Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 177 of 320
Found at i:58566392 original size:20 final size:21
Alignment explanation
Indices: 58566334--58566394 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
58566324 AAATCTCTAG
*
58566334 AAATATTGGTAAATCTTTAGAA
1 AAAT-TTGGTAAATCCTTAGAA
* * *
58566356 ACA-TCGGTAAATTCTTA-AA
1 AAATTTGGTAAATCCTTAGAA
58566375 AAATTTGGTAAATCCTTAGA
1 AAATTTGGTAAATCCTTAGA
58566395 TATTTTGATA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.13
20 23 0.77
21 1 0.03
22 2 0.07
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (21 bp):
AAATTTGGTAAATCCTTAGAA
Found at i:58566424 original size:33 final size:32
Alignment explanation
Indices: 58566380--58566446 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
58566370 TTAAAAAATT
58566380 TGGTAAATCCTTAGATATTTTGATATAACCTTA
1 TGGTAAATCCTTAGATATTTTGATA-AACCTTA
* * *
58566413 TGGTAATTCCTTGGTTATTTTGATAAACCTTA
1 TGGTAAATCCTTAGATATTTTGATAAACCTTA
58566445 TG
1 TG
58566447 TTGGTAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (32 bp):
TGGTAAATCCTTAGATATTTTGATAAACCTTA
Found at i:58576103 original size:48 final size:49
Alignment explanation
Indices: 58576021--58576151 Score: 156
Period size: 49 Copynumber: 2.7 Consensus size: 49
58576011 GTGGCCCGCT
* * * *
58576021 AACCTAGTTAACAACTTACATGTCCTACCAGTGGCCCGT-ATACACGCC
1 AACCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCATCATACACGCC
* * * * *
58576069 AATCTGGTTAGCAACTAACATGCCCTACTAGTGGCCCATCATATACTCC
1 AACCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCATCATACACGCC
* *
58576118 CACCTAGTTAGCAACTAGCATGCCCTACCAGTGG
1 AACCTAGTTAGCAACTAACATGCCCTACCAGTGG
58576152 TTTAGCACAT
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
48 32 0.47
49 36 0.53
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (49 bp):
AACCTAGTTAGCAACTAACATGCCCTACCAGTGGCCCATCATACACGCC
Found at i:58581762 original size:49 final size:47
Alignment explanation
Indices: 58581648--58581775 Score: 132
Period size: 49 Copynumber: 2.7 Consensus size: 47
58581638 GGTATAATGT
* * ** * *
58581648 CGACGTCATGTCCCAGACATGATCTTACACTGGCTCATCCATCACGT
1 CGACGCCATGTCCCAGACATGGTCTTACACTAACTCATCAATCACGC
* ** *
58581695 CGATGCCATGTCTTAGACATGGTCTTACACTAACT-ATCAAAATCGAGGC
1 CGACGCCATGTCCCAGACATGGTCTTACACTAACTCATC--AATC-ACGC
58581744 CGACGCCATGTCCCAGACATGGTCTTACACTA
1 CGACGCCATGTCCCAGACATGGTCTTACACTA
58581776 GCTCTCGTCT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
46 3 0.05
47 28 0.43
48 3 0.05
49 31 0.48
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (47 bp):
CGACGCCATGTCCCAGACATGGTCTTACACTAACTCATCAATCACGC
Found at i:58582004 original size:90 final size:91
Alignment explanation
Indices: 58581717--58582046 Score: 334
Period size: 90 Copynumber: 3.6 Consensus size: 91
58581707 TTAGACATGG
* * * * *
58581717 TCTTACACTAACTATCAAAATCGAGGCCGACGCCATGTCCCAGACATGGTCTTACACTAGCTCTC
1 TCTTACACTAGCTCTCATAAT-GTGGCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTCTC
58581782 GTCTCAATGTCAATTGTCCCAAACATTT
64 GTCTCAATGTCAATTGTCCCAAACATTT
* * *
58581810 TCTTACACTAGCTCTCATAATGTGGCCGATGCCATGTCCTAGACATGGTCTTACAGTGACACCTC
1 TCTTACACTAGCTCTCATAATGTGGCCGATG-CATGTCCCAGACATGGTCTTACACT---AGCTC
* * ** ** * *
58581875 TTGTAGTTGATG-C-A-TGTCTTAGACA-TA
62 TCGT-CTCAATGTCAATTGTCCCAAACATTT
* *** *
58581902 TCTTACACTAGCT-TACAT-CTCAAAGCCGATGCATGTCCTAGACAT-GTCTTACACTAGCTCTC
1 TCTTACACTAGCTCT-CATAAT-GTGGCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTC
58581964 GTCTCAATGTCAATTGTCCCAAACATTT
64 GTCTCAATGTCAATTGTCCCAAACATTT
58581992 TCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACAT-GTCTTACACT
1 TCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGGTCTTACACT
58582047 GGCACACAAA
Statistics
Matches: 190, Mismatches: 35, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
86 4 0.02
87 8 0.04
88 1 0.01
89 8 0.04
90 56 0.29
91 18 0.09
92 56 0.29
93 26 0.14
94 1 0.01
95 8 0.04
96 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (91 bp):
TCTTACACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCTCGT
CTCAATGTCAATTGTCCCAAACATTT
Found at i:58583542 original size:19 final size:20
Alignment explanation
Indices: 58583503--58583544 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
58583493 AGTGTTACAA
*
58583503 GTAAATCTTTAAAAATGTTG
1 GTAAATCATTAAAAATGTTG
58583523 GTAAATCATTAAAAAT-TTG
1 GTAAATCATTAAAAATGTTG
58583542 GTA
1 GTA
58583545 TGAATGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (20 bp):
GTAAATCATTAAAAATGTTG
Found at i:58583619 original size:20 final size:20
Alignment explanation
Indices: 58583594--58583717 Score: 74
Period size: 20 Copynumber: 6.2 Consensus size: 20
58583584 ACAATTTTAG
58583594 AAATTTTGATAAATCCTTAA
1 AAATTTTGATAAATCCTTAA
* * *
58583614 AAATTTTGGTAATTCCTTAG
1 AAATTTTGATAAATCCTTAA
*
58583634 ATATTTT-AGTATAA-CCTTAGA
1 AAATTTTGA-TA-AATCCTTA-A
* * * *
58583655 AATTTTTG-TAAAACTTTAG
1 AAATTTTGATAAATCCTTAA
* * *
58583674 AAATTTTAATAAATTCTTAG
1 AAATTTTGATAAATCCTTAA
* * *
58583694 ATATTCTGGTAAATCCTTAA
1 AAATTTTGATAAATCCTTAA
58583714 AAAT
1 AAAT
58583718 ATTGGTTTCG
Statistics
Matches: 75, Mismatches: 23, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
19 8 0.11
20 61 0.81
21 6 0.08
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (20 bp):
AAATTTTGATAAATCCTTAA
Found at i:58583634 original size:40 final size:39
Alignment explanation
Indices: 58583590--58583717 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 39
58583580 CAAAACAATT
* *
58583590 TTAGAAATTTTGATAAATCCTTAAAAATTTTGGTAATTCC
1 TTAGAAATTTT-ATAAATCCTTAGAAATTTTGGTAAATCC
* * * *
58583630 TTAGATATTTTAGTATAA-CCTTAGAAATTTTTGTAAAACT
1 TTAGAAATTTTA-TA-AATCCTTAGAAATTTTGGTAAATCC
* * *
58583670 TTAGAAATTTTAATAAATTCTTAGATATTCTGGTAAATCC
1 TTAGAAATTTT-ATAAATCCTTAGAAATTTTGGTAAATCC
*
58583710 TTAAAAAT
1 TTAGAAAT
58583718 ATTGGTTTCG
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
39 3 0.04
40 64 0.91
41 3 0.04
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (39 bp):
TTAGAAATTTTATAAATCCTTAGAAATTTTGGTAAATCC
Found at i:58583712 original size:60 final size:61
Alignment explanation
Indices: 58583590--58583717 Score: 138
Period size: 60 Copynumber: 2.1 Consensus size: 61
58583580 CAAAACAATT
* ** *
58583590 TTAGAAA-TTTTGATAAATCCTTAAAAATTTTGGTAATTCCTTAGATATTTTAGTATAACC
1 TTAGAAATTTTTGATAAAACCTTAAAAATTTTAATAATTCCTTAGATATTCTAGTATAACC
* * *
58583650 TTAGAAATTTTTG-TAAAACTTTAGAAATTTTAATAAATT-CTTAGATATTCTGGTA-AATCC
1 TTAGAAATTTTTGATAAAACCTTAAAAATTTTAAT-AATTCCTTAGATATTCTAGTATAA-CC
*
58583710 TTAAAAAT
1 TTAGAAAT
58583718 ATTGGTTTCG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
59 2 0.04
60 46 0.81
61 9 0.16
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (61 bp):
TTAGAAATTTTTGATAAAACCTTAAAAATTTTAATAATTCCTTAGATATTCTAGTATAACC
Found at i:58584341 original size:16 final size:16
Alignment explanation
Indices: 58584322--58584355 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58584312 TTCATTAAAA
58584322 TAATAAATTATATTAT
1 TAATAAATTATATTAT
**
58584338 TAATTCATTATATTAT
1 TAATAAATTATATTAT
58584354 TA
1 TA
58584356 TATATAAAGA
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATAAATTATATTAT
Found at i:58584424 original size:21 final size:21
Alignment explanation
Indices: 58584391--58584433 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58584381 TTAATAATAT
*
58584391 TTAACATTGTAATATTTGATA
1 TTAAAATTGTAATATTTGATA
* *
58584412 TTAAAATTTTAATATTTTATA
1 TTAAAATTGTAATATTTGATA
58584433 T
1 T
58584434 ATTTTCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAAAATTGTAATATTTGATA
Found at i:58591997 original size:95 final size:95
Alignment explanation
Indices: 58591833--58592005 Score: 310
Period size: 95 Copynumber: 1.8 Consensus size: 95
58591823 AAACAAGGAA
*
58591833 GGTGCAATTTCTGCTAAGCTTAGCGCATAGGATTATTTTAGATTTAAGGTGGGAGATGAATCATA
1 GGTGCAATTTCTGCTAAGCTTAGCGCATAGGATTATTTTAGAGTTAAGGTGGGAGATGAATCATA
58591898 TCATGTTCTCTACAACCACAAACTGCTGAT
66 TCATGTTCTCTACAACCACAAACTGCTGAT
* * *
58591928 GGTGCAATTTCTGCTAAGCTTAGCGCTTAGGATTATTTTAGGGTTAAGGTGGGAGATGAATCATT
1 GGTGCAATTTCTGCTAAGCTTAGCGCATAGGATTATTTTAGAGTTAAGGTGGGAGATGAATCATA
58591993 TCATGTTCTCTAC
66 TCATGTTCTCTAC
58592006 GACTAAGCTT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (95 bp):
GGTGCAATTTCTGCTAAGCTTAGCGCATAGGATTATTTTAGAGTTAAGGTGGGAGATGAATCATA
TCATGTTCTCTACAACCACAAACTGCTGAT
Found at i:58606689 original size:18 final size:18
Alignment explanation
Indices: 58606610--58606703 Score: 122
Period size: 18 Copynumber: 5.4 Consensus size: 18
58606600 CAAGGTCACG
*
58606610 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
58606628 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
* *
58606646 ATTAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
58606664 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
58606682 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
58606697 ATCAATA
1 ATCAATA
58606704 AGAAAACCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 59 0.83
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:58609096 original size:21 final size:21
Alignment explanation
Indices: 58609066--58609154 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
58609056 CTCACAAAGA
* *
58609066 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
58609086 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
58609107 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
58609128 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
58609152 AAA
1 AAA
58609155 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:58609147 original size:24 final size:21
Alignment explanation
Indices: 58609066--58609134 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
58609056 CTCACAAAGA
* * *
58609066 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
58609086 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
58609107 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
58609128 AAAAAGA
1 AAAAAGA
58609135 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:58613313 original size:14 final size:14
Alignment explanation
Indices: 58613294--58613320 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58613284 TACAATATAT
58613294 ATAAGAATTATACG
1 ATAAGAATTATACG
58613308 ATAAGAATTATAC
1 ATAAGAATTATAC
58613321 AAATCCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:58617216 original size:13 final size:13
Alignment explanation
Indices: 58617198--58617231 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
58617188 CAATGGAGCC
58617198 TTAATTTATTAAT
1 TTAATTTATTAAT
58617211 TTAATTTATTAAT
1 TTAATTTATTAAT
58617224 TTAATTTA
1 TTAATTTA
58617232 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTTATTAAT
Found at i:58617229 original size:18 final size:16
Alignment explanation
Indices: 58617202--58617244 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
58617192 GGAGCCTTAA
58617202 TTTA-TTAATTTAATT
1 TTTATTTAATTTAATT
58617217 TATTAATTTAATTTAATT
1 T-TT-ATTTAATTTAATT
58617235 TTTATTTAAT
1 TTTATTTAAT
58617245 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 9 0.36
17 3 0.12
18 12 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTTAATTTAATT
Found at i:58622223 original size:2 final size:2
Alignment explanation
Indices: 58622216--58622240 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58622206 ATTTGACTTT
58622216 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
58622241 TATATATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:58628036 original size:27 final size:27
Alignment explanation
Indices: 58628006--58628183 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
58627996 ATATTGAGTC
* *
58628006 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
58628033 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
58628060 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* ** ** *
58628088 CGAACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
58628115 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
58628142 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
58628169 CGTACACTTAGTGCT
1 CGCACACTTAGTGCT
58628184 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:58636135 original size:27 final size:27
Alignment explanation
Indices: 58636105--58636282 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
58636095 ATATTGAGTC
* * * *
58636105 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
58636132 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
58636159 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
58636187 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
58636214 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
58636241 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
58636268 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58636283 GTACAATTCA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:58636244 original size:82 final size:81
Alignment explanation
Indices: 58636126--58636281 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
58636116 TGCTATATAA
* *
58636126 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
58636191 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
58636208 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
58636272 CACTTAGTGC
65 CACTTAGTGC
58636282 TGTACAATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:58636294 original size:82 final size:83
Alignment explanation
Indices: 58636105--58636306 Score: 227
Period size: 82 Copynumber: 2.5 Consensus size: 83
58636095 ATATTGAGTC
* * * * *
58636105 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
58636169 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
58636187 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
58636248 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
* *
58636268 CGCACACTTAGTGCTGTACAATTCAATCCGCGCACTTAG
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAG
58636307 CGCCAATCTC
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
79 1 0.01
81 17 0.17
82 79 0.79
83 1 0.01
84 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:58636295 original size:27 final size:25
Alignment explanation
Indices: 58636105--58636306 Score: 122
Period size: 27 Copynumber: 7.4 Consensus size: 25
58636095 ATATTGAGTC
* * *
58636105 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACA-ATTCAA-T
58636132 CGCACACTTAGTGCTACGTAA-TCAAAT
1 CGCACACTTAGTGCTAC--AATTC-AAT
*
58636159 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACA-ATTC-AA-T
**
58636187 CGCACACTTAGTGCCGC-ATGGTCAATT
1 CGCACACTTAGTGCTACAAT--TCAA-T
*
58636214 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CA-ATTCA-AT
* *
58636241 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACA-ATTC-AAT
58636268 CGCACACTTAGTGCTGTACAATTCAAT
1 CGCACACTTAGTGC--TACAATTCAAT
*
58636295 CCGCGCACTTAG
1 -CGCACACTTAG
58636307 CGCCAATCTC
Statistics
Matches: 145, Mismatches: 13, Indels: 33
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.01
26 2 0.01
27 100 0.69
28 36 0.25
29 6 0.04
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (25 bp):
CGCACACTTAGTGCTACAATTCAAT
Found at i:58639859 original size:23 final size:23
Alignment explanation
Indices: 58639827--58639886 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
58639817 GTGACACCTG
* *
58639827 TGTGGAGTATTTTGTAAAGGCTT
1 TGTGGAGTATTCTGTAAAGCCTT
*
58639850 TGTGGTGTATTCTGTAAAGCCTT
1 TGTGGAGTATTCTGTAAAGCCTT
* *
58639873 TTTGGCGTATTCTG
1 TGTGGAGTATTCTG
58639887 ATACCTGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.10, G:0.28, T:0.45
Consensus pattern (23 bp):
TGTGGAGTATTCTGTAAAGCCTT
Found at i:58643037 original size:5 final size:5
Alignment explanation
Indices: 58643023--58643064 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
58643013 GAATGAAGAT
* *
58643023 GAAAT GAAAA GAAAA CTAAAA GAAAA GAAAA GAAAA GAAAA G
1 GAAAA GAAAA GAAAA -GAAAA GAAAA GAAAA GAAAA GAAAA G
58643065 GACTAACGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (5 bp):
GAAAA
Found at i:58643049 original size:16 final size:15
Alignment explanation
Indices: 58643023--58643064 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
58643013 GAATGAAGAT
*
58643023 GAAATGAAAAGAAAA
1 GAAAAGAAAAGAAAA
*
58643038 CTAAAAGAAAAGAAAA
1 -GAAAAGAAAAGAAAA
58643054 GAAAAGAAAAG
1 GAAAAGAAAAG
58643065 GACTAACGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
GAAAAGAAAAGAAAA
Found at i:58646017 original size:22 final size:21
Alignment explanation
Indices: 58645975--58646017 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
58645965 ATGCGTATTG
* *
58645975 AGTTATAATATGTAATGCATT
1 AGTTATAAAATGTAATCCATT
*
58645996 AGTTAGTAAAATGTATTCCATT
1 AGTTA-TAAAATGTAATCCATT
58646018 TATGTGTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
AGTTATAAAATGTAATCCATT
Found at i:58646900 original size:40 final size:40
Alignment explanation
Indices: 58646712--58646893 Score: 174
Period size: 40 Copynumber: 4.6 Consensus size: 40
58646702 AATGATGTCC
* * * * * *
58646712 GGGCTAAGTCCCGAA-GTATTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCT
* * * * *
58646752 GGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCT
* *
58646792 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATTT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCT
*
58646831 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCT
*
58646871 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
58646894 AACGAGTAGC
Statistics
Matches: 116, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 31 0.27
40 73 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCT
Found at i:58662500 original size:46 final size:46
Alignment explanation
Indices: 58662444--58662619 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
58662434 TGGTTGAGCA
58662444 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58662490 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
58662535 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58662583 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58662620 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:58662600 original size:93 final size:93
Alignment explanation
Indices: 58662441--58662612 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
58662431 GGATGGTTGA
* *
58662441 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58662506 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
58662534 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58662599 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
58662613 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:58667891 original size:57 final size:58
Alignment explanation
Indices: 58667817--58667927 Score: 154
Period size: 57 Copynumber: 1.9 Consensus size: 58
58667807 GTGCCCACTG
* *
58667817 ACCGATCTCGTACACATAGTGCTCGGTTGAA-G-ATCTCACACACACAGTGCCTCAATT
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAAT-TCACACACACAGTGCCTCAATT
* **
58667874 ACCGATTTCGCACACATAGTGCTCGGTTAAAGGAATTTGCACACACAGTGCCTC
1 ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCACACACACAGTGCCTC
58667928 TAATCATTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
57 28 0.60
58 17 0.36
59 2 0.04
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (58 bp):
ACCGATCTCGCACACATAGTGCTCGGTTAAAGGAATTCACACACACAGTGCCTCAATT
Found at i:58668147 original size:43 final size:43
Alignment explanation
Indices: 58668093--58668302 Score: 330
Period size: 43 Copynumber: 4.9 Consensus size: 43
58668083 CACTGGCATT
* * **
58668093 AAGCCTGCTAGGCACGAAGACCCGAATACACATCATTGGCACG
1 AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACG
* * * *
58668136 GAGCCTGCTAGGCACGAAGGCTCGAATACACATCACCGGCATG
1 AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACG
* *
58668179 AAGCCTGCTAGGCACAAAGGCCCAAATACTCATCACCGGCACG
1 AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACG
58668222 AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACG
1 AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACG
58668265 AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCG
1 AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCG
58668303 AGTTTCATGC
Statistics
Matches: 153, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 153 1.00
ACGTcount: A:0.32, C:0.33, G:0.23, T:0.12
Consensus pattern (43 bp):
AAGCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACG
Found at i:58669951 original size:38 final size:37
Alignment explanation
Indices: 58669900--58670040 Score: 210
Period size: 38 Copynumber: 3.7 Consensus size: 37
58669890 TTAAACTCAT
*
58669900 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCA-TAAGCCTGCGGGATTTAACCCGG
*
58669938 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCA-TAAGCCTGCGGGATTTAACCCGG
*
58669976 ATATATTACCAGCATGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCAT-AAGCCTGCGGGATTTAACCCGG
*
58670014 ATATAATTCCAGCATATAGCCTGCGGG
1 ATATAATACCAGCATA-AGCCTGCGGG
58670041 TCTTTAAGCT
Statistics
Matches: 95, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
37 1 0.01
38 94 0.99
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (37 bp):
ATATAATACCAGCATAAGCCTGCGGGATTTAACCCGG
Found at i:58670011 original size:76 final size:78
Alignment explanation
Indices: 58669862--58670056 Score: 236
Period size: 76 Copynumber: 2.5 Consensus size: 78
58669852 AAACCCAAAC
* * * * *
58669862 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCATATATAATACCAGCACTAGGCCTGCGGG
1 ATAATACCAGCACGAAGCCTGCGGGACTTTAAACCCAGATATAATACCAGCACTAAGCCTGCGGG
58669927 ATTTAACCCGGAT
66 ATTTAACCCGGAT
* *
58669940 ATAATACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGATATATTACCAGCA-TGAAGCCTGCGG
1 ATAATACCAGCACGAAGCCTGCGGGACTTTAAACCCAGATATAATACCAGCACT-AAGCCTGCGG
58670002 GATTTAACCCGGAT
65 GATTTAACCCGGAT
* * * * *
58670016 ATAATTCCAGCA-TATAGCCTGCGGGTCTTTAAGCTCAGATA
1 ATAATACCAGCACGA-AGCCTGCGGGACTTTAAACCCAGATA
58670057 CACATCAAAT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
75 2 0.02
76 61 0.61
77 6 0.06
78 31 0.31
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (78 bp):
ATAATACCAGCACGAAGCCTGCGGGACTTTAAACCCAGATATAATACCAGCACTAAGCCTGCGGG
ATTTAACCCGGAT
Found at i:58678747 original size:46 final size:47
Alignment explanation
Indices: 58678671--58678839 Score: 167
Period size: 45 Copynumber: 3.6 Consensus size: 47
58678661 GGGGTAGGGT
* *
58678671 GCCGATGCCATATCCCAGATATGGTCTTACACTGACTATTATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ATTATCTCGTA
*
58678719 GCCGATG-CATGTCCCAGACAT-GTCTTACACTG-C-TTACGTCTC-AA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATTA--TCTCGTA
* *
58678763 GGCCGATG-CATGTCCCGGACAT-GTCTTACACT-AGCACTTGTCTCGATA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CA-TTATCTCG-TA
58678811 -CCGATGCCATGTCCCAGACATGGTCTTAC
1 GCCGATGCCATGTCCCAGACATGGTCTTAC
58678840 GTAGGCTCTC
Statistics
Matches: 103, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 35 0.34
46 22 0.21
47 25 0.24
48 17 0.17
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGACATTATCTCGTA
Found at i:58683772 original size:15 final size:17
Alignment explanation
Indices: 58683754--58683785 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
58683744 CAGCATAATT
58683754 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
58683769 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
58683786 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:58684847 original size:24 final size:26
Alignment explanation
Indices: 58684820--58684868 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
58684810 AGTTCATGCA
58684820 ATATTAAAGC-ATTTAA-ATACAATT
1 ATATTAAAGCTATTTAACATACAATT
58684844 ATATTAAAGCTTATTTAACATACAA
1 ATATTAAAGC-TATTTAACATACAA
58684869 ACTTACCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (26 bp):
ATATTAAAGCTATTTAACATACAATT
Found at i:58690647 original size:40 final size:40
Alignment explanation
Indices: 58690592--58690816 Score: 292
Period size: 40 Copynumber: 5.6 Consensus size: 40
58690582 TATTCGGATG
58690592 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
58690632 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* *
58690675 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
58690715 ATTAT-CGAGCTAAGACCCGAAGGCATGTGTGCGAGTTACT
1 A-TATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
58690755 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTTCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
58690795 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
58690817 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
39 17 0.10
40 106 0.65
41 3 0.02
43 37 0.23
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:58690735 original size:83 final size:80
Alignment explanation
Indices: 58690596--58690816 Score: 286
Period size: 83 Copynumber: 2.7 Consensus size: 80
58690586 CGGATGATAT
* * *
58690596 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGAGCTAAGACCCGAAGGCATGTG
*
58690661 TGCGAGTAGTTGCTATAC
66 TGC--G-AGTTACTATAC
*
58690679 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATTAT-CGAGCTAAGACCCGAAGGCATGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTA-TATCCGAGCTAAGACCCGAAGGCATGT
*
58690743 GTGCGAGTTACTATAT
65 GTGCGAGTTACTATAC
* * * *
58690759 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTTCGATATCCG-GCTAA-ATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGAGCTAAGA-CCCGAAGG
58690817 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 16 0.13
80 44 0.35
81 1 0.01
83 60 0.48
84 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGAGCTAAGACCCGAAGGCATGTG
TGCGAGTTACTATAC
Found at i:58705573 original size:43 final size:42
Alignment explanation
Indices: 58705535--58705660 Score: 135
Period size: 44 Copynumber: 2.9 Consensus size: 42
58705525 TCTTACATAT
* *
58705535 AATCAAACATCGTTGCCACTGTCCCAGACAAGGTCTTACACGA
1 AATCAAACA-CGATGCCAATGTCCCAGACAAGGTCTTACACGA
* *
58705578 AATCAAATACGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCAAACACGATGCCAATGTCCCAGACAAGGTCTTACACG-A
* ** ** *
58705621 AACCAGAAGTCGATGCCAACATCCCAGACATGGTCTTACA
1 AATCA-AACACGATGCCAATGTCCCAGACAAGGTCTTACA
58705661 TGAACTCACA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
42 29 0.40
43 13 0.18
44 30 0.42
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.21
Consensus pattern (42 bp):
AATCAAACACGATGCCAATGTCCCAGACAAGGTCTTACACGA
Found at i:58705606 original size:42 final size:44
Alignment explanation
Indices: 58705548--58705660 Score: 151
Period size: 44 Copynumber: 2.6 Consensus size: 44
58705538 CAAACATCGT
* * *
58705548 TGCCACTGTCCCAGACAAGGTCTTACACG-AAATCA-AA-TACGA
1 TGCCAATGTCCCAGACATGGTCTTACACGTAAACCAGAAGT-CGA
58705590 TGCCAATGTCCCAGACATGGTCTTACACGTAAACCAGAAGTCGA
1 TGCCAATGTCCCAGACATGGTCTTACACGTAAACCAGAAGTCGA
**
58705634 TGCCAACATCCCAGACATGGTCTTACA
1 TGCCAATGTCCCAGACATGGTCTTACA
58705661 TGAACTCACA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
42 27 0.43
43 5 0.08
44 30 0.48
45 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (44 bp):
TGCCAATGTCCCAGACATGGTCTTACACGTAAACCAGAAGTCGA
Found at i:58710470 original size:58 final size:58
Alignment explanation
Indices: 58710380--58710519 Score: 253
Period size: 58 Copynumber: 2.4 Consensus size: 58
58710370 TTGCTGACGA
*
58710380 GATTTAGCCTAGACTAGTAACCCTAATATAATGTCTCTCGATCATATGTTACAATTAG
1 GATTTAGCCTAGACTAGTAATCCTAATATAATGTCTCTCGATCATATGTTACAATTAG
58710438 GATTTAGCCTAGACTAGTAATCCTAATATAATGTCTCTCGATCATATGTTACAATTAG
1 GATTTAGCCTAGACTAGTAATCCTAATATAATGTCTCTCGATCATATGTTACAATTAG
* *
58710496 GATTTAGCCTGGACTGGTAATCCT
1 GATTTAGCCTAGACTAGTAATCCT
58710520 GTCATATGTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 79 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (58 bp):
GATTTAGCCTAGACTAGTAATCCTAATATAATGTCTCTCGATCATATGTTACAATTAG
Found at i:58714801 original size:29 final size:29
Alignment explanation
Indices: 58714767--58714831 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
58714757 TAAATCAGGT
58714767 AAAGTGTAAAACTTGTGTTCTATTAGCTA
1 AAAGTGTAAAACTTGTGTTCTATTAGCTA
58714796 AAAGTGTAAAACTTGTGTTCTATTAGCTA
1 AAAGTGTAAAACTTGTGTTCTATTAGCTA
*
58714825 GAAGTGT
1 AAAGTGT
58714832 CAAATAGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (29 bp):
AAAGTGTAAAACTTGTGTTCTATTAGCTA
Found at i:58717710 original size:47 final size:46
Alignment explanation
Indices: 58717611--58717766 Score: 178
Period size: 45 Copynumber: 3.4 Consensus size: 46
58717601 TACCGATATA
* * * *
58717611 TCAGCTCGTATGAGCTTAC-TGTTCAGCTTGATAGAGTTTACCGTT
1 TCAGCTCGTAAGAGCTTACTTGTTTAGCTCGATAGAGCTTACCGTT
* *
58717656 TCAGCTCGTAAGAGCTTACTATTTTTAGCTC-ATTGGAGCTTACCGTT
1 TCAGCTCGTAAGAGCTTACT-TGTTTAGCTCGA-TAGAGCTTACCGTT
*
58717703 TCAGCTCGTATGAGCTTA-TTGTTTAGCTCGATAGAGCTTACCG-T
1 TCAGCTCGTAAGAGCTTACTTGTTTAGCTCGATAGAGCTTACCGTT
*
58717747 TCAGCTC-TATAAAGCTTACT
1 TCAGCTCGTA-AGAGCTTACT
58717767 GTTCATCAGC
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
43 2 0.02
44 14 0.15
45 39 0.41
46 3 0.03
47 36 0.38
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (46 bp):
TCAGCTCGTAAGAGCTTACTTGTTTAGCTCGATAGAGCTTACCGTT
Found at i:58717739 original size:22 final size:22
Alignment explanation
Indices: 58717613--58717769 Score: 106
Period size: 22 Copynumber: 7.0 Consensus size: 22
58717603 CCGATATATC
*
58717613 AGCTCG-TATGAGCTTACTGTTC
1 AGCTCGATA-GAGCTTACTGTTT
* * *
58717635 AGCTTGATAGAGTTTACCGTTT
1 AGCTCGATAGAGCTTACTGTTT
*
58717657 CAGCTCG-TAAGAGCTTACTATTTTT
1 -AGCTCGAT-AGAGCTTAC--TGTTT
* *
58717682 AGCTC-ATTGGAGCTTACCGTTT
1 AGCTCGA-TAGAGCTTACTGTTT
*
58717704 CAGCTCG-TATGAGCTTATTGTTT
1 -AGCTCGATA-GAGCTTACTGTTT
* *
58717727 AGCTCGATAGAGCTTACCGTTC
1 AGCTCGATAGAGCTTACTGTTT
* *
58717749 AGCTCTATAAAGCTTACTGTT
1 AGCTCGATAGAGCTTACTGTT
58717770 CATCAGCTCA
Statistics
Matches: 104, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
22 54 0.52
23 33 0.32
24 13 0.12
25 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (22 bp):
AGCTCGATAGAGCTTACTGTTT
Found at i:58717778 original size:92 final size:93
Alignment explanation
Indices: 58717611--58717793 Score: 237
Period size: 92 Copynumber: 2.0 Consensus size: 93
58717601 TACCGATATA
* * *
58717611 TCAGCTCGTATGAGCTTACTGTTCAGCTTGATAGAGTTTACCGTTTCAGCTCGTAAGAGCTTACT
1 TCAGCTCGTATGAGCTTACTGTTCAGCTCGATAGAGCTTACCGTTTCAGCTCGTAAAAGCTTACT
* * **
58717676 ATTTTTAGCTCA-TTGGAGCTTACCGTT
66 ATTATCAGCTCAGGAGGAGCTTACCGTT
* *
58717703 TCAGCTCGTATGAGCTTATTGTTTAGCTCGATAGAGCTTACCG-TTCAGCTC-TATAAAGCTTAC
1 TCAGCTCGTATGAGCTTACTGTTCAGCTCGATAGAGCTTACCGTTTCAGCTCGTA-AAAGCTTAC
*
58717766 TGTTCATCAGCTCAGGAGGAGCTTACCG
65 TATT-ATCAGCTCAGGAGGAGCTTACCG
58717794 ATCATGGGTC
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
90 2 0.03
91 19 0.24
92 46 0.59
93 11 0.14
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (93 bp):
TCAGCTCGTATGAGCTTACTGTTCAGCTCGATAGAGCTTACCGTTTCAGCTCGTAAAAGCTTACT
ATTATCAGCTCAGGAGGAGCTTACCGTT
Found at i:58721885 original size:22 final size:22
Alignment explanation
Indices: 58721814--58721932 Score: 59
Period size: 22 Copynumber: 5.1 Consensus size: 22
58721804 GCATATATGA
58721814 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
58721836 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
58721861 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* *
58721883 GATGAATG-TGAACAT-G-CATATACGT
1 GAT-AAGGCCG-A-ATGGCCA-AT--GT
58721908 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
58721930 GAT
1 GAT
58721933 GAATGTGAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 32
0.63 0.09 0.28
Matches are distributed among these distances:
22 19 0.27
23 18 0.25
24 18 0.25
25 16 0.23
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:58722092 original size:141 final size:142
Alignment explanation
Indices: 58721789--58722119 Score: 474
Period size: 141 Copynumber: 2.4 Consensus size: 142
58721779 GATTTTATGA
* *
58721789 GATGAATGTGAACATGCATATA--TGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 GATGAACGTGAACATGCATATACGTG-GATAAGGCCGAATGGCCAATGCGATGAATGTGAACATG
*
58721852 CATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATACGTGATAAGGCC
65 CATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATACGTGATAAGGCA
58721917 GAATGGCCAATGT
130 GAATGGCCAATGT
* *
58721930 GATGAATGTGAACATGCATATACGT-GATAAGGCCGAATGGCCAATGCGATGAATGTGAACTTGC
1 GATGAACGTGAACATGCATATACGTGGATAAGGCCGAATGGCCAATGCGATGAATGTGAACATGC
* * * *
58721994 ATATGTGTGATAAGGTCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGGTAG
66 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATACGTGATAAGGCAG
58722059 AATGGCCAATGT
131 AATGGCCAATGT
* * * ** *
58722071 GATGAACGTGGAA-GTGTATATATGTGGCGAA-GCCGAATGGCTAATGCGA
1 GATGAACGT-GAACATGCATATACGTGGATAAGGCCGAATGGCCAATGCGA
58722120 AATGTGTATG
Statistics
Matches: 172, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
141 165 0.96
142 6 0.03
143 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (142 bp):
GATGAACGTGAACATGCATATACGTGGATAAGGCCGAATGGCCAATGCGATGAATGTGAACATGC
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATACGTGATAAGGCAG
AATGGCCAATGT
Found at i:58722108 original size:94 final size:94
Alignment explanation
Indices: 58721789--58722116 Score: 439
Period size: 94 Copynumber: 3.5 Consensus size: 94
58721779 GATTTTATGA
* *
58721789 GATGAATGTGAACATGCATATATG-AGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 GATGAATGTGAA-ATGTATATATGTGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
58721853 ATATATGTGATAAGGCCGAATGGCCAATGT
65 ATATATGTGATAAGGCCGAATGGCCAATGT
* *
58721883 GATGAATGTGAACATGCATATACGT-GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 GATGAATGTGAA-ATGTATATATGTGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
58721947 ATATACGTGATAAGGCCGAATGGCCAATGC
65 ATATATGTGATAAGGCCGAATGGCCAATGT
* ** *
58721977 GATGAATGTGAACT-TGCATATGTGTGATAAGGTCGAATGGCCAATGTGATGAATGTGAACATGC
1 GATGAATGTGAAATGTATATATGTG-GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
**
58722041 ATATATGTGATAAGGTAGAATGGCCAATGT
65 ATATATGTGATAAGGCCGAATGGCCAATGT
* * ** *
58722071 GATGAACGTGGAAGTGTATATATGTGGCGAA-GCCGAATGGCTAATG
1 GATGAATGT-GAAATGTATATATGTGGATAAGGCCGAATGGCCAATG
58722117 CGAAATGTGT
Statistics
Matches: 208, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
92 5 0.02
93 1 0.00
94 187 0.90
95 7 0.03
96 8 0.04
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (94 bp):
GATGAATGTGAAATGTATATATGTGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
TATATGTGATAAGGCCGAATGGCCAATGT
Found at i:58722111 original size:47 final size:47
Alignment explanation
Indices: 58721789--58722076 Score: 495
Period size: 47 Copynumber: 6.1 Consensus size: 47
58721779 GATTTTATGA
*
58721789 GATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
58721836 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
58721883 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* *
58721930 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGC
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* * *
58721977 GATGAATGTGAACTTGCATATGTGTGATAAGGTCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
58722024 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
58722071 GATGAA
1 GATGAA
58722077 CGTGGAAGTG
Statistics
Matches: 230, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 230 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:58722154 original size:46 final size:46
Alignment explanation
Indices: 58722100--58722277 Score: 284
Period size: 46 Copynumber: 3.9 Consensus size: 46
58722090 ATATGTGGCG
*
58722100 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
*
58722146 AAGTCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
58722192 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
* * * ** *
58722238 AAGCCGAATGGCAAATGTGAGATATGTATGAGATGTATAT
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATAT
58722278 ATATATTGTG
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 123 1.00
ACGTcount: A:0.35, C:0.09, G:0.31, T:0.24
Consensus pattern (46 bp):
AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
Found at i:58725763 original size:29 final size:29
Alignment explanation
Indices: 58725731--58725815 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 29
58725721 CCTAACTAGC
58725731 CATATAAATGTGATTTGGGCCTAATGGGA
1 CATATAAATGTGATTTGGGCCTAATGGGA
* * *
58725760 CATATACAGGTGATTTGGGCCTAATGGGT
1 CATATAAATGTGATTTGGGCCTAATGGGA
* * *
58725789 CATATAAATAT-AATTGGGCTTAATGGG
1 CATATAAATGTGATTTGGGCCTAATGGG
58725816 CTAGATACAG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 14 0.29
29 34 0.71
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.32
Consensus pattern (29 bp):
CATATAAATGTGATTTGGGCCTAATGGGA
Found at i:58729382 original size:9 final size:9
Alignment explanation
Indices: 58729368--58729392 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
58729358 CTAAATTGGA
58729368 AATTAAATT
1 AATTAAATT
58729377 AATTAAATT
1 AATTAAATT
58729386 AATTAAA
1 AATTAAA
58729393 AGATGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:58733300 original size:55 final size:54
Alignment explanation
Indices: 58733048--58733301 Score: 242
Period size: 55 Copynumber: 4.8 Consensus size: 54
58733038 TCGCGAGTAC
* * *
58733048 CTTACC-ATTTCCATGACTTGTCATGGTCTTACATGGTATCCTT---TT--AAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
* * *
58733096 CTTACC-ATTTCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
* * * * * *
58733149 CTCACCAA-TGCCATGCCTTGGCATGGTCTTACATGGGA-CATTTACCTTATAGTAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATC-CTTGCC-T-TAGAAA
* * *
58733204 CTTATCAA-TGCCATGTCTTGACATGGTCTTACATGGAATCCTTGCCTTAGAAA
1 CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
*
58733257 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTT
58733302 AAACCCTAAT
Statistics
Matches: 169, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
48 40 0.24
51 2 0.01
52 1 0.01
53 41 0.24
54 11 0.07
55 73 0.43
56 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (54 bp):
CTTACCAATTGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAA
Found at i:58733670 original size:29 final size:29
Alignment explanation
Indices: 58733637--58733692 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
58733627 TTCTTGACTC
*
58733637 AAACTTTCGCAAAATTACACTTTTCCCTT
1 AAACTTTCACAAAATTACACTTTTCCCTT
* * *
58733666 AAACTTTTACATATTTACACTTTTCCC
1 AAACTTTCACAAAATTACACTTTTCCC
58733693 CAAGGCTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.27, G:0.02, T:0.41
Consensus pattern (29 bp):
AAACTTTCACAAAATTACACTTTTCCCTT
Found at i:58740931 original size:55 final size:53
Alignment explanation
Indices: 58740790--58740997 Score: 213
Period size: 55 Copynumber: 3.8 Consensus size: 53
58740780 ATCCTTTTGA
* * * * * *
58740790 AACTTACCATTGTCATGTCTCGACATGGTCTTACATGGTATCATTACCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAG
* * *
58740843 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG
* * *
58740897 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGA-
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAG
* *
58740951 AACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 AA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
58740998 AAACCCTAAT
Statistics
Matches: 130, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
53 43 0.33
54 8 0.06
55 76 0.58
56 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAG
Found at i:58746547 original size:24 final size:23
Alignment explanation
Indices: 58746520--58746567 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
58746510 AACAAAAGCC
58746520 GAAATGCCAAAAAGCCAAAAAGTT
1 GAAATGCCAAAAAGCC-AAAAGTT
* *
58746544 GAAATGCCGAAAAGCCGAAAGTT
1 GAAATGCCAAAAAGCCAAAAGTT
58746567 G
1 G
58746568 GGCAACAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.12
Consensus pattern (23 bp):
GAAATGCCAAAAAGCCAAAAGTT
Found at i:58746828 original size:29 final size:27
Alignment explanation
Indices: 58746781--58746892 Score: 89
Period size: 29 Copynumber: 4.0 Consensus size: 27
58746771 TGAGTATAAT
*
58746781 ATGATTTGGGCCTAATGGGCCATATGA
1 ATGAATTGGGCCTAATGGGCCATATGA
* * *
58746808 AGGTGAATTGGGCCTAGTGGGACATAAGAA
1 A--TGAATTGGGCCTAATGGGCCATATG-A
* * *
58746838 TATGAACTGGGCCAAATGGGCCATTTGA
1 -ATGAATTGGGCCTAATGGGCCATATGA
* * *
58746866 ATAAGATTGGGCCTAGTGGGCTATATG
1 ATGA-ATTGGGCCTAATGGGCCATATG
58746893 CATGTATATA
Statistics
Matches: 64, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
27 4 0.06
28 18 0.28
29 40 0.62
30 1 0.02
31 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (27 bp):
ATGAATTGGGCCTAATGGGCCATATGA
Found at i:58747784 original size:25 final size:26
Alignment explanation
Indices: 58747755--58747803 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
58747745 AAATCGTAAT
* *
58747755 TAAGG-GAAAATTATCAAAATACCCC
1 TAAGGTGAAAATGACCAAAATACCCC
58747780 TAAGGTGAAAATGACCAAAATACC
1 TAAGGTGAAAATGACCAAAATACC
58747804 GCTAGTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (26 bp):
TAAGGTGAAAATGACCAAAATACCCC
Found at i:58752511 original size:24 final size:25
Alignment explanation
Indices: 58752479--58752531 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
58752469 TTTGAATTGG
* *
58752479 ATGTTGTATATGTG-AATTGTATAA
1 ATGTCGTATATATGAAATTGTATAA
* *
58752503 ATGTCGTATGTATGAAATTGTATAT
1 ATGTCGTATATATGAAATTGTATAA
58752528 ATGT
1 ATGT
58752532 GAATTGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (25 bp):
ATGTCGTATATATGAAATTGTATAA
Found at i:58752532 original size:40 final size:39
Alignment explanation
Indices: 58752485--58752565 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 39
58752475 TTGGATGTTG
*
58752485 TATATGTGAATTGTATAAATGTCGTATGTATGAAATTGTA
1 TATATGTGAATTGTATAAATGTCGTATATATG-AATTGTA
* *
58752525 TATATGTGAATTGTATAAATGTTGTATATGTGAATTGTA
1 TATATGTGAATTGTATAAATGTCGTATATATGAATTGTA
58752564 TA
1 TA
58752566 AATCCCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 9 0.24
40 29 0.76
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (39 bp):
TATATGTGAATTGTATAAATGTCGTATATATGAATTGTA
Found at i:58752538 original size:15 final size:15
Alignment explanation
Indices: 58752518--58752568 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
58752508 GTATGTATGA
*
58752518 AATTGTATATATGTG
1 AATTGTATAAATGTG
58752533 AATTGTATAAA--TG
1 AATTGTATAAATGTG
58752546 --TTGTAT--ATGTG
1 AATTGTATAAATGTG
58752557 AATTGTATAAAT
1 AATTGTATAAAT
58752569 CCCATTTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
9 1 0.03
11 8 0.28
13 8 0.28
15 12 0.41
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (15 bp):
AATTGTATAAATGTG
Found at i:58752896 original size:25 final size:25
Alignment explanation
Indices: 58752835--58752949 Score: 142
Period size: 25 Copynumber: 4.6 Consensus size: 25
58752825 GGCTCTTCCT
* *
58752835 GAGCTTCCTGATTAAAGGCTCTTTG
1 GAGCTTCCTGATTAATGGCTCTCTG
58752860 TGAGCTTCCTGATTAATGGCTCTCTG
1 -GAGCTTCCTGATTAATGGCTCTCTG
* *
58752886 GAGCTTTCTGATTAATAGCTCTCTG
1 GAGCTTCCTGATTAATGGCTCTCTG
* * *
58752911 GAGCTTCCCGA-TATATGACTATCTG
1 GAGCTTCCTGATTA-ATGGCTCTCTG
58752936 GAGCTTCCTGATTA
1 GAGCTTCCTGATTA
58752950 GTGGTTCTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
24 2 0.03
25 50 0.65
26 25 0.32
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTCTG
Found at i:58752963 original size:25 final size:26
Alignment explanation
Indices: 58752823--58752965 Score: 138
Period size: 25 Copynumber: 5.7 Consensus size: 26
58752813 GTCCCGATAT
58752823 ATGGCTCTTCCT-GAGCTTCCTGATTA
1 ATGGCTCTT-CTGGAGCTTCCTGATTA
*
58752849 AAGGCTCTT-TGTGAGCTTCCTGATTA
1 ATGGCTCTTCTG-GAGCTTCCTGATTA
*
58752875 ATGGCTC-TCTGGAGCTTTCTGATTA
1 ATGGCTCTTCTGGAGCTTCCTGATTA
* *
58752900 ATAGCTC-TCTGGAGCTTCCCGA-TA
1 ATGGCTCTTCTGGAGCTTCCTGATTA
* *
58752924 TATGACT-ATCTGGAGCTTCCTGATTA
1 -ATGGCTCTTCTGGAGCTTCCTGATTA
* *
58752950 GTGGTTCTTC-GGAGCT
1 ATGGCTCTTCTGGAGCT
58752966 ACCCGTTATT
Statistics
Matches: 97, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
24 3 0.03
25 60 0.62
26 34 0.35
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (26 bp):
ATGGCTCTTCTGGAGCTTCCTGATTA
Found at i:58753075 original size:25 final size:25
Alignment explanation
Indices: 58752961--58753120 Score: 105
Period size: 24 Copynumber: 6.4 Consensus size: 25
58752951 TGGTTCTTCG
*
58752961 GAGCTACCCGTTAT-TGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCACAT
* * **
58752985 GAGCTT-CC-TAATTATGGATCTTAT
1 GAGCTTCCCGTTA-TATGGCTCACAT
* * * *
58753009 GAGCTTCCTGTTATATAGCCCAGAT
1 GAGCTTCCCGTTATATGGCTCACAT
** *
58753034 -AGCTTTTCGTTACATGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCACAT
* * *
58753058 GAGCTTCCCATTATATGGCTCAAGAGA
1 GAGCTTCCCGTTATATGGCTC-ACA-T
58753085 GAGCTTCCCGTT-TATGTGCTCACAT
1 GAGCTTCCCGTTATATG-GCTCACAT
58753110 GAGCATTCCCG
1 GAGC-TTCCCG
58753121 AATATGAATT
Statistics
Matches: 99, Mismatches: 28, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
22 2 0.02
23 3 0.03
24 35 0.35
25 28 0.28
26 16 0.16
27 15 0.15
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCACAT
Found at i:58758528 original size:21 final size:22
Alignment explanation
Indices: 58758487--58758528 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
58758477 GGGCTCACAC
*
58758487 GCCCGTGTGGTCCAAGGGACAT
1 GCCCGTGTGGACCAAGGGACAT
*
58758509 GCCCGTGT-GACCATGGGACA
1 GCCCGTGTGGACCAAGGGACA
58758529 CGTACATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.19, C:0.29, G:0.36, T:0.17
Consensus pattern (22 bp):
GCCCGTGTGGACCAAGGGACAT
Found at i:58765912 original size:40 final size:40
Alignment explanation
Indices: 58765860--58766213 Score: 636
Period size: 40 Copynumber: 8.8 Consensus size: 40
58765850 ATTACCACAA
* * ** *
58765860 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
58765900 GCACGAATGCCTTCGGGCCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
58765940 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAATTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
58765980 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
58766020 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
58766060 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
58766100 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
58766140 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
58766180 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
58766214 TCAAATGCTC
Statistics
Matches: 303, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 303 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:58771830 original size:29 final size:29
Alignment explanation
Indices: 58771772--58771885 Score: 140
Period size: 29 Copynumber: 4.0 Consensus size: 29
58771762 CATGCATACA
* * * *
58771772 GCCCACTAGG-CCTAATCTCATTCACATG
1 GCCCATTAGGCCCAAATCACATTCATATG
* **
58771800 GCCCATTAGGCCCAAATCATATTTGTATG
1 GCCCATTAGGCCCAAATCACATTCATATG
*
58771829 GCCCATTAGGCCCAAATCACATTCATACG
1 GCCCATTAGGCCCAAATCACATTCATATG
*
58771858 GCCTATTAGGCCCAAATCACATTCATAT
1 GCCCATTAGGCCCAAATCACATTCATAT
58771886 ACATGCTTTC
Statistics
Matches: 72, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 9 0.12
29 63 0.88
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTCATATG
Found at i:58774939 original size:27 final size:27
Alignment explanation
Indices: 58774909--58775085 Score: 158
Period size: 27 Copynumber: 6.5 Consensus size: 27
58774899 AAATTGTACA
* * *
58774909 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
58774936 GCACTCAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
58774963 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
** *
58774990 GCACTAAGTGTGCGAGCCTGACTATGTA
1 GCACTAAGTGTGCGA-ATTGACTATGTG
* * *
58775018 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * * *
58775045 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAATTGACTATGTG
*
58775072 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
58775086 GGCTCAATGT
Statistics
Matches: 122, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 99 0.81
28 23 0.19
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:58775022 original size:82 final size:81
Alignment explanation
Indices: 58774909--58775064 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
58774899 AAATTGTACA
** * * *
58774909 GCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGGGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
58774973 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
58774990 GCACTAAGTGTGCGAGCCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGGGTGCGA-CCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
58775055 TGCGAGTTGA
65 TGCGAATTGA
58775065 TTATATAGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:58775076 original size:82 final size:81
Alignment explanation
Indices: 58774905--58775085 Score: 193
Period size: 82 Copynumber: 2.2 Consensus size: 81
58774895 GATTAAATTG
* ** * * *
58774905 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
58774970 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
58774986 TGCGGCACTAAGTGTGCGAGCCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-CCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
58775050 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
58775068 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
58775086 GGCTCAATGT
Statistics
Matches: 80, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
81 17 0.21
82 63 0.79
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:58793997 original size:18 final size:18
Alignment explanation
Indices: 58793918--58794011 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
58793908 CAAGGTCACG
*
58793918 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
58793936 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
58793954 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
58793972 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
58793990 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
58794005 ATCAATA
1 ATCAATA
58794012 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:58793998 original size:9 final size:9
Alignment explanation
Indices: 58793918--58793998 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
58793908 CAAGGTCACG
*
58793918 ATCAATAGC
1 ATCAATATC
* *
58793927 GTCACTATC
1 ATCAATATC
*
58793936 ATCAATAGC
1 ATCAATATC
* * *
58793945 GTCACTAGC
1 ATCAATATC
58793954 ATCAATATC
1 ATCAATATC
* * *
58793963 GTCACTAGC
1 ATCAATATC
58793972 ATCAATATC
1 ATCAATATC
* *
58793981 GTCACTATC
1 ATCAATATC
58793990 ATCAATATC
1 ATCAATATC
58793999 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:58796401 original size:21 final size:21
Alignment explanation
Indices: 58796371--58796459 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
58796361 CTCACAAAGA
* *
58796371 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
58796391 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
58796412 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
58796433 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
58796457 AAA
1 AAA
58796460 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:58796452 original size:24 final size:21
Alignment explanation
Indices: 58796371--58796439 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
58796361 CTCACAAAGA
* * *
58796371 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
58796391 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
58796412 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
58796433 AAAAAGA
1 AAAAAGA
58796440 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:58800621 original size:14 final size:14
Alignment explanation
Indices: 58800602--58800630 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58800592 TACAATATAT
58800602 ATAAGAATTATACG
1 ATAAGAATTATACG
58800616 ATAAGAATTATACG
1 ATAAGAATTATACG
58800630 A
1 A
58800631 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:58803422 original size:13 final size:15
Alignment explanation
Indices: 58803397--58803436 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
58803387 TATTTTATTA
58803397 AATAAATATTAAATT
1 AATAAATATTAAATT
58803412 AA-AAA-ATTAAATT
1 AATAAATATTAAATT
58803425 AATAAATATTAA
1 AATAAATATTAA
58803437 TAAATTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAAATATTAAATT
Found at i:58818080 original size:27 final size:27
Alignment explanation
Indices: 58818050--58818227 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
58818040 ATATTGAGCC
* *
58818050 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
58818077 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
58818104 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
58818132 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
58818159 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
58818186 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
58818213 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58818228 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:58818162 original size:55 final size:54
Alignment explanation
Indices: 58818050--58818227 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
58818040 ATATTGAGCC
* * * * *
58818050 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
58818104 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
58818159 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
58818213 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58818228 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:58822166 original size:27 final size:27
Alignment explanation
Indices: 58822136--58822313 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
58822126 ATATTGAGTC
* *
58822136 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
58822163 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
58822190 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
58822218 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
58822245 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
58822272 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
58822299 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58822314 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:58826094 original size:25 final size:26
Alignment explanation
Indices: 58826050--58826100 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
58826040 ATTACAAGTA
58826050 TTAATAACATAAATGGTTAAT-TATT
1 TTAATAACATAAATGGTTAATATATT
* **
58826075 TTAATAACATATATTTTTAATATATT
1 TTAATAACATAAATGGTTAATATATT
58826101 ATTTATGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
TTAATAACATAAATGGTTAATATATT
Found at i:58826449 original size:27 final size:27
Alignment explanation
Indices: 58826417--58826470 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
58826407 AAAGAGTCCA
* *
58826417 AATAATACAAAACTCCCGAAATTAACT
1 AATAATACAAAACACCCAAAATTAACT
58826444 AATAATACAAAACACCCAAAATTAACT
1 AATAATACAAAACACCCAAAATTAACT
58826471 TTTAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (27 bp):
AATAATACAAAACACCCAAAATTAACT
Found at i:58826722 original size:19 final size:18
Alignment explanation
Indices: 58826682--58826723 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
58826672 GATATAGTTC
*
58826682 CAGATTCAGAATCAGATC
1 CAGATTCAGAATCAGATA
58826700 CAGATTCA-AATTACAGATA
1 CAGATTCAGAA-T-CAGATA
58826719 CAGAT
1 CAGAT
58826724 ATGCATAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 9 0.43
19 10 0.48
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (18 bp):
CAGATTCAGAATCAGATA
Found at i:58828744 original size:51 final size:50
Alignment explanation
Indices: 58828673--58828845 Score: 195
Period size: 51 Copynumber: 3.4 Consensus size: 50
58828663 TCGCATGTGT
58828673 AGTACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTCTATCACGTGTAC
1 AGTACTAAGTGCAGGCTACTATGCGTACCCGTTAACTT-TATCACGTGTAC
* * * * * * * * * *
58828724 AGTACTAAGTGTAGGTTACTACGTGTACCAGATTGA-TATGTCGCATGTAC
1 AGTACTAAGTGCAGGCTACTATGCGTACCCG-TTAACTTTATCACGTGTAC
* **
58828774 AGTACTAAGTGCAGGCTACTATACGTACCCGTTAACTTTGATCACGTGTGT
1 AGTACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTT-ATCACGTGTAC
58828825 AGTACTAAGTGCAGGCTACTA
1 AGTACTAAGTGCAGGCTACTA
58828846 CGTGTATCAG
Statistics
Matches: 96, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
49 3 0.03
50 36 0.38
51 54 0.56
52 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (50 bp):
AGTACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTTATCACGTGTAC
Found at i:58828788 original size:101 final size:101
Alignment explanation
Indices: 58828613--58828945 Score: 429
Period size: 101 Copynumber: 3.3 Consensus size: 101
58828603 TCGTTATGAG
*
58828613 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAAGTCGCATGTGTAGTAC
58828678 TAAGTGCAGGCTACTATGCGTACCCGTTAACTTCT-A
66 TAAGTGCAGGCTACTATGCGTACCCGTTAACTT-TGA
** * * * **
58828714 TCACGTGTACAGTACTAAGTGTAGGTTACTACGTGTACCAGATTGATATGTCGCATGTACAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAAGTCGCATGTGTAGTAC
*
58828779 TAAGTGCAGGCTACTATACGTACCCGTTAACTTTGA
66 TAAGTGCAGGCTACTATGCGTACCCGTTAACTTTGA
* * * ***
58828815 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAAGTCATGTGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAAGTCGCATGTGTAGTAC
* * * * *
58828880 TAAGTGCAGGCTACTATGTGTACCAGATTGA--TAGG
66 TAAGTGCAGGCTACTATGCGTACCCG-TTAACTTTGA
* *
58828915 TCGCATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
58828946 TGCGTGCCAG
Statistics
Matches: 201, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
100 32 0.16
101 166 0.83
102 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAAGTCGCATGTGTAGTAC
TAAGTGCAGGCTACTATGCGTACCCGTTAACTTTGA
Found at i:58828946 original size:50 final size:50
Alignment explanation
Indices: 58828618--58828956 Score: 317
Period size: 50 Copynumber: 6.7 Consensus size: 50
58828608 ATGAGTCACG
*
58828618 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTCGCA
* * ** *
58828668 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCG-TT-A-ACTTCTATCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTC--GCA
* * * * *
58828717 CGTGTACAGTACTAAGTGTAGGTTACTACGTGTACCAGATTGATATGTCGCA
1 TGTGT--AGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTCGCA
** ** * * * * * *
58828769 TGTACAGTACTAAGTGCAGGCTACTATACGTACCCG-TTAACTTTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGA--TAGGTCGCA
* * * * * ***
58828820 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAAGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTCGCA
58828870 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTCGCA
* *
58828920 TGTGTAGTACTAAGTGCAGGCTACTATGCGTGCCAGA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGA
58828957 GAGCTTCGGT
Statistics
Matches: 225, Mismatches: 54, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
47 3 0.01
48 1 0.00
49 11 0.05
50 140 0.62
51 59 0.26
52 7 0.03
53 1 0.00
54 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATTGATAGGTCGCA
Found at i:58829177 original size:16 final size:16
Alignment explanation
Indices: 58829156--58829187 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58829146 AGAATGGAGT
58829156 AAGTGAAATTATGTAA
1 AAGTGAAATTATGTAA
*
58829172 AAGTGAAATTTTGTAA
1 AAGTGAAATTATGTAA
58829188 TAAAACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AAGTGAAATTATGTAA
Found at i:58832628 original size:20 final size:20
Alignment explanation
Indices: 58832605--58832651 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
58832595 GGGTTAAGAT
*
58832605 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
58832625 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
58832645 TGAGCTG
1 TGAGCTG
58832652 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:58834378 original size:48 final size:48
Alignment explanation
Indices: 58834323--58834428 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
58834313 TTGTCTTTTC
*
58834323 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
58834371 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
58834419 TTTCTTTTTC
1 TTTCTTTTTC
58834429 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:58835469 original size:10 final size:9
Alignment explanation
Indices: 58835456--58835491 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
58835446 CTTTTCACTT
58835456 TTTTTTGTTC
1 TTTTTT-TTC
58835466 TTTTTTTTAC
1 TTTTTTTT-C
58835476 TTTTTTTTC
1 TTTTTTTTC
58835485 TTTTTTT
1 TTTTTTT
58835492 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:58835477 original size:22 final size:21
Alignment explanation
Indices: 58835447--58835511 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
58835437 CTCACAAGAC
*
58835447 TTTTCACTTTTTTTTGTTCTTT
1 TTTTCACTTTTTTTTCTT-TTT
*
58835469 TTTTTACTTTTTTTTCTTTTT
1 TTTTCACTTTTTTTTCTTTTT
* *
58835490 TTGCTCACTTCTTTTT-TTTTT
1 TT-TTCACTTTTTTTTCTTTTT
58835511 T
1 T
58835512 GAATTTCGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 11 0.30
22 26 0.70
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTCACTTTTTTTTCTTTTT
Found at i:58837047 original size:20 final size:20
Alignment explanation
Indices: 58837024--58837070 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
58837014 GGGTTAAGAT
*
58837024 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
58837044 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
58837064 TGAGCTG
1 TGAGCTG
58837071 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:58852371 original size:29 final size:29
Alignment explanation
Indices: 58852329--58852393 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
58852319 GGATTACAAT
*
58852329 ATATGTGTGCGAGTAAGACCATGACATCG
1 ATATGTGTGAGAGTAAGACCATGACATCG
*
58852358 ATATGTGTGAGAGTAAGACCATGGCATCG
1 ATATGTGTGAGAGTAAGACCATGACATCG
58852387 ATATGTG
1 ATATGTG
58852394 ACTCCGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (29 bp):
ATATGTGTGAGAGTAAGACCATGACATCG
Found at i:58854555 original size:33 final size:33
Alignment explanation
Indices: 58854518--58854602 Score: 82
Period size: 33 Copynumber: 2.5 Consensus size: 33
58854508 TTCTCTCTAT
* *
58854518 TTGGTGTGCTGGTTGGATTAGCTCTTA-TGAGCA
1 TTGGTGTGATGGTTGGATTAGCTC-GAGTGAGCA
* * *
58854551 TTGGTGTGATAGATGGATTGGCTCGAGTGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCGAGTGAGCA
*
58854584 TCTGGTGTGTTTGGTTGGA
1 T-TGGTGTG-ATGGTTGGA
58854603 CTGATGATGT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 1 0.02
33 27 0.66
34 7 0.17
35 6 0.15
ACGTcount: A:0.15, C:0.09, G:0.38, T:0.38
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAGCTCGAGTGAGCA
Found at i:58861181 original size:33 final size:33
Alignment explanation
Indices: 58861139--58861204 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
58861129 AAGGTGATCA
58861139 AATCCACCCAATTTGATTTCATTTTCTGCTTTT
1 AATCCACCCAATTTGATTTCATTTTCTGCTTTT
58861172 AATCCACCCAATTTGATTTCATTTTCTGCTTTT
1 AATCCACCCAATTTGATTTCATTTTCTGCTTTT
58861205 CCTTTCTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.06, T:0.48
Consensus pattern (33 bp):
AATCCACCCAATTTGATTTCATTTTCTGCTTTT
Found at i:58873829 original size:26 final size:26
Alignment explanation
Indices: 58873783--58873846 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
58873773 ATAAGAGCCA
* *
58873783 TAATCAGGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
** *
58873809 TAATCAGGAAGCTCATGAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
58873835 TAATCA-GAAGCT
1 TAATCAGGAAGCT
58873847 TCAGATAGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 6 0.18
26 27 0.82
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:58874369 original size:59 final size:59
Alignment explanation
Indices: 58874277--58874396 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
58874267 ACGAACTTAC
*
58874277 CTCGATAAATGTTCGTGTACGTAAAATCTACTAATCTAACATTTTCTTTTTTCCTCGTT
1 CTCGATAAATGTTCGTGTACGTAAAATCTACTAATCTAACATTTTCTCTTTTCCTCGTT
*
58874336 CTCGATAAATGTTCGTGTACGTAAAATCTACTAATCTAACATTTTCTCTTTTCCTTGTT
1 CTCGATAAATGTTCGTGTACGTAAAATCTACTAATCTAACATTTTCTCTTTTCCTCGTT
58874395 CT
1 CT
58874397 AACTCAAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.44
Consensus pattern (59 bp):
CTCGATAAATGTTCGTGTACGTAAAATCTACTAATCTAACATTTTCTCTTTTCCTCGTT
Found at i:58885768 original size:20 final size:20
Alignment explanation
Indices: 58885745--58885808 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
58885735 GCACACTCCT
*
58885745 GTGTGCTTTAGGACACGCCC
1 GTGTGCTTTGGGACACGCCC
*
58885765 GTGTGCTTTGGGACACGTCC
1 GTGTGCTTTGGGACACGCCC
58885785 GTGTGCTTTGGGACACGCCC
1 GTGTGCTTTGGGACACGCCC
58885805 GTGT
1 GTGT
58885809 CTTCTACCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.11, C:0.27, G:0.34, T:0.28
Consensus pattern (20 bp):
GTGTGCTTTGGGACACGCCC
Found at i:58886239 original size:32 final size:32
Alignment explanation
Indices: 58886198--58886264 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
58886188 ACCCGTATGG
58886198 ACCATGTTAGGTTATTTTCCAAGCCTTTGGTC
1 ACCATGTTAGGTTATTTTCCAAGCCTTTGGTC
58886230 ACCATGTTAGGTTATTTTCCAAGCCTTTGGTC
1 ACCATGTTAGGTTATTTTCCAAGCCTTTGGTC
58886262 ACC
1 ACC
58886265 CTCTAACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (32 bp):
ACCATGTTAGGTTATTTTCCAAGCCTTTGGTC
Found at i:58887710 original size:31 final size:31
Alignment explanation
Indices: 58887672--58887747 Score: 143
Period size: 31 Copynumber: 2.5 Consensus size: 31
58887662 TTTAACGGTT
58887672 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
58887703 ACTGGGCCGAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
58887734 ACTGGGCCGAAGCC
1 ACTGGGCCGAAGCC
58887748 GTTACTGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:58887825 original size:42 final size:42
Alignment explanation
Indices: 58887778--58887865 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
58887768 CCATAGGCCT
* *** **
58887778 ATTTCAATATCACATGTAATGTTAATGGATGTATGCAAGCCC
1 ATTTCAATATCACATGAAATACCAATAAATGTATGCAAGCCC
*
58887820 ATTTCAATATCATATGAAATACCAATAAATGTATGCAAGCCC
1 ATTTCAATATCACATGAAATACCAATAAATGTATGCAAGCCC
58887862 ATTT
1 ATTT
58887866 TGGGAGACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (42 bp):
ATTTCAATATCACATGAAATACCAATAAATGTATGCAAGCCC
Found at i:58888056 original size:26 final size:26
Alignment explanation
Indices: 58888011--58888108 Score: 162
Period size: 26 Copynumber: 3.8 Consensus size: 26
58888001 CTCTTTTAAT
58888011 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
58888036 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
58888062 AACTGGGGCATAAGCCATTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
58888088 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
58888109 GCATTTCCTC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
25 10 0.15
26 58 0.85
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:58888821 original size:20 final size:19
Alignment explanation
Indices: 58888785--58888835 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
58888775 AATGGCTATC
*
58888785 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
58888804 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
58888824 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
58888836 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:58890723 original size:27 final size:27
Alignment explanation
Indices: 58890693--58890870 Score: 162
Period size: 27 Copynumber: 6.6 Consensus size: 27
58890683 ATATTGAGTC
* *
58890693 CGCACA-TTCAGTACTATATAATCAACT
1 CGCACACTT-AGTGCTACATAATCAACT
* *
58890720 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
58890747 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
58890775 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
58890802 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
58890829 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
58890856 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58890871 GTACAATTTA
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 100 0.79
28 26 0.21
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:58890781 original size:55 final size:55
Alignment explanation
Indices: 58890693--58890870 Score: 193
Period size: 54 Copynumber: 3.3 Consensus size: 55
58890683 ATATTGAGTC
* * * * *
58890693 CGCACA-TTCAGTACTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTT-AGTGCTATCATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
58890747 CGCACACTTAGTGCTA-CATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATAGTC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ***
58890802 CGCACACTTAGTGC-ATCATATTCGTTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTATCATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
58890856 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
58890871 GTACAATTTA
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
54 56 0.54
55 47 0.46
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATAGTCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:58892910 original size:46 final size:48
Alignment explanation
Indices: 58892854--58892957 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 48
58892844 GCCATGACAT
* *
58892854 TGGGACATGCATC-GGCT-AGATTAT-GAGAGCCAGTCTAAGACATGTC
1 TGGGACATGCATCAGCCTCAGATTATAGA-AACCAGTCTAAGACATGTC
* * *
58892900 TGGGACATGCATCAGCCTCGAGATTATAGAAACTAGTGTAAGACCTGTC
1 TGGGACATGCATCAGCCTC-AGATTATAGAAACCAGTCTAAGACATGTC
58892949 TGGGACATG
1 TGGGACATG
58892958 GCGTCAGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
46 13 0.27
47 3 0.06
49 31 0.63
50 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
TGGGACATGCATCAGCCTCAGATTATAGAAACCAGTCTAAGACATGTC
Found at i:58893054 original size:49 final size:49
Alignment explanation
Indices: 58892977--58893091 Score: 142
Period size: 49 Copynumber: 2.3 Consensus size: 49
58892967 TGTTGTGTGT
* * *
58892977 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACT-GATAGATGAGAGC
1 CAGTGTAAGACCTGTCTCGGACACGGCATCGAC-CTCGATAGATGAAAGC
* * * *
58893026 CAGTGTAAGGCCTGTCTCGGACACGGCATCGGCCTCGATATATGAAAGT
1 CAGTGTAAGACCTGTCTCGGACACGGCATCGACCTCGATAGATGAAAGC
*
58893075 CAGAGTAAGACCTGTCT
1 CAGTGTAAGACCTGTCT
58893092 GGGCATGGCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 2 0.04
49 54 0.96
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTCGGACACGGCATCGACCTCGATAGATGAAAGC
Found at i:58901216 original size:28 final size:28
Alignment explanation
Indices: 58901184--58901248 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
58901174 ATTTACTAGA
*
58901184 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
58901212 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
58901240 ATACCCCTA
1 ATACCCCTA
58901249 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:58901395 original size:28 final size:29
Alignment explanation
Indices: 58901354--58901416 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
58901344 AGGAAGCGTC
*
58901354 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTAT
58901382 CTGGTGGC-ACTGCCACAAAATATCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGTAT
58901411 CTGGTG
1 CTGGTG
58901417 ACTCTGTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.75
29 7 0.22
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCTATGCCACAAAATATCTGTAT
Found at i:58901427 original size:29 final size:28
Alignment explanation
Indices: 58901364--58901427 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
58901354 CTGGTGGCTA
* *
58901364 TGCCACAAATTATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
58901392 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
58901421 TGTCACA
1 TGCCACA
58901428 TTTTCTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:58904649 original size:46 final size:47
Alignment explanation
Indices: 58904596--58904715 Score: 167
Period size: 46 Copynumber: 2.6 Consensus size: 47
58904586 TGTGCTAGTG
*
58904596 TAAGACATGTCTGGGACATGCATCGGCCACATT-ATGAGAGCCAGTC
1 TAAGACATGTCTGGGACATGCATCGGCCACATTGACGAGAGCCAGTC
* *
58904642 TAAGACATGTCTGGGACATGCATC-G--ACATTGAGACGAGAGCTAGTG
1 TAAGACATGTCTGGGACATGCATCGGCCACATT--GACGAGAGCCAGTC
58904688 TAAGACATGTCTGGGACATGCATCGGCC
1 TAAGACATGTCTGGGACATGCATCGGCC
58904716 TCGAGATATA
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
43 5 0.08
45 1 0.02
46 58 0.89
47 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (47 bp):
TAAGACATGTCTGGGACATGCATCGGCCACATTGACGAGAGCCAGTC
Found at i:58911314 original size:23 final size:23
Alignment explanation
Indices: 58911281--58911344 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
58911271 ACTAATTTAC
* *
58911281 CCTCCAAACACAACCATATG-CA
1 CCTCCGAACACAACCATATGTAA
58911303 CCTACCGAACACAACCCTATATGTAA
1 CCT-CCGAACACAA-CC-ATATGTAA
*
58911329 CCTTCGAACACAACCA
1 CCTCCGAACACAACCA
58911345 AGTATACCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
22 3 0.09
23 10 0.29
24 4 0.11
25 14 0.40
26 4 0.11
ACGTcount: A:0.39, C:0.39, G:0.06, T:0.16
Consensus pattern (23 bp):
CCTCCGAACACAACCATATGTAA
Found at i:58915344 original size:101 final size:99
Alignment explanation
Indices: 58915171--58915357 Score: 277
Period size: 101 Copynumber: 1.9 Consensus size: 99
58915161 CTGGTACGCA
* *
58915171 TAGTAGCCTGCACTTAGTACTACACATGCGACCAGCAGTCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAGCAGTCTGGTACACATAGTAGCCTGCACTTA
*
58915236 GTACTACACACGTGACCTCACCATCTAATACACC
66 GTACTACACACGCGACCTCACCATCTAATACACC
* * *
58915270 TAGTAGCCTGCACTTAGTACTACACACGTGATCA-CAGTTCTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAGCAG-TCT--GGTACACATAGTAGCCTGCAC
*
58915334 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACACGCGACCTCAC
58915358 AATAGATCAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 3 0.04
99 34 0.44
101 41 0.53
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAGCAGTCTGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTCACCATCTAATACACC
Found at i:58920681 original size:50 final size:49
Alignment explanation
Indices: 58920560--58920689 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 49
58920550 CTGGTACGCA
* * *
58920560 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
* *
58920609 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCA-TCTAATATACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAACAGTCTAATACACG
58920659 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
58920690 TCACAATTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
49 29 0.39
50 41 0.55
51 4 0.05
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAGTCTAATACACG
Found at i:58920715 original size:50 final size:50
Alignment explanation
Indices: 58920552--58920734 Score: 187
Period size: 50 Copynumber: 3.7 Consensus size: 50
58920542 GAAGCTATCT
* * * *
58920552 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCT-A
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAATCTCA
* * * *
58920602 -GTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTCACCATCTAA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGA--TCACAATCTCA
** * *
58920653 TATACG--TAGTAGCCTGCACTTAGTACTACACACGTGATCACAATTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCACAA-TCTCA
58920702 GGTACGCAT-GTAGCCTGCACTTAGTACTACACA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACA
58920735 TGCGACCTCA
Statistics
Matches: 111, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
48 5 0.05
49 40 0.36
50 60 0.54
51 3 0.03
52 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (50 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGATCACAATCTCA
Found at i:58940155 original size:18 final size:18
Alignment explanation
Indices: 58940129--58940172 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
58940119 TGGCCCAAAA
*
58940129 TCCCGCACGCACATGTGG
1 TCCCACACGCACATGTGG
*
58940147 TCCCACACGCCCATGTGG
1 TCCCACACGCACATGTGG
*
58940165 GCCCACAC
1 TCCCACAC
58940173 TCCGTGTGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.45, G:0.23, T:0.14
Consensus pattern (18 bp):
TCCCACACGCACATGTGG
Found at i:58943257 original size:27 final size:27
Alignment explanation
Indices: 58943226--58943403 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
58943216 TAAATTGTAC
*
58943226 AGCACTAAGTGTACGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
58943253 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
58943279 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
58943307 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
58943335 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
58943362 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
58943389 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
58943404 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:58943340 original size:82 final size:81
Alignment explanation
Indices: 58943227--58943382 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
58943217 AAATTGTACA
* *
58943227 GCACTAAGTGTACGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTACGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
58943291 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
58943308 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTACGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
58943373 TGCGAGTTGA
65 TGCGAATTGA
58943383 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 14 0.21
82 51 0.77
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTACGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:58943394 original size:82 final size:81
Alignment explanation
Indices: 58943223--58943403 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
58943213 GATTAAATTG
* * *
58943223 TACAGCACTAAGTGTACGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
58943288 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
58943304 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
58943368 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
58943386 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
58943404 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 17 0.20
82 66 0.80
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.