Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 5 of 66
Found at i:1677339 original size:351 final size:351
Alignment explanation
Indices: 1676647--1677324 Score: 934
Period size: 351 Copynumber: 1.9 Consensus size: 351
1676637 GTGGTGAATC
* * * *
1676647 TTCAAGTACAGAGCAGCCCGACAGATCAAGAACCTTTAGGCTGCTGAGATTTCCAACTGAAGAAG
1 TTCAAGTACAGAGCAACCCGACAGATCAAGAACCTTTAGACTGCTGAGATGTCCAAATGAAGAAG
* * * * ** **
1676712 GAAGTTCTTCCATACTTGTGCCATCTAAATGGACCTCTAGCAAATGTTCCATTTTTCCGGTAATC
66 GAAGTTCTTCAATACTTGTCCCATCTAAATAGACCTCCAGCAAACATTCCATTTCCCCGGTAATC
* * *
1676777 TCTGGAAACCTTTGAAGATTCTTACAGCCTGAAAGAATCAATATTTCAAGAGATTCCATTCCAAT
131 TCTGGAAACCTTCGAAGATTCTGACAGCCTGAAAGAATAAATATTTCAAGAGATTCCATTCCAAT
** * * *
1676842 TTTGGTTGGGAGACTCTTAAGGCTTTTGCAGTTTCTTAAATTCAAAAGTTTAAGCTTGGGCGAAA
196 TTTGGTTGGGAGACTCCGAAGGCTTATGCAGTTTCTAAAATTCAAAAGTTTAAGCTTGGGAGAAA
* * * * *
1676907 ATGCGATGGATGGATGGACATGTGCTAAGCTGGTGCAGCCTTCCAAATTCAAACTTTCGAGATTT
261 ATGCGATGGATGGATGAACATGTACTAAGCTGGTACAACCTTCCAAATTCAAACTTTCCAGATTT
1676972 TCCATCATTCTGAAGTCCGGTAAATT
326 TCCATCATTCTGAAGTCCGGTAAATT
* * * *
1676998 TTCAAGTTCAGAGCAACCCGAGAGATTAAGAA-CTTTGAGATTGCTGAGATGTCCAAATGAAG-A
1 TTCAAGTACAGAGCAACCCGACAGATCAAGAACCTTT-AGACTGCTGAGATGTCCAAATGAAGAA
* *
1677061 GGTAAGTTCTTTAATACTTGTCCCATCTAAATAGAGCTCCAGCAAACATTCCATTTCCCCGGTAA
65 GG-AAGTTCTTCAATACTTGTCCCATCTAAATAGACCTCCAGCAAACATTCCATTTCCCCGGTAA
* * * * *
1677126 TTTCTGGAAACCTTCGAAGATT-TGAGCAGCCTGAAAGAATAAATGTTTCAAGGGATTGCATTCT
129 TCTCTGGAAACCTTCGAAGATTCTGA-CAGCCTGAAAGAATAAATATTTCAAGAGATTCCATTCC
1677190 AATTTTGGTTGGGAGACTCCGAAGGCTTATGCAGTTTCTAAAATTCAAAAGTTTAAGCTTGGGTA
193 AATTTTGGTTGGGAGACTCCGAAGGCTTATGCAGTTTCTAAAATTCAAAAGTTTAAGCTTGGG-A
* *
1677255 G-AAATGCGATGGATGGATGAACATGTACTAAGTTGGTACAACCTGT-TAAATTCAAACTTTCCA
257 GAAAATGCGATGGATGGATGAACATGTACTAAGCTGGTACAACCT-TCCAAATTCAAACTTTCCA
1677318 GATTTTC
321 GATTTTC
1677325 GGTCGTTGTG
Statistics
Matches: 284, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
350 9 0.03
351 273 0.96
352 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (351 bp):
TTCAAGTACAGAGCAACCCGACAGATCAAGAACCTTTAGACTGCTGAGATGTCCAAATGAAGAAG
GAAGTTCTTCAATACTTGTCCCATCTAAATAGACCTCCAGCAAACATTCCATTTCCCCGGTAATC
TCTGGAAACCTTCGAAGATTCTGACAGCCTGAAAGAATAAATATTTCAAGAGATTCCATTCCAAT
TTTGGTTGGGAGACTCCGAAGGCTTATGCAGTTTCTAAAATTCAAAAGTTTAAGCTTGGGAGAAA
ATGCGATGGATGGATGAACATGTACTAAGCTGGTACAACCTTCCAAATTCAAACTTTCCAGATTT
TCCATCATTCTGAAGTCCGGTAAATT
Found at i:1682092 original size:34 final size:34
Alignment explanation
Indices: 1682049--1682152 Score: 190
Period size: 34 Copynumber: 3.1 Consensus size: 34
1682039 CTTTTATTAT
1682049 ATCAAATTAAAACATATAAACACGTATAAAAAAA
1 ATCAAATTAAAACATATAAACACGTATAAAAAAA
1682083 ATCAAATTAAAACATATAAACACGTATAAAAAAA
1 ATCAAATTAAAACATATAAACACGTATAAAAAAA
**
1682117 ATCAAATTAAAACATATAAACACGTACCAAAAAA
1 ATCAAATTAAAACATATAAACACGTATAAAAAAA
1682151 AT
1 AT
1682153 AAAACTATTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (34 bp):
ATCAAATTAAAACATATAAACACGTATAAAAAAA
Found at i:1683162 original size:238 final size:238
Alignment explanation
Indices: 1682736--1683209 Score: 932
Period size: 238 Copynumber: 2.0 Consensus size: 238
1682726 ATTAATTTTT
1682736 TATTTTTAAAAATTACTTTAATTTAATTTCTATCGTATTCAATATTTATATTAAAATGTTGACAT
1 TATTTTTAAAAATTACTTTAATTTAATTTCTATCGTATTCAATATTTATATTAAAATGTTGACAT
1682801 CAATGTTGACGTATAGCCAAAGTCACCGTAGAAAATGCGCACTCTTTGTTGGGATGGTAACATTT
66 CAATGTTGACGTATAGCCAAAGTCACCGTAGAAAATGCGCACTCTTTGTTGGGATGGTAACATTT
1682866 TCTTGACTTTTATTCTCATGATAAAGACTTATTCTTGGAAGATGTGTGTATGCCCATCTTTGAGC
131 TCTTGACTTTTATTCTCATGATAAAGACTTATTCTTGGAAGATGTGTGTATGCCCATCTTTGAGC
1682931 TTTGGAAAAATTAGGCCAAACACAAATATTTTCTTTTTGAATG
196 TTTGGAAAAATTAGGCCAAACACAAATATTTTCTTTTTGAATG
1682974 NTATTTTT-AAAATTACTTTAATTTAATTTCTATCGTATTCAATATTTATATTAAAATGTTGACA
1 -TATTTTTAAAAATTACTTTAATTTAATTTCTATCGTATTCAATATTTATATTAAAATGTTGACA
1683038 TCAATGTTGACGTATAGCCAAAGTCACCGTAGAAAATGCGCACTCTTTGTTGGGATGGTAACATT
65 TCAATGTTGACGTATAGCCAAAGTCACCGTAGAAAATGCGCACTCTTTGTTGGGATGGTAACATT
1683103 TTCTTGACTTTTATTCTCATGATAAAGACTTATTCTTGGAAGATGTGTGTATGCCCATCTTTGAG
130 TTCTTGACTTTTATTCTCATGATAAAGACTTATTCTTGGAAGATGTGTGTATGCCCATCTTTGAG
1683168 CTTTGGAAAAATTAGGCCAAACACAAATATTTTCTTTTTGAA
195 CTTTGGAAAAATTAGGCCAAACACAAATATTTTCTTTTTGAA
1683210 GGGCAAGACA
Statistics
Matches: 235, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
238 228 0.97
239 7 0.03
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (238 bp):
TATTTTTAAAAATTACTTTAATTTAATTTCTATCGTATTCAATATTTATATTAAAATGTTGACAT
CAATGTTGACGTATAGCCAAAGTCACCGTAGAAAATGCGCACTCTTTGTTGGGATGGTAACATTT
TCTTGACTTTTATTCTCATGATAAAGACTTATTCTTGGAAGATGTGTGTATGCCCATCTTTGAGC
TTTGGAAAAATTAGGCCAAACACAAATATTTTCTTTTTGAATG
Found at i:1684128 original size:2 final size:2
Alignment explanation
Indices: 1684113--1684165 Score: 55
Period size: 2 Copynumber: 29.0 Consensus size: 2
1684103 TAGAAATAAA
1684113 AT AT -T AT A- AT AT AT AT -T AT -T AT AT AT -T AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1684149 AT AT AT AT GAT AT AT AT
1 AT AT AT AT -AT AT AT AT
1684166 TTGCTCAGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
1 6 0.14
2 36 0.82
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1684445 original size:21 final size:22
Alignment explanation
Indices: 1684423--1684535 Score: 104
Period size: 27 Copynumber: 4.8 Consensus size: 22
1684413 ACATTGTCCT
*
1684423 TAAATAAGTTGATAAAAGTCTTA
1 TAAATAAGTTGATAAAAATC-TA
1684446 TAAAAATATAAGTTGATAAAAAT-TA
1 T---AA-ATAAGTTGATAAAAATCTA
*
1684471 TAAATAAGTTGATAAAAGTCTTA
1 TAAATAAGTTGATAAAAATC-TA
1684494 TAAAAATATAAGTTGATAAAAAT-TA
1 T---AA-ATAAGTTGATAAAAATCTA
1684519 TAAATAAGTTGATAAAA
1 TAAATAAGTTGATAAAA
1684536 TTACGACATG
Statistics
Matches: 77, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
21 29 0.38
22 4 0.05
23 4 0.05
25 6 0.08
26 4 0.05
27 30 0.39
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.33
Consensus pattern (22 bp):
TAAATAAGTTGATAAAAATCTA
Found at i:1684460 original size:27 final size:27
Alignment explanation
Indices: 1684426--1684514 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
1684416 TTGTCCTTAA
1684426 ATAAGTTGATAAAAGTCTTATAAAAAT
1 ATAAGTTGATAAAAGTCTTATAAAAAT
*
1684453 ATAAGTTGATAAAA--ATTAT---AA-
1 ATAAGTTGATAAAAGTCTTATAAAAAT
1684474 ATAAGTTGATAAAAGTCTTATAAAAAT
1 ATAAGTTGATAAAAGTCTTATAAAAAT
1684501 ATAAGTTGATAAAA
1 ATAAGTTGATAAAA
1684515 ATTATAAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
21 14 0.26
22 2 0.04
23 4 0.07
25 4 0.07
26 2 0.04
27 28 0.52
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (27 bp):
ATAAGTTGATAAAAGTCTTATAAAAAT
Found at i:1684494 original size:48 final size:48
Alignment explanation
Indices: 1684423--1684535 Score: 226
Period size: 48 Copynumber: 2.4 Consensus size: 48
1684413 ACATTGTCCT
1684423 TAAATAAGTTGATAAAAGTCTTATAAAAATATAAGTTGATAAAAATTA
1 TAAATAAGTTGATAAAAGTCTTATAAAAATATAAGTTGATAAAAATTA
1684471 TAAATAAGTTGATAAAAGTCTTATAAAAATATAAGTTGATAAAAATTA
1 TAAATAAGTTGATAAAAGTCTTATAAAAATATAAGTTGATAAAAATTA
1684519 TAAATAAGTTGATAAAA
1 TAAATAAGTTGATAAAA
1684536 TTACGACATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.33
Consensus pattern (48 bp):
TAAATAAGTTGATAAAAGTCTTATAAAAATATAAGTTGATAAAAATTA
Found at i:1684536 original size:13 final size:12
Alignment explanation
Indices: 1684453--1684534 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 12
1684443 TTATAAAAAT
1684453 ATAAGTTGATAA
1 ATAAGTTGATAA
1684465 A-AA-TT-ATAA
1 ATAAGTTGATAA
1684474 ATAAGTTGAT-A
1 ATAAGTTGATAA
*
1684485 A-AAGTCTTATAAAAA
1 ATAAGT-TGAT---AA
1684500 TATAAGTTGATAA
1 -ATAAGTTGATAA
1684513 A-AA-TT-ATAA
1 ATAAGTTGATAA
1684522 ATAAGTTGATAA
1 ATAAGTTGATAA
1684534 A
1 A
1684535 ATTACGACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 26
0.66 0.02 0.31
Matches are distributed among these distances:
9 10 0.18
10 12 0.22
11 13 0.24
12 9 0.16
13 2 0.04
15 1 0.02
16 4 0.07
17 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAAGTTGATAA
Found at i:1686427 original size:30 final size:29
Alignment explanation
Indices: 1686372--1686442 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
1686362 TACATTTTGT
1686372 TTAATTTAATTTTTATATTTTAAATTAAA
1 TTAATTTAATTTTTATATTTTAAATTAAA
* **
1686401 TTAAATTAATTTTT-TATTTTAAAAATTATT
1 TTAATTTAATTTTTATATTTT--AAATTAAA
1686431 TTAATTTAATTT
1 TTAATTTAATTT
1686443 CTATCGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.17
29 13 0.36
30 17 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTAATTTAATTTTTATATTTTAAATTAAA
Found at i:1687114 original size:29 final size:28
Alignment explanation
Indices: 1687063--1687128 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
1687053 ATGTCTATGG
* **
1687063 GTAATTTTTCAGTTTTTGGGGTAAAAAT
1 GTAATTTTTCACTTTACGGGGTAAAAAT
*
1687091 GTAATTTTTCACTTTACGAGGGTAAAAGT
1 GTAATTTTTCACTTTACG-GGGTAAAAAT
1687120 GTAATTTTT
1 GTAATTTTT
1687129 AAAAAATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (28 bp):
GTAATTTTTCACTTTACGGGGTAAAAAT
Found at i:1687117 original size:28 final size:29
Alignment explanation
Indices: 1687063--1687128 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1687053 ATGTCTATGG
* **
1687063 GTAATTTTTCAGTTTTTGGGGTAAAAA-T
1 GTAATTTTTCACTTTACGGGGTAAAAAGT
1687091 GTAATTTTTCACTTTACGAGGGT-AAAAGT
1 GTAATTTTTCACTTTACG-GGGTAAAAAGT
1687120 GTAATTTTT
1 GTAATTTTT
1687129 AAAAAATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 19 0.58
29 14 0.42
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (29 bp):
GTAATTTTTCACTTTACGGGGTAAAAAGT
Found at i:1688303 original size:13 final size:13
Alignment explanation
Indices: 1688285--1688309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1688275 AGAAAATGGG
1688285 ATTTTATAAAATA
1 ATTTTATAAAATA
1688298 ATTTTATAAAAT
1 ATTTTATAAAAT
1688310 TTTTAAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:1697821 original size:2 final size:2
Alignment explanation
Indices: 1697804--1697862 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1697794 ACATTATGAA
* *
1697804 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1697845 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1697863 GGTTTTGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1698168 original size:189 final size:188
Alignment explanation
Indices: 1697847--1698225 Score: 733
Period size: 189 Copynumber: 2.0 Consensus size: 188
1697837 TATATATTAT
1697847 ATATATATATATATATGGTTTTGTTATCCTATGGAGTTTTGTTTTAAGTTTAAGTTTGTAAATTT
1 ATATATATATATATATGGTTTTGTTATCCTATGGAGTTTTGTTTTAAGTTTAAGTTTGTAAATTT
1697912 TATATTTAAAGCTTATAAGTTTTTGTTAAAGATTCCATAAACTATCACATCTCTAATACTAAAAA
66 TATATTTAAAGCTTATAAGTTTTTGTTAAAGATTCCATAAACTATCACATCTCTAATACTAAAAA
1697977 TATTTTTTTTGTTCGTTCAAATCATGATTTTATTACGGGTATCTGATTAGATACTGTC
131 TATTTTTTTTGTTCGTTCAAATCATGATTTTATTACGGGTATCTGATTAGATACTGTC
1698035 ANTATATATATATAT-TGGGTTTTGTTATCCTATGGAGTTTTGTTTTAAGTTTAAGTTTGTAAAT
1 A-TATATATATATATAT-GGTTTTGTTATCCTATGGAGTTTTGTTTTAAGTTTAAGTTTGTAAAT
1698099 TTTATATTTAAAGCTTATAAGTTTTTGTTAAAGATTCCATAAACTATCACATCTCTAATACTAAA
64 TTTATATTTAAAGCTTATAAGTTTTTGTTAAAGATTCCATAAACTATCACATCTCTAATACTAAA
1698164 AATATTTTTTTTGTTCGTTCAAATCATGATTTTATTACGGGTATCTGATTAGATACTGTC
129 AATATTTTTTTTGTTCGTTCAAATCATGATTTTATTACGGGTATCTGATTAGATACTGTC
1698224 AT
1 AT
1698226 GATCTATTTC
Statistics
Matches: 189, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
188 3 0.02
189 186 0.98
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (188 bp):
ATATATATATATATATGGTTTTGTTATCCTATGGAGTTTTGTTTTAAGTTTAAGTTTGTAAATTT
TATATTTAAAGCTTATAAGTTTTTGTTAAAGATTCCATAAACTATCACATCTCTAATACTAAAAA
TATTTTTTTTGTTCGTTCAAATCATGATTTTATTACGGGTATCTGATTAGATACTGTC
Found at i:1698524 original size:13 final size:13
Alignment explanation
Indices: 1698508--1698546 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1698498 CGTCTCGAAG
1698508 GAGAAGAAAAAGA
1 GAGAAGAAAAAGA
*
1698521 GAGAAGAAAAGGA
1 GAGAAGAAAAAGA
*
1698534 -AGAAGAAAGAGA
1 GAGAAGAAAAAGA
1698546 G
1 G
1698547 GCGGAGCGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GAGAAGAAAAAGA
Found at i:1698667 original size:17 final size:17
Alignment explanation
Indices: 1698645--1698687 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1698635 GGGAGAAAGG
1698645 AGAAGAAAAAAAAAGAA
1 AGAAGAAAAAAAAAGAA
* * *
1698662 AGAAGAAGAAACAGGAA
1 AGAAGAAAAAAAAAGAA
1698679 AGGAAGAAA
1 A-GAAGAAA
1698688 GAATAGCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAAGAAAAAAAAAGAA
Found at i:1699363 original size:60 final size:60
Alignment explanation
Indices: 1699286--1699457 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 60
1699276 TGAAAAAGGG
** *
1699286 GGACCTGAAGCCCCGATTTATATTGGGTGTTGTGAGTAGTTCCCACGAGTAGGTAAAGAA
1 GGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGAA
* * * * **
1699346 GGACCTGAAGCCTCGATTTATATTGAGTGGCATGGGTAATTCCCACGAGTAGGTAAAGGG
1 GGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGAA
* * * *
1699406 GGACCTAAAGCCCCTATTCATA-T-GGTGGCGTGGGTAGTTCCCATGAGTAGGT
1 GGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGTAGTTCCCACGAGTAGGT
1699458 GATGATGTCT
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 25 0.26
59 1 0.01
60 69 0.73
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (60 bp):
GGACCTGAAGCCCCGATTTATATTGGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGAA
Found at i:1703076 original size:18 final size:18
Alignment explanation
Indices: 1703053--1703093 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1703043 GAGCTAAGGG
1703053 AGAAAGA-AAGAAAGAAAA
1 AGAAAGAGAA-AAAGAAAA
*
1703071 AGAAAGAGAAAAAGAAAG
1 AGAAAGAGAAAAAGAAAA
1703089 AGAAA
1 AGAAA
1703094 CGTCGGCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AGAAAGAGAAAAAGAAAA
Found at i:1703090 original size:12 final size:12
Alignment explanation
Indices: 1703055--1703093 Score: 60
Period size: 12 Copynumber: 3.1 Consensus size: 12
1703045 GCTAAGGGAG
1703055 AAAGAAAGAAAGAA
1 AAAGAAAG--AGAA
1703069 AAAGAAAGAGAA
1 AAAGAAAGAGAA
1703081 AAAGAAAGAGAA
1 AAAGAAAGAGAA
1703093 A
1 A
1703094 CGTCGGCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 17 0.68
14 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAGAA
Found at i:1703869 original size:61 final size:58
Alignment explanation
Indices: 1703771--1703945 Score: 217
Period size: 61 Copynumber: 2.9 Consensus size: 58
1703761 ATTGAGAAAA
*
1703771 AGGGACCTGAAGCCCTGATTTATATTGGGTGGCATGGGTAGTTCCCACGAGTAGGTAAAG
1 AGGGACCTGAAGCCC-AATTTATATT-GGTGGCATGGGTAGTTCCCACGAGTAGGTAAAG
*
1703831 AGGGACCTGAAGCCTCAATTTTATATTAGGTGACATGGGTAGTTCCCACGAGTAGGTAAAG
1 AGGGACCTGAAGCC-CAA-TTTATATT-GGTGGCATGGGTAGTTCCCACGAGTAGGTAAAG
* * * * **
1703892 GGGGAACTGAAGCCCCTATTCATA-TGGTGGTGTGGGTAGTTCCCACGAGTAGGT
1 AGGGACCTGAAG-CCCAATTTATATTGGTGGCATGGGTAGTTCCCACGAGTAGGT
1703946 GATGATGTCT
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
58 26 0.25
59 1 0.01
60 20 0.20
61 53 0.52
62 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (58 bp):
AGGGACCTGAAGCCCAATTTATATTGGTGGCATGGGTAGTTCCCACGAGTAGGTAAAG
Found at i:1707447 original size:12 final size:12
Alignment explanation
Indices: 1707430--1707455 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1707420 GACTGCCTGC
1707430 TTGTGTTTTAAA
1 TTGTGTTTTAAA
1707442 TTGTGTTTTAAA
1 TTGTGTTTTAAA
1707454 TT
1 TT
1707456 ATATGGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (12 bp):
TTGTGTTTTAAA
Found at i:1711961 original size:351 final size:351
Alignment explanation
Indices: 1711305--1711982 Score: 968
Period size: 351 Copynumber: 1.9 Consensus size: 351
1711295 GGAAAGATGG
*
1711305 TGGTAAAATTTCAAATACAGAGCAGCCCGAAAGATTAAGAACTTGTAGGCTGCTGAGATTTCCAA
1 TGGTAAAATTTCAAATACAGAGCAGCCCGAAAGATTAAGAACTTGTAGACTGCTGAGATTTCCAA
* * * * **
1711370 TTGAAGAGGGAAGTTCTTCAATACTTGTGCCATCTAAATGGAGCTCCAACAAACGTTCCATTTTT
66 ATGAAGAGGGAAGTTCTTCAATACTTGTCCCATCTAAATAGAGCTCCAACAAACATTCCATTTCC
* **
1711435 CCGGTGATCTCTGGAAACCTTCGAAGATCCTTGCAGCCTGAAAGAATCAATGTTTCAAGAGACTC
131 CCGGTAATCTCTGGAAACCTTCGAAGATCCGAGCAGCCTGAAAGAATCAATGTTTCAAGAGACTC
*
1711500 CATTCCAATATTGGTTGAGAGACTCCTAAGACTTGTGCAGTTTCTTAAATTCAAAAGCTTGAGCT
196 CATTCCAATATTGGTTGAGAGACTCCTAAGACTTGTGCAGTTTCTTAAATTCAAAAGCTTAAGCT
*
1711565 TGGGTAAAACTGAGATGGATGGATGGACATCTAATAAGCTGGTACAACCTTGCAAATTCAAACTT
261 TGGGTAAAACTGAGATGGATGGATGGACATCTAATAAGCTGGTACAACCTTCCAAATTCAAACTT
1711630 TCGAGATTTTCAATCATCGTGAAGTC
326 TCGAGATTTTCAATCATCGTGAAGTC
* * ** * * *
1711656 TGGTAAATTTTCAAGTTTAGAGCAGCCTGAGAGATTAAGAACTT-TGAGATTGCTGAGATGTT-C
1 TGGTAAAATTTCAAATACAGAGCAGCCCGAAAGATTAAGAACTTGT-AGACTGCTGAGAT-TTCC
* * *
1711719 AAATGAAGAGGGAAGTTCTTTAATACTTGTCCCATCTAAATAGAGCTCCAGCAAACATTTCATTT
64 AAATGAAGAGGGAAGTTCTTCAATACTTGTCCCATCTAAATAGAGCTCCAACAAACATTCCATTT
* *
1711784 CCCCGGTAATCTCTGGAAACCTTCGAAGATTCGAGCAGCTTGAAAGAA-CAAATGTTTCAAGAGA
129 CCCCGGTAATCTCTGGAAACCTTCGAAGATCCGAGCAGCCTGAAAGAATC-AATGTTTCAAGAGA
* * * * * *
1711848 TTCCATTCTAATTTTGGTTGCGAGACTCTTAAGACTTGTGCAGTTTCTTAAATTCAAAAGTTTAA
193 CTCCATTCCAATATTGGTTGAGAGACTCCTAAGACTTGTGCAGTTTCTTAAATTCAAAAGCTTAA
* * * * * *
1711913 GCTTGGGTAGAAA-TGTGATGGATGGATGGACATGTACTAAGTTGGTACAGCCTTCCAAATTCGA
258 GCTTGGGTA-AAACTGAGATGGATGGATGGACATCTAATAAGCTGGTACAACCTTCCAAATTCAA
1711977 ACTTTC
322 ACTTTC
1711983 CAAAATTTCG
Statistics
Matches: 287, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
350 2 0.01
351 280 0.98
352 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (351 bp):
TGGTAAAATTTCAAATACAGAGCAGCCCGAAAGATTAAGAACTTGTAGACTGCTGAGATTTCCAA
ATGAAGAGGGAAGTTCTTCAATACTTGTCCCATCTAAATAGAGCTCCAACAAACATTCCATTTCC
CCGGTAATCTCTGGAAACCTTCGAAGATCCGAGCAGCCTGAAAGAATCAATGTTTCAAGAGACTC
CATTCCAATATTGGTTGAGAGACTCCTAAGACTTGTGCAGTTTCTTAAATTCAAAAGCTTAAGCT
TGGGTAAAACTGAGATGGATGGATGGACATCTAATAAGCTGGTACAACCTTCCAAATTCAAACTT
TCGAGATTTTCAATCATCGTGAAGTC
Found at i:1716230 original size:6 final size:6
Alignment explanation
Indices: 1716219--1716267 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
1716209 CCATTGAGAA
* *
1716219 GAAGAT GAAGAT --A-AT GAAGAT GAAGAT GATGAT GAAGAG GAAG-T
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
1716263 GAAGA
1 GAAGA
1716268 CAGTACCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 5 0.14
6 27 0.77
ACGTcount: A:0.49, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:1716239 original size:15 final size:15
Alignment explanation
Indices: 1716219--1716250 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1716209 CCATTGAGAA
1716219 GAAGATGAAGATAAT
1 GAAGATGAAGATAAT
*
1716234 GAAGATGAAGATGAT
1 GAAGATGAAGATAAT
1716249 GA
1 GA
1716251 TGAAGAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (15 bp):
GAAGATGAAGATAAT
Found at i:1716985 original size:6 final size:6
Alignment explanation
Indices: 1716974--1717022 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
1716964 CCATTGAGAA
* *
1716974 GAAGAT GAAGAT --A-AT GAAGAT GAAGAT GATGAT GAAGAG GAAG-T
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
1717018 GAAGA
1 GAAGA
1717023 CAGTACCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 5 0.14
6 27 0.77
ACGTcount: A:0.49, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:1716994 original size:15 final size:15
Alignment explanation
Indices: 1716974--1717005 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1716964 CCATTGAGAA
1716974 GAAGATGAAGATAAT
1 GAAGATGAAGATAAT
*
1716989 GAAGATGAAGATGAT
1 GAAGATGAAGATAAT
1717004 GA
1 GA
1717006 TGAAGAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (15 bp):
GAAGATGAAGATAAT
Found at i:1724491 original size:6 final size:6
Alignment explanation
Indices: 1724480--1724528 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
1724470 CCATTGAGAA
* *
1724480 GAAGAT GAAGAT --A-AT GAAGAT GAAGAT GATGAT GAAGAG GAAG-T
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
1724524 GAAGA
1 GAAGA
1724529 CAGTACCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 5 0.14
6 27 0.77
ACGTcount: A:0.49, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:1724500 original size:15 final size:15
Alignment explanation
Indices: 1724480--1724511 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1724470 CCATTGAGAA
1724480 GAAGATGAAGATAAT
1 GAAGATGAAGATAAT
*
1724495 GAAGATGAAGATGAT
1 GAAGATGAAGATAAT
1724510 GA
1 GA
1724512 TGAAGAGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (15 bp):
GAAGATGAAGATAAT
Found at i:1725046 original size:13 final size:13
Alignment explanation
Indices: 1725009--1725046 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1724999 TAAAAAATTT
1725009 ATTTAATTTTT-A
1 ATTTAATTTTTCA
*
1725021 ATTTTAATATTTCA
1 A-TTTAATTTTTCA
1725035 ATTTAATTTTTC
1 ATTTAATTTTTC
1725047 CCTTTAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 1 0.05
13 19 0.86
14 2 0.09
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTAATTTTTCA
Found at i:1730931 original size:19 final size:19
Alignment explanation
Indices: 1730904--1730960 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
1730894 CCATTTGACT
*
1730904 TATTAGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
1730923 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
1730942 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
1730961 ATTTAGAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:1740204 original size:13 final size:13
Alignment explanation
Indices: 1740186--1740210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1740176 ATTTTTAAAA
1740186 ATTTTATAAAATT
1 ATTTTATAAAATT
1740199 ATTTTATAAAAT
1 ATTTTATAAAAT
1740211 CTCATTTTCT
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:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:1743019 original size:28 final size:29
Alignment explanation
Indices: 1742971--1743034 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1742961 GCAAACTTTT
* ** *
1742971 AAAAATTACACTTTTGCCCCCGTAAAGTG
1 AAAAATTACACTTTTGACCCCAAAAACTG
*
1743000 AAAAATTACA-TTTTTACCCCAAAAACTG
1 AAAAATTACACTTTTGACCCCAAAAACTG
1743028 AAAAATT
1 AAAAATT
1743035 GACCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTGACCCCAAAAACTG
Found at i:1747354 original size:21 final size:20
Alignment explanation
Indices: 1747298--1747359 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 20
1747288 GGTCTTTTTT
1747298 GTTAAGAATGATGGCT--TCA
1 GTTAAGAATGATGG-TAATCA
* *
1747317 ATTAAGAA-GATGATAATCA
1 GTTAAGAATGATGGTAATCA
*
1747336 GTTAAGAAATGATGGTAATTA
1 GTTAAG-AATGATGGTAATCA
1747357 GTT
1 GTT
1747360 TAAAGCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 4 0.12
19 15 0.44
20 2 0.06
21 12 0.35
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (20 bp):
GTTAAGAATGATGGTAATCA
Found at i:1748099 original size:208 final size:207
Alignment explanation
Indices: 1747741--1748157 Score: 809
Period size: 208 Copynumber: 2.0 Consensus size: 207
1747731 AATTTGAATG
1747741 ATTCATCCATTTCGAATTCGACTTGACTTTAAAAGTCAATAACTTGAATCCAAAATGAAGAGAAC
1 ATTCATCCATTTCGAATTCGACTTGACTTTAAAAGTCAATAACTTGAATCCAAAATGAAGAGAAC
1747806 CTGAATAATCTTAATGTCAAATCAGAATGACTCAAACCTAAAAATTACTTGAATTTTCTTCTATC
66 CTGAATAATCTTAATGTCAAATCAGAATGACTCAAACCTAAAAATTACTTGAATTTTCTTCTATC
1747871 CAAAATGATTGTGTATCTAATTGTCACCTCTACCTATTACGACATTATATTTATATATATATATA
131 CAAAATGATTGTGTATCTAATTGTCACCTCTACCTATTACGACATTATATTTATATATATATATA
1747936 TTAT-GTTTTGTT
196 -TATGGTTTTGTT
1747948 NATTCATCCATTTCGAATTCGACTTGACTTTAAAAGTCAATAACTTGAATCCAAAATGAAGAGAA
1 -ATTCATCCATTTCGAATTCGACTTGACTTTAAAAGTCAATAACTTGAATCCAAAATGAAGAGAA
1748013 CCTGAATAATCTTAATGTCAAATCAGAATGACTCAAACCTAAAAATTACTTGAATTTTCTTCTAT
65 CCTGAATAATCTTAATGTCAAATCAGAATGACTCAAACCTAAAAATTACTTGAATTTTCTTCTAT
1748078 CCAAAATGATTGTGTATCTAATTGTCACCTCTACCTATTACGACATTATATTTATATATATATAT
130 CCAAAATGATTGTGTATCTAATTGTCACCTCTACCTATTACGACATTATATTTATATATATATAT
1748143 ATATGGTTTTGTT
195 ATATGGTTTTGTT
1748156 AT
1 AT
1748158 CCTATGGAGT
Statistics
Matches: 208, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
207 5 0.02
208 203 0.98
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (207 bp):
ATTCATCCATTTCGAATTCGACTTGACTTTAAAAGTCAATAACTTGAATCCAAAATGAAGAGAAC
CTGAATAATCTTAATGTCAAATCAGAATGACTCAAACCTAAAAATTACTTGAATTTTCTTCTATC
CAAAATGATTGTGTATCTAATTGTCACCTCTACCTATTACGACATTATATTTATATATATATATA
TATGGTTTTGTT
Found at i:1750334 original size:25 final size:25
Alignment explanation
Indices: 1750286--1750334 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1750276 TTTTTATTTT
* *
1750286 AATATTAAAAATAAAAATATAAGAA
1 AATATTAAAAATAAAAACAAAAGAA
1750311 AATA-TAAGAAATAAAAACAAAAGA
1 AATATTAA-AAATAAAAACAAAAGA
1750335 TGATGTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.18
Consensus pattern (25 bp):
AATATTAAAAATAAAAACAAAAGAA
Found at i:1755192 original size:24 final size:26
Alignment explanation
Indices: 1755162--1755210 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
1755152 AGATGGCTAG
*
1755162 AAAAAATAAA-ATAATAA-AATATTC
1 AAAAAATAAATAAAATAATAATATTC
1755186 AAAAAATAAATAAAATAATAATATT
1 AAAAAATAAATAAAATAATAATATT
1755211 TTATTAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 6 0.27
26 6 0.27
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (26 bp):
AAAAAATAAATAAAATAATAATATTC
Found at i:1756181 original size:13 final size:13
Alignment explanation
Indices: 1756163--1756187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1756153 GGAAAATGAG
1756163 ATTTTATAAAATA
1 ATTTTATAAAATA
1756176 ATTTTATAAAAT
1 ATTTTATAAAAT
1756188 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:1762006 original size:3 final size:3
Alignment explanation
Indices: 1761998--1762022 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1761988 TGGTACTAGA
1761998 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
1762023 AGATTTACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1764920 original size:44 final size:43
Alignment explanation
Indices: 1764850--1764932 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 43
1764840 TCTAAGTAAT
1764850 AAAATCAAAATAATTTTTACTTTAATTAAATAATATTTTCACC
1 AAAATCAAAATAATTTTTACTTTAATTAAATAATATTTTCACC
*
1764893 AAAATACAAACAT-ATTTTTA-TTATAATTTAATAATATTTT
1 AAAAT-CAAA-ATAATTTTTACTT-TAATTAAATAATATTTT
1764933 GTATTAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
43 7 0.19
44 27 0.75
45 2 0.06
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (43 bp):
AAAATCAAAATAATTTTTACTTTAATTAAATAATATTTTCACC
Found at i:1764947 original size:23 final size:22
Alignment explanation
Indices: 1764904--1764947 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1764894 AAATACAAAC
* **
1764904 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAAAAGATAATA
1764926 ATATTTTGTATTAAAAGATAAT
1 ATATTTT-TATTAAAAGATAAT
1764948 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAAAAGATAATA
Found at i:1765034 original size:33 final size:32
Alignment explanation
Indices: 1764992--1765063 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
1764982 TTAAAAGACA
1764992 AAAT-ATATTCTTCATTAAATTTA-AATAATAC
1 AAATAATATTCTTCATTAAATTTATAATAAT-C
* * *
1765023 TAAATAATATTCTTTATTACATTTATTATAATC
1 -AAATAATATTCTTCATTAAATTTATAATAATC
1765056 AAATAATA
1 AAATAATA
1765064 ATATTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 12 0.34
33 18 0.51
34 5 0.14
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (32 bp):
AAATAATATTCTTCATTAAATTTATAATAATC
Found at i:1766066 original size:22 final size:22
Alignment explanation
Indices: 1766038--1766089 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1766028 TTGAAGGTAA
1766038 AAAGAAGATGGAACAAATGAGG
1 AAAGAAGATGGAACAAATGAGG
* *
1766060 AACGAAGATGGAGCAAATGAGG
1 AAAGAAGATGGAACAAATGAGG
1766082 AAAGAAGA
1 AAAGAAGA
1766090 ATTCAAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.54, C:0.06, G:0.33, T:0.08
Consensus pattern (22 bp):
AAAGAAGATGGAACAAATGAGG
Found at i:1766591 original size:19 final size:19
Alignment explanation
Indices: 1766563--1766600 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1766553 CCATTTAACT
* *
1766563 TATTGGAGTATGATTTGAG
1 TATTGAAGTATAATTTGAG
1766582 TATTGAAGTATAATTTGAG
1 TATTGAAGTATAATTTGAG
1766601 GGTTTGGGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGAAGTATAATTTGAG
Found at i:1767991 original size:13 final size:13
Alignment explanation
Indices: 1767973--1767997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1767963 AGAGAAATTG
1767973 TGATTTTATAAAA
1 TGATTTTATAAAA
1767986 TGATTTTATAAA
1 TGATTTTATAAA
1767998 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:1769697 original size:20 final size:20
Alignment explanation
Indices: 1769672--1769717 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1769662 TTTTGGCTCC
1769672 ATTTGACTTATTGAAGTATA
1 ATTTGACTTATTGAAGTATA
* *
1769692 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGAAGTATA
1769712 ATTTGA
1 ATTTGA
1769718 GATTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:1775811 original size:77 final size:76
Alignment explanation
Indices: 1775643--1775877 Score: 249
Period size: 77 Copynumber: 3.0 Consensus size: 76
1775633 AATATAATCA
*
1775643 TAAATTAAATAATAATTATTTAATTATTGGTTTGATAAAAATTATTTGGTTTACATGATTTAATT
1 TAAATTAAATAATAATTATTT-ATTA---GTTTGATAAAAATTATTT-ATTTACATGATTTAATT
*
1775708 ATTTGTTTCAACAGACAG
61 ATTTGTTT-AA-AAACAG
* * * * **
1775726 TAAA--AAATAATTATTATTTATTAATTTCATAAAAATTATTTAATTACATGATTTAATGGTTTG
1 TAAATTAAATAATAATTATTTATTAGTTTGATAAAAATTATTTATTTACATGATTTAATTATTTG
1775789 TGTTAAAAACAG
66 T-TTAAAAACAG
* * * * *
1775801 TAAATTAAATAGTAATTATTTATTGGTTTGATAAAAATTAGTTGATTTACGTGATGTAATTATTT
1 TAAATTAAATAATAATTATTTATTAGTTTGATAAAAATTA-TTTATTTACATGATTTAATTATTT
1775866 GTTTTAAAAACA
65 G-TTTAAAAACA
1775878 ATTTTCTTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
75 9 0.07
76 21 0.16
77 47 0.37
78 28 0.22
79 1 0.01
80 4 0.03
81 14 0.11
83 4 0.03
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (76 bp):
TAAATTAAATAATAATTATTTATTAGTTTGATAAAAATTATTTATTTACATGATTTAATTATTTG
TTTAAAAACAG
Found at i:1781109 original size:26 final size:26
Alignment explanation
Indices: 1781058--1781110 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1781048 AAAATAAAAG
* *
1781058 ATTTTTAAAATATGGAAAAAATAAATT
1 ATTTTTAAAATA-GAAAAAAAAAAATT
1781085 ATTTTTAAAATA-AAAAATAAAAAATT
1 ATTTTTAAAATAGAAAAA-AAAAAATT
1781111 GACATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 7 0.30
27 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
ATTTTTAAAATAGAAAAAAAAAAATT
Found at i:1787744 original size:28 final size:23
Alignment explanation
Indices: 1787664--1787752 Score: 124
Period size: 23 Copynumber: 3.8 Consensus size: 23
1787654 GTCTTTAAAT
* *
1787664 CTAATTATATTAAAATAACAATTC
1 CTAATTATATTAAGATAA-GATTC
1787688 CTAATTATATTAAGATAAGATTC
1 CTAATTATATTAAGATAAGATTC
*
1787711 CTAATTATATTAGGATAAGATTC
1 CTAATTATATTAAGATAAGATTC
* *
1787734 CTAATTAAATTAGGATAAG
1 CTAATTATATTAAGATAAG
1787753 GTTATTGTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 44 0.72
24 17 0.28
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (23 bp):
CTAATTATATTAAGATAAGATTC
Found at i:1792349 original size:20 final size:19
Alignment explanation
Indices: 1792326--1792381 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 19
1792316 ATTAAAACAC
*
1792326 ATAAACACGTACCAAAAAA
1 ATAAACAAGTACCAAAAAA
*
1792345 TATAAACAAGTATCAAAAAA
1 -ATAAACAAGTACCAAAAAA
1792365 ATAAA-AA-TA-CAAAAAA
1 ATAAACAAGTACCAAAAAA
1792381 A
1 A
1792382 AACGAATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 2 0.06
19 5 0.15
20 17 0.50
ACGTcount: A:0.70, C:0.12, G:0.04, T:0.14
Consensus pattern (19 bp):
ATAAACAAGTACCAAAAAA
Found at i:1794088 original size:2 final size:2
Alignment explanation
Indices: 1794068--1794104 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1794058 TGGAAATAAA
1794068 AT AT -T AT A- AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1794105 TTGCACAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1796900 original size:28 final size:28
Alignment explanation
Indices: 1796869--1796931 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
1796859 ATTTATCAAG
1796869 TATTAATTTATAGAATTTATACTATACA
1 TATTAATTTATAGAATTTATACTATACA
1796897 TATTAATTTATAGAATTTATACTATACA
1 TATTAATTTATAGAATTTATACTATACA
*
1796925 TTTTAAT
1 TATTAAT
1796932 GAGGTGTCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.49
Consensus pattern (28 bp):
TATTAATTTATAGAATTTATACTATACA
Found at i:1797975 original size:20 final size:20
Alignment explanation
Indices: 1797950--1797995 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1797940 TTTTGGCCTC
*
1797950 ATTTGACTTATTGGAGTATA
1 ATTTGACTTACTGGAGTATA
*
1797970 ATTTGACTTACTGGAGTATG
1 ATTTGACTTACTGGAGTATA
1797990 ATTTGA
1 ATTTGA
1797996 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (20 bp):
ATTTGACTTACTGGAGTATA
Found at i:1799338 original size:4 final size:4
Alignment explanation
Indices: 1799329--1799364 Score: 54
Period size: 4 Copynumber: 8.5 Consensus size: 4
1799319 NNNNNNNGAG
1799329 AGAA AGAA AGAA AGAA AGAA AGAAA AGAAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AG-AA AG-AA AGAA AG
1799365 GAAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 22 0.71
5 9 0.29
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1799346 original size:12 final size:13
Alignment explanation
Indices: 1799329--1799373 Score: 65
Period size: 12 Copynumber: 3.4 Consensus size: 13
1799319 NNNNNNNGAG
1799329 AGAAAGAAAG-AA
1 AGAAAGAAAGAAA
1799341 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
1799354 AGAAAAGAAAGGAAA
1 AG-AAAGAAA-GAAA
1799369 AGAAA
1 AGAAA
1799374 ATAACAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.33
13 4 0.13
14 10 0.33
15 6 0.20
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:1799357 original size:5 final size:5
Alignment explanation
Indices: 1799331--1799374 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
1799321 NNNNNGAGAG
*
1799331 AAAG- AAAG- AAAG- AAAG- AAAGA AAAGA AAAGA AAGGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1799375 TAACAAGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
4 16 0.43
5 21 0.57
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1799421 original size:27 final size:25
Alignment explanation
Indices: 1799391--1799452 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1799381 GGAAAATGGG
*
1799391 CATGGCCCAACAAGCAAGAAAAATAGA
1 CATGGTCCAACAA--AAGAAAAATAGA
* * *
1799418 CATGGTCCAATAAACGAAAAATGGA
1 CATGGTCCAACAAAAGAAAAATAGA
1799443 CATGGTCCAA
1 CATGGTCCAA
1799453 TTAAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 20 0.65
27 11 0.35
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (25 bp):
CATGGTCCAACAAAAGAAAAATAGA
Found at i:1799464 original size:25 final size:24
Alignment explanation
Indices: 1799409--1799466 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
1799399 AACAAGCAAG
*
1799409 AAAAATAGACATGGTCCAATAAAC
1 AAAAATGGACATGGTCCAATAAAC
1799433 GAAAAATGGACATGGTCCAATTAAA-
1 -AAAAATGGACATGGTCCAA-TAAAC
1799458 AAGAAATGG
1 AA-AAATGG
1799467 GAGAAGTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 2 0.07
25 24 0.80
26 4 0.13
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (24 bp):
AAAAATGGACATGGTCCAATAAAC
Found at i:1803017 original size:14 final size:14
Alignment explanation
Indices: 1803000--1803032 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1802990 TAGTTATTTC
1803000 AAAAATTAA-AAATA
1 AAAAATTAAGAAA-A
1803014 AAAAATTAAGAAAA
1 AAAAATTAAGAAAA
1803028 AAAAA
1 AAAAA
1803033 AGAAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (14 bp):
AAAAATTAAGAAAA
Found at i:1803450 original size:13 final size:13
Alignment explanation
Indices: 1803420--1803462 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1803410 TTTTAATATT
*
1803420 AAAAATAAAAATA
1 AAAAATAAAAACA
1803433 TAAAAA-AAAAGACA
1 -AAAAATAAAA-ACA
1803447 AAAAATAAAAACA
1 AAAAATAAAAACA
1803460 AAA
1 AAA
1803463 GATGATGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.84, C:0.05, G:0.02, T:0.09
Consensus pattern (13 bp):
AAAAATAAAAACA
Found at i:1803457 original size:20 final size:21
Alignment explanation
Indices: 1803426--1803464 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1803416 TATTAAAAAT
1803426 AAAAATATAAAAAAAAAGACA
1 AAAAATATAAAAAAAAAGACA
*
1803447 AAAAATA-AAAACAAAAGA
1 AAAAATATAAAAAAAAAGA
1803465 TGATGTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.08
Consensus pattern (21 bp):
AAAAATATAAAAAAAAAGACA
Found at i:1808333 original size:12 final size:13
Alignment explanation
Indices: 1808303--1808334 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1808293 TTAAATAAAG
1808303 TAAAAAATATGAT
1 TAAAAAATATGAT
1808316 T-AAAAATAT-AT
1 TAAAAAATATGAT
1808327 TAAAAAAT
1 TAAAAAAT
1808335 TAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 14 0.78
13 1 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
TAAAAAATATGAT
Found at i:1810323 original size:2 final size:2
Alignment explanation
Indices: 1810316--1810357 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1810306 TAAATTACAC
*
1810316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1810358 AAAGGATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1824843 original size:21 final size:21
Alignment explanation
Indices: 1824819--1824869 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1824809 AATATGAAAA
1824819 CATAATTAACAGTAATTATAG
1 CATAATTAACAGTAATTATAG
1824840 CATAATTAACAGTAATTATAG
1 CATAATTAACAGTAATTATAG
*
1824861 TATAATTAA
1 CATAATTAA
1824870 AACAACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (21 bp):
CATAATTAACAGTAATTATAG
Found at i:1825238 original size:2 final size:2
Alignment explanation
Indices: 1825231--1825271 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1825221 ATCAGATGAG
1825231 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1825272 ACATTATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1827522 original size:36 final size:34
Alignment explanation
Indices: 1827455--1827522 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
1827445 AATTTATTTT
* *
1827455 ATTTTTTATGAATTAATCTTAATTTATTAATCTA
1 ATTTTTTAAGAAATAATCTTAATTTATTAATCTA
* *
1827489 ATTTTTGTAAGAAATAATTTTATATTTTTTAATC
1 ATTTTT-TAAGAAATAATCTTA-ATTTATTAATC
1827523 AAGTATTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 6 0.21
35 12 0.43
36 10 0.36
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (34 bp):
ATTTTTTAAGAAATAATCTTAATTTATTAATCTA
Found at i:1827737 original size:24 final size:24
Alignment explanation
Indices: 1827710--1827765 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1827700 AAATAACATT
1827710 AATTAA-AAATATTAACTTTTATAA
1 AATTAATAAATATTAA-TTTTATAA
* * *
1827734 AATTAATATATTTTAATTTTATTA
1 AATTAATAAATATTAATTTTATAA
1827758 AATTAATA
1 AATTAATA
1827766 TTTATTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTAATAAATATTAATTTTATAA
Found at i:1828612 original size:36 final size:35
Alignment explanation
Indices: 1828554--1828621 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
1828544 AATATTCTTT
* *
1828554 ATATAATAACTGAAATTTGTAAATGATAATTTAAAA
1 ATATAATAACTGAAAATAGTAAAT-ATAATTTAAAA
* * *
1828590 ATATAATAAGTTAAAATAGTAAATATTATTTA
1 ATATAATAACTGAAAATAGTAAATATAATTTA
1828622 TCTAAAGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 7 0.26
36 20 0.74
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.38
Consensus pattern (35 bp):
ATATAATAACTGAAAATAGTAAATATAATTTAAAA
Found at i:1831016 original size:32 final size:33
Alignment explanation
Indices: 1830975--1831053 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
1830965 TATTCTTGAG
1830975 ATAAA-AATATTATTTGAATA-TA-ATAAATTTA
1 ATAAAGAATATTATTT-AATATTATATAAATTTA
* *
1831006 ATAAAGAATATTATTTAGTATTATTTAAATTTA
1 ATAAAGAATATTATTTAATATTATATAAATTTA
*
1831039 ATGAAGAATA-TATTT
1 ATAAAGAATATTATTT
1831054 TATGTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 8 0.19
32 17 0.40
33 17 0.40
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44
Consensus pattern (33 bp):
ATAAAGAATATTATTTAATATTATATAAATTTA
Found at i:1831069 original size:30 final size:32
Alignment explanation
Indices: 1830998--1831069 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 32
1830988 TTGAATATAA
1830998 TAAATTTAATAAAGAATATTATTTAGTATTATT
1 TAAATTTAATAAAGAATATTATTTA-TATTATT
*
1831031 TAAATTTAATGAAGAATA-TATTT-TATGT-TT
1 TAAATTTAATAAAGAATATTATTTATAT-TATT
*
1831061 TAACTTTAA
1 TAAATTTAA
1831070 ATATTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 13 0.36
31 1 0.03
32 5 0.14
33 17 0.47
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (32 bp):
TAAATTTAATAAAGAATATTATTTATATTATT
Found at i:1831259 original size:24 final size:24
Alignment explanation
Indices: 1831209--1831261 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1831199 ACTTAGAATA
*
1831209 TTTTTAACTTTTAACAAAATTAAT
1 TTTTTAACTTTTAACAAAAGTAAT
* *
1831233 TTTTTAA-TTTTAATAAAGAGTATT
1 TTTTTAACTTTTAACAAA-AGTAAT
1831257 TTTTT
1 TTTTT
1831262 TCTCATCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTTAACTTTTAACAAAAGTAAT
Found at i:1841754 original size:13 final size:13
Alignment explanation
Indices: 1841738--1841762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1841728 TAATAATAAC
1841738 AATTTTTAATATA
1 AATTTTTAATATA
1841751 AATTTTTAATAT
1 AATTTTTAATAT
1841763 TTTTTATTTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTTAATATA
Found at i:1863974 original size:13 final size:13
Alignment explanation
Indices: 1863956--1863984 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1863946 CAAAGTTTAG
1863956 TGCTATGTCATAC
1 TGCTATGTCATAC
1863969 TGCTATGTCATAC
1 TGCTATGTCATAC
1863982 TGC
1 TGC
1863985 CTTTAACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (13 bp):
TGCTATGTCATAC
Found at i:1865068 original size:51 final size:51
Alignment explanation
Indices: 1865012--1865109 Score: 196
Period size: 51 Copynumber: 1.9 Consensus size: 51
1865002 CACATAAGAT
1865012 AGGCTTGGTCATGTGACAAATTGTACACAAGAAAACAATATAATTTGAAAA
1 AGGCTTGGTCATGTGACAAATTGTACACAAGAAAACAATATAATTTGAAAA
1865063 AGGCTTGGTCATGTGACAAATTGTACACAAGAAAACAATATAATTTG
1 AGGCTTGGTCATGTGACAAATTGTACACAAGAAAACAATATAATTTG
1865110 CCACATCACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (51 bp):
AGGCTTGGTCATGTGACAAATTGTACACAAGAAAACAATATAATTTGAAAA
Found at i:1873512 original size:2 final size:2
Alignment explanation
Indices: 1873507--1873533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1873497 CCCCACCCCA
1873507 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1873534 AAGCATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1879747 original size:22 final size:23
Alignment explanation
Indices: 1879721--1879765 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1879711 AAAGAAAACC
* *
1879721 CCAAAACAAAAGAACA-AACAAA
1 CCAAAAAAAAAGAAAACAACAAA
1879743 CCAAAAAAAAAGAAAACAACAAA
1 CCAAAAAAAAAGAAAACAACAAA
1879766 GGTGGGGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.76, C:0.20, G:0.04, T:0.00
Consensus pattern (23 bp):
CCAAAAAAAAAGAAAACAACAAA
Found at i:1882365 original size:2 final size:2
Alignment explanation
Indices: 1882358--1882388 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1882348 GCATATAAAT
1882358 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 T
1882389 GCATTATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1891569 original size:2 final size:2
Alignment explanation
Indices: 1891562--1891592 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1891552 GCACATGCAC
1891562 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1891593 CGACCCCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1898321 original size:2 final size:2
Alignment explanation
Indices: 1898314--1898347 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1898304 ATCAGTCAAT
1898314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1898348 AGAAAGTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1899129 original size:15 final size:17
Alignment explanation
Indices: 1899099--1899138 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
1899089 ATATTAAATT
1899099 ATAGAATAATTTTATTA
1 ATAGAATAATTTTATTA
1899116 ATAGAA-AA-TTTATTA
1 ATAGAATAATTTTATTA
1899131 AGTAGAAT
1 A-TAGAAT
1899139 TATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (17 bp):
ATAGAATAATTTTATTA
Found at i:1899942 original size:18 final size:18
Alignment explanation
Indices: 1899921--1899962 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1899911 ATATATTTGT
1899921 ATATACATGTGTATACAC
1 ATATACATGTGTATACAC
*
1899939 ATAT--ATGTGTATATAC
1 ATATACATGTGTATACAC
*
1899955 ACATACAT
1 ATATACAT
1899963 ACACATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 14 0.70
18 6 0.30
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (18 bp):
ATATACATGTGTATACAC
Found at i:1899979 original size:36 final size:35
Alignment explanation
Indices: 1899939--1900027 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 35
1899929 GTGTATACAC
1899939 ATATATGTGTATATACACATAC-ATACACATGTGT
1 ATATATGTGTATATACACATACAATACACATGTGT
* * *
1899973 ATATATATATATATACATATACATATACACATGTGT
1 ATATATGTGTATATACACATACA-ATACACATGTGT
*
1900009 ATGTATGTGTATATACACA
1 ATATATGTGTATATACACA
1900028 AATATATAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
34 19 0.41
36 27 0.59
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (35 bp):
ATATATGTGTATATACACATACAATACACATGTGT
Found at i:1899993 original size:40 final size:36
Alignment explanation
Indices: 1899939--1900057 Score: 110
Period size: 36 Copynumber: 3.5 Consensus size: 36
1899929 GTGTATACAC
* * *
1899939 ATATATGTGTATATACACATAC--ATACACATGTGT
1 ATATATATATATATACATATACATATACACATGTGT
1899973 ATATATATATATATACATATACATATACACATGTGT
1 ATATATATATATATACATATACATATACACATGTGT
* * * * *
1900009 ATGTATGTGTATATACACA-A-ATATATA-A---GT
1 ATATATATATATATACATATACATATACACATGTGT
1900039 ATATATATATATATACATA
1 ATATATATATATATACATA
1900058 CATAAATAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
30 17 0.24
33 1 0.01
34 25 0.35
35 1 0.01
36 27 0.38
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (36 bp):
ATATATATATATATACATATACATATACACATGTGT
Found at i:1900111 original size:23 final size:24
Alignment explanation
Indices: 1900057--1900119 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
1900047 ATATATACAT
1900057 ACATAAATAATAATAAACACATAA
1 ACATAAATAATAATAAACACATAA
*
1900081 ACAAAAATAATAA-AAGA-ACATATA
1 ACATAAATAATAATAA-ACACATA-A
*
1900105 A-ATAAATAAAAATAA
1 ACATAAATAATAATAA
1900120 TAAAAGTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (24 bp):
ACATAAATAATAATAAACACATAA
Found at i:1900543 original size:2 final size:2
Alignment explanation
Indices: 1900536--1900602 Score: 64
Period size: 2 Copynumber: 33.0 Consensus size: 2
1900526 GATATACATG
* * * * *
1900536 TA TA TA TA CA T- TA TA TA TT TA TG TA TA TA TA CA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1900577 CTA TA CTA TA TA TA TA TA TA TA TA TA
1 -TA TA -TA TA TA TA TA TA TA TA TA TA
1900603 AGATGAATGA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
1 1 0.02
2 47 0.90
3 4 0.08
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1900544 original size:12 final size:12
Alignment explanation
Indices: 1900527--1900569 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1900517 ACAAGAAAAG
1900527 ATATACATGTAT
1 ATATACATGTAT
1900539 ATATACAT-TAT
1 ATATACATGTAT
**
1900550 ATATTTATGTAT
1 ATATACATGTAT
1900562 ATATACAT
1 ATATACAT
1900570 ACATATACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (12 bp):
ATATACATGTAT
Found at i:1905196 original size:200 final size:199
Alignment explanation
Indices: 1904838--1905240 Score: 546
Period size: 200 Copynumber: 2.0 Consensus size: 199
1904828 TTTGGGCGCA
* * **
1904838 ATTCTTGTAACGTTTTATTTTTTTAATTGATTTTGATTTAATTTTTCAAAAATCACAATTTTTTT
1 ATTCTTGTAACCTTTTATTTTTTTAATTGATTTTGATTTAATTTTTCAAAAATCACAATTATCAT
* * * *
1904903 ACAATCACAATTACAAATTTAAAATCGACCTTTAATTATAAAATACATGTCAAGCGAATCGACAT
66 ACAATCAAAATCACAAATTTAAAATCGACCTCTAATTATAAAATACATGTCAAGAGAATCGACAT
* **
1904968 TTAACCCAATTGATAGTGTCAAAGCATAATCATACTATAAG-GTAAATAAAAATATATTTTCATA
131 TTAACCCAATTGATAGTATCAAAGCATAATCATACTATAAGACAAAATAAAAATATA-TTTCATA
1905032 TTTTG
195 TTTTG
*
1905037 ATTCTTGT-ACCTTTTATTTTTTTAATTGATTTTGATTTAATTTTTTAAAAATCACAATTAATCA
1 ATTCTTGTAACCTTTTATTTTTTTAATTGATTTTGATTTAATTTTTCAAAAATCACAATT-ATCA
* ** * *
1905101 TA-AATTTTTATAAATCAC-AA-TTAAAATCGGTCTCTAATTATAAAATACATGTCGAGATAATC
65 TACAA---TCA-AAATCACAAATTTAAAATCGACCTCTAATTATAAAATACATGTCAAGAGAATC
* *
1905163 GACATTTAACCCAATTGATAGTATCAGAGCATAATCATACTATAAGACAAAATGAAAATATATTT
126 GACATTTAACCCAATTGATAGTATCAAAGCATAATCATACTATAAGACAAAATAAAAATATATTT
1905228 CATATTTTG
191 CATATTTTG
1905237 ATTC
1 ATTC
1905241 AATTGTTAGC
Statistics
Matches: 179, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
198 51 0.28
199 11 0.06
200 96 0.54
201 16 0.09
202 5 0.03
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (199 bp):
ATTCTTGTAACCTTTTATTTTTTTAATTGATTTTGATTTAATTTTTCAAAAATCACAATTATCAT
ACAATCAAAATCACAAATTTAAAATCGACCTCTAATTATAAAATACATGTCAAGAGAATCGACAT
TTAACCCAATTGATAGTATCAAAGCATAATCATACTATAAGACAAAATAAAAATATATTTCATAT
TTTG
Found at i:1908940 original size:21 final size:21
Alignment explanation
Indices: 1908916--1908955 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1908906 CTGGTTTCTC
*
1908916 CCCTAATTCTTCTATTTCTTT
1 CCCTAATTCCTCTATTTCTTT
* *
1908937 CCCTATTTCCTCTGTTTCT
1 CCCTAATTCCTCTATTTCT
1908956 CCCTTCTGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.33, G:0.03, T:0.55
Consensus pattern (21 bp):
CCCTAATTCCTCTATTTCTTT
Found at i:1911145 original size:45 final size:46
Alignment explanation
Indices: 1911092--1911209 Score: 186
Period size: 45 Copynumber: 2.6 Consensus size: 46
1911082 GTAGAACAAT
1911092 GCACAACTATACCTCAAAAGACAAATATTAATTATT-CT-TAATAAC
1 GCACAACTATACCTCAAAAGACAAATATTAATTATTGCTGT-ATAAC
*
1911137 GCACAACTATACCTCAAGAGACAAATATTAATTATTGCTGTATAAC
1 GCACAACTATACCTCAAAAGACAAATATTAATTATTGCTGTATAAC
* *
1911183 GCACAACTATATCACAAAAGACAAATA
1 GCACAACTATACCTCAAAAGACAAATA
1911210 ATAGGAAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
45 35 0.52
46 31 0.46
47 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (46 bp):
GCACAACTATACCTCAAAAGACAAATATTAATTATTGCTGTATAAC
Found at i:1917203 original size:20 final size:20
Alignment explanation
Indices: 1917178--1917215 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1917168 TTTAATTATA
*
1917178 AAATTATTAATATTTTAAAT
1 AAATTATAAATATTTTAAAT
1917198 AAATTATAAATATTTTAA
1 AAATTATAAATATTTTAA
1917216 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATAAATATTTTAAAT
Found at i:1917220 original size:27 final size:28
Alignment explanation
Indices: 1917171--1917223 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1917161 TCAAAATTTT
1917171 AATTATAAAATTATTAATATTTTAAATA
1 AATTATAAAATTATTAATATTTTAAATA
1917199 AATTATAAATATT-TTAAT-TTTTAAA
1 AATTATAAA-ATTATTAATATTTTAAA
1917224 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 7 0.29
28 14 0.58
29 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AATTATAAAATTATTAATATTTTAAATA
Found at i:1926257 original size:3 final size:3
Alignment explanation
Indices: 1926249--1926301 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
1926239 CTTGTATAGA
* * * *
1926249 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGA AGC ATC AGC AAC AGC AAC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
1926297 AGC AG
1 AGC AG
1926302 GAACTCAGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.40, C:0.30, G:0.28, T:0.02
Consensus pattern (3 bp):
AGC
Found at i:1933136 original size:1 final size:1
Alignment explanation
Indices: 1933130--1933166 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
1933120 TGGCTGCAGC
*
1933130 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1933167 CCAACCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1936438 original size:31 final size:30
Alignment explanation
Indices: 1936377--1936466 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
1936367 GGTTATGTCA
* * * * *
1936377 TTATATTTTAATTAT-ATTTAATTAAGTTT
1 TTATATTTTTATTTTAAGTTAAATAAATTT
*
1936406 TTATATTTTTTATTTTGAGTTAAATAAATTT
1 TTATA-TTTTTATTTTAAGTTAAATAAATTT
*
1936437 TTATATTTTTCTTTTAAGTTAAATAAATTT
1 TTATATTTTTATTTTAAGTTAAATAAATTT
1936467 AAAAATTAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.10
30 31 0.60
31 16 0.31
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (30 bp):
TTATATTTTTATTTTAAGTTAAATAAATTT
Found at i:1936457 original size:30 final size:31
Alignment explanation
Indices: 1936394--1936466 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
1936384 TTAATTATAT
* * *
1936394 TTAATTAAGTTTTTATATTTTTTATTTTGAG
1 TTAAATAAATTTTTATATTTTTTATTTTAAG
*
1936425 TTAAATAAATTTTTATA-TTTTTCTTTTAAG
1 TTAAATAAATTTTTATATTTTTTATTTTAAG
1936455 TTAAATAAATTT
1 TTAAATAAATTT
1936467 AAAAATTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 23 0.61
31 15 0.39
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (31 bp):
TTAAATAAATTTTTATATTTTTTATTTTAAG
Found at i:1936732 original size:22 final size:22
Alignment explanation
Indices: 1936690--1936733 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1936680 CCATAAACAT
**
1936690 TTTGATTAATAATAATGATTTA
1 TTTGATTAATAATAAAAATTTA
1936712 TTTGATTCAA-AATAAAAATTTA
1 TTTGATT-AATAATAAAAATTTA
1936734 AAAACTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTGATTAATAATAAAAATTTA
Found at i:1937072 original size:65 final size:66
Alignment explanation
Indices: 1936961--1937086 Score: 191
Period size: 65 Copynumber: 1.9 Consensus size: 66
1936951 TTATACTAAT
* *
1936961 TTTTTCATCCATATAAAAAAAAAAAAGACTCATCTTAATGTAAACCTGTCAATATCTCTCACATT
1 TTTTTCATCCA-ATAAAAAAAAAAAAGACTCATCTTAATGCAAACCTGTCAAAATCTCTCACATT
1937026 AA
65 AA
* * *
1937028 TTTTTCATCC-ATAAAAAAAAAAAAGACTTATGTTAATGCGAACCTGTCAAAATCTCTCA
1 TTTTTCATCCAATAAAAAAAAAAAAGACTCATCTTAATGCAAACCTGTCAAAATCTCTCA
1937087 GAGGAGATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 44 0.81
67 10 0.19
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (66 bp):
TTTTTCATCCAATAAAAAAAAAAAAGACTCATCTTAATGCAAACCTGTCAAAATCTCTCACATTA
A
Found at i:1945515 original size:44 final size:44
Alignment explanation
Indices: 1945465--1945548 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
1945455 TTTATCCTAG
*
1945465 GGGAATTATAATAAATCACATGGTTGACTGATTCCACGAGCTAA
1 GGGAATTATAATAAATCACATGATTGACTGATTCCACGAGCTAA
1945509 GGGAATTATAATAAATCACATGATTGACTGATTCCACGAG
1 GGGAATTATAATAAATCACATGATTGACTGATTCCACGAG
1945549 TCCAGGATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (44 bp):
GGGAATTATAATAAATCACATGATTGACTGATTCCACGAGCTAA
Found at i:1950552 original size:17 final size:18
Alignment explanation
Indices: 1950530--1950566 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1950520 TTCAATTTGT
*
1950530 TTGATCAAAA-AATCAAA
1 TTGATCAAAATAACCAAA
1950547 TTGATCAAAATAACCAAA
1 TTGATCAAAATAACCAAA
1950565 TT
1 TT
1950567 ACAAAATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (18 bp):
TTGATCAAAATAACCAAA
Found at i:1955159 original size:16 final size:16
Alignment explanation
Indices: 1955140--1955191 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1955130 TTATTTGTTG
1955140 AATTATTTACTATGTA
1 AATTATTTACTATGTA
** ***
1955156 AATT-TTTTTTAAAAA
1 AATTATTTACTATGTA
1955171 AATTATTTACTATGTA
1 AATTATTTACTATGTA
1955187 AATTA
1 AATTA
1955192 ACGTTGAAAA
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (16 bp):
AATTATTTACTATGTA
Found at i:1955202 original size:31 final size:31
Alignment explanation
Indices: 1955140--1955204 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1955130 TTATTTGTTG
****
1955140 AATTATTTACTATGTAAATTTTTTTTAAAAA
1 AATTATTTACTATGTAAATTAACGTTAAAAA
*
1955171 AATTATTTACTATGTAAATTAACGTTGAAAA
1 AATTATTTACTATGTAAATTAACGTTAAAAA
1955202 AAT
1 AAT
1955205 AAAAATGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (31 bp):
AATTATTTACTATGTAAATTAACGTTAAAAA
Found at i:1962255 original size:22 final size:22
Alignment explanation
Indices: 1962230--1962289 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1962220 TCGTTTCTTC
1962230 TTTCTCTCTCTTCTCACGTTCT
1 TTTCTCTCTCTTCTCACGTTCT
*
1962252 TTTCTCTCTCGTCTCACGTTCT
1 TTTCTCTCTCTTCTCACGTTCT
*
1962274 TTCCTCTCTCATTCTC
1 TTTCTCTCTC-TTCTC
1962290 TCTCCAAGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.05, C:0.38, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTCTCTCTCTTCTCACGTTCT
Found at i:1962719 original size:26 final size:26
Alignment explanation
Indices: 1962657--1962719 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1962647 TTTGTAAAAT
*
1962657 TTAAAATATTAATATTTTATATATAA
1 TTAAAATATTAATATATTATATATAA
* * * *
1962683 TTTAAACATTATTAATATTA-ATATGA
1 TTAAAATATTAAT-ATATTATATATAA
1962709 TTAAAATATTA
1 TTAAAATATTA
1962720 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAAAATATTAATATATTATATATAA
Found at i:1966851 original size:45 final size:47
Alignment explanation
Indices: 1966754--1966990 Score: 131
Period size: 45 Copynumber: 5.2 Consensus size: 47
1966744 CTTTCCCTTG
*
1966754 GGTTTCAAAAATGGTTACTTTGAGGTTTTGAAGATTGTTACCCAGAA
1 GGTTTCAAAAATGGTTACTTAGAGGTTTTGAAGATTGTTACCCAGAA
* * *
1966801 -TTTTCAAAGAT-GTTTCTTAGAGGTTTTGAA-ACTTGTTACCCA-AA
1 GGTTTCAAAAATGGTTACTTAGAGGTTTTGAAGA-TTGTTACCCAGAA
* * * * * *
1966845 GGTTTCAAAATTTGTTACTCGTAGA--TTTTAAAAATTATTA-CCAAAA
1 GGTTTCAAAAATGGTTACT--TAGAGGTTTTGAAGATTGTTACCCAGAA
* * * * * * * *
1966891 GGTTTC-AAAATTGTTACCCT-GAAGTTTT-AAAAATGGTATCC-GGA
1 GGTTTCAAAAATGGTTA-CTTAGAGGTTTTGAAGATTGTTACCCAGAA
* * ** *
1966935 GGATTT-AAAGATGGTTTCTCGGAGGTTTTGAAGATTGTTACCTAG-A
1 GG-TTTCAAAAATGGTTACTTAGAGGTTTTGAAGATTGTTACCCAGAA
1966981 GGTTTCAAAA
1 GGTTTCAAAA
1966991 GTTATTACCC
Statistics
Matches: 144, Mismatches: 29, Indels: 35
0.69 0.14 0.17
Matches are distributed among these distances:
43 2 0.01
44 15 0.10
45 73 0.51
46 48 0.33
47 2 0.01
48 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (47 bp):
GGTTTCAAAAATGGTTACTTAGAGGTTTTGAAGATTGTTACCCAGAA
Found at i:1966859 original size:23 final size:22
Alignment explanation
Indices: 1966833--1966909 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
1966823 GTTTTGAAAC
1966833 TTGTTACCCAAAGGTTTCAAAA
1 TTGTTACCCAAAGGTTTCAAAA
* ** * *
1966855 TTTGTTACTCGTAGATTTTAAAAA
1 -TTGTTACCCAAAG-GTTTCAAAA
* *
1966879 TTATTACCAAAAGGTTTCAAAA
1 TTGTTACCCAAAGGTTTCAAAA
1966901 TTGTTACCC
1 TTGTTACCC
1966910 TGAAGTTTTA
Statistics
Matches: 39, Mismatches: 14, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
22 14 0.36
23 18 0.46
24 7 0.18
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
TTGTTACCCAAAGGTTTCAAAA
Found at i:1966894 original size:46 final size:45
Alignment explanation
Indices: 1966836--1966924 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
1966826 TTGAAACTTG
* * *
1966836 TTACCCAAAGGTTTCAAAATTTGTTACTC-GTAGATTTTAAAAATTA
1 TTACCAAAAGGTTTCAAAA-TTGTTACCCTGAAG-TTTTAAAAATTA
1966882 TTACCAAAAGGTTTCAAAATTGTTACCCTGAAGTTTTAAAAAT
1 TTACCAAAAGGTTTCAAAATTGTTACCCTGAAGTTTTAAAAAT
1966925 GGTATCCGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (45 bp):
TTACCAAAAGGTTTCAAAATTGTTACCCTGAAGTTTTAAAAATTA
Found at i:1966968 original size:23 final size:22
Alignment explanation
Indices: 1966914--1966969 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1966904 TTACCCTGAA
*
1966914 GTTTTAAAAATGGTATCCGGAG
1 GTTTTAAAGATGGTATCCGGAG
* *
1966936 GATTTAAAGATGGTTTCTCGGAG
1 GTTTTAAAGATGGTATC-CGGAG
*
1966959 GTTTTGAAGAT
1 GTTTTAAAGAT
1966970 TGTTACCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (22 bp):
GTTTTAAAGATGGTATCCGGAG
Found at i:1966982 original size:23 final size:23
Alignment explanation
Indices: 1966956--1967035 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
1966946 TGGTTTCTCG
1966956 GAGGTTTTGAAGATTGTTACCTA
1 GAGGTTTTGAAGATTGTTACCTA
* * * *
1966979 GAGG-TTTCAAAAGTTATTACCCA
1 GAGGTTTTGAAGA-TTGTTACCTA
* *
1967002 AAAGTTTT-AAGAATTGTTACCTA
1 GAGGTTTTGAAG-ATTGTTACCTA
*
1967025 GAGATTTTGAA
1 GAGGTTTTGAA
1967036 AACAGTACCG
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
22 6 0.15
23 29 0.71
24 6 0.15
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (23 bp):
GAGGTTTTGAAGATTGTTACCTA
Found at i:1969406 original size:38 final size:39
Alignment explanation
Indices: 1969319--1969406 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 39
1969309 AGATTTCATT
* *
1969319 TCATTCATAAATTGATGTTCATTATATAAATCAACCAAA
1 TCATTCATAAAATAATGTTCATTATATAAATCAACCAAA
* * * **
1969358 ACATTTATAAAATAAT-TTCGTTATATGTAT-AACTCAAA
1 TCATTCATAAAATAATGTTCATTATATAAATCAAC-CAAA
1969396 TCATTCATAAA
1 TCATTCATAAA
1969407 TCCATTTTCC
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
37 3 0.08
38 24 0.62
39 12 0.31
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.38
Consensus pattern (39 bp):
TCATTCATAAAATAATGTTCATTATATAAATCAACCAAA
Found at i:1970824 original size:2 final size:2
Alignment explanation
Indices: 1970817--1970843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1970807 ATTAATCATT
1970817 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 T
1970844 TTGCAAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1971027 original size:29 final size:29
Alignment explanation
Indices: 1970995--1971050 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1970985 ATTTAAAAAA
1970995 ATTCAAAT-AAGTCTTTATACTTTTATTAC
1 ATTC-AATCAAGTCTTTATACTTTTATTAC
*
1971024 ATTCAATCAAGTCTTTGTACTTTTATT
1 ATTCAATCAAGTCTTTATACTTTTATT
1971051 TTAAGCCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.50
Consensus pattern (29 bp):
ATTCAATCAAGTCTTTATACTTTTATTAC
Found at i:1972194 original size:23 final size:23
Alignment explanation
Indices: 1972168--1972453 Score: 144
Period size: 23 Copynumber: 12.5 Consensus size: 23
1972158 GAATAGTTTT
* *
1972168 CCAAAGGTTTTAAGGATTTTTAC
1 CCAAAGGTTTTAAAGATTGTTAC
* *
1972191 CC-AAGGTTTCAAACATTGTTAC
1 CCAAAGGTTTTAAAGATTGTTAC
** * * *
1972213 TTAGAGGTTTTGAATATTGTTAC
1 CCAAAGGTTTTAAAGATTGTTAC
* * *
1972236 CGAAAGGTTTCAAAGATTGTTTC
1 CCAAAGGTTTTAAAGATTGTTAC
*
1972259 CCAAAGGTTTTGAAA-ATAGTTAC
1 CCAAAGGTTTT-AAAGATTGTTAC
** *
1972282 CCTGAGGTTTCAAAGATTGTTAC
1 CCAAAGGTTTTAAAGATTGTTAC
**** * * *
1972305 TTGGAGATTTTAACGATTATTAC
1 CCAAAGGTTTTAAAGATTGTTAC
** * * * *
1972328 TTAAAAGTTTCAAAAATTGTTAA
1 CCAAAGGTTTTAAAGATTGTTAC
** * *
1972351 CTTAAGGGTTTAAAGATAGTTAC
1 CCAAAGGTTTTAAAGATTGTTAC
* * ** ** *
1972374 CTAAAGGCTTCGAAGAAGGTTTC
1 CCAAAGGTTTTAAAGATTGTTAC
* * *
1972397 TCAGAGGTTTTGAAGATTGTTAC
1 CCAAAGGTTTTAAAGATTGTTAC
* *
1972420 TCAAAGGTTTCAAAGATTGTTAC
1 CCAAAGGTTTTAAAGATTGTTAC
1972443 CCAAAGGTTTT
1 CCAAAGGTTTT
1972454 GAGGATAGTT
Statistics
Matches: 191, Mismatches: 69, Indels: 6
0.72 0.26 0.02
Matches are distributed among these distances:
22 19 0.10
23 169 0.88
24 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (23 bp):
CCAAAGGTTTTAAAGATTGTTAC
Found at i:1972255 original size:46 final size:46
Alignment explanation
Indices: 1972172--1972442 Score: 212
Period size: 46 Copynumber: 5.9 Consensus size: 46
1972162 AGTTTTCCAA
* * *
1972172 AGGTTTT-AAGGATTTTTACC-CAAGGTTTCAAACATTGTTACTTAG
1 AGGTTTTGAA-GATTGTTACCTAAAGGTTTCAAAGATTGTTACTTAG
* * * ** *
1972217 AGGTTTTGAATATTGTTACCGAAAGGTTTCAAAGATTGTTTCCCAA
1 AGGTTTTGAAGATTGTTACCTAAAGGTTTCAAAGATTGTTACTTAG
* * * *
1972263 AGGTTTTGAAAATAGTTACCCT-GAGGTTTCAAAGATTGTTACTTGG
1 AGGTTTTGAAGATTGTTA-CCTAAAGGTTTCAAAGATTGTTACTTAG
* * * * *
1972309 AGATTTT-AACGATTATTACTTAAAAGTTTCAAAAATTGTTAACTTA-
1 AGGTTTTGAA-GATTGTTACCTAAAGGTTTCAAAGATTGTT-ACTTAG
* * * * * ** * *
1972355 AGGGTTTAAAGATAGTTACCTAAAGGCTTCGAAGAAGGTTTCTCAG
1 AGGTTTTGAAGATTGTTACCTAAAGGTTTCAAAGATTGTTACTTAG
1972401 AGGTTTTGAAGATTGTTA-CTCAAAGGTTTCAAAGATTGTTAC
1 AGGTTTTGAAGATTGTTACCT-AAAGGTTTCAAAGATTGTTAC
1972443 CCAAAGGTTT
Statistics
Matches: 170, Mismatches: 47, Indels: 17
0.73 0.20 0.07
Matches are distributed among these distances:
45 24 0.14
46 138 0.81
47 8 0.05
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (46 bp):
AGGTTTTGAAGATTGTTACCTAAAGGTTTCAAAGATTGTTACTTAG
Found at i:1972338 original size:92 final size:92
Alignment explanation
Indices: 1972193--1972464 Score: 282
Period size: 92 Copynumber: 3.0 Consensus size: 92
1972183 ATTTTTACCC
* *
1972193 AAGGTTTCAAACATTGTTACTTAGAGGTTTTGAATATTGTTAC-CGAAAGGTTTCAAAGATTGTT
1 AAGGTTTCAAAGATTGTTACTTAGAGGTTTTGAAGATTGTTACTC-AAAGGTTTCAAAGATTGTT
*
1972257 TCCCAAAGGTTTTGAAAATAGTTACCCT-
65 ACCCAAAGGTTTTGAAAATAGTTA-CCTA
* * * * * * *
1972285 GAGGTTTCAAAGATTGTTACTTGGAGATTTT-AACGATTATTACTTAAAAGTTTCAAAAATTGTT
1 AAGGTTTCAAAGATTGTTACTTAGAGGTTTTGAA-GATTGTTACTCAAAGGTTTCAAAGATTGTT
* ** *
1972349 AACTTAAGGGTTT-AAAGATAGTTACCTA
65 ACCCAAAGGTTTTGAAA-ATAGTTACCTA
* * ** * *
1972377 AAGGCTTCGAAGAAGGTTTCTCAGAGGTTTTGAAGATTGTTACTCAAAGGTTTCAAAGATTGTTA
1 AAGGTTTCAAAGATTGTTACTTAGAGGTTTTGAAGATTGTTACTCAAAGGTTTCAAAGATTGTTA
**
1972442 CCCAAAGGTTTTGAGGATAGTTA
66 CCCAAAGGTTTTGAAAATAGTTA
1972465 GTCAGAGGTT
Statistics
Matches: 141, Mismatches: 33, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
91 8 0.06
92 130 0.92
93 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (92 bp):
AAGGTTTCAAAGATTGTTACTTAGAGGTTTTGAAGATTGTTACTCAAAGGTTTCAAAGATTGTTA
CCCAAAGGTTTTGAAAATAGTTACCTA
Found at i:1978981 original size:52 final size:52
Alignment explanation
Indices: 1978919--1979022 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
1978909 TAATTGTTCC
1978919 TCTGTCTTTTGTAAGCTATTGTTGAGCAACAATCTTTGATTGATGGTGGATG
1 TCTGTCTTTTGTAAGCTATTGTTGAGCAACAATCTTTGATTGATGGTGGATG
*
1978971 TCTGTCTTTTGTACGCTATTGTTGAGCAACAATCTTTGATTGATGGTGGATG
1 TCTGTCTTTTGTAAGCTATTGTTGAGCAACAATCTTTGATTGATGGTGGATG
1979023 ACATCGACAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (52 bp):
TCTGTCTTTTGTAAGCTATTGTTGAGCAACAATCTTTGATTGATGGTGGATG
Found at i:1981568 original size:30 final size:30
Alignment explanation
Indices: 1981532--1981596 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1981522 AATCACTAAT
* *
1981532 TATAAGAGTTTATTTGAG-TCAAAATAAAAG
1 TATAAGAGCTTATTTG-GTTCAAAATAAAAC
*
1981562 TATAAGAGCTTATTTGGTTTAAAATAAAAC
1 TATAAGAGCTTATTTGGTTCAAAATAAAAC
1981592 TATAA
1 TATAA
1981597 AGACTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (30 bp):
TATAAGAGCTTATTTGGTTCAAAATAAAAC
Found at i:1991972 original size:29 final size:28
Alignment explanation
Indices: 1991883--1991974 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 28
1991873 ATCTTTTATT
* *
1991883 ATTGAATTTATTGTTCTAAATCATTTTACA
1 ATTGAAATTATTGTTCT-AATCATTAT-CA
* * * * *
1991913 ATGGAAAATGATTGTTCTTATCCCTTGTCA
1 ATTG-AAATTATTGTTCTAAT-CATTATCA
1991943 ATTGAAATTATTGGTTCTAATCATTATCA
1 ATTGAAATTATT-GTTCTAATCATTATCA
1991972 ATT
1 ATT
1991975 ATCCAATCTA
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
29 16 0.33
30 17 0.35
31 15 0.31
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (28 bp):
ATTGAAATTATTGTTCTAATCATTATCA
Found at i:2000062 original size:13 final size:13
Alignment explanation
Indices: 2000028--2000065 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2000018 TATATATGTA
2000028 TATATT-AATTTT
1 TATATTAAATTTT
*
2000040 TATTTATAAATTTT
1 TATAT-TAAATTTT
2000054 TATATTAAATTT
1 TATATTAAATTT
2000066 AATACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 4 0.18
13 8 0.36
14 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATATTAAATTTT
Found at i:2006391 original size:5 final size:5
Alignment explanation
Indices: 2006381--2006405 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2006371 ATCTCTTTAG
2006381 TCCCT TCCCT TCCCT TCCCT TCCCT
1 TCCCT TCCCT TCCCT TCCCT TCCCT
2006406 GGTTCTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
TCCCT
Found at i:2012100 original size:67 final size:67
Alignment explanation
Indices: 2011988--2012120 Score: 230
Period size: 67 Copynumber: 2.0 Consensus size: 67
2011978 ATGCGGCTTG
* *
2011988 TTCTGGTGTCTTATAATCTTTTTCCTTGAACGGGGTTTGCAGGAAAGTTATTTAGATTTCAAGAT
1 TTCTGGTGTCTTATAATCTTTTTCCTTGAACAGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
2012053 CA
66 CA
* *
2012055 TTCTGGTGTCTTATAATCTTTTTCCTTTAACAGGGTTTGCTGGAAAGTTATCTAGATTTCAAGAT
1 TTCTGGTGTCTTATAATCTTTTTCCTTGAACAGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
2012120 C
66 C
2012121 GCGCACAGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (67 bp):
TTCTGGTGTCTTATAATCTTTTTCCTTGAACAGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
CA
Found at i:2015110 original size:38 final size:38
Alignment explanation
Indices: 2015056--2015136 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
2015046 CAGCGATAGA
*
2015056 AAGAGATCGGTAGAGGGAGAGCTCGATTTGGGCAAAGG
1 AAGAGATCGGTAGAGGGAGAGCCCGATTTGGGCAAAGG
*
2015094 AAGAGATCGGTGGAGGGAGAGCCCGATTTGGGCAAAGG
1 AAGAGATCGGTAGAGGGAGAGCCCGATTTGGGCAAAGG
*
2015132 GAGAG
1 AAGAG
2015137 CAAATCTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.11, G:0.44, T:0.14
Consensus pattern (38 bp):
AAGAGATCGGTAGAGGGAGAGCCCGATTTGGGCAAAGG
Done.