Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, whole genome shotgun sequence
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: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 4 of 10
Found at i:1248946 original size:22 final size:23
Alignment explanation
Indices: 1248899--1248955 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
1248889 TGTTCTTTCA
*
1248899 ATTTATATTA-TT-ATTATTATT
1 ATTTATTTTATTTAATTATTATT
1248920 ATTTA-TTTATTTAATTATTTATT
1 ATTTATTTTATTTAATTA-TTATT
1248943 -TTTATTTTATTTA
1 ATTTATTTTATTTA
1248956 CTCATATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 3 0.10
21 7 0.23
22 8 0.26
23 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
ATTTATTTTATTTAATTATTATT
Found at i:1249367 original size:16 final size:17
Alignment explanation
Indices: 1249346--1249377 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1249336 TGGCTCTCAA
1249346 AATAATT-ATTTTATTT
1 AATAATTAATTTTATTT
1249362 AATAATTAATTTTATT
1 AATAATTAATTTTATT
1249378 CTTCAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATAATTAATTTTATTT
Found at i:1253387 original size:15 final size:15
Alignment explanation
Indices: 1253358--1253411 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1253348 TAGTATAATT
**
1253358 TTTTATTTTAATTTA
1 TTTTATTTTTCTTTA
1253373 TTTTATTTTTCTTTA
1 TTTTATTTTTCTTTA
*
1253388 TATTCATTTTTCTTT-
1 T-TTTATTTTTCTTTA
*
1253403 TGTTATTTT
1 TTTTATTTT
1253412 CATTTTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 6 0.18
15 15 0.45
16 12 0.36
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTATTTTTCTTTA
Found at i:1255202 original size:31 final size:31
Alignment explanation
Indices: 1255160--1255218 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1255150 TGTAATTTTT
*
1255160 ATTTTTATTTTTTTATATTTTCTTATATTTA
1 ATTTTTATTTTTTTATATTTTCTCATATTTA
* * *
1255191 ATTTTTCTTTTTTTTTCTTTTCTCATAT
1 ATTTTTATTTTTTTATATTTTCTCATAT
1255219 CTATGCCGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (31 bp):
ATTTTTATTTTTTTATATTTTCTCATATTTA
Found at i:1262572 original size:21 final size:20
Alignment explanation
Indices: 1262547--1262598 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1262537 TTTGTTGATA
*
1262547 TATTAGTTTTAATTATTAGTT
1 TATTAGTTTTAATT-TTACTT
*
1262568 TATTAGTTTCAATTTTACTT
1 TATTAGTTTTAATTTTACTT
*
1262588 T-TTAATTTTAA
1 TATTAGTTTTAA
1262599 CAGTTTAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 8 0.30
20 6 0.22
21 13 0.48
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (20 bp):
TATTAGTTTTAATTTTACTT
Found at i:1263534 original size:20 final size:20
Alignment explanation
Indices: 1263509--1263547 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1263499 ATAAATAATG
*
1263509 AATTCTTGATGATGATTGAT
1 AATTCTTGATGATAATTGAT
1263529 AATTCTTGATGATAATTGA
1 AATTCTTGATGATAATTGA
1263548 GAATGGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (20 bp):
AATTCTTGATGATAATTGAT
Found at i:1272003 original size:32 final size:32
Alignment explanation
Indices: 1271967--1272066 Score: 182
Period size: 32 Copynumber: 3.1 Consensus size: 32
1271957 TAGTCAACTA
1271967 AGAGGCTACTGCCAAAAACTAGGTTCAGAGAT
1 AGAGGCTACTGCCAAAAACTAGGTTCAGAGAT
1271999 AGAGGCTACTGCCAAAAACTAGGTTCAGAGAT
1 AGAGGCTACTGCCAAAAACTAGGTTCAGAGAT
* *
1272031 AGAGCCTACTGCCAAAAACTAGGTTCAGAGAC
1 AGAGGCTACTGCCAAAAACTAGGTTCAGAGAT
1272063 AGAG
1 AGAG
1272067 ATGACTTAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (32 bp):
AGAGGCTACTGCCAAAAACTAGGTTCAGAGAT
Found at i:1275538 original size:2 final size:2
Alignment explanation
Indices: 1275526--1275563 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1275516 TTGTATTTTC
*
1275526 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1275564 TATTCCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1277977 original size:33 final size:35
Alignment explanation
Indices: 1277940--1278015 Score: 102
Period size: 33 Copynumber: 2.2 Consensus size: 35
1277930 GTTGTTCTAC
* *
1277940 GTGAAGTAACACTTTACTTGTTCTAATTG-TT-GT
1 GTGAAGTAACACTTCACATGTTCTAATTGTTTAGT
* *
1277973 GTGAAGTAACACTTCACATGTTTTAGTTGTTTAGT
1 GTGAAGTAACACTTCACATGTTCTAATTGTTTAGT
1278008 GTGAAGTA
1 GTGAAGTA
1278016 GTGCTTCACT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 25 0.68
34 2 0.05
35 10 0.27
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (35 bp):
GTGAAGTAACACTTCACATGTTCTAATTGTTTAGT
Found at i:1282002 original size:27 final size:27
Alignment explanation
Indices: 1281971--1282022 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1281961 TTGCTCCATA
* * *
1281971 GGCTACTCAAGATGAGGTTGTTCCTCT
1 GGCTACTCAAAATAAGGATGTTCCTCT
1281998 GGCTACTCAAAATAAGGATGTTCCT
1 GGCTACTCAAAATAAGGATGTTCCT
1282023 AACAATGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (27 bp):
GGCTACTCAAAATAAGGATGTTCCTCT
Found at i:1285816 original size:29 final size:26
Alignment explanation
Indices: 1285782--1285858 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 26
1285772 GTATAAGATA
1285782 AGAAGCTGTATGTGAACAAGTACAAG
1 AGAAGCTGTATGTGAACAAGTACAAG
* ** * *
1285808 AGAATAAGCTTTACATGAATAGGTACAAG
1 AG---AAGCTGTATGTGAACAAGTACAAG
*
1285837 AGAAGGTGTATGTGAACAAGTA
1 AGAAGCTGTATGTGAACAAGTA
1285859 TACGAGAACC
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
26 16 0.43
29 21 0.57
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.22
Consensus pattern (26 bp):
AGAAGCTGTATGTGAACAAGTACAAG
Found at i:1286257 original size:35 final size:35
Alignment explanation
Indices: 1286101--1286250 Score: 192
Period size: 35 Copynumber: 4.3 Consensus size: 35
1286091 AGTAATGTTC
* * * * *
1286101 CACTTATTCTAATTGTTCTGCGTGAAGTAGCGCTT
1 CACTTGTTTTAATTGTTTTACGTGAAGTAGCACTT
* *
1286136 CGCTTGTTTTAATTGTTTTACGTGAAGTAGCATTT
1 CACTTGTTTTAATTGTTTTACGTGAAGTAGCACTT
*
1286171 CACTTGTTTTAATTGTTTTACGTGAAGTAGCATTT
1 CACTTGTTTTAATTGTTTTACGTGAAGTAGCACTT
* **
1286206 CACTTGTTTTAATTGTTTTATGTGAAGTAGTGCTT
1 CACTTGTTTTAATTGTTTTACGTGAAGTAGCACTT
*
1286241 CACTTATTTT
1 CACTTGTTTT
1286251 GGTTGTTCTC
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 102 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (35 bp):
CACTTGTTTTAATTGTTTTACGTGAAGTAGCACTT
Found at i:1288173 original size:22 final size:23
Alignment explanation
Indices: 1288147--1288221 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
1288137 GTTTAGAGTT
1288147 TGTGA-AAGGCCATGGT-GGAATG
1 TGTGACAAGG-CATGGTGGGAATG
* *
1288169 TGTGACATGGCATGGTGGGAGTG
1 TGTGACAAGGCATGGTGGGAATG
* * * * *
1288192 TGTGACACGTCATGATGAGAATA
1 TGTGACAAGGCATGGTGGGAATG
1288215 TGTGACA
1 TGTGACA
1288222 CTGTTGTGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
22 11 0.26
23 32 0.74
ACGTcount: A:0.27, C:0.11, G:0.37, T:0.25
Consensus pattern (23 bp):
TGTGACAAGGCATGGTGGGAATG
Found at i:1288205 original size:23 final size:22
Alignment explanation
Indices: 1288157--1288222 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
1288147 TGTGAAAGGC
*
1288157 CATGGTGGAATGTGTGACATGG
1 CATGGTGGAATGTGTGACACGG
* *
1288179 CATGGTGGGAGTGTGTGACACGT
1 CATGGT-GGAATGTGTGACACGG
* *
1288202 CATGATGAGAATATGTGACAC
1 CATGGTG-GAATGTGTGACAC
1288223 TGTTGTGACA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 7 0.19
23 29 0.81
ACGTcount: A:0.26, C:0.12, G:0.36, T:0.26
Consensus pattern (22 bp):
CATGGTGGAATGTGTGACACGG
Found at i:1288299 original size:23 final size:23
Alignment explanation
Indices: 1288250--1288349 Score: 94
Period size: 23 Copynumber: 4.3 Consensus size: 23
1288240 GTTTAGAGTT
** * * *
1288250 TGTGACATGCCATCGTGACAATG
1 TGTGACACACCATGGTGAGAATA
1288273 TGTGACACACCATGGT-ATGAATA
1 TGTGACACACCATGGTGA-GAATA
*
1288296 TGTGACACACTATGGTGAGAATA
1 TGTGACACACCATGGTGAGAATA
* ** *
1288319 TGTGAGACGGCATGGTGAGCATA
1 TGTGACACACCATGGTGAGAATA
1288342 TGTGACAC
1 TGTGACAC
1288350 GGTTGTGACA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 1 0.02
23 61 0.97
24 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (23 bp):
TGTGACACACCATGGTGAGAATA
Found at i:1288319 original size:104 final size:103
Alignment explanation
Indices: 1288133--1288323 Score: 240
Period size: 104 Copynumber: 1.8 Consensus size: 103
1288123 TATGTCATGG
* * *** * * *
1288133 CAGGGTTTAGAGTTTGTGAAAGGCCATGGTGGAATGTGTGACATGGCATGGTGGGAGTGTGTGAC
1 CAGGGTTTAGAGTTTGTGAAAGGCCATCGTGCAATGTGTGACACACCATGGTAGGAATATGTGAC
*
1288198 ACGTCATGATGAGAATATGTGACACTGTTGTGACACGA
66 ACCTCATGATGAGAATATGTGACACTGTTGTGACACGA
* * *
1288236 CAGGGTTTAGAGTTTGTGACATGCCATCGTGACAATGTGTGACACACCATGGTATGAATATGTGA
1 CAGGGTTTAGAGTTTGTGAAAGGCCATCGTG-CAATGTGTGACACACCATGGTAGGAATATGTGA
*
1288301 CACACT-ATGGTGAGAATATGTGA
65 CAC-CTCATGATGAGAATATGTGA
1288324 GACGGCATGG
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
103 28 0.38
104 44 0.60
105 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (103 bp):
CAGGGTTTAGAGTTTGTGAAAGGCCATCGTGCAATGTGTGACACACCATGGTAGGAATATGTGAC
ACCTCATGATGAGAATATGTGACACTGTTGTGACACGA
Found at i:1288508 original size:104 final size:104
Alignment explanation
Indices: 1288312--1288510 Score: 238
Period size: 104 Copynumber: 1.9 Consensus size: 104
1288302 ACACTATGGT
* * * ** *
1288312 GAGAATATGTGAGACGGCATGGTGAGCATATGTGACACGGTTGTGACACAACAAGGTTTAGAGTT
1 GAGAATATGTGAGACGACATGATGAGAATATGTGACACGACTGTGACACAACAAGGTTCAGAGTT
* * *
1288377 TGTGACACATCATGGAGGGAGTTTGTGACATGGAAAGGC
66 TGTGACACAGCATGGAGGGAATGTGTGACATGGAAAGGC
* * * * * *
1288416 GAGAATGTGTGAGATGACATGATGAGAATATGTGACATGACTGTGACACAGCAGGGTTCAGATTT
1 GAGAATATGTGAGACGACATGATGAGAATATGTGACACGACTGTGACACAACAAGGTTCAGAGTT
*
1288481 TGTGACA-AGCTATGGTGGGAATGTGTGACA
66 TGTGACACAGC-ATGGAGGGAATGTGTGACA
1288511 CAGTAGGGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
103 2 0.03
104 76 0.97
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (104 bp):
GAGAATATGTGAGACGACATGATGAGAATATGTGACACGACTGTGACACAACAAGGTTCAGAGTT
TGTGACACAGCATGGAGGGAATGTGTGACATGGAAAGGC
Found at i:1288583 original size:23 final size:23
Alignment explanation
Indices: 1288557--1288601 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1288547 AGTTTATGAT
*
1288557 ACCACAAGGTGAGAATGTGTGAG
1 ACCACAAGGTGAGAATATGTGAG
*
1288580 ACCACATGGTGAGAATATGTGA
1 ACCACAAGGTGAGAATATGTGA
1288602 CACAGTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (23 bp):
ACCACAAGGTGAGAATATGTGAG
Found at i:1288738 original size:23 final size:23
Alignment explanation
Indices: 1288632--1288755 Score: 106
Period size: 23 Copynumber: 5.4 Consensus size: 23
1288622 GTTCAGAGTT
* * * * *
1288632 TGTGACATGTCATGATGGGAATG
1 TGTGACACGGCATGGTGAGAATC
*
1288655 TGTGACATGGCATGGTGAGAATC
1 TGTGACACGGCATGGTGAGAATC
* *
1288678 TGTGACACGACATGTTGA-AATC
1 TGTGACACGGCATGGTGAGAATC
* *
1288700 ATGTGAGAAGGCATGGTGAGAATC
1 -TGTGACACGGCATGGTGAGAATC
* ** *
1288724 TATGACACGGCATGGTTTGAATA
1 TGTGACACGGCATGGTGAGAATC
1288747 TGTGACACG
1 TGTGACACG
1288756 TCGTGGTTTG
Statistics
Matches: 81, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
22 4 0.05
23 73 0.90
24 4 0.05
ACGTcount: A:0.29, C:0.13, G:0.31, T:0.27
Consensus pattern (23 bp):
TGTGACACGGCATGGTGAGAATC
Found at i:1289436 original size:87 final size:87
Alignment explanation
Indices: 1289289--1289473 Score: 230
Period size: 87 Copynumber: 2.1 Consensus size: 87
1289279 GTTTTTAGCT
* * * * **
1289289 TGTCACCACATTGAGTATTTTAGGACAATTTATGTAATGAGTTAGTAATTATAGTGATTGGTGTG
1 TGTCACCACATTGAGTATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTCATTGGCATG
* * *
1289354 TCACGACATGGCATGGTTGACA
66 TCACGACACGACATGGTTAACA
* *
1289376 TGTCACCACATT-AGGTATTTTA-GAGCAGTTCGTGTAACGAGTCAGTAATTATAGTCATTGGCA
1 TGTCACCACATTGA-GTATTTTAGGA-CAATTCATGTAACGAGTCAGTAATTATAGTCATTGGCA
*
1289439 TGTCACGATACGACATGGTTAACA
64 TGTCACGACACGACATGGTTAACA
1289463 TGTCACCACAT
1 TGTCACCACAT
1289474 GGCTCAGCAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
86 3 0.04
87 81 0.96
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (87 bp):
TGTCACCACATTGAGTATTTTAGGACAATTCATGTAACGAGTCAGTAATTATAGTCATTGGCATG
TCACGACACGACATGGTTAACA
Found at i:1289525 original size:31 final size:31
Alignment explanation
Indices: 1289490--1289594 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 31
1289480 GCATTGGCAC
** *
1289490 GTAACAACATTTGACTTGGTATGGTTAACGT
1 GTAACAACATTTGACTTGGTATGCATAACGA
* *
1289521 GTAACATCATTTGACTTGGTATGCATAGCGA
1 GTAACAACATTTGACTTGGTATGCATAACGA
* ** ** *
1289552 GTAACAACATTTTACTTAATATGCATAGTGT
1 GTAACAACATTTGACTTGGTATGCATAACGA
1289583 GTAACAACATTT
1 GTAACAACATTT
1289595 ATTTCTTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35
Consensus pattern (31 bp):
GTAACAACATTTGACTTGGTATGCATAACGA
Found at i:1291378 original size:150 final size:150
Alignment explanation
Indices: 1291029--1291552 Score: 516
Period size: 151 Copynumber: 3.5 Consensus size: 150
1291019 AGTAAGGATA
* * * * * * *
1291029 GTTCTAACGGTTTGTGTTCAACAATTCCATATATGTTTATCGAATAACATAGTAATATCTATGT-
1 GTTCTAACAGTTTGTGTTCAACATTTCCACATATATTTATTGAATAACACAGTAATTTCTAT-TA
* * * * ** * ** * *
1291093 TAGTAGTTAACCTATGTGACAACAACTTTTCAACCACCAACCGGTCATGCTCAGTCGCACAGTGC
65 TTGCAATTCACAGAGGTGATGACAAC-TTTCAACCACCAACCGGTCATGCTCAGTCACATAGTGC
1291158 TAATGAGCCATCGATAAGAATG
129 TAATGAGCCATCGATAAGAATG
* * * * * *
1291180 GTTATAACAGTTTGTATTCAACATTTCCATATATGTTTATTGAATAACACAGTAATTTTTGTTAT
1 GTTCTAACAGTTTGTGTTCAACATTTCCACATATATTTATTGAATAACACAGTAATTTCTATTAT
** * * * * * *
1291245 TGCAATTCATGGAGGTGATGATAGCTCTTCAACCACCAACCGGTCCTGCTCA-ACTACATAATTC
66 TGCAATTCACAGAGGTGATGACAACT-TTCAACCACCAACCGGTCATGCTCAGTC-ACATAGTGC
*
1291309 TAATGAG-CATCGGTAAGAATG
129 TAATGAGCCATCGATAAGAATG
* *
1291330 GTTCTAAC-GATTTGTGTTCAACATTTCCACATATATTTATCGAATAACATAGTAATTTCTATTA
1 GTTCTAACAG-TTTGTGTTCAACATTTCCACATATATTTATTGAATAACACAGTAATTTCTATTA
* * * *
1291394 TTCCAATTCACAGAGGTGATGACAACTTCTCAACCACCAATCTGTCTTGCTCAGTCACATAGTGC
65 TTGCAATTCACAGAGGTGATGACAACTT-TCAACCACCAACCGGTCATGCTCAGTCACATAGTGC
* * * **
1291459 TAACGAGCCGTCAATAAGAACA
129 TAATGAGCCATCGATAAGAATG
* * * * * *
1291481 GTTCGAACAGTTTGTGTTCACCATTTTCACATATAATTATTGAATAACACAATAATATCTATTAT
1 GTTCTAACAGTTTGTGTTCAACATTTCCACATATATTTATTGAATAACACAGTAATTTCTATTAT
1291546 TGCAATT
66 TGCAATT
1291553 GACCCATTCG
Statistics
Matches: 303, Mismatches: 62, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
149 2 0.01
150 126 0.42
151 174 0.57
152 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (150 bp):
GTTCTAACAGTTTGTGTTCAACATTTCCACATATATTTATTGAATAACACAGTAATTTCTATTAT
TGCAATTCACAGAGGTGATGACAACTTTCAACCACCAACCGGTCATGCTCAGTCACATAGTGCTA
ATGAGCCATCGATAAGAATG
Found at i:1292174 original size:81 final size:81
Alignment explanation
Indices: 1292048--1292235 Score: 204
Period size: 81 Copynumber: 2.3 Consensus size: 81
1292038 CACACAATTA
* * *
1292048 AGGCTAAAGGAGACCATGTTCCTCATGTCGATGCGGTAGTCAAGGCAG-TTGCCA-AAAGGGATG
1 AGGCTAAAGGAGACCATGTTCCTCAAGCCGATGCAGTAGTCAAGGCAGCTT--CAGAAAGGGATG
* *
1292111 GGAACCTTACATTAGTTC
64 GGAACCTTACATCAGTAC
* * * * * *
1292129 AGGCTGAAGGAAACCATGTTCCTTAAGCCGATGTAGTAG-CTAAGGCAGCTTCAGGAGGGGATGG
1 AGGCTAAAGGAGACCATGTTCCTCAAGCCGATGCAGTAGTC-AAGGCAGCTTCAGAAAGGGATGG
*
1292193 GCACCTTACATCAGTAC
65 GAACCTTACATCAGTAC
1292210 AGGCTAAAAGG-GACCATGTTCCTCAA
1 AGGCT-AAAGGAGACCATGTTCCTCAA
1292236 AGTACTCCCA
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
80 3 0.03
81 79 0.90
82 6 0.07
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (81 bp):
AGGCTAAAGGAGACCATGTTCCTCAAGCCGATGCAGTAGTCAAGGCAGCTTCAGAAAGGGATGGG
AACCTTACATCAGTAC
Found at i:1294049 original size:76 final size:76
Alignment explanation
Indices: 1293920--1294319 Score: 365
Period size: 76 Copynumber: 5.2 Consensus size: 76
1293910 TGACTAAGCA
* * * *
1293920 TGTCACCACAAGATGTCA-TGACATCTAACAAGTGAAGCATCGTATGTCACCCCATAATGCTGTA
1 TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGTATGTCACCCCATAATACTGCA
1293984 ACAGCTCAACG
66 ACAGCTCAACG
* ** * *
1293995 TGTCACCATAAGATGTCATTGACATCTAACAAGTGGAGTGTGGCATGTCACCCCATAATACTACA
1 TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGTATGTCACCCCATAATACTGCA
* *
1294060 A-TGACTCAATG
66 ACAG-CTCAACG
* * * * * * *
1294071 TGTCCCCACAAGATGTCATCGACATCTAACAAATGGACCATGGTGTGCCACCCCATAATACCATA
1 TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGTATGTCACCCCATAATA-C-TG
* * * *
1294136 CTACAATGACTTAGCA
64 CAAC-A-G-CTCAACG
* * *
1294152 TGTCACCACAAGATGTCATTGACATTTAACAAGTGGAGCATGGTGTGTCACCCTATAATACTGCA
1 TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGTATGTCACCCCATAATACTGCA
* * *
1294217 ACAACTCTATG
66 ACAGCTCAACG
* ** * ** * *
1294228 TGTTACCACAAGATGTCATCAACATCTAACAAGTAGAGTGTGGCATGTCACTCCATAATACTGCA
1 TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGTATGTCACCCCATAATACTGCA
* *
1294293 ACCA-CTTAGCG
66 A-CAGCTCAACG
*
1294304 TGTCACCATAAGATGT
1 TGTCACCACAAGATGT
1294320 TATCGAAATG
Statistics
Matches: 258, Mismatches: 59, Indels: 15
0.78 0.18 0.05
Matches are distributed among these distances:
75 18 0.07
76 169 0.66
77 3 0.01
78 5 0.02
79 4 0.02
80 1 0.00
81 58 0.22
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (76 bp):
TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGTATGTCACCCCATAATACTGCA
ACAGCTCAACG
Found at i:1294284 original size:157 final size:157
Alignment explanation
Indices: 1293995--1294288 Score: 381
Period size: 157 Copynumber: 1.9 Consensus size: 157
1293985 CAGCTCAACG
* **
1293995 TGTCACCATAAGATGTCATTGACATCTAACAAGTGGAGTGTGGCATGTCACCCCATAATACTACA
1 TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGCATGTCACCCCATAATACTACA
** * * * **
1294060 ATGACTCAATGTGTCCCCACAAGATGTCATCGACATCTAACAAATGGACCATGGTGTGCCACCCC
66 ACAACTCAATGTGTCACCACAAGATGTCATCAACATCTAACAAATAGACCATGGCATGCCACCCC
1294125 ATAATACCATACTACAATGACTTAGCA
131 ATAATACCATACTACAATGACTTAGCA
* ** * *
1294152 TGTCACCACAAGATGTCATTGACATTTAACAAGTGGAGCATGGTGTGTCACCCTATAATACTGCA
1 TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGCATGTCACCCCATAATACTACA
* * * *** * *
1294217 ACAACTCTATGTGTTACCACAAGATGTCATCAACATCTAACAAGTAGAGTGTGGCATGTCACTCC
66 ACAACTCAATGTGTCACCACAAGATGTCATCAACATCTAACAAATAGACCATGGCATGCCACCCC
1294282 ATAATAC
131 ATAATAC
1294289 TGCAACCACT
Statistics
Matches: 114, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
157 114 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (157 bp):
TGTCACCACAAGATGTCATTGACATCTAACAAGTGGAGCATGGCATGTCACCCCATAATACTACA
ACAACTCAATGTGTCACCACAAGATGTCATCAACATCTAACAAATAGACCATGGCATGCCACCCC
ATAATACCATACTACAATGACTTAGCA
Found at i:1294319 original size:233 final size:232
Alignment explanation
Indices: 1293907--1294325 Score: 595
Period size: 233 Copynumber: 1.8 Consensus size: 232
1293897 CATAATGTTG
1293907 CAATGACTAAGCATGTCACCACAAGATGTCATGACATCTAACAAGTGAAGCATCGTATGTCACCC
1 CAATGACTAAGCATGTCACCACAAGATGTCATGACATCTAACAAGTGAAGCATCGTATGTCACCC
* * * * ** *
1293972 CATAATGCTGTAACAGCTCAACGTGTCACCATAAGATGTCATTGACATCTAACAAGTGGAGTGTG
66 CATAATACTGCAACAACTCAACGTGTCACCACAAGATGTCATCAACATCTAACAAGTAGAGTGTG
** * *
1294037 GCATGTCACCCCATAATACTACAATGACTCAATGTGTCCCCACAAGATGTCATCGACATCTAACA
131 GCATGTCACCCCATAATACTACAACCACTCAACGTGTCACCACAAGATGTCATCGACATCTAACA
1294102 AATGGACCATGGTGTGCCACCCCATAATACCATACTA
196 AATGGACCATGGTGTGCCACCCCATAATACCATACTA
* * * * *
1294139 CAATGACTTAGCATGTCACCACAAGATGTCATTGACATTTAACAAGTGGAGCATGGTGTGTCACC
1 CAATGACTAAGCATGTCACCACAAGATGTCA-TGACATCTAACAAGTGAAGCATCGTATGTCACC
* * * *
1294204 CTATAATACTGCAACAACTCTATGTGTTACCACAAGATGTCATCAACATCTAACAAGTAGAGTGT
65 CCATAATACTGCAACAACTCAACGTGTCACCACAAGATGTCATCAACATCTAACAAGTAGAGTGT
* * * * * *
1294269 GGCATGTCACTCCATAATACTGCAACCACTTAGCGTGTCACCATAAGATGTTATCGA
130 GGCATGTCACCCCATAATACTACAACCACTCAACGTGTCACCACAAGATGTCATCGA
1294326 AATGGTTACA
Statistics
Matches: 160, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
232 30 0.19
233 130 0.81
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (232 bp):
CAATGACTAAGCATGTCACCACAAGATGTCATGACATCTAACAAGTGAAGCATCGTATGTCACCC
CATAATACTGCAACAACTCAACGTGTCACCACAAGATGTCATCAACATCTAACAAGTAGAGTGTG
GCATGTCACCCCATAATACTACAACCACTCAACGTGTCACCACAAGATGTCATCGACATCTAACA
AATGGACCATGGTGTGCCACCCCATAATACCATACTA
Found at i:1295719 original size:15 final size:16
Alignment explanation
Indices: 1295701--1295743 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1295691 AACATAAATT
*
1295701 AAAATAACTCATT-TA
1 AAAATAACTAATTATA
1295716 AAAATAAGCTAATTATA
1 AAAATAA-CTAATTATA
*
1295733 AAAACAACTAA
1 AAAATAACTAA
1295744 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 9 0.38
17 8 0.33
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAATAACTAATTATA
Found at i:1295743 original size:16 final size:15
Alignment explanation
Indices: 1295685--1295743 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
1295675 CCAAATTAAA
*
1295685 AAAAATAACATAAATT
1 AAAAATAAC-TAATTT
*
1295701 -AAAATAACTCATTT
1 AAAAATAACTAATTT
1295715 AAAAATAAGCTAATTAT
1 AAAAATAA-CTAATT-T
*
1295732 AAAAACAACTAA
1 AAAAATAACTAA
1295744 AAATAAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 4 0.11
15 15 0.42
16 9 0.25
17 8 0.22
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (15 bp):
AAAAATAACTAATTT
Found at i:1304837 original size:13 final size:14
Alignment explanation
Indices: 1304819--1304848 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1304809 GTTATGCCCG
1304819 TAGGTCTTCCT-CT
1 TAGGTCTTCCTGCT
1304832 TAGGTCTTCCTGCT
1 TAGGTCTTCCTGCT
1304846 TAG
1 TAG
1304849 CCTCACCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.10, C:0.27, G:0.20, T:0.43
Consensus pattern (14 bp):
TAGGTCTTCCTGCT
Found at i:1307795 original size:15 final size:14
Alignment explanation
Indices: 1307756--1307798 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
1307746 ATATTTTTTT
1307756 AAAAAAATATA-AC
1 AAAAAAATATATAC
1307769 ATAAATAAATATATAC
1 A-AAA-AAATATATAC
1307785 AAAAAATATATATA
1 AAAAAA-ATATATA
1307799 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.04
14 5 0.19
15 17 0.65
16 3 0.12
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAAAATATATAC
Found at i:1308255 original size:25 final size:23
Alignment explanation
Indices: 1308173--1308257 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 23
1308163 TCAATCATGT
* *
1308173 TGTTACACATCATGTTCAAAATA
1 TGTTACACACCATGTTCAAAAAA
* * *
1308196 TATTACACGCTATGTTC-AAAAA
1 TGTTACACACCATGTTCAAAAAA
**
1308218 TGTTACATGCCATGTTCAATGAAAA
1 TGTTACACACCATGTTCAA--AAAA
1308243 TGTTACACACCATGT
1 TGTTACACACCATGT
1308258 GCTAACAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
22 18 0.37
23 14 0.29
25 17 0.35
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (23 bp):
TGTTACACACCATGTTCAAAAAA
Found at i:1312569 original size:35 final size:34
Alignment explanation
Indices: 1312530--1312613 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
1312520 CATAACAAAT
1312530 ATAACCCTTACAATGCCTTTTTCACAAGAACAAGC
1 ATAACCCTTACAATGCCTTTTT-ACAAGAACAAGC
* * * *
1312565 ATAACCCATACAATGCCTTTTTACTAGAGCAGGC
1 ATAACCCTTACAATGCCTTTTTACAAGAACAAGC
*
1312599 ACAACCCTTACAATG
1 ATAACCCTTACAATG
1312614 TTACCTTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 22 0.51
35 21 0.49
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.25
Consensus pattern (34 bp):
ATAACCCTTACAATGCCTTTTTACAAGAACAAGC
Found at i:1321475 original size:72 final size:72
Alignment explanation
Indices: 1321358--1321495 Score: 276
Period size: 72 Copynumber: 1.9 Consensus size: 72
1321348 AGTAAACAAG
1321358 AAATTATATAGTTGATTAGTTTATAAGGTAAGAAATGAACTTTTATGAAGGAGGAAGTATATATT
1 AAATTATATAGTTGATTAGTTTATAAGGTAAGAAATGAACTTTTATGAAGGAGGAAGTATATATT
1321423 AAGCAAA
66 AAGCAAA
1321430 AAATTATATAGTTGATTAGTTTATAAGGTAAGAAATGAACTTTTATGAAGGAGGAAGTATATATT
1 AAATTATATAGTTGATTAGTTTATAAGGTAAGAAATGAACTTTTATGAAGGAGGAAGTATATATT
1321495 A
66 A
1321496 GATGGTGAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (72 bp):
AAATTATATAGTTGATTAGTTTATAAGGTAAGAAATGAACTTTTATGAAGGAGGAAGTATATATT
AAGCAAA
Found at i:1336921 original size:21 final size:21
Alignment explanation
Indices: 1336891--1336930 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1336881 GTGTGTGTAT
*
1336891 ATATATATATATGTACTTTAA
1 ATATAAATATATGTACTTTAA
*
1336912 ATATAAATATATTTACTTT
1 ATATAAATATATGTACTTT
1336931 TTATTTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (21 bp):
ATATAAATATATGTACTTTAA
Found at i:1344984 original size:39 final size:35
Alignment explanation
Indices: 1344958--1345037 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
1344948 AGTGTCTTGA
*
1344958 TAGAGGTTACGGCTGATCTTGCAAAAGGTAAGTTG
1 TAGAGGTTACGGCTGATCTTGCAAAAGGCAAGTTG
* * *
1344993 TTGAGGTTACGGTTGATCTTGCAAAAGACATA-TTG
1 TAGAGGTTACGGCTGATCTTGCAAAAGGCA-AGTTG
*
1345028 TAAAGGTTAC
1 TAGAGGTTAC
1345038 ACTTGACCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 37 0.97
36 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (35 bp):
TAGAGGTTACGGCTGATCTTGCAAAAGGCAAGTTG
Found at i:1349775 original size:27 final size:26
Alignment explanation
Indices: 1349737--1349787 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1349727 AACTAAATGA
1349737 GCTTTAATAGTAAAAAAATATTTTTGT
1 GCTTTAATAGT-AAAAAATATTTTTGT
*
1349764 GCTTTGAA-AGTAAAAGATATTTTT
1 GCTTT-AATAGTAAAAAATATTTTT
1349788 AAGTATGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 8 0.36
28 2 0.09
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (26 bp):
GCTTTAATAGTAAAAAATATTTTTGT
Found at i:1351595 original size:17 final size:16
Alignment explanation
Indices: 1351573--1351614 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
1351563 AATTAATATA
*
1351573 ATTTTTTTTATTTTTTT
1 ATTTTTTTTA-TTTTTC
1351590 ATTTTTTATTATTTTTC
1 ATTTTTT-TTATTTTTC
1351607 ATTTTTTT
1 ATTTTTTT
1351615 CTCTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 19 0.83
18 3 0.13
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.83
Consensus pattern (16 bp):
ATTTTTTTTATTTTTC
Found at i:1351614 original size:10 final size:9
Alignment explanation
Indices: 1351573--1351605 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
1351563 AATTAATATA
1351573 ATTTTTTTT
1 ATTTTTTTT
1351582 A-TTTTTTT
1 ATTTTTTTT
1351590 ATTTTTTATT
1 ATTTTTT-TT
1351600 ATTTTT
1 ATTTTT
1351606 CATTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 6 0.27
10 8 0.36
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:1351615 original size:9 final size:8
Alignment explanation
Indices: 1351575--1351614 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 8
1351565 TTAATATAAT
1351575 TTTTTTTA
1 TTTTTTTA
1351583 TTTTTTTA
1 TTTTTTTA
1351591 -TTTTTTA
1 TTTTTTTA
1351598 TTATTTTTCA
1 TT-TTTTT-A
1351608 TTTTTTT
1 TTTTTTT
1351615 CTCTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.24
8 9 0.31
9 10 0.34
10 3 0.10
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1359026 original size:77 final size:77
Alignment explanation
Indices: 1358933--1359096 Score: 274
Period size: 77 Copynumber: 2.1 Consensus size: 77
1358923 AATGCCATCT
*
1358933 ATTTTAATTTTGGGTGATTCATAAAAAATAAGAAATTGTTTCCTACTTTAAAAGTAATTGCTAAA
1 ATTTTAATTTTGGGTGATTCATAAAAAATAAGAAATTGTTTCCTACTTTAAAAGAAATTGCTAAA
* *
1358998 ATTAGGGATAGA
66 ATTAAGAATAGA
* *
1359010 ATTTTAATTTTGGGTGATTCATAAAGAATAAGAAATTGTTTCCTACTTTAAAAGAAATTTCTAAA
1 ATTTTAATTTTGGGTGATTCATAAAAAATAAGAAATTGTTTCCTACTTTAAAAGAAATTGCTAAA
*
1359075 ATTAAGAATAGT
66 ATTAAGAATAGA
1359087 ATTTTAATTT
1 ATTTTAATTT
1359097 CAAAAATTCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40
Consensus pattern (77 bp):
ATTTTAATTTTGGGTGATTCATAAAAAATAAGAAATTGTTTCCTACTTTAAAAGAAATTGCTAAA
ATTAAGAATAGA
Found at i:1367052 original size:167 final size:164
Alignment explanation
Indices: 1366753--1367313 Score: 522
Period size: 167 Copynumber: 3.3 Consensus size: 164
1366743 NNNNNNNNNN
* *
1366753 AATCAATTATGAGATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTA-GATGTGAC
1 AATCAATTATGAGATTATAAAT-CATTTAAAGCGAGTAATAAAGCTTTTGAA-GTATGA-GTGAC
* * * ** * * *
1366817 TATAAATAGACTTTTCTTATCAGTGAATGGCTTTTCCTTTATGTTTCTAGAGGCAAATAGTCAAT
63 TATAAATAGGCTTTTCTTGTCAATGAATGGCTTTT-CTACATGTTTCTTGAGGCAGATA-TTAAT
* *
1366882 TATAATATGTTTAACTAAAATTTAAAAAAATTCAGCCTAA
126 TATAATATGTTTAACAAAAATATAAAAAAATT-AGCCTAA
* *
1366922 ATTCAATTATGAGA-TATAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAGCTATGGGTGACTA
1 AATCAATTATGAGATTATAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAG-TATGAGTGACTA
* * ** *
1366986 TAAATAGGCTTTTCTTGTCAACGAATGGCTATTTCTACACGTTTCTTGAGATAGACACTTAATTA
65 TAAATAGGCTTTTCTTGTCAATGAATGGCT-TTTCTACATGTTTCTTGAGGCAGATA-TTAATTA
* * *
1367051 TAATCTGTTTGAACAAAAAATATAAGAAAATTTAACCTAA
128 TAATATGTTT-AAC-AAAAATATAA-AAAAATTAGCCTAA
* * * * *
1367091 AATCAATTATGAGATTACAAAACCGTTTAAAGTGAGTAAT-AAGACTTTTGAAAGAATGAGTGAC
1 AATCAATTATGAGATTA-TAAATCATTTAAAGCGAGTAATAAAG-CTTTTG-AAGTATGAGTGAC
* * * *
1367155 TCTAAAT-GGACTTTTCTTG-CAAATGAATGGCCTTTCTACATATTT-TTCAAGGCAGATATTCA
63 TATAAATAGG-CTTTTCTTGTC-AATGAATGGCTTTTCTACATGTTTCTT-GAGGCAGATATT-A
* * *
1367217 ATTATAGTATGTTTTAACAAAAAGTATAAAAAAATTTGACTTAA
124 ATTATAATATG-TTTAACAAAAA-TATAAAAAAATTAG-CCTAA
* * * * *
1367261 AATCAATTATGAGATTATAAAACAAATTACAGCGAGTAATAAGGCTTTCGAAG
1 AATCAATTATGAGATTATAAATC-ATTTAAAGCGAGTAATAAAGCTTTTGAAG
1367314 GTTTGTGTAA
Statistics
Matches: 320, Mismatches: 53, Indels: 38
0.78 0.13 0.09
Matches are distributed among these distances:
166 1 0.00
167 92 0.29
168 14 0.04
169 62 0.19
170 87 0.27
171 61 0.19
172 3 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (164 bp):
AATCAATTATGAGATTATAAATCATTTAAAGCGAGTAATAAAGCTTTTGAAGTATGAGTGACTAT
AAATAGGCTTTTCTTGTCAATGAATGGCTTTTCTACATGTTTCTTGAGGCAGATATTAATTATAA
TATGTTTAACAAAAATATAAAAAAATTAGCCTAA
Found at i:1367267 original size:170 final size:168
Alignment explanation
Indices: 1366753--1367308 Score: 522
Period size: 170 Copynumber: 3.3 Consensus size: 168
1366743 NNNNNNNNNN
* * *
1366753 AATCAATTATGAGATTATAAATCCATTTAAAGTGAGTAATAAGGCTTTTGAAGGTA-GATGTGAC
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAAGTATGA-GTGAC
* * * * * * * *
1366817 TATAAATAGACTTTTCTTATCAGTGAATGG-CTTT-TCCTTTATGTTTCTAGAGGCAAATAGTCA
65 TATAAATGGACTTTTCTT-GCAATGAATGGCCTTTCTAC-ATATTTTTC-A-AGGCAGATATTCA
* * * *
1366880 ATTATAATATG-TTTAACTAAAATTTAAAAAAATTCAGCCTAA
126 ATTATAATATGTTTTAACAAAAATATAAAAAAATTTAACCTAA
* * * *
1366922 ATTCAATTATGAGA-TAT-AAATCATTTAAAGCGAGTAATAA-AGCTTTTG-AAGCTATGGGTGA
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGA-CTTTTGAAAG-TATGAGTGA
* * ** * ** *
1366983 CTATAAATAGG-CTTTTCTTGTCAACGAATGGCTATTTCTACACGTTTCTT-GAGATAGACACTT
64 CTATAAAT-GGACTTTTCTTG-CAATGAATGGC-CTTTCTACATATTT-TTCAAGGCAGATA-TT
* * *
1367046 -AATTATAATCTGTTTGAACAAAAAATATAAGAAAATTTAACCTAA
124 CAATTATAATATGTTTTAAC-AAAAATATAAAAAAATTTAACCTAA
* * *
1367091 AATCAATTATGAGATTACAAAACCGTTTAAAGTGAGTAATAAGACTTTTGAAAGAATGAGTGACT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAAGTATGAGTGACT
*
1367156 CTAAATGGACTTTTCTTGCAAATGAATGGCCTTTCTACATATTTTTCAAGGCAGATATTCAATTA
66 ATAAATGGACTTTTCTTGC-AATGAATGGCCTTTCTACATATTTTTCAAGGCAGATATTCAATTA
* * *
1367221 TAGTATGTTTTAACAAAAAGTATAAAAAAATTTGACTTAA
130 TAATATGTTTTAACAAAAA-TATAAAAAAATTTAACCTAA
* * * * *
1367261 AATCAATTATGAGATTATAAAACAAATTACAGCGAGTAATAAGGCTTT
1 AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTT
1367309 CGAAGGTTTG
Statistics
Matches: 307, Mismatches: 59, Indels: 41
0.75 0.14 0.10
Matches are distributed among these distances:
166 2 0.01
167 72 0.23
168 11 0.04
169 60 0.20
170 100 0.33
171 58 0.19
172 4 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (168 bp):
AATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGACTTTTGAAAGTATGAGTGACT
ATAAATGGACTTTTCTTGCAATGAATGGCCTTTCTACATATTTTTCAAGGCAGATATTCAATTAT
AATATGTTTTAACAAAAATATAAAAAAATTTAACCTAA
Found at i:1368021 original size:171 final size:171
Alignment explanation
Indices: 1367776--1368164 Score: 474
Period size: 171 Copynumber: 2.3 Consensus size: 171
1367766 AGATAGATAG
* ** * * **
1367776 TCAATTATAATCTGTTTTATCCAAAATTGTTAAAAAATTCAACCTAAAATAAATTATAAGATTGT
1 TCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATAAATTATAAGATTAC
* * *
1367841 AATACCATTTAAAGTGAGTAATAAGGTTTTTGAAGGCATGGGTAACTAAAAATAGACTTTTCTTG
66 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCATGAGTAACTAAAAATAGACTTTTCTTG
* ** ** * * * *
1367906 TCAATGAATGGGTTTTTCTTCACGTTTTCCATGGCAAACAT
131 CCAATGAATGGCCTTTTCTTCACACTTTCAAAGCCAAACAA
* * *
1367947 TCAATTATAATCTGTTTTAACTAAAAAAGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAC
1 TCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATAAATTATAAGATTAC
* * * * * * *
1368012 AAAACCATTTACAGTGATTAGTAAGGCTTTTGAGGGGATGAGTTACTATAAATAGACTTTTCTTG
66 AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCATGAGTAACTAAAAATAGACTTTTCTTG
* *
1368077 CCAATGAATGTCCTTTTCTTCACACTTTCAAAGCCAGACAA
131 CCAATGAATGGCCTTTTCTTCACACTTTCAAAGCCAAACAA
*
1368118 TCAATTATAATATGTTTTAACCAAAAATA-TAAAAAAATTCAACTTAA
1 TCAATTATAATCTGTTTTAACCAAAAA-AGTAAAAAAATTCAACTTAA
1368165 NNNNNNNNNN
Statistics
Matches: 184, Mismatches: 33, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
171 183 0.99
172 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (171 bp):
TCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAATTCAACTTAAAATAAATTATAAGATTAC
AAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCATGAGTAACTAAAAATAGACTTTTCTTG
CCAATGAATGGCCTTTTCTTCACACTTTCAAAGCCAAACAA
Found at i:1370579 original size:18 final size:18
Alignment explanation
Indices: 1370557--1370594 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
1370547 TTTCCTCTCA
1370557 TTCTCTCTC-TTC-CTTT
1 TTCTCTCTCTTTCTCTTT
1370573 TTCTCTCTCTTTCTCTTT
1 TTCTCTCTCTTTCTCTTT
1370591 TTCT
1 TTCT
1370595 TTTCACCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (18 bp):
TTCTCTCTCTTTCTCTTT
Found at i:1377866 original size:17 final size:17
Alignment explanation
Indices: 1377844--1377877 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1377834 AAACATATAA
1377844 AATTAAATGCT-TAAATT
1 AATT-AATGCTATAAATT
1377861 AATTAATGCTATAAATT
1 AATTAATGCTATAAATT
1377878 GCAATGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
AATTAATGCTATAAATT
Found at i:1380459 original size:1 final size:1
Alignment explanation
Indices: 1380455--1380481 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1380445 TGAAAAAAGC
1380455 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1380482 CAACAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1383521 original size:53 final size:53
Alignment explanation
Indices: 1383440--1383602 Score: 182
Period size: 56 Copynumber: 3.0 Consensus size: 53
1383430 TTAAAGGTCT
***
1383440 TGTAAGGGTTATCGCTTGATCCCATTAAAAAGCAAGAATCCTTTAGTGGATTG
1 TGTAAGGGTTATCGCTTGATCTTGTTAAAAAGCAAGAATCCTTTAGTGGATTG
** * * *
1383493 TGTAAGGGTTATTACTTGATCTTGTTAAAAAAGCAAAAAATCCCTTTTGTGAATTG
1 TGTAAGGGTTATCGCTTGATCTTGTT-AAAAAGC-AAGAAT-CCTTTAGTGGATTG
* * * *
1383549 TGTAAGGGTTATCGTTTGATTTTGTTAAAAAGTAAGAATTCTTTTAGTGGATTG
1 TGTAAGGGTTATCGCTTGATCTTGTTAAAAAGCAAGAA-TCCTTTAGTGGATTG
1383603 AAAATTCTTT
Statistics
Matches: 89, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
53 21 0.24
54 22 0.25
55 12 0.13
56 34 0.38
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (53 bp):
TGTAAGGGTTATCGCTTGATCTTGTTAAAAAGCAAGAATCCTTTAGTGGATTG
Found at i:1384489 original size:43 final size:44
Alignment explanation
Indices: 1384442--1384561 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
1384432 AATATAATCA
* *
1384442 AAATAACTTTTACTATAATTAAATAATATTTT-CATCAAAATAC
1 AAATAACTTTTATTATAATTAAATAATATTTTGCATCAAAAGAC
* * * * * *
1384485 AAATATATTTTTATTAT-ATTTAATAGTATTTTGTATTAAAAGAT
1 AAATA-ACTTTTATTATAATTAAATAATATTTTGCATCAAAAGAC
*
1384529 AATTAAACCTTTTATTATAATTAAATAATATTT
1 AAAT-AA-CTTTTATTATAATTAAATAATATTT
1384562 AATATTAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
43 18 0.30
44 20 0.33
45 10 0.17
46 12 0.20
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (44 bp):
AAATAACTTTTATTATAATTAAATAATATTTTGCATCAAAAGAC
Found at i:1388106 original size:29 final size:30
Alignment explanation
Indices: 1388044--1388114 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
1388034 AATTAGTGAA
* *
1388044 AGGGGCTT-ATTTAAGTTAAAATAAAAGTTC
1 AGGGGCTTAATTAAAGTT-AAATAAAAGATC
1388074 AGGGGCTTAATTAAAGTT-AATAAAATGAT-
1 AGGGGCTTAATTAAAGTTAAATAAAA-GATC
*
1388103 AGGGACTTAATT
1 AGGGGCTTAATT
1388115 GATTTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 18 0.50
30 10 0.28
31 8 0.22
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (30 bp):
AGGGGCTTAATTAAAGTTAAATAAAAGATC
Found at i:1389747 original size:38 final size:38
Alignment explanation
Indices: 1389705--1389795 Score: 87
Period size: 38 Copynumber: 2.4 Consensus size: 38
1389695 ACATAGTCAC
* * *
1389705 AAAGGTGGGTATTCATTCGTCCATAC-CTACATTAACAT
1 AAAGGTGGGTATTCATTCATCCACACTC-ACATTAACAA
* * *
1389743 AAAGGCGGATACTT-ATTCATCCACACTCACATTATCAA
1 AAAGGTGGGTA-TTCATTCATCCACACTCACATTAACAA
*
1389781 AAAGGTGAGTATTCA
1 AAAGGTGGGTATTCA
1389796 AGCATTTGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
37 2 0.05
38 36 0.88
39 3 0.07
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (38 bp):
AAAGGTGGGTATTCATTCATCCACACTCACATTAACAA
Found at i:1390688 original size:21 final size:21
Alignment explanation
Indices: 1390672--1390715 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1390662 ACAAGTGTCT
*
1390672 ATGCTTAGAATATAAGTATCG
1 ATGCTTAGAATAAAAGTATCG
1390693 ATGCTTAGAATAAAAGTATCG
1 ATGCTTAGAATAAAAGTATCG
1390714 AT
1 AT
1390716 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (21 bp):
ATGCTTAGAATAAAAGTATCG
Found at i:1393727 original size:11 final size:11
Alignment explanation
Indices: 1393711--1393735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1393701 AGTGCAACCT
1393711 CAGTTGAAGGC
1 CAGTTGAAGGC
1393722 CAGTTGAAGGC
1 CAGTTGAAGGC
1393733 CAG
1 CAG
1393736 AGTTACCATA
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:0.20, G:0.36, T:0.16
Consensus pattern (11 bp):
CAGTTGAAGGC
Found at i:1395867 original size:40 final size:39
Alignment explanation
Indices: 1395821--1395903 Score: 96
Period size: 41 Copynumber: 2.1 Consensus size: 39
1395811 GTTTATTTTT
*
1395821 ATTTTT-TTAAAAAAATTATTTTTATAATTTTATTTGATAA
1 ATTTTTATTAAAAAAATTA-TTTTATAATTTAATTT-ATAA
* * *
1395861 ATTTTTTATTAATAGAATTATTTTATCATTTAATTTATAA
1 A-TTTTTATTAAAAAAATTATTTTATAATTTAATTTATAA
1395901 ATT
1 ATT
1395904 GAATAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
39 2 0.05
40 6 0.16
41 19 0.51
42 10 0.27
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (39 bp):
ATTTTTATTAAAAAAATTATTTTATAATTTAATTTATAA
Found at i:1396417 original size:18 final size:18
Alignment explanation
Indices: 1396394--1396428 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1396384 AGTTATTTTT
*
1396394 TCTCAAAAAAATCCTCTC
1 TCTCAAAAAAATACTCTC
1396412 TCTCAAAAAAATACTCT
1 TCTCAAAAAAATACTCT
1396429 TCCCTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (18 bp):
TCTCAAAAAAATACTCTC
Found at i:1434316 original size:45 final size:45
Alignment explanation
Indices: 1434252--1434340 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
1434242 TGATATTTTT
*
1434252 GATTTGTCATGATATCTACTCGATATCCACTACATAATTATCTTG
1 GATTTGTCATGATATCTACTCAATATCCACTACATAATTATCTTG
* * * *
1434297 GATTTGTCGTGATATCTACTTAATATCCACTGCTTAATTATCTT
1 GATTTGTCATGATATCTACTCAATATCCACTACATAATTATCTT
1434341 TTGATTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (45 bp):
GATTTGTCATGATATCTACTCAATATCCACTACATAATTATCTTG
Found at i:1435890 original size:30 final size:30
Alignment explanation
Indices: 1435830--1435892 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1435820 GCACTCTATC
* *
1435830 AAATTATTATATTTTTATTTTGAATTAAAT
1 AAATTATTATAATTTTATTTTGAATCAAAT
*
1435860 AAATTTTTATAATTTTATTTT-AAGTCAAAT
1 AAATTATTATAATTTTATTTTGAA-TCAAAT
1435890 AAA
1 AAA
1435893 CCTTTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
AAATTATTATAATTTTATTTTGAATCAAAT
Found at i:1435899 original size:30 final size:30
Alignment explanation
Indices: 1435836--1435899 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1435826 TATCAAATTA
* * **
1435836 TTATATTTTTATTTTGAATTAAATAAATTT
1 TTATAATTTTATTTTGAATCAAATAAACCT
1435866 TTATAATTTTATTTT-AAGTCAAATAAACCT
1 TTATAATTTTATTTTGAA-TCAAATAAACCT
1435896 TTAT
1 TTAT
1435900 TATTAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATAATTTTATTTTGAATCAAATAAACCT
Found at i:1448773 original size:17 final size:17
Alignment explanation
Indices: 1448751--1448790 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1448741 TATTTGTCAA
* *
1448751 AATATATTTTTATGTAT
1 AATATATATTTATATAT
1448768 AATATATATTTATATAT
1 AATATATATTTATATAT
1448785 AA-ATAT
1 AATATAT
1448791 CAATGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATATATATTTATATAT
Found at i:1469746 original size:23 final size:24
Alignment explanation
Indices: 1469715--1469759 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1469705 ATTAATTTTT
1469715 AATTAATTAATATATAAATTAAGA
1 AATTAATTAATATATAAATTAAGA
*
1469739 AATT-ATTAATATATCAATTAA
1 AATTAATTAATATATAAATTAA
1469760 ATAATATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTAATTAATATATAAATTAAGA
Found at i:1480455 original size:21 final size:22
Alignment explanation
Indices: 1480431--1480473 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1480421 ATTTTGCGCT
*
1480431 TATTATCATCATGTAAG-ACAA
1 TATTATCATCAAGTAAGCACAA
*
1480452 TATTATGATCAAGTAAGCACAA
1 TATTATCATCAAGTAAGCACAA
1480474 GCTTGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (22 bp):
TATTATCATCAAGTAAGCACAA
Found at i:1482681 original size:49 final size:49
Alignment explanation
Indices: 1482614--1482716 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 49
1482604 CATAATACAT
* * *
1482614 CATTAAAAACATACTTAATTCGGCTTAATTTAAGCACATGCACATCAAG
1 CATTCAAAACATACTTAATTCAGCTTAATTCAAGCACATGCACATCAAG
* * *
1482663 CATTCAAAACATATTTAATTCAGCTTAATTCAAGCCCATGCATATCAAG
1 CATTCAAAACATACTTAATTCAGCTTAATTCAAGCACATGCACATCAAG
1482712 CATTC
1 CATTC
1482717 CTAGCTCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (49 bp):
CATTCAAAACATACTTAATTCAGCTTAATTCAAGCACATGCACATCAAG
Found at i:1486187 original size:21 final size:19
Alignment explanation
Indices: 1486154--1486194 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
1486144 ACATGTTGAG
1486154 TAGTTAATTTATGTTATTT
1 TAGTTAATTTATGTTATTT
1486173 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTATGTTATTT
1486194 T
1 T
1486195 GTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
TAGTTAATTTATGTTATTT
Found at i:1487285 original size:5 final size:5
Alignment explanation
Indices: 1487262--1487340 Score: 58
Period size: 5 Copynumber: 16.2 Consensus size: 5
1487252 ATATTATAAT
* * *
1487262 TAAAA TAAAA -AATAT TAAAA TAAAA T-ATA TAATA TAAGAA T-AAA -AAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA
* * *
1487310 TAAAA TAAAA TAAAA TATAA GAAAT TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA T
1487341 TTATATAATA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 10 0.17
5 44 0.76
6 4 0.07
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:1487296 original size:41 final size:40
Alignment explanation
Indices: 1487250--1487427 Score: 114
Period size: 41 Copynumber: 4.2 Consensus size: 40
1487240 AAACATTTTG
*
1487250 TAATATTATAATTAAAATAAAAAATATTAAAATAAAATATA
1 TAATATTAAAATTAAAATAAAAAA-ATTAAAATAAAATATA
1487291 TAATA-TAAGAA-TAAAA-AAATAAAA-TAAAATAAAATATA
1 TAATATTAA-AATTAAAATAAA-AAAATTAAAATAAAATATA
*
1487329 -AGAAATTAAAATTTATATAATATAGGTAAAAGAAATTAAAATAAAATATA
1 TA-ATATT-AAA---AT-TAA-A-A--TAAAA-AAATTAAAATAAAATATA
* * * * *
1487379 TAATATAAAAAATTATATTAAAGAAATGAAAATAAAATATA
1 TAATAT-TAAAATTAAAATAAAAAAATTAAAATAAAATATA
*
1487420 TAAGATTA
1 TAATATTA
1487428 TAACAAGAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 39
0.69 0.06 0.25
Matches are distributed among these distances:
37 1 0.01
38 16 0.15
39 6 0.06
40 13 0.12
41 29 0.27
42 5 0.05
44 3 0.03
45 2 0.02
46 3 0.03
47 2 0.02
48 1 0.01
49 6 0.06
50 20 0.19
51 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (40 bp):
TAATATTAAAATTAAAATAAAAAAATTAAAATAAAATATA
Found at i:1487339 original size:33 final size:35
Alignment explanation
Indices: 1487251--1487332 Score: 113
Period size: 33 Copynumber: 2.5 Consensus size: 35
1487241 AACATTTTGT
1487251 AATATTATAAT-TAA-AATAAAAAATATTAAAATAA
1 AATA-TATAATATAAGAATAAAAAATATTAAAATAA
1487285 AATATATAATATAAGAATAAAAAA-A-TAAAATAA
1 AATATATAATATAAGAATAAAAAATATTAAAATAA
1487318 AATA-A-AATATAAGAA
1 AATATATAATATAAGAA
1487333 ATTAAAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
31 10 0.22
32 1 0.02
33 18 0.39
34 8 0.17
35 9 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (35 bp):
AATATATAATATAAGAATAAAAAATATTAAAATAA
Found at i:1487419 original size:34 final size:33
Alignment explanation
Indices: 1487367--1487452 Score: 104
Period size: 33 Copynumber: 2.5 Consensus size: 33
1487357 AAAGAAATTA
1487367 AAAT-AAAATATATAATATAAAAAATTATATTA-AAG
1 AAATGAAAATA-A-AATATAAAAAATTATA--ACAAG
* *
1487402 AAATGAAAATAAAATATATAAGATTATAACAAG
1 AAATGAAAATAAAATATAAAAAATTATAACAAG
1487435 AAATGAAAATAAAATATA
1 AAATGAAAATAAAATATA
1487453 TGACATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 1 0.02
33 21 0.45
34 14 0.30
35 5 0.11
36 6 0.13
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.27
Consensus pattern (33 bp):
AAATGAAAATAAAATATAAAAAATTATAACAAG
Found at i:1491358 original size:20 final size:20
Alignment explanation
Indices: 1491333--1491372 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1491323 CTAACCTTAC
1491333 CTCTAAAACCATGTGGTCAA
1 CTCTAAAACCATGTGGTCAA
1491353 CTCTAAAACCATGTGGTCAA
1 CTCTAAAACCATGTGGTCAA
1491373 GTGTGACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
CTCTAAAACCATGTGGTCAA
Found at i:1498199 original size:21 final size:21
Alignment explanation
Indices: 1498173--1498214 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1498163 ATATGTATTT
1498173 TCTTGTCTAAATTAAGACAAC
1 TCTTGTCTAAATTAAGACAAC
*
1498194 TCTTGTCTTAATTAAGACAAC
1 TCTTGTCTAAATTAAGACAAC
1498215 ATATAAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (21 bp):
TCTTGTCTAAATTAAGACAAC
Found at i:1513709 original size:24 final size:25
Alignment explanation
Indices: 1513682--1513749 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
1513672 TAAAAAAAAT
1513682 CATTTTCAAAATATTAAAGGGGA-A
1 CATTTTCAAAATATTAAAGGGGACA
*
1513706 CATTTTCAAAAGATT-AAGGGGAGCA
1 CATTTTCAAAATATTAAAGGGGA-CA
*
1513731 AATTTTC-AAATATTAAAGG
1 CATTTTCAAAATATTAAAGG
1513750 AGAGGAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 7 0.18
24 20 0.53
25 11 0.29
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (25 bp):
CATTTTCAAAATATTAAAGGGGACA
Found at i:1513740 original size:25 final size:26
Alignment explanation
Indices: 1513683--1513780 Score: 98
Period size: 25 Copynumber: 4.0 Consensus size: 26
1513673 AAAAAAAATC
* *
1513683 ATTTTCAAAATATTAAAGGGGA--AC
1 ATTTTCAAAAGATTAAAGGGGAGCAA
1513707 ATTTTCAAAAGATT-AAGGGGAGCAA
1 ATTTTCAAAAGATTAAAGGGGAGCAA
* * *
1513732 ATTTTC-AAATATTAAAGGAGAGGAA
1 ATTTTCAAAAGATTAAAGGGGAGCAA
* *
1513757 ATTTT-TAAAGATTGAAGGGGAGCA
1 ATTTTCAAAAGATTAAAGGGGAGCA
1513781 TTTTTTTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
23 7 0.11
24 19 0.31
25 35 0.57
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (26 bp):
ATTTTCAAAAGATTAAAGGGGAGCAA
Found at i:1517978 original size:16 final size:16
Alignment explanation
Indices: 1517957--1517989 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1517947 TTTCAACCAC
1517957 TAAACTTGTTTTCCAA
1 TAAACTTGTTTTCCAA
1517973 TAAACTTGTTTTCCAA
1 TAAACTTGTTTTCCAA
1517989 T
1 T
1517990 TTTTTGGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
TAAACTTGTTTTCCAA
Found at i:1518723 original size:69 final size:71
Alignment explanation
Indices: 1518610--1518758 Score: 185
Period size: 69 Copynumber: 2.1 Consensus size: 71
1518600 TATGAAATGC
* * * * *
1518610 ATGTATGCTAAGTTGCTACTATAGTATGTAATAATGATTTCACATACTACATGAGTTAGGAATGA
1 ATGTATGCTAAGTTGCTA-TATAGTATGTAACAATGATTCCACATACAACATGAGATAAGAATGA
*
1518675 GCACATG
65 GAACATG
* * * *
1518682 ATGTATGCTAAGTTG-T-TATTGTATGTGACGATGATTCCACATACAATATGAGATAAGAATGAG
1 ATGTATGCTAAGTTGCTATATAGTATGTAACAATGATTCCACATACAACATGAGATAAGAATGAG
1518745 AACATG
66 AACATG
1518751 ATGTATGC
1 ATGTATGC
1518759 CATTTTTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
69 51 0.76
71 1 0.01
72 15 0.22
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (71 bp):
ATGTATGCTAAGTTGCTATATAGTATGTAACAATGATTCCACATACAACATGAGATAAGAATGAG
AACATG
Found at i:1520633 original size:33 final size:34
Alignment explanation
Indices: 1520591--1520687 Score: 117
Period size: 33 Copynumber: 2.9 Consensus size: 34
1520581 CCCATTTTAT
*
1520591 ATTCACCCTTAGTAAGGGAGTGGAAATACGCC-A
1 ATTCACCCTTGGTAAGGGAGTGGAAATACGCCAA
* * *
1520624 ATTCACCCTTGGCAAGAGAGTGGAAATATGCCAA
1 ATTCACCCTTGGTAAGGGAGTGGAAATACGCCAA
**
1520658 ATT-ATCCCTTGGTTGGGGAGTGGAAATACG
1 ATTCA-CCCTTGGTAAGGGAGTGGAAATACG
1520688 TCATAGGACT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (34 bp):
ATTCACCCTTGGTAAGGGAGTGGAAATACGCCAA
Found at i:1521178 original size:21 final size:21
Alignment explanation
Indices: 1521149--1521191 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1521139 AAGTGATTAA
1521149 TTTAAGTTATTTTAGTTAAAT
1 TTTAAGTTATTTTAGTTAAAT
* *
1521170 TTTAGGTTATTTTATTTAAAT
1 TTTAAGTTATTTTAGTTAAAT
1521191 T
1 T
1521192 ACTTTTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTAAGTTATTTTAGTTAAAT
Found at i:1526174 original size:21 final size:19
Alignment explanation
Indices: 1526148--1526188 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1526138 AATTTAAAAC
1526148 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
1526169 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
1526188 A
1 A
1526189 CTCAACATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:1532469 original size:18 final size:18
Alignment explanation
Indices: 1532446--1532493 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
1532436 ACACATTTTA
1532446 ATGATGTGGCATCACCTG
1 ATGATGTGGCATCACCTG
1532464 ATGATGTGGCATCACCTG
1 ATGATGTGGCATCACCTG
1532482 ATGATGTGGCAT
1 ATGATGTGGCAT
1532494 GTCACGTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (18 bp):
ATGATGTGGCATCACCTG
Found at i:1533368 original size:15 final size:14
Alignment explanation
Indices: 1533348--1533389 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1533338 TGTAGTTTTA
1533348 AATCTAAAATATTT
1 AATCTAAAATATTT
* *
1533362 CAATCTAAAAAATAT
1 -AATCTAAAATATTT
1533377 AATCTAAAATATT
1 AATCTAAAATATT
1533390 ATACAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (14 bp):
AATCTAAAATATTT
Found at i:1540528 original size:30 final size:30
Alignment explanation
Indices: 1540492--1540550 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1540482 CCATGAGTTT
*
1540492 TCTTGATCGACAAAAAGTGAGCTGACTTAG
1 TCTTGATCAACAAAAAGTGAGCTGACTTAG
1540522 TCTTGATCAACAAAAAGTGAGCTGACTTA
1 TCTTGATCAACAAAAAGTGAGCTGACTTA
1540551 ATGAACCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (30 bp):
TCTTGATCAACAAAAAGTGAGCTGACTTAG
Found at i:1545856 original size:2 final size:2
Alignment explanation
Indices: 1545849--1545876 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1545839 CGTACATATT
1545849 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1545877 TATATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1576849 original size:26 final size:27
Alignment explanation
Indices: 1576819--1576874 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1576809 ACAAATCAAC
1576819 TCAAGATGTC-TTTTTCATAATGGCTT
1 TCAAGATGTCGTTTTTCATAATGGCTT
* * *
1576845 TCAAGGTTTCGTTTTTCTTAATGGCTT
1 TCAAGATGTCGTTTTTCATAATGGCTT
1576872 TCA
1 TCA
1576875 TGATAGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (27 bp):
TCAAGATGTCGTTTTTCATAATGGCTT
Found at i:1584516 original size:33 final size:32
Alignment explanation
Indices: 1584416--1584516 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 32
1584406 CGACACTGGG
* *
1584416 GGGCAACATGCTTTTGGATTTATGTTTTATTGC
1 GGGCAACATGCTTTT-GATTCATGTTTTATTGT
* * *
1584449 GGGCAGCATGCTTTTTGTTTCATGTTTTACTGT
1 GGGCAACATGC-TTTTGATTCATGTTTTATTGT
*
1584482 GGGCAACATGCTTTTGCATTCATGTTTCATTGT
1 GGGCAACATGCTTTTG-ATTCATGTTTTATTGT
1584515 GG
1 GG
1584517 TTAGAGTAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 5 0.09
33 48 0.84
34 4 0.07
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.45
Consensus pattern (32 bp):
GGGCAACATGCTTTTGATTCATGTTTTATTGT
Found at i:1587409 original size:7 final size:8
Alignment explanation
Indices: 1587392--1587418 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1587382 ATGATATGAT
1587392 AAAAATAA
1 AAAAATAA
1587400 AAAAATAA
1 AAAAATAA
1587408 AAAAATAA
1 AAAAATAA
1587416 AAA
1 AAA
1587419 GAAAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:1594659 original size:22 final size:22
Alignment explanation
Indices: 1594634--1594677 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1594624 TTCTTGGTAA
1594634 TACTTGG-TGCAATCTCTAATAT
1 TACTTGGCT-CAATCTCTAATAT
*
1594656 TACTTGGCTCAATCTTTAATAT
1 TACTTGGCTCAATCTCTAATAT
1594678 ATTCTCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (22 bp):
TACTTGGCTCAATCTCTAATAT
Found at i:1597256 original size:19 final size:19
Alignment explanation
Indices: 1597232--1597270 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1597222 ACTTCAAGTT
*
1597232 AACATTGATTTGTGTGAAG
1 AACATTGATTTGTGTAAAG
*
1597251 AACATTGTTTTGTGTAAAG
1 AACATTGATTTGTGTAAAG
1597270 A
1 A
1597271 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (19 bp):
AACATTGATTTGTGTAAAG
Found at i:1597329 original size:6 final size:6
Alignment explanation
Indices: 1597318--1597345 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1597308 CATTTCAAGA
1597318 AATGAT AATGAT AATGAT AATGAT AATG
1 AATGAT AATGAT AATGAT AATGAT AATG
1597346 TTAGAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (6 bp):
AATGAT
Found at i:1599497 original size:28 final size:27
Alignment explanation
Indices: 1599457--1599544 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
1599447 ATCTCTTCAC
* * *
1599457 TATTCATGCACTCGTGGTAGGTTAAAAG
1 TATTCATCCACTCCTCGT-GGTTAAAAG
* * *
1599485 TATTCATTCACTCCTTGTGGGTTAAAAC
1 TATTCATCCACTCCTCGT-GGTTAAAAG
* *
1599513 TATTTATCCACTCTTCGTGAGTTAAAAG
1 TATTCATCCACTCCTCGTG-GTTAAAAG
1599541 TATT
1 TATT
1599545 TCTATTATTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
27 1 0.02
28 48 0.98
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (27 bp):
TATTCATCCACTCCTCGTGGTTAAAAG
Found at i:1599545 original size:28 final size:28
Alignment explanation
Indices: 1599477--1599545 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
1599467 CTCGTGGTAG
* * *
1599477 GTTAAAAGTATTCATTCACTCCTTGTGG
1 GTTAAAAGTATTTATCCACTCCTTGTGA
*
1599505 GTTAAAACTATTTATCCACT-CTTCGTGA
1 GTTAAAAGTATTTATCCACTCCTT-GTGA
1599533 GTTAAAAGTATTT
1 GTTAAAAGTATTT
1599546 CTATTATTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 3 0.09
28 32 0.91
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (28 bp):
GTTAAAAGTATTTATCCACTCCTTGTGA
Found at i:1601312 original size:16 final size:16
Alignment explanation
Indices: 1601287--1601322 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1601277 TCTTTTTTGC
1601287 CTTT-AGTGCATCTCA
1 CTTTCAGTGCATCTCA
1601302 CTTTCAGTGCATCTCA
1 CTTTCAGTGCATCTCA
*
1601318 ATTTC
1 CTTTC
1601323 CTTATTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (16 bp):
CTTTCAGTGCATCTCA
Found at i:1605646 original size:18 final size:18
Alignment explanation
Indices: 1605619--1605663 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1605609 GTAAATATAA
1605619 AATT-ATAATTAATATTT
1 AATTAATAATTAATATTT
*
1605636 AATTAATAATTATTATTT
1 AATTAATAATTAATATTT
*
1605654 AATTATTAAT
1 AATTAATAAT
1605664 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTAATAATTAATATTT
Found at i:1608804 original size:4 final size:4
Alignment explanation
Indices: 1608797--1608827 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1608787 TAAATCTCCC
*
1608797 CTTT CTTT CTTC CTTT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
1608828 GTGTTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
CTTT
Found at i:1611852 original size:23 final size:21
Alignment explanation
Indices: 1611815--1611867 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
1611805 TAAATCTCGA
**
1611815 AATTAAAAATTAATTTCAATAAT
1 AATTAAAAAAGAATTT-AA-AAT
*
1611838 AGTTAAAAAAGAATTTAAAAT
1 AATTAAAAAAGAATTTAAAAT
1611859 AATTAAAAA
1 AATTAAAAA
1611868 TTTCATTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 11 0.42
22 2 0.08
23 13 0.50
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (21 bp):
AATTAAAAAAGAATTTAAAAT
Found at i:1614879 original size:18 final size:17
Alignment explanation
Indices: 1614844--1614891 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1614834 TATTTTTAAT
*
1614844 TATTTTGTAAATATATAA
1 TATTTT-TAAAAATATAA
1614862 TATTTTTAAAAATGATAA
1 TATTTTTAAAAAT-ATAA
1614880 -ATTATTTAAAAA
1 TATT-TTTAAAAA
1614892 ATTTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
TATTTTTAAAAATATAA
Found at i:1641865 original size:9 final size:9
Alignment explanation
Indices: 1641851--1641893 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
1641841 GTACAAATTA
1641851 AATATTTAT
1 AATATTTAT
1641860 AATATTTAT
1 AATATTTAT
1641869 -ATAATTCTAT
1 AAT-ATT-TAT
1641879 -ATATTTAT
1 AATATTTAT
1641887 AATATTT
1 AATATTT
1641894 TATATTACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.16
9 21 0.68
10 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
AATATTTAT
Found at i:1641897 original size:18 final size:18
Alignment explanation
Indices: 1641851--1641898 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1641841 GTACAAATTA
1641851 AATA-TTTATAATATTTAT
1 AATATTTTAT-ATATTTAT
*
1641869 -ATAATTCTATATATTTAT
1 AAT-ATTTTATATATTTAT
1641887 AATATTTTATAT
1 AATATTTTATAT
1641899 TACGAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.08
18 17 0.68
19 6 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTTTATATATTTAT
Found at i:1642135 original size:16 final size:16
Alignment explanation
Indices: 1642114--1642147 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1642104 TTAATATATT
*
1642114 TTAAGTATATTATTAA
1 TTAAGTATACTATTAA
*
1642130 TTAAGTTTACTATTAA
1 TTAAGTATACTATTAA
1642146 TT
1 TT
1642148 TTTCTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTATACTATTAA
Found at i:1644421 original size:5 final size:6
Alignment explanation
Indices: 1644396--1644428 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1644386 TAGCTCTGTC
*
1644396 TTTGCT TTTGCT TTTGCT TTTG-T TTTGTT TTTG
1 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTG
1644429 GTGCATGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.09, G:0.18, T:0.73
Consensus pattern (6 bp):
TTTGCT
Found at i:1648975 original size:254 final size:253
Alignment explanation
Indices: 1648503--1649310 Score: 1162
Period size: 254 Copynumber: 3.2 Consensus size: 253
1648493 CTTATCCCTA
* *
1648503 GTTACATTAACTCTCACACACTTACATTAAGATTTAAAATTTAGTTATTCCACCTTTACAAGTTT
1 GTTACATTAACTCTCACACACTTACATTAAGATTTAAAATTTAGTTATTCCATCTTCACAAGTTT
1648568 TTACGTCAATTCTTACAGTTTTACGTCAAGGCTTTTCCATGTCAAC-TTGAACTATAATTATTTT
66 TTACGTCAATTCTTACAGTTTTACGTCAAGGCTTTTCCATGTCAACTTTGAACTATAATTATTTT
* *
1648632 TATCCTTATTATTCTTAATTTAAAAATTAAGATTTGTATATCGTTAAACACTTTTAGTCTGAGAA
131 TATCCTTATTATTTTTAATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAG-CTGAGAA
*
1648697 AATAGAAATTTAAATACTTATTTTTTATTAAATTTACATTGTTTTTAATTAAATGGCTT
195 AATAGAAATTTAAATACTTATTTTTCATTAAATTTACATTGTTTTTAATTAAATGGCTT
* *
1648756 GTTACATTAA-TCCTCACACACTTACGTTAAGATTTAAAATTTATTTATTCCATCTTCACAAGTT
1 GTTACATTAACT-CTCACACACTTACATTAAGATTTAAAATTTAGTTATTCCATCTTCACAAGTT
* *
1648820 TTTACGTTAATTCTTACAGTTTTACGTCAAGGCTTTTCCATGTTAACTTTGAACTATAATTATTT
65 TTTACGTCAATTCTTACAGTTTTACGTCAAGGCTTTTCCATGTCAACTTTGAACTATAATTATTT
* *
1648885 TTATCCTTATTATTTTTTATTTAAAAAATAAAATTTGTATATCGTTAAACACTTTTAGCATGAGA
130 TTATCCTTATTATTTTTAATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGC-TGAGA
*
1648950 AAATAGAAATTTAAATACTTATTTTTCATTAAATTTAGATTGTTTTTAATTAAATGAG-TT
194 AAATAGAAATTTAAATACTTATTTTTCATTAAATTTACATTGTTTTTAATTAAATG-GCTT
* * ***
1649010 GTTACGTTAACTCTCGCACACTTGTGTTAAGATTTAAAATTTAGTTATTCC-TGCTTCACAAGTT
1 GTTACATTAACTCTCACACACTTACATTAAGATTTAAAATTTAGTTATTCCAT-CTTCACAAGTT
* * * * *
1649074 ATTACGTCAATTCTTACAGTATTACATCAAGGTTTTTCCATGACAACTTTGAACTATAATTATTT
65 TTTACGTCAATTCTTACAGTTTTACGTCAAGGCTTTTCCATGTCAACTTTGAACTATAATTATTT
* * * * * * *
1649139 TTATCCTTATTATTTTTAATTCAAAAATTTAAATTTTTATGTCGTTGAAC-TTTTTCAGTTCGAG
130 TTATCCTTATTATTTTTAATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTT-AGCT-GAG
* * * * * *
1649203 --AATATAAATTTAAATATTTACTTTTCATTAAATTTACATTGTTTTTACTTAATTGACTT
193 AAAATAGAAATTTAAATACTTATTTTTCATTAAATTTACATTGTTTTTAATTAAATGGCTT
* * *
1649262 GTTACGTTAACTCTTACACACTTACATTGAGATTTAAAATTTAGTTATT
1 GTTACATTAACTCTCACACACTTACATTAAGATTTAAAATTTAGTTATT
1649311 TCTCCTTATG
Statistics
Matches: 500, Mismatches: 46, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
252 95 0.19
253 110 0.22
254 293 0.59
255 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (253 bp):
GTTACATTAACTCTCACACACTTACATTAAGATTTAAAATTTAGTTATTCCATCTTCACAAGTTT
TTACGTCAATTCTTACAGTTTTACGTCAAGGCTTTTCCATGTCAACTTTGAACTATAATTATTTT
TATCCTTATTATTTTTAATTTAAAAATTAAAATTTGTATATCGTTAAACACTTTTAGCTGAGAAA
ATAGAAATTTAAATACTTATTTTTCATTAAATTTACATTGTTTTTAATTAAATGGCTT
Found at i:1652941 original size:16 final size:16
Alignment explanation
Indices: 1652920--1652953 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1652910 AAAATATTAA
1652920 AAATATATATTACTTC
1 AAATATATATTACTTC
*
1652936 AAATATATATTATTTC
1 AAATATATATTACTTC
1652952 AA
1 AA
1652954 TATTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATATATTACTTC
Found at i:1662577 original size:2 final size:2
Alignment explanation
Indices: 1662570--1662598 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1662560 AAACCAAATT
1662570 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1662599 TATTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1663121 original size:35 final size:35
Alignment explanation
Indices: 1663089--1663154 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1663079 ATATATTTAC
1663089 TCATTAT-ATAATTAA-A-ATTTTATGTAATTATTT
1 TCATTATAATAATTAATAGA-TTTATGTAATTATTT
* *
1663122 TTATTATAATTATTAATAGATTTATGTAATTAT
1 TCATTATAATAATTAATAGATTTATGTAATTAT
1663155 CTAATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 7 0.25
35 14 0.50
36 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (35 bp):
TCATTATAATAATTAATAGATTTATGTAATTATTT
Found at i:1663159 original size:21 final size:20
Alignment explanation
Indices: 1663128--1663166 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1663118 ATTTTTATTA
1663128 TAATTATTAATAGATTTATG
1 TAATTATTAATAGATTTATG
*
1663148 TAATTATCTAATATATTTA
1 TAATTAT-TAATAGATTTA
1663167 CTGATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
TAATTATTAATAGATTTATG
Found at i:1663456 original size:22 final size:24
Alignment explanation
Indices: 1663431--1663477 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1663421 ATAAATTTTA
1663431 TTAAAAT-TAA-AAATAAAAATAT
1 TTAAAATGTAATAAATAAAAATAT
* *
1663453 TTAAAATGTAATGAATAAATATAT
1 TTAAAATGTAATAAATAAAAATAT
1663477 T
1 T
1663478 CAGTTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
24 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
TTAAAATGTAATAAATAAAAATAT
Found at i:1673070 original size:2 final size:2
Alignment explanation
Indices: 1673047--1673089 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1673037 TTTTGCAATG
* * *
1673047 TA TA AA TA TA GA TA TCA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1673090 AAGTTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1676058 original size:74 final size:73
Alignment explanation
Indices: 1675974--1676209 Score: 278
Period size: 74 Copynumber: 3.2 Consensus size: 73
1675964 ACTATACTTT
* * * *
1675974 TTAGTTGATTAAGTCTTCTTTGTCTTGTATTTGAATTCTCTGGCAATGAGCTCTTAGTTGACTAG
1 TTAGTTGATTAAGT-TTCTTTGTCTTGTAATTGAAGTCTCTGGCAGTGAGCTTTTAGTTGACTAG
*
1676039 CCATTCTTC
65 CCATGCTTC
* * * * *
1676048 TTAGTCGATTAAGTTCTCTTTGTCTTGTAATTGAAGTCTCTAGTAGTGAGCTTTTAATTGA-TTG
1 TTAGTTGATTAAGTT-TCTTTGTCTTGTAATTGAAGTCTCTGGCAGTGAGCTTTTAGTTGACTAG
1676112 ACCATGCTTC
65 -CCATGCTTC
* * *
1676122 TTAGTTGATTAAG-TTCTGTCAGTCTTGTAATTGAAGTCTCTGACAGTGAGCTTTTAGTTAACTA
1 TTAGTTGATTAAGTTTCT-T-TGTCTTGTAATTGAAGTCTCTGGCAGTGAGCTTTTAGTTGACTA
*
1676186 ACCATGCTTC
64 GCCATGCTTC
*
1676196 TTAGTTGACTAAGT
1 TTAGTTGATTAAGT
1676210 CTTTTCTGTA
Statistics
Matches: 136, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
72 3 0.02
73 5 0.04
74 127 0.93
75 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.44
Consensus pattern (73 bp):
TTAGTTGATTAAGTTTCTTTGTCTTGTAATTGAAGTCTCTGGCAGTGAGCTTTTAGTTGACTAGC
CATGCTTC
Found at i:1687453 original size:14 final size:14
Alignment explanation
Indices: 1687432--1687465 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1687422 TGTTAGTTTA
1687432 AATTTTAGTTAATT
1 AATTTTAGTTAATT
*
1687446 AGTTTTAGTTAATT
1 AATTTTAGTTAATT
1687460 AATTTT
1 AATTTT
1687466 TAGTATTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (14 bp):
AATTTTAGTTAATT
Found at i:1688460 original size:75 final size:76
Alignment explanation
Indices: 1688367--1688558 Score: 216
Period size: 75 Copynumber: 2.5 Consensus size: 76
1688357 AAATTGAAAA
* *
1688367 AATCAAATTAAAGTTTTAATTATAAATTTTTATTATTTTGA-TATTTT-AAAAATAAAAAT-AAA
1 AATCATATTAAAGTTTTAATTATAAATTTTTA-TATTTTCAGTATTTTAAAAAATAAAAATGAAA
*
1688429 GAATAAGATAAAAT
65 AAATAA-AT-AAAT
*
1688443 AATC-TATTAAAGTTTTAATTATAAA-TTATATATTTTCAGTATTTTAAAAAATAAAAATAGGAA
1 AATCATATTAAAGTTTTAATTATAAATTTTTATATTTTCAGTATTTTAAAAAATAAAAAT--GAA
1688506 AAAATAAATAAAT
64 AAAATAAATAAAT
* *
1688519 AATCATATTAATGTTTTACTTGA-AAATTTATTAATATTTT
1 AATCATATTAAAGTTTTAATT-ATAAATTT-TT-ATATTTT
1688559 AAATAAATTT
Statistics
Matches: 99, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
73 7 0.07
74 10 0.10
75 32 0.32
76 12 0.12
77 19 0.19
78 11 0.11
79 1 0.01
80 7 0.07
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (76 bp):
AATCATATTAAAGTTTTAATTATAAATTTTTATATTTTCAGTATTTTAAAAAATAAAAATGAAAA
AATAAATAAAT
Found at i:1690266 original size:46 final size:46
Alignment explanation
Indices: 1690157--1690267 Score: 132
Period size: 47 Copynumber: 2.4 Consensus size: 46
1690147 TCAACAGACA
* *
1690157 AAAATACTTATACCAAAAGACAAAATACCCTTAACTATAATATAAT
1 AAAATATTTATACCAAAAGACAAAATACACTTAACTATAATATAAT
* * * *
1690203 AAAATATTTATACCAAAAGATTAAATTACACTTGACTATAATTTAAT
1 AAAATATTTATACCAAAAGA-CAAAATACACTTAACTATAATATAAT
* * *
1690250 CACATATTTATACAAAAA
1 AAAATATTTATACCAAAA
1690268 AAAATTATCC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
46 19 0.35
47 36 0.65
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (46 bp):
AAAATATTTATACCAAAAGACAAAATACACTTAACTATAATATAAT
Found at i:1690953 original size:14 final size:14
Alignment explanation
Indices: 1690931--1690961 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1690921 TTCAACCCCA
1690931 CAACAACAAGGTCC
1 CAACAACAAGGTCC
*
1690945 CAACTACAAGGTCC
1 CAACAACAAGGTCC
1690959 CAA
1 CAA
1690962 AAAGTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.35, G:0.13, T:0.10
Consensus pattern (14 bp):
CAACAACAAGGTCC
Found at i:1690966 original size:92 final size:91
Alignment explanation
Indices: 1690858--1691024 Score: 214
Period size: 92 Copynumber: 1.8 Consensus size: 91
1690848 GGTTTTAACA
** * * *
1690858 ACAAGGTTTCAAAAAGTTGCAATTTCCATTAA-CTGACCTT-TTAAAAAATTTCCAAACTTG-CC
1 ACAAGGTCCCAAAAAGTTACAATTT-CA-TAATCTGACCTTCCTAAAAAATTT-CAAACTTGTCA
1690920 ATTCAACCCCACAACAACAAGGTCCCAACT
63 ATT-AACCCCACAACAACAAGGTCCCAACT
* *
1690950 ACAAGGTCCCAAAAAGTTACAATTTCATAATTTGGCCTTCCTAAAAAATTTCAAACTTGTCAATT
1 ACAAGGTCCCAAAAAGTTACAATTTCATAATCTGACCTTCCTAAAAAATTTCAAACTTGTCAATT
1691015 AACCCCACAA
66 AACCCCACAA
1691025 TTAGCATTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
90 3 0.05
91 26 0.40
92 36 0.55
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.27
Consensus pattern (91 bp):
ACAAGGTCCCAAAAAGTTACAATTTCATAATCTGACCTTCCTAAAAAATTTCAAACTTGTCAATT
AACCCCACAACAACAAGGTCCCAACT
Found at i:1692404 original size:15 final size:16
Alignment explanation
Indices: 1692376--1692408 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1692366 AATTAGTTTA
1692376 TTATTATTAAGTTATT
1 TTATTATTAAGTTATT
*
1692392 TTATT-TTATGTTATT
1 TTATTATTAAGTTATT
1692407 TT
1 TT
1692409 TATGTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (16 bp):
TTATTATTAAGTTATT
Found at i:1694889 original size:79 final size:79
Alignment explanation
Indices: 1694758--1694914 Score: 314
Period size: 79 Copynumber: 2.0 Consensus size: 79
1694748 TCTTAATATT
1694758 GGCAAAAGCATCTAATTTTTCTTGTACTTCAGCATCATGCTTTCTTAGTGAAGCCATATTCGTTG
1 GGCAAAAGCATCTAATTTTTCTTGTACTTCAGCATCATGCTTTCTTAGTGAAGCCATATTCGTTG
1694823 AAATGTCTTCTAAA
66 AAATGTCTTCTAAA
1694837 GGCAAAAGCATCTAATTTTTCTTGTACTTCAGCATCATGCTTTCTTAGTGAAGCCATATTCGTTG
1 GGCAAAAGCATCTAATTTTTCTTGTACTTCAGCATCATGCTTTCTTAGTGAAGCCATATTCGTTG
1694902 AAATGTCTTCTAA
66 AAATGTCTTCTAA
1694915 CTCATTTTCC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (79 bp):
GGCAAAAGCATCTAATTTTTCTTGTACTTCAGCATCATGCTTTCTTAGTGAAGCCATATTCGTTG
AAATGTCTTCTAAA
Found at i:1698408 original size:25 final size:25
Alignment explanation
Indices: 1698352--1698409 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1698342 GTAAAAAGTT
* *
1698352 AGAAAGATTAGAAGAAAGAATTATA
1 AGAAGGATTAGAAGAAAGAATTACA
*
1698377 A-AGAGGATTGGAAGAAAGAATTACA
1 AGA-AGGATTAGAAGAAAGAATTACA
1698402 AGAAGGAT
1 AGAAGGAT
1698410 CAAGCTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.04
25 26 0.93
26 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (25 bp):
AGAAGGATTAGAAGAAAGAATTACA
Found at i:1702551 original size:2 final size:2
Alignment explanation
Indices: 1702544--1702569 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1702534 AATCACATCC
1702544 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1702570 GTTCTCTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1703104 original size:16 final size:16
Alignment explanation
Indices: 1703083--1703115 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1703073 GCTCCAATCT
1703083 ACTCCAAATGGCTACA
1 ACTCCAAATGGCTACA
1703099 ACTCCAAATGGCTACA
1 ACTCCAAATGGCTACA
1703115 A
1 A
1703116 AAATTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.18
Consensus pattern (16 bp):
ACTCCAAATGGCTACA
Found at i:1710225 original size:8 final size:8
Alignment explanation
Indices: 1710212--1710246 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1710202 ATGTAATCAC
1710212 ATACATAT
1 ATACATAT
1710220 ATACATAT
1 ATACATAT
*
1710228 ATATATAT
1 ATACATAT
*
1710236 ATATATAT
1 ATACATAT
1710244 ATA
1 ATA
1710247 GTTCAAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (8 bp):
ATACATAT
Found at i:1710229 original size:2 final size:2
Alignment explanation
Indices: 1710216--1710246 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1710206 AATCACATAC
*
1710216 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1710247 GTTCAAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1715277 original size:22 final size:23
Alignment explanation
Indices: 1715239--1715282 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1715229 CTATTGATGA
1715239 ATTTACTAGTTTATGTGCTTATGG
1 ATTTACTAG-TTATGTGCTTATGG
*
1715263 ATTTACTA-TTATGTGTTTAT
1 ATTTACTAGTTATGTGCTTAT
1715283 TTATGGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (23 bp):
ATTTACTAGTTATGTGCTTATGG
Found at i:1719272 original size:3 final size:3
Alignment explanation
Indices: 1719256--1719292 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1719246 TAGATTTTTT
* *
1719256 TTA TTA ATA CTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1719293 CATCATCATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1719781 original size:17 final size:17
Alignment explanation
Indices: 1719756--1719795 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1719746 GAAAACAAAA
* *
1719756 TTTGATCTAAATTTTGT
1 TTTGCTCTAAATTTCGT
1719773 TTTGCTCTAAATTTCGT
1 TTTGCTCTAAATTTCGT
1719790 TTTGCT
1 TTTGCT
1719796 TTGAACCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.57
Consensus pattern (17 bp):
TTTGCTCTAAATTTCGT
Found at i:1723622 original size:15 final size:15
Alignment explanation
Indices: 1723565--1723622 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1723555 CACGTTATTA
* *
1723565 CCTAAAGTGTTACTA
1 CCTAAGGTGTTACTG
*
1723580 CCTAAGATGTTACTG
1 CCTAAGGTGTTACTG
* **
1723595 TCTAAGGCATTACTG
1 CCTAAGGTGTTACTG
1723610 CCTAAGGTGTTAC
1 CCTAAGGTGTTAC
1723623 AACACAAAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (15 bp):
CCTAAGGTGTTACTG
Done.