Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 205 of 206
Found at i:62124099 original size:239 final size:239
Alignment explanation
Indices: 62123680--62124197 Score: 1000
Period size: 239 Copynumber: 2.2 Consensus size: 239
62123670 ATTCGATTTT
*
62123680 AAAAAATCGAAAAAAATTCAAATTTCGAATAACTTGATTCGAGTATTGAGTTCGAATTGAGTTGA
1 AAAAAATCGAAAAAAATTCAAATTTCGAATAACTTGATTCGAGTATTGAGTTCGAATTGAGTTAA
62123745 ATTTTACAATTTGAATAACAGATTGGTATAAATATCATTTTGATTTTGTCAACTTTGAAAGAAAA
66 ATTTTACAATTTGAATAACAGATTGGTATAAATATCATTTTGATTTTGTCAACTTTGAAAGAAAA
62123810 CAAATTGGTCTATCTCAGTAATGATTAAAAAAAATTAAAGTCATTTTCAAAAATTCAAAATAATT
131 CAAATTGGTCTATCTCAGTAATGATTAAAAAAAATTAAAGTCATTTTCAAAAATTCAAAATAATT
*
62123875 TTTAAAATTTTATAAAAAATTCAATATTTATAAAAACCTCAGCA
196 TTTAAAATTTTATAAAAAATTCAATATTAATAAAAACCTCAGCA
*
62123919 AAAAAATCGAAAAAAATTCAAATTTCGAATAACTTGATTCGAGTATTGAGTTTGAATTGAGTTAA
1 AAAAAATCGAAAAAAATTCAAATTTCGAATAACTTGATTCGAGTATTGAGTTCGAATTGAGTTAA
*
62123984 ATTTTATAATTTGAATAACAGATTGGTATAAATATCATTTTGATTTTGTCAACTTTGAAAGAAAA
66 ATTTTACAATTTGAATAACAGATTGGTATAAATATCATTTTGATTTTGTCAACTTTGAAAGAAAA
62124049 CAAATTGGTCTATCTCAGTAATGATTAAAAAAAATTAAAGTCATTTTCAAAAATTCAAAATAATT
131 CAAATTGGTCTATCTCAGTAATGATTAAAAAAAATTAAAGTCATTTTCAAAAATTCAAAATAATT
62124114 TTTAAAATTTTATAAAAAATTCAATATTAATAAAAACCTCAGCA
196 TTTAAAATTTTATAAAAAATTCAATATTAATAAAAACCTCAGCA
62124158 AAAAAATCGAAAAAAATTCAAATTTCGAATAACTTGATTC
1 AAAAAATCGAAAAAAATTCAAATTTCGAATAACTTGATTC
62124198 TATTCAAATT
Statistics
Matches: 275, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
239 275 1.00
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (239 bp):
AAAAAATCGAAAAAAATTCAAATTTCGAATAACTTGATTCGAGTATTGAGTTCGAATTGAGTTAA
ATTTTACAATTTGAATAACAGATTGGTATAAATATCATTTTGATTTTGTCAACTTTGAAAGAAAA
CAAATTGGTCTATCTCAGTAATGATTAAAAAAAATTAAAGTCATTTTCAAAAATTCAAAATAATT
TTTAAAATTTTATAAAAAATTCAATATTAATAAAAACCTCAGCA
Found at i:62124114 original size:20 final size:19
Alignment explanation
Indices: 62124078--62124120 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
62124068 AATGATTAAA
* *
62124078 AAAAATTAAAGTCATTTTC
1 AAAAATTAAAATAATTTTC
*
62124097 AAAAATTCAAAATAATTTTT
1 AAAAATT-AAAATAATTTTC
62124117 AAAA
1 AAAA
62124121 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATTAAAATAATTTTC
Found at i:62126429 original size:37 final size:37
Alignment explanation
Indices: 62126375--62126449 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
62126365 AGTAAGCATA
62126375 TCAGTTGTGTAAAGCAGATTGCTTCCTTGCTACACGT
1 TCAGTTGTGTAAAGCAGATTGCTTCCTTGCTACACGT
* *
62126412 TCAGTTGTGTAACGCAGATTGCTTCCTTGCTGCACGT
1 TCAGTTGTGTAAAGCAGATTGCTTCCTTGCTACACGT
62126449 T
1 T
62126450 TTTGAGCAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36
Consensus pattern (37 bp):
TCAGTTGTGTAAAGCAGATTGCTTCCTTGCTACACGT
Found at i:62127288 original size:24 final size:24
Alignment explanation
Indices: 62127260--62127307 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
62127250 TCATTTATTC
*
62127260 ATCAAGTCATGAATCAAGCTTTCA
1 ATCAAGTCATAAATCAAGCTTTCA
62127284 ATCAAGTCATAAATCAAGCTTTCA
1 ATCAAGTCATAAATCAAGCTTTCA
62127308 TCTTTGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (24 bp):
ATCAAGTCATAAATCAAGCTTTCA
Found at i:62128465 original size:41 final size:41
Alignment explanation
Indices: 62128420--62128501 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
62128410 ATCCATCACA
62128420 TAGCCCCTACTTTTTGTTGTGGTTGGCTCTGCCGATTTGGG
1 TAGCCCCTACTTTTTGTTGTGGTTGGCTCTGCCGATTTGGG
62128461 TAGCCCCTACTTTTTGTTGTGGTTGGCTCTGCCGATTTGGG
1 TAGCCCCTACTTTTTGTTGTGGTTGGCTCTGCCGATTTGGG
62128502 GTCCAATAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.07, C:0.22, G:0.29, T:0.41
Consensus pattern (41 bp):
TAGCCCCTACTTTTTGTTGTGGTTGGCTCTGCCGATTTGGG
Found at i:62137788 original size:14 final size:14
Alignment explanation
Indices: 62137769--62137798 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
62137759 TAAGAAATGG
62137769 AATATAAAATCTGT
1 AATATAAAATCTGT
62137783 AATATAAAATCTGT
1 AATATAAAATCTGT
62137797 AA
1 AA
62137799 ACAAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
AATATAAAATCTGT
Found at i:62152553 original size:13 final size:15
Alignment explanation
Indices: 62152523--62152552 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
62152513 CTGAAAGAAC
62152523 GACCAAAAAAAGAGA
1 GACCAAAAAAAGAGA
62152538 GACCAAAAAAAGAGA
1 GACCAAAAAAAGAGA
62152553 CAACCCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.13, G:0.20, T:0.00
Consensus pattern (15 bp):
GACCAAAAAAAGAGA
Found at i:62153933 original size:2 final size:2
Alignment explanation
Indices: 62153926--62153950 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62153916 GAGTAAGCTT
62153926 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
62153951 CAATTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62156941 original size:69 final size:69
Alignment explanation
Indices: 62156830--62156969 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
62156820 ATATCTTTAT
62156830 TTTCAGTTTTAGGGATGCTGGACTCACCACTGGCCGTGGCTGGAGAAGAATCCATCAAACTAGCG
1 TTTCAGTTTTAGGGATGCTGGACTCACCACTGGCCGTGGCTGGAGAAGAATCCATCAAACTAGCG
62156895 GCGA
66 GCGA
*
62156899 TTTCAGTTTTAGGGATGCTGGACTCACCGCTGGCCGTGGCTGGAGAAGAATCCATCAAACTAGCG
1 TTTCAGTTTTAGGGATGCTGGACTCACCACTGGCCGTGGCTGGAGAAGAATCCATCAAACTAGCG
62156964 GCGA
66 GCGA
62156968 TT
1 TT
62156970 GCAGCCCTCA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (69 bp):
TTTCAGTTTTAGGGATGCTGGACTCACCACTGGCCGTGGCTGGAGAAGAATCCATCAAACTAGCG
GCGA
Found at i:62165499 original size:21 final size:22
Alignment explanation
Indices: 62165475--62165517 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
62165465 TAATCTCTTG
*
62165475 TTTTTATA-TTATGAAATTTAA
1 TTTTTATACTTATCAAATTTAA
*
62165496 TTTTTATACTTTTCAAATTTAA
1 TTTTTATACTTATCAAATTTAA
62165518 AAATATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTTATACTTATCAAATTTAA
Found at i:62166525 original size:99 final size:100
Alignment explanation
Indices: 62166285--62166582 Score: 363
Period size: 99 Copynumber: 3.0 Consensus size: 100
62166275 TAGAATTCTG
* * * *
62166285 CTTTTAATTTGATGAATTTATTTTACTCTGAGTGAGCTAGCGGTTGTATTTATGATGATATATTG
1 CTTTTAATTTGATGAATTTA-TTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTG
* *
62166350 TTAATTGATTAGAGATTAGTATTTGTTATGATTTTG
65 TTAATTGATTAGAGATTAGTATATGTTATGATTTTA
* * *
62166386 CGTTTAATTTAATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGTTATAGTGT
1 CTTTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
* *
62166451 TAATTTG-TTA-ATATTTGT-TATGATT-T-AGTTTTAA
66 TAA-TTGATTAGAGATTAGTATATG-TTATGA-TTTT-A
* *
62166485 CTTTTACTTTGATGAATTTATTTACTCGGAATGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
1 CTTTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
* * * *
62166550 TAACTGATTACATATTAGTATTTGTTATGATTT
66 TAATTGATTAGAGATTAGTATATGTTATGATTT
62166583 AGTATTGATT
Statistics
Matches: 169, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
97 1 0.01
98 10 0.06
99 74 0.44
100 55 0.33
101 28 0.17
102 1 0.01
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (100 bp):
CTTTTAATTTGATGAATTTATTTACTCGGAGTGAGCTAGCTGTTGTATTTGTGATGATATAGTGT
TAATTGATTAGAGATTAGTATATGTTATGATTTTA
Found at i:62169462 original size:3 final size:3
Alignment explanation
Indices: 62169454--62169481 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
62169444 AGCAGCTGTA
62169454 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
62169482 GAGCTCCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:62174826 original size:23 final size:24
Alignment explanation
Indices: 62174782--62174837 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
62174772 TAAGATGATT
62174782 ATATATAGAATTATAATAAATTAAA
1 ATATATA-AATTATAATAAATTAAA
* *
62174807 ATATATAAATT-TATTGAATTAAA
1 ATATATAAATTATAATAAATTAAA
*
62174830 ATAAATAA
1 ATATATAA
62174838 TTAAATTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 17 0.61
24 4 0.14
25 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATATAAATTATAATAAATTAAA
Found at i:62178316 original size:22 final size:22
Alignment explanation
Indices: 62178290--62178343 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
62178280 TTTTTCTTTA
**
62178290 TTTATGAATTTCATCCTTTAGT
1 TTTATGAATTTCAAACTTTAGT
* *
62178312 TTTATGAATATCAAATTTTAGT
1 TTTATGAATTTCAAACTTTAGT
62178334 TTT-TGAATTT
1 TTTATGAATTT
62178344 TGTGATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (22 bp):
TTTATGAATTTCAAACTTTAGT
Found at i:62179846 original size:21 final size:21
Alignment explanation
Indices: 62179822--62179869 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
62179812 CCATGAAGCT
62179822 CTTGGTTCATCAAATGAAAAC
1 CTTGGTTCATCAAATGAAAAC
**
62179843 CTTGAATCATCAAATGAAAAC
1 CTTGGTTCATCAAATGAAAAC
62179864 CTTGGT
1 CTTGGT
62179870 GGAGCTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (21 bp):
CTTGGTTCATCAAATGAAAAC
Found at i:62183039 original size:8 final size:8
Alignment explanation
Indices: 62183026--62183065 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
62183016 TGTTTATTAA
*
62183026 GAATTATT
1 GAATTATC
62183034 GAATTATC
1 GAATTATC
62183042 GAATTATC
1 GAATTATC
62183050 GAATTATC
1 GAATTATC
62183058 GAATTATC
1 GAATTATC
62183066 ATTAGCCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (8 bp):
GAATTATC
Found at i:62183515 original size:19 final size:20
Alignment explanation
Indices: 62183493--62183530 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
62183483 AATAAATACC
62183493 AAAAAA-TATTTTAAAAATT
1 AAAAAAGTATTTTAAAAATT
62183512 AAAAAAGTATTTTAAAAAT
1 AAAAAAGTATTTTAAAAAT
62183531 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAAAGTATTTTAAAAATT
Found at i:62183528 original size:12 final size:11
Alignment explanation
Indices: 62183494--62183539 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
62183484 ATAAATACCA
62183494 AAAAATATTTT
1 AAAAATATTTT
*
62183505 -AAAA-A-TTA
1 AAAAATATTTT
62183513 AAAAAGTATTTT
1 AAAAA-TATTTT
62183525 AAAAATATTTT
1 AAAAATATTTT
62183536 AAAA
1 AAAA
62183540 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 2 0.07
9 5 0.17
10 4 0.14
11 11 0.38
12 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:62188388 original size:11 final size:11
Alignment explanation
Indices: 62188374--62188399 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62188364 TTTTTATTTT
62188374 ATTTTATAATA
1 ATTTTATAATA
62188385 ATTTTATAATA
1 ATTTTATAATA
62188396 ATTT
1 ATTT
62188400 ATTTAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTATAATA
Found at i:62196572 original size:19 final size:20
Alignment explanation
Indices: 62196532--62196574 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
62196522 TATCAAATTT
*
62196532 TATATAAAATAATTTATTAA
1 TATATAAAATAATTTATCAA
62196552 TATATAAAA-AA-TTATACAA
1 TATATAAAATAATTTAT-CAA
62196571 TATA
1 TATA
62196575 CTTTAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 9 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATAAAATAATTTATCAA
Found at i:62198322 original size:45 final size:43
Alignment explanation
Indices: 62198271--62198440 Score: 163
Period size: 45 Copynumber: 3.9 Consensus size: 43
62198261 ACGATTTTCG
*
62198271 ATATGTGTTCTCGTGTAAGACCACGTCTGGGAC-GATGGCATCGAT
1 ATATGTGAT-TCGTGTAAGACCACGTCTGGGACAG-TGGCATCG-T
* * *
62198316 ATATGTGATTACGTGTAAGACCATGTCTAGGACATTGGCATCGT
1 ATATGTGATT-CGTGTAAGACCACGTCTGGGACAGTGGCATCGT
*
62198360 AT-T-TGATTCGTGTAAGACC-CTGTCCGGGACAGTGGCATCG-
1 ATATGTGATTCGTGTAAGACCAC-GTCTGGGACAGTGGCATCGT
* * *
62198400 ATATGAGATAGCATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 ATATGTGAT-TCGTGTAAGACCACGTCTGGGACAG-TGGCAT
62198441 TGTTCGATAT
Statistics
Matches: 105, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
40 2 0.02
41 28 0.27
42 9 0.09
43 25 0.24
44 5 0.05
45 36 0.34
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
ATATGTGATTCGTGTAAGACCACGTCTGGGACAGTGGCATCGT
Found at i:62199219 original size:2 final size:2
Alignment explanation
Indices: 62199214--62199273 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
62199204 ACACACACAC
62199214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62199256 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
62199274 ATAAATTGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62200137 original size:40 final size:40
Alignment explanation
Indices: 62200093--62200172 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
62200083 GGTTTTAAAA
* * * * *
62200093 TTTTTGATTTTGACCATTATGGATTTGAATTATTTTGGGT
1 TTTTTGAGTTTGACCATTACGAATTCGAATAATTTTGGGT
*
62200133 TTTTTGAGTTTGATCATTACGAATTCGAATAATTTTGGGT
1 TTTTTGAGTTTGACCATTACGAATTCGAATAATTTTGGGT
62200173 CATTTGGTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51
Consensus pattern (40 bp):
TTTTTGAGTTTGACCATTACGAATTCGAATAATTTTGGGT
Found at i:62210117 original size:106 final size:106
Alignment explanation
Indices: 62209915--62210129 Score: 297
Period size: 106 Copynumber: 2.0 Consensus size: 106
62209905 AGAGATGTTA
* * ** *
62209915 TAGAATTATAATAAAACATATCATAACCCAATCTGAAGTCCAACCTACTCTGGTAATCTGGAATT
1 TAGAATTATAATAAAACATATAATAACCCAACCTGAAGTCCAACCTACTCTGGTAATCCAGAATC
*
62209980 CGACCCAAAAATCCCCTTATATACATACCAAAAACCCTATT
66 CGACCCAAAAACCCCCTTATATACATACCAAAAACCCTATT
* * ** *
62210021 TAGAATTATAATAAAATATATAATAACTCAACCTGAAGTCCAACCTGTTCTGGTGATCCAGAATC
1 TAGAATTATAATAAAACATATAATAACCCAACCTGAAGTCCAACCTACTCTGGTAATCCAGAATC
* *
62210086 CGACCC-AAACCCCCCTTATATACATATCCAAAAACCCTTTT
66 CGACCCAAAAACCCCCTTATATACATA-CCAAAAACCCTATT
62210127 TAG
1 TAG
62210130 GGGGGTTTGC
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
105 18 0.19
106 77 0.81
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.27
Consensus pattern (106 bp):
TAGAATTATAATAAAACATATAATAACCCAACCTGAAGTCCAACCTACTCTGGTAATCCAGAATC
CGACCCAAAAACCCCCTTATATACATACCAAAAACCCTATT
Found at i:62213907 original size:2 final size:2
Alignment explanation
Indices: 62213900--62213928 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62213890 TTTTCACACC
62213900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62213929 GTAGGCACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62217161 original size:13 final size:13
Alignment explanation
Indices: 62217143--62217167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62217133 ATATTGATTT
62217143 TTCAGTGTTTTAA
1 TTCAGTGTTTTAA
62217156 TTCAGTGTTTTA
1 TTCAGTGTTTTA
62217168 GTTGGATTTT
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:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
TTCAGTGTTTTAA
Found at i:62232892 original size:17 final size:19
Alignment explanation
Indices: 62232863--62232897 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62232853 TTATTGACGC
62232863 AAATTCAAAAT-AATTTTA
1 AAATTCAAAATAAATTTTA
62232881 AAATTC-AAATAAATTTT
1 AAATTCAAAATAAATTTT
62232898 GACCCTACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTCAAAATAAATTTTA
Found at i:62241386 original size:62 final size:61
Alignment explanation
Indices: 62241186--62241391 Score: 252
Period size: 62 Copynumber: 3.3 Consensus size: 61
62241176 GCATACATTC
*
62241186 TTTGCCTTCAATTCAATAAATTCAACCAAAGAAGAGGGAACTTTAGGTCATATTTACCCAACA
1 TTTGCCTTCAATTCAATAAATTCAAGCAAA-AAGAGGGAACTTTAGGTCA-ATTTACCCAACA
* * *
62241249 TTTGCCTTCAATTTACCCAACAAATTCAAGCAAAAA-AGAGGAACCTTAGGTCAATTTACCTAAC
1 TTTGCCTTCAA-TT---CAATAAATTCAAGCAAAAAGAG-GGAACTTTAGGTCAATTTACCCAAC
62241313 A
61 A
* * * *
62241314 TTTTCCTTCAATTCTATAAATTCAAGCAGAAAAGAGGGAGCTTTAGGTCAATTTACCCAATA
1 TTTGCCTTCAATTCAATAAATTCAAGCA-AAAAGAGGGAACTTTAGGTCAATTTACCCAACA
*
62241376 TTTGCTTTCAATTCAA
1 TTTGCCTTCAATTCAA
62241392 AACCCGACAT
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
61 13 0.11
62 39 0.32
63 13 0.11
64 4 0.03
65 23 0.19
66 15 0.12
67 15 0.12
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (61 bp):
TTTGCCTTCAATTCAATAAATTCAAGCAAAAAGAGGGAACTTTAGGTCAATTTACCCAACA
Found at i:62259056 original size:21 final size:21
Alignment explanation
Indices: 62259032--62259074 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62259022 TATGATAAAC
*
62259032 TAAATTAGGTCAATTTAAATT
1 TAAATTAAGTCAATTTAAATT
* *
62259053 TAAATTAATTGAATTTAAATT
1 TAAATTAAGTCAATTTAAATT
62259074 T
1 T
62259075 TTTTCTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TAAATTAAGTCAATTTAAATT
Found at i:62261065 original size:275 final size:272
Alignment explanation
Indices: 62260561--62261456 Score: 1107
Period size: 275 Copynumber: 3.3 Consensus size: 272
62260551 GTTTTACATT
* * *
62260561 ATAAATGTCATAACCAACACCCAGCATGGTAAGATATTTTCCGCTTTGAGCGCACATGGCCCTCA
1 ATAAATGTCATAACCAACACCCAGCCTGGTAAGATATTGTCCGCTTTGGGCGCACATGGCCCTCA
* * * * ** * * *
62260626 TGGTTTTGTTATTGAGAGTTTCTATACACCCCAAAAGGCCTCTTACCACTTAAGTGTTGCTACCC
66 CGGCTTTGTTCTTGGGAGTGCCCATACACTCCAAAAGGCCTTTTACCACTTAAGTGTTGCTACCC
* * *
62260691 CTTTATATAGCACATGTCTCTCTTGTGCTTTGCCGATGTGAGATTTGCCTAGGGTGTTACATTCA
131 CTTTATATAGCCCAAGTCTCTCCTGTGCTTTGCCGATGTGAGATTTGCCTAGGGTGTTACATTCA
* ** * * * *
62260756 CCTCCCTTAGGGACTCAACATCCTCGCC-GAGGTTTGCCCCACCATCGCTCAAAAAGCATAATGA
196 CC-CCCTTAGGGACTTAATGTCCTC-CCTGAGGTTTGCCCCACCATCGCTCAAGAGGCACAACGA
62260820 GTTGCTCTGATACCA
259 GTTGCTCTGATA-CA
* * ** *
62260835 ATAAATGTCATAGCCAACACCCAGTCC-GGTAAGATATTGTTCATTTTGGGCGCACATGGCCCTT
1 ATAAATGTCATAACCAACACCCAG-CCTGGTAAGATATTGTCCGCTTTGGGCGCACATGGCCCTC
* *
62260899 ACGGCTTTGTTCTTGGGAGCGCCCATACATCTCCAAAAGGCTTTTTACCACTTAAGTGTTGCTAC
65 ACGGCTTTGTTCTTGGGAGTGCCCATACA-CTCCAAAAGGCCTTTTACCACTTAAGTGTTGCTAC
* * *
62260964 CCCTTTATATAGCCCAGGTCTCTCCTGTGCTTTGCTGATGTGAGATTTTCCTAGGGTGTTACATT
129 CCCTTTATATAGCCCAAGTCTCTCCTGTGCTTTGCCGATGTGAGATTTGCCTAGGGTGTTACATT
** * *
62261029 CACTCCCCTTAAAGACTTAATGTCCTCCCTGAGGTTTGCCCCACCATCACTCAAGAGGCACAGCG
194 CAC-CCCCTTAGGGACTTAATGTCCTCCCTGAGGTTTGCCCCACCATCGCTCAAGAGGCACAACG
*
62261094 AGTGGCTCTGATATCA
258 AGTTGCTCTGATA-CA
* * *
62261110 ATAAATGTAATAACCAACACCCAGCCTGGTAAGATATTGTCCGCTTTAGGCGCACATGACCCTCA
1 ATAAATGTCATAACCAACACCCAGCCTGGTAAGATATTGTCCGCTTTGGGCGCACATGGCCCTCA
* * * * * *
62261175 TGGCTTTATTCTTGGGAGTGCTCATACACCTCTAAAAGGCCTTTTATCACTTAAGTGTTGTTACC
66 CGGCTTTGTTCTTGGGAGTGCCCATACA-CTCCAAAAGGCCTTTTACCACTTAAGTGTTGCTACC
* * *
62261240 CCTTTATATAGCCCAAGTCTCTCCCGTGCTTTGCCGATGTGGGATTTGCCTAGGGTATTACATTC
130 CCTTTATATAGCCCAAGTCTCTCCTGTGCTTTGCCGATGTGAGATTTGCCTAGGGTGTTACATTC
* * * * *
62261305 A-CCCCTTAGGGACTTAGTGTCCTCGCTAAGGTTTGCCCTACCATCGCTCAAGAGGCACGACGAG
195 ACCCCCTTAGGGACTTAATGTCCTCCCTGAGGTTTGCCCCACCATCGCTCAAGAGGCACAACGAG
**
62261369 -TGACTCTGATATT
260 TTG-CTCTGATACA
* * * * * * *
62261382 ATAAATGTTATAGCCAATATCCAACCTGGTAAGATATTGTCCGCTTTGGGCGCATATGGCCATCA
1 ATAAATGTCATAACCAACACCCAGCCTGGTAAGATATTGTCCGCTTTGGGCGCACATGGCCCTCA
*
62261447 CGACTTTGTT
66 CGGCTTTGTT
62261457 ATTAGAAATG
Statistics
Matches: 532, Mismatches: 84, Indels: 14
0.84 0.13 0.02
Matches are distributed among these distances:
272 64 0.12
273 62 0.12
274 79 0.15
275 326 0.61
276 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.31
Consensus pattern (272 bp):
ATAAATGTCATAACCAACACCCAGCCTGGTAAGATATTGTCCGCTTTGGGCGCACATGGCCCTCA
CGGCTTTGTTCTTGGGAGTGCCCATACACTCCAAAAGGCCTTTTACCACTTAAGTGTTGCTACCC
CTTTATATAGCCCAAGTCTCTCCTGTGCTTTGCCGATGTGAGATTTGCCTAGGGTGTTACATTCA
CCCCCTTAGGGACTTAATGTCCTCCCTGAGGTTTGCCCCACCATCGCTCAAGAGGCACAACGAGT
TGCTCTGATACA
Found at i:62267794 original size:24 final size:22
Alignment explanation
Indices: 62267752--62267804 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
62267742 AATGGTTTTT
*
62267752 AATTTT-AAAAAATATTTTTAT
1 AATTTTAAAAAAATATTTTTAA
*
62267773 TATTTTAAAAAAATTATATTTTAA
1 AATTTTAAAAAAA-TAT-TTTTAA
62267797 AATTTTAA
1 AATTTTAA
62267805 TTAAATGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 5 0.19
22 6 0.23
23 3 0.12
24 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATTTTAAAAAAATATTTTTAA
Found at i:62270146 original size:12 final size:11
Alignment explanation
Indices: 62270129--62270158 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
62270119 ATTGATTGTC
62270129 TTTTTTTCTTT
1 TTTTTTTCTTT
62270140 TTCTTTTTCTTT
1 TT-TTTTTCTTT
62270152 TTTTTTT
1 TTTTTTT
62270159 ATGTTGCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:62285070 original size:30 final size:28
Alignment explanation
Indices: 62285015--62285094 Score: 133
Period size: 30 Copynumber: 2.8 Consensus size: 28
62285005 GGCCTATTTT
62285015 TATTTTAAAAATTAAAAAAATTTTAAAAA
1 TATTTT-AAAATTAAAAAAATTTTAAAAA
62285044 TATTTTAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAA--ATTTTAAAAA
62285074 TATTTTAAAATTAAAAAAATT
1 TATTTTAAAATTAAAAAAATT
62285095 AAAATAGTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
28 15 0.31
29 6 0.12
30 28 0.57
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
TATTTTAAAATTAAAAAAATTTTAAAAA
Found at i:62285072 original size:11 final size:11
Alignment explanation
Indices: 62285026--62285083 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
62285016 ATTTTAAAAA
*
62285026 TTAAAAAAATT
1 TTAAAAATATT
62285037 TTAAAAATATT
1 TTAAAAATATT
62285048 TT--AAA-A-T
1 TTAAAAATATT
*
62285055 TAAAAAAGTATT
1 TTAAAAA-TATT
62285067 TTAAAAATATT
1 TTAAAAATATT
62285078 TTAAAA
1 TTAAAA
62285084 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
7 2 0.05
8 1 0.03
9 6 0.15
11 23 0.59
12 7 0.18
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:62285091 original size:19 final size:19
Alignment explanation
Indices: 62285069--62285133 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
62285059 AAAGTATTTT
62285069 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
*** **
62285088 AAAAATTAAAATAGTATGT-A
1 AAAAA-TATTTTAAAAT-TAA
62285108 AAAAATATTTTAAAATTAA
1 AAAAATATTTTAAAATTAA
62285127 AAAAATA
1 AAAAATA
62285134 AATATATTTA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATATTTTAAAATTAA
Found at i:62285129 original size:38 final size:39
Alignment explanation
Indices: 62285050--62285132 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
62285040 AAAATATTTT
* *
62285050 AAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
*
62285089 AAAATTAAAATAGTATGTAAAAAATATTTTAAAATTAAA
1 AAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
62285128 AAAAT
1 AAAAT
62285133 AAATATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.34
Consensus pattern (39 bp):
AAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAA
Found at i:62296354 original size:47 final size:47
Alignment explanation
Indices: 62296285--62296400 Score: 214
Period size: 47 Copynumber: 2.5 Consensus size: 47
62296275 TCCATTCGAG
*
62296285 TTTGGGTGTTTTAAGTTACTTGTTTTTGTCATTTTGGGGTTTAAACT
1 TTTGGGTATTTTAAGTTACTTGTTTTTGTCATTTTGGGGTTTAAACT
*
62296332 TTTGGGTATTGTAAGTTACTTGTTTTTGTCATTTTGGGGTTTAAACT
1 TTTGGGTATTTTAAGTTACTTGTTTTTGTCATTTTGGGGTTTAAACT
62296379 TTTGGGTATTTTAAGTTACTTG
1 TTTGGGTATTTTAAGTTACTTG
62296401 ATTTGAGATA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.16, C:0.06, G:0.23, T:0.54
Consensus pattern (47 bp):
TTTGGGTATTTTAAGTTACTTGTTTTTGTCATTTTGGGGTTTAAACT
Found at i:62296562 original size:15 final size:15
Alignment explanation
Indices: 62296542--62296572 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
62296532 ATGTGACATA
62296542 TTATGTGTAATTGTT
1 TTATGTGTAATTGTT
62296557 TTATGTGTAATTGTT
1 TTATGTGTAATTGTT
62296572 T
1 T
62296573 GGTAATTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (15 bp):
TTATGTGTAATTGTT
Found at i:62306357 original size:25 final size:28
Alignment explanation
Indices: 62306302--62306357 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
62306292 TTTGAAAAGT
* *
62306302 TAAGGGTCAAATTAGCTCCAAAAAATGA
1 TAAGGGTCAAATTAGCACAAAAAAATGA
62306330 TAAGGGTCAAATT-G-ACAAAAAAAT-A
1 TAAGGGTCAAATTAGCACAAAAAAATGA
62306355 TAA
1 TAA
62306358 AAGTTGAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 8 0.31
27 1 0.04
28 13 0.50
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.21
Consensus pattern (28 bp):
TAAGGGTCAAATTAGCACAAAAAAATGA
Found at i:62311935 original size:22 final size:22
Alignment explanation
Indices: 62311894--62311978 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
62311884 ATAATCCTAT
**
62311894 AGCTTAGTACGTTAGCCATGAG
1 AGCTTAGTACGTTAAACATGAG
* * *
62311916 GGTTTAGTTCGTTAAACATGAG
1 AGCTTAGTACGTTAAACATGAG
62311938 AGCTTAGTACGTTAAACATGAG
1 AGCTTAGTACGTTAAACATGAG
*
62311960 AGCTTAGTACGTGAAACAT
1 AGCTTAGTACGTTAAACAT
62311979 TGAATGATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (22 bp):
AGCTTAGTACGTTAAACATGAG
Found at i:62314980 original size:201 final size:198
Alignment explanation
Indices: 62314638--62315026 Score: 562
Period size: 201 Copynumber: 1.9 Consensus size: 198
62314628 CAAGGTAAGC
* * * *
62314638 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAATAAAAGAATATGTTTATATCCTCAAGTGC
1 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAAAAAAAAGAAAATGTTTATATCCTCAAGAGC
* * ** * *
62314703 CTAGCATGACCAGACATGATATTGGCAACAGGGAAAAGAGGAGATTGAAAAGAAATTAATCAGCT
66 CTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGATCCAAAAGAAATTAACCACCT
* **
62314768 CGGCAAAGTTGCCCAGCCTTCAAATTCTATTCTACACCTTACAGAGTGACAACCACTTTATAGTA
131 CGGCAAAGTTGCCCAGCCTTCAAATTCCAGCCTACACCTTACAGAGTGACAACCACTTTATAGTA
62314833 ACT
196 ACT
*
62314836 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAATAAAACAAGAAAATGTTTATATCCTTAAGG
1 TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAA-AAAA-AAGAAAATGTTTATATCCTCAA-G
* * * *
62314901 AGCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGTGATCCATAAGATATTGACCA
63 AGCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGATCCAAAAGAAATTAACCA
* * *
62314966 CCTCGGCAAAGTTGCCCATCCTTCAAATTCCAGCCTACATCTTACAGAGTGATAACCACTT
128 CCTCGGCAAAGTTGCCCAGCCTTCAAATTCCAGCCTACACCTTACAGAGTGACAACCACTT
62315027 CATGATAATT
Statistics
Matches: 167, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
198 34 0.20
199 3 0.02
200 20 0.12
201 110 0.66
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (198 bp):
TTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAAAAAAAAGAAAATGTTTATATCCTCAAGAGC
CTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGATCCAAAAGAAATTAACCACCT
CGGCAAAGTTGCCCAGCCTTCAAATTCCAGCCTACACCTTACAGAGTGACAACCACTTTATAGTA
ACT
Found at i:62315260 original size:486 final size:487
Alignment explanation
Indices: 62314349--62315314 Score: 1365
Period size: 486 Copynumber: 2.0 Consensus size: 487
62314339 TTATGGTATT
* *
62314349 TTTTAAAGAAAATTTAGGTCCCATAGACAATTGGAATAAAACAAGAAACTGTTTAACTCCTCAAG
1 TTTTAAAGAAAATTTAGGTCCCATAGACAATTAGAATAAAACAAGAAAATGTTTAACTCCTCAAG
* * *
62314414 GAGCCTAGCATGACCAGACATAGTATTGGCAACAGGGAAAAGAGGAGACCGATAAGAAATTGATC
66 GAGCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGACCGATAAGAAATTGACC
** **
62314479 ACCTCGGCAAAGTTGCCCAGCCTTCAAATTTTTATTCTACATCTTACATAGAGTGACAACCACTT
131 ACCTCGGCAAAGTTGCCCAGCCTTCAAATTTCCAGCCTACATCTTACA-AGAGTGACAACCACTT
* * * *
62314544 CACGATAGTTTGATAAAAACAAGCCCGAGGATAACTACTTTAGATCTAGTTTGATAAAAGTAATC
195 CACGATAATTTGATAAAAACAAGCCCGAGGATAACTACTCTAAATCTAGTTTGATAAAAGAAATC
* * *
62314609 ATGAGGGTAACACCCACTTCAAGGTAAGCTTTAAAGAAAATTTAGGTCCCTTGGGCAATTGGAAA
260 ACGAGGCTAACACCCACTTCAAGGTAAGCTTTAAAGAAAATTTAGGTCCCTTAGGCAATTGGAAA
* * *
62314674 TAAAAGAATATGTTTATATCCTCAAGTGCCTAGCATGACCAGACATGATATTGGCAACAGGGAAA
325 AAAAAGAATATGTTTATATCCTCAAGAGCCTAGCATGACCAGACATAATATTGGCAACAGGGAAA
* * * *
62314739 AGAGGAGATTGAAAAGAAATTAATCAGCTCGGCAAAGTTGCCCAGCCTTCAAA-TTCTATTCTAC
390 AGAGGAGATCGAAAAGAAATTAACCACCTCGGCAAAGTTGCCCAGCCATCAAATTTCTATTCTAC
*
62314803 ACCTTAC-AGAGTGACAACCACTTTATAGTAAC
455 ACCTTACAAGAGGGACAACCACTTTATAGTAAC
* * * *
62314835 TTTTAAAGAAAATTTAGGTCCCTTGGGCAATTAGAATAAAACAAGAAAATGTTTATA-TCCTTAA
1 TTTTAAAGAAAATTTAGGTCCCATAGACAATTAGAATAAAACAAGAAAATGTTTA-ACTCCTCAA
* *
62314899 GGAGCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGTGATCC-ATAAGATATTGA
65 GGAGCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGA-CCGATAAGAAATTGA
* *
62314963 CCACCTCGGCAAAGTTGCCCATCCTTCAAA-TTCCAGCCTACATCTTAC-AGAGTGATAACCACT
129 CCACCTCGGCAAAGTTGCCCAGCCTTCAAATTTCCAGCCTACATCTTACAAGAGTGACAACCACT
* ** * *
62315026 TCATGATAATTTGATAAAAACAATTCCTA-GAGTAACTACTCTAAATCTTGTTTGATAAAAGAAA
194 TCACGATAATTTGATAAAAACAAGCCCGAGGA-TAACTACTCTAAATCTAGTTTGATAAAAGAAA
* * ***
62315090 TCACGAGGCTAACAGCCACTTTATA-GTATTTTTTAAAGAAAATTTAGGTCCCTTAGGCAATTGG
258 TCACGAGGCTAACACCCACTTCA-AGGTAAGCTTTAAAGAAAATTTAGGTCCCTTAGGCAATTGG
*
62315154 AATAAAACAAGAA-ACTGTTTATATCCTTAAGGAGCCTAGCATGACCAGACATAATATTGGCAAC
322 AA-AAAA-AAGAATA-TGTTTATATCCTCAA-GAGCCTAGCATGACCAGACATAATATTGGCAAC
* *
62315218 AGGGAAAAGAGGAGATCGATAAGAAATTGACCACCTCGGCAAAGTTGCCCAGCCATCAAATTTCT
383 AGGGAAAAGAGGAGATCGAAAAGAAATTAACCACCTCGGCAAAGTTGCCCAGCCATCAAATTTCT
*
62315283 ATTCTACATCTTACATAGAGGGACAACCACTT
448 ATTCTACACCTTACA-AGAGGGACAACCACTT
62315315 CACAATAGGT
Statistics
Matches: 423, Mismatches: 46, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
482 2 0.00
483 122 0.29
484 5 0.01
485 33 0.08
486 226 0.53
487 20 0.05
489 15 0.04
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (487 bp):
TTTTAAAGAAAATTTAGGTCCCATAGACAATTAGAATAAAACAAGAAAATGTTTAACTCCTCAAG
GAGCCTAGCAAGACCAGACATAATATTGGCAACAGGGAAAAGAGGAGACCGATAAGAAATTGACC
ACCTCGGCAAAGTTGCCCAGCCTTCAAATTTCCAGCCTACATCTTACAAGAGTGACAACCACTTC
ACGATAATTTGATAAAAACAAGCCCGAGGATAACTACTCTAAATCTAGTTTGATAAAAGAAATCA
CGAGGCTAACACCCACTTCAAGGTAAGCTTTAAAGAAAATTTAGGTCCCTTAGGCAATTGGAAAA
AAAAGAATATGTTTATATCCTCAAGAGCCTAGCATGACCAGACATAATATTGGCAACAGGGAAAA
GAGGAGATCGAAAAGAAATTAACCACCTCGGCAAAGTTGCCCAGCCATCAAATTTCTATTCTACA
CCTTACAAGAGGGACAACCACTTTATAGTAAC
Found at i:62318585 original size:17 final size:17
Alignment explanation
Indices: 62318563--62318604 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
62318553 TTTTCTTTCT
62318563 TCTTTCTTTTGTTTGTC
1 TCTTTCTTTTGTTTGTC
62318580 TCTTTCTTTTGTTTGTC
1 TCTTTCTTTTGTTTGTC
62318597 TCTTTCTT
1 TCTTTCTT
62318605 ATACGTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.00, C:0.19, G:0.10, T:0.71
Consensus pattern (17 bp):
TCTTTCTTTTGTTTGTC
Found at i:62320282 original size:20 final size:20
Alignment explanation
Indices: 62320257--62320296 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
62320247 CCGTTTTGCT
62320257 TTTTGATCTAGCTTATAGAG
1 TTTTGATCTAGCTTATAGAG
62320277 TTTTGATCTAGCTTATAGAG
1 TTTTGATCTAGCTTATAGAG
62320297 ACCAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (20 bp):
TTTTGATCTAGCTTATAGAG
Found at i:62323847 original size:15 final size:16
Alignment explanation
Indices: 62323827--62323859 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62323817 AATTTTGATT
*
62323827 AAAAATATACA-AAAA
1 AAAAATAAACATAAAA
62323842 AAAAATAAACATAAAA
1 AAAAATAAACATAAAA
62323858 AA
1 AA
62323860 TCCAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAATAAACATAAAA
Found at i:62325997 original size:102 final size:102
Alignment explanation
Indices: 62325851--62326251 Score: 480
Period size: 102 Copynumber: 3.8 Consensus size: 102
62325841 AATTCAATGG
* ** * ** * * **
62325851 CATTTCACCTGCAAG-ATCTCTTGCATCAGAGGGTGTTGGCATATTTGGCTCTTGCGTTCCAGGC
1 CATTTCACCTGC-AGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGC
62325915 ATGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
65 ATGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
*
62325953 CATTTCACCTGCAGCATCTCTTACATCCTCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
62326018 TGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
66 TGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
*
62326055 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGCTGGAATATTCAGCTCTTGCCTTTCTTGCA
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
* * *
62326120 TGCTACGGTTCATGTTTTGATGGACTTGATCGTCGGAGCTCGATGG
66 TGCTACGGTTCGTGTTTTGAT---C--GA---T-GGAACTCGATGC
* ** * ** * *
62326166 CATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATATTCAGCTCTTGCCTTCCCTGCA
1 CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
* *
62326231 TGCTACTGTTCATGTTTTGAT
66 TGCTACGGTTCGTGTTTTGAT
62326252 AAACTTGATT
Statistics
Matches: 263, Mismatches: 26, Indels: 11
0.88 0.09 0.04
Matches are distributed among these distances:
101 2 0.01
102 171 0.65
105 1 0.00
107 2 0.01
110 1 0.00
111 86 0.33
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (102 bp):
CATTTCACCTGCAGCATCTCTTACATCATCGGGTGTTGGAATATTCAGCTCTTGCCTTTCTTGCA
TGCTACGGTTCGTGTTTTGATCGATGGAACTCGATGC
Found at i:62326210 original size:111 final size:109
Alignment explanation
Indices: 62326034--62326371 Score: 372
Period size: 111 Copynumber: 3.0 Consensus size: 109
62326024 GGTTCGTGTT
* * ** * *
62326034 TTGATCGATGGAACTCGATGCCATTTCACCTGCAGCATCTCTTACATCATCGGGTGCTGGAATAT
1 TTGATCG-TGGAACTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGGTG-TTGTATAT
* * **
62326099 TCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGAC
64 TCAGCTCTTGCCTTCCCTGCATGCTACGGTTCATGTTTTGATAAAC
* *
62326145 TTGATCGTCGGAGCTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGTCATAT
1 TTGATCGT-GGAACTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGGTGTTGT-ATAT
*
62326210 TCAGCTCTTGCCTTCCCTGCATGCTACTGTTCATGTTTTGATAAAC
64 TCAGCTCTTGCCTTCCCTGCATGCTACGGTTCATGTTTTGATAAAC
* * * * * * *
62326256 TTGATTAGTGGACCTCAATGGCCA-TTCACCTACAGCATGTCTTGCATAAAAGGGTCTCTGTATA
1 TTGA-TCGTGGAACTCGATGG-CATTTCACCTGCAGCATCTCTTGCATCAAAGGGTGT-TGTATA
* * * * * *
62326320 TTCGGTTCTTGCCATCCCTGCATGCTTCGGCTCATGTTTTCATAAAC
63 TTCAGCTCTTGCCTTCCCTGCATGCTACGGTTCATGTTTTGATAAAC
62326367 TTGAT
1 TTGAT
62326372 TAATGGAACT
Statistics
Matches: 194, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
110 4 0.02
111 182 0.94
112 8 0.04
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (109 bp):
TTGATCGTGGAACTCGATGGCATTTCACCTGCAGCATCTCTTGCATCAAAGGGTGTTGTATATTC
AGCTCTTGCCTTCCCTGCATGCTACGGTTCATGTTTTGATAAAC
Found at i:62326372 original size:111 final size:110
Alignment explanation
Indices: 62326095--62326443 Score: 351
Period size: 111 Copynumber: 3.1 Consensus size: 110
62326085 GGGTGCTGGA
* * * * ** * *
62326095 ATATTCAGCTCTTGCCTTTCTTGCATGCTACGGTTCATGTTTTGATGGACTTGA-TCGTCGGAGC
1 ATATTCGGCTCTTGCCATCCCTGCATGCTACGGTTCATGTTTTGATAAACTTGATTAGT-GGAAC
* * * * * *
62326159 TCGATGG-CATTTCACCTGCAGCATCTCTTGCATCAAAGGATGTTGT
65 TCAATGGCCA-TTCACCTACAGCATATCTTGCATAAAAGGGTATTGT
* * * *
62326205 CATATTCAGCTCTTGCCTTCCCTGCATGCTACTGTTCATGTTTTGATAAACTTGATTAGTGGACC
1 -ATATTCGGCTCTTGCCATCCCTGCATGCTACGGTTCATGTTTTGATAAACTTGATTAGTGGAAC
* *
62326270 TCAATGGCCATTCACCTACAGCATGTCTTGCATAAAAGGGTCTCTGT
65 TCAATGGCCATTCACCTACAGCATATCTTGCATAAAAGGGTAT-TGT
* * * * *
62326317 ATATTCGGTTCTTGCCATCCCTGCATGCTTCGGCTCATGTTTTCATAAACTTGATTAATGGAACT
1 ATATTCGGCTCTTGCCATCCCTGCATGCTACGGTTCATGTTTTGATAAACTTGATTAGTGGAACT
** * * * * *
62326382 CAATGGCTGTACACCTACAGCACAACTTCCATAAAAGGGTATTCGA
66 CAATGGCCATTCACCTACAGCATATCTTGCATAAAAGGGTATT-GT
62326428 ATATTCGGCTCTTGCC
1 ATATTCGGCTCTTGCC
62326444 TATATACTTG
Statistics
Matches: 202, Mismatches: 32, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
110 1 0.00
111 193 0.96
112 8 0.04
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (110 bp):
ATATTCGGCTCTTGCCATCCCTGCATGCTACGGTTCATGTTTTGATAAACTTGATTAGTGGAACT
CAATGGCCATTCACCTACAGCATATCTTGCATAAAAGGGTATTGT
Found at i:62327475 original size:2 final size:2
Alignment explanation
Indices: 62327468--62327503 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
62327458 ATGTGTTTAA
62327468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62327504 TCTTGAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62328851 original size:43 final size:43
Alignment explanation
Indices: 62328764--62328852 Score: 99
Period size: 43 Copynumber: 2.1 Consensus size: 43
62328754 AATAAAAATA
* * * * *
62328764 TTTATTTTTTTAAATTTTTAAAATAAGTTTTTAACATACCTTT
1 TTTAATTTTTTAAATTTTAAAAATAAGTTTTTAAAAGAACTTT
* *
62328807 TTTAATTTTTTAAATTTTAAAAA-ATATTTTTTAAAAGAAGTTT
1 TTTAATTTTTTAAATTTTAAAAATA-AGTTTTTAAAAGAACTTT
62328850 TTT
1 TTT
62328853 TTAATTTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (43 bp):
TTTAATTTTTTAAATTTTAAAAATAAGTTTTTAAAAGAACTTT
Found at i:62328864 original size:34 final size:35
Alignment explanation
Indices: 62328812--62328893 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 35
62328802 CCTTTTTTAA
* *
62328812 TTTTTTAAATTTTAAAAAATATTTTTTAAAAGAA-G-T
1 TTTTTTTAA-TTTAAAAAA-AATTTTTAAAA-AATGCT
62328848 TTTTTTTAATTT-AAAAAAATTTTTAAAAAATGCT
1 TTTTTTTAATTTAAAAAAAATTTTTAAAAAATGCT
*
62328882 TTTTTTTTATTT
1 TTTTTTTAATTT
62328894 TTTTTAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 11 0.27
34 17 0.41
35 3 0.07
36 8 0.20
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTTTTTAATTTAAAAAAAATTTTTAAAAAATGCT
Found at i:62328886 original size:35 final size:36
Alignment explanation
Indices: 62328812--62328894 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 36
62328802 CCTTTTTTAA
*
62328812 TTTTTTAAATTTTAAAAAATATTTTTTAAAAGAAGT
1 TTTTTTTAATTTTAAAAAATATTTTTTAAAAGAAGT
62328848 TTTTTTTAA-TTTAAAAAA-A-TTTTTAAAA-AATGCT
1 TTTTTTTAATTTTAAAAAATATTTTTTAAAAGAA-G-T
*
62328882 TTTTTTTTATTTT
1 TTTTTTTAATTTT
62328895 TTTTAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.05
33 10 0.24
34 10 0.24
35 12 0.29
36 8 0.19
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.57
Consensus pattern (36 bp):
TTTTTTTAATTTTAAAAAATATTTTTTAAAAGAAGT
Found at i:62328931 original size:45 final size:43
Alignment explanation
Indices: 62328847--62328932 Score: 102
Period size: 46 Copynumber: 1.9 Consensus size: 43
62328837 TTAAAAGAAG
*
62328847 TTTTTTTTAATTTAAAAAAATTTTTAAAAAATGCTTTTTTTTTA
1 TTTTTTTTAATTTAAAAAAATTTTTAAAAAAT-CATTTTTTTTA
* *
62328891 TTTTTTTTAAATTTTAAAATATTTTTTAGAAAAAT-ATTTTTT
1 TTTTTTTT-AA-TTTAAAAAAATTTTTA-AAAAATCATTTTTT
62328933 AAANNNNNNN
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
44 8 0.22
45 8 0.22
46 14 0.39
47 6 0.17
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (43 bp):
TTTTTTTTAATTTAAAAAAATTTTTAAAAAATCATTTTTTTTA
Found at i:62329566 original size:23 final size:23
Alignment explanation
Indices: 62329540--62329584 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
62329530 AAATTAGTTC
62329540 GTTTTGAATGAAAAAGTTGATTT
1 GTTTTGAATGAAAAAGTTGATTT
62329563 GTTTTGAATGAAAAAGTTGATT
1 GTTTTGAATGAAAAAGTTGATT
62329585 GGAGTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (23 bp):
GTTTTGAATGAAAAAGTTGATTT
Found at i:62330341 original size:22 final size:22
Alignment explanation
Indices: 62330315--62330357 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
62330305 GAATAAACTA
*
62330315 TTTTGCTACCATTTCGCTATTG
1 TTTTGCTACAATTTCGCTATTG
* *
62330337 TTTTGCTGCAATTTCGTTATT
1 TTTTGCTACAATTTCGCTATT
62330358 ATATTGTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.53
Consensus pattern (22 bp):
TTTTGCTACAATTTCGCTATTG
Found at i:62331624 original size:16 final size:17
Alignment explanation
Indices: 62331603--62331637 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
62331593 TTAATAATGT
*
62331603 AATTAAAA-TATTTTAA
1 AATTAAAATTAATTTAA
62331619 AATTAAAATTAATTTAA
1 AATTAAAATTAATTTAA
62331636 AA
1 AA
62331638 GAGGATGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTAAAATTAATTTAA
Found at i:62332222 original size:37 final size:37
Alignment explanation
Indices: 62332180--62332258 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
62332170 TTAAATTAAT
62332180 TTAATATTT-T-ATTATATTAATTAAAATATTGTTTTTA
1 TTAATATTTGTGATT-TATTAATTAAAATATT-TTTTTA
* *
62332217 TTAATATTTGTGATTTATTAGTTAAAATCTTTTTTTA
1 TTAATATTTGTGATTTATTAATTAAAATATTTTTTTA
62332254 -TAATA
1 TTAATA
62332259 CGAATAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
36 5 0.13
37 15 0.39
38 15 0.39
39 3 0.08
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.58
Consensus pattern (37 bp):
TTAATATTTGTGATTTATTAATTAAAATATTTTTTTA
Found at i:62332881 original size:123 final size:123
Alignment explanation
Indices: 62332660--62332907 Score: 399
Period size: 123 Copynumber: 2.0 Consensus size: 123
62332650 TGTTTTATTT
* * * *
62332660 AGAAAAACTTTGTGAATTAATTTTATGGAGGGATTTTGTGATGTTTTCAAATAATCGTATACATT
1 AGAAAAACTTTGTCAATTAATCTTATGGAGGGATTTTGTGATCTTTTCAAATAATCGTAGACATT
*
62332725 CAGGGTTTTTATAAAGTTGGGTGATAAAATTCTATCATATATAAGTATCGACCTTAAA
66 CAGGGTTTTTATAAAGTTGGGTGATAAAATTCTATCATAAATAAGTATCGACCTTAAA
* *
62332783 AGAAAAAGC-TTGTCAATTGATCTTATGGAGGGATTTTGTTATCTTTTCAAATAATCGTAGACAT
1 AGAAAAA-CTTTGTCAATTAATCTTATGGAGGGATTTTGTGATCTTTTCAAATAATCGTAGACAT
* *
62332847 TCAGGGTTTTTATAAAGTTGGGTGATAAAGTTCTATCATAAATAAGTATTGACCTTAAA
65 TCAGGGTTTTTATAAAGTTGGGTGATAAAATTCTATCATAAATAAGTATCGACCTTAAA
62332906 AG
1 AG
62332908 GGTTTTGTCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
123 114 0.99
124 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (123 bp):
AGAAAAACTTTGTCAATTAATCTTATGGAGGGATTTTGTGATCTTTTCAAATAATCGTAGACATT
CAGGGTTTTTATAAAGTTGGGTGATAAAATTCTATCATAAATAAGTATCGACCTTAAA
Found at i:62343725 original size:26 final size:27
Alignment explanation
Indices: 62343674--62343728 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
62343664 TTTAAAATAC
* * *
62343674 TTTTAAAATATTTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
62343701 TTTTAAAATAATTTTTTA-ATGTTTAT
1 TTTTAAAATAATTTTTTATATGTTTAT
62343727 TT
1 TT
62343729 AAAAATAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTATATGTTTAT
Found at i:62344164 original size:143 final size:143
Alignment explanation
Indices: 62343904--62344185 Score: 465
Period size: 143 Copynumber: 2.0 Consensus size: 143
62343894 AAAACACAAA
*
62343904 ACCAAGTAATTCCTTAATGTTGGTATATTAAATGTAAACATAAATGTCAGTGATGGACTAAAGCA
1 ACCAAGTAATTCCTTAATGTTGGTATATTAAATGGAAACATAAATGTCAGTGATGGACTAAAGCA
* * * *
62343969 ATTAGATTCAAGTTCAGCCTCAATTAGTTTCAAAGCCGCGATGGGCAACTCTCAATTTACTGCAT
66 ATTAGATGCAAGTTCAGCCACAATTAGTTTCAAAGCCGCAATGGGCAACTCTCAATTTACGGCAT
62344034 AAGCGTTGACCAG
131 AAGCGTTGACCAG
** *
62344047 ACCAAGTTCTTCCTTAATGTTGGTATATTAAATGGAAACATAAATGTTAGTGATGGACTAAAGCA
1 ACCAAGTAATTCCTTAATGTTGGTATATTAAATGGAAACATAAATGTCAGTGATGGACTAAAGCA
* *
62344112 ATTAGATGCAAGTTCAGCCACAATTAGTTTCAACGCCGCAATGGGCAGCTCTCAATTTACGGCAT
66 ATTAGATGCAAGTTCAGCCACAATTAGTTTCAAAGCCGCAATGGGCAACTCTCAATTTACGGCAT
*
62344177 ATGCGTTGA
131 AAGCGTTGA
62344186 TCATTAGGGT
Statistics
Matches: 128, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
143 128 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (143 bp):
ACCAAGTAATTCCTTAATGTTGGTATATTAAATGGAAACATAAATGTCAGTGATGGACTAAAGCA
ATTAGATGCAAGTTCAGCCACAATTAGTTTCAAAGCCGCAATGGGCAACTCTCAATTTACGGCAT
AAGCGTTGACCAG
Found at i:62356862 original size:13 final size:13
Alignment explanation
Indices: 62356844--62356869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62356834 CATTGTCAAG
62356844 GTGATTAACAATC
1 GTGATTAACAATC
62356857 GTGATTAACAATC
1 GTGATTAACAATC
62356870 TTCGAGGCCT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
GTGATTAACAATC
Found at i:62362653 original size:2 final size:2
Alignment explanation
Indices: 62362646--62362685 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
62362636 TAATTAAGCA
62362646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62362686 TGTTTATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62372021 original size:14 final size:16
Alignment explanation
Indices: 62371997--62372028 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62371987 TTTTTCCCTC
62371997 TTTCTATTTGTA-ATT
1 TTTCTATTTGTATATT
62372012 TTTC-ATTTGTATATT
1 TTTCTATTTGTATATT
62372027 TT
1 TT
62372029 ACAGTGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTCTATTTGTATATT
Found at i:62372683 original size:30 final size:30
Alignment explanation
Indices: 62372649--62372724 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
62372639 TAAAATTAAT
* *
62372649 AATAATAAAATTATATTTTAATTCTTCAAA
1 AATAATAAAATTATAATTTAAGTCTTCAAA
*
62372679 AATAATAATAATT-TAATTTAAGTCTTTAAA
1 AATAATAA-AATTATAATTTAAGTCTTCAAA
*
62372709 AA-ATATAAAAATATAA
1 AATA-ATAAAATTATAA
62372725 ATTATTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 4 0.10
30 31 0.79
31 4 0.10
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (30 bp):
AATAATAAAATTATAATTTAAGTCTTCAAA
Found at i:62372739 original size:16 final size:17
Alignment explanation
Indices: 62372714--62372746 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62372704 TTAAAAAATA
62372714 TAAAAATAT-AAATTAT
1 TAAAAATATAAAATTAT
*
62372730 TAAAATTATAAAATTAT
1 TAAAAATATAAAATTAT
62372747 ATTTAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATATAAAATTAT
Found at i:62375163 original size:2 final size:2
Alignment explanation
Indices: 62375156--62375183 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62375146 ATAGCTACTA
62375156 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
62375184 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62375188 original size:2 final size:2
Alignment explanation
Indices: 62375183--62375215 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62375173 TATATATATA
62375183 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
62375216 ATGATCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:62376798 original size:21 final size:20
Alignment explanation
Indices: 62376768--62376809 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
62376758 TTTAATCATT
62376768 TAATTTTAAA-TATTATAAAA
1 TAATTTTAAATTATT-TAAAA
62376788 TAATTATTAAATTATTTAAAA
1 TAATT-TTAAATTATTTAAAA
62376809 T
1 T
62376810 TTTCAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATTTTAAATTATTTAAAA
Found at i:62378762 original size:21 final size:22
Alignment explanation
Indices: 62378720--62378762 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
62378710 AATTTACCGG
62378720 ATTAAATCAATTTTGAAAAAAA
1 ATTAAATCAATTTTGAAAAAAA
62378742 ATTAAATCAATTTTGAAAAAA
1 ATTAAATCAATTTTGAAAAAA
62378763 TAGGTGCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (22 bp):
ATTAAATCAATTTTGAAAAAAA
Found at i:62396774 original size:285 final size:288
Alignment explanation
Indices: 62396222--62396835 Score: 830
Period size: 288 Copynumber: 2.1 Consensus size: 288
62396212 CCCTACTTTC
* * * * * *
62396222 AAAACCAATGAATACGA-AAACATAGCATCAAACAACAATTATACTTATCATATACCATAATCAA
1 AAAACAAAAGAATAGGACAAACATAGCATCAAACTACAACTATACTTAACATATACCATAATCAA
* * *
62396286 AAAGATGCCATCCAAATCATCATCAAACTAAGCTGAAAACCAGAAACTATGAATGCTTAAATGAT
66 AAAGATGCCATCCAAATCATCATCAAACTAAGCTGAAAACCAGAAACTATCAATGCTGAAACGAT
62396351 ACCAAAAGAACAGGAAAGTCGACTGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACAT
131 ACCAAAAGAACAGGAAAGTCGA-TGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACAT
* * * *
62396416 TTTTAAGTTAAAAAATGTAGTAATATCACTTCCGAAGCACGTTATTATATCGGCTTTTCACTACC
195 TTGTAAGTTAAAAAATGTACTAATATCACTTCCGAAGCACGTTATCATATCCGCTTTTCACTACC
* *
62396481 AATCACTACTTC-CAAACAACTTC-AGTTG
260 AATCACTAC-TCACAAACAACTTCAAGATA
* * *
62396509 AAAGCAAAAGAATGGGAC-AACATAGCATCAAACTACAAGCTATACTTAACATATTCCATAATCA
1 AAAACAAAAGAATAGGACAAACATAGCATCAAACTACAA-CTATACTTAACATATACCATAATCA
* * * * * * *
62396573 CAAAGATGCCTTCCAAATCATCATCAAACTATGTTGAAAA-TAGGAAATTA-CAAGTGCTGATAC
65 AAAAGATGCCATCCAAATCATCATCAAACTAAGCTGAAAACCA-GAAACTATCAA-TGCTGAAAC
* *
62396636 GATACCAAAAGAACAGGAAAGTCG-TGTTCTTAAACCACTTGAAAGCATAA-TCAATGACTTCAG
128 GATACCAAAAGAACAGGAAAGTCGATGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCAC
*
62396699 ATTTGTAAGTTCAAAAATGTACTAATATCACTTCCGAAGCACGTTATCATATCCGCTTTTCACTA
193 ATTTGTAAGTTAAAAAATGTACTAATATCACTTCCGAAGCACGTTATCATATCCGCTTTTCACTA
*
62396764 CCAATCACTACTCACAAACTACTTCAAAGATA
258 CCAATCACTACTCACAAACAACTTC-AAGATA
* * *
62396796 AAAACAAAAGAATAGGACAAACCTAGCATAAAACTGCAAC
1 AAAACAAAAGAATAGGACAAACATAGCATCAAACTACAAC
62396836 AAATATAAGA
Statistics
Matches: 285, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
284 2 0.01
285 92 0.32
286 26 0.09
287 54 0.19
288 111 0.39
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (288 bp):
AAAACAAAAGAATAGGACAAACATAGCATCAAACTACAACTATACTTAACATATACCATAATCAA
AAAGATGCCATCCAAATCATCATCAAACTAAGCTGAAAACCAGAAACTATCAATGCTGAAACGAT
ACCAAAAGAACAGGAAAGTCGATGTTCTTAAACCACTTGAAAGCATAATTAAATGACTTCACATT
TGTAAGTTAAAAAATGTACTAATATCACTTCCGAAGCACGTTATCATATCCGCTTTTCACTACCA
ATCACTACTCACAAACAACTTCAAGATA
Found at i:62400212 original size:92 final size:92
Alignment explanation
Indices: 62400030--62400251 Score: 322
Period size: 91 Copynumber: 2.4 Consensus size: 92
62400020 TTTTTAGATT
* *
62400030 TTAGGGTTT-GATGTTTATGGTTTTTAAGAAAATAAATAAATAAATTAGAGTTTAGAATTACTTG
1 TTAGGGTTTAG-TGTTTAAGGTTTTTAAG--GA-AAA-AAATAAATTAGAGTTTAGAATTACTTG
62400094 AGTAAATTAATTATAAATTTTAAAAAAATTAGA
61 AGTAAATTAATTATAAA-TTTAAAAAAATTAGA
* *
62400127 TTAGGGTTTAGTGTTTAAGGTTTTTAAGGAAAAAAATAAATTAGGGTTTAG-GTTACTTGAGTAA
1 TTAGGGTTTAGTGTTTAAGGTTTTTAAGGAAAAAAATAAATTAGAGTTTAGAATTACTTGAGTAA
62400191 ATTAATTATAAATTTAAAAAAATTAGA
66 ATTAATTATAAATTTAAAAAAATTAGA
* *
62400218 TTAGGGTTTAGTATTTAGGGTTTTTAAGGAAAAA
1 TTAGGGTTTAGTGTTTAAGGTTTTTAAGGAAAAA
62400252 TCAAATAGAA
Statistics
Matches: 118, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
91 47 0.40
92 24 0.20
93 17 0.14
94 3 0.03
95 1 0.01
97 25 0.21
98 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.18, T:0.40
Consensus pattern (92 bp):
TTAGGGTTTAGTGTTTAAGGTTTTTAAGGAAAAAAATAAATTAGAGTTTAGAATTACTTGAGTAA
ATTAATTATAAATTTAAAAAAATTAGA
Found at i:62400968 original size:16 final size:16
Alignment explanation
Indices: 62400929--62400971 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
62400919 TTAATTTTTT
*
62400929 CCTTAAAACCCTAAAA
1 CCTTAAAACCCAAAAA
* * *
62400945 TCTAAAAACTCAAAAA
1 CCTTAAAACCCAAAAA
62400961 CCTTAAAACCC
1 CCTTAAAACCC
62400972 TAACTCTAAT
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (16 bp):
CCTTAAAACCCAAAAA
Found at i:62401095 original size:40 final size:39
Alignment explanation
Indices: 62401022--62401136 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 39
62401012 GGAAGTGTTT
**
62401022 CCTCAAGGAAGC-ACTTTGTCCACGTGGACACAAAGCACTC
1 CCTCAAGGAAGCGTTTTTGTCCACGTGG--ACAAAGCACTC
* *
62401062 CCTCAAGGAAGCGTTTTCTGTCCACGTGGACAAAGCGCTT
1 CCTCAAGGAAGCGTTTT-TGTCCACGTGGACAAAGCACTC
**
62401102 CCTTGAGGAAGCGTTTTTTGTCCACGTGGACAAAG
1 CCTCAAGGAAGCG-TTTTTGTCCACGTGGACAAAG
62401137 TACTTCCTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
40 49 0.74
41 6 0.09
42 11 0.17
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.23
Consensus pattern (39 bp):
CCTCAAGGAAGCGTTTTTGTCCACGTGGACAAAGCACTC
Found at i:62401143 original size:40 final size:40
Alignment explanation
Indices: 62401036--62401147 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
62401026 AAGGAAGCAC
* *
62401036 TTTGTCCACGTGGACACAAAGCACTCCCTCAAGGAAGCGTTT
1 TTTGTCCACGTGG--ACAAAGCACTTCCTTAAGGAAGCGTTT
* * *
62401078 TCTGTCCACGTGGACAAAGCGCTTCCTTGAGGAAGCGTTT
1 TTTGTCCACGTGGACAAAGCACTTCCTTAAGGAAGCGTTT
*
62401118 TTTGTCCACGTGGACAAAGTACTTCCTTAA
1 TTTGTCCACGTGGACAAAGCACTTCCTTAA
62401148 ATAAGCATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 49 0.80
42 12 0.20
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
TTTGTCCACGTGGACAAAGCACTTCCTTAAGGAAGCGTTT
Found at i:62407100 original size:31 final size:29
Alignment explanation
Indices: 62407064--62407131 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 29
62407054 GGTAACAGTT
62407064 TAAAAAAATATTATTATTTATAATTTTTAAA
1 TAAAAAAATATTATTATTTAT-ATTTTT-AA
* * * *
62407095 TAAAAATATATTTTTTTTTCTATTTTTAA
1 TAAAAAAATATTATTATTTATATTTTTAA
*
62407124 TAACAAAA
1 TAAAAAAA
62407132 CAGAGCATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 8 0.26
30 6 0.19
31 17 0.55
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
TAAAAAAATATTATTATTTATATTTTTAA
Found at i:62408331 original size:22 final size:22
Alignment explanation
Indices: 62408302--62408358 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
62408292 ATATCCAAAC
* *
62408302 AATAACAACAAATTAGTAGTAA
1 AATAACAACAAAATAGTAGCAA
*
62408324 TAA-AACAACAAAATGGTAGCAA
1 -AATAACAACAAAATAGTAGCAA
62408346 AATAACAACAAAA
1 AATAACAACAAAA
62408359 AAGAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.07
22 26 0.87
23 2 0.07
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.16
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:62408748 original size:28 final size:31
Alignment explanation
Indices: 62408692--62408761 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 31
62408682 TTTAGTACAA
*
62408692 ATAAAATTATACTTTAATTCTTTTTAAAAAT
1 ATAAAATTATAATTTAATTCTTTTTAAAAAT
*
62408723 ATAAAATT-TAATTTAA-T-TTTTTAAAATT
1 ATAAAATTATAATTTAATTCTTTTTAAAAAT
*
62408751 ATAAAAATATA
1 ATAAAATTATA
62408762 GACTATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 17 0.49
29 3 0.09
30 7 0.20
31 8 0.23
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
ATAAAATTATAATTTAATTCTTTTTAAAAAT
Found at i:62409027 original size:23 final size:25
Alignment explanation
Indices: 62408986--62409033 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
62408976 TATAATTTGA
*
62408986 GATATAATTTTTATATTTTAATTTT
1 GATATAATTTTAATATTTTAATTTT
*
62409011 GATATAA-TTTAAT-TTTTTATTTT
1 GATATAATTTTAATATTTTAATTTT
62409034 AATAATGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (25 bp):
GATATAATTTTAATATTTTAATTTT
Found at i:62409353 original size:22 final size:22
Alignment explanation
Indices: 62409311--62409353 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
62409301 TATTTTTAAG
* *
62409311 TTTAGTTTTGTACTAATTATTC
1 TTTAGTTTTGTACCAACTATTC
62409333 TTTA-TTTTGTATCCAACTATT
1 TTTAGTTTTGTA-CCAACTATT
62409354 ATAATACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTAGTTTTGTACCAACTATTC
Found at i:62410591 original size:51 final size:49
Alignment explanation
Indices: 62410460--62410592 Score: 203
Period size: 50 Copynumber: 2.7 Consensus size: 49
62410450 AGTGAAAGTG
* *
62410460 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATA
*
62410509 ATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAAGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAA--TA
*
62410561 ATGGTCACATGTGTAGTACTATGTGTAGGCTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTA
62410593 TTATGTGAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
49 2 0.03
50 43 0.56
51 29 0.38
52 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (49 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCGGAATA
Found at i:62410655 original size:45 final size:45
Alignment explanation
Indices: 62410606--62410694 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
62410596 TGTGAACTAA
* * *
62410606 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGATTGCTATGTGCTGAATCCACCGG
62410651 ACATCATTGATTAATAAGGTGATTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGATTGCTATGTGCTGAATCCACCG
62410695 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGATTGCTATGTGCTGAATCCACCGG
Found at i:62418976 original size:50 final size:50
Alignment explanation
Indices: 62418917--62419018 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 50
62418907 CCTATATATT
* * *
62418917 TTTCATTCGGTT-ATTTTTGTCGCCATCTTCACTATTCTTCCTTCTTTTTC
1 TTTCATTCGGTTGATTTTTGTCACCATCTTCACTACTCTT-CTTCTTCTTC
* *
62418967 TTTCATTCGGTTGTTTTTTGTCATCATCTTCACTACTCTTCTTCTTCTTC
1 TTTCATTCGGTTGATTTTTGTCACCATCTTCACTACTCTTCTTCTTCTTC
62419017 TT
1 TT
62419019 CTTCTTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 23 0.50
51 23 0.50
ACGTcount: A:0.10, C:0.25, G:0.08, T:0.57
Consensus pattern (50 bp):
TTTCATTCGGTTGATTTTTGTCACCATCTTCACTACTCTTCTTCTTCTTC
Found at i:62423962 original size:2 final size:2
Alignment explanation
Indices: 62423952--62423996 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
62423942 TTCAAAAAAA
62423952 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62423993 AT AT
1 AT AT
62423997 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62440459 original size:2 final size:2
Alignment explanation
Indices: 62440454--62440484 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62440444 AGAAGTTTGC
62440454 AT AT AT 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 AT AT AT A
62440485 AAAGTTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62441563 original size:11 final size:11
Alignment explanation
Indices: 62441547--62441607 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
62441537 ACCCAAAATT
62441547 TATTTTAAAAA
1 TATTTTAAAAA
62441558 TATTTT--AAA
1 TATTTTAAAAA
62441567 -A--TTAAAAA
1 TATTTTAAAAA
* *
62441575 AAATTTAAAAA
1 TATTTTAAAAA
62441586 GTATTTTAAAAA
1 -TATTTTAAAAA
62441598 TATTTTAAAA
1 TATTTTAAAA
62441608 TTAAAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
6 2 0.05
8 4 0.10
9 4 0.10
11 23 0.55
12 9 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:62441591 original size:40 final size:40
Alignment explanation
Indices: 62441547--62441663 Score: 186
Period size: 39 Copynumber: 3.0 Consensus size: 40
62441537 ACCCAAAATT
*
62441547 TATTTTAAAAATATTTTAAAATTAAAAAAAATTTAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAG
*
62441587 TATTTTAAAAATATTTTAAAATTAAAAAATAA--AAAAAAT
1 TATTTTAAAAATATTTTAAAATTAAAAAA-AATTAAAAAAG
62441626 TATTTTAAAAATATTTTAAAATT-AAAAAAATTAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAA
62441664 ATAAATATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
37 2 0.03
38 5 0.07
39 34 0.47
40 29 0.40
41 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAG
Found at i:62441665 original size:40 final size:40
Alignment explanation
Indices: 62441541--62441665 Score: 191
Period size: 40 Copynumber: 3.1 Consensus size: 40
62441531 ATAAATACCC
* *
62441541 AAAATTTATTTTAAAAATATTTTAAAATTAAAAAAAATT-T
1 AAAAATTATTTTAAAAATATTTTAAAATT-AAAAAAATTAA
* *
62441581 AAAAAGTATTTTAAAAATATTTTAAAATT-AAAAAATAAA
1 AAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
62441620 AAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
1 AAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
62441660 AAAAAT
1 AAAAAT
62441666 AAATATTTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
38 7 0.09
39 28 0.36
40 42 0.55
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (40 bp):
AAAAATTATTTTAAAAATATTTTAAAATTAAAAAAATTAA
Found at i:62444397 original size:4 final size:4
Alignment explanation
Indices: 62444388--62444478 Score: 146
Period size: 4 Copynumber: 22.8 Consensus size: 4
62444378 TATGATTGCA
* * * *
62444388 TATG TATG TATG TGTG TGTG TATG TATG TATG TATG TGTG TGTG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
62444436 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
62444479 ATGTGTTACG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 83 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:62452475 original size:23 final size:23
Alignment explanation
Indices: 62452439--62452490 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
62452429 AAAAAAACAA
* * *
62452439 AAAAAAAACCCAAAGGGGGAGAG
1 AAAAAAAACACAAAGAGAGAGAG
*
62452462 AAAAAAAATACAAAGAGAGAGAG
1 AAAAAAAACACAAAGAGAGAGAG
*
62452485 GAAAAA
1 AAAAAA
62452491 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.65, C:0.08, G:0.25, T:0.02
Consensus pattern (23 bp):
AAAAAAAACACAAAGAGAGAGAG
Found at i:62487866 original size:16 final size:16
Alignment explanation
Indices: 62487828--62487866 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
62487818 TGGCAGTAGC
* *
62487828 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
62487844 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
62487860 AAAGAAA
1 AAAGAAA
62487867 ACAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:62491513 original size:16 final size:16
Alignment explanation
Indices: 62491475--62491513 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
62491465 TGGCAGTAGC
* *
62491475 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
62491491 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
62491507 AAAGAAA
1 AAAGAAA
62491514 ACAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:62491870 original size:26 final size:26
Alignment explanation
Indices: 62491833--62491882 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
62491823 TAAAATTGTA
*
62491833 CAATTTGCTGCTGTTGGTTTTTTGAC
1 CAATTTGCTGCTGTTGGTTCTTTGAC
*
62491859 CAATTTGTTGCTGTTGGTTCTTTG
1 CAATTTGCTGCTGTTGGTTCTTTG
62491883 TTGCAATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (26 bp):
CAATTTGCTGCTGTTGGTTCTTTGAC
Found at i:62495253 original size:17 final size:19
Alignment explanation
Indices: 62495226--62495260 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
62495216 TAAAACATTT
62495226 ATTGTTAATATAT-TTATA
1 ATTGTTAATATATATTATA
62495244 ATTG-TAATATATATTAT
1 ATTGTTAATATATATTAT
62495261 TAAAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (19 bp):
ATTGTTAATATATATTATA
Found at i:62505696 original size:23 final size:24
Alignment explanation
Indices: 62505640--62505699 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
62505630 CTTGTGATAG
62505640 TTTAATATTTTTATAATGTAATAT
1 TTTAATATTTTTATAATGTAATAT
**
62505664 TTGTGTTATTTTT-TAAT-TAATAAT
1 TT-TAATATTTTTATAATGTAAT-AT
62505688 TTTAATATTTTT
1 TTTAATATTTTT
62505700 GTGTCTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 12 0.40
24 10 0.33
25 8 0.27
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (24 bp):
TTTAATATTTTTATAATGTAATAT
Found at i:62512701 original size:2 final size:2
Alignment explanation
Indices: 62512694--62512722 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
62512684 CCTCTCCTCA
62512694 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62512723 TTTAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:62515531 original size:2 final size:2
Alignment explanation
Indices: 62515524--62515559 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
62515514 TATTTGACAA
62515524 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62515560 TGGTAGTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62519401 original size:6 final size:6
Alignment explanation
Indices: 62519390--62519417 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
62519380 AAAGTTGAAC
62519390 TATACA TATACA TATACA TATACA TATA
1 TATACA TATACA TATACA TATACA TATA
62519418 TATACCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
TATACA
Found at i:62520360 original size:2 final size:2
Alignment explanation
Indices: 62520353--62520386 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
62520343 ATATTCATAA
62520353 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
62520387 TCCAGTCATG
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:62523489 original size:2 final size:2
Alignment explanation
Indices: 62523482--62523514 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62523472 AATTATTGAG
62523482 AT AT AT AT 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 AT AT AT AT A
62523515 AATACATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62524690 original size:28 final size:26
Alignment explanation
Indices: 62524632--62524703 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 26
62524622 AAATAATTTT
62524632 TAAATATTT-ATAGAAATTCTAAAAATTA
1 TAAA-ATTTAATA-AAA-TCTAAAAATTA
*
62524660 TAAGTATTTAA-AAAATCTAAAAATATAA
1 TAA-AATTTAATAAAATCTAAAAAT-T-A
62524688 TAAAATTTAATAAAAT
1 TAAAATTTAATAAAAT
62524704 AATAATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 9 0.24
27 10 0.27
28 17 0.46
29 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (26 bp):
TAAAATTTAATAAAATCTAAAAATTA
Found at i:62524692 original size:18 final size:18
Alignment explanation
Indices: 62524671--62524708 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
62524661 AAGTATTTAA
62524671 AAAATCTAA-AAATATAAT
1 AAAATCTAATAAA-ATAAT
*
62524689 AAAATTTAATAAAATAAT
1 AAAATCTAATAAAATAAT
62524707 AA
1 AA
62524709 TTTTAGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATCTAATAAAATAAT
Found at i:62563514 original size:4 final size:4
Alignment explanation
Indices: 62563507--62563561 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
62563497 CATATATATA
62563507 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
62563555 TATG TAT
1 TATG TAT
62563562 TGAAGTGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:62570836 original size:29 final size:30
Alignment explanation
Indices: 62570782--62570844 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
62570772 ATATTAAAAC
* *
62570782 TATATATGAACTTTGATTCAATGTGTAATTT
1 TATACATGAACTTTAATTC-ATGTGTAATTT
62570813 TATACATGAACTTTAATTC-TGTGTAATTT
1 TATACATGAACTTTAATTCATGTGTAATTT
62570842 TAT
1 TAT
62570845 GTATACAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (30 bp):
TATACATGAACTTTAATTCATGTGTAATTT
Found at i:62576189 original size:46 final size:46
Alignment explanation
Indices: 62576136--62576226 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
62576126 TAATTAAGTC
62576136 ATTCGATCAGCTTCACCAACTCAAATTCAATATAGACATATTTAAT
1 ATTCGATCAGCTTCACCAACTCAAATTCAATATAGACATATTTAAT
* *
62576182 ATTCGATCAGCTTCACCTACTCAAATTTAATATAGACATATTTAA
1 ATTCGATCAGCTTCACCAACTCAAATTCAATATAGACATATTTAA
62576227 AACACATGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (46 bp):
ATTCGATCAGCTTCACCAACTCAAATTCAATATAGACATATTTAAT
Found at i:62584685 original size:2 final size:2
Alignment explanation
Indices: 62584678--62584703 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62584668 GGCAGAGAAG
62584678 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
62584704 ATATAGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:62585659 original size:7 final size:7
Alignment explanation
Indices: 62585643--62585688 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
62585633 GGAGTTACTC
*
62585643 ATTGGCA
1 ATTGGTA
62585650 ATTGGTA
1 ATTGGTA
62585657 ATTGGTA
1 ATTGGTA
62585664 ATTGGTA
1 ATTGGTA
62585671 ATTGGTA
1 ATTGGTA
62585678 ATTGGTA
1 ATTGGTA
62585685 ATTG
1 ATTG
62585689 CTGTATGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.28, C:0.02, G:0.28, T:0.41
Consensus pattern (7 bp):
ATTGGTA
Found at i:62587955 original size:26 final size:26
Alignment explanation
Indices: 62587919--62587970 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
62587909 GGTTTTATAC
*
62587919 TCCCTATCTTACCCTAAGCTTGGATA
1 TCCCTATCTTACCCTAAGCTTAGATA
* *
62587945 TCCCTATCTTATCCTATGCTTAGATA
1 TCCCTATCTTACCCTAAGCTTAGATA
62587971 AATATTTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38
Consensus pattern (26 bp):
TCCCTATCTTACCCTAAGCTTAGATA
Found at i:62588127 original size:6 final size:6
Alignment explanation
Indices: 62588116--62588146 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
62588106 CAATGAGTAT
62588116 CTTAGC CTTAGC CTTAGC CTTAGC CTTAGC C
1 CTTAGC CTTAGC CTTAGC CTTAGC CTTAGC C
62588147 CATTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.16, T:0.32
Consensus pattern (6 bp):
CTTAGC
Found at i:62588676 original size:6 final size:6
Alignment explanation
Indices: 62588665--62588697 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
62588655 AAAGGATTTA
62588665 CCAATG CCAATG CCAATG CCAATG CCAATG CCA
1 CCAATG CCAATG CCAATG CCAATG CCAATG CCA
62588698 CTAAGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAATG
Found at i:62598565 original size:4 final size:4
Alignment explanation
Indices: 62598556--62598604 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
62598546 CCACAAGACA
62598556 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
62598604 A
1 A
62598605 CACGTATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:62624028 original size:27 final size:29
Alignment explanation
Indices: 62623984--62624037 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
62623974 TATATAATTA
* *
62623984 ATTTTAATTTTTACAATA-CAAAATAAAT
1 ATTTTAATATTTAAAATAGCAAAATAAAT
*
62624012 ATTTT-ATATTTAAAATAGTAAAATAA
1 ATTTTAATATTTAAAATAGCAAAATAA
62624038 GTAAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (29 bp):
ATTTTAATATTTAAAATAGCAAAATAAAT
Found at i:62624326 original size:24 final size:23
Alignment explanation
Indices: 62624289--62624334 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
62624279 AAATGATAAA
62624289 AAAATATTTAAAAAAATCAAAAAT
1 AAAATATTTAAAAAAAT-AAAAAT
62624313 AAAATA-TTATAAAAAATAAAAA
1 AAAATATTTA-AAAAAATAAAAA
62624335 CTTTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATATTTAAAAAAATAAAAAT
Found at i:62624733 original size:17 final size:16
Alignment explanation
Indices: 62624711--62624756 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
62624701 CACAAACTTC
*
62624711 TTTCTACTTTATTTATT
1 TTTCTACTTT-TTCATT
62624728 TTTCTATCCTTTTTCATT
1 TTTCTA--CTTTTTCATT
62624746 TTTCTACTTTT
1 TTTCTACTTTT
62624757 AATTCCATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 11 0.42
19 4 0.15
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTCTACTTTTTCATT
Found at i:62631946 original size:113 final size:113
Alignment explanation
Indices: 62631748--62631975 Score: 402
Period size: 113 Copynumber: 2.0 Consensus size: 113
62631738 ATTAGTAGAG
**
62631748 TTAATTAAACAATTGTCACCAGTCCATCATATTTCTAGGAATTAACACACCAATAAAGGAGATGC
1 TTAATTAAACAATTGTCACCAACCCATCATATTTCTAGGAATTAACACACCAATAAAGGAGATGC
* * *
62631813 CAAGTACATATATGATATTCAATCAAGACATGTTTTTTCTTTTGCAAA
66 CAAATACATATACGATATTCAATCAAGACAGGTTTTTTCTTTTGCAAA
*
62631861 TTAATTAAACAATTGTCACCAACCCATCATATTTCTAGGAATTAACACACCAATAAAGGAGATGG
1 TTAATTAAACAATTGTCACCAACCCATCATATTTCTAGGAATTAACACACCAATAAAGGAGATGC
62631926 CAAATACATATACGATATTCAATCAAGACAGGTTTTTTCTTTTGCAAA
66 CAAATACATATACGATATTCAATCAAGACAGGTTTTTTCTTTTGCAAA
62631974 TT
1 TT
62631976 TAGTAATTAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (113 bp):
TTAATTAAACAATTGTCACCAACCCATCATATTTCTAGGAATTAACACACCAATAAAGGAGATGC
CAAATACATATACGATATTCAATCAAGACAGGTTTTTTCTTTTGCAAA
Found at i:62634701 original size:22 final size:22
Alignment explanation
Indices: 62634676--62634719 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
62634666 GGAACGGAAC
62634676 AATACTTCTGTGCGATGGGGAT
1 AATACTTCTGTGCGATGGGGAT
**
62634698 AATACTTCTGTTTGATGGGGAT
1 AATACTTCTGTGCGATGGGGAT
62634720 CAAAGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.36
Consensus pattern (22 bp):
AATACTTCTGTGCGATGGGGAT
Found at i:62640811 original size:19 final size:20
Alignment explanation
Indices: 62640774--62640817 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
62640764 TTAACAAAAA
62640774 TTATAGAAAAATTCAAAATAT
1 TTATAGAAAAATTCAAAAT-T
*
62640795 TTATA-AAAATTTC-AAATT
1 TTATAGAAAAATTCAAAATT
62640813 TTATA
1 TTATA
62640818 TTTTTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 4 0.18
20 7 0.32
21 5 0.23
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATAGAAAAATTCAAAATT
Found at i:62643854 original size:9 final size:9
Alignment explanation
Indices: 62643840--62643869 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
62643830 ATTTAATAGT
62643840 ATTTATTCA
1 ATTTATTCA
62643849 ATTTATTCA
1 ATTTATTCA
*
62643858 ATTTATTAA
1 ATTTATTCA
62643867 ATT
1 ATT
62643870 AGATTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTTATTCA
Found at i:62645953 original size:2 final size:2
Alignment explanation
Indices: 62645946--62645974 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62645936 TGGTGTTTGG
62645946 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62645975 GGCTATGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62647739 original size:18 final size:19
Alignment explanation
Indices: 62647716--62647752 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
62647706 GGACGATTTA
62647716 GAACATGAAGAA-AAAAAT
1 GAACATGAAGAAGAAAAAT
62647734 GAACATGAAGAAGAAAAAT
1 GAACATGAAGAAGAAAAAT
62647753 ATTTCTTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.65, C:0.05, G:0.19, T:0.11
Consensus pattern (19 bp):
GAACATGAAGAAGAAAAAT
Found at i:62673208 original size:22 final size:22
Alignment explanation
Indices: 62673164--62673246 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
62673154 GAACCTCAAC
62673164 GTGCTCTCTGATTATCAGCACATTA
1 GTGCTCTCTG-TT-T-AGCACATTA
*
62673189 GTGCTCTCTGTTTAGCACATTC
1 GTGCTCTCTGTTTAGCACATTA
* * *
62673211 GTGCTCTCTGTGTAACACATCA
1 GTGCTCTCTGTTTAGCACATTA
* *
62673233 CTGCTCTCTATTTA
1 GTGCTCTCTGTTTA
62673247 TTAGTGCATA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 37 0.74
23 1 0.02
24 2 0.04
25 10 0.20
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.39
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACATTA
Done.