Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2999
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: 51001
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:5897 original size:20 final size:20
Alignment explanation
Indices: 5874--5911 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5864 TTAATGTGCG
*
5874 AATATATGTATATGTGTGTA
1 AATATATATATATGTGTGTA
5894 AATATATATATATGTGTG
1 AATATATATATATGTGTG
5912 GATCGAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (20 bp):
AATATATATATATGTGTGTA
Found at i:6185 original size:41 final size:41
Alignment explanation
Indices: 6123--6380 Score: 390
Period size: 41 Copynumber: 6.3 Consensus size: 41
6113 GTTTGGAATT
* *
6123 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
6164 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * *
6205 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
6246 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * * *
6287 GGTGATATGAATCAGGTTATAAACCTAGAAGGCTAAGCGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
6328 AGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
6369 GGTGATCCGAAT
1 GGTGATCTGAAT
6381 ATGATGAATT
Statistics
Matches: 193, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 193 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:6260 original size:82 final size:82
Alignment explanation
Indices: 6123--6374 Score: 477
Period size: 82 Copynumber: 3.1 Consensus size: 82
6113 GTTTGGAATT
*
6123 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
6188 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
6205 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
6270 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
* *
6287 GGTGATATGAATCAGGTTATAAACCTAGAAGGCTAAGCGCCAGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
6352 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
6369 GGTGAT
1 GGTGAT
6375 CCGAATATGA
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 167 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:14443 original size:16 final size:16
Alignment explanation
Indices: 14410--14443 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14400 TGGTTCTGTT
* *
14410 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
14426 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
14442 AA
1 AA
14444 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:17252 original size:21 final size:21
Alignment explanation
Indices: 17226--17266 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17216 AGACGAGCAA
* *
17226 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
17247 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
17267 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:19205 original size:16 final size:16
Alignment explanation
Indices: 19172--19205 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19162 GGAGATTGTT
* *
19172 AACATTAATGGGAGAC
1 AACATTAATGGAAAAC
19188 AACATTAATGGAAAAC
1 AACATTAATGGAAAAC
19204 AA
1 AA
19206 TACAAAGTGG
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:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGAAAAC
Found at i:26342 original size:21 final size:22
Alignment explanation
Indices: 26318--26372 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
26308 TAGGGATCCT
*
26318 ACACGGGCGTGTGTT-TTG-GAC
1 ACACGGGCGTGTGTTGATGAG-C
*
26339 ACACGGTCGTGT-TTGATGAGC
1 ACACGGGCGTGTGTTGATGAGC
26360 ACACGGGCGTGTG
1 ACACGGGCGTGTG
26373 AGACCCTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.16, C:0.20, G:0.38, T:0.25
Consensus pattern (22 bp):
ACACGGGCGTGTGTTGATGAGC
Found at i:28297 original size:19 final size:19
Alignment explanation
Indices: 28237--28299 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
28227 ATAATATTAC
28237 TATTATTAAATTCAT-A-T
1 TATTATTAAATTCATCATT
* *
28254 TATTAAATTTAACTTGA-CATAT
1 TATT--A-TTAAATTCATCAT-T
28276 TATTATTAAATTCATCATT
1 TATTATTAAATTCATCATT
28295 TATTA
1 TATTA
28300 ATATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
17 4 0.11
19 14 0.40
20 12 0.34
22 5 0.14
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTATTAAATTCATCATT
Found at i:31526 original size:15 final size:15
Alignment explanation
Indices: 31508--31540 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
31498 TTATTTTTGC
31508 TTTTATTTT-CTCCCT
1 TTTTATTTTACT-CCT
31523 TTTTATTTTACTCCT
1 TTTTATTTTACTCCT
31538 TTT
1 TTT
31541 CAATTTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATTTTACTCCT
Found at i:32044 original size:16 final size:16
Alignment explanation
Indices: 32020--32060 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
32010 TATTTTATCT
*
32020 TTTATTTTGTTTATTTA
1 TTTA-TTTGTTCATTTA
32037 TTTATTTGTTCATTTA
1 TTTATTTGTTCATTTA
32053 TTTATTTG
1 TTTATTTG
32061 CCTATCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTATTTGTTCATTTA
Found at i:33613 original size:44 final size:44
Alignment explanation
Indices: 33518--33870 Score: 209
Period size: 44 Copynumber: 7.8 Consensus size: 44
33508 TCTTATCTCT
* *
33518 CTGAAGTTGCAGTGGAATAGATTAAAGCTACGAATAT-C-AT-CTCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTAC-AA-ATCCTATAC-CC
*
33562 CTAAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCC
* * * * ** *
33606 TTGAAGTTACAGTGG-GTCGGATTAAATATATCATAGTTAACCT-TATCTCC
1 CTGAAGTTGCAGTGGAGT-AGATTGAAGCTA-CA-A---ATCCTATA-C-CC
* *
33656 CTCAAGTTGCAGTGGAGTAGATTGACGCTACAAATCCTATACCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCC
* * * * * *
33700 TTGAAGTTGTAGTGG-GTCGGATTAAATCTACCATAGCAAACCT-TATCTCC
1 CTGAAGTTGCAGTGGAGT-AGATTGAAGCTA-C--A--AATCCTATA-C-CC
* * * *
33750 CTGAAGTTGCAATGGAGCAGATTGAAGCTACGAATCTTAT-CTCC
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATAC-CC
* * * * *
33794 CTGAAGTTGTAGTGGAGCAAATTGAAGCTACAATTCCTATACCA
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCC
* *
33838 CTGAAGTTGCAGTGGATTAGAATGAAGCTACAA
1 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAA
33871 CAACAAATCT
Statistics
Matches: 235, Mismatches: 50, Indels: 48
0.71 0.15 0.14
Matches are distributed among these distances:
42 2 0.01
43 7 0.03
44 141 0.60
45 14 0.06
46 4 0.02
47 1 0.00
48 5 0.02
49 14 0.06
50 44 0.19
51 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCC
Found at i:33799 original size:94 final size:94
Alignment explanation
Indices: 33556--33808 Score: 364
Period size: 94 Copynumber: 2.7 Consensus size: 94
33546 TACGAATATC
**
33556 ATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCCTTGAAGTTACAGTGG
1 ATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
* **
33621 GTCGGATTAAATATATCATAGTTAACCTT
66 GTCGGATTAAATATACCATAGCAAACCTT
* *
33650 ATCTCCCTCAAGTTGCAGTGGAGTAGATTGACGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
1 ATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
*
33715 GTCGGATTAAATCTACCATAGCAAACCTT
66 GTCGGATTAAATATACCATAGCAAACCTT
* * * * * *
33744 ATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGCTACGAATCTTAT-CTCCCTGAAGTTGTAGTG
1 ATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATAC-CCTTGAAGTTGTAGTG
33808 G
65 G
33809 AGCAAATTGA
Statistics
Matches: 143, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
93 1 0.01
94 142 0.99
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (94 bp):
ATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACAAATCCTATACCCTTGAAGTTGTAGTGG
GTCGGATTAAATATACCATAGCAAACCTT
Found at i:33801 original size:138 final size:138
Alignment explanation
Indices: 33647--33915 Score: 335
Period size: 138 Copynumber: 1.9 Consensus size: 138
33637 CATAGTTAAC
* * * *
33647 CTTATCTCCCTCAAGTTGCAGTGGAGTAGATTGACGCTACAAATCCTATACC-CTTGAAGTTGTA
1 CTTATCTCCCTCAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCCTATACCAC-TGAAGTTGCA
* * * * * * * *
33711 GTGGGTCGGATTAAATCTACCATAGCAAACCTTATCTCCCTGAAGTTGCAATGGAGC-AGATTGA
65 GTGGATCAGAATAAAGCTACAACAACAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAGA-TGA
33775 AGCTACGAAT
129 AGCTACGAAT
* * *
33785 CTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGCTACAATTCCTATACCACTGAAGTTGCAG
1 CTTATCTCCCTCAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCCTATACCACTGAAGTTGCAG
* * * *
33850 TGGATTAGAATGAAGCTACAACAACAAATCTTATCTCCTTGAAGTTGCAATAGAGCAAGATGAAG
66 TGGATCAGAATAAAGCTACAACAACAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAG
33915 C
131 C
33916 CATGATACCA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
138 106 0.96
139 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (138 bp):
CTTATCTCCCTCAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCCTATACCACTGAAGTTGCAG
TGGATCAGAATAAAGCTACAACAACAAACCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAG
CTACGAAT
Found at i:33885 original size:232 final size:232
Alignment explanation
Indices: 33453--33898 Score: 531
Period size: 232 Copynumber: 1.9 Consensus size: 232
33443 TAGTAAAACC
* ** * *
33453 ACAAATCCTATACCCCTGAAATTGCAGTGGGTCGAATTGAAGTCACCATAGTGAATCTTATCTCT
1 ACAAATCCTATACCCCTGAAATTGCAGTGGGTCGAATTGAAATCACCATAGCAAACCTTATCTCC
* * * *
33518 CTGAAGTTGCAGTGGAATAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAGTGGAGTAGA
66 CTGAAGTTGCAATGGAACAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAGTGGAGCAAA
* * * * * **
33583 TTGAAGCTACAAATCCTATACCCTTGAAGTTACAGTGGGTCGGATTAAATATATCATAGTTAACC
131 TTGAAGCTACAAATCCTATACCCTTGAAGTTACAGTGGGTAGAATGAAATACAACATAGCAAACC
33648 TTATCTCCCTCAAGTTGCAGTGGAGTAGATTGACGCT
196 TTATCTCCCTCAAGTTGCAGTGGAGTAGATTGACGCT
* * * *
33685 ACAAATCCTATACCCTTGAAGTTGTAGTGGGTCGGATT-AAATCTACCATAGCAAACCTTATCTC
1 ACAAATCCTATACCCCTGAAATTGCAGTGGGTCGAATTGAAATC-ACCATAGCAAACCTTATCTC
* * * * * *
33749 CCTGAAGTTGCAATGGAGCAGATTGAAGCTACGAATCTTATCTCCCTGAAGTTGTAGTGGAGCAA
65 CCTGAAGTTGCAATGGAACAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAGTGGAGCAA
* * * *
33814 ATTGAAGCTACAATTCCTATACCAC-TGAAGTTGCAGTGGATTAGAATGAAGCTACAACA-A-CA
130 ATTGAAGCTACAAATCCTATACC-CTTGAAGTTACAGTGG-GTAGAATGAA-ATACAACATAGCA
* * *
33876 AATCTTATCTCCTTGAAGTTGCA
192 AACCTTATCTCCCTCAAGTTGCA
33899 ATAGAGCAAG
Statistics
Matches: 177, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
231 4 0.02
232 160 0.90
233 8 0.05
234 5 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (232 bp):
ACAAATCCTATACCCCTGAAATTGCAGTGGGTCGAATTGAAATCACCATAGCAAACCTTATCTCC
CTGAAGTTGCAATGGAACAGATTAAAGCTACGAATATCATCTCCCTAAAGTTGCAGTGGAGCAAA
TTGAAGCTACAAATCCTATACCCTTGAAGTTACAGTGGGTAGAATGAAATACAACATAGCAAACC
TTATCTCCCTCAAGTTGCAGTGGAGTAGATTGACGCT
Found at i:35447 original size:23 final size:24
Alignment explanation
Indices: 35421--35465 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
35411 ATCCTTTGTT
35421 TCCTT-TTTTTTCTGTTTGCTTTC
1 TCCTTCTTTTTTCTGTTTGCTTTC
35444 TCCTTCTTTTTTCTGTTTGCTT
1 TCCTTCTTTTTTCTGTTTGCTT
35466 CACATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.00, C:0.22, G:0.09, T:0.69
Consensus pattern (24 bp):
TCCTTCTTTTTTCTGTTTGCTTTC
Found at i:36699 original size:15 final size:16
Alignment explanation
Indices: 36675--36708 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
36665 TCTTTCTCTC
*
36675 TTTTCGTTTCT-TTTT
1 TTTTCCTTTCTGTTTT
36690 TTTTCCTTTCTGTTTT
1 TTTTCCTTTCTGTTTT
36706 TTT
1 TTT
36709 ATTAATCGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTCCTTTCTGTTTT
Found at i:39420 original size:30 final size:30
Alignment explanation
Indices: 39358--39427 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
39348 TTGTATATAT
* *
39358 AAACTTTAATTTGGTGCAATTATACACGTG
1 AAACTTTAATGTGGTGCAAATATACACGTG
* * * *
39388 AAACTATAATGTGGTTCAAATATATACTTG
1 AAACTTTAATGTGGTGCAAATATACACGTG
39418 AAACTTTAAT
1 AAACTTTAAT
39428 TTTGATTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (30 bp):
AAACTTTAATGTGGTGCAAATATACACGTG
Found at i:41029 original size:41 final size:40
Alignment explanation
Indices: 40984--41082 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 40
40974 TTATTGTTAC
* *
40984 TTAGTATTATTGTTAGTAAAAAACTAATATTTTTATTATGG
1 TTAGTATTATTGTTAGTAAAAAACTAA-ATTATTATTATAG
* * * *
41025 TTAGTTATTA-GGATTAGTAAAAACCTTAATTATTATTTTAG
1 TTAG-TATTATTG-TTAGTAAAAAACTAAATTATTATTATAG
*
41066 TTAGTATGATTGTTAGT
1 TTAGTATTATTGTTAGT
41083 TTTTACACTA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
40 9 0.19
41 20 0.43
42 18 0.38
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (40 bp):
TTAGTATTATTGTTAGTAAAAAACTAAATTATTATTATAG
Found at i:41136 original size:37 final size:38
Alignment explanation
Indices: 41089--41179 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 38
41079 TAGTTTTTAC
*
41089 ACTA-TATTATTGTTAG-T-TATTATTTTTAGTA-AAA
1 ACTATTATTATTGTTAGTTATATTATTTTGAGTATAAA
*
41123 CCCTAATTATTATTGTTAGTTAGTATTATTTTGAGTATAAA
1 -ACT-ATTATTATTGTTAGTTA-TATTATTTTGAGTATAAA
41164 ACTATTATTATTGTTA
1 ACTATTATTATTGTTA
41180 TTGTGTTAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
35 2 0.04
36 1 0.02
37 12 0.26
38 1 0.02
39 13 0.28
40 15 0.32
41 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (38 bp):
ACTATTATTATTGTTAGTTATATTATTTTGAGTATAAA
Found at i:41173 original size:76 final size:77
Alignment explanation
Indices: 41016--41179 Score: 201
Period size: 76 Copynumber: 2.2 Consensus size: 77
41006 ACTAATATTT
* *
41016 TTATTATGGTTAGTTATTAGGATTAGTAAAAACCTTAATTATTATTTTAGTTAGTATGATTGTTA
1 TTATTATTGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTTAGTTAGTATGATTGTTA
* * *
41081 GTTTTTACACTA
66 GTTATAAAACTA
*** *
41093 -TATTATTGTTAGTTATTATTTTTAGT-AAAACCCTAATTATTATTGTTAGTTAGTATTATT-TT
1 TTATTATTGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATT-TTAGTTAGTATGATTGTT
41155 GAG-TATAAAACTA
65 -AGTTATAAAACTA
41168 TTATTATTGTTA
1 TTATTATTGTTA
41180 TTGTGTTAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
75 26 0.35
76 49 0.65
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (77 bp):
TTATTATTGTTAGTTATTAGGATTAGTAAAAACCCTAATTATTATTTTAGTTAGTATGATTGTTA
GTTATAAAACTA
Found at i:43216 original size:22 final size:22
Alignment explanation
Indices: 43159--43217 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
43149 TACGAGGGCT
* *
43159 GTGGAGGTATGGGACTACTGTA
1 GTGGAGGTATGGGGCCACTGTA
* *
43181 GTGGGGGTATGGGGCCGCTGTA
1 GTGGAGGTATGGGGCCACTGTA
43203 GTGGAGGTATGGGGC
1 GTGGAGGTATGGGGC
43218 TGCTTCATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.15, C:0.10, G:0.51, T:0.24
Consensus pattern (22 bp):
GTGGAGGTATGGGGCCACTGTA
Found at i:44163 original size:71 final size:72
Alignment explanation
Indices: 44085--44917 Score: 651
Period size: 73 Copynumber: 11.0 Consensus size: 72
44075 AAAAAACGAA
* * * *
44085 AAATTGAAAATACCTCAGCGTG-CGGCGAGGCTCAACTCACCTTTAGCAATATGAATTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTC-TCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
44149 GAAAACATAATTG
65 GAAAAC---A--G
* * * *
44162 AAAACAGAAATGGAAATACCTCAGCATGTC-CTGAGGCTCAACTCACCTCTCGCCAGTATGAGTT
1 -----A-AATTGAAAATACCTCAGCGTGTCTC-GAGGCTCAACTCACCTCTCG-CAATATGAGTT
* *
44226 GGTTTTTTGCCAAACAG
58 -GATTTTTG-AAAACAG
* *
44243 TAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGA
1 AAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT---
* *
44307 AAACAGACATAAAAACAG
63 --------TTGAAAACAG
* ** *** * *
44325 AAATTGAAAGTGACTC-GACACGTGAGCCAAGGCTCAACTCACCTTTCGCAATATGAGTTGATTT
1 AAATTGAAAATACCTCAG---CGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* **
44389 TTTAAAGTAG
63 TTGAAAACAG
* * * *
44399 AATTTGAAAATACCTCGGCGTG-CCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
44463 AAAAACAG
66 -AAAACAG
*
44471 AAATTGAAATTACCTCAGCGTGTC-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTCTC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
44535 GAAAAACATAAAATTAACAG
65 G----------AA--AACAG
* * *
44555 GAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCT
1 AAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-T
44620 TGAAAAGCAG
64 TGAAAA-CAG
** *
44630 AAATTGAAAATACCTCAATGTGTCTTGAGGCTC-ACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTT
*
44694 TGACAACAG
64 TGAAAACAG
* ** *
44703 AAATT-AAATTACCTCAGCGTGTC-CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
1 AAATTGAAAATACCTCAGCGTGTCTC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
44766 GAAAAGCAG
65 GAAAA-CAG
* * ** * *
44775 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTA
1 AAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
44840 AAAACAG
66 AAAACAG
** * **
44847 AAATTG-AAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTCTTT
1 AAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTT
*
44911 CAAAACA
65 GAAAACA
44918 TAATAATGAA
Statistics
Matches: 639, Mismatches: 64, Indels: 106
0.79 0.08 0.13
Matches are distributed among these distances:
71 99 0.15
72 81 0.13
73 138 0.22
74 72 0.11
75 58 0.09
76 2 0.00
81 2 0.00
82 23 0.04
83 38 0.06
84 73 0.11
85 46 0.07
86 7 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (72 bp):
AAATTGAAAATACCTCAGCGTGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
AAAACAG
Found at i:44422 original size:156 final size:154
Alignment explanation
Indices: 44086--44997 Score: 532
Period size: 158 Copynumber: 5.9 Consensus size: 154
44076 AAAAACGAAA
* * * * *
44086 AATTGAAAATACCTCAGCGTGCGGCGAGGCTCAACTCACCTTTAGCAATATGAATTGATTTTTGA
1 AATTGAAAATACCTCAGCGTGC-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAGA
* * * *
44151 AAACATAATTGAAAACAGAAATGGAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCC
64 AAACAGAATTAAAAACAGAAATGGAAATACCTCAGCATGGCCTAAGGCTCAACTCACCTCTCGCC
* *
44216 AGTATGAGTTGGTTTTTTGCCAAACAGT
129 AATATGAGTTGATTTTTT--CAAACAGT
44244 AATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGAAA
1 AATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGAAA
* *
44309 ACAGACA-TAAAAACAGAAATTGAAAGTGA-CTC-GACACGTGAGCC-AAGGCTCAACTCACCTT
66 ACAGA-ATTAAAAACAGAAATGGAAA-T-ACCTCAG-CA--TG-GCCTAAGGCTCAACTCACCTC
*
44370 TCG-CAATATGAGTTGATTTTTT-AAAGTAG-
124 TCGCCAATATGAGTTGATTTTTTCAAA-CAGT
* *
44399 AATTTGAAAATACCTCGGCGTGCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT----
1 AA-TTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGAA
* * * *
44460 -------TTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG-
65 AACAGAATT-AAAAACAGAAATGGAAA-TACCTCAGCATGGCCTAAGGCTCAACTCACCTCTCGC
* *
44517 CAATATGAGTTGATTTTTGAAAAACATAAAATTAACAGG
128 CAATATGAGTTGATTTTT--------T--CA--AACAGT
* **
44556 AATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT----
1 AATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGAA
* * * * *
44617 -TC----TTGAAAAGCAGAAATTGAAAATACCTCA--ATGTGTCTTGAGGCTC-ACTCACCTCTC
65 AACAGAATT-AAAAACAGAAA-TGGAAATACCTCAGCATG-G-CCTAAGGCTCAACTCACCTCTC
* *
44674 G-CAATATGAGTTGATTTTTTTGACAACAGA
126 GCCAATATGAGTTGA-TTTTTTCA-AACAGT
* * ** *
44704 AATT-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-
1 AATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTAGA
* * * * * * **
44767 AAA-AG---------CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCG-
64 AAACAGAATTAAAAACAGAAA-TGGAAATACCTCAGCATGGCCTAAGGCTCAACTCACCTCTCGC
* ** *
44821 CAATATGAGTTGAATTTTAAAAACAGA
128 CAATATGAGTTGATTTTTTCAAACAGT
** ** ** **
44848 AATTG-AAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTC
1 AATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TTAG
* * * ** * *
44912 AAAACATAATAATGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCT
63 AAAACAGAAT--TAAAAACAGAAATGG-AAATACCTCAGCATGGCCTAAGGCTCAACTCACCTCT
44977 CG-CAATATGAGTTGATTTTTT
125 CGCCAATATGAGTTGATTTTTT
44998 TGAAAAACAG
Statistics
Matches: 627, Mismatches: 65, Indels: 124
0.77 0.08 0.15
Matches are distributed among these distances:
143 3 0.00
144 96 0.15
145 40 0.06
146 48 0.08
147 51 0.08
148 13 0.02
149 1 0.00
151 1 0.00
152 1 0.00
155 6 0.01
156 105 0.17
157 82 0.13
158 120 0.19
159 54 0.09
160 6 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (154 bp):
AATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGAAA
ACAGAATTAAAAACAGAAATGGAAATACCTCAGCATGGCCTAAGGCTCAACTCACCTCTCGCCAA
TATGAGTTGATTTTTTCAAACAGT
Found at i:44514 original size:73 final size:73
Alignment explanation
Indices: 44354--44915 Score: 652
Period size: 73 Copynumber: 7.6 Consensus size: 73
44344 ACGTGAGCCA
* * ** * **
44354 AGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTT-TAAAGTAGAATTTGAAAATACCTCGGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAAC
***
44418 GTG-CCCA
66 GTGTCTTG
* *
44425 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAAC
*
44490 GTGTCCTG
66 GTGTCTTG
*
44498 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAAATTAACAGGAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG---------AAA--AACAGAAATTGAA
44563 AATACCTCAACGTGTCTTG
55 AATACCTCAACGTGTCTTG
*
44582 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAACAGAAATTGAAAATACCTCA
*
44647 ATGTGTCTTG
64 ACGTGTCTTG
* *
44657 AGGCTC-ACTCACCTCTCGCAATATGAGTTGATTTTTTTG-ACAACAGAAATT-AAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAAAATACCTCA
* *
44719 GCGTGTCCTG
64 ACGTGTCTTG
** * *
44729 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAAC
44794 GTGTCTTG
66 GTGTCTTG
** * *
44802 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT-AAAAACAGAAATTG-AAATACCTCAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAAC
44865 GTGTCTTG
66 GTGTCTTG
** *
44873 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTCAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAA
44916 CATAATAATG
Statistics
Matches: 437, Mismatches: 33, Indels: 40
0.86 0.06 0.08
Matches are distributed among these distances:
71 93 0.21
72 73 0.17
73 132 0.30
74 28 0.06
75 39 0.09
77 3 0.01
82 3 0.01
84 60 0.14
85 3 0.01
86 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (73 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAAC
GTGTCTTG
Found at i:44714 original size:231 final size:225
Alignment explanation
Indices: 44159--45155 Score: 915
Period size: 231 Copynumber: 4.3 Consensus size: 225
44149 GAAAACATAA
* * *
44159 TTGAAAACAGAAA-TGGAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCCAGTATGA
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG-CAATATGA
* * * * *
44223 GTTG-GTTTTTTGCCAAACAGTAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCT
65 GTTGATTTTTTTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
* *
44286 CGCAATATGAGTTGA-TTTAGAAAACAGACATAAAAACAGAAATTGAAAGTGA-CTCGACACGTG
129 CGCAATATGAGTTGATTTTTG-AAA-A-ACA-AAAAACAGAAATTGAAAAT-ACCTC-A-ACGTG
* ** *
44349 AGC-CAAGGCTCAACTCACCTTTCGCAATATGAGTTGATTT
187 -TCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
* ** * * **
44389 TTTAAAGTAGAATTTGAAAATACCTCGGCGTG-CCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
44453 TTGA--TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTC
66 TTGATTTTTTTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTC
*
44516 GCAATATGAGTTGATTTTTGAAAAACATAAAATTAACAGGAATTGAAAATACCTCAACGTGTCTT
130 GCAATATGAGTTGATTTTTGAAAAAC--AAAA--AACAGAAATTGAAAATACCTCAACGTGTCTT
44581 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
191 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
** *
44618 CTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTC-ACTCACCTCTCGCAATATG
1 -TTGAAAA-CAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
* **
44682 AGTTGATTTTTTTGACAACAGAAATT-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCT
64 AGTTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
* *
44746 CGCAATATGAGTTGAATTTTG-------AAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAG
129 CGCAATATGAGTTGATTTTTGAAAAACAAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAG
**
44804 GCTCAACTCATTTCTCGCAATATGAGTTGAATT
194 GCTCAACTCACCTCTCGCAATATGAGTTG-ATT
* ** * **
44837 TTAAAAACAGAAATTG-AAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * * *
44901 TTGATTCTTTCAAAACATAATAATGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTC
66 TTGA-T-TTT-------T--T--TGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
*
44966 AACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATCAA-AGGCTTAATTGAAAA
118 AACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACA-AAA--AACA-G--AAATTGAAAA
** * **
45030 TACCTCGGCGTGTGTCCTGAGGCTCAACTCACCTCTCGC-ATATGAGTTGAAA
175 TACCTCAAC--GTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* * * * *
45082 TT-AAAACAAAAAAAATTG-AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTTTTGCAATAT
1 TTGAAAAC---AGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
*
45145 GAGCTGATTTT
63 GAGTTGATTTT
45156 GAAAAAGTAG
Statistics
Matches: 643, Mismatches: 72, Indels: 89
0.80 0.09 0.11
Matches are distributed among these distances:
216 26 0.04
217 32 0.05
218 7 0.01
219 5 0.01
220 59 0.09
221 1 0.00
222 3 0.00
226 1 0.00
227 3 0.00
228 73 0.11
229 55 0.09
230 68 0.11
231 163 0.25
232 18 0.03
233 11 0.02
241 3 0.00
242 1 0.00
243 2 0.00
244 5 0.01
245 22 0.03
246 11 0.02
247 74 0.12
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (225 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG
CAATATGAGTTGATTTTTGAAAAACAAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGC
TCAACTCACCTCTCGCAATATGAGTTGATT
Found at i:44779 original size:304 final size:303
Alignment explanation
Indices: 44162--45161 Score: 897
Period size: 304 Copynumber: 3.2 Consensus size: 303
44152 AACATAATTG
* * *
44162 AAAACAGAAATGGAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCCAGTATGAGTTG
1 AAAACAGAAATTGAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCG-CAATATGAGTTG
* * ** * * **
44227 GTTTT-----TTGCCAAACAGTAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCT
65 ATTTTGAAAAAT-AAAAACAGAAATTG-AAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
** * * * * *
44286 CGCAATATGAGTTGATT-TAGAAAACAGACATAAAAACAGAAATTGAAAGTGA-CTCGACACGTG
128 CGCAATATGAGTTGATTCT---TTAC--ATATGAAAACAGAAATGGAAAAT-ACCTC-A-ATGTG
* * * *
44349 AGCC-AAGGCTCAACTCACCTTTCGCAATATGAGTTGA-TTTTTT-A-AAGTAGAATTTGAAAAT
185 A-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAGCAGAAATTGAAAAT
** *
44410 ACCTCGGCGTG-CCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
249 ACCTCGGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA
44464 AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAA-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
44529 ATTTTTGAAAAACATAAAATTAACAGGAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCA
65 A-TTTTG-AAAA-AT-AAA--AACAGAAATTG-AAATACCTCAACGTGTCTTGAGGCTCAACTCA
* *
44594 CCTCTCGCAATATGAGTTGA-T-TTT-C-T-TGAAAAGCAGAAATTGAAAATACCTCAATGTGTC
123 CCTCTCGCAATATGAGTTGATTCTTTACATATGAAAA-CAGAAATGGAAAATACCTCAATGTGAC
* *
44654 TTGAGGCTC-ACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAA-CAGAAATT-AAATTACC
187 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAGCAGAAATTGAAAATACC
* **
44716 TCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGA
252 TCGGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA
* * * **
44768 AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACAGAAATTG-AAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * **
44833 AATTT------TAAAAACAGAAATTGAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCG
65 ATTTTGAAAAATAAAAACAGAAATTGAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCG
**
44892 CAATATGAGTTGATTCTTTCAAAACATAATAATGAAAACAGAAATGGAAAATACCTCGGTGTGAC
130 CAATATGAGTTGATTCTTT----AC---AT-ATGAAAACAGAAATGGAAAATACCTCAATGTGAC
* *
44957 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATCAAAGGCTTA
187 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG----AC---AAGC--A-G--AA
* *
45022 ATTGAAAATACCTCGGCGTGTGTCCTGAGGCTCAACTCACCTCTCGC-ATATGAGTTGAA-ATTA
240 ATTGAAAATACCTCGGC--GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG
45085 A
303 A
* * * * * * *
45086 AACAAAAAAAATTGAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTTTTGCAATATGAGCTG
1 AA-AACAGAAATTGAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
45151 ATTTTGAAAAA
65 ATTTTGAAAAA
45162 GTAGAAATTA
Statistics
Matches: 575, Mismatches: 66, Indels: 92
0.78 0.09 0.13
Matches are distributed among these distances:
291 49 0.09
292 11 0.02
293 3 0.01
294 3 0.01
295 1 0.00
298 1 0.00
302 52 0.09
303 103 0.18
304 148 0.26
305 21 0.04
308 3 0.01
310 2 0.00
311 2 0.00
312 28 0.05
313 34 0.06
314 1 0.00
315 1 0.00
317 4 0.01
318 62 0.11
319 20 0.03
320 26 0.05
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (303 bp):
AAAACAGAAATTGAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTGAAAAATAAAAACAGAAATTGAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGC
AATATGAGTTGATTCTTTACATATGAAAACAGAAATGGAAAATACCTCAATGTGACCTGAGGCTC
AACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAGCAGAAATTGAAAATACCTCGGCGTGT
CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA
Found at i:44963 original size:87 final size:87
Alignment explanation
Indices: 44840--45079 Score: 274
Period size: 87 Copynumber: 2.8 Consensus size: 87
44830 TTGAATTTTA
** * **
44840 AAAACAGAAATTG-AAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* *
44904 A-TTCTTT-CAAAACATAATAATG
66 ATTTCTTTGAAAAACA-AA-AATC
* *
44926 AAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* *
44991 ATTTTTTTGAAAAACAGAAATC
66 ATTTCTTTGAAAAACAAAAATC
* **
45013 AAAGGC-TTAATTGAAAATACCTCGGCGTGTGTCCTGAGGCTCAACTCACCTCTCGC-ATATGAG
1 AAA-ACAGAAATTGAAAATACCTC-G-GTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
45076 TTGA
63 TTGA
45080 AATTAAAACA
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
86 12 0.09
87 66 0.50
88 19 0.14
89 35 0.27
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (87 bp):
AAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTCTTTGAAAAACAAAAATC
Found at i:45422 original size:79 final size:77
Alignment explanation
Indices: 45304--45652 Score: 401
Period size: 78 Copynumber: 4.5 Consensus size: 77
45294 AGTGTTGTAT
* *
45304 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATA
*
45369 CCTCAGCATGTGAAC
66 CCTCAGC--GTG-TC
*
45384 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTTTTGAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATA
**
45447 CCTCAAAGTGTTC
66 CCTCAGCGTG-TC
* ** * * * *
45460 TTGAGGCTCAACTCATTTCTCGCAATATTAAGTTGA-----ATTTTGAAAACAGAAATTGTAATT
1 CTGAGGCTCAACTCACCTCTCGCAATA-TGAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAAT
45520 ACCTTCAGCGTGTC
65 ACC-TCAGCGTGTC
* *
45534 CTGAGGCTCAACTCA-TTCGTCGCAAATATGAGTTGATTTTTTTTTTAAACAACAGAAATTGAAA
1 CTGAGGCTCAACTCACCTC-TCGC-AATATGAGTTGATTTTTTTTTTGAA-AACAGAAATTGAAA
45598 ATTACCTCAGCGTGTC
63 A-TACCTCAGCGTGTC
*
45614 CTGAGGCTCAACTCACCTCTAGCAATA-GAGTTGATTTTT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
45653 GAAAAACAAA
Statistics
Matches: 233, Mismatches: 23, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
73 3 0.01
74 51 0.22
75 10 0.04
76 4 0.02
77 23 0.10
78 53 0.23
79 41 0.18
80 42 0.18
81 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (77 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATA
CCTCAGCGTGTC
Found at i:45539 original size:74 final size:74
Alignment explanation
Indices: 45343--45666 Score: 279
Period size: 74 Copynumber: 4.3 Consensus size: 74
45333 AGTTGATTTT
* * *
45343 TTTTTTTAAAACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCA
1 TTTTTTGAAAACAGAAATTGAAAATACCTCAGC--GTGATCCTGAGGCTCAACTCA-TTCTCGCA
45407 ATA-TAAGTTGA
63 ATATTAAGTTGA
** * *
45418 TTTTTTTTTGAAAACAGAAATTGAAAATACCTCAAAGTGTTCTTGAGGCTCAACTCATTTCTCGC
1 ---TTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTGATCCTGAGGCTCAACTCA-TTCTCGC
45483 AATATTAAGTTGA
62 AATATTAAGTTGA
* * *
45496 -ATTTTGAAAACAGAAATTGTAATTACCTTCAGCGTG-TCCTGAGGCTCAACTCATTCGTCGCAA
1 TTTTTTGAAAACAGAAATTGAAAATACC-TCAGCGTGATCCTGAGGCTCAACTCATTC-TCGCAA
*
45559 -ATATGAGTTGA
64 TAT-TAAGTTGA
* *
45570 TTTTTTTTTTAAACAACAGAAATTGAAAATTACCTCAGCGTG-TCCTGAGGCTCAACTCACCTCT
1 ----TTTTTTGAA-AACAGAAATTGAAAA-TACCTCAGCGTGATCCTGAGGCTCAACTCA-TTCT
* *
45634 AGCAATA--GAGTTGA
59 CGCAATATTAAGTTGA
*
45648 -TTTTTGAAAAACAAAAATT
1 TTTTTTG-AAAACAGAAATT
45667 AAAGGCTTAA
Statistics
Matches: 208, Mismatches: 23, Indels: 35
0.78 0.09 0.13
Matches are distributed among these distances:
73 19 0.09
74 55 0.26
75 6 0.03
76 4 0.02
77 23 0.11
78 45 0.22
79 6 0.03
80 43 0.21
81 7 0.03
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (74 bp):
TTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTGATCCTGAGGCTCAACTCATTCTCGCAATA
TTAAGTTGA
Found at i:45647 original size:152 final size:150
Alignment explanation
Indices: 45304--45666 Score: 403
Period size: 152 Copynumber: 2.4 Consensus size: 150
45294 AGTGTTGTAT
* *
45304 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTAAAACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTGAAAACAGAAATTGAAAATA
*
45369 CCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAACA
61 CCTCAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTAAAAACA
45434 GAAATTGAAAATACCTCAAAGTGTTC
125 GAAATTGAAAATACCTCAAAGTGTTC
* ** * * * *
45460 TTGAGGCTCAACTCATTTCTCGCAATATTAAGTTGAATTTTGAAAACAGAAATTGTAATTACCTT
1 CTGAGGCTCAACTCACCTCTCGCAATA-TGAGTTGATTTTTGAAAACAGAAATTGAAAATACC-T
* * *
45525 CAGC-GTG-TCCTGAGGCTCAACTCA-TTCGTCGCAAATATGAGTTGATTTTTTTTTTAAACAAC
64 CAGCAGTGAACC-GAGGCTCAACTCACCTC-TCGC-AATATAAGTTGA-TTTTTTTTTAAA-AAC
**
45587 AGAAATTGAAAATTACCTCAGCGTG-TC
124 AGAAATTGAAAA-TACCTCAAAGTGTTC
* *
45614 CTGAGGCTCAACTCACCTCTAGCAATA-GAGTTGATTTTTGAAAAACAAAAATT
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATT
45667 AAAGGCTTAA
Statistics
Matches: 176, Mismatches: 22, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
150 4 0.02
151 20 0.11
152 45 0.26
153 27 0.15
154 40 0.23
155 10 0.06
156 23 0.13
157 7 0.04
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (150 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCA
GCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTAAAAACAGAAATT
GAAAATACCTCAAAGTGTTC
Done.