Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 80 of 144
Found at i:24224566 original size:12 final size:12
Alignment explanation
Indices: 24224549--24224573 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24224539 ATAAATTTAA
24224549 TTTATAACATAT
1 TTTATAACATAT
24224561 TTTATAACATAT
1 TTTATAACATAT
24224573 T
1 T
24224574 CTGTCATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTATAACATAT
Found at i:24230277 original size:12 final size:12
Alignment explanation
Indices: 24230260--24230289 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24230250 GAGGTCAAAA
24230260 GATGATTACGAT
1 GATGATTACGAT
*
24230272 GATGATTCCGAT
1 GATGATTACGAT
24230284 GATGAT
1 GATGAT
24230290 AAATTCAACG
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:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (12 bp):
GATGATTACGAT
Found at i:24231799 original size:59 final size:59
Alignment explanation
Indices: 24231734--24231851 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
24231724 GTGAAGACGG
24231734 ATTCATCTTTTTGGACGCTAGGTATTTATCGTTTCAATTTTTTTTTTTTTTGGG-ATTCT
1 ATTCATCTTTTTGGACGCTAGGTATTTATCGTTTCAA-TTTTTTTTTTTTTGGGAATTCT
24231793 ATTCATCTTTTTGGACGCTAGGTATTTATCGTTTCAATTTTTTTTTTTTTGGGAATTCT
1 ATTCATCTTTTTGGACGCTAGGTATTTATCGTTTCAATTTTTTTTTTTTTGGGAATTCT
24231852 TTAAGAACTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 16 0.28
59 42 0.72
ACGTcount: A:0.16, C:0.12, G:0.15, T:0.57
Consensus pattern (59 bp):
ATTCATCTTTTTGGACGCTAGGTATTTATCGTTTCAATTTTTTTTTTTTTGGGAATTCT
Found at i:24238279 original size:242 final size:238
Alignment explanation
Indices: 24237793--24238433 Score: 797
Period size: 237 Copynumber: 2.7 Consensus size: 238
24237783 CCTTCTCTGT
*
24237793 AACCATTCTTTC--ATA--TAGTTACATGCTAGTACTTTTTTGTTAATCAGG-CTCGAGTGTGAA
1 AACCATTCTTTCATATAGTTAGTTACATGCTAGTACTTTTTTGTTAATC-GGACTCGAGTCTGAA
** *
24237853 TGTTAGATATAAGCCTATTTAGAACACGGGTTTTGTTCCATTTTACTATT--AAAAAA-AATGTA
65 TGCCAGATATAAGCCTATTTAGAACACGGG-TTTGTTCCATTTTTCT-TTAAAAAAAATAATGTA
*
24237915 TTTGGAGGTCTTTGAAAGATCATGTCCTATACCCTTATACCCTTGCATGAATATGTGTCGTATCA
128 TTTGGAGGTCTTTGAAAGATCATTTCCTATACCCTTATACCCTTGCATGAATATGTGTCGTATCA
* * *
24237980 GACACGAATACTTCACTTGGAACGACGAGTCGGAGCTAGTAATTGC
193 GACACGAATACTTCAATTGAAACGACGAGTCGGAGCTACTAATTGC
* *
24238026 GACCGTTCTTTCATATAGTTAGTTACATGCTAGTACTTTTTCTGTTAATCGGACTCGAGTCTGAA
1 AACCATTCTTTCATATAGTTAGTTACATGCTAGTACTTTTT-TGTTAATCGGACTCGAGTCTGAA
*
24238091 TGCCAAATATAAGCCTATTTAGAACACGGGTTTGTTCCATTTTTCCTTTAAAAAAAAATAATGTA
65 TGCCAGATATAAGCCTATTTAGAACACGGGTTTGTTCCATTTTT-CTTT-AAAAAAAATAATGTA
* * * * *
24238156 TTTGGAGGTCTTTGAAAGATCATATTCCTATACTCTTGTTCCTTTGCATGAATATGTGTTGTATC
128 TTTGGAGGTCTTTGAAAGATCAT-TTCCTATACCCTTATACCCTTGCATGAATATGTGTCGTATC
* * * * * *
24238221 TGACATGAGTACTTCAATTGAAATGATGAGTCGGAGCTTCTAATTGC
192 AGACACGAATACTTCAATTGAAACGACGAGTCGGAGCTACTAATTGC
* *
24238268 AACCATTCTTTCATATAGTT-G---CATGTTAGTACTTTTTTGTTAATCGGACCCGAG-CAT-AA
1 AACCATTCTTTCATATAGTTAGTTACATGCTAGTACTTTTTTGTTAATCGGACTCGAGTC-TGAA
* * * * * * *
24238327 GTGGCAGATGTAAGTCTATTTAGGACACGGGTATGTTCCATTTTTCTTTAAAAAAATTCATGTAT
65 -TGCCAGATATAAGCCTATTTAGAACACGGGTTTGTTCCATTTTTCTTTAAAAAAAATAATGTAT
* *
24238392 TTGGTGGTCTTTGAAAGATCATGTTCCTATGCCCTTATACCC
129 TTGGAGGTCTTTGAAAGATCAT-TTCCTATACCCTTATACCC
24238434 GACATGGGTG
Statistics
Matches: 353, Mismatches: 41, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
233 10 0.03
235 52 0.15
236 7 0.02
237 94 0.27
238 63 0.18
240 6 0.02
241 30 0.08
242 91 0.26
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (238 bp):
AACCATTCTTTCATATAGTTAGTTACATGCTAGTACTTTTTTGTTAATCGGACTCGAGTCTGAAT
GCCAGATATAAGCCTATTTAGAACACGGGTTTGTTCCATTTTTCTTTAAAAAAAATAATGTATTT
GGAGGTCTTTGAAAGATCATTTCCTATACCCTTATACCCTTGCATGAATATGTGTCGTATCAGAC
ACGAATACTTCAATTGAAACGACGAGTCGGAGCTACTAATTGC
Found at i:24246218 original size:12 final size:12
Alignment explanation
Indices: 24246201--24246226 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24246191 CATTCCGAAG
24246201 TATATATATACA
1 TATATATATACA
24246213 TATATATATACA
1 TATATATATACA
24246225 TA
1 TA
24246227 AGTATGCCAT
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:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:24246741 original size:27 final size:27
Alignment explanation
Indices: 24246710--24246887 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
24246700 TAAATTGTAC
24246710 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
24246737 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
24246763 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
24246791 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
24246819 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
24246846 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
24246873 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
24246888 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:24246824 original size:82 final size:81
Alignment explanation
Indices: 24246711--24246866 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
24246701 AAATTGTACA
* *
24246711 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
24246775 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
24246792 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
24246857 TGCGAGTTGA
65 TGCGAATTGA
24246867 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:24246878 original size:82 final size:81
Alignment explanation
Indices: 24246707--24246887 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
24246697 GATTAAATTG
* *
24246707 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
24246772 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
24246788 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
24246852 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
24246870 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
24246888 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:24250750 original size:200 final size:200
Alignment explanation
Indices: 24250407--24250807 Score: 793
Period size: 200 Copynumber: 2.0 Consensus size: 200
24250397 GACGGAACCA
24250407 TGAGGTTGTGCATTGACTATCGACAACTGAATAAAGTGACGATAAAGAATAAGTATCCGTTACCG
1 TGAGGTTGTGCATTGACTATCGACAACTGAATAAAGTGACGATAAAGAATAAGTATCCGTTACCG
24250472 CGTATTGATGATCTGTTCGATCAATTAAAGGGAGCATCGGTGTTTTCAAAGATAGATTTGAGATC
66 CGTATTGATGATCTGTTCGATCAATTAAAGGGAGCATCGGTGTTTTCAAAGATAGATTTGAGATC
24250537 GGGTTATTATCAGTTGCGGATTCGAGATTCGGACGTACCCAAAACTGCTTTCAGAACGAGGTACG
131 GGGTTATTATCAGTTGCGGATTCGAGATTCGGACGTACCCAAAACTGCTTTCAGAACGAGGTACG
24250602 GTCAC
196 GTCAC
*
24250607 TGAGGTTGTGCATTGACTATCGTCAACTGAATAAAGTGACGATAAAGAATAAGTATCCGTTACCG
1 TGAGGTTGTGCATTGACTATCGACAACTGAATAAAGTGACGATAAAGAATAAGTATCCGTTACCG
24250672 CGTATTGATGATCTGTTCGATCAATTAAAGGGAGCATCGGTGTTTTCAAAGATAGATTTGAGATC
66 CGTATTGATGATCTGTTCGATCAATTAAAGGGAGCATCGGTGTTTTCAAAGATAGATTTGAGATC
24250737 GGGTTATTATCAGTTGCGGATTCGAGATTCGGACGTACCCAAAACTGCTTTCAGAACGAGGTACG
131 GGGTTATTATCAGTTGCGGATTCGAGATTCGGACGTACCCAAAACTGCTTTCAGAACGAGGTACG
24250802 GTCAC
196 GTCAC
24250807 T
1 T
24250808 ACGAGTTCTT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (200 bp):
TGAGGTTGTGCATTGACTATCGACAACTGAATAAAGTGACGATAAAGAATAAGTATCCGTTACCG
CGTATTGATGATCTGTTCGATCAATTAAAGGGAGCATCGGTGTTTTCAAAGATAGATTTGAGATC
GGGTTATTATCAGTTGCGGATTCGAGATTCGGACGTACCCAAAACTGCTTTCAGAACGAGGTACG
GTCAC
Found at i:24294181 original size:25 final size:26
Alignment explanation
Indices: 24294134--24294182 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
24294124 TAATCTCTAT
* *
24294134 TTTTTAAATTTTATAATATATATTTG
1 TTTTAAAATTTTATAATAAATATTTG
24294160 TTTTAAAATTTTATAA-AAATATT
1 TTTTAAAATTTTATAATAAATATT
24294183 AAATACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTTAAAATTTTATAATAAATATTTG
Found at i:24295359 original size:2 final size:2
Alignment explanation
Indices: 24295352--24295380 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24295342 CATATAAGCT
24295352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24295381 TATTGTAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24295522 original size:30 final size:30
Alignment explanation
Indices: 24295488--24295544 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
24295478 AAAATTACAT
24295488 TTTAAACCTCTTAAAAAGAA-GAAAATTTTG
1 TTTAAACC-CTTAAAAAGAATGAAAATTTTG
** *
24295518 TTTAATTCCTTAAAAATAATGAAAATT
1 TTTAAACCCTTAAAAAGAATGAAAATT
24295545 ATATAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (30 bp):
TTTAAACCCTTAAAAAGAATGAAAATTTTG
Found at i:24301879 original size:22 final size:22
Alignment explanation
Indices: 24301852--24301926 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
24301842 TTCCACATCC
24301852 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
24301874 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
24301898 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
24301921 ATCACA
1 ATCACA
24301927 CATACACATG
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 17 0.45
23 5 0.13
24 5 0.13
25 11 0.29
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:24301887 original size:47 final size:47
Alignment explanation
Indices: 24301845--24302792 Score: 1758
Period size: 47 Copynumber: 20.1 Consensus size: 47
24301835 TATACACTTC
* * *
24301845 CACATCCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTT
24301892 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24301939 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24301986 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302033 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302080 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302127 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302174 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302221 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302268 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302315 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302362 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302409 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302456 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302503 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302550 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302597 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
24302644 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
* *
24302691 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCAC--ACATACACA-TGTT
* * *
24302740 CACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACT-TT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACA-TGTT
24302787 CACATT
1 CACATT
24302793 TATTCAAATA
Statistics
Matches: 891, Mismatches: 6, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
46 1 0.00
47 847 0.95
49 42 0.05
50 1 0.00
ACGTcount: A:0.28, C:0.32, G:0.10, T:0.30
Consensus pattern (47 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTT
Found at i:24304334 original size:168 final size:169
Alignment explanation
Indices: 24304056--24304402 Score: 669
Period size: 168 Copynumber: 2.1 Consensus size: 169
24304046 TATTTTATTG
*
24304056 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
24304121 TAGCCATAACATCTTGTCCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCA
66 TAGCCATAACATCTTGTCCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCA
24304186 ACATGTTTATGAC-GTTTTTAGCCATAACATCTTGTCCA
131 ACATGTTTATGACAGTTTTTAGCCATAACATCTTGTCCA
24304224 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
24304289 TAGCCATAACATCTTGTCCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCA
66 TAGCCATAACATCTTGTCCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCA
24304354 ACATGTTTATGACATGTTTTTAGCCATAACATCTTGTCCA
131 ACATGTTTATGACA-GTTTTTAGCCATAACATCTTGTCCA
24304394 CCCATGCTC
1 CCCATGCTC
24304403 ATGGCCGGCC
Statistics
Matches: 176, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
168 142 0.81
170 34 0.19
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (169 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCACCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCA
ACATGTTTATGACAGTTTTTAGCCATAACATCTTGTCCA
Found at i:24304342 original size:85 final size:85
Alignment explanation
Indices: 24304056--24304402 Score: 671
Period size: 85 Copynumber: 4.1 Consensus size: 85
24304046 TATTTTATTG
*
24304056 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
24304121 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
24304141 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGAC--GTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
24304204 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
24304224 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
24304289 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
24304309 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
24304374 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
24304394 CCCATGCTC
1 CCCATGCTC
24304403 ATGGCCGGCC
Statistics
Matches: 259, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
83 83 0.32
85 176 0.68
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:24309708 original size:28 final size:28
Alignment explanation
Indices: 24309645--24309767 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
24309635 ATATTAAGTC
*
24309645 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
24309672 CACACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
24309700 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
24309728 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
24309757 CGCACACTTAG
1 CGCACACTTAG
24309768 CGCCAATCTC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.25
28 48 0.56
29 16 0.19
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:24318981 original size:10 final size:12
Alignment explanation
Indices: 24318956--24318981 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24318946 AGAATAGGAG
24318956 ATATACCTGAAT
1 ATATACCTGAAT
24318968 ATATACCTGAAT
1 ATATACCTGAAT
24318980 AT
1 AT
24318982 GGGGTTGACT
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:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATATACCTGAAT
Found at i:24321811 original size:25 final size:25
Alignment explanation
Indices: 24321728--24321861 Score: 129
Period size: 25 Copynumber: 5.6 Consensus size: 25
24321718 TTATTATGCA
* *
24321728 CTAATGAA-CAGAGAGCACTAAAGTG
1 CTAAT-AATCAGAGAGCACCAACGTG
* *
24321753 CT-AT-A-CAGAGAGCACAAATGTG
1 CTAATAATCAGAGAGCACCAACGTG
**
24321775 C---TAATCAGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACCAACGTG
* *
24321797 CTAGTAATCAAAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACCAACGTG
24321822 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACCAACGTG
*
24321847 CTAATAATTAGAGAG
1 CTAATAATCAGAGAG
24321862 TGCGCTAAAG
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 32 0.34
24 2 0.02
25 57 0.61
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.18
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACCAACGTG
Found at i:24322830 original size:5 final size:5
Alignment explanation
Indices: 24322820--24322877 Score: 100
Period size: 5 Copynumber: 11.8 Consensus size: 5
24322810 TTATTTCTTT
*
24322820 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TACAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
24322869 TATAA TATA
1 TATAA TATA
24322878 TAACTTAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
4 4 0.08
5 46 0.92
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:24325861 original size:14 final size:14
Alignment explanation
Indices: 24325842--24325882 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
24325832 TGATTAAAGA
*
24325842 TTAATTAATTTAGT
1 TTAATTAATTAAGT
24325856 TTAATTAACTTAAGT
1 TTAATTAA-TTAAGT
*
24325871 TCAATTAATTAA
1 TTAATTAATTAA
24325883 CCATTTAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
TTAATTAATTAAGT
Found at i:24329078 original size:15 final size:15
Alignment explanation
Indices: 24329058--24329086 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24329048 GACCTAGTAG
24329058 TTGTCTTGATCTATT
1 TTGTCTTGATCTATT
24329073 TTGTCTTGATCTAT
1 TTGTCTTGATCTAT
24329087 CCCTATAGAT
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:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TTGTCTTGATCTATT
Found at i:24332882 original size:12 final size:13
Alignment explanation
Indices: 24332865--24332893 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
24332855 CTCATACATG
24332865 AATAAATAAA-GC
1 AATAAATAAATGC
24332877 AATAAATAAATGC
1 AATAAATAAATGC
24332890 AATA
1 AATA
24332894 GTTATAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:24340862 original size:24 final size:24
Alignment explanation
Indices: 24340835--24340880 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
24340825 TATGTTATAT
*
24340835 TTATAATCTATTATTTAGTATAAA
1 TTATAATATATTATTTAGTATAAA
** *
24340859 TTATTTTATATTATTTATTATA
1 TTATAATATATTATTTAGTATA
24340881 CATATACACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATAATATATTATTTAGTATAAA
Found at i:24348632 original size:2 final size:2
Alignment explanation
Indices: 24348627--24348664 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24348617 GTGTGTGTAT
24348627 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24348665 AGCAGAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24349045 original size:6 final size:6
Alignment explanation
Indices: 24349034--24349062 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
24349024 ATAAGGGTCG
24349034 GGTTGA GGTTGA GGTTGA GGTTGA GGTTG
1 GGTTGA GGTTGA GGTTGA GGTTGA GGTTG
24349063 GGGATATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34
Consensus pattern (6 bp):
GGTTGA
Found at i:24349087 original size:18 final size:18
Alignment explanation
Indices: 24349064--24349101 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
24349054 TTGAGGTTGG
24349064 GGATATGGATACGGGTAT
1 GGATATGGATACGGGTAT
* *
24349082 GGATATTGATATGGGTAT
1 GGATATGGATACGGGTAT
24349100 GG
1 GG
24349102 TGGCATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.39, T:0.32
Consensus pattern (18 bp):
GGATATGGATACGGGTAT
Found at i:24349554 original size:15 final size:15
Alignment explanation
Indices: 24349534--24349570 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 15
24349524 CCTGAGGTAA
24349534 ACCACCGCCATTTTT
1 ACCACCGCCATTTTT
24349549 ACCACCG---TTTTT
1 ACCACCGCCATTTTT
24349561 ACCACCGCCA
1 ACCACCGCCA
24349571 CCTTGATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
12 12 0.63
15 7 0.37
ACGTcount: A:0.22, C:0.43, G:0.08, T:0.27
Consensus pattern (15 bp):
ACCACCGCCATTTTT
Found at i:24349908 original size:15 final size:15
Alignment explanation
Indices: 24349890--24349957 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
24349880 AACTCATCGC
24349890 CATCATCAAAATCAT
1 CATCATCAAAATCAT
*
24349905 CATCATCAAGATCACAAT
1 CATCATCAAAAT--C-AT
* * *
24349923 CATTATCCAAGTCAT
1 CATCATCAAAATCAT
*
24349938 CATCATCATAATCAT
1 CATCATCAAAATCAT
24349953 CATCA
1 CATCA
24349958 CTGAAATCTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
15 29 0.71
16 1 0.02
17 1 0.02
18 10 0.24
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (15 bp):
CATCATCAAAATCAT
Found at i:24349924 original size:18 final size:18
Alignment explanation
Indices: 24349900--24349957 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
24349890 CATCATCAAA
24349900 ATCATCATCAT-CAAGATC
1 ATCATCATCATCCAAG-TC
*
24349918 A-CAATCATTATCCAAGTC
1 ATC-ATCATCATCCAAGTC
24349936 ATCATCATCAT--AA-TC
1 ATCATCATCATCCAAGTC
24349951 ATCATCA
1 ATCATCA
24349958 CTGAAATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 9 0.26
16 2 0.06
17 1 0.03
18 18 0.51
19 5 0.14
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.29
Consensus pattern (18 bp):
ATCATCATCATCCAAGTC
Found at i:24350179 original size:3 final size:3
Alignment explanation
Indices: 24350171--24350208 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
24350161 CTGACCACCC
*
24350171 TTG TTG TTG TT- TTGG TTG TTG TTC TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TT-G TTG TTG TTG TTG TTG TTG TTG TT
24350209 TCCACCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.00, C:0.03, G:0.29, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:24350681 original size:12 final size:13
Alignment explanation
Indices: 24350660--24350688 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
24350650 TAGAGAAACA
24350660 AAAAATGAGAGAG
1 AAAAATGAGAGAG
24350673 AAAAA-GAGAGAG
1 AAAAATGAGAGAG
24350685 AAAA
1 AAAA
24350689 TACTTGGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (13 bp):
AAAAATGAGAGAG
Found at i:24351016 original size:6 final size:6
Alignment explanation
Indices: 24350981--24351015 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
24350971 AGAGAGTGCC
*
24350981 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAC GGCAA
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAA
24351016 CAGCAGGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.34, T:0.11
Consensus pattern (6 bp):
GGCAAT
Found at i:24353023 original size:23 final size:23
Alignment explanation
Indices: 24353008--24353061 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
24352998 TATATACACG
24353008 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
* *
24353031 TACATAATAATAATA-ATAGTAA
1 TACATAATAAAAATATATACTAA
24353053 TAC-TAATAA
1 TACATAATAA
24353062 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:24353033 original size:29 final size:26
Alignment explanation
Indices: 24353011--24353070 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
24353001 ATACACGTAC
24353011 ATAATAAAAATATATACTAATACATA
1 ATAATAAAAATATATACTAATACATA
*
24353037 ATAATAATAATAGTAATACTAATA-ATA
1 ATAATAAAAATA-T-ATACTAATACATA
*
24353064 CTAATAA
1 ATAATAA
24353071 TATAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 11 0.37
27 10 0.33
28 9 0.30
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
ATAATAAAAATATATACTAATACATA
Found at i:24353042 original size:3 final size:3
Alignment explanation
Indices: 24353011--24353081 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
24353001 ATACACGTAC
* * * *
24353011 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
24353058 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
24353082 CAAGGATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:24353568 original size:11 final size:12
Alignment explanation
Indices: 24353548--24353585 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
24353538 AGAAAAAAAA
24353548 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
24353561 GAAGAGAGAAGG
1 GAAGAGAGAAGG
24353573 G-AGAGAGAAGG
1 GAAGAGAGAAGG
24353584 GA
1 GA
24353586 GGGGGGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 4 0.17
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:24354072 original size:8 final size:8
Alignment explanation
Indices: 24354059--24354083 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
24354049 GGTGTTCGGC
24354059 GCAAGTGG
1 GCAAGTGG
24354067 GCAAGTGG
1 GCAAGTGG
24354075 GCAAGTGG
1 GCAAGTGG
24354083 G
1 G
24354084 GGGTAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:24371058 original size:296 final size:296
Alignment explanation
Indices: 24370524--24371117 Score: 1188
Period size: 296 Copynumber: 2.0 Consensus size: 296
24370514 ATTATTTTAT
24370524 TTGATAGTTTAATAAGCACAAACTCGAACAAGGGGATGTCGGGCGAATAGAATTGTTTCTCGAAT
1 TTGATAGTTTAATAAGCACAAACTCGAACAAGGGGATGTCGGGCGAATAGAATTGTTTCTCGAAT
24370589 TGGAGTGGCTCGGTTGTTTCGGATTGAAGCAAATGGTTTTGCTGGGGGGATTTGGATTCTTTGGA
66 TGGAGTGGCTCGGTTGTTTCGGATTGAAGCAAATGGTTTTGCTGGGGGGATTTGGATTCTTTGGA
24370654 ATGAAATGATTCAATTAACATATTGGTTATGTATCCCTAAATAGTTCATATGAAAGTTAGCAATG
131 ATGAAATGATTCAATTAACATATTGGTTATGTATCCCTAAATAGTTCATATGAAAGTTAGCAATG
24370719 TGTAAGATTCCTCTAGTTTTCTATGTTCAGCAATATATGTTACCCACAACAAATGATGGGGAGGG
196 TGTAAGATTCCTCTAGTTTTCTATGTTCAGCAATATATGTTACCCACAACAAATGATGGGGAGGG
24370784 AACTTTGGTATACTTTGAATTACACGGCAGATTCGA
261 AACTTTGGTATACTTTGAATTACACGGCAGATTCGA
24370820 TTGATAGTTTAATAAGCACAAACTCGAACAAGGGGATGTCGGGCGAATAGAATTGTTTCTCGAAT
1 TTGATAGTTTAATAAGCACAAACTCGAACAAGGGGATGTCGGGCGAATAGAATTGTTTCTCGAAT
24370885 TGGAGTGGCTCGGTTGTTTCGGATTGAAGCAAATGGTTTTGCTGGGGGGATTTGGATTCTTTGGA
66 TGGAGTGGCTCGGTTGTTTCGGATTGAAGCAAATGGTTTTGCTGGGGGGATTTGGATTCTTTGGA
24370950 ATGAAATGATTCAATTAACATATTGGTTATGTATCCCTAAATAGTTCATATGAAAGTTAGCAATG
131 ATGAAATGATTCAATTAACATATTGGTTATGTATCCCTAAATAGTTCATATGAAAGTTAGCAATG
24371015 TGTAAGATTCCTCTAGTTTTCTATGTTCAGCAATATATGTTACCCACAACAAATGATGGGGAGGG
196 TGTAAGATTCCTCTAGTTTTCTATGTTCAGCAATATATGTTACCCACAACAAATGATGGGGAGGG
24371080 AACTTTGGTATACTTTGAATTACACGGCAGATTCGA
261 AACTTTGGTATACTTTGAATTACACGGCAGATTCGA
24371116 TT
1 TT
24371118 TTAAAGTTGT
Statistics
Matches: 298, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
296 298 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (296 bp):
TTGATAGTTTAATAAGCACAAACTCGAACAAGGGGATGTCGGGCGAATAGAATTGTTTCTCGAAT
TGGAGTGGCTCGGTTGTTTCGGATTGAAGCAAATGGTTTTGCTGGGGGGATTTGGATTCTTTGGA
ATGAAATGATTCAATTAACATATTGGTTATGTATCCCTAAATAGTTCATATGAAAGTTAGCAATG
TGTAAGATTCCTCTAGTTTTCTATGTTCAGCAATATATGTTACCCACAACAAATGATGGGGAGGG
AACTTTGGTATACTTTGAATTACACGGCAGATTCGA
Found at i:24372600 original size:9 final size:9
Alignment explanation
Indices: 24372586--24372610 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
24372576 GAAGAATTAT
24372586 ATTGGTAAA
1 ATTGGTAAA
24372595 ATTGGTAAA
1 ATTGGTAAA
24372604 ATTGGTA
1 ATTGGTA
24372611 TTGCTTGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (9 bp):
ATTGGTAAA
Found at i:24374466 original size:17 final size:17
Alignment explanation
Indices: 24374446--24374479 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24374436 GTTTTATTTT
* *
24374446 TTTTCTTTTATATCAAC
1 TTTTCATTTATAACAAC
24374463 TTTTCATTTATAACAAC
1 TTTTCATTTATAACAAC
24374480 AATCATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTCATTTATAACAAC
Found at i:24378086 original size:42 final size:42
Alignment explanation
Indices: 24378029--24378196 Score: 151
Period size: 42 Copynumber: 4.0 Consensus size: 42
24378019 TAAAAGCCCG
* * * * *
24378029 AAGGCTGAACAGAAGCTCATGAGAGCTCAACAGAAACCCATA
1 AAGGTTGAACTGAAGCTCATTAGAGCTGAACGGAAACCCATA
* * * * *
24378071 ATGGTTGAACTGAAGCTCGTAAGAGTTGAATGGAAACCCATA
1 AAGGTTGAACTGAAGCTCATTAGAGCTGAACGGAAACCCATA
* * * * *
24378113 AGGGTTAAACAT-AAGCTCATTAAAGCTAAACGGAAACCTATA
1 AAGGTTGAAC-TGAAGCTCATTAGAGCTGAACGGAAACCCATA
* *
24378155 AAGGTT-AAATAGAAGCTCATTACAGCTGAACGGAAACCCATA
1 AAGGTTGAACT-GAAGCTCATTAGAGCTGAACGGAAACCCATA
24378197 GTGTAACACC
Statistics
Matches: 100, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 96 0.96
43 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (42 bp):
AAGGTTGAACTGAAGCTCATTAGAGCTGAACGGAAACCCATA
Found at i:24379275 original size:41 final size:41
Alignment explanation
Indices: 24379188--24379375 Score: 215
Period size: 41 Copynumber: 4.6 Consensus size: 41
24379178 TTAAACAGAT
** * * *
24379188 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAAT--GTA
* *
24379230 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
*
24379270 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTAAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
24379311 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
*
24379350 CTTCACCAGCATTAAGCCTGCTAGAC
1 --TCACCGGCATTAAGCCTGCTAGAC
24379376 GTAACGTCCG
Statistics
Matches: 129, Mismatches: 11, Indels: 13
0.84 0.07 0.08
Matches are distributed among these distances:
39 2 0.02
40 8 0.06
41 115 0.89
42 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
Found at i:24379391 original size:41 final size:42
Alignment explanation
Indices: 24379270--24379396 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 42
24379260 CTGAAATGTA
* * ** * **
24379270 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTAAAATGTA-
1 TCACCAGCATTAAGCCTGCTAGACGTAAAGTCCGAATTACAT
* * *
24379311 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAATTAC-T
1 TCACCAGCATTAAGCCTGCTAGACGTAAAGTCCGAATTACAT
* *
24379352 TCACCAGCATTAAGCCTGCTAGACGTAACGTCCGTATTACAT
1 TCACCAGCATTAAGCCTGCTAGACGTAAAGTCCGAATTACAT
24379394 TCA
1 TCA
24379397 ATCACTTTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
41 71 0.95
42 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (42 bp):
TCACCAGCATTAAGCCTGCTAGACGTAAAGTCCGAATTACAT
Found at i:24386905 original size:91 final size:91
Alignment explanation
Indices: 24386750--24386930 Score: 353
Period size: 91 Copynumber: 2.0 Consensus size: 91
24386740 TATGGGGTAA
24386750 TATATCCATTTCGGATGCCATATCCAGCATCAGCAAGATAATATTTACCTACAATTTTACAAAAC
1 TATATCCATTTCGGATGCCATATCCAGCATCAGCAAGATAATATTTACCTACAATTTTACAAAAC
24386815 ATAATTAATACTAATAAATTATGAGT
66 ATAATTAATACTAATAAATTATGAGT
*
24386841 TATATCTATTTCGGATGCCATATCCAGCATCAGCAAGATAATATTTACCTACAATTTTACAAAAC
1 TATATCCATTTCGGATGCCATATCCAGCATCAGCAAGATAATATTTACCTACAATTTTACAAAAC
24386906 ATAATTAATACTAATAAATTATGAG
66 ATAATTAATACTAATAAATTATGAG
24386931 CTTACTAAAA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (91 bp):
TATATCCATTTCGGATGCCATATCCAGCATCAGCAAGATAATATTTACCTACAATTTTACAAAAC
ATAATTAATACTAATAAATTATGAGT
Found at i:24391369 original size:47 final size:48
Alignment explanation
Indices: 24391261--24391372 Score: 129
Period size: 48 Copynumber: 2.4 Consensus size: 48
24391251 GTGGAAGAAT
* * * *
24391261 GTGGTAGTTTATCTGCAAAAGTGGTGACTTATCCATAAATTTTATTAT
1 GTGGCAGTTTATCTGCAAAAGTGATGACTTATCCATAAATTTGATTAC
* * * *
24391309 ATGGCAGTATATCTGCAAAAGTGATGGCTTGT-C-TACAATTTGATTAC
1 GTGGCAGTTTATCTGCAAAAGTGATGACTTATCCATA-AATTTGATTAC
24391356 GTGGCAGTTTATCTGCA
1 GTGGCAGTTTATCTGCA
24391373 TTACCGTGAC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
46 2 0.04
47 25 0.47
48 26 0.49
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (48 bp):
GTGGCAGTTTATCTGCAAAAGTGATGACTTATCCATAAATTTGATTAC
Found at i:24392919 original size:21 final size:21
Alignment explanation
Indices: 24392895--24393001 Score: 81
Period size: 21 Copynumber: 5.1 Consensus size: 21
24392885 TGAGTTTCCA
*
24392895 TTCAACCCTAATGGGTTTCTG
1 TTCAACCCTTATGGGTTTCTG
* ** * * *
24392916 TTCAGCTTTTTTGAGCTTCTG
1 TTCAACCCTTATGGGTTTCTG
* * *
24392937 TTTAACCCTTATAGGTTTCCG
1 TTCAACCCTTATGGGTTTCTG
* * *
24392958 TTCAGCTCTTATGAGCTTTC-G
1 TTCAACCCTTATG-GGTTTCTG
24392979 TTCAACCCTTATGGGTTTCTG
1 TTCAACCCTTATGGGTTTCTG
24393000 TT
1 TT
24393002 TAGCATTTAT
Statistics
Matches: 60, Mismatches: 24, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
20 5 0.08
21 50 0.83
22 5 0.08
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCAACCCTTATGGGTTTCTG
Found at i:24392944 original size:42 final size:42
Alignment explanation
Indices: 24392898--24393024 Score: 157
Period size: 42 Copynumber: 3.0 Consensus size: 42
24392888 GTTTCCATTC
* *
24392898 AACCCTAATGGGTTTCTGTTCAGCTTTTTTGAGCTTCTGTTT
1 AACCCTTATGGGTTTCTGTTCAGCTTTTATGAGCTTCTGTTT
* * * *
24392940 AACCCTTATAGGTTTCCGTTCAGCTCTTATGAGCTT-TCGTTC
1 AACCCTTATGGGTTTCTGTTCAGCTTTTATGAGCTTCT-GTTT
* * *
24392982 AACCCTTATGGGTTTCTGTTTAGCATTTATGTGCTTCTGTTT
1 AACCCTTATGGGTTTCTGTTCAGCTTTTATGAGCTTCTGTTT
24393024 A
1 A
24393025 GCCTTCGGGC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 1 0.01
42 68 0.97
43 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (42 bp):
AACCCTTATGGGTTTCTGTTCAGCTTTTATGAGCTTCTGTTT
Found at i:24393011 original size:21 final size:21
Alignment explanation
Indices: 24392987--24393026 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24392977 CGTTCAACCC
*
24392987 TTATGGGTTTCTGTTTAGCAT
1 TTATGGGCTTCTGTTTAGCAT
*
24393008 TTATGTGCTTCTGTTTAGC
1 TTATGGGCTTCTGTTTAGC
24393027 CTTCGGGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (21 bp):
TTATGGGCTTCTGTTTAGCAT
Found at i:24396226 original size:60 final size:60
Alignment explanation
Indices: 24396148--24396265 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
24396138 TTGTTAACGA
* ** *
24396148 AGGGGCTTAATTAATTTTTTTTATTAATGACAAGAGCTCAATTGGACGCATATTAAGTCG
1 AGGGGCTTAACTAATTTTTTTTATTAACAACAAGAGCTCAATTGGACGCAAATTAAGTCG
* * * * *
24396208 AGGGGTTTAACTAGTTTTTTTTATTAACAATAAGTGCTCAATTGGATGCAAATTAAGT
1 AGGGGCTTAACTAATTTTTTTTATTAACAACAAGAGCTCAATTGGACGCAAATTAAGT
24396266 TGATGTCTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.38
Consensus pattern (60 bp):
AGGGGCTTAACTAATTTTTTTTATTAACAACAAGAGCTCAATTGGACGCAAATTAAGTCG
Found at i:24403554 original size:5 final size:5
Alignment explanation
Indices: 24403540--24403570 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
24403530 AAGAGATGCC
*
24403540 TTTTA CTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
24403571 CCCTTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:24411067 original size:120 final size:120
Alignment explanation
Indices: 24410849--24411325 Score: 828
Period size: 120 Copynumber: 4.0 Consensus size: 120
24410839 NNNNNNNNNN
*
24410849 TTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
1 TTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
* *
24410914 ATTTTTTTAAATTATATAGTTTAATTAAAATTTATTTAATAATAATTATGTTAAT
66 ATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAAT
* * *
24410969 TTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGA
1 TTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
*
24411034 ATTTTATTAAATTATATAGTTTAATTAAAATTTATTTAATAATAATTATGTTAAT
66 ATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAAT
* *
24411089 TTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
1 TTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
* *
24411154 ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAT
66 ATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAAT
*
24411209 TTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGA
1 TTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
* *
24411274 ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 ATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTT
24411326 TAAATATGAT
Statistics
Matches: 343, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 343 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
TTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
ATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAAT
Found at i:24411193 original size:15 final size:15
Alignment explanation
Indices: 24411158--24411209 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
24411148 TTAAGAATTT
*
24411158 TATTAAATTAT-ATA
1 TATTTAATTATAATA
24411172 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
24411186 TATTTAATAATAAT-
1 TATTTAATTATAATA
24411200 TATGTTAATT
1 TAT-TTAATT
24411210 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:24411308 original size:16 final size:16
Alignment explanation
Indices: 24411287--24411328 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
24411277 TTATTAAATT
*
24411287 ATATATTTTAATTATA
1 ATATATTTTAATAATA
24411303 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
24411318 AT-TATGTTTAA
1 ATATAT-TTTAA
24411329 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:24411313 original size:15 final size:15
Alignment explanation
Indices: 24411278--24411319 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24411268 TTAAGAATTT
*
24411278 TATTAAATTAT-ATA
1 TATTTAATTATAATA
24411292 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
24411306 TATTTAATAATAAT
1 TATTTAATTATAAT
24411320 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:24411554 original size:45 final size:43
Alignment explanation
Indices: 24411454--24411563 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
24411444 TTTTCCATTA
24411454 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
24411493 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
24411538 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
24411564 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:24411565 original size:16 final size:16
Alignment explanation
Indices: 24411544--24411595 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
24411534 GATTTGCTAT
*
24411544 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
24411560 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
24411576 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
24411592 TACA
1 TACA
24411596 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:24419599 original size:14 final size:14
Alignment explanation
Indices: 24419580--24419611 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
24419570 CGACTCCAGT
24419580 AAAAGCAATAGTTC
1 AAAAGCAATAGTTC
24419594 AAAAGCAATAGTTC
1 AAAAGCAATAGTTC
24419608 AAAA
1 AAAA
24419612 ACTCTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (14 bp):
AAAAGCAATAGTTC
Found at i:24424397 original size:11 final size:11
Alignment explanation
Indices: 24424383--24424431 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
24424373 AGATAAATAT
24424383 TATTTTATTAA
1 TATTTTATTAA
*
24424394 TATTTTACTAA
1 TATTTTATTAA
* *
24424405 TATTTAATGAGA
1 TATTTTATTA-A
*
24424417 TATTTTATTAT
1 TATTTTATTAA
24424428 TATT
1 TATT
24424432 ATTTATTATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:24424431 original size:23 final size:22
Alignment explanation
Indices: 24424380--24424431 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
24424370 ATTAGATAAA
* *
24424380 TATTATTTTATTAATATTTTAC
1 TATTATTTAATGAATATTTTAC
* *
24424402 TAATATTTAATGAGATATTTTAT
1 TATTATTTAATGA-ATATTTTAC
24424425 TATTATT
1 TATTATT
24424432 ATTTATTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TATTATTTAATGAATATTTTAC
Found at i:24425829 original size:25 final size:25
Alignment explanation
Indices: 24425801--24425929 Score: 171
Period size: 25 Copynumber: 5.4 Consensus size: 25
24425791 AGAGTTTATT
24425801 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
*
24425826 GTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATCA
*
24425851 GTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATCA
* *
24425876 ATGCTCTCTGATTACTAG--CA-CA
1 GTGCTCTCTGATTATTAGCACATCA
*
24425898 ---CTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATCA
24425920 GTGCTCTCTG
1 GTGCTCTCTG
24425930 TTTAGCACAT
Statistics
Matches: 92, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
19 14 0.15
21 2 0.02
22 3 0.03
23 1 0.01
25 72 0.78
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCA
Found at i:24425903 original size:19 final size:19
Alignment explanation
Indices: 24425879--24425916 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24425869 CACGTCAATG
24425879 CTCTCTGATTACTAGCACA
1 CTCTCTGATTACTAGCACA
*
24425898 CTCTCTGATTATTAGCACA
1 CTCTCTGATTACTAGCACA
24425917 TTAGTGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (19 bp):
CTCTCTGATTACTAGCACA
Found at i:24425936 original size:22 final size:22
Alignment explanation
Indices: 24425909--24425977 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
24425899 TCTCTGATTA
24425909 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
**
24425931 TTAGCACATTTTTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* * *
24425953 ATAACACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
24425975 TTA
1 TTA
24425978 ATAGTGCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:24428975 original size:11 final size:11
Alignment explanation
Indices: 24428961--24429014 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
24428951 AGATAAATAT
24428961 TATTTTATTAA
1 TATTTTATTAA
*
24428972 TATTTTACTAA
1 TATTTTATTAA
* *
24428983 TATTTAATGAGA
1 TATTTTATTA-A
*
24428995 TATTTTATTAT
1 TATTTTATTAA
24429006 TA-TTTATTA
1 TATTTTATTA
24429015 TTTATTTGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
10 7 0.20
11 19 0.54
12 9 0.26
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:24430355 original size:23 final size:22
Alignment explanation
Indices: 24430303--24430356 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
24430293 GATATGTTGA
* *
24430303 AGGGTATATTGGTTGTGTTTGG
1 AGGGTATATTGGTAGTGTTCGG
*
24430325 AGGGTATACTTGGTAGTGTTCGT
1 AGGGTATA-TTGGTAGTGTTCGG
*
24430348 AGGTTATAT
1 AGGGTATAT
24430357 ATATAGTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.43
Consensus pattern (22 bp):
AGGGTATATTGGTAGTGTTCGG
Found at i:24430407 original size:48 final size:46
Alignment explanation
Indices: 24430314--24430417 Score: 111
Period size: 48 Copynumber: 2.2 Consensus size: 46
24430304 GGGTATATTG
* * * *
24430314 GTTGTGTTTGGAGGGTATACTTGGTAGTGTTCGTAGGTTATATATATA
1 GTTGTGTTTGGAGGGTAAACTTGGTAGTGTTCCTAGG--GTACATATA
* * *
24430362 GTTGTGTTTGGAGGGTAAATTTTGTTGTG-TCCTAAGGGTACATATA
1 GTTGTGTTTGGAGGGTAAACTTGGTAGTGTTCCT-AGGGTACATATA
24430408 GTTGTGTTTG
1 GTTGTGTTTG
24430418 AAGGCTATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
46 17 0.35
47 3 0.06
48 28 0.58
ACGTcount: A:0.19, C:0.05, G:0.32, T:0.44
Consensus pattern (46 bp):
GTTGTGTTTGGAGGGTAAACTTGGTAGTGTTCCTAGGGTACATATA
Found at i:24430421 original size:23 final size:23
Alignment explanation
Indices: 24430357--24430421 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
24430347 TAGGTTATAT
*
24430357 ATATAGTTGTGTTTGGAGGGTAA
1 ATATAGTTGTGTTTGAAGGGTAA
* * * *
24430380 ATTTTGTTGTGTCCT-AAGGGTAC
1 ATATAGTTGTGT-TTGAAGGGTAA
24430403 ATATAGTTGTGTTTGAAGG
1 ATATAGTTGTGTTTGAAGG
24430422 CTATGATTGG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.31, T:0.42
Consensus pattern (23 bp):
ATATAGTTGTGTTTGAAGGGTAA
Found at i:24432678 original size:30 final size:30
Alignment explanation
Indices: 24432644--24432705 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
24432634 GCTACAATTA
* *
24432644 TGCACAAATAAAAGTGTTAAAGGGTAGCTT
1 TGCACAAATAAAAGTATTAAAGGGGAGCTT
*
24432674 TGCACAAATAAATGTATTAAAGGGGAGCTT
1 TGCACAAATAAAAGTATTAAAGGGGAGCTT
24432704 TG
1 TG
24432706 GTAGCCTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (30 bp):
TGCACAAATAAAAGTATTAAAGGGGAGCTT
Found at i:24433049 original size:23 final size:23
Alignment explanation
Indices: 24432981--24433076 Score: 104
Period size: 23 Copynumber: 4.1 Consensus size: 23
24432971 AGTGGATATG
*
24432981 TTGAAGGGTATAT-TGGTTGTGT
1 TTGAAGGGTAAATATGGTTGTGT
* *
24433003 TTGGAGGTTATATATATGGTTGTGT
1 TTGAAGGGTA-A-ATATGGTTGTGT
*
24433028 TTGAAGGGTAAATTTGGTTGTGT
1 TTGAAGGGTAAATATGGTTGTGT
** *
24433051 CCGAAGGGTACATATGGTTGTGT
1 TTGAAGGGTAAATATGGTTGTGT
24433074 TTG
1 TTG
24433077 GAGGCTATGA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
22 8 0.14
23 31 0.53
24 3 0.05
25 17 0.29
ACGTcount: A:0.20, C:0.03, G:0.34, T:0.43
Consensus pattern (23 bp):
TTGAAGGGTAAATATGGTTGTGT
Found at i:24443414 original size:23 final size:23
Alignment explanation
Indices: 24443381--24443870 Score: 301
Period size: 23 Copynumber: 21.0 Consensus size: 23
24443371 TGATGCTTAA
* *
24443381 ATGCTGCCCAATTTGTTGCATAT
1 ATGCTGTCCAATTTGTTGTATAT
* *
24443404 ATGCTGTCCAATTTTGATGCT-TAA
1 ATGCTGTCCAA-TTTGTTG-TATAT
*
24443428 ATGTTGTCCAATTTG-TGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* *
24443450 ATGCTGCCCAATTTGTTGCATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
24443473 AAGCTGTCCAATTTTGGTGCT-TAA
1 ATGCTGTCCAA-TTTGTTG-TATAT
*
24443497 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
24443520 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
* *
24443544 ATGCT-ACTCAAATTGTTGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * * *
24443567 ACGCTGCTCAAAATTGTTTTATAT
1 ATGCTG-TCCAATTTGTTGTATAT
* * *
24443591 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
*
24443615 ATGCTG-CTCAAATTGTTGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * * *
24443638 ATGCTGCCCAAATTGTTGAATTT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
24443661 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
* *
24443685 ATGCTGTTCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * * *
24443708 ATGCTGCCCAAATTCTTGAATTT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
24443731 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
* *
24443755 ATACTG-CTCAAATTGTTGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * *
24443778 ATGCTGCCCAAATTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* *
24443801 ATGCTGTCCAAATTTTGGTGTGA-AA
1 ATGCTGTCC-AA-TTTGTTGT-ATAT
* * * * *
24443826 ATACTGTCTAATTTGGTATATAA
1 ATGCTGTCCAATTTGTTGTATAT
* *
24443849 ATGCTGTCCAAATTGATGTATA
1 ATGCTGTCCAATTTGTTGTATA
24443871 AGAGCTATCC
Statistics
Matches: 356, Mismatches: 89, Indels: 44
0.73 0.18 0.09
Matches are distributed among these distances:
21 1 0.00
22 19 0.05
23 200 0.56
24 121 0.34
25 14 0.04
26 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (23 bp):
ATGCTGTCCAATTTGTTGTATAT
Found at i:24443546 original size:47 final size:47
Alignment explanation
Indices: 24443381--24443821 Score: 285
Period size: 47 Copynumber: 9.4 Consensus size: 47
24443371 TGATGCTTAA
* * * * * *
24443381 ATGCTGCCCAA-TTTGTTGCATATATGCTGTCCAATTTTGATGCT-TAA
1 ATGCTGTCCAATTTTGGTGTATATATGCTGCCCAA-TTTGTTG-TATAT
* *
24443428 ATGTTGTCCAA-TTT-GTGTATATATGCTGCCCAATTTGTTGCATAT
1 ATGCTGTCCAATTTTGGTGTATATATGCTGCCCAATTTGTTGTATAT
* *
24443473 AAGCTGTCCAATTTTGGTGCT-TAAATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTTGGTG-TATATATGCTGCCCAATTTGTTGTATAT
* * * * *
24443520 ATGCTGTCCAATTTTGGTGTAAAAATGCTACTCAAATTGTTGTATAT
1 ATGCTGTCCAATTTTGGTGTATATATGCTGCCCAATTTGTTGTATAT
* ** * * * * * *
24443567 ACGCTG-CTCAAAATTGTTTTATATATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTC-CAATTTTGGTGTATATATGCTGCCCAA-TTTGTTGTATAT
* * * * *
24443615 ATGCTG-CTCAA-ATTGTTGTATATATGCTGCCCAAATTGTTGAATTT
1 ATGCTGTC-CAATTTTGGTGTATATATGCTGCCCAATTTGTTGTATAT
* * ** *
24443661 ATGCTGTCCAATTTTGGTGTAAAAATGCTGTTCAAATTGTTGTATAT
1 ATGCTGTCCAATTTTGGTGTATATATGCTGCCCAATTTGTTGTATAT
* * * * * * * *
24443708 ATGCTGCCCAAATTCT--TGAATTTATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGTCC-AATTTTGGTGTATATATGCTGCCCAA-TTTGTTGTATAT
* * * * *
24443755 ATACTG-CTCAA-ATTGTTGTATATATGCTGCCCAAATTGTTGTATTT
1 ATGCTGTC-CAATTTTGGTGTATATATGCTGCCCAATTTGTTGTATAT
24443801 ATGCTGTCCAAATTTTGGTGT
1 ATGCTGTCC-AATTTTGGTGT
24443822 GAAAATACTG
Statistics
Matches: 304, Mismatches: 73, Indels: 33
0.74 0.18 0.08
Matches are distributed among these distances:
45 18 0.06
46 65 0.21
47 191 0.63
48 30 0.10
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (47 bp):
ATGCTGTCCAATTTTGGTGTATATATGCTGCCCAATTTGTTGTATAT
Found at i:24443573 original size:70 final size:70
Alignment explanation
Indices: 24443497--24443869 Score: 534
Period size: 70 Copynumber: 5.3 Consensus size: 70
24443487 TGGTGCTTAA
* * *
24443497 ATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGGTGTAAAAATGCTACTCAAATTGTTG
1 ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
24443562 TATAT
66 TATAT
* * * *
24443567 ACGCTGCTCAAAATTGTTTTATATATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTT
1 ATGCTGC-CCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTT
24443632 GTATAT
65 GTATAT
* *
24443638 ATGCTGCCCAAATTGTTGAATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGTTCAAATTGTTG
1 ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
24443703 TATAT
66 TATAT
* * *
24443708 ATGCTGCCCAAATTCTTGAATTTATGCTGTCCAATTTTGGTGTAAAAATACTGCTCAAATTGTTG
1 ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
24443773 TATAT
66 TATAT
* * * *
24443778 ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAAATTTTGGTGTGAAAATACTG-TCTAATT-TG
1 ATGCTGCCCAAATTGTTGTATTTATGCTGTCC-AATTTTGGTGTAAAAATGCTGCTCAAATTGTT
24443841 GTATAT
65 GTATAT
* *
24443847 AAATGCTGTCCAAATTGATGTAT
1 --ATGCTGCCCAAATTGTTGTAT
24443870 AAGAGCTATC
Statistics
Matches: 278, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
69 7 0.03
70 167 0.60
71 104 0.37
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (70 bp):
ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
TATAT
Found at i:24443595 original size:21 final size:22
Alignment explanation
Indices: 24443553--24443595 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
24443543 AATGCTACTC
24443553 AAATTGTTGTATATACGCTGCTCA
1 AAATTGTTGTATATA--CTGCTCA
*
24443577 AAATTGTTTTATATA-TGCT
1 AAATTGTTGTATATACTGCT
24443596 GTCCAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
24 14 0.78
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (22 bp):
AAATTGTTGTATATACTGCTCA
Found at i:24445481 original size:24 final size:25
Alignment explanation
Indices: 24445443--24445500 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
24445433 TAGCTCGAAA
* *
24445443 GAGCATCCCGTTA-TTAGCTCTCAT
1 GAGCATCCCGATATTTAGCTCTCAC
* *
24445467 GAGCATCCTGATATTTGGCTCTCAC
1 GAGCATCCCGATATTTAGCTCTCAC
*
24445492 GAGCTTCCC
1 GAGCATCCC
24445501 ATTGTATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (25 bp):
GAGCATCCCGATATTTAGCTCTCAC
Found at i:24454920 original size:22 final size:23
Alignment explanation
Indices: 24454877--24454920 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24454867 CGATTGGTCC
* *
24454877 TTTTCAAATTTTTGTGGGATTAT
1 TTTTAAAATTTTTGTGGAATTAT
24454900 TTTTAAAATTTTTGT-GAATTA
1 TTTTAAAATTTTTGTGGAATTA
24454921 ATATATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTTAAAATTTTTGTGGAATTAT
Found at i:24456000 original size:54 final size:55
Alignment explanation
Indices: 24455878--24456040 Score: 161
Period size: 54 Copynumber: 3.0 Consensus size: 55
24455868 TATGATATTC
*
24455878 TTAA-ACAGCTTATATAGCAATCTCAAGTGATAAAGCGTCCAAATGACGCTACAAA
1 TTAACACAGCTTATATAGCAATCTCAAGTGA-AAAGCGTCCAAACGACGCTACAAA
* * * * * * * *
24455933 CTATCATAGCTTATATGGCAATCTTAAGTG-AAAGCGTCCAAACGATGTTATAAA
1 TTAACACAGCTTATATAGCAATCTCAAGTGAAAAGCGTCCAAACGACGCTACAAA
* * * *
24455987 TTAACACATCTTATATTA-TAATCTCAAGTGATAAAGTGTCCAAATGACGCTACA
1 TTAACACAGCTTATA-TAGCAATCTCAAGTGA-AAAGCGTCCAAACGACGCTACA
24456041 CTCAAGTGAC
Statistics
Matches: 83, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
54 41 0.49
55 3 0.04
56 39 0.47
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28
Consensus pattern (55 bp):
TTAACACAGCTTATATAGCAATCTCAAGTGAAAAGCGTCCAAACGACGCTACAAA
Found at i:24456810 original size:22 final size:22
Alignment explanation
Indices: 24456775--24456822 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
24456765 TTAGCTGTTT
24456775 TTTCGATTATATA-TTTAATTA
1 TTTCGATTATATATTTTAATTA
24456796 GTTTCGCATTA-ATATTTTAATTA
1 -TTTCG-ATTATATATTTTAATTA
24456819 TTTC
1 TTTC
24456823 TACTATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTCGATTATATATTTTAATTA
Found at i:24475911 original size:38 final size:37
Alignment explanation
Indices: 24475842--24475920 Score: 99
Period size: 36 Copynumber: 2.1 Consensus size: 37
24475832 TTTTTTCTAG
*
24475842 AAAAGATATTTATATTAAATTTAAATTAATAT-TTTT
1 AAAAGATATTTATATAAAATTTAAATTAATATATTTT
*
24475878 AAAAGATCATTTATA-AAAATATTGAACTTAATATATTTT
1 AAAAGAT-ATTTATATAAAAT-TT-AAATTAATATATTTT
24475917 AAAA
1 AAAA
24475921 TTTAATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
36 11 0.30
37 9 0.24
38 9 0.24
39 8 0.22
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (37 bp):
AAAAGATATTTATATAAAATTTAAATTAATATATTTT
Found at i:24477999 original size:136 final size:136
Alignment explanation
Indices: 24477751--24478017 Score: 489
Period size: 136 Copynumber: 2.0 Consensus size: 136
24477741 TGGGCCCATC
*
24477751 ATCAGTGCCTACGCAAGAACGGTTGACATTTTGGTTTGTGACACAATTCTCTATCGGGTAAGAAC
1 ATCAGTGCCTACGCAAGAACGGTTGACATTTTGGTTTGTGACACAATTCTCTATCAGGTAAGAAC
*
24477816 TTAAACGGAGCAATCAATATAGACGGCCACTTACGTTTATCTAGGACTAGTGGGAATACGTGTCT
66 TTAAACGGAGCAATCAATATAGACGACCACTTACGTTTATCTAGGACTAGTGGGAATACGTGTCT
24477881 TCACAT
131 TCACAT
* *
24477887 ATCAGTGTCTACGCAAGAACGGTTGACCTTTTGGTTTGTGACACAATTCTCTATCAGGTAAGAAC
1 ATCAGTGCCTACGCAAGAACGGTTGACATTTTGGTTTGTGACACAATTCTCTATCAGGTAAGAAC
*
24477952 TTAAACGGAGCAATCAATATAGACGACCACTTACGTTTATCTGGGACTAGTGGGAATACGTGTCT
66 TTAAACGGAGCAATCAATATAGACGACCACTTACGTTTATCTAGGACTAGTGGGAATACGTGTCT
24478017 T
131 T
24478018 TACACATTGT
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 126 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (136 bp):
ATCAGTGCCTACGCAAGAACGGTTGACATTTTGGTTTGTGACACAATTCTCTATCAGGTAAGAAC
TTAAACGGAGCAATCAATATAGACGACCACTTACGTTTATCTAGGACTAGTGGGAATACGTGTCT
TCACAT
Found at i:24483505 original size:23 final size:22
Alignment explanation
Indices: 24483453--24483505 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
24483443 TCCACGTCTT
*
24483453 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
24483475 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
24483498 TTTCTTTT
1 TTTCTTTT
24483506 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:24486347 original size:32 final size:32
Alignment explanation
Indices: 24486308--24486374 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
24486298 TAGAAATTAA
24486308 TAAACACTTA-AAAATAAATAAAACCCTAAAC-C
1 TAAACACTTACAAAATAAA-AAAA-CCTAAACTC
*
24486340 TAAACACTTACAAATTAAAAAAACCTAAACTC
1 TAAACACTTACAAAATAAAAAAACCTAAACTC
24486372 TAA
1 TAA
24486375 TTTAAAATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.22
32 18 0.56
33 7 0.22
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (32 bp):
TAAACACTTACAAAATAAAAAAACCTAAACTC
Found at i:24488429 original size:13 final size:14
Alignment explanation
Indices: 24488411--24488439 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24488401 CACTAGTATG
24488411 TATTTTTTTA-ATT
1 TATTTTTTTATATT
24488424 TATTTTTTTATATT
1 TATTTTTTTATATT
24488438 TA
1 TA
24488440 AAATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTTTATATT
Found at i:24489170 original size:15 final size:15
Alignment explanation
Indices: 24489140--24489169 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
24489130 ATGTTTGAAA
24489140 TGTAAAATTATATTT
1 TGTAAAATTATATTT
24489155 TGTAAAA-TATATTT
1 TGTAAAATTATATTT
24489169 T
1 T
24489170 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TGTAAAATTATATTT
Found at i:24489316 original size:11 final size:10
Alignment explanation
Indices: 24489290--24489315 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
24489280 ACTGAGGACC
24489290 AAAAAATTAA
1 AAAAAATTAA
24489300 AAAAAATTAA
1 AAAAAATTAA
24489310 AAAAAA
1 AAAAAA
24489316 AATGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:24491769 original size:335 final size:335
Alignment explanation
Indices: 24491159--24491829 Score: 1324
Period size: 335 Copynumber: 2.0 Consensus size: 335
24491149 AGCAAGCCTT
24491159 ATTTTATATCTGGGTTCTTCAACTCCTGGAGTCTCTTCTTTCTTTTTACCTTTAGGAAGTTTCAC
1 ATTTTATATCTGGGTTCTTCAACTCCTGGAGTCTCTTCTTTCTTTTTACCTTTAGGAAGTTTCAC
24491224 AAGATCCCATGTTTTGTTTTTGTCGAGTGATTACATCTCCTCTTGCATAGCAAACATCCACTTTT
66 AAGATCCCATGTTTTGTTTTTGTCGAGTGATTACATCTCCTCTTGCATAGCAAACATCCACTTTT
24491289 CTGAGTCTTCACAGCTAGTCGAATCAGAATAATTAGATGGCTCTTGTTTTGCATCTATAACTTTA
131 CTGAGTCTTCACAGCTAGTCGAATCAGAATAATTAGATGGCTCTTGTTTTGCATCTATAACTTTA
24491354 GCCACATTTAAAGCATAAGCAACTAGATCAGCCTCGACATACTTCTTTGGAAGTTTAATTTCTTT
196 GCCACATTTAAAGCATAAGCAACTAGATCAGCCTCGACATACTTCTTTGGAAGTTTAATTTCTTT
24491419 TCTAATTCTATTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTTTGAACTTTTGTAC
261 TCTAATTCTATTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTTTGAACTTTTGTAC
24491484 TGGCTTGAGA
326 TGGCTTGAGA
24491494 ATTTTATATCTGGGTTCTTCAACTCCTGGAGTCTCTTCTTTCTTTTTACCTTTAGGAAGTTTCAC
1 ATTTTATATCTGGGTTCTTCAACTCCTGGAGTCTCTTCTTTCTTTTTACCTTTAGGAAGTTTCAC
*
24491559 AAGATCCCATGTTTTGTTTTTGTGGAGTGATTACATCTCCTCTTGCATAGCAAACATCCACTTTT
66 AAGATCCCATGTTTTGTTTTTGTCGAGTGATTACATCTCCTCTTGCATAGCAAACATCCACTTTT
*
24491624 CTGAGTCTTCACAGCTAGTTGAATCAGAATAATTAGATGGCTCTTGTTTTGCATCTATAACTTTA
131 CTGAGTCTTCACAGCTAGTCGAATCAGAATAATTAGATGGCTCTTGTTTTGCATCTATAACTTTA
24491689 GCCACATTTAAAGCATAAGCAACTAGATCAGCCTCGACATACTTCTTTGGAAGTTTAATTTCTTT
196 GCCACATTTAAAGCATAAGCAACTAGATCAGCCTCGACATACTTCTTTGGAAGTTTAATTTCTTT
24491754 TCTAATTCTATTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTTTGAACTTTTGTAC
261 TCTAATTCTATTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTTTGAACTTTTGTAC
24491819 TGGCTTGAGA
326 TGGCTTGAGA
24491829 A
1 A
24491830 GTAGACTCTG
Statistics
Matches: 334, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
335 334 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (335 bp):
ATTTTATATCTGGGTTCTTCAACTCCTGGAGTCTCTTCTTTCTTTTTACCTTTAGGAAGTTTCAC
AAGATCCCATGTTTTGTTTTTGTCGAGTGATTACATCTCCTCTTGCATAGCAAACATCCACTTTT
CTGAGTCTTCACAGCTAGTCGAATCAGAATAATTAGATGGCTCTTGTTTTGCATCTATAACTTTA
GCCACATTTAAAGCATAAGCAACTAGATCAGCCTCGACATACTTCTTTGGAAGTTTAATTTCTTT
TCTAATTCTATTTTTGGCGATAGAGTATTGTGGTGAAGAAGCAACTCTATTTTGAACTTTTGTAC
TGGCTTGAGA
Found at i:24500827 original size:20 final size:19
Alignment explanation
Indices: 24500787--24500841 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
24500777 ATAAATAAAC
* *
24500787 AAATATTATAAAACATTTA
1 AAATATTATAAAAAATATA
24500806 AAATATTATAAAAAATAATA
1 AAATATTATAAAAAAT-ATA
*
24500826 AACA-ATTAAAAAAAAT
1 AA-ATATTATAAAAAAT
24500842 TTCAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.48
20 15 0.48
21 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATATTATAAAAAATATA
Found at i:24500864 original size:79 final size:81
Alignment explanation
Indices: 24500768--24500921 Score: 260
Period size: 79 Copynumber: 1.9 Consensus size: 81
24500758 AATATAATTT
24500768 AAAAAATGTATAAATAAACAAATATTATAAAACATTTAAAATATTAT-AAA-AAATAA-TAAACA
1 AAAAAATGTATAAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAATAATTAAA-A
24500830 ATTAAAAAAAATTTCAA
65 ATTAAAAAAAATTTCAA
* *
24500847 AAAAAATGTTTGAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAATAATTAAAAA
1 AAAAAATGTATAAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAATAATTAAAAA
24500912 TTAAAAAAAA
66 TTAAAAAAAA
24500922 CAAATAATAC
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
79 45 0.64
80 3 0.04
81 18 0.26
82 4 0.06
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (81 bp):
AAAAAATGTATAAATAAACAAATATTATAAAACATTTAAAATATTATAAAACAAATAATTAAAAA
TTAAAAAAAATTTCAA
Found at i:24500921 original size:24 final size:25
Alignment explanation
Indices: 24500894--24500951 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
24500884 AAAATATTAT
24500894 AAAACAAATAATTA-A-AAATTAAA-A
1 AAAACAAATAA-TACACAAA-TAAAGA
24500918 AAAACAAATAATACACAAATAAAGA
1 AAAACAAATAATACACAAATAAAGA
24500943 AAAACAAAT
1 AAAACAAAT
24500952 CAAATAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 2 0.06
24 16 0.52
25 13 0.42
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAACAAATAATACACAAATAAAGA
Found at i:24500957 original size:27 final size:25
Alignment explanation
Indices: 24500894--24500974 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 25
24500884 AAAATATTAT
24500894 AAAACAAATAATTAA-A-AATTAAA-A
1 AAAACAAATAA-TAACAGAA-TAAAGA
24500918 AAAACAAATAATACACA-AATAAAGA
1 AAAACAAATAATA-ACAGAATAAAGA
*
24500943 AAAACAAATCAAATAACAGAAAAAAGA
1 AAAACAAAT--AATAACAGAATAAAGA
24500970 TAAAA
1 -AAAA
24500975 GGTAGCAGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
23 2 0.04
24 16 0.33
25 13 0.27
26 3 0.06
27 11 0.22
28 4 0.08
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.14
Consensus pattern (25 bp):
AAAACAAATAATAACAGAATAAAGA
Found at i:24501761 original size:20 final size:20
Alignment explanation
Indices: 24501717--24501765 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
24501707 TTAATGGACT
*
24501717 TTTTATTTGTGTTTTATTTTA
1 TTTTATTT-TGTTCTATTTTA
24501738 -TTTATTTTGTTCT-TTTTA
1 TTTTATTTTGTTCTATTTTA
24501756 GTTTTATTTT
1 -TTTTATTTT
24501766 ATTTGAGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.20
19 5 0.20
20 15 0.60
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (20 bp):
TTTTATTTTGTTCTATTTTA
Found at i:24510676 original size:23 final size:22
Alignment explanation
Indices: 24510624--24510676 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
24510614 TCCACGTCTT
*
24510624 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
24510646 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
24510669 TTTCTTTT
1 TTTCTTTT
24510677 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:24516869 original size:28 final size:28
Alignment explanation
Indices: 24516833--24516908 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
24516823 AACACTAACA
*
24516833 AACAACAAAATTTTAAAA-AAACGACAAC
1 AACAGCAAAA-TTTAAAATAAACGACAAC
* * *
24516861 AACAGC-AAATTCAAAATAAATGATAAC
1 AACAGCAAAATTTAAAATAAACGACAAC
*
24516888 ACCAGCAAAATTTAAAATAAA
1 AACAGCAAAATTTAAAATAAA
24516909 GGATACACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 6 0.15
27 16 0.40
28 18 0.45
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (28 bp):
AACAGCAAAATTTAAAATAAACGACAAC
Found at i:24516916 original size:27 final size:28
Alignment explanation
Indices: 24516838--24516929 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 28
24516828 TAACAAACAA
* * *
24516838 CAAAATTTTAAAA-AAACGACAACAACAG
1 CAAAA-TTTAAAATAAAGGATAACACCAG
* *
24516866 C-AAATTCAAAATAAATGATAACACCAG
1 CAAAATTTAAAATAAAGGATAACACCAG
**
24516893 CAAAATTTAAAATAAAGGAT-ACACTTG
1 CAAAATTTAAAATAAAGGATAACACCAG
24516920 -AAAATTTAAA
1 CAAAATTTAAA
24516930 CACATGCTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
26 16 0.30
27 21 0.39
28 17 0.31
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.21
Consensus pattern (28 bp):
CAAAATTTAAAATAAAGGATAACACCAG
Found at i:24536642 original size:24 final size:24
Alignment explanation
Indices: 24536614--24536665 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
24536604 TTCAAGATGA
24536614 TTAAAAACATTTTCAATCATCATC
1 TTAAAAACATTTTCAATCATCATC
24536638 TTAAAAACATTTTCAATCATCATC
1 TTAAAAACATTTTCAATCATCATC
24536662 TTAA
1 TTAA
24536666 GTTTATAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAAACATTTTCAATCATCATC
Found at i:24538722 original size:23 final size:23
Alignment explanation
Indices: 24538696--24538739 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
24538686 TAAAAACATC
* * *
24538696 GAAGTGCTATTAATAGAAGTATT
1 GAAGTACTAATAACAGAAGTATT
24538719 GAAGTACTAATAACAGAAGTA
1 GAAGTACTAATAACAGAAGTA
24538740 CATAAGTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.27
Consensus pattern (23 bp):
GAAGTACTAATAACAGAAGTATT
Found at i:24553973 original size:27 final size:27
Alignment explanation
Indices: 24553897--24553967 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
24553887 AATACCCTAA
* **
24553897 AATAGA-TAAAATAACCAAAATACCCC
1 AATAGAGTAAAATGACTGAAATACCCC
24553923 AATAGAGTAAAATGACTGAAATACTCCC
1 AATAGAGTAAAATGACTGAAATAC-CCC
*
24553951 -ATAGGGTAAAATGACTG
1 AATAGAGTAAAATGACTG
24553968 TTATACCCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 6 0.15
27 30 0.77
28 3 0.08
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (27 bp):
AATAGAGTAAAATGACTGAAATACCCC
Found at i:24554399 original size:29 final size:32
Alignment explanation
Indices: 24554366--24554425 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 32
24554356 TCTCTGTACT
*
24554366 GATTAATGAT-TT-TGTACTGTT-ACTGCATC
1 GATTAATGATATTACGTACTGTTCACTGCATC
24554395 GATTAATGATATTACGTACTGTTCACTGCAT
1 GATTAATGATATTACGTACTGTTCACTGCAT
24554426 GACTGATATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.37
30 2 0.07
31 8 0.30
32 7 0.26
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
GATTAATGATATTACGTACTGTTCACTGCATC
Found at i:24558826 original size:21 final size:21
Alignment explanation
Indices: 24558800--24558882 Score: 94
Period size: 21 Copynumber: 3.8 Consensus size: 21
24558790 TTAAGAGAAC
24558800 AAAACAACGAAAAATAAAGAG
1 AAAACAACGAAAAATAAAGAG
* * *
24558821 AAAACAAGGAAAAATACTTGCAGAC
1 AAAACAACGAAAAATA----AAGAG
24558846 AAAACAACGAAAAATAAAGAG
1 AAAACAACGAAAAATAAAGAG
*
24558867 AAAACAAGGAAAAATA
1 AAAACAACGAAAAATA
24558883 CTTAGCAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 33 0.65
25 18 0.35
ACGTcount: A:0.67, C:0.11, G:0.14, T:0.07
Consensus pattern (21 bp):
AAAACAACGAAAAATAAAGAG
Found at i:24558850 original size:25 final size:25
Alignment explanation
Indices: 24558821--24558891 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 25
24558811 AAATAAAGAG
24558821 AAAACAAGGAAAAATACTTGCAGAC
1 AAAACAAGGAAAAATACTTGCAGAC
* * *
24558846 AAAACAACGAAAAATA----AAGAG
1 AAAACAAGGAAAAATACTTGCAGAC
24558867 AAAACAAGGAAAAATACTTAGCAGA
1 AAAACAAGGAAAAATACTT-GCAGA
24558892 TTTTTAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
21 18 0.50
25 15 0.42
26 3 0.08
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (25 bp):
AAAACAAGGAAAAATACTTGCAGAC
Found at i:24558865 original size:46 final size:47
Alignment explanation
Indices: 24558798--24558891 Score: 181
Period size: 46 Copynumber: 2.0 Consensus size: 47
24558788 AGTTAAGAGA
24558798 ACAAAACAACGAAAAATAAAGAGAAAACAAGGAAAAATACTT-GCAG
1 ACAAAACAACGAAAAATAAAGAGAAAACAAGGAAAAATACTTAGCAG
24558844 ACAAAACAACGAAAAATAAAGAGAAAACAAGGAAAAATACTTAGCAG
1 ACAAAACAACGAAAAATAAAGAGAAAACAAGGAAAAATACTTAGCAG
24558891 A
1 A
24558892 TTTTTAACTA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 42 0.89
47 5 0.11
ACGTcount: A:0.64, C:0.13, G:0.15, T:0.09
Consensus pattern (47 bp):
ACAAAACAACGAAAAATAAAGAGAAAACAAGGAAAAATACTTAGCAG
Found at i:24579243 original size:36 final size:36
Alignment explanation
Indices: 24579196--24579269 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
24579186 AAGTCCAGAG
24579196 TTTGTTTGTACGACCTCTTCAGTGTTTATGCTTCAC
1 TTTGTTTGTACGACCTCTTCAGTGTTTATGCTTCAC
24579232 TTTGTTTGTACGACCTCTTCAGTGTTTATGCTTCAC
1 TTTGTTTGTACGACCTCTTCAGTGTTTATGCTTCAC
24579268 TT
1 TT
24579270 GGATCTTGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (36 bp):
TTTGTTTGTACGACCTCTTCAGTGTTTATGCTTCAC
Found at i:24582831 original size:35 final size:35
Alignment explanation
Indices: 24582750--24582856 Score: 115
Period size: 35 Copynumber: 3.1 Consensus size: 35
24582740 AAACACATCA
* * * *
24582750 AATGCTCACAAGAGCTAGTCCAACTGTAGCACCCC
1 AATGCTCATAAGAGCTAGTCCAACCGAAACACCCC
* * * **
24582785 TATACTTATAAGAGCTAGTCCAACCGAAACAGGCC
1 AATGCTCATAAGAGCTAGTCCAACCGAAACACCCC
* *
24582820 AATGCTCATAAGAGCTAGTCCAACCAAAACACACC
1 AATGCTCATAAGAGCTAGTCCAACCGAAACACCCC
24582855 AA
1 AA
24582857 ACAGAGAGTA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.38, C:0.30, G:0.15, T:0.17
Consensus pattern (35 bp):
AATGCTCATAAGAGCTAGTCCAACCGAAACACCCC
Found at i:24588427 original size:15 final size:15
Alignment explanation
Indices: 24588402--24588442 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
24588392 TAAATTTAGT
* *
24588402 ACTTAAATTTTCAAT
1 ACTTAATTTTTCAAC
*
24588417 ATTTAATTTTTCAAC
1 ACTTAATTTTTCAAC
24588432 ACTTAATTTTT
1 ACTTAATTTTT
24588443 TTAGTTTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (15 bp):
ACTTAATTTTTCAAC
Found at i:24588976 original size:25 final size:25
Alignment explanation
Indices: 24588922--24588976 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
24588912 CTTAAGGGAT
* *
24588922 GTTTTCTCGAGTCCTTGGTAGTCCA
1 GTTTTCTCGAGTCCGTAGTAGTCCA
* *
24588947 ATTTTCTCGAGTTCGTAGTGAGT-CA
1 GTTTTCTCGAGTCCGTAGT-AGTCCA
24588972 GTTTT
1 GTTTT
24588977 ATCAAGTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (25 bp):
GTTTTCTCGAGTCCGTAGTAGTCCA
Found at i:24591329 original size:87 final size:86
Alignment explanation
Indices: 24591218--24591384 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 86
24591208 TTGTTTATTA
* * * * * *
24591218 TTTTTTTGCACTCATTTGGGTACTTGAACTTCCAAAATGTACCAAAAA-GGCCATCAAACCTTTA
1 TTTTTTTACACTCAATTGGATACTTGAACTTCCAAAATGCACAAAAAATAGCC-TCAAA-CTTTA
24591282 AAAAAAAGCAATTAAGCCCCTAC
64 AAAAAAAGCAATTAAGCCCCTAC
* * * * *
24591305 TTTTTTTACACTCAATTGGATACTTTAACTTTCGAAATGCATAAAAAATATCCTCAAACTTTAAA
1 TTTTTTTACACTCAATTGGATACTTGAACTTCCAAAATGCACAAAAAATAGCCTCAAACTTTAAA
24591370 AAAAAGCAATTAAGC
66 AAAAAGCAATTAAGC
24591385 TCATGCTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
86 22 0.32
87 44 0.65
88 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (86 bp):
TTTTTTTACACTCAATTGGATACTTGAACTTCCAAAATGCACAAAAAATAGCCTCAAACTTTAAA
AAAAAGCAATTAAGCCCCTAC
Found at i:24591421 original size:9 final size:9
Alignment explanation
Indices: 24591409--24591569 Score: 71
Period size: 9 Copynumber: 17.4 Consensus size: 9
24591399 AAAATTAGAA
24591409 AAAAATTAT
1 AAAAATTAT
24591418 AAAAA--AT
1 AAAAATTAT
* *
24591425 TAAAATCAAT
1 AAAAAT-TAT
24591435 AAAAGA-TAT
1 AAAA-ATTAT
*
24591444 AAATATTATT
1 AAAAATTA-T
**
24591454 AAATTTTAAT
1 AAAAATT-AT
**
24591464 AAAAAAAAT
1 AAAAATTAT
*
24591473 AAAAAATAT
1 AAAAATTAT
24591482 AAAAA-TAT
1 AAAAATTAT
*
24591490 AAAAAATAT
1 AAAAATTAT
**
24591499 AAAAATCGT
1 AAAAATTAT
*
24591508 AAAAAATAT
1 AAAAATTAT
*
24591517 AAAAAATTGT
1 -AAAAATTAT
24591527 AAAATATTAT
1 AAAA-ATTAT
24591537 -AAAATATAT
1 AAAAAT-TAT
* *
24591546 AGAAATATAA
1 AAAAAT-TAT
24591556 AAGAAATTAT
1 AA-AAATTAT
24591566 AAAA
1 AAAA
24591570 TTTTATAAAG
Statistics
Matches: 116, Mismatches: 23, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
7 6 0.05
8 11 0.09
9 54 0.47
10 39 0.34
11 6 0.05
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:24591421 original size:10 final size:10
Alignment explanation
Indices: 24591393--24591569 Score: 69
Period size: 10 Copynumber: 18.8 Consensus size: 10
24591383 GCTCATGCTT
*
24591393 TTATTAAAAA
1 TTATAAAAAA
*
24591403 TTAGAAAAAAA
1 TTA-TAAAAAA
24591414 TTATAAAAAA
1 TTATAAAAAA
**
24591424 TTA-AAATCA
1 TTATAAAAAA
*
24591433 --ATAAAAGA
1 TTATAAAAAA
*
24591441 -TAT-AAATA
1 TTATAAAAAA
* **
24591449 TTATTAAATT
1 TTATAAAAAA
24591459 TTAATAAAAAA
1 TT-ATAAAAAA
*
24591470 -AATAAAAAA
1 TTATAAAAAA
24591479 -TAT-AAAAA
1 TTATAAAAAA
24591487 -TATAAAAAA
1 TTATAAAAAA
24591496 -TAT-AAAAA
1 TTATAAAAAA
**
24591504 TCGTAAAAAA
1 TTATAAAAAA
24591514 -TATAAAAAA
1 TTATAAAAAA
* *
24591523 TTGTAAAATA
1 TTATAAAAAA
*
24591533 TTATAAAATA
1 TTATAAAAAA
*
24591543 -TAT-AGAAA
1 TTATAAAAAA
24591551 -TATAAAAGAAA
1 TTAT-AAA-AAA
24591562 TTATAAAA
1 TTATAAAA
24591570 TTTTATAAAG
Statistics
Matches: 129, Mismatches: 24, Indels: 28
0.71 0.13 0.15
Matches are distributed among these distances:
7 1 0.01
8 27 0.21
9 38 0.29
10 41 0.32
11 19 0.15
12 3 0.02
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:24591478 original size:8 final size:9
Alignment explanation
Indices: 24591462--24591557 Score: 90
Period size: 9 Copynumber: 10.7 Consensus size: 9
24591452 TTAAATTTTA
*
24591462 ATAAAAAAA
1 ATAAAAAAT
24591471 ATAAAAAAT
1 ATAAAAAAT
24591480 AT-AAAAAT
1 ATAAAAAAT
24591488 ATAAAAAAT
1 ATAAAAAAT
24591497 AT-AAAAAT
1 ATAAAAAAT
*
24591505 CGTAAAAAAT
1 -ATAAAAAAT
24591515 ATAAAAAAT
1 ATAAAAAAT
**
24591524 -TGTAAAAT
1 ATAAAAAAT
*
24591532 ATTATAAAAT
1 A-TAAAAAAT
*
24591542 ATATAGAAAT
1 ATA-AAAAAT
24591552 ATAAAA
1 ATAAAA
24591558 GAAATTATAA
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
8 20 0.28
9 31 0.43
10 21 0.29
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:24591491 original size:17 final size:17
Alignment explanation
Indices: 24591461--24591557 Score: 90
Period size: 17 Copynumber: 5.5 Consensus size: 17
24591451 ATTAAATTTT
*
24591461 AATA-AAAAAAATAAAA
1 AATATAAAAATATAAAA
24591477 AATATAAAAATATAAAA
1 AATATAAAAATATAAAA
*
24591494 AATATAAAAATCGTAAAA
1 AATATAAAAAT-ATAAAA
**
24591512 AATATAAAAA-ATTGTAA
1 AATATAAAAATA-TAAAA
*
24591529 AATATTATAAAATATATAGA
1 AATA-TA-AAAATATA-AAA
24591549 AATATAAAA
1 AATATAAAA
24591558 GAAATTATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
16 4 0.06
17 29 0.44
18 20 0.30
19 7 0.11
20 6 0.09
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (17 bp):
AATATAAAAATATAAAA
Found at i:24591589 original size:39 final size:37
Alignment explanation
Indices: 24591476--24591589 Score: 110
Period size: 39 Copynumber: 3.1 Consensus size: 37
24591466 AAAAAATAAA
* *
24591476 AAATAT-AAAAA-TATAAAA-AATATAAAAATCGTAAA
1 AAATATAAAAAATTATAAAATATTAT-AAAATCGTAAG
* *
24591511 AAATATAAAAAATTGTAAAATATTATAAAAT-ATATAG
1 AAATATAAAAAATTATAAAATATTATAAAATCGTA-AG
* *
24591548 AAATATAAAAGAAATTATAAAATTTTATAAAGTCGTAAG
1 AAATAT-AAA-AAATTATAAAATATTATAAAATCGTAAG
24591587 AAA
1 AAA
24591590 ATTATACAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
35 6 0.09
36 7 0.11
37 18 0.28
38 7 0.11
39 24 0.38
40 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (37 bp):
AAATATAAAAAATTATAAAATATTATAAAATCGTAAG
Found at i:24591826 original size:26 final size:25
Alignment explanation
Indices: 24591789--24591839 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
24591779 TTCTTTTATG
*
24591789 ATTTTTATAAAATTTTATAATTTTT
1 ATTTTTATAAAATTTAATAATTTTT
24591814 ATTTTTATTAAAATTTAATAATTTTT
1 ATTTTTA-TAAAATTTAATAATTTTT
24591840 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTTTATAAAATTTAATAATTTTT
Found at i:24592021 original size:87 final size:87
Alignment explanation
Indices: 24591872--24592082 Score: 300
Period size: 87 Copynumber: 2.4 Consensus size: 87
24591862 TTTTAATAAG
* * * * *
24591872 AGCAGGGGCTTAATTGCATTTTTGAAAAATTTTGGGGGTCTTTTTGATGTATTTTGACAGTTCAA
1 AGCAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAA
24591937 GTACCCAATTGAGTG-AAAAAA
66 GTACCCAATTGAGTGAAAAAAA
*
24591958 AGCAGGGGCTTAATTGCTTTTTCTGAAGAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA
1 AGCAGGGGCTTAATTGCTTTTT-TGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA
* *
24592023 AGTGCTCAATTGAGTGAAAAAAA
65 AGTACCCAATTGAGTGAAAAAAA
* *
24592046 AG-AGGGGCTTAATTACTTTTTTAAAAAAAGTTTGAGG
1 AGCAGGGGCTTAATTGCTTTTTT-GAAAAAGTTTGAGG
24592083 ACTTTTTACA
Statistics
Matches: 111, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
86 22 0.20
87 81 0.73
88 8 0.07
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (87 bp):
AGCAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAA
GTACCCAATTGAGTGAAAAAAA
Found at i:24607586 original size:13 final size:13
Alignment explanation
Indices: 24607532--24607579 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
24607522 CCTTAAGAAT
24607532 TAAGTAAATATATA
1 TAAGTAAATATA-A
*
24607546 TAA-TATA-ATAA
1 TAAGTAAATATAA
24607557 TAAAGTAAATATAA
1 T-AAGTAAATATAA
24607571 TAAGTAAAT
1 TAAGTAAAT
24607580 GAAATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 2 0.07
12 5 0.17
13 14 0.48
14 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (13 bp):
TAAGTAAATATAA
Found at i:24607636 original size:30 final size:30
Alignment explanation
Indices: 24607576--24607638 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
24607566 TATAATAAGT
* * *
24607576 AAATGAAATAAAAAGGGAAAGAAAGGAAGA
1 AAATGAAACAAAAAGGAAAAGAAAGAAAGA
24607606 AAATGAAACAAAAAGGAAAAGGAAA-AAAGA
1 AAATGAAACAAAAAGGAAAA-GAAAGAAAGA
24607636 AAA
1 AAA
24607639 AAAGAAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (30 bp):
AAATGAAACAAAAAGGAAAAGAAAGAAAGA
Found at i:24608604 original size:40 final size:40
Alignment explanation
Indices: 24608479--24608614 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 40
24608469 AACTTCGAGT
* *
24608479 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATT-ATC
* * * * *
24608520 CGGTGAGGCACTGGGTTGCCAA--T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGG-TGTCAATTTATTACTTCGGATTATC
* *
24608558 CGATGAGACACTAGGTGTCAATTTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTATC
* *
24608598 CAATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
24608615 CCAAACTGGT
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 5 0.07
38 13 0.18
39 11 0.15
40 27 0.36
41 13 0.18
42 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTATTACTTCGGATTATC
Found at i:24608904 original size:31 final size:33
Alignment explanation
Indices: 24608869--24608936 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
24608859 CAACTGATGA
* *
24608869 GAATTGAATATTGGATGAATGATGT-ATT-TAT
1 GAATTGAATATTGAATGAATAATGTCATTGTAT
*
24608900 GAATTGAATATTGAATGACTAATGTCATTGTAT
1 GAATTGAATATTGAATGAATAATGTCATTGTAT
24608933 GAAT
1 GAAT
24608937 AAATGTGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 22 0.69
32 3 0.09
33 7 0.22
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.40
Consensus pattern (33 bp):
GAATTGAATATTGAATGAATAATGTCATTGTAT
Found at i:24612416 original size:20 final size:20
Alignment explanation
Indices: 24612391--24612430 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
24612381 CCTTCTTGCT
24612391 CTTTAGAACTAAGATTTCTC
1 CTTTAGAACTAAGATTTCTC
24612411 CTTTAGAACTAAGATTTCTC
1 CTTTAGAACTAAGATTTCTC
24612431 ATTCTTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (20 bp):
CTTTAGAACTAAGATTTCTC
Found at i:24615405 original size:17 final size:17
Alignment explanation
Indices: 24615359--24615406 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
24615349 TCAACCTTTC
*
24615359 ACCTTTCATCTCCCTTA
1 ACCTTTCATCTTCCTTA
*
24615376 ATCTTTCATCTTCCTTA
1 ACCTTTCATCTTCCTTA
*
24615393 ACCTTTCACCTTCC
1 ACCTTTCATCTTCC
24615407 ATTTTCTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.17, C:0.40, G:0.00, T:0.44
Consensus pattern (17 bp):
ACCTTTCATCTTCCTTA
Found at i:24623404 original size:31 final size:31
Alignment explanation
Indices: 24623336--24623404 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
24623326 CATTTTGATA
* *
24623336 AGTCATCGTTGTCGAACAACCCAGGGTGGCG
1 AGTCATCATTGTCGAACAACCCAAGGTGGCG
* ** *
24623367 ACTCATCATTGTCGGGCAACCCAAGGTGGTG
1 AGTCATCATTGTCGAACAACCCAAGGTGGCG
*
24623398 GGTCATC
1 AGTCATC
24623405 GTTGCTGAGC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (31 bp):
AGTCATCATTGTCGAACAACCCAAGGTGGCG
Found at i:24624606 original size:16 final size:16
Alignment explanation
Indices: 24624587--24624620 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
24624577 GTAGACCATG
*
24624587 AAACTTTAGATTCTGA
1 AAACTGTAGATTCTGA
*
24624603 AAACTGTAGATTTTGA
1 AAACTGTAGATTCTGA
24624619 AA
1 AA
24624621 CTATAGTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (16 bp):
AAACTGTAGATTCTGA
Done.