Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1243
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: 213413
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:142558 original size:20 final size:20
Alignment explanation
Indices: 142533--142585 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
142523 ACATCTTTTT
142533 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
142553 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
142573 CATGTATCGATAC
1 CATGTATCGATAC
142586 TTTGAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:148315 original size:72 final size:73
Alignment explanation
Indices: 148145--148341 Score: 206
Period size: 73 Copynumber: 2.7 Consensus size: 73
148135 AGATCCTAAC
* * * * ** *
148145 AAAACATATTTAAATTTCTACAAATAAAAATAAATTATACCATTAAAAA-TTAAATTCATATTTG
1 AAAACACATTTAAACTTCTACAAATAAAAATAAATTATA-CTTTAAAAATTTTAACACATATATG
*
148209 TATATCCAA
65 CATATCCAA
* *
148218 AAAACACATTTAAACTTTTATAAATAAAAATAAATTATACTTTAAAAATTTTAACACATATAAT-
1 AAAACACATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTTAACACATAT-ATG
148282 CATA-CTCAA
65 CATATC-CAA
* * *
148291 AAATA-A-ATTTAAACTTCTACAAATAAAGATAAATAATACTCTAAAAATTTT
1 AAA-ACACATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTT
148342 TAAATACAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
72 49 0.47
73 54 0.51
74 2 0.02
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (73 bp):
AAAACACATTTAAACTTCTACAAATAAAAATAAATTATACTTTAAAAATTTTAACACATATATGC
ATATCCAA
Found at i:149660 original size:11 final size:12
Alignment explanation
Indices: 149620--149654 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
149610 CGAAAATACC
149620 AAGAAAATCAAG
1 AAGAAAATCAAG
*
149632 AATAAAATC-AG
1 AAGAAAATCAAG
149643 AAGAAAATCAAG
1 AAGAAAATCAAG
149655 CAAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
AAGAAAATCAAG
Found at i:151109 original size:16 final size:17
Alignment explanation
Indices: 151090--151121 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
151080 TTTTTATTTT
151090 ATTTAATAAT-AAAAAA
1 ATTTAATAATGAAAAAA
151106 ATTTAATAATGAAAAA
1 ATTTAATAATGAAAAA
151122 GATGATATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATTTAATAATGAAAAAA
Found at i:153688 original size:33 final size:33
Alignment explanation
Indices: 153646--153712 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
153636 ATAGTAACCC
* *
153646 ATGTATCGATACAAAAAATATTATATCGATACA
1 ATGTATCGATACAAAAAACAATATATCGATACA
* *
153679 ATGTATCGATACAAAGAACAATGTATCGATACA
1 ATGTATCGATACAAAAAACAATATATCGATACA
153712 A
1 A
153713 AGAACATTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAAAACAATATATCGATACA
Found at i:153701 original size:20 final size:20
Alignment explanation
Indices: 153676--153731 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
153666 TTATATCGAT
153676 ACAATGTATCGATACAAAGA
1 ACAATGTATCGATACAAAGA
153696 ACAATGTATCGATACAAAGA
1 ACAATGTATCGATACAAAGA
* *
153716 ACATTGTATCAATACA
1 ACAATGTATCGATACA
153732 TCTAGGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (20 bp):
ACAATGTATCGATACAAAGA
Found at i:163512 original size:52 final size:52
Alignment explanation
Indices: 163427--163551 Score: 196
Period size: 52 Copynumber: 2.4 Consensus size: 52
163417 ATATGAAAAG
* *
163427 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAAC
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAC
* * *
163479 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAC
*
163531 TTGCCTTCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
163552 AAGATCAATG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAC
Found at i:163562 original size:52 final size:52
Alignment explanation
Indices: 163427--163571 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 52
163417 ATATGAAAAG
* * *
163427 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTAGGCAAAC
1 TTGCCTGCATGTATCGATACA-TAAGATAATGTATCGATACATCTAGGCAAAC
*** * *
163479 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTAGGCAAAC
*
163531 TTGCCTTCATGTATCGATACA-AAGATCAATGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AATGTATCGATACA
163572 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 78 0.95
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTAGGCAAAC
Found at i:163575 original size:13 final size:13
Alignment explanation
Indices: 163557--163584 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
163547 ATACAAAGAT
163557 CAATGTATCGATA
1 CAATGTATCGATA
163570 CAATGTATCGATA
1 CAATGTATCGATA
163583 CA
1 CA
163585 TTTGAGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:163662 original size:33 final size:33
Alignment explanation
Indices: 163625--163691 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
163615 AGTGGCTTAA
163625 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
163658 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
163691 A
1 A
163692 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:163665 original size:13 final size:13
Alignment explanation
Indices: 163647--163671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163637 CAAAAAAATA
163647 TGTATCGATACAT
1 TGTATCGATACAT
163660 TGTATCGATACA
1 TGTATCGATACA
163672 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:165276 original size:71 final size:70
Alignment explanation
Indices: 165060--165301 Score: 403
Period size: 70 Copynumber: 3.4 Consensus size: 70
165050 TCTCATGTAC
*
165060 AATTCATGTATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGAATCTGATTCTCA
1 AATTCATGCATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGAATCTGATTCTCA
165125 GATAT
66 GATAT
*
165130 AATTAATGCATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGAATCTGATTCTCA
1 AATTCATGCATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGAATCTGATTCTCA
*
165195 GGTAT
66 GATAT
* * *
165200 AATTCATGCATTAGTCTAATCCTTGTAGTCTTTCTTTTTTTTCTATAAAAAAGAATATGATTCTC
1 AATTCATGCATTAGTCTAATCCTTGCAGTCTTTC-TTTTTTCCTATAAAAAAGAATCTGATTCTC
165265 AGATAT
65 AGATAT
**
165271 AATTCACACATTAGTCTAATCCTTGCAGTCT
1 AATTCATGCATTAGTCTAATCCTTGCAGTCT
165302 GATATTTACA
Statistics
Matches: 160, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 99 0.62
71 61 0.38
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (70 bp):
AATTCATGCATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGAATCTGATTCTCA
GATAT
Found at i:165294 original size:141 final size:140
Alignment explanation
Indices: 165048--165301 Score: 418
Period size: 141 Copynumber: 1.8 Consensus size: 140
165038 AAAAAATCCA
* *
165048 ATTCTCATGTACAATTCATGTATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGA
1 ATTCTCAGGTACAATTCATGCATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGA
* **
165113 ATCTGATTCTCAGATATAATTAATGCATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAA
66 ATATGATTCTCAGATATAATTAACACATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAA
165178 AAAGAATCTG
131 AAAGAATCTG
* * *
165188 ATTCTCAGGTATAATTCATGCATTAGTCTAATCCTTGTAGTCTTTCTTTTTTTTCTATAAAAAAG
1 ATTCTCAGGTACAATTCATGCATTAGTCTAATCCTTGCAGTCTTTC-TTTTTTCCTATAAAAAAG
*
165253 AATATGATTCTCAGATATAATTCACACATTAGTCTAATCCTTGCAGTCT
65 AATATGATTCTCAGATATAATTAACACATTAGTCTAATCCTTGCAGTCT
165302 GATATTTACA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
140 42 0.40
141 62 0.60
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (140 bp):
ATTCTCAGGTACAATTCATGCATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAAAAAGA
ATATGATTCTCAGATATAATTAACACATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCCTATAAA
AAAGAATCTG
Found at i:165340 original size:92 final size:89
Alignment explanation
Indices: 165229--165579 Score: 424
Period size: 92 Copynumber: 3.9 Consensus size: 89
165219 TCCTTGTAGT
* **
165229 CTTTCTTTTTTTTCTATAAAAAAGAATATGATTCTCAGATATAATTCACACATTAGTCTAATCCT
1 CTTTC-TTTTTTTCTAT-AAAAA-AATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCT
* * * *
165294 TGCAGTCTGATATTTACAATCAATCAA
63 TACAGTCTAACATTTACAATCAGTCAA
* **
165321 TCTTTCTTTTTTTCAATAAAAAAGAATCCAATTCTCAGATATAATTCATGCATTAGTCTAATCCT
1 -CTTTCTTTTTTTCTAT-AAAAA-AATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCT
* * * *
165386 TACAGTCTAATATTCACATTTAGTCAA
63 TACAGTCTAACATTTACAATCAGTCAA
* *
165413 -----TTTTTTTCTATAAAAAAATTTGATTATCAGATATAATTCATGCATTAGTCTAATCCTTAC
1 CTTTCTTTTTTTCTATAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTAC
165473 AGTCTAACATTTACAATCAGTCAA
66 AGTCTAACATTTACAATCAGTCAA
* * *
165497 CTTTTCTTTTTTACTATAAAAAAATCTGATTCTCAAATATAATTAATGCATTAGTCTAATCCTTA
1 C-TTTCTTTTTTTCTATAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTA
*
165562 CAGTCTGACATTTACAAT
65 CAGTCTAACATTTACAAT
165580 TGATTTTCAA
Statistics
Matches: 225, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
84 60 0.27
85 5 0.02
86 10 0.04
90 71 0.32
92 74 0.33
93 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (89 bp):
CTTTCTTTTTTTCTATAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTAC
AGTCTAACATTTACAATCAGTCAA
Found at i:165557 original size:90 final size:91
Alignment explanation
Indices: 165413--165579 Score: 243
Period size: 90 Copynumber: 1.9 Consensus size: 91
165403 ATTTAGTCAA
* *
165413 TTTTTTTCTAT-AAAAA-AATTTGATTATCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
1 TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
165476 CTAACATTTACAATCAGTCAACTTTTC
66 CTAACATTTACAATCAGTCAA-TTTTC
* * *
165503 TTTTTTACTAT-AAAAA-AATCTGATTCTCAAATATAATTAATGCATTAGTCTAATCCTTACAGT
1 TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
*
165566 CTGACATTTACAAT
66 CTAACATTTACAAT
165580 TGATTTTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (91 bp):
TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGT
CTAACATTTACAATCAGTCAATTTTC
Found at i:165611 original size:57 final size:57
Alignment explanation
Indices: 165523--165636 Score: 183
Period size: 57 Copynumber: 2.0 Consensus size: 57
165513 TAAAAAAATC
*
165523 TGATTCTCAAATATAATTAATGCATTAGTCTAATCCTTACAGTCTGACATTTACAAT
1 TGATTCTCAAATATAACTAATGCATTAGTCTAATCCTTACAGTCTGACATTTACAAT
* * * *
165580 TGATTTTCAAATATAACTCATGCATTAGTCTAATCTTTACAGTTTGACATTTACAAT
1 TGATTCTCAAATATAACTAATGCATTAGTCTAATCCTTACAGTCTGACATTTACAAT
165637 CAATCAACTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (57 bp):
TGATTCTCAAATATAACTAATGCATTAGTCTAATCCTTACAGTCTGACATTTACAAT
Found at i:165731 original size:152 final size:147
Alignment explanation
Indices: 165432--165731 Score: 431
Period size: 147 Copynumber: 2.0 Consensus size: 147
165422 ATAAAAAAAT
* * *
165432 TTGATTATCAGATATAATTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAGTCAA
1 TTGATTATCAAATATAACTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAATCAA
165497 CTTTTCTTTTTTACTATAAAAAAATCTGATTCTCAAATATAATTAATGCATTAGTCTAATCCTTA
66 CTTTTCTTTTTTACTATAAAAAAATCTGATTCTCAAATATAATTAATGCATTAGTCTAATCCTTA
*
165562 CAGTCTGACATTTACAA
131 CAGTCTAACATTTACAA
* * * *
165579 TTGATTTTCAAATATAACTCATGCATTAGTCTAATCTTTACAGTTTGACATTTACAATCAATCAA
1 TTGATTATCAAATATAACTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAATCAA
* * *
165644 CTTTTCTTTTTTTCTTTTTATAAAAAAGAAT-TGATTCTCAGATATAATTCATGCATTAGTCTAA
66 CTTTTCTTTTTTAC----TAT-AAAAA-AATCTGATTCTCAAATATAATTAATGCATTAGTCTAA
*
165708 TCCTTGCAGTCTAACATTTACAA
125 TCCTTACAGTCTAACATTTACAA
165731 T
1 T
165732 CAATCAACTT
Statistics
Matches: 135, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
147 71 0.53
151 3 0.02
152 58 0.43
153 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (147 bp):
TTGATTATCAAATATAACTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAATCAA
CTTTTCTTTTTTACTATAAAAAAATCTGATTCTCAAATATAATTAATGCATTAGTCTAATCCTTA
CAGTCTAACATTTACAA
Found at i:165740 original size:95 final size:95
Alignment explanation
Indices: 165577--165750 Score: 285
Period size: 95 Copynumber: 1.8 Consensus size: 95
165567 TGACATTTAC
* * * *
165577 AATTGATTTTCAAATATAACTCATGCATTAGTCTAATCTTTACAGTTTGACATTTACAATCAATC
1 AATTGATTCTCAAATATAACTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAATC
165642 AACTTTTCTTTTTTTCTTTTTATAAAAAAG
66 AACTTTTCTTTTTTTCTTTTTATAAAAAAG
* * *
165672 AATTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATC
1 AATTGATTCTCAAATATAACTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAATC
165737 AACTTTTCTTTTTT
66 AACTTTTCTTTTTT
165751 CAATAAAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 72 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (95 bp):
AATTGATTCTCAAATATAACTCATGCATTAGTCTAATCCTTACAGTCTAACATTTACAATCAATC
AACTTTTCTTTTTTTCTTTTTATAAAAAAG
Found at i:170535 original size:13 final size:13
Alignment explanation
Indices: 170517--170542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
170507 GATACATGGG
170517 ACATTGTATCGAT
1 ACATTGTATCGAT
170530 ACATTGTATCGAT
1 ACATTGTATCGAT
170543 TCATGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:170556 original size:33 final size:33
Alignment explanation
Indices: 170501--170567 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
170491 CTAAGTGAAA
*
170501 TGTATCGATACATGGGACATTGTATCGATACAT
1 TGTATCGATACATGAGACATTGTATCGATACAT
* *
170534 TGTATCGATTCATGAAGA-ATTGTATTGATACAT
1 TGTATCGATACATG-AGACATTGTATCGATACAT
170567 T
1 T
170568 ATGCCCAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATGAGACATTGTATCGATACAT
Found at i:177113 original size:52 final size:51
Alignment explanation
Indices: 177028--177151 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
177018 ATATGAAAAG
* *
177028 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
177079 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
177131 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
177152 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:177164 original size:51 final size:50
Alignment explanation
Indices: 177028--177171 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 50
177018 ATATGAAAAG
* *
177028 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
177080 TTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGCAAAT
177131 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
177172 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.39
52 42 0.50
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:177178 original size:13 final size:13
Alignment explanation
Indices: 177160--177184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177150 CAAAGATCAG
177160 TGTATCGATACAA
1 TGTATCGATACAA
177173 TGTATCGATACA
1 TGTATCGATACA
177185 CTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:177579 original size:13 final size:13
Alignment explanation
Indices: 177561--177585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177551 CATAAAATGT
177561 TGTATCGATACAA
1 TGTATCGATACAA
177574 TGTATCGATACA
1 TGTATCGATACA
177586 TATTTTTTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:177671 original size:13 final size:13
Alignment explanation
Indices: 177653--177677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177643 ATTACTCACA
177653 TGTATCGATACAT
1 TGTATCGATACAT
177666 TGTATCGATACA
1 TGTATCGATACA
177678 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:177814 original size:52 final size:52
Alignment explanation
Indices: 177686--177806 Score: 233
Period size: 52 Copynumber: 2.3 Consensus size: 52
177676 CACTGATCTT
177686 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
177738 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
177790 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
177807 ATAAATTTTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:181346 original size:79 final size:79
Alignment explanation
Indices: 181209--181391 Score: 251
Period size: 79 Copynumber: 2.3 Consensus size: 79
181199 ACAACGGGGC
* * *
181209 TGGAGTATCCCCGATTATGAAAAATCGGTGTTCTGGAAATAAAATCAGGTTTGTAGTATCCCCTC
1 TGGAGTATCCCCGATTATGAAAAATCGGTGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTC
**
181274 GGAAATAACAGGGT
66 AAAAATAACAGGGT
* * *
181288 TGGAGTATCGCTGATTAT-AGAAAATCGGTGTTTTGAAAATAAAATCAGGGTTGGAGTATCCCCT
1 TGGAGTATCCCCGATTATGA-AAAATCGGTGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCT
*
181352 CAAAAATAACGGGGT
65 CAAAAATAACAGGGT
* *
181367 TGGAGTATCCCCGATTGTGGAAAAT
1 TGGAGTATCCCCGATTATGAAAAAT
181392 TGATGCTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
78 1 0.01
79 88 0.99
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATGAAAAATCGGTGTTCTGAAAATAAAATCAGGGTTGGAGTATCCCCTC
AAAAATAACAGGGT
Found at i:181407 original size:79 final size:77
Alignment explanation
Indices: 181201--181429 Score: 242
Period size: 79 Copynumber: 2.9 Consensus size: 77
181191 TGGGGATAAC
* * * * *
181201 AACGGGGCTGGAGTATCCCCGATTATGAAAAATCGGTGTTCTGGAAATAAAATCAGGTTTGTAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTT-T-AAAATAAAATCAGGGTTGGAGT
**
181266 ATCCCCTCGGAAAT
64 ATCCCCTCAAAAAT
* * * *
181280 AACAGGGTTGGAGTATCGCTGATTATAGAAAATCGGTGTTTTGAAAATAAAATCAGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTG-TTT-AAAATAAAATCAGGGTTGGAGT
181345 ATCCCCTCAAAAAT
64 ATCCCCTCAAAAAT
* * * *** *
181359 AACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTATAAATAAGGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTG-TTTA-AAATAAAATCAGGGTTGGAGT
181424 ATCCCC
64 ATCCCC
181430 GATTGTGAGA
Statistics
Matches: 125, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 1 0.01
79 122 0.98
80 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (77 bp):
AACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTAAAATAAAATCAGGGTTGGAGTAT
CCCCTCAAAAAT
Found at i:181458 original size:51 final size:51
Alignment explanation
Indices: 181361--181479 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
181351 TCAAAAATAA
** * * *
181361 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGCTTTATAAATAAGGC
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATACTTTACAAATAAAGC
* *
181412 CGGGGTTGGAGTATCCCCGATTGT-GAGAAATCAATATTTTACAAATAAAGT
1 CGGGGTTGGAGTATCCCCGATTGTGGA-AAATCAATACTTTACAAATAAAGC
*
181463 CAGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
181480 TTCGAAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 2 0.03
51 57 0.97
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATACTTTACAAATAAAGC
Found at i:181539 original size:28 final size:27
Alignment explanation
Indices: 181463--181539 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 27
181453 CAAATAAAGT
181463 CAGGGTTGGAGTATCCCTTCGA-AAATAA
1 CAGGGTTGGAGTATCCC--CGATAAATAA
181491 CAGGGTTGGAGTATCCCCGATGAAATAA
1 CAGGGTTGGAGTATCCCCGAT-AAATAA
*
181519 CGGGGTTGGAGTATCCCCGAT
1 CAGGGTTGGAGTATCCCCGAT
181540 TATGAAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 3 0.07
28 43 0.93
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (27 bp):
CAGGGTTGGAGTATCCCCGATAAATAA
Found at i:181565 original size:158 final size:157
Alignment explanation
Indices: 181333--181665 Score: 375
Period size: 158 Copynumber: 2.1 Consensus size: 157
181323 AAAATAAAAT
* * *
181333 CAGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGC
1 CAGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGACGC
* ** * * *
181398 TTTATAAATAAGGCCGGGGTTGGAGTATCCCCGATTGT-GAGAAATCAATATTTTACAAATAAAG
66 TTTAGAAATAAAACCGGAGTTGAAGTATCCCCGATTATGGAG-AATCAATATTTTACAAATAAA-
* * * *
181462 TCAGGGTTGGAGTATCCCTTC-GAAAATAA
129 CCAGGGTTGAAATATCCCCTCTG-AAATAA
* * *
181491 CAGGGTTGGAGTATCCCC-GATGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGGCG
1 CAGGGTTGGAGTATCCCCTCA-AAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGACG
* * * *** * *
181555 TTTTGGAAATAAAATCGGAGTTGAAGTATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAC
65 CTTTAGAAATAAAACCGGAGTTGAAGTATCCCCGATTATGGAGAATCAATATTTTACAAATAAAC
181620 CAGGGTTGAAATATCCCCTCTGAAATAA
130 CAGGGTTGAAATATCCCCTCTGAAATAA
* *
181648 CGGGGTAGGAGTATCCCC
1 CAGGGTTGGAGTATCCCC
181666 AATTGTGAAA
Statistics
Matches: 146, Mismatches: 26, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
157 40 0.27
158 103 0.71
159 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (157 bp):
CAGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGACGC
TTTAGAAATAAAACCGGAGTTGAAGTATCCCCGATTATGGAGAATCAATATTTTACAAATAAACC
AGGGTTGAAATATCCCCTCTGAAATAA
Found at i:181685 original size:78 final size:78
Alignment explanation
Indices: 181579--181774 Score: 189
Period size: 79 Copynumber: 2.5 Consensus size: 78
181569 TCGGAGTTGA
* * * * * * *
181579 AGTATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAACCAGGGTTGAAATATCCCCTCTG-A
1 AGTATCCCCAATTATGAAAAACTAGTGTTTTGGAAATAAACCAGGATTGAAATATCCCCTC-GAA
* *
181643 AATAACGGGGTAGG
65 AATAACAGGATAGG
* * * * *
181657 AGTATCCCCAATTGTGAAAAACTAGTGTTTTGGGAATAAAATCAGGATTGGAGTATCCCCTCGAA
1 AGTATCCCCAATTATGAAAAACTAGTGTTTTGGAAAT-AAACCAGGATTGAAATATCCCCTCGAA
* *
181722 AATAATAGGATTGG
65 AATAACAGGATAGG
* * *
181736 AGTATCCCCGATTATGAAAAATTAATG-TTTGGAAATAAA
1 AGTATCCCCAATTATGAAAAACTAGTGTTTTGGAAATAAA
181775 ACCGAGGTTG
Statistics
Matches: 95, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
77 3 0.03
78 38 0.40
79 54 0.57
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (78 bp):
AGTATCCCCAATTATGAAAAACTAGTGTTTTGGAAATAAACCAGGATTGAAATATCCCCTCGAAA
ATAACAGGATAGG
Found at i:184782 original size:45 final size:44
Alignment explanation
Indices: 184689--184926 Score: 220
Period size: 45 Copynumber: 5.4 Consensus size: 44
184679 ACGAAATGCA
* **
184689 TCCTGCTCTTTGAGGACAAA-AGAAAAAGA-AAAATAAAGTGCA
1 TCCTGCTCTTTGAGGACAAAGAGAAAAAGAGGAAATAAAGTGTG
* *
184731 TCCTGCTATTTGAGGACAAAGAGAAAAATGAGGAAATGAAGTGTG
1 TCCTGCTCTTTGAGGACAAAGAGAAAAA-GAGGAAATAAAGTGTG
* * * *
184776 TCCTGCTCTATGAGGACAAAAGGGGAAAATA-AGGAAATGGAA-CGTG
1 TCCTGCTCTTTGAGGAC-AAA-GAGAAAA-AGAGGAAAT-AAAGTGTG
*
184822 TCATGCTCTTTGAGGACAAAGGAGAAAAAGA--AAATAAAGTGTG
1 TCCTGCTCTTTGAGGACAAA-GAGAAAAAGAGGAAATAAAGTGTG
* * * *
184865 TCCTACACTTTGAGGACAAA-AGGGAAAAGAAGGAAATAAAGTGCG
1 TCCTGCTCTTTGAGGACAAAGA-GAAAAAG-AGGAAATAAAGTGTG
*
184910 TCCTACTCTTTGAGGAC
1 TCCTGCTCTTTGAGGAC
184927 TAGAAGGTGC
Statistics
Matches: 163, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 27 0.17
43 32 0.20
44 3 0.02
45 62 0.38
46 28 0.17
47 9 0.06
48 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (44 bp):
TCCTGCTCTTTGAGGACAAAGAGAAAAAGAGGAAATAAAGTGTG
Found at i:184879 original size:89 final size:89
Alignment explanation
Indices: 184734--184901 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 89
184724 AAGTGCATCC
* * *
184734 TGCTATTTGAGGACAAAGAGAAAAATGAGGAAATGAAGTGTGTCCTGCTCTATGAGGACAAAAGG
1 TGCTATTTGAGGACAAAGAGAAAAATGA-GAAATAAAGTGTGTCCTACACTATGAGGACAAAA-G
*
184799 GGAAAATAAGGAAATGGAACGTGTCA
64 GGAAAAGAAGGAAATGGAACGTGTCA
* *
184825 TGCTCTTTGAGGACAAAGGAGAAAAA-GA-AAATAAAGTGTGTCCTACACTTTGAGGACAAAAGG
1 TGCTATTTGAGGACAAA-GAGAAAAATGAGAAATAAAGTGTGTCCTACACTATGAGGACAAAAGG
184888 GAAAAGAAGGAAAT
65 GAAAAGAAGGAAAT
184902 AAAGTGCGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
88 15 0.21
89 29 0.41
91 18 0.26
92 8 0.11
ACGTcount: A:0.43, C:0.10, G:0.28, T:0.19
Consensus pattern (89 bp):
TGCTATTTGAGGACAAAGAGAAAAATGAGAAATAAAGTGTGTCCTACACTATGAGGACAAAAGGG
AAAAGAAGGAAATGGAACGTGTCA
Found at i:185050 original size:62 final size:60
Alignment explanation
Indices: 184902--185412 Score: 597
Period size: 62 Copynumber: 8.5 Consensus size: 60
184892 AGAAGGAAAT
* *
184902 AAAGTGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGA
1 AAAG-GCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * *
184964 AAAGGCATCCTGCTCTTTGAGGACTAAAGGGTGCTACCAACTCGTGTGGGCTTTGAAAAGAA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAA-GGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * * *
185026 AAAGGTGTCCTGCTCTTTGAGGACTAAAATGTGCCACCAACTTGTATGGGCTTT-GAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * *
185086 GAAGGCATCCTGCTCTTTGAAGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * * *
185147 AAAGGCATCTTGCTCTTTGAGGACTAAAGGTGCCACTAACTCGTGTGGGCTTT-GAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * * * *
185206 GAAGGCGTCCTACTCTTTGAGGACTGAAGATGCCACCAGCTTGTGTGGGCTTT-----G-
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
185260 AAAGGCGTCCTGTTCTTTGAGGACTGAAATGTGCCACCAACTTGTGTGGGCTTTTAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* * *
185321 AAAGGCGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAATTTGTGTGGGCTTTAAAAGGA
1 AAAGGCGTCCTGCTCTTTGAGGACT--AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
* *
185383 AAAAGCATCCTGCTCTTTGAGGACTAAAGG
1 AAAGGCGTCCTGCTCTTTGAGGACTAAAGG
185413 GTGAAAGGAG
Statistics
Matches: 384, Mismatches: 52, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
54 22 0.06
55 25 0.07
59 50 0.13
60 82 0.21
61 93 0.24
62 109 0.28
63 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (60 bp):
AAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA
Found at i:185494 original size:100 final size:101
Alignment explanation
Indices: 185325--185507 Score: 314
Period size: 100 Copynumber: 1.8 Consensus size: 101
185315 AAAGGAAAAG
* *
185325 GCGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAATTTGTGTGGGCTTTAAAAGGAAAAAGCA
1 GCGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAGCA
185390 TCCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
66 TCCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
* * *
185426 GCGTCCTGCTTTTTGAGGACTA-AAAAGTGCCACCAACTTATGTGGGCTTTAAGAGGAAAAGGCG
1 GCGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAGCA
185490 TCCTGCTCTTTGAGGACT
66 TCCTGCTCTTTGAGGACT
185508 GGAAGGTGCC
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 55 0.71
101 22 0.29
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (101 bp):
GCGTCCTGCTTTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAGCA
TCCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
Found at i:185495 original size:61 final size:61
Alignment explanation
Indices: 185426--185731 Score: 416
Period size: 61 Copynumber: 5.0 Consensus size: 61
185416 AAAGGAGAGA
* * * * *
185426 GCGTCCTGCTTTTTGAGGACTAAAAAGTGCCACCAACTTATGTGGGCTTTAAGAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
185487 GCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
*
185548 TCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
* * * * *
185609 GCGTCCTGCTCTTTGAAGACT-GAAGGTGCCGCCAACTCGTGTGGGTTTTGAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAG
* * * * * *
185670 GCATCTTGCTCTTTGAGGACTAAAAGGGTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAAA
1 GCGTCCTGCTCTTTGAGGACTAGAA-GGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAA
185732 AAAGACGTCC
Statistics
Matches: 221, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
60 25 0.11
61 161 0.73
62 2 0.01
63 33 0.15
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG
Found at i:192004 original size:79 final size:75
Alignment explanation
Indices: 191868--192197 Score: 320
Period size: 79 Copynumber: 4.2 Consensus size: 75
191858 ACAACGGGGC
* * * *
191868 TGGAGTATCCCCGATTATGAAAAATCGGTGTTCTAGAAATAAAATCGAGGTTAGAGTATCTCTTC
1 TGGAGTATCCCCGATTATG-AAAATCGATGTT-TAGAAATAAAATCG-GGTTGGAGTATCCCCTC
191933 GAAAATAACAGGGT
63 GAAAATAAC-GGGT
* *
191947 TGGAGTATCCCTGATTATAGAAAATCGGTAGTTT-GAAAATAAAATCGGGATTGGAGTATCCCCT
1 TGGAGTATCCCCGATTAT-GAAAATCGAT-GTTTAG-AAATAAAATCGGG-TTGGAGTATCCCCT
*
192011 TGAAAATAACGGGGT
62 CGAAAATAAC-GGGT
* * *** * *
192026 TGGAGTATCCCCGATTGTGGAAAATTGATGCTTTAGAAATAAGGCCAAGGTTGGAGTATCCCCGC
1 TGGAGTATCCCCGATTAT-GAAAATCGATG-TTTAGAAATAAAATC-GGGTTGGAGTATCCCCTC
*
192091 AAAAATAACCGGGT
63 GAAAATAA-CGGGT
* * * * * *
192105 TGGAGTATCCCTGATTGTGAGAAATCAATATTTTGAAAATAAAGTCGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGATTATGA-AAATCGATGTTTAG-AAATAAAATC-GGGTTGGAGTATCCCCTC
192170 GAAAATAACGGGT
63 GAAAATAACGGGT
192183 TGGAGTATCCCCGAT
1 TGGAGTATCCCCGAT
192198 GAAATAACGG
Statistics
Matches: 211, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
78 29 0.14
79 174 0.82
80 8 0.04
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (75 bp):
TGGAGTATCCCCGATTATGAAAATCGATGTTTAGAAATAAAATCGGGTTGGAGTATCCCCTCGAA
AATAACGGGT
Found at i:192153 original size:158 final size:158
Alignment explanation
Indices: 191860--192197 Score: 439
Period size: 158 Copynumber: 2.1 Consensus size: 158
191850 TGGGGATAAC
* * * *
191860 AACGGGGCTGGAGTATCCCCGATTATGAAAAATCGGTGTTCTAGAAATAAAATCGAGGTTAGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTCTAGAAATAAAACCAAGGTTAGAGT
* ** * **
191925 ATCTCTTCGAAAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATCGGTAGTTTGAAAATAAA
66 ATCCCCGCAAAAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATCAATAGTTTGAAAATAAA
*
191990 ATCGGGATTGGAGTATCCCCTTGAAAAT
131 ATCGGGATTGGAGTATCCCCTCGAAAAT
* * * ** *
192018 AACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGCTT-TAGAAATAAGGCCAAGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATG-TTCTAGAAATAAAACCAAGGTTAGAG
* * *
192082 TATCCCCGCAAAAATAACCGGGTTGGAGTATCCCTGATTGT-GAGAAATCAATATTTTGAAAATA
65 TATCCCCGCAAAAATAACAGGGTTGGAGTATCCCTGATTATAGA-AAATCAATAGTTTGAAAATA
* *
192146 AAGTCGGGGTTGGAGTATCCCCTCGAAAAT
129 AAATCGGGATTGGAGTATCCCCTCGAAAAT
192176 AAC-GGGTTGGAGTATCCCCGAT
1 AACGGGGTTGGAGTATCCCCGAT
192198 GAAATAACGG
Statistics
Matches: 156, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
157 21 0.13
158 133 0.85
159 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (158 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTCTAGAAATAAAACCAAGGTTAGAGT
ATCCCCGCAAAAATAACAGGGTTGGAGTATCCCTGATTATAGAAAATCAATAGTTTGAAAATAAA
ATCGGGATTGGAGTATCCCCTCGAAAAT
Found at i:192211 original size:28 final size:28
Alignment explanation
Indices: 192150--192216 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 28
192140 AAAATAAAGT
192150 CGGGGTTGGAGTATCCCCTCGAAAATAA
1 CGGGGTTGGAGTATCCCCTCGAAAATAA
192178 C-GGGTTGGAGTAT-CCC-CGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCGA--AAATAA
192205 CGGGGTTGGAGT
1 CGGGGTTGGAGT
192217 TTCCTCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 3 0.08
26 3 0.08
27 19 0.53
28 11 0.31
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAA
Found at i:192264 original size:106 final size:106
Alignment explanation
Indices: 192074--192270 Score: 245
Period size: 106 Copynumber: 1.9 Consensus size: 106
192064 ATAAGGCCAA
* * *
192074 GGTTGGAGTATCCCCGCAAAAATAACCGGGTTGGAGTATCCCTGATTGTGAGAAATCAATATTTT
1 GGTTGGAGTATCCCCGCAAAAATAACCGGGTTGGAGTATCCCTAATTATGAAAAATCAATATTTT
* *
192139 GAAAATAAAGTCGGGGTTGGAGTATCCCCTCGAAAATAACG
66 GAAAATAAAATCGGAGTTGGAGTATCCCCTCGAAAATAACG
* * * *** *
192180 GGTTGGAGTATCCCCG-ATGAAATAACGGGGTTGGAGT-TTCCTCAATTATGAAAAATTGGTGTT
1 GGTTGGAGTATCCCCGCA-AAAATAACCGGGTTGGAGTATCCCT-AATTATGAAAAATCAATATT
*
192243 TTGGAAATAAAATCGGAGTTGGAGTATC
64 TTGAAAATAAAATCGGAGTTGGAGTATC
192271 ACCGATTGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
105 5 0.07
106 71 0.93
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (106 bp):
GGTTGGAGTATCCCCGCAAAAATAACCGGGTTGGAGTATCCCTAATTATGAAAAATCAATATTTT
GAAAATAAAATCGGAGTTGGAGTATCCCCTCGAAAATAACG
Found at i:192345 original size:79 final size:78
Alignment explanation
Indices: 192260--192481 Score: 234
Period size: 79 Copynumber: 2.8 Consensus size: 78
192250 TAAAATCGGA
* *
192260 GTTGGAGTATCACCGATTGTGAAGAATTGGTGTTTTAGAAATAAAACTGGGGTTTGAGTATCCCC
1 GTTGGAGTATC-CCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACTGGGGTTTGAGTATCCCC
* *
192325 TCAGAAATGACGGG
65 TCAGAAATAACGCG
* * * * *
192339 GTTGGAGTATCCCCAATTGTGAAAAACTAGTGTTTTGGGAATAAAA-TCGGGG-TTGAAATATCC
1 GTTGGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACT-GGGGTTTG-AGTATCC
* *
192402 CTTTAGAAATAACGCG
63 CCTCAGAAATAACGCG
* * * * *
192418 ATTGGAGTATCCCTGATTATGAAAAATTGATG-TTTGGAAATAAAACCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCC-GATTGTGAAAAATTGGTGTTTTGGAAATAAAACTGGGGTTTGAGTATCCCC
192482 GAGATGAAGA
Statistics
Matches: 115, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
78 30 0.26
79 84 0.73
80 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (78 bp):
GTTGGAGTATCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAACTGGGGTTTGAGTATCCCCT
CAGAAATAACGCG
Found at i:194595 original size:20 final size:20
Alignment explanation
Indices: 194570--194624 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
194560 AAAATGCTTG
*
194570 AATGTATCGATACATTGCAA-
1 AATGTATCGATACAATG-AAC
194590 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
194610 AATGTATCAATACAA
1 AATGTATCGATACAA
194625 ATTGTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:195317 original size:41 final size:41
Alignment explanation
Indices: 195223--195327 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 41
195213 GGGTGTCTCA
* * *
195223 CTTCTTGAGGACAAAGG-AAAAGAGAATGAAATGGGTCTTG
1 CTTCTTGAGGACAAAGGAAAAAGAAAAGGAAATGGGTCCTG
* * *
195263 CTCCTTGAAGACAAAGGAAGAAAGAAAAGGAAA-GTGTCCTG
1 CTTCTTGAGGACAAAGGAA-AAAGAAAAGGAAATGGGTCCTG
195304 CTTCTTGAGGACAAAGTGAAAAAG
1 CTTCTTGAGGACAAAG-GAAAAAG
195328 TGTACGTCCT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
40 15 0.28
41 25 0.46
42 14 0.26
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (41 bp):
CTTCTTGAGGACAAAGGAAAAAGAAAAGGAAATGGGTCCTG
Found at i:195467 original size:46 final size:44
Alignment explanation
Indices: 195332--195474 Score: 170
Period size: 42 Copynumber: 3.3 Consensus size: 44
195322 AAAAAGTGTA
**
195332 CGTCCTACT-TTTCGAGGAC-AAAGGAAAAAAGGGAAACGAAA-TG
1 CGTCCTACTATTT-GAGGACAAAAGGAAAAAA-GGAAAATAAAGTG
* *
195375 CATCCTACTCTTTGAGGACAAAA-G-AAAAAGGAAAATAAAGTG
1 CGTCCTACTATTTGAGGACAAAAGGAAAAAAGGAAAATAAAGTG
195417 CGTCCTACTATTTGAGGACAAAAGGGAAAAGAAGGAAAATAAAGTG
1 CGTCCTACTATTTGAGGACAAAA-GGAAAA-AAGGAAAATAAAGTG
*
195463 CGTCCTGCTATT
1 CGTCCTACTATT
195475 CGTCCCCATA
Statistics
Matches: 87, Mismatches: 6, Indels: 11
0.84 0.06 0.11
Matches are distributed among these distances:
41 8 0.09
42 28 0.32
43 15 0.17
44 7 0.08
45 3 0.03
46 26 0.30
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (44 bp):
CGTCCTACTATTTGAGGACAAAAGGAAAAAAGGAAAATAAAGTG
Found at i:197805 original size:33 final size:33
Alignment explanation
Indices: 197768--197834 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
197758 TTCAACGATT
197768 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
197801 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
197834 T
1 T
197835 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:197806 original size:13 final size:13
Alignment explanation
Indices: 197788--197812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
197778 CATAAAATGT
197788 TGTATCGATACAA
1 TGTATCGATACAA
197801 TGTATCGATACA
1 TGTATCGATACA
197813 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:197893 original size:13 final size:13
Alignment explanation
Indices: 197875--197899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
197865 ATTACTCAAA
197875 TGTATCGATACAT
1 TGTATCGATACAT
197888 TGTATCGATACA
1 TGTATCGATACA
197900 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:198001 original size:52 final size:52
Alignment explanation
Indices: 197908--198031 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
197898 CACTGATCTT
*
197908 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
197959 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
198011 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
198032 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:202173 original size:10 final size:10
Alignment explanation
Indices: 202158--202184 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
202148 TGCTAACTAA
202158 GTTTTTGTTT
1 GTTTTTGTTT
202168 GTTTTTGTTT
1 GTTTTTGTTT
202178 GTTTTTG
1 GTTTTTG
202185 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:208463 original size:12 final size:12
Alignment explanation
Indices: 208448--208482 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
208438 TAGTGAAGTT
208448 GATTCTGAAGAA
1 GATTCTGAAGAA
208460 GATTCTGAAGAA
1 GATTCTGAAGAA
208472 GATTCTGAAGA
1 GATTCTGAAGA
208483 GAACTTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (12 bp):
GATTCTGAAGAA
Found at i:211871 original size:1 final size:1
Alignment explanation
Indices: 211865--211989 Score: 106
Period size: 1 Copynumber: 125.0 Consensus size: 1
211855 GGCGTCCTCC
* ** * * * *
211865 AAAAAAAAAAAAAAAAAACAAAAAAAAAAAATGAAAAAACAAAAAAAAAACAAAAGAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * * * * *
211930 AAAAACACAAAAAAAAACCAAAAACAAAAACAAAAAAAAAACAAACAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
211990 GGGGGTCCGG
Statistics
Matches: 95, Mismatches: 29, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.87, C:0.10, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Done.