Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 3104049
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 172765 characters in sequence are not A, C, G, or T
File 16 of 18
Found at i:2665658 original size:39 final size:32
Alignment explanation
Indices: 2665585--2665663 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 32
2665575 TAACTTAATT
2665585 TTTTTAAAAAATTAATTAAATATTATTTTTAA
1 TTTTTAAAAAATTAATTAAATATTATTTTTAA
2665617 TTTTATAAAAAATAATAATTAATATATTATTTATTAAAA
1 TTTT-TAAAAAAT--TAATTAA-ATATTATTT-TT--AA
2665656 TTTTTAAA
1 TTTTTAAA
2665664 TTTAATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
32 4 0.10
33 8 0.20
35 7 0.17
36 9 0.22
37 2 0.05
38 4 0.10
39 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTTTAAAAAATTAATTAAATATTATTTTTAA
Found at i:2665995 original size:12 final size:13
Alignment explanation
Indices: 2665972--2666009 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
2665962 TATATTTGTA
2665972 AAAAAAATTATTT
1 AAAAAAATTATTT
*
2665985 TAAAAAA-TATTT
1 AAAAAAATTATTT
2665997 AAAAAAATTATTT
1 AAAAAAATTATTT
2666010 GTGAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AAAAAAATTATTT
Found at i:2671545 original size:31 final size:29
Alignment explanation
Indices: 2671473--2671545 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
2671463 ATTATTTTAT
*
2671473 ATATATATTTTAAATTTAATAAGAATTAA
1 ATATATATTTTAAATTTAATAAAAATTAA
*
2671502 ATTTATACATTTTAGAA-TTATATAAAAAATTAA
1 A--TATATATTTTA-AATTTA-AT-AAAAATTAA
2671535 ATATATATTTT
1 ATATATATTTT
2671546 TATTAAGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 1 0.03
31 22 0.61
32 4 0.11
33 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (29 bp):
ATATATATTTTAAATTTAATAAAAATTAA
Found at i:2671637 original size:22 final size:19
Alignment explanation
Indices: 2671554--2671629 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 19
2671544 TTTATTAAGA
*
2671554 ATTTAATATATTTAATATTT
1 ATTTAATATA-TTAAAATTT
*
2671574 ATTTAATATATGAAAATTT
1 ATTTAATATATTAAAATTT
*
2671593 ATTTTAAAATATATAAAATTTT
1 A-TTTAATATAT-TAAAA-TTT
2671615 ATTTAAATATATTAA
1 ATTT-AATATATTAA
2671630 TCAATTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.17
20 19 0.40
21 10 0.21
22 10 0.21
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (19 bp):
ATTTAATATATTAAAATTT
Found at i:2678334 original size:252 final size:251
Alignment explanation
Indices: 2677783--2678530 Score: 1248
Period size: 252 Copynumber: 3.0 Consensus size: 251
2677773 ACGTAATATG
* * * *
2677783 GAGAGAAAGAAACAATAGACACTTCAGGCAAGTGGAGAACAAAGTGCAAGAATTAATTGATAGAA
1 GAGAAAAAGAAACAATAGACATTTTAGGCAAGTGGAGAACAAAGTGCAAAAATTAATTGATAGAA
* * * * *
2677848 TCAGAGTGTTGATAAAATTTAAACTGACAAGTACAGAACGAACGTTTGTTGAACCAGATATCATT
66 TCAGAGTGTCGAT-AAATTTAAACTGATAGGTACAAAACGAACGTTTGTTGAATCAGATATCATT
* *
2677913 AATTTATGTGTTGTTTGG-GGAATAACTAGCATTTAGATTTAGTTTTTGTTTTTTTGATGATTGT
130 AATTTATGTGTTGCTTGGAAG-ATAACTAGCATTTAGATTTAGTTTTTG-TTTTTTGATGATTGT
2677977 TGGCTATAAGTAAACTAGTATTAATGTTATAGATTAAAAGCTGTAAATTGATAGAATAA
193 TGGCTATAAGTAAACTAGTATTAATGTTATAGATTAAAAGCTGTAAATTGATAGAATAA
*
2678036 GAGAAAAAGAAACAATAGACATTTTAGGCAAGTGGAGAATAAAGTGCAAAAATTAATTGATAGAA
1 GAGAAAAAGAAACAATAGACATTTTAGGCAAGTGGAGAACAAAGTGCAAAAATTAATTGATAGAA
2678101 TCAGAGTGTCGATAAGATTTAAACTGATAGGTACAAAACGAACGTTTGTTGAATCAGATATCATT
66 TCAGAGTGTCGATAA-ATTTAAACTGATAGGTACAAAACGAACGTTTGTTGAATCAGATATCATT
* *
2678166 AACTTATGTATTGCTTGGAAGATAACTAGCATTTAGATTTAGTTTTTGTTTTTTGAT-AGTTGTT
130 AATTTATGTGTTGCTTGGAAGATAACTAGCATTTAGATTTAGTTTTTGTTTTTTGATGA-TTGTT
*
2678230 GGCTATAAGTAAACTAGTATTAATGTTATAGATTAAAAGCTGTAAATTGATAGAATCA
194 GGCTATAAGTAAACTAGTATTAATGTTATAGATTAAAAGCTGTAAATTGATAGAATAA
* * *
2678288 GAGAAAAAGAAACAATAGACATTTTAGGCAAGTAGAAAACAAAGTGCAAAAATTAATTGATAAAA
1 GAGAAAAAGAAACAATAGACATTTTAGGCAAGTGGAGAACAAAGTGCAAAAATTAATTGATAGAA
2678353 TCAGAGTGTCGATAAAGTTTAAACTGATAGGTACAAAACGAACGTTTGTTGAATCAGATATCATT
66 TCAGAGTGTCGATAAA-TTTAAACTGATAGGTACAAAACGAACGTTTGTTGAATCAGATATCATT
*
2678418 AATTTATGTGTTGCTTGGAATATAACTAGCATTTAGATTTAGTTTTTGTTTTTTGATGATTGTTG
130 AATTTATGTGTTGCTTGGAAGATAACTAGCATTTAGATTTAGTTTTTGTTTTTTGATGATTGTTG
*
2678483 GCTATAAATAAACTAGTATTAATGTTATAGATTAAAAGCTGTAAATTG
195 GCTATAAGTAAACTAGTATTAATGTTATAGATTAAAAGCTGTAAATTG
2678531 TAACAAATTT
Statistics
Matches: 467, Mismatches: 23, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
251 2 0.00
252 304 0.65
253 160 0.34
254 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.33
Consensus pattern (251 bp):
GAGAAAAAGAAACAATAGACATTTTAGGCAAGTGGAGAACAAAGTGCAAAAATTAATTGATAGAA
TCAGAGTGTCGATAAATTTAAACTGATAGGTACAAAACGAACGTTTGTTGAATCAGATATCATTA
ATTTATGTGTTGCTTGGAAGATAACTAGCATTTAGATTTAGTTTTTGTTTTTTGATGATTGTTGG
CTATAAGTAAACTAGTATTAATGTTATAGATTAAAAGCTGTAAATTGATAGAATAA
Found at i:2680578 original size:22 final size:21
Alignment explanation
Indices: 2680531--2680579 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2680521 AAATCATGAA
2680531 ATTTTTCTTTCGTTTAAAATT
1 ATTTTTCTTTCGTTTAAAATT
2680552 ATTTTTCTTTCGTTTAAAATT
1 ATTTTTCTTTCGTTTAAAATT
2680573 ATTTTTC
1 ATTTTTC
2680580 GAGTTTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.10, G:0.04, T:0.63
Consensus pattern (21 bp):
ATTTTTCTTTCGTTTAAAATT
Found at i:2686937 original size:2 final size:2
Alignment explanation
Indices: 2686925--2686955 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2686915 CAACTTTTGT
*
2686925 TA TA GA 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 T
2686956 TTTTTATAGG
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2687775 original size:13 final size:13
Alignment explanation
Indices: 2687759--2687783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2687749 AATTTATTGC
2687759 AAAAAATAAATAT
1 AAAAAATAAATAT
2687772 AAAAAATAAATA
1 AAAAAATAAATA
2687784 ATTTATTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATAAATAT
Found at i:2688316 original size:73 final size:73
Alignment explanation
Indices: 2688230--2688367 Score: 206
Period size: 73 Copynumber: 1.9 Consensus size: 73
2688220 TATAATTAAC
* * * * *
2688230 GAATATACTTAATACTATTTATGTATATTTATAGTTCATAAATATTCAAAATTCTTGAATTTACA
1 GAATATACTTAATACCATTTATATATATTCATAGTTCATAAATATTCAAAATTCATGAATATACA
2688295 TCATTTAT
66 TCATTTAT
*
2688303 GAATATA-TATAATACCATTTATATATATTCATAGTTCATAAATATTCAAATTTCATGAATATAC
1 GAATATACT-TAATACCATTTATATATATTCATAGTTCATAAATATTCAAAATTCATGAATATAC
2688367 A
65 A
2688368 AAATAACATT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 1 0.02
73 57 0.98
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.43
Consensus pattern (73 bp):
GAATATACTTAATACCATTTATATATATTCATAGTTCATAAATATTCAAAATTCATGAATATACA
TCATTTAT
Found at i:2688349 original size:17 final size:17
Alignment explanation
Indices: 2688327--2688369 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2688317 CCATTTATAT
*
2688327 ATATTCATAGTTCATAA
1 ATATTCAAAGTTCATAA
* *
2688344 ATATTCAAATTTCATGA
1 ATATTCAAAGTTCATAA
*
2688361 ATATACAAA
1 ATATTCAAA
2688370 ATAACATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (17 bp):
ATATTCAAAGTTCATAA
Found at i:2689288 original size:14 final size:14
Alignment explanation
Indices: 2689269--2689299 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2689259 TGTTTGGTCT
2689269 ATTGGAAAGTAATC
1 ATTGGAAAGTAATC
2689283 ATTGGAAAGTAATC
1 ATTGGAAAGTAATC
2689297 ATT
1 ATT
2689300 TTTTTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (14 bp):
ATTGGAAAGTAATC
Found at i:2689997 original size:22 final size:21
Alignment explanation
Indices: 2689949--2689998 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2689939 ATTTAGTAAA
* *
2689949 TTAAATACGTTAATATATTTT
1 TTAAAGACTTTAATATATTTT
2689970 TTAAAGACTTTAAT-TATTATT
1 TTAAAGACTTTAATATATT-TT
2689991 TTCAAAGA
1 TT-AAAGA
2689999 TATATCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 16 0.64
22 5 0.20
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (21 bp):
TTAAAGACTTTAATATATTTT
Found at i:2690186 original size:17 final size:16
Alignment explanation
Indices: 2690164--2690205 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2690154 AATATTTTAA
2690164 ATTTTTTATTTAAATTT
1 ATTTTTTATTT-AATTT
*
2690181 ATTTTTAATTTAATTT
1 ATTTTTTATTTAATTT
*
2690197 AATTTTTAT
1 ATTTTTTAT
2690206 ATATTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTTATTTAATTT
Found at i:2690283 original size:22 final size:21
Alignment explanation
Indices: 2690239--2690279 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2690229 ATTAAAAAAT
2690239 TATTTTATATTAATATTTATA
1 TATTTTATATTAATATTTATA
2690260 TATTTTATAATTAA-ATTTAT
1 TATTTTAT-ATTAATATTTAT
2690280 TATAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTATATTAATATTTATA
Found at i:2698235 original size:23 final size:22
Alignment explanation
Indices: 2698209--2698259 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 22
2698199 ATTATCTAAA
2698209 TTTTAAA-AAATAAATAAAATAAT
1 TTTTAAATAAA-AAA-AAAATAAT
2698232 TTTTAAATTAAAAAAAAAATAAT
1 TTTTAAA-TAAAAAAAAAATAAT
2698255 TTTTA
1 TTTTA
2698260 TCTAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 20 0.77
24 3 0.12
25 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTAAATAAAAAAAAAATAAT
Found at i:2699779 original size:16 final size:16
Alignment explanation
Indices: 2699754--2699791 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2699744 ATGTTATTAA
*
2699754 AAAATAAAATAA-ATT
1 AAAATTAAATAATATT
2699769 ATAAATTAAATAATATT
1 A-AAATTAAATAATATT
2699786 AAAATT
1 AAAATT
2699792 CAGCTCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 15 0.75
17 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTAAATAATATT
Found at i:2703273 original size:6 final size:7
Alignment explanation
Indices: 2703256--2703281 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2703246 GGCATGAATT
2703256 TTTTTAA
1 TTTTTAA
2703263 TTTTTAA
1 TTTTTAA
2703270 TTTTTAA
1 TTTTTAA
2703277 TTTTT
1 TTTTT
2703282 TGTCCTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:2704441 original size:37 final size:38
Alignment explanation
Indices: 2704386--2704461 Score: 118
Period size: 37 Copynumber: 2.0 Consensus size: 38
2704376 GACCACACAC
* *
2704386 TAGGCCCTAAGCTCAAGTTGCAATGGAAACCGCTCAAG
1 TAGGCACTAAGCTAAAGTTGCAATGGAAACCGCTCAAG
*
2704424 TAGGCACTAA-CTAAAGTTGTAATGGAAACCGCTCAAG
1 TAGGCACTAAGCTAAAGTTGCAATGGAAACCGCTCAAG
2704461 T
1 T
2704462 CTCAACGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 26 0.74
38 9 0.26
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (38 bp):
TAGGCACTAAGCTAAAGTTGCAATGGAAACCGCTCAAG
Found at i:2707300 original size:157 final size:157
Alignment explanation
Indices: 2707013--2707486 Score: 939
Period size: 157 Copynumber: 3.0 Consensus size: 157
2707003 TAATCTATAT
2707013 TAATTAAATGAATAATGGAGAAAATAAAAAAAGGGGGTAAACTTGTCATTTTAAAAATAGTACGG
1 TAATTAAATGAATAATGGAGAAAAT-AAAAAAGGGGGTAAACTTGTCATTTTAAAAATAGTACGG
2707078 AGAAAGAAAGAAATTGCCAAATTGGAAAAAATAATAGTGAGGCCTTGGGTTTTTTTTCTAGGAGA
65 AGAAAGAAAGAAATTGCCAAATTGGAAAAAATAATAGTGAGGCCTTGGGTTTTTTTTCTAGGAGA
2707143 AGAACAATAAAGGCTGTGGTGCAAAGAA
130 AGAACAATAAAGGCTGTGGTGCAAAGAA
2707171 TAATTAAATGAATAATGGAGAAAATAAAAAAGGGGGTAAACTTGTCATTTTAAAAATAGTACGGA
1 TAATTAAATGAATAATGGAGAAAATAAAAAAGGGGGTAAACTTGTCATTTTAAAAATAGTACGGA
2707236 GAAAGAAAGAAATTGCCAAATTGGAAAAAATAATAGTGAGGCCTTGGGTTTTTTTTCTAGGAGAA
66 GAAAGAAAGAAATTGCCAAATTGGAAAAAATAATAGTGAGGCCTTGGGTTTTTTTTCTAGGAGAA
2707301 GAACAATAAAGGCTGTGGTGCAAAGAA
131 GAACAATAAAGGCTGTGGTGCAAAGAA
2707328 TAATTAAATGAATAATGGAGAAAATAAAAAAGGGGGTAAACTTGTCATTTTAAAAATAGTACGGA
1 TAATTAAATGAATAATGGAGAAAATAAAAAAGGGGGTAAACTTGTCATTTTAAAAATAGTACGGA
2707393 GAAAGAAAGAAATTGCCAAATTGGAAAAAATAATAGTGAGGCCTTGGGTTTTTTTTCTAGGAGAA
66 GAAAGAAAGAAATTGCCAAATTGGAAAAAATAATAGTGAGGCCTTGGGTTTTTTTTCTAGGAGAA
2707458 GAACAATAAAGGCTGTGGTGCAAAGAA
131 GAACAATAAAGGCTGTGGTGCAAAGAA
2707485 TA
1 TA
2707487 GCCAAGTGTT
Statistics
Matches: 316, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
157 291 0.92
158 25 0.08
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (157 bp):
TAATTAAATGAATAATGGAGAAAATAAAAAAGGGGGTAAACTTGTCATTTTAAAAATAGTACGGA
GAAAGAAAGAAATTGCCAAATTGGAAAAAATAATAGTGAGGCCTTGGGTTTTTTTTCTAGGAGAA
GAACAATAAAGGCTGTGGTGCAAAGAA
Found at i:2708444 original size:14 final size:16
Alignment explanation
Indices: 2708410--2708455 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
2708400 CTAAAATAAA
*
2708410 AAATTTTTAATATTA-
1 AAATTTTAAATATTAT
2708425 AAA-TTTAAAT-TTAT
1 AAATTTTAAATATTAT
2708439 AAATTTTAAATATTAT
1 AAATTTTAAATATTAT
2708455 A
1 A
2708456 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 9 0.33
15 10 0.37
16 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTTAAATATTAT
Found at i:2710183 original size:12 final size:13
Alignment explanation
Indices: 2710165--2710212 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
2710155 ATTTTTTTTT
2710165 AATTTTTTAAATA
1 AATTTTTTAAATA
2710178 AATTTTTTAAA-A
1 AATTTTTTAAATA
2710190 ATATTTTTTAAAATA
1 A-ATTTTTT-AAATA
*
2710205 TATTTTTT
1 AATTTTTT
2710213 TACAGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 2 0.06
13 18 0.58
14 10 0.32
15 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:2710184 original size:14 final size:14
Alignment explanation
Indices: 2710167--2710214 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2710157 TTTTTTTTAA
2710167 TTTTTTAAATAAA-
1 TTTTTTAAATAAAT
2710180 TTTTTTAAA-AATAT
1 TTTTTTAAATAA-AT
* *
2710194 TTTTTAAAATATAT
1 TTTTTTAAATAAAT
2710208 TTTTTTA
1 TTTTTTA
2710215 CAGTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.07
13 10 0.34
14 16 0.55
15 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTTAAATAAAT
Found at i:2710645 original size:52 final size:51
Alignment explanation
Indices: 2710553--2710655 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 51
2710543 TTAAAGTATG
* *
2710553 ATTTTTTTAATTATTAAAATGTATTTTGATATAATTATATAAATTTAATTTA
1 ATTTTTTTAAGTATTAAAATGTATTTTGATATAACTATAT-AATTTAATTTA
* * *
2710605 ATTTTTTTAAGTAGTTTAAAAT-TATTTT-ATTTTACTATATAATTTATTTTA
1 ATTTTTTTAAGTA--TTAAAATGTATTTTGATATAACTATATAATTTAATTTA
2710656 TTTATAAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
51 10 0.23
52 21 0.48
53 6 0.14
54 7 0.16
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (51 bp):
ATTTTTTTAAGTATTAAAATGTATTTTGATATAACTATATAATTTAATTTA
Found at i:2710669 original size:22 final size:22
Alignment explanation
Indices: 2710626--2710672 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2710616 TAGTTTAAAA
**
2710626 TTATTTTATTTTACTATATAAT
1 TTATTTTATTTTAAGATATAAT
2710648 TTATTTTATTTATAAGAT-TAAT
1 TTATTTTATTT-TAAGATATAAT
2710670 TTA
1 TTA
2710673 ATTAGAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTTTATTTTAAGATATAAT
Found at i:2710972 original size:15 final size:16
Alignment explanation
Indices: 2710951--2710996 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
2710941 AGAATAAGAC
2710951 AAAAAGAGAA-AAAAA
1 AAAAAGAGAAGAAAAA
*
2710966 GAAAAGAAGAAGAAAAA
1 AAAAAG-AGAAGAAAAA
2710983 AAATAAGAGAAGAA
1 AAA-AAGAGAAGAA
2710997 GATAGAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 14 0.54
18 3 0.12
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAAGAGAAGAAAAA
Found at i:2710985 original size:23 final size:23
Alignment explanation
Indices: 2710959--2711015 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
2710949 ACAAAAAGAG
2710959 AAAAAAAGAAAAGAAGA-AGAAA
1 AAAAAAAGAAAAGAAGATAGAAA
*
2710981 AAAAATAAGAGAAGAAGATAGAAA
1 AAAAA-AAGAAAAGAAGATAGAAA
*
2711005 GAAAAAAGAAA
1 AAAAAAAGAAA
2711016 GCTGACTGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.17
23 16 0.53
24 9 0.30
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (23 bp):
AAAAAAAGAAAAGAAGATAGAAA
Found at i:2711683 original size:14 final size:13
Alignment explanation
Indices: 2711657--2711701 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2711647 TCAACGTAAA
*
2711657 AAAAATATATTTT
1 AAAAATATTTTTT
2711670 AAAAAGTATTTTTT
1 AAAAA-TATTTTTT
2711684 AAAAA-ATTTATTT
1 AAAAATATTT-TTT
2711697 AAAAA
1 AAAAA
2711702 ATTAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 4 0.14
13 13 0.45
14 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:2711719 original size:14 final size:14
Alignment explanation
Indices: 2711656--2711703 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
2711646 CTCAACGTAA
2711656 AAAAAATATATTTT
1 AAAAAATATATTTT
* *
2711670 AAAAAGTATTTTTT
1 AAAAAATATATTTT
*
2711684 AAAAAATTTA-TTT
1 AAAAAATATATTTT
2711697 AAAAAAT
1 AAAAAAT
2711704 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AAAAAATATATTTT
Found at i:2721492 original size:4 final size:4
Alignment explanation
Indices: 2721473--2721509 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
2721463 AACTGCAATT
2721473 TTTA TTTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
2721510 TTTGTTGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 23 0.72
5 9 0.28
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2723690 original size:2 final size:2
Alignment explanation
Indices: 2723683--2723745 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
2723673 TATTCAGTTT
*
2723683 TA TA TA TA TA TA TA TA TA TA TT 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
* *
2723725 AA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2723746 TTAGGGTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2724150 original size:19 final size:21
Alignment explanation
Indices: 2724126--2724164 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2724116 TCTTTTGTTA
2724126 ATTTTA-A-GATAAAAAATTC
1 ATTTTATATGATAAAAAATTC
*
2724145 ATTTTATATTATAAAAAATT
1 ATTTTATATGATAAAAAATT
2724165 AAGATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
ATTTTATATGATAAAAAATTC
Found at i:2726931 original size:23 final size:23
Alignment explanation
Indices: 2726905--2726955 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
2726895 AGCGTTTTTG
2726905 CATCTGTATATTCGATATTATTT
1 CATCTGTATATTCGATATTATTT
2726928 CATCTGTATATTCGATATTATTT
1 CATCTGTATATTCGATATTATTT
2726951 CATCT
1 CATCT
2726956 ATTTTTGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.51
Consensus pattern (23 bp):
CATCTGTATATTCGATATTATTT
Found at i:2727024 original size:18 final size:19
Alignment explanation
Indices: 2726995--2727048 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
2726985 GAATAATTTA
*
2726995 TAAATTTAAATATTAAATT
1 TAAATATAAATATTAAATT
* *
2727014 T-ATTATAAATAATAAATT
1 TAAATATAAATATTAAATT
*
2727032 TAAATATAAATTTTAAA
1 TAAATATAAATATTAAA
2727049 ATATCTATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATAAATATTAAATT
Found at i:2727085 original size:21 final size:21
Alignment explanation
Indices: 2727061--2727102 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2727051 ATCTATTTTG
*
2727061 ATAT-TTGAATTCTATATTTAT
1 ATATATTGAATTAT-TATTTAT
*
2727082 ATATATTTAATTATTATTTAT
1 ATATATTGAATTATTATTTAT
2727103 TTTTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATATTGAATTATTATTTAT
Found at i:2728062 original size:16 final size:17
Alignment explanation
Indices: 2728041--2728094 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
2728031 AATCCAAATC
2728041 TAAAATGA-TCGAAACT
1 TAAAATGATTCGAAACT
* *
2728057 TAAAATAATTCG-AATT
1 TAAAATGATTCGAAACT
*
2728073 TGAAATGATTC-AAACT
1 TAAAATGATTCGAAACT
2728089 TAAAAT
1 TAAAAT
2728095 TACTCAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 27 0.90
17 3 0.10
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (17 bp):
TAAAATGATTCGAAACT
Found at i:2728105 original size:32 final size:32
Alignment explanation
Indices: 2728043--2728105 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2728033 TCCAAATCTA
* *
2728043 AAATGATCGAAACTTAAAATAATTCGAATTTG
1 AAATGATCGAAACTTAAAATAACTCAAATTTG
*
2728075 AAATGATTC-AAACTTAAAATTACTCAAATTT
1 AAATGA-TCGAAACTTAAAATAACTCAAATTT
2728106 AAAAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 25 0.93
33 2 0.07
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (32 bp):
AAATGATCGAAACTTAAAATAACTCAAATTTG
Found at i:2728145 original size:15 final size:16
Alignment explanation
Indices: 2728127--2728156 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2728117 AAAAGTTTAA
2728127 AATTTAAAA-TAATTT
1 AATTTAAAATTAATTT
2728142 AATTTAAAATTAATT
1 AATTTAAAATTAATT
2728157 CGATCCGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAAAATTAATTT
Found at i:2729964 original size:2 final size:2
Alignment explanation
Indices: 2729914--2729955 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2729904 CCCAAGAACA
* *
2729914 AT AT A- AT AT GT AT AT AT AT AT AT AT AT AT TT 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
2729955 A
1 A
2729956 AAGATATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2733516 original size:13 final size:13
Alignment explanation
Indices: 2733498--2733523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2733488 CAATTTTTTG
2733498 TGTATCGATACAT
1 TGTATCGATACAT
2733511 TGTATCGATACAT
1 TGTATCGATACAT
2733524 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2733538 original size:32 final size:33
Alignment explanation
Indices: 2733478--2733541 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2733468 TACAAGCCAA
** *
2733478 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2733511 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2733542 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2733607 original size:20 final size:20
Alignment explanation
Indices: 2733562--2733634 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
2733552 CTGCCAAGAA
***
2733562 ATGTATCGATACATCTTTGTC
1 ATGTATCGATACAT-TGAATC
2733583 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
2733603 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
2733623 ATGTATCGATAC
1 ATGTATCGATAC
2733635 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:2733635 original size:20 final size:20
Alignment explanation
Indices: 2733582--2733637 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2733572 ACATCTTTGT
*
2733582 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
2733602 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
2733621 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
2733638 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:2735615 original size:21 final size:20
Alignment explanation
Indices: 2735586--2735628 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2735576 GACTAGTGTG
*
2735586 GGGACTGCCCGGTTGCAACCT
1 GGGACTG-CCGGTCGCAACCT
* *
2735607 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCAACCT
2735627 GG
1 GG
2735629 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCAACCT
Found at i:2738171 original size:15 final size:15
Alignment explanation
Indices: 2738151--2738181 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2738141 ATTTCGTTTG
*
2738151 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2738166 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2738181 G
1 G
2738182 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2742267 original size:13 final size:13
Alignment explanation
Indices: 2742249--2742274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2742239 CAATTTTTTG
2742249 TGTATCGATACAT
1 TGTATCGATACAT
2742262 TGTATCGATACAT
1 TGTATCGATACAT
2742275 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2742289 original size:32 final size:33
Alignment explanation
Indices: 2742229--2742292 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2742219 TACAAGCTAA
** *
2742229 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2742262 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2742293 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2742358 original size:20 final size:20
Alignment explanation
Indices: 2742313--2742385 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
2742303 CTGCCAAGAA
***
2742313 ATGTATCGATACATCTTTGTC
1 ATGTATCGATACAT-TGAATC
2742334 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
2742354 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
2742374 ATGTATCGATAC
1 ATGTATCGATAC
2742386 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:2742386 original size:20 final size:20
Alignment explanation
Indices: 2742333--2742388 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2742323 ACATCTTTGT
*
2742333 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
2742353 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
2742372 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
2742389 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:2746143 original size:42 final size:42
Alignment explanation
Indices: 2746079--2746160 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
2746069 GCTCAGATTA
*
2746079 AATCTAATAGACGGTTACGTTTATTACTTATTTACAAAATCT
1 AATCTAATAGACGGCTACGTTTATTACTTATTTACAAAATCT
*
2746121 AATCTAATAGACGGCTAGGTTTATTACTTATTTACAAAAT
1 AATCTAATAGACGGCTACGTTTATTACTTATTTACAAAAT
2746161 TTAAAACTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (42 bp):
AATCTAATAGACGGCTACGTTTATTACTTATTTACAAAATCT
Found at i:2746445 original size:19 final size:19
Alignment explanation
Indices: 2746421--2746459 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2746411 TTCATTCATT
2746421 GTCTAAGATGGTGAGCGGC
1 GTCTAAGATGGTGAGCGGC
*
2746440 GTCTAAGATGGTGAGTGGC
1 GTCTAAGATGGTGAGCGGC
2746459 G
1 G
2746460 GTCATGGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.44, T:0.23
Consensus pattern (19 bp):
GTCTAAGATGGTGAGCGGC
Found at i:2747979 original size:2 final size:2
Alignment explanation
Indices: 2747972--2748005 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2747962 AGTTTTATGC
2747972 AT AT AT AT AT AT AT 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
2748006 GACGTAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2748928 original size:18 final size:18
Alignment explanation
Indices: 2748905--2748944 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2748895 AATTAGAAAA
*
2748905 AAAAT-AAAGAACAAGCAT
1 AAAATAAAAGAA-AAACAT
2748923 AAAATAAAAGAAAAACAT
1 AAAATAAAAGAAAAACAT
2748941 AAAA
1 AAAA
2748945 GAATTACGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.10
Consensus pattern (18 bp):
AAAATAAAAGAAAAACAT
Found at i:2749178 original size:34 final size:34
Alignment explanation
Indices: 2749134--2749347 Score: 262
Period size: 34 Copynumber: 6.4 Consensus size: 34
2749124 AAAAACCACT
*
2749134 ATTTAATCAACAATGGCAACCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* *
2749168 ATTTAGTCAACAATGGTAAGCC-ACCAAATCACCC
1 ATTTAATCAACAATGGTAA-CCTACCAAATCTCCC
* * *
2749202 ATTTAATCAACAATGGTAAGCTACCAAATTTCTC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
*
2749236 ATTTAATCAACAATGGTAAGCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* *
2749270 ATTTAGTCAACAATGGCAAACC-ACCAAATCAT-CC
1 ATTTAATCAACAATGG-TAACCTACCAAATC-TCCC
*
2749304 ATTTAATCAACAATGGTAAACTACCAAA--T--C
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
2749334 ATTTAATCAACAAT
1 ATTTAATCAACAAT
2749348 TCTCCCACTT
Statistics
Matches: 159, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
30 15 0.09
31 1 0.01
33 4 0.03
34 133 0.84
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
ATTTAATCAACAATGGTAACCTACCAAATCTCCC
Found at i:2749274 original size:102 final size:98
Alignment explanation
Indices: 2749134--2749347 Score: 338
Period size: 102 Copynumber: 2.1 Consensus size: 98
2749124 AAAAACCACT
* *
2749134 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
*
2749199 CCCATTTAATCAACAATGGTAAGCTACCAAATTTCTC
66 CCCATTTAATCAACAATGGTAAACTACCAAA----TC
* *
2749236 ATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
*
2749301 TCCATTTAATCAACAATGGTAAACTACCAAATC
66 CCCATTTAATCAACAATGGTAAACTACCAAATC
2749334 ATTTAATCAACAAT
1 ATTTAATCAACAAT
2749348 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
98 16 0.15
102 90 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (98 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATCA
CCCATTTAATCAACAATGGTAAACTACCAAATC
Found at i:2753443 original size:19 final size:19
Alignment explanation
Indices: 2753419--2753476 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
2753409 TGTACAATAT
*
2753419 CCGTATACTTGAATAGTAC
1 CCGTATACGTGAATAGTAC
2753438 CCGTATACGTGAATAGTAC
1 CCGTATACGTGAATAGTAC
**
2753457 ATGTATACGTGAATAGTAC
1 CCGTATACGTGAATAGTAC
2753476 C
1 C
2753477 TCGACAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (19 bp):
CCGTATACGTGAATAGTAC
Found at i:2753825 original size:34 final size:34
Alignment explanation
Indices: 2753782--2753970 Score: 190
Period size: 34 Copynumber: 5.6 Consensus size: 34
2753772 GTAAAAACCA
* ** *
2753782 CCATTTAATCAATAATGGCAACCTACTAAATCTC
1 CCATTTAATCAACAATGATAACCTACCAAATCTC
*
2753816 CCATTTAATCAACAAT-AGTAA-GTCACCAAATCAT-
1 CCATTTAATCAACAATGA-TAACCT-ACCAAATC-TC
* * *
2753850 CTATTTAATCAACAATGATAAGCTACCAAATTTC
1 CCATTTAATCAACAATGATAACCTACCAAATCTC
* * *
2753884 TCATTTAATCAACAATGATAAGCTACCAAATCTT
1 CCATTTAATCAACAATGATAACCTACCAAATCTC
*
2753918 CCATTTAATCAACAATGACAAACC-ACCAAAT-TAC
1 CCATTTAATCAACAATGA-TAACCTACCAAATCT-C
2753952 CCATTTAATCAACAATGAT
1 CCATTTAATCAACAATGAT
2753971 TACTACTAAA
Statistics
Matches: 130, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
33 3 0.02
34 121 0.93
35 6 0.05
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (34 bp):
CCATTTAATCAACAATGATAACCTACCAAATCTC
Found at i:2753897 original size:68 final size:68
Alignment explanation
Indices: 2753782--2753984 Score: 241
Period size: 68 Copynumber: 3.0 Consensus size: 68
2753772 GTAAAAACCA
* * * * *
2753782 CCATTTAATCAATAATGGCAACCTACTAAATCTCCCATTTAATCAACAAT-AGTAAG-TCACCAA
1 CCATTTAATCAACAATGACAAACTACCAAATTTCCCATTTAATCAACAATGA-TAAGCT-ACCAA
2753845 ATCAT
64 ATCAT
* * * *
2753850 CTATTTAATCAACAATGATAAGCTACCAAATTTCTCATTTAATCAACAATGATAAGCTACCAAAT
1 CCATTTAATCAACAATGACAAACTACCAAATTTCCCATTTAATCAACAATGATAAGCTACCAAAT
*
2753915 CTT
66 CAT
* * * *
2753918 CCATTTAATCAACAATGACAAACCACCAAATTACCCATTTAATCAACAATGATTA-CTACTAAAT
1 CCATTTAATCAACAATGACAAACTACCAAATTTCCCATTTAATCAACAATGATAAGCTACCAAAT
2753982 CAT
66 CAT
2753985 TTAATCAACA
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
67 10 0.09
68 103 0.90
69 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (68 bp):
CCATTTAATCAACAATGACAAACTACCAAATTTCCCATTTAATCAACAATGATAAGCTACCAAAT
CAT
Found at i:2753959 original size:102 final size:102
Alignment explanation
Indices: 2753783--2753970 Score: 252
Period size: 102 Copynumber: 1.8 Consensus size: 102
2753773 TAAAAACCAC
* * * * **
2753783 CATTTAATCAATAATGGCAACCTACTAAATCTCCCATTTAATCAACAATAGTAAGTCACCAAATC
1 CATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAATCAACAATAGCAAACCACCAAATC
* *
2753848 ATCTATTTAATCAACAATGATAAGCTACCAAATTTCT
66 ACCCATTTAATCAACAATGATAAGCTACCAAATTTCT
* * *
2753885 CATTTAATCAACAATGATAAGCTACCAAATCTTCCATTTAATCAACAAT-GACAAACCACCAAAT
1 CATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAATCAACAATAG-CAAACCACCAAAT
*
2753949 TACCCATTTAATCAACAATGAT
65 CACCCATTTAATCAACAATGAT
2753971 TACTACTAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 1 0.01
102 72 0.99
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.29
Consensus pattern (102 bp):
CATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAATCAACAATAGCAAACCACCAAATC
ACCCATTTAATCAACAATGATAAGCTACCAAATTTCT
Found at i:2754436 original size:16 final size:16
Alignment explanation
Indices: 2754415--2754464 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
2754405 GTGGATACCC
2754415 AATAGCTGAAGAAGAA
1 AATAGCTGAAGAAGAA
*
2754431 AATAGCTGAAGAGGAA
1 AATAGCTGAAGAAGAA
2754447 AATAGCTGAAGAAGAA
1 AATAGCTGAAGAAGAA
2754463 AA
1 AA
2754465 CCGAGGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.56, C:0.06, G:0.26, T:0.12
Consensus pattern (16 bp):
AATAGCTGAAGAAGAA
Found at i:2754924 original size:13 final size:14
Alignment explanation
Indices: 2754907--2754973 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 14
2754897 AATATGTGTA
2754907 ATAAATA-TAAATT
1 ATAAATATTAAATT
*
2754920 TTAAATATTAAATT
1 ATAAATATTAAATT
*
2754934 ATAAAT-TT--TTT
1 ATAAATATTAAATT
*
2754945 A-AAATATTATATT
1 ATAAATATTAAATT
2754958 AT-AA-ATTAAATT
1 ATAAATATTAAATT
2754970 ATAA
1 ATAA
2754974 TATAAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
10 4 0.09
11 5 0.12
12 9 0.21
13 14 0.33
14 11 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATAAATATTAAATT
Found at i:2754933 original size:14 final size:13
Alignment explanation
Indices: 2754907--2754979 Score: 57
Period size: 14 Copynumber: 5.8 Consensus size: 13
2754897 AATATGTGTA
2754907 ATAAATATAAATT
1 ATAAATATAAATT
*
2754920 TTAAATATTAAATT
1 ATAAATA-TAAATT
**
2754934 ATAAAT-T-TTTT
1 ATAAATATAAATT
*
2754945 A-AAATATTATATT
1 ATAAATA-TAAATT
2754958 ATAAAT-TAAATT
1 ATAAATATAAATT
2754970 AT-AATATAAA
1 ATAAATATAAA
2754980 AATTAAACGA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
10 4 0.08
11 6 0.12
12 13 0.27
13 10 0.21
14 15 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAAATATAAATT
Found at i:2754958 original size:24 final size:23
Alignment explanation
Indices: 2754918--2754964 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
2754908 TAAATATAAA
2754918 TTTTAAATATTAAATTATAAATT
1 TTTTAAATATTAAATTATAAATT
*
2754941 TTTTAAAATATTATATTATAAATT
1 TTTT-AAATATTAAATTATAAATT
2754965 AAATTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAATATTAAATTATAAATT
Found at i:2760314 original size:16 final size:16
Alignment explanation
Indices: 2760280--2760325 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
2760270 AAAAAAATTA
* * *
2760280 TAAATATTAAATTTAT
1 TAAATATTTATTTTTT
2760296 TAAATATTTATTTTTT
1 TAAATATTTATTTTTT
2760312 T-AAT-TTTATTTTTT
1 TAAATATTTATTTTTT
2760326 AGAAACATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 10 0.37
15 3 0.11
16 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TAAATATTTATTTTTT
Found at i:2760666 original size:2 final size:2
Alignment explanation
Indices: 2760659--2760715 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
2760649 TATTCAGTTT
* *
2760659 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2760701 TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA T
2760716 TTAGGGTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2761120 original size:19 final size:21
Alignment explanation
Indices: 2761096--2761134 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2761086 TCTTTTGTTA
2761096 ATTTTA-A-GATAAAAAATTC
1 ATTTTATATGATAAAAAATTC
*
2761115 ATTTTATATTATAAAAAATT
1 ATTTTATATGATAAAAAATT
2761135 AAGATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
ATTTTATATGATAAAAAATTC
Found at i:2766402 original size:2 final size:2
Alignment explanation
Indices: 2766354--2766393 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2766344 CCCAAGAATA
* *
2766354 AT AT A- AT AT GT AT AT AT TT 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 AT AT A
2766394 AAGATATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2768172 original size:37 final size:38
Alignment explanation
Indices: 2768122--2768197 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
2768112 GACCACACAC
*
2768122 TAGGCCCTAAGCTCAAGTTGCAATGGAAACCGCTCAAG
1 TAGGCACTAAGCTCAAGTTGCAATGGAAACCGCTCAAG
*
2768160 TAGGCACT-AGCTCAAGTTGTAATGGAAACCGCTCAAG
1 TAGGCACTAAGCTCAAGTTGCAATGGAAACCGCTCAAG
2768197 T
1 T
2768198 CTCAACGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 29 0.81
38 7 0.19
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (38 bp):
TAGGCACTAAGCTCAAGTTGCAATGGAAACCGCTCAAG
Found at i:2774431 original size:14 final size:14
Alignment explanation
Indices: 2774405--2774440 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2774395 AAGTTATAAA
2774405 AAAATTATAAATATT
1 AAAATT-TAAATATT
2774420 AAAATTTAAATATT
1 AAAATTTAAATATT
2774434 -AAATTTA
1 AAAATTTA
2774441 TTAAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.33
14 8 0.38
15 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:2774795 original size:2 final size:2
Alignment explanation
Indices: 2774788--2774831 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2774778 ATTATTCAGT
2774788 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
2774830 TA
1 TA
2774832 GGGTTTATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2777966 original size:11 final size:12
Alignment explanation
Indices: 2777938--2777978 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
2777928 ATTCAAATTT
2777938 TATATTTA--TA
1 TATATTTAGTTA
2777948 TATATTTAGTTA
1 TATATTTAGTTA
*
2777960 T-TATTTATTTA
1 TATATTTAGTTA
2777971 TATATTTA
1 TATATTTA
2777979 AAAAATAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 8 0.30
11 10 0.37
12 9 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TATATTTAGTTA
Found at i:2778030 original size:17 final size:17
Alignment explanation
Indices: 2777989--2778030 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2777979 AAAAATAATG
*
2777989 TAATAAATTTAAATATT
1 TAATAAATTTAAATATC
*
2778006 TAACAAATTTAAATATC
1 TAATAAATTTAAATATC
2778023 TAATAAAT
1 TAATAAAT
2778031 ATTACTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATAAATTTAAATATC
Found at i:2781377 original size:14 final size:14
Alignment explanation
Indices: 2781358--2781392 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2781348 CGTTTATATG
2781358 TGTAAAATTTATTA
1 TGTAAAATTTATTA
2781372 TGTAAAATTTATTA
1 TGTAAAATTTATTA
*
2781386 TTTAAAA
1 TGTAAAA
2781393 AATAATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (14 bp):
TGTAAAATTTATTA
Found at i:2782972 original size:14 final size:15
Alignment explanation
Indices: 2782953--2782988 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2782943 AATATTAAAA
2782953 TAATATTTTTAT-AT
1 TAATATTTTTATAAT
2782967 TAATATTTTTATAAT
1 TAATATTTTTATAAT
2782982 TAA-ATTT
1 TAATATTT
2782989 AAATCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATATTTTTATAAT
Found at i:2785374 original size:2 final size:2
Alignment explanation
Indices: 2785367--2785404 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2785357 GAAGCGACAA
*
2785367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2785405 TTTGATTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2785933 original size:69 final size:69
Alignment explanation
Indices: 2785805--2785933 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 69
2785795 TAATAAAAGT
* * * *
2785805 TATCATATTTATAATAAAAAATCTAATTCTATTAAAATATTTTGGTTAAATGATTTTTATAACAA
1 TATCACATTTATAATAAAAAATCTAATTCTATTAAAATATTTTGATTAAACGATATTTATAACAA
2785870 AATA
66 AATA
*
2785874 TATCACATTTAT-ATACAAGAATTCTAATTCTATTGAAAAT-TTTTGATTAAACGA-ATTTAT
1 TATCACATTTATAATA-AA-AAATCTAATTCTATT-AAAATATTTTGATTAAACGATATTTAT
2785934 TTGCTAATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
68 3 0.06
69 18 0.35
70 26 0.50
71 5 0.10
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (69 bp):
TATCACATTTATAATAAAAAATCTAATTCTATTAAAATATTTTGATTAAACGATATTTATAACAA
AATA
Found at i:2790688 original size:17 final size:20
Alignment explanation
Indices: 2790666--2790714 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2790656 AATAAAATAA
2790666 TTTTATTATTTT-TA-A-AT
1 TTTTATTATTTTATATATAT
2790683 TTTTATTATTTTATATATAT
1 TTTTATTATTTTATATATAT
2790703 TTTTA-TATTTTA
1 TTTTATTATTTTA
2790715 ATTACAGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.41
18 2 0.07
19 8 0.28
20 7 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTATTTTATATATAT
Found at i:2794314 original size:16 final size:17
Alignment explanation
Indices: 2794293--2794329 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
2794283 CTTTTTGATT
*
2794293 TTTATTTGTGAA-TAAA
1 TTTATTTGTAAATTAAA
2794309 TTTATTTGTAAATTAAA
1 TTTATTTGTAAATTAAA
2794326 TTTA
1 TTTA
2794330 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
TTTATTTGTAAATTAAA
Found at i:2794432 original size:24 final size:25
Alignment explanation
Indices: 2794390--2794438 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
2794380 AATAAAAAAT
2794390 ATATAAATTTAATTAT-AAATATTA
1 ATATAAATTTAATTATAAAATATTA
*
2794414 ATATAAA-TTAATTTTTAAAATATTA
1 ATATAAATTTAA-TTATAAAATATTA
2794439 TTTTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATAAATTTAATTATAAAATATTA
Found at i:2796907 original size:28 final size:30
Alignment explanation
Indices: 2796866--2796921 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2796856 ATTTATCATC
* *
2796866 TCATTTTATAA-T-TAAAGACAATAACTTA
1 TCATCTTATAATTATAAAAACAATAACTTA
*
2796894 TCATCTTATCATTATAAAAACAATAACT
1 TCATCTTATAATTATAAAAACAATAACT
2796922 CATAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
29 1 0.04
30 13 0.57
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (30 bp):
TCATCTTATAATTATAAAAACAATAACTTA
Found at i:2800468 original size:18 final size:19
Alignment explanation
Indices: 2800442--2800479 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2800432 GCAAAAATGG
*
2800442 ATTTCTTTTT-TTTTTAGA
1 ATTTCTTTTTACTTTTAGA
*
2800460 ATTTTTTTTTACTTTTAGA
1 ATTTCTTTTTACTTTTAGA
2800479 A
1 A
2800480 CTTTAGAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
ATTTCTTTTTACTTTTAGA
Found at i:2800528 original size:18 final size:18
Alignment explanation
Indices: 2800481--2800519 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2800471 CTTTTAGAAC
* *
2800481 TTTAGAATTTATTTATTT
1 TTTAAAATTTTTTTATTT
2800499 TTTAAAATTTTTTTATTT
1 TTTAAAATTTTTTTATTT
2800517 TTT
1 TTT
2800520 CTATTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTAAAATTTTTTTATTT
Found at i:2800795 original size:2 final size:2
Alignment explanation
Indices: 2800790--2800824 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2800780 TTCTTCAATT
2800790 TA 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 TA T
2800825 TTGTAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2802613 original size:16 final size:16
Alignment explanation
Indices: 2802594--2802627 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2802584 CAAAATTATT
2802594 TTTAATTACTATTAAA
1 TTTAATTACTATTAAA
**
2802610 TTTAATTTTTATTAAA
1 TTTAATTACTATTAAA
2802626 TT
1 TT
2802628 ATTTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAATTACTATTAAA
Found at i:2803087 original size:22 final size:23
Alignment explanation
Indices: 2803059--2803105 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2803049 AAAATATTAA
2803059 AATATTTAAAAAATTTTAT-ATT
1 AATATTTAAAAAATTTTATAATT
* *
2803081 AATATTTATATAATTTTATAATT
1 AATATTTAAAAAATTTTATAATT
2803104 AA
1 AA
2803106 ATATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTAAAAAATTTTATAATT
Found at i:2803115 original size:22 final size:22
Alignment explanation
Indices: 2803059--2803115 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
2803049 AAAATATTAA
* *
2803059 AATATTTAAAAAATTTTATATT
1 AATATATAAATAATTTTATATT
* *
2803081 AATATTTATATAATTTTATAATT
1 AATATATAAATAATTTTAT-ATT
2803104 AA-ATATAAATAA
1 AATATATAAATAA
2803116 AATAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATATAAATAATTTTATATT
Found at i:2803471 original size:16 final size:16
Alignment explanation
Indices: 2803450--2803513 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 16
2803440 TGAATTATTA
*
2803450 AAATTTATATTATTTT
1 AAATTTAAATTATTTT
*
2803466 AAATTTAAATCATTTT
1 AAATTTAAATTATTTT
* *
2803482 -AATTCAAATAATTTT
1 AAATTTAAATTATTTT
*
2803497 AAATTTAGATCTATTTT
1 AAATTTAAAT-TATTTT
2803514 TATCACTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 13 0.33
16 21 0.54
17 5 0.13
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:2804020 original size:4 final size:4
Alignment explanation
Indices: 2804013--2804060 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
2804003 TTAATTTTTT
**
2804013 TTTC TTTC TTTC TTTC TTTC TTTC -TTC TTCTC TACC TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC
2804060 T
1 T
2804061 ATGTCTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 6 0.16
4 28 0.76
5 3 0.08
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:2804837 original size:13 final size:13
Alignment explanation
Indices: 2804803--2804843 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
2804793 TTTTTTTATT
*
2804803 TTTTAAATTAAAA
1 TTTTAAACTAAAA
2804816 TTGTTAAACTAAAA
1 TT-TTAAACTAAAA
2804830 TTTTAAACGTAAAA
1 TTTTAAAC-TAAAA
2804844 ATTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (13 bp):
TTTTAAACTAAAA
Found at i:2805517 original size:20 final size:21
Alignment explanation
Indices: 2805481--2805519 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2805471 ATATTATACC
*
2805481 ATAAAATAAATAAAAATATTT
1 ATAAAATAAACAAAAATATTT
2805502 ATAAAAT-AACAAAAATAT
1 ATAAAATAAACAAAAATAT
2805520 ATATTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAAATAAACAAAAATATTT
Found at i:2805821 original size:77 final size:78
Alignment explanation
Indices: 2805721--2805878 Score: 205
Period size: 77 Copynumber: 2.0 Consensus size: 78
2805711 ATAATTAGTC
*
2805721 ATATATATATATATATTGCACAAAGGATGCTCCTATGTTAAAA-ATGAGTTAATG-AGGATCAAT
1 ATATATATATATATATT-CACAAAGGATGCTCCTATATTAAAATA-GAGTTAATGCA-GATCAAT
*
2805784 AATCAATTTCTCTTTG
63 AATCAATTTATCTTTG
* * * * *
2805800 ATATATATTTATATATT-ACAAAGGTTGCTCCTCTATTAAAATAGAGTTAATGCAGTTGAATAAT
1 ATATATATATATATATTCACAAAGGATGCTCCTATATTAAAATAGAGTTAATGCAGATCAATAAT
2805864 CAATTTATCTTTG
66 CAATTTATCTTTG
2805877 AT
1 AT
2805879 TAATGGAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
77 52 0.74
78 2 0.03
79 16 0.23
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (78 bp):
ATATATATATATATATTCACAAAGGATGCTCCTATATTAAAATAGAGTTAATGCAGATCAATAAT
CAATTTATCTTTG
Found at i:2806136 original size:11 final size:11
Alignment explanation
Indices: 2806120--2806149 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2806110 GTTTTGAACA
2806120 TTTTATTTTTC
1 TTTTATTTTTC
2806131 TTTTATTTTTC
1 TTTTATTTTTC
2806142 TTTT-TTTT
1 TTTTATTTT
2806150 GGTCTTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:2810265 original size:16 final size:17
Alignment explanation
Indices: 2810244--2810278 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2810234 AATTATAAAT
*
2810244 ATTTTAATATCAAA-AA
1 ATTTTAAAATCAAATAA
2810260 ATTTTAAAATCAAATAA
1 ATTTTAAAATCAAATAA
2810277 AT
1 AT
2810279 AAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTTTAAAATCAAATAA
Found at i:2811922 original size:19 final size:19
Alignment explanation
Indices: 2811875--2811922 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2811865 ATGAATAATG
*
2811875 AAATATTTTTAAATTTTAA
1 AAATATTTTTAAATTTAAA
*
2811894 AAATATTTTT-TATATTAAA
1 AAATATTTTTAAAT-TTAAA
2811913 TAAATATTTT
1 -AAATATTTT
2811923 CATAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATATTTTTAAATTTAAA
Found at i:2811931 original size:19 final size:20
Alignment explanation
Indices: 2811894--2811931 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2811884 TAAATTTTAA
* *
2811894 AAATATTTTTTATATTAAAT
1 AAATATTTTTCATAATAAAT
2811914 AAATA-TTTTCATAATAAA
1 AAATATTTTTCATAATAAA
2811932 AATAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATTTTTCATAATAAAT
Found at i:2814322 original size:16 final size:16
Alignment explanation
Indices: 2814303--2814334 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2814293 GATGACATCT
2814303 GTGTCAAACAAACAAC
1 GTGTCAAACAAACAAC
2814319 GTGTCAAACAAACAAC
1 GTGTCAAACAAACAAC
2814335 AACGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
GTGTCAAACAAACAAC
Found at i:2819460 original size:24 final size:23
Alignment explanation
Indices: 2819406--2819470 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 23
2819396 CTCCATTTGA
2819406 TTTAGTTTT-TTTAATTGATGAT
1 TTTAGTTTTATTTAATTGATGAT
2819428 TTT-GATTTTATTATAATT-ATGTAT
1 TTTAG-TTTTATT-TAATTGATG-AT
2819452 TTTAGTTTTGATTTTAATT
1 TTTAGTTTT-A-TTTAATT
2819471 TTGACATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
21 1 0.03
22 7 0.19
23 5 0.14
24 14 0.39
25 7 0.19
26 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.65
Consensus pattern (23 bp):
TTTAGTTTTATTTAATTGATGAT
Found at i:2819467 original size:12 final size:12
Alignment explanation
Indices: 2819414--2819474 Score: 52
Period size: 13 Copynumber: 5.0 Consensus size: 12
2819404 GATTTAGTTT
*
2819414 TTTTAATTGATGA
1 TTTTAATT-TTGA
*
2819427 TTTTGATTTT-A
1 TTTTAATTTTGA
* *
2819438 TTATAATTATGTA
1 TTTTAATTTTG-A
*
2819451 TTTTAGTTTTGA
1 TTTTAATTTTGA
2819463 TTTTAATTTTGA
1 TTTTAATTTTGA
2819475 CATTTTTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
11 8 0.22
12 13 0.35
13 16 0.43
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.62
Consensus pattern (12 bp):
TTTTAATTTTGA
Found at i:2822116 original size:19 final size:19
Alignment explanation
Indices: 2822094--2822149 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
2822084 AAGACAAAAA
2822094 AAAAAATAAAATATAATAT
1 AAAAAATAAAATATAATAT
* *
2822113 AAAATATAAAAAATAATAT
1 AAAAAATAAAATATAATAT
2822132 AAATATAATATAAATATA
1 AAA-A-AATA-AAATATA
2822150 TAAACATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 20 0.67
20 1 0.03
21 3 0.10
22 6 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATAAAATATAATAT
Found at i:2822136 original size:30 final size:30
Alignment explanation
Indices: 2822091--2822153 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
2822081 TATAAGACAA
2822091 AAAAAAAAATAAAATATAATATAAA-ATAT
1 AAAAAAAAATAAAATATAATATAAATATAT
*
2822120 AAAAAATAATATAAATATAATATAAATATAT
1 AAAAAAAAATA-AAATATAATATAAATATAT
2822151 AAA
1 AAA
2822154 CATATCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 10 0.32
30 14 0.45
31 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAAAAAAATAAAATATAATATAAATATAT
Found at i:2822168 original size:10 final size:9
Alignment explanation
Indices: 2822109--2822262 Score: 74
Period size: 9 Copynumber: 16.8 Consensus size: 9
2822099 ATAAAATATA
2822109 ATATAAAAT
1 ATATAAAAT
*
2822118 ATAAAAAAT
1 ATATAAAAT
2822127 A-ATATAAAT
1 ATATA-AAAT
2822136 ATAATATAAAT
1 AT-ATA-AAAT
2822147 ATATAAACAT
1 ATATAAA-AT
*
2822157 AT-CAAAAT
1 ATATAAAAT
2822165 ATAT-AAA-
1 ATATAAAAT
*
2822172 ACAT-AAAT
1 ATATAAAAT
*
2822180 GAT-TAATAT
1 -ATATAAAAT
*
2822189 ATCT-AAAT
1 ATATAAAAT
*
2822197 TTATATAAAT
1 ATATA-AAAT
*
2822207 ATATAATAT
1 ATATAAAAT
2822216 ATCA-AAAAT
1 AT-ATAAAAT
2822225 A-ATTATAAAT
1 ATA-TA-AAAT
2822235 ATATAAAATT
1 ATATAAAA-T
2822245 ATATAAATAT
1 ATATAAA-AT
2822255 AATATAAA
1 -ATATAAA
2822263 TACGATATAA
Statistics
Matches: 113, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
7 7 0.06
8 17 0.15
9 38 0.34
10 32 0.28
11 19 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (9 bp):
ATATAAAAT
Found at i:2822238 original size:28 final size:27
Alignment explanation
Indices: 2822199--2822264 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 27
2822189 ATCTAAATTT
2822199 ATATAAATATATAATATATCAAAAATA
1 ATATAAATATATAATATATCAAAAATA
*
2822226 ATTATAAATATATAAAATTATAT-AAATATA
1 A-TATAAATATAT--AA-TATATCAAAAATA
2822256 ATATAAATA
1 ATATAAATA
2822265 CGATATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 1 0.03
28 11 0.32
29 8 0.24
30 9 0.26
31 5 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
ATATAAATATATAATATATCAAAAATA
Found at i:2822239 original size:30 final size:28
Alignment explanation
Indices: 2822109--2822169 Score: 56
Period size: 29 Copynumber: 2.2 Consensus size: 28
2822099 ATAAAATATA
*
2822109 ATATAAAATATA-AAAAATAATATAAAT
1 ATATATAATATATAAAAATAATATAAAT
*
2822136 ATAATATAAATATATAAACAT-ATCA-AAAT
1 AT-ATAT-AATATATAAAAATAAT-ATAAAT
2822165 ATATA
1 ATATA
2822170 AAACATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
27 2 0.07
28 6 0.21
29 14 0.50
30 6 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (28 bp):
ATATATAATATATAAAAATAATATAAAT
Found at i:2822273 original size:46 final size:44
Alignment explanation
Indices: 2822125--2822274 Score: 114
Period size: 46 Copynumber: 3.4 Consensus size: 44
2822115 AATATAAAAA
* *
2822125 ATAATATAAATATAA-TATAAATATATAAACA-TAT-CAAA-ATAT
1 ATAA-ATACATATAATTATAAATATATAAA-ATTATATAAATATAT
* * *
2822167 ATAAA-ACATA-AATGATTAATATATCTAAATTTATATAAATATAT
1 ATAAATACATATAATTA-TAA-ATATATAAAATTATATAAATATAT
* * *
2822211 AATATATCAAAAATAATTATAAATATATAAAATTATATAAATATAAT
1 -ATAAAT-ACATATAATTATAAATATATAAAATTATATAAATAT-AT
2822258 ATAAATACGATATAATT
1 ATAAATAC-ATATAATT
2822275 TTTATATGAA
Statistics
Matches: 82, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
39 2 0.02
40 5 0.06
41 4 0.05
42 15 0.18
43 3 0.04
44 4 0.05
45 5 0.06
46 32 0.39
47 8 0.10
48 4 0.05
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (44 bp):
ATAAATACATATAATTATAAATATATAAAATTATATAAATATAT
Found at i:2823514 original size:12 final size:11
Alignment explanation
Indices: 2823495--2823519 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2823485 AATGAAATTT
2823495 AATTTTTTTAA
1 AATTTTTTTAA
2823506 AATTTTTTTAA
1 AATTTTTTTAA
2823517 AAT
1 AAT
2823520 ATGCGCATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTTTTTTAA
Found at i:2824134 original size:28 final size:28
Alignment explanation
Indices: 2824101--2824169 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
2824091 TTAACTTGTG
*
2824101 CTTAAATATTTTCAGCT-TAATATGTTTTT
1 CTTAAATATTTTCA-ATGTAATAT-TTTTT
*
2824130 -TTAAATAGTTTCAATGTAATATTTTTT
1 CTTAAATATTTTCAATGTAATATTTTTT
2824157 CTTAAATTATTTT
1 CTTAAA-TATTTT
2824170 AAAAATACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 6 0.18
28 23 0.68
29 5 0.15
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (28 bp):
CTTAAATATTTTCAATGTAATATTTTTT
Found at i:2824297 original size:2 final size:2
Alignment explanation
Indices: 2824290--2824316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2824280 TTAAAATGCA
2824290 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 A
2824317 AAGTTTTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2825882 original size:20 final size:21
Alignment explanation
Indices: 2825845--2825884 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2825835 ATTCAAACAA
2825845 AAAATTTTAATTTATAAATCT
1 AAAATTTTAATTTATAAATCT
*
2825866 AAAATTTT-ATTTCTAAATC
1 AAAATTTTAATTTATAAATC
2825885 GCCCCTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATTTTAATTTATAAATCT
Found at i:2826051 original size:3 final size:3
Alignment explanation
Indices: 2826043--2826097 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
2826033 AATTACTATT
*
2826043 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2826091 TAA TAA T
1 TAA TAA T
2826098 TTAATTTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2829016 original size:2 final size:2
Alignment explanation
Indices: 2829011--2829056 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2829001 TTTTTTTAGA
2829011 AT AT AT AT AT AT AT AT AT AT AT 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
2829053 AT AT
1 AT AT
2829057 GATGTCTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2831848 original size:334 final size:334
Alignment explanation
Indices: 2831239--2832910 Score: 3058
Period size: 334 Copynumber: 5.0 Consensus size: 334
2831229 CTTTACCCTC
2831239 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCACGA
1 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCACGA
*
2831304 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTGCTGTAACC
66 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
* * *
2831369 TCATTGCATTACTAGTCTTGCCCATCAGGGCAATAATTGCATTTCTATTGTCCACTCCATTCATT
131 TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCACTCCATTCATT
2831434 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTCA
196 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTCA
2831499 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGATC
261 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGATC
2831564 CCAAGATCA
326 CCAAGATCA
*
2831573 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTTGCATGCATCATCACATCACGA
1 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCACGA
* * *
2831638 TCATTCTTTGTTTCGTTATGAGCCTGCATTTATAGTCATCTGACTTTCATTTGGTTGCTGTAATC
66 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
* * * *
2831703 TCATTGCATTACTAGTCTTGCCCATTAGGGCAATAATTGCATTTCTATTGTCCACTCCATTCATT
131 TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCACTCCATTCATT
2831768 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTCA
196 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTCA
2831833 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGATC
261 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGATC
2831898 CCAAGATCA
326 CCAAGATCA
* *
2831907 ATTCTTTTATTTGCATGCCATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCATGA
1 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCACGA
2831972 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
66 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
* *
2832037 TTATTGCATTACTAGTTTTGCCCATCAAAGCAATAATTGCATTTCTATTGTCCATTCCATTCATT
131 TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCACTCCATTCATT
* *
2832102 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATTATCTCATGTCCACCGTCA
196 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTCA
*
2832167 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGTAATGGCCATAAAAGTGCAAGGGATC
261 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGATC
2832232 CCAAGATCA
326 CCAAGATCA
*
2832241 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTTGCATGCATCATCACATCACGA
1 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCACGA
2832306 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
66 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
2832371 TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCA-TCCCATTCAT
131 TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCACT-CCATTCAT
*
2832435 TTAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCATC
195 TTAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTC
*
2832500 ATCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATAGCCATAAAAGTGCAAGGGAT
260 ATCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGAT
*
2832565 CCCAATATCA
325 CCCAAGATCA
*
2832575 ATTCTTTTATTTGCATGCTATAAAATTTTGCTTTTGTGATTTTCGCATGCATCATCACATCACGA
1 ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCACGA
2832640 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
66 TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
* *
2832705 TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCATTCTATTCATT
131 TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCACTCCATTCATT
* *
2832770 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATTATCTCATGTCCACCGTCA
196 TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTCA
* *
2832835 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGTAATGGCCATAAAAGTGCAAAGGATC
261 TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGATC
2832900 CCAAGATCA
326 CCAAGATCA
2832909 AT
1 AT
2832911 CAAGGAACAT
Statistics
Matches: 1297, Mismatches: 39, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
333 1 0.00
334 1295 1.00
335 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (334 bp):
ATTCTTTTATTTGCATGCTATAAAATTTTACTTTTGTGATTTTCGCATGCATCATCACATCACGA
TCATTCTTTGTTTCGTTATGAGCCTGCACTTATAGTCATCTGACTTTCATTTGGTTACTGTAACC
TTATTGCATTACTAGTTTTGCCCATCAAGGCAATAATTGCATTTCTATTGTCCACTCCATTCATT
TAATTATCTTAATCGTGCATCCGCATCACTAGTCATTCATTGTCATGATCTTATGTCCACCGTCA
TCTTATCATAAGCTCATTTAGAATAAAAATCTAATATGGGAATGGCCATAAAAGTGCAAGGGATC
CCAAGATCA
Found at i:2835151 original size:22 final size:21
Alignment explanation
Indices: 2835086--2835153 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
2835076 AAAATGACGT
2835086 AAAAGTCAAAAGCAAAAGCATAA
1 AAAAGTCAAAAGCAAAA-CA-AA
* *
2835109 AAAA-TAAAAAGAAAAACAAA
1 AAAAGTCAAAAGCAAAACAAA
*
2835129 AAAAGTGCAAAAGCAAAATAAA
1 AAAAGT-CAAAAGCAAAACAAA
2835151 AAA
1 AAA
2835154 GAAAATAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.16
21 3 0.08
22 25 0.66
23 4 0.11
ACGTcount: A:0.74, C:0.09, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAGTCAAAAGCAAAACAAA
Found at i:2840060 original size:52 final size:52
Alignment explanation
Indices: 2839982--2840110 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
2839972 CGAAATATGA
*
2839982 AAATTTGCTTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
2840034 AAATTTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
2840086 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2840111 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:2842596 original size:34 final size:34
Alignment explanation
Indices: 2842558--2842662 Score: 105
Period size: 34 Copynumber: 3.2 Consensus size: 34
2842548 ATAATATCCT
2842558 TAATTTTGCAATATATAATACCAACAACACGTGA
1 TAATTTTGCAATATATAATACCAACAACACGTGA
* * * *
2842592 TAA-TTT--AATATATATATA-TATATAATATCCT--
1 TAATTTTGCAATATATA-ATACCA-ACAACA-CGTGA
2842623 TAATTTTGCAATATATAATACCAACAACACGTGA
1 TAATTTTGCAATATATAATACCAACAACACGTGA
2842657 TAATTT
1 TAATTT
2842663 AATATATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
31 12 0.22
32 12 0.22
33 12 0.22
34 18 0.33
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (34 bp):
TAATTTTGCAATATATAATACCAACAACACGTGA
Found at i:2842605 original size:31 final size:31
Alignment explanation
Indices: 2842567--2842670 Score: 97
Period size: 31 Copynumber: 3.3 Consensus size: 31
2842557 TTAATTTTGC
2842567 AATATATAATACCAACAACACGTGATAATTT
1 AATATATAATACCAACAACACGTGATAATTT
* * * *
2842598 AATATATATATA-TATATAATATCCT--TAATTTT
1 AATATATA-ATACCA-ACAACA-CGTGATAA-TTT
2842630 GCAATATATAATACCAACAACACGTGATAATTT
1 --AATATATAATACCAACAACACGTGATAATTT
2842663 AATATATA
1 AATATATA
2842671 TATATATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
31 20 0.36
32 12 0.21
33 12 0.21
34 12 0.21
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (31 bp):
AATATATAATACCAACAACACGTGATAATTT
Found at i:2842614 original size:65 final size:65
Alignment explanation
Indices: 2842534--2842685 Score: 295
Period size: 65 Copynumber: 2.3 Consensus size: 65
2842524 CATTTACAAT
2842534 ATATATATATATATATAATATCCTTAATTTTGCAATATATAATACCAACAACACGTGATAATTTA
1 ATATATATATATATATAATATCCTTAATTTTGCAATATATAATACCAACAACACGTGATAATTTA
2842599 ATATATATATATATATAATATCCTTAATTTTGCAATATATAATACCAACAACACGTGATAATTTA
1 ATATATATATATATATAATATCCTTAATTTTGCAATATATAATACCAACAACACGTGATAATTTA
2842664 ATATATATATATATATATATAT
1 ATATATATATATATATA-ATAT
2842686 ATATAATTAT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 82 0.95
66 4 0.05
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (65 bp):
ATATATATATATATATAATATCCTTAATTTTGCAATATATAATACCAACAACACGTGATAATTTA
Found at i:2842671 original size:2 final size:2
Alignment explanation
Indices: 2842664--2842690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2842654 TGATAATTTA
2842664 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 A
2842691 ATTATATGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2842696 original size:10 final size:11
Alignment explanation
Indices: 2842664--2842704 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
2842654 TGATAATTTA
2842664 ATATAT-ATAT
1 ATATATAATAT
2842674 ATATAT-ATAT
1 ATATATAATAT
2842684 ATATATAAT-T
1 ATATATAATAT
*
2842694 ATATGTAATAT
1 ATATATAATAT
2842705 CATTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 25 0.89
11 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
ATATATAATAT
Found at i:2842768 original size:16 final size:15
Alignment explanation
Indices: 2842741--2842772 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
2842731 ATAAAACGTG
2842741 ATAATTTCAATATAT
1 ATAATTTCAATATAT
2842756 ATAATTATCAATATAT
1 ATAATT-TCAATATAT
2842772 A
1 A
2842773 ATTTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATTTCAATATAT
Found at i:2844209 original size:3 final size:3
Alignment explanation
Indices: 2844201--2844238 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2844191 TATTTTGAAC
2844201 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
2844239 TCTTAAGGCA
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:2848423 original size:24 final size:24
Alignment explanation
Indices: 2848391--2848453 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
2848381 GTTTTTATTC
*
2848391 TTTTATCATTAATTATT-TCTTTT
1 TTTTTTCATTAATTATTCTCTTTT
2848414 TATTTTTCATTTAACTT-TTCTCTTTT
1 T-TTTTTCA-TTAA-TTATTCTCTTTT
2848440 TTTTTTCA-TAATTA
1 TTTTTTCATTAATTA
2848454 AATAGAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.06
23 4 0.12
24 6 0.18
25 13 0.38
26 9 0.26
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTTCATTAATTATTCTCTTTT
Done.