Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 202 of 202
Found at i:61958277 original size:81 final size:80
Alignment explanation
Indices: 61958135--61958687 Score: 609
Period size: 81 Copynumber: 6.9 Consensus size: 80
61958125 ATTGACTCAT
* * * *
61958135 ACCACTCATTTAAGA-TTTTTTTTGAACAATCTCATCATAGATTCTGATCATATCTGTTCTTTTT
1 ACCACCCATTTAAGATTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCTCTTTTT
* * *
61958199 TACACAACGTCTAGA
66 GACACAATGCCTAGA
* * *
61958214 ATCACCCATTTAAGATTTTTTTTTTGAACAATCTCATTATAGGTTTTGATTATATCTGCTCTTTT
1 ACCACCCATTTAAGA-TTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCTCTTTT
* *
61958279 TAACACAATGGCTAGA
65 TGACACAATGCCTAGA
* * * * * * *
61958295 ACCACTCATTTAAGATTTTTTTTTTCAACAATCTTATTATAGATTCTGATCATATAT-ATATTTT
1 ACCACCCATTTAAGA-TTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCT-CTTT
61958359 TTGACACAATGCCTAGA
64 TTGACACAATGCCTAGA
* * *
61958376 A-CA--AATTCAAGAGTTTTTTTTTTGAACAATCTCATTATAGGTTTTGATCATATCTGCTCTTT
1 ACCACCCATTTAAGA--TTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCTCTTT
*
61958438 TTGACACAATGACTAGA
64 TTGACACAATGCCTAGA
* * * * *
61958455 ACCATCCATTTAAGA-TTTTTTTTGAACAATCTTATTATAAGTTCTGATCATATATGTTC-TTTT
1 ACCACCCATTTAAGATTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCTCTTTTT
61958518 GACACAATGCCTAGAAGA
66 GACACAATGCCT---AGA
* * * *
61958536 ACCACCCATTTAAGATTATTTTTTGAACAATCTAATTATAAGTTTTGATCATATCTGCTCTTTTT
1 ACCACCCATTTAAGATTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCTCTTTTT
* * *
61958601 GACATAACGTCTAGA
66 GACACAATGCCTAGA
* * ** * *
61958616 ACCACCCATTTAAGATATTTTTTTAAACAATCTCATTATAAATTCCGATCATATTTGCT-TTTTT
1 ACCACCCATTTAAGATTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCTCTTTTT
61958680 GACACAAT
66 GACACAAT
61958688 ACTTAAAACT
Statistics
Matches: 402, Mismatches: 59, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
78 22 0.05
79 120 0.30
80 60 0.15
81 141 0.35
82 46 0.11
83 13 0.03
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (80 bp):
ACCACCCATTTAAGATTTTTTTTTGAACAATCTCATTATAGGTTCTGATCATATCTGCTCTTTTT
GACACAATGCCTAGA
Found at i:61958639 original size:241 final size:239
Alignment explanation
Indices: 61958135--61958687 Score: 636
Period size: 241 Copynumber: 2.3 Consensus size: 239
61958125 ATTGACTCAT
* * *
61958135 ACCACTCATTTAAGATTTTTTTTGAACAATCTCATCATAGATTCTGATCATATCTGTTCTTTTTT
1 ACCAC-CATTTAAGATTTTTTTTGAACAATCTCATTATAGATTCTGATCATATCTGCTCTTTTTG
* * * * * *
61958200 ACACAACGTCTAGAATCACCCATTTAAGATTTTTTTTTTGAACAATCTCATTATAGGTTTTGATT
65 ACACAATGACTAGAACCACCCATTTAAGA-TTTTTTTTTGAACAATCTCATTATAAGTTCTGATC
* * * * *
61958265 ATATCTGCTCTTTTTAACACAATGGCTAGAACCACTCATTTAAGATTTTTTTTTTCAACAATCTT
129 ATATATGCTCTTTTTAACACAATGCCTAGAACCACCCATTTAAGATTTATTTTTTCAACAATCTA
* *
61958330 ATTATAGATTCTGATCATATATATATTTTTTGACACAATGCCTAGA
194 ATTATAGATTCTGATCATATATATACTTTTTGACACAACGCCTAGA
* * * *
61958376 A-CA-AATTCAAGAGTTTTTTTTTTGAACAATCTCATTATAGGTTTTGATCATATCTGCTCTTTT
1 ACCACCATTTAAGA---TTTTTTTTGAACAATCTCATTATAGATTCTGATCATATCTGCTCTTTT
* *
61958439 TGACACAATGACTAGAACCATCCATTTAAGA-TTTTTTTTGAACAATCTTATTATAAGTTCTGAT
63 TGACACAATGACTAGAACCACCCATTTAAGATTTTTTTTTGAACAATCTCATTATAAGTTCTGAT
* * *
61958503 CATATATGTTC-TTTTGACACAATGCCTAGAAGAACCACCCATTTAAGA-TTATTTTTTGAACAA
128 CATATATGCTCTTTTTAACACAATGCCT---AGAACCACCCATTTAAGATTTATTTTTTCAACAA
* * * * *
61958566 TCTAATTATA-AGTTTTGATCATATCTGCT-CTTTTTGACATAACGTCTAGA
190 TCTAATTATAGA-TTCTGATCATATAT-ATACTTTTTGACACAACGCCTAGA
* * * *
61958616 ACCACCCATTTAAGATATTTTTTTAAACAATCTCATTATAAATTCCGATCATATTTGCT-TTTTT
1 ACCA-CCATTTAAGAT-TTTTTTTGAACAATCTCATTATAGATTCTGATCATATCTGCTCTTTTT
61958680 GACACAAT
64 GACACAAT
61958688 ACTTAAAACT
Statistics
Matches: 262, Mismatches: 38, Indels: 25
0.81 0.12 0.08
Matches are distributed among these distances:
238 21 0.08
239 39 0.15
240 68 0.26
241 127 0.48
243 7 0.03
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (239 bp):
ACCACCATTTAAGATTTTTTTTGAACAATCTCATTATAGATTCTGATCATATCTGCTCTTTTTGA
CACAATGACTAGAACCACCCATTTAAGATTTTTTTTTGAACAATCTCATTATAAGTTCTGATCAT
ATATGCTCTTTTTAACACAATGCCTAGAACCACCCATTTAAGATTTATTTTTTCAACAATCTAAT
TATAGATTCTGATCATATATATACTTTTTGACACAACGCCTAGA
Found at i:61963274 original size:21 final size:21
Alignment explanation
Indices: 61963253--61963293 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
61963243 ATAAATTTTA
61963253 AAATTTT-TAAAATATAATTT
1 AAATTTTATAAAATATAATTT
* *
61963273 AAATTTTATAATATTTAATTT
1 AAATTTTATAAAATATAATTT
61963294 TGTAAAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATTTTATAAAATATAATTT
Found at i:61971571 original size:27 final size:29
Alignment explanation
Indices: 61971541--61971597 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
61971531 AAAATTTCTG
*
61971541 AAAATTAAAA-ATTCATTAAAA-TTATAA
1 AAAATAAAAATATTCATTAAAATTTATAA
**
61971568 AAAATAAAAATATTTTTTAAAATTTATAA
1 AAAATAAAAATATTCATTAAAATTTATAA
61971597 A
1 A
61971598 CATGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.36
28 9 0.36
29 7 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATAAAAATATTCATTAAAATTTATAA
Found at i:61971849 original size:21 final size:20
Alignment explanation
Indices: 61971821--61971861 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
61971811 CACCATAATA
*
61971821 TATGTAAATAGGTATTTTTT
1 TATGTAAATAGATATTTTTT
*
61971841 TATGATAAATATATATTTTTT
1 TATG-TAAATAGATATTTTTT
61971862 GTTATGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
TATGTAAATAGATATTTTTT
Found at i:61982218 original size:174 final size:174
Alignment explanation
Indices: 61981928--61982382 Score: 721
Period size: 174 Copynumber: 2.6 Consensus size: 174
61981918 TACTTTTACC
* * * *
61981928 GGATTACACATTAAGTTTTCAAGTTCTATGAGCTCACATACTTGGATTATACTAGTATTAACAAG
1 GGATTACACATTAAGTTTTCAAGTTCTATGAGCTCATAGACATGGAATATACTAGTATTAACAAG
* * * ** *
61981993 CTTACATTCACCATTTTGAAACGATACAATTTCGTTTCCATTGAGAAAACAATGACAACGAGGTT
66 CTTACCTTCACCATTTCGAAACGATACAATTTCATTTCCATCAAGAAAACAATGACAACGAGGTA
61982058 ATTGCAACCAAATTTAGTACTGATTCGAGCACTTAATGAATTAA
131 ATTGCAACCAAATTTAGTACTGATTCGAGCACTTAATGAATTAA
* * * * *
61982102 GGATTACACATCAAGTTTTCATGTTCTATGAGCTCATAGACATGGAGTATACTGGTATCAACAAG
1 GGATTACACATTAAGTTTTCAAGTTCTATGAGCTCATAGACATGGAATATACTAGTATTAACAAG
* *
61982167 CTTACCTTCACCATTTCGAAACAAAACAATTTCATTTCCATCAAGAAAACAATGACAACGAGGTA
66 CTTACCTTCACCATTTCGAAACGATACAATTTCATTTCCATCAAGAAAACAATGACAACGAGGTA
61982232 ATTGCAACCAAATTTAGTACTGATTCGAGCACTTAATGAATTAA
131 ATTGCAACCAAATTTAGTACTGATTCGAGCACTTAATGAATTAA
* * *
61982276 GGATCACACATTAAGTTTTCAAGTTCCATGAGCTCCTAGACATGGAATATACTAGTATTAACAAG
1 GGATTACACATTAAGTTTTCAAGTTCTATGAGCTCATAGACATGGAATATACTAGTATTAACAAG
*
61982341 CTTACCTTCACCATTTCGAATCGATACAATTTCATTTCCATC
66 CTTACCTTCACCATTTCGAAACGATACAATTTCATTTCCATC
61982383 TGAAAATAAC
Statistics
Matches: 254, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
174 254 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (174 bp):
GGATTACACATTAAGTTTTCAAGTTCTATGAGCTCATAGACATGGAATATACTAGTATTAACAAG
CTTACCTTCACCATTTCGAAACGATACAATTTCATTTCCATCAAGAAAACAATGACAACGAGGTA
ATTGCAACCAAATTTAGTACTGATTCGAGCACTTAATGAATTAA
Found at i:61984276 original size:26 final size:28
Alignment explanation
Indices: 61984228--61984282 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
61984218 TTTAACCCTA
61984228 AAAGAAAAAACAAGAAATATCTAAGCTC
1 AAAGAAAAAACAAGAAATATCTAAGCTC
*
61984256 AAAGGAAAAA-AA-AAATATCTAAGCTC
1 AAAGAAAAAACAAGAAATATCTAAGCTC
61984282 A
1 A
61984283 TGCAAAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 15 0.58
27 2 0.08
28 9 0.35
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.15
Consensus pattern (28 bp):
AAAGAAAAAACAAGAAATATCTAAGCTC
Found at i:61986196 original size:3 final size:3
Alignment explanation
Indices: 61986188--61986234 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
61986178 CATGTGAGAC
61986188 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
61986235 ATGCAACAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:61990382 original size:54 final size:54
Alignment explanation
Indices: 61990320--61990468 Score: 148
Period size: 54 Copynumber: 2.8 Consensus size: 54
61990310 TCGTAATGAC
* *
61990320 CCTATCAGAAGT-AGAGGTTGATTCCCTTCTAGAAATTC-GATTTATG-GTAA-CAAT
1 CCTATCAG-AGTGA-AGGTTGATTCCCTTCTAGAAATTCTGATTT-CGAGCAATC-AT
* *
61990374 CCTATCAGAGGCGAAGGTTGATTCCTTTCTAG-AATTCTGATTTCGAGCAATCAT
1 CCTATCAGA-GTGAAGGTTGATTCCCTTCTAGAAATTCTGATTTCGAGCAATCAT
* *
61990428 CCTACCGGGAGTGAAGGTTGATTCCCTTCTAGAAATT-TGAT
1 CCTATC-AGAGTGAAGGTTGATTCCCTTCTAGAAATTCTGAT
61990469 CTCCAGAAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
53 7 0.09
54 65 0.81
55 8 0.10
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (54 bp):
CCTATCAGAGTGAAGGTTGATTCCCTTCTAGAAATTCTGATTTCGAGCAATCAT
Found at i:61991765 original size:30 final size:27
Alignment explanation
Indices: 61991706--61991765 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
61991696 TCAATTAGTT
* * *
61991706 TCCCTATTATTAAATAGATCAATTTAG
1 TCCCTATTATTAAAAAGATCAAATAAG
61991733 TCCCTATACTATTAAAAAGAATCAAATAAG
1 TCCCTAT--TATTAAAAAG-ATCAAATAAG
61991763 TCC
1 TCC
61991766 AAACTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
29 9 0.33
30 11 0.41
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (27 bp):
TCCCTATTATTAAAAAGATCAAATAAG
Found at i:61994539 original size:41 final size:42
Alignment explanation
Indices: 61994486--61994590 Score: 176
Period size: 41 Copynumber: 2.5 Consensus size: 42
61994476 AATTCGTAAT
*
61994486 AAAATGCAAAATAAGCTACGAACTAACTTCA-AAATTAAATA
1 AAAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATA
*
61994527 AAAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTGAATA
1 AAAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATA
61994569 AAAATGCAAAAATAAGCTAAGA
1 AAAATGC-AAAATAAGCTAAGA
61994591 GAAAACAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
41 30 0.50
42 16 0.27
43 14 0.23
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.20
Consensus pattern (42 bp):
AAAATGCAAAATAAGCTAAGAACTAACTTCAGAAATTAAATA
Found at i:61996258 original size:15 final size:16
Alignment explanation
Indices: 61996233--61996265 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
61996223 ATAAAATGTA
61996233 TTTATATTATTTTAAT
1 TTTATATTATTTTAAT
*
61996249 TTTATA-TATTTTTAT
1 TTTATATTATTTTAAT
61996264 TT
1 TT
61996266 AATAAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATATTATTTTAAT
Found at i:62001261 original size:121 final size:122
Alignment explanation
Indices: 62001046--62001268 Score: 421
Period size: 121 Copynumber: 1.8 Consensus size: 122
62001036 AAAGAAAGAA
62001046 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAATTTTCTTACATAAAGGCATAGCTAA
1 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAATTTTCTTACATAAAGGCATAGCTAA
*
62001111 CTTCTAATTTATATATATGAACTAAAACAACTTCAAAGAACAACTTCTAATCTATAT
66 CTTCTAATCTATATATATGAACTAAAACAACTTCAAAGAACAACTTCTAATCTATAT
*
62001168 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAA-TTTCTTACATAAGGGCATAGCTAA
1 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAATTTTCTTACATAAAGGCATAGCTAA
62001232 CTTCTAATCTATATATATGAACTAAAACAACTTCAAA
66 CTTCTAATCTATATATATGAACTAAAACAACTTCAAA
62001269 TTCTTAAAAC
Statistics
Matches: 99, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
121 59 0.60
122 40 0.40
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (122 bp):
AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAATTTTCTTACATAAAGGCATAGCTAA
CTTCTAATCTATATATATGAACTAAAACAACTTCAAAGAACAACTTCTAATCTATAT
Found at i:62001495 original size:192 final size:184
Alignment explanation
Indices: 62001168--62001809 Score: 992
Period size: 192 Copynumber: 3.5 Consensus size: 184
62001158 TAATCTATAT
*
62001168 AGATACCATTTGTTCTTGGATTTCAGCTAATAG-AAAAAAATTTC-TTACATAAGGGCATAGCTA
1 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAATTCTTTACATAAGGGCATAGCTA
*
62001231 ACTTCTAATCTATATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAATAAATTGA
66 ACTTCTAAT-TTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAA-AAATTGA
*
62001296 CCAAATTATCCATAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAA
129 TCAAATTATCCATAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAA
*
62001352 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAATTCTTTACATATGGCCTATGAGC
1 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAATTCTTTACATA------A-GGGC
*
62001417 ACAGCTAACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAA
59 ATAGCTAACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAA
*
62001482 GATTGATCAAATTATCCACAATTATCAAATCAAAATTAATAAACAAAAACAGAAAG--A-AA
124 -ATTGATCAAATTATCCATAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAA
* * *
62001541 ATATATCATTTGTTCTTGAATTTCAGCTAATAGAAAAAAAAATTCTTTACATAAGGGCATAGCTA
1 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAATTCTTTACATAAGGGCATAGCTA
62001606 ACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAAAATTTGA
66 ACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGT-AAAAAA-TTGA
62001671 TCAAATTATCCATAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAA
129 TCAAATTATCCATAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAA
* * *
62001727 AGAAACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAAAT-TAT-CATATAGGGCATAGCT
1 AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAATTCTTTACATA-AGGGCATAGCT
*
62001790 AACTTCTAATATATATATAT
65 AACTTCTAAT-TTTATATAT
62001810 ATGTGTGTGG
Statistics
Matches: 422, Mismatches: 19, Indels: 32
0.89 0.04 0.07
Matches are distributed among these distances:
182 63 0.15
183 59 0.14
184 37 0.09
185 34 0.08
186 56 0.13
189 52 0.12
190 1 0.00
191 2 0.00
192 100 0.24
193 18 0.04
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (184 bp):
AGATACCATTTGTTCTTGGATTTCAGCTAATAGAAAAAAAAATTCTTTACATAAGGGCATAGCTA
ACTTCTAATTTTATATATGAACTAAAACAACTTCAAATTCTTAAAACAAGAGTAAAAAATTGATC
AAATTATCCATAATTATCAAATCAAAATTAATAAACAAAAACAGAAAGAAAGAA
Found at i:62002570 original size:41 final size:38
Alignment explanation
Indices: 62002503--62002589 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 38
62002493 GTTTTATATG
* *
62002503 TTTATAAATATAATATGTTAAGTTATATATATATATATAA
1 TTTATAAATATAATAAGTTAAGTTATAGA-A-ATATATAA
*
62002543 TTTATAACATATAA-AAGTTAAATTTATAGAAATATATAA
1 TTTATAA-ATATAATAAGTT-AAGTTATAGAAATATATAA
62002582 TGTTATAA
1 T-TTATAA
62002590 TGTAATATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 9 0.22
40 18 0.44
41 14 0.34
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (38 bp):
TTTATAAATATAATAAGTTAAGTTATAGAAATATATAA
Found at i:62003385 original size:30 final size:30
Alignment explanation
Indices: 62003349--62003409 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
62003339 CTTAACAACG
62003349 TCAATTAAATTGTATTGAGTTTTATTTGAA
1 TCAATTAAATTGTATTGAGTTTTATTTGAA
62003379 TCAATTAAATTGTATTGAGTTTTATTTGAA
1 TCAATTAAATTGTATTGAGTTTTATTTGAA
62003409 T
1 T
62003410 TTGGGTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (30 bp):
TCAATTAAATTGTATTGAGTTTTATTTGAA
Found at i:62003883 original size:2 final size:2
Alignment explanation
Indices: 62003876--62003904 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62003866 TTCCAGATCT
62003876 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
62003905 TGTTCAGGTT
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:62004668 original size:13 final size:13
Alignment explanation
Indices: 62004652--62004676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62004642 AAATAAAATT
62004652 TATAAAATTATTG
1 TATAAAATTATTG
62004665 TATAAAATTATT
1 TATAAAATTATT
62004677 TTAAAGAATA
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TATAAAATTATTG
Found at i:62006484 original size:14 final size:15
Alignment explanation
Indices: 62006458--62006489 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
62006448 CAGGGAATTG
62006458 ATTTAGGGTTTTTGA
1 ATTTAGGGTTTTTGA
62006473 ATTTAGGGTTTTT-A
1 ATTTAGGGTTTTTGA
62006487 ATT
1 ATT
62006490 ATAGAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
ATTTAGGGTTTTTGA
Found at i:62011079 original size:29 final size:29
Alignment explanation
Indices: 62011037--62011094 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
62011027 TGACAGAGAT
* *
62011037 TGGATCAAATTAGTACCTCTATTATTAAA
1 TGGATCAAATTAGTACCTATACTATTAAA
* *
62011066 TGGATCAATTTAGTCCCTATACTATTAAA
1 TGGATCAAATTAGTACCTATACTATTAAA
62011095 AAGAATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (29 bp):
TGGATCAAATTAGTACCTATACTATTAAA
Found at i:62016789 original size:183 final size:183
Alignment explanation
Indices: 62016481--62016811 Score: 502
Period size: 183 Copynumber: 1.8 Consensus size: 183
62016471 AGTTTCACGC
* *
62016481 TAGAATCTAGATTTAAATTTAAAAAATCCATCGCAAAATTAACACTTCCCAGATGCCCAAATAAA
1 TAGAATCTACATTCAAATTTAAAAAATCCATCGCAAAATTAACACTTCCCAGATGCCCAAATAAA
* *
62016546 TAATCCGTTTGAATCATACTAGAATCTACATCAAAATTCCAAAAATCCATAAAAAAATTAACACT
66 TAATCCATTTGAATCATACTAGAATCTACATCAAAATTCCAAAAATCCACAAAAAAATTAACACT
62016611 ACCCAGATGCCCAAATCAATAGTCCATTTGAATAAAAAAAATAACAGCCATGT
131 ACCCAGATGCCCAAATCAATAGTCCATTTGAATAAAAAAAATAACAGCCATGT
* * *
62016664 TAGAATCTACATTCAAATTTCAAAAATCGATCGCAAAATTAACACTTCCCAGATGCCCAAAATCA
1 TAGAATCTACATTCAAATTTAAAAAATCCATCGCAAAATTAACACTTCCCAGATGCCC-AAATAA
* * * * * *** *
62016729 CTAGTCCATTTGAATCATACTAGAATCTACATCCAAATTTCAATAATCC-CCGCAAAATTAACAT
65 ATAATCCATTTGAATCATACTAGAATCTACATCAAAATTCCAAAAATCCACAAAAAAATTAACAC
62016793 TACCCAGATGCCCAAATCA
130 TACCCAGATGCCCAAATCA
62016812 CTAAATTCCC
Statistics
Matches: 131, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
183 83 0.63
184 48 0.37
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (183 bp):
TAGAATCTACATTCAAATTTAAAAAATCCATCGCAAAATTAACACTTCCCAGATGCCCAAATAAA
TAATCCATTTGAATCATACTAGAATCTACATCAAAATTCCAAAAATCCACAAAAAAATTAACACT
ACCCAGATGCCCAAATCAATAGTCCATTTGAATAAAAAAAATAACAGCCATGT
Found at i:62017656 original size:30 final size:31
Alignment explanation
Indices: 62017622--62017681 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
62017612 TAAAATAGTC
*
62017622 ATTAAA-TATTTGAAATTTTTCATTAAATTT
1 ATTAAACTATTTAAAATTTTTCATTAAATTT
* *
62017652 ATTAAACTATTTAAAATTTTTTATTTAATT
1 ATTAAACTATTTAAAATTTTTCATTAAATT
62017682 CACTTGAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTAAACTATTTAAAATTTTTCATTAAATTT
Found at i:62018999 original size:9 final size:9
Alignment explanation
Indices: 62018985--62019024 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
62018975 TTTGGTTAAA
62018985 AATTAACCG
1 AATTAACCG
62018994 AATTAACCG
1 AATTAACCG
* *
62019003 GATTACCCG
1 AATTAACCG
62019012 AATTAACCG
1 AATTAACCG
62019021 AATT
1 AATT
62019025 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:62021019 original size:103 final size:101
Alignment explanation
Indices: 62020825--62021283 Score: 332
Period size: 88 Copynumber: 4.8 Consensus size: 101
62020815 ATCATTGATA
* * **
62020825 TTTTCTTTTGGTAATATTTTTTTTTCTGGGACGAGAAAATTAGGGAAAACAATTTCGAAAATCAA
1 TTTTCTTTTAGTAATA-TTTTTTGTCTAAGACGAGAAAATTAGGGAAAACAA-TTCGAAAATCAA
62020890 CAGATTTCTGGATCTAGAGGTTTTTTTTTTCTTCATGT
64 CAGATTTCTGGATCTAGAGGTTTTTTTTTTCTTCATGT
* *
62020928 TTTTCTTTTAGTAATA-TTTTTGTCTAAGACGGGAAAATTAGGGGGAAA-AA-TCGAAAATCAAC
1 TTTTCTTTTAGTAATATTTTTTGTCTAAGACGAGAAAATTA-GGGAAAACAATTCGAAAATCAAC
62020990 AGATTTCTGGATCT--A-------TTTTT-TT-ATGT
65 AGATTTCTGGATCTAGAGGTTTTTTTTTTCTTCATGT
* * **
62021016 TTTTCTTTTAGTAATA-TTTTTCTCTAAGACGGGAAAATTAGGGGGGAA-AA-TCGAAAATCAAC
1 TTTTCTTTTAGTAATATTTTTTGTCTAAGACGAGAAAATTA-GGGAAAACAATTCGAAAATCAAC
* * *
62021078 AAAATTCTGGATCTAG-GGTATTTTTTTTC--C-TGT
65 AGATTTCTGGATCTAGAGGTTTTTTTTTTCTTCATGT
* * * * * * * *
62021111 TTTTCTTTTGGTAATATTTTTTCTCTGAGACGGGAAAATTAGGG-GAA-ATTTTGAAAATTAACA
1 TTTTCTTTTAGTAATATTTTTTGTCTAAGACGAGAAAATTAGGGAAAACAATTCGAAAATCAACA
* * * * * * **
62021174 AATTTATGGCTTTCGA---TTCTTTTCCCTGT--TGT
66 GATTTCTGGATCTAGAGGTTTTTTTTTTCT-TCATGT
* * * ** *
62021206 TTTTCTTTTAGTAATA-TTTTTCTCTGAGACGGGAAAATTAGGGGGAA-AATT-GAAAATTAACA
1 TTTTCTTTTAGTAATATTTTTTGTCTAAGACGAGAAAATTAGGGAAAACAATTCGAAAATCAACA
*
62021268 AATTTCTGGATCTAGA
66 GATTTCTGGATCTAGA
62021284 TTTTTTCCCC
Statistics
Matches: 307, Mismatches: 30, Indels: 47
0.80 0.08 0.12
Matches are distributed among these distances:
88 76 0.25
89 2 0.01
90 5 0.02
93 6 0.02
94 54 0.18
95 66 0.21
96 28 0.09
97 1 0.00
99 26 0.08
101 22 0.07
102 6 0.02
103 15 0.05
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (101 bp):
TTTTCTTTTAGTAATATTTTTTGTCTAAGACGAGAAAATTAGGGAAAACAATTCGAAAATCAACA
GATTTCTGGATCTAGAGGTTTTTTTTTTCTTCATGT
Found at i:62021244 original size:94 final size:91
Alignment explanation
Indices: 62020925--62021307 Score: 400
Period size: 94 Copynumber: 4.1 Consensus size: 91
62020915 TTTTTCTTCA
* * * *
62020925 TGTTTTTCTTTTAGTAATATTTTTGTCTAAGACGGGAAAATTAGGGGGAAAAATCGAAAATCAAC
1 TGTTTTTCTTTTAGTAATATTTTTCTCTGAGACGGGAAAATTAGGGGG-AAAATTGAAAATTAAC
* ** **
62020990 AGATTTCTGG--ATCTATTTTTT--TA
65 AAATTTCTGGCTATAGATTTTTTCCCG
* * *
62021013 TGTTTTTCTTTTAGTAATATTTTTCTCTAAGACGGGAAAATTAGGGGGGAAAATCGAAAATCAAC
1 TGTTTTTCTTTTAGTAATATTTTTCTCTGAGACGGGAAAATTA-GGGGGAAAATTGAAAATTAAC
* ** *
62021078 AAAATTCTGGATCTAGGGTATTTTTTTTCC-
65 AAATTTCTGG--CTATAG-A-TTTTTTCCCG
* *
62021108 TGTTTTTCTTTTGGTAATATTTTTTCTCTGAGACGGGAAAATTA-GGGGAAATTTTGAAAATTAA
1 TGTTTTTCTTTTAGTAATA-TTTTTCTCTGAGACGGGAAAATTAGGGGGAAA-ATTGAAAATTAA
* * *
62021172 CAAATTTATGGCTTTCGATTCTTTTCCCTG
64 CAAATTTCTGGCTATAGATT-TTTTCCC-G
62021202 TTGTTTTTCTTTTAGTAATATTTTTCTCTGAGACGGGAAAATTAGGGGGAAAATTGAAAATTAAC
1 -TGTTTTTCTTTTAGTAATATTTTTCTCTGAGACGGGAAAATTAGGGGGAAAATTGAAAATTAAC
* *
62021267 AAATTTCTGGATCTAGATTTTTTCCCCG
65 AAATTTCTGGCTATAGATTTTTT-CCCG
62021295 CTGTTTTTCTTTT
1 -TGTTTTTCTTTT
62021308 TTTGAGACTG
Statistics
Matches: 253, Mismatches: 25, Indels: 29
0.82 0.08 0.09
Matches are distributed among these distances:
88 66 0.26
89 5 0.02
91 2 0.01
92 8 0.03
93 21 0.08
94 67 0.26
95 61 0.24
96 23 0.09
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (91 bp):
TGTTTTTCTTTTAGTAATATTTTTCTCTGAGACGGGAAAATTAGGGGGAAAATTGAAAATTAACA
AATTTCTGGCTATAGATTTTTTCCCG
Found at i:62029277 original size:29 final size:30
Alignment explanation
Indices: 62029240--62029298 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
62029230 TTTGGTTTAA
*
62029240 TGTGCAATTATATATAT-AAATTTTGATTT
1 TGTGCAATTATATAAATGAAATTTTGATTT
* * *
62029269 TGTGTAATTTTATAAATGAAGTTTTGATTT
1 TGTGCAATTATATAAATGAAATTTTGATTT
62029299 GATTTAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGCAATTATATAAATGAAATTTTGATTT
Found at i:62029331 original size:12 final size:12
Alignment explanation
Indices: 62029314--62029338 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62029304 AATTCTCATA
62029314 AATTATTAATAT
1 AATTATTAATAT
62029326 AATTATTAATAT
1 AATTATTAATAT
62029338 A
1 A
62029339 GCATCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTAATAT
Found at i:62029966 original size:24 final size:24
Alignment explanation
Indices: 62029938--62029986 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
62029928 CTTCTAACAT
*
62029938 ATCATGAAATGAACACTTAAAATA
1 ATCATGAAATGAACACGTAAAATA
62029962 ATCATGAAATGAACACGTAAAATA
1 ATCATGAAATGAACACGTAAAATA
62029986 A
1 A
62029987 CCAAGCGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.22
Consensus pattern (24 bp):
ATCATGAAATGAACACGTAAAATA
Found at i:62043490 original size:11 final size:11
Alignment explanation
Indices: 62043470--62043556 Score: 66
Period size: 11 Copynumber: 8.6 Consensus size: 11
62043460 TAAAAATTAA
62043470 AAAAAGTATTTT
1 AAAAA-TATTTT
62043482 AAAAATATTTT
1 AAAAATATTTT
62043493 --AAA-A--TT
1 AAAAATATTTT
* **
62043499 AAAAAAATTAA
1 AAAAATATTTT
62043510 AAAAATATTTT
1 AAAAATATTTT
62043521 AAAAATATTTT
1 AAAAATATTTT
62043532 --AAA-ATTTT
1 AAAAATATTTT
*
62043540 AAAAAT-TTTA
1 AAAAATATTTT
62043550 AAAAATA
1 AAAAATA
62043557 AATATATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
6 2 0.03
8 9 0.15
9 7 0.12
10 12 0.20
11 25 0.42
12 5 0.08
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:62043519 original size:39 final size:40
Alignment explanation
Indices: 62043461--62043556 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
62043451 AATTTATTTT
62043461 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA-TTAA
1 AAAAATTAAAAAAA-TATTTTAAAAATATTTTAAAATTTAA
*
62043501 AAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTTTA
1 AAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTTAA
* *
62043541 AAAATTTTAAAAAATA
1 AAAAATTAAAAAAATA
62043557 AATATATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 21 0.40
40 31 0.60
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (40 bp):
AAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTTAA
Found at i:62043546 original size:9 final size:9
Alignment explanation
Indices: 62043477--62043553 Score: 64
Period size: 9 Copynumber: 8.1 Consensus size: 9
62043467 TAAAAAAAGT
62043477 ATTTTAAAA
1 ATTTTAAAA
*
62043486 ATATTTTAAA
1 AT-TTTAAAA
**
62043496 ATTAAAAAA
1 ATTTTAAAA
**
62043505 ATTAAAAAAA
1 ATT-TTAAAA
62043515 TATTTTAAAA
1 -ATTTTAAAA
*
62043525 ATATTTTAAA
1 AT-TTTAAAA
62043535 ATTTTAAAA
1 ATTTTAAAA
62043544 ATTTTAAAA
1 ATTTTAAAA
62043553 A
1 A
62043554 ATAAATATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
9 27 0.48
10 26 0.46
11 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:62043553 original size:40 final size:39
Alignment explanation
Indices: 62043456--62043556 Score: 157
Period size: 39 Copynumber: 2.5 Consensus size: 39
62043446 CTAAAAATTT
62043456 ATTTTAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTTAAAAATTAAAAAAA-TATTTTAAAAATATTTTAAA
**
62043496 ATTAAAAAAATTAAAAAAATATTTTAAAAATATTTTAAA
1 ATTTTAAAAATTAAAAAAATATTTTAAAAATATTTTAAA
*
62043535 ATTTTAAAAATTTTAAAAAATA
1 ATTTTAAAAA-TTAAAAAAATA
62043557 AATATATTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 28 0.51
40 27 0.49
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (39 bp):
ATTTTAAAAATTAAAAAAATATTTTAAAAATATTTTAAA
Found at i:62044901 original size:2 final size:2
Alignment explanation
Indices: 62044894--62044918 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62044884 ATGTCTTATT
62044894 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 T
62044919 TTTTTTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62045993 original size:313 final size:312
Alignment explanation
Indices: 62045397--62046010 Score: 925
Period size: 313 Copynumber: 2.0 Consensus size: 312
62045387 CAGTTTATAC
*
62045397 GATACGTTATTGCTGCATTCTTCATTATTTTTGTTGATCGTCATTTCCATGCATACTTGAGTTCA
1 GATACGTTATTGCTGCATTCTTCATTATTTTTGTTGATCGTCATTTCCATACATACTTGAGTTCA
* * **
62045462 AAATTAGTTGTTAATCTCTATATATTGTTAAAAATTAAATATGTTCTGCAAGTTCAGTGAAATTA
66 AAATTAGTTGTTAACCTCTATATATTCTTAAAAATTAAATATACTCTGCAAGTTCAGTGAAATTA
62045527 TGAATTTGAAGTCATAAAGTTTGTCTATGTTGTTTGCGATGGATAATTTAGTAGATGTAAGTTGT
131 TGAATTTGAAGTCATAAAGTTTGTCTATGTTGTTTGCGATGGATAATTTAGTAGATGTAAGTTGT
* * *
62045592 TTATTAATTGTTTTTCACTTAATTAGGAATATGAAATTTTTTATTATTTTTGCTTTTTCTTTTTG
196 TTAGT-ATTGTTTTTCACTTAATTAAGAATATGAAATTTTTTATTATTTTTGCTTTTTCTTTTCG
*
62045657 ATTAAAATGAGATCATTATCCATGTTTGGAAATCTTATTTTTTTATTTTAGAT
260 ATTAAAATAAGATCATTATCCATGTTTGGAAATCTTATTTTTTTATTTTAGAT
* * * * * * *
62045710 GATACGTTATTGTTGCATTCTTCA-TATTTTTTTTTATGGTCATTTCCTTACTTACTTGAGTTGA
1 GATACGTTATTGCTGCATTCTTCATTATTTTTGTTGATCGTCATTTCCATACATACTTGAGTTCA
* *
62045774 AAATTAGTTGTTAACCTCTATGTATTCTTAAAAATTAAATATACTCTGCAAGTTTGAGTGAAATT
66 AAATTAGTTGTTAACCTCTATATATTCTTAAAAATTAAATATACTCTGCAAG-TTCAGTGAAATT
62045839 ATGAAATTTGAAGTCATAAAGTTTGTCTATGTTGTTTGCGATGGATAATTTAGTAGATGTAAGTT
130 ATG-AATTTGAAGTCATAAAGTTTGTCTATGTTGTTTGCGATGGATAATTTAGTAGATGTAAGTT
* *
62045904 G-TT-GT-TT-TTTTTCACTTACTTAAGAATA-GGAATTTTATTATTTTTATTTTTTGCTTTTTC
194 GTTTAGTATTGTTTTTCACTTAATTAAGAATATGAAATTTT-TTA---TTA-TTTTTGCTTTTTC
*
62045964 TTTTCGATTAAAATAAGATGATTATCCATGTTTGGAAATCTTATTTT
254 TTTTCGATTAAAATAAGATCATTATCCATGTTTGGAAATCTTATTTT
62046011 CAGTTTTAAG
Statistics
Matches: 273, Mismatches: 21, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
308 7 0.03
309 22 0.08
310 2 0.01
312 84 0.31
313 96 0.35
314 62 0.23
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (312 bp):
GATACGTTATTGCTGCATTCTTCATTATTTTTGTTGATCGTCATTTCCATACATACTTGAGTTCA
AAATTAGTTGTTAACCTCTATATATTCTTAAAAATTAAATATACTCTGCAAGTTCAGTGAAATTA
TGAATTTGAAGTCATAAAGTTTGTCTATGTTGTTTGCGATGGATAATTTAGTAGATGTAAGTTGT
TTAGTATTGTTTTTCACTTAATTAAGAATATGAAATTTTTTATTATTTTTGCTTTTTCTTTTCGA
TTAAAATAAGATCATTATCCATGTTTGGAAATCTTATTTTTTTATTTTAGAT
Found at i:62052978 original size:15 final size:15
Alignment explanation
Indices: 62052958--62052989 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
62052948 ATGAAGAGTC
62052958 GGTGGCAAAATAGAT
1 GGTGGCAAAATAGAT
62052973 GGTGGCAAAATAGAT
1 GGTGGCAAAATAGAT
62052988 GG
1 GG
62052990 AGATTAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.19
Consensus pattern (15 bp):
GGTGGCAAAATAGAT
Found at i:62054627 original size:28 final size:28
Alignment explanation
Indices: 62054596--62054685 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
62054586 ATAAAATGCC
62054596 AAAAAATTATTTTAAAAATTAAAAAATT
1 AAAAAATTATTTTAAAAATTAAAAAATT
* **
62054624 AAAAAAGTATTTTAAAATATTTTAAAATT
1 AAAAAATTATTTTAAAA-ATTAAAAAATT
62054653 AAAAAA-TATTTT-AAAATTAAAAAATT
1 AAAAAATTATTTTAAAAATTAAAAAATT
*
62054679 TAAAAAT
1 AAAAAAT
62054686 AAATATATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 14 0.26
27 3 0.06
28 22 0.41
29 15 0.28
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAAAATTATTTTAAAAATTAAAAAATT
Found at i:62054656 original size:16 final size:16
Alignment explanation
Indices: 62054635--62054695 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 16
62054625 AAAAAGTATT
62054635 TTAAAATATTTTAAAA
1 TTAAAATATTTTAAAA
62054651 TTAAAAAATATTTTAAAA
1 TT--AAAATATTTTAAAA
*
62054669 TTAAAA-AATTTAAAA
1 TTAAAATATTTTAAAA
*
62054684 ATAAATATATTT
1 TTAAA-ATATTT
62054696 ATTATATTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 12 0.32
16 7 0.18
17 3 0.08
18 16 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAATATTTTAAAA
Found at i:62054660 original size:18 final size:18
Alignment explanation
Indices: 62054637--62054677 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
62054627 AAAGTATTTT
62054637 AAAATATTTTAAAATTAA
1 AAAATATTTTAAAATTAA
62054655 AAAATATTTTAAAATTAA
1 AAAATATTTTAAAATTAA
62054673 AAAAT
1 AAAAT
62054678 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATATTTTAAAATTAA
Found at i:62054696 original size:16 final size:16
Alignment explanation
Indices: 62054638--62054696 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
62054628 AAGTATTTTA
62054638 AAATAT-TTTAAAATT
1 AAATATATTTAAAATT
*
62054653 AAAAAATATTTTAAAATT
1 -AAATATA-TTTAAAATT
* *
62054671 AAA-AAATTTAAAAAT
1 AAATATATTTAAAATT
62054686 AAATATATTTA
1 AAATATATTTA
62054697 TTATATTGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 11 0.31
16 13 0.36
17 3 0.08
18 9 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATATTTAAAATT
Found at i:62055903 original size:16 final size:17
Alignment explanation
Indices: 62055884--62055917 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
62055874 TTTTAAGAAG
*
62055884 CATTTTTG-GGACAAAA
1 CATTTTTGAGGAAAAAA
62055900 CATTTTTGAGGAAAAAA
1 CATTTTTGAGGAAAAAA
62055917 C
1 C
62055918 TAAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
CATTTTTGAGGAAAAAA
Found at i:62057619 original size:15 final size:14
Alignment explanation
Indices: 62057597--62057631 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
62057587 TCTTTCTTTC
62057597 TTTTTTTTTT-CAA
1 TTTTTTTTTTCCAA
62057610 TTTTTATTTTTCCAA
1 TTTTT-TTTTTCCAA
62057625 TTTTTTT
1 TTTTTTT
62057632 CACTATGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 7 0.35
15 8 0.40
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTTCCAA
Found at i:62060383 original size:6 final size:6
Alignment explanation
Indices: 62060374--62060409 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
62060364 ATAAAGTTTA
* *
62060374 TATATA TATATT TATGTT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT
62060410 AAATTATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:62060401 original size:18 final size:20
Alignment explanation
Indices: 62060369--62060406 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
62060359 GTTAAATAAA
62060369 GTTTATATATATATATTTAT
1 GTTTATATATATATATTTAT
62060389 GTTTATAT-T-TATATTTAT
1 GTTTATATATATATATTTAT
62060407 ATTAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
GTTTATATATATATATTTAT
Found at i:62063858 original size:60 final size:60
Alignment explanation
Indices: 62063759--62063871 Score: 172
Period size: 60 Copynumber: 1.9 Consensus size: 60
62063749 AGAGTTTACA
* * *
62063759 CTAATAATTAAGTCTAGAATCATCTAGAAGCAATTAATCATTGTTATCCAAGGCCGTATG
1 CTAATAATTAAGTCTAGAATCATATAGAAACAATCAATCATTGTTATCCAAGGCCGTATG
* * *
62063819 CTAATAATTAAGTCTAGGATCATATGGAAACAATCAATCATTGTTATGCAAGG
1 CTAATAATTAAGTCTAGAATCATATAGAAACAATCAATCATTGTTATCCAAGG
62063872 ACATAGTTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (60 bp):
CTAATAATTAAGTCTAGAATCATATAGAAACAATCAATCATTGTTATCCAAGGCCGTATG
Found at i:62066342 original size:20 final size:20
Alignment explanation
Indices: 62066302--62066342 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
62066292 AAATACTTTA
*
62066302 AAAATATATTTTTTATTTTT
1 AAAATATATTTTTTATGTTT
* *
62066322 AAAATATTTTTTTTGTGTTT
1 AAAATATATTTTTTATGTTT
62066342 A
1 A
62066343 TTAAAAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
AAAATATATTTTTTATGTTT
Found at i:62067134 original size:27 final size:27
Alignment explanation
Indices: 62067097--62067165 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
62067087 AAAAATAAAA
**
62067097 ATTTACCAAAATATAATCCCTTTTTTT
1 ATTTACCAAAATATAATAACTTTTTTT
* * *
62067124 ATTTACTAAAATATTATAATTTTTTTT
1 ATTTACCAAAATATAATAACTTTTTTT
62067151 ATTTACCAAAATATA
1 ATTTACCAAAATATA
62067166 CCAAAAAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATAATAACTTTTTTT
Found at i:62067241 original size:27 final size:27
Alignment explanation
Indices: 62067203--62067287 Score: 118
Period size: 27 Copynumber: 3.2 Consensus size: 27
62067193 GCCTGATCAG
* *
62067203 GCCACTGCCATTGGCGGCATCAAAGGT
1 GCCAATGCCATTGGCGGCACCAAAGGT
*
62067230 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAAAGGT
* *
62067257 GCCAATGCCATTAGCGGCACC-AATGT
1 GCCAATGCCATTGGCGGCACCAAAGGT
62067283 GCCAA
1 GCCAA
62067288 AGGATTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 8 0.15
27 44 0.85
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.18
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAAAGGT
Found at i:62077561 original size:14 final size:15
Alignment explanation
Indices: 62077542--62077575 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
62077532 CAATTGCCTG
62077542 CAAAAAAACAAAAA-
1 CAAAAAAACAAAAAT
62077556 CAAAAAAACAAAAAT
1 CAAAAAAACAAAAAT
62077571 CAAAA
1 CAAAA
62077576 CAAAATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (15 bp):
CAAAAAAACAAAAAT
Found at i:62077569 original size:21 final size:21
Alignment explanation
Indices: 62077544--62077586 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
62077534 ATTGCCTGCA
62077544 AAAAAACAAAAACAAAA-AAAC
1 AAAAAAC-AAAACAAAATAAAC
*
62077565 AAAAATCAAAACAAAATAAAC
1 AAAAAACAAAACAAAATAAAC
62077586 A
1 A
62077587 TATAAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.81, C:0.14, G:0.00, T:0.05
Consensus pattern (21 bp):
AAAAAACAAAACAAAATAAAC
Found at i:62081368 original size:9 final size:9
Alignment explanation
Indices: 62081351--62081384 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
62081341 GCCATGTCAA
*
62081351 TAAATAATT
1 TAAAAAATT
62081360 TAAAAAATT
1 TAAAAAATT
62081369 ATAAAAAATT
1 -TAAAAAATT
62081379 TAAAAA
1 TAAAAA
62081385 TATAAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAAAATT
Found at i:62081378 original size:19 final size:17
Alignment explanation
Indices: 62081350--62081392 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
62081340 CGCCATGTCA
*
62081350 ATAAATAATTTAAAAAATT
1 ATAAAAAATTT-AAAAA-T
62081369 ATAAAAAATTTAAAAAT
1 ATAAAAAATTTAAAAAT
62081386 ATAAAAA
1 ATAAAAA
62081393 GTTCATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAAAATTTAAAAAT
Found at i:62086903 original size:5 final size:6
Alignment explanation
Indices: 62086888--62086918 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
62086878 TAAAATACTT
62086888 TTTTTA TTTTTA TTTTTA TTTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA
62086919 AAATAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:62086903 original size:13 final size:12
Alignment explanation
Indices: 62086888--62086918 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
62086878 TAAAATACTT
62086888 TTTTTATTTTTA
1 TTTTTATTTTTA
62086900 TTTTTATTTTTTA
1 TTTTTA-TTTTTA
62086913 TTTTTA
1 TTTTTA
62086919 AAATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:62086927 original size:19 final size:19
Alignment explanation
Indices: 62086872--62086930 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
62086862 TATTTTAAAA
*
62086872 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATA-ATTTTT
*** *
62086892 TATTTTTATTTTTATTTTT
1 TATTTTTAAAATAATTTTT
62086911 TATTTTTAAAATAATTTTT
1 TATTTTTAAAATAATTTTT
62086930 T
1 T
62086931 GGTGTTTATT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTAAAATAATTTTT
Found at i:62092577 original size:30 final size:31
Alignment explanation
Indices: 62092543--62092608 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
62092533 GTTGCAAAAT
* *
62092543 AGTTACTAAACTATTCTAAAG-TTGCATTTA
1 AGTTAATAAACTATTCAAAAGATTGCATTTA
* **
62092573 AGTTAATGAACTATTCAAAAGATTTTATTTA
1 AGTTAATAAACTATTCAAAAGATTGCATTTA
62092604 AGTTA
1 AGTTA
62092609 TTAGACTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (31 bp):
AGTTAATAAACTATTCAAAAGATTGCATTTA
Found at i:62093726 original size:9 final size:9
Alignment explanation
Indices: 62093708--62093743 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
62093698 TATTTGTTTC
62093708 AAAA-TAAA
1 AAAATTAAA
62093716 AAAATTAAA
1 AAAATTAAA
62093725 AAAATTAAAA
1 AAAATT-AAA
62093735 AAAATTAAA
1 AAAATTAAA
62093744 TTGAGGTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 4 0.15
9 13 0.50
10 9 0.35
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATTAAA
Found at i:62093728 original size:10 final size:10
Alignment explanation
Indices: 62093713--62093743 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
62093703 GTTTCAAAAT
62093713 AAAAAAATT-
1 AAAAAAATTA
62093722 AAAAAAATTA
1 AAAAAAATTA
62093732 AAAAAAATTA
1 AAAAAAATTA
62093742 AA
1 AA
62093744 TTGAGGTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:62093934 original size:13 final size:13
Alignment explanation
Indices: 62093882--62093934 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
62093872 AATTCTTCAT
62093882 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
62093895 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
62093908 TGCTTTT-AATAAG
1 TGCTTTTGAA-AAG
*
62093921 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
62093934 T
1 T
62093935 TTGGTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 2 0.06
13 29 0.88
14 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:62097134 original size:19 final size:20
Alignment explanation
Indices: 62097110--62097147 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62097100 ATATATAATC
62097110 TTAAAAA-TACAAAAAAATA
1 TTAAAAATTACAAAAAAATA
*
62097129 TTAAAAATTATAAAAAAAT
1 TTAAAAATTACAAAAAAAT
62097148 TAGATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
TTAAAAATTACAAAAAAATA
Found at i:62097429 original size:2 final size:2
Alignment explanation
Indices: 62097422--62097454 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62097412 ATTCCTTTTG
62097422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62097455 TAGCTCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62102061 original size:30 final size:31
Alignment explanation
Indices: 62101990--62102065 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
62101980 TTGGATAAAA
* *
62101990 AAGTTTAGGCCCCAATCTAGAAACAATTGTC
1 AAGTTTAGGCCCCAATATAGAAACAATTGAC
*
62102021 AAGTTCAGGCCCCAATATA-AAA-AAGTTGAC
1 AAGTTTAGGCCCCAATATAGAAACAA-TTGAC
62102051 AAGTTTAGGCCCCAA
1 AAGTTTAGGCCCCAA
62102066 AAAATAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.05
30 21 0.52
31 17 0.43
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (31 bp):
AAGTTTAGGCCCCAATATAGAAACAATTGAC
Found at i:62103370 original size:22 final size:22
Alignment explanation
Indices: 62103340--62103390 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
62103330 TATTTTTTAA
*
62103340 TTTTAAAATACTTT-AAAAATAC
1 TTTTTAAAT-CTTTAAAAAATAC
*
62103362 TTTTTAAATTTTTAAAAAATAC
1 TTTTTAAATCTTTAAAAAATAC
62103384 TTTTTAA
1 TTTTTAA
62103391 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTTAAATCTTTAAAAAATAC
Found at i:62103395 original size:22 final size:22
Alignment explanation
Indices: 62103354--62103398 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
62103344 AAAATACTTT
62103354 AAAAATACTTTTTAAATTTTTA
1 AAAAATACTTTTTAAATTTTTA
*
62103376 AAAAATACTTTTTAATTTTTTA
1 AAAAATACTTTTTAAATTTTTA
62103398 A
1 A
62103399 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAAATACTTTTTAAATTTTTA
Found at i:62103438 original size:65 final size:66
Alignment explanation
Indices: 62103311--62103438 Score: 188
Period size: 66 Copynumber: 1.9 Consensus size: 66
62103301 CGAATATAAT
*
62103311 AAATATTTTTATTATTTTTTATTTTTTAATTTTAAAATACTTTAAAAATACTTTTTAAATTTTTA
1 AAATATTTTTA-TATTTTTTAATTTTTAATTTTAAAATACTTTAAAAATACTTTTTAAATTTTTA
62103376 AA
65 AA
** *
62103378 AAATACTTTTTA-ATTTTTTAATTTTTAATTTTAAAATA-TTTTTAAATACTTTTTTAATTTT
1 AAATA-TTTTTATATTTTTTAATTTTTAATTTTAAAATACTTTAAAAATACTTTTTAAATTTT
62103439 GTTTTAATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
65 20 0.36
66 25 0.45
67 5 0.09
68 6 0.11
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (66 bp):
AAATATTTTTATATTTTTTAATTTTTAATTTTAAAATACTTTAAAAATACTTTTTAAATTTTTAA
A
Found at i:62112944 original size:51 final size:51
Alignment explanation
Indices: 62112848--62112945 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
62112838 ATTCTATGTA
* ** *
62112848 AATGTTACGGGATAAAATTATTAAATCAAGATTAGTTTGATAGAATGCGAG
1 AATGTTACGGGATAAAATTATTAAATCAAGATCAAATTGACAGAATGCGAG
* * * *
62112899 AATGTTGCGGGCTAAATTTGTTAAATCAAGATCAAATTGACAGAATG
1 AATGTTACGGGATAAAATTATTAAATCAAGATCAAATTGACAGAATG
62112946 TATAAACTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (51 bp):
AATGTTACGGGATAAAATTATTAAATCAAGATCAAATTGACAGAATGCGAG
Found at i:62114693 original size:76 final size:76
Alignment explanation
Indices: 62114567--62114718 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
62114557 TCAATATATA
62114567 TATGATCCTAATGAGTGATCTGTAATTACAGTTAGTTGAGTCAGTTATTCTGTTTACTGCATGCT
1 TATGATCCTAATGAGTGATCTGTAATTACAGTTAGTTGAGTCAGTTATTCTGTTTACTGCATGCT
*
62114632 TAGATACTTGT
66 TAAATACTTGT
62114643 TATGATCCTAATGAGTGATCTGTAATTACAGTTAGTTGAGTCAGTTATTCTGTTTACTGCATGCT
1 TATGATCCTAATGAGTGATCTGTAATTACAGTTAGTTGAGTCAGTTATTCTGTTTACTGCATGCT
62114708 TAAATACTTGT
66 TAAATACTTGT
62114719 AACAGTCATA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (76 bp):
TATGATCCTAATGAGTGATCTGTAATTACAGTTAGTTGAGTCAGTTATTCTGTTTACTGCATGCT
TAAATACTTGT
Found at i:62114822 original size:43 final size:43
Alignment explanation
Indices: 62114767--62114865 Score: 173
Period size: 43 Copynumber: 2.3 Consensus size: 43
62114757 CCCCCCAAAA
62114767 CTTTTCTTTGTTCCTCTTGTTAGCTTTCAAGACCCAACTT-CT
1 CTTTTCTTTGTTCCTCTTGTTAGCTTTCAAGACCCAACTTCCT
*
62114809 CCTTTTCTCTGTTCCTCTTGTTAGCTTTCAAGACCCAACTTCCT
1 -CTTTTCTTTGTTCCTCTTGTTAGCTTTCAAGACCCAACTTCCT
62114853 CTTTTCTTTGTTC
1 CTTTTCTTTGTTC
62114866 TTTTGTTTCG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
43 51 0.96
44 2 0.04
ACGTcount: A:0.12, C:0.30, G:0.09, T:0.48
Consensus pattern (43 bp):
CTTTTCTTTGTTCCTCTTGTTAGCTTTCAAGACCCAACTTCCT
Found at i:62116213 original size:290 final size:291
Alignment explanation
Indices: 62115686--62116262 Score: 935
Period size: 290 Copynumber: 2.0 Consensus size: 291
62115676 CAGGTGATTG
* *** * *
62115686 TTTGAGGAATTTAAGGTCATGTTGTGCTATATGCTTCTTAATTTGTGAAAACCATCATAGTCCTT
1 TTTGAGGAATTTAAGATCATGTACAGCTATATACTTATTAATTTGTGAAAACCATCATAGTCCTT
* * *
62115751 TTCCTCATTAATGACTGATTTGCGATGAATCAGATGAGTAAACAAATGATGCAAACCGAAGAACA
66 TTCCCCATTAAAGACTGATTT-CGATAAATCAGATGAGTAAACAAATGATGCAAACCGAAGAACA
62115816 TCAAAACACAGATGATATGCTACAGCAACAGCAGGTAATATGCGATCAGTCATGAGGTTTCTTTA
130 TCAAAACACAGATGATATGCTACAGCAACAGCAGGTAATATGCGATCAGTCATGAGGTTTCTTTA
*
62115881 CCAAAGATGGCAAATTCCATGTCAGTGGAAAGTGTCATACAGATTTGCATCAG-AAACGTTGGCT
195 CCAAAGATAGCAAATTCCATGTCAGTGGAAAGTGTCATACAGATTTGCATC-GTAAACGTTGGCT
*
62115945 ACTTAATGAAAAT-TTCATCTGCAGGATTAATGA
259 ACTAAATG-AAATGTTCATCTGCAGGATTAATGA
* *
62115978 TTTGTGGAATTTAAGATCATGTACAGCTATATACTTATTAATTTGTGAAAACCATCATAGTTCTT
1 TTTGAGGAATTTAAGATCATGTACAGCTATATACTTATTAATTTGTGAAAACCATCATAGTCCTT
* * *
62116043 TTCCCCATTAAAGACTGATTT-GTTAAATCAGATGAGTAACCACATGATGCAAACCGAAGAACAT
66 TTCCCCATTAAAGACTGATTTCGATAAATCAGATGAGTAAACAAATGATGCAAACCGAAGAACAT
* *
62116107 CAAAACACAGATGATATGCTACAGCAACAGCAGGTAATATGTGATCAGTCATTAGGTTTCTTTAC
131 CAAAACACAGATGATATGCTACAGCAACAGCAGGTAATATGCGATCAGTCATGAGGTTTCTTTAC
*
62116172 CAAAGATAGCAAATTCCATGTCAGTGGAAAGTGTCATACAGATTTGCATCGTAAATGTTGGCTAC
196 CAAAGATAGCAAATTCCATGTCAGTGGAAAGTGTCATACAGATTTGCATCGTAAACGTTGGCTAC
62116237 TAAATGAAATGTTCATCTGCAGGATT
261 TAAATGAAATGTTCATCTGCAGGATT
62116263 CTGTTGGTAA
Statistics
Matches: 264, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
289 5 0.02
290 183 0.69
292 76 0.29
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (291 bp):
TTTGAGGAATTTAAGATCATGTACAGCTATATACTTATTAATTTGTGAAAACCATCATAGTCCTT
TTCCCCATTAAAGACTGATTTCGATAAATCAGATGAGTAAACAAATGATGCAAACCGAAGAACAT
CAAAACACAGATGATATGCTACAGCAACAGCAGGTAATATGCGATCAGTCATGAGGTTTCTTTAC
CAAAGATAGCAAATTCCATGTCAGTGGAAAGTGTCATACAGATTTGCATCGTAAACGTTGGCTAC
TAAATGAAATGTTCATCTGCAGGATTAATGA
Found at i:62131658 original size:31 final size:31
Alignment explanation
Indices: 62131623--62131686 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
62131613 ACAACCCAAA
*
62131623 GACTTAAATAAAAAGT-TCTGAATAGTTCAGT
1 GACTTAAATAAAAACTAT-TGAATAGTTCAGT
*
62131654 GACTTAAATGAAAACTATTGAATAGTTCAGT
1 GACTTAAATAAAAACTATTGAATAGTTCAGT
62131685 GA
1 GA
62131687 TCATTCTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.31
Consensus pattern (31 bp):
GACTTAAATAAAAACTATTGAATAGTTCAGT
Found at i:62144221 original size:2 final size:2
Alignment explanation
Indices: 62144214--62144238 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62144204 CTATTAATAC
62144214 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
62144239 ACTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62146814 original size:2 final size:2
Alignment explanation
Indices: 62146807--62146850 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
62146797 GCAACCTTTC
62146807 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62146847 AT AT
1 AT AT
62146851 CTTTTAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62147142 original size:10 final size:10
Alignment explanation
Indices: 62147127--62147153 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
62147117 TATAAACATT
62147127 TTCTAAAATA
1 TTCTAAAATA
62147137 TTCTAAAATA
1 TTCTAAAATA
62147147 TTCTAAA
1 TTCTAAA
62147154 CTCTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (10 bp):
TTCTAAAATA
Found at i:62148046 original size:12 final size:12
Alignment explanation
Indices: 62148026--62148064 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
62148016 ATTGAGCTGT
* *
62148026 TATGTATATGTA
1 TATGGATATGGA
62148038 TATGGATATGGA
1 TATGGATATGGA
62148050 TATGGATATGGA
1 TATGGATATGGA
62148062 TAT
1 TAT
62148065 ACGTATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (12 bp):
TATGGATATGGA
Found at i:62148052 original size:18 final size:18
Alignment explanation
Indices: 62148026--62148064 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
62148016 ATTGAGCTGT
* *
62148026 TATGTATATGTATATGGA
1 TATGGATATGGATATGGA
62148044 TATGGATATGGATATGGA
1 TATGGATATGGATATGGA
62148062 TAT
1 TAT
62148065 ACGTATACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (18 bp):
TATGGATATGGATATGGA
Found at i:62159872 original size:15 final size:15
Alignment explanation
Indices: 62159852--62159901 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
62159842 TTCAGAGTCT
62159852 TCATCTCTTTCAACA
1 TCATCTCTTTCAACA
* *
62159867 TCATCTCTTTCCACC
1 TCATCTCTTTCAACA
*
62159882 TCATCTCTTTCAACT
1 TCATCTCTTTCAACA
62159897 TCATC
1 TCATC
62159902 AGCATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (15 bp):
TCATCTCTTTCAACA
Found at i:62165386 original size:22 final size:22
Alignment explanation
Indices: 62165345--62165386 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
62165335 ATAAGCTTTT
* *
62165345 CTTTATCCCTTTTTTTTCTCTC
1 CTTTATCCCTTTTCTCTCTCTC
*
62165367 CTTTATTCCTTTTCTCTCTC
1 CTTTATCCCTTTTCTCTCTC
62165387 AAAAAAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (22 bp):
CTTTATCCCTTTTCTCTCTCTC
Found at i:62165563 original size:17 final size:17
Alignment explanation
Indices: 62165534--62165566 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
62165524 GAATAATTAA
62165534 TCTTTATTTTTTCTTTT
1 TCTTTATTTTTTCTTTT
62165551 TCTTT-TTTGTTTCTTT
1 TCTTTATTT-TTTCTTT
62165567 ATTGAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (17 bp):
TCTTTATTTTTTCTTTT
Found at i:62166416 original size:9 final size:9
Alignment explanation
Indices: 62166404--62166449 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
62166394 ATTAAGCCCA
62166404 TTAAAATTT
1 TTAAAATTT
*
62166413 TTAAATTTT
1 TTAAAATTT
*
62166422 TTAAATTTT
1 TTAAAATTT
62166431 TTAAAATTT
1 TTAAAATTT
62166440 TTAAAATTT
1 TTAAAATTT
62166449 T
1 T
62166450 AAATTAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTAAAATTT
Found at i:62166420 original size:8 final size:8
Alignment explanation
Indices: 62166407--62166454 Score: 60
Period size: 9 Copynumber: 5.6 Consensus size: 8
62166397 AAGCCCATTA
62166407 AAATTTTT
1 AAATTTTT
62166415 AAATTTTTT
1 AAA-TTTTT
62166424 AAATTTTTT
1 AAA-TTTTT
62166433 AAAATTTTT
1 -AAATTTTT
*
62166442 AAAATTTT
1 AAATTTTT
62166450 AAATT
1 AAATT
62166455 AGTAAATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 14 0.39
9 19 0.53
10 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
AAATTTTT
Found at i:62168947 original size:60 final size:60
Alignment explanation
Indices: 62168882--62169063 Score: 355
Period size: 60 Copynumber: 3.0 Consensus size: 60
62168872 ACAATCTCCA
62168882 CCTTGACACGAATTCTCAATGAATAAGTTATTCATCGCGAACTCTCAACAAACAAGTTCT
1 CCTTGACACGAATTCTCAATGAATAAGTTATTCATCGCGAACTCTCAACAAACAAGTTCT
62168942 CCTTGACACGAATTCTCAATGAATAAGTTATTCATCGCGAACTCTCAACAAACAAGTTCT
1 CCTTGACACGAATTCTCAATGAATAAGTTATTCATCGCGAACTCTCAACAAACAAGTTCT
*
62169002 CCTTGACACGAATTCTCAATGAATAAGTTTTTCATCGCGAACTCTCAACAAACAAGTTCT
1 CCTTGACACGAATTCTCAATGAATAAGTTATTCATCGCGAACTCTCAACAAACAAGTTCT
62169062 CC
1 CC
62169064 ACCTCTTCTA
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 121 1.00
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (60 bp):
CCTTGACACGAATTCTCAATGAATAAGTTATTCATCGCGAACTCTCAACAAACAAGTTCT
Found at i:62168959 original size:31 final size:31
Alignment explanation
Indices: 62168919--62169063 Score: 120
Period size: 29 Copynumber: 4.8 Consensus size: 31
62168909 TTATTCATCG
62168919 CGAACTCTCAACAAACAAGTTCTCCTTGACA
1 CGAACTCTCAACAAACAAGTTCTCCTTGACA
* ** * * * * *
62168950 CGAATTCTCAATGAATAAGTTATTCAT--CG
1 CGAACTCTCAACAAACAAGTTCTCCTTGACA
62168979 CGAACTCTCAACAAACAAGTTCTCCTTGACA
1 CGAACTCTCAACAAACAAGTTCTCCTTGACA
* ** * * *
62169010 CGAATTCTCAATGAATAAGTT-T--TTCATCG
1 CGAACTCTCAACAAACAAGTTCTCCTTGA-CA
62169039 CGAACTCTCAACAAACAAGTTCTCC
1 CGAACTCTCAACAAACAAGTTCTCC
62169064 ACCTCTTCTA
Statistics
Matches: 82, Mismatches: 26, Indels: 11
0.69 0.22 0.09
Matches are distributed among these distances:
28 3 0.04
29 39 0.48
30 2 0.02
31 38 0.46
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (31 bp):
CGAACTCTCAACAAACAAGTTCTCCTTGACA
Done.