACTGTTAATAATGAATTGAGCACATGTT
1 CATGTCTACTGTTAATAATGAATTGAGTACATGTT
2483977 GTACCTGTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 3 0.05
38 61 0.95
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (38 bp):
CATGTCTACTGTTAATAATGAATTGAGTACATGTTAAA
Found at i:2485454 original size:38 final size:38
Alignment explanation
Indices: 2485337--2485461 Score: 153
Period size: 38 Copynumber: 3.3 Consensus size: 38
2485327 ACATAATTTG
* *
2485337 CATGTCTACTGTTAATAATAAATTAAGTACTTGTTAAA
1 CATGTCTACTGTTAATAATGAATTAAGTACATGTTAAA
* * * *
2485375 CATGTCTACTATTAATGATGAATTAAGTATATATTAAA
1 CATGTCTACTGTTAATAATGAATTAAGTACATGTTAAA
* **
2485413 CATGTCTACTGTTAATAATGAATTGAA-CACATGTTGTA
1 CATGTCTACTGTTAATAATGAATT-AAGTACATGTTAAA
2485451 CATGTCTACTG
1 CATGTCTACTG
2485462 CTACTGTTGA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 71 0.97
39 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (38 bp):
CATGTCTACTGTTAATAATGAATTAAGTACATGTTAAA
Found at i:2485751 original size:89 final size:89
Alignment explanation
Indices: 2485584--2485754 Score: 200
Period size: 89 Copynumber: 1.9 Consensus size: 89
2485574 CTAGAAGCAA
* * * * **
2485584 ATTTTATTTACGAGATTTTTCTGTGTATCCACAGCCAAAGGTAGATTCTAATTTTGGGATAATTG
1 ATTTTATCTACGAGATTTTTCTGTGCATCCACAGCCAAAGGCAGATTCTAACTGCGGGATAATTG
** *
2485649 TTGTGTTTTCATAGCCAGAGGCTG
66 TTGTGCGTCCATAGCCAGAGGCTG
* * * * *
2485673 ATTTTATCTGCGAGATTTTTGTTGTGCATCCATAGCCAGAGGCAGATTCTAACTGCGGGAT-TTT
1 ATTTTATCTACGAGATTTTT-CTGTGCATCCACAGCCAAAGGCAGATTCTAACTGCGGGATAATT
2485737 GTTGTGCGTCCATAGCCA
65 GTTGTGCGTCCATAGCCA
2485755 CTGACAGTTT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
89 35 0.52
90 32 0.48
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (89 bp):
ATTTTATCTACGAGATTTTTCTGTGCATCCACAGCCAAAGGCAGATTCTAACTGCGGGATAATTG
TTGTGCGTCCATAGCCAGAGGCTG
Found at i:2485752 original size:44 final size:45
Alignment explanation
Indices: 2485658--2485754 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
2485648 GTTGTGTTTT
* * *
2485658 CATAGCCAGAGGCTGATTTTATCTGCGAGATTTTTGTTGTGCATC
1 CATAGCCAGAGGCAGATTCTAACTGCGAGATTTTTGTTGTGCATC
* *
2485703 CATAGCCAGAGGCAGATTCTAACTGCGGGA-TTTTGTTGTGCGTC
1 CATAGCCAGAGGCAGATTCTAACTGCGAGATTTTTGTTGTGCATC
2485747 CATAGCCA
1 CATAGCCA
2485755 CTGACAGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 21 0.45
45 26 0.55
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (45 bp):
CATAGCCAGAGGCAGATTCTAACTGCGAGATTTTTGTTGTGCATC
Found at i:2487670 original size:11 final size:11
Alignment explanation
Indices: 2487654--2487679 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2487644 AAAACTAATC
2487654 TTAATTAATAA
1 TTAATTAATAA
2487665 TTAATTAATAA
1 TTAATTAATAA
2487676 TTAA
1 TTAA
2487680 AATAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAATTAATAA
Found at i:2491278 original size:6 final size:7
Alignment explanation
Indices: 2491260--2491285 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2491250 ATAACGGGTA
2491260 ATTTTTT
1 ATTTTTT
2491267 ATTTTTT
1 ATTTTTT
2491274 ATTTTTT
1 ATTTTTT
2491281 ATTTT
1 ATTTT
2491286 GTAATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:2497369 original size:7 final size:7
Alignment explanation
Indices: 2497357--2497381 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2497347 CATTTCTAAA
2497357 CATCCCT
1 CATCCCT
2497364 CATCCCT
1 CATCCCT
2497371 CATCCCT
1 CATCCCT
2497378 CATC
1 CATC
2497382 ATTCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.56, G:0.00, T:0.28
Consensus pattern (7 bp):
CATCCCT
Found at i:2505036 original size:27 final size:27
Alignment explanation
Indices: 2504997--2505050 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2504987 AAAAAGACTA
2504997 AGTGATGCAGTAATGGGAATGAACATG
1 AGTGATGCAGTAATGGGAATGAACATG
**
2505024 AGTGATGTGGTAATGGGAATGAACATG
1 AGTGATGCAGTAATGGGAATGAACATG
2505051 TCTAGGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (27 bp):
AGTGATGCAGTAATGGGAATGAACATG
Found at i:2506004 original size:117 final size:117
Alignment explanation
Indices: 2505798--2506029 Score: 428
Period size: 117 Copynumber: 2.0 Consensus size: 117
2505788 CAAAAAGGAA
* * *
2505798 AAATGTATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCTAAAGGTTCGCTTAAAGAAAAAGG
1 AAATGCATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
2505863 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACTG
66 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACTG
*
2505915 AAATGCATGAGCTTAAGTTCAAAATATGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
1 AAATGCATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
2505980 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAAC
66 TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAAC
2506030 CAAAATGTCC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 111 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (117 bp):
AAATGCATGAGCTTAAGTTCAAAATAAGTTTGGGGGTGTTCCAAAGGTTCACTTAAAGAAAAAGG
TTGTATTACGAGAAAACCAAGACAAAGTTAAAGGTTAAGATTTTTAAAACTG
Found at i:2507277 original size:19 final size:19
Alignment explanation
Indices: 2507250--2507291 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2507240 CATCTCTAAA
*
2507250 TTCTCTTAGCATTCTTCTT
1 TTCTATTAGCATTCTTCTT
2507269 TTCTATTAGCATTCTTCTT
1 TTCTATTAGCATTCTTCTT
2507288 TTCT
1 TTCT
2507292 CCCCACGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.12, C:0.24, G:0.05, T:0.60
Consensus pattern (19 bp):
TTCTATTAGCATTCTTCTT
Found at i:2508085 original size:19 final size:22
Alignment explanation
Indices: 2508052--2508091 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2508042 AGTTTATTTA
2508052 TGTTATAATTGTTGC-AAAATG
1 TGTTATAATTGTTGCTAAAATG
2508073 TGTT-TAATT-TTGCTAAAAT
1 TGTTATAATTGTTGCTAAAAT
2508092 CTATTTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (22 bp):
TGTTATAATTGTTGCTAAAATG
Found at i:2509104 original size:25 final size:25
Alignment explanation
Indices: 2509004--2509097 Score: 68
Period size: 24 Copynumber: 3.8 Consensus size: 25
2508994 GGTTGTATAA
**
2509004 CAGGAAGCTCATAAGAGCCA-TAAT
1 CAGGAAGCTCCGAAGAGCCATTAAT
* * * *
2509028 CAGAAAGCTCATGTA-AGCCAATAA-
1 CAGGAAGCTC-CGAAGAGCCATTAAT
* *
2509052 CGGGTAGCTCCGAAGAGCCATTAAT
1 CAGGAAGCTCCGAAGAGCCATTAAT
* *
2509077 CAGGAAGCTCCGGATAGCCAT
1 CAGGAAGCTCCGAAGAGCCAT
2509098 ATATCAGAAG
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
23 2 0.04
24 29 0.56
25 21 0.40
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (25 bp):
CAGGAAGCTCCGAAGAGCCATTAAT
Found at i:2518450 original size:17 final size:16
Alignment explanation
Indices: 2518414--2518459 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
2518404 TTTAGTATAG
2518414 ATATTTATAAAAACAT
1 ATATTTATAAAAACAT
2518430 ATATTTATGAAACAA-AT
1 ATATTTAT-AAA-AACAT
2518447 ATATTTATAAAAA
1 ATATTTATAAAAA
2518460 AAGTAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (16 bp):
ATATTTATAAAAACAT
Found at i:2522506 original size:18 final size:18
Alignment explanation
Indices: 2522483--2522517 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2522473 ATGTGTCCCT
2522483 TCCACAAGGGCGCGTGTC
1 TCCACAAGGGCGCGTGTC
* *
2522501 TCCACACGGGCGTGTGT
1 TCCACAAGGGCGCGTGT
2522518 AGCTTTCACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.34, T:0.20
Consensus pattern (18 bp):
TCCACAAGGGCGCGTGTC
Found at i:2522564 original size:19 final size:19
Alignment explanation
Indices: 2522540--2522578 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2522530 GGCATGTAGG
*
2522540 CTTCCACACGGCCAAGGCA
1 CTTCCACACAGCCAAGGCA
2522559 CTTCCACACAGCCAAGGCA
1 CTTCCACACAGCCAAGGCA
2522578 C
1 C
2522579 ACAACTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.44, G:0.18, T:0.10
Consensus pattern (19 bp):
CTTCCACACAGCCAAGGCA
Found at i:2524611 original size:16 final size:16
Alignment explanation
Indices: 2524590--2524646 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
2524580 TTTGGTTCGC
*
2524590 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
2524606 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
2524622 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
2524638 TGTAATGGA
1 TGTAATGGA
2524647 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:2524913 original size:18 final size:17
Alignment explanation
Indices: 2524892--2524926 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2524882 TTATTATTAA
*
2524892 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2524910 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2524927 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2525061 original size:153 final size:156
Alignment explanation
Indices: 2524779--2525091 Score: 560
Period size: 153 Copynumber: 2.0 Consensus size: 156
2524769 TAGAATACCC
2524779 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
2524844 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
2524909 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAAAAA
* *
2524936 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAA-TTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
2524998 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
2525063 ATATAATTTAATAAAATTCTTAAAAA
131 ATATAATTTAATAAAATTCTTAAAAA
2525089 TTA
1 TTA
2525092 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
153 92 0.61
154 1 0.01
156 13 0.09
157 46 0.30
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAAAAA
Found at i:2525062 original size:16 final size:16
Alignment explanation
Indices: 2525025--2525066 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2525015 TTAATCATAT
*
2525025 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
2525041 TT-AAATATATTATAA
1 TTAAAATATATTATAA
2525056 TTAAAATATAT
1 TTAAAATATAT
2525067 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:2525073 original size:14 final size:15
Alignment explanation
Indices: 2525034--2525075 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2525024 TTTAAACATA
*
2525034 ATTATTATTAAATAT
1 ATTATAATTAAATAT
2525049 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
2525063 A-TATAATTTAATA
1 ATTATAATTAAATA
2525076 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:2525160 original size:120 final size:120
Alignment explanation
Indices: 2525028--2525250 Score: 412
Period size: 120 Copynumber: 1.9 Consensus size: 120
2525018 ATCATATTTA
2525028 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-AAATTA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAA-TA
*
2525092 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 AAATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
2525148 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
2525213 AATTCTTCTATGAATTTACTCAAATCATAATATATGAT
66 AATTCTTATATGAATTTACTCAAATCATAATATATGAT
2525251 TATAACTAAT
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 97 0.97
121 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
AATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:2525193 original size:14 final size:15
Alignment explanation
Indices: 2525144--2525195 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2525134 GTAAAATATA
2525144 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2525159 TATTAAATATATTAT
1 AATTAAATATATTAT
2525174 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2525187 AATTTAATA
1 AATTAAATA
2525196 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2525210 original size:44 final size:43
Alignment explanation
Indices: 2525121--2525211 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
2525111 CTCAAATCAT
* * *
2525121 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
2525164 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
2525208 AATA
1 AATA
2525212 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:2525246 original size:59 final size:59
Alignment explanation
Indices: 2525063--2525246 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 59
2525053 TAATTAAAAT
2525063 ATATAATTTAATAAAATTCTTAA-AAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAA-TAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * *
2525122 ATAT-ATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-ATAA-TATTCTTATATGA-ATT-TACTCAAATCA
2525182 T-
58 TA
* *
2525183 ATATAATTTAATAAAATTCTTAATAAATAAAATTCTTCTATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
2525242 ATATA
1 ATATA
2525247 TGATTATAAC
Statistics
Matches: 92, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 8 0.09
61 11 0.12
62 10 0.11
63 13 0.14
64 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
Found at i:2525262 original size:17 final size:16
Alignment explanation
Indices: 2525240--2525286 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2525230 ACTCAAATCA
2525240 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
2525257 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
2525271 TAAATATATGATTTAA
1 T-AATATATGATTTAA
2525287 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:2525287 original size:17 final size:17
Alignment explanation
Indices: 2525259--2525292 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2525249 ATTATAACTA
*
2525259 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
2525276 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
2525293 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:2525435 original size:93 final size:92
Alignment explanation
Indices: 2525325--2525519 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
2525315 GATTATAGTT
* * *
2525325 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
2525388 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
2525418 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
2525483 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
2525510 TATGAATTTA
1 TATGAATTTA
2525520 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:2527943 original size:12 final size:12
Alignment explanation
Indices: 2527926--2527951 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2527916 TACAAAAAAT
2527926 AGAAGCTGCTAC
1 AGAAGCTGCTAC
2527938 AGAAGCTGCTAC
1 AGAAGCTGCTAC
2527950 AG
1 AG
2527952 CAATAACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (12 bp):
AGAAGCTGCTAC
Found at i:2533684 original size:16 final size:17
Alignment explanation
Indices: 2533652--2533684 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2533642 ATTTTATAAG
2533652 TTTAATACAAAGGTTAA
1 TTTAATACAAAGGTTAA
*
2533669 TTTAATA-AATGGTTAA
1 TTTAATACAAAGGTTAA
2533685 ATGTAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (17 bp):
TTTAATACAAAGGTTAA
Found at i:2535035 original size:35 final size:35
Alignment explanation
Indices: 2534933--2535035 Score: 109
Period size: 35 Copynumber: 2.9 Consensus size: 35
2534923 CAATGTTATC
* * *
2534933 TGGCGTGCTGGATGGTACTGGCTCTAATGAACAAT
1 TGGCGTGCTGGATGGTACTGACTCTTATGAGCAAT
* * * *
2534968 TGGTGTGCTAGATGGTACTGACT-TTCACGAGCAGT
1 TGGCGTGCTGGATGGTACTGACTCTT-ATGAGCAAT
* *
2535003 TGGCGTGTTGGATGGTACTGCCTCTTATGAGCA
1 TGGCGTGCTGGATGGTACTGACTCTTATGAGCA
2535036 TCTAGTATGT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
34 1 0.02
35 51 0.94
36 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.31
Consensus pattern (35 bp):
TGGCGTGCTGGATGGTACTGACTCTTATGAGCAAT
Found at i:2537714 original size:17 final size:18
Alignment explanation
Indices: 2537701--2537825 Score: 100
Period size: 19 Copynumber: 6.9 Consensus size: 18
2537691 TAATCTTCAA
2537701 TGATATGCAATCTTAGATG
1 TGATATGCAATCTTAGA-G
2537720 TGATATGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
2537737 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
2537756 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
2537772 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
*
2537791 TGAT-TGCAATCTTAGATA
1 TGATATGCAATCTTAGA-G
*
2537809 TGATATACAATCTTAGA
1 TGATATGCAATCTTAGA
2537826 AGATATGATT
Statistics
Matches: 91, Mismatches: 5, Indels: 20
0.78 0.04 0.17
Matches are distributed among these distances:
15 2 0.02
16 3 0.03
17 24 0.26
18 28 0.31
19 30 0.33
20 4 0.04
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (18 bp):
TGATATGCAATCTTAGAG
Found at i:2537770 original size:35 final size:35
Alignment explanation
Indices: 2537708--2537825 Score: 200
Period size: 35 Copynumber: 3.3 Consensus size: 35
2537698 CAATGATATG
*
2537708 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
2537744 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
2537779 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
2537816 CAATCTTAGA
1 CAATCTTAGA
2537826 AGATATGATT
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 51 0.65
36 15 0.19
37 13 0.16
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:2540108 original size:25 final size:25
Alignment explanation
Indices: 2540074--2540124 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2540064 CTACTTGTTT
2540074 GCCAATCTTTCTTTCAAGGTAATCA
1 GCCAATCTTTCTTTCAAGGTAATCA
2540099 GCCAATCTTTCTTTCAAGGTAATCA
1 GCCAATCTTTCTTTCAAGGTAATCA
2540124 G
1 G
2540125 AGCAACTTCA
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:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (25 bp):
GCCAATCTTTCTTTCAAGGTAATCA
Found at i:2543047 original size:1 final size:1
Alignment explanation
Indices: 2543041--2543105 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
2543031 CTTCTATTTC
* * * * * * * *
2543041 AAAAAAAAAAAGAAAAAAGAAAAAAAAGAAAAGAAAAAGAGAAAAAAAAGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2543106 TGGAGAGGCC
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:2543072 original size:22 final size:23
Alignment explanation
Indices: 2543041--2543099 Score: 90
Period size: 21 Copynumber: 2.7 Consensus size: 23
2543031 CTTCTATTTC
2543041 AAAAAA-AAAAAGAAAAA-AGAA
1 AAAAAAGAAAAAGAAAAAGAGAA
2543062 AAAAAAG-AAAAGAAAAAGAGAA
1 AAAAAAGAAAAAGAAAAAGAGAA
2543084 AAAAAAGAAAAA-AAAA
1 AAAAAAGAAAAAGAAAA
2543100 GAAAAATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 16 0.46
22 15 0.43
23 4 0.11
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAGAAAAAGAGAA
Found at i:2543080 original size:27 final size:27
Alignment explanation
Indices: 2543045--2543105 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
2543035 TATTTCAAAA
* *
2543045 AAAAAAAGAAAAAAGAAAAAAAAGAAAAG
1 AAAAAGAGAAAAAA-AAGAAAAA-AAAAG
2543074 AAAAAGAGAAAAAAAAGAAAAAAAAAG
1 AAAAAGAGAAAAAAAAGAAAAAAAAAG
2543101 AAAAA
1 AAAAA
2543106 TGGAGAGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.33
28 7 0.23
29 13 0.43
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (27 bp):
AAAAAGAGAAAAAAAAGAAAAAAAAAG
Found at i:2544204 original size:79 final size:81
Alignment explanation
Indices: 2544096--2544250 Score: 251
Period size: 79 Copynumber: 1.9 Consensus size: 81
2544086 TTAAATTTGC
* *
2544096 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA-A-GACTCGCCTAAATCCCCTAAGTAGT
1 AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAGACGACTCGCCTAAATCCCCTAAGCAGT
2544159 AGGGTAACAGGTTCGT
66 AGGGTAACAGGTTCGT
* *
2544175 AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGATGACTACTCGCCTTAATCCCCTAAGCAG
1 AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGA-GACGACTCGCCTAAATCCCCTAAGCAG
2544240 TAGGGTAACAG
65 TAGGGTAACAG
2544251 ATCTTATCCC
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
79 36 0.52
81 1 0.01
82 32 0.46
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (81 bp):
AGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAGACGACTCGCCTAAATCCCCTAAGCAGT
AGGGTAACAGGTTCGT
Found at i:2544687 original size:206 final size:206
Alignment explanation
Indices: 2544329--2545115 Score: 1333
Period size: 206 Copynumber: 3.8 Consensus size: 206
2544319 TAGACCAAAG
* * * * *
2544329 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
* * * * *
2544394 CTTATAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAATCT
* * * * *
2544459 AAGATGATTTGGCATATCTGTATTGTCAGAGAACAAATCGAATTTTAGCGTCTCCATATTCGACG
131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGCCTCCATATTCGACG
2544524 GAGGGCAGACA
196 GAGGGCAGACA
2544535 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
* * *
2544600 CTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTTGCGTGCTTACGCTGAAGCAAGTCT
66 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAATCT
2544665 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGCCTCCATATTCGACG
131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGCCTCCATATTCGACG
2544730 GAGGGCAGACA
196 GAGGGCAGACA
2544741 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
* * *
2544806 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGAGTGCTTACGCCGAAGCAAGTCT
66 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAATCT
*
2544871 AAGATAATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGCCTCCATATTCGACG
131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGCCTCCATATTCGACG
*
2544936 GAGGGTAGACA
196 GAGGGCAGACA
*
2544947 CATAGCAGCTCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
*
2545012 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAACCT
66 CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAATCT
2545077 AAGATGATTTGGCATCTCTGTATTGTCA-AGAAACAAATC
131 AAGATGATTTGGCATCTCTGTATTGTCAGAG-AACAAATC
2545116 GAAGAAGCAG
Statistics
Matches: 552, Mismatches: 28, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
205 2 0.00
206 550 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (206 bp):
CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
CTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGAAGCAAATCT
AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGCGCCTCCATATTCGACG
GAGGGCAGACA
Found at i:2545539 original size:19 final size:19
Alignment explanation
Indices: 2545514--2545639 Score: 192
Period size: 19 Copynumber: 6.9 Consensus size: 19
2545504 ATGATCTTCA
2545514 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
2545533 TTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2545552 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2545569 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2545587 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
2545604 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
2545622 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
2545640 AGATATGATT
Statistics
Matches: 98, Mismatches: 3, Indels: 12
0.87 0.03 0.11
Matches are distributed among these distances:
17 32 0.33
18 32 0.33
19 34 0.35
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:2545563 original size:17 final size:17
Alignment explanation
Indices: 2545522--2545639 Score: 155
Period size: 17 Copynumber: 6.6 Consensus size: 17
2545512 CAATGATATG
*
2545522 CAATCTTAGATTTGATA
1 CAATCTTAGATATGATA
2545539 TGCAATCTTAGATATGATA
1 --CAATCTTAGATATGATA
*
2545558 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
2545576 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
2545593 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
2545611 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
2545630 CAATCTTAGA
1 CAATCTTAGA
2545640 AGATATGATT
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
17 31 0.34
18 31 0.34
19 27 0.30
20 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:2545584 original size:35 final size:35
Alignment explanation
Indices: 2545522--2545639 Score: 200
Period size: 35 Copynumber: 3.3 Consensus size: 35
2545512 CAATGATATG
*
2545522 CAATCTTAGATTTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
2545558 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
2545593 CAATCTTAGATATGATTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
2545630 CAATCTTAGA
1 CAATCTTAGA
2545640 AGATATGATT
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 51 0.65
36 15 0.19
37 13 0.16
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:2560141 original size:29 final size:30
Alignment explanation
Indices: 2560095--2560196 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 30
2560085 ATTTGAGCAC
* *
2560095 TTTTGAAAAGGCTAGGCCCTTCTCTGACCA
1 TTTTGAAAAGGTTAGGCCCTTCTATGACCA
* * *
2560125 TTTTG-AAAGGTTTGG-CCTTCATTTGAGCA
1 TTTTGAAAAGGTTAGGCCCTTC-TATGACCA
* *
2560154 CTTTTGTAAAA-GTTAGGCTCTTATATGACCA
1 -TTTTG-AAAAGGTTAGGCCCTTCTATGACCA
*
2560185 TCTTG-AAAGGTT
1 TTTTGAAAAGGTT
2560197 TGGTTCTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
28 8 0.14
29 17 0.30
30 14 0.25
31 11 0.20
32 6 0.11
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.37
Consensus pattern (30 bp):
TTTTGAAAAGGTTAGGCCCTTCTATGACCA
Found at i:2560159 original size:60 final size:59
Alignment explanation
Indices: 2560081--2560199 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 59
2560071 TTTGAGAAGC
* * *
2560081 CCTTATTTGAGCACTTTTG-AAAAGGCTAGGCCCTTCTCTGACCATTTTGAAAGGTTTGG
1 CCTTATTTGAGCACTTTTGTAAAA-GCTAGGCCCTTATATGACCATCTTGAAAGGTTTGG
* *
2560140 CCTTCATTTGAGCACTTTTGTAAAAGTTAGGCTCTTATATGACCATCTTGAAAGGTTTGG
1 CCTT-ATTTGAGCACTTTTGTAAAAGCTAGGCCCTTATATGACCATCTTGAAAGGTTTGG
2560200 TTCTTATATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 4 0.08
60 45 0.85
61 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (59 bp):
CCTTATTTGAGCACTTTTGTAAAAGCTAGGCCCTTATATGACCATCTTGAAAGGTTTGG
Found at i:2560205 original size:29 final size:28
Alignment explanation
Indices: 2560119--2560210 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
2560109 GGCCCTTCTC
* *
2560119 TGACCATTTTGAAAGGTTTGGCCTTCATT
1 TGACCATTTTGAAAGGTTTGGTCTT-ATA
* * *
2560148 TGAGCACTTTTGTAAAAGTTAGGCTCTTATA
1 TGACCA-TTTTG-AAAGGTTTGG-TCTTATA
*
2560179 TGACCATCTTGAAAGGTTTGGTTCTTATA
1 TGACCATTTTGAAAGGTTTGG-TCTTATA
2560208 TGA
1 TGA
2560211 ACAACCCCTA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 23 0.46
30 9 0.18
31 15 0.30
32 3 0.06
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (28 bp):
TGACCATTTTGAAAGGTTTGGTCTTATA
Found at i:2560633 original size:6 final size:6
Alignment explanation
Indices: 2560622--2560656 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2560612 CGGAGAAATT
2560622 ATTATG ATTATG ATTATG ATTATG ATTATG ATTAT
1 ATTATG ATTATG ATTATG ATTATG ATTATG ATTAT
2560657 TTTTTATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
ATTATG
Done.