Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 15 of 141
Found at i:5027513 original size:21 final size:21
Alignment explanation
Indices: 5027389--5027554 Score: 70
Period size: 21 Copynumber: 8.0 Consensus size: 21
5027379 TTTGCTTTCC
*
5027389 GTTTAGCTCTCATGAGCTTCA
1 GTTTAGCTCTTATGAGCTTCA
** * *
5027410 GTCAAG-TCATATGAGTTTCA
1 GTTTAGCTCTTATGAGCTTCA
* * * *
5027430 GTTTAACCCTT-TTACGTTTCA
1 GTTTAGCTCTTATGA-GCTTCA
* *
5027451 GTTCAGCTCTTTTGAGCTTCA
1 GTTTAGCTCTTATGAGCTTCA
* * * * * *
5027472 ATTTAACCCTAATGGGTTTCA
1 GTTTAGCTCTTATGAGCTTCA
*
5027493 GTTTAGCTCTTCTGAGCTTCA
1 GTTTAGCTCTTATGAGCTTCA
* * * *
5027514 -TATTAACCCTTATGGGTTTCCA
1 GT-TTAGCTCTTATGAGCTT-CA
*
5027536 -TTTAGCTCCTATGAGCTTC
1 GTTTAGCTCTTATGAGCTTC
5027555 TGTTCAACCC
Statistics
Matches: 99, Mismatches: 41, Indels: 11
0.66 0.27 0.07
Matches are distributed among these distances:
20 18 0.18
21 76 0.77
22 5 0.05
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTTAGCTCTTATGAGCTTCA
Found at i:5027529 original size:42 final size:42
Alignment explanation
Indices: 5027419--5027589 Score: 154
Period size: 42 Copynumber: 4.1 Consensus size: 42
5027409 AGTCAAGTCA
* * ** *
5027419 TATGAGTTTCAGT-TTAACCCTTTTACGTTTCAGTTCAGCTCT
1 TATGAGCTTCA-TATTAACCCTTATGGGTTTCAGTTTAGCTCT
* *
5027461 TTTGAGCTTCA-ATTTAACCCTAATGGGTTTCAGTTTAGCTCT
1 TATGAGCTTCATA-TTAACCCTTATGGGTTTCAGTTTAGCTCT
* *
5027503 TCTGAGCTTCATATTAACCCTTATGGGTTTCCA-TTTAGCTCC
1 TATGAGCTTCATATTAACCCTTATGGGTTT-CAGTTTAGCTCT
* * *
5027545 TATGAGCTTC-TGTTCAACCCTTACGGGTTGTC-GTTTAGCACT
1 TATGAGCTTCATATT-AACCCTTATGGGTT-TCAGTTTAGCTCT
5027587 TAT
1 TAT
5027590 ATGCTTCTGT
Statistics
Matches: 107, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
41 3 0.03
42 100 0.93
43 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.42
Consensus pattern (42 bp):
TATGAGCTTCATATTAACCCTTATGGGTTTCAGTTTAGCTCT
Found at i:5031315 original size:24 final size:24
Alignment explanation
Indices: 5031288--5031385 Score: 101
Period size: 25 Copynumber: 4.0 Consensus size: 24
5031278 GTTATTAGGG
*
5031288 TTACTGATTACAGCTCTTATGAGC
1 TTACTGATTACAGCTCGTATGAGC
* *
5031312 TTACTGATT-CTTAGCTTGCATGAGC
1 TTACTGATTAC--AGCTCGTATGAGC
*
5031337 TTACTG-TTAATCAGCTCGTAAGAGC
1 TTACTGATT-A-CAGCTCGTATGAGC
*
5031362 TTACTGTTTACAGCTCGTATGAGC
1 TTACTGATTACAGCTCGTATGAGC
5031386 ATACATGTAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
23 1 0.02
24 24 0.39
25 33 0.54
26 2 0.03
27 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (24 bp):
TTACTGATTACAGCTCGTATGAGC
Found at i:5033162 original size:45 final size:45
Alignment explanation
Indices: 5033097--5033270 Score: 170
Period size: 45 Copynumber: 3.9 Consensus size: 45
5033087 TCATTTTTCG
* ** * ** *
5033097 TTGTGTTGCCATAGTGTCTTTCAGCTATGGTCTTATTTCTTTA-AT
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTA-CTCGATAGAA
*
5033142 TTGTGATGCCATAGCATCTTTTAGCTATGGTCTTACTCGATAGAA
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCGATAGAA
* * * *
5033187 TTGTGATGCCATAACTTCTTTCAGCCATGGTCTTACTCGATTGAA
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCGATAGAA
* * ** * *
5033232 TCGTGATTCCATAATATCTTTTAGCCATGGTCTTACTCG
1 TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCG
5033271 TTTCTGGTAT
Statistics
Matches: 110, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
44 4 0.04
45 106 0.96
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.42
Consensus pattern (45 bp):
TTGTGATGCCATAGCATCTTTCAGCTATGGTCTTACTCGATAGAA
Found at i:5033297 original size:90 final size:89
Alignment explanation
Indices: 5033054--5033312 Score: 204
Period size: 90 Copynumber: 2.9 Consensus size: 89
5033044 ATTCTCGTCT
* * * * * * * *
5033054 TGATTCCATATTATCTTTCAGTCATGTTCTTATTCATTTTTCGTTGTGTTGCCATAGTGTCTTTC
1 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGTTG-G-TGCCATAGTGTCTTTC
* * *
5033119 AGCTATGGTCTTATTTCTTTAATTTG
64 AGCTATGGTCTTATCTCTTGAATTCG
* ** * * ** * *
5033145 TGATGCCATAGCATCTTTTAGCTATGGTCTTACTCG-ATAGAATTGTGATGCCATAACT-TCTTT
1 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGTTG-G-TGCCAT-AGTGTCTTT
*
5033208 CAGCCATGGTCTTA-CTCGATTGAA-TCG
63 CAGCTATGGTCTTATCTC--TTGAATTCG
*
5033235 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTGGTATGGTGCCATAGTGTCTTTCT
1 TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGT-TGGTGCCATAGTGTCTTTC-
5033300 A-CTATGGTCTTAT
64 AGCTATGGTCTTAT
5033313 TTATTTTCGG
Statistics
Matches: 129, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
89 4 0.03
90 86 0.67
91 37 0.29
92 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (89 bp):
TGATTCCATAATATCTTTTAGCCATGGTCTTACTCGTTTCTAGTTGGTGCCATAGTGTCTTTCAG
CTATGGTCTTATCTCTTGAATTCG
Found at i:5033411 original size:15 final size:15
Alignment explanation
Indices: 5033382--5033415 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5033372 CCAACAAACT
5033382 CAATTCATATATAAA
1 CAATTCATATATAAA
5033397 CAATT-ATATATTAAA
1 CAATTCATATA-TAAA
5033412 CAAT
1 CAAT
5033416 CAAAAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (15 bp):
CAATTCATATATAAA
Found at i:5034992 original size:24 final size:23
Alignment explanation
Indices: 5034965--5035012 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
5034955 GAGTAAAGAA
* *
5034965 TTTTATTTTTTTATTTCATTTAGT
1 TTTTATTTTTTAATTT-AATTAGT
5034989 TTTTATTTTTTAATTTAATTAGT
1 TTTTATTTTTTAATTTAATTAGT
5035012 T
1 T
5035013 AAAGTTGACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTAATTTAATTAGT
Found at i:5039439 original size:27 final size:27
Alignment explanation
Indices: 5039399--5039480 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
5039389 AACACGTCAG
* *
5039399 GAAAGAAAAACCTTTATGGCAAACTCT
1 GAAAGAAAAGCCTTTATGGCGAACTCT
5039426 GAAAGAAAAGCCTTTATGGCGAACTCT
1 GAAAGAAAAGCCTTTATGGCGAACTCT
* *
5039453 GAAAGAAGAGCCTTTATGGTGAACTCT
1 GAAAGAAAAGCCTTTATGGCGAACTCT
5039480 G
1 G
5039481 TATGGACTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTATGGCGAACTCT
Found at i:5039705 original size:35 final size:35
Alignment explanation
Indices: 5039623--5039719 Score: 131
Period size: 35 Copynumber: 2.8 Consensus size: 35
5039613 TTCATGATGT
* *
5039623 CACTTCGTAGAGCCAATAGATCATTTTCGTGATGC
1 CACTTCGTAGAGCCAGTAGATCATTTTCGTGATAC
* **
5039658 CACTCCACAGAGCCAGTAGATCATTTTCGTGATAC
1 CACTTCGTAGAGCCAGTAGATCATTTTCGTGATAC
* *
5039693 CACTTTGTAGAGCTAGTAGATCATTTT
1 CACTTCGTAGAGCCAGTAGATCATTTT
5039720 TCCAACCAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (35 bp):
CACTTCGTAGAGCCAGTAGATCATTTTCGTGATAC
Found at i:5040306 original size:20 final size:20
Alignment explanation
Indices: 5040281--5040329 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5040271 CTAGAAACTT
*
5040281 ACAGAAACCTTTCAAATTTG
1 ACAGAAACCTTTCAAATATG
*
5040301 ACAGAAACTTTTCAAATATG
1 ACAGAAACCTTTCAAATATG
*
5040321 ACAAAAACC
1 ACAGAAACC
5040330 GTTAACTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (20 bp):
ACAGAAACCTTTCAAATATG
Found at i:5041481 original size:23 final size:23
Alignment explanation
Indices: 5041451--5041505 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
5041441 GCTCTATACG
*
5041451 TGTTATATTCAAAGCTTTATGCA
1 TGTTATATTCAAAGCTATATGCA
* *
5041474 TGTTATATTCCATGCTATATGCA
1 TGTTATATTCAAAGCTATATGCA
5041497 TGTTATATT
1 TGTTATATT
5041506 TGATTCAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (23 bp):
TGTTATATTCAAAGCTATATGCA
Found at i:5044085 original size:3 final size:3
Alignment explanation
Indices: 5044077--5044140 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
5044067 CTTTTTAAGC
*
5044077 CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
5044125 CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT C
5044141 ACACCACCGC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:5052191 original size:27 final size:27
Alignment explanation
Indices: 5052155--5052232 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
5052145 AAATATAAAG
5052155 GGGGTTGCTAAGTGCTGAATCCCCCAA
1 GGGGTTGCTAAGTGCTGAATCCCCCAA
5052182 GGGGTTGCTAAGTGCTGAATCCCCCAA
1 GGGGTTGCTAAGTGCTGAATCCCCCAA
* *
5052209 GGGCTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGAATCCCC
5052233 GATTCATTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.24
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGAATCCCCCAA
Found at i:5052255 original size:33 final size:33
Alignment explanation
Indices: 5052213--5052448 Score: 126
Period size: 33 Copynumber: 6.7 Consensus size: 33
5052203 CCCCAAGGGC
5052213 TTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
1 TTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
* *
5052246 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGG
1 TTGCTAAGTGCTGATTCC-CCG-A---TT-CAT-TG--GTGG
*
5052288 CTTGCTAAGTGCTGATTCCCC---T-A-AGG-GG
1 -TTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
* * *
5052316 TTGCTAAGTGTTGATTCCCCGAATCATTCGTGG
1 TTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
*
5052349 TTGCTAAGTGCTGATTCCACC-ATATCTTTGAATGTGAAAGGG
1 TTGCTAAGTGCTGATTCC-CCGAT-TCATTG---GT-----GG
* * *
5052391 ATTGCTAAGTGCTGATCCCCCGAATCAGTGGTGG
1 -TTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
*
5052425 TTGCTAAGTGCTGAATCCACCGAT
1 TTGCTAAGTGCTGATTCC-CCGAT
5052449 AACGATTGAT
Statistics
Matches: 157, Mismatches: 17, Indels: 57
0.68 0.07 0.25
Matches are distributed among these distances:
27 19 0.12
28 2 0.01
29 1 0.01
30 1 0.01
31 2 0.01
32 1 0.01
33 55 0.35
34 15 0.10
35 2 0.01
37 2 0.01
38 2 0.01
39 4 0.03
40 2 0.01
42 13 0.08
43 36 0.23
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (33 bp):
TTGCTAAGTGCTGATTCCCCGATTCATTGGTGG
Found at i:5052308 original size:103 final size:101
Alignment explanation
Indices: 5052180--5052411 Score: 356
Period size: 103 Copynumber: 2.3 Consensus size: 101
5052170 TGAATCCCCC
* *
5052180 AAGGGGTTGCTAAGTGCTGAATCCCCCAAGGGCTTGCTAAGTGCTGATTCCCCGATTCATTGGTG
1 AAGGGGTTGCTAAGTGCTG-ATCCCCCAAGGGCTTGCTAAGTGCTGATTCCCCGAATCATTCGTG
*
5052245 GTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTG
65 GTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTG
* * *
5052282 AAGGGGCTTGCTAAGTGCTGATTCCCCTAAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTCGT
1 AAGGGG-TTGCTAAGTGCTGA-TCCCCCAAGGGCTTGCTAAGTGCTGATTCCCCGAATCATTCGT
*
5052347 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGTG
64 GGTTGCTAAGTGCTGATTCCACCATATCTTTAAATGTG
*
5052385 AAAGGGATTGCTAAGTGCTGATCCCCC
1 -AAGGGGTTGCTAAGTGCTGATCCCCC
5052412 GAATCAGTGG
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
102 12 0.10
103 101 0.86
104 5 0.04
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (101 bp):
AAGGGGTTGCTAAGTGCTGATCCCCCAAGGGCTTGCTAAGTGCTGATTCCCCGAATCATTCGTGG
TTGCTAAGTGCTGATTCCACCATATCTTTAAATGTG
Found at i:5052321 original size:27 final size:28
Alignment explanation
Indices: 5052282--5052335 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
5052272 TTTAAATGTG
5052282 AAGGGGCTTGCTAAGTGCTGATTCCCCT
1 AAGGGGCTTGCTAAGTGCTGATTCCCCT
*
5052310 AAGGGG-TTGCTAAGTGTTGATTCCCC
1 AAGGGGCTTGCTAAGTGCTGATTCCCC
5052336 GAATCATTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (28 bp):
AAGGGGCTTGCTAAGTGCTGATTCCCCT
Found at i:5052335 original size:130 final size:130
Alignment explanation
Indices: 5052101--5052335 Score: 398
Period size: 130 Copynumber: 1.8 Consensus size: 130
5052091 ATTCAATATA
*
5052101 CCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAAATATAAAGGGGGTTGCTAA
1 CCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAAATATAAAGGGGCTTGCTAA
5052166 GTGCTGAATCCCCCAAGGGGTTGCTAAGTGCTGAATCCCCCAAGGGCTTGCTAAGTGCTGATTCC
66 GTGCTGAATCCCCCAAGGGGTTGCTAAGTGCTGAATCCCCCAAGGGCTTGCTAAGTGCTGATTCC
* * *
5052231 CCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGGGCTTGCTAA
1 CCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAAATATAAAGGGGCTTGCTAA
* * * *
5052296 GTGCTGATTCCCCTAAGGGGTTGCTAAGTGTTGATTCCCC
66 GTGCTGAATCCCCCAAGGGGTTGCTAAGTGCTGAATCCCC
5052336 GAATCATTCG
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 97 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (130 bp):
CCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAAATATAAAGGGGCTTGCTAA
GTGCTGAATCCCCCAAGGGGTTGCTAAGTGCTGAATCCCCCAAGGGCTTGCTAAGTGCTGATTCC
Found at i:5059646 original size:76 final size:75
Alignment explanation
Indices: 5059557--5059815 Score: 394
Period size: 76 Copynumber: 3.4 Consensus size: 75
5059547 GAATACATTG
* *
5059557 AATATGAA-GGGGTTGCTAAGTGCTGATTCCGCAACTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCC-CAATTCATTGGTGGTTGCTAAGTGCTGATTCCA
5059621 CCGTATCCTTA
65 CCGTATCCTTA
*
5059632 AATATAAAGGGGGTTGCTAAGTGTTGATTCCCTAATTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCCC-AATTCATTGGTGGTTGCTAAGTGCTGATTCCA
*
5059697 CCATATCCTTA
65 CCGTATCCTTA
* *
5059708 AATATAAAGAGGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 AATATAAAGGGGGTTGCTAAGTGCTGATTC-CCAATTCATTGGTGGTTGCTAAGTGCTGATTCCA
**
5059773 CCGTATTTTTA
65 CCGTATCCTTA
* *
5059784 AATGTGAAGGGGGTTGCTAAGTGCTGATTCCC
1 AATATAAAGGGGGTTGCTAAGTGCTGATTCCC
5059816 CCAAGGGGTT
Statistics
Matches: 168, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
75 10 0.06
76 156 0.93
77 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (75 bp):
AATATAAAGGGGGTTGCTAAGTGCTGATTCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCAC
CGTATCCTTA
Found at i:5059661 original size:43 final size:40
Alignment explanation
Indices: 5059600--5059814 Score: 161
Period size: 43 Copynumber: 5.5 Consensus size: 40
5059590 ACTCATTGGT
5059600 GGTTGCTAAGTGCTGATTCCACCGTATCCTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-CTTAAAT-T-AAGGG
* * * *
5059643 GGTTGCTAAGTGTTGATT-C-CC-TA-ATT-CATT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATTAAGGG
* *
5059676 GGTTGCTAAGTGCTGATTCCACCATATCCTTAAATATAAAGAG
1 GGTTGCTAAGTGCTGATTCCACCGTAT-CTTAAAT-T-AAGGG
* * *
5059719 GGTTGCTAAGTGCTGATT-CTCCG-A--TT-CATT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATTAAGGG
*
5059752 GGTTGCTAAGTGCTGATTCCACCGTATTTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTA-TCTTAAAT-T-AAGGG
5059795 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
5059815 CCCAAGGGGT
Statistics
Matches: 135, Mismatches: 17, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
33 38 0.28
34 5 0.04
35 3 0.02
36 4 0.03
37 4 0.03
38 8 0.06
39 4 0.03
40 4 0.03
41 3 0.02
42 4 0.03
43 58 0.43
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (40 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATTAAGGG
Found at i:5059851 original size:103 final size:103
Alignment explanation
Indices: 5059718--5059919 Score: 332
Period size: 103 Copynumber: 2.0 Consensus size: 103
5059708 AATATAAAGA
* * * * *
5059718 GGGTTGCTAAGTGCTGATTCTCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTT
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
*
5059783 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAG
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAG
*
5059821 GGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
*
5059886 GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
5059920 GAATCACTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (103 bp):
GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGAGCTGATTCCACCATATCTTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAG
Found at i:5059864 original size:33 final size:33
Alignment explanation
Indices: 5059795--5059942 Score: 103
Period size: 33 Copynumber: 4.4 Consensus size: 33
5059785 ATGTGAAGGG
*
5059795 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
5059822 GGTTGCTAAGTGTTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
5059855 GGTTGCTAAGAGCTGATTCCACC-ATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGA-ATC-----AT-TG---GT
*
5059898 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
5059931 GGTTGCTAAGTG
1 GGTTGCTAAGTG
5059943 ATGAATCCAC
Statistics
Matches: 95, Mismatches: 8, Indels: 30
0.71 0.06 0.23
Matches are distributed among these distances:
27 21 0.22
31 2 0.02
32 2 0.02
33 32 0.34
34 5 0.05
36 2 0.02
37 1 0.01
39 2 0.02
40 2 0.02
42 5 0.05
43 21 0.22
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:5065249 original size:22 final size:21
Alignment explanation
Indices: 5065174--5065256 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 21
5065164 CCTTCCTCTC
5065174 CCTTTTCTTTTCTTATCGTTC-TT
1 CCTTTTCTTTTCTT-T--TTCTTT
*
5065197 CCTTTTCTATTTCCTTATTCTTT
1 CCTTTTCT-TTT-CTTTTTCTTT
*
5065220 -ATTCTTCTTTTCTTTTTCCTTT
1 CCTT-TTCTTTTCTTTTT-CTTT
*
5065242 CCTTTTCTTTCCTTT
1 CCTTTTCTTTTCTTT
5065257 GGGTTGTTGT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
21 5 0.10
22 22 0.45
23 16 0.33
24 3 0.06
25 3 0.06
ACGTcount: A:0.05, C:0.27, G:0.01, T:0.67
Consensus pattern (21 bp):
CCTTTTCTTTTCTTTTTCTTT
Found at i:5066972 original size:127 final size:128
Alignment explanation
Indices: 5066819--5067075 Score: 426
Period size: 127 Copynumber: 2.0 Consensus size: 128
5066809 GATTGTTGAA
*
5066819 TTATCGACTGGGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
1 TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
*
5066884 TGG-TTTTTTTATAATAACGTTACTGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
66 TGGTTTTTTTTATAATAACGTTAATGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
*
5066946 TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATACAAGT
1 TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
* * * * * *
5067011 TGGTTTTTTTTCTAATAATGTTAATGTAACTTTTTAGAGTTGGTCTTAACGTCTAGGCTGAGT
66 TGGTTTTTTTTATAATAACGTTAATGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
5067074 TT
1 TT
5067076 GGGGTGTTAC
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
127 66 0.55
128 54 0.45
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.47
Consensus pattern (128 bp):
TTATCGACTGAGTTTTTATGATTGTTATAATCTGTCAGATGGTTTTTAACTGTGTTTATAAAAGT
TGGTTTTTTTTATAATAACGTTAATGTAACTTTTCAGACTTGGTCTTAACATCTAGGCCGAGT
Found at i:5067356 original size:30 final size:30
Alignment explanation
Indices: 5067322--5067378 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
5067312 ACAGGAATAA
5067322 GTTGCTCACACAAGCTGACAGTATATCAAG
1 GTTGCTCACACAAGCTGACAGTATATCAAG
* *
5067352 GTTGCTCACACAAGTTGACATTATATC
1 GTTGCTCACACAAGCTGACAGTATATC
5067379 GAGACTACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
GTTGCTCACACAAGCTGACAGTATATCAAG
Found at i:5069798 original size:13 final size:13
Alignment explanation
Indices: 5069780--5069827 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
5069770 CCACTCGCTC
5069780 TATTATTAAATTT
1 TATTATTAAATTT
* *
5069793 TATTATTAGA-TA
1 TATTATTAAATTT
*
5069805 TAATATTAAATTT
1 TATTATTAAATTT
5069818 TATTATTAAA
1 TATTATTAAA
5069828 ATTGTCCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (13 bp):
TATTATTAAATTT
Found at i:5070837 original size:22 final size:23
Alignment explanation
Indices: 5070811--5070854 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5070801 GTGATGAGGT
**
5070811 TATCTTATGAATATGTT-AAATC
1 TATCTTAAAAATATGTTGAAATC
5070833 TATCTTAAAAATATGTTGAAAT
1 TATCTTAAAAATATGTTGAAAT
5070855 ATATTGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (23 bp):
TATCTTAAAAATATGTTGAAATC
Found at i:5080033 original size:13 final size:13
Alignment explanation
Indices: 5080015--5080040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5080005 TCTGTTGCTG
5080015 CACAAAACTTTAT
1 CACAAAACTTTAT
5080028 CACAAAACTTTAT
1 CACAAAACTTTAT
5080041 TTTGTTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CACAAAACTTTAT
Found at i:5080290 original size:5 final size:5
Alignment explanation
Indices: 5080282--5080307 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5080272 TAACTAAGAT
5080282 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
5080308 TAAATCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:5090063 original size:18 final size:18
Alignment explanation
Indices: 5090023--5090059 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5090013 CCATGATGTT
*
5090023 TGCCCGTGTGGGCCGACA
1 TGCCCGTGTGGGCCCACA
5090041 TGCCCGTGT-GGCCCACA
1 TGCCCGTGTGGGCCCACA
5090058 TG
1 TG
5090060 GCCCAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.35, G:0.35, T:0.19
Consensus pattern (18 bp):
TGCCCGTGTGGGCCCACA
Found at i:5091640 original size:16 final size:16
Alignment explanation
Indices: 5091619--5091688 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
5091609 TTTGGTTCGC
* *
5091619 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
5091635 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
5091651 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
5091667 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
5091683 TGTAAT
1 TGTAAT
5091689 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:5091772 original size:39 final size:43
Alignment explanation
Indices: 5091667--5091776 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
5091657 GGAATAGAGG
5091667 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
5091712 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
5091752 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
5091777 TAATAGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:5091939 original size:16 final size:16
Alignment explanation
Indices: 5091902--5091943 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5091892 TTAATCATAT
*
5091902 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5091918 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5091933 TTAAAATATAT
1 TTAAAATATAT
5091944 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5091950 original size:14 final size:15
Alignment explanation
Indices: 5091911--5091952 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5091901 TTTAAACATA
*
5091911 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5091926 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5091940 A-TATAATTTAATA
1 ATTATAATTAAATA
5091953 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5092164 original size:24 final size:25
Alignment explanation
Indices: 5092118--5092165 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
5092108 TATGAATTTG
5092118 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
5092144 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
5092166 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:5092217 original size:22 final size:22
Alignment explanation
Indices: 5092192--5092236 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5092182 TGATAACTTG
5092192 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
5092214 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
5092236 A
1 A
5092237 GTTAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTCATTAAATTACTTTCAA
Found at i:5095199 original size:19 final size:19
Alignment explanation
Indices: 5095175--5095214 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
5095165 AATAAAAGAG
5095175 TCATCTTCCAAAAACCAAT
1 TCATCTTCCAAAAACCAAT
*
5095194 TCATCTTCCAAAAATCAAT
1 TCATCTTCCAAAAACCAAT
5095213 TC
1 TC
5095215 CCACTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (19 bp):
TCATCTTCCAAAAACCAAT
Found at i:5095952 original size:40 final size:40
Alignment explanation
Indices: 5095897--5095999 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 40
5095887 TTATTGAATT
*
5095897 ATTGCACTTACGTGCCCCTGTTTGTTCTTCGGTACCCCTG
1 ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
* *
5095937 ATTGCACTTACGTGCCCCCTATTTGTACTTCGGTACCCTTG
1 ATTGCACTTACGTG-CCCCTGTTTGTACTTCGGTACCCCTG
* * *
5095978 AATGCACATATGTGCCCCTGTT
1 ATTGCACTTACGTGCCCCTGTT
5096000 GCACTTTGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 21 0.38
41 34 0.62
ACGTcount: A:0.15, C:0.31, G:0.18, T:0.36
Consensus pattern (40 bp):
ATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTG
Found at i:5095954 original size:20 final size:19
Alignment explanation
Indices: 5095897--5096055 Score: 72
Period size: 20 Copynumber: 7.9 Consensus size: 19
5095887 TTATTGAATT
5095897 ATTGCACTTACGTGCCCCTG
1 ATTGCACTT-CGTGCCCCTG
* ** *
5095917 TTTGTTCTTCGGTACCCCTG
1 ATTGCACTTC-GTGCCCCTG
5095937 ATTGCACTTACGTGCCCCCT-
1 ATTGCACTT-CGTG-CCCCTG
* * *
5095957 ATTTGTACTTCGGTACCCTTG
1 A-TTGCACTTC-GTGCCCCTG
*
5095978 AATGCACATAT-GTGCCCCTG
1 ATTGCAC-T-TCGTGCCCCTG
* *
5095998 -TTGCACTTTGATGCCTCTG
1 ATTGCACTTCG-TGCCCCTG
* * *
5096017 ATCGCACATTCATGCTCCTG
1 ATTGCAC-TTCGTGCCCCTG
*
5096037 ATTGCACTTTGGTGCCCCT
1 ATTGCAC-TTCGTGCCCCT
5096056 ATTATGCGTC
Statistics
Matches: 100, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
17 1 0.01
18 2 0.02
19 13 0.13
20 64 0.64
21 19 0.19
22 1 0.01
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.35
Consensus pattern (19 bp):
ATTGCACTTCGTGCCCCTG
Found at i:5102455 original size:12 final size:13
Alignment explanation
Indices: 5102438--5102471 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
5102428 TTTACTAGGG
5102438 TTAGGGTTTTTA-
1 TTAGGGTTTTTAT
5102450 TTAGGGTTTTTAT
1 TTAGGGTTTTTAT
5102463 TTAGGGTTT
1 TTAGGGTTT
5102472 AGAGTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (13 bp):
TTAGGGTTTTTAT
Found at i:5104114 original size:9 final size:9
Alignment explanation
Indices: 5104102--5104152 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
5104092 ATTAAAAAGA
5104102 AGAGAGTTG
1 AGAGAGTTG
*
5104111 AGAGACTTG
1 AGAGAGTTG
* *
5104120 AAAGGGTTTG
1 AGAGAG-TTG
5104130 AGAG-GATTG
1 AGAGAG-TTG
5104139 AGAGAGTTG
1 AGAGAGTTG
5104148 AGAGA
1 AGAGA
5104153 AGAATGTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 27 0.79
10 7 0.21
ACGTcount: A:0.35, C:0.02, G:0.41, T:0.22
Consensus pattern (9 bp):
AGAGAGTTG
Found at i:5105784 original size:3 final size:3
Alignment explanation
Indices: 5105776--5105807 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5105766 GAGTGAAAAA
5105776 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
5105808 CGACAAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:5106421 original size:3 final size:3
Alignment explanation
Indices: 5106413--5106443 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5106403 TTTGAATTTA
5106413 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5106444 GTAAGAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5107319 original size:6 final size:6
Alignment explanation
Indices: 5107304--5107337 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5107294 ATCTACCCAA
* *
5107304 CCCTGG CCCTGC CCCTGC CCCTGC CTCTGC CCCT
1 CCCTGC CCCTGC CCCTGC CCCTGC CCCTGC CCCT
5107338 TTTCTCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.62, G:0.18, T:0.21
Consensus pattern (6 bp):
CCCTGC
Found at i:5109684 original size:3 final size:3
Alignment explanation
Indices: 5109676--5109709 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5109666 CCATGATCTT
5109676 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5109710 CATCATCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5121169 original size:47 final size:45
Alignment explanation
Indices: 5121093--5121215 Score: 113
Period size: 46 Copynumber: 2.6 Consensus size: 45
5121083 GTGGTTTAAC
* * * *
5121093 CACATATCTATTCTGGCAGCTTAGTTGCAATTATAGTGGCTCGACCA
1 CACATATCTATTTTGGTAGCTTA-CTGCAA-TATAGTAGCTCGACCA
* *
5121140 CACATATCTATTTTGGTAGCTTGACTGCAATGTAGTAGCTTGACCA
1 CACATATCTATTTTGGTAGCTT-ACTGCAATATAGTAGCTCGACCA
* * *
5121186 CATATATTTGA-TTTGGTAGTTTAACTGCAA
1 CACATATCT-ATTTTGGTAGCTT-ACTGCAA
5121216 CTTTGGTGGC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
46 37 0.58
47 26 0.41
48 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (45 bp):
CACATATCTATTTTGGTAGCTTACTGCAATATAGTAGCTCGACCA
Found at i:5122011 original size:29 final size:30
Alignment explanation
Indices: 5121968--5122045 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
5121958 AAATTGAATC
* *
5121968 AAATCAAATTTTCATGTATAAAATCGCACA-
1 AAATCAAA-GTTCATGTACAAAATCGCACAT
* * *
5121998 AAATCAAAGTTCATGTACGACATTGCACATT
1 AAATCAAAGTTCATGTACAAAATCGCACA-T
5122029 AAATCAAAGTTCATGTA
1 AAATCAAAGTTCATGTA
5122046 AATATTCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.39
30 8 0.20
31 17 0.41
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (30 bp):
AAATCAAAGTTCATGTACAAAATCGCACAT
Found at i:5124236 original size:18 final size:18
Alignment explanation
Indices: 5124215--5124259 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5124205 CATTCGTTTG
5124215 CAAAACATTATTC-ATTT
1 CAAAACATTATTCAATTT
* *
5124232 ACAAATCGTTATTCAATTT
1 -CAAAACATTATTCAATTT
5124251 CAAAACATT
1 CAAAACATT
5124260 TTCTTATTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (18 bp):
CAAAACATTATTCAATTT
Found at i:5128015 original size:20 final size:20
Alignment explanation
Indices: 5127990--5128054 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
5127980 AGTACAACAA
5127990 GGGTACGTAAGTGCGTTCAG
1 GGGTACGTAAGTGCGTTCAG
* ** *
5128010 GGGTACCG-AAGTAC-AACAA
1 GGGTA-CGTAAGTGCGTTCAG
*
5128029 GGGCACGTAAGTGCGTTCAG
1 GGGTACGTAAGTGCGTTCAG
5128049 GGGTAC
1 GGGTAC
5128055 CGAAGTACAA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.34
20 17 0.53
21 2 0.06
ACGTcount: A:0.26, C:0.18, G:0.37, T:0.18
Consensus pattern (20 bp):
GGGTACGTAAGTGCGTTCAG
Found at i:5128027 original size:39 final size:39
Alignment explanation
Indices: 5127968--5128106 Score: 188
Period size: 39 Copynumber: 3.6 Consensus size: 39
5127958 AAAGTACTAA
* * *
5127968 CAGGAGTACCAAAGTACAACAAGGGTACGTAAGTGCGTT
1 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
5128007 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
1 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
* * *
5128046 CAGGGGTACCGAAGTACAACAGGGGCACGTACGTGCATT
1 CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
** **
5128085 CAAAGGTACTTAAGTACAACAA
1 CAGGGGTACCGAAGTACAACAA
5128107 TTTTTCTACA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.17
Consensus pattern (39 bp):
CAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCGTT
Found at i:5128068 original size:19 final size:20
Alignment explanation
Indices: 5127959--5128070 Score: 63
Period size: 19 Copynumber: 5.8 Consensus size: 20
5127949 TGCGATACGA
* * *
5127959 AAGTACTAACAGGAGTACCA
1 AAGTACGAACAGGGGTACCG
*
5127979 AAGTAC-AACAAGGGTA-CG
1 AAGTACGAACAGGGGTACCG
* **
5127997 TAAGTGCGTTCAGGGGTACCG
1 -AAGTACGAACAGGGGTACCG
* *
5128018 AAGTAC-AACAAGGGCA-CG
1 AAGTACGAACAGGGGTACCG
* **
5128036 TAAGTGCGTTCAGGGGTACCG
1 -AAGTACGAACAGGGGTACCG
5128057 AAGTAC-AACAGGGG
1 AAGTACGAACAGGGG
5128071 CACGTACGTG
Statistics
Matches: 66, Mismatches: 20, Indels: 13
0.67 0.20 0.13
Matches are distributed among these distances:
18 3 0.05
19 30 0.45
20 29 0.44
21 4 0.06
ACGTcount: A:0.35, C:0.19, G:0.31, T:0.15
Consensus pattern (20 bp):
AAGTACGAACAGGGGTACCG
Found at i:5134936 original size:22 final size:22
Alignment explanation
Indices: 5134900--5134943 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5134890 TAGCATGTTG
*
5134900 AAATTTTCTTAATTTT-ATAAT
1 AAATTTTATTAATTTTGATAAT
5134921 AAATTTTGATTAATTTTGATAAT
1 AAATTTT-ATTAATTTTGATAAT
5134944 TTTCGACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
AAATTTTATTAATTTTGATAAT
Found at i:5135636 original size:54 final size:54
Alignment explanation
Indices: 5135572--5135681 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
5135562 CCCTTTCTGA
*
5135572 TTTCATCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
1 TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
5135626 TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
1 TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
5135680 TT
1 TT
5135682 CATAAGAGCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (54 bp):
TTTCACCTCTTGAAAAAGAGTCAATCTACCACCATTTGAAGCAGCATTCAAGTT
Found at i:5135664 original size:26 final size:26
Alignment explanation
Indices: 5135581--5135665 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
5135571 ATTTCATCTC
5135581 TTGAAAAAGAGTCAATCTACCACCAT
1 TTGAAAAAGAGTCAATCTACCACCAT
** * * **
5135607 TTGAAGCAGCATTCAAGTTTTTCACC-T
1 TTGAAAAAG-AGTCAA-TCTACCACCAT
5135634 CTTGAAAAAGAGTCAATCTACCACCAT
1 -TTGAAAAAGAGTCAATCTACCACCAT
5135661 TTGAA
1 TTGAA
5135666 GCAGCATTCA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
26 18 0.42
27 12 0.28
28 13 0.30
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (26 bp):
TTGAAAAAGAGTCAATCTACCACCAT
Found at i:5145473 original size:28 final size:28
Alignment explanation
Indices: 5145441--5145496 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5145431 CAGTGACGGT
* *
5145441 ACAGTGAGGGCCTTAGCCCAATTCAGTA
1 ACAGTGAGGGCCTTAACCCAATACAGTA
*
5145469 ACAGTGTGGGCCTTAACCCAATACAGTA
1 ACAGTGAGGGCCTTAACCCAATACAGTA
5145497 TCATTACAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.21
Consensus pattern (28 bp):
ACAGTGAGGGCCTTAACCCAATACAGTA
Found at i:5145900 original size:26 final size:27
Alignment explanation
Indices: 5145871--5146007 Score: 170
Period size: 27 Copynumber: 5.1 Consensus size: 27
5145861 TATAAAGATC
*
5145871 ATTTTACCCTTAG-GGGTATTACGGTA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
**
5145897 ATTTTACCCTTAG-GGGTATTTTAGTA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
* *
5145923 ATTTTACCCTTTGAGGGTATTTCGATA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
* **
5145950 ATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
* *
5145977 ATTTTACCCTTTGAGGGTATTTCGATA
1 ATTTTACCCTTAGAGGGTATTTCGGTA
5146004 ATTT
1 ATTT
5146008 ACTCATGAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
26 35 0.37
27 60 0.63
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTAGAGGGTATTTCGGTA
Found at i:5145983 original size:54 final size:53
Alignment explanation
Indices: 5145871--5146007 Score: 222
Period size: 54 Copynumber: 2.6 Consensus size: 53
5145861 TATAAAGATC
* * *
5145871 ATTTTACCCTTAG-GGGTATTACGGTAATTTTACCCTTAGGGGTATTTTAGTA
1 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTAGGGGTATTTTAGTA
*
5145923 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTTAGTA
1 ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTAG-GGGTATTTTAGTA
5145977 ATTTTACCCTTTGAGGGTATTTCGATAATTT
1 ATTTTACCCTTTGAGGGTATTTCGATAATTT
5146008 ACTCATGAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
52 12 0.15
53 23 0.29
54 44 0.56
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (53 bp):
ATTTTACCCTTTGAGGGTATTTCGATAATTTTACCCTTAGGGGTATTTTAGTA
Found at i:5147167 original size:570 final size:570
Alignment explanation
Indices: 5146088--5147228 Score: 1957
Period size: 570 Copynumber: 2.0 Consensus size: 570
5146078 ACGGCTTTTT
*
5146088 GGCTTTTCGCTGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
1 GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
* * *
5146153 TCCACGGACACCAACCTAGATTTCATCAAATCACAAGTCAGCCGTTAAAGCAATACACCCTATTA
66 TCCACGCACACCAACCTAGATTTCATCAAATCACAAGTCAGCCCTTAAAGCAAGACACCCTATTA
* * *
5146218 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAGGGTGACTTAACTCCTTCAATAT
131 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
** *
5146283 TCCCAACCGAAAATGGTCACCCACTTAATGATTACCTGTACCACAACACAAATCTTCATAAACTA
196 TCCCAACCGAAAATGGTCACCCACTTAATGATTACCAATACCACAACACAAATATTCATAAACTA
* *
5146348 ACTTGGCCAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAAT
261 ACTAGGACAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAAT
5146413 TTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGAC
326 TTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGAC
* *
5146478 AGTAAAAATAGTGAAGAGAAGATCGGTGTAGAGGAATAGAGCAAAAGGTGATAATCGGCTGAACC
391 AGTAAAAATAGTCAAGAGAAGATCGGTGCAGAGGAATAGAGCAAAAGGTGATAATCGGCTGAACC
5146543 ACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAATAAAA
456 ACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAATAAAA
5146608 TCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
521 TCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
*
5146658 GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGTGCAAACC
1 GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
* * *
5146723 TCCATGCACACCAACCTAGATTTCATCAAATCACAAGTTAGCCCTTAAAGCAAGACACCCTTTTA
66 TCCACGCACACCAACCTAGATTTCATCAAATCACAAGTCAGCCCTTAAAGCAAGACACCCTATTA
5146788 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
131 ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
*
5146853 TCCCAACCGAAAATGGTCACCCACTTAACT-ATTACCAATACCACAACACAGATATTCATAAACT
196 TCCCAACCGAAAATGGTCACCCACTTAA-TGATTACCAATACCACAACACAAATATTCATAAACT
* * *
5146917 AACTAGGACAAAATAGTGGCTAAGAGGAGTATTCGATTTTAATGAAAAGAAAGAAAGAGAACCGA
260 AACTAGGACAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAA
* * *
5146982 TTTTAAACAAAAATTGAAGAGTATTCAAACTTTACCGATAATCAGGAATACTTGCAGCACTGAGA
325 TTTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGA
* * *
5147047 CAGTAAAAATAG-CAAGGAGAATATCGGCT-CAGAGGAATA-ATGCAAAAGGTGATAATCTGTTG
390 CAGTAAAAATAGTCAA-GAGAAGATCGG-TGCAGAGGAATAGA-GCAAAAGGTGATAATCGGCTG
*
5147109 AACTACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAAT
452 AACCACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAAT
5147174 AAAATCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
517 AAAATCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
5147228 G
1 G
5147229 AGGTCAGAGA
Statistics
Matches: 538, Mismatches: 29, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
569 3 0.01
570 533 0.99
571 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (570 bp):
GGCTTTTCGCCGATCTACGGTTGCAGTGGGTGATTACACACCTGATTACGAGAAACGCGCAAACC
TCCACGCACACCAACCTAGATTTCATCAAATCACAAGTCAGCCCTTAAAGCAAGACACCCTATTA
ATAACACTTAAACCACACACCATCCTTACCTTGCTTGATAGAAGGTGACTTAACTCCTTCAAGAC
TCCCAACCGAAAATGGTCACCCACTTAATGATTACCAATACCACAACACAAATATTCATAAACTA
ACTAGGACAAAATAGTGGCCAAGAGGAGTATTCAATTTTAATGAAAAGAAAGAAAGAGAACCAAT
TTTAAACAAAAAGTGAAGAGTATTCAAACTTTACCGATAACCAGGAATACTTGCAGCACCGAGAC
AGTAAAAATAGTCAAGAGAAGATCGGTGCAGAGGAATAGAGCAAAAGGTGATAATCGGCTGAACC
ACACTCCAAATAGAGAGATCGCTCTCAGTCAAAAAGAGAAGAAAATAATAAAAGGTAAAATAAAA
TCAGAACAGAAAGAAAGAGAGGGATAACCTGTCAAAGAAAAAGAGGAGGA
Found at i:5149410 original size:22 final size:22
Alignment explanation
Indices: 5149374--5149417 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5149364 TAGCATGTTG
*
5149374 AAATTTTCTTAATTTT-ATAAT
1 AAATTTTATTAATTTTGATAAT
5149395 AAATTTTGATTAATTTTGATAAT
1 AAATTTT-ATTAATTTTGATAAT
5149418 TTTCGACAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
AAATTTTATTAATTTTGATAAT
Found at i:5156130 original size:13 final size:13
Alignment explanation
Indices: 5156112--5156136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5156102 CGGCGATCAT
5156112 CCATCTGATTCCC
1 CCATCTGATTCCC
5156125 CCATCTGATTCC
1 CCATCTGATTCC
5156137 ATCATTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.08, T:0.32
Consensus pattern (13 bp):
CCATCTGATTCCC
Found at i:5158602 original size:21 final size:22
Alignment explanation
Indices: 5158544--5158602 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
5158534 AAATTAAATC
*
5158544 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATATATCATA--T
**
5158567 TCTAAGATTGTATATATCATA-
1 TCTAAGATTACATATATCATAT
5158588 TCTAAGATTACATAT
1 TCTAAGATTACATAT
5158603 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 13 0.43
23 10 0.33
24 7 0.23
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (22 bp):
TCTAAGATTACATATATCATAT
Found at i:5163381 original size:29 final size:30
Alignment explanation
Indices: 5163339--5163401 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 30
5163329 ACAATATCAA
*
5163339 AAATAATTTGATCTTTATCCAGCCAA-TTT
1 AAATAATTTAATCTTTATCCAGCCAACTTT
5163368 CAAAT-ATTTAATCTTTATCCAGCCAACTTT
1 -AAATAATTTAATCTTTATCCAGCCAACTTT
5163398 AAAT
1 AAAT
5163402 CTCCAATCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATAATTTAATCTTTATCCAGCCAACTTT
Found at i:5163409 original size:29 final size:29
Alignment explanation
Indices: 5163349--5163412 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
5163339 AAATAATTTG
**
5163349 ATCTTTATCCAGCCAATTTCAAATATTTA
1 ATCTTTATCCAGCCAATTTCAAATATCCA
*
5163378 ATCTTTATCCAGCCAACTTT-AAATCTCCA
1 ATCTTTATCCAGCCAA-TTTCAAATATCCA
5163407 ATCTTT
1 ATCTTT
5163413 CAATCTACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (29 bp):
ATCTTTATCCAGCCAATTTCAAATATCCA
Found at i:5164277 original size:26 final size:27
Alignment explanation
Indices: 5164189--5164297 Score: 118
Period size: 26 Copynumber: 4.2 Consensus size: 27
5164179 TCATTAGGCG
* *
5164189 TAGCAGGCTTTGTGCCA-ATGTATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
* * * *
5164215 TAGTAGGCTTCGAGCC-GATATATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
*
5164241 TAGTAAGCTTTGAG-CAGATGTATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
*
5164267 TAGCAAGCTTTGTGCCAG-TGTATATT
1 TAGCAAGCTTTGAGCCAGATGTATATT
5164293 TAGCA
1 TAGCA
5164298 GGTACTATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.01
26 67 0.94
27 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (27 bp):
TAGCAAGCTTTGAGCCAGATGTATATT
Found at i:5169749 original size:30 final size:31
Alignment explanation
Indices: 5169715--5169782 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
5169705 TTCCCCAAGA
** * * *
5169715 GTAAATACTCAAAATTTGAGGGGTTAA-AGT
1 GTAAATACGAAAAATTTGAAGGATCAATAGT
5169745 GTAAATACGAAAAATTTGAAGGATCAATAGT
1 GTAAATACGAAAAATTTGAAGGATCAATAGT
5169776 GTAAATA
1 GTAAATA
5169783 TTTTAAGAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.28
Consensus pattern (31 bp):
GTAAATACGAAAAATTTGAAGGATCAATAGT
Found at i:5174220 original size:50 final size:50
Alignment explanation
Indices: 5174162--5174284 Score: 165
Period size: 50 Copynumber: 2.5 Consensus size: 50
5174152 ATTGAGGTTC
* * *
5174162 TGAGAGGTCCCATGTAAGACCATGTCTCGGACATGGCGTTGGCACCGAGA
1 TGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGA
* * * *
5174212 TGAGAGGTCCCCTGTAAAACCATGTCTATGACATGGCATGGGCACCGATA
1 TGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGA
**
5174262 TGAGAACTCCCATGTAAGACCAT
1 TGAGAGGTCCCATGTAAGACCAT
5174285 ATCTGGGTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (50 bp):
TGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGA
Found at i:5174582 original size:20 final size:20
Alignment explanation
Indices: 5174557--5174595 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5174547 TGATTTATTT
5174557 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
5174577 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
5174596 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:5197810 original size:24 final size:24
Alignment explanation
Indices: 5197751--5197815 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 24
5197741 TTAAAACGTT
5197751 TTCTAT-A-AGTCTTTTTTGTCTG
1 TTCTATAAGAGTCTTTTTTGTCTG
5197773 TTCTGTACTTTAAGAGTCTTTTTTGTCTG
1 TTC--TA---TAAGAGTCTTTTTTGTCTG
5197802 TTCTATAAGAGTCT
1 TTCTATAAGAGTCT
5197816 ATAATACTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
22 3 0.08
24 11 0.31
27 3 0.08
28 1 0.03
29 18 0.50
ACGTcount: A:0.17, C:0.14, G:0.15, T:0.54
Consensus pattern (24 bp):
TTCTATAAGAGTCTTTTTTGTCTG
Found at i:5198167 original size:21 final size:21
Alignment explanation
Indices: 5198143--5198182 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5198133 TTTTACGTTT
5198143 TTTCTCTCAAAGGCCTAAAAC
1 TTTCTCTCAAAGGCCTAAAAC
5198164 TTTCTCTCAAAGGCCTAAA
1 TTTCTCTCAAAGGCCTAAA
5198183 GTCTCACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCTCTCAAAGGCCTAAAAC
Found at i:5201633 original size:29 final size:29
Alignment explanation
Indices: 5201601--5201658 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
5201591 TGTATAACCC
* *
5201601 ATATTAATTTGA-AAATAATTTCTTATTTT
1 ATATTAATTTGATAAA-AATCTCTAATTTT
*
5201630 ATATTATTTTGATAAAAATCTCTAATTTT
1 ATATTAATTTGATAAAAATCTCTAATTTT
5201659 TAAACTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (29 bp):
ATATTAATTTGATAAAAATCTCTAATTTT
Found at i:5202926 original size:18 final size:17
Alignment explanation
Indices: 5202903--5202962 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
5202893 TATGATATGG
5202903 AACTTATTCAGTTTATTA
1 AACTTATTCAGTTTA-TA
*
5202921 AACTTAATTAAAG--TATA
1 AACTT-ATT-CAGTTTATA
5202938 AACTTATTTCAGTTTATA
1 AACTTA-TTCAGTTTATA
5202956 AA-TTATT
1 AACTTATT
5202963 TGAAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
16 5 0.14
17 12 0.34
18 13 0.37
19 3 0.09
20 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (17 bp):
AACTTATTCAGTTTATA
Found at i:5204124 original size:22 final size:22
Alignment explanation
Indices: 5204096--5204145 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
5204086 ACAAATCCTA
5204096 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
* *
5204118 TCTCAATTTCCTTTCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
5204140 TCTCAA
1 TCTCAA
5204146 ACTCTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:5204151 original size:30 final size:30
Alignment explanation
Indices: 5204117--5204175 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5204107 TTCCAAAATC
* *
5204117 CTCTCAATTTCCTTTCAAAATTCTCTCAAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAAA
5204147 CTCTCAATTTCCTTCCAAAATCCTCTCAA
1 CTCTCAATTTCCTTCCAAAATCCTCTCAA
5204176 TTTCCTTNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (30 bp):
CTCTCAATTTCCTTCCAAAATCCTCTCAAA
Found at i:5205256 original size:7 final size:7
Alignment explanation
Indices: 5205244--5205275 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5205234 AGTAGATTGA
5205244 TATTTAG
1 TATTTAG
5205251 TATTTAG
1 TATTTAG
5205258 TATTTAG
1 TATTTAG
*
5205265 TATTTTG
1 TATTTAG
5205272 TATT
1 TATT
5205276 ATGTATGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
TATTTAG
Found at i:5206975 original size:29 final size:29
Alignment explanation
Indices: 5206485--5206974 Score: 863
Period size: 29 Copynumber: 16.7 Consensus size: 29
5206475 AAAAATTTAA
* *
5206485 TTTAATTAAAAACCCTAAACACTAACCTAA
1 TTTAATTAAAAACCCT-AACCCTAACCTAT
5206515 TTTAATTAAAAACCCTAACCCTAACCTAATT
1 TTTAATTAAAAACCCTAACCCTAACCT-A-T
*
5206546 TAATTAAAATAAAAACCCTAACCCTAACCTAT
1 T--TT-AATTAAAAACCCTAACCCTAACCTAT
5206578 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206607 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206636 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206665 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206694 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206723 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206752 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206781 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206810 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206839 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206868 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAACCCTAACCTAT
*
5206897 TTTAATTAAAAACCCTAACCCTAACCTAA
1 TTTAATTAAAAACCCTAACCCTAACCTAT
* * *
5206926 TTTAATTAAAACCCCTAACCTTAACCTAA
1 TTTAATTAAAAACCCTAACCCTAACCTAT
5206955 TTTAATTAAAAACCCTAACC
1 TTTAATTAAAAACCCTAACC
5206975 TAGTTTATTT
Statistics
Matches: 447, Mismatches: 8, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
29 399 0.89
30 19 0.04
31 1 0.00
32 2 0.00
33 3 0.01
34 23 0.05
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (29 bp):
TTTAATTAAAAACCCTAACCCTAACCTAT
Found at i:5207057 original size:56 final size:56
Alignment explanation
Indices: 5206997--5207121 Score: 205
Period size: 56 Copynumber: 2.2 Consensus size: 56
5206987 AAACCATAAC
* * **
5206997 ATAATTTTACCTAATTTGATAATCTTACTAACCATTAACACACTTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAATCTTACTAACCATTAACAAAAGTTTTTGGGCTTA
*
5207053 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAAGTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAATCTTACTAACCATTAACAAAAGTTTTTGGGCTTA
5207109 ATAATTTTACATA
1 ATAATTTTACATA
5207122 GTTTTATATA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAATCTTACTAACCATTAACAAAAGTTTTTGGGCTTA
Found at i:5210163 original size:123 final size:123
Alignment explanation
Indices: 5209945--5210221 Score: 459
Period size: 123 Copynumber: 2.3 Consensus size: 123
5209935 TCACGAGGGC
*
5209945 GCGATTTTATA-TATTTGCTCAGAAACGTCAAAAAAATTATTGCTTACATGACCAACTGTAGCGA
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTGCTTACATGACCAACTGTAGCGA
* *
5210009 AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTGGTATAA
66 AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTAGTAGAA
* *
5210067 GCGATTTTATACTATTTGCTCAGAAATGTCAAAAAAAATATTTCTTACATGACCAACTGTAGCGA
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTGCTTACATGACCAACTGTAGCGA
*
5210132 AATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
66 AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTAGTAGAA
* *
5210190 GCTATTTTATACTATTTGAC-CAGAACCGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
5210222 CTCGAAATAA
Statistics
Matches: 144, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
122 11 0.08
123 132 0.92
124 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (123 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTGCTTACATGACCAACTGTAGCGA
AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTAGTAGAA
Found at i:5211690 original size:43 final size:43
Alignment explanation
Indices: 5211550--5211693 Score: 180
Period size: 43 Copynumber: 3.3 Consensus size: 43
5211540 TTTATGTGAA
* * *
5211550 AAAAATGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTATA
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
* * * * *
5211593 AAAAATGCCGCTAAAGAACATGTCTTTTAGCGGCGCTTTAACC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
* *
5211636 ACAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTATC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
* *
5211679 ATAAACACCGCTAAA
1 AAAAACGCCGCTAAA
5211694 CAAACTCCGT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
Found at i:5211709 original size:57 final size:57
Alignment explanation
Indices: 5211636--5211750 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
5211626 CGCTTTAACC
* *
5211636 ACAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTATCATAAACACCGCTAA
1 ACAAACGCCGCTAAAGAACATAACCTTTAGCAGCGCTTTTATCACAAACACCGCTAA
* * * * *
5211693 ACAAACTCCGTTAAAGAATATAACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 ACAAACGCCGCTAAAGAACATAACCTTTAGCAGCGCTTTTATCACAAACACCGCTAA
5211750 A
1 A
5211751 GAGCATGACC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.23
Consensus pattern (57 bp):
ACAAACGCCGCTAAAGAACATAACCTTTAGCAGCGCTTTTATCACAAACACCGCTAA
Found at i:5211762 original size:43 final size:43
Alignment explanation
Indices: 5211715--5211879 Score: 188
Period size: 43 Copynumber: 3.8 Consensus size: 43
5211705 AAAGAATATA
5211715 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
* * *
5211758 ACCTTTTGCGGCGCTTTTATCACAAACGCTGCTATAA-AGAATG
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTA-AAGAGCATG
* * ** * ** *
5211801 ACTTTTAGTGGCTTTTTTTTCACAAATTCCGCTAAAGAACATG
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
* * *
5211844 ATCTTTAGCGGCGCTTTTATCACAAATGCCGTTAAA
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAA
5211880 AGTACCGTTC
Statistics
Matches: 98, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
42 2 0.02
43 94 0.96
44 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (43 bp):
ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
Found at i:5214959 original size:42 final size:43
Alignment explanation
Indices: 5214905--5215015 Score: 136
Period size: 42 Copynumber: 2.6 Consensus size: 43
5214895 TATTTGAGAT
5214905 TTACGTGTAAGACCATGTCTGGGAC-GTTGACATCG-TATATGA
1 TTACGTGTAAGACCATGTCTGGGACAG-TGACATCGTTATATGA
* * * *
5214947 TTACGTGTAAGACCCTGTCTAGGACAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
* * *
5214990 TTGCATGTAAGACCATGTTTGGGACA
1 TTACGTGTAAGACCATGTCTGGGACA
5215016 TTGGCATTGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 30 0.52
43 28 0.48
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
Found at i:5215002 original size:43 final size:42
Alignment explanation
Indices: 5214905--5215022 Score: 130
Period size: 43 Copynumber: 2.8 Consensus size: 42
5214895 TATTTGAGAT
* *
5214905 TTACGTGTAAGACCATGTCTGGGAC-GTTGACATCGTATATGA
1 TTACATGTAAGACCATGTCTGGGACAG-TGGCATCGTATATGA
* * * *
5214947 TTACGTGTAAGACCCTGTCTAGGACAGTGGCATCGTTATTTGA
1 TTACATGTAAGACCATGTCTGGGACAGTGGCATCG-TATATGA
* * *
5214990 TTGCATGTAAGACCATGTTTGGGACATTGGCAT
1 TTACATGTAAGACCATGTCTGGGACAGTGGCAT
5215023 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 30 0.47
43 34 0.53
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACAGTGGCATCGTATATGA
Found at i:5215491 original size:2 final size:2
Alignment explanation
Indices: 5215484--5215512 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5215474 TTTGAAATTG
5215484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5215513 GTAAAGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5218048 original size:7 final size:7
Alignment explanation
Indices: 5218018--5218180 Score: 90
Period size: 7 Copynumber: 23.6 Consensus size: 7
5218008 CTTAGGCCCC
5218018 TAAACCT
1 TAAACCT
5218025 TAAA-CT
1 TAAACCT
*
5218031 CTAAACTT
1 -TAAACCT
5218039 TAAACCT
1 TAAACCT
*
5218046 TAAACCC
1 TAAACCT
* *
5218053 TAAGCCCC
1 TAA-ACCT
5218061 T-AACACT
1 TAAAC-CT
5218068 TAAACCT
1 TAAACCT
5218075 TAAACCT
1 TAAACCT
5218082 TAAACAC-
1 TAAAC-CT
*
5218089 TAAACCA
1 TAAACCT
5218096 TAAACC-
1 TAAACCT
* *
5218102 TACACCC
1 TAAACCT
*
5218109 TAAA-TT
1 TAAACCT
5218115 GTAAACAC-
1 -TAAAC-CT
* *
5218123 TAAATCA
1 TAAACCT
*
5218130 TAAACCC
1 TAAACCT
5218137 TAAACCT
1 TAAACCT
5218144 TAAA-CT
1 TAAACCT
* *
5218150 CAAACCA
1 TAAACCT
5218157 TAAACC-
1 TAAACCT
*
5218163 TACACCT
1 TAAACCT
5218170 TAAACCT
1 TAAACCT
5218177 TAAA
1 TAAA
5218181 TATATATTAC
Statistics
Matches: 122, Mismatches: 20, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
6 20 0.16
7 93 0.76
8 9 0.07
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAACCT
Found at i:5218070 original size:43 final size:43
Alignment explanation
Indices: 5218002--5218094 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
5217992 AAATTAGACC
* * *
5218002 CTAAACCTTAGGCCCCTAAACCTTAAA-CTCTAAACTTTAAAC-
1 CTAAACCCTAAGCCCCTAAACCTTAAACCT-TAAACCTTAAACA
5218044 CTTAAACCCTAAGCCCCT-AACACTTAAACCTTAAACCTTAAACA
1 C-TAAACCCTAAGCCCCTAAAC-CTTAAACCTTAAACCTTAAACA
5218088 CTAAACC
1 CTAAACC
5218095 ATAAACCTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
42 4 0.09
43 37 0.84
44 3 0.07
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.24
Consensus pattern (43 bp):
CTAAACCCTAAGCCCCTAAACCTTAAACCTTAAACCTTAAACA
Found at i:5218355 original size:7 final size:7
Alignment explanation
Indices: 5218343--5218389 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
5218333 TATAAAATAG
5218343 TAAACCC
1 TAAACCC
5218350 TAAACCC
1 TAAACCC
*
5218357 TAAACTC
1 TAAACCC
*
5218364 TAAACCA
1 TAAACCC
*
5218371 TAAACCA
1 TAAACCC
5218378 TAAACCC
1 TAAACCC
5218385 TAAAC
1 TAAAC
5218390 TCAAAACTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:5218366 original size:14 final size:14
Alignment explanation
Indices: 5218343--5218401 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
5218333 TATAAAATAG
*
5218343 TAAACCCTAAACCC
1 TAAACTCTAAACCC
*
5218357 TAAACTCTAAACCA
1 TAAACTCTAAACCC
5218371 TAAAC-CATAAACCC
1 TAAACTC-TAAACCC
* *
5218385 TAAACTCAAAACTC
1 TAAACTCTAAACCC
5218399 TAA
1 TAA
5218402 TCCTAAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 1 0.03
14 36 0.95
15 1 0.03
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:5218460 original size:14 final size:14
Alignment explanation
Indices: 5218426--5218486 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
5218416 ATATATATCA
* *
5218426 TAAACCCTAAAAAGC
1 TAAACCATAAACA-C
*
5218441 TAAACCATAAACAT
1 TAAACCATAAACAC
* *
5218455 TAAACCTTAAATAC
1 TAAACCATAAACAC
* *
5218469 TAAACCCTAAACCC
1 TAAACCATAAACAC
5218483 TAAA
1 TAAA
5218487 ATAAAATGAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACAC
Found at i:5218479 original size:28 final size:29
Alignment explanation
Indices: 5218426--5218480 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
5218416 ATATATATCA
5218426 TAAACCCTAAAAAGCTAAACCATAAACAT
1 TAAACCCTAAAAAGCTAAACCATAAACAT
* * *
5218455 TAAACCTTAAATA-CTAAACCCTAAAC
1 TAAACCCTAAAAAGCTAAACCATAAAC
5218481 CCTAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.53, C:0.25, G:0.02, T:0.20
Consensus pattern (29 bp):
TAAACCCTAAAAAGCTAAACCATAAACAT
Found at i:5218905 original size:72 final size:71
Alignment explanation
Indices: 5218779--5218937 Score: 273
Period size: 72 Copynumber: 2.2 Consensus size: 71
5218769 ATTTTTTGAC
* *
5218779 AAAGCACCGCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTTGTGACGT
1 AAAGCGCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAAC-TTTTTGTGACGT
5218844 TTTCCAA
65 TTTCCAA
* *
5218851 ATAGCTCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTGTGACGTT
1 AAAGCGCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTGTGACGTT
5218916 TTCCAA
66 TTCCAA
5218922 AAAGCGCCCCTAATGC
1 AAAGCGCCCCTAATGC
5218938 TAGATCTATA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 33 0.40
72 49 0.60
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (71 bp):
AAAGCGCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTGTGACGTT
TTCCAA
Found at i:5219049 original size:81 final size:80
Alignment explanation
Indices: 5218913--5219062 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 80
5218903 TTTTTGTGAC
* * *
5218913 GTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATATCGGCGTTTTTCCAATAGCACCGCTAATGC
1 GTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGC
5218978 TTGATTTATAACGGT
66 TTGATTTATAACGGT
* * * *
5218993 GTTTTTCAAAAAGTGCCCACTAATGCTCGATCTATAGCGGCGTTTTTTAAAAAGCACCGCTAATG
1 GTTTTCCAAAAAGCGCCC-CTAATGCTAGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATG
5219058 CTTGA
65 CTTGA
5219063 CCTATAGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 16 0.26
81 46 0.74
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (80 bp):
GTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGC
TTGATTTATAACGGT
Found at i:5219069 original size:40 final size:40
Alignment explanation
Indices: 5218912--5219071 Score: 169
Period size: 40 Copynumber: 4.0 Consensus size: 40
5218902 CTTTTTGTGA
* * * * *
5218912 CGTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATATCGG
1 CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCGG
* * * *
5218952 CGTTTTTCCAATAGCACCGCTAATGCTTGATTTATAACGG
1 CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCGG
* * *
5218992 TGTTTTTCAAAAAGTGC-CCACTAATGCTCGATCTATAGCGG
1 CGTTTTTCAAAAA--GCACCGCTAATGCTTGATCTATAGCGG
* *
5219033 CGTTTTTTAAAAAGCACCGCTAATGCTTGACCTATAGCG
1 CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCG
5219072 ACATTTGTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 2 0.02
40 62 0.64
41 31 0.32
42 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCGG
Found at i:5221945 original size:48 final size:48
Alignment explanation
Indices: 5221744--5221945 Score: 116
Period size: 46 Copynumber: 4.3 Consensus size: 48
5221734 CTATTTTTTG
* * * *
5221744 TGTAGGTTTAACCCTTACGAGTGATC-AGACACTATTATCCGAT-TCG-
1 TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTC-ATATTGT
* * * *
5221790 TGTAAGTTCAACCCTTACG-GTTGACCAAG-GACTATGATTTATTATT-T
1 TGTAGGTTTAACCCTTACGAG-TGACCAAGACACTATGATTCA-TATTGT
* * * * * * * **
5221837 GTGTAGGTTTAATCCTTATGGGTGA-CTAGACAGTATTATTC-GATTCA
1 -TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTCATATTGT
* * *
5221884 TGTAGATTCAACCCTTACGAGTGACCAAGA-ATTATGATTCATTATTGT
1 TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTCA-TATTGT
5221932 TGTAGGTTTAACCC
1 TGTAGGTTTAACCC
5221946 AAATGGGTAA
Statistics
Matches: 112, Mismatches: 32, Indels: 22
0.67 0.19 0.13
Matches are distributed among these distances:
45 2 0.02
46 59 0.53
47 10 0.09
48 40 0.36
49 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (48 bp):
TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTCATATTGT
Found at i:5221952 original size:94 final size:94
Alignment explanation
Indices: 5221740--5221968 Score: 277
Period size: 94 Copynumber: 2.4 Consensus size: 94
5221730 CATGCTATTT
* * *
5221740 TTTGTGTAGGTTTAACCCTTACGAGTGA-TCAGACACTATTATCCGATTCGTGTAAGTTCAACCC
1 TTTGTGTAGGTTTAACCCTTATGGGTGACT-AGACACTATTATCCGATTCATGTAAGTTCAACCC
* *
5221804 TTACGGTTGACCAAGGACTATGATTTATTA
65 TTACGGTTGACCAAGAACTATGATTCATTA
* * *
5221834 TTTGTGTAGGTTTAATCCTTATGGGTGACTAGACAGTATTATTCGATTCATGT-AGATTCAACCC
1 TTTGTGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCATGTAAG-TTCAACCC
*
5221898 TTACGAG-TGACCAAGAATTATGATTCATTA
65 TTACG-GTTGACCAAGAACTATGATTCATTA
** * *
5221928 -TTGTTGTAGGTTTAACCCAAATGGGTAACCAGACACTATTA
1 TTTG-TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTA
5221969 CTTTTACCTG
Statistics
Matches: 116, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
93 5 0.04
94 109 0.94
95 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (94 bp):
TTTGTGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCATGTAAGTTCAACCCT
TACGGTTGACCAAGAACTATGATTCATTA
Found at i:5224578 original size:24 final size:24
Alignment explanation
Indices: 5224551--5224600 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5224541 CGATGTACTA
5224551 TCAGTCTAATCACTCACATCTATG
1 TCAGTCTAATCACTCACATCTATG
*
5224575 TCAGTCTAATCAGTCACATCTATG
1 TCAGTCTAATCACTCACATCTATG
5224599 TC
1 TC
5224601 TTTATCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (24 bp):
TCAGTCTAATCACTCACATCTATG
Found at i:5236761 original size:25 final size:25
Alignment explanation
Indices: 5236733--5236805 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 25
5236723 CCTGATATAT
5236733 GGCTCTTCGAAGCTTCTCGATTAAA
1 GGCTCTTCGAAGCTTCTCGATTAAA
*
5236758 GGCTCTTTC-ATGAGCTTC-CTGATTAAT
1 GGCTC-TTCGA--AGCTTCTC-GATTAAA
* *
5236785 GGCTCTGCGGAGCTTCTCGAT
1 GGCTCTTCGAAGCTTCTCGAT
5236806 ATTGGCTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
25 15 0.38
26 7 0.18
27 17 0.44
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (25 bp):
GGCTCTTCGAAGCTTCTCGATTAAA
Found at i:5236848 original size:24 final size:24
Alignment explanation
Indices: 5236794--5236848 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
5236784 TGGCTCTGCG
5236794 GAGCTTCTCGATATTGGCTCGCTT
1 GAGCTTCTCGATATTGGCTCGCTT
*
5236818 GAACTTCTCGATATTGGCTCG-TAT
1 GAGCTTCTCGATATTGGCTCGCT-T
5236842 GAGCTTC
1 GAGCTTC
5236849 CTGTAAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (24 bp):
GAGCTTCTCGATATTGGCTCGCTT
Found at i:5236929 original size:24 final size:24
Alignment explanation
Indices: 5236880--5236935 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
5236870 TTTTTGTTAC
* *
5236880 ATGGCTC-ACATATCTTCCCTTAT
1 ATGGCTCGAAATAGCTTCCCTTAT
5236903 ATGGCTCGAAATAGCTTCCCGTT-T
1 ATGGCTCGAAATAGCTTCCC-TTAT
5236927 ATGTGCTCG
1 ATG-GCTCG
5236936 TATAAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 14 0.50
25 7 0.25
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (24 bp):
ATGGCTCGAAATAGCTTCCCTTAT
Found at i:5237423 original size:107 final size:107
Alignment explanation
Indices: 5237237--5237453 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 107
5237227 ATGATATGTG
5237237 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
1 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
**
5237302 AAGTTAATTACCATGTTATATGAACTTACTAAGCTTTAAAGC
66 AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
*
5237344 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGT
1 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
5237409 AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
66 AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
5237451 TTA
1 TTA
5237454 CTCTATTTTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.41
Consensus pattern (107 bp):
TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
Found at i:5240382 original size:20 final size:22
Alignment explanation
Indices: 5240357--5240398 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
5240347 GATATTTATG
*
5240357 TATATTTGTTT-T-TTATTTTA
1 TATATTTATTTATCTTATTTTA
5240377 TATATTTATTTATCTTATTTTA
1 TATATTTATTTATCTTATTTTA
5240399 GTTAGTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TATATTTATTTATCTTATTTTA
Found at i:5241172 original size:21 final size:20
Alignment explanation
Indices: 5241126--5241181 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
5241116 CATGGGCTGC
5241126 TCACACGGGCGTGTGCCCCT
1 TCACACGGGCGTGTGCCCCT
*
5241146 TCCACACGGGCATGTGTG-GCCT
1 T-CACACGGGC--GTGTGCCCCT
*
5241168 TCACATGGGCGTGT
1 TCACACGGGCGTGT
5241182 AGACCCCCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 4 0.13
20 1 0.03
21 17 0.55
22 4 0.13
23 5 0.16
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.23
Consensus pattern (20 bp):
TCACACGGGCGTGTGCCCCT
Found at i:5245511 original size:3 final size:3
Alignment explanation
Indices: 5245505--5245538 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5245495 TGATGATGAT
*
5245505 GAG GAG GAG GAG GAG GAG GAG GAG AAG GATG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA-G GAG
5245539 ATGGAGAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.62, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:5248135 original size:16 final size:16
Alignment explanation
Indices: 5248116--5248156 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5248106 AAACTTAAGG
5248116 TGATTTGAACTAGAAA
1 TGATTTGAACTAGAAA
* * *
5248132 TGATTAGGACTCGAAA
1 TGATTTGAACTAGAAA
5248148 TGATTTGAA
1 TGATTTGAA
5248157 TAAATAATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (16 bp):
TGATTTGAACTAGAAA
Found at i:5251420 original size:45 final size:44
Alignment explanation
Indices: 5251369--5251461 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
5251359 AGGTGGCTGT
** *
5251369 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAAACGTAACAGT-ATTC-ATGTGTTTGGTTGAATGG
* *
5251414 AATGGAATAGAAATGTAACAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAAACGTAACAGTATTCATGTGTTTGGTTGAATGG
5251458 AATG
1 AATG
5251462 ATGTTGCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.55
45 18 0.43
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (44 bp):
AATGGAATAGAAACGTAACAGTATTCATGTGTTTGGTTGAATGG
Found at i:5254246 original size:34 final size:34
Alignment explanation
Indices: 5254207--5254275 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
5254197 ATCACAAACT
5254207 TTAGACAGTAATCAAAATACCATGATCAAATATA
1 TTAGACAGTAATCAAAATACCATGATCAAATATA
*
5254241 TTAGACAGTAATTAAAATACCATGATCAAATATA
1 TTAGACAGTAATCAAAATACCATGATCAAATATA
5254275 T
1 T
5254276 CTTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (34 bp):
TTAGACAGTAATCAAAATACCATGATCAAATATA
Found at i:5257839 original size:67 final size:67
Alignment explanation
Indices: 5257709--5257839 Score: 156
Period size: 67 Copynumber: 2.0 Consensus size: 67
5257699 AGAGGTTTAA
* * * * *
5257709 AGGTGTAAAACCATAGCTCGGCTATGGCAACCACTAGAGTCTACCAGGACATTGAACATGGGGTT
1 AGGTGTAAAACCATAGCTCGACTATGGCAACCAATAGAGTCTACCAGGACAATAAACACGGGGTT
5257774 AT
66 AT
* * * * *
5257776 AGGTGTAAGATCATAGCTCGACTATGGTAACCAAT-GAAGTCTACCGGGACAATAAATACGGGGT
1 AGGTGTAAAACCATAGCTCGACTATGGCAACCAATAG-AGTCTACCAGGACAATAAACACGGGGT
5257840 AGTTCATCAG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 1 0.02
67 52 0.98
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (67 bp):
AGGTGTAAAACCATAGCTCGACTATGGCAACCAATAGAGTCTACCAGGACAATAAACACGGGGTT
AT
Found at i:5260371 original size:16 final size:16
Alignment explanation
Indices: 5260350--5260384 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5260340 ACAAAAAGAA
5260350 TTTTTTGCAGTTTACT
1 TTTTTTGCAGTTTACT
5260366 TTTTTTGCAGTTTACT
1 TTTTTTGCAGTTTACT
5260382 TTT
1 TTT
5260385 CTTAGCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTTTTGCAGTTTACT
Found at i:5268038 original size:27 final size:27
Alignment explanation
Indices: 5268008--5268284 Score: 267
Period size: 27 Copynumber: 10.3 Consensus size: 27
5267998 CAAGATACGA
* *
5268008 CACAAATGCATTCCTTTCAGAGCAAGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* *
5268035 CAC-AA-GCATTTCTTTCAGAGTATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
5268060 CACAAAGGCATTCCTTTCAGAGTACA-C
1 CACAAAGGCATTCCTTTCAGAGTA-AGC
*
5268087 TACAAAGGCATTCCTTTCAGAGTACA-C
1 CACAAAGGCATTCCTTTCAGAGTA-AGC
* *
5268114 TACAAAGGCATTCCTTTCAGAGTATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* * *
5268141 CACAAAGGCATTCTTTTCAGAATATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* * * *
5268168 CATAAATGCATTCCTGTCAGAGTACGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* ** *
5268195 CATAAAGTTATTCCTTTTAGAGTACA-C
1 CACAAAGGCATTCCTTTCAGAGTA-AGC
* * *
5268222 CAAAAAGGCATTTCTTTCAGAGTACGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
** * *
5268249 CACAAAGGCATTTATTTCAAAGTATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
5268276 CACAAAGGC
1 CACAAAGGC
5268285 TAACACGATG
Statistics
Matches: 212, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
25 20 0.09
26 4 0.02
27 188 0.89
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (27 bp):
CACAAAGGCATTCCTTTCAGAGTAAGC
Found at i:5268144 original size:81 final size:81
Alignment explanation
Indices: 5267977--5268284 Score: 291
Period size: 81 Copynumber: 3.8 Consensus size: 81
5267967 CATACAGAAC
* * ** * * *
5267977 ATGCCACAAAAGCAATCCACTCA-AGATACGACACAAATGCATTCCTTTCAGAGCA-AGCCAC-A
1 ATGCCACAAAGGCATTCCTTTCAGAG-TACGCCACAAAGGCATTCCTTTCAGAGTACA-CCACAA
*
5268039 A-GCATTTCTTTCAGAGT
64 AGGCATTCCTTTCAGAGT
* * *
5268056 ATGCCACAAAGGCATTCCTTTCAGAGTACACTACAAAGGCATTCCTTTCAGAGTACACTACAAAG
1 ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
5268121 GCATTCCTTTCAGAGT
66 GCATTCCTTTCAGAGT
* * * * * * * *
5268137 ATGCCACAAAGGCATTCTTTTCAGAATATGCCATAAATGCATTCCTGTCAGAGTACGCCATAAAG
1 ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
** *
5268202 TTATTCCTTTTAGAGT
66 GCATTCCTTTCAGAGT
** * * ** * **
5268218 ACACCAAAAAGGCATTTCTTTCAGAGTACGCCACAAAGGCATTTATTTCAAAGTATGCCACAAAG
1 ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
5268283 GC
66 GC
5268285 TAACACGATG
Statistics
Matches: 183, Mismatches: 42, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
79 46 0.25
80 5 0.03
81 132 0.72
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (81 bp):
ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
GCATTCCTTTCAGAGT
Found at i:5272022 original size:36 final size:36
Alignment explanation
Indices: 5271982--5272058 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
5271972 GGTTCTATGA
*
5271982 ATATATTTTTTAAACACTATTTCTATGAATCAATCC
1 ATATATTTTTTAAACACTATTTCCATGAATCAATCC
5272018 ATATATTTTTTAAACACTATTTCCATGAATCAATCC
1 ATATATTTTTTAAACACTATTTCCATGAATCAATCC
5272054 ATATA
1 ATATA
5272059 ATTTAGTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.43
Consensus pattern (36 bp):
ATATATTTTTTAAACACTATTTCCATGAATCAATCC
Found at i:5272190 original size:19 final size:18
Alignment explanation
Indices: 5272144--5272191 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
5272134 GTTAAATTCT
*
5272144 TGTTGAAAAAAATTAAATA
1 TGTT-AAAATAATTAAATA
5272163 T-TATAAAATAATTAAATTA
1 TGT-TAAAATAATTAAA-TA
5272182 TGTTAAAATA
1 TGTTAAAATA
5272192 TGAACATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TGTTAAAATAATTAAATA
Found at i:5278892 original size:27 final size:27
Alignment explanation
Indices: 5278873--5279098 Score: 310
Period size: 27 Copynumber: 8.4 Consensus size: 27
5278863 GGGTATAAAA
5278873 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
5278900 ATCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
5278927 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
5278954 GTCATTTTACCTTATGAGGGCATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
5278981 CTCATTTTACCCTATGGGGGTGTTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
5279008 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
5279035 ATCATTTTACCCTAT-GGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
5279061 ATCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
5279088 GTCATTTTACC
1 GTCATTTTACC
5279099 TATTTTAGGG
Statistics
Matches: 173, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 24 0.14
27 149 0.86
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:5279923 original size:23 final size:23
Alignment explanation
Indices: 5279889--5279948 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
5279879 TTCACACCAA
5279889 AATTT-GGACAGCATATATACAAC
1 AATTTAGG-CAGCATATATACAAC
5279912 AATTTAGGCAGCATATATACAAC
1 AATTTAGGCAGCATATATACAAC
*
5279935 ATATTGA-GCAGCAT
1 A-ATTTAGGCAGCAT
5279949 TTTTGCACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 28 0.82
24 6 0.18
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (23 bp):
AATTTAGGCAGCATATATACAAC
Found at i:5279994 original size:70 final size:71
Alignment explanation
Indices: 5279883--5280020 Score: 192
Period size: 70 Copynumber: 2.0 Consensus size: 71
5279873 AGCAATTTCA
* * * *
5279883 CACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGC-ATATATACAACATATTGAGCAGC
1 CACCAAAATTTGGACAGCATATACACAACAAATTAGGCAGCAAT-TACACAACAAATTGAGCAGC
5279947 ATTTTTG
65 ATTTTTG
*
5279954 CACCAAAA-TTGGACAGCTTATACACAACAAATT-GGACAGCAATTACACAACAAATTGAGCAGC
1 CACCAAAATTTGGACAGCATATACACAACAAATTAGG-CAGCAATTACACAACAAATTGAGCAGC
5280017 ATTT
65 ATTT
5280021 AAGCATAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
69 2 0.03
70 48 0.80
71 10 0.17
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (71 bp):
CACCAAAATTTGGACAGCATATACACAACAAATTAGGCAGCAATTACACAACAAATTGAGCAGCA
TTTTTG
Found at i:5280017 original size:23 final size:23
Alignment explanation
Indices: 5279959--5280010 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5279949 TTTTGCACCA
*
5279959 AAATTGGACAGC-TTATACACAAC
1 AAATTGGACAGCAAT-TACACAAC
5279982 AAATTGGACAGCAATTACACAAC
1 AAATTGGACAGCAATTACACAAC
5280005 AAATTG
1 AAATTG
5280011 AGCAGCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.21
Consensus pattern (23 bp):
AAATTGGACAGCAATTACACAAC
Found at i:5280785 original size:28 final size:28
Alignment explanation
Indices: 5280753--5280878 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
5280743 TTTAATAAGT
* * *
5280753 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
*
5280781 TCGCACACTTAGTGCTTCT-CCATTAAAC
1 TCGCACACTTAGTGC-TCTACAATTAAAC
*
5280809 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
* *
5280837 TCGCACACTTAGTGCTTTCCAATTAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
5280865 TCGCACACTTAGTG
1 TCGCACACTTAGTG
5280879 TCGAAAGTCA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
27 2 0.02
28 85 0.96
29 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (28 bp):
TCGCACACTTAGTGCTCTACAATTAAAC
Found at i:5280819 original size:56 final size:56
Alignment explanation
Indices: 5280753--5280878 Score: 200
Period size: 56 Copynumber: 2.2 Consensus size: 56
5280743 TTTAATAAGT
*
5280753 TCGCACACTTAGTGCTCAATAATCAAACTCGCACACTTAGTGCTTCTCC-ATTAAAC
1 TCGCACACTTAGTGCTCAACAATCAAACTCGCACACTTAGTGCTT-TCCAATTAAAC
** *
5280809 TCGCACACTTAGTGCTTTACAATTAAACTCGCACACTTAGTGCTTTCCAATTAAAC
1 TCGCACACTTAGTGCTCAACAATCAAACTCGCACACTTAGTGCTTTCCAATTAAAC
5280865 TCGCACACTTAGTG
1 TCGCACACTTAGTG
5280879 TCGAAAGTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
55 3 0.05
56 62 0.95
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (56 bp):
TCGCACACTTAGTGCTCAACAATCAAACTCGCACACTTAGTGCTTTCCAATTAAAC
Found at i:5288771 original size:25 final size:24
Alignment explanation
Indices: 5288743--5288798 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
5288733 TATTATAAAA
*
5288743 ATAATTTATATGTTATAAAAATATT
1 ATAATTTATATATTATAAAAA-ATT
* * * *
5288768 ATAATATATTTATTTTAAAAAGTT
1 ATAATTTATATATTATAAAAAATT
5288792 ATAATTT
1 ATAATTT
5288799 TTTTTATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
ATAATTTATATATTATAAAAAATT
Found at i:5288823 original size:16 final size:16
Alignment explanation
Indices: 5288802--5288840 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5288792 ATAATTTTTT
* *
5288802 TTATAAATGCTGTATA
1 TTATAAATGATATATA
*
5288818 TTATAAATTATATATA
1 TTATAAATGATATATA
5288834 TTATAAA
1 TTATAAA
5288841 ATTATTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (16 bp):
TTATAAATGATATATA
Found at i:5289629 original size:44 final size:44
Alignment explanation
Indices: 5289561--5289647 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
5289551 TGTAAGTGTT
*
5289561 TAATTACAATTTGTACTACCAAACATG-ACATAAGAAATTACAATG
1 TAATTACAATTTGTACAACCAAACATGTACA-AAG-AATTACAATG
* *
5289606 TAATTACAGTTTG-ACAACCAAACATGTCCAAAGAATTACAAT
1 TAATTACAATTTGTACAACCAAACATGTACAAAGAATTACAAT
5289648 TCTTTGTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 9 0.24
44 15 0.39
45 14 0.37
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (44 bp):
TAATTACAATTTGTACAACCAAACATGTACAAAGAATTACAATG
Found at i:5300093 original size:49 final size:49
Alignment explanation
Indices: 5300003--5300147 Score: 164
Period size: 49 Copynumber: 2.9 Consensus size: 49
5299993 ATGTGAAAAT
* * *
5300003 GTGATTATGTGATTCCCGTGTAAGATCATATCTGGGATATGGCATCGGTAA
1 GTGA-TATGTGATT-CCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
5300054 GTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* ** * * * *
5300103 GTGATAAGTGATTATGTGTAAGACCACAGTTGGACTACGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
5300148 AGAAAACGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
49 68 0.84
50 9 0.11
51 4 0.05
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Done.