Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 108 of 322
Found at i:35063314 original size:11 final size:11
Alignment explanation
Indices: 35063298--35063323 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35063288 TGAATGCAAA
35063298 AAAATAAAAAT
1 AAAATAAAAAT
35063309 AAAATAAAAAT
1 AAAATAAAAAT
35063320 AAAA
1 AAAA
35063324 CCGTTTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:35083768 original size:133 final size:131
Alignment explanation
Indices: 35083506--35083887 Score: 331
Period size: 133 Copynumber: 2.9 Consensus size: 131
35083496 TTTAAAAATT
* * * * *
35083506 CTTTAAAACGAAGGTAATGTTCGATATTTGGCAA-CTCACGAAATCGTGCCCTAACGTGCTGGGT
1 CTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTTGA-G-AATCGTGCCCTATCGTGCTGGGT
* * * ** *
35083570 TGCAATTTCTCGTTTGCTCAAGATAATCGAAAGTCTCTTTAGAATTTCGTTCATGATTTAAAAAA
64 TGCAATTTCTCATTTGCTCAAAACAATCGAAAGTCTCTTTAGAATTTCACTCACGATTT--AAAA
35083635 AAAAC
127 AAAAC
** *
35083640 CTTTAAAACGAAGGCGATATTCGATGTTTGGCAATTTGAGAATCGTGCCCTATCGTGCTGGGTTG
1 CTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTTGAGAATCGTGCCCTATCGTGCTGGGTTG
** * * * * * **
35083705 CGCTTTTTCATTTGTTCAAAACAATCGAAGATTC-CTTTAGAATTTTACTCACGTTTTCTAAAAA
66 CAATTTCTCATTTGCTCAAAACAATCGAA-AGTCTCTTTAGAATTTCACTCACGATTTAAAAAAA
*
35083769 CC
130 AC
* * ** * * *
35083771 CTTTAAAACGAAAGAAATGTTCGGTGTTTGGTGATTCGGGGAATAGTGCCCTATCGTGCTGGGTT
1 CTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATT-TGAGAATCGTGCCCTATCGTGCTGGGTT
* * * * * *
35083836 GCAATCTCCCGTTTGTTCAAAATAATCGAATA-TCTC-TTCGAAATTTCACTCA
65 GCAATTTCTCATTTGCTCAAAACAATCGAA-AGTCTCTTTAG-AATTTCACTCA
35083888 TGTTTTCTAA
Statistics
Matches: 200, Mismatches: 43, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
131 40 0.20
132 60 0.30
133 64 0.32
134 34 0.17
135 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (131 bp):
CTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTTGAGAATCGTGCCCTATCGTGCTGGGTTG
CAATTTCTCATTTGCTCAAAACAATCGAAAGTCTCTTTAGAATTTCACTCACGATTTAAAAAAAA
C
Found at i:35084816 original size:9 final size:9
Alignment explanation
Indices: 35084804--35084828 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
35084794 TGCAACTGAG
35084804 CTTTCAACT
1 CTTTCAACT
35084813 CTTTCAACT
1 CTTTCAACT
35084822 CTTTCAA
1 CTTTCAA
35084829 AGCCATTCTG
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:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTTCAACT
Found at i:35090268 original size:46 final size:46
Alignment explanation
Indices: 35090201--35090370 Score: 189
Period size: 46 Copynumber: 3.7 Consensus size: 46
35090191 TGTAACCCGC
* * *
35090201 CCATAAGTGAACTCGAACTCAACTCAATGAGCTCGGCCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * * * *
35090247 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACG-TTCGCAT
* *** * *
35090293 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
35090340 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
35090371 TTCAGATGCC
Statistics
Matches: 98, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
46 64 0.65
47 34 0.35
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:35090316 original size:93 final size:93
Alignment explanation
Indices: 35090209--35090380 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
35090199 GCCCATAAGT
* * *
35090209 GAACTCGAACTCAACTCAATGAGCTCGGCCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
35090274 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCAGATGCCTAGTTACATCTCTC
* * *
35090302 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
35090367 CGAGTTCAGATGCC
66 CGAGCTCAGATGCC
35090381 CAAACATCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCTC
Found at i:35090395 original size:46 final size:46
Alignment explanation
Indices: 35090252--35090395 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 46
35090242 CGCATCCATA
* * * *
35090252 AGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCA--TACATC-CT
* * * * * *
35090301 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTC--AGATGCCCATACATCCT
*
35090345 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCATACATCCT
35090391 AGTGA
1 AGTGA
35090396 CATGTCACTT
Statistics
Matches: 72, Mismatches: 17, Indels: 15
0.69 0.16 0.14
Matches are distributed among these distances:
44 9 0.12
46 31 0.43
47 28 0.39
49 4 0.06
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCCATACATCCT
Found at i:35097888 original size:27 final size:27
Alignment explanation
Indices: 35097858--35098035 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35097848 ATATTGAGCC
* * * *
35097858 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
35097885 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35097912 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
35097940 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
35097967 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
35097994 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
35098021 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35098036 GTACAATTTA
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:35097997 original size:82 final size:81
Alignment explanation
Indices: 35097879--35098034 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
35097869 TGCTATATAA
* *
35097879 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
35097944 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
35097961 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
35098025 CACTTAGTGC
65 CACTTAGTGC
35098035 TGTACAATTT
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:35100221 original size:15 final size:15
Alignment explanation
Indices: 35100201--35100234 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35100191 AGCGTATACA
*
35100201 CACAACCAATTCAAC
1 CACAACCAAGTCAAC
*
35100216 CACAACCAAGTCATC
1 CACAACCAAGTCAAC
35100231 CACA
1 CACA
35100235 CATCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.41, G:0.03, T:0.12
Consensus pattern (15 bp):
CACAACCAAGTCAAC
Found at i:35100853 original size:20 final size:20
Alignment explanation
Indices: 35100830--35100867 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35100820 CTTGCAACTC
35100830 ACCATAATCTTTCACAACAT
1 ACCATAATCTTTCACAACAT
* *
35100850 ACCATAGTCTTTCCCAAC
1 ACCATAATCTTTCACAAC
35100868 TTTAACATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (20 bp):
ACCATAATCTTTCACAACAT
Found at i:35101031 original size:43 final size:42
Alignment explanation
Indices: 35100953--35101074 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
35100943 TACCATACCA
* **
35100953 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * * *
35100995 ATGCCAATAGCCCAGCTATGGTCTTACACAAAATCTCATATTG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* * *
35101038 ATGCTATATCCTAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCA
35101075 ACTAACCTTA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
42 32 0.48
43 34 0.52
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:35108101 original size:27 final size:27
Alignment explanation
Indices: 35108071--35108147 Score: 67
Period size: 27 Copynumber: 3.1 Consensus size: 27
35108061 GATACATTGA
35108071 TTTGGCTTCGGGCCATGATATCGGCAC
1 TTTGGCTTCGGGCCATGATATCGGCAC
* * * * *
35108098 TTTGGGTGCGAG-CTTCAT-T--G-A-
1 TTTGGCTTCGGGCCATGATATCGGCAC
35108119 TTTGGCTTCGGGCCATGATATCGGCAC
1 TTTGGCTTCGGGCCATGATATCGGCAC
35108146 TT
1 TT
35108148 CAGGTGCGAG
Statistics
Matches: 34, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
21 9 0.26
22 5 0.15
23 2 0.06
25 2 0.06
26 5 0.15
27 11 0.32
ACGTcount: A:0.14, C:0.22, G:0.30, T:0.34
Consensus pattern (27 bp):
TTTGGCTTCGGGCCATGATATCGGCAC
Found at i:35108963 original size:48 final size:48
Alignment explanation
Indices: 35108065--35108955 Score: 1692
Period size: 48 Copynumber: 18.6 Consensus size: 48
35108055 TTAGGGGATA
**
35108065 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTTGGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108113 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108161 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108209 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108257 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108305 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108353 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108401 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108449 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108497 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108545 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108593 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108641 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108689 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108737 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108785 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
35108833 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
* ** * ***
35108881 CATTGATTTGGCTTCGGGCCATGAGATTAGCACTTCGGGTGCGAGAGA
1 CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
*
35108929 CATTGAGTTGGCTTCGGGCCATGATAT
1 CATTGATTTGGCTTCGGGCCATGATAT
35108956 TAGCACTTAG
Statistics
Matches: 832, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 832 1.00
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.31
Consensus pattern (48 bp):
CATTGATTTGGCTTCGGGCCATGATATCGGCACTTCAGGTGCGAGCTT
Found at i:35110485 original size:37 final size:37
Alignment explanation
Indices: 35110435--35110510 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
35110425 TAATGCTCCA
35110435 TAACCCTATTTCGACATTGAATACGAGTGAGAGGTGT
1 TAACCCTATTTCGACATTGAATACGAGTGAGAGGTGT
35110472 TAACCCTATTTCGACATTGAATACGAGTGAGAGGTGT
1 TAACCCTATTTCGACATTGAATACGAGTGAGAGGTGT
35110509 TA
1 TA
35110511 CATTATGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (37 bp):
TAACCCTATTTCGACATTGAATACGAGTGAGAGGTGT
Found at i:35111373 original size:22 final size:22
Alignment explanation
Indices: 35111348--35111393 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
35111338 GTAAAGTTAC
*
35111348 TTTGTTATGGTATGAATCTAAA
1 TTTGTTATGGTACGAATCTAAA
35111370 TTTGTTATGGTACGAATCTAAA
1 TTTGTTATGGTACGAATCTAAA
35111392 TT
1 TT
35111394 GGTAAGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (22 bp):
TTTGTTATGGTACGAATCTAAA
Found at i:35112918 original size:40 final size:39
Alignment explanation
Indices: 35112854--35112983 Score: 152
Period size: 40 Copynumber: 3.3 Consensus size: 39
35112844 TAGATAACAC
* * **
35112854 CGACACAAAGCCTGTTAGGCACAAAGCCCAATAAATACA
1 CGACACAAAACCTGCTAGGCACAAAGCCTGATAAATACA
* * *
35112893 TCGACACAAAACTTGCTAGGAACAAAGCCTGATAAACACA
1 -CGACACAAAACCTGCTAGGCACAAAGCCTGATAAATACA
* *
35112933 CTGGCACAAAGCCTGCTAGGCACAAAGCCTGATAAATACA
1 C-GACACAAAACCTGCTAGGCACAAAGCCTGATAAATACA
35112973 CCGACACAAAA
1 -CGACACAAAA
35112984 GCCTAATAGA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 72 0.97
41 1 0.01
ACGTcount: A:0.43, C:0.28, G:0.16, T:0.13
Consensus pattern (39 bp):
CGACACAAAACCTGCTAGGCACAAAGCCTGATAAATACA
Found at i:35138292 original size:46 final size:46
Alignment explanation
Indices: 35138202--35138455 Score: 214
Period size: 46 Copynumber: 5.5 Consensus size: 46
35138192 CCGTACTGAC
* * * * *
35138202 GCATGTCCTAGACATGTCTTATACTAGC--ACAT-CTCATAGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTAACATACTGA-GGCCGAT
* * *
35138246 GCATGTCCCGGAGATGTCTGACACTGGCTAACAT-CTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTAACATACT-GAGGCCGAT
** * *
35138292 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTAACATACTGAGGCCGAT
* *** * * *
35138338 GCATGTCCCAGACATGTCTTACACTAGCCCTCGT-CTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTAACATACT-GAGGCCGAT
* * *
35138384 GCCATGTCCCAGTCATGGTCTTACACTGGCTATCATAAT-ATGGCCGAT
1 G-CATGTCCCAGACAT-GTCTTACACTGGCTAACATACTGA-GGCCGAT
35138432 GCATGTCCCAGACATGTCTTACAC
1 GCATGTCCCAGACATGTCTTACAC
35138456 GGGCACAAAA
Statistics
Matches: 171, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
44 22 0.13
45 2 0.01
46 94 0.55
47 30 0.18
48 22 0.13
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTACACTGGCTAACATACTGAGGCCGAT
Found at i:35138438 original size:94 final size:92
Alignment explanation
Indices: 35138202--35138455 Score: 280
Period size: 94 Copynumber: 2.8 Consensus size: 92
35138192 CCGTACTGAC
* * * * * * *
35138202 GCATGTCCTAGACATGTCTTATACTAGC-A-CAT-CTCATAGCCGATGCATGTCCCGGAGATGTC
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATAAT-ATGGCCGATGCATGTCCCAGACATGTC
* * * *
35138264 TGACACTGGCTAACATCTCGAGGCCGAT
65 TTACACTAGCCAACATCTCAAGGCCGAT
* * * *
35138292 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACTGTGGCTGATGCATGTCCCAGACATGTCT
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATAATATGGCCGATGCATGTCCCAGACATGTCT
** * *
35138357 TACACTAGCCCTCGTCTCAATGCCGAT
66 TACACTAGCCAACATCTCAAGGCCGAT
*
35138384 GCCATGTCCCAGTCATGGTCTTACACTGGCTATCATAATATGGCCGATGCATGTCCCAGACATGT
1 G-CATGTCCCAGACAT-GTCTTACACTGGCTATCATAATATGGCCGATGCATGTCCCAGACATGT
35138449 CTTACAC
64 CTTACAC
35138456 GGGCACAAAA
Statistics
Matches: 137, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
90 25 0.18
92 46 0.34
93 15 0.11
94 51 0.37
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (92 bp):
GCATGTCCCAGACATGTCTTACACTGGCTATCATAATATGGCCGATGCATGTCCCAGACATGTCT
TACACTAGCCAACATCTCAAGGCCGAT
Found at i:35138451 original size:140 final size:135
Alignment explanation
Indices: 35138197--35138455 Score: 333
Period size: 140 Copynumber: 1.9 Consensus size: 135
35138187 TGTAACCGTA
* * * *
35138197 CTGACGCATGTCCTAGACATGTCTTATACTAGCACATCTCATAGCCGATGCATGTCCCGGAGATG
1 CTGACGCATGTCCCAGACATGTCTTACACTAGCACATCTCATAGCCGATGCATGTCCCAGACATG
*
35138262 TCTGACACTGGCTAACATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATA
66 TCTGACACTGGCTAACATATC-AGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATA
35138327 CTGTGG
130 CTGTGG
* * * *
35138333 CTGATGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCA-ATGCCGATGCCATGTCCCAGT
1 CTGACGCATGTCCCAGACATGTCTTACACTAG--CACATCTCATA-GCCGATG-CATGTCCCAGA
* *
35138397 CATGGTCTTACACTGGCTATCATAAT-ATGGCCGATGCATGTCCCAGACATGTCTTACAC
62 CAT-GTCTGACACTGGCTAACAT-ATCA-GGCCGATGCATGTCCCAGACATGTCTTACAC
35138456 GGGCACAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
136 29 0.28
137 1 0.01
138 14 0.13
139 12 0.11
140 48 0.46
141 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (135 bp):
CTGACGCATGTCCCAGACATGTCTTACACTAGCACATCTCATAGCCGATGCATGTCCCAGACATG
TCTGACACTGGCTAACATATCAGGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAC
TGTGG
Found at i:35142851 original size:27 final size:27
Alignment explanation
Indices: 35142814--35142974 Score: 166
Period size: 27 Copynumber: 6.0 Consensus size: 27
35142804 TAAGACCCCA
*
35142814 ATTTTTAAAATTATCGAAATACCCCTG
1 ATTTGTAAAATTATCGAAATACCCCTG
*
35142841 ATTTGTGAAATTA-CTGAAATA-CCCTCG
1 ATTTGTAAAATTATC-GAAATACCCCT-G
* *
35142868 ATTTGTAAAATTACCAAAATACCCCTG
1 ATTTGTAAAATTATCGAAATACCCCTG
*
35142895 ATTTGTAAAATTATCGAAATACCCTTG
1 ATTTGTAAAATTATCGAAATACCCCTG
** ** * *
35142922 GGTTGTAAAGGTACCGAAATACCCC-C
1 ATTTGTAAAATTATCGAAATACCCCTG
*
35142948 AGTTTGTAAAATTATCGTAATACCCCT
1 A-TTTGTAAAATTATCGAAATACCCCT
35142975 ATAAGATAAA
Statistics
Matches: 108, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
26 5 0.05
27 98 0.91
28 5 0.05
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.32
Consensus pattern (27 bp):
ATTTGTAAAATTATCGAAATACCCCTG
Found at i:35142906 original size:54 final size:54
Alignment explanation
Indices: 35142814--35142972 Score: 187
Period size: 54 Copynumber: 2.9 Consensus size: 54
35142804 TAAGACCCCA
* * *
35142814 ATTTTTAAAATTATCGAAATACCCCTGATTTGTGAAATTA-CTGAAATACCCTCG
1 ATTTGTAAAATTACCGAAATACCCCTGATTTGTAAAATTATC-GAAATACCCTCG
* *
35142868 ATTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTTG
1 ATTTGTAAAATTACCGAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCG
** ** * *
35142922 GGTTGTAAAGGTACCGAAATACCCC-CAGTTTGTAAAATTATCGTAATACCC
1 ATTTGTAAAATTACCGAAATACCCCTGA-TTTGTAAAATTATCGAAATACCC
35142973 CTATAAGATA
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 89 0.98
55 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (54 bp):
ATTTGTAAAATTACCGAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCG
Found at i:35142984 original size:27 final size:27
Alignment explanation
Indices: 35142953--35143097 Score: 164
Period size: 27 Copynumber: 5.4 Consensus size: 27
35142943 CCCCCAGTTT
* *
35142953 GTAAAATTATCGTAATACCCCTATAAG
1 GTAAAATGACCGTAATACCCCTATAAG
* * * *
35142980 ATAAAATGACCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTATAAG
* *
35143007 GTAAAATGACCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATACCCCTATAAG
* * *
35143034 GTAAAATGACTGTAATACCTCTGTAAG
1 GTAAAATGACCGTAATACCCCTATAAG
* * *
35143061 GTAAAATGACCGTAATACCCTTGTATG
1 GTAAAATGACCGTAATACCCCTATAAG
35143088 GTAAAATGAC
1 GTAAAATGAC
35143098 GATGATGCCC
Statistics
Matches: 99, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTATAAG
Found at i:35142985 original size:81 final size:81
Alignment explanation
Indices: 35142819--35143002 Score: 194
Period size: 81 Copynumber: 2.3 Consensus size: 81
35142809 CCCCAATTTT
* * * * *
35142819 TAAAATTATCGAAATACCCCTGATTTGTGAAATTACTGAAATACCCTCGATTTGTAAAATTACCA
1 TAAAATTATCGAAATACCCTTGAGTTGTGAAAGTACCGAAATACCCCCGATTTGTAAAATTACCA
**
35142884 AAATACCCCTGATTTG
66 AAATACCCCTGATAAG
* *
35142900 TAAAATTATCGAAATACCCTTGGGTTGT-AAAGGTACCGAAATACCCCC-AGTTTGTAAAATTAT
1 TAAAATTATCGAAATACCCTTGAGTTGTGAAA-GTACCGAAATACCCCCGA-TTTGTAAAATTAC
**
35142963 CGTAATACCCCT-ATAAG
64 CAAAATACCCCTGATAAG
* * *
35142980 ATAAAATGACCGTAATACCCTTG
1 -TAAAATTATCGAAATACCCTTG
35143003 TAGGGTAAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 7 0.08
81 79 0.92
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (81 bp):
TAAAATTATCGAAATACCCTTGAGTTGTGAAAGTACCGAAATACCCCCGATTTGTAAAATTACCA
AAATACCCCTGATAAG
Found at i:35142997 original size:54 final size:55
Alignment explanation
Indices: 35142934--35143080 Score: 147
Period size: 54 Copynumber: 2.7 Consensus size: 55
35142924 TTGTAAAGGT
* ** * *
35142934 ACCGAAATACCCCCAGT-TTGTAAAATTATCGTAATACCCCTATAAGATAAAATG
1 ACCGTAATACCCCCAGTAGGGTAAAATGACCGTAATACCCCTATAAGATAAAATG
** * * *
35142988 ACCGTAATA-CCCTTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATG
1 ACCGTAATACCCCCAGTAGGGTAAAATGACCGTAATACCCCTATAAGATAAAATG
* * * *
35143042 ACTGTAATA-CCTCTGTAAGGTAAAATGACCGTAATACCC
1 ACCGTAATACCCCCAGTAGGGTAAAATGACCGTAATACCC
35143081 TTGTATGGTA
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 5 0.06
54 72 0.94
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (55 bp):
ACCGTAATACCCCCAGTAGGGTAAAATGACCGTAATACCCCTATAAGATAAAATG
Found at i:35143011 original size:81 final size:81
Alignment explanation
Indices: 35142934--35143097 Score: 206
Period size: 81 Copynumber: 2.0 Consensus size: 81
35142924 TTGTAAAGGT
** *
35142934 ACCGAAATACCCCCAGT-TTGTAAAATTA-TCGTAATACCCCTATAAGATAAAATGACCGTAATA
1 ACCGAAATACCCCCA-TAGGGTAAAATGACT-GTAATACCCCTATAAGATAAAATGACCGTAATA
35142997 CCCTTGTAGGGTAAAATG
64 CCCTTGTAGGGTAAAATG
* * * * * *
35143015 ACCGTAATGCCCCTATAGGGTAAAATGACTGTAATACCTCTGTAAGGTAAAATGACCGTAATACC
1 ACCGAAATACCCCCATAGGGTAAAATGACTGTAATACCCCTATAAGATAAAATGACCGTAATACC
*
35143080 CTTGTATGGTAAAATG
66 CTTGTAGGGTAAAATG
35143096 AC
1 AC
35143098 GATGATGCCC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
80 1 0.01
81 69 0.97
82 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (81 bp):
ACCGAAATACCCCCATAGGGTAAAATGACTGTAATACCCCTATAAGATAAAATGACCGTAATACC
CTTGTAGGGTAAAATG
Found at i:35143091 original size:54 final size:54
Alignment explanation
Indices: 35142953--35143097 Score: 184
Period size: 54 Copynumber: 2.7 Consensus size: 54
35142943 CCCCCAGTTT
* * * *
35142953 GTAAAATTATCGTAATACCCCTATAAGATAAAATGACCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTATAAGGTAAAATGACCGTAATACCCTTGTAAG
* * *
35143007 GTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACTGTAATA-CCTCTGTAAG
1 GTAAAATGACCGTAATACCCCTATAAGGTAAAATGACCGTAATACCCT-TGTAAG
* * *
35143061 GTAAAATGACCGTAATACCCTTGTATGGTAAAATGAC
1 GTAAAATGACCGTAATACCCCTATAAGGTAAAATGAC
35143098 GATGATGCCC
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 3 0.04
54 76 0.96
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (54 bp):
GTAAAATGACCGTAATACCCCTATAAGGTAAAATGACCGTAATACCCTTGTAAG
Found at i:35143290 original size:27 final size:27
Alignment explanation
Indices: 35143247--35143332 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
35143237 GTACTAATGA
*
35143247 CTATGTCA-AATTCACTGTTACTGGTGG
1 CTATGCCACAATT-ACTGTTACTGGTGG
* **
35143274 CTATGCCACAATTACTGATACCAGTGG
1 CTATGCCACAATTACTGTTACTGGTGG
* * **
35143301 CT-TGCCACATTTACTGTTTCTGGCAG
1 CTATGCCACAATTACTGTTACTGGTGG
35143327 CTATGC
1 CTATGC
35143333 TGCATTATTA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
26 19 0.41
27 23 0.50
28 4 0.09
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (27 bp):
CTATGCCACAATTACTGTTACTGGTGG
Found at i:35143527 original size:28 final size:28
Alignment explanation
Indices: 35143482--35143535 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
35143472 GTACTAATAA
* * *
35143482 TGTATTGGGCTTAGGCCCACACTGTTAT
1 TGTATAGGGCTAAAGCCCACACTGTTAT
*
35143510 TGTATAGGGCTAAAGCCCAGACTGTT
1 TGTATAGGGCTAAAGCCCACACTGTT
35143536 CTGTTACTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (28 bp):
TGTATAGGGCTAAAGCCCACACTGTTAT
Found at i:35143547 original size:33 final size:33
Alignment explanation
Indices: 35143502--35143586 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
35143492 TTAGGCCCAC
*
35143502 ACTGTTATTGTATAGGGCTAAAGCCCAGACTGT
1 ACTGTTACTGTATAGGGCTAAAGCCCAGACTGT
* * * **
35143535 TCTGTTACTGTATAAGGCTAAGGCCTTGACTGT
1 ACTGTTACTGTATAGGGCTAAAGCCCAGACTGT
* *
35143568 ACTGATACTGGATAGGGCT
1 ACTGTTACTGTATAGGGCT
35143587 CAGGCTTAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (33 bp):
ACTGTTACTGTATAGGGCTAAAGCCCAGACTGT
Found at i:35143599 original size:33 final size:34
Alignment explanation
Indices: 35143528--35143600 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
35143518 GCTAAAGCCC
* * *
35143528 AGACTGTTCTGTTACTGTATAAGGCTAAGGCCTT
1 AGACTGTACTGATACTGGATAAGGCTAAGGCCTT
* *
35143562 -GACTGTACTGATACTGGATAGGGCTCAGG-CTT
1 AGACTGTACTGATACTGGATAAGGCTAAGGCCTT
35143594 AGACTGT
1 AGACTGT
35143601 TACTACATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (34 bp):
AGACTGTACTGATACTGGATAAGGCTAAGGCCTT
Found at i:35147590 original size:27 final size:27
Alignment explanation
Indices: 35147549--35147764 Score: 174
Period size: 27 Copynumber: 8.0 Consensus size: 27
35147539 GTTAGGACCT
35147549 TGATTTGTAAAATTACTAAAATACCCC
1 TGATTTGTAAAATTACTAAAATACCCC
* * *
35147576 TGCTTTGTAAAATTA-TCGAAATACCCT
1 TGATTTGTAAAATTACT-AAAATACCCC
*
35147603 TGATTTGTAAAATTA-TCGAAATACCCC
1 TGATTTGTAAAATTACT-AAAATACCCC
* * * *
35147630 T-ACTTTGTGAAATTACCAAAATACTCT
1 TGA-TTTGTAAAATTACTAAAATACCCC
** * *
35147657 TGGGTTGTAAAATTACCAAAATACCCT
1 TGATTTGTAAAATTACTAAAATACCCC
* *
35147684 TGATTTGTGAAATTACCAAAATACCCC
1 TGATTTGTAAAATTACTAAAATACCCC
* *
35147711 TAATTTGTAAAATTA-TCGAAATA-CCC
1 TGATTTGTAAAATTACT-AAAATACCCC
* * *
35147737 TCAGTTTGTAAAATGACTATAAT-CCCC
1 TGA-TTTGTAAAATTACTAAAATACCCC
35147764 T
1 T
35147765 ATAGGGTAAA
Statistics
Matches: 155, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
26 7 0.05
27 147 0.95
28 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (27 bp):
TGATTTGTAAAATTACTAAAATACCCC
Found at i:35147628 original size:54 final size:54
Alignment explanation
Indices: 35147546--35147750 Score: 234
Period size: 54 Copynumber: 3.8 Consensus size: 54
35147536 GTCGTTAGGA
* *
35147546 CCTTGATTTGTAAAATTA-CTAAAATACCCCTGCTTTGTAAAATTATCGAAATAC
1 CCTTGATTTGTAAAATTATC-AAAATACCCCTGCTTTGTAAAATTACCAAAATAC
* * *
35147600 CCTTGATTTGTAAAATTATCGAAATACCCCTACTTTGTGAAATTACCAAAATAC
1 CCTTGATTTGTAAAATTATCAAAATACCCCTGCTTTGTAAAATTACCAAAATAC
* ** * * * *
35147654 TCTTGGGTTGTAAAATTACCAAAATACCCTTGATTTGTGAAATTACCAAAATAC
1 CCTTGATTTGTAAAATTATCAAAATACCCCTGCTTTGTAAAATTACCAAAATAC
* * * *
35147708 CCCTAATTTGTAAAATTATCGAAATACCCTCAG-TTTGTAAAAT
1 CCTTGATTTGTAAAATTATCAAAATACCC-CTGCTTTGTAAAAT
35147751 GACTATAATC
Statistics
Matches: 126, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
54 124 0.98
55 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (54 bp):
CCTTGATTTGTAAAATTATCAAAATACCCCTGCTTTGTAAAATTACCAAAATAC
Found at i:35147687 original size:81 final size:81
Alignment explanation
Indices: 35147551--35147736 Score: 246
Period size: 81 Copynumber: 2.3 Consensus size: 81
35147541 TAGGACCTTG
* * * *
35147551 ATTTGTAAAATTACTAAAATACCCCTGCTTTGTAAAATTATCGAAATACCCTTGATTTGTAAAAT
1 ATTTGTAAAATTACCAAAATACCCCTGCGTTGTAAAATTACCAAAATACCCTTGATTTGTAAAAT
* *
35147616 TATCGAAATACCCCTA
66 TACCAAAATACCCCTA
* * * * * *
35147632 CTTTGTGAAATTACCAAAATACTCTTGGGTTGTAAAATTACCAAAATACCCTTGATTTGTGAAAT
1 ATTTGTAAAATTACCAAAATACCCCTGCGTTGTAAAATTACCAAAATACCCTTGATTTGTAAAAT
35147697 TACCAAAATACCCCTA
66 TACCAAAATACCCCTA
* *
35147713 ATTTGTAAAATTATCGAAATACCC
1 ATTTGTAAAATTACCAAAATACCC
35147737 TCAGTTTGTA
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (81 bp):
ATTTGTAAAATTACCAAAATACCCCTGCGTTGTAAAATTACCAAAATACCCTTGATTTGTAAAAT
TACCAAAATACCCCTA
Found at i:35147801 original size:27 final size:26
Alignment explanation
Indices: 35147744--35147887 Score: 146
Period size: 27 Copynumber: 5.4 Consensus size: 26
35147734 CCCTCAGTTT
** *
35147744 GTAAAATGACTATAAT-CCCCTATAGG
1 GTAAAATGACCGTAATACCCCTGTA-G
* *
35147770 GTAAAATGACCGTAATACTCCTATAG
1 GTAAAATGACCGTAATACCCCTGTAG
* * *
35147796 GTTAAAATGTCTGTAATGCCCCTGTAAG
1 G-TAAAATGACCGTAATACCCCTGT-AG
* *
35147824 GTAAAATGATCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTA-G
35147851 GTAAAATGACCGTAATACCCCTGTATG
1 GTAAAATGACCGTAATACCCCTGTA-G
35147878 GTAAAATGAC
1 GTAAAATGAC
35147888 GATTATGCCC
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
26 17 0.17
27 78 0.80
28 3 0.03
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (26 bp):
GTAAAATGACCGTAATACCCCTGTAG
Found at i:35147829 original size:54 final size:53
Alignment explanation
Indices: 35147744--35147887 Score: 173
Period size: 54 Copynumber: 2.7 Consensus size: 53
35147734 CCCTCAGTTT
* * *
35147744 GTAAAATGACTATAATCCCCTATAGGGTAAAATGACCGTAATACTCC-TATAGG
1 GTAAAATGACTGTAATCCCCTGTAAGGTAAAATGACCGTAATAC-CCTTATAGG
* * * *
35147797 TTAAAATGTCTGTAATGCCCCTGTAAGGTAAAATGATCGTAATACCCTTGTAGG
1 GTAAAATGACTGTAAT-CCCCTGTAAGGTAAAATGACCGTAATACCCTTATAGG
* *
35147851 GTAAAATGACCGTAATACCCCTGTATGGTAAAATGAC
1 GTAAAATGACTGTAAT-CCCCTGTAAGGTAAAATGAC
35147888 GATTATGCCC
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 15 0.20
54 61 0.80
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (53 bp):
GTAAAATGACTGTAATCCCCTGTAAGGTAAAATGACCGTAATACCCTTATAGG
Found at i:35148104 original size:26 final size:27
Alignment explanation
Indices: 35148050--35148106 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
35148040 CGTCATATTC
*
35148050 ACTGTTACTGGTGGCTATGCCACAATT
1 ACTGATACTGGTGGCTATGCCACAATT
*
35148077 ACTGATACTGGTGGCT-TGCCACATTT
1 ACTGATACTGGTGGCTATGCCACAATT
35148103 ACTG
1 ACTG
35148107 TTTCTGGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
ACTGATACTGGTGGCTATGCCACAATT
Found at i:35148113 original size:26 final size:27
Alignment explanation
Indices: 35148050--35148113 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
35148040 CGTCATATTC
35148050 ACTGTTACTGGTGGCTATGCCACAATT
1 ACTGTTACTGGTGGCTATGCCACAATT
* *
35148077 ACTGATACTGGTGGCT-TGCCACATTT
1 ACTGTTACTGGTGGCTATGCCACAATT
*
35148103 ACTGTTTCTGG
1 ACTGTTACTGG
35148114 CAGCTATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (27 bp):
ACTGTTACTGGTGGCTATGCCACAATT
Found at i:35148157 original size:26 final size:28
Alignment explanation
Indices: 35148110--35148168 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
35148100 TTTACTGTTT
*
35148110 CTGGCAGCTATGTTGCATTATT-AT-TA
1 CTGGCAGCTATGCTGCATTATTGATGTA
*
35148136 CTGGCAGCTTTGCTGCGA-TATTGATGTA
1 CTGGCAGCTATGCTGC-ATTATTGATGTA
35148164 CTGGC
1 CTGGC
35148169 TGGGTGGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 18 0.64
27 3 0.11
28 7 0.25
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (28 bp):
CTGGCAGCTATGCTGCATTATTGATGTA
Found at i:35148333 original size:33 final size:33
Alignment explanation
Indices: 35148296--35148391 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 33
35148286 GCCCACACTA
* *
35148296 TTACTGTATAGGGCTAAAGCCCAGACTGTTTTG
1 TTACTGTATAGGGCTAAGGCCCAGACTGTTCTG
* *
35148329 TTACTGTATAGGGCTAAGGCCTAGACTGTACTG
1 TTACTGTATAGGGCTAAGGCCCAGACTGTTCTG
* * *
35148362 ATACTGGATAGGGCTTAGGCCCAGACTGTT
1 TTACTGTATAGGGCTAAGGCCCAGACTGTT
35148392 ACTGCATGCA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (33 bp):
TTACTGTATAGGGCTAAGGCCCAGACTGTTCTG
Found at i:35153246 original size:64 final size:62
Alignment explanation
Indices: 35153177--35153375 Score: 163
Period size: 64 Copynumber: 3.1 Consensus size: 62
35153167 TTATCAAAAT
*
35153177 TTTAAAAAAGTGTAAACTTTATTTAGTACTAAAAATTATAATAATATTTTATAATCTTTAGAAA
1 TTTAAAAAAGTGTAAA-TTTATTTAATACTAAAAATTATAATAATATTTTATAAT-TTTAGAAA
* * * * *** * * * * *
35153241 TTTAAAAAAAT-TAATTAATTGTTTACCTA-TAAAAAACCTAA-AA-ACTTAACAATTATCAAAA
1 TTTAAAAAAGTGTAA--ATTTATTTA-ATACTAAAAATTATAATAATATTTTATAATT-TTAGAA
35153302 A
62 A
* *
35153303 TTTTAAAAAGTGTAAAATTTATTTAATACTAAAAATTATAATAATATTCTATAATTTTTAGAAA
1 TTTAAAAAAGTGT-AAATTTATTTAATACTAAAAATTATAATAATATTTTATAA-TTTTAGAAA
35153367 TTTAAAAAA
1 TTTAAAAAA
35153376 ATTAATTAAT
Statistics
Matches: 98, Mismatches: 27, Indels: 20
0.68 0.19 0.14
Matches are distributed among these distances:
61 3 0.03
62 37 0.38
63 8 0.08
64 45 0.46
65 5 0.05
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (62 bp):
TTTAAAAAAGTGTAAATTTATTTAATACTAAAAATTATAATAATATTTTATAATTTTAGAAA
Found at i:35153288 original size:126 final size:126
Alignment explanation
Indices: 35153145--35153391 Score: 424
Period size: 126 Copynumber: 2.0 Consensus size: 126
35153135 TAATTTTTTA
* * *
35153145 AAAAAATCTAAAAACTTAAAAATTATC-AAAATTTTAAAAAAGTGTAAACTTTATTTAGTACTAA
1 AAAAAACCTAAAAACTTAAAAATTATCAAAAATTTT-AAAAAGTGTAAAATTTATTTAATACTAA
*
35153209 AAATTATAATAATATTTTATAATCTTTAGAAATTTAAAAAAATTAATTAATTGTTTACCTAT
65 AAATTATAATAATATTCTATAATCTTTAGAAATTTAAAAAAATTAATTAATTGTTTACCTAT
*
35153271 AAAAAACCTAAAAACTTAACAATTATCAAAAATTTTAAAAAGTGTAAAATTTATTTAATACTAAA
1 AAAAAACCTAAAAACTTAAAAATTATCAAAAATTTTAAAAAGTGTAAAATTTATTTAATACTAAA
*
35153336 AATTATAATAATATTCTATAATTTTTAGAAATTTAAAAAAATTAATTAATTGTTTA
66 AATTATAATAATATTCTATAATCTTTAGAAATTTAAAAAAATTAATTAATTGTTTA
35153392 AGTAAACACA
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
126 106 0.93
127 8 0.07
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (126 bp):
AAAAAACCTAAAAACTTAAAAATTATCAAAAATTTTAAAAAGTGTAAAATTTATTTAATACTAAA
AATTATAATAATATTCTATAATCTTTAGAAATTTAAAAAAATTAATTAATTGTTTACCTAT
Found at i:35153908 original size:42 final size:43
Alignment explanation
Indices: 35153833--35153970 Score: 156
Period size: 44 Copynumber: 3.2 Consensus size: 43
35153823 TTTCATCCAA
* *
35153833 TCTTACATGTAATCAAATATCGATGCCACTGTCCCAGATAG-GG
1 TCTTACATGAAATCAAATATCGATGCCAATGTCCCAGA-AGTGG
* * *
35153876 TCTTACACGAAATCAGATA-CGATGCCAATGTCCCAGACGTGG
1 TCTTACATGAAATCAAATATCGATGCCAATGTCCCAGAAGTGG
* * *
35153918 TCTTACATGCAAAACATAA-ATCGATGCCAATGTCTCAGACGTGG
1 TCTTACATG-AAATCA-AATATCGATGCCAATGTCCCAGAAGTGG
35153962 TCTTACATG
1 TCTTACATG
35153971 CAGAACAGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 27 0.33
43 22 0.27
44 32 0.39
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
TCTTACATGAAATCAAATATCGATGCCAATGTCCCAGAAGTGG
Found at i:35161138 original size:27 final size:29
Alignment explanation
Indices: 35161090--35161144 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
35161080 TATTTAATTT
35161090 ACAATTTAGTCCTTCAAAAGCTC-ATTTTC
1 ACAATTTAGTCC-TCAAAAGCTCGATTTTC
35161119 ACAATTTAGT-C-CAAATAGCTCGATTT
1 ACAATTTAGTCCTCAAA-AGCTCGATTT
35161145 CATCAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 4 0.17
27 5 0.21
28 5 0.21
29 10 0.42
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (29 bp):
ACAATTTAGTCCTCAAAAGCTCGATTTTC
Found at i:35161146 original size:27 final size:27
Alignment explanation
Indices: 35161086--35161146 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 27
35161076 AACATATTTA
35161086 ATTT-ACAATTTAGTCCTTCAAAAGCTC
1 ATTTCACAATTTAGTCC-TCAAAAGCTC
35161113 ATTTTCACAATTTAGT-C-CAAATAGCTC
1 A-TTTCACAATTTAGTCCTCAAA-AGCTC
35161140 GATTTCA
1 -ATTTCA
35161147 TCAAAAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 4 0.13
27 11 0.37
28 5 0.17
29 10 0.33
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (27 bp):
ATTTCACAATTTAGTCCTCAAAAGCTC
Found at i:35179207 original size:27 final size:27
Alignment explanation
Indices: 35179168--35179247 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
35179158 TAGCCGTGAG
*
35179168 TTTGACTATGTAGCACTAAGTGTGCGA
1 TTTGATTATGTAGCACTAAGTGTGCGA
*
35179195 TTTGATTACGTAGCACTAAGTGTGCGA
1 TTTGATTATGTAGCACTAAGTGTGCGA
* * *
35179222 GTTGATTATATAGCACTGAGTGTGCG
1 TTTGATTATGTAGCACTAAGTGTGCG
35179248 GACTCAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (27 bp):
TTTGATTATGTAGCACTAAGTGTGCGA
Found at i:35188812 original size:18 final size:18
Alignment explanation
Indices: 35188789--35188852 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
35188779 GGACTGAACC
*
35188789 TGGCGAACTCTCCCATAT
1 TGGCGAACTCTCCAATAT
35188807 TGGCGAA-TCATCCAATAT
1 TGGCGAACTC-TCCAATAT
** *
35188825 TGGTAAACTCTACAATAT
1 TGGCGAACTCTCCAATAT
*
35188843 TGGCGGACTC
1 TGGCGAACTC
35188853 ACAAGAAGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 2 0.05
18 33 0.89
19 2 0.05
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (18 bp):
TGGCGAACTCTCCAATAT
Found at i:35189011 original size:24 final size:24
Alignment explanation
Indices: 35188959--35189011 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
35188949 AAGATTTAAA
*
35188959 ATTTATTAGCATAATATATTTGTT
1 ATTTCTTAGCATAATATATTTGTT
*
35188983 ATTTCTTAGCATACA-ATCTTTGTT
1 ATTTCTTAGCATA-ATATATTTGTT
35189007 ATTTC
1 ATTTC
35189012 CTTATGTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (24 bp):
ATTTCTTAGCATAATATATTTGTT
Found at i:35190009 original size:20 final size:20
Alignment explanation
Indices: 35189964--35190009 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
35189954 GGTCATGGAT
*
35189964 ATATTATGCTGAAATTAGAA
1 ATATTATGCTGAAAATAGAA
*
35189984 AT-TTATGGTGGAAAATA-AA
1 ATATTATGCT-GAAAATAGAA
35190003 ATATTAT
1 ATATTAT
35190010 TGATAGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (20 bp):
ATATTATGCTGAAAATAGAA
Found at i:35190094 original size:20 final size:20
Alignment explanation
Indices: 35190069--35190107 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35190059 AGAGACTAAA
*
35190069 ATGAAAAGTTATAAAATTTG
1 ATGAAAAATTATAAAATTTG
*
35190089 ATGAAAAATTCTAAAATTT
1 ATGAAAAATTATAAAATTT
35190108 TAGGAATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:35190783 original size:56 final size:58
Alignment explanation
Indices: 35190651--35190799 Score: 175
Period size: 56 Copynumber: 2.6 Consensus size: 58
35190641 CATTGACCTT
* *
35190651 GTTATAAAAAGGATTTAGCCCAGA-TGGGTAATCCTAATGTAATACCTCTCGAGCATAC
1 GTTATATAAAGGATTTAGCCTAGACT-GGTAATCCTAATGTAATACCTCTCGAGCATAC
* * *
35190709 GTTATGAT-TAGGGTTTAGCCTGGACTGGTAATCCTAAT-TGAACT-CC-CT-GAGCATAC
1 GTTAT-ATAAAGGATTTAGCCTAGACTGGTAATCCTAATGT-AA-TACCTCTCGAGCATAC
35190765 GTTATATAAAGGATTTAGCCTAGACTGGTAATCCT
1 GTTATATAAAGGATTTAGCCTAGACTGGTAATCCT
35190800 GTTAAACGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
55 2 0.03
56 37 0.47
57 3 0.04
58 33 0.42
59 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (58 bp):
GTTATATAAAGGATTTAGCCTAGACTGGTAATCCTAATGTAATACCTCTCGAGCATAC
Found at i:35197725 original size:20 final size:21
Alignment explanation
Indices: 35197679--35197725 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
35197669 GGTCATGGAT
*
35197679 ATATTATGCTGGAAATTAGAA
1 ATATTATGCTGGAAAATAGAA
*
35197700 AT-TTATGGTGGAAAAT-GAA
1 ATATTATGCTGGAAAATAGAA
35197719 ATATTAT
1 ATATTAT
35197726 TGATAGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 16 0.70
21 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (21 bp):
ATATTATGCTGGAAAATAGAA
Found at i:35199325 original size:518 final size:517
Alignment explanation
Indices: 35198349--35199380 Score: 1654
Period size: 518 Copynumber: 2.0 Consensus size: 517
35198339 AGCTTGGACA
* * *
35198349 AGTAACCCCATTGACCTTGTTATAAAAAGGATTTAGCCCAGATGGGTAATCCTAATGTAATACCT
1 AGTAACCCCATTAACCTTGTTATAAAAAGGATTTAGCCCAGACGGGTAATCCCAATGTAATACCT
* *
35198414 CTCGAGCATACGTTATGATTAGGGTTTAGCTTGGACCGGTAATCCTAATTGAGCTCCTTGAGCAT
66 CTCGAGCATACGTTATGATTAGGGTTTAGCCTGGACCGGTAATCCTAATTGAGCTCCCTGAGCAT
*
35198479 ACGTTATATAAAGGATTTAGCCTAGACTGGTAATCCTGTTAAACGATATGTGGCTCGAGAGAGTG
131 ACGTTATATAAAGGATTTAGCCTAGACTAGTAATCCTGTTAAACGATATGTGGCTCGAGAGAGTG
* *
35198544 CTTCTTAGCTAAGTGCCCTAATGGGTACCCCTGACTAAGAAATTGAAGAATGGTTGAATTGTACA
196 CTTCTTAGCTAAGTGCCCTAATGGGTACCCCTGAATAAGAAATTGAAGAATGGTTAAATTGTACA
* * * * * * *
35198609 CTTTGTGTGTACTACTTGAGCATTCATTGGAATTCAATGATTCAAATGACATATAACTTTTGATT
261 CTTCGGGTGTACCACTTGAGCATTCATTGGAATTCAATGATTCAAAGGACATAAAACTCTTGACT
*
35198674 TGGCATGAAAACCTTGAGATGAAATAGTAATGACTAGATAGAATATTGCTTGATGAGCTCATTTA
326 TGGCATGAAAACCTTGAGATGAAATAGTAATGACTAGATAGAATATTGCTTGATGAGCTCATCTA
* * *
35198739 TGTTACTTGATTTATATAAAGATTTCAGGGACTGACATGTTTGATTAAATGTATGTGCTTAGGCA
391 TGTTACTTGATTTATATAAAGATTTCAGGGACTAACATATTTGATTAAATGTATATGCTTAGGCA
* *
35198804 AATTTAGCCAAATGGATGGAAACATGATATTGTATGTTTAGATTTAATAATCAATATTGACG
456 AATTTAACCAAATGGATGGAAACATGATATTGTATGTTTAGATTTAATAATCAAGATTGACG
* * *
35198866 AGTAACCCCATTAACCTTGTTATAAAAAGTATTTAG-CCTGAACGGGTAATCCCAGTGTAATACC
1 AGTAACCCCATTAACCTTGTTATAAAAAGGATTTAGCCCAG-ACGGGTAATCCCAATGTAATACC
* * **
35198930 TTTCGAGCATACGTTATGGTTAGGGTTTAGCCTGGATTGGTAATCCTAATTGAGCTTCCCTGAGC
65 TCTCGAGCATACGTTATGATTAGGGTTTAGCCTGGACCGGTAATCCTAATTGAGC-TCCCTGAGC
* * *
35198995 ATACGTTATATAAAGGATTTAGCCTGGACTAGTAATCCTGTTAAATGATATGTGGCTCGAGATAG
129 ATACGTTATATAAAGGATTTAGCCTAGACTAGTAATCCTGTTAAACGATATGTGGCTCGAGAGAG
* * * * *
35199060 TGTTTCTTTGTTAAGTGCCCTAATGGGTAGCCCTGAATAAGAAATTGATGAATGGTTAAATTGTA
194 TGCTTCTTAGCTAAGTGCCCTAATGGGTACCCCTGAATAAGAAATTGAAGAATGGTTAAATTGTA
35199125 CACTTCGGGTGTACCACTTGAGCATTCATTGGAATTCAATGATTCAAAGGACATAAAACTCTTGA
259 CACTTCGGGTGTACCACTTGAGCATTCATTGGAATTCAATGATTCAAAGGACATAAAACTCTTGA
35199190 CTTGGCATGAAAACCTTGAGATGAAATAGTAATGACTAGATAGAATATTGCTTGATGAGCTCATC
324 CTTGGCATGAAAACCTTGAGATGAAATAGTAATGACTAGATAGAATATTGCTTGATGAGCTCATC
* * * *
35199255 TATGTTGCTTGATTTATATGAAGATTT-TGGTGACTAACATATTTGATTGAATGTATATGCTTAG
389 TATGTTACTTGATTTATATAAAGATTTCAGG-GACTAACATATTTGATTAAATGTATATGCTTAG
*
35199319 GCAAATTTAACCAAATGGATGGGAACATGATATTGTATGTTTAGATTTAATAATCAAGATTG
453 GCAAATTTAACCAAATGGATGGAAACATGATATTGTATGTTTAGATTTAATAATCAAGATTG
35199381 GTAAGTTTAA
Statistics
Matches: 471, Mismatches: 41, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
516 3 0.01
517 106 0.23
518 362 0.77
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (517 bp):
AGTAACCCCATTAACCTTGTTATAAAAAGGATTTAGCCCAGACGGGTAATCCCAATGTAATACCT
CTCGAGCATACGTTATGATTAGGGTTTAGCCTGGACCGGTAATCCTAATTGAGCTCCCTGAGCAT
ACGTTATATAAAGGATTTAGCCTAGACTAGTAATCCTGTTAAACGATATGTGGCTCGAGAGAGTG
CTTCTTAGCTAAGTGCCCTAATGGGTACCCCTGAATAAGAAATTGAAGAATGGTTAAATTGTACA
CTTCGGGTGTACCACTTGAGCATTCATTGGAATTCAATGATTCAAAGGACATAAAACTCTTGACT
TGGCATGAAAACCTTGAGATGAAATAGTAATGACTAGATAGAATATTGCTTGATGAGCTCATCTA
TGTTACTTGATTTATATAAAGATTTCAGGGACTAACATATTTGATTAAATGTATATGCTTAGGCA
AATTTAACCAAATGGATGGAAACATGATATTGTATGTTTAGATTTAATAATCAAGATTGACG
Found at i:35204609 original size:24 final size:24
Alignment explanation
Indices: 35204580--35204626 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35204570 CATTTTTAGA
35204580 ATATTTAG-AATTTATTAGCATAAT
1 ATATTT-GTAATTTATTAGCATAAT
*
35204604 ATATTTGTTATTTATTAGCATAA
1 ATATTTGTAATTTATTAGCATAA
35204627 AATCTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
ATATTTGTAATTTATTAGCATAAT
Found at i:35210704 original size:96 final size:96
Alignment explanation
Indices: 35210540--35210714 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 96
35210530 AGAGGGTTGT
* * *
35210540 CGATGCCATGTCCCAAACATGGTCTTACACCAGCTCTCGTCTCAATGTCGATGCCATGTCCCAAA
1 CGATGCCATGTCCCAAACATGGTCTTACACCAGCTCTCATATCAATGCCGATGCCATGTCCCAAA
35210605 CATGGTCTTACACTAGCTCTCACAACATCGC
66 CATGGTCTTACACTAGCTCTCACAACATCGC
* ** * *
35210636 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATC-GTGGCCGATGCCATGTCCCAG
1 CGATGCCATGTCCCAAACATGGTCTTACACCAGCTCTCATATCAAT-GCCGATGCCATGTCCCAA
35210700 ACATGGTCTTACACT
65 ACATGGTCTTACACT
35210715 GGCACACATA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
95 1 0.01
96 69 0.99
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (96 bp):
CGATGCCATGTCCCAAACATGGTCTTACACCAGCTCTCATATCAATGCCGATGCCATGTCCCAAA
CATGGTCTTACACTAGCTCTCACAACATCGC
Found at i:35210717 original size:48 final size:47
Alignment explanation
Indices: 35210540--35210714 Score: 233
Period size: 48 Copynumber: 3.7 Consensus size: 47
35210530 AGAGGGTTGT
* * * *
35210540 CGATGCCATGTCCCAAACATGGTCTTACACCAGCTCTCGTCTCAATGT
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATC-ATGC
* *
35210588 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCACAACATCGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAT-GC
* * *
35210636 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAT-GC
*
35210684 CGATGCCATGTCCCAGACATGGTCTTACACT
1 CGATGCCATGTCCCAAACATGGTCTTACACT
35210715 GGCACACATA
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
47 2 0.02
48 110 0.98
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCATGC
Found at i:35223337 original size:12 final size:12
Alignment explanation
Indices: 35223320--35223360 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
35223310 TTTATCAAAA
35223320 TTAATTAGTTAT
1 TTAATTAGTTAT
* *
35223332 TTAATTA-TAAA
1 TTAATTAGTTAT
35223343 TTAATTAGTTAT
1 TTAATTAGTTAT
35223355 TTAATT
1 TTAATT
35223361 TATCAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (12 bp):
TTAATTAGTTAT
Found at i:35223345 original size:23 final size:23
Alignment explanation
Indices: 35223317--35223360 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
35223307 TAATTTATCA
35223317 AAATTAATTAGTTATTTAATTAT
1 AAATTAATTAGTTATTTAATTAT
35223340 AAATTAATTAGTTATTTAATT
1 AAATTAATTAGTTATTTAATT
35223361 TATCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
AAATTAATTAGTTATTTAATTAT
Found at i:35230089 original size:35 final size:35
Alignment explanation
Indices: 35229920--35230092 Score: 197
Period size: 35 Copynumber: 5.0 Consensus size: 35
35229910 CGATTCACTA
* * * *
35229920 CTCAGTATGGTTAATACCATACCTAAGTTTCACAA
1 CTCAGTATGGATAATACCATACCTACGTTTCATAG
* * *
35229955 CTCGGTATGGAAAATACCATACTTACGTATT-ATAG
1 CTCAGTATGGATAATACCATACCTACGT-TTCATAG
* ** * * *
35229990 CTTAGTATGGAGGATACCATACCTACATCTCATGG
1 CTCAGTATGGATAATACCATACCTACGTTTCATAG
*
35230025 ATCAGTATGGA-AATACCATACCTACGTTTCATAG
1 CTCAGTATGGATAATACCATACCTACGTTTCATAG
35230059 CTCAGTATGGATAATACCATACCTACGTTTCATA
1 CTCAGTATGGATAATACCATACCTACGTTTCATA
35230093 ACTTTGCCAT
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
34 30 0.27
35 81 0.72
36 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (35 bp):
CTCAGTATGGATAATACCATACCTACGTTTCATAG
Found at i:35240702 original size:35 final size:35
Alignment explanation
Indices: 35240623--35240795 Score: 188
Period size: 35 Copynumber: 5.0 Consensus size: 35
35240613 CAATTCGCTA
** * * *
35240623 CTCAGTATGGTTAATACCATACCTACGTTTCACAA
1 CTCAGTATGGAAAATACCATACCTACGTATCATAG
* * *
35240658 CT-TGATATGGAAAATATCATACCTACGTATTATAG
1 CTCAG-TATGGAAAATACCATACCTACGTATCATAG
* ** * *
35240693 CTCGGTATGGAGGATACCATACCTACATCTCATAG
1 CTCAGTATGGAAAATACCATACCTACGTATCATAG
35240728 CTCAGTATGG-AAATACCATACCTACGTATCATAG
1 CTCAGTATGGAAAATACCATACCTACGTATCATAG
* *
35240762 CTCAGTATGGATAATACCATACCTACGTTTCATA
1 CTCAGTATGGAAAATACCATACCTACGTATCATA
35240796 ACTTTGCCAT
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
34 31 0.27
35 81 0.72
36 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (35 bp):
CTCAGTATGGAAAATACCATACCTACGTATCATAG
Found at i:35240795 original size:69 final size:70
Alignment explanation
Indices: 35240623--35240798 Score: 230
Period size: 69 Copynumber: 2.5 Consensus size: 70
35240613 CAATTCGCTA
* * * *
35240623 CTCAGTATGGTTAATACCATACCTACGTTTCACAACTTGATATGGAAAATATCATACCTACGTAT
1 CTCAGTATGGATAATACCATACCTACGTTTCATAACTAGATATGGAAAATACCATACCTACGTAT
*
35240688 TATAG
66 CATAG
* ** * * *
35240693 CTCGGTATGGAGGATACCATACCTACATCTCATAGCTCAG-TATGG-AAATACCATACCTACGTA
1 CTCAGTATGGATAATACCATACCTACGTTTCATAACT-AGATATGGAAAATACCATACCTACGTA
35240756 TCATAG
65 TCATAG
35240762 CTCAGTATGGATAATACCATACCTACGTTTCATAACT
1 CTCAGTATGGATAATACCATACCTACGTTTCATAACT
35240799 TTGCCATGGA
Statistics
Matches: 88, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
69 53 0.60
70 34 0.39
71 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (70 bp):
CTCAGTATGGATAATACCATACCTACGTTTCATAACTAGATATGGAAAATACCATACCTACGTAT
CATAG
Found at i:35251252 original size:2 final size:2
Alignment explanation
Indices: 35251245--35251272 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35251235 AACATAAATC
35251245 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35251273 GGGGGGGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35257971 original size:9 final size:8
Alignment explanation
Indices: 35257941--35257967 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
35257931 TTATCTTTAT
35257941 TTTATAAC
1 TTTATAAC
35257949 TTTATAAC
1 TTTATAAC
35257957 TTTATAAC
1 TTTATAAC
35257965 TTT
1 TTT
35257968 TATATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTATAAC
Found at i:35258737 original size:20 final size:21
Alignment explanation
Indices: 35258692--35258739 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
35258682 AAGATTTAAC
*
35258692 TTTTTTATATATTTTTTAGAA
1 TTTTTTATATATTTTGTAGAA
* *
35258713 GTTTTTATA-ATTTTGTATAA
1 TTTTTTATATATTTTGTAGAA
35258733 TTTTTTA
1 TTTTTTA
35258740 AAAATATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTTTTATATATTTTGTAGAA
Found at i:35258797 original size:10 final size:10
Alignment explanation
Indices: 35258782--35258807 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
35258772 TTGAATTTTA
35258782 AAAATTATTG
1 AAAATTATTG
35258792 AAAATTATTG
1 AAAATTATTG
35258802 AAAATT
1 AAAATT
35258808 TTTTAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (10 bp):
AAAATTATTG
Found at i:35259640 original size:29 final size:28
Alignment explanation
Indices: 35259539--35259648 Score: 68
Period size: 27 Copynumber: 3.8 Consensus size: 28
35259529 TATTATACTA
*
35259539 AAAATTATTAT-AAAATATAAATAATTAC-
1 AAAA-TATTATAAAAATATAAAAAATT-CT
* ** *
35259567 AAAATTTTATAAAGCT-TAGAAAAAAT-T
1 AAAATATTATAAAAATATA-AAAAATTCT
35259594 AAAA-AGTTATAAACAAATATAGAAAAATTCT
1 AAAATA-TTAT-AA-AAATATA-AAAAATTCT
35259625 AAAATATTATAAAAATCATAAAAA
1 AAAATATTATAAAAAT-ATAAAAA
35259649 GAATAAGATA
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
27 15 0.24
28 14 0.22
29 10 0.16
30 14 0.22
31 9 0.14
32 1 0.02
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.30
Consensus pattern (28 bp):
AAAATATTATAAAAATATAAAAAATTCT
Found at i:35259925 original size:28 final size:28
Alignment explanation
Indices: 35259894--35259953 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
35259884 CTATTAAATT
35259894 ATAATTTT-TATATGCCTTATAATTTTTA
1 ATAATTTTCTATATGCCTTAT-ATTTTTA
***
35259922 ATAATTTTCTATATTTTTTATATTTTTA
1 ATAATTTTCTATATGCCTTATATTTTTA
35259950 ATAA
1 ATAA
35259954 GTTAATTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (28 bp):
ATAATTTTCTATATGCCTTATATTTTTA
Found at i:35260995 original size:5 final size:5
Alignment explanation
Indices: 35260985--35261020 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
35260975 AAGCCAAAAG
*
35260985 TATTT TATTT TATTT TATTT TATTT TATTT TGTTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
35261021 CATATAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:35261758 original size:21 final size:20
Alignment explanation
Indices: 35261729--35261774 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 20
35261719 TATACTCAGT
35261729 TTCATCAAACACGTAAAGGATA
1 TTCATCAAACA--TAAAGGATA
35261751 TTCA-CAAACATAAAGGATA
1 TTCATCAAACATAAAGGATA
35261770 TTCAT
1 TTCAT
35261775 GGTTGGGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.57
21 6 0.26
22 4 0.17
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (20 bp):
TTCATCAAACATAAAGGATA
Found at i:35268917 original size:24 final size:23
Alignment explanation
Indices: 35268889--35268947 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
35268879 ATAGCTCGAA
*
35268889 AGAGCATCTCGTTATTAGCCCTCTT
1 AGAGCATCTCGTTAGTAG--CTCTT
* *
35268914 -GAGCTTCCCGTTAGTAGCTCTT
1 AGAGCATCTCGTTAGTAGCTCTT
35268936 CAGAGCATCTCG
1 -AGAGCATCTCG
35268948 ATAGATTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
22 5 0.19
24 22 0.81
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (23 bp):
AGAGCATCTCGTTAGTAGCTCTT
Found at i:35269163 original size:25 final size:24
Alignment explanation
Indices: 35269097--35269163 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
35269087 CTATCCAGAG
35269097 CTTCCCGATATGGTTCTTTGTGAA
1 CTTCCCGATATGGTTCTTTGTGAA
35269121 CTTCCCGATATGGTTCTTTGTGAA
1 CTTCCCGATATGGTTCTTTGTGAA
* *
35269145 CTTCCTGATTATGGCTCTT
1 CTTCCCGA-TATGGTTCTT
35269164 ATGAGCTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 31 0.77
25 9 0.22
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (24 bp):
CTTCCCGATATGGTTCTTTGTGAA
Found at i:35279430 original size:29 final size:31
Alignment explanation
Indices: 35279380--35279445 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
35279370 ACAACTTAAG
* * **
35279380 AATTAATTTAAGTTTTTGAATT-ATT-AATT
1 AATTAAATGAAGTTTTAAAATTAATTAAATT
35279409 AATTAAATGAAGTTTTAAAATTGAATTAAATT
1 AATTAAATGAAGTTTTAAAATT-AATTAAATT
35279441 AATTA
1 AATTA
35279446 TTCATTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 18 0.60
31 3 0.10
32 9 0.30
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (31 bp):
AATTAAATGAAGTTTTAAAATTAATTAAATT
Found at i:35282592 original size:69 final size:70
Alignment explanation
Indices: 35282462--35282592 Score: 210
Period size: 69 Copynumber: 1.9 Consensus size: 70
35282452 GTTTATTACC
* * * * *
35282462 AATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTACT
1 AATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTACT
35282527 TAGTT
66 TAGTT
35282532 AATTAATATGCTGCTATAATACT-TAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
1 AATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
35282593 GTTATGTGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
69 36 0.64
70 20 0.36
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (70 bp):
AATTAATATGCTGCTATAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTACT
TAGTT
Found at i:35283579 original size:118 final size:117
Alignment explanation
Indices: 35283338--35283601 Score: 348
Period size: 118 Copynumber: 2.2 Consensus size: 117
35283328 ATATTTGATG
* * *
35283338 TATATCCGGACTTAAGGTCCGCAGGCTTCGTGCTAGAATTGTATCCGGACTTAAGGTCTACAGGC
1 TATATCCGGACTTAAGGTCCGCAGGCTTCATGCTAGAATTGTATCCGGACTTAAGATCCACAGGC
* * * * * * *
35283403 TTCGTGCTGGAATTGTATCCTGACTTAAGGTCCGCAGGCTTCGTGCTGGAAT
66 TTCGTGCTGGAACTATATCCGGACTTAAGGTCCACAAGCTTCGTACTGGAAC
* * ** * *
35283455 TGTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGGAATTGTATCCGGACTTAAGATCCGCAGG
1 TATATCCGGACTT-AAGGTCCGCAGGCTTCATGCTAGAATTGTATCCGGACTTAAGATCCACAGG
* *
35283520 CTTCGTGCTGGTACTATATCCGGACTTAAGGTCCACAAGCTTCGTACTGGTAC
65 CTTCGTGCTGGAACTATATCCGGACTTAAGGTCCACAAGCTTCGTACTGGAAC
*
35283573 TATATCCAGACTTAAGGTCCGCAGGCTTC
1 TATATCCGGACTTAAGGTCCGCAGGCTTC
35283602 GTACTGGTAC
Statistics
Matches: 123, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
117 25 0.20
118 98 0.80
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (117 bp):
TATATCCGGACTTAAGGTCCGCAGGCTTCATGCTAGAATTGTATCCGGACTTAAGATCCACAGGC
TTCGTGCTGGAACTATATCCGGACTTAAGGTCCACAAGCTTCGTACTGGAAC
Found at i:35283612 original size:39 final size:39
Alignment explanation
Indices: 35283340--35283608 Score: 349
Period size: 39 Copynumber: 6.9 Consensus size: 39
35283330 ATTTGATGTA
*
35283340 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTAGAATTG
1 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
**
35283379 TATCCGGACTTAAGGTCTACAGGCTTCGTGCTGGAATTG
1 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
*
35283418 TATCCTGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
1 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
* ** *
35283457 TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGGAATTG
1 TATCCGGACTT-AAGGTCCGCAGGCTTCGTGCTGGAATTG
* * * *
35283497 TATCCGGACTTAAGATCCGCAGGCTTCGTGCTGGTACTA
1 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
* * * * * *
35283536 TATCCGGACTTAAGGTCCACAAGCTTCGTACTGGTACTA
1 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
* *
35283575 TATCCAGACTTAAGGTCCGCAGGCTTCGTACTGG
1 TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGG
35283609 TACTGTAACA
Statistics
Matches: 205, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 170 0.83
40 35 0.17
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (39 bp):
TATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAATTG
Found at i:35284362 original size:31 final size:31
Alignment explanation
Indices: 35284321--35284384 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
35284311 CCTTTTCATA
*
35284321 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
35284352 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
35284383 TT
1 TT
35284385 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:35284629 original size:23 final size:24
Alignment explanation
Indices: 35284578--35284743 Score: 214
Period size: 23 Copynumber: 7.0 Consensus size: 24
35284568 GCTTTATCAT
*
35284578 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
35284603 ATAACTGGGGCA-AAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
35284626 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* * *
35284649 ATAATTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
35284673 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
35284697 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
35284720 ATAATTGGGGCATAAGCCCATTTT
1 ATAACTGGGGCATAAGCCC-TTTT
35284744 CACTTCCTCC
Statistics
Matches: 126, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
23 58 0.46
24 57 0.45
25 11 0.09
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:35284677 original size:47 final size:47
Alignment explanation
Indices: 35284578--35284743 Score: 203
Period size: 47 Copynumber: 3.5 Consensus size: 47
35284568 GCTTTATCAT
* * *
35284578 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAGCCCTTTTT
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCTAAGCCCTTTTA
* *
35284626 ATAACTGGGGCATAAGCCC-TTTAATAATTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGC-TAAGCCCTTTTA
*
35284673 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGC-TAAGCCCTTTTA
*
35284720 ATAATTGGGGCATAAGCCCATTTT
1 ATAACTGGGGCATAAGCCC-TTTT
35284744 CACTTCCTCC
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
46 14 0.13
47 55 0.52
48 36 0.34
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCTAAGCCCTTTTA
Found at i:35284703 original size:71 final size:70
Alignment explanation
Indices: 35284592--35284743 Score: 250
Period size: 71 Copynumber: 2.1 Consensus size: 70
35284582 CTGGAGGCCT
*
35284592 AGCCTCTTTTAATAACTGGGGCAAAGCCCTTTTTATAACTGGGGCATAAGCCCTTTAATAATTGG
1 AGCC-CTTTTAATAACTGGGGCAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAATTGG
*
35284657 GGCGTA
65 GGCATA
*
35284663 AGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAATTGG
1 AGCCCTTTTAATAACTGGGGCA-AAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAATTGG
35284728 GGCATA
65 GGCATA
35284734 AGCCCATTTT
1 AGCCC-TTTT
35284744 CACTTCCTCC
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
70 17 0.22
71 55 0.72
72 4 0.05
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (70 bp):
AGCCCTTTTAATAACTGGGGCAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAATTGGG
GCATA
Found at i:35284838 original size:20 final size:20
Alignment explanation
Indices: 35284793--35284831 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35284783 TATGAATACA
35284793 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
35284813 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
35284832 AGCATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:35288512 original size:68 final size:66
Alignment explanation
Indices: 35288434--35288632 Score: 193
Period size: 68 Copynumber: 3.0 Consensus size: 66
35288424 ATTTTAACAA
*
35288434 ATTTAATATTAAATTTAATTTAATAGTTATCTTGATAGTATTTTATTAATTTAATATTAAAGTGA
1 ATTTAATATTAAATTTAATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAAAG-GA
35288499 TT
65 TT
* *
35288501 ATCTTAATATTAAATTAAATTTAATATTTATATT-ATAGGTAAATATTTTATTAATTT-A-A-T-
1 AT-TTAATATTAAATTTAATTTAATATTTATCTTGATA-G----TATTTTATTAATTTAATATTA
35288561 AAGG---
60 AAGGATT
* *
35288565 -TTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAA-TTATATATTAAAGC
1 ATTTAATATTAAATTTAATTTAATATTTATCTTGAT-AGTATTTTATTAATTTA-ATATTAAAG-
35288628 GATT
63 GATT
35288632 A
1 A
35288633 AGTTTAATCA
Statistics
Matches: 107, Mismatches: 7, Indels: 35
0.72 0.05 0.23
Matches are distributed among these distances:
58 2 0.02
59 10 0.09
60 1 0.01
61 1 0.01
62 29 0.27
63 7 0.07
64 2 0.02
67 6 0.06
68 32 0.30
69 1 0.01
70 1 0.01
71 1 0.01
72 14 0.13
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (66 bp):
ATTTAATATTAAATTTAATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTAAAGGAT
T
Found at i:35289211 original size:15 final size:15
Alignment explanation
Indices: 35289191--35289220 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35289181 TAGATTCTCC
35289191 TATCTCTCCCTATAA
1 TATCTCTCCCTATAA
*
35289206 TATCTCTCCTTATAA
1 TATCTCTCCCTATAA
35289221 ATAGATAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (15 bp):
TATCTCTCCCTATAA
Found at i:35289710 original size:49 final size:49
Alignment explanation
Indices: 35289638--35289731 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
35289628 TGGTATCGAG
*
35289638 CCAAGGTTGAGCTATGTTTATAGTATAAACCAATACCGAATTTTCTATC
1 CCAAGGTTGAGCTATGTCTATAGTATAAACCAATACCGAATTTTCTATC
* *
35289687 CCAAGGTTGAGCTATGTCTATAGTATAAACCGATACTGAATTTTC
1 CCAAGGTTGAGCTATGTCTATAGTATAAACCAATACCGAATTTTC
35289732 GATCTTCTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (49 bp):
CCAAGGTTGAGCTATGTCTATAGTATAAACCAATACCGAATTTTCTATC
Found at i:35293528 original size:58 final size:58
Alignment explanation
Indices: 35293463--35293576 Score: 219
Period size: 58 Copynumber: 2.0 Consensus size: 58
35293453 TGGATTAGCT
*
35293463 GGAAGCTCACATTATCTAGCCATTTGGTAGTTTTTGTATTTTGCTCTTGGGATGTGCA
1 GGAAGCTCACACTATCTAGCCATTTGGTAGTTTTTGTATTTTGCTCTTGGGATGTGCA
35293521 GGAAGCTCACACTATCTAGCCATTTGGTAGTTTTTGTATTTTGCTCTTGGGATGTG
1 GGAAGCTCACACTATCTAGCCATTTGGTAGTTTTTGTATTTTGCTCTTGGGATGTG
35293577 GCATGTATAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (58 bp):
GGAAGCTCACACTATCTAGCCATTTGGTAGTTTTTGTATTTTGCTCTTGGGATGTGCA
Found at i:35298401 original size:20 final size:20
Alignment explanation
Indices: 35298378--35298416 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35298368 TAAGATTTAG
35298378 AAAACAAAGTTAAGGGTTTC
1 AAAACAAAGTTAAGGGTTTC
* **
35298398 AAAACTATTTTAAGGGTTT
1 AAAACAAAGTTAAGGGTTT
35298417 TCATGTTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (20 bp):
AAAACAAAGTTAAGGGTTTC
Found at i:35300988 original size:23 final size:23
Alignment explanation
Indices: 35300958--35301008 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
35300948 TACTATTTCA
*
35300958 TATTTAAGCTTTATTCACCGAAG
1 TATTTAAGCTTTATTCACCAAAG
35300981 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
35301004 TATTT
1 TATTT
35301009 CAAATATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (23 bp):
TATTTAAGCTTTATTCACCAAAG
Found at i:35301704 original size:42 final size:42
Alignment explanation
Indices: 35301654--35301768 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
35301644 CTTCATTTTC
** * * *
35301654 TCGATGCCATAGTTCAACTATGGTCTTACATATCTTCAGATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGAT-A
*
35301697 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
35301738 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
35301769 GAATCACATA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.03
42 62 0.95
43 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCAGATA
Found at i:35301842 original size:47 final size:47
Alignment explanation
Indices: 35301739--35302049 Score: 543
Period size: 47 Copynumber: 6.6 Consensus size: 47
35301729 ATTCATATAT
* * * * * * *
35301739 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
*
35301785 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
35301832 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
35301879 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
35301926 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
35301973 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
35302020 CGATGCCATATCCCAGATATGGTCTTATAC
1 CGATGCCATATCCCAGATATGGTCTTATAC
35302050 GAAAATCACT
Statistics
Matches: 255, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
46 26 0.10
47 229 0.90
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
Found at i:35302103 original size:31 final size:31
Alignment explanation
Indices: 35302068--35302185 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
35302058 CTTGTCACTT
*
35302068 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
35302099 GTAGCC-AGGGCTACCATTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
35302130 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
35302161 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
35302186 TGTTATTTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
30 1 0.01
31 77 0.99
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:35302266 original size:50 final size:50
Alignment explanation
Indices: 35302161--35303037 Score: 1682
Period size: 50 Copynumber: 17.5 Consensus size: 50
35302151 CACTGATCAG
* * * * *
35302161 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCCTTGATCAGATAAGT
35302212 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302262 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302312 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302362 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302412 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302462 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302512 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302562 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302612 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302662 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302712 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302762 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302812 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302862 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35302912 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
* *
35302962 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
35303012 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
35303038 GTTGCCATGG
Statistics
Matches: 818, Mismatches: 8, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
50 794 0.97
51 24 0.03
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
Found at i:35314735 original size:21 final size:21
Alignment explanation
Indices: 35314711--35314758 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
35314701 AACTATTATT
35314711 ATTATTATTATTATATT-TTAA
1 ATTATTATTATTAT-TTCTTAA
*
35314732 ATTATAATTATTATTTCTTAA
1 ATTATTATTATTATTTCTTAA
35314753 A-TATTA
1 ATTATTA
35314759 AGTAAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTATTATTATTTCTTAA
Found at i:35318565 original size:21 final size:21
Alignment explanation
Indices: 35318541--35318582 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
35318531 TTGTCAAATC
35318541 ACCCCAAAATGGATAACAAAA
1 ACCCCAAAATGGATAACAAAA
35318562 ACCCCAAAATGGATAACAAAA
1 ACCCCAAAATGGATAACAAAA
35318583 TTAACGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.24, G:0.10, T:0.10
Consensus pattern (21 bp):
ACCCCAAAATGGATAACAAAA
Found at i:35328557 original size:17 final size:18
Alignment explanation
Indices: 35328525--35328559 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35328515 CGATGTGATC
35328525 TGCCTGTGTGGGCCCACA
1 TGCCTGTGTGGGCCCACA
35328543 TGCCTGTGT-GGCCCACA
1 TGCCTGTGTGGGCCCACA
35328560 CGGCCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.11, C:0.34, G:0.31, T:0.23
Consensus pattern (18 bp):
TGCCTGTGTGGGCCCACA
Found at i:35342431 original size:61 final size:61
Alignment explanation
Indices: 35342358--35342477 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
35342348 CAGATTTTTC
35342358 TTTCTTTCTTATGCCGCCTCATCCATTCCCTTTTGGCTAATTTGCCTTTTAAGTCCTCCTT
1 TTTCTTTCTTATGCCGCCTCATCCATTCCCTTTTGGCTAATTTGCCTTTTAAGTCCTCCTT
35342419 TTTCTTGT-TTATGCCGCCTCATCCATTCCCTTTTGGCTAATTTGCCTTTTAAGTCCTCC
1 TTTCTT-TCTTATGCCGCCTCATCCATTCCCTTTTGGCTAATTTGCCTTTTAAGTCCTCC
35342478 CTCATTTAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 57 0.98
62 1 0.02
ACGTcount: A:0.12, C:0.31, G:0.11, T:0.47
Consensus pattern (61 bp):
TTTCTTTCTTATGCCGCCTCATCCATTCCCTTTTGGCTAATTTGCCTTTTAAGTCCTCCTT
Found at i:35343982 original size:15 final size:15
Alignment explanation
Indices: 35343953--35344002 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
35343943 CAAAGATAAG
*
35343953 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
35343967 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
35343982 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
35343997 AAGAAA
1 AAGAAA
35344003 CCCAAGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:35344011 original size:15 final size:15
Alignment explanation
Indices: 35343964--35344011 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
35343954 AGAAAACCGA
35343964 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
35343978 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
35343994 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
35344009 ATA
1 ATA
35344012 CGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:35347401 original size:52 final size:49
Alignment explanation
Indices: 35347218--35347410 Score: 200
Period size: 47 Copynumber: 4.0 Consensus size: 49
35347208 TGCACATAGT
* ** * *
35347218 CACATATCACA-TACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACACT-CCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* * *
35347266 CACATATCACACT--GATGCCATATCCCAGATATGGTCTTATACAGTAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
35347313 CACATATCACA--CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
* *
35347360 CACATATCACATTTCTCCGAAGCCATAGCCCAGCTATGGTCTTATACGGAA
1 CACATATCACA---CTCCGATGCCATAGCCCAGATATGGTCTTATACGGAA
35347411 ATCACATTTC
Statistics
Matches: 122, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
46 25 0.20
47 54 0.44
48 11 0.09
49 1 0.01
52 31 0.25
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
CACATATCACACTCCGATGCCATAGCCCAGATATGGTCTTATACGGAAG
Found at i:35354545 original size:48 final size:48
Alignment explanation
Indices: 35354493--35354588 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
35354483 GGATCAATTG
35354493 ATGACATGAAAAGTACCTTAGGGTATCTATTTACCCTTGGATCAGCTA
1 ATGACATGAAAAGTACCTTAGGGTATCTATTTACCCTTGGATCAGCTA
35354541 ATGACATGAAAAGTACCTTAGGGTATCTATTTACCCTTGGATCAGCTA
1 ATGACATGAAAAGTACCTTAGGGTATCTATTTACCCTTGGATCAGCTA
35354589 TTTTCTGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (48 bp):
ATGACATGAAAAGTACCTTAGGGTATCTATTTACCCTTGGATCAGCTA
Found at i:35355573 original size:10 final size:10
Alignment explanation
Indices: 35355558--35355582 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35355548 TTGACCTCTA
35355558 AAATTTAACC
1 AAATTTAACC
35355568 AAATTTAACC
1 AAATTTAACC
35355578 AAATT
1 AAATT
35355583 AGATATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTTAACC
Found at i:35357882 original size:15 final size:15
Alignment explanation
Indices: 35357862--35357892 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35357852 ATTCATTTTA
35357862 ATTCTTTATGTATTT
1 ATTCTTTATGTATTT
35357877 ATTCTTTATGTATTT
1 ATTCTTTATGTATTT
35357892 A
1 A
35357893 CTTGTTAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (15 bp):
ATTCTTTATGTATTT
Found at i:35358214 original size:12 final size:12
Alignment explanation
Indices: 35358170--35358216 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
35358160 TATTTTGTCA
35358170 TTATTATTATT-T
1 TTATT-TTATTAT
*
35358182 TTATCATTATTAT
1 TTAT-TTTATTAT
*
35358195 TTACTTTATTAT
1 TTATTTTATTAT
35358207 TTATTTTATT
1 TTATTTTATT
35358217 TTTCTTTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 25 0.86
13 4 0.14
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTTTATTAT
Found at i:35358307 original size:30 final size:30
Alignment explanation
Indices: 35358271--35358329 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
35358261 TGATTATCGA
35358271 CATTATGTGCATTATGAAATATTCTATTAC
1 CATTATGTGCATTATGAAATATTCTATTAC
*
35358301 CATTATGTGCATTATGAAATGTTCTATTA
1 CATTATGTGCATTATGAAATATTCTATTA
35358330 GTAATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (30 bp):
CATTATGTGCATTATGAAATATTCTATTAC
Found at i:35361797 original size:42 final size:42
Alignment explanation
Indices: 35361750--35361909 Score: 178
Period size: 42 Copynumber: 3.6 Consensus size: 42
35361740 GCATCAGTGA
* *
35361750 GATATGTGATTACGTGTAAGACCACAGCTGGGCTATGGCATC
1 GATATGTGAATACGTGTAAGACCATAGCTGGGCTATGGCATC
*
35361792 GATATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCTTC
1 GATATGTG--A----A-TACGTGTAAGACCATAGCTGGGCTATGGCATC
* *
35361841 GATATGTGAATATGTGTGAGACCATAGCTGGGCTATGGCATC
1 GATATGTGAATACGTGTAAGACCATAGCTGGGCTATGGCATC
* *
35361883 -ATTATGTGAAGATGTGTAAGACCATAG
1 GA-TATGTGAATACGTGTAAGACCATAG
35361910 TTGAACTATG
Statistics
Matches: 102, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
41 1 0.01
42 60 0.59
43 1 0.01
44 1 0.01
47 1 0.01
49 38 0.37
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (42 bp):
GATATGTGAATACGTGTAAGACCATAGCTGGGCTATGGCATC
Found at i:35361820 original size:49 final size:49
Alignment explanation
Indices: 35361598--35361856 Score: 240
Period size: 47 Copynumber: 5.2 Consensus size: 49
35361588 CCATGGCAAC
* * * *
35361598 ATGTGATATGAGATTTCCGTATAAGACTATAGCTGGGCTATGGCATCAGAGAG
1 ATGTGATATGTGA-TTACGTATAAGACCATAGCTGGGCTATGGCATC---GAT
* * * * *
35361651 ATGTGATTATGTGCTTCCGTATAATACCATATCTGGGATATGGCATC--T
1 ATGTGA-TATGTGATTACGTATAAGACCATAGCTGGGCTATGGCATCGAT
* * * * *
35361699 GTGTGATATATG-CTACTGTATAAGACCATATCTGGGATATGGCATC-A-
1 ATGTGATATGTGATTAC-GTATAAGACCATAGCTGGGCTATGGCATCGAT
* * * *
35361746 GTGAGATATGTGATTACGTGTAAGACCACAGCTGGGCTATGGCATCGAT
1 ATGTGATATGTGATTACGTATAAGACCATAGCTGGGCTATGGCATCGAT
* *
35361795 ATGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCTTCGAT
1 ATGTGATATGTGATTACGTATAAGACCATAGCTGGGCTATGGCATCGAT
35361844 ATGTGAATATGTG
1 ATGTG-ATATGTG
35361857 TGAGACCATA
Statistics
Matches: 176, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
46 2 0.01
47 68 0.39
48 9 0.05
49 50 0.28
50 7 0.04
53 35 0.20
54 5 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (49 bp):
ATGTGATATGTGATTACGTATAAGACCATAGCTGGGCTATGGCATCGAT
Found at i:35363112 original size:19 final size:20
Alignment explanation
Indices: 35363060--35363104 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
35363050 ACCTCTTTTT
*
35363060 TGCATT-CATTTCATCCATC
1 TGCATTACATTTCATCCATA
35363079 TGCATTACATTTCAT-CATA
1 TGCATTACATTTCATCCATA
35363098 TGCATTA
1 TGCATTA
35363105 AGTTTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (20 bp):
TGCATTACATTTCATCCATA
Found at i:35371252 original size:44 final size:43
Alignment explanation
Indices: 35371189--35371490 Score: 223
Period size: 44 Copynumber: 6.9 Consensus size: 43
35371179 CATCGTGGTG
* * * *
35371189 AATCTTATCTCCCTAAAGTTGTAGTGGAACAGATTAAGGCCACA
1 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAA-GCTACA
* *
35371233 AATCTTATCTCCTTGAAGTTATAGTGGAGCAGATTGAAGATAGCA
1 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATT-AAGCTA-CA
* * * *
35371278 AATCTTATCT-CTCTAAAGTTGTGGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCT-TGAAGTTGTAGTGGAGCAGATT-AAGCTACA
* * *
35371322 AACCTTATCTCCTTGAAGTTGTAGTGGAGCAGGTTGAAGTTACA
1 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATT-AAGCTACA
* * * * * * *
35371366 AACCTTATCT-CTTGAATTTTTAGTGGAGTAGGTTGAAGTTAAA
1 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATT-AAGCTACA
* * * * * *
35371409 AATCTTATCTCCCTGAAATTG-CGTTGGAGCAGATAGAAGACAATA
1 AATCTTATCTCCTTGAAGTTGTAG-TGGAGCAGAT-TAAG-CTACA
* * * *
35371454 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAA
1 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAA
35371491 AGTTATAAAC
Statistics
Matches: 208, Mismatches: 41, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
43 39 0.19
44 99 0.48
45 69 0.33
46 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (43 bp):
AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAGCTACA
Found at i:35371311 original size:89 final size:88
Alignment explanation
Indices: 35371189--35371377 Score: 261
Period size: 89 Copynumber: 2.1 Consensus size: 88
35371179 CATCGTGGTG
* * * *
35371189 AATCTTATCTCCCTAAAGTTGTAGTGGAACAGATTAAGGCCACAAATCTTATCTCCTTGAAGTTA
1 AATCTTATCTCTCTAAAGTTGTAGTAGAACAGATTAAAGCCACAAACCTTATCTCCTTGAAGTTA
35371254 TAGTGGAGCAGATTGAAGATAGCA
66 TAGTGGAGCAGATTGAAGATA-CA
* * * * *
35371278 AATCTTATCTCTCTAAAGTTGTGGTAGAGCAGATTAAAGCTATAAACCTTATCTCCTTGAAGTTG
1 AATCTTATCTCTCTAAAGTTGTAGTAGAACAGATTAAAGCCACAAACCTTATCTCCTTGAAGTTA
* *
35371343 TAGTGGAGCAGGTTGAAGTTACA
66 TAGTGGAGCAGATTGAAGATACA
*
35371366 AACCTTATCTCT
1 AATCTTATCTCT
35371378 TGAATTTTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 13 0.15
89 75 0.85
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (88 bp):
AATCTTATCTCTCTAAAGTTGTAGTAGAACAGATTAAAGCCACAAACCTTATCTCCTTGAAGTTA
TAGTGGAGCAGATTGAAGATACA
Found at i:35371583 original size:44 final size:44
Alignment explanation
Indices: 35371520--35371630 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
35371510 TATCTTCTTG
* * * *
35371520 AAGTTACAATGAAGAAGATTGAAGATACGAGTCTCATCTCCCTA
1 AAGTTACAGTGGAGAAGATTGAAGATACAAGTCTAATCTCCCTA
* * * * *
35371564 AAGTTACAGTGGAGCAGATTAAAGCTATAAGTCTAATCTCCCTG
1 AAGTTACAGTGGAGAAGATTGAAGATACAAGTCTAATCTCCCTA
*
35371608 AAGTTACAGTGGAGTAGATTGAA
1 AAGTTACAGTGGAGAAGATTGAA
35371631 ACACTAATTC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (44 bp):
AAGTTACAGTGGAGAAGATTGAAGATACAAGTCTAATCTCCCTA
Found at i:35372343 original size:32 final size:28
Alignment explanation
Indices: 35372300--35372362 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 28
35372290 TTCATTTTTT
35372300 AAAAAGAAAATAGACACGAAAAAGCAATCA
1 AAAAAGAAAATAGACACGAAAAA--AATCA
*
35372330 AAAATAGAGAAATAGAGACGAAAAAAATCA
1 AAAA-AGA-AAATAGACACGAAAAAAATCA
35372360 AAA
1 AAA
35372363 GAGGAAGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 12 0.40
31 3 0.10
32 15 0.50
ACGTcount: A:0.68, C:0.10, G:0.14, T:0.08
Consensus pattern (28 bp):
AAAAAGAAAATAGACACGAAAAAAATCA
Found at i:35373207 original size:3 final size:3
Alignment explanation
Indices: 35373199--35373226 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
35373189 CGTTAGCTTA
35373199 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35373227 TAAAACTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35386945 original size:24 final size:24
Alignment explanation
Indices: 35386913--35386962 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
35386903 AAGAAGAGGA
*
35386913 TGCTTAATTGGATAAAAGAAAATT
1 TGCTCAATTGGATAAAAGAAAATT
*
35386937 TGCTCAATTGTATAAAAGAAAATT
1 TGCTCAATTGGATAAAAGAAAATT
35386961 TG
1 TG
35386963 ACAAACTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (24 bp):
TGCTCAATTGGATAAAAGAAAATT
Found at i:35395726 original size:34 final size:34
Alignment explanation
Indices: 35395683--35395749 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
35395673 TTTTTTCTTT
*
35395683 TTATTCTGTCACGGTTGGAGTCGTGGGCACGACC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACC
35395717 TTATTCTGTCACGGCTGGAGTCGTGGGCACGAC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGAC
35395750 GCTGGGCACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.28
Consensus pattern (34 bp):
TTATTCTGTCACGGCTGGAGTCGTGGGCACGACC
Found at i:35397907 original size:20 final size:21
Alignment explanation
Indices: 35397864--35397909 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
35397854 AATGTTTTGT
35397864 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
35397884 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
35397903 TATGGGC
1 TATGGGC
35397910 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:35405641 original size:29 final size:29
Alignment explanation
Indices: 35405608--35405663 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
35405598 TCACTCAACT
* *
35405608 ATAAAAAATTTTCATTTTAAGCACCCAAA
1 ATAAAAAATTTGCAATTTAAGCACCCAAA
*
35405637 ATAAAAAGTTTGCAATTTAAGCACCCA
1 ATAAAAAATTTGCAATTTAAGCACCCA
35405664 CGTTACATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (29 bp):
ATAAAAAATTTGCAATTTAAGCACCCAAA
Found at i:35415664 original size:27 final size:27
Alignment explanation
Indices: 35415634--35415720 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 27
35415624 TCAAAATAAT
* *
35415634 TTTAAAAT-TTTTTAAATAATTTTAAAA
1 TTTAAAATATTTATAAA-AATTTCAAAA
35415661 TTTAAAATATTTATAAAAATTTCAAAA
1 TTTAAAATATTTATAAAAATTTCAAAA
* * *
35415688 -CT-ATATATTT-TAAAAAATTATAAAAA
1 TTTAAAATATTTAT-AAAAATT-TCAAAA
35415714 TTTAAAA
1 TTTAAAA
35415721 GAATACATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
24 1 0.02
25 14 0.29
26 6 0.12
27 18 0.38
28 9 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTAAAATATTTATAAAAATTTCAAAA
Found at i:35415720 original size:17 final size:17
Alignment explanation
Indices: 35415644--35415720 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
35415634 TTTAAAATTT
*
35415644 TTTAAATAATT-TTAAAA
1 TTTAAA-AATTATAAAAA
35415661 TTTAAAATATTTATAAAAA
1 TTTAAAA-A-TTATAAAAA
* * * *
35415680 TTTCAAAACTAT-ATAT
1 TTTAAAAATTATAAAAA
35415696 TTTAAAAAATTATAAAAA
1 TTT-AAAAATTATAAAAA
35415714 TTTAAAA
1 TTTAAAA
35415721 GAATACATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
16 6 0.13
17 21 0.46
18 8 0.17
19 11 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAAATTATAAAAA
Found at i:35417348 original size:77 final size:77
Alignment explanation
Indices: 35417221--35417376 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 77
35417211 ACAAAATTAA
*
35417221 AAGCCAATTTTGCTCATCTTCAACCCCATGGCCGAATGTAGCAAGGAGAAACCATGGCTAGGGTT
1 AAGCCAATTTTGCTCATCTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTT
35417286 TTTCAAGCTTCC
66 TTTCAAGCTTCC
*
35417298 AAGCCAATTTTGCTCATCTTCAACCCCATGGCTGAATATAGCAAGGAGAAACCATGGCTAGGGTT
1 AAGCCAATTTTGCTCATCTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTT
35417363 TTTCAAGCTTCC
66 TTTCAAGCTTCC
35417375 AA
1 AA
35417377 TCTCGATTGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (77 bp):
AAGCCAATTTTGCTCATCTTCAACCCCATGGCCGAATATAGCAAGGAGAAACCATGGCTAGGGTT
TTTCAAGCTTCC
Found at i:35420591 original size:46 final size:45
Alignment explanation
Indices: 35420455--35420617 Score: 129
Period size: 46 Copynumber: 3.6 Consensus size: 45
35420445 ATGCCGATTC
* * * *
35420455 CATGTCCCAGACATGGTCTTACACTG-ACACATCTC-CTAGCGATG
1 CATGTCCCAGACATAGTCTTACACTGCACTCGTCTCAC-ACCGATG
* * * * ** *
35420499 CATGTCCCAGACAT-GTCTTAGATTGGC-TTACGTTTCGAGGCTGATG
1 CATGTCCCAGACATAGTCTTACACT-GCACT-CGTCTC-ACACCGATG
35420545 CATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCAACACCGATG
1 CATGTCCCAGACATAGTCTTACACT-GCACTCGTCTC-ACACCGATG
35420591 CCATGTCCCAGACATAGTCTTACACTG
1 -CATGTCCCAGACATAGTCTTACACTG
35420618 GCTCACACCA
Statistics
Matches: 92, Mismatches: 19, Indels: 13
0.74 0.15 0.10
Matches are distributed among these distances:
43 8 0.09
44 15 0.16
45 4 0.04
46 39 0.42
47 16 0.17
48 10 0.11
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
CATGTCCCAGACATAGTCTTACACTGCACTCGTCTCACACCGATG
Found at i:35424571 original size:21 final size:21
Alignment explanation
Indices: 35424547--35424591 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35424537 CATGGGCATA
* * *
35424547 TGTCCTCTCTACATGGGTGTG
1 TGTCCTCTCCACACGGGAGTG
35424568 TGTCCTCTCCACACGGGAGTG
1 TGTCCTCTCCACACGGGAGTG
35424589 TGT
1 TGT
35424592 GGCCTTCACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.27, G:0.29, T:0.33
Consensus pattern (21 bp):
TGTCCTCTCCACACGGGAGTG
Found at i:35426130 original size:30 final size:28
Alignment explanation
Indices: 35426091--35426148 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 28
35426081 ATGGATTTAA
35426091 ATTACTTATTATTTAAGTAAATAGATATTT
1 ATTACTTATTA-TTAAGTAAA-AGATATTT
*
35426121 ATTATTTATTATTAAGTAAAAGATATTT
1 ATTACTTATTATTAAGTAAAAGATATTT
35426149 TTTAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 8 0.30
29 9 0.33
30 10 0.37
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (28 bp):
ATTACTTATTATTAAGTAAAAGATATTT
Found at i:35427496 original size:39 final size:39
Alignment explanation
Indices: 35427448--35427598 Score: 185
Period size: 39 Copynumber: 3.9 Consensus size: 39
35427438 TTAATCGGGG
*
35427448 TAAACTACTGTACTGAATGATTGATAGTTACTGAATAAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * * * *
35427487 TAAATTACTGTATTAAATAATTGATAGTTATTGAATAAA
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * * *
35427526 TAAACTACTGCACTGAATATTTGATAGTTACTAAATGAC
1 TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
* * *
35427565 TAAATTACTGTACCGAATAATTGATTGTTACTGA
1 TAAACTACTGTACTGAATAATTGATAGTTACTGA
35427599 TTAAATATGA
Statistics
Matches: 91, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (39 bp):
TAAACTACTGTACTGAATAATTGATAGTTACTGAATAAC
Done.