Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 140 of 230
Found at i:41211675 original size:29 final size:28
Alignment explanation
Indices: 41211595--41211676 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 28
41211585 GCGGAAAAGG
* *
41211595 TAAGTGTGCGAACTTGAAATGCATGGCAC
1 TAAGTGTGCGAAC-TCAAATACATGGCAC
* ** *
41211624 TAAGTGTGTGAGTTTAAAGTACATGGCAC
1 TAAGTGTGCGAACTCAAA-TACATGGCAC
41211653 TAAGTGTGCGAACTCAATATACAT
1 TAAGTGTGCGAACTCAA-ATACAT
41211677 TTTCTATAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
28 4 0.10
29 37 0.88
30 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (28 bp):
TAAGTGTGCGAACTCAAATACATGGCAC
Found at i:41219056 original size:29 final size:28
Alignment explanation
Indices: 41219008--41219080 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
41218998 TCATGAGATT
* *
41219008 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCAATAAGTGTGCGAGTTTAAA--GTACA
41219038 -GCAATAAGTGTGCGAGTTTAAAGTACA
1 GGCAATAAGTGTGCGAGTTTAAAGTACA
*
41219065 TGGCACTAAGTGTGCG
1 -GGCAATAAGTGTGCG
41219081 CGGTTGATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 5 0.13
29 33 0.87
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (28 bp):
GGCAATAAGTGTGCGAGTTTAAAGTACA
Found at i:41219303 original size:174 final size:174
Alignment explanation
Indices: 41219042--41219539 Score: 924
Period size: 174 Copynumber: 2.9 Consensus size: 174
41219032 TGTACAGCAA
*
41219042 TAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTG
1 TAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTG
41219107 CGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATTTT
66 CGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATTTT
*
41219172 GGATAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGCAC
131 GGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGCAC
* *
41219216 TAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTGAGCACTATGTGTG
1 TAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTG
41219281 CGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATTTT
66 CGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATTTT
41219346 GGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGCAC
131 GGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGCAC
*
41219390 TAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGCG
1 TAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTG
* * *
41219455 CGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAATTTT
66 CGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATTTT
41219520 GGACAGCGGAAAAGGTAAGT
131 GGACAGCGGAAAAGGTAAGT
41219540 ACCTTGAGTT
Statistics
Matches: 314, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 314 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
TAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTG
CGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATTTT
GGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGCAC
Found at i:41221061 original size:28 final size:28
Alignment explanation
Indices: 41221030--41221083 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
41221020 TTGTCTTTTT
* *
41221030 TTATAATAA-GTTTATAATATACTATATA
1 TTATAATAACCTTTATAA-ATAATATATA
*
41221058 TTATTATAACCTTTATAAATAATATA
1 TTATAATAACCTTTATAAATAATATA
41221084 AAAACTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (28 bp):
TTATAATAACCTTTATAAATAATATATA
Found at i:41229789 original size:28 final size:28
Alignment explanation
Indices: 41229699--41229848 Score: 223
Period size: 27 Copynumber: 5.4 Consensus size: 28
41229689 ATATTAAGTC
*
41229699 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41229726 CGCACACTTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41229753 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41229781 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41229809 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41229838 CGCACACTTAG
1 CGCACACTTAG
41229849 CGCCAATCTC
Statistics
Matches: 114, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 49 0.43
28 49 0.43
29 16 0.14
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41229802 original size:55 final size:56
Alignment explanation
Indices: 41229699--41229848 Score: 223
Period size: 55 Copynumber: 2.7 Consensus size: 56
41229689 ATATTAAGTC
* *
41229699 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
41229753 CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
* * * *
41229809 CGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTAG
1 CGCACACTTAGTGCTATATAA-TCAAACTCGCACACTTAG
41229849 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 22 0.25
55 26 0.30
56 23 0.26
57 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (56 bp):
CGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:41238754 original size:43 final size:43
Alignment explanation
Indices: 41238707--41238817 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
41238697 AAAAGTTAGT
* * * * *
41238707 AGAATGCCATAAAGGGCATATCAGAATTACCACAGAGGATAAC
1 AGAATGCCACAAAGGGCATATCAAAAATACCACAAACGATAAC
* * *
41238750 AGAATGCCACAAAGGTCATAT-AAAAATACCACAAACGCTAAG
1 AGAATGCCACAAAGGGCATATCAAAAATACCACAAACGATAAC
41238792 AGAATGCCACAAA-GGCAATATCAAAA
1 AGAATGCCACAAAGGGC-ATATCAAAA
41238818 TACACCATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.04
42 32 0.56
43 23 0.40
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (43 bp):
AGAATGCCACAAAGGGCATATCAAAAATACCACAAACGATAAC
Found at i:41243246 original size:17 final size:18
Alignment explanation
Indices: 41243213--41243247 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41243203 CAGCGAAAGT
*
41243213 AAACTTTTTTCCTTTTCC
1 AAACTTTATTCCTTTTCC
41243231 AAACTTTATT-CTTTTCC
1 AAACTTTATTCCTTTTCC
41243248 TTTCTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.26, G:0.00, T:0.54
Consensus pattern (18 bp):
AAACTTTATTCCTTTTCC
Found at i:41247406 original size:25 final size:26
Alignment explanation
Indices: 41247378--41247442 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 26
41247368 TGTAGATTGG
41247378 TATGCTCTCATGAGCC-ATAAATCGA
1 TATGCTCTCATGAGCCTATAAATCGA
* *
41247403 TATGCTCTCAGGA-CCTATAAATCGG
1 TATGCTCTCATGAGCCTATAAATCGA
41247428 TATGCTCTCATGAGC
1 TATGCTCTCATGAGC
41247443 TTTGGGTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.06
25 32 0.91
26 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (26 bp):
TATGCTCTCATGAGCCTATAAATCGA
Found at i:41256127 original size:25 final size:25
Alignment explanation
Indices: 41256098--41256188 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
41256088 CGGATACACC
*
41256098 ACAGCTCGT-ATGAGCTTACTGATTT
1 ACAGCTCGTGA-GAGCATACTGATTT
* *
41256123 ACAGCTTGTGAGAGCATATTGATTT
1 ACAGCTCGTGAGAGCATACTGATTT
* * *
41256148 ACAGCTCAAGAGAGAACATACTAATTT
1 ACAGCTC--GTGAGAGCATACTGATTT
* *
41256175 ACAACTCGAGAGAG
1 ACAGCTCGTGAGAG
41256189 AGCATACCAA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
25 32 0.60
26 1 0.02
27 20 0.38
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACTGATTT
Found at i:41256174 original size:27 final size:27
Alignment explanation
Indices: 41256144--41256207 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
41256134 GAGCATATTG
*
41256144 ATTTACAGCTCAAGAGAGAACATACTA
1 ATTTACAGCTCAAGAGAGAACATACCA
* * *
41256171 ATTTACAACTCGAGAGAGAGCATACCA
1 ATTTACAGCTCAAGAGAGAACATACCA
*
41256198 ATTCACAGCT
1 ATTTACAGCT
41256208 TGTATGAGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
ATTTACAGCTCAAGAGAGAACATACCA
Found at i:41258495 original size:26 final size:26
Alignment explanation
Indices: 41258464--41258521 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
41258454 AACTTGTACT
*
41258464 TAAATTATTAACATATTTAATTTTAA
1 TAAATTATTAACATATTGAATTTTAA
41258490 TAAATTATTAACATATTGAATTTTAA
1 TAAATTATTAACATATTGAATTTTAA
*
41258516 TTAATT
1 TAAATT
41258522 TTGTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (26 bp):
TAAATTATTAACATATTGAATTTTAA
Found at i:41262092 original size:951 final size:953
Alignment explanation
Indices: 41260187--41262095 Score: 2564
Period size: 967 Copynumber: 2.0 Consensus size: 953
41260177 CATCATTCCA
* *
41260187 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTTTTTAGTTTTCTTTCTTTCATCCCATGTGTG
1 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCATGTGTG
* * * * * * * * *
41260252 CCGCCCCCCAAGCCACCAAGATTTACCATTAATTTCTCTTCTTTTTGCAATGGGTTCTTGAGCCA
66 CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
* * ** * * * *
41260317 TTCTTTTCCTCTTCTTTTTTTCATTTAATCATAATATTTCTAGCCTTAAATTTGAGATTTAACCA
131 TTATTTCCCTCTTCTTGCTTTCATTTAATCATAAAATTTCAAGCCTTAAATATGAAATTTAACCA
* * * *
41260382 CTCAATATCGGCCTCCAATGATTCCCCAAAAGAACTACATTGCTGCACCTATCTTCTTGCTTGAG
196 CTCAAGATCGGCCTCCAATGATGCCCCAAAAGAACTACATTCCCGCACCTATCTTCTTGCTTGAG
** * *
41260447 TAAGTGCCATTTTCTTGGGTTTTTCTTGATGGATCTTTCAATAAAATACCAAGTTTTCTAGATCC
261 TAAGTGCCATTTTCTTGCATTTTTCTTGATGGATCTTTAAATAAAATACAAAGTTTTCTAGATCC
41260512 AAAATTGGGGTAATATTTTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGT
326 ------------ATA--TTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGT
* * ** *
41260577 GGTTTTGAATCAGCCCCAATTTCACCACCGTTGGTGGTGGTGCATCGTGCCTAGAGGCAAAAATG
377 GGTTATGAATCAGCCCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATA
** ** * * * *
41260642 GGGGTTGTTGTTTCTTTAGTTTTTCTCATATATTTCCAGCAATAACTTTGCTTCCTGAACTCTTC
442 GGGGTTACTGTTTCTTTAAATTTTCTCATATATTTCCAGAAATAACTTTCCTTCCTCAACCCTTC
* *** *
41260707 CTAATCAGCCTTTAATAATGTGTAAACTAGGAAAAATCAAACTTGGACAATCGGTAACTCAGATC
507 CTAATCAGCCTTTAATAATGTGTAAACTAGGAAAAAGCAAACTTGGACAATCAACAACTCAAATC
* * * *
41260772 TGACAATTCGGGAATCGTAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTGAGTTTTGATGTTG
572 TGAAAATTCGGGAAGCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTTG
**
41260837 GGAAATTGTTAATTGATTGAATTAATGATTTTTAAGATGGAATAGCTACTAGTTTTTCAGTATTT
637 GGAAATTGTTAATTGAGCGAATTAATGATTTTTAAGATGGAATAGCTACTAGTTTTTCAGTATTT
* * * **
41260902 AAATGTGTTCAGTGCCAACTTAAATTGCAAAATTATTTCAAGAATAAGGAAATAACCCAATGGTT
702 AAATGTGGTCAGTGCCAACTTAAATTACAAAAGTATTTCAAGAATAACAAAATAACCCAATGGTT
* ** * *
41260967 CAAAGAAATATGAGAAAGCATGGAAATTAGATTTACGTTCCAAGTTTGATTCCCTTCCCCTGCAA
767 CAAAGAAATATGAGAAAGCACGGAAATTAGATTTACGGCCCAAGTTCGATTCCCTTCACCTGCAA
* * * **
41261032 AATAGCTTCATTTTTACTAAAATTTCTCCTTCTCCTTATTTTATGTCGCCCAATCCTTGAACCCT
832 AATAGCTTAATTTTTACTAAAATTTCTCCTTCTCCTTATTTTATGTCACCCAAGCCTCAAACCCT
41261097 AGGTATAAATACAACTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATTACTCCCTAC
897 AGGTATAAATACAACTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATTACTCCCTAC
* *
41261154 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCTTGTGTT
1 CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCATGTGTG
41261219 CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
66 CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
* * *
41261284 TTATTTCCCTCTTCTTGCTTTCATTTTATCATAAAATTTCAAGCCTTCAAA-ATGAAATTTTAGC
131 TTATTTCCCTCTTCTTGCTTTCATTTAATCATAAAATTTCAAGCCTT-AAATATGAAATTTAACC
* * * * * *
41261348 ACTGAAGATTGGCCTCTATTGATGCCCCAAAAGAACTTCATTCCCGCCCCTATCTTCTTGCTTGA
195 ACTCAAGATCGGCCTCCAATGATGCCCCAAAAGAACTACATTCCCGCACCTATCTTCTTGCTTGA
* * * *
41261413 GTAAGTGTCATTTTCTTTCATTTTTCTTGATGGCTCTTTAAATAAAATACAAATTTTTCTAGAT-
260 GTAAGTGCCATTTTCTTGCATTTTTCTTGATGGATCTTTAAATAAAATACAAAGTTTTCTAGATC
* * *
41261477 C-TA-TAAGATTTAATGGTTATTTTTTCAGCCTTTATAGTAATTTCAATTGTGGTTATGAATCAG
325 CATATTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGTGGTTATGAATCAG
41261540 CCCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATAGGGGTTACTGTTT
390 CCCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATAGGGGTTACTGTTT
* * *
41261605 CTTTAAATTTTC-CAATCTATTTCCA-AAATTA-TGCTTCCTTCTTCAACCCTTCCTAATCAGCC
455 CTTTAAATTTTCTC-ATATATTTCCAGAAATAACT--TTCCTTCCTCAACCCTTCCTAATCAGCC
* * *
41261667 TTTAGTAATGTGTAAATTAGGAAAACGCAATA-TT-GATCAATCAACAACTCAAATCTGAAAATT
517 TTTAATAATGTGTAAACTAGGAAAAAGCAA-ACTTGGA-CAATCAACAACTCAAATCTGAAAATT
*
41261730 CGGGTAGCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTTGGGGAAATT
580 CGGGAAGCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTT-GGGAAATT
*
41261795 GTTAATTGAGCGAATTAATGATTTTTATGATGGAATAGCTACTAGCTTTTT-AGTATTTAAATGT
644 GTTAATTGAGCGAATTAATGATTTTTAAGATGGAATAGCTACTAG-TTTTTCAGTATTTAAATGT
* * * *
41261859 GGT-AGGTGCCGAA-TTAAATTACAAAAGTATTTCAAGGATGACAAAATAGCCCAATGGTTCAAG
708 GGTCA-GTGCC-AACTTAAATTACAAAAGTATTTCAAGAATAACAAAATAACCCAATGGTTCAAA
* * *
41261922 GAAATATGAGAAAGCACGGAAATTAGATTTAGGGCCCAAGTTCGATTCCCTTCACTTGTAAAATA
771 GAAATATGAGAAAGCACGGAAATTAGATTTACGGCCCAAGTTCGATTCCCTTCACCTGCAAAATA
* * *
41261987 GCTTAATTTTTGCTAAAATTTCTCCTTCTCCTTATTTTGTGTCACCCAAGCCTCAAACCCTTGGT
836 GCTTAATTTTTACTAAAATTTCTCCTTCTCCTTATTTTATGTCACCCAAGCCTCAAACCCTAGGT
* * * *
41262052 ATAAATACAACTTTTTCTTGTATTTTTTAGCTTTTAAGTCAATT
901 ATAAATACAACTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATT
41262096 TTTGTAACAC
Statistics
Matches: 826, Mismatches: 106, Indels: 36
0.85 0.11 0.04
Matches are distributed among these distances:
948 1 0.00
949 7 0.01
950 261 0.32
951 267 0.32
952 7 0.01
953 2 0.00
966 1 0.00
967 277 0.34
968 3 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (953 bp):
CCTAGCCATTCACCCTCTTCCTCTCCTCTTTTCTCTTTAATTTTCTTTCTTTCATCCCATGTGTG
CCACCACCCAAGCCACCAAGATTCACCATCAATTTCTCTTCTTATTACAATAGGTTCTTAAACCA
TTATTTCCCTCTTCTTGCTTTCATTTAATCATAAAATTTCAAGCCTTAAATATGAAATTTAACCA
CTCAAGATCGGCCTCCAATGATGCCCCAAAAGAACTACATTCCCGCACCTATCTTCTTGCTTGAG
TAAGTGCCATTTTCTTGCATTTTTCTTGATGGATCTTTAAATAAAATACAAAGTTTTCTAGATCC
ATATTAAGATTTAATGGGTACTTTTCCAGCCTTTATAGTAATTTCAATTGTGGTTATGAATCAGC
CCCAATTTCACCACCGTTGGTGGTGGTGCACCGCACCTAGAGGCAAAAATAGGGGTTACTGTTTC
TTTAAATTTTCTCATATATTTCCAGAAATAACTTTCCTTCCTCAACCCTTCCTAATCAGCCTTTA
ATAATGTGTAAACTAGGAAAAAGCAAACTTGGACAATCAACAACTCAAATCTGAAAATTCGGGAA
GCATAAGTGTGGTTGATTATGGGCTAGTGTGTAGTTTCAGTTTTGATGTTGGGAAATTGTTAATT
GAGCGAATTAATGATTTTTAAGATGGAATAGCTACTAGTTTTTCAGTATTTAAATGTGGTCAGTG
CCAACTTAAATTACAAAAGTATTTCAAGAATAACAAAATAACCCAATGGTTCAAAGAAATATGAG
AAAGCACGGAAATTAGATTTACGGCCCAAGTTCGATTCCCTTCACCTGCAAAATAGCTTAATTTT
TACTAAAATTTCTCCTTCTCCTTATTTTATGTCACCCAAGCCTCAAACCCTAGGTATAAATACAA
CTCTTTCTTGTATTTTTCAGCCTCTAAGTCAATTACTCCCTAC
Found at i:41263277 original size:27 final size:27
Alignment explanation
Indices: 41263232--41263499 Score: 295
Period size: 27 Copynumber: 9.9 Consensus size: 27
41263222 ATCTGCATCG
* *
41263232 AAATACCCTCATAGTGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGACCA
* * *
41263259 AAATACCCCCACAAGGTAAAAAGACCA
1 AAATACCCCCATAGGGTAAAATGACCA
* *
41263286 AAATACCCCTATAGGATAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGACCA
* * *
41263313 AAATACCTCCATTGGGTAAAATGACTA
1 AAATACCCCCATAGGGTAAAATGACCA
* *
41263340 AAATACCCCTATAAGGTAAAATGA-CA
1 AAATACCCCCATAGGGTAAAATGACCA
*
41263366 GAAATACCCCCATAGGGTAAAATGACTA
1 -AAATACCCCCATAGGGTAAAATGACCA
* *** *
41263394 GAATACTTTCATAGGGTAAAATGACTA
1 AAATACCCCCATAGGGTAAAATGACCA
* * ** *
41263421 AAATAACCCCATAGGTTAGGATGACCG
1 AAATACCCCCATAGGGTAAAATGACCA
*
41263448 AAATACCCCCATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCA
*
41263475 AAATACCCTCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
41263500 TGTTATACCC
Statistics
Matches: 197, Mismatches: 42, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 1 0.01
27 195 0.99
28 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCA
Found at i:41264947 original size:22 final size:22
Alignment explanation
Indices: 41264917--41264959 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41264907 ATTGGCCTCT
41264917 ATTGACACCCCAAAAGAACTCA
1 ATTGACACCCCAAAAGAACTCA
* *
41264939 ATTGTCACCCTAAAAGAACTC
1 ATTGACACCCCAAAAGAACTC
41264960 CACTACCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (22 bp):
ATTGACACCCCAAAAGAACTCA
Found at i:41285747 original size:28 final size:28
Alignment explanation
Indices: 41285713--41285772 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
41285703 TTCATTAAAC
*
41285713 TAATTAAATTAATTA-TCCTAAAATAACT
1 TAATTAAATGAATTAGT-CTAAAATAACT
41285741 TAATTAAATGAATTAGTCTAAAATAACT
1 TAATTAAATGAATTAGTCTAAAATAACT
41285769 TAAT
1 TAAT
41285773 GGAATTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.38
Consensus pattern (28 bp):
TAATTAAATGAATTAGTCTAAAATAACT
Found at i:41288184 original size:26 final size:26
Alignment explanation
Indices: 41288150--41288201 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
41288140 TTTGAGTAAA
41288150 AAAATTTCAAGTCGAATTAACGAATC
1 AAAATTTCAAGTCGAATTAACGAATC
41288176 AAAATTTCAAGTCGAATTAACGAATC
1 AAAATTTCAAGTCGAATTAACGAATC
41288202 TTATTATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (26 bp):
AAAATTTCAAGTCGAATTAACGAATC
Found at i:41288382 original size:21 final size:21
Alignment explanation
Indices: 41288356--41288396 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41288346 TCAAAACGAC
41288356 ATAGTTTTG-CATTTTAACTTG
1 ATAGTTTTGAC-TTTTAACTTG
41288377 ATAGTTTTGACTTTTAACTT
1 ATAGTTTTGACTTTTAACTT
41288397 TAGAAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (21 bp):
ATAGTTTTGACTTTTAACTTG
Found at i:41288746 original size:20 final size:20
Alignment explanation
Indices: 41288723--41288760 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41288713 TTTATATATT
*
41288723 TTTATATTTTTTTAAAAAAA
1 TTTATAATTTTTTAAAAAAA
41288743 TTTATAATTTTTTAAAAA
1 TTTATAATTTTTTAAAAA
41288761 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATAATTTTTTAAAAAAA
Found at i:41288837 original size:20 final size:19
Alignment explanation
Indices: 41288776--41288835 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
41288766 ATTTTATAAT
*
41288776 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
*
41288794 TTTTAAAAATTATTTTCAAA
1 TTTTAAAAATTATTTT-GAA
*
41288814 TTTTGAAAATTATTTTG-A
1 TTTTAAAAATTATTTTGAA
41288832 TTTT
1 TTTT
41288836 TTTTTGTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.36
19 6 0.17
20 17 0.47
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:41292965 original size:16 final size:16
Alignment explanation
Indices: 41292917--41292965 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
41292907 AAAAATATTT
*
41292917 AAATAAATA-AAATTA
1 AAATAAATATTAATTA
*
41292932 ACAA-AAAT-TTAATGA
1 A-AATAAATATTAATTA
41292947 AAATAAATATTAATTA
1 AAATAAATATTAATTA
41292963 AAA
1 AAA
41292966 ATTAACACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 2 0.07
15 14 0.52
16 11 0.41
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
AAATAAATATTAATTA
Found at i:41294667 original size:16 final size:16
Alignment explanation
Indices: 41294658--41294692 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41294648 AAACTGAAGC
41294658 AAATAAAAACTAAAAA
1 AAATAAAAACTAAAAA
41294674 AAATAAAAAC-AAAATA
1 AAATAAAAACTAAAA-A
41294690 AAA
1 AAA
41294693 ACATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (16 bp):
AAATAAAAACTAAAAA
Found at i:41294687 original size:11 final size:11
Alignment explanation
Indices: 41294669--41294705 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
41294659 AATAAAAACT
41294669 AAAA-AAAATA
1 AAAACAAAATA
41294679 AAAACAAAATA
1 AAAACAAAATA
*
41294690 AAAAC-ATATA
1 AAAACAAAATA
41294700 AAAACA
1 AAAACA
41294706 CTAGAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 13 0.54
11 11 0.46
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAACAAAATA
Found at i:41294687 original size:21 final size:21
Alignment explanation
Indices: 41294663--41294705 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
41294653 GAAGCAAATA
41294663 AAAACTAAAAA-AAATAAAAAC
1 AAAA-TAAAAACAAATAAAAAC
*
41294684 AAAATAAAAACATATAAAAAC
1 AAAATAAAAACAAATAAAAAC
41294705 A
1 A
41294706 CTAGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAATAAAAACAAATAAAAAC
Found at i:41295019 original size:65 final size:67
Alignment explanation
Indices: 41294771--41295046 Score: 358
Period size: 68 Copynumber: 4.1 Consensus size: 67
41294761 TGACAAATTA
* * * * *
41294771 ATAACCCTATGTTTAATGTCTTGGAAGACTCTATTAGTTGGCATAGTTGAGTTATGGTCTTACAC
1 ATAACCC-ATGTTTAATGTCCTGGAGGACTCTATTAGTTGTCATAGTCGAGCTATGGTCTTACAC
41294836 CTT
65 CTT
* * * * * * *
41294839 ATAAATCCATGTTTAATGTCCTGGTGGACTCTATTGGTTGTCATATTCGAGGTATGATCTTTCAC
1 AT-AACCCATGTTTAATGTCCTGGAGGACTCTATTAGTTGTCATAGTCGAGCTATGGTCTTACAC
41294904 CTT
65 CTT
* * *
41294907 ATAACCCCATCTTTAATGTCCTGGTGGACTCTATTGGTTGTCATAGTCGAGCTATGGTCTTACAC
1 ATAA-CCCATGTTTAATGTCCTGGAGGACTCTATTAGTTGTCATAGTCGAGCTATGGTCTTACAC
41294972 CTT
65 CTT
* *
41294975 ATAA-CC-TGTTTAATGTCCTAGAGGACTCTATTAGTTGTCATAGTCGAGCTATTGTCTTACACC
1 ATAACCCATGTTTAATGTCCTGGAGGACTCTATTAGTTGTCATAGTCGAGCTATGGTCTTACACC
41295038 TT
66 TT
41295040 ATAACCC
1 ATAACCC
41295047 TATTGAGGTG
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
65 58 0.32
66 4 0.02
67 2 0.01
68 115 0.63
69 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (67 bp):
ATAACCCATGTTTAATGTCCTGGAGGACTCTATTAGTTGTCATAGTCGAGCTATGGTCTTACACC
TT
Found at i:41301810 original size:25 final size:25
Alignment explanation
Indices: 41301776--41301832 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
41301766 AACGGCTTTT
41301776 GCTCCCTTTGAGGGCAGCAGTGTAG
1 GCTCCCTTTGAGGGCAGCAGTGTAG
41301801 GCTCCCTTTGAGGGCAGCAGTGTAG
1 GCTCCCTTTGAGGGCAGCAGTGTAG
41301826 GCTCCCT
1 GCTCCCT
41301833 CCGCTTCGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (25 bp):
GCTCCCTTTGAGGGCAGCAGTGTAG
Found at i:41310791 original size:275 final size:275
Alignment explanation
Indices: 41310300--41310845 Score: 961
Period size: 275 Copynumber: 2.0 Consensus size: 275
41310290 TTGATATATA
* *
41310300 TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACGACGTTACGACGAATATTGA
1 TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACAACGTTACGACGAATATTAA
*
41310365 ACCCCGTATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
66 ACCCCATATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
*
41310430 GGTGCTGGTCTTGAATGTCCTACTGATGTTTGAGGTCCTGCATTTGTTGCGGATACTTGTCAGCT
131 GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGATACTTGTCAGCT
* *
41310495 TGTGTGAGTGACATTGTGTAGCTTACATTCTGA-TCGTCAGCTTGTGTGAGTAGACCCATTTTAT
196 TGTGTGAGCGACATCGTGTAGCTTACATTCTGACT-GTCAGCTTGTGTGAGTAGACCCATTTTAT
41310559 GGCTCGAGTGAGCAAC
260 GGCTCGAGTGAGCAAC
* *
41310575 TATTATTGTGTTATTTATCATGTAAACGATTGTTGGAAATCCAACAACGTTATGACGAATATTAA
1 TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACAACGTTACGACGAATATTAA
* * *
41310640 ACCCCATGTGAACCTTAGGAATATATAGGATACAACTGACATGTCACTAGGGTTACCATGTTTCG
66 ACCCCATATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
41310705 GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGA-AGCTTGTCAGC
131 GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGATA-CTTGTCAGC
41310769 TTGTGTGAGCGACATCGTGTAGCTTACATTCTGACTGTCAGCTTGTGTGAGTAGACCCATTTTAT
195 TTGTGTGAGCGACATCGTGTAGCTTACATTCTGACTGTCAGCTTGTGTGAGTAGACCCATTTTAT
41310834 GGCTCGAGTGAG
260 GGCTCGAGTGAG
41310846 AAGCTATCTA
Statistics
Matches: 258, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
274 1 0.00
275 256 0.99
276 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (275 bp):
TATTATTGTGTTATTTATCATGGAAACGATTGTTGGAAATCCAACAACGTTACGACGAATATTAA
ACCCCATATGAACCTTAGGAATATATAGGATACAAATGACATGTCACTAGGGTTACCATGTTTCA
GGTGCTGGTCTTGAATGTCCTACTGATGGTTGAGGTCCTGCATTTGTTGCGGATACTTGTCAGCT
TGTGTGAGCGACATCGTGTAGCTTACATTCTGACTGTCAGCTTGTGTGAGTAGACCCATTTTATG
GCTCGAGTGAGCAAC
Found at i:41311438 original size:7 final size:7
Alignment explanation
Indices: 41311428--41311458 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
41311418 TAAAGTTTGA
41311428 GTTAAAT
1 GTTAAAT
41311435 GTTAAAT
1 GTTAAAT
41311442 GTTAAAT
1 GTTAAAT
41311449 GTTAAAT
1 GTTAAAT
41311456 GTT
1 GTT
41311459 GCTTTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (7 bp):
GTTAAAT
Found at i:41322123 original size:50 final size:51
Alignment explanation
Indices: 41322058--41322167 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 51
41322048 TTTCAACAGG
*
41322058 CATGAAAAGGGAAAGGAATGGTATGTGTTCAAATGAACTAT-TTCATGAAAT
1 CATGAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTT-ATGAAAT
*
41322109 TA-GAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTTATGAAAT
1 CATGAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTTATGAAAT
41322159 CATGAAAAG
1 CATGAAAAG
41322168 AATTGAAATG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
50 45 0.83
51 9 0.17
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (51 bp):
CATGAAAAGGGAAAGGAATGGTATGTATTCAAATGAACTATGTTATGAAAT
Found at i:41324701 original size:51 final size:50
Alignment explanation
Indices: 41324615--41325056 Score: 372
Period size: 51 Copynumber: 8.7 Consensus size: 50
41324605 TATCGATGAA
* *
41324615 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-ATGGT
* * * * * *
41324666 CACTTGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAA-ATATGGT
* * * * *
41324717 CACGTGTATAGTACTGTGTGAAGGCTACTATCTGAATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-ATGGT
* * * * * * *
41324768 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAA-ATATGGT
* * * *
41324819 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-ATGGT
* * *
41324870 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAATCTTCGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-AT-GGT
* * ** * *
41324921 CACGTGTGTGGTACTATGTGATGGCTACTACATGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATA--TGGT
* * * * * * *
41324971 CACATGTGTAGTACAATCTGAAGGCTAGTACGTGAACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATA--TGGT
* *
41325021 CACGTGTGTAGTACTATCTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
41325057 TCGAATGATA
Statistics
Matches: 313, Mismatches: 70, Indels: 17
0.78 0.17 0.04
Matches are distributed among these distances:
50 84 0.27
51 227 0.73
52 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATATGGT
Found at i:41324791 original size:102 final size:102
Alignment explanation
Indices: 41324615--41325060 Score: 580
Period size: 102 Copynumber: 4.4 Consensus size: 102
41324605 TATCGATGAA
* *
41324615 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACTTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
41324680 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* *
41324717 CACGTGTATAGTACTGTGTGAAGGCTACTATC-TGAATCGATAAATAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTA-CGTGAATCGATAAATAATGGTCACATGTGTAGTA
*
41324781 CTAAGTGAAGGCTACAATGTGTACCAAGAAGCTTTGGT
65 CTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* *
41324819 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* * * *
41324884 TAAGTGAAGGCTACTATGTGTACCGAAAATCTTCGGT
66 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* * * * * *
41324921 CACGTGTGTGGTACTATGTGATGGCTACTACATGAACCG-TAAA-ACTTGATCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTGTAGTA
* ** * * * *
41324984 C-AATCTGAAGGCTAGTACGTGAACCGTA-AAAC-TTGAT
65 CTAA-GTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
* *
41325021 CACGTGTGTAGTACTATCTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
41325061 ATGATAAAAG
Statistics
Matches: 305, Mismatches: 33, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
100 38 0.12
101 43 0.14
102 223 0.73
103 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
Found at i:41331711 original size:39 final size:39
Alignment explanation
Indices: 41331668--41331808 Score: 219
Period size: 39 Copynumber: 3.6 Consensus size: 39
41331658 AACATGTTTT
* *
41331668 TGAGTATTGTGATATATACTTAAATGTTATATGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
41331707 TGAGTATTGTGATATATGCTCAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
41331746 TGCGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
41331785 TGTGTAATGTGATATACGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
41331809 GGTGAATATG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 94 1.00
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:41331739 original size:22 final size:23
Alignment explanation
Indices: 41331714--41331786 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
41331704 ATATGAGTAT
41331714 TGTGA-TATATGCTCAAATGTTA
1 TGTGATTATATGCTCAAATGTTA
41331736 TGTGATTATATG--C----G-TA
1 TGTGATTATATGCTCAAATGTTA
*
41331752 TTGTGA-TATATGCTTAAATGTTA
1 -TGTGATTATATGCTCAAATGTTA
41331775 TGTGATTATATG
1 TGTGATTATATG
41331787 TGTAATGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 19
0.67 0.02 0.32
Matches are distributed among these distances:
16 8 0.20
17 6 0.15
21 1 0.03
22 11 0.28
23 14 0.35
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (23 bp):
TGTGATTATATGCTCAAATGTTA
Found at i:41332188 original size:9 final size:9
Alignment explanation
Indices: 41332174--41332198 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41332164 GGGATTATTT
41332174 GTATATTGC
1 GTATATTGC
41332183 GTATATTGC
1 GTATATTGC
41332192 GTATATT
1 GTATATT
41332199 TGTATATAAG
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (9 bp):
GTATATTGC
Found at i:41340649 original size:9 final size:9
Alignment explanation
Indices: 41340635--41340671 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
41340625 TATAGTTTGA
41340635 TATTCGAAT
1 TATTCGAAT
41340644 TATTCGAAT
1 TATTCGAAT
*
41340653 TATTCGAGT
1 TATTCGAAT
41340662 TATTCGAAT
1 TATTCGAAT
41340671 T
1 T
41340672 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41340779 original size:20 final size:22
Alignment explanation
Indices: 41340737--41340780 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
41340727 AATAACTCGA
*
41340737 TTAACTCGAATAACTTGATTTT
1 TTAACTCGAATAACTTGAATTT
*
41340759 TTAACTCG-A-AATTTGAATTT
1 TTAACTCGAATAACTTGAATTT
41340779 TT
1 TT
41340781 TTGGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (22 bp):
TTAACTCGAATAACTTGAATTT
Found at i:41340904 original size:23 final size:23
Alignment explanation
Indices: 41340869--41340986 Score: 148
Period size: 23 Copynumber: 5.1 Consensus size: 23
41340859 AGTGTTATTG
*
41340869 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
41340892 TTCAATGGTAGCTAT-GGCTACAT
1 ATCAGTGGTAGCT-TCGGCTACAT
* *
41340915 ATCAGTGGTAACTTCGCCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
41340938 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
41340961 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41340984 ATC
1 ATC
41340987 TGTGTGGCAC
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
22 1 0.01
23 77 0.97
24 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:41340921 original size:46 final size:46
Alignment explanation
Indices: 41340869--41340983 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
41340859 AGTGTTATTG
* *
41340869 ATCAGTGGTAGCTTTGGCTACATTTCAATGGTAGCTATGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGGCTACAT
* * * *
41340915 ATCAGTGGTAACTTCGCCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGGCTACAT
41340961 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
41340984 ATCTGTGTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGGCTACAT
Found at i:41349250 original size:24 final size:24
Alignment explanation
Indices: 41349202--41349248 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41349192 ACTGGTCATA
*
41349202 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
41349226 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
41349249 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:41349973 original size:28 final size:27
Alignment explanation
Indices: 41349915--41350005 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
41349905 GAGAGTCAAT
* *
41349915 AAATGACTGAATTACCCCCTACAGGGT-
1 AAATTACTGAATTACCCCC-ATAGGGTA
41349942 AAATTAACTGAATTACCCCCATAGGGTA
1 AAATT-ACTGAATTACCCCCATAGGGTA
** *
41349970 AAATTACCAAAATACCCCCATAGGGTA
1 AAATTACTGAATTACCCCCATAGGGTA
*
41349997 AAATGACTG
1 AAATTACTG
41350006 TTATAACCCT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
27 35 0.65
28 19 0.35
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (27 bp):
AAATTACTGAATTACCCCCATAGGGTA
Found at i:41350409 original size:28 final size:28
Alignment explanation
Indices: 41350368--41350467 Score: 128
Period size: 28 Copynumber: 3.6 Consensus size: 28
41350358 ACTGTACCGA
* * *
41350368 TACTGTATCGGGCTAATGCTTACATTGT
1 TACTGTATTGGGCTAAGGCTCACATTGT
* * * *
41350396 TACTATATTGGGCTAAGGCCCACGTTAT
1 TACTGTATTGGGCTAAGGCTCACATTGT
*
41350424 TAATGTATTGGGCTAAGGCTCACATTGT
1 TACTGTATTGGGCTAAGGCTCACATTGT
41350452 TACTGTATTGGGCTAA
1 TACTGTATTGGGCTAA
41350468 AGCCCACACT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCTCACATTGT
Found at i:41356415 original size:3 final size:3
Alignment explanation
Indices: 41356407--41356441 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
41356397 TGTCGATAGA
*
41356407 AAC AAC AAC AAC AAC AAC AAA AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
41356442 ATGCAAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:41358543 original size:22 final size:22
Alignment explanation
Indices: 41358515--41358561 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
41358505 GGCTGAGTCG
* * *
41358515 TAAACAGGATAGCTATAAGCTA
1 TAAACAGAATAGCTACAAGCCA
*
41358537 TAAACAGAATGGCTACAAGCCA
1 TAAACAGAATAGCTACAAGCCA
41358559 TAA
1 TAA
41358562 GTACAGTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (22 bp):
TAAACAGAATAGCTACAAGCCA
Found at i:41358614 original size:32 final size:32
Alignment explanation
Indices: 41358553--41358755 Score: 230
Period size: 32 Copynumber: 6.4 Consensus size: 32
41358543 GAATGGCTAC
* *
41358553 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
41358584 AAGCCATCAGTAGCAGTGATATGACCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
41358616 CAGCCATCAGTAACGGTAATATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
41358648 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
41358680 AAGCCATTAGTAGCAGTGATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * *
41358712 CAA-CCATCAATAACGGTAATATGATGGGGACA
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
41358744 AAGCCATCAGTA
1 AAGCCATCAGTA
41358756 GCATCGCAAC
Statistics
Matches: 143, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
31 12 0.08
32 129 0.90
33 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:41358731 original size:96 final size:96
Alignment explanation
Indices: 41358553--41358755 Score: 309
Period size: 96 Copynumber: 2.1 Consensus size: 96
41358543 GAATGGCTAC
* *
41358553 AAGCCATAAGT-ACAGTAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACAC
1 AAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACAC
* * *
41358617 AGCCATCAGTAACGGTAATATGATCGGTACA
66 AACCATCAATAACGGTAATATGATCGGGACA
* * **
41358648 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATTAGTAGCAGTGATATGATTGGCACAC
1 AAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACAC
*
41358713 AACCATCAATAACGGTAATATGATGGGGACA
66 AACCATCAATAACGGTAATATGATCGGGACA
41358744 AAGCCATCAGTA
1 AAGCCATCAGTA
41358756 GCATCGCAAC
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 10 0.10
96 87 0.90
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (96 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACAC
AACCATCAATAACGGTAATATGATCGGGACA
Found at i:41358756 original size:64 final size:64
Alignment explanation
Indices: 41358553--41358758 Score: 254
Period size: 64 Copynumber: 3.2 Consensus size: 64
41358543 GAATGGCTAC
* * * * *
41358553 AAGCCATAAGTA-CAGTAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGACCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATTGGCACAAAGCCATCAGTAACGGTAATATGATCGGCACA
* * * * *
41358616 CAGCCATCAGTAACGGTAATATGATCGGTACAAAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATTGGCACAAAGCCATCAGTAACGGTAATATGATCGGCACA
* * * * *
41358680 AAGCCATTAGTAGCAGTGATATGATTGGCACACAA-CCATCAATAACGGTAATATGATGGGGACA
1 AAGCCATCAGTAGCAGTAATATGATTGGCACA-AAGCCATCAGTAACGGTAATATGATCGGCACA
41358744 AAGCCATCAGTAGCA
1 AAGCCATCAGTAGCA
41358759 TCGCAACAAA
Statistics
Matches: 121, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
63 10 0.08
64 109 0.90
65 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (64 bp):
AAGCCATCAGTAGCAGTAATATGATTGGCACAAAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:41358780 original size:26 final size:26
Alignment explanation
Indices: 41358746--41358798 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
41358736 TGGGGACAAA
* *
41358746 GCCATCAGTAGCATCGCAACAAAGCT
1 GCCAGCAGTAGCATCCCAACAAAGCT
*
41358772 GCCAGCAGTAGTATCCCAACAAAGCT
1 GCCAGCAGTAGCATCCCAACAAAGCT
41358798 G
1 G
41358799 TCAGTAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (26 bp):
GCCAGCAGTAGCATCCCAACAAAGCT
Found at i:41358809 original size:26 final size:26
Alignment explanation
Indices: 41358762--41358811 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
41358752 AGTAGCATCG
*
41358762 CAACAAAGCTGCCAGCAGTAGTATCC
1 CAACAAAGCTGCCAGCAATAGTATCC
* *
41358788 CAACAAAGCTGTCAGTAATAGTAT
1 CAACAAAGCTGCCAGCAATAGTAT
41358812 ATGTGGCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (26 bp):
CAACAAAGCTGCCAGCAATAGTATCC
Found at i:41358832 original size:27 final size:26
Alignment explanation
Indices: 41358800--41358865 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
41358790 ACAAAGCTGT
41358800 CAGTAATAGTATATGTGGCTA-AGACAC
1 CAGTAATAGTAT-TGTGGC-AGAGACAC
* *
41358827 CAGTAACAGTGATTGTGGCAGAGCCAC
1 CAGTAATAGT-ATTGTGGCAGAGACAC
41358854 CAGT-ATAGTATT
1 CAGTAATAGTATT
41358866 TCCTCCATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.09
26 5 0.15
27 24 0.71
28 2 0.06
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (26 bp):
CAGTAATAGTATTGTGGCAGAGACAC
Found at i:41358954 original size:24 final size:23
Alignment explanation
Indices: 41358927--41358998 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 23
41358917 CCATGCTCAG
41358927 AATCAGTCATTCAAATCACAGACA
1 AATCAGTCATTCAAA-CACAGACA
41358951 AATCAGTCATATCAAACACAGACA
1 AATCAGTCAT-TCAAACACAGACA
* * *
41358975 AATTAGTCATTTAACCACAGACA
1 AATCAGTCATTCAAACACAGACA
41358998 A
1 A
41358999 GTCAATCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
23 12 0.27
24 27 0.61
25 5 0.11
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (23 bp):
AATCAGTCATTCAAACACAGACA
Found at i:41359061 original size:27 final size:27
Alignment explanation
Indices: 41359022--41359147 Score: 171
Period size: 27 Copynumber: 4.7 Consensus size: 27
41359012 CGTCGAGGGT
* *
41359022 ATTATGGTTATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGC
*
41359049 ATTAGGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGC
*
41359076 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGC
* * *
41359103 ATTACGATCATTTTACCCTAGAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGC
* *
41359130 GTTATGGTCATTTTACCC
1 ATTACGGTCATTTTACCC
41359148 ATTGAGGGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 90 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGC
Found at i:41359156 original size:27 final size:27
Alignment explanation
Indices: 41359016--41359186 Score: 109
Period size: 27 Copynumber: 6.3 Consensus size: 27
41359006 TTTTGGCGTC
* *
41359016 GAGGGTATTATGGTTATTTTACCC-TA
1 GAGGGTATTATAGTCATTTTACCCATA
* * **
41359042 CAGGGGCATTAGGGTCATTTTACCC-TA
1 GA-GGGTATTATAGTCATTTTACCCATA
* * **
41359069 CAGGGGCATTACGGTCATTTTACCC-TA
1 GA-GGGTATTATAGTCATTTTACCCATA
* *
41359096 CAGGGGTATTA-CGATCATTTTACCC-TA
1 GA-GGGTATTATAG-TCATTTTACCCATA
* * *
41359123 GAGGGGTGTTATGGTCATTTTACCCATT
1 GA-GGGTATTATAGTCATTTTACCCATA
* *
41359151 GAGGGTATTTTAGTCATTTTACCCATC
1 GAGGGTATTATAGTCATTTTACCCATA
41359178 GAGGGTATT
1 GAGGGTATT
41359187 TCATTCATTT
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
26 2 0.02
27 120 0.95
28 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (27 bp):
GAGGGTATTATAGTCATTTTACCCATA
Found at i:41359184 original size:81 final size:80
Alignment explanation
Indices: 41359014--41359186 Score: 179
Period size: 81 Copynumber: 2.1 Consensus size: 80
41359004 TCTTTTGGCG
* * *
41359014 TCGAGGGTATTATGGTTATTTTACCCTACAGGGGCATTAGGGTCATTTTACCCTACAGGGGCATT
1 TCGAGGGTATTACGATCATTTTACCCTACAGGGGCATTAGGGTCATTTTACCCTACAGGGGCATT
*
41359079 ACGGTCATTTTACCC
66 ACAGTCATTTTACCC
* ** * ** *
41359094 TAC-AGGGGTATTACGATCATTTTACCCTAGAGGGGTGTTATGGTCATTTTACCC-ATTGAGGGT
1 T-CGA-GGGTATTACGATCATTTTACCCTACAGGGGCATTAGGGTCATTTTACCCTACAG-GGGC
**
41359157 ATTTTAGTCATTTTACCC
63 ATTACAGTCATTTTACCC
41359175 ATCGAGGGTATT
1 -TCGAGGGTATT
41359187 TCATTCATTT
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
80 4 0.05
81 69 0.92
82 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (80 bp):
TCGAGGGTATTACGATCATTTTACCCTACAGGGGCATTAGGGTCATTTTACCCTACAGGGGCATT
ACAGTCATTTTACCC
Found at i:41359187 original size:27 final size:27
Alignment explanation
Indices: 41359110--41359197 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
41359100 GGTATTACGA
* * *
41359110 TCATTTTACCC-TAGAGGGGTGTTATGG
1 TCATTTTACCCATAGA-GGGTATTTTAG
*
41359137 TCATTTTACCCATTGAGGGTATTTTAG
1 TCATTTTACCCATAGAGGGTATTTTAG
* * *
41359164 TCATTTTACCCATCGAGGGTATTTCAT
1 TCATTTTACCCATAGAGGGTATTTTAG
41359191 TCATTTT
1 TCATTTT
41359198 TCCTATTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
27 50 0.94
28 3 0.06
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCATAGAGGGTATTTTAG
Found at i:41360432 original size:5 final size:5
Alignment explanation
Indices: 41360422--41360448 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41360412 TTAACTACAG
41360422 AAAAC AAAAC AAAAC AAAAC AAAAC AA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AA
41360449 GTAAGCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:41384552 original size:23 final size:25
Alignment explanation
Indices: 41384525--41384582 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
41384515 TTATTTTACA
**
41384525 AAAATTAAATCCTAATTA-CTAAAG
1 AAAATTAAATCCTAAAGACCTAAAG
41384549 -AAA-TAAATTCCTAAAGACCTAAAG
1 AAAATTAAA-TCCTAAAGACCTAAAG
41384573 AAAATTAAAT
1 AAAATTAAAT
41384583 AAATAACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.14
23 10 0.36
24 6 0.21
25 4 0.14
26 4 0.14
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.26
Consensus pattern (25 bp):
AAAATTAAATCCTAAAGACCTAAAG
Found at i:41388574 original size:43 final size:43
Alignment explanation
Indices: 41388522--41388605 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
41388512 TATATATACA
*
41388522 TTTGCTTTGTCAACTTCAATTCCTTTTTTTGAAATTATATGCC
1 TTTGCTTTGTCAACTTCAATTCCTTTCTTTGAAATTATATGCC
* * *
41388565 TTTGTTTTGTCGACTTCAATTCCTTTCTTTGAAATTCTATG
1 TTTGCTTTGTCAACTTCAATTCCTTTCTTTGAAATTATATG
41388606 GCCTAAGACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.19, C:0.18, G:0.11, T:0.52
Consensus pattern (43 bp):
TTTGCTTTGTCAACTTCAATTCCTTTCTTTGAAATTATATGCC
Found at i:41388589 original size:23 final size:23
Alignment explanation
Indices: 41388522--41388590 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
41388512 TATATATACA
*
41388522 TTTGCTTTGTCAACTTCAATTCC
1 TTTGTTTTGTCAACTTCAATTCC
* *
41388545 TTT-TTTTG--AAATT-ATATGCC
1 TTTGTTTTGTCAACTTCA-ATTCC
*
41388565 TTTGTTTTGTCGACTTCAATTCC
1 TTTGTTTTGTCAACTTCAATTCC
41388588 TTT
1 TTT
41388591 CTTTGAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 5 0.14
22 4 0.11
23 13 0.37
24 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (23 bp):
TTTGTTTTGTCAACTTCAATTCC
Found at i:41394560 original size:8 final size:8
Alignment explanation
Indices: 41394547--41394575 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
41394537 ATGAGTGAGA
41394547 GATGATGG
1 GATGATGG
41394555 GATGATGG
1 GATGATGG
41394563 GATGA-GG
1 GATGATGG
41394570 GATGAT
1 GATGAT
41394576 TAAAAAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (8 bp):
GATGATGG
Found at i:41397945 original size:137 final size:138
Alignment explanation
Indices: 41397674--41398007 Score: 485
Period size: 137 Copynumber: 2.4 Consensus size: 138
41397664 TTTTGTGATT
* * *
41397674 TTAAATTCGGTCAAAATATAAAAGGCATGGAAAATAATATTCTTTTGGAAATAATATAATTAATA
1 TTAAATTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATA
* * * * *
41397739 TATCAGTTTTATTCATACACAATATTAATTGTATATATTTTACCGAATTTATTAATATAAATAGT
66 TATCAGATTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTATTAATATAAACAGT
41397804 TATATTAA
131 TATATTAA
* * *
41397812 TTAATTTCCGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTTGAAAGAATATAATTAATA
1 TTAAATTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATA
* * * *
41397877 TATGA-ATTGATTCATACAAAATATTAATTGTATATATTTTATAGAATTTCTTACTATAAACAGT
66 TATCAGATTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTATTAATATAAACAGT
41397941 TATATTAA
131 TATATTAA
* * *
41397949 TTAACTTAGGTCAAAATGTAAAAGACA--GAAATTAATATTCTTTTGGAAAGAATATAATT
1 TTAAATTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATT
41398008 CATTTTTCTA
Statistics
Matches: 176, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
135 31 0.18
137 82 0.47
138 63 0.36
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (138 bp):
TTAAATTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAATATAATTAATA
TATCAGATTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTATTAATATAAACAGT
TATATTAA
Found at i:41399011 original size:34 final size:35
Alignment explanation
Indices: 41398963--41399030 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 35
41398953 GTAATTTGTT
41398963 CACTAAAAAAAACCAACACAAACCATTCAAAAACG
1 CACTAAAAAAAACCAACACAAACCATTCAAAAACG
41398998 CACT-AAAAAAACCAACACAAACCATTCAAAAAC
1 CACTAAAAAAAACCAACACAAACCATTCAAAAAC
41399031 TAACCTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.60, C:0.29, G:0.01, T:0.09
Consensus pattern (35 bp):
CACTAAAAAAAACCAACACAAACCATTCAAAAACG
Found at i:41399917 original size:25 final size:26
Alignment explanation
Indices: 41399889--41399945 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
41399879 AGCTCCTCCG
* *
41399889 AGCTGAA-TAACAGTAAGCTCATGCA
1 AGCTGAAGTAACAGTAAACTCATACA
*
41399914 AGCT-AAGTATCAGTAAACTCATACA
1 AGCTGAAGTAACAGTAAACTCATACA
41399939 AGCTGAA
1 AGCTGAA
41399946 ATTGGTAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 23 0.85
26 2 0.07
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (26 bp):
AGCTGAAGTAACAGTAAACTCATACA
Found at i:41402811 original size:27 final size:27
Alignment explanation
Indices: 41402766--41402831 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
41402756 TAGTGTCCGT
*
41402766 GTAAAATGA-CTGAGATACCCCTGA-AGG
1 GTAAAATGATC-GAGATACCCCT-ATAAG
*
41402793 GTAAAATGATCGAGCTACCCCTATAAG
1 GTAAAATGATCGAGATACCCCTATAAG
41402820 GTAAAATGATCG
1 GTAAAATGATCG
41402832 TAATGTCGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 1 0.03
27 33 0.94
28 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (27 bp):
GTAAAATGATCGAGATACCCCTATAAG
Found at i:41402902 original size:24 final size:24
Alignment explanation
Indices: 41402872--41402933 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
41402862 CCCCTCAAGG
*
41402872 TTAAATGATTGATTTGTCCATGAT
1 TTAAATGACTGATTTGTCCATGAT
* * *
41402896 TTAAATGACTGTTTTGTCTATGAA
1 TTAAATGACTGATTTGTCCATGAT
**
41402920 TTGTATGACTGATT
1 TTAAATGACTGATT
41402934 CTGAGCATGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCCATGAT
Found at i:41403809 original size:16 final size:16
Alignment explanation
Indices: 41403788--41403857 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
41403778 TTTGGTTTGC
* *
41403788 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
41403804 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
41403820 TGTAATGGAATAGAAG
1 TGTAATGGAATAGAGG
41403836 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
41403852 TGTAAT
1 TGTAAT
41403858 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.00, G:0.34, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:41404110 original size:18 final size:17
Alignment explanation
Indices: 41404089--41404125 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
41404079 AATTATTATT
*
41404089 ATATATATTTTAATTAAA
1 ATATATAATTTAA-TAAA
41404107 ATATATAATTTAATAAA
1 ATATATAATTTAATAAA
41404124 AT
1 AT
41404126 TCTTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATAATTTAATAAA
Found at i:41404179 original size:157 final size:157
Alignment explanation
Indices: 41403978--41404292 Score: 585
Period size: 157 Copynumber: 2.0 Consensus size: 157
41403968 TAGAATACCC
*
41403978 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * *
41404043 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTATATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
41404108 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
41404135 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
41404200 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
41404265 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
41404292 T
1 T
41404293 AAATATTCTT
Statistics
Matches: 153, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:41404265 original size:16 final size:16
Alignment explanation
Indices: 41404228--41404269 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
41404218 TTAATCATAT
*
41404228 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
41404244 TT-AAATATATTATAA
1 TTAAAATATATTATAA
41404259 TTAAAATATAT
1 TTAAAATATAT
41404270 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:41404276 original size:14 final size:15
Alignment explanation
Indices: 41404237--41404278 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
41404227 TTTAAACATA
*
41404237 ATTATTATTAAATAT
1 ATTATAATTAAATAT
41404252 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
41404266 A-TATAATTTAATA
1 ATTATAATTAAATA
41404279 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:41404294 original size:15 final size:16
Alignment explanation
Indices: 41404274--41404303 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41404264 ATATATAATT
41404274 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
41404289 TAATAAATATTCTTA
1 TAATAAATATTCTTA
41404304 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:41404366 original size:120 final size:120
Alignment explanation
Indices: 41404231--41404523 Score: 498
Period size: 120 Copynumber: 2.4 Consensus size: 120
41404221 ATCATATTTA
41404231 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
* *
41404296 TATTCTTATATGAATTTACTCAAATCATAATATATGATAGTGTAAAATAAAAAT-T
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA-AAAAATAT
*
41404351 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
*
41404416 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAAATAT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAAAAAATAT
* * * *
41404471 AAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
41404524 TAAAATAATT
Statistics
Matches: 164, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
119 5 0.03
120 159 0.97
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAAAAAATAT
Found at i:41404396 original size:14 final size:15
Alignment explanation
Indices: 41404347--41404398 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41404337 GTAAAATAAA
41404347 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
41404362 TATTAAATATATTAT
1 AATTAAATATATTAT
41404377 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
41404390 AATTTAATA
1 AATTAAATA
41404399 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:41404633 original size:101 final size:93
Alignment explanation
Indices: 41404470--41404746 Score: 287
Period size: 91 Copynumber: 2.9 Consensus size: 93
41404460 AAAGAAAATA
* * *
41404470 TAAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATT-TAAAATAAT
1 TAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTCT----T-A-
* * * *
41404533 TATAACTAATAAATTATATTTTATGAATTTGTATAATT
59 -ATAA-T-ATAAATTTTATTATATGAATTTATACAATT
* *
41404571 TAAAATAA-TAATTATTACATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT-A-A
1 TAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATA
*
41404633 TAAATTTTCTTATATGAATTTATACAATT
65 TAAATTTTATTATATGAATTTATACAATT
* *
41404662 TAAAATAATTAATATTAAATATAATTTAATAGTGATATATAATTTCATAAAATTCTTAATAATA-
1 TAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATAT
* *
41404726 AAATGTTCTTATATGAATTTA
66 AAATTTTATTATATGAATTTA
41404747 CTAAAATCAA
Statistics
Matches: 155, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
91 77 0.50
92 24 0.15
93 1 0.01
94 1 0.01
95 2 0.01
98 1 0.01
100 6 0.04
101 42 0.27
102 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (93 bp):
TAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATAATAT
AAATTTTATTATATGAATTTATACAATT
Found at i:41406115 original size:2 final size:2
Alignment explanation
Indices: 41406108--41406132 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41406098 CTATGCAATT
41406108 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
41406133 TTTACATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:41407211 original size:23 final size:24
Alignment explanation
Indices: 41407151--41407213 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
41407141 TGTACTGACT
*
41407151 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAAAACAATTTCCAGC
41407175 AA-ACAAT-AAAAACAATTTCCAG-
1 AACA-AATCAAAAACAATTTCCAGC
*
41407197 AACAAATCAATAACAAT
1 AACAAATCAAAAACAAT
41407214 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 5 0.15
23 24 0.71
24 5 0.15
ACGTcount: A:0.57, C:0.21, G:0.05, T:0.17
Consensus pattern (24 bp):
AACAAATCAAAAACAATTTCCAGC
Found at i:41409962 original size:50 final size:50
Alignment explanation
Indices: 41409908--41410014 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
41409898 ATGTGAGAGT
* ***
41409908 TCTCATATCAGTGCCCATGTCATGTCCCAGACATGGTCTTACGGGGGACA
1 TCTCATATCAGTGCCAACACCATGTCCCAGACATGGTCTTACGGGGGACA
* * * *
41409958 TCTCATCTCGGTGCCAACACCATGTCCCAGACATGGTCTTACGTGGGACC
1 TCTCATATCAGTGCCAACACCATGTCCCAGACATGGTCTTACGGGGGACA
41410008 TCTCATA
1 TCTCATA
41410015 ACCTCAATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (50 bp):
TCTCATATCAGTGCCAACACCATGTCCCAGACATGGTCTTACGGGGGACA
Found at i:41410212 original size:22 final size:21
Alignment explanation
Indices: 41410168--41410212 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
41410158 TCAACATTAA
* **
41410168 ATAATTTCATGAAATAAGTAC
1 ATAATTTCATAAAATAACAAC
41410189 ATAATTTCTATAAAATAACAAC
1 ATAATTTC-ATAAAATAACAAC
41410211 AT
1 AT
41410213 TAATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (21 bp):
ATAATTTCATAAAATAACAAC
Found at i:41410439 original size:30 final size:30
Alignment explanation
Indices: 41410404--41410461 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41410394 CCTTGACTCG
41410404 AACTTTTGCAAAATTACAATTTTGCCCCTA
1 AACTTTTGCAAAATTACAATTTTGCCCCTA
* * * *
41410434 AACTTTTGCATATTTACACTTTTTCCCC
1 AACTTTTGCAAAATTACAATTTTGCCCC
41410462 AAAGCTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTGCCCCTA
Found at i:41411999 original size:26 final size:27
Alignment explanation
Indices: 41411941--41411999 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
41411931 TCACATAGGA
* * *
41411941 GAGTTCACATAGGTAGTTCAGTGATAG
1 GAGTTCACAAAGGCAGTTCAGCGATAG
41411968 GAGTTCACAAAGGCAGTTC-GCGATAG
1 GAGTTCACAAAGGCAGTTCAGCGATAG
*
41411994 GGGTTC
1 GAGTTC
41412000 GCACAAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.25
Consensus pattern (27 bp):
GAGTTCACAAAGGCAGTTCAGCGATAG
Found at i:41412190 original size:17 final size:18
Alignment explanation
Indices: 41412151--41412191 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
41412141 CCTCGCATAC
41412151 ATATAGGCTTGCACACTA
1 ATATAGGCTTGCACACTA
*
41412169 A-ATAGGCTTGCATA-TA
1 ATATAGGCTTGCACACTA
41412185 ATATAGG
1 ATATAGG
41412192 GCTCGCTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 17 0.81
18 1 0.05
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (18 bp):
ATATAGGCTTGCACACTA
Found at i:41412384 original size:51 final size:51
Alignment explanation
Indices: 41412281--41412386 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 51
41412271 CAAATGTGAA
* ** * *
41412281 TTCGCCAATCATAGGGGTTTGGCAGTCATAAGGGTTCGTTGGTGATAGGTG
1 TTCGCCAATCATAGGGGTTTGCCAGTCATAAGGGTTCGCAGGTGACAAGTG
* *
41412332 TTCGCCAATGAT-GGTGGTTTTCCAGTCATAAGGGTTCGCCAGGT-ACAAGTG
1 TTCGCCAATCATAGG-GGTTTGCCAGTCATAAGGGTTCG-CAGGTGACAAGTG
41412383 TTCG
1 TTCG
41412387 TCGATCTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
50 2 0.04
51 41 0.89
52 3 0.07
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (51 bp):
TTCGCCAATCATAGGGGTTTGCCAGTCATAAGGGTTCGCAGGTGACAAGTG
Found at i:41413112 original size:29 final size:29
Alignment explanation
Indices: 41413070--41413131 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
41413060 GTTATAAGAT
*
41413070 ACCTTAATTCTCTTATTTATGTTTTTGTA
1 ACCTTAATTCTCTTATTTATGTTTTCGTA
41413099 ACCTTAATTCTCTTATTTATGTTTTCGTA
1 ACCTTAATTCTCTTATTTATGTTTTCGTA
41413128 ACCT
1 ACCT
41413132 ATGGTGTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.55
Consensus pattern (29 bp):
ACCTTAATTCTCTTATTTATGTTTTCGTA
Found at i:41413296 original size:20 final size:19
Alignment explanation
Indices: 41413271--41413317 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
41413261 CAAAGACAAT
41413271 TATTTTAAGTATTAATATAA
1 TATTTTAAGTATTAA-ATAA
*
41413291 TATTTT-AGTATTAAATAT
1 TATTTTAAGTATTAAATAA
41413309 TATTATTAA
1 TATT-TTAA
41413318 AATATTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.29
19 10 0.42
20 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TATTTTAAGTATTAAATAA
Found at i:41413388 original size:24 final size:22
Alignment explanation
Indices: 41413361--41413405 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
41413351 TTACTTTTTA
41413361 ATAATAAATATCAGTAAATATTTC
1 ATAATAAATA--AGTAAATATTTC
*
41413385 ATAATTAATAAGTAAATATTT
1 ATAATAAATAAGTAAATATTT
41413406 ATTACTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
ATAATAAATAAGTAAATATTTC
Found at i:41418723 original size:16 final size:16
Alignment explanation
Indices: 41418673--41418724 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
41418663 TGTATAGATA
41418673 AATTTTGATTTTATAT-
1 AATTTTGA-TTTATATC
*
41418689 AATTTT-ATATATA-C
1 AATTTTGATTTATATC
*
41418703 AATTTTGATTTAAATC
1 AATTTTGATTTATATC
41418719 AATTTT
1 AATTTT
41418725 TGTAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.37
15 6 0.20
16 13 0.43
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (16 bp):
AATTTTGATTTATATC
Found at i:41418723 original size:30 final size:29
Alignment explanation
Indices: 41418665--41418724 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
41418655 TTTGTAAGTG
*
41418665 TATAGATAAATTTTGATTTTATATAATTT
1 TATAGATAAATTTTGATTTTAAATAATTT
*
41418694 TATATATACAATTTTGA-TTTAAATCAATTT
1 TATAGATA-AATTTTGATTTTAAAT-AATTT
41418724 T
1 T
41418725 TGTAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (29 bp):
TATAGATAAATTTTGATTTTAAATAATTT
Found at i:41419065 original size:21 final size:21
Alignment explanation
Indices: 41419041--41419081 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41419031 TATAAAAAAA
*
41419041 TTATATTTCAGAAATTTTAAT
1 TTATATTTAAGAAATTTTAAT
* *
41419062 TTATTTTTAATAAATTTTAA
1 TTATATTTAAGAAATTTTAA
41419082 AAAATTAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATATTTAAGAAATTTTAAT
Found at i:41420370 original size:40 final size:40
Alignment explanation
Indices: 41420309--41420420 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 40
41420299 ATATAAAAAC
* * * * * *
41420309 AAATCATTTTAAAAATAAATTGAG-ATCATTTTTATTTTTA
1 AAATAATTTAAAAAATAAATTG-GAATAACTTTCATTTTAA
41420349 AAATAATTTAAAAAATAAATTGGAATAACTTTCATTTTAA
1 AAATAATTTAAAAAATAAATTGGAATAACTTTCATTTTAA
* *
41420389 AAATGATTT-AAAATTAAATTAGG-ATAACTTTC
1 AAATAATTTAAAAAATAAATT-GGAATAACTTTC
41420421 TCTCTCTCTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
39 20 0.32
40 42 0.68
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (40 bp):
AAATAATTTAAAAAATAAATTGGAATAACTTTCATTTTAA
Found at i:41420683 original size:16 final size:16
Alignment explanation
Indices: 41420662--41420701 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
41420652 TGTTTGATTC
41420662 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
41420678 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
41420694 ACTGTAAT
1 GCTGTAAT
41420702 AGTAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:41420770 original size:44 final size:44
Alignment explanation
Indices: 41420683--41420773 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 44
41420673 ATAGAGCTGT
*
41420683 AATGGAATAGAACTGTAATAGTAATTTAATTGTTTAGTTGAATGG
1 AATGAAATAGAACTGTAATAGTAATTT-ATTGTTTAGTTGAATGG
* *
41420728 AATGAAATATAACTGTAATAGT-ATTCT-TCTGTTTGGTTGAATGG
1 AATGAAATAGAACTGTAATAGTAATT-TAT-TGTTTAGTTGAATGG
41420772 AA
1 AA
41420774 CGATGTTGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 19 0.46
45 21 0.51
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.38
Consensus pattern (44 bp):
AATGAAATAGAACTGTAATAGTAATTTATTGTTTAGTTGAATGG
Found at i:41420997 original size:55 final size:56
Alignment explanation
Indices: 41420883--41421012 Score: 133
Period size: 55 Copynumber: 2.3 Consensus size: 56
41420873 AATAAGATTA
* **
41420883 TTAATAAAAATAATAAATAATTTAATCATGTTTTAACATAATTATTATTAAATATAAT
1 TTAATAAAAATAAT-AATAATTTAATAAAATTTTAACATAATTATTATT-AATATAAT
* *
41420941 TTAATAAAAAT-AT-ATAATTTAATAAAATTCTTAATATAATTATTGTT-ATATGAAT
1 TTAATAAAAATAATAATAATTTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
41420996 TTACT-AAAATCATAATA
1 TTAATAAAAATAATAATA
41421013 TAAAATACTA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
54 9 0.15
55 22 0.35
56 18 0.29
57 2 0.03
58 11 0.18
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (56 bp):
TTAATAAAAATAATAATAATTTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:41421434 original size:47 final size:47
Alignment explanation
Indices: 41421375--41421464 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
41421365 GTTTGTTGAG
41421375 ATAACTTTTAATCAAACAATATAAGTAATATAAAACATTGTTTAATT
1 ATAACTTTTAATCAAACAATATAAGTAATATAAAACATTGTTTAATT
* *
41421422 ATAATTTTTAATCAGACAATATAAGTAATATAAAACATTGTTT
1 ATAACTTTTAATCAAACAATATAAGTAATATAAAACATTGTTT
41421465 GAAGACCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.39
Consensus pattern (47 bp):
ATAACTTTTAATCAAACAATATAAGTAATATAAAACATTGTTTAATT
Found at i:41425642 original size:27 final size:27
Alignment explanation
Indices: 41425608--41425668 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
41425598 AAAAATAACT
*
41425608 AAAATATTATAACTTTTTTTATTTACC
1 AAAATATTATAAATTTTTTTATTTACC
41425635 AAAATATTATAAATTTTTTTATTTACC
1 AAAATATTATAAATTTTTTTATTTACC
41425662 AAAATAT
1 AAAATAT
41425669 ACCAAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (27 bp):
AAAATATTATAAATTTTTTTATTTACC
Found at i:41426098 original size:18 final size:18
Alignment explanation
Indices: 41426075--41426138 Score: 92
Period size: 18 Copynumber: 3.5 Consensus size: 18
41426065 TAAAATAGAG
41426075 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* * *
41426093 TTATTAAATTAAAATAGAG
1 TTATTAAATGAGAATAG-T
41426112 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
41426130 TTATTAAAT
1 TTATTAAAT
41426139 TAAAATAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 24 0.62
19 15 0.38
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:41426101 original size:37 final size:36
Alignment explanation
Indices: 41426059--41426326 Score: 208
Period size: 37 Copynumber: 7.6 Consensus size: 36
41426049 CTTAATTTTT
41426059 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATA-TTTA
41426096 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATA-TTTA
*
41426133 TTAAATTAAAATAGAGTTATTACTTAATTAGAAT-TCTCTCA
1 TTAAATTAAAATAGAGTTATTA---AATGAGAATAT-T-T-A
* * ** * * **
41426174 TTTAA-T-AACTCTA-TT-TTAATTTA-AA-A-AAA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATATTTA
* * *
41426203 TTAAATTAAAAT--AG-T-TT-ACTTA-ACT-TTT-
1 TTAAATTAAAATAGAGTTATTAAATGAGAATATTTA
41426231 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAAT-ATTTA
* *
41426268 TTAAATTAAAATAGAGTTATTAGATGGGAATATTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATA-TTTA
41426305 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
41426327 CTTAATTAGA
Statistics
Matches: 190, Mismatches: 19, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
28 17 0.09
29 9 0.05
30 3 0.02
31 4 0.02
32 2 0.01
33 5 0.03
34 6 0.03
36 4 0.02
37 117 0.62
38 3 0.02
39 5 0.03
40 10 0.05
41 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (36 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATATTTA
Found at i:41426159 original size:18 final size:19
Alignment explanation
Indices: 41426059--41426154 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
41426049 CTTAATTTTT
41426059 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
41426078 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
41426096 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
41426115 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
41426133 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
41426152 TTA
1 TTA
41426155 CTTAATTAGA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
18 30 0.48
19 33 0.52
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:41426255 original size:19 final size:19
Alignment explanation
Indices: 41426231--41426326 Score: 97
Period size: 19 Copynumber: 5.2 Consensus size: 19
41426221 CTTAACTTTT
41426231 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
41426250 TTAAATGAGAATA-ATTTA
1 TTAAATTAAAATAGAGTTA
41426268 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* *** **
41426287 TTAGATGGGAATA-TTTTA
1 TTAAATTAAAATAGAGTTA
41426305 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
41426324 TTA
1 TTA
41426327 CTTAATTAGA
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
18 27 0.47
19 30 0.53
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:41426255 original size:172 final size:173
Alignment explanation
Indices: 41425968--41426341 Score: 687
Period size: 172 Copynumber: 2.2 Consensus size: 173
41425958 ATAAGCTCTT
*
41425968 AAATAGAGTTATTACTTAATTATAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT
1 AAATAGAGTTATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT
* *
41426033 AAATTAAAATAGTTTACTTAATTTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
66 AAATTAAAATAGTTTACTTAACTTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAATTTATT
41426098 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
131 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
41426141 AAATAGAGTTATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAA-TTTAAAAAAATT
1 AAATAGAGTTATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT
41426205 AAATTAAAATAGTTTACTTAACTTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAATTTATT
66 AAATTAAAATAGTTTACTTAACTTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAATTTATT
* * *
41426270 AAATTAAAATAGAGTTATTAGATGGGAATATTTTATTAAATTA
131 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
41426313 AAATAGAGTTATTACTTAATTAGAATTCT
1 AAATAGAGTTATTACTTAATTAGAATTCT
41426342 AAGTATCTTA
Statistics
Matches: 195, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
172 144 0.74
173 51 0.26
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.43
Consensus pattern (173 bp):
AAATAGAGTTATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT
AAATTAAAATAGTTTACTTAACTTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAATTTATT
AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
Found at i:41426270 original size:18 final size:18
Alignment explanation
Indices: 41426247--41426310 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
41426237 TAAAATAGAG
41426247 TTATTAAATGAGAATAAT
1 TTATTAAATGAGAATAAT
* * *
41426265 TTATTAAATTAAAATAGAG
1 TTATTAAATGAGAATA-AT
* * *
41426284 TTATTAGATGGGAATATT
1 TTATTAAATGAGAATAAT
41426302 TTATTAAAT
1 TTATTAAAT
41426311 TAAAATAGAG
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTATTAAATGAGAATAAT
Found at i:41426870 original size:27 final size:27
Alignment explanation
Indices: 41426826--41426877 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
41426816 CATTTTAGTC
41426826 CTTTGGCACCATTAGTGCCGCCAATCT
1 CTTTGGCACCATTAGTGCCGCCAATCT
* *
41426853 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTAGTGCCGCCAAT
41426878 GTGATTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTAGTGCCGCCAATCT
Found at i:41426885 original size:27 final size:27
Alignment explanation
Indices: 41426828--41426886 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
41426818 TTTTAGTCCT
*
41426828 TTGGCACCATTAGTGCCGCCAATCTCT
1 TTGGCACCATTAGTGCCGCCAATCTCA
* * * *
41426855 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTAGTGCCGCCAATCTCA
41426882 TTGGC
1 TTGGC
41426887 CTGTTGTCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTAGTGCCGCCAATCTCA
Found at i:41426943 original size:29 final size:28
Alignment explanation
Indices: 41426911--41426980 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
41426901 TTTTTCTGTT
41426911 TTTTTATATATATTTTGATAAATAAAAAA
1 TTTTTATA-ATATTTTGATAAATAAAAAA
*
41426940 TTTTTATAATATTTTGGTAAATAAAAAA
1 TTTTTATAATATTTTGATAAATAAAAAA
*
41426968 --ATTATAATATTTT
1 TTTTTATAATATTTT
41426981 AGTTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
26 12 0.31
28 19 0.49
29 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTTTATAATATTTTGATAAATAAAAAA
Found at i:41432466 original size:229 final size:227
Alignment explanation
Indices: 41431736--41432609 Score: 835
Period size: 229 Copynumber: 3.8 Consensus size: 227
41431726 TTACCACAAA
* * *
41431736 GCGCCGCAAAATATCTTAACCAAAATACAACGTTTTCGTCTTGACGTATACTAGAATTAGTGGCG
1 GCGCCGCAAAATATCTTAACCAAAACACAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * * * ** *
41431801 ATTATGAG-AAAACGCCACTAAA-G--CGTATTAGCAGCGTTTTGCGAA-ATGCGCCGCAAAAAT
66 CTTA-CAGTAAAACGCCACTAAAGGATAGTATTAGCGGCACTTTGTGAATA-GCGCCGC-AAAAT
* * *
41431861 ATCTTAACCAAAACGCATCGTTTTGGTCTTGATGTATCCTAGAATTAGTGGCGCTTAAGGGAAAA
128 ATCTTAACCAAAACGCA-AGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTT-ACGGAAAA
* * *** *
41431926 CACCG-TTAAGGCATAGTATTAGCGGCGCTTTGCCAAAA
191 CGCCGCTAAAGG-ATAGTATTAGCGGCGCTTT-CTGGAT
* * * *
41431964 GCGCCGCAAAATATCTTTACC-AAACGCAGA-G-TTTGGTCTTGAGGTATGCTAGAATTAGTGGC
1 GCGCCGCAAAATATCTTAACCAAAACACA-ACGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * * ** ** * *
41432026 GCTTATAGGAAAACGCTAC-AAACAAATAGTATTAGCGGGGCTTTTTGAA-AGCGCTGCAAAATA
65 GCTTACAGTAAAACGCCACTAAA-GGATAGTATTAGCGGCACTTTGTGAATAGCGCCGCAAAATA
* * * * *
41432089 TCTGAACCAAAATGCATCA-TTTTGGTCTTGCT-TATACTAGAATTAGTGGCGTTTACCGAAAAC
129 TCTTAACCAAAACGCA--AGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGAAAAC
* * ** ** *
41432152 GCCGCTATAGCATAGTATTAGCGGCGAATAGTGGCT
192 GCCGCTAAAGGATAGTATTAGCGGCGCTTTCTGGAT
*
41432188 GGCGCCGCAAAATATCTTAACCAAAACACAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
1 -GCGCCGCAAAATATCTTAACCAAAACACAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
*
41432253 GCTTACAGTAAAACGCCATTAAAGGATAGTATTAGCGGCACTTTG-GTAATAGCGCCGCAAAATA
65 GCTTACAGTAAAACGCCACTAAAGGATAGTATTAGCGGCACTTTGTG-AATAGCGCCGCAAAATA
* ** ** *
41432317 TCTTAACCAAAACGCAGAGTTTTGGTCTTGAGGTATGTTAGCGTTAGTGGCGCTTATTGGAAAAC
129 TCTTAACCAAAACGCA-AGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTA-CGGAAAAC
* *
41432382 GCGGCTAAAGGATAGTATTAGCGGCGCTTTTTGGAT
192 GCCGCTAAAGGATAGTATTAGCGGCGCTTTCTGGAT
* * * *
41432418 GCGCCGCAAAATATCTAAACCAAAACGCAACGTTTTGGT-TTGGATGTATACTTGAATTATTGGC
1 GCGCCGCAAAATATCTTAACCAAAACACAACGTTTTGGTCTT-GATGTATACTAGAATTAGTGGC
* * * * ** * **
41432482 GCTTACGGTGAAACGCCGCTAAAGCATAGTATTAGCGGCGA-TTTGTGGCTAGTGCCATAAAATA
65 GCTTACAGTAAAACGCCACTAAAGGATAGTATTAGCGGC-ACTTTGTGAATAGCGCCGCAAAATA
* * * *
41432546 CCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAAAATTTGTGGCGCTTACGGTAAAC
129 TCTTAACCAAAACGCAA-GTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGAAAAC
41432610 CGTCGCGAAA
Statistics
Matches: 525, Mismatches: 99, Indels: 44
0.79 0.15 0.07
Matches are distributed among these distances:
225 51 0.10
226 72 0.14
227 102 0.19
228 77 0.15
229 187 0.36
230 36 0.07
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (227 bp):
GCGCCGCAAAATATCTTAACCAAAACACAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
CTTACAGTAAAACGCCACTAAAGGATAGTATTAGCGGCACTTTGTGAATAGCGCCGCAAAATATC
TTAACCAAAACGCAAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGAAAACGCCG
CTAAAGGATAGTATTAGCGGCGCTTTCTGGAT
Found at i:41432603 original size:115 final size:114
Alignment explanation
Indices: 41431735--41432609 Score: 839
Period size: 113 Copynumber: 7.7 Consensus size: 114
41431725 TTTACCACAA
** * *
41431735 AGCGCCGCAAAATATCTTAACCAAAATACAACGTTTTCGTCTTGACGTATACTAGAATTAGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * * * *
41431800 GATTATGAGAAAACGCCACTAAAGC---GTATTAGCAGCG-TTT-TGCGAA
66 GCTTACG-GAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTG-GAT
* *
41431846 ATGCGCCGCAAAAATATCTTAACCAAAACGCATCGTTTTGGTCTTGATGTATCCTAGAATTAGTG
1 A-GCGCCGC-AAAATATCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAGAATTAGTG
* * * * * *** *
41431911 GCGCTTAAGGGAAAACACCGTTAAGGCATAGTATTAGCGGCGCTTTGCCAAA
64 GCGCTT-ACGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
* * *
41431963 AGCGCCGCAAAATATCTTTACC-AAACGCAGA-G-TTTGGTCTTGAGGTATGCTAGAATTAGTGG
1 AGCGCCGCAAAATATCTTAACCAAAACGCA-ACGTTTTGGTCTTGATGTATACTAGAATTAGTGG
* ** * * * *
41432025 CGCTTATAGGAAAACGCTAC-AAA-CAAATAGTATTAGCGGGGCTTT-TTGAA
65 CGCTTA-CGGAAAACGCCGCTAAAGC--ATAGTATTAGCGGCGATTTGTGGAT
* * * * * *
41432075 AGCGCTGCAAAATATCTGAACCAAAATGCATCATTTTGGTCTTGCT-TATACTAGAATTAGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* * * * * *
41432139 GTTTACCGAAAACGCCGCTATAGCATAGTATTAGCGGCGAATAGTGGCT
66 GCTTACGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
* * *
41432188 GGCGCCGCAAAATATCTTAACCAAAACACAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
* ** * *
41432253 GCTTACAGTAAAACGCCATTAAAGGATAGTATTAGCGGC-ACTTTG-GTAAT
66 GCTTAC-GGAAAACGCCGCTAAAGCATAGTATTAGCGGCGA-TTTGTG-GAT
* ** **
41432303 AGCGCCGCAAAATATCTTAACCAAAACGCAGA-GTTTTGGTCTTGAGGTATGTTAGCGTTAGTGG
1 AGCGCCGCAAAATATCTTAACCAAAACGCA-ACGTTTTGGTCTTGATGTATACTAGAATTAGTGG
* * * * *
41432367 CGCTTATTGGAAAACGCGGCTAAAGGATAGTATTAGCGGCGCTTTTTGGAT
65 CGCTTA-CGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
* * *
41432418 -GCGCCGCAAAATATCTAAACCAAAACGCAACGTTTTGGT-TTGGATGTATACTTGAATTATTGG
1 AGCGCCGCAAAATATCTTAACCAAAACGCAACGTTTTGGTCTT-GATGTATACTAGAATTAGTGG
* *
41432481 CGCTTACGGTGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGCT
65 CGCTTACGG-AAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
* ** * * *
41432532 AGTGCCATAAAATACCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAAAATTTGTGGC
1 AGCGCCGCAAAATATCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
*
41432597 GCTTACGGTAAAC
66 GCTTACGGAAAAC
41432610 CGTCGCGAAA
Statistics
Matches: 621, Mismatches: 112, Indels: 59
0.78 0.14 0.07
Matches are distributed among these distances:
111 2 0.00
112 55 0.09
113 200 0.32
114 141 0.23
115 196 0.32
116 21 0.03
117 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (114 bp):
AGCGCCGCAAAATATCTTAACCAAAACGCAACGTTTTGGTCTTGATGTATACTAGAATTAGTGGC
GCTTACGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTTGTGGAT
Found at i:41432795 original size:20 final size:20
Alignment explanation
Indices: 41432770--41432811 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41432760 TACAGTTTAG
41432770 GGTTTAGGGTTTACGATATA
1 GGTTTAGGGTTTACGATATA
* * *
41432790 GGTTTAGTGTTTTCGATTTA
1 GGTTTAGGGTTTACGATATA
41432810 GG
1 GG
41432812 GTTTGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.31, T:0.45
Consensus pattern (20 bp):
GGTTTAGGGTTTACGATATA
Found at i:41433337 original size:14 final size:13
Alignment explanation
Indices: 41433302--41433361 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
41433292 ATTAGCGGCG
*
41433302 TTAGGATTACGGT
1 TTAGGTTTACGGT
*
41433315 TTGGGGTTTACGGT
1 TT-AGGTTTACGGT
41433329 TTAGAGTTTA-GAGTT
1 TTAG-GTTTACG-G-T
*
41433344 TTAGGTTTAGGGT
1 TTAGGTTTACGGT
41433357 TTAGG
1 TTAGG
41433362 AATTATGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 10 0.26
14 23 0.59
15 6 0.15
ACGTcount: A:0.18, C:0.03, G:0.35, T:0.43
Consensus pattern (13 bp):
TTAGGTTTACGGT
Found at i:41433451 original size:8 final size:7
Alignment explanation
Indices: 41433428--41433496 Score: 66
Period size: 7 Copynumber: 9.3 Consensus size: 7
41433418 AGTTTTAAGA
*
41433428 TTTAAGG
1 TTTAGGG
41433435 TTTAGGG
1 TTTAGGG
41433442 TTTAAGGG
1 TTT-AGGG
41433450 TTTAGTGG
1 TTTAG-GG
* *
41433458 CTTAGGAT
1 TTTAGG-G
41433466 TTTAGGG
1 TTTAGGG
41433473 TTTAAGGG
1 TTT-AGGG
*
41433481 TTTAAGG
1 TTTAGGG
41433488 TTTAGGG
1 TTTAGGG
41433495 TT
1 TT
41433497 AAATCCCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
7 26 0.51
8 25 0.49
ACGTcount: A:0.20, C:0.01, G:0.35, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:41433451 original size:15 final size:15
Alignment explanation
Indices: 41433428--41433496 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
41433418 AGTTTTAAGA
41433428 TTTAA-GGTTTAGGG
1 TTTAAGGGTTTAGGG
41433442 TTTAAGGGTTTAGTGG
1 TTTAAGGGTTTAG-GG
* *
41433458 CTT-AGGATTTTAGGG
1 TTTAAGG-GTTTAGGG
*
41433473 TTTAAGGGTTTAAGG
1 TTTAAGGGTTTAGGG
41433488 TTT-AGGGTT
1 TTTAAGGGTT
41433497 AAATCCCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
14 11 0.24
15 23 0.50
16 12 0.26
ACGTcount: A:0.20, C:0.01, G:0.35, T:0.43
Consensus pattern (15 bp):
TTTAAGGGTTTAGGG
Found at i:41434114 original size:148 final size:148
Alignment explanation
Indices: 41433961--41434243 Score: 372
Period size: 148 Copynumber: 1.9 Consensus size: 148
41433951 TTTACTACGA
* * * *
41433961 GTTGAGGAAACG-GGACCGTTTCCTCCTTTTATTAGTGGCACTTCAGCTAAAGCGCCGCAAAAAT
1 GTTGAGGAAACGACG-CCGTTTCCTACTTTTATTAGTGGCACTTCAGATAAAACGCCGCAAAAAT
* * *
41434025 GTTTAAGGTTATCTGATAACAGTGCCGTTTTGTCCATGTTATTTGTGGCGTTTTTACTGC-AAGC
65 GTTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTTGTGGCGTTTTTACT-CTAAGC
41434089 GCCACAAATATTTATTAGTG
129 GCCACAAATATTTATTAGTG
* * * ** *
41434109 GTTGAGGTAACGACGCCGTTTCCTATTTTTATTAGTGGCGCTTTTGATAAAACGCCGTAAAAATG
1 GTTGAGGAAACGACGCCGTTTCCTACTTTTATTAGTGGCACTTCAGATAAAACGCCGCAAAAATG
* * * * *
41434174 TTTATGGTTATCTAATAGCGGTGTCATTTTGTCCATGGTATTTGTGGCGTTTTTGCTCTAAGCGC
66 TTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTTGTGGCGTTTTTACTCTAAGCGC
41434239 CACAA
131 CACAA
41434244 GTTTTAGCTT
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
147 1 0.01
148 113 0.98
149 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (148 bp):
GTTGAGGAAACGACGCCGTTTCCTACTTTTATTAGTGGCACTTCAGATAAAACGCCGCAAAAATG
TTTAAGGTTATCTAATAACAGTGCCATTTTGTCCATGGTATTTGTGGCGTTTTTACTCTAAGCGC
CACAAATATTTATTAGTG
Found at i:41434700 original size:14 final size:14
Alignment explanation
Indices: 41434683--41434734 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
41434673 ACTTTGGAAT
41434683 ATATACTTGCTGGA
1 ATATACTTGCTGGA
41434697 ATATATTCCAGTTGCTGGA
1 ATATA---C--TTGCTGGA
41434716 ATATACTTGCTGGA
1 ATATACTTGCTGGA
41434730 ATATA
1 ATATA
41434735 TGGCCAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 18 0.55
16 1 0.03
17 1 0.03
19 13 0.39
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (14 bp):
ATATACTTGCTGGA
Found at i:41436262 original size:25 final size:25
Alignment explanation
Indices: 41436234--41436284 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
41436224 ATATTTTCAA
* *
41436234 ACATCTTTGATATATATATTTATAT
1 ACATCTTTAATATATATATATATAT
*
41436259 ACATTTTTAATATATATATATATAT
1 ACATCTTTAATATATATATATATAT
41436284 A
1 A
41436285 TTAAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (25 bp):
ACATCTTTAATATATATATATATAT
Found at i:41436284 original size:27 final size:27
Alignment explanation
Indices: 41436243--41436302 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
41436233 AACATCTTTG
* * *
41436243 ATATATATATTTATA-TACATTTTTAAT
1 ATATATATATATATATTAAAATTTT-AT
41436270 ATATATATATATATATTAAAATTTTAT
1 ATATATATATATATATTAAAATTTTAT
41436297 ATATAT
1 ATATAT
41436303 TTGAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATATATATATATATATTAAAATTTTAT
Found at i:41436297 original size:19 final size:19
Alignment explanation
Indices: 41436249--41436315 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
41436239 TTTGATATAT
* *
41436249 ATATTTATATACATTTTTAAT
1 ATATTTATAT--ATATTTAAA
*
41436270 ATATATATATATATATTAAA
1 ATATTTATATATAT-TTAAA
*
41436290 AT-TTTATATATATTTGAA
1 ATATTTATATATATTTAAA
41436308 ATATTTAT
1 ATATTTAT
41436316 CAATCATATC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 6 0.15
19 18 0.46
20 6 0.15
21 9 0.23
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
ATATTTATATATATTTAAA
Found at i:41436397 original size:21 final size:21
Alignment explanation
Indices: 41436371--41436442 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
41436361 CTTACACAAC
41436371 ACATAACTTACATAATAACTT
1 ACATAACTTACATAATAACTT
*
41436392 ACATAACTTATAT-ATAAACTTAT
1 ACATAACTTACATAAT-AAC-T-T
* *
41436415 ATATAACTTACATACATAGCTT
1 ACATAACTTACATA-ATAACTT
*
41436437 AAATAA
1 ACATAA
41436443 AATTTATATG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
20 2 0.05
21 15 0.37
22 7 0.17
23 13 0.32
24 2 0.05
25 2 0.05
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (21 bp):
ACATAACTTACATAATAACTT
Found at i:41436420 original size:23 final size:23
Alignment explanation
Indices: 41436394--41436556 Score: 82
Period size: 23 Copynumber: 6.9 Consensus size: 23
41436384 AATAACTTAC
41436394 ATAACTTATATATAAACTTATAT
1 ATAACTTATATATAAACTTATAT
* * * *
41436417 ATAACTTACATACATAGCTTAAAT
1 ATAACTTATATATA-AACTTATAT
* * * * *
41436441 AAAATTTATATGTAAACTTACACAACAG
1 ATAACTTATATATAAACTT-----ATAT
* *
41436469 ATAACTTACATA-ATAAC-T-TAC
1 ATAACTTATATATA-AACTTATAT
41436490 ATAACTTATATATAAACTTATAT
1 ATAACTTATATATAAACTTATAT
* *
41436513 ATAACTTACATACATAACTTA-ACT
1 ATAACTTATATATA-AACTTATA-T
* *
41436537 AAAATTTATATATAAACTTA
1 ATAACTTATATATAAACTTA
41436557 CACAACACAT
Statistics
Matches: 102, Mismatches: 26, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
21 15 0.15
22 2 0.02
23 37 0.36
24 33 0.32
27 2 0.02
28 13 0.13
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAACTTATATATAAACTTATAT
Found at i:41436446 original size:96 final size:95
Alignment explanation
Indices: 41436332--41436634 Score: 491
Period size: 96 Copynumber: 3.2 Consensus size: 95
41436322 TATCATAATT
*
41436332 TACATACATAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATA
1 TACATACTTAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATA
41436397 ACTTATATATAAACTTATATATAACTTACA
66 ACTTATATATAAACTTATATATAACTTACA
* *
41436427 TACATAGCTTAAATAAAATTTATATGTAAACTTACACAACAGATAACTTACATAATAACTTACAT
1 TACATA-CTTAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACAT
41436492 AACTTATATATAAACTTATATATAACTTACA
65 AACTTATATATAAACTTATATATAACTTACA
*
41436523 TACATAACTTAACTAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACAT
1 TACAT-ACTTAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACAT
* * *
41436588 AACTTATACAT-GACTTATATATAACTTTCA
65 AACTTATATATAAACTTATATATAACTTACA
*
41436618 TAACTTACTTATAATAA
1 T-ACATACTTA-AATAA
41436635 CTTACATAAC
Statistics
Matches: 193, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
95 29 0.15
96 163 0.84
97 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (95 bp):
TACATACTTAAATAAAATTTATATATAAACTTACACAACACATAACTTACATAATAACTTACATA
ACTTATATATAAACTTATATATAACTTACA
Found at i:41436459 original size:36 final size:36
Alignment explanation
Indices: 41436391--41436462 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
41436381 CATAATAACT
*
41436391 TACATAACTTATATATAAACTTATATATAACTTACA
1 TACATAACTTAAATATAAACTTATATATAACTTACA
* * *
41436427 TACATAGCTTAAATA-AAATTTATATGTAAACTTACA
1 TACATAACTTAAATATAAACTTATATAT-AACTTACA
41436463 CAACAGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 10 0.32
36 21 0.68
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (36 bp):
TACATAACTTAAATATAAACTTATATATAACTTACA
Found at i:41436577 original size:9 final size:9
Alignment explanation
Indices: 41436551--41436670 Score: 53
Period size: 9 Copynumber: 13.7 Consensus size: 9
41436541 TTTATATATA
*
41436551 AACTTACAC
1 AACTTACAT
41436560 AAC--ACAT
1 AACTTACAT
41436567 AACTTACATAAT
1 AACTTAC---AT
41436579 AACTTACAT
1 AACTTACAT
41436588 AACTTATACAT
1 AAC-T-TACAT
* *
41436599 GACTTATATAT
1 AAC-T-TACAT
*
41436610 AACTTTCAT
1 AACTTACAT
41436619 AACTTAC-T
1 AACTTACAT
*
41436627 TA--TA-AT
1 AACTTACAT
41436633 AACTTACAT
1 AACTTACAT
41436642 AACTTAC-T
1 AACTTACAT
*
41436650 TA--TA-AT
1 AACTTACAT
41436656 AACTTACAT
1 AACTTACAT
41436665 AACTTA
1 AACTTA
41436671 TTAATATTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
6 8 0.09
7 6 0.07
8 8 0.09
9 36 0.42
10 2 0.02
11 16 0.19
12 9 0.11
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.36
Consensus pattern (9 bp):
AACTTACAT
Found at i:41436603 original size:11 final size:11
Alignment explanation
Indices: 41436563--41436624 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
41436553 CTTACACAAC
41436563 ACATAACTTACAT
1 ACATAACTT--AT
41436576 A-ATAAC-T-T
1 ACATAACTTAT
41436584 ACATAACTTAT
1 ACATAACTTAT
*
41436595 ACATGACTTAT
1 ACATAACTTAT
*
41436606 ATATAACTT-T
1 ACATAACTTAT
41436616 -CATAACTTA
1 ACATAACTTA
41436625 CTTATAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
8 2 0.05
9 12 0.29
10 2 0.05
11 19 0.46
12 5 0.12
13 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.37
Consensus pattern (11 bp):
ACATAACTTAT
Found at i:41436613 original size:43 final size:45
Alignment explanation
Indices: 41436565--41436668 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 45
41436555 TACACAACAC
* *
41436565 ATAACTTACATAA-TAACTTA-CATAACTTATACATGACTTA-TAT-
1 ATAACTTACATAACTAACTTATAATAAC-T-TACATAACTTACTATA
* *
41436608 ATAACTTTCATAACTTACTTATAATAACTTACATAACTTACTTATA
1 ATAACTTACATAACTAACTTATAATAACTTACATAACTTAC-TATA
41436654 ATAACTTACATAACT
1 ATAACTTACATAACT
41436669 TATTAATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 22 0.43
44 7 0.14
45 8 0.16
46 14 0.27
ACGTcount: A:0.43, C:0.17, G:0.01, T:0.38
Consensus pattern (45 bp):
ATAACTTACATAACTAACTTATAATAACTTACATAACTTACTATA
Done.