Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 122 of 135
Found at i:44182242 original size:228 final size:225
Alignment explanation
Indices: 44181845--44183071 Score: 1707
Period size: 228 Copynumber: 5.5 Consensus size: 225
44181835 TACTGCTCCA
** * * *
44181845 TTAACATAAACATCTAAGCTACCGGAGCCAACCTTAACGCAAATCGCGTTGGCGCCAATGAGAAG
1 TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAG
* *
44181910 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGTAATTGTAA
66 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
* * *
44181975 CCGAATCAGGTTCGGATTTCACTTCGTGGTCCTCTTCGACAATGCAATTGTCACCCGATTCCACA
131 CCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACT
44182040 ACAACTCCATTAACGGAGTCGCTTCCATTTACG
196 ACAACTCCATTAACGGAGTCG-TTCCA-TTA-G
* * * *
44182073 TTAACATAAACATCCGTGCTGCCGGTGCCAACCTTAACGCTACTCGTGTTGGCGCCATTGAGAAG
1 TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAG
* * * *
44182138 ATATCTCGTTTCATTCTCTTTCTCATCTACTATATCCGCCTCCTGCTGATTCATAGTAATAGTGA
66 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
* * * *
44182203 CCGAATCAGATTCGGATTTCACTTCGTGGTTTTCTTCGACAATGCAATTGCCATCTGATTCCACT
131 CCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACT
*
44182268 ACAGCTCCATTAACGGAGTCGTTTCC---A-
196 ACAACTCCATTAACGGAGTCG-TTCCATTAG
* * * * *
44182295 TTAACATAGACATCTGAGCTGCCGGAGCCAACCTTAACGCAAATCGCGTTGGCGCCAATAAGAAG
1 TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAG
* *
44182360 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGTAATTGTAA
66 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
*
44182425 CCGAATCAGATTCGGATTTCACTTCGTGTTCTTCTTCGACAATGCAATTGTCACCCGATTCCACT
131 CCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACT
44182490 ACAACTCCATTAACGGAGTCGTTGCCATCTAGG
196 ACAACTCCATTAACGGAGTCGTT-CCAT-TA-G
* * *** * * *
44182523 TTAGCATAAGCATCCGAGCCATCGGAGCCAACGTTAACGCTACTCGTGTTGGCGCCATTGAGAAG
1 TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAG
*
44182588 ATATCTCGTTTCATTCTGTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
66 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
* * *
44182653 CCGAATCAGATTCGGATTGCACTTCGTGGTCTTCTTCGACAATGCAATTGTCTCCCGGTTCCACT
131 CCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACT
44182718 ACAACTCCATTAACGGAGTCGTTCCCATCTAGG
196 ACAACTCCATTAACGGAGTCGTT-CCAT-TA-G
** **
44182751 TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCTGCTCATGTTGGCGCCATTGAGAAG
1 TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAG
44182816 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
66 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
* * * *
44182881 CCGAATCAGATTCGG-TTGGCACTTCGTGGTCTTCTTCGACAATGCAATTGCCATCCGATTCCAT
131 CCGAATCAGATTCGGATT-TCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCAC
*
44182945 TACAACTCCATTATCGGAGTCGTTTCC---A-
195 TACAACTCCATTAACGGAGTCG-TTCCATTAG
* *
44182973 TTAACATAAACATCCGAGCTCCCGGAACCAACCTTAACGCAACT--C----GCG---TTGAGAAG
1 TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAG
* * *
44183029 ATATTTCTTTTCATTCCCTTTCTCAGCTACAATATCCACCTCC
66 ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCC
44183072 GCGGCTACAT
Statistics
Matches: 901, Mismatches: 89, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
213 48 0.05
216 3 0.00
221 2 0.00
222 237 0.26
224 2 0.00
226 1 0.00
227 2 0.00
228 604 0.67
229 2 0.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (225 bp):
TTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCATTGAGAAG
ATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGTAATAGTAA
CCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATTCCACT
ACAACTCCATTAACGGAGTCGTTCCATTAG
Found at i:44182682 original size:450 final size:450
Alignment explanation
Indices: 44181840--44183071 Score: 1798
Period size: 450 Copynumber: 2.8 Consensus size: 450
44181830 TCCACTACTG
* *
44181840 CTCCATTAACATAAACATCTAAGCTACCGGAGCCAACCTTAACGCAAATCGCGTTGGCGCCAATG
1 CTCCATTAACATAAACATCTGAGCTGCCGGAGCCAACCTTAACGCAAATCGCGTTGGCGCCAATG
44181905 AGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGTAAT
66 AGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGTAAT
* *
44181970 TGTAACCGAATCAGGTTCGGATTTCACTTCGTGGTCCTCTTCGACAATGCAATTGTCACCCGATT
131 TGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATT
* * * ** *
44182035 CCACAACAACTCCATTAACGGAGTCGCTTCCATTTACGTTAACATAAACATCCGTGCTGCCGGTG
196 CCACTACAACTCCATTAACGGAGTCG-TTCCATCTACGTTAACATAAACATCCGAGCCACCGGAG
*
44182100 CCAACCTTAACGCTACTCGTGTTGGCGCCATTGAGAAGATATCTCGTTTCATTCTCTTTCTCATC
260 CCAACCTTAACGCTACTCGTGTTGGCGCCATTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGC
* * * *
44182165 TACTATATCCGCCTCCTGCTGATTCATAGTAATAGTGACCGAATCAGATTCGGATTTCACTTCGT
325 TACAATATCCACCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTGCACTTCGT
* * *
44182230 GGTTTTCTTCGACAATGCAATTGCCAT-CTGATTCCACTACAGCTCCATTAACGGAGTCGTT
390 GGTCTTCTTCGACAATGCAATTGCC-TCCCGATTCCACTACAACTCCATTAACGGAGTCGTT
* *
44182291 -TCCATTAACATAGACATCTGAGCTGCCGGAGCCAACCTTAACGCAAATCGCGTTGGCGCCAATA
1 CTCCATTAACATAAACATCTGAGCTGCCGGAGCCAACCTTAACGCAAATCGCGTTGGCGCCAATG
44182355 AGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGTAAT
66 AGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGTAAT
*
44182420 TGTAACCGAATCAGATTCGGATTTCACTTCGTGTTCTTCTTCGACAATGCAATTGTCACCCGATT
131 TGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATT
* * * *
44182485 CCACTACAACTCCATTAACGGAGTCGTTGCCATCTAGGTTAGCATAAGCATCCGAGCCATCGGAG
196 CCACTACAACTCCATTAACGGAGTCGTT-CCATCTACGTTAACATAAACATCCGAGCCACCGGAG
* *
44182550 CCAACGTTAACGCTACTCGTGTTGGCGCCATTGAGAAGATATCTCGTTTCATTCTGTTTCTCAGC
260 CCAACCTTAACGCTACTCGTGTTGGCGCCATTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGC
44182615 TACAATATCCACCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTGCACTTCGT
325 TACAATATCCACCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTGCACTTCGT
* *
44182680 GGTCTTCTTCGACAATGCAATTGTCTCCCGGTTCCACTACAACTCCATTAACGGAGTCGTT
390 GGTCTTCTTCGACAATGCAATTGCCTCCCGATTCCACTACAACTCCATTAACGGAGTCGTT
* * *** **
44182741 CCCATCTAGGTTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCTGCTCATGTTGGCGC
1 --C-TCCA--TTAACATAAACATCTGAGCTGCCGGAGCCAACCTTAACGCAAATCGCGTTGGCGC
* *
44182806 CATTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATA
61 CAATGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATA
* * * *
44182871 GTAATAGTAACCGAATCAGATTCGG-TTGGCACTTCGTGGTCTTCTTCGACAATGCAATTGCCAT
126 GTAATTGTAACCGAATCAGATTCGGATT-TCACTTCGTGGTCTTCTTCGACAATGCAATTGTCAC
* * *
44182935 CCGATTCCATTACAACTCCATTATCGGAGTCGTT---TC--CATTAACATAAACATCCGAGCTC-
190 CCGATTCCACTACAACTCCATTAACGGAGTCGTTCCATCTACGTTAACATAAACATCCGAGC-CA
* * * * *
44182994 CCGGAACCAACCTTAACGCAACTC------GCG---TTGAGAAGATATTTCTTTTCATTCCCTTT
254 CCGGAGCCAACCTTAACGCTACTCGTGTTGGCGCCATTGAGAAGATATCTCGTTTCATTCTCTTT
44183050 CTCAGCTACAATATCCACCTCC
319 CTCAGCTACAATATCCACCTCC
44183072 GCGGCTACAT
Statistics
Matches: 712, Mismatches: 59, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
441 47 0.07
444 3 0.00
449 3 0.00
450 453 0.64
451 1 0.00
452 2 0.00
454 3 0.00
455 2 0.00
456 198 0.28
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (450 bp):
CTCCATTAACATAAACATCTGAGCTGCCGGAGCCAACCTTAACGCAAATCGCGTTGGCGCCAATG
AGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGTAAT
TGTAACCGAATCAGATTCGGATTTCACTTCGTGGTCTTCTTCGACAATGCAATTGTCACCCGATT
CCACTACAACTCCATTAACGGAGTCGTTCCATCTACGTTAACATAAACATCCGAGCCACCGGAGC
CAACCTTAACGCTACTCGTGTTGGCGCCATTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCT
ACAATATCCACCTCCTGCTGATTCATAGTAATAGTAACCGAATCAGATTCGGATTGCACTTCGTG
GTCTTCTTCGACAATGCAATTGCCTCCCGATTCCACTACAACTCCATTAACGGAGTCGTT
Found at i:44183929 original size:176 final size:174
Alignment explanation
Indices: 44183600--44183952 Score: 429
Period size: 176 Copynumber: 2.0 Consensus size: 174
44183590 ATTCACTTTG
* * * *
44183600 GTTTCAATTCAGTCATTCAACTTTTAAAAAATAACAAAACAATCACTAATGTTATCAAAAAGTGA
1 GTTTCAATTCAGCCACTCAACTTTCAAAAAATAACAAAACAATCACTAACGTTATCAAAAAGTGA
* * ** * *
44183665 CAAAATAGTCACCCATTAACATTTTCTGTTACAGGCCTAACGGGACAGGTGATGTGGCCAGTTAA
66 CAAAATAGTCACCCATTAACATTTTCTGTTACAGACCTAACGAGACAGGTGACATGACCAGTAAA
* * * * * *
44183730 CTAGCTGACGTGGCCAGTTAACTTGCCACGTTGGATGAGGCTAA
131 CTAGCTAACGTGACCAATTAACTTGCCACGTTAGACGAGGCAAA
* *
44183774 GTTTCAATTCAGCCACTCAACTTTACAAAAAATTAACAAATCAGTCACTAACGTTATCAAAAAGT
1 GTTTCAATTCAGCCACTCAACTTT-CAAAAAA-TAACAAAACAATCACTAACGTTATCAAAAAGT
* * * *
44183839 GACAAATTAGTCACCCATTAACATTTT-TGGTTATAGACCTAACGAGACAGGTGGCATGACTAGT
64 GACAAAATAGTCACCCATTAACATTTTCT-GTTACAGACCTAACGAGACAGGTGACATGACCAGT
* * ** *
44183903 AAATTAGCTAATGTGATTAATTAACTTGCCATGTTAGACGAGGCAAA
128 AAACTAGCTAACGTGACCAATTAACTTGCCACGTTAGACGAGGCAAA
44183950 GTT
1 GTT
44183953 GAGTGACTAT
Statistics
Matches: 149, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
174 22 0.15
175 7 0.05
176 120 0.81
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (174 bp):
GTTTCAATTCAGCCACTCAACTTTCAAAAAATAACAAAACAATCACTAACGTTATCAAAAAGTGA
CAAAATAGTCACCCATTAACATTTTCTGTTACAGACCTAACGAGACAGGTGACATGACCAGTAAA
CTAGCTAACGTGACCAATTAACTTGCCACGTTAGACGAGGCAAA
Found at i:44184024 original size:29 final size:29
Alignment explanation
Indices: 44183986--44184042 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
44183976 TCCTTTTTCA
* *
44183986 TTTTTTCATAAATGTCCCAATATCTTTAC
1 TTTTTGCATAAATGGCCCAATATCTTTAC
*
44184015 TTTTTGCATAAATGGCCCAATATGTTTA
1 TTTTTGCATAAATGGCCCAATATCTTTA
44184043 TACTTCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (29 bp):
TTTTTGCATAAATGGCCCAATATCTTTAC
Found at i:44185002 original size:62 final size:62
Alignment explanation
Indices: 44184932--44185117 Score: 177
Period size: 62 Copynumber: 3.2 Consensus size: 62
44184922 GAAAGTTGAG
44184932 TGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCTTATATTTTT
1 TGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCTTATATTTTT
* * * * * * *
44184994 TGACTGTTTTGTTATT--TTTCAAAAGTTG-AGTGACTGA-ATTG--A---A-AC-TAGA----G
1 TGACTGTTTTGTCATTGATATC-AAAGTTGAAG-AACT-ATTTTGTCATTTACCCTTATATTTTT
44185044 TGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCTTATATTTTT
1 TGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCTTATATTTTT
44185106 TGACTGTTTTGT
1 TGACTGTTTTGT
44185118 TATTTTTCAA
Statistics
Matches: 92, Mismatches: 14, Indels: 36
0.65 0.10 0.25
Matches are distributed among these distances:
50 16 0.17
51 13 0.14
52 5 0.05
53 1 0.01
54 3 0.03
55 1 0.01
56 2 0.02
57 1 0.01
58 3 0.03
59 1 0.01
60 5 0.05
61 13 0.14
62 28 0.30
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (62 bp):
TGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCTTATATTTTT
Found at i:44185117 original size:112 final size:112
Alignment explanation
Indices: 44184920--44185169 Score: 482
Period size: 112 Copynumber: 2.2 Consensus size: 112
44184910 TTGTTATTTT
* *
44184920 TTGAAAGTTGAGTGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCT
1 TTGAAACTAGAGTGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCT
44184985 TATATTTTTTGACTGTTTTGTTATTTTTCAAAAGTTGAGTGACTGAA
66 TATATTTTTTGACTGTTTTGTTATTTTTCAAAAGTTGAGTGACTGAA
44185032 TTGAAACTAGAGTGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCT
1 TTGAAACTAGAGTGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCT
44185097 TATATTTTTTGACTGTTTTGTTATTTTTCAAAAGTTGAGTGACTGAA
66 TATATTTTTTGACTGTTTTGTTATTTTTCAAAAGTTGAGTGACTGAA
44185144 TTGAAACTAGAGTGACTGTTTTGTCA
1 TTGAAACTAGAGTGACTGTTTTGTCA
44185170 GCTACCTGAA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 136 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.44
Consensus pattern (112 bp):
TTGAAACTAGAGTGACTGTTTTGTCATTGATATCAAAGTTGAAGAACTATTTTGTCATTTACCCT
TATATTTTTTGACTGTTTTGTTATTTTTCAAAAGTTGAGTGACTGAA
Found at i:44186032 original size:23 final size:21
Alignment explanation
Indices: 44185993--44186041 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 21
44185983 AGGTTCAAAA
44185993 TTCAA-GTTCGAGGTTTAGGG
1 TTCAAGGTTCGAGGTTTAGGG
44186013 TTCAAGGTTCGAAGGGTTTAGGG
1 TTCAAGGTTCG-A-GGTTTAGGG
44186036 TTCAAG
1 TTCAAG
44186042 TTTGAGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.19
21 5 0.19
22 1 0.04
23 15 0.58
ACGTcount: A:0.22, C:0.10, G:0.35, T:0.33
Consensus pattern (21 bp):
TTCAAGGTTCGAGGTTTAGGG
Found at i:44195519 original size:23 final size:23
Alignment explanation
Indices: 44195484--44195529 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
44195474 CGCTTATCTT
* *
44195484 CATGTTGAGCTGCTGCTAGTCTC
1 CATGCTGAACTGCTGCTAGTCTC
*
44195507 CATGCTGAACTGCTGCTGGTCTC
1 CATGCTGAACTGCTGCTAGTCTC
44195530 TTGTTGCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.28, G:0.26, T:0.33
Consensus pattern (23 bp):
CATGCTGAACTGCTGCTAGTCTC
Found at i:44200723 original size:112 final size:113
Alignment explanation
Indices: 44200541--44200758 Score: 393
Period size: 112 Copynumber: 1.9 Consensus size: 113
44200531 CATAAACTTA
44200541 TAATTGAACATGTTCACAATCAATATTCATGAATAATTAATAAACAAATAAATAAACATAAACAT
1 TAATTGAACA-GTTCACAATCAATATTCATGAATAATTAATAAACAAATAAATAAACATAAACAT
*
44200606 ATGATTATATATATTTAGATATAAAATGTCAAATATTAATATTTATAGT
65 ATGATTATATATATTTAGATATAAAATATCAAATATTAATATTTATAGT
44200655 TAATTGAACA-TTCACAATCAATATTCATGAATAATTAATAAACAAATAAATAAACATAAACATA
1 TAATTGAACAGTTCACAATCAATATTCATGAATAATTAATAAACAAATAAATAAACATAAACATA
**
44200719 TGATTATATATATTTAGATATAAAATATGTAATATTAATA
66 TGATTATATATATTTAGATATAAAATATCAAATATTAATA
44200759 AAACATAAAT
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
112 91 0.90
114 10 0.10
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (113 bp):
TAATTGAACAGTTCACAATCAATATTCATGAATAATTAATAAACAAATAAATAAACATAAACATA
TGATTATATATATTTAGATATAAAATATCAAATATTAATATTTATAGT
Found at i:44213584 original size:28 final size:29
Alignment explanation
Indices: 44213540--44213605 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
44213530 AAAAAATTAT
*
44213540 CAAAATGT-TATACATTTTTTTAATTTAC
1 CAAAATATATATACATTTTTTTAATTTAC
*
44213568 CAAAATATATATA-ATTTTTTTTATTTAC
1 CAAAATATATATACATTTTTTTAATTTAC
44213596 CAAAATATAT
1 CAAAATATAT
44213606 CAAAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 31 0.89
29 4 0.11
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (29 bp):
CAAAATATATATACATTTTTTTAATTTAC
Found at i:44216940 original size:18 final size:18
Alignment explanation
Indices: 44216914--44216951 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
44216904 ATCCCAATGA
*
44216914 TCGCCACCACCTTCTTCT
1 TCGCAACCACCTTCTTCT
44216932 TCGCAACCACCTTCTTCT
1 TCGCAACCACCTTCTTCT
44216950 TC
1 TC
44216952 ACCACCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.47, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACCTTCTTCT
Found at i:44216958 original size:18 final size:18
Alignment explanation
Indices: 44216917--44216958 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
44216907 CCAATGATCG
*
44216917 CCACCACCTTCTTCTTCG
1 CCACCACCTTCTTCTTCA
*
44216935 CAACCACCTTCTTCTTCA
1 CCACCACCTTCTTCTTCA
44216953 CCACCA
1 CCACCA
44216959 ACCATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.50, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACCTTCTTCTTCA
Found at i:44217706 original size:3 final size:3
Alignment explanation
Indices: 44217688--44217722 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
44217678 AGTAACATCT
* *
44217688 TAA TAC TAA CAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
44217723 CTAACTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:44218005 original size:27 final size:27
Alignment explanation
Indices: 44217965--44218025 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
44217955 ACGAGTAGTC
* *
44217965 CCGCCAATCAGTATGGCACCATTGGTG
1 CCGCCAAGCAGTATGGCACCATCGGTG
*
44217992 CTGCCAAGCAGTATGGCACCATCGGTG
1 CCGCCAAGCAGTATGGCACCATCGGTG
44218019 CCGCCAA
1 CCGCCAA
44218026 TCAAAATCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (27 bp):
CCGCCAAGCAGTATGGCACCATCGGTG
Found at i:44218151 original size:29 final size:30
Alignment explanation
Indices: 44218116--44218191 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
44218106 AATAAAAAAA
44218116 TTATAATATTTTAG--ATATTTTTTATTTTT
1 TTATAATATTTTAGTAAT-TTTTTTATTTTT
*
44218145 TTATAATAATTTAGTAATTTTTTTATTTTT
1 TTATAATATTTTAGTAATTTTTTTATTTTT
* *
44218175 TTATATTATTTTTGTAA
1 TTATAATATTTTAGTAA
44218192 AAAACCCTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 13 0.32
30 26 0.63
31 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (30 bp):
TTATAATATTTTAGTAATTTTTTTATTTTT
Found at i:44227214 original size:33 final size:33
Alignment explanation
Indices: 44227172--44227314 Score: 286
Period size: 33 Copynumber: 4.3 Consensus size: 33
44227162 TCTGAAGAAA
44227172 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
1 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
44227205 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
1 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
44227238 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
1 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
44227271 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
1 GAAAAATGTTGCTTGATCAACAAGGAAACAACC
44227304 GAAAAATGTTG
1 GAAAAATGTTG
44227315 ATACTTAAGG
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 110 1.00
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (33 bp):
GAAAAATGTTGCTTGATCAACAAGGAAACAACC
Found at i:44230099 original size:222 final size:223
Alignment explanation
Indices: 44229690--44230543 Score: 1154
Period size: 222 Copynumber: 3.8 Consensus size: 223
44229680 ACTGATAGTA
* * * *
44229690 ACTTTGTGGTCTTCTTCGACAATACAATTGTCACCCGATTCCACTACAACTCCATTAACGGGGTC
1 ACTTCGTGGTCTTCTTCGACAATGCAATTGCCACCCGATTCCACTACAACTCCATTAACGGAGTC
* * * * * *
44229755 GCTTCTATTTACGTTAACATAAACATCCGTGCTGCCGGTGCCAACCTTAACTCTACTCGTGTTGG
66 G----T-TTTACATTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGG
* * * *
44229820 CGCCATTGAGAAGATATCTCGTTTCATTCTCTTTCTCATCTACTATATCCGCCTCCTGGTGATTC
126 CGCCATTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTC
44229885 ATAGTAATAGTGACCGAATCAGATTCGGATTTC
191 ATAGTAATAGTGACCGAATCAGATTCGGATTTC
* * * *
44229918 ACTTCATGGTCTTCTTCGACAATGCAATTGCCATCTGATTCCACTACAACTCCATTAACAGAGTC
1 ACTTCGTGGTCTTCTTCGACAATGCAATTGCCACCCGATTCCACTACAACTCCATTAACGGAGTC
* * * *
44229983 G-TTTCCATTAACATAAACATCTGAGCTGCCGGAGCTAACCTTAACGCAAATCGCGTTGGCGCCA
66 GTTTTACATTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCA
* *
44230047 ATGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGAGTCATAGT
131 TTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGT
* *
44230112 AATTGTAACCGAATCAGATTCGGATTTC
196 AATAGTGACCGAATCAGATTCGGATTTC
* * *
44230140 ACTTCGTGTTCTTCTTCGACAATGCAATTGTCACCCGATTCCACTACAACTCCATTAACGGGGTC
1 ACTTCGTGGTCTTCTTCGACAATGCAATTGCCACCCGATTCCACTACAACTCCATTAACGGAGTC
* * * * *
44230205 GCTTCTATTTACGTTAACATAAACATCCGTGCTGCCGGTGCCAACCTTAACGCTACTCGTGTTGG
66 G----T-TTTACATTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGG
* * ** *
44230270 CGCCATTGAGAAGATATATCGTTTCATTCTCTTTCTCATCTACCTTATCCGCCTCCTGCTGATTC
126 CGCCATTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTC
44230335 ATAGTAATAGTGACCGAATCAGATTCGGATTTC
191 ATAGTAATAGTGACCGAATCAGATTCGGATTTC
* *
44230368 ACTTCGTGGTCTTCTTCGACAATGCAATTGCCATCCGATTCCACTAGAACTCCATTAACGGAGTC
1 ACTTCGTGGTCTTCTTCGACAATGCAATTGCCACCCGATTCCACTACAACTCCATTAACGGAGTC
* ** * * *
44230433 G-TTTCCATTAACATCGACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCACTTTGGCGCTA
66 GTTTTACATTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCA
* * *
44230497 TTGAGAAGATATCTCTTTTCATTGTCTTTCTCAGCTACAACATCCAC
131 TTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCAC
44230544 GTCCGCGGCT
Statistics
Matches: 545, Mismatches: 75, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
222 288 0.53
228 257 0.47
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.32
Consensus pattern (223 bp):
ACTTCGTGGTCTTCTTCGACAATGCAATTGCCACCCGATTCCACTACAACTCCATTAACGGAGTC
GTTTTACATTAACATAAACATCCGAGCTGCCGGAGCCAACCTTAACGCAACTCGCGTTGGCGCCA
TTGAGAAGATATCTCGTTTCATTCTCTTTCTCAGCTACAATATCCACCTCCTGCTGATTCATAGT
AATAGTGACCGAATCAGATTCGGATTTC
Found at i:44231336 original size:20 final size:20
Alignment explanation
Indices: 44231311--44231356 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
44231301 AAACCCTAAA
44231311 TTCAAGA-TTAGGATT-CGAGG
1 TTCAAGATTTAGG-TTCCG-GG
44231331 TTCAAGATTTAGGTTCCGGG
1 TTCAAGATTTAGGTTCCGGG
44231351 TTCAAG
1 TTCAAG
44231357 GTTCGAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
TTCAAGATTTAGGTTCCGGG
Found at i:44231393 original size:29 final size:29
Alignment explanation
Indices: 44231338--44231393 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
44231328 AGGTTCAAGA
*
44231338 TTTAGGTTCCGGGTTCAAGGTTCGAGGGG
1 TTTAGGTTCCGGGTTCAAGATTCGAGGGG
* * * *
44231367 TTTAGGTTCTGTGTTCGAGATTTGAGG
1 TTTAGGTTCCGGGTTCAAGATTCGAGG
44231394 TTAAAGGTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.14, C:0.11, G:0.38, T:0.38
Consensus pattern (29 bp):
TTTAGGTTCCGGGTTCAAGATTCGAGGGG
Found at i:44231430 original size:21 final size:21
Alignment explanation
Indices: 44231400--44231452 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
44231390 GAGGTTAAAG
*
44231400 GTTTAGGGTTCAGAATTTGAT
1 GTTTAAGGTTCAGAATTTGAT
* * *
44231421 GTTTATGGTTTAGGATTTGAT
1 GTTTAAGGTTCAGAATTTGAT
44231442 GTTTAAGGTTC
1 GTTTAAGGTTC
44231453 GGGGGTTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (21 bp):
GTTTAAGGTTCAGAATTTGAT
Found at i:44235333 original size:19 final size:19
Alignment explanation
Indices: 44235289--44235337 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
44235279 TTAATTTTTA
*
44235289 TAATTAAAAATATCATAAT
1 TAATTAAAAATATCATAAC
* *
44235308 TAATTAAAAATATTATTAC
1 TAATTAAAAATATCATAAC
*
44235327 TACTTAAAAAT
1 TAATTAAAAAT
44235338 TAAGTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATTAAAAATATCATAAC
Found at i:44237240 original size:240 final size:241
Alignment explanation
Indices: 44236805--44237286 Score: 948
Period size: 240 Copynumber: 2.0 Consensus size: 241
44236795 TAATTAGGAT
44236805 ATATTTTTCTAAAATATAATTATATATTATTTTATTAATCTTATTTTAGATAATTTAATTTTTTT
1 ATATTTTTCT-AAATATAATTATATATTATTTTATTAATCTTATTTTAGATAATTTAATTTTTTT
44236870 ATTAACGAGAAATAATTTCTTATATATTTTGACCTATTAAAACATAAAATAAAATAAAATTGTAT
65 ATTAACGAGAAATAATTTCTTATATATTTTGACCTATTAAAACATAAAATAAAATAAAATTGTAT
44236935 TTAGAATAAATAAATTGTACTAATTTAAACTAAATTAGTTTTTAATTATTTATACTTAACCAATG
130 TTAGAATAAATAAATTGTACTAATTTAAACTAAATTAGTTTTTAATTATTTATACTTAACCAATG
44237000 ATTAATTGATGATGACAAAGAGTATATATTTAGTGCTAGAGAGCGAA
195 ATTAATTGATGATGACAAAGAGTATATATTTAGTGCTAGAGAGCGAA
44237047 ATATTTTTCT-AATATAATTATATATTATTTTATTAATCTTATTTTAGATAATTTAATTTTTTTA
1 ATATTTTTCTAAATATAATTATATATTATTTTATTAATCTTATTTTAGATAATTTAATTTTTTTA
44237111 TTAACGAGAAATAATTTCTTATATATTTTGACCTATTAAAACATAAAATAAAATAAAATTGTATT
66 TTAACGAGAAATAATTTCTTATATATTTTGACCTATTAAAACATAAAATAAAATAAAATTGTATT
44237176 TAGAATAAATAAATTGTACTAATTTAAACTAAATTAGTTTTTAATTATTTATACTTAACCAATGA
131 TAGAATAAATAAATTGTACTAATTTAAACTAAATTAGTTTTTAATTATTTATACTTAACCAATGA
44237241 TTAATTGATGATGACAAAGAGTATATATTTAGTGCTAGAGAGCGAA
196 TTAATTGATGATGACAAAGAGTATATATTTAGTGCTAGAGAGCGAA
44237287 TAACCCAATA
Statistics
Matches: 240, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
240 230 0.96
242 10 0.04
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (241 bp):
ATATTTTTCTAAATATAATTATATATTATTTTATTAATCTTATTTTAGATAATTTAATTTTTTTA
TTAACGAGAAATAATTTCTTATATATTTTGACCTATTAAAACATAAAATAAAATAAAATTGTATT
TAGAATAAATAAATTGTACTAATTTAAACTAAATTAGTTTTTAATTATTTATACTTAACCAATGA
TTAATTGATGATGACAAAGAGTATATATTTAGTGCTAGAGAGCGAA
Found at i:44250968 original size:21 final size:21
Alignment explanation
Indices: 44250944--44250983 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44250934 TAAACATTAA
**
44250944 ATTTTTTAAATTTATTTATGT
1 ATTTTTTAAAAATATTTATGT
44250965 ATTTTTTAAAAATATTTAT
1 ATTTTTTAAAAATATTTAT
44250984 TTAAATCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTTTTTAAAAATATTTATGT
Found at i:44251221 original size:3 final size:3
Alignment explanation
Indices: 44251215--44251248 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
44251205 TAATAAAATT
44251215 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
44251249 AGGAAAGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:44263506 original size:9 final size:9
Alignment explanation
Indices: 44263494--44263534 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
44263484 ATATACATTA
44263494 TTTTAAATT
1 TTTTAAATT
44263503 TTTT-AATT
1 TTTTAAATT
44263511 TTTTAAATT
1 TTTTAAATT
44263520 TCTTTATAATT
1 T-TTTA-AATT
44263531 TTTT
1 TTTT
44263535 TAGAACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.28
9 9 0.31
10 7 0.24
11 5 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTAAATT
Found at i:44263536 original size:11 final size:11
Alignment explanation
Indices: 44263501--44263566 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
44263491 TTATTTTAAA
44263501 TTTTT-TAA-T
1 TTTTTATAATT
44263510 TTTTTA-AATT
1 TTTTTATAATT
*
44263520 TCTTTATAATT
1 TTTTTATAATT
*
44263531 TTTTTAGAACTT
1 TTTTTATAA-TT
*
44263543 TTTTT-TAA-A
1 TTTTTATAATT
*
44263552 ATTTTATAATT
1 TTTTTATAATT
44263563 TTTT
1 TTTT
44263567 GAAAAATATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
9 11 0.26
10 9 0.21
11 16 0.37
12 7 0.16
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:44263546 original size:12 final size:10
Alignment explanation
Indices: 44263494--44263566 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 10
44263484 ATATACATTA
44263494 TTTTAAA-TT
1 TTTTAAATTT
44263503 TTTT-AA-TT
1 TTTTAAATTT
44263511 TTTTAAATTT
1 TTTTAAATTT
*
44263521 CTTTATAATTT
1 TTTTA-AATTT
44263532 TTTTAGAACTTTT
1 TTTTA-AA--TTT
*
44263545 TTTTAAAATT
1 TTTTAAATTT
*
44263555 TTAT-AATTT
1 TTTTAAATTT
44263564 TTT
1 TTT
44263567 GAAAAATATA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
8 8 0.15
9 12 0.23
10 11 0.21
11 11 0.21
12 2 0.04
13 8 0.15
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:44263603 original size:20 final size:19
Alignment explanation
Indices: 44263578--44263649 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
44263568 AAAAATATAA
44263578 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTA-AAATT
* *
44263598 ATTTTG-AGTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
44263616 ATTTTTGAATTTTTGAAAATT
1 A-TTTTGAATTTTT-AAAATT
44263637 ATTTTGAATTTTT
1 ATTTTGAATTTTT
44263650 TGTAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.07
18 7 0.16
19 6 0.14
20 21 0.48
21 7 0.16
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:44275336 original size:31 final size:31
Alignment explanation
Indices: 44275301--44275361 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
44275291 TCAGCATCTA
44275301 GGCATTTTTTGTATCAATTCTTTTCCAAAAT
1 GGCATTTTTTGTATCAATTCTTTTCCAAAAT
*
44275332 GGCATTTTTTGTATTAATTCTTTTCCAAAA
1 GGCATTTTTTGTATCAATTCTTTTCCAAAA
44275362 AGGTTGAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (31 bp):
GGCATTTTTTGTATCAATTCTTTTCCAAAAT
Found at i:44275951 original size:76 final size:76
Alignment explanation
Indices: 44275822--44275975 Score: 256
Period size: 76 Copynumber: 2.0 Consensus size: 76
44275812 GATCCACGAC
* * *
44275822 TATCAATTGTTTTATGGCTTTGAACCATTATCTCTTGTGATAATTTAATGTTCATATCATGG-GC
1 TATCAATTGTTTTATGGCTTTGAACCATTAGCTCTTGTGATAACTTAAAGTTCATATCA-GGAGC
44275886 AAAAATTATCCA
65 AAAAATTATCCA
*
44275898 TATCAATTGTTTTATGGCTTTTAACCATTAGCTCTTGTGATAACTTAAAGTTCATATCAGGAGCA
1 TATCAATTGTTTTATGGCTTTGAACCATTAGCTCTTGTGATAACTTAAAGTTCATATCAGGAGCA
44275963 AAAATTATCCA
66 AAAATTATCCA
44275974 TA
1 TA
44275976 ATGGTCTCTT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 2 0.03
76 71 0.97
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (76 bp):
TATCAATTGTTTTATGGCTTTGAACCATTAGCTCTTGTGATAACTTAAAGTTCATATCAGGAGCA
AAAATTATCCA
Found at i:44277210 original size:70 final size:70
Alignment explanation
Indices: 44277097--44277237 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
44277087 TTTTATATTT
44277097 TTTAATGAAATCAATGAGAATTTTCAGTTATCTTCCCGTTCAAACTCTTTCCTCTCGATTTTGCT
1 TTTAATGAAATCAATGAGAATTTTCAGTTATCTTCCCGTTCAAACTCTTTCCTCTCGATTTTGCT
44277162 TCTGC
66 TCTGC
*
44277167 TTTAATGAAATCAATGAGAATTTTCAGTTATCTTCCTGTTCAAACTCTTTCCTCTCGATTTTGCT
1 TTTAATGAAATCAATGAGAATTTTCAGTTATCTTCCCGTTCAAACTCTTTCCTCTCGATTTTGCT
44277232 TCTGC
66 TCTGC
44277237 T
1 T
44277238 CTCTTTTGTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (70 bp):
TTTAATGAAATCAATGAGAATTTTCAGTTATCTTCCCGTTCAAACTCTTTCCTCTCGATTTTGCT
TCTGC
Found at i:44286957 original size:50 final size:50
Alignment explanation
Indices: 44286900--44287030 Score: 244
Period size: 50 Copynumber: 2.6 Consensus size: 50
44286890 TTCGATACAT
44286900 GTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAGTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAGTTCAC
*
44286950 GTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAGTTCAC
*
44287000 GTAGTAGCCTTCACACAGTACTACACACGTG
1 GTAGTAGCCTTCACATAGTACTACACACGTG
44287031 TTCATCGATA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (50 bp):
GTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAGTTCAC
Found at i:44291094 original size:50 final size:51
Alignment explanation
Indices: 44291019--44291118 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 51
44291009 GTAGCCAAAG
*
44291019 CTACCACTGATCAATAATACTGGAAA-GTCCACGGGCCTGCTCACACAAGA
1 CTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCACACAAGA
44291069 CTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCACACAAG
1 CTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCACACAAG
44291119 CTGTCAGGTG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 25 0.52
51 23 0.48
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (51 bp):
CTACCACTGATCAATAACACTGGAAATGTCCACGGGCCTGCTCACACAAGA
Found at i:44294961 original size:12 final size:12
Alignment explanation
Indices: 44294944--44294968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44294934 GAAGAAAACT
44294944 ATTTGGATTTTG
1 ATTTGGATTTTG
44294956 ATTTGGATTTTG
1 ATTTGGATTTTG
44294968 A
1 A
44294969 CCTGTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (12 bp):
ATTTGGATTTTG
Found at i:44301407 original size:32 final size:32
Alignment explanation
Indices: 44301338--44301407 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
44301328 ATTTATTACT
44301338 TATT-TATTAATATTTTTAATTTTAAGTTTAA
1 TATTATATTAATATTTTTAATTTTAAGTTTAA
* * *
44301369 -AGTTATATTAAT-TATTTTATTTTTTATTTTAA
1 TA-TTATATTAATAT-TTTTAATTTTAAGTTTAA
44301401 TATTATA
1 TATTATA
44301408 AATGTATTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
30 1 0.03
31 3 0.09
32 27 0.84
33 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (32 bp):
TATTATATTAATATTTTTAATTTTAAGTTTAA
Found at i:44306068 original size:20 final size:21
Alignment explanation
Indices: 44306031--44306070 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44306021 TTTGACCTAC
44306031 TAAATTAAATAGTATTTATTA
1 TAAATTAAATAGTATTTATTA
*
44306052 TAAATTAATTA-TATTTATT
1 TAAATTAAATAGTATTTATT
44306071 TTATTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TAAATTAAATAGTATTTATTA
Found at i:44309400 original size:10 final size:10
Alignment explanation
Indices: 44309386--44309458 Score: 62
Period size: 10 Copynumber: 7.5 Consensus size: 10
44309376 TTATGTTTTA
*
44309386 AATATATTAA
1 AATATATTAT
44309396 AATATTATT-T
1 AATA-TATTAT
*
44309406 AAT-TA-TAA
1 AATATATTAT
44309414 AATATATTAT
1 AATATATTAT
*
44309424 ATTATATTAT
1 AATATATTAT
*
44309434 ATTATATTAT
1 AATATATTAT
*
44309444 ATTATATTAT
1 AATATATTAT
*
44309454 TATAT
1 AATAT
44309459 TAGGTAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
7 1 0.02
8 5 0.09
9 2 0.04
10 41 0.77
11 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATATATTAT
Found at i:44309460 original size:5 final size:5
Alignment explanation
Indices: 44309416--44309453 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
44309406 AATTATAAAA
44309416 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
44309454 TATATTAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:44309578 original size:3 final size:3
Alignment explanation
Indices: 44309572--44309612 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
44309562 TAAGTAAGAC
44309572 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
44309613 AGCAAATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:44310929 original size:45 final size:45
Alignment explanation
Indices: 44310860--44310961 Score: 152
Period size: 45 Copynumber: 2.3 Consensus size: 45
44310850 GCCGACTACT
* *
44310860 GTTACTGTTACTAATTCGATACTTTGTGTGTCGAATATTGTTACC
1 GTTACTGTTACTAATTCAACACTTTGTGTGTCGAATATTGTTACC
* *
44310905 GTTACTGTTAC-AGATTCAACACTTTGTGTGTTGAATATTGTTACT
1 GTTACTGTTACTA-ATTCAACACTTTGTGTGTCGAATATTGTTACC
44310950 GTTACTGTTACT
1 GTTACTGTTACT
44310962 GCTATCGTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.02
45 50 0.98
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.45
Consensus pattern (45 bp):
GTTACTGTTACTAATTCAACACTTTGTGTGTCGAATATTGTTACC
Found at i:44315240 original size:22 final size:23
Alignment explanation
Indices: 44315197--44315240 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
44315187 AAATATATGC
* **
44315197 AAAATAATAATAATGATGACAAT
1 AAAATAATAATAATAAAAACAAT
44315220 AAAATAA-AATAATAAAAACAA
1 AAAATAATAATAATAAAAACAA
44315241 AGGCTATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (23 bp):
AAAATAATAATAATAAAAACAAT
Found at i:44316103 original size:23 final size:22
Alignment explanation
Indices: 44316047--44316105 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
44316037 AGATATACAT
*
44316047 ATATATATATATAAAAAGTATTT
1 ATATATATATATAAAAAG-ATTA
* *
44316070 ATGTATTTATATCAAATAAG-TTA
1 ATATATATATAT-AAA-AAGATTA
44316093 ATATATATATATA
1 ATATATATATATA
44316106 TACGTATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 1 0.03
23 22 0.76
24 3 0.10
25 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATATATATATATAAAAAGATTA
Found at i:44316105 original size:25 final size:23
Alignment explanation
Indices: 44316045--44316107 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
44316035 ATAGATATAC
44316045 ATATATATATATATAAAAAGTAT
1 ATATATATATATATAAAAAGTAT
* * *
44316068 TTATGTATTTATATCAAATAAGT-T
1 ATATATATATATAT-AAA-AAGTAT
44316092 AATATATATATATATA
1 -ATATATATATATATA
44316108 CGTATATATG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 11 0.35
24 5 0.16
25 15 0.48
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
ATATATATATATATAAAAAGTAT
Found at i:44316153 original size:12 final size:12
Alignment explanation
Indices: 44316133--44316167 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
44316123 AATTATATAG
*
44316133 TAATAATAATAT
1 TAATAATAATAC
*
44316145 TAGTAATAATAC
1 TAATAATAATAC
44316157 TAATAATAATA
1 TAATAATAATA
44316168 GCATGAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:44316414 original size:12 final size:12
Alignment explanation
Indices: 44316394--44316428 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
44316384 AATTATATAG
*
44316394 TAATAATAATAT
1 TAATAATAATAC
*
44316406 TAGTAATAATAC
1 TAATAATAATAC
44316418 TAATAATAATA
1 TAATAATAATA
44316429 GCATGGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:44321052 original size:13 final size:13
Alignment explanation
Indices: 44321034--44321061 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
44321024 CTTTGAAATT
44321034 CTTGAAATTTTTG
1 CTTGAAATTTTTG
44321047 CTTGAAATTTTTG
1 CTTGAAATTTTTG
44321060 CT
1 CT
44321062 ATTTTTAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (13 bp):
CTTGAAATTTTTG
Found at i:44332879 original size:732 final size:732
Alignment explanation
Indices: 44331476--44332938 Score: 2908
Period size: 732 Copynumber: 2.0 Consensus size: 732
44331466 GCTGGTGGAC
44331476 TTGCCGGTAATCGGCCACAAAGTTGAGTACAGAGTCAAGCAACTTGGCAGACAACAGCTCCAAAA
1 TTGCCGGTAATCGGCCACAAAGTTGAGTACAGAGTCAAGCAACTTGGCAGACAACAGCTCCAAAA
44331541 AGGCAGAAAGAGCAGCCTCTCCAAAGACAGACATGGTGGAATTGGGACAAAGAAATCAAAGAGAG
66 AGGCAGAAAGAGCAGCCTCTCCAAAGACAGACATGGTGGAATTGGGACAAAGAAATCAAAGAGAG
44331606 ATGAAGGAGGAAGGGGAGATTGAGGGAAAGGAATGGAGATGGAATGTGTATAGTTGGGGATAACA
131 ATGAAGGAGGAAGGGGAGATTGAGGGAAAGGAATGGAGATGGAATGTGTATAGTTGGGGATAACA
44331671 GGGAATGGAGTTGAAGTCAACGAATAGAGACAAATGAGATGGAAAACACAAGAAATACATTATAT
196 GGGAATGGAGTTGAAGTCAACGAATAGAGACAAATGAGATGGAAAACACAAGAAATACATTATAT
44331736 TTTGTAAATTAATTCAGTAATTATGACTATTTAATTGTAATTATTTACGCCATACAAGTCTTTGT
261 TTTGTAAATTAATTCAGTAATTATGACTATTTAATTGTAATTATTTACGCCATACAAGTCTTTGT
44331801 GTTTTAATTTTATTCAATGGATTTGAGTTATATACATTATTTTTTAGTTAAAGATTAGAATTTAT
326 GTTTTAATTTTATTCAATGGATTTGAGTTATATACATTATTTTTTAGTTAAAGATTAGAATTTAT
44331866 TACTTATTTTTTATTATTTTAATTTTAAATTTAAATTTATATTAACTATTTTATTTTTTTTATTT
391 TACTTATTTTTTATTATTTTAATTTTAAATTTAAATTTATATTAACTATTTTATTTTTTTTATTT
44331931 TGATATTATAAATGTATTGATTATTTATTAAAATATGTATCTTCAAAATTGTTTTTTGAAATATA
456 TGATATTATAAATGTATTGATTATTTATTAAAATATGTATCTTCAAAATTGTTTTTTGAAATATA
44331996 TTTTTTAGGGATATTTTAACACTTATAAGAGTCAAGTTATGATTATAGTACTTTGACATCTATGG
521 TTTTTTAGGGATATTTTAACACTTATAAGAGTCAAGTTATGATTATAGTACTTTGACATCTATGG
44332061 ATAGAAGTGAGCGATTGATTGAATCGAGTGAAAAATTTTCATATTAATCGAATTCGTGAATCTTA
586 ATAGAAGTGAGCGATTGATTGAATCGAGTGAAAAATTTTCATATTAATCGAATTCGTGAATCTTA
44332126 TTTTATCATTCTAACTCGATTTGAATTTTTTCGAATCGGGTCAAGTGAAATAAAATTCAAGTCGA
651 TTTTATCATTCTAACTCGATTTGAATTTTTTCGAATCGGGTCAAGTGAAATAAAATTCAAGTCGA
44332191 GCCAAATCGAGTGAAAG
716 GCCAAATCGAGTGAAAG
* *
44332208 TTGCCGGTGATCGGCCATAAAGTTGAGTACAGAGTCAAGCAACTTGGCAGACAACAGCTCCAAAA
1 TTGCCGGTAATCGGCCACAAAGTTGAGTACAGAGTCAAGCAACTTGGCAGACAACAGCTCCAAAA
44332273 AGGCAGAAAGAGCAGCCTCTCCAAAGACAGACATGGTGGAATTGGGACAAAGAAATCAAAGAGAG
66 AGGCAGAAAGAGCAGCCTCTCCAAAGACAGACATGGTGGAATTGGGACAAAGAAATCAAAGAGAG
44332338 ATGAAGGAGGAAGGGGAGATTGAGGGAAAGGAATGGAGATGGAATGTGTATAGTTGGGGATAACA
131 ATGAAGGAGGAAGGGGAGATTGAGGGAAAGGAATGGAGATGGAATGTGTATAGTTGGGGATAACA
44332403 GGGAATGGAGTTGAAGTCAACGAATAGAGACAAATGAGATGGAAAACACAAGAAATACATTATAT
196 GGGAATGGAGTTGAAGTCAACGAATAGAGACAAATGAGATGGAAAACACAAGAAATACATTATAT
44332468 TTTGTAAATTAATTCAGTAATTATGACTATTTAATTGTAATTATTTACGCCATACAAGTCTTTGT
261 TTTGTAAATTAATTCAGTAATTATGACTATTTAATTGTAATTATTTACGCCATACAAGTCTTTGT
44332533 GTTTTAATTTTATTCAATGGATTTGAGTTATATACATTATTTTTTAGTTAAAGATTAGAATTTAT
326 GTTTTAATTTTATTCAATGGATTTGAGTTATATACATTATTTTTTAGTTAAAGATTAGAATTTAT
44332598 TACTTATTTTTTATTATTTTAATTTTAAATTTAAATTTATATTAACTATTTTATTTTTTTTATTT
391 TACTTATTTTTTATTATTTTAATTTTAAATTTAAATTTATATTAACTATTTTATTTTTTTTATTT
44332663 TGATATTATAAATGTATTGATTATTTATTAAAATATGTATCTTCAAAATTGTTTTTTGAAATATA
456 TGATATTATAAATGTATTGATTATTTATTAAAATATGTATCTTCAAAATTGTTTTTTGAAATATA
44332728 TTTTTTAGGGATATTTTAACACTTATAAGAGTCAAGTTATGATTATAGTACTTTGACATCTATGG
521 TTTTTTAGGGATATTTTAACACTTATAAGAGTCAAGTTATGATTATAGTACTTTGACATCTATGG
44332793 ATAGAAGTGAGCGATTGATTGAATCGAGTGAAAAATTTTCATATTAATCGAATTCGTGAATCTTA
586 ATAGAAGTGAGCGATTGATTGAATCGAGTGAAAAATTTTCATATTAATCGAATTCGTGAATCTTA
44332858 TTTTATCATTCTAACTCGATTTGAATTTTTTCGAATCGGGTCAAGTGAAATAAAATTCAAGTCGA
651 TTTTATCATTCTAACTCGATTTGAATTTTTTCGAATCGGGTCAAGTGAAATAAAATTCAAGTCGA
44332923 GCCAAATCGAGTGAAA
716 GCCAAATCGAGTGAAA
44332939 TTGTTCAAGT
Statistics
Matches: 729, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
732 729 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (732 bp):
TTGCCGGTAATCGGCCACAAAGTTGAGTACAGAGTCAAGCAACTTGGCAGACAACAGCTCCAAAA
AGGCAGAAAGAGCAGCCTCTCCAAAGACAGACATGGTGGAATTGGGACAAAGAAATCAAAGAGAG
ATGAAGGAGGAAGGGGAGATTGAGGGAAAGGAATGGAGATGGAATGTGTATAGTTGGGGATAACA
GGGAATGGAGTTGAAGTCAACGAATAGAGACAAATGAGATGGAAAACACAAGAAATACATTATAT
TTTGTAAATTAATTCAGTAATTATGACTATTTAATTGTAATTATTTACGCCATACAAGTCTTTGT
GTTTTAATTTTATTCAATGGATTTGAGTTATATACATTATTTTTTAGTTAAAGATTAGAATTTAT
TACTTATTTTTTATTATTTTAATTTTAAATTTAAATTTATATTAACTATTTTATTTTTTTTATTT
TGATATTATAAATGTATTGATTATTTATTAAAATATGTATCTTCAAAATTGTTTTTTGAAATATA
TTTTTTAGGGATATTTTAACACTTATAAGAGTCAAGTTATGATTATAGTACTTTGACATCTATGG
ATAGAAGTGAGCGATTGATTGAATCGAGTGAAAAATTTTCATATTAATCGAATTCGTGAATCTTA
TTTTATCATTCTAACTCGATTTGAATTTTTTCGAATCGGGTCAAGTGAAATAAAATTCAAGTCGA
GCCAAATCGAGTGAAAG
Found at i:44338420 original size:13 final size:13
Alignment explanation
Indices: 44338402--44338465 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
44338392 ACATTCAAAT
44338402 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
44338415 TTTTCAAAAACAC
1 TTTTCAAAAGCAC
** *
44338428 TTTTTTACAGCAC
1 TTTTCAAAAGCAC
44338441 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
44338454 TTTTTAAAAGCA
1 TTTTCAAAAGCA
44338466 ATGAAGAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:44338431 original size:26 final size:26
Alignment explanation
Indices: 44338401--44338465 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
44338391 AACATTCAAA
44338401 TTTTTCAAAAGCACTTTTCAAAAACAC
1 TTTTT-AAAAGCACTTTTCAAAAACAC
* * *
44338428 TTTTTTACAGCACTTTTCAAAAGCAC
1 TTTTTAAAAGCACTTTTCAAAAACAC
44338454 TTTTTAAAAGCA
1 TTTTTAAAAGCA
44338466 ATGAAGAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
26 28 0.85
27 5 0.15
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (26 bp):
TTTTTAAAAGCACTTTTCAAAAACAC
Found at i:44346874 original size:43 final size:43
Alignment explanation
Indices: 44346827--44346911 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
44346817 TGAAAGAATG
*
44346827 TTTTTGATTTTATTTGCTTATATATATTGTTATTTTGTATGTA
1 TTTTTGATTTTATTTGCTTATATATATGGTTATTTTGTATGTA
* * * *
44346870 TTTTTTATTTTATTTGCTTCTATGTGTGGTTATTTTGTATGT
1 TTTTTGATTTTATTTGCTTATATATATGGTTATTTTGTATGT
44346912 CATTGATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.66
Consensus pattern (43 bp):
TTTTTGATTTTATTTGCTTATATATATGGTTATTTTGTATGTA
Found at i:44347286 original size:109 final size:108
Alignment explanation
Indices: 44347006--44347345 Score: 506
Period size: 110 Copynumber: 3.1 Consensus size: 108
44346996 CACGCATACT
* * *
44347006 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAATGTACC
1 AATATCCTTTTAAAAATTTCAAAATAA-GCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* * *
44347071 CTAATGTGTTGGGTTTCGATTCTTCTAG-TTGAACCAAATAGCCA
65 CTAATGTGCTGGGTTTCGATTTTTCTCGTTTG-ACCAAATAGCCA
44347115 AATATCCTTTTTAAAAATTTCAAAATAATGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGC
1 AATATCC-TTTTAAAAATTTCAAAATAA-GCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGC
44347180 CCTAATGTGCTGGGTTTCGATTTTTCTCGTTTGACCAAATAGCCA
64 CCTAATGTGCTGGGTTTCGATTTTTCTCGTTTGACCAAATAGCCA
* * * *
44347225 AATATCCTTTTAAAAATTTCAACATAAGATAATGTTTTACGTTTGGAAATTTGAGAAAACGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAG-CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
*
44347290 CTAATGTGCTGGGTTTCGA--TTTCTCGTTCGACCAAATAGCCA
65 CTAATGTGCTGGGTTTCGATTTTTCTCGTTTGACCAAATAGCCA
*
44347332 AATATCCTCTTAAA
1 AATATCCTTTTAAA
44347346 TCTTAATCCA
Statistics
Matches: 215, Mismatches: 13, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
107 35 0.16
108 1 0.00
109 78 0.36
110 98 0.46
111 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (108 bp):
AATATCCTTTTAAAAATTTCAAAATAAGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCC
TAATGTGCTGGGTTTCGATTTTTCTCGTTTGACCAAATAGCCA
Found at i:44349480 original size:20 final size:20
Alignment explanation
Indices: 44349451--44349492 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44349441 GGATTTTTTT
* *
44349451 TTCTTTATTTCTCCTTATTC
1 TTCTTCATTTCTACTTATTC
*
44349471 TTCTTCATTTCTATTTATTC
1 TTCTTCATTTCTACTTATTC
44349491 TT
1 TT
44349493 ATTCTTCTAC
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:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTCATTTCTACTTATTC
Found at i:44349750 original size:10 final size:10
Alignment explanation
Indices: 44349737--44349764 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
44349727 TAATTTTGTT
44349737 AAATTTAAGA
1 AAATTTAAGA
44349747 AAATTTAAGA
1 AAATTTAAGA
44349757 AAATTTAA
1 AAATTTAA
44349765 TACATTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (10 bp):
AAATTTAAGA
Found at i:44351864 original size:52 final size:53
Alignment explanation
Indices: 44351799--44351903 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 53
44351789 CTTCTTTACG
44351799 TTGCTTCCAACAATCATCAAATTCAGCAATATTTGCCCATAGCTTTGGAATTA
1 TTGCTTCCAACAATCATCAAATTCAGCAATATTTGCCCATAGCTTTGGAATTA
44351852 TTGCTT-CAACAATCATCAAATTCAGCAATATTTGCCCATAGCTTTGGAATTA
1 TTGCTTCCAACAATCATCAAATTCAGCAATATTTGCCCATAGCTTTGGAATTA
44351904 GGGTGAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 46 0.88
53 6 0.12
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.34
Consensus pattern (53 bp):
TTGCTTCCAACAATCATCAAATTCAGCAATATTTGCCCATAGCTTTGGAATTA
Found at i:44352301 original size:23 final size:23
Alignment explanation
Indices: 44352267--44352312 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
44352257 AATGCAACAA
* * *
44352267 GAGACCAGCAGCAGTTCAGCATG
1 GAGACCAACAGCAGCTCAACATG
44352290 GAGACCAACAGCAGCTCAACATG
1 GAGACCAACAGCAGCTCAACATG
44352313 AAGATAAGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.26, T:0.11
Consensus pattern (23 bp):
GAGACCAACAGCAGCTCAACATG
Found at i:44355759 original size:19 final size:19
Alignment explanation
Indices: 44355737--44355790 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
44355727 ATATCCAAAT
44355737 AAGTAATAAATAATAAAGA
1 AAGTAATAAATAATAAAGA
44355756 AAGTAATAAATAAAGTAAAGA
1 AAGTAATAAAT-AA-TAAAGA
44355777 AA--AAT-AATAATAAA
1 AAGTAATAAATAATAAA
44355791 TAATAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 3 0.09
19 14 0.42
20 2 0.06
21 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (19 bp):
AAGTAATAAATAATAAAGA
Found at i:44355788 original size:21 final size:20
Alignment explanation
Indices: 44355733--44355811 Score: 67
Period size: 23 Copynumber: 3.9 Consensus size: 20
44355723 ATTAATATCC
44355733 AAATAAGTAATAAATAATA-AA
1 AAATAA-TAATAAATAA-AGAA
44355754 GAAAGTAATAAATAAAGTAAAGAA
1 -AAA-TAAT-AATAAA-TAAAGAA
*
44355778 AAATAATAATAAAT-AA-TA
1 AAATAATAATAAATAAAGAA
44355796 AAATAATAA-AAATAAA
1 AAATAATAATAAATAAA
44355812 AATTGGGTTG
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.08
18 12 0.24
19 2 0.04
20 1 0.02
21 6 0.12
22 8 0.16
23 13 0.25
24 5 0.10
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (20 bp):
AAATAATAATAAATAAAGAA
Found at i:44355800 original size:15 final size:14
Alignment explanation
Indices: 44355782--44355812 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
44355772 AAAGAAAAAT
44355782 AATAATAAATAATAA
1 AATAATAAA-AATAA
44355797 AATAATAAAAATAA
1 AATAATAAAAATAA
44355811 AA
1 AA
44355813 ATTGGGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAATAAAAATAA
Found at i:44355814 original size:15 final size:17
Alignment explanation
Indices: 44355776--44355813 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
44355766 TAAAGTAAAG
44355776 AAAAATAATAATAAATA
1 AAAAATAATAATAAATA
44355793 ATAAAATAATAA-AAATA
1 A-AAAATAATAATAAATA
44355810 AAAA
1 AAAA
44355814 TTGGGTTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 7 0.35
18 10 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAATAATAAATA
Found at i:44358680 original size:350 final size:350
Alignment explanation
Indices: 44358039--44358738 Score: 1355
Period size: 350 Copynumber: 2.0 Consensus size: 350
44358029 TTCGATAATT
44358039 TTTTCCACATATTCAGAAAATATACTCATCATACATCTTTGGAAGGTGGCCGGCGCATTGCAAAG
1 TTTTCCACATATTCAGAAAATATACTCATCATACATCTTTGGAAGGTGGCCGGCGCATTGCAAAG
* *
44358104 ACCGAATGGCATCCTTCTATATGCAAATGTACCGAATGGGCATGTAAAAGTGGTCTTTTCTTGGT
66 ACCGAATGGCATCCTTCTATATGCAAATGTACCGAATGGGCATCTAAAAGTGGTCTTTTATTGGT
44358169 CCTCCGGTGCGACTGGAATTTGAAAGAAACCTGAGTATCCATCAAGACAACAAAAATGAGTTTTT
131 CCTCCGGTGCGACTGGAATTTGAAAGAAACCTGAGTATCCATCAAGACAACAAAAATGAGTTTTT
44358234 CCGGCTAATCTTTCAAGCATTTGATCTATAAAAGGAAGAGGGAAATGATCTTTTCTAGTGTATGA
196 CCGGCTAATCTTTCAAGCATTTGATCTATAAAAGGAAGAGGGAAATGATCTTTTCTAGTGTATGA
44358299 ATTCAACTTCCTGTAATCAATGCAGACGCGCCACCCATTTTGTACTCGGGTAGGTACCAAGTCAC
261 ATTCAACTTCCTGTAATCAATGCAGACGCGCCACCCATTTTGTACTCGGGTAGGTACCAAGTCAC
44358364 CTTCAGCATTTTTCTTTACTGTCAC
326 CTTCAGCATTTTTCTTTACTGTCAC
44358389 TTTTCCACATATTCAGAAAATATACTCATCATACATCTTTGGAAGGTGGCCGGCGCATTGCAAAG
1 TTTTCCACATATTCAGAAAATATACTCATCATACATCTTTGGAAGGTGGCCGGCGCATTGCAAAG
44358454 ACCGAATGGCATCCTTCTATATGCAAATGTACCGAATGGGCATCTAAAAGTGGTCTTTTATTGGT
66 ACCGAATGGCATCCTTCTATATGCAAATGTACCGAATGGGCATCTAAAAGTGGTCTTTTATTGGT
*
44358519 CCTCCGGTGCGACTGGAATTTGAAAGAAACCTGAGTATTCATCAAGACAACAAAAATGAGTTTTT
131 CCTCCGGTGCGACTGGAATTTGAAAGAAACCTGAGTATCCATCAAGACAACAAAAATGAGTTTTT
* *
44358584 CCGGCTAATCTTTCAAGCATTTGATCTATATAATGAAGAGGGAAATGATCTTTTCTAGTGTATGA
196 CCGGCTAATCTTTCAAGCATTTGATCTATAAAAGGAAGAGGGAAATGATCTTTTCTAGTGTATGA
44358649 ATTCAACTTCCTGTAATCAATGCAGACGCGCCACCCATTTTGTACTCGGGTAGGTACCAAGTCAC
261 ATTCAACTTCCTGTAATCAATGCAGACGCGCCACCCATTTTGTACTCGGGTAGGTACCAAGTCAC
44358714 CTTCAGCATTTTTCTTTACTGTCAC
326 CTTCAGCATTTTTCTTTACTGTCAC
44358739 GCCTATTTTC
Statistics
Matches: 345, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
350 345 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (350 bp):
TTTTCCACATATTCAGAAAATATACTCATCATACATCTTTGGAAGGTGGCCGGCGCATTGCAAAG
ACCGAATGGCATCCTTCTATATGCAAATGTACCGAATGGGCATCTAAAAGTGGTCTTTTATTGGT
CCTCCGGTGCGACTGGAATTTGAAAGAAACCTGAGTATCCATCAAGACAACAAAAATGAGTTTTT
CCGGCTAATCTTTCAAGCATTTGATCTATAAAAGGAAGAGGGAAATGATCTTTTCTAGTGTATGA
ATTCAACTTCCTGTAATCAATGCAGACGCGCCACCCATTTTGTACTCGGGTAGGTACCAAGTCAC
CTTCAGCATTTTTCTTTACTGTCAC
Found at i:44367108 original size:18 final size:19
Alignment explanation
Indices: 44367075--44367114 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
44367065 AGGAGAGAAT
*
44367075 AAAAAAAAGGGAAAATGGA
1 AAAAAAAAGGGAAAATAGA
*
44367094 AAAAAAAAGTG-AAATAGA
1 AAAAAAAAGGGAAAATAGA
44367112 AAA
1 AAA
44367115 TTAGAATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAAAAAAAGGGAAAATAGA
Found at i:44375352 original size:3 final size:3
Alignment explanation
Indices: 44375346--44375380 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
44375336 ATCAAAGTAA
44375346 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44375381 ATACTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44385065 original size:15 final size:15
Alignment explanation
Indices: 44385043--44385078 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
44385033 ATTTTATTTT
44385043 ATTTTAT-TTTAAT-
1 ATTTTATATTTAATA
44385056 ATTTTATATTTAATA
1 ATTTTATATTTAATA
44385071 ATTTTATA
1 ATTTTATA
44385079 CATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTATATTTAATA
Found at i:44385083 original size:17 final size:14
Alignment explanation
Indices: 44385042--44385078 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
44385032 TATTTTATTT
44385042 TATTTTAT-TTTAA
1 TATTTTATATTTAA
44385055 TATTTTATATTTAA
1 TATTTTATATTTAA
44385069 TAATTTTATA
1 T-ATTTTATA
44385079 CATTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 6 0.27
15 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTATATTTAA
Found at i:44385170 original size:15 final size:15
Alignment explanation
Indices: 44385150--44385178 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44385140 AAGTAGTATT
44385150 ATATATTTAGTATAG
1 ATATATTTAGTATAG
44385165 ATATATTTAGTATA
1 ATATATTTAGTATA
44385179 TCTCATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
ATATATTTAGTATAG
Found at i:44385229 original size:40 final size:40
Alignment explanation
Indices: 44385185--44385264 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
44385175 TATATCTCAT
*
44385185 GTTTACATTAGAATAGTAAATAACATAATATAAAATATTA
1 GTTTACATTAGAATAATAAATAACATAATATAAAATATTA
44385225 GTTTACATTAGAATAATAAATAACATAATATAAAATATTA
1 GTTTACATTAGAATAATAAATAACATAATATAAAATATTA
44385265 TAAACTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (40 bp):
GTTTACATTAGAATAATAAATAACATAATATAAAATATTA
Found at i:44390155 original size:15 final size:15
Alignment explanation
Indices: 44390133--44390168 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
44390123 ATTTTATTTT
44390133 ATTTTAT-TTTAAT-
1 ATTTTATATTTAATA
44390146 ATTTTATATTTAATA
1 ATTTTATATTTAATA
44390161 ATTTTATA
1 ATTTTATA
44390169 CATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
15 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTATATTTAATA
Found at i:44390173 original size:17 final size:14
Alignment explanation
Indices: 44390132--44390168 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
44390122 TATTTTATTT
44390132 TATTTTAT-TTTAA
1 TATTTTATATTTAA
44390145 TATTTTATATTTAA
1 TATTTTATATTTAA
44390159 TAATTTTATA
1 T-ATTTTATA
44390169 CATTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 6 0.27
15 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTTATATTTAA
Found at i:44390260 original size:15 final size:15
Alignment explanation
Indices: 44390240--44390268 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
44390230 AAGTAGTATT
44390240 ATATATTTAGTATAG
1 ATATATTTAGTATAG
44390255 ATATATTTAGTATA
1 ATATATTTAGTATA
44390269 TCTCATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
ATATATTTAGTATAG
Found at i:44390558 original size:7 final size:7
Alignment explanation
Indices: 44390546--44390570 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
44390536 ACATCAATAA
44390546 ATAATTT
1 ATAATTT
44390553 ATAATTT
1 ATAATTT
44390560 ATAATTT
1 ATAATTT
44390567 ATAA
1 ATAA
44390571 AATATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATAATTT
Found at i:44394162 original size:12 final size:12
Alignment explanation
Indices: 44394145--44394171 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
44394135 GTAAGCATAT
44394145 TTTCGAACCTAG
1 TTTCGAACCTAG
44394157 TTTCGAACCTAG
1 TTTCGAACCTAG
44394169 TTT
1 TTT
44394172 TAAGATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (12 bp):
TTTCGAACCTAG
Found at i:44400009 original size:16 final size:17
Alignment explanation
Indices: 44399971--44400012 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
44399961 ACAAACTTGA
44399971 TTATTATA-ATGAAATG
1 TTATTATAGATGAAATG
* *
44399987 TTGTTATAGATGATA-G
1 TTATTATAGATGAAATG
44400003 TTATTATAGA
1 TTATTATAGA
44400013 GATGGCTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (17 bp):
TTATTATAGATGAAATG
Found at i:44401335 original size:6 final size:6
Alignment explanation
Indices: 44401320--44401377 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
44401310 GAGTAGGATC
* * * * * *
44401320 TGTATA TGTATT TGTATC TGTATC TATATC TGCATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
44401368 TGTATA TGTA
1 TGTATA TGTA
44401378 ATTGCACCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:44403946 original size:29 final size:29
Alignment explanation
Indices: 44403910--44403986 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
44403900 AAAAAAATGA
44403910 ATAGTTGGGTGACCATTTTTCAACTTTTC
1 ATAGTTGGGTGACCATTTTTCAACTTTTC
*
44403939 ATAGTTGGGTGACCAATTTTCAACTTTTC
1 ATAGTTGGGTGACCATTTTTCAACTTTTC
*
44403968 ATAGTTGGATGACCATTTT
1 ATAGTTGGGTGACCATTTT
44403987 GTAGTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (29 bp):
ATAGTTGGGTGACCATTTTTCAACTTTTC
Found at i:44405082 original size:274 final size:273
Alignment explanation
Indices: 44404447--44405072 Score: 769
Period size: 274 Copynumber: 2.3 Consensus size: 273
44404437 CCACTAAACC
** *
44404447 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATAT-TCACAATTCGTTATATTCATC
1 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGT-ACAATTTATTATCTTCATC
* * * * ** *
44404511 AGTTGTATATCTATACTTACTATTTATTAAGCCCTTGACTGAGTTGGTGTCACCCTCAACCGGGT
65 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGT
* * * *
44404576 CACCAACTTGATCAAGAAATTATAAAAATGTTCTTTCATAATTAAAAAAAGGTTATATTATTCAA
130 CACCAACTTGATCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCAA
* * *
44404641 GGGTATTTTAGTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATACGGTGAGATTTGAA
195 GGGTATTTTAGTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATAAGATGAGACTTGAA
*
44404706 CCTATGCCAATTCT
260 CCCATGCCAATTCT
* * * *
44404720 AAACCTTTATTTTAATGTATTTTTATACATTTTGGTTTTAATATGCACAATATATTATCTTCATC
1 AAAACTTTATTTTAATATA-TTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATC
* * *
44404785 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTTTCACTCTCAATCGAGT
65 AATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGT
* * *
44404850 CACCAACTT-AGTCAAAAAATTACGAAAATGTCCTTTCGTAATT-AGAAAA-GTTATATAATTCA
130 CACCAACTTGA-TCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCA
** *
44404912 AGGGTATTTTAGGT-TTTTCATTTT-AGGAAAACCAATTAAAAAATATACATAAGATGGGACTTG
194 AGGGTATTTTA-GTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATAAGATGAGACTTG
* *
44404975 AACCCGTGCCAATTAAATTATT
258 AACCCATGCC-----AATT-CT
* * * *
44404997 AAAACTTTATCTTAATATATTTTATACATTTTGATTTTAATATGTATAATTTATTATCTCCATCA
1 AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATCA
* *
44405062 CTTATATATAT
66 ATTGTATATAT
44405073 TAATAATATT
Statistics
Matches: 300, Mismatches: 43, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
271 41 0.14
272 33 0.11
273 25 0.08
274 130 0.43
276 54 0.18
277 17 0.06
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (273 bp):
AAAACTTTATTTTAATATATTTTATACATTTTGGTTTTAATATGTACAATTTATTATCTTCATCA
ATTGTATATATATACTTAATATTTATTAAGCCCCTGACTGAGTCAGTGTCACCCTCAACCGAGTC
ACCAACTTGATCAAAAAATTACAAAAATGTCCTTTCATAATTAAAAAAAGGTTATATAATTCAAG
GGTATTTTAGTCTTTTCATTTTAACAAAAACCAATTAAAAAATATACATAAGATGAGACTTGAAC
CCATGCCAATTCT
Found at i:44419728 original size:3 final size:3
Alignment explanation
Indices: 44419722--44419759 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
44419712 TTTAATAATT
*
44419722 ATG ATG ATG ATG ACG ATG ATG ATG ATG ATG AT- ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
44419760 TTGCATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:44441232 original size:6 final size:6
Alignment explanation
Indices: 44441223--44441266 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
44441213 AAAAGAGAAT
* * *
44441223 GAGACA GAGACA GAGACA GTGACA GTGACA GGAGACA GTGACA G
1 GAGACA GAGACA GAGACA GAGACA GAGACA -GAGACA GAGACA G
44441267 CTAAAGGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.41, C:0.16, G:0.36, T:0.07
Consensus pattern (6 bp):
GAGACA
Found at i:44441259 original size:19 final size:18
Alignment explanation
Indices: 44441225--44441266 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
44441215 AAGAGAATGA
44441225 GACAGAGACAGAGACAGT
1 GACAGAGACAGAGACAGT
*
44441243 GACAGTGACAGGAGACAGT
1 GACAGAGACA-GAGACAGT
44441262 GACAG
1 GACAG
44441267 CTAAAGGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.40, C:0.17, G:0.36, T:0.07
Consensus pattern (18 bp):
GACAGAGACAGAGACAGT
Found at i:44441274 original size:19 final size:19
Alignment explanation
Indices: 44441235--44441278 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
44441225 GACAGAGACA
*
44441235 GAGACAGTGACAGTGACAG
1 GAGACAGTGACAGTGAAAG
44441254 GAGACAGTGACAGCT-AAAG
1 GAGACAGTGACAG-TGAAAG
44441273 GAGACA
1 GAGACA
44441279 ATATAGGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.34, T:0.09
Consensus pattern (19 bp):
GAGACAGTGACAGTGAAAG
Found at i:44441642 original size:3 final size:3
Alignment explanation
Indices: 44441636--44441661 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44441626 AACTTGTCGG
44441636 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
44441662 AACTCCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:44441952 original size:15 final size:12
Alignment explanation
Indices: 44441916--44441944 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44441906 TTCTCTCTCC
44441916 TCCTC-TCTTCT
1 TCCTCGTCTTCT
44441927 TCCTCGTCTTCT
1 TCCTCGTCTTCT
44441939 TCCTCG
1 TCCTCG
44441945 AAGTCTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.00, C:0.45, G:0.07, T:0.48
Consensus pattern (12 bp):
TCCTCGTCTTCT
Found at i:44442551 original size:2 final size:2
Alignment explanation
Indices: 44442546--44442571 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44442536 ACACACGCCC
44442546 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
44442572 TCTGTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:44442588 original size:6 final size:6
Alignment explanation
Indices: 44442579--44442605 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
44442569 TCTTCTGTTG
44442579 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
44442606 CCACTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:44443385 original size:16 final size:16
Alignment explanation
Indices: 44443362--44443394 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
44443352 TATGCTTATA
44443362 AAATTAA-TTAAAAAT
1 AAATTAATTTAAAAAT
44443377 AAATATAATTTAAAAAT
1 AAAT-TAATTTAAAAAT
44443394 A
1 A
44443395 TCATCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 3 0.19
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATTAATTTAAAAAT
Found at i:44444066 original size:20 final size:19
Alignment explanation
Indices: 44444043--44444089 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
44444033 GGATTTTGAG
*
44444043 GTTTTTTTTTTATTTTTTAA
1 GTTTTTTTTATATTTTTT-A
* *
44444063 GTTTATTATATATTTTTTA
1 GTTTTTTTTATATTTTTTA
44444082 GTTTTTTT
1 GTTTTTTT
44444090 AATAAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (19 bp):
GTTTTTTTTATATTTTTTA
Found at i:44447941 original size:26 final size:25
Alignment explanation
Indices: 44447901--44447968 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
44447891 ATAAACAAAC
* *
44447901 ATATTTTCTTCTTTTGCAAATTTTA
1 ATATTTTCTTTTTTTGCAAATGTTA
* * *
44447926 ATCATTTTGTTTTTTTCCATATGTTA
1 AT-ATTTTCTTTTTTTGCAAATGTTA
*
44447952 ATATTTTTTTATTTTTG
1 ATATTTTCTT-TTTTTG
44447969 TGCAACCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 9 0.26
26 25 0.74
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (25 bp):
ATATTTTCTTTTTTTGCAAATGTTA
Found at i:44448108 original size:20 final size:21
Alignment explanation
Indices: 44448083--44448121 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
44448073 ATCCAAAATC
*
44448083 CTGAACCTTGAA-CTTGAACT
1 CTGAACCTTAAATCTTGAACT
44448103 CTGAACCTTAAATCTTGAA
1 CTGAACCTTAAATCTTGAA
44448122 TCACAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (21 bp):
CTGAACCTTAAATCTTGAACT
Found at i:44454224 original size:2 final size:2
Alignment explanation
Indices: 44454217--44454264 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
44454207 AATATTAGTG
*
44454217 TA TA TA TA TA TA T- TA GTG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
44454259 TA TA TA
1 TA TA TA
44454265 AAATATTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44454231 original size:18 final size:18
Alignment explanation
Indices: 44454208--44454263 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
44454198 CGTTCAATAA
44454208 ATATTAGTGTATATATAT
1 ATATTAGTGTATATATAT
44454226 ATATTAGTGTATATATAT
1 ATATTAGTGTATATATAT
*
44454244 ATA-TA-TATATATATAT
1 ATATTAGTGTATATATAT
44454260 ATAT
1 ATAT
44454264 AAAATATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
16 13 0.36
17 2 0.06
18 21 0.58
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (18 bp):
ATATTAGTGTATATATAT
Found at i:44465088 original size:14 final size:15
Alignment explanation
Indices: 44465069--44465097 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44465059 ACCACCTTTA
44465069 TTTTTATT-TTATTT
1 TTTTTATTATTATTT
44465083 TTTTTATTATTATTT
1 TTTTTATTATTATTT
44465098 AAATTATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTATTATTT
Found at i:44467937 original size:35 final size:35
Alignment explanation
Indices: 44467898--44467967 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
44467888 ACGATCTTCA
44467898 ATTAGTACTTTTAACAAATTTACTATGACATACTT
1 ATTAGTACTTTTAACAAATTTACTATGACATACTT
*
44467933 ATTAGTACTTTTAACAAATTTTCTATGACATACTT
1 ATTAGTACTTTTAACAAATTTACTATGACATACTT
44467968 TAACCATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (35 bp):
ATTAGTACTTTTAACAAATTTACTATGACATACTT
Found at i:44469396 original size:31 final size:31
Alignment explanation
Indices: 44469335--44469400 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
44469325 TTATTATACC
* **
44469335 ATTTGGTACATGAGTTTGGCTTTGAGGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
*
44469366 ATTTGGTACATGAATTTGGCTTCAATGTTCA
1 ATTTGGTACATGAATTTGGCTTCAAGGTTCA
44469397 ATTT
1 ATTT
44469401 AATACCTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.44
Consensus pattern (31 bp):
ATTTGGTACATGAATTTGGCTTCAAGGTTCA
Found at i:44471551 original size:15 final size:15
Alignment explanation
Indices: 44471513--44471553 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
44471503 TAAATAACTG
44471513 AATTTAATAAGT-CAA
1 AATTTAA-AAGTACAA
44471528 AATTT-AAAGTACAA
1 AATTTAAAAGTACAA
*
44471542 ATTTTAAAAGTA
1 AATTTAAAAGTA
44471554 AAGCGAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 11 0.48
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (15 bp):
AATTTAAAAGTACAA
Found at i:44475332 original size:117 final size:116
Alignment explanation
Indices: 44475151--44475363 Score: 311
Period size: 117 Copynumber: 1.8 Consensus size: 116
44475141 TTTCAGGACA
**
44475151 AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCATGTTTTTCCATAC
1 AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCACATTTTTCCATAC
*
44475216 AGTTCATGTTTCTCAAACTCAAATGCTGTATGCAGCCACATTTCTCAAATTC
66 AGTT-ATGTTTCTCAAACTCAAAAGCTGTATGCAGCCACATTTCTCAAATTC
* * ** *
44475268 AAATTGAATCACTAACTGAAATGACTCCTGAAATTGAGAACCATTTGCTCCACATTTCTT-CATA
1 AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCACATTT-TTCCATA
* *
44475332 CGGTTATGTTTCTCAAACTCAAAAGTTGTATG
65 CAGTTATGTTTCTCAAACTCAAAAGCTGTATG
44475364 TAGCTAAGGA
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
116 25 0.29
117 58 0.68
118 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (116 bp):
AAATTAAACCACTAACTGAAATGACTCCTGAAACCGAGAACAATTTGCTCCACATTTTTCCATAC
AGTTATGTTTCTCAAACTCAAAAGCTGTATGCAGCCACATTTCTCAAATTC
Found at i:44490171 original size:3 final size:3
Alignment explanation
Indices: 44490163--44490191 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44490153 CTTAAAATGA
44490163 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44490192 AGTTTAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44491478 original size:25 final size:27
Alignment explanation
Indices: 44491428--44491487 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
44491418 TTTTAGTTCT
44491428 TTTATATATTTATATATATTTCATAAA
1 TTTATATATTTATATATATTTCATAAA
* *
44491455 TTTATA-ATTTATA-ATTTTTGATAAA
1 TTTATATATTTATATATATTTCATAAA
*
44491480 TGTATATA
1 TTTATATA
44491488 ATATNNNNNN
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 15 0.52
26 8 0.28
27 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (27 bp):
TTTATATATTTATATATATTTCATAAA
Found at i:44499560 original size:20 final size:21
Alignment explanation
Indices: 44499520--44499560 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
44499510 AAGTGTTGAA
*
44499520 TGGATTAAAAATTATTTTAAT
1 TGGATTAAAAATTAATTTAAT
*
44499541 TGGATT-AAAGTTAATTTAAT
1 TGGATTAAAAATTAATTTAAT
44499561 CATCTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (21 bp):
TGGATTAAAAATTAATTTAAT
Found at i:44512365 original size:25 final size:25
Alignment explanation
Indices: 44512331--44512383 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
44512321 TAGAGCACTT
*
44512331 AGTGCCTTTAGGTCAGTACATC-CA
1 AGTGCCTTTAAGTCAGTACATCTCA
44512355 AGTGCTCTTTAAGTCAGTACATCTCA
1 AGTGC-CTTTAAGTCAGTACATCTCA
44512381 AGT
1 AGT
44512384 TGCAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 5 0.19
25 16 0.62
26 5 0.19
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (25 bp):
AGTGCCTTTAAGTCAGTACATCTCA
Found at i:44519039 original size:199 final size:199
Alignment explanation
Indices: 44518697--44519059 Score: 501
Period size: 199 Copynumber: 1.8 Consensus size: 199
44518687 CCGTTGGCAC
*
44518697 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTATTGATCTAGTCAATA
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATA
* * * *
44518762 ATCAGTATAATGATGATGGGCCACTTCAAACTTTAGTAAGAGTTCGAAAGAATAACTCACCTACT
66 ATCAGTATAATAATGATGGGACACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
* *
44518827 AATATACTTGGTGATAATCATGATAAGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
131 AACATAATTGGTGATAATCATGATAAGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
44518892 ACAT
196 ACAT
* * * *
44518896 TGCTAAGTCTAAAGAAAAGTTAGAAGTAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAGTG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATA
* * * * * * * * *
44518961 ATCAGTCTAATAATGATGTGACACTTTAACCTTTAGCAAGAGTTAGGAAGAATCACTTATCTATT
66 ATCAGTATAATAATGATGGGACACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
* ** **
44519026 GACATAATTGGTGATGTTCATGATGGGATCAAAA
131 AACATAATTGGTGATAATCATGATAAGATCAAAA
44519060 TAAGGGGTAG
Statistics
Matches: 139, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
199 139 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (199 bp):
TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATA
ATCAGTATAATAATGATGGGACACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
AACATAATTGGTGATAATCATGATAAGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
ACAT
Found at i:44520475 original size:21 final size:22
Alignment explanation
Indices: 44520434--44520476 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
44520424 TAAATAAATG
44520434 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
44520457 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
44520477 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:44520617 original size:27 final size:26
Alignment explanation
Indices: 44520570--44520626 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
44520560 GCAGAATAGC
* * *
44520570 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGAAGAAA-CAAAG
44520597 AAAAAGAAAA-AGGGAAGGAAACAAAG
1 AAAAAGAAAACAGGGAA-GAAACAAAG
44520623 AAAA
1 AAAA
44520627 TTTAGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAACAGGGAAGAAACAAAG
Found at i:44521348 original size:39 final size:38
Alignment explanation
Indices: 44521228--44521361 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 38
44521218 GACCTTGAGT
* *
44521228 CGATGAGACACTGGGTGTCATACTGTTACTTCGAA-TAGATT
1 CGATGAGACACTGGGTGTCA-ACT-TTGCTTCGAACT--ATC
** ** * *
44521269 CGATGAGGTACTGGGTACCAAC-TTGCTTCG-GCTTTGC
1 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTAT-C
44521306 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACT-TTGCTTCGAACTATC
*
44521345 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
44521362 CCATTCTGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
36 1 0.01
37 18 0.25
38 8 0.11
39 25 0.34
40 5 0.07
41 16 0.22
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTATC
Found at i:44527139 original size:16 final size:16
Alignment explanation
Indices: 44527105--44527157 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
44527095 ATAGCATTAG
44527105 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
44527121 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
44527137 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
44527153 TCATG
1 TCATG
44527158 AGTATATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:44527423 original size:37 final size:39
Alignment explanation
Indices: 44527376--44527478 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 39
44527366 AATTCAAAGT
* *
44527376 AGTAAATTGACACCCAGTGTCTCATC-AGTTAAACCG-A
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAAACCGAA
* *
44527413 AGTAAATTGACACCCAATGCCTCATCGAATAAAACCGAA
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAAACCGAA
*
44527452 ATGATGAATTGACACCCAGTGTCTCAT
1 A-G-TAAATTGACACCCAGTGTCTCAT
44527479 TGACTTTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 24 0.44
38 8 0.15
39 2 0.04
40 1 0.02
41 20 0.36
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (39 bp):
AGTAAATTGACACCCAGTGTCTCATCGAATAAAACCGAA
Found at i:44527618 original size:2 final size:2
Alignment explanation
Indices: 44527611--44527670 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
44527601 ATCATATTTG
* * *
44527611 CA CA CA CA CA CA CA CA AA CA CA CA CA AA CA CA CA CA CA GA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
44527653 CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA
44527671 TATATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.53, C:0.45, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:44529895 original size:3 final size:3
Alignment explanation
Indices: 44529889--44529926 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
44529879 GACGACCACG
44529889 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
44529927 TCAATTAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:44537970 original size:13 final size:13
Alignment explanation
Indices: 44537952--44537979 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
44537942 TATAGGTAAA
44537952 CCTAGTTGTTTCT
1 CCTAGTTGTTTCT
44537965 CCTAGTTGTTTCT
1 CCTAGTTGTTTCT
44537978 CC
1 CC
44537980 ACTCTCGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.29, G:0.14, T:0.50
Consensus pattern (13 bp):
CCTAGTTGTTTCT
Found at i:44541019 original size:55 final size:55
Alignment explanation
Indices: 44540940--44541072 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 55
44540930 AGACTTATAG
* * * * *
44540940 GGCCATGTGACCTTATTTCAAATACACACAC-GGTCTAGCACACGATTTGAGACAC
1 GGCCGTGTGACCTTATTTCGAATACACACACATG-CGAGCACACGAGTTGAGACAC
* * * *
44540995 GGTCGTGTGACCTTATTTCGAATACTCACACATGCGGGCACACGGGTTGAGACAC
1 GGCCGTGTGACCTTATTTCGAATACACACACATGCGAGCACACGAGTTGAGACAC
*
44541050 GGCCGTGTGACCCATATTTCGAA
1 GGCCGTGTGA-CCTTATTTCGAA
44541073 CTGTACACGA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
55 53 0.82
56 12 0.18
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (55 bp):
GGCCGTGTGACCTTATTTCGAATACACACACATGCGAGCACACGAGTTGAGACAC
Found at i:44565252 original size:16 final size:17
Alignment explanation
Indices: 44565217--44565255 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
44565207 AATAAATGAA
44565217 AAATATAAAAATATATT
1 AAATATAAAAATATATT
44565234 AAAT-TAAAAATA-ATAT
1 AAATATAAAAATATAT-T
44565250 AAATAT
1 AAATAT
44565256 TTTTTCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 13 0.65
17 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATAAAAATATATT
Found at i:44565253 original size:25 final size:24
Alignment explanation
Indices: 44565195--44565255 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
44565185 AATTATCTAT
* * *
44565195 ATATAAAATTGTAATAAATGAAAA
1 ATATAAAAATATATTAAATGAAAA
*
44565219 ATATAAAAATATATTAAATTAAAA
1 ATATAAAAATATATTAAATGAAAA
*
44565243 ATAATATAAATAT
1 AT-ATAAAAATAT
44565256 TTTTTCAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (24 bp):
ATATAAAAATATATTAAATGAAAA
Found at i:44571357 original size:72 final size:68
Alignment explanation
Indices: 44571281--44571418 Score: 195
Period size: 72 Copynumber: 2.0 Consensus size: 68
44571271 TGATTAAACT
* *
44571281 TAATCACTTTAATATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAAATTAATTTAAT
1 TAATCACTTTAATATTAAATTAATAAAATA-TTAT-T--AAAATAAGTATTAAAATTAATTTAAT
44571346 ATTAAGC
62 ATTAAGC
* * *
44571353 TAATCACTTTAATATTAAATTAATAAAATATTATTAAGATGAGTATTAAATTTAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATATTATTAAAATAAGTATTAAAATTAATTTAATATTA
44571418 A
66 A
44571419 ATCTATTAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 27 0.44
70 1 0.02
71 4 0.07
72 29 0.48
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATATTATTAAAATAAGTATTAAAATTAATTTAATATTA
AGC
Found at i:44571373 original size:36 final size:36
Alignment explanation
Indices: 44571281--44571385 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 36
44571271 TGATTAAACT
* * *
44571281 TAATCACTTTAATATTAAATTAATAGAATATTTATC
1 TAATCACTTTAATATTAAATTAATAAAATATTAAGC
*** **
44571317 T-A-CAAAATAATTATTAAAATTAATTTAATATTAAGC
1 TAATCACTTTAA-TATT-AAATTAATAAAATATTAAGC
44571353 TAATCACTTTAATATTAAATTAATAAAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATATTA
44571386 TTAAGATGAG
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
34 5 0.09
35 5 0.09
36 33 0.62
37 5 0.09
38 5 0.09
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (36 bp):
TAATCACTTTAATATTAAATTAATAAAATATTAAGC
Found at i:44571437 original size:68 final size:71
Alignment explanation
Indices: 44571290--44571437 Score: 160
Period size: 68 Copynumber: 2.1 Consensus size: 71
44571280 TTAATCACTT
* *
44571290 TAATATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAAATTAATTTAATATTAAGCTA
1 TAATATTAAATTAATAAAATATTTATCTA-AAAATAAGTATTAAAATTAATTTAATATTAAGCTA
***
44571355 ATCACTT
65 ATCAAAA
* * * *
44571362 TAATATTAAATTAATAAAATA-TTAT-T-AAGATGAGTATTAAATTTAATTTAATATTAAATCT-
1 TAATATTAAATTAATAAAATATTTATCTAAAAATAAGTATTAAAATTAATTTAATATT-AAGCTA
*
44571423 ATTAAAA
65 ATCAAAA
44571430 TAATATTA
1 TAATATTA
44571438 TTTTTGGAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
68 36 0.55
69 4 0.06
70 1 0.02
71 4 0.06
72 20 0.31
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (71 bp):
TAATATTAAATTAATAAAATATTTATCTAAAAATAAGTATTAAAATTAATTTAATATTAAGCTAA
TCAAAA
Found at i:44576163 original size:21 final size:21
Alignment explanation
Indices: 44576139--44576250 Score: 100
Period size: 21 Copynumber: 5.3 Consensus size: 21
44576129 GTGTTTTACT
* *
44576139 TTCTGTTTAGCTCTTTTGAGC
1 TTCTGTTCAGCTCTTTCGAGC
44576160 TTCTGTTCAGCTCTTTCGAGC
1 TTCTGTTCAGCTCTTTCGAGC
* * *
44576181 TTTTGTCCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTTCGAGC
* ** *
44576202 TTCTATTCAATTCTTAT-GAGT
1 TTCTGTTCAGCTCTT-TCGAGC
** *
44576223 TTCTGTTCAGCTCTCACGTGC
1 TTCTGTTCAGCTCTTTCGAGC
44576244 TTCTGTT
1 TTCTGTT
44576251 GGCGTGTTCA
Statistics
Matches: 70, Mismatches: 19, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTTCGAGC
Found at i:44576234 original size:42 final size:43
Alignment explanation
Indices: 44576137--44576247 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 43
44576127 TCGTGTTTTA
* ** * *
44576137 CTTTCTGTTTAGCTCTTTTGAGCTTCTGTTCAGCTCTTTCGAG
1 CTTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTTCGAG
* *
44576180 CTTT-TGTCCAGCTCTTACGAGCTTCTATTCAATTCTTAT-GAG
1 CTTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTT-TCGAG
* *
44576222 -TTTCTGTTCAGCTCTCACGTGCTTCT
1 CTTTCTGTTCAGCTCTTACGAGCTTCT
44576248 GTTGGCGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.05
42 48 0.86
43 5 0.09
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (43 bp):
CTTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTTCGAG
Found at i:44579215 original size:51 final size:52
Alignment explanation
Indices: 44579125--44579243 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
44579115 ATAGAAATTG
* *
44579125 TGAAAATGGAGAAATGAGAAACATTTGGAAATGATTGTGG-TTTTCTCCAAAA
1 TGAAAATGGAGAAATGAG-AACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
*
44579177 TGAAAATGGAGAAATGTAG-TCATTTGGAAATGAATGTGGTTTTTCTCAAAAA
1 TGAAAATGGAGAAATG-AGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
44579229 TGAAAAT-GA-AAATGA
1 TGAAAATGGAGAAATGA
44579244 CTTGGAAATG
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 1 0.02
50 5 0.08
51 20 0.32
52 34 0.55
53 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
Found at i:44580180 original size:22 final size:22
Alignment explanation
Indices: 44580152--44580197 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
44580142 ACTACGATTT
*
44580152 AAAAAAA-AAGTTACTCTCTTGA
1 AAAAAAATAAATTAC-CTCTTGA
*
44580174 AAAAAAATAAATTTCCTCTTGA
1 AAAAAAATAAATTACCTCTTGA
44580196 AA
1 AA
44580198 GTTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (22 bp):
AAAAAAATAAATTACCTCTTGA
Found at i:44580464 original size:10 final size:10
Alignment explanation
Indices: 44580430--44580456 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
44580420 CGAGCATAAA
44580430 TTAAAAAAAT
1 TTAAAAAAAT
44580440 TTAAAAAAAT
1 TTAAAAAAAT
44580450 TTAAAAA
1 TTAAAAA
44580457 TATATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:44582066 original size:18 final size:18
Alignment explanation
Indices: 44582043--44582093 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
44582033 TTTAGAGTTA
44582043 TGGGCCCACATGCCCGTG
1 TGGGCCCACATGCCCGTG
* *
44582061 TGGGCCTATATGCCCGTG
1 TGGGCCCACATGCCCGTG
*
44582079 TAGGCCCACATGCCC
1 TGGGCCCACATGCCC
44582094 ATATTGGCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.37, G:0.29, T:0.20
Consensus pattern (18 bp):
TGGGCCCACATGCCCGTG
Found at i:44586289 original size:20 final size:20
Alignment explanation
Indices: 44586264--44586302 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44586254 TACTCGCTTC
44586264 TTTACTTACTCGCTTACTTG
1 TTTACTTACTCGCTTACTTG
*
44586284 TTTACTTACTTGCTTACTT
1 TTTACTTACTCGCTTACTT
44586303 AAATAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTACTTACTCGCTTACTTG
Done.