Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 73 of 214
Found at i:20903421 original size:14 final size:14
Alignment explanation
Indices: 20903402--20903461 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 14
20903392 AAAAAATAAG
20903402 AAAATTTCGAAAAA
1 AAAATTTCGAAAAA
*
20903416 AAAATTGATTGAAAAA
1 AAAATT--TCGAAAAA
*
20903432 AAAA-TTCAAAAAA
1 AAAATTTCGAAAAA
**
20903445 AAAAAGT-GAAAAA
1 AAAATTTCGAAAAA
20903458 AAAA
1 AAAA
20903462 ATCGAGCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 19 0.50
14 7 0.18
15 1 0.03
16 11 0.29
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (14 bp):
AAAATTTCGAAAAA
Found at i:20903447 original size:13 final size:14
Alignment explanation
Indices: 20903427--20903462 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20903417 AAATTGATTG
20903427 AAAAAAAAATTCAA
1 AAAAAAAAATTCAA
* *
20903441 AAAAAAAAAGTGAA
1 AAAAAAAAATTCAA
20903455 AAAAAAAA
1 AAAAAAAA
20903463 TCGAGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.08
Consensus pattern (14 bp):
AAAAAAAAATTCAA
Found at i:20903472 original size:16 final size:16
Alignment explanation
Indices: 20903453--20903496 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
20903443 AAAAAAAGTG
*
20903453 AAAAAAAAAATCGAGC
1 AAAAAAAAAATCGACC
*
20903469 AAAAAAAAAGGT-GACC
1 AAAAAAAAA-ATCGACC
20903485 AAAAAAAAAATC
1 AAAAAAAAAATC
20903497 AAGTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.07
Consensus pattern (16 bp):
AAAAAAAAAATCGACC
Found at i:20904569 original size:17 final size:18
Alignment explanation
Indices: 20904537--20904570 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20904527 AAAAGAGAGT
*
20904537 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
20904555 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
20904571 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:20905859 original size:20 final size:20
Alignment explanation
Indices: 20905836--20905889 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
20905826 AGTTTTTCCC
*
20905836 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
20905856 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
20905876 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
20905890 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:20905871 original size:30 final size:30
Alignment explanation
Indices: 20905836--20905909 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
20905826 AGTTTTTCCC
20905836 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
20905866 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
20905896 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
20905910 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:20905899 original size:20 final size:20
Alignment explanation
Indices: 20905836--20905900 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
20905826 AGTTTTTCCC
* * * *
20905836 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
20905856 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
20905875 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
20905896 AGCTC
1 AGCTC
20905901 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:20916871 original size:43 final size:43
Alignment explanation
Indices: 20916791--20916873 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
20916781 CAAGTACCTG
* *
20916791 TTCAACATGATCAGCTATTGGCTTGGGAGTGCACATTTGCTAC
1 TTCAACATGATCAACTATTGGCTTGGGACTGCACATTTGCTAC
**
20916834 TTCAACATGATCAACTATTGGCTTGGGACTGTGCATTTGC
1 TTCAACATGATCAACTATTGGCTTGGGACTGCACATTTGC
20916874 AATGTAGATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (43 bp):
TTCAACATGATCAACTATTGGCTTGGGACTGCACATTTGCTAC
Found at i:20918330 original size:23 final size:24
Alignment explanation
Indices: 20918292--20918343 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
20918282 TGTAGCCAAG
20918292 CCACTCATTAGCGTTGTGGACAAA
1 CCACTCATTAGCGTTGTGGACAAA
* *
20918316 CCACTCA-TAGCGTTGTTGACAAG
1 CCACTCATTAGCGTTGTGGACAAA
20918339 CCACT
1 CCACT
20918344 TAATTTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (24 bp):
CCACTCATTAGCGTTGTGGACAAA
Found at i:20919244 original size:85 final size:85
Alignment explanation
Indices: 20919101--20919271 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
20919091 TACTTACGGT
20919101 AGTTCCAAGAATTAAAAGAGTCCTTGATTCCACGGTTGTTCGATTTATGGAGGAGGAACGATGGC
1 AGTTCCAAGAATTAAAAGAGTCCTTGATTCCACGGTTGTTCGATTTATGGAGGAGGAACGATGGC
20919166 TAACAAAATAGTAAAATTAA
66 TAACAAAATAGTAAAATTAA
20919186 AGTTCCAAGAATTAAAAGAGTCCTTGATTCCACGGTTGTTCGATTTATGGAGGAGGAACGATGGC
1 AGTTCCAAGAATTAAAAGAGTCCTTGATTCCACGGTTGTTCGATTTATGGAGGAGGAACGATGGC
20919251 TAACAAAATAGTAAAATTAA
66 TAACAAAATAGTAAAATTAA
20919271 A
1 A
20919272 AAGAATGGAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (85 bp):
AGTTCCAAGAATTAAAAGAGTCCTTGATTCCACGGTTGTTCGATTTATGGAGGAGGAACGATGGC
TAACAAAATAGTAAAATTAA
Found at i:20926795 original size:26 final size:26
Alignment explanation
Indices: 20926738--20926794 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 26
20926728 TAAAATGGTA
* * *
20926738 ATTTTACCCTTAGGGGTATTTCGGTT
1 ATTTTACCCTTAAGGGTATTTCAGTC
20926764 ATTTTACCCTTCAAGGGTATTTCAGTC
1 ATTTTACCCTT-AAGGGTATTTCAGTC
20926791 ATTT
1 ATTT
20926795 AATAACCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.46
Consensus pattern (26 bp):
ATTTTACCCTTAAGGGTATTTCAGTC
Found at i:20934953 original size:23 final size:22
Alignment explanation
Indices: 20934910--20934954 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
20934900 TTCTAAGTCA
20934910 ATATTCAATTCAATTCCACACTC
1 ATATTCAATTCAATT-CACACTC
20934933 ATATTCATTATTCAATT-ACACT
1 ATATTCA--ATTCAATTCACACT
20934955 TAGTCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACTC
Found at i:20935155 original size:51 final size:51
Alignment explanation
Indices: 20935097--20935283 Score: 236
Period size: 51 Copynumber: 3.7 Consensus size: 51
20935087 TTGGTTCACA
* * *
20935097 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACTATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATTCGGTACACG
* * * *
20935148 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACTATTCGGTACACG
* * * *
20935199 TAGTAGCCTTCACACAGTACTACACATGTGACC-TATC-ATTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATAACTA-TTCGGTACACG
20935249 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
20935284 CACTTTCACT
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 41 0.36
51 70 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATTCGGTACACG
Found at i:20935271 original size:101 final size:102
Alignment explanation
Indices: 20935095--20935279 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 102
20935085 GTTTGGTTCA
* *
20935095 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACTATTCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACACAGTACTACACATGTGACCATCACTATTCGATACACGTAGTAGCCTGCA
20935160 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* *
20935197 CATAGTAGCCTTCACACAGTACTACACATGTGACCTATCA-T-TTCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACACAGTACTACACATGTGACC-ATCACTATTCGATACACGTAGTAGCCTGC
20935260 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
20935280 CCATCACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
101 41 0.53
102 34 0.44
103 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACACAGTACTACACATGTGACCATCACTATTCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:20949568 original size:50 final size:50
Alignment explanation
Indices: 20949442--20949683 Score: 220
Period size: 50 Copynumber: 4.7 Consensus size: 50
20949432 GATAATAACA
* * *
20949442 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * * *
20949491 TGCCAATGTCATATCCCAGATATGGTCTTACATAGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * * ** *
20949541 TGCCCATGCCATGTCCCAGACAAGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * ** *
20949591 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC---GG
*
20949647 TGCTAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
20949684 TCTCTTTACC
Statistics
Matches: 157, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
48 4 0.03
49 36 0.23
50 80 0.51
53 2 0.01
56 35 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:20953607 original size:17 final size:17
Alignment explanation
Indices: 20953568--20953626 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
20953558 AAAACAAATA
*
20953568 GAGGCCCAAA-CCTA-T
1 GAGGCCCAAACCCAACT
*
20953583 GTGGCCCAAACCCAACT
1 GAGGCCCAAACCCAACT
* *
20953600 GAGGCCCAAACCAAACA
1 GAGGCCCAAACCCAACT
*
20953617 GAAGCCCAAA
1 GAGGCCCAAA
20953627 GCAGATTCGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
15 9 0.25
16 3 0.08
17 24 0.67
ACGTcount: A:0.39, C:0.36, G:0.19, T:0.07
Consensus pattern (17 bp):
GAGGCCCAAACCCAACT
Found at i:20961899 original size:17 final size:17
Alignment explanation
Indices: 20961877--20961909 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20961867 TTAATAAAAA
*
20961877 CAAATAGAGGCCCAAAC
1 CAAATAGAAGCCCAAAC
20961894 CAAATAGAAGCCCAAA
1 CAAATAGAAGCCCAAA
20961910 GCAGATTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.27, G:0.15, T:0.06
Consensus pattern (17 bp):
CAAATAGAAGCCCAAAC
Found at i:20968058 original size:21 final size:22
Alignment explanation
Indices: 20968009--20968060 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
20967999 TTCAAAAAAT
20968009 ATATATAAATACATAAATCCAAA
1 ATATAT-AATACATAAATCCAAA
* **
20968032 AAATATAATA-ATAAATTTAAA
1 ATATATAATACATAAATCCAAA
20968053 ATATATAA
1 ATATATAA
20968061 AAGTATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 16 0.64
22 4 0.16
23 5 0.20
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (22 bp):
ATATATAATACATAAATCCAAA
Found at i:20971279 original size:38 final size:38
Alignment explanation
Indices: 20971237--20971537 Score: 395
Period size: 38 Copynumber: 7.9 Consensus size: 38
20971227 CACCAGACAA
* *
20971237 AAGCTCATAAGAGCTAATCCAACCGAAACACCAAACAG
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
**
20971275 AAGCTCATAAGAGCTGATCCAACCGAATTGCCAAACAG
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
* *
20971313 AAGCTCATAAGAGCTGATCCAATCGAAACACCAAACAG
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
* * *
20971351 AAGCTCAAAAGAGCTGATCCAACTGAATCGCCAAACAG
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
* * *
20971389 ACGCTCATAAGAGCTGGTCCAACCGAAACACCAAACAG
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
* * ** * *
20971427 AAGCTCATAATAGGTGATTAAACCAAAACGCCAAATAG
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
* * *
20971465 AAGCTCATAAGAGCTGATCGAATCGAAATGCCAAACAG
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
* *
20971503 AAGCTCATAAGAGCTGATACAACTGAAACGCCAAA
1 AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAA
20971538 TAAAAAGTAT
Statistics
Matches: 222, Mismatches: 41, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 222 1.00
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.14
Consensus pattern (38 bp):
AAGCTCATAAGAGCTGATCCAACCGAAACGCCAAACAG
Found at i:20978551 original size:22 final size:21
Alignment explanation
Indices: 20978521--20978571 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
20978511 AAGTCATCAA
*
20978521 TTCCCTTCTTTCTCTTCTCTTT
1 TTCCTTTCTTTCTC-TCTCTTT
* *
20978543 TTCCTTTCTTTTTCTCTTTTT
1 TTCCTTTCTTTCTCTCTCTTT
*
20978564 TTCTTTTC
1 TTCCTTTC
20978572 GAAAGCAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCCTTTCTTTCTCTCTCTTT
Found at i:20978552 original size:11 final size:12
Alignment explanation
Indices: 20978529--20978565 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
20978519 AATTCCCTTC
20978529 TTTCTCTTCTCTT
1 TTTCTCTT-TCTT
20978542 TTTC-CTTTCTT
1 TTTCTCTTTCTT
20978553 TTTCTCTTT-TT
1 TTTCTCTTTCTT
20978564 TT
1 TT
20978566 CTTTTCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 12 0.52
12 7 0.30
13 4 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTCTTTCTT
Found at i:20987313 original size:38 final size:38
Alignment explanation
Indices: 20987273--20987501 Score: 235
Period size: 38 Copynumber: 6.0 Consensus size: 38
20987263 CACAGCAGAT
*
20987273 AGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAAT
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAAC
* * * **
20987311 AGAAGCTCATAAGAGCTAATCTC-ATCGAATCGTCAAAC
1 AGAAGCTCATAAGAGCTGATC-CAACCGAAACACCAAAC
* * *
20987349 AGAAGCTCATAAGAGCTGATCGAACCAAAACACCAAAT
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAAC
* ** * **
20987387 AGAAGCTCATAAGAGTTGATTGAATCGAAATGCCAAAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAAC
* * * * * *
20987425 AAAAGCTCATAAGAGCTGAACGAATCGAAATAACAAAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAAC
* *
20987463 AGAAGCTCATAAGAGTTGATCCAACCGAAACGCCAAAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAAC
20987501 A
1 A
20987502 TAAAGTATAA
Statistics
Matches: 154, Mismatches: 35, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
38 153 0.99
39 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (38 bp):
AGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAAC
Found at i:20987435 original size:114 final size:114
Alignment explanation
Indices: 20987255--20987499 Score: 287
Period size: 114 Copynumber: 2.1 Consensus size: 114
20987245 ATCATCAAAT
* * * *
20987255 CAACCAAACACAGCAGATAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAATAGAAGCTCA
1 CAACCAAA-ACACCAAATAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAACAAAAGCTCA
** **
20987320 TAAGAGCT-AATCTCATCG-AATCGTCAAACAGAAGCTCATAAGAGCTGATC
65 TAAGAGCTGAA-CGAATCGAAAT-AACAAACAGAAGCTCATAAGAGCTGATC
* * ** * **
20987370 GAACCAAAACACCAAATAGAAGCTCATAAGAGTTGATTGAATCGAAATGCCAAACAAAAGCTCAT
1 CAACCAAAACACCAAATAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAACAAAAGCTCAT
*
20987435 AAGAGCTGAACGAATCGAAATAACAAACAGAAGCTCATAAGAGTTGATC
66 AAGAGCTGAACGAATCGAAATAACAAACAGAAGCTCATAAGAGCTGATC
* *
20987484 CAACCGAAACGCCAAA
1 CAACCAAAACACCAAA
20987500 CATAAAGTAT
Statistics
Matches: 109, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
114 97 0.89
115 12 0.11
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (114 bp):
CAACCAAAACACCAAATAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAAACAAAAGCTCAT
AAGAGCTGAACGAATCGAAATAACAAACAGAAGCTCATAAGAGCTGATC
Found at i:20987478 original size:76 final size:75
Alignment explanation
Indices: 20987275--20987506 Score: 277
Period size: 76 Copynumber: 3.0 Consensus size: 75
20987265 CAGCAGATAG
* * * *
20987275 AAGCTCATAAGAGCTGATCCAACCGAAACACCAAATAGAAGCTCATAAGAGCTAATCTCATCG-A
1 AAGCTCATAAGAGCTGATCGAACCGAAACACCAAATAGAAGCTCATAAGAGTTGAT-TAATCGAA
* *
20987339 ATCGTCAAACAG
65 AT-GCCAAACAA
*
20987351 AAGCTCATAAGAGCTGATCGAACCAAAACACCAAATAGAAGCTCATAAGAGTTGATTGAATCGAA
1 AAGCTCATAAGAGCTGATCGAACCGAAACACCAAATAGAAGCTCATAAGAGTTGATT-AATCGAA
20987416 ATGCCAAACAA
65 ATGCCAAACAA
* * * * * * *
20987427 AAGCTCATAAGAGCTGAACGAATCGAAATAACAAACAGAAGCTCATAAGAGTTGATCCAACCGAA
1 AAGCTCATAAGAGCTGATCGAACCGAAACACCAAATAGAAGCTCATAAGAGTTGAT-TAATCGAA
*
20987492 ACGCCAAACATA
65 ATGCCAAACA-A
20987504 AAG
1 AAG
20987507 TATAACACGA
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
75 1 0.01
76 128 0.94
77 7 0.05
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (75 bp):
AAGCTCATAAGAGCTGATCGAACCGAAACACCAAATAGAAGCTCATAAGAGTTGATTAATCGAAA
TGCCAAACAA
Found at i:20995410 original size:23 final size:23
Alignment explanation
Indices: 20995366--20995410 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
20995356 ATAATAAGCT
* *
20995366 TAAAAATAATATTAAACCAATAA
1 TAAAAATAATATAAAAACAATAA
* *
20995389 TAAAAATAATGTAAAAATAATA
1 TAAAAATAATATAAAAACAATA
20995411 TATGAATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAAAATAATATAAAAACAATAA
Found at i:20997014 original size:50 final size:50
Alignment explanation
Indices: 20996859--20997002 Score: 218
Period size: 50 Copynumber: 2.9 Consensus size: 50
20996849 CGCAAGTTTT
* * * * *
20996859 GGGAAGTAAGATTCGTCATTT-TAGCTTCAATATTTTTAACTGCACCGCCA
1 GGGAAGTAAGATTCGAC-TTTGTGGCTTTAATCTTTTTAACTGCACTGCCA
*
20996909 GGGAAGTAAGATTCGCCTTTGTGGCTTTAATCTTTTTAACTGCACTGCCA
1 GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCACTGCCA
20996959 GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCA
1 GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCA
20997003 GTATCGGGGA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 3 0.03
50 84 0.97
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (50 bp):
GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCACTGCCA
Found at i:20997020 original size:50 final size:50
Alignment explanation
Indices: 20996859--20997041 Score: 208
Period size: 50 Copynumber: 3.7 Consensus size: 50
20996849 CGCAAGTTTT
* * * * **
20996859 GGGAAGTAAGATTCGTCATTT-TAGCTTCAATATTTTTAACTGCACCGCCA
1 GGGAAGTAAGATTCGAC-TTTGTGGCTTTAATCTTTTTAACTGCACTACCA
* *
20996909 GGGAAGTAAGATTCGCCTTTGTGGCTTTAATCTTTTTAACTGCACTGCCA
1 GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCACTACCA
* * *
20996959 GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCAGTATCG
1 GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCACTACCA
* **
20997009 GGGAAGCAAGATTC-ACCGATGTGGCTTTAATCT
1 GGGAAGTAAGATTCGA-CTTTGTGGCTTTAATCT
20997042 GCTCCACTGC
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
49 4 0.03
50 114 0.97
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (50 bp):
GGGAAGTAAGATTCGACTTTGTGGCTTTAATCTTTTTAACTGCACTACCA
Found at i:20997032 original size:100 final size:100
Alignment explanation
Indices: 20996859--20997041 Score: 233
Period size: 100 Copynumber: 1.8 Consensus size: 100
20996849 CGCAAGTTTT
* * * *
20996859 GGGAAGTAAGATTCGTCATTTTAGCTTCAATATTTTTAACTGCACCGCCAGGGAAGTAAGATTCG
1 GGGAAGTAAGATTCGACATTTTAGCTTCAATATTTTTAACTGCACCACCAGGGAAGCAAGATTCA
**
20996924 CCTTTGTGGCTTTAATCTTTTTAACTGCACTGCCA
66 CCGATGTGGCTTTAATCTTTTTAACTGCACTGCCA
* * * ** * *
20996959 GGGAAGTAAGATTCGAC-TTTGTGGCTTTAATCTTTTTAACTGCAGTATCGGGGAAGCAAGATTC
1 GGGAAGTAAGATTCGACATTT-TAGCTTCAATATTTTTAACTGCACCACCAGGGAAGCAAGATTC
20997023 ACCGATGTGGCTTTAATCT
65 ACCGATGTGGCTTTAATCT
20997042 GCTCCACTGC
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
99 3 0.04
100 66 0.96
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (100 bp):
GGGAAGTAAGATTCGACATTTTAGCTTCAATATTTTTAACTGCACCACCAGGGAAGCAAGATTCA
CCGATGTGGCTTTAATCTTTTTAACTGCACTGCCA
Found at i:20997197 original size:44 final size:44
Alignment explanation
Indices: 20997165--20997545 Score: 159
Period size: 44 Copynumber: 8.2 Consensus size: 44
20997155 GATCCTTTAT
* *
20997165 TTTAAT-TCGCTCCATTGTAATCTCAAGGAGATAGGATTACTAGC
1 TTTAATCT-GCTCCACTGTAATCTCAAGGAGATAAGATTACTAGC
* * *
20997209 TTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGC
1 TTTAATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGC
* * * *
20997253 TTCAATCTGATGCGATCTACTCTACTGTAA-CTTC-AGAGAGATAAGA-TCCTTTGT
1 TTTAATC---T--G--CT-C-C-ACTGTAATC-TCAAG-GAGATAAGATTAC-TAGC
** * * * *
20997307 TTTAATCCACTCTACTATAATCTCAGGGAGATAGGATTACTAGC
1 TTTAATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGC
* * * *
20997351 TTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGC
1 TTTAATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGC
* * *
20997395 TTCAATCTGATGCGATCTACTCTACTGTAA-CATC-AGAGAGATAAGATCCT-TTA-T
1 TTTAATC---T--G--CT-C-C-ACTGTAATC-TCAAG-GAGATAAGAT--TACTAGC
* * * *
20997449 TTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTAGC
1 TTTAATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGC
* * * *
20997493 TTCAATCTGCT-CAGCTGTAATCTCAGGGAGATAAGATTTCTGGC
1 TTTAATCTGCTCCA-CTGTAATCTCAAGGAGATAAGATTACTAGC
*
20997537 TTCAATCTG
1 TTTAATCTG
20997546 ATGCGATCTA
Statistics
Matches: 254, Mismatches: 47, Indels: 72
0.68 0.13 0.19
Matches are distributed among these distances:
42 1 0.00
43 4 0.02
44 165 0.65
45 7 0.03
46 2 0.01
47 6 0.02
49 3 0.01
51 4 0.02
52 2 0.01
53 8 0.03
54 50 0.20
55 1 0.00
56 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGTAATCTCAAGGAGATAAGATTACTAGC
Found at i:20997373 original size:142 final size:142
Alignment explanation
Indices: 20997117--20997593 Score: 783
Period size: 142 Copynumber: 3.4 Consensus size: 142
20997107 GAGATAAGAC
* * * * *
20997117 CTGATGCGATCTACTCAATTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATTCGCTCCATTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
20997182 TAATCTCAAGGAGATAGGATTACTAGCTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
20997247 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* * * *
20997259 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCACTCTACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
20997324 TAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
20997389 TCTGGCTTCAAT
131 TCTGGCTTCAAT
*
20997401 CTGATGCGATCTACTCTACTGTAACATCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
20997466 TAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCAGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
20997531 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* * * *
20997543 CTGATGCGATCTACTCCATTGTAATTTTAGAGAGATAAGATCCTTTATTTT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTT
20997594 CGATTAGGAA
Statistics
Matches: 311, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 311 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:20997436 original size:98 final size:97
Alignment explanation
Indices: 20997315--20997501 Score: 225
Period size: 98 Copynumber: 1.9 Consensus size: 97
20997305 GTTTTAATCC
* * * * *
20997315 ACTCTACTATAATCTCAGGGAGATAGGAT-TACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGG
1 ACTCTACTATAATCTCAGAGAGATAAGATCT-CTA-CTTTAATCCGCTCCACTGTAATATCAGGG
* *
20997379 AGATAAGATTTCTGGCTTCAATCTGATGCGATCT
64 AGATAAGATTACTAGCTTCAATCTGATGCGATCT
* * *
20997413 ACTCTACTGTAA-CATCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATATCAGGG
1 ACTCTACTATAATC-TCAGAGAGATAAGAT-CTCTACTTTAATCCGCTCCACTGTAATATCAGGG
*
20997477 AGATAGGATTACTAGCTTCAATCTG
64 AGATAAGATTACTAGCTTCAATCTG
20997502 CTCAGCTGTA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
97 1 0.01
98 71 0.95
99 2 0.03
100 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (97 bp):
ACTCTACTATAATCTCAGAGAGATAAGATCTCTACTTTAATCCGCTCCACTGTAATATCAGGGAG
ATAAGATTACTAGCTTCAATCTGATGCGATCT
Found at i:20998894 original size:42 final size:42
Alignment explanation
Indices: 20998842--20998934 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
20998832 CACGCCCCGA
* *
20998842 TCTGATCAAGATACAAGTTGCTCTAAACACATCATGCCCCAT
1 TCTGATCAAGATACAAGCTACTCTAAACACATCATGCCCCAT
* *
20998884 TCTGATCAAGATACAAGCTACTCTAAACACTTCATGCCCTAT
1 TCTGATCAAGATACAAGCTACTCTAAACACATCATGCCCCAT
20998926 TCTGATCAA
1 TCTGATCAA
20998935 TATTTGAGCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (42 bp):
TCTGATCAAGATACAAGCTACTCTAAACACATCATGCCCCAT
Found at i:21004557 original size:79 final size:78
Alignment explanation
Indices: 21004455--21004677 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
21004445 GCTCCTCGTT
* *
21004455 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
21004520 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
21004535 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
21004598 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * * *
21004613 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCA-AGA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
21004676 GA
63 GA
21004678 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 47 0.38
79 57 0.46
80 19 0.15
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:21004572 original size:39 final size:40
Alignment explanation
Indices: 21004455--21004677 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
21004445 GCTCCTCGTT
* *
21004455 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
21004495 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
21004535 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
21004574 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
21004613 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
*
21004654 -AGA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
21004678 CATCATTCAA
Statistics
Matches: 165, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 89 0.54
40 64 0.39
41 10 0.06
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:21017476 original size:13 final size:12
Alignment explanation
Indices: 21017433--21017505 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 12
21017423 TAGCTTCGAA
21017433 AAAAAAAAAGTT-
1 AAAAAAAAA-TTG
*
21017445 AAAAAAAAGTTTCG
1 AAAAAAAA-ATT-G
21017459 AAAAAAAAAATCTG
1 -AAAAAAAAAT-TG
*
21017473 AAAAAAAAA-GG
1 AAAAAAAAATTG
21017484 AAAAAAAAATTG
1 AAAAAAAAATTG
21017496 CAAAAAAAAA
1 -AAAAAAAAA
21017506 AATTGCATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 10 0.20
12 11 0.22
13 18 0.36
14 2 0.04
15 9 0.18
ACGTcount: A:0.74, C:0.04, G:0.10, T:0.12
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:21017476 original size:28 final size:28
Alignment explanation
Indices: 21017427--21017480 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
21017417 AAATCATAGC
* *
21017427 TTCGAAAAAAAAAAAGTTAAAAAAAAGT
1 TTCGAAAAAAAAAAACTGAAAAAAAAGT
*
21017455 TTCGAAAAAAAAAATCTGAAAAAAAA
1 TTCGAAAAAAAAAAACTGAAAAAAAA
21017481 AGGAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (28 bp):
TTCGAAAAAAAAAAACTGAAAAAAAAGT
Found at i:21017487 original size:24 final size:24
Alignment explanation
Indices: 21017460--21017505 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
21017450 AAAGTTTCGA
21017460 AAAAAAAAATCTG-AAAAAAAAAGG
1 AAAAAAAAAT-TGCAAAAAAAAAGG
21017484 AAAAAAAAATTGCAAAAAAAAA
1 AAAAAAAAATTGCAAAAAAAAA
21017506 AATTGCATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (24 bp):
AAAAAAAAATTGCAAAAAAAAAGG
Found at i:21017488 original size:39 final size:40
Alignment explanation
Indices: 21017433--21017508 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
21017423 TAGCTTCGAA
* * * *
21017433 AAAAAAAAAGTTAAAAAAAAGTTTCGAAAAAAAAAATCTG
1 AAAAAAAAAGTGAAAAAAAAATTGCAAAAAAAAAAATCTG
21017473 AAAAAAAAAG-GAAAAAAAAATTGCAAAAAAAAAAAT
1 AAAAAAAAAGTGAAAAAAAAATTGCAAAAAAAAAAAT
21017509 TGCATACGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 22 0.69
40 10 0.31
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (40 bp):
AAAAAAAAAGTGAAAAAAAAATTGCAAAAAAAAAAATCTG
Found at i:21017502 original size:15 final size:15
Alignment explanation
Indices: 21017484--21017512 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21017474 AAAAAAAAGG
21017484 AAAAAAAAATTGCAA
1 AAAAAAAAATTGCAA
21017499 AAAAAAAAATTGCA
1 AAAAAAAAATTGCA
21017513 TACGGTCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAAAATTGCAA
Found at i:21020779 original size:20 final size:20
Alignment explanation
Indices: 21020756--21020809 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21020746 AGCTAAAGTA
21020756 AGCTAAATTTAGCTCACATG
1 AGCTAAATTTAGCTCACATG
* ***
21020776 AGCTTAATTTAGCTCGTTTG
1 AGCTAAATTTAGCTCACATG
*
21020796 AGCTCAATTTAGCT
1 AGCTAAATTTAGCT
21020810 GGGAAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (20 bp):
AGCTAAATTTAGCTCACATG
Found at i:21021360 original size:24 final size:23
Alignment explanation
Indices: 21021333--21021386 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
21021323 GATGAGTGAT
21021333 AAAAAAAAGAGAGTGATTCAAAA-G
1 AAAAAAAA-AGAGTGA-TCAAAATG
* *
21021357 AAAAAGAAACGAGTGATGAAAATG
1 AAAAA-AAAAGAGTGATCAAAATG
21021381 AAAAAA
1 AAAAAA
21021387 GAATTTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.23
24 17 0.65
25 3 0.12
ACGTcount: A:0.65, C:0.04, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAAAAAAAGAGTGATCAAAATG
Found at i:21021362 original size:21 final size:19
Alignment explanation
Indices: 21021313--21021363 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 19
21021303 GAAAAGAAGA
21021313 AAAACAAAAAGATGAGTGAT
1 AAAA-AAAAAGATGAGTGAT
21021333 -AAAAAAAAGA-GAGTGATT
1 AAAAAAAAAGATGAGTGA-T
21021351 CAAAAGAAAAAGA
1 -AAAA-AAAAAGA
21021364 AACGAGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 3 0.11
20 3 0.11
21 7 0.26
ACGTcount: A:0.65, C:0.04, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAAAAAAAGATGAGTGAT
Found at i:21025644 original size:20 final size:20
Alignment explanation
Indices: 21025621--21025674 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21025611 AGTTTTTCCC
*
21025621 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21025641 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21025661 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21025675 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21025656 original size:30 final size:30
Alignment explanation
Indices: 21025621--21025694 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21025611 AGTTTTTCCC
21025621 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21025651 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21025681 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21025695 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21025684 original size:20 final size:20
Alignment explanation
Indices: 21025621--21025685 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21025611 AGTTTTTCCC
* * * *
21025621 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21025641 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21025660 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21025681 AGCTC
1 AGCTC
21025686 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21027279 original size:12 final size:12
Alignment explanation
Indices: 21027262--21027332 Score: 61
Period size: 12 Copynumber: 5.6 Consensus size: 12
21027252 TTGGAGTAAC
21027262 AAAAAAAATCAA
1 AAAAAAAATCAA
*
21027274 AAAAAAATTCGAA
1 AAAAAAAATC-AA
*
21027287 AAAAAAATTGATTAA
1 AAAAAAA---ATCAA
*
21027302 AAAAAAATTCAA
1 AAAAAAAATCAA
* *
21027314 AAAAAAAGTGAA
1 AAAAAAAATCAA
21027326 AAAAAAA
1 AAAAAAA
21027333 TCGAGCAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
12 29 0.60
13 9 0.19
15 9 0.19
16 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:21027280 original size:13 final size:13
Alignment explanation
Indices: 21027262--21027320 Score: 68
Period size: 13 Copynumber: 4.5 Consensus size: 13
21027252 TTGGAGTAAC
21027262 AAAAAAAA-TC-A
1 AAAAAAAATTCAA
*
21027273 AAAAAAAATTCGA
1 AAAAAAAATTCAA
*
21027286 AAAAAAAATTGATTA
1 AAAAAAAATTCA--A
21027301 AAAAAAAATTCAA
1 AAAAAAAATTCAA
21027314 AAAAAAA
1 AAAAAAA
21027321 GTGAAAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 8 0.20
12 2 0.05
13 19 0.46
15 12 0.29
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:21027303 original size:27 final size:26
Alignment explanation
Indices: 21027272--21027332 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
21027262 AAAAAAAATC
*
21027272 AAAAAAAAATTCGAAAAAAAAATTGA
1 AAAAAAAAATTCGAAAAAAAAAGTGA
21027298 TTAAAAAAAAATTC-AAAAAAAAAGTGA
1 --AAAAAAAAATTCGAAAAAAAAAGTGA
21027325 AAAAAAAA
1 AAAAAAAA
21027333 TCGAGCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 8 0.25
27 12 0.38
28 12 0.38
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (26 bp):
AAAAAAAAATTCGAAAAAAAAAGTGA
Found at i:21027316 original size:39 final size:38
Alignment explanation
Indices: 21027262--21027347 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 38
21027252 TTGGAGTAAC
* * **
21027262 AAAAAAAATCAAAAAAAAATTCGAAAAAAAAATTGATTA
1 AAAAAAAATCAAAAAAAAAGT-GAAAAAAAAATCGAGCA
21027301 AAAAAAAATTCAAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAA-TCAAAAAAAAAGTGAAAAAAAAATCGAGCA
21027340 AAAAAAAA
1 AAAAAAAA
21027348 AAGGTGACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 30 0.71
40 12 0.29
ACGTcount: A:0.74, C:0.06, G:0.07, T:0.13
Consensus pattern (38 bp):
AAAAAAAATCAAAAAAAAAGTGAAAAAAAAATCGAGCA
Found at i:21027328 original size:13 final size:13
Alignment explanation
Indices: 21027272--21027332 Score: 63
Period size: 13 Copynumber: 4.6 Consensus size: 13
21027262 AAAAAAAATC
21027272 AAAAAAAAATTCG-
1 AAAAAAAAATT-GA
21027285 AAAAAAAAATTGA
1 AAAAAAAAATTGA
*
21027298 TTAAAAAAAAATT-C
1 --AAAAAAAAATTGA
*
21027312 AAAAAAAAAGTGA
1 AAAAAAAAATTGA
21027325 AAAAAAAA
1 AAAAAAAA
21027333 TCGAGCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 11 0.27
13 19 0.46
15 11 0.27
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:21027375 original size:31 final size:29
Alignment explanation
Indices: 21027312--21027385 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
21027302 AAAAAAATTC
*
21027312 AAAAAAAAAGTGAAAAAAAAATCGAGCAA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCAA
* *
21027341 AAAAAAAAAGGTGACCAAAAAAATCAAG--T
1 AAAAAAAAA-GTGA-AAAAAAAATCAAGCAA
*
21027370 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
21027386 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.05
28 4 0.11
29 17 0.45
30 4 0.11
31 11 0.29
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (29 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCAA
Found at i:21028289 original size:17 final size:16
Alignment explanation
Indices: 21028269--21028306 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
21028259 GTGAGCGAGA
21028269 AAATGAAAAAGAAAAAG
1 AAATG-AAAAGAAAAAG
21028286 AAATG-AAAGAAAAAG
1 AAATGAAAAGAAAAAG
*
21028301 AGATGA
1 AAATGA
21028307 GTGTGAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 14 0.74
17 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (16 bp):
AAATGAAAAGAAAAAG
Found at i:21028296 original size:15 final size:15
Alignment explanation
Indices: 21028276--21028306 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21028266 AGAAAATGAA
21028276 AAAGAAAAAGAAATG
1 AAAGAAAAAGAAATG
*
21028291 AAAGAAAAAGAGATG
1 AAAGAAAAAGAAATG
21028306 A
1 A
21028307 GTGTGAGATA
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:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (15 bp):
AAAGAAAAAGAAATG
Found at i:21028420 original size:17 final size:18
Alignment explanation
Indices: 21028388--21028421 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21028378 AAAAGAGAGT
*
21028388 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
21028406 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
21028422 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:21029706 original size:20 final size:20
Alignment explanation
Indices: 21029683--21029736 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21029673 TAGTTTTCCC
*
21029683 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21029703 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21029723 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21029737 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21029717 original size:30 final size:30
Alignment explanation
Indices: 21029683--21029756 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21029673 TAGTTTTCCC
21029683 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21029713 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21029743 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21029757 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21029746 original size:20 final size:20
Alignment explanation
Indices: 21029683--21029747 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21029673 TAGTTTTCCC
* * * *
21029683 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21029703 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21029722 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21029743 AGCTC
1 AGCTC
21029748 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21031363 original size:14 final size:14
Alignment explanation
Indices: 21031344--21031404 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 14
21031334 AAAAAAAAAT
21031344 AAAAAATTTCGAAA
1 AAAAAATTTCGAAA
*
21031358 AAAAAATTGATTGAAA
1 AAAAAATT--TCGAAA
21031374 AAAAAA-TTC-AAA
1 AAAAAATTTCGAAA
*
21031386 AAAAAA-GT-GAAA
1 AAAAAATTTCGAAA
21031398 AAAAAAT
1 AAAAAAT
21031405 CGAGCAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 19 0.47
13 1 0.03
14 8 0.20
15 1 0.03
16 11 0.28
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.18
Consensus pattern (14 bp):
AAAAAATTTCGAAA
Found at i:21032511 original size:17 final size:18
Alignment explanation
Indices: 21032479--21032512 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21032469 AAAAGAGAGT
*
21032479 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
21032497 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
21032513 GGAGTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:21033796 original size:20 final size:20
Alignment explanation
Indices: 21033773--21033826 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21033763 AGTTTTTCCC
*
21033773 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21033793 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21033813 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21033827 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21033808 original size:30 final size:30
Alignment explanation
Indices: 21033773--21033846 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
21033763 AGTTTTTCCC
21033773 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
21033803 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
21033833 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
21033847 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:21033836 original size:20 final size:20
Alignment explanation
Indices: 21033773--21033837 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
21033763 AGTTTTTCCC
* * * *
21033773 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
21033793 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
21033812 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
21033833 AGCTC
1 AGCTC
21033838 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:21038562 original size:72 final size:73
Alignment explanation
Indices: 21038449--21038596 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 73
21038439 TTTAATGCTA
* * *
21038449 TCCCAAGTCCCATGCACACACTAAATTCGACTGGTTGGG-AAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTT-GCTT
21038512 TAAATGCCG
65 TAAATGCCG
* * * * * * *
21038521 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
21038586 AAATGCCG
66 AAATGCCG
21038594 TCC
1 TCC
21038597 ATGTACCTGC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 33 0.52
73 25 0.39
74 6 0.09
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:21038804 original size:16 final size:16
Alignment explanation
Indices: 21038783--21038814 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21038773 CATTCTGCAT
21038783 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
21038799 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
21038815 AAACACATTA
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):
TTAAACAACAGCAGCA
Found at i:21039477 original size:17 final size:17
Alignment explanation
Indices: 21039457--21039500 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
21039447 GAGAGACGAG
21039457 AGAAAAAGAAACTGAAA
1 AGAAAAAGAAACTGAAA
*
21039474 AGAAACAA-AAATTGAAA
1 AGAAA-AAGAAACTGAAA
21039491 AGATAAAAGA
1 AGA-AAAAGA
21039501 TTGGAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (17 bp):
AGAAAAAGAAACTGAAA
Found at i:21040498 original size:30 final size:30
Alignment explanation
Indices: 21040464--21040560 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
21040454 AGCTCACTCC
21040464 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
21040494 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
21040524 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
21040554 TAGCTCA
1 TAGCTCA
21040561 TTTTACTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:21045598 original size:19 final size:20
Alignment explanation
Indices: 21045562--21045610 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
21045552 TTTTTTCTTC
*
21045562 TTTTTTTTCGAATTTTTCAAA
1 TTTTTTTTGGAA-TTTTCAAA
* *
21045583 TTTTTTTTGGAA-TTTCGAT
1 TTTTTTTTGGAATTTTCAAA
21045602 TTTTTTTTG
1 TTTTTTTTG
21045611 TGATACTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 14 0.56
21 11 0.44
ACGTcount: A:0.16, C:0.06, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTTTTTTGGAATTTTCAAA
Found at i:21047665 original size:21 final size:23
Alignment explanation
Indices: 21047620--21047666 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21047610 TCACCTGCAA
* *
21047620 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
21047643 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
21047664 TAA
1 TAA
21047667 TCCTAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:21057322 original size:18 final size:18
Alignment explanation
Indices: 21057301--21057335 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21057291 TTTTTCTTTT
21057301 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
21057319 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
21057336 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:21058270 original size:17 final size:17
Alignment explanation
Indices: 21058230--21058274 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
21058220 TTTTTAACTT
*
21058230 GATTTTTTTTTTTGGTC
1 GATTTTTTTTTTTGCTC
*
21058247 -ACCTTTTTTTTTTGCTC
1 GA-TTTTTTTTTTTGCTC
21058264 GATTTTTTTTT
1 GATTTTTTTTT
21058275 CACTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 1 0.04
17 21 0.91
18 1 0.04
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.71
Consensus pattern (17 bp):
GATTTTTTTTTTTGCTC
Found at i:21058297 original size:28 final size:27
Alignment explanation
Indices: 21058210--21058299 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 27
21058200 CTCGCAAGAC
21058210 TTTTCACTTTTTTTTAACTTGATTTTTTTT
1 TTTTCACTTTTTTTT---TTGATTTTTTTT
* **
21058240 TTTGGTCACCTTTTTTTTTTGCTCGATTTTT
1 TTT--TCA-CTTTTTTTTTTGAT-TTTTTTT
*
21058271 TTTTCACTTTTTTTTTTGAATTTTTTT
1 TTTTCACTTTTTTTTTTGATTTTTTTT
21058298 TT
1 TT
21058300 CAATCAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
27 7 0.14
28 12 0.24
29 3 0.06
30 7 0.14
31 8 0.16
32 3 0.06
33 9 0.18
ACGTcount: A:0.10, C:0.11, G:0.07, T:0.72
Consensus pattern (27 bp):
TTTTCACTTTTTTTTTTGATTTTTTTT
Found at i:21061528 original size:18 final size:18
Alignment explanation
Indices: 21061507--21061541 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21061497 TTTTTCTTTT
21061507 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
21061525 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
21061542 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:21062473 original size:16 final size:16
Alignment explanation
Indices: 21062435--21062478 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
21062425 TTTTTAACTT
*
21062435 GATTTTTTTTTTGGTC
1 GATTTTTTTTTTGCTC
21062451 -ACCTTTTTTTTTTGCTC
1 GA--TTTTTTTTTTGCTC
21062468 GATTTTTTTTT
1 GATTTTTTTTT
21062479 CACTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.38
17 13 0.54
18 1 0.04
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.70
Consensus pattern (16 bp):
GATTTTTTTTTTGCTC
Found at i:21062498 original size:11 final size:12
Alignment explanation
Indices: 21062469--21062539 Score: 63
Period size: 12 Copynumber: 5.7 Consensus size: 12
21062459 TTTTTGCTCG
*
21062469 ATTTTTTTTTCA
1 ATTTTTTTTTGA
*
21062481 CTTTTTTTTTTGA
1 -ATTTTTTTTTGA
*
21062494 ATTTTTTTTTCA
1 ATTTTTTTTTGA
*
21062506 ATCAATTTTTTTCGA
1 AT---TTTTTTTTGA
21062521 ATTTTTTTTTG-
1 ATTTTTTTTTGA
21062532 ATTTTTTT
1 ATTTTTTT
21062540 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
11 8 0.17
12 20 0.42
13 10 0.21
15 10 0.21
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.73
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:21065729 original size:18 final size:18
Alignment explanation
Indices: 21065708--21065742 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21065698 TTTTTCTTTT
21065708 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
21065726 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
21065743 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:21066670 original size:29 final size:29
Alignment explanation
Indices: 21066616--21066689 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
21066606 GCAAGACTTT
* *
21066616 TCACTTTTTTTTTTAACTTGATTTTTTTGG
1 TCACTTTTTTTTTT-GCTCGATTTTTTTGG
*
21066646 TCACCTTTTTTTTTTGCTCGATTTTTTT-T
1 TCA-CTTTTTTTTTTGCTCGATTTTTTTGG
21066675 TCACTTTTTTTTTTG
1 TCACTTTTTTTTTTG
21066690 AATTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 12 0.30
29 3 0.08
30 14 0.35
31 11 0.28
ACGTcount: A:0.09, C:0.14, G:0.08, T:0.69
Consensus pattern (29 bp):
TCACTTTTTTTTTTGCTCGATTTTTTTGG
Found at i:21066698 original size:28 final size:28
Alignment explanation
Indices: 21066613--21066728 Score: 76
Period size: 28 Copynumber: 4.0 Consensus size: 28
21066603 CTCGCAAGAC
21066613 TTTTCACTTTTTTTTTT-AACTTGATTTTTT
1 TTTTCACTTTTTTTTTTGAA-TT--TTTTTT
** * **
21066643 TGGTCACCTTTTTTTTTTG-CTCGATTTTT
1 TTTTCA-CTTTTTTTTTTGAAT-TTTTTTT
21066672 TTTTCACTTTTTTTTTTGAATTTTTTTT
1 TTTTCACTTTTTTTTTTGAATTTTTTTT
** * *
21066700 TCAATCA-ATTTTTTTTCGAATTTTTTTT
1 T-TTTCACTTTTTTTTTTGAATTTTTTTT
21066728 T
1 T
21066729 GATTTTTTTG
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
28 38 0.57
29 13 0.19
30 5 0.07
31 11 0.16
ACGTcount: A:0.13, C:0.11, G:0.06, T:0.70
Consensus pattern (28 bp):
TTTTCACTTTTTTTTTTGAATTTTTTTT
Found at i:21071369 original size:11 final size:12
Alignment explanation
Indices: 21071342--21071399 Score: 80
Period size: 12 Copynumber: 4.7 Consensus size: 12
21071332 CCGCATGCAA
21071342 TTTTTTTTCAAAT
1 TTTTTTTTC-AAT
21071355 TTTTTTTTCAAT
1 TTTTTTTTCAAT
*
21071367 TTTTTTTTCATTT
1 TTTTTTTTCA-AT
*
21071380 TTTTTTTTCGAT
1 TTTTTTTTCAAT
21071392 TTTTTTTT
1 TTTTTTTT
21071400 GAATCTACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
12 22 0.54
13 19 0.46
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:21071376 original size:25 final size:25
Alignment explanation
Indices: 21071342--21071399 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
21071332 CCGCATGCAA
21071342 TTTTTTTTCAAATTTTTTTTTCAAT
1 TTTTTTTTCAAATTTTTTTTTCAAT
** *
21071367 TTTTTTTTCATTTTTTTTTTTCGAT
1 TTTTTTTTCAAATTTTTTTTTCAAT
21071392 TTTTTTTT
1 TTTTTTTT
21071400 GAATCTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTTTTCAAATTTTTTTTTCAAT
Found at i:21075277 original size:15 final size:15
Alignment explanation
Indices: 21075257--21075310 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 15
21075247 TAGCTTCTTC
21075257 TTTTTTTCACGAAAA
1 TTTTTTTCACGAAAA
**
21075272 TTTTTTTTTCACGAATT
1 --TTTTTTTCACGAAAA
21075289 TTTTTTTCACG--AA
1 TTTTTTTCACGAAAA
21075302 TTTTTTTCA
1 TTTTTTTCA
21075311 ACTTGATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.27
15 11 0.33
17 13 0.39
ACGTcount: A:0.22, C:0.13, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTTTTTCACGAAAA
Found at i:21075307 original size:17 final size:15
Alignment explanation
Indices: 21075257--21075308 Score: 86
Period size: 15 Copynumber: 3.3 Consensus size: 15
21075247 TAGCTTCTTC
21075257 TTTTTTTCACGAAAATT
1 TTTTTTTCACG--AATT
21075274 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
21075289 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
21075304 TTTTT
1 TTTTT
21075309 CAACTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 24 0.69
17 11 0.31
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:21075365 original size:12 final size:12
Alignment explanation
Indices: 21075348--21075396 Score: 82
Period size: 12 Copynumber: 4.2 Consensus size: 12
21075338 ATGGAAACCA
21075348 AATTTTTTTTTG
1 AATTTTTTTTTG
21075360 AA-TTTTTTTTG
1 AATTTTTTTTTG
21075371 AATTTTTTTTTG
1 AATTTTTTTTTG
*
21075383 AAATTTTTTTTG
1 AATTTTTTTTTG
21075395 AA
1 AA
21075397 GAAACTACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
11 11 0.31
12 24 0.69
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:21076430 original size:21 final size:23
Alignment explanation
Indices: 21076385--21076431 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21076375 TCACCTGCAA
* *
21076385 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
21076408 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
21076429 TAA
1 TAA
21076432 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:21077348 original size:10 final size:10
Alignment explanation
Indices: 21077333--21077381 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
21077323 TTGGGTTAAG
21077333 ATTGAGCTGA
1 ATTGAGCTGA
21077343 ATTGAGCTCGA
1 ATTGAGCT-GA
21077354 A-TGAGCTGA
1 ATTGAGCTGA
* *
21077363 CTTGAGCTCA
1 ATTGAGCTGA
*
21077373 AGTGAGCTG
1 ATTGAGCTG
21077382 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:21077360 original size:20 final size:20
Alignment explanation
Indices: 21077335--21077381 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
21077325 GGGTTAAGAT
21077335 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
21077355 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
21077375 TGAGCTG
1 TGAGCTG
21077382 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:21077732 original size:18 final size:17
Alignment explanation
Indices: 21077709--21077747 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21077699 CTCTTTTTGC
21077709 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
21077727 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
21077745 TCT
1 TCT
21077748 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:21086556 original size:10 final size:10
Alignment explanation
Indices: 21086543--21086604 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 10
21086533 AAAAAATTCG
21086543 AAAAAAAAGA
1 AAAAAAAAGA
21086553 AAAAAAAAGA
1 AAAAAAAAGA
21086563 AGTGAGCAAAAAAG-
1 A---A--AAAAAAGA
21086577 AAAAAAAAGTA
1 AAAAAAAAG-A
21086588 AAAAAAGAAGA
1 AAAAAA-AAGA
21086599 AAAAAA
1 AAAAAA
21086605 GTGAAAAGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
9 7 0.16
10 11 0.25
11 14 0.32
12 3 0.07
13 1 0.02
14 1 0.02
15 7 0.16
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:21086586 original size:21 final size:20
Alignment explanation
Indices: 21086530--21086611 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
21086520 ATCAAAATTC
*
21086530 AAAAAAAAATTCGAAAAAAAAG
1 AAAAAAAAAGT-G-AAAAAAAG
21086552 AAAAAAAAAGAAGTGAGCAAAAAAG
1 --AAAAAAA-AAGTGA--AAAAAAG
21086577 -AAAAAAAAGT-AAAAAAAG
1 AAAAAAAAAGTGAAAAAAAG
21086595 AAGAAAAAAAGTGAAAA
1 AA-AAAAAAAGTGAAAA
21086612 GTCTTGCGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
18 7 0.14
19 1 0.02
20 10 0.20
21 8 0.16
22 6 0.12
23 1 0.02
24 8 0.16
25 10 0.20
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (20 bp):
AAAAAAAAAGTGAAAAAAAG
Found at i:21087361 original size:20 final size:20
Alignment explanation
Indices: 21087338--21087391 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
21087328 AGTTTTTCCT
*
21087338 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
21087358 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
21087378 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
21087392 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:21087371 original size:30 final size:30
Alignment explanation
Indices: 21087337--21087411 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
21087327 TAGTTTTTCC
21087337 TAGCTCGATTT-AGCTCACA-TGAGCTTAATT
1 TAGCTCG-TTTGAGCTCA-ATTGAGCTTAATT
* *
21087367 TAGCTCGTTTGAGCTCAATTTAGCTTACTT
1 TAGCTCGTTTGAGCTCAATTGAGCTTAATT
21087397 TAGCTCGTTTGAGCT
1 TAGCTCGTTTGAGCT
21087412 TGGCTTAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 37 0.90
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (30 bp):
TAGCTCGTTTGAGCTCAATTGAGCTTAATT
Found at i:21087401 original size:20 final size:20
Alignment explanation
Indices: 21087337--21087402 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
21087327 TAGTTTTTCC
* * *
21087337 TAGCTCGATTTAGCTCACAT
1 TAGCTCAATTTAGCTTACTT
* *
21087357 GAGCTTAATTTAGC-T-CGTT
1 TAGCTCAATTTAGCTTAC-TT
21087376 TGAGCTCAATTTAGCTTACTT
1 T-AGCTCAATTTAGCTTACTT
21087397 TAGCTC
1 TAGCTC
21087403 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (20 bp):
TAGCTCAATTTAGCTTACTT
Found at i:21093271 original size:56 final size:56
Alignment explanation
Indices: 21093166--21093272 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
21093156 ATTAATGTCG
* * * * *
21093166 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
21093222 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
21093273 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:21093922 original size:20 final size:20
Alignment explanation
Indices: 21093897--21093951 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
21093887 ACAAGTTAAA
* *
21093897 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
21093917 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
21093937 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
21093952 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:21094182 original size:14 final size:15
Alignment explanation
Indices: 21094163--21094201 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
21094153 AACTAGCTCT
*
21094163 TTTTTTTTCAC-GAA
1 TTTTTTTTCACAAAA
21094177 TTTTTTTTCACAAAA
1 TTTTTTTTCACAAAA
21094192 TTTTTTTTCA
1 TTTTTTTTCA
21094202 ACTTGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTTTTTCACAAAA
Found at i:21094256 original size:13 final size:13
Alignment explanation
Indices: 21094238--21094284 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
21094228 AAAGGAAACC
21094238 AATTTTTTTTTTG
1 AATTTTTTTTTTG
21094251 AA--TTTTTTTTG
1 AATTTTTTTTTTG
*
21094262 AATTTTTTTTTCG
1 AATTTTTTTTTTG
21094275 AATTTTTTTT
1 AATTTTTTTT
21094285 GAAGAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 11 0.35
13 20 0.65
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:21094258 original size:11 final size:11
Alignment explanation
Indices: 21094242--21094287 Score: 74
Period size: 12 Copynumber: 4.0 Consensus size: 11
21094232 GAAACCAATT
21094242 TTTTTTTTGAA
1 TTTTTTTTGAA
21094253 TTTTTTTTGAA
1 TTTTTTTTGAA
21094264 TTTTTTTTTCGAA
1 -TTTTTTTT-GAA
21094277 TTTTTTTTGAA
1 TTTTTTTTGAA
21094288 GAAACTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 14 0.42
12 16 0.48
13 3 0.09
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:21094270 original size:24 final size:24
Alignment explanation
Indices: 21094238--21094287 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
21094228 AAAGGAAACC
*
21094238 AATTTTTTTTTTGAATTTTTTTTG
1 AATTTTTTTTTCGAATTTTTTTTG
21094262 AATTTTTTTTTCGAATTTTTTTTG
1 AATTTTTTTTTCGAATTTTTTTTG
21094286 AA
1 AA
21094288 GAAACTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.70
Consensus pattern (24 bp):
AATTTTTTTTTCGAATTTTTTTTG
Found at i:21096299 original size:11 final size:11
Alignment explanation
Indices: 21096279--21096325 Score: 67
Period size: 11 Copynumber: 4.0 Consensus size: 11
21096269 TAGTAGTTTC
21096279 TTCAAAAAAAA
1 TTCAAAAAAAA
21096290 TTTCAAAAAAAA
1 -TTCAAAAAAAA
21096302 TTCAAAAAAAAAA
1 TTC--AAAAAAAA
21096315 TTCAAAAAAAA
1 TTCAAAAAAAA
21096326 AAATTTGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.33
12 11 0.33
13 11 0.33
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:21096326 original size:12 final size:12
Alignment explanation
Indices: 21096279--21096326 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
21096269 TAGTAGTTTC
*
21096279 TTCAAAAAAAAT
1 TTCAAAAAAAAA
21096291 TTC-AAAAAAAA
1 TTCAAAAAAAAA
21096302 TTCAAAAAAAAAA
1 TTC-AAAAAAAAA
21096315 TTCAAAAAAAAA
1 TTCAAAAAAAAA
21096327 AATTTGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
11 10 0.30
12 12 0.36
13 11 0.33
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:21096330 original size:14 final size:13
Alignment explanation
Indices: 21096282--21096327 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
21096272 TAGTTTCTTC
*
21096282 AAAAAAAATTTC-
1 AAAAAAAAATTCA
21096294 -AAAAAAAATTCA
1 AAAAAAAAATTCA
21096306 AAAAAAAAATTCA
1 AAAAAAAAATTCA
21096319 AAAAAAAAA
1 AAAAAAAAA
21096328 ATTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 10 0.32
13 21 0.68
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:21096388 original size:15 final size:16
Alignment explanation
Indices: 21096368--21096410 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
21096358 GATATCAAGT
21096368 TGAAAAAAAAA-TTCG
1 TGAAAAAAAAATTTCG
21096383 TGAAAAAAAAATTTTCG
1 TGAAAAAAAAA-TTTCG
21096400 TGAAAAAAAAA
1 TGAAAAAAAAA
21096411 AGAAGAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.21
Consensus pattern (16 bp):
TGAAAAAAAAATTTCG
Found at i:21099367 original size:22 final size:22
Alignment explanation
Indices: 21099339--21099382 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21099329 TTTTGAACCA
21099339 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
21099361 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
21099383 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:21100176 original size:12 final size:12
Alignment explanation
Indices: 21100159--21100196 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
21100149 AGGAAATTTG
21100159 AAAAAAATTCAAA
1 AAAAAAATTC-AA
21100172 AAAAAAATTCAA
1 AAAAAAATTCAA
*
21100184 AAAAAAAATCAA
1 AAAAAAATTCAA
21100196 A
1 A
21100197 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:21100177 original size:13 final size:13
Alignment explanation
Indices: 21100159--21100196 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
21100149 AGGAAATTTG
21100159 AAAAAAATTCAAA
1 AAAAAAATTCAAA
21100172 AAAAAAATTCAAA
1 AAAAAAATTCAAA
21100185 AAAAAAA-TCAAA
1 AAAAAAATTCAAA
21100197 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:21108494 original size:15 final size:15
Alignment explanation
Indices: 21108474--21108528 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
21108464 ACTCTCCTCA
*
21108474 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
21108489 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
21108504 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
21108518 TTCTTTT-TCTC
1 TTCTTTTCTCTC
21108529 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:21110694 original size:13 final size:13
Alignment explanation
Indices: 21110676--21110707 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
21110666 AAGACGACGA
21110676 TTCTTTATGAGCT
1 TTCTTTATGAGCT
21110689 TTCTTTATGAGCT
1 TTCTTTATGAGCT
21110702 TTCTTT
1 TTCTTT
21110708 GCCATTAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (13 bp):
TTCTTTATGAGCT
Found at i:21113417 original size:24 final size:20
Alignment explanation
Indices: 21113389--21113442 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 20
21113379 GAAGTTGAAG
21113389 GAAAAGATTGAAAAAGAGAGACAA
1 GAAAA-ATTGAAAAA-A-AGA-AA
21113413 GAAAAA-TGAAAAAAAGAAA
1 GAAAAATTGAAAAAAAGAAA
21113432 GAAAAAATTGA
1 G-AAAAATTGA
21113443 GGGAGTGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 3 0.11
20 8 0.29
21 4 0.14
22 7 0.25
23 1 0.04
24 5 0.18
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (20 bp):
GAAAAATTGAAAAAAAGAAA
Found at i:21113423 original size:22 final size:19
Alignment explanation
Indices: 21113397--21113437 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
21113387 AGGAAAAGAT
21113397 TGAAAAAGAGAGACAAGAAAAA
1 TGAAAAA-A-AGA-AAGAAAAA
21113419 TGAAAAAAAGAAAGAAAAA
1 TGAAAAAAAGAAAGAAAAA
21113438 ATTGAGGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 3 0.16
21 1 0.05
22 7 0.37
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (19 bp):
TGAAAAAAAGAAAGAAAAA
Found at i:21118286 original size:20 final size:20
Alignment explanation
Indices: 21118263--21118309 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21118253 GGGTTAAGAT
*
21118263 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
21118283 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
21118303 TGAGCTG
1 TGAGCTG
21118310 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:21120006 original size:18 final size:18
Alignment explanation
Indices: 21119985--21120019 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21119975 TTTTTCTTTT
21119985 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
21120003 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
21120020 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:21120932 original size:15 final size:14
Alignment explanation
Indices: 21120914--21120962 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
21120904 TTTAACTTGA
21120914 TTTTTTTTGCTCACC
1 TTTTTTTTGCTCA-C
21120929 TTTTTTTTGCTCGA-
1 TTTTTTTTGCTC-AC
21120943 TTTTTTTT--TCAC
1 TTTTTTTTGCTCAC
21120955 TTTTTTTT
1 TTTTTTTT
21120963 TGAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.03
12 10 0.31
14 8 0.25
15 12 0.38
16 1 0.03
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:21120970 original size:11 final size:12
Alignment explanation
Indices: 21120942--21121014 Score: 76
Period size: 12 Copynumber: 5.9 Consensus size: 12
21120932 TTTTTGCTCG
*
21120942 ATTTTTTTTTCA
1 ATTTTTTTTTGA
*
21120954 CTTTTTTTTTGA
1 ATTTTTTTTTGA
*
21120966 ATTTTTTTTTCA
1 ATTTTTTTTTGA
*
21120978 ATCAATTTTTTTCGA
1 AT---TTTTTTTTGA
21120993 ATTTTTTTTTG-
1 ATTTTTTTTTGA
21121004 ATTTTTTTTTG
1 ATTTTTTTTTG
21121015 TTACTCCAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
11 11 0.22
12 30 0.59
15 10 0.20
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.73
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:21120973 original size:27 final size:27
Alignment explanation
Indices: 21120891--21121002 Score: 68
Period size: 27 Copynumber: 4.0 Consensus size: 27
21120881 CTCGCAAGAC
21120891 TTTTCACTTTTTTTTT-AACTTGATTTTTT
1 TTTTCACTTTTTTTTTGAA-TT--TTTTTT
* * * **
21120920 TTGCTCACCTTTTTTTTG-CTCGATTTTT
1 TT-TTCACTTTTTTTTTGAAT-TTTTTTT
21120948 TTTTCACTTTTTTTTTGAATTTTTTTT
1 TTTTCACTTTTTTTTTGAATTTTTTTT
** * *
21120975 TCAATCA-ATTTTTTTCGAATTTTTTTT
1 T-TTTCACTTTTTTTTTGAATTTTTTTT
21121002 T
1 T
21121003 GATTTTTTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
27 38 0.59
28 11 0.17
29 3 0.05
30 12 0.19
ACGTcount: A:0.13, C:0.12, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTTCACTTTTTTTTTGAATTTTTTTT
Found at i:21122529 original size:20 final size:20
Alignment explanation
Indices: 21122506--21122552 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21122496 GGGTTAAGAT
*
21122506 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
21122526 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
21122546 TGAGCTG
1 TGAGCTG
21122553 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:21125346 original size:12 final size:12
Alignment explanation
Indices: 21125277--21125358 Score: 55
Period size: 12 Copynumber: 6.9 Consensus size: 12
21125267 TTTCCACTCG
21125277 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
21125288 AGCTCTCTTTCA
1 ATTTCTTTTTCA
21125300 ATTTCTTTTTTCA
1 ATTTC-TTTTTCA
*
21125313 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
21125326 --TTCTCTTTCA
1 ATTTCTTTTTCA
21125336 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
21125348 ATCTCTTTTTC
1 ATTTCTTTTTC
21125359 CTTTTCACTC
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 27 0.50
13 6 0.11
14 6 0.11
15 4 0.07
ACGTcount: A:0.12, C:0.24, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:21125363 original size:18 final size:18
Alignment explanation
Indices: 21125337--21125374 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21125327 TCTCTTTCAA
*
21125337 TTTCTTTTTCAATCTCTT
1 TTTCCTTTTCAATCTCTT
*
21125355 TTTCCTTTTCACTCTCTT
1 TTTCCTTTTCAATCTCTT
21125373 TT
1 TT
21125375 ATTTTTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTCCTTTTCAATCTCTT
Found at i:21127886 original size:11 final size:10
Alignment explanation
Indices: 21127861--21127921 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
21127851 ACCAATAAAA
21127861 TAAA-TGAGC
1 TAAATTGAGC
*
21127870 TGAATTGTAGC
1 TAAATTG-AGC
21127881 TAAATTGAGC
1 TAAATTGAGC
**
21127891 TCGATTGAGC
1 TAAATTGAGC
21127901 TGAAA-TGAGC
1 T-AAATTGAGC
*
21127911 TCAATTGAGC
1 TAAATTGAGC
21127921 T
1 T
21127922 GGTTGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:21127922 original size:20 final size:20
Alignment explanation
Indices: 21127862--21127922 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
21127852 CCAATAAAAT
*
21127862 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
21127882 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
21127903 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
21127923 GTTGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:21127935 original size:30 final size:30
Alignment explanation
Indices: 21127878--21127942 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
21127868 GCTGAATTGT
*
21127878 AGCTAAATTGAGCTCGATTGAGCTGAAATG
1 AGCTAAATTGAGCTCGATTGAGCTGAAACG
* * *
21127908 AGCTCAATTGAGCT-GGTTGGAGTTGAAACG
1 AGCTAAATTGAGCTCGATT-GAGCTGAAACG
21127938 AGCTA
1 AGCTA
21127943 GAAAAGCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (30 bp):
AGCTAAATTGAGCTCGATTGAGCTGAAACG
Found at i:21130015 original size:18 final size:18
Alignment explanation
Indices: 21129994--21130028 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
21129984 TTTTTCTTTT
21129994 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
21130012 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
21130029 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Done.