Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 38 of 120
Found at i:9925286 original size:17 final size:17
Alignment explanation
Indices: 9925264--9925296 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9925254 CATTGGGATG
9925264 GAACT-GAGGAATGAAAT
1 GAACTGGAGGAA-GAAAT
9925281 GAACTGGAGGAAGAAA
1 GAACTGGAGGAAGAAA
9925297 ACTTTATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.33, T:0.12
Consensus pattern (17 bp):
GAACTGGAGGAAGAAAT
Found at i:9926251 original size:23 final size:21
Alignment explanation
Indices: 9926222--9926277 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
9926212 AATTAATAAT
9926222 AAAATAAATT-AATTAAGTTCCCA
1 AAAATAAATTCAA--AAG-TCCCA
9926245 AAAATAAAATATCAAAAGTCCCA
1 AAAAT-AAAT-TCAAAAGTCCCA
9926268 AAAATAAATT
1 AAAATAAATT
9926278 TTATTTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 1 0.03
22 4 0.13
23 15 0.50
24 7 0.23
25 1 0.03
26 2 0.07
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAATAAATTCAAAAGTCCCA
Found at i:9926350 original size:3 final size:3
Alignment explanation
Indices: 9926336--9926382 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
9926326 CCAAAATCAA
* *
9926336 AAT AAT ACT AAT AAT AAC AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9926382 A
1 A
9926383 TTATAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:9927472 original size:7 final size:7
Alignment explanation
Indices: 9927457--9927552 Score: 86
Period size: 7 Copynumber: 13.9 Consensus size: 7
9927447 ACAGTCAAAA
*
9927457 TCAATGG
1 TCAACGG
9927464 TCAACGG
1 TCAACGG
*
9927471 TCAACAG
1 TCAACGG
9927478 TCAACGG
1 TCAACGG
*
9927485 TTAACGG
1 TCAACGG
**
9927492 TCAA-AA
1 TCAACGG
9927498 TCAACGG
1 TCAACGG
*
9927505 TCAATGG
1 TCAACGG
*
9927512 TCAACGA
1 TCAACGG
*
9927519 TCAATGG
1 TCAACGG
*
9927526 TCAATGG
1 TCAACGG
**
9927533 TCAAAAG
1 TCAACGG
9927540 TCAACGG
1 TCAACGG
9927547 TCAACG
1 TCAACG
9927553 ATTGGTCAAC
Statistics
Matches: 70, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
6 4 0.06
7 66 0.94
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (7 bp):
TCAACGG
Found at i:9927489 original size:41 final size:41
Alignment explanation
Indices: 9927443--9927552 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
9927433 TTTCGAAAAA
* *
9927443 GTTAACAGTCAAAATCAATGGTCAACGGTCAAC-AGTCAACG
1 GTTAACGGTCAAAATCAACGGTCAACGGTCAACGA-TCAACG
* *
9927484 GTTAACGGTCAAAATCAACGGTCAATGGTCAACGATCAATG
1 GTTAACGGTCAAAATCAACGGTCAACGGTCAACGATCAACG
* *
9927525 GTCAATGGTCAAAAGTCAACGGTCAACG
1 GTTAACGGTCAAAA-TCAACGGTCAACG
9927553 ATTGGTCAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 47 0.78
42 13 0.22
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (41 bp):
GTTAACGGTCAAAATCAACGGTCAACGGTCAACGATCAACG
Found at i:9927501 original size:27 final size:27
Alignment explanation
Indices: 9927471--9927522 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
9927461 TGGTCAACGG
* *
9927471 TCAACAGTCAACGGTTAACGGTCAAAA
1 TCAACAGTCAACGGTCAACGATCAAAA
* *
9927498 TCAACGGTCAATGGTCAACGATCAA
1 TCAACAGTCAACGGTCAACGATCAA
9927523 TGGTCAATGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (27 bp):
TCAACAGTCAACGGTCAACGATCAAAA
Found at i:9927528 original size:34 final size:34
Alignment explanation
Indices: 9927464--9927529 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
9927454 AAATCAATGG
* *
9927464 TCAACGGTCAACAGTCAACGGTTAACGGTCAAAA
1 TCAACGGTCAACAGTCAACGATCAACGGTCAAAA
** *
9927498 TCAACGGTCAATGGTCAACGATCAATGGTCAA
1 TCAACGGTCAACAGTCAACGATCAACGGTCAA
9927530 TGGTCAAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (34 bp):
TCAACGGTCAACAGTCAACGATCAACGGTCAAAA
Found at i:9931042 original size:17 final size:17
Alignment explanation
Indices: 9931022--9931067 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
9931012 CCACTCATTG
*
9931022 ATAAACACAGCTCACAT
1 ATAAACACAACTCACAT
*
9931039 ATAAAGACAACTCACAT
1 ATAAACACAACTCACAT
9931056 ATAAACACAACT
1 ATAAACACAACT
9931068 TGCATGTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.52, C:0.26, G:0.04, T:0.17
Consensus pattern (17 bp):
ATAAACACAACTCACAT
Found at i:9936161 original size:20 final size:21
Alignment explanation
Indices: 9936136--9936184 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
9936126 TAATAGTATT
9936136 TTATTAAT-TTAATATTAAAG
1 TTATTAATCTTAATATTAAAG
*
9936156 TTATT-ATCTTAATATTAAAT
1 TTATTAATCTTAATATTAAAG
9936176 TTAATTAAT
1 TT-ATTAAT
9936185 AGAATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 18 0.72
21 3 0.12
22 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TTATTAATCTTAATATTAAAG
Found at i:9936239 original size:12 final size:12
Alignment explanation
Indices: 9936222--9936285 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
9936212 ATTTAATAAG
9936222 ATTTAATATTAA
1 ATTTAATATTAA
9936234 ATTTAATA-TAA
1 ATTTAATATTAA
* *
9936245 TATTTATCTTTATAA
1 -ATTTA-ATAT-TAA
9936260 ATATT-ATATT-A
1 AT-TTAATATTAA
9936271 ATTTAATATTAA
1 ATTTAATATTAA
9936283 ATT
1 ATT
9936286 GATTAAGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
10 2 0.05
11 11 0.27
12 18 0.44
13 3 0.07
14 2 0.05
15 5 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:9936242 original size:38 final size:37
Alignment explanation
Indices: 9936200--9936281 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 37
9936190 ATTATAGATA
*
9936200 AATATTCTATTAAT-TTAATAAGAT-TTAATATTAAATTT
1 AATATTATATTAATCTTAATAA-ATATT-ATATT-AATTT
* * *
9936238 AATATAATATTTATCTTTATAAATATTATATTAATTT
1 AATATTATATTAATCTTAATAAATATTATATTAATTT
9936275 AATATTA
1 AATATTA
9936282 AATTGATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
37 11 0.30
38 18 0.49
39 8 0.22
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (37 bp):
AATATTATATTAATCTTAATAAATATTATATTAATTT
Found at i:9938681 original size:52 final size:51
Alignment explanation
Indices: 9938593--9938804 Score: 262
Period size: 52 Copynumber: 4.1 Consensus size: 51
9938583 ATTTCACTTC
* ** *
9938593 ATTCATATACTCACGATGACACATAGCCATCAGACCTTATAATCCACAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACCTT-TAATCCGTAAAGG
* * * * *
9938645 ATTCGTATACTTACGATGACACAGAGTCATCGGACCTCTTAATTCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACCT-TTAATCCGTAAAGG
* * * *
9938697 ATCCATATACTCACGATGATACTTAGTCATCAGACCTTTTAATTCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCAGACC-TTTAATCCGTAAAGG
*
9938749 ATTCATATACTCACGATGACACTTAGTCATCAGACCCTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACATAGTCATCAGA-CCTTTAATCCGTAAAGG
9938801 ATTC
1 ATTC
9938805 TGATAAAATT
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
52 134 0.97
53 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACATAGTCATCAGACCTTTAATCCGTAAAGG
Found at i:9951828 original size:31 final size:31
Alignment explanation
Indices: 9951790--9951849 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
9951780 AACGATGGTG
9951790 GTTCAGATAGTAGTAAAAATATGGATGATTA
1 GTTCAGATAGTAGTAAAAATATGGATGATTA
9951821 GTTCAGATAGTAGTAAAAATATGGATGAT
1 GTTCAGATAGTAGTAAAAATATGGATGAT
9951850 CATGCTGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (31 bp):
GTTCAGATAGTAGTAAAAATATGGATGATTA
Found at i:9952329 original size:20 final size:20
Alignment explanation
Indices: 9952293--9952330 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9952283 AAAATAAACA
*
9952293 ATTTTTTAAAATTAACATTT
1 ATTTTTTAAAATCAACATTT
9952313 ATTTTTATAAAA-CAACAT
1 ATTTTT-TAAAATCAACAT
9952331 AAAAAGGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTTTAAAATCAACATTT
Found at i:9954374 original size:67 final size:66
Alignment explanation
Indices: 9954268--9954441 Score: 266
Period size: 67 Copynumber: 2.6 Consensus size: 66
9954258 GTTATTTATT
*
9954268 TATTTATTTATCTATATTCAT-AA-AAT-AATAAATAAATAATAAAACAAAATTAATACTATTTT
1 TATTTATTTATTTATATTCATAAATAATAAATAAATAAATAATAAAACAAAATTAATACTATTTT
9954330 A
66 A
*
9954331 CT-TTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAACAAAATTAATATTATT
1 -TATTTATTTATTTATATTCATA-AATAATAAATAAATAAATAATAAAACAAAATTAATACTATT
9954395 TTA
64 TTA
9954398 TATTTATTTATTTATATTCATAAAAATAATAAATAAATAAATAA
1 TATTTATTTATTTATATTCAT--AAATAATAAATAAATAAATAA
9954442 AAATAATAAG
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
63 18 0.18
64 1 0.01
65 2 0.02
66 4 0.04
67 55 0.54
68 20 0.20
69 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (66 bp):
TATTTATTTATTTATATTCATAAATAATAAATAAATAAATAATAAAACAAAATTAATACTATTTT
A
Found at i:9955043 original size:40 final size:40
Alignment explanation
Indices: 9954992--9955440 Score: 444
Period size: 40 Copynumber: 11.3 Consensus size: 40
9954982 ATTGGATCAT
* *
9954992 TTCAATCTGCCCCTTAGTCGGGGTAAGAGATCGAATGGTC
1 TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
* * *** * * *
9955032 TTCAATTTG-CCCTCTAGTTATGGTAAAAGATTGGATTG-C
1 TTCAATCTGCCCCT-TGGTCGGGGTAAGAGATCGGATGGTC
*
9955071 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
1 TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
** * * *
9955111 TTCAATCTG-CCCTCTGGTTAGGGTAAAAGATTGGATTG-C
1 TTCAATCTGCCCCT-TGGTCGGGGTAAGAGATCGGATGGTC
* * *
9955150 TTCAATCTGCACCATGGTCGGGGTAAGAGATCGGGTGGTC
1 TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
* * ** * * *
9955190 TTTAATCTGCCCTTTGGTTAGGGTAAAAGATTGGATTG-C
1 TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
* *
9955229 TTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTC
1 TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
* * ** *
9955269 TTCAATCTG-CCCTCTAGTCGGGGTAAAAGATTAGATGATC
1 TTCAATCTGCCCCT-TGGTCGGGGTAAGAGATCGGATGGTC
* * *
9955309 TTCAATCTACCCCATGGTCGAGGTAAGAGATCGGATGGTC
1 TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
* * *
9955349 TTCAATCTGCCCTTTGGTCTGAGTAAGAGATCGGATGGTC
1 TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
* *
9955389 TTCAATCTG-CCCTCTGGTCTGAGTAAGAGATCGGATGGTC
1 TTCAATCTGCCCCT-TGGTCGGGGTAAGAGATCGGATGGTC
9955429 TTCAATCTGCCC
1 TTCAATCTGCCC
9955441 GTTTCAGCTT
Statistics
Matches: 328, Mismatches: 70, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
39 99 0.30
40 224 0.68
41 5 0.02
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
TTCAATCTGCCCCTTGGTCGGGGTAAGAGATCGGATGGTC
Found at i:9955083 original size:79 final size:79
Alignment explanation
Indices: 9954973--9955440 Score: 618
Period size: 79 Copynumber: 5.9 Consensus size: 79
9954963 ATAATTTTAG
*** * * *
9954973 GGGTAAAAGATTGGATCATTTCAATCTGCCCCTTAGTCGGGGTAAGAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
*
9955038 TTGCCCTCTAGTTA
66 CTGCCCTCTAGTTA
*
9955052 TGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
*
9955117 CTGCCCTCTGGTTA
66 CTGCCCTCTAGTTA
* * *
9955131 GGGTAAAAGATTGGATTGCTTCAATCTGCACCATGGTCGGGGTAAGAGATCGGGTGGTCTTTAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
* *
9955196 CTGCCCTTTGGTTA
66 CTGCCCTCTAGTTA
*
9955210 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTTGGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
**
9955275 CTGCCCTCTAGTCG
66 CTGCCCTCTAGTTA
* * *
9955289 GGGTAAAAGATTAGA-TGATCTTCAATCTACCCCATGGTCGAGGTAAGAGATCGGATGGTCTTCA
1 GGGTAAAAGATTGGATTG--CTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCA
* *
9955353 ATCTGCCCTTTGGTCT-
64 ATCTGCCCTCTAGT-TA
* * * * * *
9955369 GAGTAAGAGATCGGATGGTCTTCAATCTGCCCTC-TGGTCTGAGTAAGAGATCGGATGGTCTTCA
1 GGGTAAAAGATTGGATTG-CTTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTCTTCA
9955433 ATCTGCCC
64 ATCTGCCC
9955441 GTTTCAGCTT
Statistics
Matches: 346, Mismatches: 38, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
78 2 0.01
79 229 0.66
80 113 0.33
81 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
CTGCCCTCTAGTTA
Found at i:9955566 original size:50 final size:49
Alignment explanation
Indices: 9955428--9955603 Score: 169
Period size: 50 Copynumber: 3.6 Consensus size: 49
9955418 ATCGGATGGT
* * * * *
9955428 CTTCAATCTGCCCGT-TTCAGCTTCAGGAGTATAT-GATTCGTCCTTGCGA
1 CTTCAATCTGCCCCTCTACAGCTTTA-GA-TATATGGATTCGTCATTGCGG
* * *
9955477 CTTCAATATGCCCCTCTACAACTTTAGGTGA-ATGTGATTCGTCATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGAT-ATATG-GATTCGTCATTGCGG
* * *
9955527 CTTCAATCTGCCCCTCTACAGCTTTAGATATATGAGATTCGCCATCGTGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGATATATG-GATTCGTCATTGCGG
**
9955577 CTTCAATCTGTTCCTCTACAGCTTTAG
1 CTTCAATCTGCCCCTCTACAGCTTTAG
9955604 GGGTATAGGA
Statistics
Matches: 105, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
48 3 0.03
49 16 0.15
50 86 0.82
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (49 bp):
CTTCAATCTGCCCCTCTACAGCTTTAGATATATGGATTCGTCATTGCGG
Found at i:9960857 original size:24 final size:24
Alignment explanation
Indices: 9960830--9961005 Score: 262
Period size: 24 Copynumber: 7.3 Consensus size: 24
9960820 CCCATGCGAT
* * * *
9960830 CCCAAAATGGTTAGTTCTTACAAG
1 CCCAGAATGATTAGCTCTTACGAG
*
9960854 CCCAGAATAATTAGCTCTTACGAG
1 CCCAGAATGATTAGCTCTTACGAG
9960878 CCCAGAATGATTAGCTCTTACGAG
1 CCCAGAATGATTAGCTCTTACGAG
*
9960902 TCCAGAATGATTAGCTCTTACGAG
1 CCCAGAATGATTAGCTCTTACGAG
* *
9960926 CCTAGAATGGTTAGCTCTTACGAG
1 CCCAGAATGATTAGCTCTTACGAG
* *
9960950 CCTAGAATGGTTAGCTCTTACGAG
1 CCCAGAATGATTAGCTCTTACGAG
9960974 CCCAGAATGATTAGCTCTTACGAG
1 CCCAGAATGATTAGCTCTTACGAG
9960998 CCCAGAAT
1 CCCAGAAT
9961006 CAGAATAAGG
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 140 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (24 bp):
CCCAGAATGATTAGCTCTTACGAG
Found at i:9964060 original size:31 final size:29
Alignment explanation
Indices: 9964014--9964093 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
9964004 CGTCTTTCTC
9964014 AAACTTT-TAATGCATGAAAATGCGATGCA
1 AAACTTTATAATGCATGAAAATGCGAT-CA
*
9964043 AAACTTTATAAATGCATGAAAATGCGATCC
1 AAACTTTAT-AATGCATGAAAATGCGATCA
*
9964073 AGACTTTTATGAATGCATGAA
1 AAAC-TTTAT-AATGCATGAA
9964094 TGCATATGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
29 7 0.16
30 5 0.11
31 33 0.73
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (29 bp):
AAACTTTATAATGCATGAAAATGCGATCA
Found at i:9966513 original size:13 final size:13
Alignment explanation
Indices: 9966495--9966523 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
9966485 GGACTTTGAT
9966495 TTTGGGTTTATTA
1 TTTGGGTTTATTA
9966508 TTTGGGTTTATTA
1 TTTGGGTTTATTA
9966521 TTT
1 TTT
9966524 TTTTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.66
Consensus pattern (13 bp):
TTTGGGTTTATTA
Found at i:9966613 original size:63 final size:63
Alignment explanation
Indices: 9966525--9966701 Score: 246
Period size: 71 Copynumber: 2.7 Consensus size: 63
9966515 TTATTATTTT
9966525 TTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACA
1 TTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACA
9966588 TTTATTTATTTATATTCATACAATAATAAATAAATAAATAAATAATAAAACAAAATTAATATTAT
1 TTTATTTATTTATA-T--T-C-AT-A-AAAT-AATAAATAAATAATAAAACAAAATTAATATTAT
*
9966653 TTTATA
58 TTTACA
* *
9966659 TTTATTTATTTATATTCAAAAAATAATAAGTAAATACATAAAA
1 TTTATTTATTTATATTCATAAAATAATAAATAAATA-ATAAAA
9966702 ATAATAAGAA
Statistics
Matches: 102, Mismatches: 3, Indels: 17
0.84 0.02 0.14
Matches are distributed among these distances:
63 25 0.25
64 11 0.11
65 1 0.01
66 2 0.02
67 2 0.02
68 3 0.03
69 1 0.01
70 5 0.05
71 52 0.51
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (63 bp):
TTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACA
Found at i:9966624 original size:71 final size:71
Alignment explanation
Indices: 9966545--9966705 Score: 263
Period size: 71 Copynumber: 2.3 Consensus size: 71
9966535 TATATTCATA
* *
9966545 AAAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCATAC
1 AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAAAA
9966609 AATAAT
66 AATAAT
*
9966615 AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTATATTTATTTATTTATATTCAAAA
1 AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAAAA
9966680 AATAAT
66 AATAAT
* *
9966686 AAGTAAATACATAAA-AATAA
1 AAATAAATAAATAAATAATAA
9966706 TAAGAAAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
70 9 0.11
71 76 0.89
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (71 bp):
AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAAAA
AATAAT
Found at i:9967487 original size:29 final size:30
Alignment explanation
Indices: 9967431--9967494 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 30
9967421 CAACTTAACA
*
9967431 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
9967461 AACAAATGCCTCT-AAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
9967490 AACAA
1 AACAA
9967495 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.58, C:0.16, G:0.03, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:9975219 original size:25 final size:24
Alignment explanation
Indices: 9975162--9975220 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
9975152 AAAAATAGGT
* *
9975162 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
9975185 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
9975209 TATTTTAATAAT
1 TATATT-ATAAT
9975221 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:9975280 original size:58 final size:58
Alignment explanation
Indices: 9975194--9975339 Score: 181
Period size: 58 Copynumber: 2.5 Consensus size: 58
9975184 ATATATTATA
* * *
9975194 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAAT
* * *
9975254 A-TTTTATTAAATTTTATTTAACAATAATTATGTTAAAATATAATTAAATTAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
9975311 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
9975340 CATTAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
57 19 0.25
58 43 0.57
59 8 0.11
60 5 0.07
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
Found at i:9975530 original size:16 final size:16
Alignment explanation
Indices: 9975509--9975548 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
9975499 TGAATTACTG
*
9975509 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
9975525 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
9975541 ATTACAGC
1 ATTACAGC
9975549 GAACCAAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:9976894 original size:10 final size:10
Alignment explanation
Indices: 9976872--9976912 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
9976862 AAAAAAATTG
*
9976872 TTTTT-ATAA
1 TTTTTAATAT
9976881 TTTTTAATA-
1 TTTTTAATAT
9976890 TTTTTAATAT
1 TTTTTAATAT
*
9976900 TTTTTAAAAT
1 TTTTTAATAT
9976910 TTT
1 TTT
9976913 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:9976894 original size:19 final size:19
Alignment explanation
Indices: 9976872--9976912 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9976862 AAAAAAATTG
*
9976872 TTTTT-ATAATTTTTAATA
1 TTTTTAATAATTTTTAAAA
*
9976890 TTTTTAATATTTTTTAAAA
1 TTTTTAATAATTTTTAAAA
9976909 TTTT
1 TTTT
9976913 AAAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTAATAATTTTTAAAA
Found at i:9980414 original size:22 final size:22
Alignment explanation
Indices: 9980375--9980419 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
9980365 GGCCATGACA
* * * *
9980375 GGCCTTTGACTGATCGTTGATC
1 GGCCGTTGACGGACCGTTAATC
9980397 GGCCGTTGACGGACCGTTAATC
1 GGCCGTTGACGGACCGTTAATC
9980419 G
1 G
9980420 TTGACAGTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (22 bp):
GGCCGTTGACGGACCGTTAATC
Found at i:9981394 original size:2 final size:2
Alignment explanation
Indices: 9981353--9981377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9981343 TTTTTTGAGT
9981353 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
9981378 GTTTGTTGTG
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:10000791 original size:42 final size:42
Alignment explanation
Indices: 10000725--10000927 Score: 149
Period size: 42 Copynumber: 4.8 Consensus size: 42
10000715 GGAAAAATGC
*
10000725 CGCTAAAGAACATGTTCTATAGCGGCGTTTGTGAAAAAAACGT
1 CGCTAAAG-ACATATTCTATAGCGGCGTTTGTGAAAAAAACGT
* * ** *
10000768 CGCTAAAGACATATTCTGTAGCGGTGTTTGTGGGAAAAGCGT
1 CGCTAAAGACATATTCTATAGCGGCGTTTGTGAAAAAAACGT
* * ** * * *
10000810 CGCTAAAGACCATGTTCAATAGC-ATGTTTGT-AGGAAAAATGC
1 CGCTAAAGA-CATATTCTATAGCGGCGTTTGTGA-AAAAAACGT
** ** * *
10000852 CGCTAAAGACCATGCTCTATAGCGGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGA-CATATTCTATAGCGGCGTTTGTGAAAAAAACGT
* * *
10000895 CACTAAAGACCATGTTCTATAGCGACGTTTGTG
1 CGCTAAAGA-CATATTCTATAGCGGCGTTTGTG
10000928 GGAAAAGGAA
Statistics
Matches: 132, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
42 71 0.54
43 61 0.46
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (42 bp):
CGCTAAAGACATATTCTATAGCGGCGTTTGTGAAAAAAACGT
Found at i:10000817 original size:85 final size:85
Alignment explanation
Indices: 10000682--10001004 Score: 316
Period size: 85 Copynumber: 3.8 Consensus size: 85
10000672 GTACAAATGC
* * * * * * *
10000682 CGCTAAATATCATGTTTTATAACGGCGTTTATGGGAAAAATGC-CGCTAAAGAACATGTTCTATA
1 CGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGG-AAAA-GCGCACTAAAGACCATGTTCTATA
* * *
10000746 GCGGCGTTTGTGAAAAAAACGT
64 GCGACGTTTGTGAGAAAAACGA
* * * * *
10000768 CGCTAAAGA-CATATTCTGTAGCGGTGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCAATAG
1 CGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGCG-CACTAAAGACCATGTTCTATAG
* * *
10000832 C-ATGTTTGT-AGGAAAAATGC
65 CGACGTTTGTGA-GAAAAACGA
*
10000852 CGCTAAAGACCATGCTCTATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAG
1 CGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGCG-CACTAAAGACCATGTTCTATAG
* *
10000917 CGACGTTTGTG-GGAAAAGGAA
65 CGACGTTTGTGAGAAAAACG-A
* * *
10000938 CGCTAAAGACCATGTTCTATAGTC-ACGTTTGTGGGAAAAGCGCTATTAAAGATCATGTTCTATA
1 CGCTAAAGACCATGTTCTATAG-CGGCGTTTGTGGGAAAAGCGC-ACTAAAGACCATGTTCTATA
10001002 GCG
64 GCG
10001005 GCATTTTCTC
Statistics
Matches: 199, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
83 3 0.02
84 25 0.13
85 96 0.48
86 74 0.37
87 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (85 bp):
CGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCACTAAAGACCATGTTCTATAGC
GACGTTTGTGAGAAAAACGA
Found at i:10000977 original size:43 final size:43
Alignment explanation
Indices: 10000680--10001004 Score: 316
Period size: 43 Copynumber: 7.6 Consensus size: 43
10000670 TGGTACAAAT
* * * * * * **
10000680 GCCGCTAAATATCATGTTTTATAACGGCGTTTATGGGAAAAAT
1 GCCGCTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAGC
* * ** *
10000723 GCCGCTAAAGAACATGTTCTATAGCGGCGTTTGTGAAAAAAAC
1 GCCGCTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAGC
* * * **
10000766 GTCGCTAAAGA-CATATTCTGTAGCGGTGTTTGTGGGAAAAGC
1 GCCGCTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAGC
* * * * **
10000808 GTCGCTAAAGACCATGTTCAATAGC-ATGTTTGTAGGAAAAAT
1 GCCGCTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAGC
* *
10000850 GCCGCTAAAGACCATGCTCTATAGCGGCGTTTGTGGGAAAAGC
1 GCCGCTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAGC
*
10000893 GCCACTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAG-
1 GCCGCTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAGC
*
10000935 GAACGCTAAAGACCATGTTCTATAGTC-ACGTTTGTGGGAAAAGC
1 G-CCGCTAAAGACCATGTTCTATAG-CGACGTTTGTGGGAAAAGC
*** *
10000979 GCTATTAAAGATCATGTTCTATAGCG
1 GCCGCTAAAGACCATGTTCTATAGCG
10001005 GCATTTTCTC
Statistics
Matches: 236, Mismatches: 40, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
42 73 0.31
43 161 0.68
44 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
GCCGCTAAAGACCATGTTCTATAGCGACGTTTGTGGGAAAAGC
Found at i:10001143 original size:13 final size:13
Alignment explanation
Indices: 10001125--10001149 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10001115 TTAATTTTTA
10001125 ATATATAAAATTC
1 ATATATAAAATTC
10001138 ATATATAAAATT
1 ATATATAAAATT
10001150 TTTTTTCACC
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATAAAATTC
Found at i:10001450 original size:11 final size:11
Alignment explanation
Indices: 10001420--10001456 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
10001410 AACAAACCTT
*
10001420 AAAATTTGCAA
1 AAAATTTACAA
10001431 AACAATTTACAA
1 AA-AATTTACAA
10001443 AAAATTTACAA
1 AAAATTTACAA
10001454 AAA
1 AAA
10001457 TAACATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAATTTACAA
Found at i:10001525 original size:16 final size:19
Alignment explanation
Indices: 10001488--10001527 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
10001478 TTACTAATTT
10001488 TTTTAATATATATTAGAAA
1 TTTTAATATATATTAGAAA
10001507 TTTTAATAT-T-TTA-AAA
1 TTTTAATATATATTAGAAA
10001523 TTTTA
1 TTTTA
10001528 TAAATCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 3 0.14
18 1 0.05
19 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTTAATATATATTAGAAA
Found at i:10001813 original size:29 final size:29
Alignment explanation
Indices: 10001780--10001837 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
10001770 TTTGTAACCT
*
10001780 AAAAAATATAAATATTTATAATATTTTTA
1 AAAAAAAATAAATATTTATAATATTTTTA
* * *
10001809 AAAAAAAATAATTATTTTTTATATTTTTA
1 AAAAAAAATAAATATTTATAATATTTTTA
10001838 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AAAAAAAATAAATATTTATAATATTTTTA
Found at i:10001853 original size:17 final size:17
Alignment explanation
Indices: 10001821--10001854 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10001811 AAAAAATAAT
*
10001821 TATTTTTTATATTTTTA
1 TATTTTTTATAATTTTA
*
10001838 TATTTTTTTTAATTTTA
1 TATTTTTTATAATTTTA
10001855 CAATTTTACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTTATAATTTTA
Found at i:10004191 original size:28 final size:28
Alignment explanation
Indices: 10004145--10004198 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
10004135 AATATTAAAA
* ** *
10004145 AATATTTTTTTAGTTTTTTAATAATTCT
1 AATATTTTTTAAGAATTTTAAAAATTCT
10004173 AATATTTTTTAAGAATTTTAAAAATT
1 AATATTTTTTAAGAATTTTAAAAATT
10004199 AGTTAATGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (28 bp):
AATATTTTTTAAGAATTTTAAAAATTCT
Found at i:10005143 original size:20 final size:20
Alignment explanation
Indices: 10005120--10005174 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
10005110 AAAGTTTATT
10005120 AAAATTATTAAAA-ATAGAA
1 AAAATTATTAAAATATAGAA
* *
10005139 AAAA-AATATAAAATATAGTA
1 AAAATTAT-TAAAATATAGAA
10005159 AAAATT-TTAAAATATA
1 AAAATTATTAAAATATA
10005175 TATTAGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 2 0.07
19 18 0.60
20 10 0.33
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAATTATTAAAATATAGAA
Found at i:10005544 original size:21 final size:20
Alignment explanation
Indices: 10005518--10005556 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
10005508 TAATAAATTT
10005518 GTAATTTTTAAATAATTTTTC
1 GTAATTTTTAAAT-ATTTTTC
10005539 GTAATTTTTAAATATTTT
1 GTAATTTTTAAATATTTT
10005557 AAAGATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (20 bp):
GTAATTTTTAAATATTTTTC
Found at i:10007608 original size:23 final size:23
Alignment explanation
Indices: 10007562--10007604 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
10007552 ATTATATTGA
10007562 TTTAATATTTTAAAAATTACATT
1 TTTAATATTTTAAAAATTACATT
*
10007585 TTTACTATTTT-AAAATTACA
1 TTTAATATTTTAAAAATTACA
10007605 ATTTAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAATATTTTAAAAATTACATT
Found at i:10013983 original size:39 final size:39
Alignment explanation
Indices: 10013888--10014007 Score: 150
Period size: 39 Copynumber: 3.1 Consensus size: 39
10013878 ATTTTCAATT
* * * *
10013888 TTAGTTTGACCCAATCTATTAATGACCTAATTAATAAGC
1 TTAGTTTGACACAATCTGTTAATGGCCCAATTAATAAGC
* *
10013927 TTAGTTTGGCTCAATCTGTTAATGGCCCAATTAATAAGC
1 TTAGTTTGACACAATCTGTTAATGGCCCAATTAATAAGC
* * * *
10013966 TTAGTTTGACACAATCTGTTCATGGGCCGATTAACAAGC
1 TTAGTTTGACACAATCTGTTAATGGCCCAATTAATAAGC
10014005 TTA
1 TTA
10014008 TTGTTAGTCA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (39 bp):
TTAGTTTGACACAATCTGTTAATGGCCCAATTAATAAGC
Found at i:10014723 original size:28 final size:28
Alignment explanation
Indices: 10014691--10014746 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
10014681 TTATATTTTT
10014691 ATAAAAAAATTTC-TAATTTTTAATAAAA
1 ATAAAAAAATTTCAT-ATTTTTAATAAAA
* **
10014719 ATAAATATTTTTCATATTTTTAATAAAA
1 ATAAAAAAATTTCATATTTTTAATAAAA
10014747 TTTAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (28 bp):
ATAAAAAAATTTCATATTTTTAATAAAA
Found at i:10014758 original size:28 final size:29
Alignment explanation
Indices: 10014706--10014768 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
10014696 AAAATTTCTA
10014706 ATTTTTAATAAAAATAAATATTTTTCA-T
1 ATTTTTAATAAAAATAAATATTTTTCATT
* *
10014734 ATTTTTAATAAAATTTAATTATTTTT-ATT
1 ATTTTTAATAAAA-ATAAATATTTTTCATT
10014763 ATTTTT
1 ATTTTT
10014769 TTATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTTTTAATAAAAATAAATATTTTTCATT
Found at i:10014967 original size:3 final size:3
Alignment explanation
Indices: 10014959--10014999 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
10014949 TTTAATAACG
10014959 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
10015000 GCATTCTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10022886 original size:119 final size:119
Alignment explanation
Indices: 10022671--10022918 Score: 290
Period size: 119 Copynumber: 2.1 Consensus size: 119
10022661 CTCTAAACTA
* * * *
10022671 TCCAAAAA-TCATATTTTGACCCCCAAACTTTTCAAAAAAATTACATTTTGACCCCTAAACTTCT
1 TCCAAAAATTCATATTTTGACCCCCAAACTTTCCAAAAAAATCACATTTTGACCCCCAAACTTCC
* * **
10022735 AAAAATTCCATTTTGACCCCAAATTTCACAAAAATTACCATTTTGCCCTCGAATT
66 AAAAATTCCATTTTGACCCCAAATTT-ACAAAAATTACCATTTTACCCCCGAACC
* *
10022790 TCCAAAAATTC-TATTTTTTACCCTCAAAC-TTCCAAAAAAATCACATTTT-ACCCCCAAACTCT
1 TCCAAAAATTCATA-TTTTGACCCCCAAACTTTCCAAAAAAATCACATTTTGACCCCCAAACT-T
* * * *
10022852 CCAAAAATTGCATTTTTACCCCTCAACTTT-CAAAAATTACTATTTTACCCCCGAACC
64 CCAAAAATTCCATTTTGA-CCC-CAAATTTACAAAAATTACCATTTTACCCCCGAACC
10022909 TCCAAAAATT
1 TCCAAAAATT
10022919 ACCATTTTAC
Statistics
Matches: 110, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
118 10 0.09
119 76 0.69
120 18 0.16
121 6 0.05
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (119 bp):
TCCAAAAATTCATATTTTGACCCCCAAACTTTCCAAAAAAATCACATTTTGACCCCCAAACTTCC
AAAAATTCCATTTTGACCCCAAATTTACAAAAATTACCATTTTACCCCCGAACC
Found at i:10022933 original size:29 final size:29
Alignment explanation
Indices: 10022665--10022932 Score: 183
Period size: 29 Copynumber: 9.0 Consensus size: 29
10022655 GAAGGTCTCT
* *
10022665 AAACTATCCAAAAATCA-TATTTTGACCCCC
1 AAACT-TCCAAAAATTACCATTTT-ACCCCC
* *
10022695 AAACTTTTCAAAAAAATTA-CATTTTGACCCCT
1 AAAC--TTC-CAAAAATTACCATTTT-ACCCCC
*
10022727 AAACTTCTAAAAATT-CCATTTTGA-CCCC
1 AAACTTCCAAAAATTACCATTTT-ACCCCC
* * *
10022755 AAATTTCACAAAAATTACCATTTTGCCCTC
1 AAACTTC-CAAAAATTACCATTTTACCCCC
* * * *
10022785 GAATTTCCAAAAATT-CTATTTTTTACCCTC
1 AAACTTCCAAAAATTACCA--TTTTACCCCC
*
10022815 AAACTTCCAAAAA-AATCACATTTTACCCCC
1 AAACTTCCAAAAATTA-C-CATTTTACCCCC
*
10022845 AAACTCTCCAAAAATT-GCATTTTTACCCCTC
1 AAACT-TCCAAAAATTACCA-TTTTACCCC-C
* *
10022876 -AACTTTCAAAAATTACTATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* *
10022904 GAACCTCCAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
10022933 GGGTATCCAA
Statistics
Matches: 194, Mismatches: 26, Indels: 37
0.75 0.10 0.14
Matches are distributed among these distances:
28 12 0.06
29 75 0.39
30 71 0.37
31 12 0.06
32 24 0.12
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCC
Found at i:10024289 original size:121 final size:120
Alignment explanation
Indices: 10024069--10024290 Score: 365
Period size: 121 Copynumber: 1.8 Consensus size: 120
10024059 GGCATAAGGG
* *
10024069 TTTATTTAGCTCTTCGATTATATAAAAAAATTCATTTTAACTTTTAATTTAATTTTTTTTAAATT
1 TTTATTTAGCTCTTCAATTATATAAAAAAAATCATTTTAACTTTTAATTTAATTTTTTTTAAATT
*
10024134 TGTTTTTGTAAAATTACCGTAAAATAGATGCAAAAATAACATTTTTTTAACTTTGT
66 TGTATTTGTAAAATTACCGTAAAATAGA-GCAAAAATAACATTTTTTTAACTTTGT
*
10024190 TTTATTTAGCTCTTCAATTCTATAAAAAAAATCATTTTAACTTTTAATTTAATTTTTTTCTTAAA
1 TTTATTTAGCTCTTCAATTATATAAAAAAAATCATTTTAACTTTTAATTTAA-TTTTTT-TTAAA
*
10024255 TTTGTATTTGTAAAATTACCGTGAAATAGA-CAAAAA
64 TTTGTATTTGTAAAATTACCGTAAAATAGAGCAAAAA
10024291 AAAATAATAT
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
121 55 0.59
122 6 0.06
123 33 0.35
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (120 bp):
TTTATTTAGCTCTTCAATTATATAAAAAAAATCATTTTAACTTTTAATTTAATTTTTTTTAAATT
TGTATTTGTAAAATTACCGTAAAATAGAGCAAAAATAACATTTTTTTAACTTTGT
Found at i:10030539 original size:24 final size:25
Alignment explanation
Indices: 10030512--10030566 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
10030502 TTGTAACAGA
*
10030512 TTTAATAAAAAT-TTCGTAAAAT-TT
1 TTTAATAAAAATGAT-GTAAAATATT
* *
10030536 TTTAACAAGAATGATGTAAAATATT
1 TTTAATAAAAATGATGTAAAATATT
10030561 TTTAAT
1 TTTAAT
10030567 GAGATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (25 bp):
TTTAATAAAAATGATGTAAAATATT
Found at i:10032058 original size:31 final size:30
Alignment explanation
Indices: 10032010--10032088 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
10032000 GAGCTGATGG
* * *
10032010 ATTTAGGTACTTGAACTTGATATTTTTTCTTA
1 ATTT-GGTACTTAAACTTAACATTTTTT-TTA
10032042 ATTTGGTACTTAAACTTAACATTTTTTTTA
1 ATTTGGTACTTAAACTTAACATTTTTTTTA
* * *
10032072 AGTTAGTATTTAAACTT
1 ATTTGGTACTTAAACTT
10032089 TCTGAGATCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 17 0.41
31 20 0.49
32 4 0.10
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.52
Consensus pattern (30 bp):
ATTTGGTACTTAAACTTAACATTTTTTTTA
Found at i:10032396 original size:59 final size:60
Alignment explanation
Indices: 10032314--10032426 Score: 156
Period size: 59 Copynumber: 1.9 Consensus size: 60
10032304 TAAATCTTAA
* *
10032314 AAAAAAAACTTAAGTATTAAATTAAGAAAAAA-TATCAAGTTCAAGTATAAAATTAGGTT
1 AAAAAAAACTTAAGTATCAAATTAAAAAAAAAGTATCAAGTTCAAGTATAAAATTAGGTT
* * * * *
10032373 AAAAAAAATTTAGGTATCAAATTAAAAAAAAAGTGTCAAGTTTAAGTATCAAAT
1 AAAAAAAACTTAAGTATCAAATTAAAAAAAAAGTATCAAGTTCAAGTATAAAAT
10032427 GTTATATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 28 0.61
60 18 0.39
ACGTcount: A:0.56, C:0.05, G:0.11, T:0.28
Consensus pattern (60 bp):
AAAAAAAACTTAAGTATCAAATTAAAAAAAAAGTATCAAGTTCAAGTATAAAATTAGGTT
Found at i:10035217 original size:20 final size:21
Alignment explanation
Indices: 10035177--10035217 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
10035167 AAGATTGACA
*
10035177 ATCTTAGATTTGATAGGTAAT
1 ATCTTAGATTTGATAGATAAT
*
10035198 ATCTTAGA-TTGATATATAAT
1 ATCTTAGATTTGATAGATAAT
10035218 CTTTAGAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.44
Consensus pattern (21 bp):
ATCTTAGATTTGATAGATAAT
Found at i:10061015 original size:21 final size:21
Alignment explanation
Indices: 10060991--10061044 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
10060981 TCTAAGACAG
*
10060991 TTCTACCGATACAAGTGA-GAC
1 TTCTACCGATACAAGTCATG-C
*
10061012 TTCTACCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATGC
10061033 TTCTACCGATAC
1 TTCTACCGATAC
10061045 TAAAAACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:10061237 original size:21 final size:21
Alignment explanation
Indices: 10061199--10061238 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
10061189 TGCCTTGTAC
* *
10061199 TTCTACCGATACATGTATGAG
1 TTCTACCGAAACAAGTATGAG
*
10061220 TTCTACTGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
10061239 CAGAATTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGAG
Found at i:10069814 original size:68 final size:69
Alignment explanation
Indices: 10069740--10069874 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 69
10069730 TTTTAATAGT
* * * * *
10069740 TTAATATTAAATTTAATTTAATGCTTATTTTAAT-AGTATTTTATTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATATAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGAT
10069804 TATC
66 TATC
* * *
10069808 TTAATATTAAATTTAATATAATATTTATCTTGATAAATATTATGTTAATTTAATATTAAAGTGAT
1 TTAATATTAAATTTAATATAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGAT
10069873 TA
66 TA
10069875 AGTTTAATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
68 29 0.50
69 29 0.50
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (69 bp):
TTAATATTAAATTTAATATAATACTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGAT
TATC
Found at i:10071355 original size:8 final size:8
Alignment explanation
Indices: 10071342--10071373 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
10071332 TTAACTTTGG
10071342 GATGATGA
1 GATGATGA
10071350 GATGATGA
1 GATGATGA
10071358 GATGATGA
1 GATGATGA
10071366 GATGATGA
1 GATGATGA
10071374 ATCATTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (8 bp):
GATGATGA
Found at i:10072918 original size:49 final size:49
Alignment explanation
Indices: 10072858--10072995 Score: 206
Period size: 49 Copynumber: 2.8 Consensus size: 49
10072848 GTATAGGGTT
*
10072858 GTTCAAGGTTTAAGG-GTTTGGGGTTATAAAATATGAGTTTATGGTTCAA
1 GTTCAATGTTT-AGGAGTTTGGGGTTATAAAATATGAGTTTATGGTTCAA
* *
10072907 GTTCAATGTTTAGGAGTTTGGGGTTAAAAAATATGAGTTTATGGTTCGA
1 GTTCAATGTTTAGGAGTTTGGGGTTATAAAATATGAGTTTATGGTTCAA
* **
10072956 GTTCAATGTTTAGGAGTTTGGGATTATATGATATGAGTTT
1 GTTCAATGTTTAGGAGTTTGGGGTTATAAAATATGAGTTT
10072996 GGAGTTTGGG
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 3 0.04
49 78 0.96
ACGTcount: A:0.28, C:0.04, G:0.28, T:0.41
Consensus pattern (49 bp):
GTTCAATGTTTAGGAGTTTGGGGTTATAAAATATGAGTTTATGGTTCAA
Found at i:10073413 original size:21 final size:22
Alignment explanation
Indices: 10073378--10073418 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
10073368 TAAGATAACC
10073378 ATATATAAAATTTTAATTAAAAA
1 ATATATAAAATTTT-ATTAAAAA
10073401 ATATAT-AAA-TTTATTAAA
1 ATATATAAAATTTTATTAAA
10073419 TATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 3 0.17
23 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATATAAAATTTTATTAAAAA
Found at i:10073441 original size:16 final size:15
Alignment explanation
Indices: 10073392--10073442 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
10073382 ATAAAATTTT
10073392 AATTAAAAAATATATA
1 AATT-AAAAATATATA
*
10073408 AATTTATTAAATAT-TA
1 AA-TTA-AAAATATATA
10073424 AATTAAAAATCATATA
1 AATTAAAAAT-ATATA
10073440 AAT
1 AAT
10073443 ACAGATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.14
15 5 0.17
16 12 0.41
17 8 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAAAAATATATA
Found at i:10073981 original size:28 final size:29
Alignment explanation
Indices: 10073922--10073983 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
10073912 TATCAATTTT
*
10073922 TTTAAATAATACATATTTTTATAATTAAA
1 TTTAAATAATACATATTATTATAATTAAA
* *
10073951 TTTAAAT-ATA-ATATATATTATTATTTAA
1 TTTAAATAATACATAT-TATTATAATTAAA
10073979 TTTAA
1 TTTAA
10073984 TTCAACTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 4 0.14
28 18 0.62
29 7 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTAAATAATACATATTATTATAATTAAA
Found at i:10079197 original size:18 final size:18
Alignment explanation
Indices: 10079163--10079197 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10079153 ACTTCTGCAG
*
10079163 CTCGAGGTCGTGGTAGTA
1 CTCGAGGTCGTGCTAGTA
*
10079181 CTCGAGGTGGTGCTAGT
1 CTCGAGGTCGTGCTAGT
10079198 GGCAGAGGTA
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:0.14, C:0.17, G:0.40, T:0.29
Consensus pattern (18 bp):
CTCGAGGTCGTGCTAGTA
Found at i:10085154 original size:17 final size:17
Alignment explanation
Indices: 10085134--10085198 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
10085124 AAAAAAGTGT
10085134 AATTAT-AAAAATATTAA
1 AATTATAAAAAATA-TAA
*
10085151 AATTCTAAAAAATATAA
1 AATTATAAAAAATATAA
*
10085168 AAATATAAAAAAGTACTAA
1 AATTATAAAAAA-TA-TAA
*
10085187 AAATA-AAAAAAT
1 AATTATAAAAAAT
10085199 TAGAAACGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 19 0.45
18 15 0.36
19 8 0.19
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (17 bp):
AATTATAAAAAATATAA
Found at i:10085177 original size:7 final size:8
Alignment explanation
Indices: 10085137--10085198 Score: 52
Period size: 9 Copynumber: 7.1 Consensus size: 8
10085127 AAAGTGTAAT
10085137 TATAAAAA
1 TATAAAAA
*
10085145 TATTAAAAT
1 TA-TAAAAA
*
10085154 TCTAAAAAA
1 TAT-AAAAA
10085163 TATAAAAA
1 TATAAAAA
10085171 TATAAAAAA
1 TAT-AAAAA
10085180 GTACTAAAAA
1 -TA-TAAAAA
*
10085190 TAAAAAAA
1 TATAAAAA
10085198 T
1 T
10085199 TAGAAACGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 17 0.39
9 19 0.43
10 7 0.16
11 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (8 bp):
TATAAAAA
Found at i:10085730 original size:19 final size:18
Alignment explanation
Indices: 10085706--10085750 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
10085696 GGTGTCAAGT
* *
10085706 AAAAAAAATTAGACATTTG
1 AAAAAAAA-AAGAAATTTG
10085725 AAAAAAAAAAGAAATTTG
1 AAAAAAAAAAGAAATTTG
10085743 AAAAAAAA
1 AAAAAAAA
10085751 GGTGTTGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAAAAAAAAGAAATTTG
Found at i:10086620 original size:39 final size:37
Alignment explanation
Indices: 10086540--10086621 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 37
10086530 TTTTATTAAA
10086540 AATA-TTTTAAGATAAAATTTTTATAAAAAAATTATT
1 AATATTTTTAAGATAAAATTTTTATAAAAAAATTATT
* **
10086576 -GTATTTTTAAGGATATACAATTTTTATATCAAAATT-TT
1 AATATTTTTAA-GATA-A-AATTTTTATAAAAAAATTATT
10086614 AATATTTT
1 AATATTTT
10086622 AAATGTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
35 2 0.05
36 6 0.16
37 4 0.11
38 3 0.08
39 22 0.59
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (37 bp):
AATATTTTTAAGATAAAATTTTTATAAAAAAATTATT
Found at i:10095469 original size:18 final size:18
Alignment explanation
Indices: 10095446--10095480 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10095436 TTTACCGCTT
10095446 TTTCTTCTT-TTTTATTTC
1 TTTCTT-TTCTTTTATTTC
10095464 TTTCTTTTCTTTTATTT
1 TTTCTTTTCTTTTATTT
10095481 TTTTAATCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTCTTTTCTTTTATTTC
Found at i:10096560 original size:32 final size:32
Alignment explanation
Indices: 10096524--10096588 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
10096514 GTGGGTTTGG
* *
10096524 TGGAGGTAAGCTGAGGACTGGGGTAGAAATGA
1 TGGAGGTAAGCCGAGGACTGAGGTAGAAATGA
* *
10096556 TGGAGGTAGGCCGAGGACTGAGGTGGAAATGA
1 TGGAGGTAAGCCGAGGACTGAGGTAGAAATGA
10096588 T
1 T
10096589 CTCCAGAGTA
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:0.29, C:0.08, G:0.45, T:0.18
Consensus pattern (32 bp):
TGGAGGTAAGCCGAGGACTGAGGTAGAAATGA
Found at i:10098304 original size:53 final size:51
Alignment explanation
Indices: 10098224--10098410 Score: 236
Period size: 51 Copynumber: 3.6 Consensus size: 51
10098214 ATTTCGTTTA
**
10098224 ATACTCACGATGACA-TATAGTCATCGGAACTCTTGTTCCATATAGGAATTCAT
1 ATACTCACGATGACACTA-AGTCATCGGAACT-TTAATCCATATAGG-ATTCAT
10098277 ATACTCACGATGACACTAAGTCATCGGAACTTTAATCCATCAT-GGATTCAT
1 ATACTCACGATGACACTAAGTCATCGGAACTTTAATCCAT-ATAGGATTCAT
* * * * *
10098328 ATGCTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACTAAGTCATCGGAACTTTAATCCATATAGGATTCAT
* *
10098379 TTACTCACGATGACACTTAGTCATCGG-ACTTT
1 ATACTCACGATGACACTAAGTCATCGGAACTTT
10098411 TTCGTTTATA
Statistics
Matches: 121, Mismatches: 10, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
50 5 0.04
51 75 0.62
52 9 0.07
53 30 0.25
54 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (51 bp):
ATACTCACGATGACACTAAGTCATCGGAACTTTAATCCATATAGGATTCAT
Found at i:10105546 original size:51 final size:50
Alignment explanation
Indices: 10105420--10105607 Score: 191
Period size: 51 Copynumber: 3.7 Consensus size: 50
10105410 AATTCTTTTA
**
10105420 ATACTCACGATGACA-TATAGTCATCGGACCTCTTTTTACATATAGGAATTCAT
1 ATACTCACGATGACACT-TAGTCATCGGACCT-TTAATACATAT-GG-ATTCAT
* *
10105473 ATACTCACGATGACACTAAGTCATCAGACCTTTAATACATCATGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTTTAATACAT-ATGGATTCAT
* * * * * *
10105524 GTACTCATGATGACATTTAGTCATCGGAGCTTTAAT-CTGTAAAGGATTCAT
1 ATACTCACGATGACACTTAGTCATCGGACCTTTAATAC-AT-ATGGATTCAT
* *
10105575 TTAATCACGATGACACTTAGTCATCGGACCTTT
1 ATACTCACGATGACACTTAGTCATCGGACCTTT
10105608 TCGTTTATAG
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.01
51 74 0.65
52 9 0.08
53 29 0.25
54 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (50 bp):
ATACTCACGATGACACTTAGTCATCGGACCTTTAATACATATGGATTCAT
Found at i:10110321 original size:14 final size:14
Alignment explanation
Indices: 10110302--10110328 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10110292 CCCATTTTTT
10110302 CATTTTTTAGCATG
1 CATTTTTTAGCATG
10110316 CATTTTTTAGCAT
1 CATTTTTTAGCAT
10110329 TTTTAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (14 bp):
CATTTTTTAGCATG
Found at i:10116700 original size:26 final size:26
Alignment explanation
Indices: 10116646--10116700 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
10116636 TCTTTCTTAC
*
10116646 TTAACTTCTTGTTTTTACTAATCTGT
1 TTAACTTCTTGTTTTTACTAATCTCT
*
10116672 TTAACTTCCTT-TTGTTTA-TATTCTCT
1 TTAACTT-CTTGTT-TTTACTAATCTCT
10116698 TTA
1 TTA
10116701 TTTTTTAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.18, C:0.16, G:0.05, T:0.60
Consensus pattern (26 bp):
TTAACTTCTTGTTTTTACTAATCTCT
Found at i:10130801 original size:14 final size:14
Alignment explanation
Indices: 10130782--10130808 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10130772 TACTAATCTT
10130782 TTAATTTTCTTTTG
1 TTAATTTTCTTTTG
10130796 TTAATTTTCTTTT
1 TTAATTTTCTTTT
10130809 ATTTCTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (14 bp):
TTAATTTTCTTTTG
Found at i:10136261 original size:15 final size:15
Alignment explanation
Indices: 10136241--10136278 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
10136231 TTTACATTTT
10136241 CTTTTATATGTTTCA
1 CTTTTATATGTTTCA
10136256 CTTTTACT-TGTTTCA
1 CTTTTA-TATGTTTCA
10136271 -TTTTATAT
1 CTTTTATAT
10136279 TCTTTGCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 6 0.29
15 13 0.62
16 1 0.05
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (15 bp):
CTTTTATATGTTTCA
Found at i:10138122 original size:3 final size:3
Alignment explanation
Indices: 10138116--10138153 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
10138106 GAAGATGGCC
*
10138116 AGA AGA AGA AGA ATGA AGA AGA AGA AAA AGA AGA AGA A
1 AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA A
10138154 AATGACATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:10138622 original size:19 final size:19
Alignment explanation
Indices: 10138598--10138642 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
10138588 ATAGTTTTCA
*
10138598 TGCATTTTTATTCTGTCAT
1 TGCATTTTTATTCTGTCAG
* *
10138617 TGCATTTTTATTTTGTTAG
1 TGCATTTTTATTCTGTCAG
10138636 TGCATTT
1 TGCATTT
10138643 CTTTTGTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (19 bp):
TGCATTTTTATTCTGTCAG
Found at i:10142300 original size:27 final size:28
Alignment explanation
Indices: 10142269--10142328 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
10142259 GCATAGGAAT
*
10142269 TTAATTTAGTTTTAGCTTAA-AC-TTAGA
1 TTAATTTAG-TTTAGATTAATACTTTAGA
10142296 TTAATTTAGTTTAGATTAATACTTTAGA
1 TTAATTTAGTTTAGATTAATACTTTAGA
10142324 TTAAT
1 TTAAT
10142329 ATCTCTCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.30
27 11 0.37
28 10 0.33
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (28 bp):
TTAATTTAGTTTAGATTAATACTTTAGA
Found at i:10142323 original size:13 final size:13
Alignment explanation
Indices: 10142279--10142329 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
10142269 TTAATTTAGT
*
10142279 TTTAGCTTAA-AC
1 TTTAGATTAATAC
*
10142291 -TTAGATTAATTTAG
1 TTTAGATTAA--TAC
10142305 TTTAGATTAATAC
1 TTTAGATTAATAC
10142318 TTTAGATTAATA
1 TTTAGATTAATA
10142330 TCTCTCAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 8 0.25
13 14 0.44
14 1 0.03
15 9 0.28
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:10148615 original size:20 final size:20
Alignment explanation
Indices: 10148594--10148661 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
10148584 GAGTTTTATT
*
10148594 TTTAAAAATCTAAACTTTTTT
1 TTTAAAAATCTAAAC-TTTTA
10148615 TTTAAAAA--TAATAC-TTTA
1 TTTAAAAATCTAA-ACTTTTA
* *
10148633 TATAAAAATCCAAACTTTTA
1 TTTAAAAATCTAAACTTTTA
*
10148653 TTTCAAAAT
1 TTTAAAAAT
10148662 AGTTAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
18 10 0.26
19 5 0.13
20 15 0.39
21 8 0.21
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTAAAAATCTAAACTTTTA
Found at i:10148620 original size:143 final size:141
Alignment explanation
Indices: 10148465--10148958 Score: 567
Period size: 143 Copynumber: 3.5 Consensus size: 141
10148455 AAAAAGTTCT
* *
10148465 CTTTTTTTTTAAAAAAATACTATTTTTCTTAAAAATCAAAATTTTTATTTCGAAATGGTT-AAAA
1 CTTTTTTTTTAAAAAAATACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAA
* * * *
10148529 AAATCAAATTTTATTTAAAAATTTAAAATTTTCTCTTTTAAAATGCCTAAAAAGAGAGTTTTATT
66 AAATCAAATTTTATTTAAAAATTTAAACTTTT-TC-TTTAAAATGACTAAAAACA-ATTTTTATT
10148594 TTTAAAAATCTAAA
128 TTTAAAAATCTAAA
* * * *
10148608 CTTTTTTTTTAAAAATAATAC--TTTAT-ATAAAAATCCAAACTTTTATTTCAAAATAGTTAAAA
1 CTTTTTTTTTAAAAA-AATACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAA
* * * *
10148670 AAAATCAAAACTTTGTTTAAAAATTCAAACTTTTTCTTTAAAATGATTAAAAAAACAAATTTTTA
65 AAAATC-AAATTTTATTTAAAAATTTAAACTTTTTCTTTAAAATGACT--AAAAAC-AATTTTTA
* *
10148735 TTTTAAAAAATCTAAG
126 TTTTTAAAAATCTAAA
* * * *
10148751 CTTTTTTTTTAATGAAAATTACTATTTTTCTTAAAACTCCAAACTTTTATTTCTAAATAGTTAAA
1 CTTTTTTTTTAA--AAAAATACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAA
*
10148816 AAAAATC-AATTTTATTT-AAAATTTAAACTTTTTCTTTAAAATAACTAAGAAACAATTTTTTAT
64 AAAAATCAAATTTTATTTAAAAATTTAAACTTTTTCTTTAAAATGACTAA-AAACAA-TTTTTAT
10148879 TTTTAAAAATCT--A
127 TTTTAAAAATCTAAA
* * * *
10148892 --TTTTTTTTAAAGAAAATCACCATTTTTCTTAAAACTCAAAATTTTTATTTCGAAATTGTTAAA
1 CTTTTTTTTTAAA-AAAAT-ACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAA
10148955 AAAA
64 AAAA
10148959 TTAAAACTTT
Statistics
Matches: 302, Mismatches: 34, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
137 1 0.00
138 4 0.01
139 54 0.18
141 37 0.12
142 19 0.06
143 97 0.32
144 36 0.12
145 11 0.04
146 4 0.01
147 39 0.13
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (141 bp):
CTTTTTTTTTAAAAAAATACTATTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAA
AAATCAAATTTTATTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAACAATTTTTATTTTT
AAAAATCTAAA
Found at i:10148691 original size:52 final size:51
Alignment explanation
Indices: 10148618--10148724 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 51
10148608 CTTTTTTTTT
*
10148618 AAAAATAATACTTTATATAAAAATCCAAACTTTTAT-TTCAAAAT-AGTTAAA
1 AAAAATAAAACTTTATATAAAAATCCAAACTTTT-TCTTCAAAATGA-TTAAA
* * * *
10148669 AAAAATCAAAACTTTGTTTAAAAATTCAAACTTTTTCTTTAAAATGATTAAA
1 AAAAAT-AAAACTTTATATAAAAATCCAAACTTTTTCTTCAAAATGATTAAA
10148721 AAAA
1 AAAA
10148725 CAAATTTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
51 7 0.15
52 40 0.83
53 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (51 bp):
AAAAATAAAACTTTATATAAAAATCCAAACTTTTTCTTCAAAATGATTAAA
Found at i:10156706 original size:16 final size:16
Alignment explanation
Indices: 10156676--10156732 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
10156666 GGTGGTAAGA
*
10156676 AATTTATTTATTTTTCT
1 AATTTATTAATTTTT-T
10156693 AATTT-TTAATTTTTTT
1 AATTTATTAA-TTTTTT
*
10156709 AATTTATTAACTTTTT
1 AATTTATTAATTTTTT
10156725 AATTTATT
1 AATTTATT
10156733 TTAAATTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 22 0.61
17 14 0.39
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTATTAATTTTTT
Found at i:10156750 original size:26 final size:24
Alignment explanation
Indices: 10156692--10156751 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
10156682 TTTATTTTTC
*
10156692 TAATTTTTAATTTTTTTAATTTAT
1 TAATTTTTAATTTTTTTAAATTAT
*
10156716 TAACTTTTTAATTTATTTTAAATTGT
1 TAA-TTTTTAATTT-TTTTAAATTAT
10156742 TAATATTTTA
1 TAAT-TTTTA
10156752 TACTAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 3 0.10
25 11 0.35
26 17 0.55
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TAATTTTTAATTTTTTTAAATTAT
Found at i:10157659 original size:21 final size:21
Alignment explanation
Indices: 10157621--10157662 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10157611 CAACAGCAAG
*
10157621 CTGAAGAAGAAGAAGAAGATC
1 CTGAAGAACAAGAAGAAGATC
* *
10157642 CTGAAGAACATGAGGAAGATC
1 CTGAAGAACAAGAAGAAGATC
10157663 TTTTGGTGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.29, T:0.12
Consensus pattern (21 bp):
CTGAAGAACAAGAAGAAGATC
Found at i:10161989 original size:18 final size:18
Alignment explanation
Indices: 10161940--10161982 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
10161930 GTAGGCACAT
* *
10161940 CATGATCAGATGTAATCA
1 CATGCTCAGATGCAATCA
10161958 CATGCTCAGATGCAATCA
1 CATGCTCAGATGCAATCA
10161976 CATGCTC
1 CATGCTC
10161983 GTATGCAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (18 bp):
CATGCTCAGATGCAATCA
Found at i:10161995 original size:18 final size:18
Alignment explanation
Indices: 10161940--10161995 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
10161930 GTAGGCACAT
* * *
10161940 CATGATCAGATGTAATCA
1 CATGCTCAGATGCAACCA
*
10161958 CATGCTCAGATGCAATCA
1 CATGCTCAGATGCAACCA
*
10161976 CATGCTC-GTATGCAGCCA
1 CATGCTCAG-ATGCAACCA
10161994 CA
1 CA
10161996 ACAGACTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 1 0.03
18 32 0.97
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (18 bp):
CATGCTCAGATGCAACCA
Found at i:10165865 original size:22 final size:23
Alignment explanation
Indices: 10165837--10165901 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
10165827 GCAATAGTAG
10165837 GCACACAAAGTGCTAAACAGA-A
1 GCACACAAAGTGCTAAACAGAGA
* *
10165859 GCACACACAGTGCTAAACAGAGG
1 GCACACAAAGTGCTAAACAGAGA
*
10165882 GCACGA-AACGTGCTAAACAG
1 GCAC-ACAAAGTGCTAAACAG
10165902 TAGGCGCGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 20 0.54
23 16 0.43
24 1 0.03
ACGTcount: A:0.43, C:0.25, G:0.23, T:0.09
Consensus pattern (23 bp):
GCACACAAAGTGCTAAACAGAGA
Found at i:10173951 original size:57 final size:57
Alignment explanation
Indices: 10173879--10173995 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
10173869 TTTTTCCAGG
10173879 TAAGGTCGGTCCAACATCAAGCAAAATTGTGCTTTATAATTATATTTTTAATTCAAT
1 TAAGGTCGGTCCAACATCAAGCAAAATTGTGCTTTATAATTATATTTTTAATTCAAT
10173936 TAAGGTCGGTCCAACATCAAGCAAAATTGTGCTTTATAATTATATTTTTAATTCAAT
1 TAAGGTCGGTCCAACATCAAGCAAAATTGTGCTTTATAATTATATTTTTAATTCAAT
10173993 TAA
1 TAA
10173996 TTTGGATTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (57 bp):
TAAGGTCGGTCCAACATCAAGCAAAATTGTGCTTTATAATTATATTTTTAATTCAAT
Found at i:10190703 original size:18 final size:19
Alignment explanation
Indices: 10190676--10190723 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
10190666 TGCAGTCTGT
*
10190676 TGTGGCTGCATTC-AAGCA
1 TGTGACTGCATTCTAAGCA
* *
10190694 TGTGATTGCA-TCTATGCA
1 TGTGACTGCATTCTAAGCA
10190712 TGTGACTGCATT
1 TGTGACTGCATT
10190724 TGATCATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.08
18 21 0.88
19 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (19 bp):
TGTGACTGCATTCTAAGCA
Found at i:10198446 original size:26 final size:25
Alignment explanation
Indices: 10198391--10198446 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
10198381 TTCTTCTACT
* *
10198391 TTTTAATTTATTTAATTTATTAACG
1 TTTTAATTTATTTAAATTATTAACA
* * *
10198416 CTTTAATTTAATTTAAATTGTTAATA
1 TTTTAATTT-ATTTAAATTATTAACA
10198442 TTTTA
1 TTTTA
10198447 TACTAATTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (25 bp):
TTTTAATTTATTTAAATTATTAACA
Found at i:10199363 original size:18 final size:18
Alignment explanation
Indices: 10199324--10199364 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
10199314 ACAGCAAGTT
*
10199324 GAAGAAGAAGAAGACCCT
1 GAAGAAGAAGAAGACCCA
* *
10199342 GAAGAAGAAGTAGATCCA
1 GAAGAAGAAGAAGACCCA
10199360 GAAGA
1 GAAGA
10199365 GGATTTTGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.29, T:0.07
Consensus pattern (18 bp):
GAAGAAGAAGAAGACCCA
Found at i:10205573 original size:24 final size:24
Alignment explanation
Indices: 10205459--10205579 Score: 136
Period size: 24 Copynumber: 5.0 Consensus size: 24
10205449 TTTGATGCTT
10205459 TGTGCATTGCGAACTCTTGT-GAAC
1 TGTGCATTGCGAACTCTT-TCGAAC
* *
10205483 TGTGCATTCCGAACTCTTTCAAAC
1 TGTGCATTGCGAACTCTTTCGAAC
* *
10205507 TGTGCATTGTGAACTCTTGCGAAC
1 TGTGCATTGCGAACTCTTTCGAAC
* * * * *
10205531 TGTACAATGTGAACTCTTTTGAAT
1 TGTGCATTGCGAACTCTTTCGAAC
*
10205555 TGTGCATTGCGAACTCTTTCAAAC
1 TGTGCATTGCGAACTCTTTCGAAC
10205579 T
1 T
10205580 ATTTGTAACC
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 1 0.01
24 78 0.99
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (24 bp):
TGTGCATTGCGAACTCTTTCGAAC
Found at i:10206460 original size:48 final size:48
Alignment explanation
Indices: 10206385--10206531 Score: 197
Period size: 48 Copynumber: 3.1 Consensus size: 48
10206375 ACATAAACAA
* * * * *
10206385 ATAATCACTTCGCATATAAACTATCACATATTTTCCAATAATGGTCAC
1 ATAATCACTTTGCAAATAAACTTTCACATAATTGCCAATAATGGTCAC
*
10206433 ATAATCACTTTGCAGATAAACTTTCACATAATTGCCAATAATGGTCAC
1 ATAATCACTTTGCAAATAAACTTTCACATAATTGCCAATAATGGTCAC
* * *
10206481 ATAATCACTTTGCAAACAAA-TTGCCACATAATTGCCAATAATGGCCAC
1 ATAATCACTTTGCAAATAAACTT-TCACATAATTGCCAATAATGGTCAC
10206529 ATA
1 ATA
10206532 TCTACCACCT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 2 0.02
48 87 0.98
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (48 bp):
ATAATCACTTTGCAAATAAACTTTCACATAATTGCCAATAATGGTCAC
Found at i:10206513 original size:11 final size:11
Alignment explanation
Indices: 10206499--10206531 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
10206489 TTTGCAAACA
10206499 AATTGCCACAT
1 AATTGCCACAT
10206510 AATTGCCA-AT
1 AATTGCCACAT
*
10206520 AATGGCCACAT
1 AATTGCCACAT
10206531 A
1 A
10206532 TCTACCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (11 bp):
AATTGCCACAT
Found at i:10211853 original size:24 final size:24
Alignment explanation
Indices: 10211826--10211934 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
10211816 TTGTGCATTG
*
10211826 CGAACTGTGCATTGTAAACTCTTA
1 CGAACTGTGCATTGCAAACTCTTA
* *
10211850 CGAACTGTGCATTGCATACTCTTG
1 CGAACTGTGCATTGCAAACTCTTA
* *
10211874 TGAA-TAGTGCATTGCAACCTCTT-
1 CGAACT-GTGCATTGCAAACTCTTA
** * * *
10211897 CTGAACTACGCATTGCGAGCTCTTG
1 C-GAACTGTGCATTGCAAACTCTTA
*
10211922 CGAAATGTGCATT
1 CGAACTGTGCATT
10211935 TCCAACCCCT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.01
24 64 0.96
25 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (24 bp):
CGAACTGTGCATTGCAAACTCTTA
Found at i:10214805 original size:21 final size:21
Alignment explanation
Indices: 10214781--10214837 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
10214771 GAACTAAGAC
* *
10214781 TTCTATCGATACAGCTCTAGG
1 TTCTACCGATACAACTCTAGG
* * *
10214802 TTCTACCAATATAACTCTGGG
1 TTCTACCGATACAACTCTAGG
10214823 TTCTACCGATACAAC
1 TTCTACCGATACAAC
10214838 CCAGACTTCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACAACTCTAGG
Found at i:10219391 original size:20 final size:20
Alignment explanation
Indices: 10219366--10219410 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
10219356 CAATAAAAAA
10219366 GTCAACAATCAAAGTCAACG
1 GTCAACAATCAAAGTCAACG
** *
10219386 GTCAACGGTTAAAGTCAACG
1 GTCAACAATCAAAGTCAACG
10219406 GTCAA
1 GTCAA
10219411 GTCAATGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
GTCAACAATCAAAGTCAACG
Found at i:10229596 original size:31 final size:31
Alignment explanation
Indices: 10229561--10229637 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
10229551 ATAACCTATC
*
10229561 GTTTCCAAGCAACCCTGAGTAACGGATCATT
1 GTTTCCAAGCAACCCGGAGTAACGGATCATT
* * *
10229592 GTTTCCAAGCAACCCGGGGTAGCGGGTCATT
1 GTTTCCAAGCAACCCGGAGTAACGGATCATT
10229623 GTTTCCAAGCAACCC
1 GTTTCCAAGCAACCC
10229638 AGGATGACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (31 bp):
GTTTCCAAGCAACCCGGAGTAACGGATCATT
Found at i:10229950 original size:19 final size:20
Alignment explanation
Indices: 10229925--10229970 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
10229915 ATTCGAAATG
10229925 TTATGTGAAAGTATGTG-ATA
1 TTATGTGAAA-TATGTGAATA
10229945 -TATGTGAAATATGTGAATA
1 TTATGTGAAATATGTGAATA
10229964 TTATGTG
1 TTATGTG
10229971 TGTTTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (20 bp):
TTATGTGAAATATGTGAATA
Found at i:10229970 original size:11 final size:9
Alignment explanation
Indices: 10229926--10229961 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
10229916 TTCGAAATGT
10229926 TATGTGAAA
1 TATGTGAAA
*
10229935 GTATGTGATA
1 -TATGTGAAA
10229945 TATGTGAAA
1 TATGTGAAA
10229954 TATGTGAA
1 TATGTGAA
10229962 TATTATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (9 bp):
TATGTGAAA
Found at i:10231674 original size:30 final size:30
Alignment explanation
Indices: 10231638--10231710 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
10231628 CTTAGCTTAA
* * *
10231638 ATAGCCACAGAGG-AGTCCACACATTATTAG
1 ATAGCCACAAAGGCA-TCCAAACATCATTAG
*
10231668 ATAGCCACAAAGGCATCCAAACATCATTTG
1 ATAGCCACAAAGGCATCCAAACATCATTAG
*
10231698 ATAGCCATAAAGG
1 ATAGCCACAAAGG
10231711 TGTCCAGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (30 bp):
ATAGCCACAAAGGCATCCAAACATCATTAG
Found at i:10231883 original size:30 final size:29
Alignment explanation
Indices: 10231831--10231922 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 29
10231821 TCACAAAGCC
10231831 TCACATATAACAGAGAACAGCCACAATGGCTT
1 TCACATATAA-A-AGAACAGCCACAAT-GCTT
* * *
10231863 TCACATATCAAAGAATAGCCATAAATGCTT
1 TCACATATAAAAGAACAGCCA-CAATGCTT
*
10231893 TCACATATAAAAGAACAACCACAAATGCTT
1 TCACATATAAAAGAACAGCCAC-AATGCTT
10231923 CCATTTCTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 38 0.75
31 4 0.08
32 9 0.18
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.22
Consensus pattern (29 bp):
TCACATATAAAAGAACAGCCACAATGCTT
Found at i:10232921 original size:20 final size:21
Alignment explanation
Indices: 10232882--10232962 Score: 69
Period size: 19 Copynumber: 4.0 Consensus size: 21
10232872 GTTTGAAACA
* *
10232882 ATTTTAAAATCAAGTTAAAATG
1 ATTTTAAAA-CAAGTCAAAATC
10232904 ATTTT-AAACAAGTCAAAATC
1 ATTTTAAAACAAGTCAAAATC
** *
10232924 ATTTT--AACACTTCAAAATT
1 ATTTTAAAACAAGTCAAAATC
* *
10232943 TTTTTCAAACAAGTCAAAAT
1 ATTTTAAAACAAGTCAAAAT
10232963 AGCGTCAGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
19 15 0.31
20 15 0.31
21 14 0.29
22 5 0.10
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTTTAAAACAAGTCAAAATC
Found at i:10234147 original size:27 final size:27
Alignment explanation
Indices: 10234069--10234148 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
10234059 TAACGGAGTA
* * *
10234069 TAGCTCATTCGATCCCAGAATAGAGTT
1 TAGCTCATTTGAGCCCAGAATAGATTT
*
10234096 TAGCTCATTTGAGCCTAGAATAGATTT
1 TAGCTCATTTGAGCCCAGAATAGATTT
* *
10234123 TAGCTCATTTGAGCCCAAAACAGATT
1 TAGCTCATTTGAGCCCAGAATAGATT
10234149 ATTTCTCTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (27 bp):
TAGCTCATTTGAGCCCAGAATAGATTT
Found at i:10234240 original size:27 final size:28
Alignment explanation
Indices: 10234179--10234248 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
10234169 ATAGAATAAC
* *
10234179 GCTCTTATCGAGCCAAAGTCCAGAATATT
1 GCTCTT-TCGAGCCAAAATCCAAAATATT
10234208 GCTCTTTCGAGCCAAAAT-CAAAATATCT
1 GCTCTTTCGAGCCAAAATCCAAAATAT-T
*
10234236 -CTCTTTTGAGCCA
1 GCTCTTTCGAGCCA
10234249 GAATAAGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 19 0.51
28 12 0.32
29 6 0.16
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (28 bp):
GCTCTTTCGAGCCAAAATCCAAAATATT
Found at i:10241613 original size:21 final size:21
Alignment explanation
Indices: 10241587--10241633 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10241577 AATTTTTTAC
* *
10241587 ATTTTT-TGAATTTTATTTAAT
1 ATTTTTATAAATTTTA-ATAAT
10241608 ATTTTTATAAATTTTAATAAT
1 ATTTTTATAAATTTTAATAAT
10241629 ATTTT
1 ATTTT
10241634 ACAAACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTTATAAATTTTAATAAT
Found at i:10250328 original size:2 final size:2
Alignment explanation
Indices: 10250321--10250347 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10250311 CTCTAAAAAT
10250321 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
10250348 AAAAGACTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:10261251 original size:70 final size:67
Alignment explanation
Indices: 10261125--10261257 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
10261115 ATAAACAATA
* * *
10261125 TAATGGTTTTGCCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACATTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACATTTTAA
10261190 CT
66 CT
* * *
10261192 TAATGGTTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGACGTAGTTTTACCTTT
1 TAATGGTTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACATTT
10261257 T
63 T
10261258 CTTATTCGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 2 0.04
70 36 0.63
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACATTTTAA
CT
Found at i:10262383 original size:10 final size:10
Alignment explanation
Indices: 10262368--10262393 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
10262358 AAGAGAGGGA
10262368 GAGGGGACGG
1 GAGGGGACGG
10262378 GAGGGGACGG
1 GAGGGGACGG
10262388 GAGGGG
1 GAGGGG
10262394 TTTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.73, T:0.00
Consensus pattern (10 bp):
GAGGGGACGG
Found at i:10262441 original size:26 final size:25
Alignment explanation
Indices: 10262404--10262455 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
10262394 TTTTTTTATT
10262404 ATTATTTCTATTTAATATTAAATATA
1 ATTATTTCTATTTAATATT-AATATA
*
10262430 ATTATTTTTATTTAATATTAATATA
1 ATTATTTCTATTTAATATTAATATA
10262455 A
1 A
10262456 AATTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTATTTCTATTTAATATTAATATA
Found at i:10269503 original size:42 final size:42
Alignment explanation
Indices: 10268766--10269504 Score: 793
Period size: 42 Copynumber: 17.5 Consensus size: 42
10268756 AAGGAAAGCA
* * * * *
10268766 TTCATTACATTTAGAGGTCCAGGTGTCGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * ** * *
10268808 TTTATTGCATTTAAAGGCCTTAGTATGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
10268850 TTCATCGCACTTAGAGGCCCAAGTGTGGAAG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCC-ATTTACTT
* * * * *
10268892 TTTATCGCATTTAGAGGCCTAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
10268934 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * * *
10268976 TTCATTACA-TTAGAGGCCTAGGTGTGAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * ** * * *
10269017 TTCATGGCATTTAAATACCTAAGTATGGAGGTCCATTTACTC
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
10269059 TTCATTGCATTTAGAGGCCCAAGTGTGAAGGTCCGTTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
*
10269101 TTCATTGCATTTAGAGGCCTAAGTGTGGAGGTCCATTTA-TT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
10269142 CTTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCTATTTACTT
1 -TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * *
10269185 TTCATCGCTTTTGGAGACCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * ** * *
10269227 TTTATCGCATTTAGAGGATCAGGTGTGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * *
10269269 TTTATCGCATTTAGAGGCAGAGGTCCAAGTGTGGAGGTTCGTTTA-TT
1 TTCATTGCATTTAGAGGC------CCAAGTGTGGAGGTCCATTTACTT
* * *
10269316 TTCAGTGCATTTAGAGGCCCAAGTGTGAAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
10269358 TTCATTACATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * * * * *
10269400 TTCAATGCATTTAAAGGCCTAGGTGTAGAGATTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
*
10269442 TTCATCGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
10269484 TTCATTGCATTTAGAGGCCCA
1 TTCATTGCATTTAGAGGCCCA
10269505 TCTATTTGCA
Statistics
Matches: 581, Mismatches: 104, Indels: 24
0.82 0.15 0.03
Matches are distributed among these distances:
41 58 0.10
42 487 0.84
43 3 0.01
47 17 0.03
48 16 0.03
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:10269918 original size:3 final size:3
Alignment explanation
Indices: 10269910--10269961 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
10269900 CAAGGGCCCA
*
10269910 ATT ATT ATT -TT CATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10269955 ATT ATT A
1 ATT ATT A
10269962 GGGTTTCATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:10270789 original size:24 final size:23
Alignment explanation
Indices: 10270745--10270790 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
10270735 GATTTTCATT
* *
10270745 AAAAAATAAAATTTTAGATTTTA
1 AAAAAATAAAAATCTAGATTTTA
*
10270768 AAAAAATAAAAAATCTATATTTT
1 AAAAAAT-AAAAATCTAGATTTT
10270791 TAGTCATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AAAAAATAAAAATCTAGATTTTA
Found at i:10270897 original size:149 final size:146
Alignment explanation
Indices: 10270388--10271029 Score: 707
Period size: 148 Copynumber: 4.4 Consensus size: 146
10270378 TTTTTTGGTG
* * * * ** *
10270388 TTTTAAACAATTTCGAAATAAAAGTTTTG-ATTTTCAACAAAAATAGTGATTTTCTTTAAAAAAA
1 TTTTTAACTATTTCGAAATAAAA-ATTTGAATTTTTAAGTAAAATAGTGATTTTCATT----AAA
* *
10270452 AAAAGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAAAAAGTTTAA
61 AAAA-AAAGTTTAGATTTTAAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAAAAAGTTTAA
*
10270517 ATTTTTAAACAAAGTTTTAATTT
125 ATTTTTAAACAAAGTTTTGA-TT
* * * *
10270540 TTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTAATTTTCTTTATAAAAAG
1 TTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCATTA-AAAAA-
* * **
10270605 AGAAAGTTTATATTTTTAATCATAAAAATATATTTTTTTAGTCATTTTAAAGAAAAA-TTTAAAT
64 A-AAAGTTTAGATTTTAAAAAATAAAAATATA-TTTTTTAGTCATTTTAAAGAAAAAGTTTAAAT
10270669 TTTTAAACAAA-TTCTTGA-T
127 TTTTAAACAAAGTT-TTGATT
* *
10270688 TTTTTAACTATTTCGAAATGAAAATTTGAATTTGTAAGTAAAATAGTGATTTTCATTAAAAAATA
1 TTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCATTAAAAAA-A
* * *
10270753 AAATTTTAGATTTTAAAAAAATAAAAAATCTATATTTTTAGTCATTTTAAAG-AAAAGTTTAAAA
65 AAAGTTTAGATTTT-AAAAAAT-AAAAATATAT-TTTTTAGTCATTTTAAAGAAAAAGTTTAAAT
*
10270817 TTTTAAGCAAAGTTTTGATT
127 TTTTAAACAAAGTTTTGATT
* ** *
10270837 TTTTTAACTATTTCAAAATAAAAATTT-AATTTTTTTTGTAAAATAGTGATTTTGATT----AAA
1 TTTTTAACTATTTCGAAATAAAAATTTGAA-TTTTTAAGTAAAATAGTGATTTTCATTAAAAAAA
* * * *
10270897 AAAGTTTAGA-TTTAAAAAA-AAAAAAATCTTTTTTAGTGATTTTAAAGAAAAATTTTAAATTTT
65 AAAGTTTAGATTTTAAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTT
*
10270960 TAAACAAAATTTTGATT
130 TAAACAAAGTTTTGATT
* * *
10270977 TTTTTAACTATTTCGAAATAAAAGTTCTG-ATTTTGAAGTAAAGTAGTGATTTT
1 TTTTTAACTATTTCGAAATAAAAATT-TGAATTTTTAAGTAAAATAGTGATTTT
10271030 GTTTTAATCA
Statistics
Matches: 427, Mismatches: 48, Indels: 42
0.83 0.09 0.08
Matches are distributed among these distances:
139 17 0.04
140 78 0.18
141 2 0.00
142 6 0.01
143 3 0.01
144 10 0.02
145 2 0.00
146 12 0.03
147 15 0.04
148 102 0.24
149 58 0.14
150 49 0.11
151 28 0.07
152 45 0.11
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (146 bp):
TTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCATTAAAAAAAA
AAGTTTAGATTTTAAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAAAAAGTTTAAATTTTT
AAACAAAGTTTTGATT
Found at i:10275733 original size:4 final size:4
Alignment explanation
Indices: 10275724--10275755 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
10275714 AGCGACTGAG
*
10275724 TGAA TGAA TGGA TGAA TGAA TGAA TGAA TGAA
1 TGAA TGAA TGAA TGAA TGAA TGAA TGAA TGAA
10275756 ATTAGGGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (4 bp):
TGAA
Found at i:10280563 original size:149 final size:151
Alignment explanation
Indices: 10280312--10281117 Score: 950
Period size: 149 Copynumber: 5.4 Consensus size: 151
10280302 TGATTAAAAT
* * * * * *
10280312 AAAATCACTACTTTATTTCAAAATCAAAACTTTTATTTTGAAATAGTT-AAAAAAATCAAAATTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* * *
10280376 TATTTAAAAATTTAAACTTTTTCTTTAAAATTACTAAAAAATAAATTTTTATTTTTTAAAAATCT
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTTAAAAATAT
*
10280441 AAACTTTCTTTATTTTTAATG
131 AAACTTTCTTTTTTTTTAATG
*
10280462 AAAATAACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAAAT-AAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
* * * *
10280525 TGTTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAACAGATTTTTATATTTTAAAAAT-T
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTTAAAAATAT
*
10280589 ATACTTTCTTTCTTTTTTAATG
131 AAACTTTCTTT-TTTTTTAATG
* * * * *
10280611 AAAATC-CTTACTTTACTTAAAAATCTAAACTTTTATTTCAAAATATTTAAAAAAAATTAAAACT
1 AAAATCAC-TATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACT
* * * * * ****
10280675 TTGTTTAAGAATTTAAAACTTTTTC-TTAAATTGACAAAAAAATAGA-TTTT-TTAAAAAAAAAT
65 TTGTTTAAAAATTT-AAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTTAAAAAT
*
10280737 CTAAA----C-TTTTTTTTAATG
129 ATAAACTTTCTTTTTTTTTAATG
* ** *
10280755 AAAATTACTATTTTACTTAAAAATTTAAACTTGTATTTCGAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAAC-T
* *
10280820 TTGTTTAAAAATTTAAATTTTTTCTTTAAAATAACT-AAAAATCATATTTTTA-TTTTTAAAAAT
65 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAT-AAATTTTTATTTTTTAAAAAT
**
10280883 ATAAACTTTCTCTTTTTTTTTAAAA
129 ATAAAC-TT-TCTTTTTTTTTAATG
* *
10280908 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAATTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
*
10280973 TGTTTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAATAAATTTTTA-TTTTTAAAAATAT
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTTAAAAATAT
* * *
10281037 TAACTTTC--TCTTTTTAAAG
131 AAACTTTCTTTTTTTTTAATG
* ** *
10281056 AAAATCATTATTTTACTTAAAAA-CCAATTTTTTTATTTCGAAATTA-TTTAAAAAAATCAAAA
1 AAAATCACTATTTTACTTAAAAATCCAA-ACTTTTATTTCGAAA-TAGTTAAAAAAAATCAAAA
10281118 TTTTTCCAAA
Statistics
Matches: 569, Mismatches: 65, Indels: 46
0.84 0.10 0.07
Matches are distributed among these distances:
144 79 0.14
145 27 0.05
146 16 0.03
147 4 0.01
148 71 0.12
149 123 0.22
150 67 0.12
151 38 0.07
152 71 0.12
153 73 0.13
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (151 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAAATTTTTATTTTTTAAAAATAT
AAACTTTCTTTTTTTTTAATG
Found at i:10280987 original size:297 final size:295
Alignment explanation
Indices: 10280295--10281022 Score: 959
Period size: 297 Copynumber: 2.4 Consensus size: 295
10280285 AATCAAAAGT
* * * *
10280295 TTTTTTTTGATTAAAATAAAATCACTACTTTATTTCAAAATCAAAACTTTTATTTTGAAATAGTT
1 TTTTTTTT--TTAAAA-AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAATT
*
10280360 -AAAAAAATCAAAATTTTATTTAAAAATTT-AAACTTTTTCTTTAAAATTACTAAAAAATAAATT
63 AAAAAAAATCAAAATTTTGTTTAAAAATTTAAAACTTTTTCTTT-AAATTACTAAAAAATAAA-T
****
10280423 TTTATTTTTTAAAAATCTAAACTTTCTTTATTTTTAATGAAAATAACTATTTTACTTAAAAATCC
126 TTT-TTAAAAAAAAATCTAAA---TCTTTATTTTTAATGAAAATAACTATTTTACTTAAAAATCC
*
10280488 AAACTTTTATTTCGAAATAGTTAAAAAAATAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAA
187 AAACTTGTATTTCGAAATAGTTAAAAAAATAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAA
* *
10280553 AATCACTAAAAAACAGATTTTTATATTTTAAAAATTATACTTTC
252 AATAACTAAAAAACAGATTTTTATATTTTAAAAATTAAACTTTC
* ** * * *
10280597 TTTCTTTTTTAATGAAAATC-CTTACTTTACTTAAAAATCTAAACTTTTATTTCAAAATATTTAA
1 TTTTTTTTTTAAAAAAAATCAC-TACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAATTAA
* * * * *
10280661 AAAAAATTAAAACTTTGTTTAAGAATTTAAAACTTTTTC-TTAAATTGACAAAAAAATAGATTTT
65 AAAAAATCAAAATTTTGTTTAAAAATTTAAAACTTTTTCTTTAAATT-ACTAAAAAATAAATTTT
* **
10280725 TTAAAAAAAAATCTAAA-CTTT-TTTTTAATGAAAATTACTATTTTACTTAAAAATTTAAACTTG
129 TTAAAAAAAAATCTAAATCTTTATTTTTAATGAAAATAACTATTTTACTTAAAAATCCAAACTTG
*
10280788 TATTTCGAAATAGTTAAAAAAAATCAAAACTTTTGTTTAAAAATTTAAATTTTTTCTTTAAAATA
194 TATTTCGAAATAGTT-AAAAAAAT-AAAAC-TTTGTTTAAAAATTTAAACTTTTTCTTTAAAATA
* *
10280853 ACTAAAAATCATATTTTTAT-TTTTAAAAATATAAACTTTC
256 ACTAAAAAACAGATTTTTATATTTTAAAAAT-TAAACTTTC
* *
10280893 TCTTTTTTTTTAAAAAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAA
1 T-TTTTTTTTTAAAAAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAATTAA
*
10280958 AAAAAATCAAAATTTTGTTTAAAAATTTAAAA-TTTTTCTTTAAAATAACTAAAAAATAAATTTT
65 AAAAAATCAAAATTTTGTTTAAAAATTTAAAACTTTTTCTTT-AAATTACTAAAAAATAAATTTT
10281022 T
129 T
10281023 ATTTTTAAAA
Statistics
Matches: 373, Mismatches: 41, Indels: 29
0.84 0.09 0.07
Matches are distributed among these distances:
293 53 0.14
294 12 0.03
295 15 0.04
296 65 0.17
297 101 0.27
298 19 0.05
299 49 0.13
300 42 0.11
301 10 0.03
302 7 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (295 bp):
TTTTTTTTTTAAAAAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAATTAAA
AAAAATCAAAATTTTGTTTAAAAATTTAAAACTTTTTCTTTAAATTACTAAAAAATAAATTTTTT
AAAAAAAAATCTAAATCTTTATTTTTAATGAAAATAACTATTTTACTTAAAAATCCAAACTTGTA
TTTCGAAATAGTTAAAAAAATAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAA
AAAACAGATTTTTATATTTTAAAAATTAAACTTTC
Found at i:10281004 original size:52 final size:52
Alignment explanation
Indices: 10280771--10281013 Score: 169
Period size: 52 Copynumber: 4.7 Consensus size: 52
10280761 ACTATTTTAC
* ** *
10280771 TTAAAAATTTAAACTTGTAT-TTCGAAATAGTTAAAAAAAATCAAAACTTTTGT
1 TTAAAAATTTAAACTT-TTTCTTTAAAATAATTAAAAAAAATCAAAA-TTTTGT
* * ** *
10280824 TTAAAAATTTAAATTTTTTCTTTAAAATAACT---AAAAATCATATTTTTATTT
1 TTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAAAATCA-AAATTT-TGT
* * * ** ** **
10280875 TTAAAAATATAAACTTTCTCTTT---TTTTTTAAAAAAAATCACTATTTTAC
1 TTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAAAATCAAAATTTTGT
** **
10280924 TTAAAAATCCAAACTTTTAT-TTCGAAATAATTAAAAAAAATCAAAATTTTGT
1 TTAAAAATTTAAACTTTT-TCTTTAAAATAATTAAAAAAAATCAAAATTTTGT
* *
10280976 TTAAAAATTTAAAATTTTTCTTTAAAATAACTAAAAAA
1 TTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAA
10281014 TAAATTTTTA
Statistics
Matches: 142, Mismatches: 37, Indels: 23
0.70 0.18 0.11
Matches are distributed among these distances:
48 2 0.01
49 18 0.13
50 16 0.11
51 32 0.23
52 51 0.36
53 23 0.16
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.42
Consensus pattern (52 bp):
TTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAAAATCAAAATTTTGT
Found at i:10283291 original size:2 final size:2
Alignment explanation
Indices: 10283284--10283339 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
10283274 TAGTATTAGA
10283284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10283326 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
10283340 TAAAGTTTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.