Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_pilon, 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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 20
Found at i:1121056 original size:26 final size:26
Alignment explanation
Indices: 1120909--1121255 Score: 207
Period size: 26 Copynumber: 13.7 Consensus size: 26
1120899 ATTAATAATA
*
1120909 ATTATTAAATCATTAGTATTAAATCATT
1 ATTATTAAATCATTATTA-T-AATCATT
* * *
1120937 ATTATAAAATCATTACTA-AATAATT
1 ATTATTAAATCATTATTATAATCATT
* * *
1120962 ACTATTAAATCATTATTATCATTATT
1 ATTATTAAATCATTATTATAATCATT
1120988 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATCATT
*
1121011 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATT
* **
1121037 ATTACTAAATCATTATTATAAGGATT
1 ATTATTAAATCATTATTATAATCATT
* * *
1121063 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATCAT--T
*
1121090 ATCATTAAAT-A-T-TTA-AATCATT
1 ATTATTAAATCATTATTATAATCATT
*
1121112 ATTA-T-AATGATTATTACTAAATCATT
1 ATTATTAAATCATTATTA-T-AATCATT
*
1121138 ATTA-T-AATGATTATTATCAAATCATT
1 ATTATTAAATCATTATTAT--AATCATT
* * *
1121164 ACTA-T-AATGATTATTATCAA--ATC
1 ATTATTAAATCATTATTAT-AATCATT
* *
1121187 ATTATTAAATCATCAAATATTAA--ATT
1 ATTATTAAATCAT-TATTA-TAATCATT
*
1121213 CATTATTAAATCAATATT-TAA--ATT
1 -ATTATTAAATCATTATTATAATCATT
* *
1121237 ATTATTAAATTATTTTTAT
1 ATTATTAAATCATTATTAT
1121256 GGTTAATTGA
Statistics
Matches: 262, Mismatches: 38, Indels: 42
0.77 0.11 0.12
Matches are distributed among these distances:
20 3 0.01
21 2 0.01
22 4 0.02
23 42 0.16
24 18 0.07
25 36 0.14
26 120 0.46
27 21 0.08
28 16 0.06
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATCATT
Found at i:1121065 original size:12 final size:12
Alignment explanation
Indices: 1120964--1121180 Score: 102
Period size: 12 Copynumber: 17.5 Consensus size: 12
1120954 AAATAATTAC
*
1120964 TATTA-AATCAT
1 TATTATAATGAT
* *
1120975 TATTATCATTAT
1 TATTATAATGAT
*
1120987 TATTATTAAATCAT
1 TATTA-T-AATGAT
* *
1121001 TATTATCATTAT
1 TATTATAATGAT
*
1121013 TATTA-AATCAT
1 TATTATAATGAT
1121024 TATTATAATGAT
1 TATTATAATGAT
*
1121036 TATTACTAAATCAT
1 TATTA-T-AATGAT
*
1121050 TATTATAAGGAT
1 TATTATAATGAT
*
1121062 TATTATCAAATCAT
1 TATTAT--AATGAT
* *
1121076 TACTA-AATCAT
1 TATTATAATGAT
* * * * *
1121087 CA-AATCATTAAA
1 TATTAT-AATGAT
*
1121099 TATT-TAAATCAT
1 TATTAT-AATGAT
1121111 TATTATAATGAT
1 TATTATAATGAT
*
1121123 TATTACTAAATCAT
1 TATTA-T-AATGAT
1121137 TATTATAATGAT
1 TATTATAATGAT
*
1121149 TATTATCAAATCAT
1 TATTAT--AATGAT
*
1121163 TACTATAATGAT
1 TATTATAATGAT
1121175 TATTAT
1 TATTAT
1121181 CAAATCATTA
Statistics
Matches: 157, Mismatches: 33, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
10 1 0.01
11 21 0.13
12 81 0.52
13 7 0.04
14 47 0.30
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (12 bp):
TATTATAATGAT
Found at i:1121110 original size:87 final size:85
Alignment explanation
Indices: 1120915--1121167 Score: 328
Period size: 87 Copynumber: 2.9 Consensus size: 85
1120905 AATAATTATT
* * * * * *
1120915 AAATCATTAGTATTAAATCATTATTATAA-AATCATTACTAAATAATTACTATTAAATCATTATT
1 AAATCATTAATATTAAATCATTATTATAATGATTATTACTAAATCATTATTA-T-AATGATTATT
* * * *
1120979 ATCATTATTATTATTAAATCATT
64 ATCA-AATCATTACTAAATCATC
* * *
1121002 ATTATCATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAAGGATTATTA
1 A-AATCATTAATATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTA
1121067 TCAAATCATTACTAAATCATC
65 TCAAATCATTACTAAATCATC
1121088 AAATCATTAAATATTTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATT
1 AAATCATT-AATA-TTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATT
1121153 ATCAAATCATTACTA
64 ATCAAATCATTACTA
1121168 TAATGATTAT
Statistics
Matches: 147, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
85 6 0.04
86 18 0.12
87 78 0.53
88 27 0.18
89 18 0.12
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (85 bp):
AAATCATTAATATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTAT
CAAATCATTACTAAATCATC
Found at i:1121220 original size:27 final size:24
Alignment explanation
Indices: 1121185--1121246 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 24
1121175 TATTATCAAA
1121185 TCATTATTAAATCATCAAATATTAAAT
1 TCATTATTAAATCA--AAAT-TTAAAT
*
1121212 TCATTATTAAATCAATATTTAAAT
1 TCATTATTAAATCAAAATTTAAAT
1121236 T-ATTATTAAAT
1 TCATTATTAAAT
1121247 TATTTTTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.29
24 7 0.21
25 3 0.09
27 14 0.41
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (24 bp):
TCATTATTAAATCAAAATTTAAAT
Found at i:1121221 original size:12 final size:12
Alignment explanation
Indices: 1121176--1121247 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 12
1121166 TATAATGATT
*
1121176 ATTATCAAA-TC
1 ATTATTAAATTC
1121187 ATTATTAAATCATC
1 ATTATTAAAT--TC
*
1121201 AAATATTAAATTC
1 -ATTATTAAATTC
1121214 ATTATTAAA-TC
1 ATTATTAAATTC
*
1121225 AATATTTAAATT-
1 ATTA-TTAAATTC
1121237 ATTATTAAATT
1 ATTATTAAATT
1121248 ATTTTTATGG
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
11 20 0.40
12 16 0.32
13 3 0.06
14 2 0.04
15 9 0.18
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTATTAAATTC
Found at i:1121238 original size:113 final size:112
Alignment explanation
Indices: 1120979--1121255 Score: 368
Period size: 113 Copynumber: 2.5 Consensus size: 112
1120969 AATCATTATT
* *
1120979 ATCATT-ATTATTATTAAATCATTA-TTATCATTATTATTAAATCATTATTATAATGATTATTAC
1 ATCATTAAATATTATTAAATCATTATTTA-AATTATTATTAAATCATTATTATAATGATTATTAC
*
1121042 TAAATCATTATTATAAGGATTATTATCAAATCATTACTAAATCATCAA
65 TAAATCATTACTATAAGGATTATTATCAAATCATTACTAAATCATCAA
*
1121090 ATCATTAAATA-T-TTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATT
1 ATCATTAAATATTATTAAATCATTATT-TAA--ATTATTATTAAATCATTATTATAATGATTATT
* *
1121153 A-TCAAATCATTACTATAATGATTATTATCAAATCATTATTAAATCATCAA
63 ACT-AAATCATTACTATAAGGATTATTATCAAATCATTACTAAATCATCAA
* * *
1121203 AT-ATTAAATTCATTATTAAATCAATATTTAAATTATTATTAAATTATTTTTAT
1 ATCATTAAA-T-ATTATTAAATCATTATTTAAATTATTATTAAATCATTATTAT
1121256 GGTTAATTGA
Statistics
Matches: 146, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
110 11 0.08
111 8 0.05
112 12 0.08
113 98 0.67
114 1 0.01
115 4 0.03
116 12 0.08
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (112 bp):
ATCATTAAATATTATTAAATCATTATTTAAATTATTATTAAATCATTATTATAATGATTATTACT
AAATCATTACTATAAGGATTATTATCAAATCATTACTAAATCATCAA
Found at i:1121247 original size:11 final size:11
Alignment explanation
Indices: 1121204--1121250 Score: 58
Period size: 12 Copynumber: 4.1 Consensus size: 11
1121194 AATCATCAAA
1121204 TATTAAATTCAT
1 TATTAAATT-AT
* *
1121216 TATTAAATCAA
1 TATTAAATTAT
1121227 TATTTAAATTAT
1 TA-TTAAATTAT
1121239 TATTAAATTAT
1 TATTAAATTAT
1121250 T
1 T
1121251 TTTATGGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 13 0.43
12 17 0.57
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTAAATTAT
Found at i:1121445 original size:17 final size:18
Alignment explanation
Indices: 1121425--1121459 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1121415 TATTAGTAAA
1121425 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
1121442 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
1121460 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:1121514 original size:49 final size:49
Alignment explanation
Indices: 1121457--1121693 Score: 411
Period size: 49 Copynumber: 4.8 Consensus size: 49
1121447 ATTATTAATA
* *
1121457 ATTACTAATCATTTCTATCAAATCATTAAATATTAATAATAATTTTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
1121506 ATTACTAATCATTGCTATCAAATCATTAAATATTAAAAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1121555 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
1121604 ATTACTAATAATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
1121653 ATTACTAATCATTACTATCAAATCATTAGATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1121694 GATGGGTACC
Statistics
Matches: 178, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 178 1.00
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:1125117 original size:22 final size:21
Alignment explanation
Indices: 1125083--1125123 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1125073 CGTATTTATG
1125083 CCTTCTTCCTTTCCTTTCTTTT
1 CCTTCTTCCTTT-CTTTCTTTT
**
1125105 CCTTCTTTGTTTCTTTCTT
1 CCTTCTTCCTTTCTTTCTT
1125124 CGAATCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (21 bp):
CCTTCTTCCTTTCTTTCTTTT
Found at i:1125518 original size:28 final size:28
Alignment explanation
Indices: 1125458--1125511 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1125448 ATAATAAAAT
1125458 ATATAACTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
*
1125486 ATATAACTTAAACTAATAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1125512 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1125521 original size:21 final size:21
Alignment explanation
Indices: 1125488--1125536 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1125478 CTAATATAAT
*
1125488 ATAACTTAAACTAATAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1125509 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1125530 ATTAACT
1 A-TAACT
1125537 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1126068 original size:65 final size:65
Alignment explanation
Indices: 1125931--1126057 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
1125921 TACAGCTACG
* * *
1125931 GATGCAGGAATCTCCCAGCTATGGATGCAACGCATGCATGAGGGATAGGGTTAAAGCTTGGTCAC
1 GATGCAGGAATCTCCCAACTATGGATGCAACGCATGCATGAGGAATAGGATTAAAGCTTGGTCAC
1125996 GATGCAGGAATCTCCCAACTATGGATGCAACGCATGCATGAGGAATAGGATTAAAGCTTGGT
1 GATGCAGGAATCTCCCAACTATGGATGCAACGCATGCATGAGGAATAGGATTAAAGCTTGGT
1126058 TGTGGTGCAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (65 bp):
GATGCAGGAATCTCCCAACTATGGATGCAACGCATGCATGAGGAATAGGATTAAAGCTTGGTCAC
Found at i:1126236 original size:29 final size:29
Alignment explanation
Indices: 1126203--1126272 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
1126193 ACATGCATCG
*
1126203 CTCCTTGGTCGCCCCGAGTGCATGGCGAC
1 CTCCTTGGTCACCCCGAGTGCATGGCGAC
* *
1126232 CTCCTTGGTCACCCGGAGTGTATGGCGAC
1 CTCCTTGGTCACCCCGAGTGCATGGCGAC
1126261 CTCCTTGGTCAC
1 CTCCTTGGTCAC
1126273 TGTAGAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.11, C:0.36, G:0.29, T:0.24
Consensus pattern (29 bp):
CTCCTTGGTCACCCCGAGTGCATGGCGAC
Found at i:1126831 original size:65 final size:65
Alignment explanation
Indices: 1126738--1126864 Score: 218
Period size: 65 Copynumber: 2.0 Consensus size: 65
1126728 CTGCACCACA
* * * *
1126738 ACCAAGCTTTAACCCTATCCCTCATGCATTCGTTGCATCCATAGCTGGGAGATTCCTGCATCGTG
1 ACCAAGCTTTAACCCTATCCCTCATGCATGCGTTGCATCCAAAACTGGGAGATTCCTACATCGTG
1126803 ACCAAGCTTTAACCCTATCCCTCATGCATGCGTTGCATCCAAAACTGGGAGATTCCTACATC
1 ACCAAGCTTTAACCCTATCCCTCATGCATGCGTTGCATCCAAAACTGGGAGATTCCTACATC
1126865 CGTAGTTGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (65 bp):
ACCAAGCTTTAACCCTATCCCTCATGCATGCGTTGCATCCAAAACTGGGAGATTCCTACATCGTG
Found at i:1127308 original size:21 final size:21
Alignment explanation
Indices: 1127260--1127308 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1127250 ACTAAAATCT
*
1127260 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTATTAGTATA
* * *
1127282 AATTATTAGTTTATTCGTTTA
1 AGTTATTAGTTTATTAGTATA
1127303 AGTTAT
1 AGTTAT
1127309 ATTATATTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (21 bp):
AGTTATTAGTTTATTAGTATA
Found at i:1127317 original size:28 final size:30
Alignment explanation
Indices: 1127285--1127347 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
1127275 TAGTATAAAT
*
1127285 TATTAGTTTATTCGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
*
1127313 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1127343 TATTA
1 TATTA
1127348 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:1131172 original size:49 final size:49
Alignment explanation
Indices: 1131096--1131283 Score: 331
Period size: 49 Copynumber: 3.8 Consensus size: 49
1131086 GGCACCCATC
* *
1131096 TATTATTAATATTTAATTATTTGATAGTAATGATCAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* * *
1131145 TATTATTAATTTTTAATGATTTAATAGTTATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1131194 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1131243 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
1 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAAT
1131284 TATTAATAAT
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 131 1.00
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.47
Consensus pattern (49 bp):
TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:1131506 original size:11 final size:11
Alignment explanation
Indices: 1131490--1131536 Score: 67
Period size: 12 Copynumber: 4.1 Consensus size: 11
1131480 TAACCATAAA
1131490 AATAATTTAAT
1 AATAATTTAAT
1131501 AATAATTTAAAT
1 AATAATTT-AAT
*
1131513 AATGATTTAAT
1 AATAATTTAAT
1131524 AATGAATTTAAT
1 AAT-AATTTAAT
1131536 A
1 A
1131537 TTTAATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
11 14 0.44
12 18 0.56
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (11 bp):
AATAATTTAAT
Found at i:1131514 original size:20 final size:21
Alignment explanation
Indices: 1131489--1131542 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
1131479 TTAACCATAA
1131489 AAATAATTTAATAAT-AATTT
1 AAATAATTTAATAATGAATTT
1131509 AAATAATGATTTAATAATGAATTT
1 AAAT-A--ATTTAATAATGAATTT
1131533 -AAT-ATTTAAT
1 AAATAATTTAAT
1131543 GATTTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 1 0.03
23 13 0.43
24 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
AAATAATTTAATAATGAATTT
Found at i:1131515 original size:12 final size:12
Alignment explanation
Indices: 1131486--1131534 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
1131476 CAATTAACCA
1131486 TAAA-AATAATT
1 TAAATAATAATT
1131497 T-AATAATAATT
1 TAAATAATAATT
*
1131508 TAAATAATGATT
1 TAAATAATAATT
1131520 T-AATAATGAATT
1 TAAATAAT-AATT
1131532 TAA
1 TAA
1131535 TATTTAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 2 0.06
11 15 0.47
12 14 0.44
13 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (12 bp):
TAAATAATAATT
Found at i:1131524 original size:23 final size:24
Alignment explanation
Indices: 1131485--1131818 Score: 162
Period size: 26 Copynumber: 13.3 Consensus size: 24
1131475 TCAATTAACC
* *
1131485 ATAAAAATAATTTAATAATAATTT
1 ATAATAATGATTTAATAATAATTT
1131509 A-AATAATGATTTAATAATGAATTT
1 ATAATAATGATTTAATAAT-AATTT
* *
1131533 AATATTTAATGATTTGATAATAATCATT
1 -ATA-ATAATGATTTAATAATAAT--TT
* *
1131561 ATAGTAATGATTTGATAATAATCATT
1 ATAATAATGATTTAATAATAAT--TT
1131587 ATAATAATGATTT-A-AAT-ATTT
1 ATAATAATGATTTAATAATAATTT
* * * *
1131608 AATGATTTGATGATTTAGTAATGATTT
1 -AT-A-ATAATGATTTAATAATAATTT
* *
1131635 CATAATAATCATTATAATAATGATTT
1 -ATAATAATGATT-TAATAATAATTT
* *
1131661 AGTAATAATCATTATAATAATGATTT
1 A-TAATAATGATT-TAATAATAATTT
*
1131687 AATAATAATGA--TAATAATGATTT
1 -ATAATAATGATTTAATAATAATTT
* * *
1131710 AATAATAATAATGATAATAATGATTT
1 -ATAATAATGAT-TTAATAATAATTT
* * * *
1131736 AATAGTAATTATTTAGTAATTATTT
1 -ATAATAATGATTTAATAATAATTT
* * *
1131761 AGTAATGAT-TTTATAATAATGATTT
1 A-TAATAATGATT-TAATAATAATTT
* * *
1131786 AATACTAAGGATTTAATAATTA-TT
1 -ATAATAATGATTTAATAATAATTT
1131810 ACTAATAAT
1 A-TAATAAT
1131819 TATAGAATAA
Statistics
Matches: 254, Mismatches: 33, Indels: 46
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.01
22 2 0.01
23 41 0.16
24 27 0.11
25 46 0.18
26 110 0.43
27 24 0.09
28 2 0.01
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (24 bp):
ATAATAATGATTTAATAATAATTT
Found at i:1131592 original size:12 final size:12
Alignment explanation
Indices: 1131549--1131594 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
1131539 TAATGATTTG
1131549 ATAATAATCATT
1 ATAATAATCATT
* *
1131561 ATAGTAATGATTT
1 ATAATAATCA-TT
1131574 GATAATAATCATT
1 -ATAATAATCATT
1131587 ATAATAAT
1 ATAATAAT
1131595 GATTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 16 0.57
13 4 0.14
14 8 0.29
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (12 bp):
ATAATAATCATT
Found at i:1131608 original size:87 final size:86
Alignment explanation
Indices: 1131523--1131715 Score: 254
Period size: 87 Copynumber: 2.3 Consensus size: 86
1131513 AATGATTTAA
* *
1131523 TAATGAATTTAAT-A-TT-TAATGATTTGATAATAATCATTATAGTAATGATTT-GATAATAATC
1 TAATG-ATTTAATGATTTATAATGATTTCATAATAATCATTATAATAATGATTTAG-TAATAATC
1131584 ATTATAATAATGATTTAAATATT
64 ATTATAATAATGATTTAAATATT
*
1131607 TAATGATTTGATGATTTAGTAATGATTTCATAATAATCATTATAATAATGATTTAGTAATAATCA
1 TAATGATTTAATGATTTA-TAATGATTTCATAATAATCATTATAATAATGATTTAGTAATAATCA
*
1131672 TTATAATAATGATTT-AATA-A
65 TTATAATAATGATTTAAATATT
*
1131692 TAATGATAATAATGATTTAATAAT
1 TAATGAT-TTAATGATTT-ATAAT
1131716 AATAATGATA
Statistics
Matches: 96, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
83 6 0.06
84 6 0.06
85 9 0.09
86 16 0.17
87 58 0.60
88 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (86 bp):
TAATGATTTAATGATTTATAATGATTTCATAATAATCATTATAATAATGATTTAGTAATAATCAT
TATAATAATGATTTAAATATT
Found at i:1131633 original size:11 final size:12
Alignment explanation
Indices: 1131617--1131818 Score: 117
Period size: 14 Copynumber: 16.2 Consensus size: 12
1131607 TAATGATTTG
*
1131617 ATGATT-TAGTA
1 ATGATTATAATA
1131628 ATGATTTCATAATA
1 ATGA-TT-ATAATA
*
1131642 ATCATTATAATA
1 ATGATTATAATA
1131654 ATGATTTAGTAATA
1 ATGA-TTA-TAATA
*
1131668 ATCATTATAATA
1 ATGATTATAATA
1131680 ATGATT-TAATA
1 ATGATTATAATA
* *
1131691 ATAATGATAATA
1 ATGATTATAATA
1131703 ATGATTTAATAATA
1 ATGA-TT-ATAATA
* *
1131717 ATAATGATAATA
1 ATGATTATAATA
1131729 ATGATT-TAATA
1 ATGATTATAATA
* * *
1131740 GTAATTATTTAGTA
1 ATGATTA--TAATA
* *
1131754 ATTATT-TAGTA
1 ATGATTATAATA
1131765 ATGATTTTATAATA
1 ATGA--TTATAATA
*
1131779 ATGATTTAATACTA
1 ATGA-TT-ATAATA
*
1131793 AGGATT-TAATA
1 ATGATTATAATA
*
1131804 ATTATTACTAATA
1 ATGATTA-TAATA
1131817 AT
1 AT
1131819 TATAGAATAA
Statistics
Matches: 149, Mismatches: 25, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
11 38 0.26
12 39 0.26
13 24 0.16
14 48 0.32
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (12 bp):
ATGATTATAATA
Found at i:1131654 original size:3 final size:3
Alignment explanation
Indices: 1131636--1131730 Score: 52
Period size: 3 Copynumber: 32.7 Consensus size: 3
1131626 TAATGATTTC
* * * * * * * *
1131636 ATA ATA ATC ATT ATA ATA ATG AT- TTA GTA ATA ATC ATT ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
1131683 AT- TTA ATA ATA ATG ATA ATA ATG AT- TTA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1131729 AT
1 AT
1131731 GATTTAATAG
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
2 3 0.04
3 66 0.96
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:1131702 original size:9 final size:9
Alignment explanation
Indices: 1131688--1131733 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
1131678 TAATGATTTA
1131688 ATAATAATG
1 ATAATAATG
1131697 ATAATAATG
1 ATAATAATG
* *
1131706 AT-TTAATA
1 ATAATAATG
1131714 ATAATAATG
1 ATAATAATG
1131723 ATAATAATG
1 ATAATAATG
1131732 AT
1 AT
1131734 TTAATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (9 bp):
ATAATAATG
Found at i:1131738 original size:17 final size:17
Alignment explanation
Indices: 1131692--1131724 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1131682 GATTTAATAA
*
1131692 TAATGATAATAATGATT
1 TAATAATAATAATGATT
1131709 TAATAATAATAATGAT
1 TAATAATAATAATGAT
1131725 AATAATGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
TAATAATAATAATGATT
Found at i:1131970 original size:24 final size:24
Alignment explanation
Indices: 1131922--1131966 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1131912 AATTTGATAC
*
1131922 TAATGATTTACTAATTATTATTAA
1 TAATGATTTACTAATTAATATTAA
*
1131946 TAATGATTTA-TTATTAATATT
1 TAATGATTTACTAATTAATATT
1131967 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
TAATGATTTACTAATTAATATTAA
Found at i:1131973 original size:17 final size:17
Alignment explanation
Indices: 1131933--1131974 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1131923 AATGATTTAC
1131933 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
1131950 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
1131967 TAATTATT
1 TAATTATT
1131975 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:1133228 original size:14 final size:14
Alignment explanation
Indices: 1133195--1133228 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1133185 TTTTAATCAA
*
1133195 AATAAATATTTTCT
1 AATAAATATTTTAT
1133209 AATAAATATTTTAT
1 AATAAATATTTTAT
*
1133223 ATTAAA
1 AATAAA
1133229 ATAAAGGATT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAAATATTTTAT
Found at i:1134366 original size:22 final size:22
Alignment explanation
Indices: 1134341--1134386 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1134331 ACTAAGAAAT
*
1134341 TATTCTTTAATATAACTTTAAC
1 TATTCTTTAATATAACGTTAAC
1134363 TATTCTTTAATATAACGTTAAC
1 TATTCTTTAATATAACGTTAAC
1134385 TA
1 TA
1134387 ATAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTCTTTAATATAACGTTAAC
Found at i:1134394 original size:30 final size:30
Alignment explanation
Indices: 1134360--1134455 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
1134350 ATATAACTTT
1134360 AACTATTCTTTAATATAACGTT-AACTAATA
1 AACTATTCTTTAATATAAC-TTAAACTAATA
1134390 AACTATTCTTTAATATAACTTAAACTAATA
1 AACTATTCTTTAATATAACTTAAACTAATA
* * *
1134420 AA-TGATT-TTTAATTATAATTTACTACTAAAA
1 AACT-ATTCTTTAA-TATAACTTA-AACTAATA
1134451 AACTA
1 AACTA
1134456 ATTAACTACT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
29 8 0.14
30 40 0.69
31 9 0.16
32 1 0.02
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (30 bp):
AACTATTCTTTAATATAACTTAAACTAATA
Found at i:1134414 original size:22 final size:22
Alignment explanation
Indices: 1134341--1134416 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 22
1134331 ACTAAGAAAT
*
1134341 TATTCTTTAATATAACTTTAAC
1 TATTCTTTAATATAACTTAAAC
1134363 TATTCTTTAATATAACGTTAACTAATAAAC
1 TATTCTTT-A-AT-A---TAACT--TAAAC
1134393 TATTCTTTAATATAACTTAAAC
1 TATTCTTTAATATAACTTAAAC
1134415 TA
1 TA
1134417 ATAAATGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
22 15 0.33
23 1 0.02
24 7 0.16
25 1 0.02
27 1 0.02
28 7 0.16
29 1 0.02
30 12 0.27
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.45
Consensus pattern (22 bp):
TATTCTTTAATATAACTTAAAC
Found at i:1134660 original size:21 final size:21
Alignment explanation
Indices: 1134636--1134675 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1134626 TTTCTATACG
1134636 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1134657 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1134676 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1134738 original size:29 final size:29
Alignment explanation
Indices: 1134705--1134798 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 29
1134695 TGTTTTACCC
1134705 TAATTTATAATAATAAACTAATTAACTAA
1 TAATTTATAATAATAAACTAATTAACTAA
* *
1134734 TAATTTATAACAATAAACTAATTTAAATAA
1 TAATTTATAATAATAAACTAA-TTAACTAA
* *
1134764 TTATTCTTTTATATAACTTAAACTAATTAACTAA
1 -TAAT-TTATA-ATAA--TAAACTAATTAACTAA
1134798 T
1 T
1134799 TTTTTTATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 20 0.38
30 7 0.13
31 3 0.06
32 4 0.08
33 4 0.08
34 7 0.13
35 8 0.15
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (29 bp):
TAATTTATAATAATAAACTAATTAACTAA
Found at i:1134757 original size:18 final size:18
Alignment explanation
Indices: 1134704--1134758 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1134694 TTGTTTTACC
*
1134704 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
1134722 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
1134734 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
1134751 CTAATTTA
1 CTAATTTA
1134759 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:1134787 original size:35 final size:31
Alignment explanation
Indices: 1134747--1134810 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 31
1134737 TTTATAACAA
1134747 TAAACTAATTTAAATAATTATTCTTTTATATAACT
1 TAAACTAA-TTAAATAA-T-TT-TTTTATATAACT
*
1134782 TAAACTAATTAACTAATTTTTTTATATAA
1 TAAACTAATTAAATAATTTTTTTATATAA
1134811 TATAAATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 10 0.36
32 2 0.07
33 1 0.04
34 7 0.25
35 8 0.29
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAACTAATTAAATAATTTTTTTATATAACT
Found at i:1135312 original size:23 final size:23
Alignment explanation
Indices: 1135286--1135375 Score: 153
Period size: 23 Copynumber: 3.9 Consensus size: 23
1135276 CACGTGAGCT
*
1135286 TAAGGGCTACAATAATGCAGCAA
1 TAAGGGCTGCAATAATGCAGCAA
*
1135309 TAAGGGCTGCAATAATGCAACAA
1 TAAGGGCTGCAATAATGCAGCAA
1135332 TAAGGGCTGCAATAATGCAGCAA
1 TAAGGGCTGCAATAATGCAGCAA
*
1135355 TAAGTGCTGCAATAATGCAGC
1 TAAGGGCTGCAATAATGCAGC
1135376 TGAATTCACG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (23 bp):
TAAGGGCTGCAATAATGCAGCAA
Found at i:1135322 original size:12 final size:12
Alignment explanation
Indices: 1135295--1135369 Score: 75
Period size: 12 Copynumber: 6.5 Consensus size: 12
1135285 TTAAGGGCTA
*
1135295 CAATAA-TGCAG
1 CAATAAGTGCTG
*
1135306 CAATAAGGGCTG
1 CAATAAGTGCTG
**
1135318 CAATAA-TGCAA
1 CAATAAGTGCTG
*
1135329 CAATAAGGGCTG
1 CAATAAGTGCTG
*
1135341 CAATAA-TGCAG
1 CAATAAGTGCTG
1135352 CAATAAGTGCTG
1 CAATAAGTGCTG
1135364 CAATAA
1 CAATAA
1135370 TGCAGCTGAA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
11 23 0.46
12 27 0.54
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (12 bp):
CAATAAGTGCTG
Found at i:1136070 original size:25 final size:25
Alignment explanation
Indices: 1136039--1136087 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
1136029 AATTTTAAAT
1136039 TTTTTGTCAATAATATACTGACGAA
1 TTTTTGTCAATAATATACTGACGAA
* *
1136064 TTTTTGTCAGTAATATTCTGACGA
1 TTTTTGTCAATAATATACTGACGA
1136088 CTTACTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (25 bp):
TTTTTGTCAATAATATACTGACGAA
Found at i:1138898 original size:17 final size:18
Alignment explanation
Indices: 1138862--1138902 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1138852 ATATTATGTA
*
1138862 TTTAATTTATTTAAACAT
1 TTTACTTTATTTAAACAT
*
1138880 TTTACTTTATTT-AATAT
1 TTTACTTTATTTAAACAT
1138897 TTTACT
1 TTTACT
1138903 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAACAT
Found at i:1141261 original size:35 final size:33
Alignment explanation
Indices: 1141222--1141306 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 33
1141212 GTATTTCAGT
1141222 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
1141257 TAATTTTGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
1141292 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1141307 TAAAATTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
33 2 0.04
34 1 0.02
35 26 0.58
36 1 0.02
37 3 0.07
38 12 0.27
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:1148777 original size:13 final size:13
Alignment explanation
Indices: 1148723--1148771 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
1148713 TGCGTCATAA
*
1148723 ATTTATGACGCGC
1 ATTTATGACGCAC
*
1148736 ATTTATGACACAC
1 ATTTATGACGCAC
1148749 ATTTATGACGCAC
1 ATTTATGACGCAC
1148762 ATTTATGACG
1 ATTTATGACG
1148772 TTCATTGAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:1153755 original size:8 final size:8
Alignment explanation
Indices: 1153739--1153780 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
1153729 GGGAGGTTGC
1153739 AAAGAGAA
1 AAAGAGAA
*
1153747 AAAGGGAA
1 AAAGAGAA
1153755 AAAGAGAA
1 AAAGAGAA
*
1153763 AAGGAGAA
1 AAAGAGAA
1153771 AAAGAGAA
1 AAAGAGAA
1153779 AA
1 AA
1153781 GCATGTGGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (8 bp):
AAAGAGAA
Found at i:1162299 original size:20 final size:20
Alignment explanation
Indices: 1162276--1162336 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
1162266 TTTTTTGAAA
*
1162276 TTTTGACTTTTTTGGGTTTTT
1 TTTTG-CTTTTTTGGCTTTTT
*
1162297 TTTTGTTTTTTTGGCTTTTT
1 TTTTGCTTTTTTGGCTTTTT
*
1162317 TTGTT--TTTTTTTGCTTTTT
1 TT-TTGCTTTTTTGGCTTTTT
1162336 T
1 T
1162337 GAAAAGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 14 0.39
20 15 0.42
21 7 0.19
ACGTcount: A:0.02, C:0.05, G:0.15, T:0.79
Consensus pattern (20 bp):
TTTTGCTTTTTTGGCTTTTT
Found at i:1162305 original size:18 final size:18
Alignment explanation
Indices: 1162283--1162325 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1162273 AAATTTTGAC
*
1162283 TTTTTTGGGTTTTTTTTTG
1 TTTTTTGGG-CTTTTTTTG
*
1162302 TTTTTTTGGCTTTTTTTG
1 TTTTTTGGGCTTTTTTTG
1162320 TTTTTT
1 TTTTTT
1162326 TTTGCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (18 bp):
TTTTTTGGGCTTTTTTTG
Found at i:1162326 original size:19 final size:20
Alignment explanation
Indices: 1162283--1162336 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1162273 AAATTTTGAC
* *
1162283 TTTTTTGGGTTTTTTTTTGT
1 TTTTTTGGCTTTTTTTGTGT
1162303 TTTTTTGGCTTTTTTTGT-T
1 TTTTTTGGCTTTTTTTGTGT
*
1162322 TTTTTTTGCTTTTTT
1 TTTTTTGGCTTTTTT
1162337 GAAAAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.81
Consensus pattern (20 bp):
TTTTTTGGCTTTTTTTGTGT
Found at i:1162334 original size:10 final size:10
Alignment explanation
Indices: 1162293--1162336 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
1162283 TTTTTTGGGT
1162293 TTTTTTTTG-
1 TTTTTTTTGC
*
1162302 TTTTTTTGGC
1 TTTTTTTTGC
*
1162312 -TTTTTTTGT
1 TTTTTTTTGC
1162321 TTTTTTTTGC
1 TTTTTTTTGC
1162331 TTTTTT
1 TTTTTT
1162337 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:1162337 original size:18 final size:18
Alignment explanation
Indices: 1162294--1162336 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
1162284 TTTTTGGGTT
1162294 TTTTTTTGTTTTTTTGGC
1 TTTTTTTGTTTTTTTGGC
*
1162312 TTTTTTTGTTTTTTTTTGC
1 TTTTTTTG-TTTTTTTGGC
1162331 TTTTTT
1 TTTTTT
1162337 GAAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.84
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTGGC
Found at i:1169611 original size:14 final size:15
Alignment explanation
Indices: 1169578--1169611 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1169568 TCAAAGTCAA
*
1169578 CGGGTTGACTCGGTT
1 CGGGTTGACTCGGAT
1169593 CGGGTTGACTC-GAT
1 CGGGTTGACTCGGAT
1169607 CGGGT
1 CGGGT
1169612 CAAATAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.09, C:0.21, G:0.41, T:0.29
Consensus pattern (15 bp):
CGGGTTGACTCGGAT
Found at i:1180040 original size:20 final size:20
Alignment explanation
Indices: 1180015--1180060 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1180005 TGAGGAAATT
1180015 ATGGAAAAATTATATAAGGG
1 ATGGAAAAATTATATAAGGG
*
1180035 ATGG-AAAATTATATAATGG
1 ATGGAAAAATTATATAAGGG
*
1180054 CTGGAAA
1 ATGGAAA
1180061 TGATGTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (20 bp):
ATGGAAAAATTATATAAGGG
Found at i:1180133 original size:30 final size:30
Alignment explanation
Indices: 1180091--1180154 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1180081 AAGCCTTAGA
*
1180091 AAAATTTAGGGACC-ATTAT-GTAATTTTGG
1 AAAAGTTAGGGACCAATT-TGGTAATTTTGG
*
1180120 AAAAGTTAGGGGACCAATTTGGTATTTTTGG
1 AAAAGTTA-GGGACCAATTTGGTAATTTTGG
1180151 AAAA
1 AAAA
1180155 ATTGTGAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 7 0.23
30 7 0.23
31 16 0.53
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAAGTTAGGGACCAATTTGGTAATTTTGG
Found at i:1180531 original size:24 final size:24
Alignment explanation
Indices: 1180504--1180551 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1180494 GCATGACATG
*
1180504 GTACATAGATGTTT-TATACATCAT
1 GTACATAAAT-TTTATATACATCAT
1180528 GTACATAAATTTTATATACATCAT
1 GTACATAAATTTTATATACATCAT
1180552 AAGGAAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
GTACATAAATTTTATATACATCAT
Found at i:1183589 original size:23 final size:23
Alignment explanation
Indices: 1183541--1183599 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
1183531 CATCTTATAT
* *
1183541 GCACTTCGGTGCATTTCTACGCG
1 GCACTTAGGTGCAATTCTACGCG
* * *
1183564 GCATTTAGGTGCAATTCTATGTG
1 GCACTTAGGTGCAATTCTACGCG
*
1183587 GCACTTCGGTGCA
1 GCACTTAGGTGCA
1183600 TTTATACGAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.32
Consensus pattern (23 bp):
GCACTTAGGTGCAATTCTACGCG
Found at i:1184037 original size:2 final size:2
Alignment explanation
Indices: 1184030--1184085 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1184020 AAAGGAAATG
1184030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184072 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1184086 TATGTTTGGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1193837 original size:51 final size:51
Alignment explanation
Indices: 1193778--1193878 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
1193768 TCAGGGGGAG
* *
1193778 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
*
1193829 AGTTACAAGGAATTTCAACCTTTTCAAACCGATATTTCTTTACAACCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTAT
1193879 CCTTTCCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAACCTATT
Found at i:1203115 original size:45 final size:45
Alignment explanation
Indices: 1203059--1203166 Score: 139
Period size: 46 Copynumber: 2.4 Consensus size: 45
1203049 TGCACCAATC
1203059 CATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACTCA-GAATTAAA-TGAAACATCGAATGCATTT
* **
1203104 CATGCATCGATGCACTGAGAATTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGAATTAAATG-AAACATCGAATGCATTT
*
1203150 GATGCATCGATGCACTC
1 CATGCATCGATGCACTC
1203167 TTAGTACACC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
44 2 0.04
45 21 0.38
46 32 0.58
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (45 bp):
CATGCATCGATGCACTCAGAATTAAATGAAACATCGAATGCATTT
Found at i:1205551 original size:65 final size:65
Alignment explanation
Indices: 1205421--1205573 Score: 195
Period size: 65 Copynumber: 2.4 Consensus size: 65
1205411 AGAGTACATT
* * * * *
1205421 GATGCATCAAGTTCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTAGTGTATC
1 GATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGCTAGTGCATC
* *
1205485 GATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCAATGCATGG-TATGTGCA
1 GATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCAATGCATGGCTA-GTGCA
1205548 TC
64 TC
*
1205550 GATGCATGAAATGCATTCGATGTT
1 GATGCATCAAATGCATTCGATGTT
1205574 CAATTTAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 22 0.28
65 53 0.68
66 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
GATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCAATGCATGGCTAGTGCATC
Found at i:1205612 original size:65 final size:62
Alignment explanation
Indices: 1205421--1205623 Score: 180
Period size: 65 Copynumber: 3.1 Consensus size: 62
1205411 AGAGTACATT
* * * * *
1205421 GATGCATCAAGTTCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCTAGTGTAT
1 GATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGG-TTGTGCAT
1205484 C
62 C
*
1205485 GATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCAATGCATGGTATGTGCATC
1 GATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGTGCATC
* **
1205550 GATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGTGCA
1 GATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TT-GTGCA
1205613 TC
61 TC
*
1205615 GGTGCATCA
1 GATGCATCA
1205624 CTCTGAAAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 42 0.36
65 64 0.55
66 4 0.03
67 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (62 bp):
GATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGTGCATC
Found at i:1208299 original size:43 final size:44
Alignment explanation
Indices: 1208232--1208328 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
1208222 GGCCTTATGC
* * * *
1208232 ATCGATGCACATTCAAGGCGTGCATCGGTGTACCTTCATA-GTGT
1 ATCGATGCATATTCAAGGCATGCATCGATGCA-CTTCATAGGTGT
**
1208276 ATCGATGCATATTCAAGG-ATGCATCGATGCACTTGTTAGGTGT
1 ATCGATGCATATTCAAGGCATGCATCGATGCACTTCATAGGTGT
1208319 ATCGATGCAT
1 ATCGATGCAT
1208329 GAAGCACAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 5 0.11
43 24 0.52
44 17 0.37
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (44 bp):
ATCGATGCATATTCAAGGCATGCATCGATGCACTTCATAGGTGT
Found at i:1212223 original size:15 final size:15
Alignment explanation
Indices: 1212205--1212250 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1212195 TATTCATCTA
1212205 ATAACTCATCATAAG
1 ATAACTCATCATAAG
*
1212220 ATAAATCATC-T-A-
1 ATAACTCATCATAAG
1212232 ATAACTCATCATAAG
1 ATAACTCATCATAAG
1212247 ATAA
1 ATAA
1212251 ATAATCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 2 0.08
15 13 0.50
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.28
Consensus pattern (15 bp):
ATAACTCATCATAAG
Found at i:1212228 original size:27 final size:27
Alignment explanation
Indices: 1212198--1212260 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
1212188 CCCATTATAT
1212198 TCATCTAATAACTCATCATAAGATAAA
1 TCATCTAATAACTCATCATAAGATAAA
1212225 TCATCTAATAACTCATCATAAGATAAA
1 TCATCTAATAACTCATCATAAGATAAA
*
1212252 TAATCTAAT
1 TCATCTAAT
1212261 TCAGATGAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (27 bp):
TCATCTAATAACTCATCATAAGATAAA
Found at i:1214223 original size:46 final size:45
Alignment explanation
Indices: 1214131--1214231 Score: 139
Period size: 46 Copynumber: 2.2 Consensus size: 45
1214121 CTAAGATTTT
* * *
1214131 ATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTCAAAAAAGCCACAGTGC
* *
1214176 ATCGATGCATCAAATGCATTCGATGTTTTCAAAAAATCCTCAGTGC
1 ATCGATGCATCAAATGCATTCGATG-TTTCAAAAAAGCCACAGTGC
*
1214222 ATCAATGCAT
1 ATCGATGCAT
1214232 GGTATGTGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
45 24 0.49
46 25 0.51
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (45 bp):
ATCGATGCATCAAATGCATTCGATGTTTCAAAAAAGCCACAGTGC
Found at i:1217030 original size:51 final size:51
Alignment explanation
Indices: 1216954--1217189 Score: 276
Period size: 51 Copynumber: 4.6 Consensus size: 51
1216944 CATACTACAA
* * *** *
1216954 AAAAAAATATAGCACTTAACTCATACTTACATTGGTGTAAGTGAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCAGTGTAAGTAAATAAAAT
* *
1217005 AAAAAATTGTAGCACTTAACACATACTTACACCAGTGTAAGTAAATAAAAC
1 AAAAAAATGTAGCACTTAACACATACTTACACCAGTGTAAGTAAATAAAAT
* * *
1217056 AAAAAAGTGTAGCACTTAACACATAC-TACACCGGTGTAAGTGAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCAGTGTAAGTAAATAAAAT
** ** ** * *
1217106 AAAAAAATAAAATAAATAACACATTCTTACAACAGTGTAAGTAAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTACACCAGTGTAAGTAAATAAAAT
* *
1217157 AAAAAAGTGTAGCATTTAACACATACTTACACC
1 AAAAAAATGTAGCACTTAACACATACTTACACC
1217190 GATGCAAGTA
Statistics
Matches: 152, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
50 39 0.26
51 113 0.74
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.25
Consensus pattern (51 bp):
AAAAAAATGTAGCACTTAACACATACTTACACCAGTGTAAGTAAATAAAAT
Found at i:1217135 original size:101 final size:102
Alignment explanation
Indices: 1216954--1217190 Score: 323
Period size: 101 Copynumber: 2.3 Consensus size: 102
1216944 CATACTACAA
* * * ** * ** *
1216954 AAAAAAATATAGCACTTAACTCATACTTACATTGGTGTAAGTGAATAAAATAAAAAATTGTAGCA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAATAAAACA
** *
1217019 CTTAACACATACTTACACCAGTGTAAGTAAATAAAAC
66 AATAACACATACTTACAACAGTGTAAGTAAATAAAAC
*
1217056 AAAAAAGTGTAGCACTTAACACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAATAAAATA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAATAAAACA
* *
1217120 AATAACACATTCTTACAACAGTGTAAGTAAATAAAAT
66 AATAACACATACTTACAACAGTGTAAGTAAATAAAAC
*
1217157 AAAAAAGTGTAGCATTTAACACATACTTACACCG
1 AAAAAAGTGTAGCACTTAACACATACTTACACCG
1217191 ATGCAAGTAT
Statistics
Matches: 118, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
101 88 0.75
102 30 0.25
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (102 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAATAAAACA
AATAACACATACTTACAACAGTGTAAGTAAATAAAAC
Found at i:1218557 original size:3 final size:3
Alignment explanation
Indices: 1218536--1218628 Score: 105
Period size: 3 Copynumber: 30.0 Consensus size: 3
1218526 CAAAATTTAA
* * * *
1218536 TAT TAT TAG TAG TAG TAT TAT TGT TAT TAT TAT TAT TAT TAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* *
1218582 TGT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TAAC TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
1218629 AAGTAAATAC
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
3 72 0.91
4 7 0.09
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1218589 original size:16 final size:15
Alignment explanation
Indices: 1218536--1218628 Score: 105
Period size: 16 Copynumber: 6.0 Consensus size: 15
1218526 CAAAATTTAA
* * *
1218536 TATTATTAGTAGTAG
1 TATTATTATTATTAT
*
1218551 TATTATTGTTATTAT
1 TATTATTATTATTAT
1218566 TATTATTATTATTAGT
1 TATTATTATTATTA-T
*
1218582 TGTTATTATTATTAAT
1 TATTATTATTATT-AT
1218598 TATTATTATTATTAT
1 TATTATTATTATTAT
*
1218613 TAACTATTATTATTAT
1 T-ATTATTATTATTAT
1218629 AAGTAAATAC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
15 27 0.40
16 39 0.58
17 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAT
Found at i:1218615 original size:19 final size:19
Alignment explanation
Indices: 1218559--1218628 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
1218549 AGTATTATTG
1218559 TTATTATTATTATTATT-A
1 TTATTATTATTATTATTAA
*
1218577 TTAGTTGTTATTATTATTAA
1 TTA-TTATTATTATTATTAA
1218597 TTATTATTATTATTATTAA
1 TTATTATTATTATTATTAA
*
1218616 CTATTATTATTAT
1 TTATTATTATTAT
1218629 AAGTAAATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 3 0.06
19 40 0.85
20 4 0.09
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (19 bp):
TTATTATTATTATTATTAA
Found at i:1227313 original size:24 final size:24
Alignment explanation
Indices: 1227273--1227319 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1227263 AAATAGATCG
*
1227273 ACTCTAAATGTAATTCCATTTGAC
1 ACTCTAAATGTAATTCCAGTTGAC
*
1227297 ACTCTAAATAG-ACTTCCAGTTGA
1 ACTCTAAAT-GTAATTCCAGTTGA
1227320 TACCACCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (24 bp):
ACTCTAAATGTAATTCCAGTTGAC
Found at i:1231865 original size:16 final size:16
Alignment explanation
Indices: 1231844--1231910 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 16
1231834 ATTACACCTG
*
1231844 AAGAAAAAAAGGAAAA
1 AAGAAAAAAAAGAAAA
1231860 AAGAAAAAAAAGAAAAA
1 AAGAAAAAAAAG-AAAA
* *
1231877 AAGATAAGAAAGATAAGA
1 AAGAAAAAAAAGA-AA-A
1231895 AAGAAAAATAAAGAAA
1 AAGAAAAA-AAAGAAA
1231911 TATGAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
16 12 0.29
17 16 0.38
18 9 0.21
19 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAGAAAAAAAAGAAAA
Found at i:1231885 original size:22 final size:23
Alignment explanation
Indices: 1231859--1231910 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1231849 AAAAAGGAAA
1231859 AAAGAAAAAAAAGAAA-AAAAGAT
1 AAAGAAAAAAAAGAAAGAAAA-AT
* *
1231882 -AAGAAAGATAAGAAAGAAAAAT
1 AAAGAAAAAAAAGAAAGAAAAAT
1231904 AAAGAAA
1 AAAGAAA
1231911 TATGAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (23 bp):
AAAGAAAAAAAAGAAAGAAAAAT
Found at i:1231888 original size:26 final size:25
Alignment explanation
Indices: 1231845--1231902 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
1231835 TTACACCTGA
*
1231845 AGAAAAAAAGGAAAAAAGAAAAAAA
1 AGAAAAAAAGAAAAAAAGAAAAAAA
* * *
1231870 AGAAAAAAAGATAAGAAAGATAAGAA
1 AGAAAAAAAGA-AAAAAAGAAAAAAA
1231896 AGAAAAA
1 AGAAAAA
1231903 TAAAGAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (25 bp):
AGAAAAAAAGAAAAAAAGAAAAAAA
Found at i:1231905 original size:13 final size:13
Alignment explanation
Indices: 1231868--1231910 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1231858 AAAAGAAAAA
1231868 AAAGAAAAA-AAG
1 AAAGAAAAATAAG
*
1231880 ATAAGAAAGATAAG
1 A-AAGAAAAATAAG
1231894 AAAGAAAAATAAAG
1 AAAGAAAAAT-AAG
1231908 AAA
1 AAA
1231911 TATGAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 1 0.04
13 15 0.58
14 10 0.38
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (13 bp):
AAAGAAAAATAAG
Found at i:1233835 original size:2 final size:2
Alignment explanation
Indices: 1233828--1233874 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1233818 GTCCTTTATG
1233828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1233870 TA TA T
1 TA TA T
1233875 GCATACTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1234246 original size:11 final size:11
Alignment explanation
Indices: 1234230--1234279 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1234220 ATGATAGTAA
1234230 TATTTTTATTT
1 TATTTTTATTT
**
1234241 TATTTTTATAA
1 TATTTTTATTT
*
1234252 TATTTTATTTTT
1 TATTTT-TATTT
*
1234264 TATTTTTATTC
1 TATTTTTATTT
1234275 TATTT
1 TATTT
1234280 AATTTACTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:1234279 original size:23 final size:23
Alignment explanation
Indices: 1234227--1234272 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1234217 AAAATGATAG
*
1234227 TAATATTTT-TATTTTATTTTTA
1 TAATATTTTATTTTTTATTTTTA
1234249 TAATATTTTATTTTTTATTTTTA
1 TAATATTTTATTTTTTATTTTTA
1234272 T
1 T
1234273 TCTATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TAATATTTTATTTTTTATTTTTA
Found at i:1234284 original size:23 final size:23
Alignment explanation
Indices: 1234238--1234284 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1234228 AATATTTTTA
*
1234238 TTTTATTTTTATAATATTTTATT
1 TTTTATTTTTATAATATTTAATT
**
1234261 TTTTATTTTTATTCTATTTAATT
1 TTTTATTTTTATAATATTTAATT
1234284 T
1 T
1234285 ACTTTTAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTATTTTTATAATATTTAATT
Found at i:1235386 original size:35 final size:35
Alignment explanation
Indices: 1235347--1235423 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
1235337 AACACAATCA
1235347 TCAATTATATTATAAACCCCAAATTCCAAAATACT
1 TCAATTATATTATAAACCCCAAATTCCAAAATACT
* *
1235382 TCAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTATATTATAAACCCCAAATTCCAAAATACT
*
1235417 TTAATTA
1 TCAATTA
1235424 CATGCCCAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTATATTATAAACCCCAAATTCCAAAATACT
Found at i:1235440 original size:35 final size:35
Alignment explanation
Indices: 1235360--1235442 Score: 112
Period size: 35 Copynumber: 2.4 Consensus size: 35
1235350 ATTATATTAT
* * *
1235360 AAACCCCAAATTCCAAAATACTTCAATTATATTCT
1 AAACCCCAAATTCCAAAATACTTCAATTACATGCC
* *
1235395 AAACCTCAAATTCCAAAATACTTTAATTACATGCC
1 AAACCCCAAATTCCAAAATACTTCAATTACATGCC
*
1235430 CAACCCCAAATTC
1 AAACCCCAAATTC
1235443 ATAATTCATT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.28
Consensus pattern (35 bp):
AAACCCCAAATTCCAAAATACTTCAATTACATGCC
Found at i:1236107 original size:143 final size:145
Alignment explanation
Indices: 1235927--1236209 Score: 453
Period size: 148 Copynumber: 1.9 Consensus size: 145
1235917 AAACTATTTA
* * *
1235927 AATTAGAATAAAATAATATTATAGTATTATAAATATTTATAATTAAATTTCAACAGAAACTCG-A
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
** *
1235991 A-AATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAATATTTTTTGAGTTAACTATT
66 ATAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAATAAATTTTGAGTCAACTATT
1236055 TTATAAACTAAACTG
131 TTATAAACTAAACTG
*
1236070 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACATAAACTCGAA
1 AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCG-A
*
1236135 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGTATAAATTTTGAGTCAACT
65 AA-T-AATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAATAAATTTTGAGTCAACT
1236200 ATTTTATAAA
128 ATTTTATAAA
1236210 TTGAATTGAG
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
143 59 0.46
145 2 0.02
148 66 0.52
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (145 bp):
AATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
ATAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAATAAATTTTGAGTCAACTATT
TTATAAACTAAACTG
Found at i:1236427 original size:35 final size:35
Alignment explanation
Indices: 1236388--1236464 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
1236378 GTTGGGCATG
* *
1236388 TAATTGAAGTATTTTGAAATTT-GAGGTTTAGAATA
1 TAATTAAAGCATTTTGAAATTTAG-GGTTTAGAATA
* *
1236423 TAATTAAAGCATTTTGGAATTTAGGGTTTAGAATG
1 TAATTAAAGCATTTTGAAATTTAGGGTTTAGAATA
1236458 TAATTAA
1 TAATTAA
1236465 TGATTGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 36 0.97
36 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
TAATTAAAGCATTTTGAAATTTAGGGTTTAGAATA
Found at i:1237394 original size:12 final size:12
Alignment explanation
Indices: 1237377--1237402 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1237367 AGAAAGTAAC
1237377 CTTCAAAACTCA
1 CTTCAAAACTCA
1237389 CTTCAAAACTCA
1 CTTCAAAACTCA
1237401 CT
1 CT
1237403 GGATTCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (12 bp):
CTTCAAAACTCA
Found at i:1237820 original size:124 final size:124
Alignment explanation
Indices: 1237562--1237811 Score: 378
Period size: 124 Copynumber: 2.0 Consensus size: 124
1237552 TGAAGAATAC
1237562 AAAAAAGTATTTTCAACATTTTCATTAAAATTGTTTTAGAAATTTGAAAATAGAAAAACACAAGA
1 AAAAAA-TATTTTCAACATTTTCATTAAAATTGTTTTAGAAATTTGAAAATAGAAAAACACAAGA
* *
1237627 TTTATATTTTTTAACTTAACTTACACAAATTCAAATACTTTTAACAATATTTTTTGACTT
65 TTTAGATTTTTAAACTTAACTTACACAAATTCAAATACTTTTAACAATATTTTTTGACTT
** * * *
1237687 AAAAAATATTTTCAATGTTTTCATTAAAATTGTTTTAGAAATTTGAAAATAGAAAAATACGATAT
1 AAAAAATATTTTCAACATTTTCATTAAAATTGTTTTAGAAATTTGAAAATAGAAAAACACAAGAT
* * *
1237752 TTAGA-TTTTAAACTTAACTTACATGAACTT-AAATACTTTTAACAATATTTTTTTACTT
66 TTAGATTTTTAAACTTAACTTACA-CAAATTCAAATACTTTTAACAATATTTTTTGACTT
1237810 AA
1 AA
1237812 TATTATATTA
Statistics
Matches: 114, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
123 46 0.40
124 62 0.54
125 6 0.05
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (124 bp):
AAAAAATATTTTCAACATTTTCATTAAAATTGTTTTAGAAATTTGAAAATAGAAAAACACAAGAT
TTAGATTTTTAAACTTAACTTACACAAATTCAAATACTTTTAACAATATTTTTTGACTT
Found at i:1249214 original size:16 final size:16
Alignment explanation
Indices: 1249173--1249215 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1249163 TTACAAGAAA
*
1249173 TAATCTAAACCACTCAT
1 TAATCTAAA-CACTAAT
**
1249190 TAAAATAAACACTAAT
1 TAATCTAAACACTAAT
1249206 TAATCTAAAC
1 TAATCTAAAC
1249216 CATTAAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATCTAAACACTAAT
Found at i:1249299 original size:29 final size:29
Alignment explanation
Indices: 1249257--1249315 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1249247 ATTTTAATCT
1249257 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1249286 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1249315 A
1 A
1249316 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1254004 original size:29 final size:29
Alignment explanation
Indices: 1253950--1254008 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1253940 ATTTTCAGCT
*
1253950 AACTAAATTGATGTAAGTAATAACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
* *
1253979 AACTAAATTGATGTAAGCATTGACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
1254008 A
1 A
1254009 TTAATTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATAACATCAA
Found at i:1256545 original size:35 final size:35
Alignment explanation
Indices: 1256505--1256576 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1256495 TTGTTGGGGT
1256505 CTCGAACTTGAAGGAATTGATTTCTGCTTCTGCTG
1 CTCGAACTTGAAGGAATTGATTTCTGCTTCTGCTG
1256540 CTCGAACTTGAAGGAATTGATTTCTGCTTCTGCTG
1 CTCGAACTTGAAGGAATTGATTTCTGCTTCTGCTG
1256575 CT
1 CT
1256577 GCTGCTGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (35 bp):
CTCGAACTTGAAGGAATTGATTTCTGCTTCTGCTG
Found at i:1259680 original size:54 final size:54
Alignment explanation
Indices: 1259619--1259738 Score: 177
Period size: 54 Copynumber: 2.2 Consensus size: 54
1259609 TTGCACAGCT
* *
1259619 ACAGGAGTCATGACCTGAACACCCATATCACCACCTTGACTCTCTTACACATCA
1 ACAGGAGTCATGACCTAAACACCCATATCACCACATTGACTCTCTTACACATCA
* * * * *
1259673 ATAGGAGTCGTGATCTAAACACCCATATCACCACATTGACTCTCTTGCACATCT
1 ACAGGAGTCATGACCTAAACACCCATATCACCACATTGACTCTCTTACACATCA
1259727 ACAGGAGTCATG
1 ACAGGAGTCATG
1259739 TTGTGAAACT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (54 bp):
ACAGGAGTCATGACCTAAACACCCATATCACCACATTGACTCTCTTACACATCA
Found at i:1272294 original size:34 final size:34
Alignment explanation
Indices: 1272251--1272330 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 34
1272241 TGAATAAACG
* *
1272251 AACGGACATAAAAAAACATACAAGGACATAAATA
1 AACGAACATAAAAAAACATACAAGAACATAAATA
*** * **
1272285 AACGAACATAAACGGACTTACACTAACATAAATA
1 AACGAACATAAAAAAACATACAAGAACATAAATA
1272319 AACGAACATAAA
1 AACGAACATAAA
1272331 CGGACATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.14
Consensus pattern (34 bp):
AACGAACATAAAAAAACATACAAGAACATAAATA
Found at i:1272337 original size:24 final size:24
Alignment explanation
Indices: 1272310--1272379 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
1272300 ACTTACACTA
*
1272310 ACATAAATAAACGAACATAAACGG
1 ACATAAATGAACGAACATAAACGG
*
1272334 ACATAAATGAACGAACATAAATGG
1 ACATAAATGAACGAACATAAACGG
*
1272358 ACATAAATGAATGAACATAAAC
1 ACATAAATGAACGAACATAAAC
1272380 AAACGGATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.57, C:0.14, G:0.13, T:0.16
Consensus pattern (24 bp):
ACATAAATGAACGAACATAAACGG
Found at i:1272354 original size:34 final size:34
Alignment explanation
Indices: 1272266--1272338 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1272256 ACATAAAAAA
**
1272266 ACATACAAGGACATAAATAAACGAACATAAACGG
1 ACATACAATAACATAAATAAACGAACATAAACGG
* *
1272300 ACTTACACTAACATAAATAAACGAACATAAACGG
1 ACATACAATAACATAAATAAACGAACATAAACGG
1272334 ACATA
1 ACATA
1272339 AATGAACGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (34 bp):
ACATACAATAACATAAATAAACGAACATAAACGG
Found at i:1272356 original size:14 final size:14
Alignment explanation
Indices: 1272309--1272378 Score: 57
Period size: 14 Copynumber: 5.6 Consensus size: 14
1272299 GACTTACACT
*
1272309 AACATAAATAAACG
1 AACATAAATGAACG
1272323 AACAT--A--AACG
1 AACATAAATGAACG
*
1272333 GACATAAATGAACG
1 AACATAAATGAACG
1272347 AACATAAATG---G
1 AACATAAATGAACG
*
1272358 -ACATAAATGAATG
1 AACATAAATGAACG
1272371 AACATAAA
1 AACATAAA
1272379 CAAACGGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
10 17 0.37
11 1 0.02
12 2 0.04
13 1 0.02
14 25 0.54
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.16
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:1276263 original size:20 final size:20
Alignment explanation
Indices: 1276196--1276268 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1276186 GGCATTCATT
1276196 TGACTATCGCAACACGAAAA
1 TGACTATCGCAACACGAAAA
* **
1276216 TGACGT-TCACAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGAAAA
* *
1276237 TGTCTATCGCAACACGGAAA
1 TGACTATCGCAACACGAAAA
1276257 TGACTATCGCAA
1 TGACTATCGCAA
1276269 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.03
20 25 0.62
21 13 0.32
22 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAACACGAAAA
Found at i:1276284 original size:19 final size:18
Alignment explanation
Indices: 1276262--1276320 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
1276252 GGAAATGACT
1276262 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
1276281 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
1276295 ATCGCAAAGCGAAATAAAA
1 ATCGC-AAGCGAAATGAAA
1276314 ATCGCAA
1 ATCGCAA
1276321 CGAGGGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
14 8 0.25
15 3 0.09
16 2 0.06
17 2 0.06
18 3 0.09
19 14 0.44
ACGTcount: A:0.49, C:0.19, G:0.20, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1276307 original size:33 final size:33
Alignment explanation
Indices: 1276262--1276355 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
1276252 GGAAATGACT
* *
1276262 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAAAGCGAAATAAAAATCGCAACGAGAGA
*
1276295 ATCGCAAAGCGAAATAAAAATCGCAACGAGGGA
1 ATCGCAAAGCGAAATAAAAATCGCAACGAGAGA
*
1276328 ATCGCAAAGCGAAATAAAAATCACAACG
1 ATCGCAAAGCGAAATAAAAATCGCAACG
1276356 CGATTTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAAAGCGAAATAAAAATCGCAACGAGAGA
Found at i:1276377 original size:19 final size:19
Alignment explanation
Indices: 1276355--1276412 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1276345 AAATCACAAC
1276355 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1276374 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
1276388 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
1276407 GCGATT
1 GCGATT
1276413 CTCTCGTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 12 0.36
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.10, C:0.17, G:0.26, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1276402 original size:33 final size:33
Alignment explanation
Indices: 1276355--1276444 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
1276345 AAATCACAAC
* *
1276355 GCGATTTT-AGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCA-TTTCGCGTTGCGATTCTCTCGTT
1276388 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
* * *
1276421 GTGATTTTCATTTTGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
1276445 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 50 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:1276570 original size:14 final size:14
Alignment explanation
Indices: 1276551--1276584 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1276541 CATCAATTAA
1276551 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1276565 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1276579 ACAAAT
1 ACAAAT
1276585 AAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1278503 original size:19 final size:19
Alignment explanation
Indices: 1278481--1278547 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
1278471 AAAAATAACT
*
1278481 ATCGCAGCGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1278500 ATCGCAACGAGAGAATGAAA
1 ATCGCAACGCGA-AATGAAA
*
1278520 ATCGCAACGCGAAACGAAA
1 ATCGCAACGCGAAATGAAA
1278539 ATCGCAACG
1 ATCGCAACG
1278548 AGAGAATCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 25 0.58
20 18 0.42
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.09
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1278518 original size:20 final size:20
Alignment explanation
Indices: 1278493--1278554 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
1278483 CGCAGCGCGA
1278493 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1278513 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
1278532 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1278552 AAT
1 AAT
1278555 CACAATGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1278633 original size:33 final size:33
Alignment explanation
Indices: 1278591--1278674 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
1278581 CGATTTTTGG
*
1278591 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
* *
1278624 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
1278657 TTTCGCGTTGCGATTTTC
1 TTTCGCGTTGCGATTTTC
1278675 ATTCTCTCGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCA
Found at i:1278634 original size:19 final size:19
Alignment explanation
Indices: 1278610--1278699 Score: 109
Period size: 19 Copynumber: 4.9 Consensus size: 19
1278600 GCGATTTTGT
1278610 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1278629 CGTTGCGA--TT-A--TCT
1 CGTTGCGATTTTCATTTCG
*
1278643 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
*
1278662 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
1278682 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
1278700 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.17
16 3 0.05
17 2 0.03
19 27 0.45
20 18 0.30
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1278694 original size:39 final size:33
Alignment explanation
Indices: 1278591--1278699 Score: 137
Period size: 33 Copynumber: 3.1 Consensus size: 33
1278581 CGATTTTTGG
* *
1278591 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
*
1278624 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1278657 TTTCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGA--TT-A---TCTCGTTGCGATTTTCA
1278696 TTTC
1 TTTC
1278700 AACCAAAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
33 43 0.65
35 2 0.03
36 1 0.02
39 20 0.30
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
Found at i:1278901 original size:94 final size:94
Alignment explanation
Indices: 1278790--1279165 Score: 620
Period size: 94 Copynumber: 4.1 Consensus size: 94
1278780 ATGGATTGCA
* * *
1278790 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1278854 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1278883 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACGGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1278948 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1278977 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1279042 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1279071 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1279131 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1279161 TTACT
1 TTACT
1279166 AAGCAATCTA
Statistics
Matches: 271, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
90 41 0.15
93 23 0.08
94 207 0.76
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1280910 original size:20 final size:19
Alignment explanation
Indices: 1280887--1280937 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1280877 GAGAATTAAA
1280887 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
**
1280907 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
1280926 ATCGCAATGCGA
1 ATCGCAACGCGA
1280938 TTTTGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1280922 original size:19 final size:19
Alignment explanation
Indices: 1280858--1280937 Score: 88
Period size: 20 Copynumber: 4.1 Consensus size: 19
1280848 TCTTTTGGTT
* *
1280858 GAAATGAAAATCTCAACGA
1 GAAATGAAAATCGCAACGC
*
1280877 GAGAATTAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1280897 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
1280917 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1280936 GA
1 GA
1280938 TTTTGGTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
19 20 0.40
20 28 0.56
21 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1280981 original size:33 final size:33
Alignment explanation
Indices: 1280933--1281013 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
1280923 AAAATCGCAA
**
1280933 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
1280966 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
1280999 TGTGATTTTCATTTC
1 TGCGATTTTCATTTC
1281014 TCTCGTTGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:1281016 original size:21 final size:21
Alignment explanation
Indices: 1280990--1281053 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1280980 CGCGTTGCGA
1280990 TTCTCTCGTTGTGATTTTCAT
1 TTCTCTCGTTGTGATTTTCAT
**
1281011 TTCTCTCGTTGTGATAGTCAT
1 TTCTCTCGTTGTGATTTTCAT
*
1281032 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGTGATTTTCAT
1281052 TT
1 TT
1281054 TCATGTTGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.55
Consensus pattern (21 bp):
TTCTCTCGTTGTGATTTTCAT
Found at i:1281051 original size:20 final size:19
Alignment explanation
Indices: 1280997--1281068 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1280987 CGATTCTCTC
*
1280997 GTTGTGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
* **
1281017 CGTTGTGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
1281038 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
1281058 GTTGCGATTTT
1 GTTGCGATTTT
1281069 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.54
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:1281423 original size:22 final size:22
Alignment explanation
Indices: 1281361--1281426 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
1281351 TGACCGTGAA
* *
1281361 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
1281383 TGATATCGTCAGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1281405 TGATTTTGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1281427 GGATGTCGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1281628 original size:20 final size:20
Alignment explanation
Indices: 1281603--1281714 Score: 102
Period size: 20 Copynumber: 5.5 Consensus size: 20
1281593 GCTATGTAAA
*
1281603 TCGCATTGCGATAGT-CAAAT
1 TCGCATTGCGAT-TTACAAAT
**
1281623 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACAAAT
* *
1281643 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGA-TTTACAAAT
*
1281664 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTAC-AAAT
* **
1281684 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACAAAT
1281704 TCGCATTGCGA
1 TCGCATTGCGA
1281715 ATTAGGAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
19 2 0.03
20 55 0.71
21 20 0.26
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:1281672 original size:41 final size:41
Alignment explanation
Indices: 1281601--1281714 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 41
1281591 GCGCTATGTA
** *
1281601 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
*
1281641 ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
* * *
1281682 AATCGCGTTGCGATTTACGT-ATTCGCATTGCGA
1 AATCGCATTGCGATTTTCCTAATTCGCATTGCGA
1281715 ATTAGGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
40 27 0.42
41 38 0.58
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (41 bp):
AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
Found at i:1281737 original size:21 final size:21
Alignment explanation
Indices: 1281711--1281756 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1281701 TATTCGCATT
1281711 GCGAA-TTAGGAAAATCACAAC
1 GCGAATTTA-GAAAATCACAAC
* *
1281732 GCGAATTTAGAAAATCGCAAT
1 GCGAATTTAGAAAATCACAAC
1281753 GCGA
1 GCGA
1281757 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
GCGAATTTAGAAAATCACAAC
Found at i:1282561 original size:226 final size:226
Alignment explanation
Indices: 1282203--1283825 Score: 2477
Period size: 226 Copynumber: 7.2 Consensus size: 226
1282193 ATTATAAAAA
* * * *** *
1282203 ATAAAAACATATTAGGTAGCACTTATGTAACGTACTAGGTAGAATCTTTTTAAAGTTGATGGGGC
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
*
1282268 CTTAGAAATCCGACGATAACAAAATATGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
66 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
*
1282333 TAGGTAACACCTAAAATGTTAACC-AAGTTTAAGCTGATAGAGCCTTAGAAATCCGACGATAACA
131 TAGGTAACACCTAAAATGTT-ACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACA
*
1282397 TAACTGGTTAATTACTTGATTTGCTATCAACC
195 TAACTGGTTAATTACTTGATTTGTTATCAACC
* * * * * *
1282429 ATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGTAGCACCTTTTTAAAGATGATGAGAC
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
* *
1282494 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTATTATCAGTATTATCAATATAT
66 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
**
1282559 TAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATTTGACGATAACAT
131 TAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAT
**
1282624 AACCAGTTAATTACTTGATTTGTTATCAACC
196 AACTGGTTAATTACTTGATTTGTTATCAACC
* *
1282655 ATAATAACATATTAGATAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGAGC
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
* *
1282720 CTTAGAAATCTGACGATAACAAAATAGCTTAATTACTTAATTTGTTATCA-TAATTATCAACATA
66 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGT-ATTATCAACATA
**
1282784 TTAGGTAACAAATAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACA
130 TTAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACA
*
1282849 TAACAT-GTTAATTACTTTATTTGTTATCAACC
195 TAAC-TGGTTAATTACTTGATTTGTTATCAACC
* * * *
1282881 ATAATAACATATTAGGTAGCTCTTATGTAACGTAATATGTAGCACCTTTTTAAAGCTAATGGGGC
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
* * * *
1282946 CTTAGAAATCTGACGATAACAAGATATGTTAATTACTTAATTTGTTATCAGAATTATCAACATAT
66 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
* * * * * * *
1283011 TAGGTAACGCCCAAAATATTACCGAAGTTTAAGTTGATAGAGCCTTAAAAATCCGACGATAACAT
131 TAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAT
1283076 AACAT-GTTAATTACTTGATTTGTTATCAACC
196 AAC-TGGTTAATTACTTGATTTGTTATCAACC
** *
1283107 ATAATAACATATTAGGTAGCGCTTATGTAATATAATAGGTAGCGCCTTTTTAAAGCTGACGGGGC
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
* *
1283172 CTTAGAAATCAGACGATAACAAAATAGTTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
66 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
* * * * * *
1283237 TAGGTAACGCTTAAAATGTTGCCAAAGTTTAAGTTGATGGAGCCTTA-AAATCTGATGATAACAT
131 TAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAT
* *
1283301 AACCGATTAATTACTTGATTTGTTATCAACC
196 AACTGGTTAATTACTTGATTTGTTATCAACC
* *
1283332 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGTGCCTTTTTAAAGCTGATGGGGT
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
* * *
1283397 CTTAGAAATCCGACGATAACAAAATATGTTAATTACTTAATTTGTTATCAGTATTATCAATATTT
66 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
* * *
1283462 TAGGTAACGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCATTGGAAATCCGACGATAACAT
131 TAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAT
*
1283527 AA-TCGGTTAATTAATTGATTTGTTATCAACC
196 AACT-GGTTAATTACTTGATTTGTTATCAACC
* *
1283558 ATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
* * * *
1283623 CTTAGAAATCGGACGATAACAAAACAGGTTAATTACTTAATTTATTATCAGTATTATCAACTTAT
66 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
1283688 TAGGTAACGA-CTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACA
131 TAGGTAAC-ACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACA
1283752 TAACTGGTTAATTACTTGATTTGTTATCAACC
195 TAACTGGTTAATTACTTGATTTGTTATCAACC
* *
1283784 ATAATAACATATTAGGAAGCGCTTATGTAACGTAATAAGTAG
1 ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAG
1283826 TTCCTTAACG
Statistics
Matches: 1270, Mismatches: 118, Indels: 18
0.90 0.08 0.01
Matches are distributed among these distances:
225 209 0.16
226 1060 0.83
227 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (226 bp):
ATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGC
CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATAT
TAGGTAACACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGCCTTAGAAATCCGACGATAACAT
AACTGGTTAATTACTTGATTTGTTATCAACC
Found at i:1283433 original size:118 final size:117
Alignment explanation
Indices: 1283307--1283825 Score: 429
Period size: 108 Copynumber: 4.6 Consensus size: 117
1283297 ACATAACCGA
* *
1283307 TTAATTACTTGATTTGTTATCAACCATAATAACATATTAGGTAGCGCTTATGTAACGTAATAGGT
1 TTAATTACTTAATTTGTTATCAACCATAATAACATATTAGGTAGCGCTTATGTAATGTAATAGGT
* *
1283372 AGTGCCTTTTTAAAGCTGATGGGGTCTTAGAAATCCGACGATAACAAAATATG
66 AGAGCCTTTTTAAAGCTGATGGGG-CTTAGAAATCCGACGATAACAAAATAGG
** * * * * * * *
1283425 TTAATTACTTAATTTGTTATC-AGTATTATCAATATTTTAGGTAACGCCTA--AAATGT--TA-C
1 TTAATTACTTAATTTGTTATCAACCATAAT-AACATATTAGGTAGCGCTTATGTAATGTAATAGG
* * * * * *
1283484 CAAAG----TTT-AAGCTGATGGAGCATTGGAAATCCGACGATAACATAATCGG
65 TAGAGCCTTTTTAAAGCTGATGGGGC-TTAGAAATCCGACGATAACAAAATAGG
* * *
1283533 TTAATTAATTGATTTGTTATCAACCATAATAACATATTAGGTAGTGCTTATGTAATGTAATAGGT
1 TTAATTACTTAATTTGTTATCAACCATAATAACATATTAGGTAGCGCTTATGTAATGTAATAGGT
* * *
1283598 AGCGCCTTTTTAAAGCTGATGGGGCCTTAGAAATCGGACGATAACAAAACAGG
66 AGAGCCTTTTTAAAGCTGATGGGG-CTTAGAAATCCGACGATAACAAAATAGG
* ** * * * *
1283651 TTAATTACTTAATTTATTATC-AGTATTATCAACTTATTAGGTAACGAC-TA--AAATGT--TA-
1 TTAATTACTTAATTTGTTATCAACCATAAT-AACATATTAGGTAGCG-CTTATGTAATGTAATAG
** * * *
1283709 CCAAAG----TTT-AAGCTGATGGAGCCTTAGAAATCCGACGATAACATAACT-GG
64 GTAGAGCCTTTTTAAAGCTGATGG-GGCTTAGAAATCCGACGATAACA-AAATAGG
* * * *
1283759 TTAATTACTTGATTTGTTATCAACCATAATAACATATTAGGAAGCGCTTATGTAACGTAATAAGT
1 TTAATTACTTAATTTGTTATCAACCATAATAACATATTAGGTAGCGCTTATGTAATGTAATAGGT
1283824 AG
66 AG
1283826 TTCCTTAACG
Statistics
Matches: 305, Mismatches: 71, Indels: 55
0.71 0.16 0.13
Matches are distributed among these distances:
107 2 0.01
108 134 0.44
109 19 0.06
110 9 0.03
112 4 0.01
113 7 0.02
114 4 0.01
116 9 0.03
117 13 0.04
118 102 0.33
119 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (117 bp):
TTAATTACTTAATTTGTTATCAACCATAATAACATATTAGGTAGCGCTTATGTAATGTAATAGGT
AGAGCCTTTTTAAAGCTGATGGGGCTTAGAAATCCGACGATAACAAAATAGG
Found at i:1284053 original size:2 final size:2
Alignment explanation
Indices: 1284042--1284075 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1284032 AAATTATAAG
1284042 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1284076 GTGTGCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1288637 original size:15 final size:15
Alignment explanation
Indices: 1288613--1288642 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1288603 CTAAACATAC
1288613 ATACAAAACAATGTT
1 ATACAAAACAATGTT
*
1288628 ATACATAACAATGTT
1 ATACAAAACAATGTT
1288643 CTAATTGTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (15 bp):
ATACAAAACAATGTT
Found at i:1289949 original size:15 final size:15
Alignment explanation
Indices: 1289925--1289954 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1289915 CTTCAGCTCT
*
1289925 AGCGTTTTCCATCAG
1 AGCGTCTTCCATCAG
1289940 AGCGTCTTCCATCAG
1 AGCGTCTTCCATCAG
1289955 TTGGTGATCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (15 bp):
AGCGTCTTCCATCAG
Found at i:1299414 original size:201 final size:200
Alignment explanation
Indices: 1299071--1299850 Score: 909
Period size: 201 Copynumber: 3.9 Consensus size: 200
1299061 TCGTTCACAG
* * **
1299071 CATAGCTCAAGGCTAGAAGGTTTATCTGTCAATGAAAACTTTTGAGTTCGATTCCATTCAGCTCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACTTTCAAGTTCGATTCCATTCAGCTCG
** * * * * * * *
1299136 ATAGTGTATCAACCGCATTGTAGTAGTGAGGAACTACTTTCTGGTTGAAGTTTAAACTGAGGTCT
66 AGGGTGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGTTTAAACCGAGGTCT
* * * * * *
1299201 TTTAGTCAAGAAGAAGGCTTAGGTTCGATGTGATTTAGCAACGAGAAACTATCTCCCAGCCTAAT
131 TTAAGTCAAGAAGAAGACTTAGGTTGGCTGCGATTTAGCAACAAG-AACTATCTCCCAGCCTAAT
* *
1299266 TTATAG
195 TTACAA
* * * *
1299272 CATAGCTCAAGACGAGAAGGGTTATCTGTCAACGAAAACTTTCAAGTTTGATTCCATTCATCTCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACTTTCAAGTTCGATTCCATTCAGCTCG
* * *
1299337 AGGGTGTATCAACTGCAAGGTAGCAGCGAGGAACTACTTCCCGATTGAAGTTTAAACCGAGGTAT
66 AGGGTGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGTTTAAACCGAGGTCT
* * *
1299402 TTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAATAATGAACTATCTCCTAGCCTAAT
131 TTAAGTCAAGAAGAAGACTTAGGTTGGCTGCGATTTAGCAACAA-GAACTATCTCCCAGCCTAAT
1299467 TTACAA
195 TTACAA
* * * *
1299473 CATAGCTCAAGGCGAGAAGGGTTATCTATCAATGAAAACTTTTAAGTTTGATTCCATTCAGATCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACTTTCAAGTTCGATTCCATTCAGCTCG
* * *
1299538 AGGGCGTATCAACTGCATGGTAGCAGCAAGGAACTACTTTCCGGTTGAAGTTTAAACCGAGGTCT
66 AGGGTGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGTTTAAACCGAGGTCT
* *
1299603 TTAAGTCAAGAAGAAGACTTAGGTTGGCTACGATTTAGCAACTAGGAACTATCTCCCAGCCTAAT
131 TTAAGTCAAGAAGAAGACTTAGGTTGGCTGCGATTTAGCAAC-AAGAACTATCTCCCAGCCTAAT
1299668 TTACAA
195 TTACAA
* * ** * ** * * * *
1299674 CATCGCTTAAGTTGATAAAAGTTGTTTGTCAATGAAAACTTTCGAGTTCGATTCCATTCAGGTCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACTTTCAAGTTCGATTCCATTCAGCTCG
* * * * *
1299739 AGGGCT-TATCAA-TCGCATGGTAGCAGCGAAGAACTACTTTTC-AGTTGAATTTTAAACCAAGA
66 AGGG-TGTATCAACT-GCATGGTAGCAGCGAGGAACTACTTTCCGA-TTGAAGTTTAAACCGAGG
* * ** * ** *
1299801 TCTTTAAGCCAAGAAGAAAACCAAGGTTGACTAAGATTTGGCAACAAGAA
128 TCTTTAAGTCAAGAAGAAGACTTAGGTTGGCTGCGATTTAGCAACAAGAA
1299851 GCCACTTTCC
Statistics
Matches: 496, Mismatches: 78, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
200 5 0.01
201 489 0.99
202 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (200 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAAACTTTCAAGTTCGATTCCATTCAGCTCG
AGGGTGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGTTTAAACCGAGGTCT
TTAAGTCAAGAAGAAGACTTAGGTTGGCTGCGATTTAGCAACAAGAACTATCTCCCAGCCTAATT
TACAA
Done.