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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 87 of 97
Found at i:34172799 original size:2 final size:2
Alignment explanation
Indices: 34172792--34172824 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34172782 TTTCATGCAC
34172792 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34172825 GTGGTNAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:34172851 original size:85 final size:85
Alignment explanation
Indices: 34172745--34172910 Score: 316
Period size: 85 Copynumber: 2.0 Consensus size: 85
34172735 AACTGAAAAA
34172745 TAATATTTTCTGATACCATTTTTAGGTAGATACCATATTTCATGCACTATATATATATATATATA
1 TAATATTTTCTGATACCATTTTTAGGTAGATACCATATTTCATGCACTATATATATATATATATA
34172810 TATAT-AATATATATAGTGG
66 TATATAAATATATATAGTGG
34172829 TNAATATTTTCTGATACCATTTTTAGGTAGATACCATATTTCATGCACTATATATATATATATAT
1 T-AATATTTTCTGATACCATTTTTAGGTAGATACCATATTTCATGCACTATATATATATATATAT
34172894 ATATATAAATATATATA
65 ATATATAAATATATATA
34172911 TGGGTGAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 1 0.01
85 69 0.86
86 10 0.12
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (85 bp):
TAATATTTTCTGATACCATTTTTAGGTAGATACCATATTTCATGCACTATATATATATATATATA
TATATAAATATATATAGTGG
Found at i:34172884 original size:2 final size:2
Alignment explanation
Indices: 34172877--34172911 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
34172867 TTTCATGCAC
*
34172877 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34172912 GGGTGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34174869 original size:16 final size:16
Alignment explanation
Indices: 34174845--34174880 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34174835 AAGTGTGAGG
34174845 TATACATATATAATTA
1 TATACATATATAATTA
* *
34174861 TATATATATATATTTA
1 TATACATATATAATTA
34174877 TATA
1 TATA
34174881 ATGAGTCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TATACATATATAATTA
Found at i:34175382 original size:2 final size:2
Alignment explanation
Indices: 34175375--34175401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34175365 AATTAAAATG
34175375 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
34175402 GAGNTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34175489 original size:111 final size:110
Alignment explanation
Indices: 34175295--34175512 Score: 427
Period size: 111 Copynumber: 2.0 Consensus size: 110
34175285 TATATATATA
34175295 TATATATATATGCATTTATTTCAAGTGGTTGTGAGAGGGTTTTCTAATGGAGAAAAAGACAGTGA
1 TATATATATATGCATTTATTTCAAGTGGTTGTGAGAGGGTTTTCTAATGGAGAAAAAGACAGTGA
34175360 AAATTAATTAAAATGGAGAGAGAGAGAGAGAGAGAGAGAGAGGAG
66 AAATTAATTAAAATGGAGAGAGAGAGAGAGAGAGAGAGAGAGGAG
34175405 NTATATATATATGCATTTATTTCAAGTGGTTGTGAGAGGGTTTTCTAATGGAGAAAAAGACAGTG
1 -TATATATATATGCATTTATTTCAAGTGGTTGTGAGAGGGTTTTCTAATGGAGAAAAAGACAGTG
34175470 AAAATTAATTAAAATGGAGAGAGAGAGAGAGAGAGAGAGAGAG
65 AAAATTAATTAAAATGGAGAGAGAGAGAGAGAGAGAGAGAGAG
34175513 AGGGATTTTG
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.41, C:0.04, G:0.29, T:0.26
Consensus pattern (110 bp):
TATATATATATGCATTTATTTCAAGTGGTTGTGAGAGGGTTTTCTAATGGAGAAAAAGACAGTGA
AAATTAATTAAAATGGAGAGAGAGAGAGAGAGAGAGAGAGAGGAG
Found at i:34175493 original size:2 final size:2
Alignment explanation
Indices: 34175486--34175514 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34175476 AATTAAAATG
34175486 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
34175515 GGATTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34176779 original size:2 final size:2
Alignment explanation
Indices: 34176767--34176829 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
34176757 ATCAAACAGG
*
34176767 AT AT AT GT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34176808 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
34176830 TATTTATAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34177731 original size:2 final size:2
Alignment explanation
Indices: 34177718--34177748 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34177708 AGAGGCAGAC
*
34177718 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34177749 AAGGAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:34185585 original size:38 final size:37
Alignment explanation
Indices: 34185532--34185605 Score: 121
Period size: 38 Copynumber: 2.0 Consensus size: 37
34185522 AAAAGAAAAG
*
34185532 AACAACTGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
1 AACAACCGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
*
34185569 NAACAACCGTGCGAAAAAGCCTCTGAATTGCAGGCAA
1 -AACAACCGTGAGAAAAAGCCTCTGAATTGCAGGCAA
34185606 GCTATATAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (37 bp):
AACAACCGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
Found at i:34185689 original size:166 final size:162
Alignment explanation
Indices: 34185404--34185731 Score: 584
Period size: 166 Copynumber: 2.0 Consensus size: 162
34185394 AAAAGAAAAG
*
34185404 AACACCCGTGAGAAAAAGCCTCTGAATTGCAGGCAAGCTATATAACATCTAAATATGACAATCAG
1 AACAACCGTGAGAAAAAGCCTCTGAATTGCAGGCAAGCTATATAACATCTAAATATGACAATCAG
*
34185469 CATCAAAATCAAGATAAAATGTGCACAATGTACATGTGCAGACAGAAAAAAAAAAAAGAAAAGAA
66 CATCAAAATCAAGATAAAATATGCACAATGTACATGTGCAGACAG--AAAAAAAAAA-AAAAGAA
34185534 CAACTGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
128 CAACTGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
* *
34185569 NAACAACCGTGCGAAAAAGCCTCTGAATTGCAGGCAAGCTATATAACATCTAAATATGACAATCG
1 -AACAACCGTGAGAAAAAGCCTCTGAATTGCAGGCAAGCTATATAACATCTAAATATGACAATCA
34185634 GCATCAAAATCAAGATAAAATATGCACAATGTACATGTGCAGACAGAAAAAAAAAAAAAAGAACA
65 GCATCAAAATCAAGATAAAATATGCACAATGTACATGTGCAGACAGAAAAAAAAAAAAAAGAACA
34185699 ACTGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
130 ACTGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
34185732 CTATATAACC
Statistics
Matches: 158, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
163 42 0.27
164 10 0.06
166 106 0.67
ACGTcount: A:0.48, C:0.18, G:0.17, T:0.17
Consensus pattern (162 bp):
AACAACCGTGAGAAAAAGCCTCTGAATTGCAGGCAAGCTATATAACATCTAAATATGACAATCAG
CATCAAAATCAAGATAAAATATGCACAATGTACATGTGCAGACAGAAAAAAAAAAAAAAGAACAA
CTGTGAGAAAAAGCCTCTGAATTGCAGGCAAA
Found at i:34187177 original size:15 final size:16
Alignment explanation
Indices: 34187145--34187177 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34187135 TCAACCAGGC
*
34187145 AAAGAAAGATTTTTAA
1 AAAGAAAGATTTTGAA
34187161 AAAGAAA-ATTTTGAA
1 AAAGAAAGATTTTGAA
34187176 AA
1 AA
34187178 TTTAAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (16 bp):
AAAGAAAGATTTTGAA
Found at i:34187873 original size:232 final size:230
Alignment explanation
Indices: 34187468--34187921 Score: 865
Period size: 232 Copynumber: 2.0 Consensus size: 230
34187458 TACGTCGTCA
34187468 CTTTTATTTTCTTTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCTT
1 CTTTTATTTTCTTTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCTT
34187533 ATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCTT
66 ATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCTT
34187598 AAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAATA
131 AAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAATA
34187663 AATTCCTTAACTATATTCAAAAATTTAATTNTAGCT
196 AATTCCTTAACTATATTCAAAAATTTAATT-TAGCT
34187699 CTTTTATTTTC-TTTTTCAATTTTTCTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGC
1 CTTTTATTTTCTTTTTTCAA-TTTT-TTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGC
34187763 TTATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTC
64 TTATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTC
34187828 TTAAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAA
129 TTAAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAA
*
34187893 TAAATTCTTTAACTATATTCAAAAATTTA
194 TAAATTCCTTAACTATATTCAAAAATTTA
34187922 TTAAACCCAT
Statistics
Matches: 220, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
230 8 0.04
231 15 0.07
232 197 0.90
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (230 bp):
CTTTTATTTTCTTTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCTT
ATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCTT
AAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAATA
AATTCCTTAACTATATTCAAAAATTTAATTTAGCT
Found at i:34190161 original size:17 final size:17
Alignment explanation
Indices: 34190139--34190171 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34190129 AGTTTTCAAG
34190139 TTCTATCCAATTAGAAC
1 TTCTATCCAATTAGAAC
34190156 TTCTATCCAATTAGAA
1 TTCTATCCAATTAGAA
34190172 ATGCTGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
TTCTATCCAATTAGAAC
Found at i:34190316 original size:29 final size:29
Alignment explanation
Indices: 34190253--34190330 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 29
34190243 CCTAACATTA
* *
34190253 ACGTGTAACAA-AATA-CTTTTAAATATG
1 ACGTGTAACAACAATATTTTTTAAACATG
* * *
34190280 TCATGTAACAACAATATTTTTTCAACATG
1 ACGTGTAACAACAATATTTTTTAAACATG
34190309 ACGTGTAACAACAATATTTTTT
1 ACGTGTAACAACAATATTTTTT
34190331 TTTCAACATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.21
28 4 0.10
29 29 0.69
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (29 bp):
ACGTGTAACAACAATATTTTTTAAACATG
Found at i:34190332 original size:32 final size:29
Alignment explanation
Indices: 34190283--34190348 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 29
34190273 AAATATGTCA
34190283 TGTAACAACAATATTTTTTCAACA-TGACG
1 TGTAACAACAATATTTTTTCAACATTG-CG
34190312 TGTAACAACAATATTTTTTTTTCAACATTGCG
1 TGTAACAACAATA---TTTTTTCAACATTGCG
34190344 TGTAA
1 TGTAA
34190349 TAACCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 13 0.39
32 18 0.55
33 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (29 bp):
TGTAACAACAATATTTTTTCAACATTGCG
Found at i:34190473 original size:24 final size:24
Alignment explanation
Indices: 34190439--34190573 Score: 175
Period size: 24 Copynumber: 5.6 Consensus size: 24
34190429 ACAATCTAAT
*
34190439 CATGACTTGTCACATGTTTTTGTA
1 CATGACGTGTCACATGTTTTTGTA
*
34190463 CATGACGTGTCACATGTTTCTGTA
1 CATGACGTGTCACATGTTTTTGTA
* *
34190487 TATGGCGTGTCACATGTTTCTT-TA
1 CATGACGTGTCACATGTTT-TTGTA
*
34190511 CATGACGAGTCACATGTTTTTGTA
1 CATGACGTGTCACATGTTTTTGTA
* *
34190535 CATGGCGTGTCACATGTTCCTT-TA
1 CATGACGTGTCACATGTT-TTTGTA
34190559 CATGACGTGTCACAT
1 CATGACGTGTCACAT
34190574 ATTCTATACG
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 2 0.02
24 91 0.95
25 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
CATGACGTGTCACATGTTTTTGTA
Found at i:34190502 original size:48 final size:47
Alignment explanation
Indices: 34190446--34190573 Score: 193
Period size: 48 Copynumber: 2.7 Consensus size: 47
34190436 AATCATGACT
*
34190446 TGTCACATGTTTTTGTACATGACGTGTCACATGTTTCTGTATATGGCG
1 TGTCACATGTTTTT-TACATGACGTGTCACATGTTTCTGTACATGGCG
* *
34190494 TGTCACATGTTTCTTTACATGACGAGTCACATGTTTTTGTACATGGCG
1 TGTCACATGTTT-TTTACATGACGTGTCACATGTTTCTGTACATGGCG
*
34190542 TGTCACATGTTCCTTTACATGACGTGTCACAT
1 TGTCACATGTT-TTTTACATGACGTGTCACAT
34190574 ATTCTATACG
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
48 71 0.97
49 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (47 bp):
TGTCACATGTTTTTTACATGACGTGTCACATGTTTCTGTACATGGCG
Found at i:34190612 original size:24 final size:23
Alignment explanation
Indices: 34190446--34190608 Score: 157
Period size: 24 Copynumber: 6.9 Consensus size: 23
34190436 AATCATGACT
*
34190446 TGTCACATGTTTTTGTACATGACG
1 TGTCACATGTTTCTGTACATG-CG
*
34190470 TGTCACATGTTTCTGTATATGGCG
1 TGTCACATGTTTCTGTACAT-GCG
*
34190494 TGTCACATGTTTCTTTACATGACG
1 TGTCACATGTTTCTGTACATG-CG
* *
34190518 AGTCACATGTTTTTGTACATGGCG
1 TGTCACATGTTTCTGTACAT-GCG
* *
34190542 TGTCACATGTTCCTTTACATGACG
1 TGTCACATGTTTCTGTACATG-CG
* * * *
34190566 TGTCACAT-ATTCTATACGTAGTG
1 TGTCACATGTTTCTGTACAT-GCG
*
34190589 TGTCACGTGTTTCTGTACAT
1 TGTCACATGTTTCTGTACAT
34190609 AGTGAAAACA
Statistics
Matches: 113, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
23 17 0.15
24 94 0.83
25 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (23 bp):
TGTCACATGTTTCTGTACATGCG
Found at i:34194262 original size:27 final size:25
Alignment explanation
Indices: 34194232--34194320 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 25
34194222 AAATTTAAAA
*
34194232 TAAAATATACAATATAAAAAATTATAT
1 TAAAATATA-AAAATAAAAAA-TATAT
*
34194259 TAAAA-ATAAAAATAAAATATATACT
1 TAAAATATAAAAATAAAAAATATA-T
*
34194284 TATAATA-AAAAATAAAAAATATAT
1 TAAAATATAAAAATAAAAAATATAT
*
34194308 T-TAAT-TAAAAATA
1 TAAAATATAAAAATA
34194321 TATTTAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
23 11 0.20
24 6 0.11
25 29 0.53
26 4 0.07
27 5 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TAAAATATAAAAATAAAAAATATAT
Found at i:34198843 original size:15 final size:16
Alignment explanation
Indices: 34198811--34198843 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
34198801 TCAACCAGGC
*
34198811 AAAGAAAGATTTTTAA
1 AAAGAAAGATTTTGAA
34198827 AAAGAAA-ATTTTGAA
1 AAAGAAAGATTTTGAA
34198842 AA
1 AA
34198844 TTTAAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (16 bp):
AAAGAAAGATTTTGAA
Found at i:34199538 original size:230 final size:230
Alignment explanation
Indices: 34199134--34199594 Score: 906
Period size: 230 Copynumber: 2.0 Consensus size: 230
34199124 TACGTCGTCA
34199134 CTTTTATTTTCTTTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCTT
1 CTTTTATTTTCTTTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCTT
34199199 ATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCTT
66 ATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCTT
34199264 AAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAATA
131 AAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAATA
34199329 AATTCCTTAACTATATTCAAAAATTTAATTAAGTT
196 AATTCCTTAACTATATTCAAAAATTTAATTAAGTT
34199364 NCTTTTATTTTC-TTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCT
1 -CTTTTATTTTCTTTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCT
34199428 TATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCT
65 TATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCT
34199493 TAAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAAT
130 TAAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAAT
34199558 AAATTCCTTAACTATATTCAAAAATTTAATTAAGTT
195 AAATTCCTTAACTATATTCAAAAATTTAATTAAGTT
34199594 C
1 C
34199595 ATATCTTTTT
Statistics
Matches: 230, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
229 1 0.00
230 218 0.95
231 11 0.05
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.49
Consensus pattern (230 bp):
CTTTTATTTTCTTTTTTCAATTTTTTAATGTTGCCTTACCGCGTGCACGTGTTGACGTTATGCTT
ATGCAGGTATATTTAGAGTAATTACATTTTTTTTTTCAATTGACACCTTTCTATTTTTTTCTCTT
AAAAACTGCTATTTAAGTTTAATTACTTCTGTAAATTAATTTTTATTTAATTAAATACTCAAATA
AATTCCTTAACTATATTCAAAAATTTAATTAAGTT
Found at i:34208914 original size:19 final size:19
Alignment explanation
Indices: 34208878--34208913 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34208868 ATTCATCAAT
*
34208878 TTTTAAAATAGATATTTTA
1 TTTTAAAATAAATATTTTA
34208897 TTTTAAAA-AAATATTTT
1 TTTTAAAATAAATATTTT
34208914 TTATTAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTAAAATAAATATTTTA
Found at i:34210841 original size:21 final size:20
Alignment explanation
Indices: 34210772--34210841 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
34210762 TTGTAGAAGC
34210772 CTTTTTCGATCAAAATTGAGT
1 CTTTTTCGAT-AAAATTGAGT
* *
34210793 -TTCTTTGGATAGAAATTGAAT
1 CTT-TTTCGATA-AAATTGAGT
*
34210814 ATATTTTCGATAAAATTTGAGT
1 CT-TTTTCGATAAAA-TTGAGT
34210836 CTTTTT
1 CTTTTT
34210842 AGATGAAAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.08
21 21 0.54
22 14 0.36
23 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (20 bp):
CTTTTTCGATAAAATTGAGT
Found at i:34211626 original size:19 final size:18
Alignment explanation
Indices: 34211601--34211661 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
34211591 TACCTATATC
*
34211601 TAAATTTTAAATTTTAAT
1 TAAATTTTAAATTTTAAA
*
34211619 TGAAATTTCAAA-TTTAAA
1 T-AAATTTTAAATTTTAAA
34211637 TAAATCTATTAAATTTTAAAA
1 TAAAT-T-TTAAATTTT-AAA
34211658 TAAA
1 TAAA
34211662 CTCTCTACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 4 0.11
18 8 0.23
19 13 0.37
20 3 0.09
21 7 0.20
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAATTTTAAATTTTAAA
Found at i:34211840 original size:31 final size:34
Alignment explanation
Indices: 34211762--34211841 Score: 112
Period size: 33 Copynumber: 2.4 Consensus size: 34
34211752 TATTGAAATA
* *
34211762 ATAATTTTATTTTTTATTAATTTTAAAAATTATT
1 ATAATTATATTTTTTATTAATTTTAAAAATTACT
*
34211796 ATTA-TATATTTTTTATTAA-TTT-AAAATTACT
1 ATAATTATATTTTTTATTAATTTTAAAAATTACT
34211827 ATAATTATATTTTTT
1 ATAATTATATTTTTT
34211842 TAAAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.27
32 13 0.32
33 14 0.34
34 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (34 bp):
ATAATTATATTTTTTATTAATTTTAAAAATTACT
Found at i:34219300 original size:2 final size:2
Alignment explanation
Indices: 34219293--34219343 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
34219283 TTACTGTATG
* *
34219293 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34219335 TA TA TA TA T
1 TA TA TA TA T
34219344 GTGTACACGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34219318 original size:18 final size:18
Alignment explanation
Indices: 34219295--34219343 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
34219285 ACTGTATGTA
34219295 TATATATATATATATATG
1 TATATATATATATATATG
34219313 TATATATATATATATATG
1 TATATATATATATATATG
34219331 TATATATATATAT
1 TATATATATATAT
34219344 GTGTACACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TATATATATATATATATG
Found at i:34222348 original size:287 final size:286
Alignment explanation
Indices: 34221832--34222400 Score: 1084
Period size: 287 Copynumber: 2.0 Consensus size: 286
34221822 GTAAAGGAAC
* * * *
34221832 AATAATAGAAGATAGATAAAGCCAAAAGAATGGTTGAAACAAAATGTTGACGGGTAGAATTTTTA
1 AATAATAGAAGACAGATAAAGCCAAAAGAATGGTCGAAACAAAAAGTTAACGGGTAGAATTTTTA
34221897 ATTAGCAAAAAGTTAGAAGATCAGATTATAATATATGAAAAGTTTGAAAGATTAAATTATAAAAG
66 ATTAGCAAAAAGTTAGAAGATCAGATTATAATATATGAAAAGTTTGAAAGATTAAATTATAAAAG
34221962 AGAAAAAGTTTGGAGGGTTAAACAGAGAATAAAAAAAAGTTAGAGAACTTATTGGCAATTAATCT
131 AGAAAAAGTTTGGAGGGTTAAACAGAGAATAAAAAAAAGTTAGAGAACTTATTGGCAATTAATCT
34222027 ATCCTTAAATTATATTAAAAACAAATACGTATGTAGAAGATGTTAAGGATTAAATGGGCGGTCAA
196 ATCCTTAAATTATATTAAAAACAAATACGTATGTAGAAGATGTTAAGGATTAAATGGGCGGTCAA
34222092 CACAAAGTTGACCACCCATGCANGAAA
261 CACAAAGTTGACCACCCATGCA-GAAA
*
34222119 AATAATAGAAGACAGATAAAGCCAAAAGAATGGTCGAAACAAAAAGTTAACGGGTTGAATTTTTA
1 AATAATAGAAGACAGATAAAGCCAAAAGAATGGTCGAAACAAAAAGTTAACGGGTAGAATTTTTA
34222184 ATTAGCAAAAAGTTAGAAGATCAGATTATAATATATGAAAAGTTTGAAAGATTAAATTATAAAAG
66 ATTAGCAAAAAGTTAGAAGATCAGATTATAATATATGAAAAGTTTGAAAGATTAAATTATAAAAG
34222249 AGAAAAAGTTTGGAGGGTTAAACAGAGAATAAAAAAAAGTTAGAGAACTTATTGGCAATTAATCT
131 AGAAAAAGTTTGGAGGGTTAAACAGAGAATAAAAAAAAGTTAGAGAACTTATTGGCAATTAATCT
34222314 ATCCTTAAATTATATTAAAAACAAATACGTATGTAGAAGATGTTAAGGATTAAATGGGCGGTCAA
196 ATCCTTAAATTATATTAAAAACAAATACGTATGTAGAAGATGTTAAGGATTAAATGGGCGGTCAA
34222379 CACAAAGTTGACCACCCATGCA
261 CACAAAGTTGACCACCCATGCA
34222401 ACAACCAAAG
Statistics
Matches: 277, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
287 277 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (286 bp):
AATAATAGAAGACAGATAAAGCCAAAAGAATGGTCGAAACAAAAAGTTAACGGGTAGAATTTTTA
ATTAGCAAAAAGTTAGAAGATCAGATTATAATATATGAAAAGTTTGAAAGATTAAATTATAAAAG
AGAAAAAGTTTGGAGGGTTAAACAGAGAATAAAAAAAAGTTAGAGAACTTATTGGCAATTAATCT
ATCCTTAAATTATATTAAAAACAAATACGTATGTAGAAGATGTTAAGGATTAAATGGGCGGTCAA
CACAAAGTTGACCACCCATGCAGAAA
Found at i:34224696 original size:161 final size:160
Alignment explanation
Indices: 34224425--34224737 Score: 518
Period size: 161 Copynumber: 1.9 Consensus size: 160
34224415 AGAAGGCTTG
*
34224425 TGACAGACTTAAATGGTCCTTTCTTCAAGATTTCCTAATAGAGATAGGCCTTCCTCCGCAATGGA
1 TGACAAACTTAAATGGTCCTTTCTTCAAGATTTCCTAATAGAGATAGGCCTTCCTCCGCAATGGA
* * *
34224490 TCTCTTTAATTTTGTATATTGTCTGGACTCTTTCTTTCTCTGTTATATGGAATGGCAAACAGCCT
66 TCTCTTTAATTTGGTATATTGTCTAGACTCCTTCTTTCTCTGTTATATGGAATGGCAAACAGCCT
* *
34224555 CACAAAATTCACTCTAGCTAGAGTAGGCCTA
131 -AAAAAATTCACTCCAGCTAGAGTAGGCCTA
* *
34224586 TGACAAACTTAAATGGTCTTTTCTTCAAGATTTCCTAGTAGAGATAGGCCTTCCTCCGCAATGGA
1 TGACAAACTTAAATGGTCCTTTCTTCAAGATTTCCTAATAGAGATAGGCCTTCCTCCGCAATGGA
* *
34224651 TCTCTTTAATTTGGTATATTGTCTAGACTCCTTCTTTCTCTGTTATATGGAATGGTAAACAGTCT
66 TCTCTTTAATTTGGTATATTGTCTAGACTCCTTCTTTCTCTGTTATATGGAATGGCAAACAGCCT
*
34224716 AAAAAATTCACTCCATCTAGAG
131 AAAAAATTCACTCCAGCTAGAG
34224738 GCATTAGCTA
Statistics
Matches: 141, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
160 19 0.13
161 122 0.87
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (160 bp):
TGACAAACTTAAATGGTCCTTTCTTCAAGATTTCCTAATAGAGATAGGCCTTCCTCCGCAATGGA
TCTCTTTAATTTGGTATATTGTCTAGACTCCTTCTTTCTCTGTTATATGGAATGGCAAACAGCCT
AAAAAATTCACTCCAGCTAGAGTAGGCCTA
Found at i:34235608 original size:20 final size:20
Alignment explanation
Indices: 34235583--34235633 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
34235573 CATAAATATC
*
34235583 CAAGTTTCTAGCA-ACTTCTT
1 CAAGTTTCCAGCAGA-TTCTT
34235603 CAAGTTTCCAGCAGATTCTT
1 CAAGTTTCCAGCAGATTCTT
*
34235623 CAAGCTTCCAG
1 CAAGTTTCCAG
34235634 TAACTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (20 bp):
CAAGTTTCCAGCAGATTCTT
Found at i:34235748 original size:2 final size:2
Alignment explanation
Indices: 34235741--34235769 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34235731 TTCTTTNTGT
34235741 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
34235770 TTTCCCACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34239384 original size:27 final size:28
Alignment explanation
Indices: 34239354--34239407 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
34239344 ATGTCCTAGT
*
34239354 GGTGG-AAAATTACAATTTTTCCCCTAA
1 GGTGGCAAAATTACAATTTTACCCCTAA
* *
34239381 GGTGGCAACATTACCATTTTACCCCTA
1 GGTGGCAAAATTACAATTTTACCCCTA
34239408 TACTCCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (28 bp):
GGTGGCAAAATTACAATTTTACCCCTAA
Found at i:34239475 original size:19 final size:19
Alignment explanation
Indices: 34239451--34239488 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
34239441 ACTTATAAAC
34239451 CTCAAATCATACTCAAATA
1 CTCAAATCATACTCAAATA
*
34239470 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCAAATA
34239489 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCAAATA
Found at i:34240003 original size:63 final size:63
Alignment explanation
Indices: 34239904--34240035 Score: 255
Period size: 63 Copynumber: 2.1 Consensus size: 63
34239894 TTAAAGGAGT
34239904 AAATAATCAAAGGCTAAATTATGGGGTTTTAACAAGAAATTAAACTAAATTGCATTATTTTTA
1 AAATAATCAAAGGCTAAATTATGGGGTTTTAACAAGAAATTAAACTAAATTGCATTATTTTTA
*
34239967 AAATAATCAAAGGCTAAATTATGGGGTTTTAACAAGAAATTAAACTAAATTGCATTGTTTTTA
1 AAATAATCAAAGGCTAAATTATGGGGTTTTAACAAGAAATTAAACTAAATTGCATTATTTTTA
34240030 AAATAA
1 AAATAA
34240036 GTGCATCATG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (63 bp):
AAATAATCAAAGGCTAAATTATGGGGTTTTAACAAGAAATTAAACTAAATTGCATTATTTTTA
Found at i:34240015 original size:31 final size:31
Alignment explanation
Indices: 34239917--34240017 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 31
34239907 TAATCAAAGG
34239917 CTAAATTATGGGGTTTTAACAAGAAATTAAA
1 CTAAATTATGGGGTTTTAACAAGAAATTAAA
*** * *
34239948 CTAAATTGCAT-TATTTTTAA-AA-TAATCAAA
1 CTAAATT--ATGGGGTTTTAACAAGAAATTAAA
34239978 GGCTAAATTATGGGGTTTTAACAAGAAATTAAA
1 --CTAAATTATGGGGTTTTAACAAGAAATTAAA
34240011 CTAAATT
1 CTAAATT
34240018 GCATTGTTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
30 8 0.15
31 22 0.42
32 15 0.28
33 8 0.15
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (31 bp):
CTAAATTATGGGGTTTTAACAAGAAATTAAA
Found at i:34240027 original size:31 final size:31
Alignment explanation
Indices: 34239929--34240027 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
34239919 AAATTATGGG
34239929 GTTTTAACAAGAAATTAAACTAAATTGCATT
1 GTTTTAACAAGAAATTAAACTAAATTGCATT
* * * *
34239960 ATTTTTAA-AA-TAATCAAAGGCTAAATT--ATGGG
1 -GTTTTAACAAGAAATTAAA--CTAAATTGCAT--T
34239992 GTTTTAACAAGAAATTAAACTAAATTGCATT
1 GTTTTAACAAGAAATTAAACTAAATTGCATT
34240023 GTTTT
1 GTTTT
34240028 TAAAATAAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 17
0.67 0.11 0.22
Matches are distributed among these distances:
30 8 0.16
31 20 0.39
32 15 0.29
33 8 0.16
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (31 bp):
GTTTTAACAAGAAATTAAACTAAATTGCATT
Found at i:34241750 original size:31 final size:31
Alignment explanation
Indices: 34241684--34241764 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
34241674 TTTAATTAGC
*
34241684 AAAAAGTTTGAGGATTAAATTATAATATATG
1 AAAAAGTTTGAGGATTAAATTATAATAGATG
34241715 -AAAAGTTTGAAGGATTAAATTATGAA-AGA-G
1 AAAAAGTTTG-AGGATTAAATTAT-AATAGATG
*
34241745 AAAAAGTTTGGAGGGTTAAA
1 AAAAAGTTT-GAGGATTAAA
34241765 CGGAAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 10 0.23
31 31 0.70
32 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (31 bp):
AAAAAGTTTGAGGATTAAATTATAATAGATG
Found at i:34241857 original size:9 final size:9
Alignment explanation
Indices: 34241841--34241902 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
34241831 AAAAAAATTA
*
34241841 AAATTAAAT
1 AAATAAAAT
34241850 AAAATAAAAT
1 -AAATAAAAT
34241860 AAAT-AAAT
1 AAATAAAAT
34241868 AAAATAAAAT
1 -AAATAAAAT
*
34241878 AATTAAAA-
1 AAATAAAAT
*
34241886 AAATTAAA-
1 AAATAAAAT
34241894 AAA-AAAAT
1 AAATAAAAT
34241902 A
1 A
34241903 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 3 0.07
8 14 0.32
9 15 0.34
10 12 0.27
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:34241866 original size:18 final size:18
Alignment explanation
Indices: 34241845--34241902 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
34241835 AAATTAAAAT
34241845 TAAATAAAATAAAATAAA
1 TAAATAAAATAAAATAAA
*
34241863 TAAATAAAATAAAATAAT
1 TAAATAAAATAAAATAAA
34241881 TAAA-AAAATTAAAA-AAA
1 TAAATAAAA-TAAAATAAA
34241898 -AAATA
1 TAAATA
34241903 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 3 0.08
17 7 0.19
18 26 0.72
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAATAAAATAAAATAAA
Found at i:34251786 original size:22 final size:22
Alignment explanation
Indices: 34251743--34251791 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
34251733 AATATTATTG
**
34251743 ATAATTAAATTATTAATTTTAT
1 ATAATTAAATTATTAAAATTAT
34251765 ATAATTAAA-TATATAAAATTAT
1 ATAATTAAATTAT-TAAAATTAT
34251787 -TAATT
1 ATAATT
34251792 TTTTTGGCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATTAAATTATTAAAATTAT
Found at i:34252967 original size:24 final size:24
Alignment explanation
Indices: 34252940--34252999 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
34252930 AAGAGAAAGG
*
34252940 TTAGAGGGAAAGGTGGATTAGAGT
1 TTAGAGGGAAAGATGGATTAGAGT
34252964 TTAGAGGGAAAGATGGATTAGAGT
1 TTAGAGGGAAAGATGGATTAGAGT
*
34252988 TTAGAGAGAAAG
1 TTAGAGGGAAAG
34253000 TTACTCTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (24 bp):
TTAGAGGGAAAGATGGATTAGAGT
Found at i:34253051 original size:25 final size:26
Alignment explanation
Indices: 34253017--34253068 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
34253007 TCCCCTTTGC
34253017 ACTTTAAACCTG-AAAGAA-AAAAACA
1 ACTTTAAACC-GAAAAGAAGAAAAACA
34253042 ACTTTAAACCGAAAAGAAGAAAAACA
1 ACTTTAAACCGAAAAGAAGAAAAACA
34253068 A
1 A
34253069 GATCCTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 1 0.04
25 16 0.64
26 8 0.32
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.13
Consensus pattern (26 bp):
ACTTTAAACCGAAAAGAAGAAAAACA
Found at i:34260310 original size:2 final size:2
Alignment explanation
Indices: 34260303--34260375 Score: 55
Period size: 2 Copynumber: 36.5 Consensus size: 2
34260293 AACTCCGGAG
34260303 GA GA GA GA GA GA GA GA GA GA GA GA GA GCA G- GTA -A GTA CGA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA G-A GA G-A -GA GA
* * *
34260344 G- GG GT NA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
34260376 CAGGAATCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
1 4 0.07
2 50 0.85
3 4 0.07
4 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.48, T:0.04
Consensus pattern (2 bp):
GA
Found at i:34261628 original size:14 final size:14
Alignment explanation
Indices: 34261609--34261640 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
34261599 TTTTTTATTA
34261609 TATTTTAAATTTTT
1 TATTTTAAATTTTT
34261623 TATTTTAAATTTTT
1 TATTTTAAATTTTT
34261637 TATT
1 TATT
34261641 ATTTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTTAAATTTTT
Found at i:34261634 original size:21 final size:20
Alignment explanation
Indices: 34261595--34261635 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34261585 CTATATAAGA
*
34261595 AAATTTTTTTATTATATTTT
1 AAATTTTTTTATTAAATTTT
*
34261615 AAATTTTTTATTTTAAATTTT
1 AAATTTTTT-TATTAAATTTT
34261636 TTATTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AAATTTTTTTATTAAATTTT
Found at i:34283704 original size:2 final size:2
Alignment explanation
Indices: 34283697--34283725 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34283687 CATCAATTAT
34283697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34283726 TTAACGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34295944 original size:19 final size:20
Alignment explanation
Indices: 34295903--34295944 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
34295893 TTAATAAATT
*
34295903 ATTAAAATAATAAATATTTTA
1 ATTAAAAT-ATAAATATTATA
*
34295924 ATTAAAAT-TAAATGTTATA
1 ATTAAAATATAAATATTATA
34295943 AT
1 AT
34295945 AAATGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.58
21 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTAAAATATAAATATTATA
Found at i:34302018 original size:110 final size:108
Alignment explanation
Indices: 34301820--34302024 Score: 243
Period size: 110 Copynumber: 1.9 Consensus size: 108
34301810 GTAAAGGGTT
* * *
34301820 GTTAATGGCTTTTGCTGTACATAATCACCTCTTAACATCTCTGCGATAAAGGCAGATAAAGTATC
1 GTTAATGACTTTTGCTGTACATAATCACCCCTTAACATATCTGCGATAAAGGCAGATAAAGTATC
** * *
34301885 GGTGTAGTGCACTGGCTCTAAAATCTGAATCTGATCAATGTTGAC
66 AATGTAATGCACT-G-TCTAAAATATGAATCTGATCAATGTTGAC
* * * *
34301930 GTTAATGACTTTTGCTGTACATGATCACCCCTTAACATATCTGTGATTGAA-GCAGATACAGTAT
1 GTTAATGACTTTTGCTGTACATAATCACCCCTTAACATATCTGCGA-TAAAGGCAGATAAAGTAT
34301994 CTAATGTAATGCACT-TCGTAAAAATATGAAT
65 C-AATGTAATGCACTGTC-T-AAAATATGAAT
34302025 TTAGCCCGTC
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
108 2 0.03
109 1 0.01
110 64 0.80
111 13 0.16
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (108 bp):
GTTAATGACTTTTGCTGTACATAATCACCCCTTAACATATCTGCGATAAAGGCAGATAAAGTATC
AATGTAATGCACTGTCTAAAATATGAATCTGATCAATGTTGAC
Found at i:34305748 original size:28 final size:28
Alignment explanation
Indices: 34305717--34305771 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
34305707 TTATTTTATT
*
34305717 TTTAAAATATTAATATTTTTATAATTTC
1 TTTAAAATATTAATATTTTGATAATTTC
34305745 TTTAAAATATTAATATTTTGATAATTT
1 TTTAAAATATTAATATTTTGATAATTT
34305772 AAATATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAAAATATTAATATTTTGATAATTTC
Found at i:34306126 original size:21 final size:22
Alignment explanation
Indices: 34306097--34306139 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
34306087 TTAAGTATTA
* *
34306097 GTATGTTTTTTATTTTTATTTT
1 GTATGTTTTTAATTTATATTTT
34306119 GTAT-TTTTTAATTTATATTTT
1 GTATGTTTTTAATTTATATTTT
34306140 TACTTAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (22 bp):
GTATGTTTTTAATTTATATTTT
Found at i:34308658 original size:21 final size:20
Alignment explanation
Indices: 34308625--34308664 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34308615 CTCATAATTG
*
34308625 TATAATAATAATATAATAAAT
1 TATAATAAAAATAT-ATAAAT
*
34308646 TATATTAAAAATATATAAA
1 TATAATAAAAATATATAAA
34308665 AATTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATAATAAAAATATATAAAT
Found at i:34311947 original size:28 final size:29
Alignment explanation
Indices: 34311892--34311964 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
34311882 ATAAAATTAA
*
34311892 AAAAATTTAATTAAATGTAATAA-ATTTT
1 AAAAATTTATTTAAATGTAATAATATTTT
* *
34311920 AAAAATTTATTTAAATAGT-TTAATTTTTT
1 AAAAATTTATTTAAAT-GTAATAATATTTT
*
34311949 AAAAATATTATGTAAA
1 AAAAAT-TTATTTAAA
34311965 AAAAATTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 18 0.47
29 12 0.32
30 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (29 bp):
AAAAATTTATTTAAATGTAATAATATTTT
Found at i:34315888 original size:18 final size:18
Alignment explanation
Indices: 34315865--34315901 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34315855 AATTGAAATT
34315865 AGAAAAAGAGAAAAA-AAA
1 AGAAAAA-AGAAAAATAAA
34315883 AGAAAAAAGAAAAATAAA
1 AGAAAAAAGAAAAATAAA
34315901 A
1 A
34315902 AGCCTCCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (18 bp):
AGAAAAAAGAAAAATAAA
Found at i:34315891 original size:19 final size:19
Alignment explanation
Indices: 34315867--34315903 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
34315857 TTGAAATTAG
34315867 AAAAAGAGAAAA-AAAAAGA
1 AAAAAGA-AAAATAAAAAGA
34315886 AAAAAGAAAAATAAAAAG
1 AAAAAGAAAAATAAAAAG
34315904 CCTCCACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAATAAAAAGA
Found at i:34317643 original size:20 final size:20
Alignment explanation
Indices: 34317606--34317643 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34317596 TTTTTTTTCT
*
34317606 GTTATGTTGCTTATCTGATG
1 GTTATGTTGCTTAACTGATG
34317626 GTTATGTTTG-TTAACTGA
1 GTTATG-TTGCTTAACTGA
34317644 CAAAATTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.18, C:0.08, G:0.24, T:0.50
Consensus pattern (20 bp):
GTTATGTTGCTTAACTGATG
Found at i:34332440 original size:21 final size:21
Alignment explanation
Indices: 34332411--34332464 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
34332401 TTCAAGAGAC
*
34332411 AGTTTTATGTTTGTGCTCTTA
1 AGTTATATGTTTGTGCTCTTA
34332432 AGTTATATGTTTGTGCTCTTA
1 AGTTATATGTTTGTGCTCTTA
34332453 AGTTATATGTTT
1 AGTTATATGTTT
34332465 CACTGTACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (21 bp):
AGTTATATGTTTGTGCTCTTA
Found at i:34341802 original size:23 final size:21
Alignment explanation
Indices: 34341783--34341826 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
34341773 TATTTTTGAC
34341783 ATAATATT-TTAAAAAGTTTTA
1 ATAA-ATTATTAAAAAGTTTTA
34341804 ATAAATTATTAAAAA--TTTA
1 ATAAATTATTAAAAAGTTTTA
34341823 ATAA
1 ATAA
34341827 TTTTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.36
20 3 0.14
21 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAATTATTAAAAAGTTTTA
Found at i:34342377 original size:21 final size:20
Alignment explanation
Indices: 34342336--34342384 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
34342326 CGATAACTTC
** *
34342336 TCAAAAATATTTTTTTTTGTT
1 TCAAAAATATTTTCATCTG-T
34342357 TCAAAAATATTTTCATCTGT
1 TCAAAAATATTTTCATCTGT
34342377 T-AAAAATA
1 TCAAAAATA
34342385 ATCTCAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.28
20 2 0.08
21 16 0.64
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (20 bp):
TCAAAAATATTTTCATCTGT
Found at i:34343716 original size:2 final size:2
Alignment explanation
Indices: 34343709--34343733 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34343699 GAAGCTTTCC
34343709 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34343734 GGTAGATAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34347425 original size:17 final size:17
Alignment explanation
Indices: 34347403--34347436 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34347393 TATGAAATTG
*
34347403 ACTTTGTATGATATCTA
1 ACTTTGTAGGATATCTA
34347420 ACTTTGTAGGATATCTA
1 ACTTTGTAGGATATCTA
34347437 TTTTTACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (17 bp):
ACTTTGTAGGATATCTA
Found at i:34347702 original size:27 final size:27
Alignment explanation
Indices: 34347656--34347720 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
34347646 CACTAATCAA
*
34347656 GATACCTTTACCTACCAGAAGTGGATG
1 GATACCTTTACCTACAAGAAGTGGATG
34347683 GATACCTTTATCC-ACAAGAAGTGGATG
1 GATACCTTTA-CCTACAAGAAGTGGATG
* *
34347710 AATAACTTTAC
1 GATACCTTTAC
34347721 TCACCGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 31 0.91
28 2 0.06
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (27 bp):
GATACCTTTACCTACAAGAAGTGGATG
Found at i:34356718 original size:15 final size:16
Alignment explanation
Indices: 34356688--34356722 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34356678 ATAAAATATT
34356688 ATGTTTTTCAATTAAA
1 ATGTTTTTCAATTAAA
* *
34356704 ATGTTTTTTAATAAAA
1 ATGTTTTTCAATTAAA
34356720 ATG
1 ATG
34356723 AGATTTATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATGTTTTTCAATTAAA
Found at i:34359108 original size:2 final size:2
Alignment explanation
Indices: 34359084--34359314 Score: 435
Period size: 2 Copynumber: 115.5 Consensus size: 2
34359074 AAGGAAAGGT
* * *
34359084 GA GA GC GA GA GC GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34359126 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34359168 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34359210 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34359252 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34359294 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
34359315 GAATAACTTG
Statistics
Matches: 223, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 223 1.00
ACGTcount: A:0.49, C:0.01, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34368508 original size:21 final size:21
Alignment explanation
Indices: 34368473--34368565 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
34368463 TCTCTGAAAC
*
34368473 TTAGGCATTGCGTGACTGGTT
1 TTAGGCATTGTGTGACTGGTT
* * *
34368494 TTAGGTATTTTGTGACTGATTT
1 TTAGGCATTGTGTGACTG-GTT
* **
34368516 TTAGGCATTGCGTGACTTATT
1 TTAGGCATTGTGTGACTGGTT
* *
34368537 TTAGGCGTTGTGTGATTGGTT
1 TTAGGCATTGTGTGACTGGTT
34368558 TTAGGCAT
1 TTAGGCAT
34368566 AGGCATTACG
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
21 40 0.71
22 16 0.29
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (21 bp):
TTAGGCATTGTGTGACTGGTT
Found at i:34368520 original size:22 final size:22
Alignment explanation
Indices: 34368473--34368646 Score: 102
Period size: 22 Copynumber: 7.7 Consensus size: 22
34368463 TCTCTGAAAC
*
34368473 TTAGGCATTGCGTGACTG-GTT
1 TTAGGCATTGCGTGACTGATTT
* **
34368494 TTAGGTATTTTGTGACTGATTT
1 TTAGGCATTGCGTGACTGATTT
*
34368516 TTAGGCATTGCGTGACTTA-TT
1 TTAGGCATTGCGTGACTGATTT
* * * *
34368537 TTAGGCGTTGTGTGATTGGTTT
1 TTAGGCATTGCGTGACTGATTT
* * *
34368559 TAGGCATAGGCATTACGTGATTGAATT
1 T-----TAGGCATTGCGTGACTGATTT
* *
34368586 GTAGGCATTGCGTGACT-AGGTT
1 TTAGGCATTGCGTGACTGA-TTT
** * *
34368608 GCAAGCTTTGCGTGACTGATTTT
1 TTAGGCATTGCGTGACTGA-TTT
34368631 TTAGGCATTGCGTGAC
1 TTAGGCATTGCGTGAC
34368647 ACGTTTTTGA
Statistics
Matches: 113, Mismatches: 31, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
21 32 0.28
22 50 0.44
23 15 0.13
27 16 0.14
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.40
Consensus pattern (22 bp):
TTAGGCATTGCGTGACTGATTT
Found at i:34368551 original size:43 final size:42
Alignment explanation
Indices: 34368473--34368565 Score: 114
Period size: 43 Copynumber: 2.2 Consensus size: 42
34368463 TCTCTGAAAC
* * * *
34368473 TTAGGCATTGCGTGACTGGTTTTAGGTATTTTGTGACTGATTT
1 TTAGGCATTGCGTGACTGATTTTAGGCATTGTGTGACTG-GTT
* * *
34368516 TTAGGCATTGCGTGACTTATTTTAGGCGTTGTGTGATTGGTT
1 TTAGGCATTGCGTGACTGATTTTAGGCATTGTGTGACTGGTT
34368558 TTAGGCAT
1 TTAGGCAT
34368566 AGGCATTACG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 10 0.23
43 33 0.77
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (42 bp):
TTAGGCATTGCGTGACTGATTTTAGGCATTGTGTGACTGGTT
Found at i:34375629 original size:25 final size:28
Alignment explanation
Indices: 34375578--34375629 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
34375568 TAATTTTAAG
*
34375578 TATATATATTATTATAAGTTTACATAAAA
1 TATATATATTATTATAAG-CTACATAAAA
34375607 TATATATA-TATTATAA-CTA-ATAA
1 TATATATATTATTATAAGCTACATAA
34375630 TTTTATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 4 0.18
26 2 0.09
28 8 0.36
29 8 0.36
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (28 bp):
TATATATATTATTATAAGCTACATAAAA
Found at i:34375637 original size:15 final size:16
Alignment explanation
Indices: 34375617--34375655 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
34375607 TATATATATA
*
34375617 TTATAACTAATAA-TT
1 TTATAAATAATAATTT
*
34375632 TTATAAATTATAATTT
1 TTATAAATAATAATTT
34375648 TTATAAAT
1 TTATAAAT
34375656 TACAAAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TTATAAATAATAATTT
Found at i:34375651 original size:16 final size:15
Alignment explanation
Indices: 34375626--34375657 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
34375616 ATTATAACTA
34375626 ATAATTTTATAAATT
1 ATAATTTTATAAATT
34375641 ATAATTTTTATAAATT
1 ATAA-TTTTATAAATT
34375657 A
1 A
34375658 CAAAATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATAATTTTATAAATT
Found at i:34378728 original size:15 final size:16
Alignment explanation
Indices: 34378708--34378742 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
34378698 TTCCCTTGAA
34378708 TTTTTTTCTA-TAAAG
1 TTTTTTTCTAGTAAAG
*
34378723 TTTTTTTCTAGTAAGG
1 TTTTTTTCTAGTAAAG
34378739 TTTT
1 TTTT
34378743 AACGAGGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (16 bp):
TTTTTTTCTAGTAAAG
Found at i:34378853 original size:16 final size:17
Alignment explanation
Indices: 34378827--34378863 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
34378817 TATGTATTTC
34378827 TAAATTTGGATGTAAA-T
1 TAAATTTGGAT-TAAAGT
34378844 TAAA-TTGGATTAAAGT
1 TAAATTTGGATTAAAGT
34378860 TAAA
1 TAAA
34378864 ATTTAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (17 bp):
TAAATTTGGATTAAAGT
Found at i:34383493 original size:20 final size:20
Alignment explanation
Indices: 34383470--34383518 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
34383460 TTTTTTTTTA
* **
34383470 TATTATTTTATATTTTAGTT
1 TATTATTTTATAATTTAAAT
34383490 TATT-TTATTATAATTTAAAT
1 TATTATT-TTATAATTTAAAT
34383510 TATTATTTT
1 TATTATTTT
34383519 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATTTTATAATTTAAAT
Found at i:34383522 original size:27 final size:27
Alignment explanation
Indices: 34383461--34383523 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
34383451 AGCCATCCTT
* *
34383461 TTTTTTTTATATTATTTTATATTTTAG
1 TTTTTTTTATATTAATTTAAATTTTAG
* *
34383488 TTTATTTTAT-TATAATTTAAATTATTAT
1 TTTTTTTTATAT-TAATTTAAATT-TTAG
34383516 TTTTTTTT
1 TTTTTTTT
34383524 TTTTTAAGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.03
27 18 0.62
28 10 0.34
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTTTTTTATATTAATTTAAATTTTAG
Found at i:34384209 original size:80 final size:80
Alignment explanation
Indices: 34384102--34384264 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
34384092 CAACACAAAG
*
34384102 TTTAAACGCGAAAGCATGCATGTTGTAAGAAAAGAAGAAATTGAGTAGTACCTCACCAATCTAAT
1 TTTAAACGCGAAAGCATGCATGCTGTAAGAAAAGAAGAAATTGAGTAGTACCTCACCAATCTAAT
34384167 TAATGTTTCAACAAC
66 TAATGTTTCAACAAC
34384182 TTTAAACGCGAAAGCATGCATGCTGTAAGAAAAGAAGAAATTGAGTAGTACCTCACCAATCTAAT
1 TTTAAACGCGAAAGCATGCATGCTGTAAGAAAAGAAGAAATTGAGTAGTACCTCACCAATCTAAT
34384247 TAATGTTTCAACAAC
66 TAATGTTTCAACAAC
34384262 TTT
1 TTT
34384265 CTTTTTTTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (80 bp):
TTTAAACGCGAAAGCATGCATGCTGTAAGAAAAGAAGAAATTGAGTAGTACCTCACCAATCTAAT
TAATGTTTCAACAAC
Found at i:34395817 original size:5 final size:5
Alignment explanation
Indices: 34395807--34395832 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34395797 ACTCAAAATC
34395807 CATCT CATCT CATCT CATCT CATCT C
1 CATCT CATCT CATCT CATCT CATCT C
34395833 TAATTAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.38
Consensus pattern (5 bp):
CATCT
Found at i:34400782 original size:2 final size:2
Alignment explanation
Indices: 34400775--34400811 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34400765 AATCTAATTC
34400775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34400812 ATCATCACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34404714 original size:12 final size:13
Alignment explanation
Indices: 34404687--34404724 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
34404677 TTATTCATTA
*
34404687 AAAAATGATTAAAT
1 AAAAAT-ATAAAAT
34404701 AAAAAT-TAAAAT
1 AAAAATATAAAAT
34404713 AAAAATATAAAA
1 AAAAATATAAAA
34404725 ATAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 5 0.23
14 6 0.27
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (13 bp):
AAAAATATAAAAT
Found at i:34406437 original size:22 final size:22
Alignment explanation
Indices: 34406412--34406454 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34406402 AACAATTCAA
34406412 TTTAAAATAAAA-ATAAATTATT
1 TTTAAAATAAAATA-AAATTATT
34406434 TTTAAAATAAAATAAAATTAT
1 TTTAAAATAAAATAAAATTAT
34406455 AATATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAAATAAAATTATT
Found at i:34410778 original size:22 final size:24
Alignment explanation
Indices: 34410750--34410793 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
34410740 TTCGAATCGA
34410750 TTATTTT-AT-TATTAAAATATTT
1 TTATTTTCATATATTAAAATATTT
*
34410772 TTATTTTCATATTTTAAAATAT
1 TTATTTTCATATATTAAAATAT
34410794 AATTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATTTTCATATATTAAAATATTT
Found at i:34419600 original size:12 final size:12
Alignment explanation
Indices: 34419530--34419620 Score: 53
Period size: 12 Copynumber: 7.3 Consensus size: 12
34419520 CCTGAAAAAG
34419530 AAAAATAATAAATA
1 AAAAATAAT--ATA
*
34419544 AATAAATAATTTA
1 AA-AAATAATATA
**
34419557 AATTATAATA-A
1 AAAAATAATATA
*
34419568 AACAAACTAAAATA
1 AA-AAA-TAATATA
*
34419582 TAAAATAATATA
1 AAAAATAATATA
34419594 AAAAATAATA-A
1 AAAAATAATATA
*
34419605 TAATAATAATA-A
1 -AAAAATAATATA
34419617 AAAA
1 AAAA
34419621 GGGGGATGGC
Statistics
Matches: 60, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
11 7 0.12
12 31 0.52
13 11 0.18
14 4 0.07
15 7 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:34422688 original size:2 final size:2
Alignment explanation
Indices: 34422641--34422676 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34422631 GCATTATAGA
34422641 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34422677 CATGTGGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34426098 original size:14 final size:14
Alignment explanation
Indices: 34426079--34426106 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34426069 GCGTTTTCAG
34426079 ATAAATTTCTAGCT
1 ATAAATTTCTAGCT
34426093 ATAAATTTCTAGCT
1 ATAAATTTCTAGCT
34426107 TTATGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
ATAAATTTCTAGCT
Found at i:34426578 original size:2 final size:2
Alignment explanation
Indices: 34426571--34426625 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
34426561 AACAAAATTT
34426571 TA TA TA TA TA TA TA TA TA 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
34426613 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
34426626 TAAACCAGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34431768 original size:2 final size:2
Alignment explanation
Indices: 34431761--34431793 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34431751 TATGTATGTG
34431761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34431794 GTTTAATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34442857 original size:18 final size:18
Alignment explanation
Indices: 34442820--34442857 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
34442810 TATATAAAGA
34442820 ATAATAAAAATAATTATT
1 ATAATAAAAATAATTATT
*
34442838 ATAAGTAAATATAATT-TT
1 ATAA-TAAAAATAATTATT
34442856 AT
1 AT
34442858 GCAAAACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATAATAAAAATAATTATT
Found at i:34443164 original size:29 final size:30
Alignment explanation
Indices: 34443131--34443205 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
34443121 TCTTTTCTTA
*
34443131 TTCTCTTATATTATTTCACGTACA-CTTTT
1 TTCTCTTATATTATTTCACATACATCTTTT
* *
34443160 TTCTCTTTTATCTA-TTCACATATATCTTTT
1 TTCTCTTATAT-TATTTCACATACATCTTTT
*
34443190 TT-TCGTA-ATTATTTCA
1 TTCTCTTATATTATTTCA
34443206 ATATTTACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.05
28 6 0.16
29 21 0.55
30 9 0.24
ACGTcount: A:0.21, C:0.19, G:0.03, T:0.57
Consensus pattern (30 bp):
TTCTCTTATATTATTTCACATACATCTTTT
Found at i:34461433 original size:18 final size:17
Alignment explanation
Indices: 34461391--34461435 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
34461381 TTCAGGCTTG
34461391 TGTAAACAAAAGAATGA
1 TGTAAACAAAAGAATGA
* *
34461408 AGTAAAACCAAAGAATGA
1 TGT-AAACAAAAGAATGA
34461426 TTGTAAACAA
1 -TGTAAACAA
34461436 GCTGATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 2 0.09
18 18 0.82
19 2 0.09
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.18
Consensus pattern (17 bp):
TGTAAACAAAAGAATGA
Found at i:34477557 original size:92 final size:94
Alignment explanation
Indices: 34477378--34477562 Score: 299
Period size: 92 Copynumber: 2.0 Consensus size: 94
34477368 CAGAAGGAAG
34477378 GAGGGAGAGAGAGAGAGAGAGAGGTAGGGGTTTTCTGACCAAAACCCGCAGGCATGTGGACGGGG
1 GAGGGAGAGAGAGAGAGAGAGAGGTAGGGGTTTTCTGA-CAAAACCCGCAGGCATGTGGACGGGG
34477443 GAAGGGATAAAGTCGTTTCCGCGCTCTGTA
65 GAAGGGATAAAGTCGTTTCCGCGCTCTGTA
34477473 NGAGGGAGAGAGAGAGAGAGAGA-G-AGGGGTTTTCTG-CAAAACCCGCAGGCATGT-GACGGGG
1 -GAGGGAGAGAGAGAGAGAGAGAGGTAGGGGTTTTCTGACAAAACCCGCAGGCATGTGGACGGGG
34477534 GAAGGGATAAAG-CGTTTTCCCGCGCTCTG
65 GAAGGGATAAAGTCG-TTT-CCGCGCTCTG
34477563 ATTTTGGTGT
Statistics
Matches: 87, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
90 2 0.02
91 22 0.25
92 28 0.32
94 12 0.14
95 1 0.01
96 22 0.25
ACGTcount: A:0.27, C:0.16, G:0.40, T:0.16
Consensus pattern (94 bp):
GAGGGAGAGAGAGAGAGAGAGAGGTAGGGGTTTTCTGACAAAACCCGCAGGCATGTGGACGGGGG
AAGGGATAAAGTCGTTTCCGCGCTCTGTA
Found at i:34483026 original size:15 final size:18
Alignment explanation
Indices: 34482996--34483035 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
34482986 AAATTAAATC
34482996 ATAAAATAATTTTATT-A
1 ATAAAATAATTTTATTAA
34483013 ATAAAA-AA-TTTATTAA
1 ATAAAATAATTTTATTAA
34483029 ATAAAAT
1 ATAAAAT
34483036 TACAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.29
16 9 0.43
17 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAAATAATTTTATTAA
Found at i:34489928 original size:42 final size:42
Alignment explanation
Indices: 34489881--34489966 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
34489871 TACCTCATAC
* *
34489881 TATGAATAGACATGTAAGTATTCTAGATAAGAAGCATGATCA
1 TATGAATAGACACGTAAATATTCTAGATAAGAAGCATGATCA
* * * *
34489923 TATGAATAGACACGTAAATATTCTCGTTAGGATGCATGATCA
1 TATGAATAGACACGTAAATATTCTAGATAAGAAGCATGATCA
34489965 TA
1 TA
34489967 GTTACATCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (42 bp):
TATGAATAGACACGTAAATATTCTAGATAAGAAGCATGATCA
Found at i:34490188 original size:2 final size:2
Alignment explanation
Indices: 34490181--34490212 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34490171 GCATATGAGT
34490181 TA TA TA TA 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
34490213 GATCGAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34490772 original size:12 final size:13
Alignment explanation
Indices: 34490755--34490783 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
34490745 AGAACACATC
34490755 AAAAAAAA-GAAA
1 AAAAAAAACGAAA
34490767 AAAAAAAACGAAA
1 AAAAAAAACGAAA
34490780 AAAA
1 AAAA
34490784 TACCATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAACGAAA
Found at i:34492232 original size:1 final size:1
Alignment explanation
Indices: 34492226--34492257 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
34492216 ACGATGTCTC
34492226 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34492258 GCCATTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34498237 original size:8 final size:8
Alignment explanation
Indices: 34498224--34498253 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
34498214 GGATCAATTG
*
34498224 AAGAAAAA
1 AAGAAACA
34498232 AAGAAACA
1 AAGAAACA
34498240 AAGAAACA
1 AAGAAACA
34498248 AAGAAA
1 AAGAAA
34498254 GTTTAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (8 bp):
AAGAAACA
Found at i:34504145 original size:3 final size:3
Alignment explanation
Indices: 34504137--34504183 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
34504127 GACTTCGCTT
* ** *
34504137 TTG TTG TTG TTG ATG TTG TTG TTG TTG TTG TTG CCG TTG TTT TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
34504184 TGTGTTGGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.04, G:0.30, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:34529220 original size:63 final size:62
Alignment explanation
Indices: 34529119--34529236 Score: 148
Period size: 63 Copynumber: 1.9 Consensus size: 62
34529109 GAAGAAAAGA
* ** **
34529119 AGAAGAGCCCATCACCATAGTGCAAGGAGGAAGCAGAGA-AAAAAAGAAAGAAAAGAAAAATAT
1 AGAAGAGCCCATCACCAGAAAGCAACAAGGAAGCAGAGAGAAAAAA-AAA-AAAAGAAAAATAT
* *
34529182 AGAAGAGCCCATCACCAGAAAGCAACAAGGTAGGAGAGAGAAAAAAAAAAAAAGA
1 AGAAGAGCCCATCACCAGAAAGCAACAAGGAAGCAGAGAGAAAAAAAAAAAAAGA
34529237 GGAGCCCATT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
62 6 0.13
63 35 0.74
64 6 0.13
ACGTcount: A:0.57, C:0.14, G:0.24, T:0.06
Consensus pattern (62 bp):
AGAAGAGCCCATCACCAGAAAGCAACAAGGAAGCAGAGAGAAAAAAAAAAAAAGAAAAATAT
Found at i:34529920 original size:11 final size:11
Alignment explanation
Indices: 34529906--34529946 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
34529896 AGTATTAAGA
34529906 AAATTTTAAAT
1 AAATTTTAAAT
34529917 AAATTTTTAAGA-
1 AAA-TTTTAA-AT
34529929 AAATTTTAAAT
1 AAATTTTAAAT
34529940 AAATTTT
1 AAATTTT
34529947 TATATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 16 0.59
12 9 0.33
13 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
AAATTTTAAAT
Found at i:34529926 original size:12 final size:12
Alignment explanation
Indices: 34529909--34529948 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
34529899 ATTAAGAAAA
34529909 TTTTAAATAAAT
1 TTTTAAATAAAT
34529921 TTTTAAGA-AAA-
1 TTTTAA-ATAAAT
34529932 TTTTAAATAAAT
1 TTTTAAATAAAT
34529944 TTTTA
1 TTTTA
34529949 TATTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.04
11 9 0.36
12 14 0.56
13 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
TTTTAAATAAAT
Found at i:34529926 original size:23 final size:23
Alignment explanation
Indices: 34529900--34529948 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
34529890 TTCTGAAGTA
34529900 TTAAGAAAATTTTAAATAAATTT
1 TTAAGAAAATTTTAAATAAATTT
34529923 TTAAGAAAATTTTAAATAAATTT
1 TTAAGAAAATTTTAAATAAATTT
34529946 TTA
1 TTA
34529949 TATTTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAAGAAAATTTTAAATAAATTT
Found at i:34531866 original size:21 final size:21
Alignment explanation
Indices: 34531816--34531866 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
34531806 GTTTTTATAT
* *
34531816 ATGATGTGTAACAACCTAACC
1 ATGACGTGTAACAACATAACC
* *
34531837 ATTACGTGTAACAATATAACC
1 ATGACGTGTAACAACATAACC
*
34531858 ATGAGGTGT
1 ATGACGTGT
34531867 CACATGTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (21 bp):
ATGACGTGTAACAACATAACC
Found at i:34531967 original size:66 final size:66
Alignment explanation
Indices: 34531777--34531970 Score: 246
Period size: 66 Copynumber: 2.9 Consensus size: 66
34531767 CAATATGGCG
* * * ** *
34531777 TGTAACAACCTAACCATGACGTGTCATATGTTTTTATATATGATGTGTAACAACCTAACCATTAC
1 TGTAACAACTTAACCATGACGTGTCACATGTTTTTATACATGATGTGTAACAACCTAATTATGAC
*
34531842 G
66 A
* *
34531843 TGTAACAA-TATAACCATGAGGTGTCACATGTTTTTATACATGATGTGTAACAATCTAATTATGA
1 TGTAACAACT-TAACCATGACGTGTCACATGTTTTTATACATGATGTGTAACAACCTAATTATGA
34531907 CA
65 CA
** * * *
34531909 TGTAACAACTTAACCATGATATGTCACATGTTTTTCTACATGACGTATAACAACCTAATTAT
1 TGTAACAACTTAACCATGACGTGTCACATGTTTTTATACATGATGTGTAACAACCTAATTAT
34531971 AGTGTTACAT
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
66 110 0.99
67 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (66 bp):
TGTAACAACTTAACCATGACGTGTCACATGTTTTTATACATGATGTGTAACAACCTAATTATGAC
A
Found at i:34532990 original size:20 final size:19
Alignment explanation
Indices: 34532962--34533004 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
34532952 AATGAATAAA
*
34532962 TAAAAAACTACTAATAATAC
1 TAAAAAACTA-TAATAACAC
* *
34532982 TAAACAACTATTATAACAC
1 TAAAAAACTATAATAACAC
34533001 TAAA
1 TAAA
34533005 TGAATAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAACTATAATAACAC
Found at i:34548070 original size:2 final size:2
Alignment explanation
Indices: 34548063--34548099 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34548053 TTGTGAATAT
34548063 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
34548100 GATGGTACCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:34566556 original size:63 final size:63
Alignment explanation
Indices: 34566478--34566602 Score: 205
Period size: 63 Copynumber: 2.0 Consensus size: 63
34566468 GCATATAATT
* * *
34566478 TGGATTATGAACATGACAAGGTGGTCCCAAACGCTGCTTTATACTTTTCCTAGTAGAAGGATA
1 TGGATTATGAACATGACAAGGCGGCCCCAAACGCTGCTTTACACTTTTCCTAGTAGAAGGATA
* *
34566541 TGGATTATGACCATGACAAGGCGGCCCCAAACGCTGCTTTACACTTTTCCTATTAGAAGGAT
1 TGGATTATGAACATGACAAGGCGGCCCCAAACGCTGCTTTACACTTTTCCTAGTAGAAGGAT
34566603 GTGCAAATTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (63 bp):
TGGATTATGAACATGACAAGGCGGCCCCAAACGCTGCTTTACACTTTTCCTAGTAGAAGGATA
Found at i:34569363 original size:2 final size:2
Alignment explanation
Indices: 34569356--34569385 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34569346 TTCTCTAATT
*
34569356 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34569386 AACTTCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:34582531 original size:2 final size:2
Alignment explanation
Indices: 34582526--34582572 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
34582516 CTGAGGTACG
*
34582526 TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
34582568 TC TC T
1 TC TC T
34582573 TTATGTCTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:34584909 original size:31 final size:31
Alignment explanation
Indices: 34584873--34584931 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
34584863 TCATCTACAT
34584873 CTTCCTTTTACAGATGCTTCTGATCCTGCCC
1 CTTCCTTTTACAGATGCTTCTGATCCTGCCC
34584904 CTTCCTTTTACAGATGCTTCTGATCCTG
1 CTTCCTTTTACAGATGCTTCTGATCCTG
34584932 GATAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.14, C:0.32, G:0.14, T:0.41
Consensus pattern (31 bp):
CTTCCTTTTACAGATGCTTCTGATCCTGCCC
Found at i:34586505 original size:21 final size:20
Alignment explanation
Indices: 34586468--34586507 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34586458 AGTATAGTAT
**
34586468 TTAAAAAAATATTTAAATTA
1 TTAAAAAAATAAATAAATTA
34586488 TTAAAAAAATTAAATAAATT
1 TTAAAAAAA-TAAATAAATT
34586508 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAAAATAAATAAATTA
Found at i:34593200 original size:108 final size:105
Alignment explanation
Indices: 34592814--34593237 Score: 794
Period size: 105 Copynumber: 4.0 Consensus size: 105
34592804 TGAAGAAGAG
*
34592814 TTTGTAGAAGATATTTTCTTTGATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
1 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
34592879 TTCATCAATGATCTTCATCTCACATACATATATATATATA
66 TTCATCAATGATCTTCATCTCACATACATATATATATATA
34592919 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
1 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
34592984 TTCATCAATGATCTTCATCTCACATACATATATATATATA
66 TTCATCAATGATCTTCATCTCACATACATATATATATATA
34593024 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
1 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
34593089 TTCATCAATGATCTTCATCTCACAATACATATATATATATATA
66 TTCATCAATGATCTTCATCTCAC-ATAC--ATATATATATATA
34593132 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
1 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
* *
34593197 TTCATCAATGATCTTCATCTCACATACATACATACATATA
66 TTCATCAATGATCTTCATCTCACATACATATATATATATA
34593237 T
1 T
34593238 ACATACATAC
Statistics
Matches: 313, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
105 204 0.65
106 4 0.01
107 4 0.01
108 101 0.32
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.41
Consensus pattern (105 bp):
TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
TTCATCAATGATCTTCATCTCACATACATATATATATATA
Found at i:34593206 original size:213 final size:210
Alignment explanation
Indices: 34592814--34593237 Score: 794
Period size: 213 Copynumber: 2.0 Consensus size: 210
34592804 TGAAGAAGAG
*
34592814 TTTGTAGAAGATATTTTCTTTGATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
1 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
34592879 TTCATCAATGATCTTCATCTCACATACATATATATATATATTTGTAGAAGATATTTTCTTTAATA
66 TTCATCAATGATCTTCATCTCACATACATATATATATATATTTGTAGAAGATATTTTCTTTAATA
34592944 TTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAATTCATCAATGATCTTCATCTCACAT
131 TTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAATTCATCAATGATCTTCATCTCACAT
* *
34593009 ACATATATATATATA
196 ACATACATACATATA
34593024 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
1 TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
34593089 TTCATCAATGATCTTCATCTCACAATACATATATATATATATATTTGTAGAAGATATTTTCTTTA
66 TTCATCAATGATCTTCATCTCAC-ATAC--ATATATATATATATTTGTAGAAGATATTTTCTTTA
34593154 ATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAATTCATCAATGATCTTCATCTCA
128 ATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAATTCATCAATGATCTTCATCTCA
34593219 CATACATACATACATATA
193 CATACATACATACATATA
34593237 T
1 T
34593238 ACATACATAC
Statistics
Matches: 208, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
210 87 0.42
211 4 0.02
213 117 0.56
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.41
Consensus pattern (210 bp):
TTTGTAGAAGATATTTTCTTTAATATTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAA
TTCATCAATGATCTTCATCTCACATACATATATATATATATTTGTAGAAGATATTTTCTTTAATA
TTAGAACTTTCAATTCTTGGTAGTTACACATACTCAACAATTCATCAATGATCTTCATCTCACAT
ACATACATACATATA
Found at i:34593227 original size:4 final size:4
Alignment explanation
Indices: 34593218--34593250 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
34593208 TCTTCATCTC
*
34593218 ACAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
34593251 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:34593241 original size:16 final size:16
Alignment explanation
Indices: 34593220--34593254 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
34593210 TTCATCTCAC
34593220 ATACATACATACATAT
1 ATACATACATACATAT
34593236 ATACATACATACATAT
1 ATACATACATACATAT
34593252 ATA
1 ATA
34593255 TATATATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (16 bp):
ATACATACATACATAT
Found at i:34593259 original size:8 final size:8
Alignment explanation
Indices: 34593220--34593262 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
34593210 TTCATCTCAC
*
34593220 ATACATAC
1 ATACATAT
34593228 ATACATAT
1 ATACATAT
*
34593236 ATACATAC
1 ATACATAT
34593244 ATACATAT
1 ATACATAT
*
34593252 ATATATAT
1 ATACATAT
34593260 ATA
1 ATA
34593263 GTGGTGGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (8 bp):
ATACATAT
Found at i:34596693 original size:42 final size:42
Alignment explanation
Indices: 34596620--34596725 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
34596610 TACAGCATAA
* *
34596620 GTCATAATCATAACAGAAACCATAATTAACCCCAATGGCATGG
1 GTCATAATCATATC-GAAACCACAATTAACCCCAATGGCATGG
*
34596663 GTCATAATCATATCGAAACCACAATTAACCCCAGTGGCATGG
1 GTCATAATCATATCGAAACCACAATTAACCCCAATGGCATGG
34596705 GTCATAAGT-ATATCGAAACCA
1 GTCATAA-TCATATCGAAACCA
34596726 ACTATTGACT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
42 45 0.76
43 14 0.24
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.22
Consensus pattern (42 bp):
GTCATAATCATATCGAAACCACAATTAACCCCAATGGCATGG
Found at i:34600059 original size:30 final size:30
Alignment explanation
Indices: 34599992--34600071 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
34599982 CCCACCTTCC
*
34599992 TCTGAAGAAGCGTCAAGAAATAGTAATTCA
1 TCTGAAGAAGCATCAAGAAATAGTAATTCA
* * *
34600022 TCCGAAGAAGTATCAAGAAATAGTACTTCCA
1 TCTGAAGAAGCATCAAGAAATAGTAATT-CA
*
34600053 T-TGAAGAAACATCAAGAAA
1 TCTGAAGAAGCATCAAGAAA
34600072 GAGCAGTTCG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 39 0.93
31 3 0.07
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.21
Consensus pattern (30 bp):
TCTGAAGAAGCATCAAGAAATAGTAATTCA
Found at i:34603232 original size:22 final size:21
Alignment explanation
Indices: 34603207--34603256 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
34603197 TTTAATTTTA
34603207 AAAATT-ACAAATTTAAACTTAT
1 AAAATTAAC-AATTTAAA-TTAT
*
34603229 AAAATTAACATTTTAAATTAT
1 AAAATTAACAATTTAAATTAT
34603250 -AAATTAA
1 AAAATTAA
34603257 AAAACTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
21 4 0.15
22 13 0.50
23 2 0.08
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTAACAATTTAAATTAT
Found at i:34603294 original size:16 final size:16
Alignment explanation
Indices: 34603275--34603305 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34603265 TAATATTTTC
*
34603275 ATATTTTAATTATAAT
1 ATATTTAAATTATAAT
34603291 ATATTTAAATTATAA
1 ATATTTAAATTATAA
34603306 ATAAAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTAAATTATAAT
Found at i:34603326 original size:20 final size:21
Alignment explanation
Indices: 34603266--34603326 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
34603256 AAAAACTATT
*
34603266 AATATTTTCATATTTTAATTATAA
1 AATA-TTTAATATTTTAA--ATAA
* *
34603290 TATATTTAA-ATTATAAATAA
1 AATATTTAATATTTTAAATAA
34603310 AATA-TTAATATTTTAAA
1 AATATTTAATATTTTAAA
34603327 ATATTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.13
20 14 0.45
22 6 0.19
23 4 0.13
24 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTAATATTTTAAATAA
Found at i:34603328 original size:16 final size:16
Alignment explanation
Indices: 34603307--34603348 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
34603297 AAATTATAAA
34603307 TAAAATATTAATATTT
1 TAAAATATTAATATTT
*
34603323 TAAAATATT-ATTTTT
1 TAAAATATTAATATTT
*
34603338 TAAATTATTAA
1 TAAAATATTAA
34603349 GTGAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAATATTAATATTT
Done.