Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008662.1 Hibiscus syriacus cultivar Beakdansim tig00111662_pilon, whole genome shotgun sequence
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: 1703488
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:238462 original size:5 final size:5
Alignment explanation
Indices: 238454--238486 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
238444 CCATCTCGTC
238454 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG
238487 TGGTAATACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.21, G:0.58, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:238607 original size:21 final size:21
Alignment explanation
Indices: 238583--238887 Score: 169
Period size: 21 Copynumber: 14.8 Consensus size: 21
238573 TGCGATTTTG
*
238583 GACTACCGCAATGCGATAGTC
1 GACTATCGCAATGCGATAGTC
*
238604 GACTATCGTAATGCGAATA-T-
1 GACTATCGCAATGCG-ATAGTC
*
238624 GTA-AATCGCAATGCGATAGTCC
1 G-ACTATCGCAATGCGATAGT-C
* * * *
238646 AAGT-TTGCATTGCGATAGTC
1 GACTATCGCAATGCGATAGTC
238666 GACTATCGCAATGCGATAGTAC
1 GACTATCGCAATGCGATAGT-C
* * *
238688 AAGT-TCGCATTGCGATAGTC
1 GACTATCGCAATGCGATAGTC
* * *
238708 GATTATCGTATTGCGAT--T-
1 GACTATCGCAATGCGATAGTC
*
238726 TACATATTCGC-ATGCGATAGTC
1 GAC-TA-TCGCAATGCGATAGTC
*
238748 GACTATCGCATTGCGAT--T-
1 GACTATCGCAATGCGATAGTC
* *
238766 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCAATGCGATAGTC
*
238789 GACTATCGCATTGCGAT--T-
1 GACTATCGCAATGCGATAGTC
*
238807 TACATATTCGCAATGCGATAGTC
1 GAC-TA-TCGCAATGCGATAGTC
*
238830 GACTATCGCATTGCGAT--T-
1 GACTATCGCAATGCGATAGTC
* *
238848 TACATATTCGCATTGCGATAGTC
1 GAC-TA-TCGCAATGCGATAGTC
*
238871 GACTATCGCATTGCGAT
1 GACTATCGCAATGCGAT
238888 TTACATATTC
Statistics
Matches: 222, Mismatches: 32, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
18 7 0.03
19 21 0.09
20 60 0.27
21 111 0.50
22 17 0.08
23 6 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (21 bp):
GACTATCGCAATGCGATAGTC
Found at i:238795 original size:41 final size:41
Alignment explanation
Indices: 238652--238928 Score: 434
Period size: 41 Copynumber: 6.8 Consensus size: 41
238642 GTCCAAGTTT
* *
238652 GCATTGCGATAGTCGACTATCGCAATGCGATAGTACA-AGTTC
1 GCATTGCGATAGTCGACTATCGCATTGCGAT-TTACATA-TTC
* *
238694 GCATTGCGATAGTCGATTATCGTATTGCGATTTACATATTC
1 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
238735 GCA-TGCGATAGTCGACTATCGCATTGCGATTTACATATTC
1 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
238775 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
1 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
*
238816 GCAATGCGATAGTCGACTATCGCATTGCGATTTACATATTC
1 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
238857 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
1 GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
* * *
238898 GCATTGCAATAGTCCAAGT-TCGCATTGCGAT
1 GCATTGCGATAGT-CGACTATCGCATTGCGAT
238929 AGTCCAAGTT
Statistics
Matches: 221, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
40 38 0.17
41 151 0.68
42 32 0.14
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (41 bp):
GCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
Found at i:238947 original size:21 final size:21
Alignment explanation
Indices: 238629--238948 Score: 152
Period size: 21 Copynumber: 15.5 Consensus size: 21
238619 AATATGTAAA
*
238629 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* * *
238650 TTGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
238670 ATCGCAATGCGATAGTACAAGT
1 -TCGCATTGCGATAGTCCAAGT
* *
238692 TCGCATTGCGATAGT-CGATT
1 TCGCATTGCGATAGTCCAAGT
* * *
238712 ATCGTATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* *
238733 TCGCA-TGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
238752 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* *
238773 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
238793 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* * *
238814 TCGCAATGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
238834 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* *
238855 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
238875 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
238896 TCGCATTGCAATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
238917 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
238938 TCGCGTTGCGA
1 TCGCATTGCGA
238949 ATCTGGAAAC
Statistics
Matches: 233, Mismatches: 38, Indels: 56
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.00
19 11 0.05
20 74 0.32
21 139 0.60
22 8 0.03
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:239223 original size:76 final size:75
Alignment explanation
Indices: 239106--239253 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
239096 TTCTAAATCA
239106 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAAT-ATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATAAAATGATAAAAATAAT
239170 ATCCTAAAACT
65 ATCCTAAAACT
* * * *
239181 TAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAAAATATT
1 TAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAAT
239246 ATCCTAAA
65 ATCCTAAA
239254 TTTGAGTTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 19 0.28
76 48 0.72
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAAAATGATAAAAATAATA
TCCTAAAACT
Found at i:241104 original size:15 final size:15
Alignment explanation
Indices: 241084--241112 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
241074 GTTCGCTAAA
241084 AAAATGAAAAAAAAT
1 AAAATGAAAAAAAAT
241099 AAAATGAAAAAAAA
1 AAAATGAAAAAAAA
241113 ACAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATGAAAAAAAAT
Found at i:241109 original size:16 final size:15
Alignment explanation
Indices: 241084--241118 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
241074 GTTCGCTAAA
*
241084 AAAATGAAAAAAAAT
1 AAAATGAAAAAAAAC
241099 AAAATGAAAAAAAAAC
1 AAAATG-AAAAAAAAC
241115 AAAA
1 AAAA
241119 ATATAACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAATGAAAAAAAAC
Found at i:247517 original size:75 final size:76
Alignment explanation
Indices: 247461--247610 Score: 223
Period size: 75 Copynumber: 2.0 Consensus size: 76
247451 TAAAATACCT
* * *
247461 ACAAAAAAT-AATATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATA
1 ACAAAAAATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATA
247524 CAAAGATAAAG
66 CAAAGATAAAG
* * *
247535 ATAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAAAT
1 ACAAAAAATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACT-AAAAT
247600 ACAAAGATAAA
65 ACAAAGATAAA
247611 ATATAATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 7 0.10
75 28 0.42
76 16 0.24
77 16 0.24
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (76 bp):
ACAAAAAATAAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATA
CAAAGATAAAG
Found at i:247633 original size:77 final size:75
Alignment explanation
Indices: 247473--247637 Score: 233
Period size: 77 Copynumber: 2.2 Consensus size: 75
247463 AAAAAATAAT
* * *
247473 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
1 ATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
247538 AAATATAAAA
66 AAATATAAAA
247548 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAAATACAAAGATAAA-A
1 ATAATATCCTAAAACTTAATTAAAATACT-AAAACCTATTTAAACT-AAAATACAAAGATAAAGA
* * *
247612 TATAATTTTTAAA
64 TA-AAATATAAAA
*
247625 ATATTATCCTAAA
1 ATAATATCCTAAA
247638 TTTGAGTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
75 26 0.32
76 19 0.24
77 35 0.44
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
AAATATAAAA
Found at i:250240 original size:40 final size:41
Alignment explanation
Indices: 250194--250298 Score: 106
Period size: 41 Copynumber: 2.6 Consensus size: 41
250184 GGTTATTTTG
* *
250194 GCGGCGTTTTTTTACAAACGCCGCCACAGGTCTA-TA-TATA
1 GCGGCGTTTTTTTACAAACGCCGCAACAGAT-TAGTACTATA
* * * * *
250234 GTGGCGTTTTTTCAATAAACGCCGCAACATATTAGTACTTTA
1 GCGGCGTTTTTT-TACAAACGCCGCAACAGATTAGTACTATA
*
250276 GCGGCGTTTTTATACAAACGCCG
1 GCGGCGTTTTTTTACAAACGCCG
250299 TAATAGGGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
40 13 0.25
41 25 0.49
42 13 0.25
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (41 bp):
GCGGCGTTTTTTTACAAACGCCGCAACAGATTAGTACTATA
Found at i:253473 original size:29 final size:30
Alignment explanation
Indices: 253431--253503 Score: 130
Period size: 29 Copynumber: 2.5 Consensus size: 30
253421 ACTACGGCGT
253431 TGAATGTGGAGCAGCGTAACA-CTCGGTTC
1 TGAATGTGGAGCAGCGTAACACCTCGGTTC
253460 TGAATGTGGAGCAGCGTAACACCTCGGTTC
1 TGAATGTGGAGCAGCGTAACACCTCGGTTC
*
253490 TGAATGTTGAGCAG
1 TGAATGTGGAGCAG
253504 AAAATGCAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 21 0.50
30 21 0.50
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (30 bp):
TGAATGTGGAGCAGCGTAACACCTCGGTTC
Found at i:253908 original size:43 final size:42
Alignment explanation
Indices: 253810--254119 Score: 334
Period size: 43 Copynumber: 7.2 Consensus size: 42
253800 AAGGAAATTA
* *
253810 GCGGCGTTTGTATCCAAAAAAACGCCGCTATATATCTGATCTTTT
1 GCGGCGTTTGT-TCC--AAAAACGCCGCTATAGATCTGACCTTTT
* * * *
253855 ACGGTG-TTGTTCAAAAAAACGCCGCTATAGATCTGACTTTTT
1 GCGGCGTTTGTTC-CAAAAACGCCGCTATAGATCTGACCTTTT
* *
253897 GCGGCGTTTGTTCCAAAAACGCCGTTATAGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
253939 GCGGCGTTTGTTCCAAAAACCCCGCTATATATATCATCCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGA-CCTTTT
* * * *
253982 GCGGCGTTTGTTCCAAAAACGCCACTATAGACCTCAACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
254025 GCGGCGTTTGTTCTAAAAACGCCGCTATAAATCTCAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * * *
254068 GCGGCATTTATTCCAAAAACGCCGCTATAGATCTTGACCTATA
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
254111 GCGGCGTTT
1 GCGGCGTTT
254120 TTTGTTCTCA
Statistics
Matches: 224, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
42 86 0.38
43 128 0.57
44 6 0.03
45 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:256198 original size:36 final size:36
Alignment explanation
Indices: 256151--256228 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
256141 CGGTCTGCAG
256151 ACAAGTAACATATTCAGTTTTTAACATTGGAATTTT
1 ACAAGTAACATATTCAGTTTTTAACATTGGAATTTT
256187 ACAAGTAACATATTCAGTTTTTAACATTGGAATTTT
1 ACAAGTAACATATTCAGTTTTTAACATTGGAATTTT
256223 ACAAGT
1 ACAAGT
256229 TTCTATCAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (36 bp):
ACAAGTAACATATTCAGTTTTTAACATTGGAATTTT
Found at i:264077 original size:38 final size:39
Alignment explanation
Indices: 264026--264101 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
264016 TGTCCAGGTT
264026 CATTTTGTATTATATAGATGATATCA-ATATTACATGTC
1 CATTTTGTATTATATAGATGATATCACATATTACATGTC
* *
264064 CATTTTGTATTATATAGATGATGTCACGTATTACATGT
1 CATTTTGTATTATATAGATGATATCACATATTACATGT
264102 TTACATAGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (39 bp):
CATTTTGTATTATATAGATGATATCACATATTACATGTC
Found at i:264209 original size:26 final size:27
Alignment explanation
Indices: 264180--264238 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
264170 ATTTAGTTTT
*
264180 TATATATATA-AT-AATATAGTATATAG
1 TATATATATACATGAAAATA-TATATAG
*
264206 TATAT-TATACTTGAAAATATATATAG
1 TATATATATACATGAAAATATATATAG
264232 TATATAT
1 TATATAT
264239 TGTTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 4 0.14
26 18 0.64
27 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (27 bp):
TATATATATACATGAAAATATATATAG
Found at i:264285 original size:2 final size:2
Alignment explanation
Indices: 264280--264317 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
264270 TATTTTAAAA
*
264280 AT AT AT -T A- AT AT AT AT AT GT 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
264318 CAGTACATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264288 original size:27 final size:26
Alignment explanation
Indices: 264244--264297 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
264234 TATATTGTTT
*
264244 TTTTAAAAATGTATTTAAATTATATATA
1 TTTTAAAAATATATTT-AA-TATATATA
264272 TTTTAAAAATATA-TTAATATATATA
1 TTTTAAAAATATATTTAATATATATA
264297 T
1 T
264298 GTATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 9 0.36
26 2 0.08
27 2 0.08
28 12 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTAAAAATATATTTAATATATATA
Found at i:264295 original size:10 final size:11
Alignment explanation
Indices: 264262--264317 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 11
264252 ATGTATTTAA
264262 ATTATATATAT
1 ATTATATATAT
* * *
264273 TTTAAAAATAT
1 ATTATATATAT
264284 ATTAATATATAT
1 ATT-ATATATAT
264296 ATGTATATATAT
1 AT-TATATATAT
264308 A-TATATATAT
1 ATTATATATAT
264318 CAGTACATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
10 9 0.24
11 10 0.27
12 17 0.46
13 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
ATTATATATAT
Found at i:265557 original size:115 final size:117
Alignment explanation
Indices: 265362--265573 Score: 265
Period size: 116 Copynumber: 1.8 Consensus size: 117
265352 ATATATATTT
* * * *
265362 AAATAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCCTTAAGACAGCTCTTT
1 AAATAAATATTTATTTATTTAAAAATATCAGAAAATGACATCTAGGTACCTTAAGACAGCTCCTT
*
265427 TCTTTGATATTAAAAA-AAAT-AATAATTAAAACAATTAATATATAATTTATA
66 TCTTTAATATTAAAAATAAATAAAT-ATTAAAACAATTAATATATAATTTATA
* ** *
265478 AAATAAGATA-TTA-TTATTTAAAAATATCAGAAAATGGACATCTAGTTATTTTAAGACTGC-CC
1 AAATAA-ATATTTATTTATTTAAAAATATCAGAAAAT-GACATCTAGGTACCTTAAGACAGCTCC
265540 TTTC-TTAATATTGAAAAATAAATAAATATTAAAA
64 TTTCTTTAATATT-AAAAATAAATAAATATTAAAA
265574 TAGGATTAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
114 7 0.09
115 31 0.38
116 38 0.46
117 6 0.07
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (117 bp):
AAATAAATATTTATTTATTTAAAAATATCAGAAAATGACATCTAGGTACCTTAAGACAGCTCCTT
TCTTTAATATTAAAAATAAATAAATATTAAAACAATTAATATATAATTTATA
Found at i:265599 original size:18 final size:18
Alignment explanation
Indices: 265554--265605 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
265544 TTAATATTGA
*
265554 AAAATAAATAAAT-A-TT
1 AAAATAATTAAATAAGTT
265570 AAAATAGGATTAAATAAGTT
1 AAAATA--ATTAAATAAGTT
*
265590 AAAATAATTAACTAAG
1 AAAATAATTAAATAAG
265606 ATTTAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 6 0.20
18 15 0.50
19 1 0.03
20 8 0.27
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (18 bp):
AAAATAATTAAATAAGTT
Found at i:265632 original size:23 final size:23
Alignment explanation
Indices: 265606--265653 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
265596 ATTAACTAAG
265606 ATTTAATAAATAAAATACATATT
1 ATTTAATAAATAAAATACATATT
* * * *
265629 ATTTATTATATAATATATATATT
1 ATTTAATAAATAAAATACATATT
265652 AT
1 AT
265654 GGTTAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATAAATAAAATACATATT
Found at i:266942 original size:3 final size:3
Alignment explanation
Indices: 266934--267014 Score: 103
Period size: 3 Copynumber: 26.7 Consensus size: 3
266924 GGCCTGTTTG
**
266934 TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA-A
266980 TAA -AA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
267015 GAAAATGGAG
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 4 0.06
3 56 0.81
4 9 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:266972 original size:21 final size:21
Alignment explanation
Indices: 266946--267014 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
266936 ATAATAATTT
266946 TAATAATAATAAATAAAATAA
1 TAATAATAATAAATAAAATAA
*
266967 TAATAATAATATATAAAATAA
1 TAATAATAATAAATAAAATAA
266988 TAATAATAAT-AAT-AAATAA
1 TAATAATAATAAATAAAATAA
267007 TAATAATA
1 TAATAATA
267015 GAAAATGGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 14 0.30
20 2 0.04
21 30 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
TAATAATAATAAATAAAATAA
Found at i:267399 original size:124 final size:122
Alignment explanation
Indices: 267153--267778 Score: 504
Period size: 124 Copynumber: 5.3 Consensus size: 122
267143 ATGTTGAATA
* *
267153 AATTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG----G--GATGAT
1 AATTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAAGTTGATGCT
* * * * *
267211 AA--TATCTCCTTTTGTGAT-GTAAT-TTGGAAAAGGGTTGAACAAGTTCTTCTTATTATAA
64 AACCTATCTCCTTCTGTGATAG-AATCATGCAAAA-GGTTGAACAAGTTCTTCTCATTAT-G
* * *
267269 AATTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAGTTGATGTTA
1 AATTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTA
* * * *
267334 ACCTATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTCATTATG
65 ACCTATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGTTCTTCTCATTATG
*
267392 AACTTCTTATTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCT
1 AA-TTCTT-CTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCT
* * * * * *
267457 GATCTATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTTTCATTGTG
64 AACCTATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGTTCTTCTCATTATG
* *
267516 AA--CTTCTTCTTCTTCAGATGAGTTTTTCTCATTATGAACTTTCTCTGGAAAAGCTGA---T--
1 AATTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAA
** * * * *
267574 CC-A--T-C--AAGTGATGGATTTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATG
66 CCTATCTCCTTCTGTGATAGA-ATCATGCAAAAGGTTGAACAAGTTCTTCTCATTATG
* *
267625 AA--CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTATAC-CTGGAAATGTTGA---T
1 AATTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGCT
** * * * *
267684 --CC-A--T-C--AAGTGAT-GAATTCAAGCAAAAAGTTGAACAAATTATTCTCATTATG
64 AACCTATCTCCTTCTGTGATAGAA-TCATGCAAAAGGTTGAACAAGTTCTTCTCATTATG
*
267735 AATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACT
1 AA-TTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACT
267779 CTAACTGGCA
Statistics
Matches: 440, Mismatches: 48, Indels: 47
0.82 0.09 0.09
Matches are distributed among these distances:
109 46 0.10
110 88 0.20
111 3 0.01
112 1 0.00
113 38 0.09
114 1 0.00
115 1 0.00
116 13 0.03
117 34 0.08
118 1 0.00
120 50 0.11
121 3 0.01
122 7 0.02
123 2 0.00
124 144 0.33
125 8 0.02
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (122 bp):
AATTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGCTAA
CCTATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGTTCTTCTCATTATG
Found at i:267798 original size:223 final size:223
Alignment explanation
Indices: 267518--267922 Score: 587
Period size: 223 Copynumber: 1.8 Consensus size: 223
267508 TCATTGTGAA
* * ** *
267518 CTTCTTCTTCTTCAGATGAGTTTTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGT
1 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCACCAAGT
* * *
267583 GATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-CTTCTTCCTTCTTCAGATGA
66 GATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGA
* *
267647 GTTCTTCTCATTATGAACTATACCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAAG
131 GTTCTTCTCATTATGAACTATAACTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAAG
267712 TTGAACAAATTATTCTCATTATGAATTT
196 TTGAACAAATTATTCTCATTATGAATTT
* * ** *
267740 CTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTCTAACTGGCACTGCTGATCCACCGAG
1 CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCACCAAG
* *
267805 TGATGAATTTAAGTAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
65 TGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA--TCTTCTTCCTTCTTCAGA
* * * *
267870 TGAGTTCTTCTCATTATGAACTCTAACTGGCACTGTTGATCCATTAAATGATG
128 TGAGTTCTTCTCATTATGAACTATAACTGGAAATGTTGATCCATCAAATGATG
267923 GATTTAAATC
Statistics
Matches: 158, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
222 6 0.04
223 88 0.56
226 64 0.41
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (223 bp):
CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCACCAAGT
GATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAATCTTCTTCCTTCTTCAGATGA
GTTCTTCTCATTATGAACTATAACTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAAG
TTGAACAAATTATTCTCATTATGAATTT
Found at i:267807 original size:113 final size:112
Alignment explanation
Indices: 267362--267929 Score: 572
Period size: 113 Copynumber: 5.0 Consensus size: 112
267352 TAGAGTCATT
* * * * *
267362 CAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTATTTCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * ** *
267427 TTATGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TTATG
65 TTATGAACTCTAACTGG--AA----ATGCTGATCCA--T-C--AAGTGAT-GAATTTAAG
* ** * * *
267486 CAAAAGGTTGAACAAGCTCTTTTCATTGTGAA--CTTCTT-CTTCTTCAGATGAGTTTTTCTCAT
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** * * *
267548 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TATGAACTCTAACTGGAAATGCTGATCCATCAAGTGATGAATTTAAG
*
267595 CAAAAGGTTGAACAAATTCTTCTCATTATGAA--CTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
267658 TATGAACTATACCTGGAAATGTTGATCCATCAAGTGATGAATTCAAG
66 TATGAACTCTAACTGGAAATGCTGATCCATCAAGTGATGAATTTAAG
* *
267705 CAAAAAGTTGAACAAATTATTCTCATTATGAATTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
267770 TTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAG
65 TTATGAACTCTAACTGGAAATGCTGATCCATCAAGTGATGAATTTAAG
* *
267818 TAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
267883 TTATGAACTCTAACTGGCACTGTTGATCCATTAAATGATGGATTTAA
65 TTATGAACTCTAACTGGAAATGCTGATCCATCAAGTGATGAATTTAA
267930 ATCTTTGCTA
Statistics
Matches: 391, Mismatches: 48, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
108 2 0.01
109 42 0.11
110 92 0.24
111 1 0.00
112 1 0.00
113 170 0.43
114 9 0.02
118 2 0.01
120 39 0.10
121 5 0.01
124 28 0.07
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (112 bp):
CAAAAAGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTAACTGGAAATGCTGATCCATCAAGTGATGAATTTAAG
Found at i:268782 original size:114 final size:114
Alignment explanation
Indices: 268619--268952 Score: 551
Period size: 114 Copynumber: 2.9 Consensus size: 114
268609 GATCATGCAG
* * * * * * * * *
268619 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAAATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
268684 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
268733 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
268798 ACACTTTCAGAATATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
268847 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
268912 ACACTTTCAGAAGATTCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
268953 CGAGAACGTG
Statistics
Matches: 206, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 206 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:269659 original size:16 final size:16
Alignment explanation
Indices: 269633--269711 Score: 83
Period size: 16 Copynumber: 5.0 Consensus size: 16
269623 TGACCCCCTT
*
269633 TTTTCTCTTTTTCTTC
1 TTTTATCTTTTTCTTC
*
269649 TCTTATCTTTTTTCTTC
1 TTTTATC-TTTTTCTTC
*
269666 TTTTTTCTTTTTCTT-
1 TTTTATCTTTTTCTTC
*
269681 TTTTTTC-TTTTCTTC
1 TTTTATCTTTTTCTTC
269696 TTTTCAT-TTTTTCTTC
1 TTTT-ATCTTTTTCTTC
269712 AAGCATAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
14 7 0.13
15 11 0.20
16 22 0.41
17 14 0.26
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTTTCTTC
Found at i:269659 original size:23 final size:22
Alignment explanation
Indices: 269632--269710 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 22
269622 TTGACCCCCT
269632 TTTTTCTCTTTTTCTTCTCTTATC
1 TTTTT-TCTTTTTCTTCT-TTATC
* *
269656 TTTTTTCTTCTTTTTTCTTTTTC
1 TTTTTTCTT-TTTCTTCTTTATC
*
269679 TTTTTTTTCTTTTCTTCTTT-TC
1 TTTTTTCT-TTTTCTTCTTTATC
269701 ATTTTTTCTT
1 -TTTTTTCTT
269711 CAAGCATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 3 0.06
23 31 0.66
24 13 0.28
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTCTTTTTCTTCTTTATC
Found at i:269680 original size:33 final size:31
Alignment explanation
Indices: 269633--269699 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 31
269623 TGACCCCCTT
269633 TTTTCTCTTTTTCTTCTCTTATCTT-TTTTCTTCT
1 TTTTCTCTTTTTCTT-T-TT-T-TTCTTTTCTTCT
269667 TTTT-TCTTTTTCTTTTTTTTCTTTTCTTCT
1 TTTTCTCTTTTTCTTTTTTTTCTTTTCTTCT
269697 TTT
1 TTT
269700 CATTTTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
29 2 0.06
30 13 0.41
31 2 0.06
32 1 0.03
33 10 0.31
34 4 0.12
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (31 bp):
TTTTCTCTTTTTCTTTTTTTTCTTTTCTTCT
Found at i:269682 original size:22 final size:23
Alignment explanation
Indices: 269632--269699 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 23
269622 TTGACCCCCT
*
269632 TTTTTC-TCTTTTTCTTCTCTTATC
1 TTTTTCTTC-TTTTCTTCT-TTTTC
269656 TTTTTTCTTCTTTT-TTCTTTTTC
1 -TTTTTCTTCTTTTCTTCTTTTTC
*
269679 TTTTTTTTCTTTTCTTCTTTT
1 TTTTTCTTCTTTTCTTCTTTT
269700 CATTTTTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 12 0.31
23 11 0.28
24 4 0.10
25 10 0.26
26 2 0.05
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTCTTCTTTTCTTCTTTTTC
Found at i:269709 original size:13 final size:12
Alignment explanation
Indices: 269630--269710 Score: 64
Period size: 13 Copynumber: 6.8 Consensus size: 12
269620 TCTTGACCCC
269630 CTTTTTTCTCTTT
1 CTTTTTTCT-TTT
* *
269643 -TTCTTCTCTTAT
1 CTT-TTTTCTTTT
269655 CTTTTTTC--TT
1 CTTTTTTCTTTT
269665 CTTTTTTCTTTT
1 CTTTTTTCTTTT
*
269677 -TCTTTT-TTTT
1 CTTTTTTCTTTT
269687 CTTTTCTTCTTTT
1 CTTTT-TTCTTTT
269700 CATTTTTTCTT
1 C-TTTTTTCTT
269711 CAAGCATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
10 13 0.24
11 8 0.15
12 12 0.22
13 17 0.31
14 4 0.07
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
CTTTTTTCTTTT
Found at i:277045 original size:15 final size:15
Alignment explanation
Indices: 277022--277053 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
277012 TGCAATGAAT
277022 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
277037 AATGCATGTATGCAA
1 AATGAATGTATGCAA
277052 AA
1 AA
277054 GGTATTGATC
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:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:280557 original size:20 final size:19
Alignment explanation
Indices: 280518--280569 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
280508 TTTCTTTGAT
280518 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
280537 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
280557 ATTTATAAAATAA
1 A-TTAAAAAATAA
280570 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:280670 original size:120 final size:120
Alignment explanation
Indices: 280427--280661 Score: 284
Period size: 120 Copynumber: 2.0 Consensus size: 120
280417 AATATATATT
* * *
280427 AATTTATATAT-ATTTAT-AAATAAAATATTTATGTATTTAGAAATATCAGAAAATGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATGTATTTAAAAATATCAGAAAATGACATCTAG
* * *
280490 GTGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
* *
280545 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAAATATCAG-AAATGGACATCT
1 AATTAATATATAATTTATAAAATAAAATATTTATGTATTT-AAAAATATCAGAAAAT-GACATCT
* ** * **
280609 AGTTATTTTAAGACTG-TCCTTTC-TTAATATTGGAAAATAAATAAAT-ATTAAAA
64 AGGTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
280662 TAGGATTAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
118 17 0.17
119 26 0.26
120 29 0.29
121 27 0.27
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATGTATTTAAAAATATCAGAAAATGACATCTAG
GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:280724 original size:23 final size:25
Alignment explanation
Indices: 280698--280749 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 25
280688 TAACTAAGAT
280698 TTTAATAAATAAA-ATACATA-ATA
1 TTTAATAAATAAATATACATATATA
* * *
280721 TTTATTATATAAATATATATATATA
1 TTTAATAAATAAATATACATATATA
280746 TTTA
1 TTTA
280750 TGGTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
24 6 0.25
25 7 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTAATAAATAAATATACATATATA
Found at i:282126 original size:3 final size:3
Alignment explanation
Indices: 282118--282198 Score: 94
Period size: 3 Copynumber: 26.7 Consensus size: 3
282108 GGCTTGTTTG
** *
282118 TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAG TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TA-A
282164 TAA -AA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA
282199 GAAAATGGAG
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 4 0.06
3 54 0.81
4 9 0.13
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:282156 original size:21 final size:21
Alignment explanation
Indices: 282130--282198 Score: 111
Period size: 21 Copynumber: 3.2 Consensus size: 21
282120 ATAATAATTT
*
282130 TAATAATAATAAATAAAATAG
1 TAATAATAATAAATAAAATAA
*
282151 TAATAATAATATATAAAATAA
1 TAATAATAATAAATAAAATAA
282172 TAATAATAATAAATAATAATAA
1 TAATAATAATAAATAA-AATAA
282194 TAATA
1 TAATA
282199 GAAAATGGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 34 0.77
22 10 0.23
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (21 bp):
TAATAATAATAAATAAAATAA
Found at i:290003 original size:21 final size:21
Alignment explanation
Indices: 289979--290019 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
289969 TGGAAAATGG
289979 TAAAAAGAAAGAAACTAACTT
1 TAAAAAGAAAGAAACTAACTT
290000 TAAAAAGAAAGAAACTAACT
1 TAAAAAGAAAGAAACTAACT
290020 CGCTTCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (21 bp):
TAAAAAGAAAGAAACTAACTT
Found at i:299860 original size:4 final size:4
Alignment explanation
Indices: 299851--299879 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
299841 TTAACCATTG
299851 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
299880 GTTTCTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:300060 original size:131 final size:142
Alignment explanation
Indices: 299728--300101 Score: 456
Period size: 144 Copynumber: 2.7 Consensus size: 142
299718 TTAACCATTG
* * **
299728 TTTATTTATT-ATTCATAATATTTG-TTTCGACCTTGTGGTGACCCGATCCGGGGTATGATCTAC
1 TTTATTTATTGTTTC-TAATATTCGATTTCGACCTTGTGGTGA-CCGATCCGGGGTATGATCCGC
* *
299791 ATTATTATGGTTCGGACTCTACTAACTACTAACTTTTATTTTATTGCACTTTAACCATTGTTATT
64 ATTATTATAGTTCGGACTCTGCTAACTACTAACTTTTATTTTATTGCACTTTAACCATTGTTATT
299856 TATTTATTTATTTA
129 TATTTATTTATTTA
*
299870 TTTATTTATTGTTTCTAATATTCGATTTTCGACCTTGTGGTGACTCGATCCTGGGTATGATCCGC
1 TTTATTTATTGTTTCTAATATTCGA-TTTCGACCTTGTGGTGAC-CGATCCGGGGTATGATCCGC
* *
299935 ATTATTATAGTTCGGACTCTGTTAACTACTGACTTTTATTTTATTGCA-TTCTAACCATTGGTTA
64 ATTATTATAGTTCGGACTCTGCTAACTACTAACTTTTATTTTATTGCACTT-TAACCATT-GTTA
299999 -TT-TTTA-TT-TTTA
127 TTTATTTATTTATTTA
*
300011 TTTA-TTA-T-TTT-T-A-ATT-GA-TTCGACCTTGTGGTGACCGATCCGGGGTATGATCCGTAT
1 TTTATTTATTGTTTCTAATATTCGATTTCGACCTTGTGGTGACCGATCCGGGGTATGATCCGCAT
* * * *
300068 TACTATAGTTTGGATTCTGCTAAC-GCTAACTTTT
66 TATTATAGTTCGGACTCTGCTAACTACTAACTTTT
300102 CTAACATCTA
Statistics
Matches: 209, Mismatches: 17, Indels: 24
0.84 0.07 0.10
Matches are distributed among these distances:
130 8 0.04
131 40 0.19
132 17 0.08
134 2 0.01
135 3 0.01
136 1 0.00
137 1 0.00
138 3 0.01
139 1 0.00
140 3 0.01
141 8 0.04
142 20 0.10
143 10 0.05
144 88 0.42
145 4 0.02
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.47
Consensus pattern (142 bp):
TTTATTTATTGTTTCTAATATTCGATTTCGACCTTGTGGTGACCGATCCGGGGTATGATCCGCAT
TATTATAGTTCGGACTCTGCTAACTACTAACTTTTATTTTATTGCACTTTAACCATTGTTATTTA
TTTATTTATTTA
Found at i:307235 original size:149 final size:150
Alignment explanation
Indices: 307045--307360 Score: 548
Period size: 150 Copynumber: 2.1 Consensus size: 150
307035 GGGTAGAGGG
*
307045 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
307109 TGCTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
307174 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
307194 TCTACGCGGTCCTTCGGGATATATATATATT-TTGTGGAACATGTGTGAAGTCTTGGAAAGACAC
1 TCTACGCGGTCCTTCGGGACATATATATATTCTT-TGGAACATGTGTGAAGTCTTGGAAAGACAC
307258 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCAT
65 ATACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCAT
307323 TATATGGCACTACGGTGCAAT
130 TATATGGCACTACGGTGCAAT
307344 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
307361 TGCATTTATA
Statistics
Matches: 159, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
148 2 0.01
149 50 0.31
150 107 0.67
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:307372 original size:23 final size:23
Alignment explanation
Indices: 307328--307372 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
307318 ATCATTATAT
*
307328 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
307351 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
307373 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:314278 original size:150 final size:149
Alignment explanation
Indices: 314008--314323 Score: 544
Period size: 150 Copynumber: 2.1 Consensus size: 149
313998 GGGTAGAGGG
* *
314008 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* * *
314073 GCTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
314138 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
**
314157 TCTACGCGGTCCTTCGGGATGTATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACACA
314222 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
314287 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
314307 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
314324 TGCATTTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
149 51 0.32
150 107 0.68
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:314335 original size:23 final size:23
Alignment explanation
Indices: 314291--314335 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
314281 ATCATTATAT
*
314291 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
314314 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
314336 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:316075 original size:16 final size:16
Alignment explanation
Indices: 316051--316082 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
316041 GACGAGAGCC
*
316051 AAAGTAAATCATATTT
1 AAAGAAAATCATATTT
316067 AAAGAAAATCATATTT
1 AAAGAAAATCATATTT
316083 TTTCATCTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (16 bp):
AAAGAAAATCATATTT
Found at i:327395 original size:22 final size:22
Alignment explanation
Indices: 327367--327413 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
327357 TTTGCATGAG
327367 ATCTAAGACAACCTCCAATGGC
1 ATCTAAGACAACCTCCAATGGC
327389 ATCTAAGACAACCTCCAATGGC
1 ATCTAAGACAACCTCCAATGGC
327411 ATC
1 ATC
327414 ATCCTTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.19
Consensus pattern (22 bp):
ATCTAAGACAACCTCCAATGGC
Found at i:328175 original size:21 final size:21
Alignment explanation
Indices: 328145--328193 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
328135 GAGACGAATT
*
328145 AAAAGTGTTTTGATTATTTCC
1 AAAAGAGTTTTGATTATTTCC
328166 AAAAGAGTTTTGATTATTTCC
1 AAAAGAGTTTTGATTATTTCC
328187 AAAAGAG
1 AAAAGAG
328194 AACCCTTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (21 bp):
AAAAGAGTTTTGATTATTTCC
Found at i:334049 original size:14 final size:14
Alignment explanation
Indices: 334030--334056 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
334020 ATATTATATC
334030 TTTAATTTAATTAT
1 TTTAATTTAATTAT
334044 TTTAATTTAATTA
1 TTTAATTTAATTA
334057 ATAGACTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATTTAATTAT
Found at i:343223 original size:19 final size:19
Alignment explanation
Indices: 343199--343236 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
343189 TTAGGTATTT
*
343199 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
343218 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
343237 GATATTTTTT
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:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:344001 original size:21 final size:22
Alignment explanation
Indices: 343966--344018 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
343956 TTTTAAATCA
* * *
343966 TTATTTATTATTTTATTATT-T
1 TTATTTTTTAATTTATAATTAT
*
343987 TTCTTTTTTAATTTATAATTAT
1 TTATTTTTTAATTTATAATTAT
344009 TTATTTTTTA
1 TTATTTTTTA
344019 TACATTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTTTTTAATTTATAATTAT
Found at i:348783 original size:19 final size:19
Alignment explanation
Indices: 348759--348796 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
348749 TTAGGTATTT
*
348759 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
348778 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
348797 GATATTATTT
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:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:348882 original size:12 final size:12
Alignment explanation
Indices: 348867--348893 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
348857 TTTAATTAGG
348867 ATTTAAAATATT
1 ATTTAAAATATT
348879 ATTTAAAATATT
1 ATTTAAAATATT
348891 ATT
1 ATT
348894 ATTTTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTAAAATATT
Found at i:348930 original size:74 final size:76
Alignment explanation
Indices: 348733--348946 Score: 274
Period size: 76 Copynumber: 2.8 Consensus size: 76
348723 TTTAAACATT
* * * * * * **
348733 ATATTTTATCTTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGG
1 ATATTATATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAAA
**
348798 ATATTATTTTT
66 ATATTATTTAA
* *
348809 ATATTTTATATTTGTTTTATGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAAA
1 ATATTATATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAAA
348874 ATATTATTTAAA
66 ATATTATTT-AA
348886 ATATTAT-TA-TT-TTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTAA
1 ATATTATATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTGTTTTAATTAGGATTTAA
348947 GATGTTTTAG
Statistics
Matches: 124, Mismatches: 12, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
73 5 0.04
74 43 0.35
75 2 0.02
76 68 0.55
77 6 0.05
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (76 bp):
ATATTATATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAAA
ATATTATTTAA
Found at i:349549 original size:11 final size:11
Alignment explanation
Indices: 349523--349563 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
349513 TTTATCCCAA
*
349523 TTTATTTATTTT
1 TTTATTTA-ATT
349535 TTTATTTAATT
1 TTTATTTAATT
349546 TTTATTTAATT
1 TTTATTTAATT
349557 TTTATTT
1 TTTATTT
349564 CATTATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTATTTAATT
Found at i:359059 original size:10 final size:9
Alignment explanation
Indices: 359006--359057 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
358996 TTAACTTCAA
359006 TTTTTTAACT
1 TTTTTTAA-T
359016 TTTTTTAAT
1 TTTTTTAAT
**
359025 TTCATTAA-
1 TTTTTTAAT
359033 TTTTTTATAT
1 TTTTTTA-AT
*
359043 GTTTTTAAT
1 TTTTTTAAT
359052 TTTTTT
1 TTTTTT
359058 TATAAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 5 0.15
9 15 0.44
10 14 0.41
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:359509 original size:163 final size:163
Alignment explanation
Indices: 359236--359547 Score: 450
Period size: 163 Copynumber: 1.9 Consensus size: 163
359226 TGTTCAGTTA
* * * *
359236 TTTTTTAATTTATTGATAATGTATATACATCATATAAATGTAATTTTTGGAATCTTAAACCTCTA
1 TTTTTTAATTTATTGATAATATATATACATCATATAAATATAATTATTCGAATCTTAAACCTCTA
* * * *
359301 AAATGAATAATACTCTTTTTTACCACTGGAATTATTTAGTAAAACCTTTATGATGGTACGAGCAG
66 AAA-GAATAATACTCTTTTTTACCACTGAAATCATTTAGTAAAACCTTTATGATGGTACAAGCAA
359366 GCAGATTAGTGAAGCGAGTTGTTTGTTCGATTGT
130 GCAGATTAGTGAAGCGAGTTGTTTGTTCGATTGT
* *
359400 TTTTTTATTTTATTGATAATATATATACATCATATAAATATAATTATTCGAATTTTAAACACT-T
1 TTTTTTAATTTATTGATAATATATATACATCATATAAATATAATTATTCGAATCTTAAAC-CTCT
* *
359464 AACAA-AATAATACTCTTTTTTATC-GTGTAAATCATTTAGTAAAACCTTTATGATGGTACAAGC
65 AA-AAGAATAATACTCTTTTTTACCACTG-AAATCATTTAGTAAAACCTTTATGATGGTACAAGC
*
359527 AAGCGGATTAGTGAAGCGAGT
128 AAGCAGATTAGTGAAGCGAGT
359548 GATGGTTATA
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
162 2 0.02
163 69 0.52
164 57 0.43
165 4 0.03
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (163 bp):
TTTTTTAATTTATTGATAATATATATACATCATATAAATATAATTATTCGAATCTTAAACCTCTA
AAAGAATAATACTCTTTTTTACCACTGAAATCATTTAGTAAAACCTTTATGATGGTACAAGCAAG
CAGATTAGTGAAGCGAGTTGTTTGTTCGATTGT
Found at i:367809 original size:18 final size:18
Alignment explanation
Indices: 367783--367823 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
367773 ATTGTTCGAA
*
367783 AAGACTGAAGTAAATGAT
1 AAGACTGAAGTAAATAAT
* *
367801 AAGATTGAATTAAATAAT
1 AAGACTGAAGTAAATAAT
367819 AAGAC
1 AAGAC
367824 CGGATGGAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.17, T:0.24
Consensus pattern (18 bp):
AAGACTGAAGTAAATAAT
Found at i:370403 original size:25 final size:27
Alignment explanation
Indices: 370355--370407 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
370345 GGCATTTTTA
370355 GTTGCAACCCAAAAATGGCTTGTTGAAAG
1 GTTGCAACCC-AAAAT-GCTTGTTGAAAG
370384 GTTGCAACCC-AAAT-CTTGTTGAAA
1 GTTGCAACCCAAAATGCTTGTTGAAA
370408 AGGAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.42
27 4 0.17
29 10 0.42
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
GTTGCAACCCAAAATGCTTGTTGAAAG
Found at i:371349 original size:18 final size:19
Alignment explanation
Indices: 371326--371374 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
371316 GCCATTTTTT
371326 GTATCGATACTCAAGGG-A
1 GTATCGATACTCAAGGGTA
*
371344 GTATCGATA-TCTAGGGTA
1 GTATCGATACTCAAGGGTA
371362 GATTATCGATACT
1 G--TATCGATACT
371375 TTCAGTAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
20 8 0.31
21 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (19 bp):
GTATCGATACTCAAGGGTA
Found at i:374750 original size:20 final size:20
Alignment explanation
Indices: 374725--374762 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
374715 AATTATTTTG
374725 AATTTTTAAATAATTTTATT
1 AATTTTTAAATAATTTTATT
* *
374745 AATTTTTATATATTTTTA
1 AATTTTTAAATAATTTTA
374763 AAATATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTTTAAATAATTTTATT
Found at i:376583 original size:18 final size:18
Alignment explanation
Indices: 376562--376600 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
376552 TCAATTGGCG
376562 ACCCTAATGCTATTGACA
1 ACCCTAATGCTATTGACA
* *
376580 ACCCTAATGTTATTGGCA
1 ACCCTAATGCTATTGACA
376598 ACC
1 ACC
376601 AAATAGTTGA
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:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (18 bp):
ACCCTAATGCTATTGACA
Found at i:378088 original size:18 final size:18
Alignment explanation
Indices: 378060--378102 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
378050 TGCCCGGGCT
* * *
378060 AGTCCACATACCTCGGTA
1 AGTCCATATACATCGATA
*
378078 ATTCCATATACATCGATA
1 AGTCCATATACATCGATA
378096 AGTCCAT
1 AGTCCAT
378103 CAATCAGATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (18 bp):
AGTCCATATACATCGATA
Found at i:381848 original size:14 final size:13
Alignment explanation
Indices: 381799--381854 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
381789 AGAGATGAAT
*
381799 AAATAATTATTAA
1 AAATTATTATTAA
381812 ATAATTA-TATTAA
1 A-AATTATTATTAA
*
381825 AATATAATTATTAA
1 AA-ATTATTATTAA
381839 AAATTCATTATATAA
1 AAATT-ATTAT-TAA
381854 A
1 A
381855 TTTAATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 1 0.03
13 13 0.37
14 17 0.49
15 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTATTATTAA
Found at i:383886 original size:17 final size:17
Alignment explanation
Indices: 383864--383897 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
383854 CTTTTAAAAC
383864 TAAAATATTAGATATAT
1 TAAAATATTAGATATAT
383881 TAAAATATTAGATATAT
1 TAAAATATTAGATATAT
383898 AAAGAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
TAAAATATTAGATATAT
Found at i:389548 original size:2 final size:2
Alignment explanation
Indices: 389541--389593 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
389531 TTATTTTTAT
389541 TA TA TA TA 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 TA TA TA TA
389583 TA TA TA TA TA T
1 TA TA TA TA TA T
389594 TGTCCATGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:389938 original size:10 final size:10
Alignment explanation
Indices: 389906--389938 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
389896 GACGTGGCCT
389906 AATGTCTTCA
1 AATGTCTTCA
*
389916 AAGGTCTTCA
1 AATGTCTTCA
389926 AATGTCTTCA
1 AATGTCTTCA
389936 AAT
1 AAT
389939 AAACAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (10 bp):
AATGTCTTCA
Found at i:390487 original size:32 final size:32
Alignment explanation
Indices: 390431--390491 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
390421 GATTTATATA
*
390431 TATATGTATGTATATATTGTATTTGTTGTTTG
1 TATATGTATGTATATATTGAATTTGTTGTTTG
*
390463 TATATGTATGTATGT-TATGAATTTGTTGT
1 TATATGTATGTATATAT-TGAATTTGTTGT
390492 GACAGTATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (32 bp):
TATATGTATGTATATATTGAATTTGTTGTTTG
Found at i:391445 original size:32 final size:32
Alignment explanation
Indices: 391409--391475 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
391399 TATATATATA
*
391409 TATATGTATGTATA-TATTGTATTTGTTGTTTG
1 TATATGTATGTATATTA-TGAATTTGTTGTTTG
*
391441 TATATGTATGTATGTTATGAATTTGTTGTTTG
1 TATATGTATGTATATTATGAATTTGTTGTTTG
391473 TAT
1 TAT
391476 GTTATGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.58
Consensus pattern (32 bp):
TATATGTATGTATATTATGAATTTGTTGTTTG
Found at i:391475 original size:22 final size:22
Alignment explanation
Indices: 391449--391530 Score: 139
Period size: 22 Copynumber: 3.8 Consensus size: 22
391439 TGTATATGTA
*
391449 TGTATGTTATGAATTTGTTGTT
1 TGTATGTTATGAATTTGCTGTT
391471 TGTATGTTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGCTGTT
391493 TGTATGTTATGAATTTGCTGTT
1 TGTATGTTATGAATTTGCTGTT
*
391515 TG-ATGTTATGTATTTG
1 TGTATGTTATGAATTTG
391531 TTGTGTATGC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
21 13 0.22
22 45 0.78
ACGTcount: A:0.18, C:0.02, G:0.23, T:0.56
Consensus pattern (22 bp):
TGTATGTTATGAATTTGCTGTT
Found at i:391477 original size:26 final size:24
Alignment explanation
Indices: 391445--391539 Score: 114
Period size: 22 Copynumber: 4.2 Consensus size: 24
391435 TGTTTGTATA
391445 TGTATGTATGTTATGAATTTG-T-
1 TGTATGTATGTTATGAATTTGCTG
*
391467 TGTTTGTATGTTATGAATTTGCTG
1 TGTATGTATGTTATGAATTTGCTG
391491 T-T-TGTATGTTATGAATTTGCTG
1 TGTATGTATGTTATGAATTTGCTG
* *
391513 T-T-TG-ATGTTATGTATTTGTTG
1 TGTATGTATGTTATGAATTTGCTG
391534 TGTATG
1 TGTATG
391540 CTGATTTGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.24
22 45 0.68
23 4 0.06
24 1 0.02
ACGTcount: A:0.18, C:0.02, G:0.24, T:0.56
Consensus pattern (24 bp):
TGTATGTATGTTATGAATTTGCTG
Found at i:392617 original size:30 final size:30
Alignment explanation
Indices: 392583--392752 Score: 203
Period size: 30 Copynumber: 5.9 Consensus size: 30
392573 TCTTTTTGAT
*
392583 TATGTAAGAAATATTATATGGTTTGTGGTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
392613 TATGTTAGAAATATTATATGG-TT-T-GTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* * * *
392640 GATGTTCA-AAACATTATATGGTTTATGGTT
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
392670 TATGTTAGAAATATTATATGG-TT-T-GTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* *
392697 GATGTTCA-AAACATTATATGGTTTGTGGTC
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
392727 TATGTTAGAAATATTATATGGTTTGT
1 TATGTTAGAAATATTATATGGTTTGT
392753 ATTAAAGTTA
Statistics
Matches: 119, Mismatches: 11, Indels: 20
0.79 0.07 0.13
Matches are distributed among these distances:
27 39 0.33
28 8 0.07
29 8 0.07
30 64 0.54
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (30 bp):
TATGTTAGAAATATTATATGGTTTGTGGTC
Found at i:392655 original size:27 final size:27
Alignment explanation
Indices: 392625--392722 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 27
392615 TGTTAGAAAT
392625 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
** *
392652 ATTATATGGTTTATGGTTTATGTT-AGAAAT
1 ATTATATGG-TT-T-GTCGATGTTCA-AAAC
392682 ATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTCGATGTTCAAAAC
392709 ATTATATGGTTTGT
1 ATTATATGGTTTGT
392723 GGTCTATGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 33 0.55
28 4 0.07
29 4 0.07
30 19 0.32
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (27 bp):
ATTATATGGTTTGTCGATGTTCAAAAC
Found at i:392683 original size:57 final size:57
Alignment explanation
Indices: 392595--392752 Score: 298
Period size: 57 Copynumber: 2.8 Consensus size: 57
392585 TGTAAGAAAT
392595 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
* *
392652 ATTATATGGTTTATGGTTTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
392709 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
1 ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
392753 ATTAAAGTTA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 97 1.00
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (57 bp):
ATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCAAAAC
Found at i:394078 original size:31 final size:31
Alignment explanation
Indices: 394040--394098 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
394030 AATTGTATGG
*
394040 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATTTCAATATTGCAAAACTAAA
*
394071 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTGCAAAACT
394099 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTGCAAAACTAAA
Found at i:395014 original size:18 final size:18
Alignment explanation
Indices: 394987--395021 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
394977 AGCATTGAAA
394987 AAAAAGGAAAA-GAAAAT
1 AAAAAGGAAAAGGAAAAT
395004 AAAAAGAGAAAAGGAAAA
1 AAAAAG-GAAAAGGAAAA
395022 GGAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (18 bp):
AAAAAGGAAAAGGAAAAT
Found at i:400568 original size:26 final size:25
Alignment explanation
Indices: 400538--400602 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 25
400528 ATGTTCACAA
* * *
400538 GATTTTAAGATTTTGGATAATTTAT
1 GATTTTAAGATTTTAGAAAATTAAT
*
400563 GAATTTTAAGAGTTTAGAAAATTAAT
1 G-ATTTTAAGATTTTAGAAAATTAAT
400589 GATTTTAAGATTTT
1 GATTTTAAGATTTT
400603 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (25 bp):
GATTTTAAGATTTTAGAAAATTAAT
Found at i:402454 original size:18 final size:18
Alignment explanation
Indices: 402409--402460 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
402399 CTCCTATGGG
402409 GAGTATCGATACTCTACCCT
1 GAGTATCGATAC-C-ACCCT
*
402429 GGGTATCGATACC-CCCGT
1 GAGTATCGATACCACCC-T
402447 GAGTATCGATACCA
1 GAGTATCGATACCA
402461 AATTTGGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.11
18 13 0.46
19 1 0.04
20 11 0.39
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (18 bp):
GAGTATCGATACCACCCT
Found at i:409175 original size:16 final size:15
Alignment explanation
Indices: 409150--409188 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
409140 TTTAATTTTT
409150 AAAT-TTTTAATAATA
1 AAATATTTTAATAA-A
*
409165 AAATATTTTAATTAA
1 AAATATTTTAATAAA
409180 AAATATTTT
1 AAATATTTT
409189 TTTTGTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATATTTTAATAAA
Found at i:409189 original size:16 final size:17
Alignment explanation
Indices: 409152--409189 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
409142 TAATTTTTAA
409152 ATTTTTAATAATAAAAT
1 ATTTTTAATAATAAAAT
*
409169 A-TTTTAATTA-AAAAT
1 ATTTTTAATAATAAAAT
409184 ATTTTT
1 ATTTTT
409190 TTTGTAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 12 0.63
17 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTAATAATAAAAT
Found at i:410119 original size:29 final size:29
Alignment explanation
Indices: 410087--410148 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
410077 AAAAAAGTGA
*
410087 TATTCAAGGAATTAATTC-AAAATTGGTGC
1 TATTCAAGGAATTAATTCGAAAA-GGGTGC
***
410116 TATTTTGGGAATTAATTCGAAAAGGGTGC
1 TATTCAAGGAATTAATTCGAAAAGGGTGC
410145 TATT
1 TATT
410149 TTGGTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (29 bp):
TATTCAAGGAATTAATTCGAAAAGGGTGC
Found at i:410149 original size:29 final size:28
Alignment explanation
Indices: 410094--410178 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
410084 TGATATTCAA
*
410094 GGAATTAATTCAAAATTGGTGCTATTTTG
1 GGAATTAATTCAAAA-GGGTGCTATTTTG
410123 GGAATTAATTCGAAAAGGGTGCTATTTTG
1 GGAATTAATTC-AAAAGGGTGCTATTTTG
* * * *
410152 GTAATTATTTTAAAAAGGTTGCTATTT
1 GGAATTA-ATTCAAAAGGGTGCTATTT
410179 GTCTAAAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 43 0.88
30 6 0.12
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (28 bp):
GGAATTAATTCAAAAGGGTGCTATTTTG
Found at i:410167 original size:86 final size:85
Alignment explanation
Indices: 410008--410167 Score: 230
Period size: 86 Copynumber: 1.8 Consensus size: 85
409998 TGCTATTCTG
*** * * *
410008 GGAATTAATTCAGTTTTGGTGCTATTCTGGGAATTAATTCGAAATGTTGTTATTTTGGTAATTTT
1 GGAATTAATTCAAAATTGGTGCTATTCTGGGAATTAATTCGAAAGGGTGCTATTTTGGTAATTTT
410073 TTGAAAAAAAGTGATATTCAA
66 TT-AAAAAAAGTGATATTCAA
*
410094 GGAATTAATTCAAAATTGGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTATTTTGGTAATTA
1 GGAATTAATTCAAAATTGGTGCTATTCTGGGAATTAATTCG-AAAGGGTGCTATTTTGGTAATT-
410159 TTTTAAAAA
64 TTTTAAAAA
410168 GGTTGCTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 37 0.57
87 24 0.37
88 4 0.06
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (85 bp):
GGAATTAATTCAAAATTGGTGCTATTCTGGGAATTAATTCGAAAGGGTGCTATTTTGGTAATTTT
TTAAAAAAAGTGATATTCAA
Found at i:411389 original size:70 final size:71
Alignment explanation
Indices: 411276--411416 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 71
411266 TTTTTCTTAT
*
411276 ATACTGTATGGAGCACACTGAGCTTTTTAGCTCATTCTGTAGTTTTTACCCTTTTTC-AGCAGTA
1 ATACTGTATGGAGCACACTGAGCTTTTTAGCTCATTCTGTAGTTTTTACCCTTTTTCAAACAGTA
411340 GCAGAC
66 GCAGAC
411346 ATACTGTATGGAGCACACTGAGCTTTTTAGCTCATTCTGTAGTTTTTACCCTTTTTCAAACAGTA
1 ATACTGTATGGAGCACACTGAGCTTTTTAGCTCATTCTGTAGTTTTTACCCTTTTTCAAACAGTA
411411 GCAGAC
66 GCAGAC
411417 CGTAAGCTAG
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 57 0.83
71 12 0.17
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (71 bp):
ATACTGTATGGAGCACACTGAGCTTTTTAGCTCATTCTGTAGTTTTTACCCTTTTTCAAACAGTA
GCAGAC
Found at i:411568 original size:17 final size:19
Alignment explanation
Indices: 411541--411579 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
411531 ATATCTGTAT
411541 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
411559 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
411578 TA
1 TA
411580 AGTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:414006 original size:51 final size:49
Alignment explanation
Indices: 413930--414029 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 49
413920 TTGATTATAG
413930 AAAACTGAACAAGCTCACTGTTAAAATAAATATCCTCTGCCCAGGATCGAT
1 AAAACTGAACAAGCTCACTGTTAAAA-AAATATCCTCTGCCC-GGATCGAT
413981 AAAACTGAACAAGCTCACTGTTAAAAAAATATCCTCTGCCCGGATCGAT
1 AAAACTGAACAAGCTCACTGTTAAAAAAATATCCTCTGCCCGGATCGAT
414030 GATCTATTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 8 0.16
50 15 0.31
51 26 0.53
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (49 bp):
AAAACTGAACAAGCTCACTGTTAAAAAAATATCCTCTGCCCGGATCGAT
Found at i:416936 original size:32 final size:34
Alignment explanation
Indices: 416895--416960 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
416885 CGTTGACGGC
416895 GGCGCGT-GGGAGGT-GATCAGTCAAAGATTCGG
1 GGCGCGTGGGGAGGTGGATCAGTCAAAGATTCGG
416927 GGCGCGTGGGGAGGTGGATCAGTCAAAGATTCGG
1 GGCGCGTGGGGAGGTGGATCAGTCAAAGATTCGG
416961 CCGAGTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 7 0.22
33 7 0.22
34 18 0.56
ACGTcount: A:0.21, C:0.15, G:0.45, T:0.18
Consensus pattern (34 bp):
GGCGCGTGGGGAGGTGGATCAGTCAAAGATTCGG
Found at i:417169 original size:18 final size:18
Alignment explanation
Indices: 417143--417179 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
417133 GACCGGTCAT
*
417143 GACCCGTTGGCCCGACCC
1 GACCCGTTGACCCGACCC
*
417161 GACCTGTTGACCCGACCC
1 GACCCGTTGACCCGACCC
417179 G
1 G
417180 TTGACCCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.46, G:0.27, T:0.14
Consensus pattern (18 bp):
GACCCGTTGACCCGACCC
Found at i:417172 original size:13 final size:13
Alignment explanation
Indices: 417156--417188 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
417146 CCGTTGGCCC
*
417156 GACCCGACCTGTT
1 GACCCGACCCGTT
417169 GACCCGACCCGTT
1 GACCCGACCCGTT
417182 GACCCGA
1 GACCCGA
417189 ACTGACCGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:417178 original size:31 final size:30
Alignment explanation
Indices: 417143--417202 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
417133 GACCGGTCAT
* *
417143 GACCCGTTGGCCCGACCCGACCTGTTGACCC
1 GACCCGTTGACCCGAACCGACC-GTTGACCC
*
417174 GACCCGTTGACCCGAACTGACCGTTGACC
1 GACCCGTTGACCCGAACCGACCGTTGACC
417203 GGTGTTATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.17, C:0.42, G:0.25, T:0.17
Consensus pattern (30 bp):
GACCCGTTGACCCGAACCGACCGTTGACCC
Found at i:417366 original size:58 final size:58
Alignment explanation
Indices: 417237--417386 Score: 149
Period size: 58 Copynumber: 2.6 Consensus size: 58
417227 GTTTTGGTAC
* ** * ** *
417237 TATTCTGGGAATTAATTGGAAATGGGTGCTATTTTGGTAATTTTTTTTGAAAAAGTGA
1 TATTTTGGGAATTAATTCAAAATGGGTGCTATTTTGGGAATTTAATTCGAAAAAGTGA
* * * *
417295 TATGTTGGGAATTAATTCAAAATTGGTGCTATTTTGGGAA-TTAATTCGAAAAGTGTGT
1 TATTTTGGGAATTAATTCAAAATGGGTGCTATTTTGGGAATTTAATTCGAAAA-AGTGA
* * * *
417353 TATTTTGGTAATTATTTTAAAAAGGGTGCTATTT
1 TATTTTGGGAATTAATTCAAAATGGGTGCTATTT
417387 GTGTAAAATG
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
57 9 0.12
58 65 0.88
ACGTcount: A:0.30, C:0.04, G:0.23, T:0.43
Consensus pattern (58 bp):
TATTTTGGGAATTAATTCAAAATGGGTGCTATTTTGGGAATTTAATTCGAAAAAGTGA
Found at i:417375 original size:29 final size:29
Alignment explanation
Indices: 417236--417386 Score: 108
Period size: 29 Copynumber: 5.2 Consensus size: 29
417226 AGTTTTGGTA
* ** *
417236 CTATTCTGGGAATTAATTGGAAATGGGTG
1 CTATTTTGGGAATTAATTCAAAAAGGGTG
* ** *
417265 CTATTTTGGTAATTTTTTTTGAAAAA--GTG
1 CTATTTTGGGAA--TTAATTCAAAAAGGGTG
* * **
417294 ATATGTTGGGAATTAATTCAAAATTGGTG
1 CTATTTTGGGAATTAATTCAAAAAGGGTG
* *
417323 CTATTTTGGGAATTAATTCGAAAAGTGTG
1 CTATTTTGGGAATTAATTCAAAAAGGGTG
* * * *
417352 TTATTTTGGTAATTATTTTAAAAAGGGTG
1 CTATTTTGGGAATTAATTCAAAAAGGGTG
417381 CTATTT
1 CTATTT
417387 GTGTAAAATG
Statistics
Matches: 92, Mismatches: 26, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
27 8 0.09
29 76 0.83
31 8 0.09
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (29 bp):
CTATTTTGGGAATTAATTCAAAAAGGGTG
Found at i:420585 original size:28 final size:28
Alignment explanation
Indices: 420545--420602 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
420535 CGGCCACTCG
420545 CGCTGGGGGGTCTAGTGACAACTTGAAC
1 CGCTGGGGGGTCTAGTGACAACTTGAAC
420573 CGCTGGGGGGTCTAGTGACAACTTGAAC
1 CGCTGGGGGGTCTAGTGACAACTTGAAC
420601 CG
1 CG
420603 TGTTTTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.22, G:0.36, T:0.21
Consensus pattern (28 bp):
CGCTGGGGGGTCTAGTGACAACTTGAAC
Found at i:448235 original size:216 final size:214
Alignment explanation
Indices: 447855--448286 Score: 801
Period size: 216 Copynumber: 2.0 Consensus size: 214
447845 TGTCATTCGG
447855 CCCCAGTGGAGGCCATTTTGGTGGAGCAAGGACTGATGCTAAGGTCCTGCAATCAGGCTTTTACT
1 CCCCAGTGGAGGCCATTTTGGTGGAGCAAGGACTGATGCTAAGGTCCTGCAATCAGGCTTTTACT
*
447920 AGCCAACTTTGTTTAGAGATGCCCAAGCATTTTACAAAGGATGTGATCGATGCCAACGGACTGGA
66 ACCCAACTTTGTTTAGAGATGCCCAAGCATTTTACAAAGGATGTGATCGATGCCAACGGACTGGA
*
447985 AACATCCCCAGACGACATGAGATGCCGTTGTAAAAATATTTTGGAGATAGAGCTGTTTGATGTGT
131 AACATCCCCAGACGACATGAGATGCCGCTGT-AAAATATTTTGGAGATAGAGCTGTTTGATGTGT
*
448050 GGGGCATCGACTTCATGGGA
195 GGGGCATCGACTTCATAGGA
448070 CCCCAAGTGGAGGCCATTTTGGTGGAGCAAGGACTGATGCTAAGGTCCTGCAATCAGGCTTTTAC
1 CCCC-AGTGGAGGCCATTTTGGTGGAGCAAGGACTGATGCTAAGGTCCTGCAATCAGGCTTTTAC
*
448135 TACCCAACTTTGTTTAGAGATGCCCAAGCATTTTACAAAGGATGTGATCGATGCCAATGGACTGG
65 TACCCAACTTTGTTTAGAGATGCCCAAGCATTTTACAAAGGATGTGATCGATGCCAACGGACTGG
*
448200 AAACATCTCCAGACGACATGAGATGCCGCTGTAAAATATTTTGGAGATAGAGCTGTTTGATGTGT
130 AAACATCCCCAGACGACATGAGATGCCGCTGTAAAATATTTTGGAGATAGAGCTGTTTGATGTGT
448265 GGGGCATCGACTTCATAGGA
195 GGGGCATCGACTTCATAGGA
448285 CC
1 CC
448287 ATTCCCATCT
Statistics
Matches: 211, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
215 58 0.27
216 153 0.73
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (214 bp):
CCCCAGTGGAGGCCATTTTGGTGGAGCAAGGACTGATGCTAAGGTCCTGCAATCAGGCTTTTACT
ACCCAACTTTGTTTAGAGATGCCCAAGCATTTTACAAAGGATGTGATCGATGCCAACGGACTGGA
AACATCCCCAGACGACATGAGATGCCGCTGTAAAATATTTTGGAGATAGAGCTGTTTGATGTGTG
GGGCATCGACTTCATAGGA
Found at i:455201 original size:8 final size:8
Alignment explanation
Indices: 455182--455279 Score: 60
Period size: 8 Copynumber: 11.8 Consensus size: 8
455172 TAACGCAGAG
*
455182 AAAAGAAG
1 AAAAGAAA
455190 AAAAGAAA
1 AAAAGAAA
455198 AAAA-AAA
1 AAAAGAAA
455205 AAATAGAAA
1 AAA-AGAAA
455214 TAAATAGAAA
1 -AAA-AGAAA
455224 TAAAAGAAA
1 -AAAAGAAA
*
455233 CAAAGAAA
1 AAAAGAAA
455241 TAAAA-AAA
1 -AAAAGAAA
455249 TAAAA-AAA
1 -AAAAGAAA
455257 TAAAA-AAA
1 -AAAAGAAA
* *
455265 TAGAGAGAA
1 AAAAGA-AA
455274 AAAAGA
1 AAAAGA
455280 TAGAGAAGGG
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
7 8 0.10
8 39 0.51
9 17 0.22
10 13 0.17
ACGTcount: A:0.80, C:0.01, G:0.11, T:0.08
Consensus pattern (8 bp):
AAAAGAAA
Found at i:455218 original size:10 final size:9
Alignment explanation
Indices: 455190--455266 Score: 78
Period size: 8 Copynumber: 9.1 Consensus size: 9
455180 AGAAAAGAAG
455190 AAAAGAAA-
1 AAAAGAAAT
455198 AAAA-AAA-
1 AAAAGAAAT
455205 AAATAGAAAT
1 AAA-AGAAAT
455215 AAATAGAAAT
1 AAA-AGAAAT
455225 AAAAGAAA-
1 AAAAGAAAT
*
455233 CAAAGAAAT
1 AAAAGAAAT
455242 AAAA-AAAT
1 AAAAGAAAT
455250 AAAA-AAAT
1 AAAAGAAAT
455258 AAAA-AAAT
1 AAAAGAAAT
455266 A
1 A
455267 GAGAGAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
7 6 0.10
8 33 0.52
9 11 0.17
10 13 0.21
ACGTcount: A:0.82, C:0.01, G:0.06, T:0.10
Consensus pattern (9 bp):
AAAAGAAAT
Found at i:457417 original size:90 final size:90
Alignment explanation
Indices: 457211--457464 Score: 388
Period size: 90 Copynumber: 2.8 Consensus size: 90
457201 CAACATGATA
* * *
457211 TTTTCAAATAAGATTTTAGAAACTAAGCCTTTGGGGGTTTCTTGATTTGTAAGTCCTTCAGG-C-
1 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCA
* *
457274 TCTATAAGACCTTCAGTGCTGGAGG
66 TCCATAAGACCTTCAGTGCTAGAGG
* *
457299 TTTTAAAATGAGATTTTAGAAACTAAGCCTTCGGGGGATTCTTGATTTGTAAGTCCTTCGGGCCA
1 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCA
*
457364 TCCATAAGACCTTCAGTG-TAAGATG
66 TCCATAAGACCTTCAGTGCT-AGAGG
* *
457389 TTTTCAAATGAGATTTTAGAAATTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTTGGGCCA
1 TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCA
457454 TCCATAAGACC
66 TCCATAAGACC
457465 CTTGGGCAGG
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
88 57 0.38
89 2 0.01
90 92 0.61
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (90 bp):
TTTTCAAATGAGATTTTAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCA
TCCATAAGACCTTCAGTGCTAGAGG
Found at i:457673 original size:34 final size:34
Alignment explanation
Indices: 457630--457699 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
457620 AGTCAGTTTC
457630 TTTTGAAACAAAG-TTTATCTCCCTTGAGACATGT
1 TTTTGAAACAAAGTTTTATCTCCCTTGAGACA-GT
* *
457664 TTTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
1 TTTTGAAACAAAGTTTTATCTCCCTTGAGACAGT
457698 TT
1 TT
457700 CCCTTGAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (34 bp):
TTTTGAAACAAAGTTTTATCTCCCTTGAGACAGT
Found at i:457786 original size:66 final size:65
Alignment explanation
Indices: 457666--457843 Score: 189
Period size: 66 Copynumber: 2.7 Consensus size: 65
457656 AGACATGTTT
* * * *
457666 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAACATCTTTGA-ATATGTTTC
1 TTGAAACAAA-TTTTGTCTCACTTGAGACAATTTCCCTTGAAACAAAACCTTTGAGAT-TGTTTC
457730 CC
64 CC
* **
457732 TTGAAACAAATTTTGTCTCCCTTGAGA-AATTTTTCTTGAAACACAAAACCTTTGAGATTGTTTC
1 TTGAAACAAATTTTGTCTCACTTGAGACAATTTCCCTTG-AA-ACAAAACCTTTGAGATTGTTTC
457796 CC
64 CC
* ** * *
457798 TTGGAACAAATTGCGTCTCACTTGAGACAGTTTTCCCCTGAAACAA
1 TTGAAACAAATTTTGTCTCACTTGAGACA-ATTTCCCTTGAAACAA
457844 GAAATTTTAT
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
64 8 0.09
65 18 0.19
66 56 0.60
67 5 0.05
68 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (65 bp):
TTGAAACAAATTTTGTCTCACTTGAGACAATTTCCCTTGAAACAAAACCTTTGAGATTGTTTCCC
Found at i:458249 original size:44 final size:44
Alignment explanation
Indices: 458177--458647 Score: 207
Period size: 44 Copynumber: 10.9 Consensus size: 44
458167 AGAGATTGTT
* * * *
458177 CAACTGTTT-GCTCGATTCTACCATAGAATGAGGTAGATCAACAC
1 CAACT-TTTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
* * *
458221 CAACATTTCGTTCGATTCCATCACAGAATGAGGTGGATC--GA-
1 CAACTTTTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
* * * * * * **
458262 C-ATTTGTTCGCTCAAATCCATCGCAG---GAGTTGGATCAGCGT
1 CAACTT-TTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
* * * * * ** *
458303 CAACTTTTTGCTCGTTTCTATCACATAAGGAGGAAGATTAACAC
1 CAACTTTTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
* * * * *
458347 CAACATTTCGTTCGATTTCCATCACAGAATGAGATGGATCGACATT
1 CAACTTTTCGCTCGA-TTCCATCACAGAATGAGGTGGATCAACA-C
** * * * * * * * **
458393 TTA-TTTTCGCTCAAATCCATCGCAAAAGGAGTTGGATCAGCGT
1 CAACTTTTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
* * * *
458436 CAACTTTTTGCTCG-TTCCTATCACGGAAGGAGGTAGATCAACAC
1 CAACTTTTCGCTCGATTCC-ATCACAGAATGAGGTGGATCAACAC
* * *
458480 CAACATTTCGTTCGATTCCATCACAGAATGAGGTGGATC--GA-
1 CAACTTTTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
* * * * * * **
458521 C-ATTTGTTCGCTCAAATCCAT-AGAAGAAGGAGTTGGATCAACGT
1 CAACTT-TTCGCTCGATTCCATCA-CAGAATGAGGTGGATCAACAC
* * ** * *
458565 CAACTTTTTGCTCGTTTATATCACAGAATGAGGTAGATCAGCAC
1 CAACTTTTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
* * *
458609 CAACATTTCGCTCGATTCCATCACTGAAGGAGGTGGATC
1 CAACTTTTCGCTCGATTCCATCACAGAATGAGGTGGATC
458648 GATATTTGTT
Statistics
Matches: 297, Mismatches: 109, Indels: 42
0.66 0.24 0.09
Matches are distributed among these distances:
38 9 0.03
40 5 0.02
41 57 0.19
42 5 0.02
43 8 0.03
44 176 0.59
45 36 0.12
46 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
CAACTTTTCGCTCGATTCCATCACAGAATGAGGTGGATCAACAC
Found at i:458769 original size:129 final size:128
Alignment explanation
Indices: 458176--458765 Score: 799
Period size: 129 Copynumber: 4.6 Consensus size: 128
458166 AAGAGATTGT
* * * *
458176 TCAACTGTTTGCTCGATTCTACCATAGAATGAGGTAGATCAACACCAACATTTCGTTCGATTCCA
1 TCAACTTTTTGCTCG-TTTTATCACAGAATGAGGTAGATCAACACCAACATTTCGTTCGATTCCA
*
458241 TCACAGAATGAGGTGGATCGACATTTGTTCGCTCAAATCCAT--C-GCAGGAGTTGGATCAGCG
65 TCACAGAATGAGGTGGATCGACATTTGTTCGCTCAAATCCATAGCAGAAGGAGTTGGATCAGCG
* * * *
458302 TCAACTTTTTGCTCGTTTCTATCACATAAGGAGGAAGATTAACACCAACATTTCGTTCGATTTCC
1 TCAACTTTTTGCTCGTTT-TATCACAGAATGAGGTAGATCAACACCAACATTTCGTTCGA-TTCC
* * * *
458367 ATCACAGAATGAGATGGATCGACATTTTATTTTCGCTCAAATCCATCGCAAAAGGAGTTGGATCA
64 ATCACAGAATGAGGTGGATCGACA--TT-TGTTCGCTCAAATCCATAGCAGAAGGAGTTGGATCA
458432 GCG
126 GCG
* * *
458435 TCAACTTTTTGCTCGTTCCTATCACGGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCCA
1 TCAACTTTTTGCTCGTT-TTATCACAGAATGAGGTAGATCAACACCAACATTTCGTTCGATTCCA
* *
458500 TCACAGAATGAGGTGGATCGACATTTGTTCGCTCAAATCCATAGAAGAAGGAGTTGGATCAACG
65 TCACAGAATGAGGTGGATCGACATTTGTTCGCTCAAATCCATAGCAGAAGGAGTTGGATCAGCG
* *
458564 TCAACTTTTTGCTCGTTTATATCACAGAATGAGGTAGATCAGCACCAACATTTCGCTCGATTCCA
1 TCAACTTTTTGCTCGTTT-TATCACAGAATGAGGTAGATCAACACCAACATTTCGTTCGATTCCA
* * * *
458629 TCACTGAAGGAGGTGGATCGATATTTGTTCGCTCAAATCCATAGCAGAAGGAGTTGGATCAGCA
65 TCACAGAATGAGGTGGATCGACATTTGTTCGCTCAAATCCATAGCAGAAGGAGTTGGATCAGCG
* * * * * * *
458693 TCAACGTTTAGCTCAATTTTATCATAGAATGAGGTAGATCACCACCAACATCTCGTTCGATTCTA
1 TCAACTTTTTGCTC-GTTTTATCACAGAATGAGGTAGATCAACACCAACATTTCGTTCGATTCCA
458758 TCACAGAA
65 TCACAGAA
458766 GGAGACGGAG
Statistics
Matches: 410, Mismatches: 43, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
125 2 0.00
126 49 0.12
127 27 0.07
129 213 0.52
130 21 0.05
132 28 0.07
133 70 0.17
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (128 bp):
TCAACTTTTTGCTCGTTTTATCACAGAATGAGGTAGATCAACACCAACATTTCGTTCGATTCCAT
CACAGAATGAGGTGGATCGACATTTGTTCGCTCAAATCCATAGCAGAAGGAGTTGGATCAGCG
Found at i:472030 original size:30 final size:30
Alignment explanation
Indices: 471994--472063 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
471984 CACAATATAT
* *
471994 AACTTTTAAAAA-TTATATTTTTGGTCCCTA
1 AACTTTTAAAAATTTATA-CTTTGGTCACTA
*
472024 AACTTTTACAAATTTATACTTTGGTCACTA
1 AACTTTTAAAAATTTATACTTTGGTCACTA
472054 AACTTTTAAA
1 AACTTTTAAA
472064 GCTTGCATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (30 bp):
AACTTTTAAAAATTTATACTTTGGTCACTA
Found at i:475872 original size:44 final size:44
Alignment explanation
Indices: 475732--475886 Score: 233
Period size: 43 Copynumber: 3.6 Consensus size: 44
475722 TCCAAAAACG
* * * * *
475732 CCGCTAAATGACCTAACCTTTTGCGGCGTTTGTTC-CAAAAACA
1 CCGCTAAATTACCTAACCTTTTGCGGCATTTATTCAAAAAAATA
475775 CCGCTAAATTACCTAACCTTTTGCGGCATTTATT-AAAAAAATA
1 CCGCTAAATTACCTAACCTTTTGCGGCATTTATTCAAAAAAATA
*
475818 CCGCTAAATTACCTAACCTTTTGTGGCATTTATTCAAAAAAATA
1 CCGCTAAATTACCTAACCTTTTGCGGCATTTATTCAAAAAAATA
*
475862 CCACTAAATTACCTAACCTTTTGCG
1 CCGCTAAATTACCTAACCTTTTGCG
475887 ATGTTTCTTG
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
43 70 0.69
44 32 0.31
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.32
Consensus pattern (44 bp):
CCGCTAAATTACCTAACCTTTTGCGGCATTTATTCAAAAAAATA
Found at i:481795 original size:18 final size:19
Alignment explanation
Indices: 481756--481796 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
481746 TAACGGCGTT
*
481756 AAAACAAAACCGTTTTAGA
1 AAAACAAAACCGTTTTACA
*
481775 AAAACAAAA-C-TTTTACC
1 AAAACAAAACCGTTTTACA
481792 AAAAC
1 AAAAC
481797 GACATCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.20
Consensus pattern (19 bp):
AAAACAAAACCGTTTTACA
Found at i:482722 original size:14 final size:14
Alignment explanation
Indices: 482702--482749 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
482692 GCTTTAAAAT
482702 AAACAAACAAACAC
1 AAACAAACAAACAC
* **
482716 GAACAAACGTACAC
1 AAACAAACAAACAC
482730 AAACAAACAGAAACAC
1 AAACAAAC--AAACAC
482746 AAAC
1 AAAC
482750 TTATTCGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 18 0.69
16 8 0.31
ACGTcount: A:0.65, C:0.27, G:0.06, T:0.02
Consensus pattern (14 bp):
AAACAAACAAACAC
Found at i:483329 original size:2 final size:2
Alignment explanation
Indices: 483322--483356 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
483312 CCTCATGGCC
483322 TA 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 TA T
483357 CTAGAAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:493719 original size:68 final size:70
Alignment explanation
Indices: 493608--493745 Score: 253
Period size: 68 Copynumber: 2.0 Consensus size: 70
493598 TTTTATCAGG
*
493608 TTCCAGCTAGAGATTTCTTGTAACACTTTAGTAAATCTTGTCGGGAATCATATACATAATGTACT
1 TTCCAGCTAGAGATTTATTGTAACACTTTAGTAAATCTTGTCGGGAATCATATACATAATGTACT
493673 TAGAT
66 TAGAT
493678 TTCCAGCTAGAGA-TTATTGT-ACACTTTAGTAAATCTTGTCGGGAATCATATACATAATGTACT
1 TTCCAGCTAGAGATTTATTGTAACACTTTAGTAAATCTTGTCGGGAATCATATACATAATGTACT
493741 TAGAT
66 TAGAT
493746 CATCCTAGAC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 48 0.72
69 6 0.09
70 13 0.19
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (70 bp):
TTCCAGCTAGAGATTTATTGTAACACTTTAGTAAATCTTGTCGGGAATCATATACATAATGTACT
TAGAT
Found at i:496042 original size:442 final size:439
Alignment explanation
Indices: 495220--496102 Score: 1572
Period size: 442 Copynumber: 2.0 Consensus size: 439
495210 CAAAGATAAA
* *
495220 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCGTAGATTGAAACTTATCACTAAGCATGTG
1 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATCACTAAGCACGTG
*
495285 GAGCCTGTTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAAAT
66 GAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAAAT
495350 AACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAGGCATTATTAACA
131 AACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAGGCATTATTAACA
*
495415 TCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAATAACAGTCGCATTGTCATCATT
196 TCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAAGAACAGTCGCATTGTCATCATT
* *
495480 TTTGCCACGGTACGAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTTGAGGGCCACC
261 TTTGCCACGGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGGGCCACC
*
495545 AACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCTATTTACA
326 AACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCATTTACA
495610 ACCAATGGGTTTAACACCAGTAGGACATGAAACAATATATCAAGTATGAT
391 ACCAATGGGTTTAACACCA-TAGGACATGAAACAATATATCAAGTATGAT
495660 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATCAGACTAAGCACG
1 TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATC--ACTAAGCACG
*
495725 TGGAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTGTAGAAA
64 TGGAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAA
495790 ATAACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAGGCA-T-TTAA
129 ATAACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAGGCATTATTAA
*
495853 CATCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCTAGAACAAGTCGCATTGTCATC
194 CATCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAAGAAC-AGTCGCATTGTCATC
* *
495918 ATTTTTTCCACTGGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGTGC
258 ATTTTTGCCAC-GGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGGGC
*
495983 CACCAACCTCGATTTGTATCAGTCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCATT
322 CACCAACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCATT
* * *
496048 TACAACCAATGGGTTTAACACTATAGGACATGAAGCAATATCTCAAGTATGAT
387 TACAACCAATGGGTTTAACACCATAGGACATGAAACAATATATCAAGTATGAT
496101 TC
1 TC
496103 CCAACATACA
Statistics
Matches: 424, Mismatches: 15, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
440 103 0.24
441 56 0.13
442 265 0.62
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (439 bp):
TCATATTGACTCGAGATGAAAGAGAAACTAATGAGCATAGATTGAAACTTATCACTAAGCACGTG
GAGCCTATTTTAAACCATAGAGTGACTTTTTTAGTTTACAAACATCAGAAGAGGCTATAGAAAAT
AACCCTTGTAAAGGAGTCATATAAATTCCTTCCTTAATATCCCCATGCAAAAGGCATTATTAACA
TCCATTTGTCGTAATGACCAGCCCTTGGAAGCAGCAATAGCAAGAACAGTCGCATTGTCATCATT
TTTGCCACGGTACAAATATCTCCTCATAATCAACTCCATACTCTTGTTGATTTTCGAGGGCCACC
AACCTCGATTTGTATCAATCAAGTGACCCATCAGATCTTAGTTTAATGGAATATACCCATTTACA
ACCAATGGGTTTAACACCATAGGACATGAAACAATATATCAAGTATGAT
Found at i:497844 original size:22 final size:21
Alignment explanation
Indices: 497814--497863 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
497804 GTCAAGGGTT
* *
497814 CTATATGGTTCTTCGGGACAAA
1 CTATGTGGTCCTTCGGG-CAAA
*
497836 CTATGTGGTCCTTCGTGCAAA
1 CTATGTGGTCCTTCGGGCAAA
*
497857 TTATGTG
1 CTATGTG
497864 AGCTGTGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (21 bp):
CTATGTGGTCCTTCGGGCAAA
Found at i:500349 original size:30 final size:29
Alignment explanation
Indices: 500313--500372 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
500303 CTGATGACCG
*
500313 TTGGGCTTGATATGGGCCTCCAGCTTGGTT
1 TTGGGCTTGAGATGGGCCTCCAGC-TGGTT
500343 TTGGGCTTGAGATGGGCCTCCAGCTGGTT
1 TTGGGCTTGAGATGGGCCTCCAGCTGGTT
500372 T
1 T
500373 GGGATCGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 6 0.21
30 23 0.79
ACGTcount: A:0.10, C:0.20, G:0.35, T:0.35
Consensus pattern (29 bp):
TTGGGCTTGAGATGGGCCTCCAGCTGGTT
Found at i:500677 original size:53 final size:54
Alignment explanation
Indices: 500587--500741 Score: 244
Period size: 53 Copynumber: 2.9 Consensus size: 54
500577 TCTTCAAATG
* * * *
500587 ACGGGTCCGCTCCCTCTTG-TTCAGGGATTAGAACTCGAACAATCATCTG-TTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTT
500639 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTT
*
500693 -CGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTG
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
500742 GTGTGATTAT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
52 18 0.19
53 76 0.79
54 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (54 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTT
Found at i:501030 original size:21 final size:21
Alignment explanation
Indices: 501002--501080 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
500992 GGCTTAAAAT
* *
501002 TGCCCGAAGGACTTATCATCT
1 TGCCCGAAAGACTTATCATCA
* *
501023 TGCTCGAAAGACTTA-CA-AA
1 TGCCCGAAAGACTTATCATCA
* *
501042 TGACCCGAAGGATTTCATCATCA
1 TG-CCCGAAAGACTT-ATCATCA
*
501065 TGCTCGAAAGACTTAT
1 TGCCCGAAAGACTTAT
501081 TGATGGATTT
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
19 2 0.05
20 11 0.26
21 16 0.37
22 11 0.26
23 3 0.07
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCCCGAAAGACTTATCATCA
Found at i:501234 original size:93 final size:93
Alignment explanation
Indices: 501075--501258 Score: 289
Period size: 93 Copynumber: 2.0 Consensus size: 93
501065 TGCTCGAAAG
* *
501075 ACTTATTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCTGAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACCACTCTTCGGTGAAGGCTTACAAATTACCTGAAGGATTTAAT
501140 CATCATGCTCGAAAGACTTACTGATGAC
66 CATCATGCTCGAAAGACTTACTGATGAC
* * * **
501168 ACTTACTGATGGGTTTGCTTCACCGCTTTTTTGTGAAGGCTTACAAATTACCCT-AAGGATTTAA
1 ACTTACTGATGGATTTGCTTCACCACTCTTCGGTGAAGGCTTACAAATTA-CCTGAAGGATTTAA
501232 TCATCATGCTCGAAAGACTTACTGATG
65 TCATCATGCTCGAAAGACTTACTGATG
501259 GCCCTAAGGA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 80 0.96
94 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (93 bp):
ACTTACTGATGGATTTGCTTCACCACTCTTCGGTGAAGGCTTACAAATTACCTGAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGAC
Found at i:501266 original size:42 final size:42
Alignment explanation
Indices: 501218--501310 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
501208 TTACAAATTA
*
501218 CCCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
*
501260 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
*
501302 CCCGAAGGA
1 CCCTAAGGA
501311 CTTACTAAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (42 bp):
CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
Found at i:507547 original size:6 final size:6
Alignment explanation
Indices: 507522--507557 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
507512 AGCTAATAAG
* *
507522 AATGCA AATGCG AATACA AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
507558 CAAGGTGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:520570 original size:2 final size:2
Alignment explanation
Indices: 520565--520620 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
520555 AACTTAATTA
520565 AT AT AT AT AT AT AT AT AT 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 AT
520607 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
520621 CTACAATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:520684 original size:38 final size:38
Alignment explanation
Indices: 520633--520709 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
520623 ACAATATAAG
520633 TGTACAATTATGACTCGTTTAATATGTACTCATTTCAA
1 TGTACAATTATGACTCGTTTAATATGTACTCATTTCAA
520671 TGTACAATTATGACTCGTTTAATATGTACTCATTTCAA
1 TGTACAATTATGACTCGTTTAATATGTACTCATTTCAA
520709 T
1 T
520710 CATGGGTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (38 bp):
TGTACAATTATGACTCGTTTAATATGTACTCATTTCAA
Found at i:523214 original size:30 final size:30
Alignment explanation
Indices: 523150--523217 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
523140 GAGCCGAAGC
* **
523150 AGAAGCAGGAGTAGAGACAGGAGGAGGCGA
1 AGAAGCAGGAGTAGAGACAGAAGGACACGA
* * *
523180 AGAAGCAGGAGTATAGAGAGAAGGACACGG
1 AGAAGCAGGAGTAGAGACAGAAGGACACGA
523210 AGAAGCAG
1 AGAAGCAG
523218 AAGCAGGAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.43, T:0.04
Consensus pattern (30 bp):
AGAAGCAGGAGTAGAGACAGAAGGACACGA
Found at i:523257 original size:24 final size:24
Alignment explanation
Indices: 523223--523268 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
523213 AGCAGAAGCA
*
523223 GGAGTATGTCGCCGCGTAGAGATC
1 GGAGTAGGTCGCCGCGTAGAGATC
* *
523247 GGAGTAGGTCGCCTCGTCGAGA
1 GGAGTAGGTCGCCGCGTAGAGA
523269 AGGGAAGTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.20
Consensus pattern (24 bp):
GGAGTAGGTCGCCGCGTAGAGATC
Found at i:527987 original size:36 final size:36
Alignment explanation
Indices: 527946--528019 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
527936 GAACTTGACT
* **
527946 TCAAAATAAAACACAGAAATGATATTTACTTGAAAA
1 TCAAAATAAAACACAGAAATCATATTTACACGAAAA
* * *
527982 TCAAAATTATACATAGAAATCATATTTACACGAAAA
1 TCAAAATAAAACACAGAAATCATATTTACACGAAAA
528018 TC
1 TC
528020 GTATAGCATC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.27
Consensus pattern (36 bp):
TCAAAATAAAACACAGAAATCATATTTACACGAAAA
Done.