Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 5 of 290
Found at i:1408239 original size:6 final size:6
Alignment explanation
Indices: 1408228--1408254 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1408218 ATAACTTAAT
1408228 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
1408255 AGATATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:1408331 original size:18 final size:18
Alignment explanation
Indices: 1408310--1408350 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1408300 GTAATTCGAG
1408310 TAATTCAGTTAATTTGAT
1 TAATTCAGTTAATTTGAT
* * *
1408328 TAATGCGGTTAATTTGGT
1 TAATTCAGTTAATTTGAT
1408346 TAATT
1 TAATT
1408351 TTATACTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (18 bp):
TAATTCAGTTAATTTGAT
Found at i:1408331 original size:27 final size:27
Alignment explanation
Indices: 1408274--1408341 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
1408264 TTTATACAAA
* *
1408274 TAATTCGGTTAATTTAGTTAACTTGGG
1 TAATTCGGTTAATTCAGTTAACTTGAG
* *
1408301 TAATTCGAG-TAATTCAGTTAATTTGAT
1 TAATTCG-GTTAATTCAGTTAACTTGAG
*
1408328 TAATGCGGTTAATT
1 TAATTCGGTTAATT
1408342 TGGTTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.03
27 32 0.94
28 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.44
Consensus pattern (27 bp):
TAATTCGGTTAATTCAGTTAACTTGAG
Found at i:1412370 original size:28 final size:28
Alignment explanation
Indices: 1412307--1412457 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
1412297 ACATTAAGTC
*
1412307 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
1412334 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
1412362 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
*
1412390 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
1412418 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
1412447 CGCACACTTAG
1 CGCACACTTAG
1412458 CGCCAATCTC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.19
28 75 0.66
29 16 0.14
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:1416701 original size:27 final size:26
Alignment explanation
Indices: 1416655--1416706 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
1416645 GCGAGACTGC
1416655 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGTCACCAGAA
* *
1416681 CAGATATTTGTGGCGAGGTCACCAGA
1 CAGATA-TTGTGACGAAGTCACCAGA
1416707 TTGCAGCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGACGAAGTCACCAGAA
Found at i:1424096 original size:33 final size:32
Alignment explanation
Indices: 1424045--1424108 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
1424035 ACGAAGTCAC
* *
1424045 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCAAAGCCACCAGAA
* *
1424077 CAGATATATATATATGTGGCAAAGCCACCAGA
1 CAGATACAGATAT-TGTGGCAAAGCCACCAGA
1424109 TTGCAGCGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCAAAGCCACCAGAA
Found at i:1424172 original size:27 final size:26
Alignment explanation
Indices: 1424124--1424175 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
1424114 GCGACGCTGC
*
1424124 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
1424150 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
1424176 TTGCAATGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:1429669 original size:18 final size:19
Alignment explanation
Indices: 1429621--1429663 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1429611 CATTTGAATT
1429621 GTTATCAGAAAAATTTAGA
1 GTTATCAGAAAAATTTAGA
1429640 GTTATCAGAAAAATTTAGA
1 GTTATCAGAAAAATTTAGA
1429659 GTTAT
1 GTTAT
1429664 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (19 bp):
GTTATCAGAAAAATTTAGA
Found at i:1430374 original size:11 final size:11
Alignment explanation
Indices: 1430343--1430388 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
1430333 ATGAATATAA
1430343 CATGTGCATAT
1 CATGTGCATAT
*
1430354 CA--TACATAT
1 CATGTGCATAT
1430363 CATGTGCATAT
1 CATGTGCATAT
*
1430374 CATGT-CAAAT
1 CATGTGCATAT
1430384 CATGT
1 CATGT
1430389 ATATCAAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 8 0.27
10 9 0.30
11 13 0.43
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (11 bp):
CATGTGCATAT
Found at i:1433969 original size:40 final size:39
Alignment explanation
Indices: 1433907--1434021 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 39
1433897 GATTTAGATT
* * *
1433907 TACCGGAGTATAAATAGGGCACATATGTGCAATCAGGGG
1 TACCGAAGTATAAAAAGGGCACATATGTGCAATCAAGGG
* * *
1433946 TACTGAAGTATAAAGAAGGGCACATATGTGCACTTAAGGG
1 TACCGAAGTATAAA-AAGGGCACATATGTGCAATCAAGGG
* *
1433986 TACCGAAGTACAAACAGGGGCACATATGTGCAATCA
1 TACCGAAGTATAAA-AAGGGCACATATGTGCAATCA
1434022 TAAAATAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 12 0.19
40 51 0.81
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.20
Consensus pattern (39 bp):
TACCGAAGTATAAAAAGGGCACATATGTGCAATCAAGGG
Found at i:1438521 original size:50 final size:49
Alignment explanation
Indices: 1438415--1438544 Score: 179
Period size: 50 Copynumber: 2.6 Consensus size: 49
1438405 CTCGTACGCA
* * * * ** *
1438415 TAGTAGCCTACACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCCGATACACG
*
1438464 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACCATCCGATACACG
1438514 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
1438545 TCGAAGTTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
49 29 0.40
50 43 0.60
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACCATCCGATACACG
Found at i:1439530 original size:11 final size:11
Alignment explanation
Indices: 1439514--1439546 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1439504 CATAGACCTC
1439514 AAAATAATTAT
1 AAAATAATTAT
1439525 AAAATAATTAT
1 AAAATAATTAT
1439536 AAAATAATTAT
1 AAAATAATTAT
1439547 TTCTATCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATAATTAT
Found at i:1440279 original size:15 final size:15
Alignment explanation
Indices: 1440227--1440280 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1440217 TAAAGATAAC
*
1440227 AAGAAAGCC-GAATA
1 AAGAAACCCAGAATA
*
1440241 AAGAAATCCA-AGATA
1 AAGAAACCCAGA-ATA
1440256 GAA-AAACCCAGAATA
1 -AAGAAACCCAGAATA
1440271 AAGAAACCCA
1 AAGAAACCCA
1440281 AGATACGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 11 0.33
15 19 0.58
16 3 0.09
ACGTcount: A:0.59, C:0.19, G:0.15, T:0.07
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:1443345 original size:49 final size:49
Alignment explanation
Indices: 1443281--1443476 Score: 212
Period size: 50 Copynumber: 3.9 Consensus size: 49
1443271 TAGCTAAAGC
* * *
1443281 TATCTGGTACGCATAGTAGCTTGCACATAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* ** *
1443330 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATATGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC-AAT
* ** * * * *
1443380 CATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
* * *
1443431 TATCGGGTACGCATTGTAGCCTGCACTTAGTACTACACATGCGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
1443477 TCACAATAGA
Statistics
Matches: 118, Mismatches: 26, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
49 40 0.34
50 42 0.36
51 36 0.31
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:1443369 original size:26 final size:26
Alignment explanation
Indices: 1443337--1443418 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
1443327 AATTATCCGG
1443337 TACACATAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
* * * *
1443363 TACACATA-T-GACCT-AAC-CATCTAA
1 TACACATAGTAG-CCTGCACTTA-GTAC
*
1443387 TACACGTAGTAGCCTGCACTTAGTAC
1 TACACATAGTAGCCTGCACTTAGTAC
1443413 TACACA
1 TACACA
1443419 CGTGATCGAA
Statistics
Matches: 40, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 1 0.03
24 12 0.30
25 8 0.20
26 18 0.45
27 1 0.03
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (26 bp):
TACACATAGTAGCCTGCACTTAGTAC
Found at i:1443477 original size:101 final size:99
Alignment explanation
Indices: 1443294--1443477 Score: 260
Period size: 101 Copynumber: 1.8 Consensus size: 99
1443284 CTGGTACGCA
* *
1443294 TAGTAGCTTGCACATAGTACTACACATGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
1 TAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
*
1443359 GTACTACACATATGACCTAACCATCTAATACACG
66 GTACTACACATACGACCTAACCATCTAATACACG
* * * * * *
1443393 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATTGTAGCCTGCACT
1 TAGTAGCCTGCACATAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
*
1443458 TAGTACTACACATGCGACCT
64 TAGTACTACACATACGACCT
1443478 CACAATAGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 27 0.37
100 3 0.04
101 43 0.59
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACATACGACCTAACCATCTAATACACG
Found at i:1448565 original size:19 final size:20
Alignment explanation
Indices: 1448527--1448565 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1448517 ATAATATTTG
*
1448527 AAATATACATAAAGTAGTAA
1 AAATATACATAAACTAGTAA
*
1448547 AAATATATAT-AACTAGTAA
1 AAATATACATAAACTAGTAA
1448566 TGTTAAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (20 bp):
AAATATACATAAACTAGTAA
Found at i:1448864 original size:19 final size:18
Alignment explanation
Indices: 1448840--1448880 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1448830 AATATATACC
*
1448840 TATATATATATTAAAGACA
1 TATATATATAATAAA-ACA
1448859 TATATATATAATAAAACA
1 TATATATATAATAAAACA
1448877 TATA
1 TATA
1448881 CTTAAGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (18 bp):
TATATATATAATAAAACA
Found at i:1449300 original size:21 final size:22
Alignment explanation
Indices: 1449252--1449316 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 22
1449242 TAAATACTAT
1449252 TAATATTAAAAAAATAACTTATTAA
1 TAATATTAAAAAAAT-A--TATTAA
* *
1449277 TAATATTACATAAATATATT-A
1 TAATATTAAAAAAATATATTAA
1449298 TAATATTAAAAAAATATAT
1 TAATATTAAAAAAATATAT
1449317 ACGTCATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 18 0.50
22 4 0.11
24 1 0.03
25 13 0.36
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATATTAAAAAAATATATTAA
Found at i:1449408 original size:15 final size:16
Alignment explanation
Indices: 1449373--1449414 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1449363 AATATATTGA
*
1449373 TAATAAATAATAAGAG
1 TAATAAATAATAACAG
*
1449389 GAATAAA-AATAACAG
1 TAATAAATAATAACAG
1449404 TAATAATATAA
1 TAATAA-ATAA
1449415 ATAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.57
16 7 0.33
17 2 0.10
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (16 bp):
TAATAAATAATAACAG
Found at i:1451333 original size:89 final size:85
Alignment explanation
Indices: 1451051--1451345 Score: 258
Period size: 86 Copynumber: 3.4 Consensus size: 85
1451041 TGATCTTGAA
** * * * * * * *
1451051 CTCAACTCATTTCTCGCAACATGAATTGACTCTTT-AAAACAGACATTAAAACAGAAATTTAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGATATGAAAAAAGAAATTGAAAA
* * * *
1451115 TAGCTCAGTGCA-TGAGCCAAGG
65 AACCTC-G-ACAGTGACCCAAGG
* * *
1451137 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGATATGATAATAGAATTTGAAAAA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGATATGAAAAAAGAAATTGAAAAA
1451202 ACCTCGACATGTGACCCAAGG
66 ACCTCGACA-GTGACCCAAGG
* *
1451223 CTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAA-ATATAAATTGAAAAAAAAAGAAATT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAT--A-TG---AAAAAAGAAATT
* * **
1451287 GAAAATACCTC-AGC-GTGTCCTGAGG
60 GAAAAAACCTCGA-CAGTGACCCAAGG
1451312 CTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1451346 TTGATGAACA
Statistics
Matches: 174, Mismatches: 25, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
84 2 0.01
85 8 0.05
86 99 0.57
87 1 0.01
88 2 0.01
89 41 0.24
90 1 0.01
91 20 0.11
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (85 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGATATGAAAAAAGAAATTGAAAAA
ACCTCGACAGTGACCCAAGG
Found at i:1451403 original size:75 final size:75
Alignment explanation
Indices: 1451280--1451441 Score: 274
Period size: 75 Copynumber: 2.2 Consensus size: 75
1451270 TGAAAAAAAA
1451280 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1451345 TTTGATGAAC
66 TTTGATGAAC
1451355 AGAAATT-AAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AGAAATTGAAAA-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
*
1451419 TTTTGA-AACAC
65 TTTTGATGA-AC
*
1451430 ATAAATTGAAAA
1 AGAAATTGAAAA
1451442 GCAGAAATTG
Statistics
Matches: 82, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
74 5 0.06
75 73 0.89
76 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (75 bp):
AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTTGATGAAC
Found at i:1451505 original size:89 final size:86
Alignment explanation
Indices: 1451352--1451618 Score: 315
Period size: 89 Copynumber: 3.0 Consensus size: 86
1451342 TTTTTTGATG
*
1451352 AACAGAAATT-AAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AACAGAAATTGAAAA-TACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1451416 TTTTTTTGAAACACATAAATTGAAA
65 --TTTTTGAAA-ACATAAATTGAAA
* *
1451441 AGCAGAAATTGAAAATACCTCAGCATGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
1451506 TTTTGACAAACAGAGATTTGAAAAA
66 TTTTGA-AAACATA-AATTG--AAA
* ** * *
1451531 AATAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTT
1 AACAGAAATTGAAAATACCTCAG-CATGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
1451595 GATATTTG-AAACATAAATTGAAA
63 GATTTTTGAAAACATAAATTGAAA
1451618 A
1 A
1451619 TACCTCGCGT
Statistics
Matches: 155, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
87 15 0.10
88 6 0.04
89 61 0.39
90 35 0.23
92 38 0.25
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (86 bp):
AACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGAAAACATAAATTGAAA
Found at i:1451715 original size:74 final size:73
Alignment explanation
Indices: 1451557--1451783 Score: 327
Period size: 73 Copynumber: 3.1 Consensus size: 73
1451547 ACCTCGACAT
* * ** *
1451557 GTGACCCGAGGCTCAACTCA-CTTCTCGCAATATGAGTTGATATTTG--AAACATAAATTGAAAA
1 GTGACCTGAGGCTCAACTCACCTT-TCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAA
1451619 TACCTC-GC
65 TACCTCAGC
*
1451627 GTGACCTGAGGCTCAAGTCACCTTTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAAAA
1 GTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGA-TTTTTGAAAAACAGGAATTAAAAA
1451692 TACCTCAGC
65 TACCTCAGC
* *
1451701 GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGT
1 GTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAAT
1451766 ACCTCAGC
66 ACCTCAGC
*
1451774 ATGACCTGAG
1 GTGACCTGAG
1451784 TGTAACACCC
Statistics
Matches: 142, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
70 34 0.24
71 8 0.06
73 60 0.42
74 40 0.28
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (73 bp):
GTGACCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAAT
ACCTCAGC
Found at i:1452729 original size:27 final size:27
Alignment explanation
Indices: 1452671--1453074 Score: 471
Period size: 27 Copynumber: 15.0 Consensus size: 27
1452661 AAAGTACTCC
*
1452671 CGATTTACAGAATTACCATTTT-CCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
1452697 CGATTTATAGATTTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1452724 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
1452751 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* * *
1452778 CAATTTATAGAATTACCGTTTTACCCC
1 CGATTTACAGAATTACCGTTTTACCCT
** *
1452805 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
1452832 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* **
1452859 C-AGTTTATAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
1452886 CGATTTACAGAATTACCGTTTTACCC-
1 CGATTTACAGAATTACCGTTTTACCCT
* **
1452912 CCAGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
1452940 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1452967 CGATTAGTA-A-AATTACCGTTTTACCCT
1 CGATT--TACAGAATTACCGTTTTACCCT
* * *
1452994 TGATTTACAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
1453021 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
1453048 CGATTTACAAAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
1453075 TAATTGTGAA
Statistics
Matches: 327, Mismatches: 38, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
25 2 0.01
26 25 0.08
27 292 0.89
28 6 0.02
29 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:1452809 original size:81 final size:82
Alignment explanation
Indices: 1452672--1453074 Score: 530
Period size: 81 Copynumber: 5.0 Consensus size: 82
1452662 AAGTACTCCC
* * * *
1452672 GATTTACAGAATTACCATTTT-CCCTCGATTTATAGATTTACCGTTTTACCCTCGATTTACAGAA
1 GATTTACAGAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAAAA
*
1452736 TTACCATTTTACCCTCA
66 TTACCGTTTTACCCTCA
* **
1452753 G-TTTACAGAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCCCGATTTGTAAAA
1 GATTTACAGAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAAAA
1452817 TTACCGTTTTACCCTC-
66 TTACCGTTTTACCCTCA
* * ** *
1452833 GATTTACAGAATTACTGTTTTACCCTCAGTTTATAGAATTACTATTTTACCCTCGATTTACAGAA
1 GATTTACAGAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAAAA
*
1452898 TTACCGTTTTACCCCCA
66 TTACCGTTTTACCCTCA
* * *
1452915 G-TTTACAGAATTACTATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGA-TTAGTAAA
1 GATTTACAGAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTA-CAAA
*
1452978 ATTACCGTTTTACCCT-T
65 ATTACCGTTTTACCCTCA
** * * * *
1452995 GATTTACAGAATTACTGGTTTACCCTCAGTTTACAAAATTATCGTTTTACCCTCGATTTACAAAA
1 GATTTACAGAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAAAA
*
1453060 TTATCGTTTTACCCT
66 TTACCGTTTTACCCT
1453075 TAATTGTGAA
Statistics
Matches: 281, Mismatches: 35, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
80 23 0.08
81 254 0.90
82 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (82 bp):
GATTTACAGAATTACTATTTTACCCTCAATTTATAGAATTACCGTTTTACCCTCGATTTACAAAA
TTACCGTTTTACCCTCA
Found at i:1453114 original size:27 final size:27
Alignment explanation
Indices: 1453084--1453278 Score: 248
Period size: 27 Copynumber: 7.2 Consensus size: 27
1453074 TTAATTGTGA
*
1453084 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* *
1453111 AATTTCTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
1453138 AATTACTGAAATACCCTTATAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
1453165 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
1453192 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* *
1453219 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
1453246 AATTACTGAGATACCCTTGTAGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
1453273 AATTAC
1 AATTAC
1453279 CATTTTGCCC
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:1453150 original size:54 final size:54
Alignment explanation
Indices: 1453084--1453279 Score: 277
Period size: 54 Copynumber: 3.6 Consensus size: 54
1453074 TTAATTGTGA
* * * * *
1453084 AATTACTAAAATACCCCTGTAGGGTAGAATTTCTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
1453138 AATTACTGAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
*
1453192 AATTA-TCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* *
1453246 AATTACTGAGATACCCTTGTAGGGTAAAATTACC
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACC
1453280 ATTTTGCCCC
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.01
54 123 0.98
55 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:1453516 original size:27 final size:26
Alignment explanation
Indices: 1453478--1453560 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 26
1453468 CGGAGGAAGC
*
1453478 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTAGTGGCTATGCCAC-AATATCT
*
1453505 GTTCTAGTGGCTCTGCCACAATATCT
1 GTTCTAGTGGCTATGCCACAATATCT
* * * * *
1453531 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTAGTGGCTATGCCACAATATCT
1453558 GTT
1 GTT
1453561 GACCGATCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 10 0.20
27 39 0.80
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
GTTCTAGTGGCTATGCCACAATATCT
Found at i:1453680 original size:22 final size:22
Alignment explanation
Indices: 1453648--1453706 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1453638 CCCGTTATTA
*
1453648 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
1453670 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
1453692 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
1453707 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:1453893 original size:27 final size:27
Alignment explanation
Indices: 1453871--1453944 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
1453861 TAGGTGGGTT
*
1453871 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
1453898 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
1453925 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
1453945 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.86
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:1454071 original size:6 final size:6
Alignment explanation
Indices: 1454062--1454163 Score: 95
Period size: 6 Copynumber: 16.8 Consensus size: 6
1454052 TTGCATTCAC
* *
1454062 ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
*
1454111 -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG
1 ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
*
1454159 GTTCT
1 ATTCT
1454164 CATTTTGGTT
Statistics
Matches: 80, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
5 6 0.08
6 67 0.84
7 5 0.06
8 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:1454125 original size:30 final size:30
Alignment explanation
Indices: 1454062--1454163 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
1454052 TTGCATTCAC
*
1454062 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTA-CTAATTCTG
1454093 ATTCTGATTCTGATTCTGTTACTAATAT-TG
1 ATTCTGATTCTGATTCTGTTACTAAT-TCTG
*
1454123 ATTCTGATTCTGATTCTGTTACTGATTCTG
1 ATTCTGATTCTGATTCTGTTACTAATTCTG
*
1454153 ATTCTGGTTCT
1 ATTCTGATTCT
1454164 CATTTTGGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
29 1 0.02
30 44 0.67
31 21 0.32
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATTCTG
Found at i:1463119 original size:43 final size:43
Alignment explanation
Indices: 1462964--1463330 Score: 466
Period size: 43 Copynumber: 8.5 Consensus size: 43
1462954 AGACCAGGAC
* * * *
1462964 CTTTTTTAAAAAATGCCGCTAGAAACCAGGACCTTTAGCGGCG
1 CTTTTATAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
* * *
1463007 CTTTTAT-AAAAACGCCGCTATAGACCTGTACTTTTAGCGGCG
1 CTTTTATAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
* * *
1463049 CTTTTATAAAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCA
1 CTTTTAT-AAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
* * *
1463093 CTTTTATAAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCG
1 CTTTTATAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
* * *
1463136 CTTTTATAAAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCA
1 CTTTTAT-AAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
* * *
1463180 CTTTTATAAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCG
1 CTTTTATAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
* * *
1463223 CTTTTATAAAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCA
1 CTTTTAT-AAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
* * *
1463267 CTTTTATAAAAAACGCCGCTATAGACCTGTACTTTTAGCGGCG
1 CTTTTATAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
*
1463310 CTTTTTTAAAAAACGCCGCTA
1 CTTTTATAAAAAACGCCGCTA
1463331 ATTTTCCTAG
Statistics
Matches: 276, Mismatches: 44, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
42 36 0.13
43 130 0.47
44 110 0.40
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
CTTTTATAAAAAACGCCGCTATAGACCAGGACCTTTAGCGGCG
Found at i:1463127 original size:87 final size:87
Alignment explanation
Indices: 1462971--1463331 Score: 647
Period size: 87 Copynumber: 4.2 Consensus size: 87
1462961 GACCTTTTTT
* * *
1462971 AAAAAATGCCGCTAGAA-ACCAGGACCTTTAGCGGCGCTTTTAT-AAAAACGCCGCTATAGACCT
1 AAAAAACGCTGCTA-AAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCT
1463034 GTACTTTTAGCGGCGCTTTTATA
65 GTACTTTTAGCGGCGCTTTTATA
1463057 AAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCTG
1 AAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCTG
1463122 TACTTTTAGCGGCGCTTTTATA
66 TACTTTTAGCGGCGCTTTTATA
1463144 AAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCTG
1 AAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCTG
1463209 TACTTTTAGCGGCGCTTTTATA
66 TACTTTTAGCGGCGCTTTTATA
1463231 AAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCTG
1 AAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCTG
*
1463296 TACTTTTAGCGGCGCTTTT-TT
66 TACTTTTAGCGGCGCTTTTATA
*
1463317 AAAAAACGCCGCTAA
1 AAAAAACGCTGCTAA
1463332 TTTTCCTAGT
Statistics
Matches: 268, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
85 2 0.01
86 52 0.19
87 214 0.80
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (87 bp):
AAAAAACGCTGCTAAAGACCAGGACCTTTAGCGGCACTTTTATAAAAAACGCCGCTATAGACCTG
TACTTTTAGCGGCGCTTTTATA
Found at i:1464243 original size:18 final size:18
Alignment explanation
Indices: 1464211--1464248 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1464201 TACAATATAG
1464211 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
1464230 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
1464247 TA
1 TA
1464249 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:1464412 original size:41 final size:41
Alignment explanation
Indices: 1464367--1464468 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 41
1464357 GCAAAAAATA
* *
1464367 GAGCAATAGCGGCGTTTTTGATCCAAACGCTACTAAAAACT
1 GAGCAATAGCGGCGTTTTTGACCCAAACGCCACTAAAAACT
* * *
1464408 GAGCAATAGTGGCGTTTTTGGCCCAAACGCCGCTAAAAACT
1 GAGCAATAGCGGCGTTTTTGACCCAAACGCCACTAAAAACT
* *
1464449 GAACAATAGCGGCGCTTTTG
1 GAGCAATAGCGGCGTTTTTG
1464469 GAAAAACGCC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (41 bp):
GAGCAATAGCGGCGTTTTTGACCCAAACGCCACTAAAAACT
Found at i:1464469 original size:41 final size:40
Alignment explanation
Indices: 1464370--1464482 Score: 136
Period size: 41 Copynumber: 2.8 Consensus size: 40
1464360 AAAAATAGAG
* ** *
1464370 CAATAGCGGCGTTTTTGATCCAAACGCTACTAAAAACTGAG
1 CAATAGCGGCGTTTTTG-GCCAAACGCCGCTAAAAACTGAA
*
1464411 CAATAGTGGCGTTTTTGGCCCAAACGCCGCTAAAAACTGAA
1 CAATAGCGGCGTTTTTGG-CCAAACGCCGCTAAAAACTGAA
* **
1464452 CAATAGCGGCGCTTTTGGAAAAACGCCGCTA
1 CAATAGCGGCGTTTTTGGCCAAACGCCGCTA
1464483 TAGGTCGAGG
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
40 11 0.18
41 51 0.82
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (40 bp):
CAATAGCGGCGTTTTTGGCCAAACGCCGCTAAAAACTGAA
Found at i:1464500 original size:41 final size:41
Alignment explanation
Indices: 1464455--1464685 Score: 390
Period size: 41 Copynumber: 5.6 Consensus size: 41
1464445 AACTGAACAA
*
1464455 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGCCGAGGTTT
* *
1464496 TAGCGGCGCTTCTGGAAAAACGCTGCTATAGGCCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGCCGAGGTTT
*
1464537 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGTCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGCCGAGGTTT
* *
1464578 TAGCGGCGCTTCTGGAAAAACGCTGCTATAGGCCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGCCGAGGTTT
*
1464619 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGCCGATGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGCCGAGGTTT
*
1464660 TAGCGGCGCTTTTGGAAAAATGCCGC
1 TAGCGGCGCTTTTGGAAAAACGCCGC
1464686 AAAAAAGTAA
Statistics
Matches: 177, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 177 1.00
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGAAAAACGCCGCTATAGGCCGAGGTTT
Found at i:1465017 original size:18 final size:18
Alignment explanation
Indices: 1464990--1465038 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1464980 TTGTCCCTTG
1464990 TTAT-ATATATATTAA-A
1 TTATAATATATATTAAGA
*
1465006 CTTCTAATATATATTAAGA
1 -TTATAATATATATTAAGA
1465025 TTATAATATATATT
1 TTATAATATATATT
1465039 TAGGGTGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 24 0.86
19 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATAATATATATTAAGA
Found at i:1465481 original size:15 final size:15
Alignment explanation
Indices: 1465461--1465492 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1465451 TTTAATGTAG
*
1465461 AAGATAAATGTATAT
1 AAGATAAATATATAT
1465476 AAGATAAATATATAT
1 AAGATAAATATATAT
1465491 AA
1 AA
1465493 ATTATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.31
Consensus pattern (15 bp):
AAGATAAATATATAT
Found at i:1465531 original size:24 final size:23
Alignment explanation
Indices: 1465464--1465531 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
1465454 AATGTAGAAG
*
1465464 ATAAATGTATATAAGATAAATATAT
1 ATAAAT-TATATATGA-AAATATAT
* *
1465489 ATAAATTATTATTTTAAAATATAT
1 ATAAATTA-TATATGAAAATATAT
1465513 ATAAATATATATATGAAAA
1 ATAAAT-TATATATGAAAA
1465532 GTGGTTTAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (23 bp):
ATAAATTATATATGAAAATATAT
Found at i:1476633 original size:31 final size:31
Alignment explanation
Indices: 1476557--1476634 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 31
1476547 AATTAATGTT
* * *
1476557 TTTGGTTGTATTTTTATGTTAAATTTGCTGTT
1 TTTGGTTGCA-TTTTATATTAAATTTGCTGTA
* * * *
1476589 TTTGGCTACATTTTATATTATATTTGTTGTA
1 TTTGGTTGCATTTTATATTAAATTTGCTGTA
*
1476620 TTTGGTTGGATTTTA
1 TTTGGTTGCATTTTA
1476635 ATGCAGGAAG
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
31 29 0.81
32 7 0.19
ACGTcount: A:0.18, C:0.04, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTGGTTGCATTTTATATTAAATTTGCTGTA
Found at i:1476734 original size:43 final size:43
Alignment explanation
Indices: 1476709--1476926 Score: 327
Period size: 43 Copynumber: 5.1 Consensus size: 43
1476699 GTAAAAAAAG
* *
1476709 CGCCACTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCC-CTAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAC-AAA
1476752 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
*
1476795 ---CGCTAAAAGCCTTGACCTTTAGTGGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
*
1476835 CGCCGCTAAAAGCCTTGACCTCTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
* *
1476878 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGTTTTTTCCCAATAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCG-CTTTTCCC-ACAAA
1476923 CGCC
1 CGCC
1476927 ACAAATTTTT
Statistics
Matches: 161, Mismatches: 8, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
40 39 0.24
43 106 0.66
44 8 0.05
45 8 0.05
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:1476829 original size:83 final size:85
Alignment explanation
Indices: 1476714--1476926 Score: 342
Period size: 83 Copynumber: 2.5 Consensus size: 85
1476704 AAAAGCGCCA
*
1476714 CTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCC-CTAAACGCCGCTAAAAGCCTTGACCTTTAGC
1 CTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACTAAACGCCGCTAAAAGCCTTGACCTCTAGC
1476778 GGCGCTTTTCCCACAAA-CG
66 GGCGCTTTTCCCACAAACCG
* *
1476797 CTAAAAGCCTTGACCTTTAGTGGCGCTTTTCCCAC-AAACGCCGCTAAAAGCCTTGACCTCTAGC
1 CTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACTAAACGCCGCTAAAAGCCTTGACCTCTAGC
1476861 GGCGCTTTTCCCACAAACGCCG
66 GGCGCTTTTCCCACAAA--CCG
*
1476883 CTAAAAGCCTTGACCTTTAGCGGCGTTTTTTCCCAATAAACGCC
1 CTAAAAGCCTTGACCTTTAGCGGCG-TTTTTCCCACTAAACGCC
1476927 ACAAATTTTT
Statistics
Matches: 118, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
83 76 0.64
84 1 0.01
86 26 0.22
87 8 0.07
88 7 0.06
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (85 bp):
CTAAAAGCCTTGACCTTTAGCGGCGTTTTTCCCACTAAACGCCGCTAAAAGCCTTGACCTCTAGC
GGCGCTTTTCCCACAAACCG
Found at i:1478716 original size:7 final size:8
Alignment explanation
Indices: 1478695--1478723 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1478685 TAAAGTTTCA
1478695 GCTTTTTG
1 GCTTTTTG
1478703 GCTTTTTG
1 GCTTTTTG
1478711 GCTTTTTG
1 GCTTTTTG
1478719 GCTTT
1 GCTTT
1478724 CGCCGATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.24, T:0.62
Consensus pattern (8 bp):
GCTTTTTG
Found at i:1483973 original size:40 final size:40
Alignment explanation
Indices: 1483929--1484019 Score: 173
Period size: 40 Copynumber: 2.3 Consensus size: 40
1483919 GCTACTTGCT
1483929 CAAATGCCTTCAAGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCAAGACTTAGCCCGGTTATAGTAACTCGCA
*
1483969 CAAATGCCTTCAGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCAAGACTTAGCCCGGTTATAGTAACTCGCA
1484009 CAAATGCCTTC
1 CAAATGCCTTC
1484020 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCAAGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:1491171 original size:294 final size:294
Alignment explanation
Indices: 1490642--1491229 Score: 1149
Period size: 294 Copynumber: 2.0 Consensus size: 294
1490632 TACGGCTCAT
1490642 ATGATCGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACATAATTTACTCCC
1 ATGATCGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACATAATTTACTCCC
1490707 TATTTAATTCCATTCCTACTATTTTTAGTGATTTTTCAAATCCACACCACTGCTACTATCAGCAT
66 TATTTAATTCCATTCCTACTATTTTTAGTGATTTTTCAAATCCACACCACTGCTACTATCAGCAT
1490772 CTGTTTTTAAGGTAAACTTTACCTATTTCATGGTTTTCCATGAATCAACTAGAATTTGTCATACA
131 CTGTTTTTAAGGTAAACTTTACCTATTTCATGGTTTTCCATGAATCAACTAGAATTTGTCATACA
*
1490837 AAGCACCAAAATGATCATGTTTAACCATTCCAATGGCTAATCCTTACCAAACATTTCCATACCTC
196 AAGCACCAAAATGATCATGATTAACCATTCCAATGGCTAATCCTTACCAAACATTTCCATACCTC
*
1490902 TCAATGAACAACATACAAAACGATTATAATGCTA
261 TCAATGAACAACATAAAAAACGATTATAATGCTA
1490936 ATGATCGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACATAATTTACTCCC
1 ATGATCGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACATAATTTACTCCC
1491001 TATTTAATTCCATTCCTACTATTTTTAGTGATTTTTCAAATCCACACCACTGCTACTATCAGCAT
66 TATTTAATTCCATTCCTACTATTTTTAGTGATTTTTCAAATCCACACCACTGCTACTATCAGCAT
1491066 CTGTTTTTAAGGTAAACTTTACCTATTTCATGGTTTTCCATGAATCAACTAGAATTTGTCATACA
131 CTGTTTTTAAGGTAAACTTTACCTATTTCATGGTTTTCCATGAATCAACTAGAATTTGTCATACA
1491131 AAGCACCAAAATGATCATGATTAACCATTCCAATGGCTAATCCTTACCAAACATTTCCATACCTC
196 AAGCACCAAAATGATCATGATTAACCATTCCAATGGCTAATCCTTACCAAACATTTCCATACCTC
*
1491196 TCAATGAACAACATAAAAAATGATTATAATGCTA
261 TCAATGAACAACATAAAAAACGATTATAATGCTA
1491230 TGCTCAAAAT
Statistics
Matches: 291, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
294 291 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (294 bp):
ATGATCGTTTCGTTACTTTCATATGAAAATAGATTCATCAAGGTTCGATTACATAATTTACTCCC
TATTTAATTCCATTCCTACTATTTTTAGTGATTTTTCAAATCCACACCACTGCTACTATCAGCAT
CTGTTTTTAAGGTAAACTTTACCTATTTCATGGTTTTCCATGAATCAACTAGAATTTGTCATACA
AAGCACCAAAATGATCATGATTAACCATTCCAATGGCTAATCCTTACCAAACATTTCCATACCTC
TCAATGAACAACATAAAAAACGATTATAATGCTA
Found at i:1491852 original size:40 final size:40
Alignment explanation
Indices: 1491808--1492031 Score: 317
Period size: 40 Copynumber: 5.6 Consensus size: 40
1491798 CTTGCTCAAC
* *
1491808 TGCCTTCGAGACTTAGCTCGGTTATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
*
1491848 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
* * *
1491888 TACCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
* *
1491928 TGCCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
* * * *
1491968 TGTCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAA
1492007 TGCCTTCGGGACTTAGCCCGGTTAT
1 TGCCTTCGGGACTTAGCCCGGTTAT
1492032 CATCCGAATA
Statistics
Matches: 162, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.01
39 32 0.20
40 128 0.79
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
Found at i:1499983 original size:40 final size:40
Alignment explanation
Indices: 1499938--1500164 Score: 325
Period size: 40 Copynumber: 5.7 Consensus size: 40
1499928 GCTACTTGCT
*
1499938 CAAATGCCTTCAGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
1499978 TAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
** *
1500018 CAAATGCCTTCGAAACTTAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
1500058 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
1500098 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
1500137 CAAATGCCTTCGGGACTTAG-CCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1500165 CATCCGAATA
Statistics
Matches: 166, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.01
39 38 0.23
40 127 0.77
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:1500036 original size:80 final size:80
Alignment explanation
Indices: 1499903--1500158 Score: 333
Period size: 80 Copynumber: 3.2 Consensus size: 80
1499893 CCAAACCAAG
* * * * *
1499903 TGCCTTCGGAATTTAG-CCAGATATAGCT-ACTTGCTCAAATGCCTTC-AGGACTTAGCCCGGTT
1 TGCCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGA-GACTTAGCCCGGTT
*
1499965 ATAGTAACTCGCATAAA
64 ATAGTAACTCGCACAAA
*
1499982 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAAACTTAGCCCGGTTAT
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGTTAT
*
1500047 AGTAATTCGCACAAA
66 AGTAACTCGCACAAA
* * *
1500062 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATGCCTTCG-GGCTTAGCCCGG-AAT
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGTTA-
* *
1500125 TAGTCACTAGCACAAA
65 TAGTAACTCGCACAAA
1500141 TGCCTTCGGGACTTAGCC
1 TGCCTTCGGGACTTAGCC
1500159 GGTTATCATC
Statistics
Matches: 158, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 56 0.35
80 100 0.63
81 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (80 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGTTAT
AGTAACTCGCACAAA
Found at i:1502976 original size:40 final size:40
Alignment explanation
Indices: 1502919--1503176 Score: 360
Period size: 40 Copynumber: 6.5 Consensus size: 40
1502909 TGGATGATAA
* * *
1502919 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
1502959 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
1502999 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
1503039 CCGGGCTAAGTCCCGAAGGCATTAGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
1503079 CCGGGCTAAGTCCCGAAGGCATTCATGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
1503119 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
1503159 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
1503177 TACTTGGCTT
Statistics
Matches: 201, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
39 16 0.08
40 185 0.92
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:1505526 original size:27 final size:27
Alignment explanation
Indices: 1505439--1505826 Score: 352
Period size: 27 Copynumber: 14.4 Consensus size: 27
1505429 TTTTTAAAAT
* *
1505439 CGAAATACCCCCGATTTGTAAAATTAT
1 CGAAATACCCTCGATTTGTAAAATTAC
* * *
1505466 TGAAATACCCTCG-GTTGTGAAATTAC
1 CGAAATACCCTCGATTTGTAAAATTAC
* *
1505492 TGAAATACCTTCGATTTG-AAAATTTAC
1 CGAAATACCCTCGATTTGTAAAA-TTAC
* * *
1505519 CGAAATACCCCCAATTTGTGAAATTAC
1 CGAAATACCCTCGATTTGTAAAATTAC
* * * *
1505546 CAAAACACCATCGATTTGTAAAATTAT
1 CGAAATACCCTCGATTTGTAAAATTAC
* *
1505573 C-AAAGTACCCTTGATTTGTAAAATTAT
1 CGAAA-TACCCTCGATTTGTAAAATTAC
* * * *
1505600 CGAAATGCCCTTGATTTGTGAAATTAT
1 CGAAATACCCTCGATTTGTAAAATTAC
* * *
1505627 CGAAACACCCTCAATTTGTAAATTTAC
1 CGAAATACCCTCGATTTGTAAAATTAC
* * * *
1505654 CAAAACACCCTCTATTTGTAAAATTAG
1 CGAAATACCCTCGATTTGTAAAATTAC
* * *
1505681 CGAAACACCCTTGATTTGTAAAATTAT
1 CGAAATACCCTCGATTTGTAAAATTAC
* *
1505708 TGAAATAACCTCGATTTGTAAAATTAC
1 CGAAATACCCTCGATTTGTAAAATTAC
* *
1505735 CAAAATACCCTCAATTTGTAAAATTAC
1 CGAAATACCCTCGATTTGTAAAATTAC
* * *
1505762 TGAAACACCCCCGATTTGTAAAATTAC
1 CGAAATACCCTCGATTTGTAAAATTAC
* * * *
1505789 CGAAATACCCTTG-TAGTGCAAAATTAT
1 CGAAATACCCTCGAT-TTGTAAAATTAC
1505816 CGAAATACCCT
1 CGAAATACCCT
1505827 TGTAGTGTAA
Statistics
Matches: 294, Mismatches: 61, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
26 29 0.10
27 259 0.88
28 6 0.02
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
CGAAATACCCTCGATTTGTAAAATTAC
Found at i:1505850 original size:27 final size:27
Alignment explanation
Indices: 1505751--1505871 Score: 102
Period size: 27 Copynumber: 4.5 Consensus size: 27
1505741 ACCCTCAATT
* ** *
1505751 TGTAAAATTACTGAAACACCCCCG-ATT
1 TGTAAAATTACTGAAATACCCTTGTA-G
*
1505778 TGTAAAATTACCGAAATACCCTTGTAG
1 TGTAAAATTACTGAAATACCCTTGTAG
*
1505805 TGCAAAATTA-TCGAAATACCCTTGTAG
1 TGTAAAATTACT-GAAATACCCTTGTAG
* * * *
1505832 TGTAAAATAACTGACATACCCCTGGAG
1 TGTAAAATTACTGAAATACCCTTGTAG
* *
1505859 GGTAAAATGACTG
1 TGTAAAATTACTG
1505872 TTTTACCCTT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
27 75 0.97
28 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (27 bp):
TGTAAAATTACTGAAATACCCTTGTAG
Found at i:1506344 original size:11 final size:11
Alignment explanation
Indices: 1506328--1506352 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1506318 TTGCATGTAC
1506328 GATATTATTGT
1 GATATTATTGT
1506339 GATATTATTGT
1 GATATTATTGT
1506350 GAT
1 GAT
1506353 GTGGTCTTCG
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:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (11 bp):
GATATTATTGT
Found at i:1513553 original size:33 final size:33
Alignment explanation
Indices: 1513511--1513575 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1513501 CTGCGGTATT
1513511 TATGGATTTGATGAATCGGATCTTCAGACAGTA
1 TATGGATTTGATGAATCGGATCTTCAGACAGTA
1513544 TATGGATTTGATGAATCGGATCTTCAGACAGT
1 TATGGATTTGATGAATCGGATCTTCAGACAGT
1513576 TTCGATCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (33 bp):
TATGGATTTGATGAATCGGATCTTCAGACAGTA
Found at i:1519232 original size:28 final size:28
Alignment explanation
Indices: 1519169--1519287 Score: 159
Period size: 28 Copynumber: 4.3 Consensus size: 28
1519159 TGCGAAGTAG
*
1519169 TTGGGCTTGATGGGCCATAT-AATGTGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
*
1519196 TTGGTCCTGATGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
*
1519224 TTGGGCCTGGTGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
* * * * *
1519252 TTGGACCTGATAGGCCATGTGAACGAGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
1519280 TTGGGCCT
1 TTGGGCCT
1519288 AAAGGGGTCA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 18 0.22
28 62 0.77
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.29
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAATGTGA
Found at i:1521094 original size:29 final size:28
Alignment explanation
Indices: 1521027--1521122 Score: 111
Period size: 29 Copynumber: 3.4 Consensus size: 28
1521017 AAGTCTACAT
* * * *
1521027 ACATGCATATGGCCTACTAGGCCCAATC
1 ACATTCATATGGCCCATTAGGCCAAATC
*
1521055 TCATTCATATGGCCCATTAGGCCAAAATC
1 ACATTCATATGGCCCATTAGGCC-AAATC
* *
1521084 ACATTCGTATGGCTCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGG-CCAAATC
1521113 ACATTCATAT
1 ACATTCATAT
1521123 TCATGCTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 19 0.33
29 36 0.63
30 2 0.04
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCAAATC
Found at i:1526963 original size:20 final size:21
Alignment explanation
Indices: 1526925--1526963 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1526915 AATGGTCATG
*
1526925 GATGATTTAAGAGTGACTTAA
1 GATGATTTAAGAGTCACTTAA
*
1526946 GATGA-TTACGAGTCACTT
1 GATGATTTAAGAGTCACTT
1526964 GTTGTTTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (21 bp):
GATGATTTAAGAGTCACTTAA
Found at i:1527499 original size:28 final size:28
Alignment explanation
Indices: 1527466--1527567 Score: 159
Period size: 28 Copynumber: 3.6 Consensus size: 28
1527456 ATTGCATGAC
*
1527466 TATGAATGTGATTGGGCCTGACGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
* *
1527494 TATGAAAGTGATTGGGCTTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
*
1527522 TATGAATGTGATTGGGCCCGATGGGCCA
1 TATGAATGTGATTGGGCCTGATGGGCCA
*
1527550 TATGAATGAGATTGGGCC
1 TATGAATGTGATTGGGCC
1527568 CAAAGGGGCC
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATGGGCCA
Found at i:1527585 original size:29 final size:28
Alignment explanation
Indices: 1527466--1527585 Score: 98
Period size: 28 Copynumber: 4.2 Consensus size: 28
1527456 ATTGCATGAC
* ** *
1527466 TATGAATGTGATTGGGCCTGACGGGCCA
1 TATGAATGAGATTGGGCCCAAGGGGCCA
* * *** *
1527494 TATGAAAGTGATTGGGCTTGATGGGCCA
1 TATGAATGAGATTGGGCCCAAGGGGCCA
* * *
1527522 TATGAATGTGATTGGGCCCGATGGGCCA
1 TATGAATGAGATTGGGCCCAAGGGGCCA
1527550 TATGAATGAGATTGGGCCCAAAGGGGCC-
1 TATGAATGAGATTGGGCCC-AAGGGGCCA
1527578 TAATGAAT
1 T-ATGAAT
1527586 AAGTATGGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 69 0.85
29 12 0.15
ACGTcount: A:0.26, C:0.15, G:0.34, T:0.25
Consensus pattern (28 bp):
TATGAATGAGATTGGGCCCAAGGGGCCA
Found at i:1529856 original size:74 final size:75
Alignment explanation
Indices: 1529772--1529920 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 75
1529762 TACACAAAAC
1529772 ACAAAATACACAAAATTTCAGCATAACCATGTTGAGTCGAATTTTTCTCACTCTT-AAAAAGTCC
1 ACAAAATACACAAAATTTCAGCATAACCATGTTGAGTCGAATTTTTCTCACTCTTAAAAAAGTCC
1529836 AATATTTAAT
66 AATATTTAAT
* *
1529846 ACAAAATACACAAAATTTCAGCATACCCATGTTGATTCGAATTTTTCTCACTCTTAAAAAAGTCC
1 ACAAAATACACAAAATTTCAGCATAACCATGTTGAGTCGAATTTTTCTCACTCTTAAAAAAGTCC
1529911 AATATTTAAT
66 AATATTTAAT
1529921 GTATTTTACA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 53 0.74
75 19 0.26
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.33
Consensus pattern (75 bp):
ACAAAATACACAAAATTTCAGCATAACCATGTTGAGTCGAATTTTTCTCACTCTTAAAAAAGTCC
AATATTTAAT
Found at i:1537905 original size:43 final size:43
Alignment explanation
Indices: 1537835--1537943 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 43
1537825 AGGATTTACG
* * * * * *
1537835 ATATGTGATTGCGTGCAAGACAATGTCTTGGACATTGGCATCGT
1 ATATGTGATTACGTGTAAGACCATGTCTAGGACAGTGGCATC-A
*
1537879 ATATGTGATT-CGTGTAAGACCCTGTCTAGGACAGTGGCATCA
1 ATATGTGATTACGTGTAAGACCATGTCTAGGACAGTGGCATCA
*
1537921 ATATGTGATTACATGTAAGACCA
1 ATATGTGATTACGTGTAAGACCA
1537944 CATTTGGGAC
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 10 0.18
43 36 0.64
44 10 0.18
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCATGTCTAGGACAGTGGCATCA
Found at i:1539883 original size:48 final size:48
Alignment explanation
Indices: 1539823--1539928 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
1539813 CGGCCACAAT
* *
1539823 ATATACACATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
1539871 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
1 ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
* *
1539919 ACATATATAT
1 ATATACATAT
1539929 ATTTATCTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (48 bp):
ATATACATATCTCATACATATTTCACACTAGCCATTCGGCTTTACCAC
Found at i:1554174 original size:30 final size:30
Alignment explanation
Indices: 1554116--1554174 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1554106 ATTTTCGAGC
* **
1554116 CTAGGGGTAAAATGGTCATTTTGTCAAAGT
1 CTAGGGGCAAAATGGTCATTTTACCAAAGT
*
1554146 CTAGGGGCAAAATGGTTATTTTACCAAAG
1 CTAGGGGCAAAATGGTCATTTTACCAAAG
1554175 AAGTGAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (30 bp):
CTAGGGGCAAAATGGTCATTTTACCAAAGT
Found at i:1554658 original size:46 final size:46
Alignment explanation
Indices: 1554515--1554688 Score: 169
Period size: 47 Copynumber: 3.7 Consensus size: 46
1554505 TTGTGAGCTG
* ** * * *
1554515 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATGTTATAAGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGG-CACGAGATGATAG-TA
* * *
1554561 GCGTAAGACCATGTCTAGGACATGGCATCGGCATCGAGACG-TAAGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGAGATGAT-AG-TA
1554609 GTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATGATAGTAA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGAGATGATAGT-A
1554655 GTGTAAGACCATGTCTGGGACATGGCATCGGCAC
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCAC
1554689 CTTACCCCAC
Statistics
Matches: 107, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
45 1 0.01
46 32 0.30
47 46 0.43
48 28 0.26
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (46 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGATAGTA
Found at i:1554676 original size:94 final size:94
Alignment explanation
Indices: 1554510--1554687 Score: 257
Period size: 94 Copynumber: 1.9 Consensus size: 94
1554500 GGTTATTGTG
* * ** *
1554510 AGCTGGTGTAAGACATGTCTGGGACATGCATCGGCCATGTTATAAGAGCCAGCGTAAGACCATGT
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATAAGAGCAAGCGTAAGACCATGT
1554575 CTAGGACATGGCATCGGCATCGAGACGTA
66 CTAGGACATGGCATCGGCATCGAGACGTA
* * * * *
1554604 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAGTAAGTGTAAGACCATGT
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATAAGAGCAAGCGTAAGACCATGT
*
1554669 CTGGGACATGGCATCGGCA
66 CTAGGACATGGCATCGGCA
1554688 CCTTACCCCA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 73 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (94 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATAAGAGCAAGCGTAAGACCATGT
CTAGGACATGGCATCGGCATCGAGACGTA
Found at i:1566534 original size:178 final size:178
Alignment explanation
Indices: 1566225--1566587 Score: 627
Period size: 178 Copynumber: 2.0 Consensus size: 178
1566215 AATCCCCAAC
* * *
1566225 TTTCTAAAAGTAGATAGTGGCATTAGGTTAATGCTAGTTCCCAAGTCGCATAAAGCATTGCTTAA
1 TTTCCAAAAGTAGATAATGGCATTAGGTTAATGCTAGTTCCCAAGTCGCATAAAACATTGCTTAA
* * * *
1566290 ATAATGGTTTCCAATTGAACATGGGATAGTAAAGCTCCCAGGATCTTTCATTTTGGGGGTAACTT
66 ATAATGGTTTCCAATTGAACAGGGGATAGTAAAGATCCCAAGATCTTTCATTTTGGGGGCAACTT
*
1566355 ATTTGTCAAAACAGCACTACAGCCTTCTGTGAGTGCAATAATTCAGAA
131 ATTTCTCAAAACAGCACTACAGCCTTCTGTGAGTGCAATAATTCAGAA
*
1566403 TTTCCAAAAGTAGATAATGGCATTAGGTTAATGCTAGTTCCCAAGTCGCATAAAACCTTGCTTAA
1 TTTCCAAAAGTAGATAATGGCATTAGGTTAATGCTAGTTCCCAAGTCGCATAAAACATTGCTTAA
1566468 ATAATGGTTTCCAATTGAACAGGGGATAGTAAAGATCCCAAGATCTTTCATTTTGGGGGCAACTT
66 ATAATGGTTTCCAATTGAACAGGGGATAGTAAAGATCCCAAGATCTTTCATTTTGGGGGCAACTT
* *
1566533 ATTTCTCAAAACAGCACTACAGCTTTTTGTGAGTGCAATAATTCAGAA
131 ATTTCTCAAAACAGCACTACAGCCTTCTGTGAGTGCAATAATTCAGAA
1566581 TTTCCAA
1 TTTCCAA
1566588 TAATTCCAAT
Statistics
Matches: 174, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
178 174 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (178 bp):
TTTCCAAAAGTAGATAATGGCATTAGGTTAATGCTAGTTCCCAAGTCGCATAAAACATTGCTTAA
ATAATGGTTTCCAATTGAACAGGGGATAGTAAAGATCCCAAGATCTTTCATTTTGGGGGCAACTT
ATTTCTCAAAACAGCACTACAGCCTTCTGTGAGTGCAATAATTCAGAA
Found at i:1570102 original size:27 final size:27
Alignment explanation
Indices: 1570072--1570262 Score: 222
Period size: 27 Copynumber: 7.1 Consensus size: 27
1570062 TAATGAAATG
*
1570072 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* * * *
1570099 CCCTCGATTTATAGAATTATCGTTTCA
1 CCCTCGATTTACAGAATTACCATTTTA
* * *
1570126 CCATCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* * * *
1570153 GCTTCGATTTATAGAATTAACATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
1570180 CCCTCGATTTACAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
1570207 CCCCCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
1570234 CCCTC-AGTTTACAAAATTACCGTTTTA
1 CCCTCGA-TTTACAGAATTACCATTTTA
1570261 CC
1 CC
1570263 TTCAATTGTG
Statistics
Matches: 141, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
26 1 0.01
27 140 0.99
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCATTTTA
Found at i:1570187 original size:81 final size:81
Alignment explanation
Indices: 1570075--1570233 Score: 246
Period size: 81 Copynumber: 2.0 Consensus size: 81
1570065 TGAAATGCCC
* * * * *
1570075 TCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATCGTTTCACCATCGATTTACAA
1 TCGATTTATAGAATTAACATTTTACCCTCGATTTACAGAATTACCATTTCACCACCGATTTACAA
*
1570140 AATTACCGTTTTAGCT
66 AATTACCATTTTAGCT
* *
1570156 TCGATTTATAGAATTAACATTTTACCCTCGATTTACAGAATTACCATTTTACCCCCGATTTACAA
1 TCGATTTATAGAATTAACATTTTACCCTCGATTTACAGAATTACCATTTCACCACCGATTTACAA
1570221 AATTACCATTTTA
66 AATTACCATTTTA
1570234 CCCTCAGTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (81 bp):
TCGATTTATAGAATTAACATTTTACCCTCGATTTACAGAATTACCATTTCACCACCGATTTACAA
AATTACCATTTTAGCT
Found at i:1570312 original size:27 final size:27
Alignment explanation
Indices: 1570273--1570422 Score: 92
Period size: 27 Copynumber: 5.6 Consensus size: 27
1570263 TTCAATTGTG
**
1570273 AAATTACTGAAATACTCCT-GTAGGATA
1 AAATTACCAAAATACTCCTAGTAGG-TA
* **
1570300 GAATTACCAAAATAC-CACTAGTTTGTA
1 AAATTACCAAAATACTC-CTAGTAGGTA
**
1570327 AAATTACCAAAATACTCCTAGTTTGTA
1 AAATTACCAAAATACTCCTAGTAGGTA
* * ** *
1570354 AAATTACCGAAATAC-CACTGGTTTGTG
1 AAATTACCAAAATACTC-CTAGTAGGTA
* * **
1570381 AAATTACCGAAATAC-CCTCAATCTGTA
1 AAATTACCAAAATACTCCT-AGTAGGTA
1570408 AAATTACCAAAATAC
1 AAATTACCAAAATAC
1570423 CCCTGATTTA
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
26 4 0.04
27 96 0.92
28 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACTCCTAGTAGGTA
Found at i:1570340 original size:54 final size:54
Alignment explanation
Indices: 1570268--1570423 Score: 181
Period size: 54 Copynumber: 2.9 Consensus size: 54
1570258 TTACCTTCAA
* *
1570268 TTGTGAAATTACTGAAATACTCCT-GTAGGATAGAATTACCAAAATACCACTAGT
1 TTGTGAAATTACCGAAATACTCCTAGTAGG-TAAAATTACCAAAATACCACTAGT
* * ** * *
1570322 TTGTAAAATTACCAAAATACTCCTAGTTTGTAAAATTACCGAAATACCACTGGT
1 TTGTGAAATTACCGAAATACTCCTAGTAGGTAAAATTACCAAAATACCACTAGT
* **
1570376 TTGTGAAATTACCGAAATAC-CCTCAATCTGTAAAATTACCAAAATACC
1 TTGTGAAATTACCGAAATACTCCT-AGTAGGTAAAATTACCAAAATACC
1570424 CCTGATTTAC
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
53 3 0.03
54 81 0.93
55 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (54 bp):
TTGTGAAATTACCGAAATACTCCTAGTAGGTAAAATTACCAAAATACCACTAGT
Found at i:1570423 original size:27 final size:26
Alignment explanation
Indices: 1570301--1570424 Score: 158
Period size: 27 Copynumber: 4.6 Consensus size: 26
1570291 TGTAGGATAG
1570301 AATTACCAAAATACCACTAGTTTGTAA
1 AATTACCAAAATACC-CTAGTTTGTAA
1570328 AATTACCAAAATACTCCTAGTTTGTAA
1 AATTACCAAAATAC-CCTAGTTTGTAA
* * *
1570355 AATTACCGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACC-CTAGTTTGTAA
* * *
1570382 AATTACCGAAATACCCTCAATCTGTAA
1 AATTACCAAAATACCCT-AGTTTGTAA
1570409 AATTACCAAAATACCC
1 AATTACCAAAATACCC
1570425 CTGATTTACA
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.03
27 82 0.95
28 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (26 bp):
AATTACCAAAATACCCTAGTTTGTAA
Found at i:1570437 original size:27 final size:26
Alignment explanation
Indices: 1570301--1570440 Score: 136
Period size: 27 Copynumber: 5.2 Consensus size: 26
1570291 TGTAGGATAG
*
1570301 AATTACCAAAATACCACTAGTTTGTAA
1 AATTACCAAAATACCCCTA-TTTGTAA
*
1570328 AATTACCAAAATACTCCTAGTTTGTAA
1 AATTACCAAAATACCCCTA-TTTGTAA
* * * *
1570355 AATTACCGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCT-ATTTGTAA
* * *
1570382 AATTACCGAAATACCCTCAATCTGTAA
1 AATTACCAAAATACCC-CTATTTGTAA
**
1570409 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCCT-ATTTGTAA
1570436 AATTA
1 AATTA
1570441 TAGAAATACC
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.01
27 91 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (26 bp):
AATTACCAAAATACCCCTATTTGTAA
Found at i:1570438 original size:81 final size:81
Alignment explanation
Indices: 1570301--1570450 Score: 196
Period size: 81 Copynumber: 1.9 Consensus size: 81
1570291 TGTAGGATAG
* * * ** *
1570301 AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACTCCTAGTTTGTAAAATTACCGAAA
1 AATTACCAAAATACCACTAATCTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAGAAA
1570366 TACCACTGGTTTGTGA
66 TACCACTGGTTTGTGA
* *
1570382 AATTACCGAAATACC-CTCAATCTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTATAGA
1 AATTACCAAAATACCACT-AATCTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTACAGA
1570445 AATACC
64 AATACC
1570451 CTTGACTTTC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
80 3 0.05
81 56 0.95
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCACTAATCTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:1570439 original size:54 final size:53
Alignment explanation
Indices: 1570301--1570452 Score: 171
Period size: 54 Copynumber: 2.8 Consensus size: 53
1570291 TGTAGGATAG
* * *
1570301 AATTACCAAAATACCACT-AGTTTGTAAAATTACCAAAATACTCCTAGTTTGTAA
1 AATTACCAAAATACCACTGA-TTTGTAAAATTACCGAAATAC-CCTAATCTGTAA
* * *
1570355 AATTACCGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATCTGTAA
1 AATTACCAAAATACCACTGATTTGTAAAATTACCGAAATACCCT-AATCTGTAA
* ** **
1570409 AATTACCAAAATACCCCTGATTTACAAAATTATAGAAATACCCT
1 AATTACCAAAATACCACTGATTTGTAAAATTACCGAAATACCCT
1570453 TGACTTTCTA
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
53 3 0.04
54 79 0.96
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (53 bp):
AATTACCAAAATACCACTGATTTGTAAAATTACCGAAATACCCTAATCTGTAA
Found at i:1570511 original size:27 final size:27
Alignment explanation
Indices: 1570407--1570514 Score: 76
Period size: 27 Copynumber: 3.9 Consensus size: 27
1570397 CTCAATCTGT
** * *
1570407 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTATAAAAATACCCTTGGTTTAC
* *
1570434 AAAATTATAGAAATACCCTTGACTTT-C
1 AAAATTATAAAAATACCCTTG-GTTTAC
** *
1570461 TAAAAATTATAAAAATGTCATTGGTTTAC
1 --AAAATTATAAAAATACCCTTGGTTTAC
*
1570490 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAAAAATACCCTTGGTTT
1570515 GTAGCTTTAC
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
27 37 0.60
28 7 0.11
29 18 0.29
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (27 bp):
AAAATTATAAAAATACCCTTGGTTTAC
Found at i:1571743 original size:31 final size:31
Alignment explanation
Indices: 1571707--1571790 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
1571697 CATTTACAGT
*
1571707 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
1571738 AAAGGCTTCAGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1571769 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
1571791 TCAAGACTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 5 0.10
31 44 0.90
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:1574083 original size:27 final size:27
Alignment explanation
Indices: 1574065--1574243 Score: 252
Period size: 27 Copynumber: 6.6 Consensus size: 27
1574055 CTCAATTTGT
*
1574065 AGAATTACCATTTTACCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
* *
1574092 AGAATTACCGTTTCACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
* * * *
1574119 AAAATTACCGTTTTAGCCTCGATTTAT
1 AGAATTACCATTTTACCCTCGATTTAC
1574146 AGAATTACCATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
1574173 AGAATTACCATTTTACCCTCGATTTAC
1 AGAATTACCATTTTACCCTCGATTTAC
*
1574200 AAAATTACCATTTTACCCTC-AGTTTAC
1 AGAATTACCATTTTACCCTCGA-TTTAC
* *
1574227 AAAATTACCGTTTTACC
1 AGAATTACCATTTTACC
1574244 ATCAATTATG
Statistics
Matches: 138, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
26 1 0.01
27 137 0.99
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (27 bp):
AGAATTACCATTTTACCCTCGATTTAC
Found at i:1574311 original size:53 final size:54
Alignment explanation
Indices: 1574254--1574374 Score: 140
Period size: 53 Copynumber: 2.3 Consensus size: 54
1574244 ATCAATTATG
* * *
1574254 AAATTACTGAAATACCCCT-GTAGGAT-AGAATTACCAAAATACCC-TAGTTTGTA
1 AAATTACCGAAATACCACTAGTAGG-TGA-AATTACCAAAATACCCTTAATTTGTA
** *
1574307 AAATTACCGAAATACCACTAGTTTGTGAAATTACCGAAATACCCTTAATTTGTA
1 AAATTACCGAAATACCACTAGTAGGTGAAATTACCAAAATACCCTTAATTTGTA
*
1574361 AAATTACCAAAATA
1 AAATTACCGAAATA
1574375 ACCCTTGATT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
53 33 0.57
54 25 0.43
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (54 bp):
AAATTACCGAAATACCACTAGTAGGTGAAATTACCAAAATACCCTTAATTTGTA
Found at i:1574337 original size:27 final size:26
Alignment explanation
Indices: 1574282--1574379 Score: 133
Period size: 27 Copynumber: 3.7 Consensus size: 26
1574272 TGTAGGATAG
1574282 AATTACCAAAATACCCTAGTTTGTAA
1 AATTACCAAAATACCCTAGTTTGTAA
* *
1574308 AATTACCGAAATACCACTAGTTTGTGA
1 AATTACCAAAATACC-CTAGTTTGTAA
* *
1574335 AATTACCGAAATACCCTTAATTTGTAA
1 AATTACCAAAATACCC-TAGTTTGTAA
1574362 AATTACCAAAATAACCCT
1 AATTACCAAAAT-ACCCT
1574380 TGATTTACCA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.23
27 45 0.70
28 4 0.06
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (26 bp):
AATTACCAAAATACCCTAGTTTGTAA
Found at i:1574457 original size:27 final size:26
Alignment explanation
Indices: 1574414--1574469 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
1574404 TCCTTGACTT
1574414 TTTAAAAATTATAGAAATAC-CATTGG
1 TTTAAAAATTATAGAAATACGC-TTGG
1574440 TTTACAAAATTACT-GAAATACGCTTGG
1 TTTA-AAAATTA-TAGAAATACGCTTGG
1574467 TTT
1 TTT
1574470 GTAGATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.15
27 21 0.78
28 2 0.07
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTAAAAATTATAGAAATACGCTTGG
Found at i:1575435 original size:25 final size:24
Alignment explanation
Indices: 1575397--1575466 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
1575387 AGGAAGTGCT
*
1575397 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
* *
1575421 GAAAAGGGCTTTGCCCCAATTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
* *
1575446 AGAAAGGGCCTTGCCCTAGTT
1 A-AAAGGGCTTTGCCCCAGTT
1575467 ATTAAAAGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:1575673 original size:42 final size:42
Alignment explanation
Indices: 1575614--1575747 Score: 241
Period size: 42 Copynumber: 3.2 Consensus size: 42
1575604 TAGTCTCCCC
*
1575614 AAATGGGCTTGCATACATTCATTGACATTACATGTAATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
*
1575656 AAATGGGCTTGCATACATTCATTGATATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
*
1575698 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1575740 AAATGGGC
1 AAATGGGC
1575748 CTAAGGGCCA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
Found at i:1575831 original size:30 final size:31
Alignment explanation
Indices: 1575770--1575883 Score: 196
Period size: 31 Copynumber: 3.7 Consensus size: 31
1575760 TCGTTTACAT
1575770 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1575801 AAAGGCTTCGGCCCAGTGATATGA-TTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
1575831 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
1575862 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
1575884 TCAAGACTAA
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
30 35 0.44
31 45 0.56
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:1575845 original size:61 final size:60
Alignment explanation
Indices: 1575770--1575883 Score: 201
Period size: 61 Copynumber: 1.9 Consensus size: 60
1575760 TCGTTTACAT
*
1575770 AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCAGCCCAGT-ATATGATTATGA
*
1575831 AAAGGCTTCGGCCCAGTGATATGATTTATGGAAAGGCTTCAGCCCAGTATATG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCAGCCCAGTATATG
1575884 TCAAGACTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
60 5 0.10
61 46 0.90
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (60 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGAAAAGGCTTCAGCCCAGTATATGATTATGA
Found at i:1576813 original size:49 final size:49
Alignment explanation
Indices: 1576752--1576978 Score: 292
Period size: 49 Copynumber: 4.6 Consensus size: 49
1576742 CTAGTATGCA
*
1576752 TAGTAGCATGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
* * * ** * *
1576801 TGGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCGGTACACG
* * * * * * *
1576851 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACACG
1576902 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1576951 TAGTAGCCTGCACTTAGTACTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
1576979 TGTCCTCACA
Statistics
Matches: 151, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
49 68 0.45
50 46 0.30
51 37 0.25
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
Found at i:1576878 original size:28 final size:27
Alignment explanation
Indices: 1576796--1576880 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 27
1576786 ATTATCCGGT
*
1576796 ACACGTGGTAGCCTGCACTTAGTACTAC
1 ACACGT-GTAGCCTACACTTAGTACTAC
* *
1576824 ACACGTG-A-CCTA-AC-CA-T-CTGAT
1 ACACGTGTAGCCTACACTTAGTACT-AC
1576846 ACACGTAGTAGCCTACACTTAGTACTAC
1 ACACGT-GTAGCCTACACTTAGTACTAC
1576874 ACACGTG
1 ACACGTG
1576881 ATCGAAGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
21 2 0.05
22 8 0.18
23 2 0.05
24 3 0.07
25 7 0.16
26 3 0.07
27 3 0.07
28 14 0.32
29 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (27 bp):
ACACGTGTAGCCTACACTTAGTACTAC
Found at i:1576925 original size:101 final size:98
Alignment explanation
Indices: 1576752--1576976 Score: 288
Period size: 101 Copynumber: 2.3 Consensus size: 98
1576742 CTAGTATGCA
* * * *
1576752 TAGTAGCATGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTGGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
* *
1576817 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGCGACC-AACCATCCGATACACG
* * * * *
1576851 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
* ** *
1576916 TAGTACTACACATGCGACCAATTATCCGGTACACG
64 TAGTACTACACACGCGACCAACCATCCGATACACG
1576951 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
1576977 TGTGTCCTCA
Statistics
Matches: 108, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
99 27 0.25
100 40 0.37
101 41 0.38
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCAACCATCCGATACACG
Found at i:1578794 original size:12 final size:12
Alignment explanation
Indices: 1578777--1578803 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1578767 ATTCCGAAGT
1578777 ATATATATATAC
1 ATATATATATAC
1578789 ATATATATATAC
1 ATATATATATAC
1578801 ATA
1 ATA
1578804 AGTATGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:1579332 original size:27 final size:28
Alignment explanation
Indices: 1579248--1579345 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
1579238 CATGAGATTG
* * * *
1579248 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
1579277 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
1579305 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
1579332 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
1579346 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:1579356 original size:27 final size:27
Alignment explanation
Indices: 1579276--1579358 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
1579266 TAAATTGTAC
* *
1579276 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
1579304 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
1579331 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
1579358 A
1 A
1579359 CTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:1586797 original size:50 final size:50
Alignment explanation
Indices: 1586624--1586953 Score: 365
Period size: 50 Copynumber: 6.5 Consensus size: 50
1586614 TGAGAACATA
* * * * **
1586624 TGTGTAGTACTATGTGCAGGCTACAATGTGTTTAAGATGGTTTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGG--TTAGGTCACG
* ** * * * *
1586676 TGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGAT-GGTTAGGTCACG
* *
1586727 TGAGTAGTACTAAGTTCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
* ** * * * *
1586777 TGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGAT-GGTTAGGTCACG
* *
1586828 TGAGTAGTACTAAGTTCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
* * *
1586878 TGTGTAGTACTAAGTGCAGGCTACTACATGTA-CCAGATTGTTAGGTCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCC-GATGGTTAGGTCACG
1586928 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
1586954 TGCATACCAG
Statistics
Matches: 232, Mismatches: 43, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
49 2 0.01
50 118 0.51
51 81 0.35
52 30 0.13
53 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCCGATGGTTAGGTCACG
Found at i:1586804 original size:101 final size:101
Alignment explanation
Indices: 1586666--1586903 Score: 476
Period size: 101 Copynumber: 2.4 Consensus size: 101
1586656 TAAGATGGTT
1586666 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACGTGAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACGTGAG
1586731 TAGTACTAAGTTCAGGCTACTACGTGTATCCGATGG
66 TAGTACTAAGTTCAGGCTACTACGTGTATCCGATGG
1586767 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACGTGAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACGTGAG
1586832 TAGTACTAAGTTCAGGCTACTACGTGTATCCGATGG
66 TAGTACTAAGTTCAGGCTACTACGTGTATCCGATGG
1586868 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
1586904 CATGTACCAG
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 137 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (101 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACGTGAG
TAGTACTAAGTTCAGGCTACTACGTGTATCCGATGG
Found at i:1586921 original size:151 final size:152
Alignment explanation
Indices: 1586671--1586961 Score: 424
Period size: 151 Copynumber: 1.9 Consensus size: 152
1586661 TGGTTTTAGG
* * *
1586671 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCCTACCCGATAGCTTCGATCACGTGAGTAGTA
1 TCACGTGAGTAGTACTAAGTGCAGGCTACTACGCCTACCCGATAGCTTAGATCACGTGAGTAGTA
* * *
1586736 CTAAGTTCAGGCTACTACGTGTATCCGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTAC
66 CTAAGTGCAGGCTACTACATGTATCCGATGGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTAC
*
1586801 TATGCCTACCCGATAGCTTCGA
131 TATGCATACCCGATAGCTTCGA
* ** * * * *
1586823 TCACGTGAGTAGTACTAAGTTCAGGCTACTACGTGTATCCGAT-GGTTAGGTCACGTGTGTAGTA
1 TCACGTGAGTAGTACTAAGTGCAGGCTACTACGCCTACCCGATAGCTTAGATCACGTGAGTAGTA
*
1586887 CTAAGTGCAGGCTACTACATGTA-CCAGATTGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTA
66 CTAAGTGCAGGCTACTACATGTATCC-GATGGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTA
1586951 CTATGCATACC
130 CTATGCATACC
1586962 AGAGAACTTC
Statistics
Matches: 123, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
150 2 0.02
151 84 0.68
152 37 0.30
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (152 bp):
TCACGTGAGTAGTACTAAGTGCAGGCTACTACGCCTACCCGATAGCTTAGATCACGTGAGTAGTA
CTAAGTGCAGGCTACTACATGTATCCGATGGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTAC
TATGCATACCCGATAGCTTCGA
Found at i:1592081 original size:46 final size:45
Alignment explanation
Indices: 1592031--1592206 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 45
1592021 TGGTTGAGCA
*
1592031 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
1592077 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
* * *
1592122 CATCCGAACTCGTTGAGTTGAGTCCAAGCTCACTTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
1592170 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1592207 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.57
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:1592187 original size:93 final size:93
Alignment explanation
Indices: 1592028--1592199 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
1592018 GGATGGTTGA
* * * * *
1592028 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGCTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1592093 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
1592121 GCATCCGAACTCGTTGAGTTGAGTCCAAGCTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGCTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1592186 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
1592200 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGCTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:1597403 original size:27 final size:27
Alignment explanation
Indices: 1597363--1597447 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
1597353 AGCATGGCTG
* *
1597363 CCAGA-ACAGATATTGTGACAGTGTCA
1 CCAGATACAGATATTGTGACAGAGCCA
*
1597389 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGATACAGATATTGTGACAGAGCCA
* * * *
1597416 CCAGAT-TAGATATTTTTGGCATAGCCA
1 CCAGATACAGATA-TTGTGACAGAGCCA
1597443 CCAGA
1 CCAGA
1597448 ACGCTTCCTC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (27 bp):
CCAGATACAGATATTGTGACAGAGCCA
Found at i:1605186 original size:27 final size:27
Alignment explanation
Indices: 1605142--1605252 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
1605132 GGGCTGCCAA
* *
1605142 AACAGATA-TTATGACAGAGTCACCAG
1 AACAGATATTTATGGCAGAGCCACCAG
*
1605168 ATACAGATA-TTGTGGCAGAGCCACCAG
1 A-ACAGATATTTATGGCAGAGCCACCAG
* * *
1605195 AACAGATATTTGTGGCATAGCCACTAG
1 AACAGATATTTATGGCAGAGCCACCAG
*
1605222 AAACAGATATTTATGGCATAGCCACCAG
1 -AACAGATATTTATGGCAGAGCCACCAG
1605250 AAC
1 AAC
1605253 GCTTCCTCCA
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 8 0.11
27 42 0.56
28 25 0.33
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (27 bp):
AACAGATATTTATGGCAGAGCCACCAG
Found at i:1611096 original size:27 final size:27
Alignment explanation
Indices: 1611049--1611150 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 27
1611039 ATGTTGATTA
* * *
1611049 TGGCTTTGTGCAAATCGTATTTACCAG
1 TGGCTATGTGCCAATCATATTTACCAG
* *
1611076 TGGCTATGTGCCTATCATATTTATC-G
1 TGGCTATGTGCCAATCATATTTACCAG
* * *
1611102 ATGACTCTGTGTCAATCATATTTACCCAG
1 -TGGCTATGTGCCAATCATATTTA-CCAG
* * *
1611131 -GGCTGTGTGCCGATTATATT
1 TGGCTATGTGCCAATCATATT
1611151 ACTGTCGCTG
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
26 1 0.02
27 54 0.95
28 1 0.02
29 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
TGGCTATGTGCCAATCATATTTACCAG
Found at i:1617602 original size:55 final size:56
Alignment explanation
Indices: 1617541--1617653 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
1617531 AGATCGGTGA
1617541 TAGAGTATTCTTGAAAGTATCTTCCT-GAAAAAGATCCTTCGATTTGTCACAAAGG
1 TAGAGTATTCTTGAAAGTATCTTCCTGGAAAAAGATCCTTCGATTTGTCACAAAGG
* *
1617596 TAGAGTATTCTTGAAAGTATCTTCGTGGGAAAAGATCCTTCGATTTGTCACAAAGG
1 TAGAGTATTCTTGAAAGTATCTTCCTGGAAAAAGATCCTTCGATTTGTCACAAAGG
1617652 TA
1 TA
1617654 AATTGAGTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 25 0.45
56 30 0.55
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (56 bp):
TAGAGTATTCTTGAAAGTATCTTCCTGGAAAAAGATCCTTCGATTTGTCACAAAGG
Found at i:1622311 original size:23 final size:23
Alignment explanation
Indices: 1622283--1622334 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
1622273 TTTTCTCTTC
*
1622283 TTTCATTCTCTTGCTCTCTTAGT
1 TTTCATTCTCTTGCGCTCTTAGT
1622306 TTTCATTCTCTTGCGCTCTTAGT
1 TTTCATTCTCTTGCGCTCTTAGT
1622329 TCTTCA
1 T-TTCA
1622335 AGCCGAGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.10, C:0.27, G:0.10, T:0.54
Consensus pattern (23 bp):
TTTCATTCTCTTGCGCTCTTAGT
Found at i:1623690 original size:27 final size:27
Alignment explanation
Indices: 1623562--1623703 Score: 180
Period size: 27 Copynumber: 5.3 Consensus size: 27
1623552 ATGGAGGAAG
1623562 TGTTCTGGTGGCTATGCCACAAATATC
1 TGTTCTGGTGGCTATGCCACAAATATC
*
1623589 TGTTCTAGTGGCTATGCCACAAATATC
1 TGTTCTGGTGGCTATGCCACAAATATC
*
1623616 TGTTCTGGTGGCTATACCACAAATATC
1 TGTTCTGGTGGCTATGCCACAAATATC
* * *
1623643 TATTCTGGTGGCTCTACCAC-AATATC
1 TGTTCTGGTGGCTATGCCACAAATATC
* * * *
1623669 TGTATCTGGTGACTCTGTCAC-AATATT
1 TGT-TCTGGTGGCTATGCCACAAATATC
1623696 TGTTCTGG
1 TGTTCTGG
1623704 AAGCCATGCT
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
26 13 0.12
27 91 0.88
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (27 bp):
TGTTCTGGTGGCTATGCCACAAATATC
Found at i:1628871 original size:27 final size:27
Alignment explanation
Indices: 1628841--1629100 Score: 331
Period size: 27 Copynumber: 9.6 Consensus size: 27
1628831 TTAGTTTACC
1628841 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
1628868 AAATCACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
1628895 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * **
1628922 AAATTACCAAAATACCCTTGGTCTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
1628949 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** * * *
1628976 AAATTATTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
1629003 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
1629030 AAATTATCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
1629057 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
*
1629084 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
1629101 TCGACCTGTA
Statistics
Matches: 201, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 201 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:1628906 original size:54 final size:54
Alignment explanation
Indices: 1628841--1629101 Score: 380
Period size: 54 Copynumber: 4.8 Consensus size: 54
1628831 TTAGTTTACC
*
1628841 AAATTACCAAAATACCCCTGGTTTGTAAAATCACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * * *
1628895 AAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTCTACA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* *
1628949 AAATTACCAAAATACCCCTGGTTTGTAAAATTATTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
* * * * *
1629003 AAATTACCAAAATACCCCTAGTTTGTAAAATTA-TCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACT-AAAATACCCTTGGTTTATA
* *
1629057 AAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCT
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCT
1629102 CGACCTGTAA
Statistics
Matches: 184, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 182 0.99
55 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATA
Found at i:1629111 original size:81 final size:81
Alignment explanation
Indices: 1628841--1629161 Score: 292
Period size: 81 Copynumber: 4.0 Consensus size: 81
1628831 TTAGTTTACC
* * * * * * *
1628841 AAATTACCAAAATACCC-CTGGTTTGTAAAATCA-CTAAAATACCCTTGGTTTATAAAATCACCA
1 AAATTACCAAAATACCCTC-GATCTGTAAAATTATC-AAAATACCCCTGATTTGTAAAATTACCA
*
1628904 AAATACCCCTGGTTTGTA
64 AAATACCCCTGATTTGTA
* * ** * * **
1628922 AAATTACCAAAATACCCTTGGTCTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTATTAAA
1 AAATTACCAAAATACCCTCGATCTGTAAAATTATCAAAATACCCCTGATTTGTAAAATTACCAAA
* *
1628987 ATACCCTTTG-TTTATA
66 ATACCC-CTGATTTGTA
* * *
1629003 AAATTACCAAAATACCC-CTAGTTTGTAAAATTATCAAAATACCCCTGATTTGTGAAATTACCAA
1 AAATTACCAAAATACCCTCGA-TCTGTAAAATTATCAAAATACCCCTGATTTGTAAAATTACCAA
*
1629067 AATACCCCTGATTTGTG
65 AATACCCCTGATTTGTA
* * ** * *
1629084 AAATTACTAAAATACCCTCGACCTGTAAAATTATTGAAATA-CCATCGACTTGTAAAATTACCAA
1 AAATTACCAAAATACCCTCGATCTGTAAAATTATCAAAATACCCCT-GATTTGTAAAATTACCAA
* *
1629148 AGTACCCTTGATTT
65 AATACCCCTGATTT
1629162 ACAGAATTAC
Statistics
Matches: 196, Mismatches: 37, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
80 5 0.03
81 186 0.95
82 5 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (81 bp):
AAATTACCAAAATACCCTCGATCTGTAAAATTATCAAAATACCCCTGATTTGTAAAATTACCAAA
ATACCCCTGATTTGTA
Found at i:1629114 original size:27 final size:28
Alignment explanation
Indices: 1628841--1629155 Score: 190
Period size: 27 Copynumber: 11.6 Consensus size: 28
1628831 TTAGTTTACC
* **
1628841 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTCTGACTTGTA
* ** *
1628868 AAATCACTAAAATACCCT-TGGTTTATA
1 AAATTACTAAAATACCCTCTGACTTGTA
* * **
1628895 AAATCACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTCTGACTTGTA
* * **
1628922 AAATTACCAAAATACCCT-TG-GTCTACA
1 AAATTACTAAAATACCCTCTGACT-TGTA
* **
1628949 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTCTGACTTGTA
* * * *
1628976 AAATTATTAAAATACCCTTTG-TTTATA
1 AAATTACTAAAATACCCTCTGACTTGTA
* *
1629003 AAATTACCAAAATACCC-CT-AGTTTGTA
1 AAATTACTAAAATACCCTCTGA-CTTGTA
* *
1629030 AAATTA-TCAAAATACCC-CTGATTTGTG
1 AAATTACT-AAAATACCCTCTGACTTGTA
* * *
1629057 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACTAAAATACCCTCTGACTTGTA
*
1629084 AAATTACTAAAATACCCTC-GACCTGTA
1 AAATTACTAAAATACCCTCTGACTTGTA
* * *
1629111 AAATTATTGAAATACCATC-GACTTGTA
1 AAATTACTAAAATACCCTCTGACTTGTA
* *
1629138 AAATTACCAAAGTACCCT
1 AAATTACTAAAATACCCT
1629156 TGATTTACAG
Statistics
Matches: 239, Mismatches: 36, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
26 2 0.01
27 232 0.97
28 5 0.02
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (28 bp):
AAATTACTAAAATACCCTCTGACTTGTA
Found at i:1629115 original size:54 final size:54
Alignment explanation
Indices: 1628841--1629172 Score: 364
Period size: 54 Copynumber: 6.1 Consensus size: 54
1628831 TTAGTTTACC
* *
1628841 AAATTACCAAAATACCCCTGGTTTGTAAAATCACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGATTTATA
* * * * *
1628895 AAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTCTACA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGATTTATA
*
1628949 AAATTACCAAAATACCCCTGGTTTGTAAAATTATTAAAATACCCTTTG-TTTATA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCC-TTGATTTATA
* * * *
1629003 AAATTACCAAAATACCCCTAGTTTGTAAAATTA-TCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACT-AAAATACCCTTGATTTATA
* * * ** *
1629057 AAATTACCAAAATACCCCTGATTTGTGAAATTACTAAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGATTTATA
*** * ** * * *
1629111 AAATTATTGAAATA-CCATCGACTTGTAAAATTACCAAAGTACCCTTGATTTACA
1 AAATTACCAAAATACCCCT-GGTTTGTAAAATTACTAAAATACCCTTGATTTATA
*
1629165 GAATTACC
1 AAATTACC
1629173 GTTTTACCCT
Statistics
Matches: 235, Mismatches: 38, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
53 6 0.03
54 225 0.96
55 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGATTTATA
Found at i:1629169 original size:27 final size:27
Alignment explanation
Indices: 1629137--1629197 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1629127 ATCGACTTGT
1629137 AAAATTACCAAAGTACCCTTGATTTAC
1 AAAATTACCAAAGTACCCTTGATTTAC
* ****
1629164 AGAATTACCGTTTTACCCTTGATTTAC
1 AAAATTACCAAAGTACCCTTGATTTAC
1629191 AAAATTA
1 AAAATTA
1629198 TCGAAATACC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (27 bp):
AAAATTACCAAAGTACCCTTGATTTAC
Found at i:1629223 original size:27 final size:27
Alignment explanation
Indices: 1629193--1629468 Score: 401
Period size: 27 Copynumber: 10.3 Consensus size: 27
1629183 TGATTTACAA
*
1629193 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1629220 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1629247 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1629274 AATTACCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
1629301 AATTATCGCAATACCCATGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
1629328 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
1629355 AATTACCGAAATACCCCTGTAGTGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
1629382 AATTACCAAAATACTCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
1629409 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
1629436 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
1629462 AATTACC
1 AATTACC
1629469 ATTTTGCCCC
Statistics
Matches: 224, Mismatches: 25, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
26 16 0.07
27 208 0.93
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:1629947 original size:22 final size:22
Alignment explanation
Indices: 1629895--1629959 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
1629885 TTAAAGCCTT
* *
1629895 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
1629917 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
1629939 TTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
1629960 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:1630713 original size:18 final size:17
Alignment explanation
Indices: 1630685--1630718 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1630675 GATCTTAGCC
1630685 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
1630702 CATTATCAGAATTAGAA
1 CATTA-CAGAATAAGAA
1630719 CCAAAATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:1630736 original size:6 final size:6
Alignment explanation
Indices: 1630706--1630822 Score: 96
Period size: 6 Copynumber: 19.3 Consensus size: 6
1630696 AAGAAACATT
* * * * *
1630706 ATCAGA ATTAGA ACCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
1630755 ATCAGA ATCAGT ATCAGTA A-CAGA ATCAAA ATCAGA ATCAGT ATTAGTA
1 ATCAGA ATCAGA ATCAG-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A
1630804 A-CAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
1630823 GTGAATGCAA
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
5 5 0.06
6 75 0.87
7 5 0.06
8 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:1630782 original size:24 final size:24
Alignment explanation
Indices: 1630727--1630819 Score: 116
Period size: 24 Copynumber: 3.8 Consensus size: 24
1630717 AACCAAAATG
*
1630727 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCA-GTAAC
*
1630752 AGAATCAGAATCAGTATCAGTAAC
1 AGAATCAGAATCAGAATCAGTAAC
* **
1630776 AGAATCAAAATCAGAATCAGTATT
1 AGAATCAGAATCAGAATCAGTAAC
1630800 AGTAA-CAGAATCAGAATCAG
1 AG-AATCAGAATCAGAATCAG
1630820 AATGTGAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
24 40 0.67
25 20 0.33
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.19
Consensus pattern (24 bp):
AGAATCAGAATCAGAATCAGTAAC
Found at i:1630790 original size:30 final size:30
Alignment explanation
Indices: 1630754--1630822 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
1630744 CAGGTGACAG
1630754 AATCAGAATCAGTATCAGTAACAGAATCAA
1 AATCAGAATCAGTATCAGTAACAGAATCAA
* *
1630784 AATCAGAATCAGTATTAGTAACAGAATCAG
1 AATCAGAATCAGTATCAGTAACAGAATCAA
1630814 AATCAGAAT
1 AATCAGAAT
1630823 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.22
Consensus pattern (30 bp):
AATCAGAATCAGTATCAGTAACAGAATCAA
Found at i:1630976 original size:27 final size:26
Alignment explanation
Indices: 1630940--1631019 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
1630930 AGCATGGCTG
*
1630940 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGACAGAGCCA
* *
1630966 CCAGATACAGATATTGTGGCTGAGCCA
1 CCAGA-ACAGATATTGTGACAGAGCCA
* * * *
1630993 CCAAAACAGATAATGTGGCAAAGCCA
1 CCAGAACAGATATTGTGACAGAGCCA
1631019 C
1 C
1631020 TTAACAGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
26 24 0.52
27 22 0.48
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATTGTGACAGAGCCA
Found at i:1631211 original size:22 final size:22
Alignment explanation
Indices: 1631163--1631221 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
1631153 GTAAATACGT
*
1631163 TTGGCACAAAGCGATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
1631185 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
1631207 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
1631222 CAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:1631368 original size:27 final size:26
Alignment explanation
Indices: 1631329--1631411 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
1631319 TCGATTGGTC
* * *
1631329 AACAGATGTTGTGACAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
1631355 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
1631382 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
1631409 AAC
1 AAC
1631412 GCTTCCTCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 8 0.16
27 43 0.84
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:1631875 original size:27 final size:27
Alignment explanation
Indices: 1631638--1631877 Score: 270
Period size: 27 Copynumber: 8.9 Consensus size: 27
1631628 GCAAAATGGA
* * * *
1631638 AATTTTACCCCACAAGGGTATCTCTG-T
1 AATTCTACCCTACAGGGGTATTTC-GAT
*
1631665 AATTCTACCCTACAGGGGTATTTCGGT
1 AATTCTACCCTACAGGGGTATTTCGAT
* * **
1631692 ATTTTTACCCTACAATGGTATTTCGAT
1 AATTCTACCCTACAGGGGTATTTCGAT
* * *
1631719 AATACTACCCTAAAGGGGTATTT-TAGT
1 AATTCTACCCTACAGGGGTATTTCGA-T
*
1631746 AATTCTACCCTGCAGGGGTATTTC-AGT
1 AATTCTACCCTACAGGGGTATTTCGA-T
* *
1631773 AATTCTACCCTACATGGGTATTTCGGT
1 AATTCTACCCTACAGGGGTATTTCGAT
* *
1631800 AATTCTACCCTACAGGCGTATTTCGGT
1 AATTCTACCCTACAGGGGTATTTCGAT
*
1631827 AATTCTACCATACAGGGGTATTTCGAT
1 AATTCTACCCTACAGGGGTATTTCGAT
1631854 AATTCTACCCTACAGGGGTATTTC
1 AATTCTACCCTACAGGGGTATTTC
1631878 AGTAAATTCA
Statistics
Matches: 181, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.01
27 179 0.99
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (27 bp):
AATTCTACCCTACAGGGGTATTTCGAT
Found at i:1631925 original size:27 final size:27
Alignment explanation
Indices: 1631889--1632331 Score: 517
Period size: 27 Copynumber: 16.4 Consensus size: 27
1631879 GTAAATTCAC
* *
1631889 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* *
1631916 AATTAAGGGTAAAACGATAATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* ** *
1631943 ACTCAAGGGTAAAATAGTGATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
*
1631970 AATCAAGGGTAAAACGGTAATTCTATA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* *
1631997 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* ** *
1632024 ACTCAAGGGTAAAATAGTGATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
*
1632051 AATCAAGGGTAAAACGGTAATTCTGTG
1 AATCAAGGGTAAAACGGTAATTCTGTA
* *
1632078 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* * ** *
1632105 ACTCAATGGTAAAACAATGATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
*
1632132 AATCAAGGGTAAAACGGTAATTCTATA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* *
1632159 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* ** *
1632186 ACTCAAGGGTAAAATAGTGATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* * *
1632213 AATCAATGGTAAAACGATAATTCTGTG
1 AATCAAGGGTAAAACGGTAATTCTGTA
* * *
1632240 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCAAGGGTAAAACGGTAATTCTGTA
* **
1632267 AATCGAGGGTAAAACAATAATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
*
1632294 AATCAAGAGTAAAACGGTAATTCTGTA
1 AATCAAGGGTAAAACGGTAATTCTGTA
*
1632321 AATCAGGGGTA
1 AATCAAGGGTA
1632332 CTTTGGTAAT
Statistics
Matches: 343, Mismatches: 73, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 343 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (27 bp):
AATCAAGGGTAAAACGGTAATTCTGTA
Done.