Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 11 of 17
Found at i:1385305 original size:13 final size:13
Alignment explanation
Indices: 1385287--1385311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1385277 TAGCCAAACT
1385287 TGTATCGATACAA
1 TGTATCGATACAA
1385300 TGTATCGATACA
1 TGTATCGATACA
1385312 CCAAAAAATT
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:1389398 original size:15 final size:15
Alignment explanation
Indices: 1389378--1389408 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1389368 TAAAAATGTC
*
1389378 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1389393 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1389408 C
1 C
1389409 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1391501 original size:13 final size:13
Alignment explanation
Indices: 1391483--1391521 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1391473 ACATTTTTCT
1391483 TTGTATCGATACA
1 TTGTATCGATACA
1391496 TTGTATCGATACA
1 TTGTATCGATACA
*
1391509 CTGTATCGATACA
1 TTGTATCGATACA
1391522 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1391685 original size:20 final size:19
Alignment explanation
Indices: 1391644--1391686 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1391634 ATCTTTTGCA
1391644 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1391664 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1391684 AAA
1 AAA
1391687 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1394068 original size:13 final size:13
Alignment explanation
Indices: 1394050--1394074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1394040 TAGCCAAACT
1394050 TGTATCGATACAA
1 TGTATCGATACAA
1394063 TGTATCGATACA
1 TGTATCGATACA
1394075 CCAAAAAATT
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:1398314 original size:21 final size:22
Alignment explanation
Indices: 1398272--1398314 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1398262 GAGTTATGAA
**
1398272 CAAATGTTTTTGAACTTTAAAT
1 CAAATGTTTTTGAACTGGAAAT
*
1398294 CAAATGTTTTT-AAGTGGAAAT
1 CAAATGTTTTTGAACTGGAAAT
1398315 ATTCCAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (22 bp):
CAAATGTTTTTGAACTGGAAAT
Found at i:1398567 original size:20 final size:20
Alignment explanation
Indices: 1398542--1398592 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1398532 CTACTGTTTT
* *
1398542 TATCGATACATGGCATATTG
1 TATCGATACATGACAAATTG
*
1398562 TATCGATACATGATAAATTG
1 TATCGATACATGACAAATTG
*
1398582 TATCAATACAT
1 TATCGATACAT
1398593 TGCTTCAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
TATCGATACATGACAAATTG
Found at i:1400033 original size:18 final size:19
Alignment explanation
Indices: 1400012--1400052 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1400002 AAAAAAATAC
1400012 TTTTTTGTTATT-TTTTTG
1 TTTTTTGTTATTATTTTTG
*
1400030 TTTTTTGTTTTTGATTTTTG
1 TTTTTTGTTATT-ATTTTTG
1400050 TTT
1 TTT
1400053 GCTTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
20 9 0.45
ACGTcount: A:0.05, C:0.00, G:0.12, T:0.83
Consensus pattern (19 bp):
TTTTTTGTTATTATTTTTG
Found at i:1400040 original size:13 final size:13
Alignment explanation
Indices: 1400024--1400076 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1400014 TTTTGTTATT
1400024 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
*
1400037 TTTTTGATTTTTG
1 TTTTTGTTTTTTG
1400050 --TTTGCTTTTTTG
1 TTTTTG-TTTTTTG
1400062 -TTTTGTTTGTTTG
1 TTTTTGTTT-TTTG
1400075 TT
1 TT
1400077 AAGGTCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 4 0.12
12 9 0.26
13 20 0.59
14 1 0.03
ACGTcount: A:0.02, C:0.02, G:0.17, T:0.79
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:1400053 original size:17 final size:16
Alignment explanation
Indices: 1400014--1400073 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
1400004 AAAAATACTT
1400014 TTTTGTTAT-TTTTTTG
1 TTTTGTT-TGTTTTTTG
1400030 -TTT-TTTG-TTTTTG
1 TTTTGTTTGTTTTTTG
1400043 ATTTTTGTTTGCTTTTTTG
1 --TTTTGTTTG-TTTTTTG
1400062 TTTTGTTTGTTT
1 TTTTGTTTGTTT
1400074 GTTAAGGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 7 0.19
14 2 0.05
15 3 0.08
16 6 0.16
17 13 0.35
19 6 0.16
ACGTcount: A:0.03, C:0.02, G:0.15, T:0.80
Consensus pattern (16 bp):
TTTTGTTTGTTTTTTG
Found at i:1400058 original size:25 final size:24
Alignment explanation
Indices: 1400013--1400065 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1400003 AAAAAATACT
*
1400013 TTTTTGTTATTTTTTTGTTTTTTG
1 TTTTTGTTATTTGTTTGTTTTTTG
1400037 TTTTTGATT-TTTGTTTGCTTTTTTG
1 TTTTTG-TTATTTGTTTG-TTTTTTG
1400062 TTTT
1 TTTT
1400066 GTTTGTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.04, C:0.02, G:0.13, T:0.81
Consensus pattern (24 bp):
TTTTTGTTATTTGTTTGTTTTTTG
Found at i:1400741 original size:12 final size:12
Alignment explanation
Indices: 1400724--1400754 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1400714 TATAATAGCT
1400724 TCATCATTATCA
1 TCATCATTATCA
1400736 TCATCATTATCA
1 TCATCATTATCA
*
1400748 TCCTCAT
1 TCATCAT
1400755 CGTTGAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (12 bp):
TCATCATTATCA
Found at i:1402977 original size:12 final size:12
Alignment explanation
Indices: 1402959--1402988 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1402949 ATCATTTATG
1402959 ATTATATAACAT
1 ATTATATAACAT
*
1402971 GTTATATAACAT
1 ATTATATAACAT
1402983 ATTATA
1 ATTATA
1402989 ACATGTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (12 bp):
ATTATATAACAT
Found at i:1403154 original size:90 final size:90
Alignment explanation
Indices: 1403000--1403473 Score: 546
Period size: 90 Copynumber: 5.3 Consensus size: 90
1402990 CATGTTCTAT
* * *
1403000 TAAAATTAATCTTGGAACCCGGAAGATGTGACAAATGCATGGGGTATCAGATTCTTACTGACACG
1 TAAAATTAATCTTGAAACCCGAAAGATGTGACAAATGCAT-GGGTATCAGATTCCTACTGACACG
*
1403065 ATAGAAACTATTTGACTAATGCCTAA
65 ATAGAAAATATTTGACTAATGCCTAA
* * * *
1403091 TAAAATTAATCTTGGAACCCGAAA-ATGTGACAGATGCATGGGGTATCAAATTCTTACTGACACG
1 TAAAATTAATCTTGAAACCCGAAAGATGTGACAAATGCAT-GGGTATCAGATTCCTACTGACACG
*
1403155 ATAGAAAATATTTAACTAATGCCTAA
65 ATAGAAAATATTTGACTAATGCCTAA
* * * * **
1403181 TAAAAATTAAATCAT-AGAACCCGAAAGATATGAC-AATGCATGAGTATCATATTCCTACCAACA
1 T-AAAATT-AATCTTGA-AACCCGAAAGATGTGACAAATGCATGGGTATCAGATTCCTACTGACA
* * *
1403244 CGATAAAAAATTTTTGACTAATACCTAA
63 CGATAGAAAATATTTGACTAATGCCTAA
* *
1403272 TAAAATTAATCTTGAAACCTGAAAGATGTGACAAATGCATGGGTATCAGATTCCTACTAACACGA
1 TAAAATTAATCTTGAAACCCGAAAGATGTGACAAATGCATGGGTATCAGATTCCTACTGACACGA
* *
1403337 CAAAAAATATTTGACTAATGCCTAA
66 TAGAAAATATTTGACTAATGCCTAA
* * * * * * * * *
1403362 T-AAATT--TTTTGAAACCTGAAAGATATGATAGATGCAAAGGATTTTAGATTCCTACTGACACG
1 TAAAATTAATCTTGAAACCCGAAAGATGTGACAAATGC-ATGGGTATCAGATTCCTACTGACACG
* *
1403424 ACAGAAAATATTTGACTAATACCTAA
65 ATAGAAAATATTTGACTAATGCCTAA
*
1403450 TAAAATTAATCTTGAAACCTGAAA
1 TAAAATTAATCTTGAAACCCGAAA
1403474 TCCTACTTAC
Statistics
Matches: 334, Mismatches: 39, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
87 25 0.07
88 46 0.14
89 30 0.09
90 122 0.37
91 85 0.25
92 20 0.06
93 6 0.02
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (90 bp):
TAAAATTAATCTTGAAACCCGAAAGATGTGACAAATGCATGGGTATCAGATTCCTACTGACACGA
TAGAAAATATTTGACTAATGCCTAA
Found at i:1403318 original size:181 final size:179
Alignment explanation
Indices: 1403000--1403473 Score: 564
Period size: 181 Copynumber: 2.6 Consensus size: 179
1402990 CATGTTCTAT
* * * * *
1403000 TAAAATTAATCTTGGAACCCGGAAGATGTGACAAATGCATGGGGTATCAGATTCTTACTGACACG
1 TAAAATTAATCTTAGAACCCGAAAGATATGAC-AATGCAT-GAGTATCAGATTCCTACTGACACG
* * * * *
1403065 ATAGAAACTATTTGACTAATGCCTAATAAAATTAATCTTGGAACCCGAAAATGTGACAGATGCAT
64 ATAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAAATGTGACAAATGCAT
* * * *
1403130 GGGGTATCAAATTCTTACTGACACGATAGAAAATATTTAACTAATGCCTAA
129 GGGGTATCAAATTCCTACTAACACGACAAAAAATATTTAACTAATGCCTAA
* * **
1403181 TAAAAATTAAATCATAGAACCCGAAAGATATGACAATGCATGAGTATCATATTCCTACCAACACG
1 T-AAAATT-AATCTTAGAACCCGAAAGATATGACAATGCATGAGTATCAGATTCCTACTGACACG
* *
1403246 ATAAAAAATTTTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAAGATGTGACAAATGCA
64 ATAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAA-ATGTGACAAATGCA
* *
1403311 T-GGGTATCAGATTCCTACTAACACGACAAAAAATATTTGACTAATGCCTAA
128 TGGGGTATCAAATTCCTACTAACACGACAAAAAATATTTAACTAATGCCTAA
* * * * * *
1403362 T-AAATT--T-TTTGAAACCTGAAAGATATGATAGATGCA-AAGGATTTTAGATTCCTACTGACA
1 TAAAATTAATCTTAG-AACCCGAAAGATATGACA-ATGCATGA-G-TATCAGATTCCTACTGACA
*
1403422 CGACAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAA
62 CGATAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAA
1403474 TCCTACTTAC
Statistics
Matches: 251, Mismatches: 35, Indels: 17
0.83 0.12 0.06
Matches are distributed among these distances:
175 2 0.01
176 18 0.07
177 6 0.02
178 63 0.25
179 5 0.02
181 109 0.43
182 27 0.11
183 21 0.08
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.28
Consensus pattern (179 bp):
TAAAATTAATCTTAGAACCCGAAAGATATGACAATGCATGAGTATCAGATTCCTACTGACACGAT
AGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAAATGTGACAAATGCATGG
GGTATCAAATTCCTACTAACACGACAAAAAATATTTAACTAATGCCTAA
Found at i:1403510 original size:63 final size:63
Alignment explanation
Indices: 1403411--1403536 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
1403401 GATTTTAGAT
* *
1403411 TCCTACTGACACGACAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAA
1 TCCTACTGACACGACAGAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAA
* *
1403474 TCCTACTTACACGATAGAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAA
1 TCCTACTGACACGACAGAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAA
1403537 GATGTGATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (63 bp):
TCCTACTGACACGACAGAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAA
Found at i:1403603 original size:154 final size:147
Alignment explanation
Indices: 1403323--1403623 Score: 361
Period size: 154 Copynumber: 2.0 Consensus size: 147
1403313 GGTATCAGAT
* * * *
1403323 TCCTACTAACACGACAAAAAATATTTGACTAATGCCTAATAAATTTTTTGAAACCTGAAAGATAT
1 TCCTACTAACACGACAAAAAATATTTGACGAATACCTAATAAATTTCTTGAAACCCGAAAGATAT
** * *
1403388 GATAGATGCAAAGGATTTTAGATTCCTACTGACACGACAGAAAATATTTGACTAATACCTAATAA
66 GATAGATGCAAAGGATTCGAGATTCCTACTAACACGACAAAAAATATTTGACTAATACCTAAT-A
1403453 AATTAATCTTGAAACCTGAAA
130 AATT--TCTTGAAA-CTGAAA
* * *
1403474 TCCTACTTACACGATAGAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAAGA
1 TCCTACTAACACGACAAAAAATATTTGACGAATACCTAAT-AAATT--TCTTGAAACCCGAAAGA
* * * * * * *
1403539 TGTGATAGATGCATAGGGTATCGA-ATTCCTTCTAACATGGCAAAAAATATTTGACTAATGCCTA
63 TATGATAGATGCAAAGGAT-TCGAGATTCCTACTAACACGACAAAAAATATTTGACTAATACCTA
1403603 ATAAATTTCTTGAAACTGAAA
127 ATAAATTTCTTGAAACTGAAA
1403624 GATATGACAG
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
150 6 0.05
151 43 0.34
152 5 0.04
153 5 0.04
154 67 0.52
155 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (147 bp):
TCCTACTAACACGACAAAAAATATTTGACGAATACCTAATAAATTTCTTGAAACCCGAAAGATAT
GATAGATGCAAAGGATTCGAGATTCCTACTAACACGACAAAAAATATTTGACTAATACCTAATAA
ATTTCTTGAAACTGAAA
Found at i:1403654 original size:87 final size:88
Alignment explanation
Indices: 1403482--1403767 Score: 297
Period size: 87 Copynumber: 3.2 Consensus size: 88
1403472 AATCCTACTT
* * * * *
1403482 ACACGATAGAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAAGATGTGATAG
1 ACACGACAAAAAATATTTGACTAATGCCTAAT-AAATT--TCTTGAAACCCGAAAGATGTGACAG
* *
1403547 ATGCATAGGGTATC-GAATTCCTTCTA
63 ATGTATGGGGTATCAG-ATTCCTTCTA
* * * *
1403573 ACATGGCAAAAAATATTTGACTAATGCCTAATAAATTTCTTGAAA-CTGAAAGATATGACAGATG
1 ACACGACAAAAAATATTTGACTAATGCCTAATAAATTTCTTGAAACCCGAAAGATGTGACAGATG
* *
1403637 TATGGGGTATCAGATTCCTACTG
66 TATGGGGTATCAGATTCCTTCTA
* * * * * *
1403660 ACACGATAGAAAATATTTGACTAGTGCCTAATAAATTTTTTGAAACCCAAAAGATGTGACAAATG
1 ACACGACAAAAAATATTTGACTAATGCCTAATAAATTTCTTGAAACCCGAAAGATGTGACAGATG
* * *
1403725 TAAGGGATATCAGATTCCTTCTG
66 TATGGGGTATCAGATTCCTTCTA
* * *
1403748 ATACAACAGAAAATATTTGA
1 ACACGACAAAAAATATTTGA
1403768 TGACAATGAG
Statistics
Matches: 164, Mismatches: 29, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
87 72 0.44
88 61 0.37
90 5 0.03
91 26 0.16
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (88 bp):
ACACGACAAAAAATATTTGACTAATGCCTAATAAATTTCTTGAAACCCGAAAGATGTGACAGATG
TATGGGGTATCAGATTCCTTCTA
Found at i:1403664 original size:241 final size:241
Alignment explanation
Indices: 1403241--1403694 Score: 696
Period size: 241 Copynumber: 1.9 Consensus size: 241
1403231 ATTCCTACCA
* * *
1403241 ACACGATAAAAAATTTTTGACTAATACCTAATAAAATTAATCTTGAAACCTGAAAGATGTGACAA
1 ACACGATAAAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAAGATGTGACAA
*
1403306 ATGCATGGGTATCAGATTCCTACTAACACGACAAAAAATATTTGACTAATGCCTAATAAATTTTT
66 ATGCATGGGTATCAGATTCCTACTAACACGACAAAAAATATTTGACTAATGCCTAATAAATTTCT
* * *
1403371 TGAAACCTGAAAGATATGATAGATGCAAAGGATTTTAGATTCCTACTGACACGACAGAAAATATT
131 TGAAACCTGAAAGATATGACAGATGCAAAGGATATCAGATTCCTACTGACACGACAGAAAATATT
1403436 TGACTAATACCTAATAAAATTAATCTTGAAACCTGAAATCCTACTT
196 TGACTAATACCTAATAAAATTAATCTTGAAACCTGAAATCCTACTT
* * *
1403482 ACACGATAGAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAAGATGTGATAG
1 ACACGATAAAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAAGATGTGACAA
* * *
1403547 ATGCATAGGGTATC-GAATTCCTTCTAACATGGCAAAAAATATTTGACTAATGCCTAATAAATTT
66 ATGCAT-GGGTATCAG-ATTCCTACTAACACGACAAAAAATATTTGACTAATGCCTAATAAATTT
* ** * *
1403611 CTTGAAA-CTGAAAGATATGACAGATGTATGGGGTATCAGATTCCTACTGACACGATAGAAAATA
129 CTTGAAACCTGAAAGATATGACAGATGCAAAGGATATCAGATTCCTACTGACACGACAGAAAATA
* *
1403675 TTTGACTAGTGCCTAATAAA
194 TTTGACTAATACCTAATAAA
1403695 TTTTTTGAAA
Statistics
Matches: 191, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
241 133 0.70
242 58 0.30
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (241 bp):
ACACGATAAAAAATATTTGACGAATACCTAATAAAATTAATCTTGAAACCCGAAAGATGTGACAA
ATGCATGGGTATCAGATTCCTACTAACACGACAAAAAATATTTGACTAATGCCTAATAAATTTCT
TGAAACCTGAAAGATATGACAGATGCAAAGGATATCAGATTCCTACTGACACGACAGAAAATATT
TGACTAATACCTAATAAAATTAATCTTGAAACCTGAAATCCTACTT
Found at i:1403759 original size:329 final size:331
Alignment explanation
Indices: 1403145--1403767 Score: 837
Period size: 329 Copynumber: 1.9 Consensus size: 331
1403135 ATCAAATTCT
* *
1403145 TACTGACACGATAGAAAATATTTAACTAATGCCTAATAAAAATTAAATCATAGAACCCGAAAGAT
1 TACTGACACGATAGAAAATATTTAACGAATACCTAATAAAAATTAAATCATAGAACCCGAAAGAT
* *
1403210 ATGACAATGCATGAGTATCATATTCCTACCAACACGATAAAAAATTTTTGACTAATACCTAATAA
66 ATGACAATGCATGAGTATCATATTCCTACCAACACGACAAAAAATATTTGACTAATACCTAATAA
*
1403275 AATTAATCTTGAAACCTGAAAGATGTGACAAATGCATGGGTATCAGATTCCTACTAACACGACAA
131 AATT-ATCTTGAAACCTGAAAGATATGACAAATGCATGGGTATCAGATTCCTACTAACACGACAA
** * * *
1403340 AAAATATTTGACTAATGCCTAATAAATTTTTTGAAACCTGAAAGATATGATAGATGCAAAGGATT
195 AAAATATTTGACTAATGCCTAATAAATTTTTTGAAACCCAAAAGATATGACAAATGCAAAGGATA
* *
1403405 TTAGATTCCTACTGACACGACAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCT
260 TCAGATTCCTACTGACACAACAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCT
1403470 GAAATCC
325 GAAATCC
* * *
1403477 TACTTACACGATAGAAAATATTTGACGAATACCTAAT-AAAATT-AATC-TTGAAACCCGAAAGA
1 TACTGACACGATAGAAAATATTTAACGAATACCTAATAAAAATTAAATCATAG-AACCCGAAAGA
* * * * * * * *
1403539 TGTGATAGATGCATAGGGTATCGA-ATTCCTTCTAACATGGCAAAAAATATTTGACTAATGCCTA
65 TATGACA-ATGCAT-GAGTATC-ATATTCCTACCAACACGACAAAAAATATTTGACTAATACCTA
* * *
1403603 AT-AAATT-TCTTGAAA-CTGAAAGATATGACAGATGTATGGGGTATCAGATTCCTACTGACACG
127 ATAAAATTATCTTGAAACCTGAAAGATATGACAAATGCAT-GGGTATCAGATTCCTACTAACACG
* * * * * *
1403665 ATAGAAAATATTTGACTAGTGCCTAATAAATTTTTTGAAACCCAAAAGATGTGACAAATGTAAGG
191 ACAAAAAATATTTGACTAATGCCTAATAAATTTTTTGAAACCCAAAAGATATGACAAATGCAAAG
* *
1403730 GATATCAGATTCCTTCTGATACAACAGAAAATATTTGA
256 GATATCAGATTCCTACTGACACAACAGAAAATATTTGA
1403768 TGACAATGAG
Statistics
Matches: 252, Mismatches: 34, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
328 19 0.08
329 121 0.48
330 20 0.08
331 17 0.07
332 74 0.29
333 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (331 bp):
TACTGACACGATAGAAAATATTTAACGAATACCTAATAAAAATTAAATCATAGAACCCGAAAGAT
ATGACAATGCATGAGTATCATATTCCTACCAACACGACAAAAAATATTTGACTAATACCTAATAA
AATTATCTTGAAACCTGAAAGATATGACAAATGCATGGGTATCAGATTCCTACTAACACGACAAA
AAATATTTGACTAATGCCTAATAAATTTTTTGAAACCCAAAAGATATGACAAATGCAAAGGATAT
CAGATTCCTACTGACACAACAGAAAATATTTGACTAATACCTAATAAAATTAATCTTGAAACCTG
AAATCC
Found at i:1408294 original size:15 final size:15
Alignment explanation
Indices: 1408274--1408304 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1408264 ATGAAAAGTT
*
1408274 ATGAAAGTGTATAAA
1 ATGAAAGTATATAAA
1408289 ATGAAAGTATATAAA
1 ATGAAAGTATATAAA
1408304 A
1 A
1408305 CTAATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (15 bp):
ATGAAAGTATATAAA
Found at i:1412118 original size:154 final size:155
Alignment explanation
Indices: 1411912--1412312 Score: 481
Period size: 154 Copynumber: 2.6 Consensus size: 155
1411902 CCATAAGGGT
* * * **
1411912 ATTTTTGTAATTTTTTAAAACCAAATCCTAGGTTGTCACTGAGTTTGCTTTTATGCAGAAGATGG
1 ATTTTCGTAATTTTTTAAAACCGAATCCTAGGTTGTCACTGGGTCAGCTTTTATGCAGAAG-TGG
* * * **
1411977 GTATTTAGAATGGGTTCATCCCTTCTAAAATCCTTTTTAAGTCCTTTAGAGGTATTGGGTACTTC
65 GTATTTAGGATAGGTTCATCCCTTCTAAAATCCATTTTAAGTCCTTTAGAGGTAGCGGGTACTTC
* * *
1412042 TATGTC-AAGGTTATC-CCTTAGGGGC
130 TACGTCGAAGGTTAGCTCC-TAGAGGC
* * * *
1412067 ATTTTCGT-ATTTTTTAAAACCGAGTCCTAGGTTGTCACTGGGTCAGTTTTTATGCTGAAGGTTG
1 ATTTTCGTAATTTTTTAAAACCGAATCCTAGGTTGTCACTGGGTCAGCTTTTATGCAGAA-GTGG
* * * *
1412131 GTATTTAGGATAGGTTCATCCCATCTACAATCCATTTTAAGTCCTTTAGGGGTAGCGGGTACTTT
65 GTATTTAGGATAGGTTCATCCCTTCTAAAATCCATTTTAAGTCCTTTAGAGGTAGCGGGTACTTC
1412196 TACGTCGAAGGTTAGCTCCTAGAGGC
130 TACGTCGAAGGTTAGCTCCTAGAGGC
* * * *
1412222 ATCTTCGTAATTTTTTATAA-CGAACTCCTAGGTTGTTACT-GGTCTA-CTTTTATGTAGAATGT
1 ATTTTCGTAATTTTTTAAAACCGAA-TCCTAGGTTGTCACTGGGTC-AGCTTTTATGCAGAA-GT
1412284 GGGTATTTAGGATAGGTTCATCCCTTCTA
63 GGGTATTTAGGATAGGTTCATCCCTTCTA
1412313 TAATTTGTTT
Statistics
Matches: 209, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
154 107 0.51
155 75 0.36
156 27 0.13
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.39
Consensus pattern (155 bp):
ATTTTCGTAATTTTTTAAAACCGAATCCTAGGTTGTCACTGGGTCAGCTTTTATGCAGAAGTGGG
TATTTAGGATAGGTTCATCCCTTCTAAAATCCATTTTAAGTCCTTTAGAGGTAGCGGGTACTTCT
ACGTCGAAGGTTAGCTCCTAGAGGC
Found at i:1412374 original size:155 final size:153
Alignment explanation
Indices: 1411866--1412381 Score: 460
Period size: 154 Copynumber: 3.3 Consensus size: 153
1411856 TAATGTCCAC
* * * * *
1411866 TAGGGTTATCGAGATACTTTCATCTCGAAGGTATA-TCCATA-AGGGTATTTTTGTAATTTTTTA
1 TAGGGTTATCG-GATACTTTTATGTCGAAGGT-TAGCCCATAGA-GGCATTTTCGTAATTTTTTA
* * * * * *
1411929 AAACCAAATCCTAGGTTGTCACTGAGTTTGCTTTTATGCAGAAGATGGGTATTTAGAATGGGTTC
63 AAACGAAATCCTAGGTTGTCACTG-GTCTACTTTTATGTAGAAG-TGGGTATTTAGGATAGGTTC
1411994 ATCCCTTCTAAAATCCTTTTTAAGTCCTT
126 ATCCCTTCTAAAAT-CTTTTTAAGTCCTT
* * * * * *
1412023 TAGAGG-TATTGGGTACTTCTATGTC-AAGGTTATCCCTTAGGGGCATTTTCGT-ATTTTTTAAA
1 TAG-GGTTATCGGATACTTTTATGTCGAAGGTTAGCCCATAGAGGCATTTTCGTAATTTTTTAAA
* * *
1412085 ACCG-AGTCCTAGGTTGTCACTGGGTC-AGTTTTTATGCT-GAAGGTTGGTATTTAGGATAGGTT
65 A-CGAAATCCTAGGTTGTCACT-GGTCTA-CTTTTATG-TAGAA-GTGGGTATTTAGGATAGGTT
* * *
1412147 CATCCCATCTACAATCCATTTTAAGTCCTT
125 CATCCCTTCTAAAAT-CTTTTTAAGTCCTT
* * * * * *
1412177 TAGGGGTAGCGGGTACTTTTACGTCGAAGGTTAGCTCC-TAGAGGCATCTTCGTAATTTTTTATA
1 TAGGGTTATCGGATACTTTTATGTCGAAGGTTAGC-CCATAGAGGCATTTTCGTAATTTTTTAAA
* *
1412241 ACGAACTCCTAGGTTGTTACTGGTCTACTTTTATGTAGAATGTGGGTATTTAGGATAGGTTCATC
65 ACGAAATCCTAGGTTGTCACTGGTCTACTTTTATGTAGAA-GTGGGTATTTAGGATAGGTTCATC
* *
1412306 CCTTCTATAAT-TTGTTTAAGTTCTT
129 CCTTCTAAAATCTT-TTTAAGTCCTT
* * * *
1412331 AAGGGTTACCGAGATACTTTTATGTCGAAGATATA-CCCATAGAGGCTTTTT
1 TAGGGTTATCG-GATACTTTTATGTCGAAGGT-TAGCCCATAGAGGCATTTT
1412382 TTTTAGAACT
Statistics
Matches: 293, Mismatches: 47, Indels: 40
0.77 0.12 0.11
Matches are distributed among these distances:
153 3 0.01
154 123 0.42
155 118 0.40
156 40 0.14
157 7 0.02
158 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (153 bp):
TAGGGTTATCGGATACTTTTATGTCGAAGGTTAGCCCATAGAGGCATTTTCGTAATTTTTTAAAA
CGAAATCCTAGGTTGTCACTGGTCTACTTTTATGTAGAAGTGGGTATTTAGGATAGGTTCATCCC
TTCTAAAATCTTTTTAAGTCCTT
Found at i:1416095 original size:23 final size:22
Alignment explanation
Indices: 1416029--1416110 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
1416019 TAGAAGAATG
* *
1416029 AAAAAGAAAAAGCAAAAAATA-A
1 AAAAAGTAAAAG-AAAAAAAAGA
*
1416051 AAAAA-TACAAAGAAAAGCAAAGA
1 AAAAAGTA-AAAGAAAA-AAAAGA
1416074 AAAAAGTAAAAGAAAATAAAAGA
1 AAAAAGTAAAAGAAAA-AAAAGA
*
1416097 AAAAGAATAAAAGA
1 AAAA-AGTAAAAGA
1416111 TCAAGGAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
21 5 0.10
22 11 0.22
23 23 0.47
24 10 0.20
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.06
Consensus pattern (22 bp):
AAAAAGTAAAAGAAAAAAAAGA
Found at i:1416100 original size:24 final size:23
Alignment explanation
Indices: 1416044--1416110 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
1416034 GAAAAAGCAA
*
1416044 AAAATAAAAAAATACAAAGAAAAG
1 AAAAGAAAAAAATA-AAAGAAAAG
* * *
1416068 CAAAGAAAAAAGTAAAAGAAAAT
1 AAAAGAAAAAAATAAAAGAAAAG
1416091 AAAAGAAAAAGAATAAAAGA
1 AAAAGAAAAA-AATAAAAGA
1416111 TCAAGGAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.78, C:0.03, G:0.12, T:0.07
Consensus pattern (23 bp):
AAAAGAAAAAAATAAAAGAAAAG
Found at i:1416122 original size:15 final size:14
Alignment explanation
Indices: 1416030--1416110 Score: 51
Period size: 14 Copynumber: 5.4 Consensus size: 14
1416020 AGAAGAATGA
1416030 AAAAGAAAAAGCAA-
1 AAAAGAAAAAG-AAT
*
1416044 AAAATAAAAA-AAT
1 AAAAGAAAAAGAAT
1416057 ACAAAGAAAAGCAAAGAA-
1 A-AAAG--AA--AAAGAAT
*
1416075 AAAAGTAAAAGAAAAT
1 AAAAG-AAAA-AGAAT
1416091 AAAAGAAAAAGAAT
1 AAAAGAAAAAGAAT
1416105 AAAAGA
1 AAAAGA
1416111 TCAAGGAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
12 2 0.04
13 1 0.02
14 24 0.45
15 7 0.13
16 9 0.17
17 4 0.08
18 4 0.08
19 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.06
Consensus pattern (14 bp):
AAAAGAAAAAGAAT
Found at i:1418460 original size:53 final size:54
Alignment explanation
Indices: 1418359--1418460 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
1418349 AATGTTGCTA
*
1418359 GTAAATTAGTTGCAACTAATAGGTCATTTTCAAGAGTTAAGCTCAATGATATCG
1 GTAAATTAGTTGCAACTAATAGGTCATTTTCAAGAGTTAACCTCAATGATATCG
* * *
1418413 GTAAA-TAGTTTCAGCTAATTGG-CATTTTTCAAGAGTTAATCCT-AATGA
1 GTAAATTAGTTGCAACTAATAGGTCA-TTTTCAAGAGTTAA-CCTCAATGA
1418461 ATATGTTAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
52 2 0.05
53 33 0.79
54 7 0.17
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (54 bp):
GTAAATTAGTTGCAACTAATAGGTCATTTTCAAGAGTTAACCTCAATGATATCG
Found at i:1419367 original size:24 final size:23
Alignment explanation
Indices: 1419322--1419367 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1419312 GATCCAAATG
* * *
1419322 CCTATTTATTTAGTTTGTTTAGA
1 CCTATTTATTTAATTAGGTTAGA
1419345 CCTATTTTATTTAATTAGGTTAG
1 CCTA-TTTATTTAATTAGGTTAG
1419368 GGTAATTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (23 bp):
CCTATTTATTTAATTAGGTTAGA
Found at i:1421431 original size:19 final size:19
Alignment explanation
Indices: 1421407--1421443 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1421397 CATCTTTTTA
1421407 TCAAAAA-TACCTAAATTTC
1 TCAAAAATTACC-AAATTTC
1421426 TCAAAAATTACCAAATTT
1 TCAAAAATTACCAAATTT
1421444 TCATCAGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (19 bp):
TCAAAAATTACCAAATTTC
Found at i:1421445 original size:20 final size:20
Alignment explanation
Indices: 1421402--1421445 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1421392 TAACCCATCT
*
1421402 TTTTATCAAAAATACCTAAA
1 TTTTCTCAAAAATACCTAAA
1421422 -TTTCTCAAAAATTACC-AAA
1 TTTTCTCAAAAA-TACCTAAA
1421441 TTTTC
1 TTTTC
1421446 ATCAGCCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTCTCAAAAATACCTAAA
Found at i:1424042 original size:2 final size:2
Alignment explanation
Indices: 1424037--1424067 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1424027 TGTGTGTGTG
1424037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1424068 GGTTTGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1424434 original size:20 final size:20
Alignment explanation
Indices: 1424406--1424484 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
1424396 ACTGCCAAGG
* *
1424406 AAATATATCGATACATTACT
1 AAATGTATCAATACATTACT
*
1424426 AAATGTATCAATACA-TGCTT
1 AAATGTATCAATACATTAC-T
* *
1424446 ACAATGGTATCGATACATTTCT
1 A-AAT-GTATCAATACATTACT
* *
1424468 CATTGTATCAATACATT
1 AAATGTATCAATACATT
1424485 CTGGGCTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 2 0.04
20 27 0.57
21 5 0.11
22 11 0.23
23 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (20 bp):
AAATGTATCAATACATTACT
Found at i:1433825 original size:18 final size:19
Alignment explanation
Indices: 1433782--1433822 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1433772 AGTTAAAACC
*
1433782 AAAAGCATAAAAAAATAAA
1 AAAAGAATAAAAAAATAAA
*
1433801 AAAAGAATAAGAAAATAAA
1 AAAAGAATAAAAAAATAAA
1433820 AAA
1 AAA
1433823 GAAGTGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAGAATAAAAAAATAAA
Found at i:1435139 original size:29 final size:30
Alignment explanation
Indices: 1435058--1435154 Score: 124
Period size: 31 Copynumber: 3.2 Consensus size: 30
1435048 AAATCTTTTT
* * *
1435058 CCTTTTTCATAGTCCACGACTCAATGGCATT
1 CCTTTTTCAAAGTCCATGACTCAATGGCA-C
1435089 CCTTTTTCAAAGTCCATGACTCAATGGCAC
1 CCTTTTTCAAAGTCCATGACTCAATGGCAC
* **
1435119 CCCTTTT-AAAGTCCATGACTCCGTGGCAC
1 CCTTTTTCAAAGTCCATGACTCAATGGCAC
1435148 CCTTTTT
1 CCTTTTT
1435155 TTACGCCCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 26 0.44
30 6 0.10
31 27 0.46
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (30 bp):
CCTTTTTCAAAGTCCATGACTCAATGGCAC
Found at i:1435246 original size:33 final size:32
Alignment explanation
Indices: 1435209--1435309 Score: 148
Period size: 32 Copynumber: 3.1 Consensus size: 32
1435199 CAGTGGTACC
*
1435209 TTTTCCTTTTAAGTCCACAACTCCGTGGCACAA
1 TTTTCCTTTTAAGTCCACAACTTCGTGGCAC-A
*
1435242 TTTTCCTTTTAAGTCCACAACTTCGTGGCACT
1 TTTTCCTTTTAAGTCCACAACTTCGTGGCACA
* * *
1435274 TTTTTCTTTAAAGTCCACAACTTCGTGGCACC
1 TTTTCCTTTTAAGTCCACAACTTCGTGGCACA
1435306 TTTT
1 TTTT
1435310 TTTTCCAAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 33 0.52
33 30 0.48
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.40
Consensus pattern (32 bp):
TTTTCCTTTTAAGTCCACAACTTCGTGGCACA
Found at i:1435311 original size:33 final size:33
Alignment explanation
Indices: 1435183--1435310 Score: 145
Period size: 32 Copynumber: 3.9 Consensus size: 33
1435173 GACATCCCTT
* * *
1435183 TTTAAAGTTCACAGC-TCAGTGGTACC-TTTTCC
1 TTTAAAGTCCACAACTTC-GTGGCACCTTTTTCC
* * **
1435215 TTTTAAGTCCACAACTCCGTGGCACAATTTTCC
1 TTTAAAGTCCACAACTTCGTGGCACCTTTTTCC
* *
1435248 TTTTAAGTCCACAACTTCGTGGCA-CTTTTTTC
1 TTTAAAGTCCACAACTTCGTGGCACCTTTTTCC
1435280 TTTAAAGTCCACAACTTCGTGGCACCTTTTT
1 TTTAAAGTCCACAACTTCGTGGCACCTTTTT
1435311 TTTCCAAAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
32 46 0.56
33 36 0.44
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.38
Consensus pattern (33 bp):
TTTAAAGTCCACAACTTCGTGGCACCTTTTTCC
Found at i:1435328 original size:35 final size:32
Alignment explanation
Indices: 1435219--1435328 Score: 87
Period size: 33 Copynumber: 3.3 Consensus size: 32
1435209 TTTTCCTTTT
* * * * **
1435219 AAGTCCACAACTCCGTGGCACAATTTTCCTTTT
1 AAGTACACAACTTCGTGGCAC-TTTTTTCTTCA
* *
1435252 AAGTCCACAACTTCGTGGCACTTTTTTCTTTA
1 AAGTACACAACTTCGTGGCACTTTTTTCTTCA
*
1435284 AAGTCCACAACTTCGTGGCACCTTTTTT-TTCCA
1 AAGTACACAACTTCGTGGCA-CTTTTTTCTT-CA
1435317 AAGCCTACACAA
1 AAG--TACACAA
1435329 GTCGATGGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
32 30 0.45
33 31 0.46
35 6 0.09
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (32 bp):
AAGTACACAACTTCGTGGCACTTTTTTCTTCA
Found at i:1435362 original size:33 final size:33
Alignment explanation
Indices: 1435311--1435407 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
1435301 GCACCTTTTT
*
1435311 TTTCCAAAGCCTACACAAGTCGATGGCAACCCC
1 TTTCTAAAGCCTACACAAGTCGATGGCAACCCC
* * *
1435344 TTTCTAAAACCTACACAAG-CTAGTGGCAACCTC
1 TTTCTAAAGCCTACACAAGTCGA-TGGCAACCCC
*
1435377 -TTCTAAAGCCTACACAAGTCGATGGTAACCC
1 TTTCTAAAGCCTACACAAGTCGATGGCAACCC
1435408 TTCTAAGCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
32 26 0.48
33 28 0.52
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (33 bp):
TTTCTAAAGCCTACACAAGTCGATGGCAACCCC
Found at i:1435544 original size:52 final size:53
Alignment explanation
Indices: 1435461--1436144 Score: 434
Period size: 52 Copynumber: 12.9 Consensus size: 53
1435451 TTGTCAAATC
* * * * *
1435461 TTCTTTCTTTAAGTCCAATGTCATTGACCTTGAATAAGCACATTGGCACCTTT
1 TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
* ** * *
1435514 TTCTTTC-TTAAGTCTAATATCACTGGCCTTGAATCAACATATTGGCACCTAT
1 TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
* * * * *
1435566 GTC-ATCTTTAAGTCCAATGTCGTT-G----GAATCAGCACATTGGCACATTT
1 TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
* * * * *
1435613 GTC-ATCTTTAAG-CCTAATATCGCTAGCCTTAAATCAGCATATTGGCACCTTTCT
1 TTCTTTCTTTAAGTCC-AATATCGTTGGCCTTGAATCAGCATATTGGCACC-TT-T
* * * * *
1435667 CATTCTTCTCATCTTTAAATCCAATGTTGTTGGCCATGAATCAGCATATTAGCACCTTT
1 --TTC-T-T--TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
* ** * * *
1435726 CTCCTTTC-TTAAGTCCAATATCAAT-ACCTCGAATTAGCATATTGGCACCTTT
1 -TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
* * * * * * *
1435778 GTC-ATCTTTAAGTCCCATGTCATTGGCCTTGAATCAGCACATTAGCA-CTTT
1 TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
** * * * *
1435829 TGT-AATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCATTTTTCTCATTC
1 T-TCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCA-----C-C-TTT
* * * * * *
1435889 TTGTTATCTTTAAGTCCAATGTCGTTGGCCGTAAATCAGCACATTGGCACTTTT
1 TTCTT-TCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
* * *
1435943 TTCCTTTC-TTAAGTCCGATATCGTTGGCCGTGAATCAGCACATTGGCACCTTTT
1 TT-CTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACC-TTT
* * **
1435997 TTCTTTC-TTAAGTCCAATATCGTTGGTCTTGAATAAGCATATTGGCGTCTTT
1 TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
* * * * * * * *
1436049 CTC-ATCTTCAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGCTCATTT
1 TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
** *
1436101 TTCTTTC-TTAAGTCCAATATCACT-GCCTTAAATCAGCATATTGG
1 TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGG
1436145 TGTCTTTGTC
Statistics
Matches: 487, Mismatches: 109, Indels: 72
0.73 0.16 0.11
Matches are distributed among these distances:
46 2 0.00
47 37 0.08
48 1 0.00
50 2 0.00
51 41 0.08
52 200 0.41
53 101 0.21
54 14 0.03
55 2 0.00
56 4 0.01
57 1 0.00
58 2 0.00
59 3 0.01
60 5 0.01
61 70 0.14
62 2 0.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (53 bp):
TTCTTTCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTT
Found at i:1435774 original size:113 final size:112
Alignment explanation
Indices: 1435466--1435990 Score: 382
Period size: 113 Copynumber: 4.9 Consensus size: 112
1435456 AAATCTTCTT
* * * * * *
1435466 TCTTTAAGTCCAATGTCATTGACCTTGAATAAGCACATTGGCACCTTTT-T-CTTTCTTAAGTCT
1 TCTTTAAGTCCAATGTCGTTGGCCATGAATCAGCACATTAGCA-CTTTTCTCCTTTCTTAAGTCC
* * * * *
1435529 AATATCACTGGCCTTGAATCAACATATTGGCA---C-C--T-ATGTCA
65 AATATCAATAGCCTCGAATCAGCATATTGGCATTTCTCATTCTTGTCA
* * * * *
1435570 TCTTTAAGTCCAATGTCGTT-G----GAATCAGCACATTGGCACATTTGTCATCT-TTAAG-CCT
1 TCTTTAAGTCCAATGTCGTTGGCCATGAATCAGCACATTAGCACTTTTCTCCTTTCTTAAGTCC-
** ** *
1435628 AATATCGCTAGCCTTAAATCAGCATATTGGCACCTTTCTCATTCTTCTCA
65 AATATCAATAGCCTCGAATCAGCATATTGGCA--TTTCTCATTCTTGTCA
* * * *
1435678 TCTTTAAATCCAATGTTGTTGGCCATGAATCAGCATATTAGCACCTTTCTCCTTTCTTAAGTCCA
1 TCTTTAAGTCCAATGTCGTTGGCCATGAATCAGCACATTAGCACTTTTCTCCTTTCTTAAGTCCA
*
1435743 ATATCAATA-CCTCGAATTAGCATATTGGCA---C-C--T-TTGTCA
66 ATATCAATAGCCTCGAATCAGCATATTGGCATTTCTCATTCTTGTCA
* * * * ** * *
1435782 TCTTTAAGTCCCATGTCATTGGCCTTGAATCAGCACATTAGCACTTTTGTAATCT-TTAAGCCCA
1 TCTTTAAGTCCAATGTCGTTGGCCATGAATCAGCACATTAGCACTTTTCTCCTTTCTTAAGTCCA
** * *
1435846 ATATCGCTAGCCTTGAATCAGCATATTGGCATTTTTCTCATTCTTGTTA
66 ATATCAATAGCCTCGAATCAGCATATTGGCA--TTTCTCATTCTTGTCA
* * * * *
1435895 TCTTTAAGTCCAATGTCGTTGGCCGTAAATCAGCACATTGGCACTTTTTTCCTTTCTTAAGTCCG
1 TCTTTAAGTCCAATGTCGTTGGCCATGAATCAGCACATTAGCACTTTTCTCCTTTCTTAAGTCCA
** * *
1435960 ATATCGTTGGCCGT-GAATCAGCACATTGGCA
66 ATATCAATAGCC-TCGAATCAGCATATTGGCA
1435991 CCTTTTTTCT
Statistics
Matches: 332, Mismatches: 58, Indels: 52
0.75 0.13 0.12
Matches are distributed among these distances:
98 5 0.02
99 50 0.15
100 2 0.01
103 15 0.05
104 88 0.27
105 2 0.01
107 2 0.01
108 23 0.07
109 2 0.01
110 1 0.00
112 1 0.00
113 92 0.28
114 46 0.14
115 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (112 bp):
TCTTTAAGTCCAATGTCGTTGGCCATGAATCAGCACATTAGCACTTTTCTCCTTTCTTAAGTCCA
ATATCAATAGCCTCGAATCAGCATATTGGCATTTCTCATTCTTGTCA
Found at i:1435873 original size:217 final size:212
Alignment explanation
Indices: 1435428--1435964 Score: 650
Period size: 217 Copynumber: 2.5 Consensus size: 212
1435418 AATGTCATTG
* * * * * * *
1435428 GCCTTAAATCAACACATTGGCA-CTTGTC-AAATCTTCT-TTCTTTAAGTCCAATGTCATTGACC
1 GCCTTAAATCAGCATATTGGCACCTT-TCTCATTCTTCTCATCTTTAAGTCCAATGTCGTTGGCC
* * * * * * *
1435490 TTGAATAAGCACATTGGCACCTTTTTCTTTCTTAAGTCTAATATCACTGGCCTTGAATCAACATA
65 ATGAATCAGCACATTGGCACCTTTTCCTTTCTTAAGTCCAATATCAATGACCTCGAATCAACATA
* * *
1435555 TTGGCACCTATGTCATCTTTAAGTCCAATGTCGTTGGAATCAGCACATTGGCACATTTGTCATCT
130 TTGGCACCTATGTCATCTTTAAGTCCAATGTCATTGGAATCAGCACATTAGCACATTTGTAATCT
*
1435620 TTAAGCCTAATATCGCTA
195 TTAAGCCCAATATCGCTA
* *
1435638 GCCTTAAATCAGCATATTGGCACCTTTCTCATTCTTCTCATCTTTAAATCCAATGTTGTTGGCCA
1 GCCTTAAATCAGCATATTGGCACCTTTCTCATTCTTCTCATCTTTAAGTCCAATGTCGTTGGCCA
* * * *
1435703 TGAATCAGCATATTAGCACCTTTCTCCTTTCTTAAGTCCAATATCAAT-ACCTCGAATTAGCATA
66 TGAATCAGCACATTGGCACCTTT-TCCTTTCTTAAGTCCAATATCAATGACCTCGAATCAACATA
* * *
1435767 TTGGCACCTTTGTCATCTTTAAGTCCCATGTCATTGGCCTTGAATCAGCACATTAGCACTTTTGT
130 TTGGCACCTATGTCATCTTTAAGTCCAATGTCATT-G----GAATCAGCACATTAGCACATTTGT
1435832 AATCTTTAAGCCCAATATCGCTA
190 AATCTTTAAGCCCAATATCGCTA
* ** * * *
1435855 GCCTTGAATCAGCATATTGGCATTTTTCTCATTCTTGTTATCTTTAAGTCCAATGTCGTTGGCCG
1 GCCTTAAATCAGCATATTGGCACCTTTCTCATTCTTCTCATCTTTAAGTCCAATGTCGTTGGCCA
* * *
1435920 TAAATCAGCACATTGGCACTTTTTTCCTTTCTTAAGTCCGATATC
66 TGAATCAGCACATTGGCAC-CTTTTCCTTTCTTAAGTCCAATATC
1435965 GTTGGCCGTG
Statistics
Matches: 277, Mismatches: 40, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
210 22 0.08
211 10 0.04
212 84 0.30
213 22 0.08
217 136 0.49
218 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (212 bp):
GCCTTAAATCAGCATATTGGCACCTTTCTCATTCTTCTCATCTTTAAGTCCAATGTCGTTGGCCA
TGAATCAGCACATTGGCACCTTTTCCTTTCTTAAGTCCAATATCAATGACCTCGAATCAACATAT
TGGCACCTATGTCATCTTTAAGTCCAATGTCATTGGAATCAGCACATTAGCACATTTGTAATCTT
TAAGCCCAATATCGCTA
Found at i:1435928 original size:61 final size:62
Alignment explanation
Indices: 1435828--1435943 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 62
1435818 ATTAGCACTT
* * *
1435828 TTGTAATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA-TTTTTCTCATTC
1 TTGTAATCTTTAAGCCCAATATCGCTAGCCGTAAATCAGCACATTGGCACTTTTTCTCATTC
* * * * *
1435889 TTGTTATCTTTAAGTCCAATGTCGTTGGCCGTAAATCAGCACATTGGCACTTTTT
1 TTGTAATCTTTAAGCCCAATATCGCTAGCCGTAAATCAGCACATTGGCACTTTTT
1435944 TCCTTTCTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
61 41 0.89
62 5 0.11
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.40
Consensus pattern (62 bp):
TTGTAATCTTTAAGCCCAATATCGCTAGCCGTAAATCAGCACATTGGCACTTTTTCTCATTC
Found at i:1435979 original size:53 final size:52
Alignment explanation
Indices: 1435898--1436121 Score: 263
Period size: 53 Copynumber: 4.3 Consensus size: 52
1435888 CTTGTTATCT
* *
1435898 TTAAGTCCAATGTCGTTGGCCGTAAATCAGCACATTGGCACTTTTTTCCTTTC
1 TTAAGTCCAATATCGTTGGCCGTGAATCAGCACATTGGCACTTTTTT-CTTTC
*
1435951 TTAAGTCCGATATCGTTGGCCGTGAATCAGCACATTGGCACCTTTTTTCTTTC
1 TTAAGTCCAATATCGTTGGCCGTGAATCAGCACATTGGCA-CTTTTTTCTTTC
* * * * * * *
1436004 TTAAGTCCAATATCGTTGGTCTTGAATAAGCATATTGG--CGTCTTTCTCATC
1 TTAAGTCCAATATCGTTGGCCGTGAATCAGCACATTGGCACTTTTTTCT-TTC
* * * * *
1436055 TTCAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGCTCATTTTTCTTTC
1 TT-AAGTCCAATATCGTTGGCCGTGAATCAGCACATTGGCACTTTTTTCTTTC
1436108 TTAAGTCCAATATC
1 TTAAGTCCAATATC
1436122 ACTGCCTTAA
Statistics
Matches: 146, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
50 7 0.05
51 4 0.03
52 42 0.29
53 79 0.54
54 14 0.10
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (52 bp):
TTAAGTCCAATATCGTTGGCCGTGAATCAGCACATTGGCACTTTTTTCTTTC
Found at i:1436163 original size:51 final size:51
Alignment explanation
Indices: 1435894--1436186 Score: 187
Period size: 53 Copynumber: 5.6 Consensus size: 51
1435884 CATTCTTGTT
* * * * ** *
1435894 ATCTTTAAGTCCAATGTCGTTGGCCGTAAATCAGCACATTGGCACTTTTTTC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGGTC-TTTCTC
* * * * * ** *
1435946 CTTTCTTAAGTCCGATATCGTTGGCCGTGAATCAGCACATTGGCACCTTTTTTC
1 ATCT-TTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGG-GTC-TTTCTC
* * *
1436000 -TTTCTTAAGTCCAATATCGTTGGTCTTGAATAAGCATATTGGCGTCTTTCTC
1 ATCT-TTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGG-GTCTTTCTC
* * * * * *
1436052 ATCTTCAAGTCCAATGTCGTTGGCCTTGAATCAACACATTGGCTCATTTTTC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGGTC-TTTCTC
* ** * *
1436104 -TTTCTTAAGTCCAATATCACT-GCCTTAAATCAGCATATTGGTGTCTTTGTC
1 ATCT-TTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGG-GTCTTTCTC
** * *
1436155 ATCTTTAAGTTAAATCTCGTTTGCCTTGAATC
1 ATCTTTAAGTCCAATATCGTTGGCCTTGAATC
1436187 TTTGGCACCT
Statistics
Matches: 192, Mismatches: 41, Indels: 16
0.77 0.16 0.06
Matches are distributed among these distances:
51 38 0.20
52 70 0.36
53 76 0.40
54 8 0.04
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (51 bp):
ATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGGTCTTTCTC
Found at i:1436181 original size:103 final size:105
Alignment explanation
Indices: 1435963--1436186 Score: 290
Period size: 103 Copynumber: 2.2 Consensus size: 105
1435953 AAGTCCGATA
* * * ** * *
1435963 TCGTTGGCCGTGAATCAGCACATTGGCACCTTTTTTCTTTCTTAAGTCCAATATCGTTGGTCTTG
1 TCGTTGGCCTTGAATCAACACATTGGCACCATTTTTCTTTCTTAAGTCCAATATCACTGGCCTTA
* *
1436028 AATAAGCATATTGGCGTCTTTCTCATCTTCAAGTCCAATG
66 AATAAGCATATTGGCGTCTTTCTCATCTTCAAGTCAAATC
*
1436068 TCGTTGGCCTTGAATCAACACATTGGC-TCATTTTTCTTTCTTAAGTCCAATATCACT-GCCTTA
1 TCGTTGGCCTTGAATCAACACATTGGCACCATTTTTCTTTCTTAAGTCCAATATCACTGGCCTTA
* * * * *
1436131 AATCAGCATATTGGTGTCTTTGTCATCTTTAAGTTAAATC
66 AATAAGCATATTGGCGTCTTTCTCATCTTCAAGTCAAATC
*
1436171 TCGTTTGCCTTGAATC
1 TCGTTGGCCTTGAATC
1436187 TTTGGCACCT
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
103 52 0.50
104 26 0.25
105 25 0.24
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (105 bp):
TCGTTGGCCTTGAATCAACACATTGGCACCATTTTTCTTTCTTAAGTCCAATATCACTGGCCTTA
AATAAGCATATTGGCGTCTTTCTCATCTTCAAGTCAAATC
Found at i:1440490 original size:94 final size:96
Alignment explanation
Indices: 1440277--1440506 Score: 236
Period size: 94 Copynumber: 2.4 Consensus size: 96
1440267 CTTCATTGGG
* ** *
1440277 GATACTCCAACCCCATTATTCTGAGGGGATACTCCAACCTTGTTTTTAGAAATTATCAAGATTTA
1 GATACTCCAACCCCATTTTTC-GAGGGGATACTCCAACCTTACTTTTAGAAATTATCAAGATATA
***
1440342 AACATTATTTTGCTTAAATTATCATCATTGGA
65 AACATTATTTTGCTTAAATTATCATCATCAAA
* *
1440374 GATACTCCAACCCCATTATTTCGAGGGGATACTCCAACC-TACTTTTA-AACTTGTCAA-A-ATA
1 GATACTCCAACCCCATT-TTTCGAGGGGATACTCCAACCTTACTTTTAGAAATTATCAAGATATA
* * **
1440435 ATTC-TTATTTTTGCTTAAATTGTCATTGTCAAA
65 A-ACATTA-TTTTGCTTAAATTATCATCATCAAA
** *
1440468 GATACTCCAACCCCATTCTTTCGAATGGATACTCAAACC
1 GATACTCCAACCCCATT-TTTCGAGGGGATACTCCAACC
1440507 CCATTTTTTA
Statistics
Matches: 113, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
93 6 0.05
94 56 0.50
95 8 0.07
96 6 0.05
97 34 0.30
98 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Consensus pattern (96 bp):
GATACTCCAACCCCATTTTTCGAGGGGATACTCCAACCTTACTTTTAGAAATTATCAAGATATAA
ACATTATTTTGCTTAAATTATCATCATCAAA
Found at i:1443463 original size:23 final size:24
Alignment explanation
Indices: 1443419--1443463 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1443409 ATTTATATAA
* *
1443419 ATATATAATACCTTAAACTTAATT
1 ATATATAATACATAAAACTTAATT
*
1443443 ATATA-AATACATAAAAGTTAA
1 ATATATAATACATAAAACTTAA
1443464 ACCTTTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATATAATACATAAAACTTAATT
Found at i:1444366 original size:13 final size:14
Alignment explanation
Indices: 1444338--1444365 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1444328 AAAATTAATT
1444338 ATTTTTATTTTAAA
1 ATTTTTATTTTAAA
1444352 ATTTTTATTTTAAA
1 ATTTTTATTTTAAA
1444366 TAATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTTATTTTAAA
Found at i:1446680 original size:26 final size:26
Alignment explanation
Indices: 1446651--1446703 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1446641 TTTTTATGGG
*
1446651 TGTTTTGTTGTTCATACTTTTTAGCT
1 TGTTTTGTTGTTCAGACTTTTTAGCT
1446677 TGTTTTGTTGTTCAGACTTTTTAGCT
1 TGTTTTGTTGTTCAGACTTTTTAGCT
1446703 T
1 T
1446704 ATGGTGGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.60
Consensus pattern (26 bp):
TGTTTTGTTGTTCAGACTTTTTAGCT
Found at i:1449705 original size:35 final size:35
Alignment explanation
Indices: 1449648--1449716 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
1449638 AAGGAATTAC
* *
1449648 AATTTACATCGTGACTCAAGGTTTAATGGCTTTAT
1 AATTTACATCATGACTCAAGGTTTAATAGCTTTAT
* *
1449683 AATTTACATCATGAGTCTAGGTTTAATAGCTTTA
1 AATTTACATCATGACTCAAGGTTTAATAGCTTTA
1449717 CTTTGCTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (35 bp):
AATTTACATCATGACTCAAGGTTTAATAGCTTTAT
Found at i:1462164 original size:10 final size:11
Alignment explanation
Indices: 1462151--1462179 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1462141 TAGATTTTTG
1462151 TTTATTTTA-T
1 TTTATTTTATT
1462161 TTTATTTTATT
1 TTTATTTTATT
1462172 TTTATTTT
1 TTTATTTT
1462180 CGTAAGGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:1466334 original size:33 final size:33
Alignment explanation
Indices: 1466280--1466342 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1466270 AAAAGTTTTG
1466280 AAAATAACATTCATCCTCAATACTA-TTAAATTA
1 AAAATAACATTCATCCTCAATA-TAGTTAAATTA
*
1466313 AAAATAATATTCAT-CTCCAATATAGTTAAA
1 AAAATAACATTCATCCT-CAATATAGTTAAA
1466343 ATCAAGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (33 bp):
AAAATAACATTCATCCTCAATATAGTTAAATTA
Found at i:1467370 original size:36 final size:37
Alignment explanation
Indices: 1467320--1467393 Score: 114
Period size: 36 Copynumber: 2.0 Consensus size: 37
1467310 GAGTGATAAA
* * *
1467320 ATCATTTTTCTTATATTTAG-TTTTTTACAGTAAATT
1 ATCATATTTATTATATTTAGTTTTTTTACAATAAATT
1467356 ATCATATTTATTATATTTAGTTTTTTTACAATAAATT
1 ATCATATTTATTATATTTAGTTTTTTTACAATAAATT
1467393 A
1 A
1467394 AGTTTAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 18 0.53
37 16 0.47
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (37 bp):
ATCATATTTATTATATTTAGTTTTTTTACAATAAATT
Found at i:1471326 original size:63 final size:63
Alignment explanation
Indices: 1471227--1471350 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
1471217 TCATTCAAGT
1471227 AGAAAACATGATAGCAAATTTATTTTATGTGATATTATAAAAGCTATGCATGCTAACAAAGGC
1 AGAAAACATGATAGCAAATTTATTTTATGTGATATTATAAAAGCTATGCATGCTAACAAAGGC
* *
1471290 AGAAAACATGATAGTAGATTTATTTTATGTGATATTATAAAAGCTATGCATGCTAACAAAG
1 AGAAAACATGATAGCAAATTTATTTTATGTGATATTATAAAAGCTATGCATGCTAACAAAG
1471351 ATAAGACCTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (63 bp):
AGAAAACATGATAGCAAATTTATTTTATGTGATATTATAAAAGCTATGCATGCTAACAAAGGC
Found at i:1480829 original size:18 final size:18
Alignment explanation
Indices: 1480796--1480830 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1480786 TATGGGGTTA
* *
1480796 TTTTAATTTTTTATAAAT
1 TTTTAATTTATAATAAAT
1480814 TTTTAATTTATAATAAA
1 TTTTAATTTATAATAAA
1480831 AATTAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATTTATAATAAAT
Found at i:1481702 original size:20 final size:21
Alignment explanation
Indices: 1481679--1481717 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1481669 ATACATCAAT
1481679 TAAAAATAAAA-TAAAAAATC
1 TAAAAATAAAACTAAAAAATC
*
1481699 TAAAACTAAAACTAAAAAA
1 TAAAAATAAAACTAAAAAA
1481718 AAAAAAGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (21 bp):
TAAAAATAAAACTAAAAAATC
Found at i:1481969 original size:16 final size:18
Alignment explanation
Indices: 1481948--1481980 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1481938 AATAATAAAT
1481948 CTAAAA-TAAA-AAAAAA
1 CTAAAACTAAAGAAAAAA
1481964 CTAAAACTAAAGAAAAA
1 CTAAAACTAAAGAAAAA
1481981 GCTCAACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (18 bp):
CTAAAACTAAAGAAAAAA
Found at i:1483618 original size:61 final size:61
Alignment explanation
Indices: 1483544--1483668 Score: 223
Period size: 61 Copynumber: 2.0 Consensus size: 61
1483534 GACTTGAGCT
*
1483544 ATATATGAACTTTTCTTCTTTTTGCAGCAAATCTTTTAAATATTTTTGAAGTTTTTCTTCC
1 ATATATGAACTTTTCTTCTTTTTGCAACAAATCTTTTAAATATTTTTGAAGTTTTTCTTCC
* *
1483605 ATATATGATCTTTTCTTCTTTTTGCAACAGATCTTTTAAATATTTTTGAAGTTTTTCTTCC
1 ATATATGAACTTTTCTTCTTTTTGCAACAAATCTTTTAAATATTTTTGAAGTTTTTCTTCC
1483666 ATA
1 ATA
1483669 ACTCTTGCTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (61 bp):
ATATATGAACTTTTCTTCTTTTTGCAACAAATCTTTTAAATATTTTTGAAGTTTTTCTTCC
Found at i:1484303 original size:20 final size:21
Alignment explanation
Indices: 1484278--1484328 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1484268 CTACAATTGA
*
1484278 TATCGATACATAAGT-AAATG
1 TATCGATACATAACTAAAATG
**
1484298 TATCGATACATGCCTAAAATG
1 TATCGATACATAACTAAAATG
1484319 TATCGATACA
1 TATCGATACA
1484329 AAGCCACCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (21 bp):
TATCGATACATAACTAAAATG
Found at i:1487614 original size:52 final size:52
Alignment explanation
Indices: 1487536--1487664 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1487526 CGAAATATGA
* *
1487536 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAATGTATCGATACATCTGGGC
**
1487588 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAATGTATCGATACATCTGGGC
1487640 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1487665 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTAAATAATGTATCGATACATCTGGGC
Found at i:1487677 original size:52 final size:51
Alignment explanation
Indices: 1487536--1487684 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
1487526 CGAAATATGA
*
1487536 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TAAATAGTGTATCGATACATCTGGGC
** *
1487588 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TAAATAGTGTATCGATACATCTGGGC
1487640 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATAA-AT-AGTGTATCGATACA
1487685 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATAAATAGTGTATCGATACATCTGGGC
Found at i:1487691 original size:13 final size:13
Alignment explanation
Indices: 1487673--1487697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1487663 CAAAGATCAG
1487673 TGTATCGATACAA
1 TGTATCGATACAA
1487686 TGTATCGATACA
1 TGTATCGATACA
1487698 TTTAAGTGAT
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:1487778 original size:33 final size:33
Alignment explanation
Indices: 1487741--1487804 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1487731 AGCTTGAATT
1487741 GTATCGATACAAAAAAATATGTATCGATACATG
1 GTATCGATACAAAAAAATATGTATCGATACATG
* ***
1487774 GTATCGATACAACACTTTATGTATCGATACA
1 GTATCGATACAAAAAAATATGTATCGATACA
1487805 AATCGTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (33 bp):
GTATCGATACAAAAAAATATGTATCGATACATG
Found at i:1494086 original size:155 final size:155
Alignment explanation
Indices: 1493797--1494178 Score: 378
Period size: 155 Copynumber: 2.5 Consensus size: 155
1493787 TCAATTCAAG
* * * * * * * * *
1493797 AAAAATTACGAAAGTACCCCTAGGAGATACTTTTGACTTAAAAGTA-TCTAATGCCTCTAAAGAA
1 AAAAATTACGAAAATGCCCCTAGGAGATACTTTCGACGTAAAAGTACCCGATTCCCT-TAAAGGA
* * * *
1493861 CTTAAAAAGGATTTTAAAAAGGGTAAACATATCCTAAATATCTACCTTCAACGTAAAAATGGACT
65 CTTAAAAAAGATCTTAAAAAGGATAAACATATCCTAAATATCTACCTTCAACATAAAAATGGACT
* * * *
1493926 TGGTGACAACCTAATAGTTGGTTATA
130 CGGTGACAACCTAAGAATTAGTTATA
*
1493952 AAAAACTACGAAAATGCCCCTAGGAGATACTTTCGACGTAAAAGTACCCGATTCCCTTAAAGGAC
1 AAAAATTACGAAAATGCCCCTAGGAGATACTTTCGACGTAAAAGTACCCGATTCCCTTAAAGGAC
* * **
1494017 TTAAAAAAGATCTTAAAAAGGATGAATC-TATCCTAAATATTTACCTTCGGCATAAAAGCA-GG-
66 TTAAAAAAGATCTTAAAAAGGAT-AAACATATCCTAAATATCTACCTTCAACATAAAA--ATGGA
** * *
1494079 CTCGGTGATGACCTAGGAATTAGTTCTA
128 CTCGGTGACAACCTAAGAATTAGTTATA
** * * * * *
1494107 AAAAATTACGAAAATGCTTCTAAGG-GATACCTTCAACGTAAAAGTACCCGATACCCCTAAGGGA
1 AAAAATTACGAAAATGCCCCT-AGGAGATACTTTCGACGTAAAAGTACCCGATTCCCTTAAAGGA
*
1494171 TTTAAAAA
65 CTTAAAAA
1494179 TGTAAAGGAA
Statistics
Matches: 187, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
155 172 0.92
156 14 0.07
157 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (155 bp):
AAAAATTACGAAAATGCCCCTAGGAGATACTTTCGACGTAAAAGTACCCGATTCCCTTAAAGGAC
TTAAAAAAGATCTTAAAAAGGATAAACATATCCTAAATATCTACCTTCAACATAAAAATGGACTC
GGTGACAACCTAAGAATTAGTTATA
Found at i:1494580 original size:16 final size:16
Alignment explanation
Indices: 1494554--1494598 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
1494544 TTAATAAGAA
1494554 TATTT-ATTCATTTTT
1 TATTTAATTCATTTTT
1494569 TATTTAATTCATTTTT
1 TATTTAATTCATTTTT
*
1494585 TATTTAATTTATTT
1 TATTTAATTCATTT
1494599 AATTTTGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTAATTCATTTTT
Found at i:1494595 original size:9 final size:9
Alignment explanation
Indices: 1494567--1494603 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1494557 TTATTCATTT
1494567 TTTATTTAA
1 TTTATTTAA
*
1494576 TTCATTT--
1 TTTATTTAA
1494583 TTTATTTAA
1 TTTATTTAA
1494592 TTTATTTAA
1 TTTATTTAA
1494601 TTT
1 TTT
1494604 TGCTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.25
9 18 0.75
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTATTTAA
Found at i:1496438 original size:165 final size:164
Alignment explanation
Indices: 1496149--1496530 Score: 423
Period size: 164 Copynumber: 2.3 Consensus size: 164
1496139 TAGAATCCTC
* * *
1496149 CAAAACTGATTTAATATGAATTTAATAATAATATTATATG-ATTTTAAAAATTATAAACAAAGAA
1 CAAAACTGATTTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACAAAGAA
* * * * ****
1496213 AAATCCTCTCAAAAACATTTACAGAGTAGGAAACTCAATTTTTTTTGGAAAGGAAAATTTCAAAG
66 AAATCCTCTCAAAAAAATTTACAGAGGAGGAAACTC-AGTATTTCAAAAAAGGAAAATTTCAAAG
** * *
1496278 AAAAAATTCAAAACTCATGAATAA-GAATTAATTTTT
130 -AAAAATAAAAAACTCATGAA-AATAAATGAATTTTT
* * * **
1496314 CAAGACTGATTTAATATAAATCAAATAATAATATTTTATGAATTTTAAAAATTGAAAAACCGAGA
1 CAAAACTGATTTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATT-AAAAACAAAGA
*
1496379 AAAATCCTCTTAAAAAAATTTACAGAGGA-GAAACTTC-GTATTTCAAAAAA-GAGAAATTTCAA
65 AAAATCCTCTCAAAAAAATTTACAGAGGAGGAAAC-TCAGTATTTCAAAAAAGGA-AAATTTCAA
* *
1496441 AGAAAAATAAAAAATTTATGAAAATAAATGAATTTTT
128 AGAAAAATAAAAAACTCATGAAAATAAATGAATTTTT
* * ** *
1496478 GAAAACTAATTTAACGTGAATTAAATAATAATATTTTATAAATTTTAAAAATT
1 CAAAACTGATTTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATT
1496531 TTGAATCAAT
Statistics
Matches: 181, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
163 2 0.01
164 73 0.40
165 53 0.29
166 17 0.09
167 36 0.20
ACGTcount: A:0.51, C:0.08, G:0.09, T:0.32
Consensus pattern (164 bp):
CAAAACTGATTTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACAAAGAA
AAATCCTCTCAAAAAAATTTACAGAGGAGGAAACTCAGTATTTCAAAAAAGGAAAATTTCAAAGA
AAAATAAAAAACTCATGAAAATAAATGAATTTTT
Found at i:1496463 original size:18 final size:19
Alignment explanation
Indices: 1496442--1496482 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1496432 AAATTTCAAA
1496442 GAAAAATAAA-AAATTTAT
1 GAAAAATAAATAAATTTAT
* *
1496460 G-AAAATAAATGAATTTTT
1 GAAAAATAAATAAATTTAT
1496478 GAAAA
1 GAAAA
1496483 CTAATTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 8 0.42
18 8 0.42
19 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (19 bp):
GAAAAATAAATAAATTTAT
Found at i:1496466 original size:17 final size:18
Alignment explanation
Indices: 1496444--1496482 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1496434 ATTTCAAAGA
1496444 AAAATAAA-AAATTTATG
1 AAAATAAATAAATTTATG
* *
1496461 AAAATAAATGAATTTTTG
1 AAAATAAATAAATTTATG
1496479 AAAA
1 AAAA
1496483 CTAATTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAAATAAATAAATTTATG
Found at i:1505212 original size:63 final size:63
Alignment explanation
Indices: 1505094--1505259 Score: 188
Period size: 63 Copynumber: 2.6 Consensus size: 63
1505084 TCATAATTGA
* * * * * * * *
1505094 ATTGTATCGATACATCATAAATTGTGTTGATATATTAAGCCCAATAGCTATAATTTCAAATGT
1 ATTGTATCGATACATCATAAATTGTATCGATACATTGAGCCAAACAGCTAGAATTTCAAATGC
* ** *
1505157 ATTGTACCGATACATGGTAAATTGTATCGATACATTGAGCCAAACGGCTAGAATTTCAAATGC
1 ATTGTATCGATACATCATAAATTGTATCGATACATTGAGCCAAACAGCTAGAATTTCAAATGC
* * * *
1505220 ATTGTATCGATACATTATGAATTGTATCAATACATGGAGC
1 ATTGTATCGATACATCATAAATTGTATCGATACATTGAGC
1505260 GTGTATGCAC
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 85 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (63 bp):
ATTGTATCGATACATCATAAATTGTATCGATACATTGAGCCAAACAGCTAGAATTTCAAATGC
Found at i:1506698 original size:3 final size:3
Alignment explanation
Indices: 1506690--1506735 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1506680 TATAAGGAAA
1506690 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1506736 ATGCTGAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1508367 original size:2 final size:2
Alignment explanation
Indices: 1508362--1508386 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1508352 CTAAAAAAAC
1508362 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1508387 GAAAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1508645 original size:20 final size:19
Alignment explanation
Indices: 1508620--1508663 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
1508610 TTTTTATCTA
1508620 AATTAA-AAGAAAAATAATTT
1 AATTAATAA-AAAAATAA-TT
1508640 AATTAATTAAAAAAATAATT
1 AATTAA-TAAAAAAATAATT
1508660 AATT
1 AATT
1508664 TTACACCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 12 0.55
21 8 0.36
22 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AATTAATAAAAAAATAATT
Found at i:1509014 original size:19 final size:20
Alignment explanation
Indices: 1508990--1509028 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1508980 TCTAATTTTT
1508990 ATATGAT-TTATATTTTATA
1 ATATGATATTATATTTTATA
1509009 ATATGATAATTATATTTTAT
1 ATATGAT-ATTATATTTTAT
1509029 GTCCTATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
ATATGATATTATATTTTATA
Found at i:1510045 original size:34 final size:30
Alignment explanation
Indices: 1510006--1510081 Score: 82
Period size: 34 Copynumber: 2.4 Consensus size: 30
1509996 AAAAATTAAT
1510006 TTTTAATAAAAATTTAAATTATGATTGTAATTGA
1 TTTTAATAAAAA--TAAA-TATGATTGTAATT-A
*
1510040 TTTTAATAATATAATAAATATTATTGTAATTA
1 TTTTAATAA-A-AATAAATATGATTGTAATTA
1510072 TTTT-ATAAAA
1 TTTTAATAAAA
1510082 TATTATCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
29 1 0.03
30 1 0.03
31 4 0.10
32 5 0.13
33 12 0.31
34 13 0.33
35 1 0.03
36 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTAATAAAAATAAATATGATTGTAATTA
Found at i:1510084 original size:33 final size:34
Alignment explanation
Indices: 1510020--1510084 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
1510010 AATAAAAATT
*
1510020 TAAATTATGATTGTAATTGATTTTAATAATATAA
1 TAAATTATGATTGTAATTGATTTTAAAAATATAA
*
1510054 TAAA-TATTATTGTAATT-ATTTTATAAAATAT
1 TAAATTATGATTGTAATTGATTTTA-AAAATAT
1510085 TATCTTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 6 0.21
33 18 0.64
34 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (34 bp):
TAAATTATGATTGTAATTGATTTTAAAAATATAA
Found at i:1514572 original size:46 final size:46
Alignment explanation
Indices: 1514518--1514709 Score: 181
Period size: 46 Copynumber: 4.0 Consensus size: 46
1514508 AAAAATTTAT
*
1514518 TTTTTTTATTTATCTGTTAATTAATTTAATTTAATTAAAAATAAAA
1 TTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAAAAATAAAA
* *
1514564 TTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAGATATAAAA
1 TTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAAAAATAAAA
* * *
1514610 TTTAATTATTTATCTTTATCTCTTAATTTATTTAATTTAACTAGATAA-AAAA
1 -TT--TT-TTTA--TTTATCTCTTAATTAATTTAATTTAATTA-AAAATAAAA
** * * * * *
1514662 TTTAATTATTTAT-TTTTGAATTACTTTGAGTTAATTAAATATAAAA
1 TTTTTTTATTTATCTCTT-AATTAATTTAATTTAATTAAAAATAAAA
1514708 TT
1 TT
1514710 GAATTCATCA
Statistics
Matches: 119, Mismatches: 18, Indels: 18
0.77 0.12 0.12
Matches are distributed among these distances:
45 5 0.04
46 68 0.57
47 2 0.02
48 3 0.03
49 3 0.03
50 4 0.03
51 2 0.02
52 31 0.26
53 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (46 bp):
TTTTTTTATTTATCTCTTAATTAATTTAATTTAATTAAAAATAAAA
Found at i:1514634 original size:52 final size:50
Alignment explanation
Indices: 1514509--1514677 Score: 202
Period size: 52 Copynumber: 3.4 Consensus size: 50
1514499 AACAATTTAA
* * * * *
1514509 AAAATTTATTTTTTTTATTTATCTGTTAATTAATTTAATTTAATTAAAAAT
1 AAAATTTATTATTTAT-TTTATCTCTTAATTAATTTAATTTAATTAGATAT
1514560 AAAA-TT-TT-TTTA-TTTATCTCTTAATTAATTTAATTTAATTAGATAT
1 AAAATTTATTATTTATTTTATCTCTTAATTAATTTAATTTAATTAGATAT
* * *
1514606 AAAATTTAATTATTTATCTTTATCTCTTAATTTATTTAATTTAACTAGATAA
1 AAAATTT-ATTATTTAT-TTTATCTCTTAATTAATTTAATTTAATTAGATAT
1514658 AAAATTTAATTATTTATTTT
1 AAAATTT-ATTATTTATTTT
1514678 TGAATTACTT
Statistics
Matches: 105, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
46 35 0.33
47 2 0.02
48 3 0.03
49 4 0.04
50 6 0.06
51 7 0.07
52 48 0.46
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (50 bp):
AAAATTTATTATTTATTTTATCTCTTAATTAATTTAATTTAATTAGATAT
Found at i:1514636 original size:98 final size:98
Alignment explanation
Indices: 1514509--1514714 Score: 238
Period size: 98 Copynumber: 2.1 Consensus size: 98
1514499 AACAATTTAA
* * * * **
1514509 AAAATTT-ATTTTTTTTATTTATCTGTTAATTAATTTAATTTAATTA-AAAATAAAATTTTTTTA
1 AAAATTTAATTATTTATATTTATCTCTTAATTAATTTAATTTAACTAGAAAA-AAAATTTAATTA
* *
1514572 TTTATCTCTT-AATTAATTTAATTTAATTAGATAT
65 TTTAT-TCTTGAATTAATTTAAGTTAATTAAATAT
* * *
1514606 AAAATTTAATTATTTATCTTTATCTCTTAATTTATTTAATTTAACTAGATAAAAAATTTAATTAT
1 AAAATTTAATTATTTATATTTATCTCTTAATTAATTTAATTTAACTAGAAAAAAAATTTAATTAT
* * *
1514671 TTATTTTTGAATTACTTTGAGTTAATTAAATAT
66 TTATTCTTGAATTAATTTAAGTTAATTAAATAT
*
1514704 AAAATTGAATT
1 AAAATTTAATT
1514715 CATCAACTAT
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
97 10 0.11
98 78 0.86
99 3 0.03
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (98 bp):
AAAATTTAATTATTTATATTTATCTCTTAATTAATTTAATTTAACTAGAAAAAAAATTTAATTAT
TTATTCTTGAATTAATTTAAGTTAATTAAATAT
Found at i:1514789 original size:15 final size:16
Alignment explanation
Indices: 1514769--1514802 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1514759 CAATACATAA
1514769 TTTAATT-AAAAATTT
1 TTTAATTAAAAAATTT
1514784 TTTAATTAAAAAATTT
1 TTTAATTAAAAAATTT
1514800 TTT
1 TTT
1514803 TTGGTACGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAAATTT
Found at i:1517143 original size:45 final size:45
Alignment explanation
Indices: 1517079--1517170 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
1517069 AGGTCTTCTA
*
1517079 ATCCTACAACTGGAAAGTGTCATGTTTCAAGAAATGTTGTGTTTG
1 ATCCTACAACTGGAAAGTGTCATGTTTCAAGAAATATTGTGTTTG
* *
1517124 ATCCTACAACTGTAAAGTGTCGTGTTTCAAGAAATATTGTGTTTG
1 ATCCTACAACTGGAAAGTGTCATGTTTCAAGAAATATTGTGTTTG
1517169 AT
1 AT
1517171 GAACCATCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (45 bp):
ATCCTACAACTGGAAAGTGTCATGTTTCAAGAAATATTGTGTTTG
Found at i:1519137 original size:34 final size:34
Alignment explanation
Indices: 1519099--1519184 Score: 109
Period size: 34 Copynumber: 2.5 Consensus size: 34
1519089 TGTTAAGTGC
* * *
1519099 GTTAGGTGATATGTTAGGCAAACTTATTAAGTAT
1 GTTAGGTGGTGTGTTAGGCAAACATATTAAGTAT
** *
1519133 GTTAGGTGGTGTGTTAGGTGAGCATATTAAGTAT
1 GTTAGGTGGTGTGTTAGGCAAACATATTAAGTAT
*
1519167 GTCAGGTGGTGTGTTAGG
1 GTTAGGTGGTGTGTTAGG
1519185 TGAGCAAGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (34 bp):
GTTAGGTGGTGTGTTAGGCAAACATATTAAGTAT
Found at i:1519185 original size:34 final size:34
Alignment explanation
Indices: 1519123--1519190 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1519113 TAGGCAAACT
*
1519123 TATTAAGTATGTTAGGTGGTGTGTTAGGTGAGCA
1 TATTAAGTATGTCAGGTGGTGTGTTAGGTGAGCA
1519157 TATTAAGTATGTCAGGTGGTGTGTTAGGTGAGCA
1 TATTAAGTATGTCAGGTGGTGTGTTAGGTGAGCA
1519191 AGACAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.04, G:0.35, T:0.37
Consensus pattern (34 bp):
TATTAAGTATGTCAGGTGGTGTGTTAGGTGAGCA
Found at i:1523924 original size:46 final size:45
Alignment explanation
Indices: 1523873--1524183 Score: 380
Period size: 46 Copynumber: 6.9 Consensus size: 45
1523863 TCTTTTTCAC
* *
1523873 TTATCTCTTAATTAATTTAACTTAATTAGAGAAAAAATTTATTTAT
1 TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTT-TTTAT
* *
1523919 TTATCTCTTAATTAATTTAATTTATTTAAAGATAAAATTTTTTTAT
1 TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAA-TTTTTTAT
* * * *
1523965 TTATCCCTTAAATAATATAATTTAATTAGAGATAAAACTCTTTTAT
1 TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAA-TTTTTTAT
* *
1524011 TTATCTCTTAATTAACTTAATTTAATTAAAGAT-AAATTTTGATTAT
1 TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTTT--TTAT
* * *
1524057 TTATCTC----TTAATTTAATTTAATTAAAGATAAAACTCTTTTAA
1 TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAA-TTTTTTAT
* * *
1524099 TTATCTCTAAATTGATTTAATTTAATTAGAGATAAAACTTTTTAT
1 TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTTTTTAT
*
1524144 TTATCTCTTAATCAATTTAATTTAATTAGAGATAAAATTT
1 TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTT
1524184 GATTGATCAA
Statistics
Matches: 227, Mismatches: 29, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
42 31 0.14
43 3 0.01
44 6 0.03
45 44 0.19
46 140 0.62
47 3 0.01
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (45 bp):
TTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTTTTTAT
Found at i:1524103 original size:134 final size:134
Alignment explanation
Indices: 1523864--1524187 Score: 438
Period size: 134 Copynumber: 2.4 Consensus size: 134
1523854 AAAAACTTAT
* * *
1523864 CTTTTTCACTTATCTCTTAATTAATTTAACTTAATTAGAGAAAAAATTT-ATTTATTTATCTCTT
1 CTTTTT-ATTTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTTGA-TTATTTATCTC--
* * * *
1523928 AATTAATTTAATTTATTTAAAGATAAAATTTTTTTATTTATCCCTTAAA-TAATATAATTTAATT
62 -ATTAATTTAATTTAATTAAAGATAAAACTCTTTTAATTATCCC-TAAATTAATATAATTTAATT
1523992 AGAGATAAAA
125 AGAGATAAAA
* * *
1524002 CTCTTTTATTTATCTCTTAATTAACTTAATTTAATTAAAGATAAATTTTGATTATTTATCTC-TT
1 CT-TTTTATTTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTTGATTATTTATCTCATT
* * *
1524066 AATTTAATTTAATTAAAGATAAAACTCTTTTAATTATCTCTAAATTGATTTAATTTAATTAGAGA
65 AATTTAATTTAATTAAAGATAAAACTCTTTTAATTATCCCTAAATTAATATAATTTAATTAGAGA
1524131 TAAAA
130 TAAAA
*
1524136 CTTTTTATTTATCTCTTAATCAATTTAATTTAATTAGAGATAAAATTTGATT
1 CTTTTTATTTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTTGATT
1524188 GATCAATCAT
Statistics
Matches: 166, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
133 50 0.30
134 62 0.37
138 49 0.30
139 5 0.03
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (134 bp):
CTTTTTATTTATCTCTTAATTAATTTAATTTAATTAGAGATAAAATTTGATTATTTATCTCATTA
ATTTAATTTAATTAAAGATAAAACTCTTTTAATTATCCCTAAATTAATATAATTTAATTAGAGAT
AAAA
Found at i:1524279 original size:15 final size:15
Alignment explanation
Indices: 1524256--1524286 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1524246 TGATGCATAA
*
1524256 TTTAGTTAAAAAATT
1 TTTAATTAAAAAATT
1524271 TTTAATTAAAAAATT
1 TTTAATTAAAAAATT
1524286 T
1 T
1524287 CAGTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTAATTAAAAAATT
Found at i:1524713 original size:16 final size:16
Alignment explanation
Indices: 1524689--1524719 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1524679 ATTTTTATTA
1524689 TTTAATTAATTATTTG
1 TTTAATTAATTATTTG
*
1524705 TTTATTTAATTATTT
1 TTTAATTAATTATTT
1524720 TATTTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTAATTAATTATTTG
Found at i:1526611 original size:37 final size:38
Alignment explanation
Indices: 1526565--1526637 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
1526555 TTAACATATA
* *
1526565 TATTAAAATTATATTTATGTTGAATAAT-AATTAAAAT
1 TATTAAAATTATATTTACGTTGAAAAATAAATTAAAAT
* *
1526602 TATTGAAATTATATTTACGTTTAAAAATAAATTAAA
1 TATTAAAATTATATTTACGTTGAAAAATAAATTAAA
1526638 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 24 0.77
38 7 0.23
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (38 bp):
TATTAAAATTATATTTACGTTGAAAAATAAATTAAAAT
Found at i:1527194 original size:22 final size:24
Alignment explanation
Indices: 1527160--1527204 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1527150 TTATTATAAT
1527160 AATAAATAATTAT-T-AGAAAGAA
1 AATAAATAATTATGTAAGAAAGAA
1527182 AATAAA-AATTTATGTAAGAAAGA
1 AATAAATAA-TTATGTAAGAAAGA
1527205 TTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.10
22 10 0.50
23 1 0.05
24 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (24 bp):
AATAAATAATTATGTAAGAAAGAA
Found at i:1527417 original size:16 final size:17
Alignment explanation
Indices: 1527396--1527428 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1527386 TTGAAATTCG
1527396 TTTA-TTAAAAATATTT
1 TTTATTTAAAAATATTT
*
1527412 TTTATTTATAAATATTT
1 TTTATTTAAAAATATTT
1527429 ATATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATTTAAAAATATTT
Found at i:1527460 original size:8 final size:8
Alignment explanation
Indices: 1527420--1527475 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
1527410 TTTTTATTTA
1527420 TAAATATT
1 TAAATATT
1527428 T--ATATT
1 TAAATATT
*
1527434 TTAATATTT
1 TAAATA-TT
1527443 TAATATATAT
1 TAA-ATAT-T
1527453 TAAAATATT
1 T-AAATATT
1527462 TAAATATT
1 TAAATATT
1527470 TAAATA
1 TAAATA
1527476 AATTATTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 6 0.15
8 17 0.41
9 7 0.17
10 9 0.22
11 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TAAATATT
Found at i:1527482 original size:21 final size:19
Alignment explanation
Indices: 1527453--1527491 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1527443 TAATATATAT
1527453 TAAAATATTTAAATATTTAAA
1 TAAAATATTT--ATATTTAAA
*
1527474 TAAATTATTTATATTTAA
1 TAAAATATTTATATTTAA
1527492 TACAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATATTTATATTTAAA
Found at i:1536626 original size:44 final size:43
Alignment explanation
Indices: 1536555--1536643 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 43
1536545 CATAAATTTG
*
1536555 AAATCAATTAGCTTTTCCTTAATCATTCATGTCCATCCACTTA
1 AAATCAATTAGCTTTTCCTTAATCATTCATGTCAATCCACTTA
*
1536598 AAATCAATTAGCTTTTTCCTTAATCATTCATTTCAATCCACTTA
1 AAATCAATTAGC-TTTTCCTTAATCATTCATGTCAATCCACTTA
1536642 AA
1 AA
1536644 CTTGATTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 12 0.28
44 31 0.72
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (43 bp):
AAATCAATTAGCTTTTCCTTAATCATTCATGTCAATCCACTTA
Found at i:1538725 original size:11 final size:11
Alignment explanation
Indices: 1538709--1538764 Score: 69
Period size: 11 Copynumber: 5.1 Consensus size: 11
1538699 ATATTTTAGG
1538709 TATTTTTATAT
1 TATTTTTATAT
*
1538720 TATTTTTATGT
1 TATTTTTATAT
1538731 TATTTTTATAT
1 TATTTTTATAT
*
1538742 TATGATTTA-AT
1 TAT-TTTTATAT
*
1538753 TAATTTTATAT
1 TATTTTTATAT
1538764 T
1 T
1538765 TTATATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
10 4 0.11
11 30 0.79
12 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:1538787 original size:34 final size:33
Alignment explanation
Indices: 1538749--1538823 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
1538739 TATTATGATT
*
1538749 TAATTAATTTTATATTTTATA-TAATTTATCATAA
1 TAATTAATTTTA-ATTTTAAATTAATTTAT-ATAA
* *
1538783 TAATTTAATTTTAATTTTAAATTTATTTATTTAA
1 TAA-TTAATTTTAATTTTAAATTAATTTATATAA
1538817 TAATTAA
1 TAATTAA
1538824 ACAATTACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 4 0.11
34 16 0.44
35 16 0.44
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
TAATTAATTTTAATTTTAAATTAATTTATATAA
Found at i:1538811 original size:35 final size:34
Alignment explanation
Indices: 1538752--1538821 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
1538742 TATGATTTAA
*
1538752 TTAATTTTATATTTTATATAATTTATCATAATAAT
1 TTAATTTTATATTTTAAATAATTTAT-ATAATAAT
* *
1538787 TTAATTTTA-ATTTTAAATTTATTTATTTAATAAT
1 TTAATTTTATATTTTAAA-TAATTTATATAATAAT
1538821 T
1 T
1538822 AAACAATTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (34 bp):
TTAATTTTATATTTTAAATAATTTATATAATAAT
Found at i:1540119 original size:17 final size:17
Alignment explanation
Indices: 1540075--1540126 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
1540065 ATGTTTCTTA
*
1540075 TTTTATATTATTATAATAT
1 TTTTA-ATTATT-TAAAAT
1540094 TTATTAATTATTTAAAAT
1 TT-TTAATTATTTAAAAT
1540112 TTTTAATTATATTAA
1 TTTTAATTAT-TTAA
1540127 TACCGCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.27
18 11 0.37
19 8 0.27
20 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAATTATTTAAAAT
Found at i:1541061 original size:22 final size:21
Alignment explanation
Indices: 1541005--1541062 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1540995 TTTTATTATT
*
1541005 TAATATATTATTTTAATTAAA
1 TAATATAATATTTTAATTAAA
* *
1541026 TTATATCATAATTTTAATTAAAA
1 TAATATAAT-ATTTTAATT-AAA
*
1541049 TAATTTAATATTTT
1 TAATATAATATTTT
1541063 TTATTACACT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.21
22 14 0.48
23 9 0.31
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATATAATATTTTAATTAAA
Found at i:1541453 original size:19 final size:18
Alignment explanation
Indices: 1541401--1541453 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1541391 ATTAAATTAT
1541401 ATAATTAAATATATAAAA
1 ATAATTAAATATATAAAA
**
1541419 ATAATTATTTATTATAAAA
1 ATAATTAAATA-TATAAAA
*
1541438 ATTATTAAAATATATA
1 ATAATT-AAATATATA
1541454 TTTATTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 9 0.32
19 16 0.57
20 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATTAAATATATAAAA
Found at i:1541455 original size:28 final size:29
Alignment explanation
Indices: 1541407--1541461 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
1541397 TTATATAATT
1541407 AAATATATAAAAATAATTATTTATTATAA
1 AAATATATAAAAATAATTATTTATTATAA
*
1541436 AAAT-TATTAAAAT-ATATATTTATTAT
1 AAATATATAAAAATAAT-TATTTATTAT
1541462 TTAATTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 2 0.08
28 18 0.75
29 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAATATATAAAAATAATTATTTATTATAA
Found at i:1542312 original size:19 final size:19
Alignment explanation
Indices: 1542290--1542341 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1542280 AGATTAAAAT
1542290 AAAATAGAAGAATGATAAA
1 AAAATAGAAGAATGATAAA
* * *
1542309 AAAATATAAG-ATTACAAA
1 AAAATAGAAGAATGATAAA
*
1542327 AAAAAAGAA-AATGAT
1 AAAATAGAAGAATGAT
1542342 CCAAAACTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (19 bp):
AAAATAGAAGAATGATAAA
Found at i:1542327 original size:18 final size:17
Alignment explanation
Indices: 1542273--1542330 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 17
1542263 CAACACAAAT
1542273 AATAGTAAGATTAAAATAA
1 AATA-TAAGATTAAAA-AA
* *
1542292 AATAGAAGAATGATAAAAA
1 AATATAAG-ATTA-AAAAA
1542311 AATATAAGATTACAAAAA
1 AATATAAGATTA-AAAAA
1542329 AA
1 AA
1542331 AAGAAAATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 13 0.41
19 16 0.50
20 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (17 bp):
AATATAAGATTAAAAAA
Found at i:1547649 original size:18 final size:19
Alignment explanation
Indices: 1547623--1547668 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1547613 TATTATATTA
1547623 TATATTTAAATAAATT-TAT
1 TATA-TTAAATAAATTGTAT
*
1547642 TATATT-AATAATTTGTAT
1 TATATTAAATAAATTGTAT
1547660 TATA-TAAAT
1 TATATTAAAT
1547669 TTTAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTAAATAAATTGTAT
Found at i:1547697 original size:16 final size:16
Alignment explanation
Indices: 1547678--1547727 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1547668 TTTTAAAATA
1547678 TATATTTATATTTTAT
1 TATATTTATATTTTAT
1547694 TATA-TTATATTTTAAT
1 TATATTTATATTTT-AT
*
1547710 TAT-TTTATAATTT-T
1 TATATTTATATTTTAT
1547724 TATA
1 TATA
1547728 AGTAGATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
16 17 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATTTATATTTTAT
Found at i:1547717 original size:21 final size:23
Alignment explanation
Indices: 1547667--1547720 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
1547657 TATTATATAA
*
1547667 ATTTTAAAATATATATTTATATT
1 ATTTTATAATATATATTTATATT
*
1547690 -TTATTATATTATAT-TTTA-ATT
1 ATT-TTATAATATATATTTATATT
1547711 ATTTTATAAT
1 ATTTTATAAT
1547721 TTTTATAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTATAATATATATTTATATT
Found at i:1547926 original size:24 final size:24
Alignment explanation
Indices: 1547871--1547927 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1547861 TTATTCTTTC
*
1547871 AATAAAAGC-AAAAATAAAAAATA
1 AATAAAAACGAAAAATAAAAAATA
* *
1547894 AAGACAAACGAAAAATAATAAAA-A
1 AATAAAAACGAAAAATAA-AAAATA
1547918 AATAAAAACG
1 AATAAAAACG
1547928 TCAATAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 6 0.22
24 17 0.63
25 4 0.15
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.11
Consensus pattern (24 bp):
AATAAAAACGAAAAATAAAAAATA
Found at i:1548088 original size:31 final size:32
Alignment explanation
Indices: 1548037--1548102 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
1548027 GGTATAAAAA
1548037 ATATATTTAATATAAATATATTTAATT-TTTT
1 ATATATTTAATATAAATATATTTAATTATTTT
*
1548068 ATATATTTTAA-A-AAATTATATTTTATTATTTT
1 ATATA-TTTAATATAAA-TATATTTAATTATTTT
1548100 ATA
1 ATA
1548103 GGCATTATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 3 0.10
31 16 0.52
32 12 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATATATTTAATATAAATATATTTAATTATTTT
Found at i:1552683 original size:2 final size:2
Alignment explanation
Indices: 1552676--1552709 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1552666 TGCTACATGC
1552676 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
1552710 TACCTTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1557522 original size:16 final size:16
Alignment explanation
Indices: 1557500--1557547 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
1557490 TATTTAAATG
1557500 AATTTTAATATAT-TA
1 AATTTTAATATATATA
1557515 ATATTTT-ATATTATATA
1 A-ATTTTAATA-TATATA
*
1557532 AATTTTAAAATATATA
1 AATTTTAATATATATA
1557548 TTTATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 19 0.68
17 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTTAATATATATA
Found at i:1557547 original size:36 final size:35
Alignment explanation
Indices: 1557507--1557574 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 35
1557497 ATGAATTTTA
1557507 ATATATTAATATTTTATATTATATAAATTTTAAAAT
1 ATATATTAATATTTTATATTAT-TAAATTTTAAAAT
* * * *
1557543 ATATATTTATATTTTGTTTTATTATATTTTAA
1 ATATATTAATATTTTATATTATTAAATTTTAA
1557575 TTATTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 9 0.32
36 19 0.68
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
ATATATTAATATTTTATATTATTAAATTTTAAAAT
Found at i:1557816 original size:24 final size:23
Alignment explanation
Indices: 1557761--1557826 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
1557751 TTTATTTTTC
*
1557761 AATAAAAGCAAAAATAAAAAATA
1 AATAAAAACAAAAATAAAAAATA
* *
1557784 AAGACAAACGAAAAATAATAAAA-A
1 AATAAAAAC-AAAAATAA-AAAATA
**
1557808 AATAAAAACATCAATAAAA
1 AATAAAAACAAAAATAAAA
1557827 CGAAGCAGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 2 0.06
23 12 0.35
24 16 0.47
25 4 0.12
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.12
Consensus pattern (23 bp):
AATAAAAACAAAAATAAAAAATA
Found at i:1557975 original size:31 final size:34
Alignment explanation
Indices: 1557925--1557990 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
1557915 TCGGTATAAA
1557925 AAATATATTTAATATAAATATA-TTTAATT-TTTT
1 AAATATATTTAATATAAATATACTTT-ATTATTTT
*
1557958 AAATATTTTTAA-A-AAATATACTTTATTATTTT
1 AAATATATTTAATATAAATATACTTTATTATTTT
1557990 A
1 A
1557991 TAGGCATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 10 0.33
32 9 0.30
33 11 0.37
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (34 bp):
AAATATATTTAATATAAATATACTTTATTATTTT
Found at i:1565237 original size:19 final size:18
Alignment explanation
Indices: 1565213--1565276 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
1565203 TTTCAACGAC
1565213 TTGTATCGATACATAAGT
1 TTGTATCGATACATAAGT
1565231 GTTGTATCGATAC--AA--
1 -TTGTATCGATACATAAGT
1565246 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAG-T
1565264 TTGTATCGATACA
1 TTGTATCGATACA
1565277 ATGTACAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTGTATCGATACATAAGT
Found at i:1565251 original size:13 final size:13
Alignment explanation
Indices: 1565233--1565257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1565223 ACATAAGTGT
1565233 TGTATCGATACAA
1 TGTATCGATACAA
1565246 TGTATCGATACA
1 TGTATCGATACA
1565258 TAAGTTTTGT
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:1565255 original size:32 final size:32
Alignment explanation
Indices: 1565214--1565281 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
1565204 TTCAACGACT
1565214 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1565246 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1565278 TGTA
1 TGTA
1565282 CAGTTACGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1569969 original size:13 final size:13
Alignment explanation
Indices: 1569951--1569975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1569941 TTAGGCTTCA
1569951 TGTATCGATACAT
1 TGTATCGATACAT
1569964 TGTATCGATACA
1 TGTATCGATACA
1569976 ATGCCCCATG
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:1570067 original size:19 final size:19
Alignment explanation
Indices: 1570024--1570079 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1570014 CTGCCAGTTT
*
1570024 CATGTATCAATACAATTAAG
1 CATGTATCGATACAA-TAAG
*
1570044 TATGTATCGATACAATAAG
1 CATGTATCGATACAATAAG
*
1570063 CATGTATTGATACAATA
1 CATGTATCGATACAATA
1570080 TATCGATACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATAAG
Found at i:1570127 original size:32 final size:32
Alignment explanation
Indices: 1570086--1570150 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1570076 AATATATCGA
* **
1570086 TACTAGGCATAATGTATTGATAAATCTGGATG
1 TACTAGGCATAATATATCAATAAATCTGGATG
*
1570118 TACTAGGCATAATATATCAATATATCTGGATG
1 TACTAGGCATAATATATCAATAAATCTGGATG
1570150 T
1 T
1570151 GTATTGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.35
Consensus pattern (32 bp):
TACTAGGCATAATATATCAATAAATCTGGATG
Found at i:1570896 original size:10 final size:10
Alignment explanation
Indices: 1570866--1570898 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1570856 AATACTTATA
1570866 TAGATTTTTT
1 TAGATTTTTT
*
1570876 T-GAATTTTT
1 TAGATTTTTT
1570885 TAGATTTTTT
1 TAGATTTTTT
1570895 TAGA
1 TAGA
1570899 GTGAATATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (10 bp):
TAGATTTTTT
Found at i:1571371 original size:26 final size:26
Alignment explanation
Indices: 1571312--1571371 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 26
1571302 GATGATTCGG
*
1571312 ATAAAATTAAATTTTTATAATTAATA
1 ATAAAATTTAATTTTTATAATTAATA
* *
1571338 A-AATATTTAA-TTTTATATTTAATA
1 ATAAAATTTAATTTTTATAATTAATA
1571362 TATAAAATTT
1 -ATAAAATTT
1571372 TATAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 13 0.46
25 8 0.29
26 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATAAAATTTAATTTTTATAATTAATA
Done.