Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 10 of 325
Found at i:3486749 original size:24 final size:24
Alignment explanation
Indices: 3486716--3486764 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3486706 TAACAGTTCA
*
3486716 GTTTAGTGTAAAGACTTCTAACTC
1 GTTTACTGTAAAGACTTCTAACTC
3486740 GTTTACTGTAAAGACTTCTAACTC
1 GTTTACTGTAAAGACTTCTAACTC
3486764 G
1 G
3486765 AAGAGTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (24 bp):
GTTTACTGTAAAGACTTCTAACTC
Found at i:3491129 original size:13 final size:13
Alignment explanation
Indices: 3491111--3491139 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3491101 AATACCCAGA
3491111 AAGCGTACAAAGG
1 AAGCGTACAAAGG
3491124 AAGCGTACAAAGG
1 AAGCGTACAAAGG
3491137 AAG
1 AAG
3491140 AACCAGGAGT
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:0.48, C:0.14, G:0.31, T:0.07
Consensus pattern (13 bp):
AAGCGTACAAAGG
Found at i:3497430 original size:21 final size:21
Alignment explanation
Indices: 3497404--3497444 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3497394 ATCTGCTCAA
* *
3497404 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3497425 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3497445 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3502109 original size:56 final size:57
Alignment explanation
Indices: 3502023--3502136 Score: 212
Period size: 56 Copynumber: 2.0 Consensus size: 57
3502013 AAGTAATGCA
*
3502023 TTCAAAACTACTATCTTTAATTGGTATAA-TTTTTATGAAAAGTAGCAAGTTTCGCT
1 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
3502079 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
1 TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
3502136 T
1 T
3502137 CTAATGTATT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 28 0.50
57 28 0.50
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (57 bp):
TTCAAAACTACTATCTTTAACTGGTATAATTTTTTATGAAAAGTAGCAAGTTTCGCT
Found at i:3504829 original size:9 final size:9
Alignment explanation
Indices: 3504812--3504843 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
3504802 GCATCATCTT
3504812 CATCTTCCTC
1 CATC-TCCTC
3504822 CATCTCCTC
1 CATCTCCTC
3504831 CATCTCCTC
1 CATCTCCTC
3504840 CATC
1 CATC
3504844 ACATAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.34
Consensus pattern (9 bp):
CATCTCCTC
Found at i:3510096 original size:46 final size:46
Alignment explanation
Indices: 3510049--3510276 Score: 271
Period size: 46 Copynumber: 5.0 Consensus size: 46
3510039 GCTATCTGAT
* * *
3510049 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
3510095 ATGAAATGTGTAAGACCATGGTTGAAATATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *** * *
3510141 GA-GAAATGAATAAGACCATGGTTGAAAGATATGGTGGCAGCATAAC
1 -ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
3510187 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
3510233 A-GAAAAAGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
3510277 TCAAGGATAA
Statistics
Matches: 157, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
45 2 0.01
46 154 0.98
47 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:3515623 original size:39 final size:37
Alignment explanation
Indices: 3515556--3515648 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
3515546 ACCAGAATGG
* *
3515556 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
3515595 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
3515632 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
3515649 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:3516012 original size:3 final size:3
Alignment explanation
Indices: 3516004--3516050 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
3515994 ATTCCCACTC
* * * *
3516004 ATA ATA ATA ATA ATA ATA CTA ATA AT- ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3516051 CTTACCTCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3516052 original size:12 final size:12
Alignment explanation
Indices: 3516004--3516050 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3515994 ATTCCCACTC
*
3516004 ATAATAATAATA
1 ATAATACTAATA
3516016 ATAATACTAATA
1 ATAATACTAATA
3516028 AT-ATACTAATA
1 ATAATACTAATA
* *
3516039 CTAATATTAATA
1 ATAATACTAATA
3516051 CTTACCTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:3516727 original size:11 final size:11
Alignment explanation
Indices: 3516713--3516738 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3516703 CTTTTTCTTC
3516713 TTTCTCCCCTG
1 TTTCTCCCCTG
3516724 TTTCTCCCCTG
1 TTTCTCCCCTG
3516735 TTTC
1 TTTC
3516739 GTCTCTTCTA
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:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:3517120 original size:21 final size:21
Alignment explanation
Indices: 3517096--3517138 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3517086 AATAATAACT
3517096 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
3517117 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
3517138 A
1 A
3517139 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:3525221 original size:19 final size:21
Alignment explanation
Indices: 3525180--3525226 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3525170 TCTTATATAT
*
3525180 AAATAAAAGTCATAAATTT-A
1 AAATAAAAATCATAAATTTAA
*
3525200 AAATAAAAAT-ATATATTTAA
1 AAATAAAAATCATAAATTTAA
3525220 AAATAAA
1 AAATAAA
3525227 TAATGAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATAAAAATCATAAATTTAA
Found at i:3529204 original size:39 final size:38
Alignment explanation
Indices: 3529137--3529271 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 38
3529127 ACCAATATGG
* *
3529137 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGTAATAGTTGA
* *
3529176 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGTAATAGTTGA
* * * * * *
3529214 TACCCAATACCTCATCGAATCTATCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGTAATAGT--TGA
*
3529255 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
3529272 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
38 18 0.24
39 37 0.50
40 4 0.05
41 15 0.20
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGTAATAGTTGA
Found at i:3533521 original size:18 final size:17
Alignment explanation
Indices: 3533486--3533518 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3533476 CTTTTTATTC
3533486 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
3533503 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
3533519 TATCATTTAA
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:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:3537978 original size:39 final size:37
Alignment explanation
Indices: 3537911--3538003 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
3537901 ACCAGAATGG
* *
3537911 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
3537950 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
3537987 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
3538004 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:3539177 original size:14 final size:14
Alignment explanation
Indices: 3539118--3539168 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3539108 CTTTTGTTTC
*
3539118 TTTTATTT-TTTTA
1 TTTTATTTCCTTTA
* *
3539131 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
3539146 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
3539160 TTTTATTTC
1 TTTTATTTC
3539169 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 19 0.63
15 7 0.23
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:3539337 original size:14 final size:17
Alignment explanation
Indices: 3539318--3539354 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
3539308 ATTTATTTCT
3539318 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
3539332 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
3539349 TAATAT
1 TAATAT
3539355 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:3546124 original size:25 final size:25
Alignment explanation
Indices: 3546096--3546154 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3546086 ATGGCTCTTA
* *
3546096 TGAGCTTGCCGATATACAGCTCGAT
1 TGAGCTTCCCGATATACAACTCGAT
* *
3546121 TGAGCTTCCCGTTATACAACTCGAA
1 TGAGCTTCCCGATATACAACTCGAT
*
3546146 AGAGCTTCC
1 TGAGCTTCC
3546155 TGTTTACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (25 bp):
TGAGCTTCCCGATATACAACTCGAT
Found at i:3558037 original size:38 final size:38
Alignment explanation
Indices: 3557990--3558063 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
3557980 GTTATATAGA
*
3557990 ATAAGAGTAGTACTTAAATAGACAAATCTAAACAATAT
1 ATAACAGTAGTACTTAAATAGACAAATCTAAACAATAT
3558028 ATAACAGTAGTACTTAAATAGACAAATCTAAACAAT
1 ATAACAGTAGTACTTAAATAGACAAATCTAAACAAT
3558064 CAAAAGATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (38 bp):
ATAACAGTAGTACTTAAATAGACAAATCTAAACAATAT
Found at i:3562304 original size:8 final size:8
Alignment explanation
Indices: 3562291--3562319 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3562281 TTATGTTTAG
3562291 TATATTAT
1 TATATTAT
3562299 TATATTAT
1 TATATTAT
3562307 TATATTAT
1 TATATTAT
3562315 TATAT
1 TATAT
3562320 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:3562352 original size:5 final size:5
Alignment explanation
Indices: 3562342--3562387 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
3562332 TTATGTTTTA
3562342 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
3562388 AAACTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:3562894 original size:23 final size:23
Alignment explanation
Indices: 3562868--3562928 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
3562858 AGGCACTTTA
3562868 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTATTTTAGGCACCTCG
*
3562891 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTTAGGCACCTCG
3562912 TGTGTCG--TTTTAGGCAC
1 TGTGTCGTATTTTAGGCAC
3562929 TTTATGTGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 25 0.74
23 9 0.26
ACGTcount: A:0.13, C:0.23, G:0.28, T:0.36
Consensus pattern (23 bp):
TGTGTCGTATTTTAGGCACCTCG
Found at i:3562936 original size:21 final size:21
Alignment explanation
Indices: 3562858--3562940 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
3562848 TTTATCGATC
* *
3562858 AGGCACTTTATGTGTCGTATTTT
1 AGGCACCTCATGTGTCG--TTTT
* * *
3562881 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCATGTGTCGTTTT
*
3562902 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCATGTGTCGTTTT
* *
3562923 AGGCACTTTATGTGTCGT
1 AGGCACCTCATGTGTCGT
3562941 ACTCTAATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 36 0.72
23 14 0.28
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (21 bp):
AGGCACCTCATGTGTCGTTTT
Found at i:3573440 original size:44 final size:45
Alignment explanation
Indices: 3573390--3573702 Score: 139
Period size: 44 Copynumber: 7.2 Consensus size: 45
3573380 ACTACTGCTT
* *
3573390 AGGGAGATAAGATCTGTGC-TCTTCACTCTATTCCACTGTTGCCC
1 AGGGAGATAAGATCTGTCCATCTTCACTCTACTCCACTGTTGCCC
* * ** * * * ***
3573434 AGGGAGAT-AGAACT-ACCAGATTCAATGTACTCCACCG-TAATC
1 AGGGAGATAAGATCTGTCCATCTTCACTCTACTCCACTGTTGCCC
* * * **
3573476 AGGGAGGTAAAATCTG-CCATCTTCGAC-CTACTCCACTATTGCTT
1 AGGGAGATAAGATCTGTCCATCTTC-ACTCTACTCCACTGTTGCCC
* *
3573520 AGGGAGATAAGATCTGT-AATCTTCACTCTATTCCACTGTTGCCC
1 AGGGAGATAAGATCTGTCCATCTTCACTCTACTCCACTGTTGCCC
* * *** * * * * ***
3573564 AGGGAGAT-AGAACT-ACTGGCTTTAATGTACTCCACCG-TAATC
1 AGGGAGATAAGATCTGTCCATCTTCACTCTACTCCACTGTTGCCC
* * * ** * * * *
3573606 AGTGAGGTAAAATC-CACCATCTTCGAC-CTGCTCCACTATTGTCT
1 AGGGAGATAAGATCTGTCCATCTTC-ACTCTACTCCACTGTTGCCC
* *
3573650 AGGGAGATAAGATCTGT-AATCTTCACTCTATTCCACTGTTGCCC
1 AGGGAGATAAGATCTGTCCATCTTCACTCTACTCCACTGTTGCCC
3573694 AGGGAGATA
1 AGGGAGATA
3573703 GAACTACTGG
Statistics
Matches: 183, Mismatches: 72, Indels: 28
0.65 0.25 0.10
Matches are distributed among these distances:
42 18 0.10
43 73 0.40
44 92 0.50
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (45 bp):
AGGGAGATAAGATCTGTCCATCTTCACTCTACTCCACTGTTGCCC
Found at i:3573613 original size:130 final size:130
Alignment explanation
Indices: 3573373--3573795 Score: 688
Period size: 130 Copynumber: 3.3 Consensus size: 130
3573363 TGGATGTGAT
* **
3573373 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGCTCTTCACTCTATTCCACTGTTGCCCAGGG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCACTCTATTCCACTGTTGCCCAGGG
** * * * *
3573438 AGATAGAACTACCAGATTCAATGTACTCCACCGTAATCAGGGAGGTAAAATCTGCCATCTTCGAC
66 AGATAGAACTACTGGCTTTAATGTACTCCACCGTAATCAGAGAGGTAAAATCTACCATCTTCGAC
*
3573503 CTACTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCACTCTATTCCACTGTTGCCCAGGG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCACTCTATTCCACTGTTGCCCAGGG
* *
3573568 AGATAGAACTACTGGCTTTAATGTACTCCACCGTAATCAGTGAGGTAAAATCCACCATCTTCGAC
66 AGATAGAACTACTGGCTTTAATGTACTCCACCGTAATCAGAGAGGTAAAATCTACCATCTTCGAC
3573633 CTGCTCCACTATTG-TCTAGGGAGATAAGATCTGTAATCTTCACTCTATTCCACTGTTGCCCAGG
1 CTGCTCCACTATTGCT-TAGGGAGATAAGATCTGTAATCTTCACTCTATTCCACTGTTGCCCAGG
*
3573697 GAGATAGAACTACTGGCTTTAATGTACTCCACCGTAATCGGAGAGGTAAAAT-TCACCATCTTCG
65 GAGATAGAACTACTGGCTTTAATGTACTCCACCGTAATCAGAGAGGTAAAATCT-ACCATCTTCG
3573761 AC
129 AC
*
3573763 CTGTTCCACTATTGCTTAGGGAGATAAGATCTG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTG
3573796 GTTTCTTTCG
Statistics
Matches: 274, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
129 1 0.00
130 272 0.99
131 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (130 bp):
CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCACTCTATTCCACTGTTGCCCAGGG
AGATAGAACTACTGGCTTTAATGTACTCCACCGTAATCAGAGAGGTAAAATCTACCATCTTCGAC
Found at i:3573861 original size:40 final size:40
Alignment explanation
Indices: 3573809--3573957 Score: 192
Period size: 40 Copynumber: 3.7 Consensus size: 40
3573799 TCTTTCGTCT
* *
3573809 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATATGATCC
* *
3573849 GCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATATGATCC
* * *
3573891 GTTCCGCTACTGCTTAGGGAGATAAGACTTGATACGATCC
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATATGATCC
*
3573931 GCTCCACTATTGCTTAGGGAGATAAGA
1 GCTCCACTACTGCTTAGGGAGATAAGA
3573958 TCTGTGGTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
39 3 0.03
40 55 0.59
41 4 0.04
42 28 0.30
43 4 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (40 bp):
GCTCCACTACTGCTTAGGGAGATAAGACTTGATATGATCC
Found at i:3573935 original size:82 final size:83
Alignment explanation
Indices: 3573767--3573969 Score: 302
Period size: 82 Copynumber: 2.4 Consensus size: 83
3573757 TTCGACCTGT
* *
3573767 TCCACTATTGCTTAGGGAGATAAGATCTG-GTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
1 TCCACTATTGCTTAGGGAGATAAGATCTGTG-GT-TTTCGTCCGCTCCACTACTGCTTAGGGAGA
** *
3573831 TAAGACTTGATGTGATCTGC
64 TAAGACTTGATACGATCCGC
* * *
3573851 TCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTT-GTCCGTTCCGCTACTGCTTAGGGAGATA
1 TCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTCGTCCGCTCCACTACTGCTTAGGGAGATA
3573915 AGACTTGATACGATCCGC
66 AGACTTGATACGATCCGC
3573933 TCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTC
1 TCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTC
3573970 ACTCTATTCC
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
82 75 0.69
83 3 0.03
84 29 0.27
85 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (83 bp):
TCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTCGTCCGCTCCACTACTGCTTAGGGAGATA
AGACTTGATACGATCCGC
Found at i:3574233 original size:44 final size:45
Alignment explanation
Indices: 3574073--3574593 Score: 431
Period size: 44 Copynumber: 11.8 Consensus size: 45
3574063 GCTTCGCTGC
* * * * * *
3574073 CCAATACAGGAAGGCAAGATCTGCAATCCTCAATCTA-TTCCACTGT
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT-CACT-A
* * * *
3574119 CAAATACAGG--GACAAGATCTGCTTTCTTCGATCTACTTCACCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * *
3574162 CCAGTATGGGAAGACAAGATCTG-TATCTTGGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * *
3574205 TCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-G
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * * *
3574249 CCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * *
3574294 CCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
** * *
3574337 CCAATATAGGAAGACCGGACCTGCTATCTTCGATCTACTTCAC-G
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * * *
3574381 CCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* *
3574426 CCAA-ATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * *
3574468 CTAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCAC-G
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* * * * * * *
3574512 CCAATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCA
1 CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
* *
3574557 CCAATATGGGAAGACAAGATCTG-TAATCTTCAATCTA
1 CCAATATAGGAAGACAAGATCTGCT-ATCTTCGATCTA
3574594 TTCCACTGCC
Statistics
Matches: 372, Mismatches: 89, Indels: 29
0.76 0.18 0.06
Matches are distributed among these distances:
42 5 0.01
43 76 0.20
44 213 0.57
45 69 0.19
46 9 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (45 bp):
CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTA
Found at i:3574311 original size:132 final size:131
Alignment explanation
Indices: 3574129--3574579 Score: 769
Period size: 132 Copynumber: 3.4 Consensus size: 131
3574119 CAAATACAGG
* * * * *
3574129 GACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
3574194 TCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTA-CAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
3574259 AA
130 AA
*
3574261 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
**
3574326 TCCACTTCCTACCAATATAGGAAGACCGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTA-CAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
3574391 AA
130 AA
3574393 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAA-ATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
* *
3574457 TCCACTTCCTACTAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTAC-AATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
3574522 AA
130 AA
*
3574524 GATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTG
3574580 TAATCTTCAA
Statistics
Matches: 302, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
130 1 0.00
131 123 0.41
132 178 0.59
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (131 bp):
GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
TCCACTTCCTACAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGA
A
Found at i:3574726 original size:136 final size:136
Alignment explanation
Indices: 3574565--3575000 Score: 791
Period size: 136 Copynumber: 3.2 Consensus size: 136
3574555 CACCAATATG
* * * * *
3574565 GGAAGACAAGATCTGTAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATTGAC
1 GGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGC
*
3574630 TTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCA
66 TTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCA
3574695 AATACA
131 AATACA
3574701 GGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGC
1 GGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGC
* *
3574766 TTCAATGTACTCCACTGTAGTCATAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTTGCTGCCA
66 TTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCA
3574831 AATACA
131 AATACA
3574837 GGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGC
1 GGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGC
*
3574902 TTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTACTTCGCTGCCA
66 TTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCA
3574967 AATACA
131 AATACA
3574973 GGAAGGCAAGATCTGCAATCTTCAATCT
1 GGAAGGCAAGATCTGCAATCTTCAATCT
3575001 GCTCTGCTAC
Statistics
Matches: 289, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
136 289 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (136 bp):
GGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGTTATCGGC
TTCAATGTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCA
AATACA
Found at i:3575074 original size:86 final size:87
Alignment explanation
Indices: 3574944--3575122 Score: 270
Period size: 86 Copynumber: 2.1 Consensus size: 87
3574934 AAAATCTGCC
* * *
3574944 ATCTTCGATCTACTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTGCTCTGCT
1 ATCTTCGATCTACTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTACT
3575009 ACAAACGAGAGAGGCAAGGTTT
66 ACAAACGAGAGAGGCAAGGTTT
* * * * * *
3575031 GTCTTCGATCTGCTTCGCTGTC-AGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACT
1 ATCTTCGATCTACTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTACT
3575095 ACAAACGAGAGAGGCAAGGTTT
66 ACAAACGAGAGAGGCAAGGTTT
3575117 ATCTTC
1 ATCTTC
3575123 AATTTTTACT
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 63 0.77
87 19 0.23
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (87 bp):
ATCTTCGATCTACTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTACT
ACAAACGAGAGAGGCAAGGTTT
Found at i:3585057 original size:16 final size:16
Alignment explanation
Indices: 3585036--3585087 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
3585026 TTTGGTTCGC
*
3585036 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
*
3585052 TGTATTGGATTAGAGT
1 TGTATTGGATTAGAGG
3585068 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3585084 TGTA
1 TGTA
3585088 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3585471 original size:14 final size:15
Alignment explanation
Indices: 3585422--3585473 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3585412 ATAAAATATA
3585422 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3585437 TATTAAATATATTAT
1 AATTAAATATATTAT
3585452 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3585465 AATTTAATA
1 AATTAAATA
3585474 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3585475 original size:59 final size:58
Alignment explanation
Indices: 3585306--3585602 Score: 164
Period size: 59 Copynumber: 5.0 Consensus size: 58
3585296 ATCATATTTA
* * *
3585306 AACATAATTATTATTAGATATATTATAATTAAAATATA-GAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATG-ATTTAATAAAA-TATAAAT
* * * * *
3585365 AATCA-ATATTCTTATATGAATTTACTCA-AA-TAATAATATATGATACT-ATAAAATATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAA-AATATATGAT-TTAATAAAATATAAA-T
* * *
3585426 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAA-TATAAAT
* * * * * * * *
3585485 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAAGATAATTT
1 AACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATGAT-TTAATAAAATATAA-AT
* * *
3585546 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAA
3585603 ATAATTATAA
Statistics
Matches: 176, Mismatches: 38, Indels: 49
0.67 0.14 0.19
Matches are distributed among these distances:
57 10 0.06
58 11 0.06
59 53 0.30
60 34 0.19
61 46 0.26
62 13 0.07
63 9 0.05
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (58 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAAT
Found at i:3585521 original size:120 final size:121
Alignment explanation
Indices: 3585306--3585598 Score: 491
Period size: 120 Copynumber: 2.4 Consensus size: 121
3585296 ATCATATTTA
* *
3585306 AACATAATTATTATTAGATATATTATAATTAAAATATAGAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
3585371 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
*
3585426 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
3585491 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
* * *
3585547 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
3585599 TAAAATAATT
Statistics
Matches: 163, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 161 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
Found at i:3588422 original size:15 final size:15
Alignment explanation
Indices: 3588402--3588431 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3588392 AGAGGGTAAA
3588402 ACAGAGAGCAAATCG
1 ACAGAGAGCAAATCG
3588417 ACAGAGAGCAAATCG
1 ACAGAGAGCAAATCG
3588432 GCCGAAAAAG
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:0.47, C:0.20, G:0.27, T:0.07
Consensus pattern (15 bp):
ACAGAGAGCAAATCG
Found at i:3590500 original size:20 final size:21
Alignment explanation
Indices: 3590475--3590522 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
3590465 ATCAATTAAT
* *
3590475 TTTATAAT-TTAACTTTAAAA
1 TTTATAATGGTAACTCTAAAA
3590495 TTTAT-ATGGTAACTCTAAAA
1 TTTATAATGGTAACTCTAAAA
*
3590515 TATATAAT
1 TTTATAAT
3590523 AATTTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
TTTATAATGGTAACTCTAAAA
Found at i:3608641 original size:12 final size:12
Alignment explanation
Indices: 3608624--3608649 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3608614 ACATGTAAAA
3608624 GTTTACTAATGG
1 GTTTACTAATGG
3608636 GTTTACTAATGG
1 GTTTACTAATGG
3608648 GT
1 GT
3608650 CTTTTCTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.27, T:0.42
Consensus pattern (12 bp):
GTTTACTAATGG
Found at i:3611730 original size:28 final size:28
Alignment explanation
Indices: 3611690--3611746 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3611680 TTATAGAGGT
3611690 TGACGAAAATTCTATTTGGCACATCAAA
1 TGACGAAAATTCTATTTGGCACATCAAA
3611718 TGACGAAAATTCTATTTGGCACATCAAA
1 TGACGAAAATTCTATTTGGCACATCAAA
3611746 T
1 T
3611747 CATTCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (28 bp):
TGACGAAAATTCTATTTGGCACATCAAA
Found at i:3621880 original size:4 final size:4
Alignment explanation
Indices: 3621871--3621895 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3621861 CAATAGAGAT
3621871 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
3621896 GGAGGAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3626916 original size:29 final size:29
Alignment explanation
Indices: 3626874--3626931 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3626864 CTGTCAGCAG
3626874 ATAGTCAGGTTTGAGACTTATCTATCATT
1 ATAGTCAGGTTTGAGACTTATCTATCATT
3626903 ATAGTCAGGTTTGAGACTTATCTATCATT
1 ATAGTCAGGTTTGAGACTTATCTATCATT
3626932 CACATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (29 bp):
ATAGTCAGGTTTGAGACTTATCTATCATT
Found at i:3628549 original size:21 final size:21
Alignment explanation
Indices: 3628525--3628564 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3628515 TCTCCATCTC
* *
3628525 CACCTCCACCACGGCCACCCT
1 CACCCCCACCACCGCCACCCT
*
3628546 CACCCCCACCCCCGCCACC
1 CACCCCCACCACCGCCACC
3628565 ACCAGCACCT
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:0.17, C:0.70, G:0.07, T:0.05
Consensus pattern (21 bp):
CACCCCCACCACCGCCACCCT
Found at i:3631577 original size:16 final size:16
Alignment explanation
Indices: 3631544--3631577 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3631534 CCTCAGTGTT
* *
3631544 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
3631560 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
3631576 AA
1 AA
3631578 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:3634404 original size:21 final size:21
Alignment explanation
Indices: 3634378--3634418 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3634368 AGACGAGCAA
* *
3634378 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3634399 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3634419 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3636338 original size:16 final size:16
Alignment explanation
Indices: 3636305--3636338 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3636295 GGAGATTGTT
* *
3636305 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
3636321 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
3636337 AA
1 AA
3636339 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:3639245 original size:11 final size:11
Alignment explanation
Indices: 3639229--3639274 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
3639219 TACTCATCCA
3639229 TTGCCCATACC
1 TTGCCCATACC
3639240 TTGCCCATACC
1 TTGCCCATACC
* *
3639251 TTTCTCATACC
1 TTGCCCATACC
*
3639262 -TACCCATACC
1 TTGCCCATACC
3639272 TTG
1 TTG
3639275 GAAAGGTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.20, C:0.41, G:0.07, T:0.33
Consensus pattern (11 bp):
TTGCCCATACC
Found at i:3639836 original size:18 final size:18
Alignment explanation
Indices: 3639812--3639882 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
3639802 ATCGTTTATA
3639812 GTACTATTCACGTATACG
1 GTACTATTCACGTATACG
* * *
3639830 ATACTATTTATGTATACG
1 GTACTATTCACGTATACG
* *
3639848 GTACTATTCACATATATG
1 GTACTATTCACGTATACG
*
3639866 GTACTGTTCACGTATAC
1 GTACTATTCACGTATAC
3639883 AGTAGTTGAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (18 bp):
GTACTATTCACGTATACG
Found at i:3643951 original size:11 final size:11
Alignment explanation
Indices: 3643937--3643968 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3643927 TACCCATCCC
3643937 TTGCCCATACA
1 TTGCCCATACA
3643948 TTGCCCATACA
1 TTGCCCATACA
*
3643959 TTTCCCATAC
1 TTGCCCATAC
3643969 CTACCCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.38, G:0.06, T:0.31
Consensus pattern (11 bp):
TTGCCCATACA
Found at i:3646121 original size:39 final size:39
Alignment explanation
Indices: 3646072--3646192 Score: 224
Period size: 39 Copynumber: 3.1 Consensus size: 39
3646062 AATCTAGCTA
*
3646072 AAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
1 AAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
*
3646111 AAGCATATAAGTGCTAAACTGAAGCCCGAAGGCTAACTG
1 AAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
3646150 AAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
1 AAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
3646189 AAGC
1 AAGC
3646193 TCATCAGAGC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (39 bp):
AAGCATATAAGTGCTAAACGGAAGCCCGAAGGCTAACTG
Found at i:3646131 original size:21 final size:21
Alignment explanation
Indices: 3646072--3646174 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
3646062 AATCTAGCTA
*
3646072 AAGCACATAAGTGCTAAACGG
1 AAGCACATAAGTGCTAAACTG
**
3646093 AAGC-CCGAAG-GCT-AACTG
1 AAGCACATAAGTGCTAAACTG
*
3646111 AAGCATATAAGTGCTAAACTG
1 AAGCACATAAGTGCTAAACTG
**
3646132 AAGC-CCGAAG-GCT-AACTG
1 AAGCACATAAGTGCTAAACTG
* *
3646150 AAGCATATAAGTGCTAAACGG
1 AAGCACATAAGTGCTAAACTG
3646171 AAGC
1 AAGC
3646175 CCGAAGGCTA
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
18 17 0.27
19 12 0.19
20 13 0.21
21 21 0.33
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (21 bp):
AAGCACATAAGTGCTAAACTG
Found at i:3646150 original size:18 final size:18
Alignment explanation
Indices: 3646092--3646192 Score: 85
Period size: 18 Copynumber: 5.3 Consensus size: 18
3646082 GTGCTAAACG
3646092 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
***
3646110 GAAGCATATAAGTGCTAAACT
1 GAAGC-CCGAAG-GCT-AACT
3646131 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
*** *
3646149 GAAGCATATAAGTGCTAAACG
1 GAAGC-CCGAAG-GCT-AACT
3646170 GAAGCCCGAAGGCTAACT
1 GAAGCCCGAAGGCTAACT
3646188 GAAGC
1 GAAGC
3646193 TCATCAGAGC
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
18 22 0.35
19 12 0.19
20 12 0.19
21 17 0.27
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.15
Consensus pattern (18 bp):
GAAGCCCGAAGGCTAACT
Found at i:3647635 original size:16 final size:16
Alignment explanation
Indices: 3647614--3647646 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3647604 ATGTATATAA
3647614 ACTTTCAATTTCTTTC
1 ACTTTCAATTTCTTTC
3647630 ACTTTCAATTTCTTTC
1 ACTTTCAATTTCTTTC
3647646 A
1 A
3647647 TAGAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (16 bp):
ACTTTCAATTTCTTTC
Found at i:3652374 original size:2 final size:2
Alignment explanation
Indices: 3652367--3652392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3652357 GAGAAAAAGT
3652367 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
3652393 AGTGGATGAC
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:3657903 original size:18 final size:20
Alignment explanation
Indices: 3657877--3657918 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
3657867 ATTTCATGTT
*
3657877 ATTTTAAAG-AAAGCCAA-A
1 ATTTAAAAGTAAAGCCAATA
*
3657895 ATTTAAAAGTAAAGTCAATA
1 ATTTAAAAGTAAAGCCAATA
3657915 ATTT
1 ATTT
3657919 TTAAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 7 0.35
20 5 0.25
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (20 bp):
ATTTAAAAGTAAAGCCAATA
Found at i:3664144 original size:37 final size:37
Alignment explanation
Indices: 3664083--3664228 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
3664073 TACGTATGAT
* *
3664083 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
3664118 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
3664155 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
**
3664192 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
3664229 TAAAGCTATC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 91 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:3664243 original size:46 final size:46
Alignment explanation
Indices: 3664192--3664414 Score: 257
Period size: 52 Copynumber: 4.6 Consensus size: 46
3664182 TAAGTGTAGC
*
3664192 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* * *
3664238 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
3664284 CACTTATCACTTTTCACTTATCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
* *
3664336 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
*
3664388 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
3664415 AGTACTCAAA
Statistics
Matches: 158, Mismatches: 12, Indels: 14
0.86 0.07 0.08
Matches are distributed among these distances:
46 67 0.42
49 1 0.01
50 1 0.01
51 3 0.02
52 86 0.54
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTAT
Found at i:3664293 original size:7 final size:7
Alignment explanation
Indices: 3664281--3664314 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3664271 TAGCCGAAGC
3664281 TATCACT
1 TATCACT
3664288 TATCACT
1 TATCACT
*
3664295 TTTCACT
1 TATCACT
3664302 TATCACT
1 TATCACT
3664309 TGATCA
1 T-ATCA
3664315 GATAAGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.44
Consensus pattern (7 bp):
TATCACT
Found at i:3664380 original size:98 final size:98
Alignment explanation
Indices: 3664191--3664414 Score: 253
Period size: 98 Copynumber: 2.3 Consensus size: 98
3664181 ATAAGTGTAG
* * * *
3664191 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
*
3664256 TTGATCAGATAAGTATAGCCGAAGCTATCA-CTTA
66 TTGATCAGATAAGTATAGCCGAAGCTA-AAGC-TA
* * *
3664290 TCACTTTTCAC-TTATCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT-CCAC
1 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
* * *
3664353 TTG-TCACTTGATCAG-ATAAG-TGTAGCTAAAGCTA
66 TTGATCA---GATAAGTAT-AGCCGAAGCTAAAGCTA
3664387 CCACTTATCACTTTATCACTTGATCAGA
1 CCACTTATCACTTTATCACTTGATCAGA
3664415 AGTACTCAAA
Statistics
Matches: 106, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
96 3 0.03
97 17 0.16
98 70 0.66
99 16 0.15
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (98 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGCCAC
TTGATCAGATAAGTATAGCCGAAGCTAAAGCTA
Found at i:3667304 original size:18 final size:17
Alignment explanation
Indices: 3667283--3667326 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3667273 TTAATTTTTT
3667283 AAAATTATATAATATATA
1 AAAATTATATAATATA-A
*
3667301 AAAATAATATAATATAA
1 AAAATTATATAATATAA
*
3667318 AATATTATA
1 AAAATTATA
3667327 AACTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTATATAATATAA
Found at i:3680658 original size:42 final size:42
Alignment explanation
Indices: 3680599--3680683 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
3680589 GGAATGGCCA
*
3680599 TAATTATAAAGTTTGGTGGGACAACTATCTTATAGATTTGAT
1 TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
*
3680641 TAATTATAAAGTTTGGTGGGACAAGTATCTTACAGATTTGAT
1 TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
3680683 T
1 T
3680684 TAATAATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (42 bp):
TAATTATAAAGTTTGGTGGGACAACTATCTTACAGATTTGAT
Found at i:3682933 original size:31 final size:33
Alignment explanation
Indices: 3682898--3682968 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
3682888 ATATCCAAAA
*
3682898 TCAAAATAACT-TGAATAAAAAAT-ACTTAAAT-
1 TCAAAATAA-TATAAATAAAAAATGACTTAAATC
**
3682929 TCAAAATAATATAAATCTAAAATGACTTAAATC
1 TCAAAATAATATAAATAAAAAATGACTTAAATC
3682962 TCAAAAT
1 TCAAAAT
3682969 CAATCTAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.03
31 18 0.53
32 8 0.24
33 7 0.21
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (33 bp):
TCAAAATAATATAAATAAAAAATGACTTAAATC
Found at i:3682934 original size:15 final size:15
Alignment explanation
Indices: 3682916--3682968 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
3682906 ACTTGAATAA
3682916 AAAATACTTAAATTC
1 AAAATACTTAAATTC
*
3682931 AAAATAATATAAA-TC
1 AAAATACT-TAAATTC
3682946 TAAAATGACTTAAATCTC
1 -AAAAT-ACTTAAAT-TC
3682964 AAAAT
1 AAAAT
3682969 CAATCTAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 9 0.29
16 13 0.42
17 7 0.23
18 2 0.06
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (15 bp):
AAAATACTTAAATTC
Found at i:3689640 original size:14 final size:14
Alignment explanation
Indices: 3689621--3689648 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3689611 CTGCTTTCTA
3689621 AATTTGTTTTAAGG
1 AATTTGTTTTAAGG
3689635 AATTTGTTTTAAGG
1 AATTTGTTTTAAGG
3689649 CTGACAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
AATTTGTTTTAAGG
Found at i:3693185 original size:12 final size:12
Alignment explanation
Indices: 3693168--3693192 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3693158 GGTGTTCATT
3693168 CGGTTAACCGAC
1 CGGTTAACCGAC
3693180 CGGTTAACCGAC
1 CGGTTAACCGAC
3693192 C
1 C
3693193 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:3693367 original size:9 final size:9
Alignment explanation
Indices: 3693353--3693399 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
3693343 TTTGGTTAAA
*
3693353 AATTACCCG
1 AATTAACCG
*
3693362 AATTACCCG
1 AATTAACCG
3693371 AATTAACCG
1 AATTAACCG
3693380 AATTAACCG
1 AATTAACCG
3693389 AATTAACCG
1 AATTAACCG
3693398 AA
1 AA
3693400 AAATACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:3697279 original size:18 final size:19
Alignment explanation
Indices: 3697240--3697291 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3697230 TTTATTTATA
3697240 ATTACAAATTAAA-TACATT
1 ATTA-AAATTAAATTACATT
*
3697259 ATTAAAATTAAATTAGA-T
1 ATTAAAATTAAATTACATT
3697277 ATTTAAAATATAAAT
1 A-TTAAAAT-TAAAT
3697292 AACAGTACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 14 0.48
20 5 0.17
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTAAAATTAAATTACATT
Found at i:3697936 original size:19 final size:20
Alignment explanation
Indices: 3697911--3697954 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3697901 TAGATTTCAA
3697911 AATAATTTATTA-GT-ATATT
1 AATAA-TTATTATGTGATATT
*
3697930 TATAATTATTATGTGATATT
1 AATAATTATTATGTGATATT
3697950 AATAA
1 AATAA
3697955 AAATTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
AATAATTATTATGTGATATT
Found at i:3698434 original size:22 final size:22
Alignment explanation
Indices: 3698392--3698433 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3698382 ATGTTTAGCT
*
3698392 GAAAATTATAAAAATAGTTTTA
1 GAAAATTAAAAAAATAGTTTTA
*
3698414 GAAAA-TAAAAAAATATTTTT
1 GAAAATTAAAAAAATAGTTTT
3698434 TTAAATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
GAAAATTAAAAAAATAGTTTTA
Found at i:3725667 original size:16 final size:16
Alignment explanation
Indices: 3725646--3725681 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3725636 TTTGGTTCGC
3725646 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3725662 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3725678 TGTA
1 TGTA
3725682 ATACCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3725937 original size:18 final size:17
Alignment explanation
Indices: 3725916--3725950 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3725906 TTATTATTAA
*
3725916 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3725934 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3725951 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3732198 original size:30 final size:30
Alignment explanation
Indices: 3732147--3732205 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3732137 GAAAATCTTT
*
3732147 TATAAAAATCGTAAAAAAAATTACAAAATA
1 TATAAAAATCATAAAAAAAATTACAAAATA
* *
3732177 TATAAAAAT-ATAGAAATAAATTATAAAAT
1 TATAAAAATCATA-AAAAAAATTACAAAAT
3732206 TTTATAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (30 bp):
TATAAAAATCATAAAAAAAATTACAAAATA
Found at i:3732242 original size:21 final size:22
Alignment explanation
Indices: 3732201--3732274 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 22
3732191 AATAAATTAT
* * *
3732201 AAAATTTTATAAAGTCG-AAAG
1 AAAATTATAAAAAATCGTAAAG
3732222 AAAATTATAAAAAAT-GTAAAG
1 AAAATTATAAAAAATCGTAAAG
* *
3732243 -AAA-TAT-AAAATTCGTAAAA
1 AAAATTATAAAAAATCGTAAAG
3732262 AAAATTATAAAAA
1 AAAATTATAAAAA
3732275 TTATCATACT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 5 0.12
19 8 0.19
20 7 0.16
21 19 0.44
22 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (22 bp):
AAAATTATAAAAAATCGTAAAG
Found at i:3766520 original size:22 final size:22
Alignment explanation
Indices: 3766494--3766539 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3766484 ATGCAAGTCG
3766494 TTGAATAATTTAAAAGTTTTCA
1 TTGAATAATTTAAAAGTTTTCA
*
3766516 TTGAATAGTTTAAAAGTTTTCA
1 TTGAATAATTTAAAAGTTTTCA
3766538 TT
1 TT
3766540 TAAATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (22 bp):
TTGAATAATTTAAAAGTTTTCA
Found at i:3770869 original size:47 final size:47
Alignment explanation
Indices: 3770816--3770909 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
3770806 AAGGCAAGGG
3770816 GAGCTGTTAAATAGAGATGAATTATCAAAGGAATGGAGCAAAGACTT
1 GAGCTGTTAAATAGAGATGAATTATCAAAGGAATGGAGCAAAGACTT
3770863 GAGCTGTTAAATAGAGATGAATTATCAAAGGAATGGAGCAAAGACTT
1 GAGCTGTTAAATAGAGATGAATTATCAAAGGAATGGAGCAAAGACTT
3770910 ACACTTTGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (47 bp):
GAGCTGTTAAATAGAGATGAATTATCAAAGGAATGGAGCAAAGACTT
Found at i:3778751 original size:23 final size:23
Alignment explanation
Indices: 3778724--3778822 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
3778714 AGTGTTATTG
*
3778724 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
3778747 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
3778770 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
3778793 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3778816 ATCAGTG
1 ATCAGTG
3778823 TTGCACTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:3784150 original size:12 final size:12
Alignment explanation
Indices: 3784135--3784165 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3784125 TTCTCTTTTA
3784135 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
3784147 TTTTTCTTTCTC
1 TTTTTCTTTCCC
3784159 TTTTTCT
1 TTTTTCT
3784166 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:3784266 original size:16 final size:16
Alignment explanation
Indices: 3784245--3784275 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3784235 TTTATTATTT
3784245 TATTAACATAATATAA
1 TATTAACATAATATAA
*
3784261 TATTAATATAATATA
1 TATTAACATAATATA
3784276 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:3786171 original size:18 final size:19
Alignment explanation
Indices: 3786148--3786185 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3786138 TTTAAACTAA
*
3786148 ATTTAACTCCCT-AATTTC
1 ATTTAAATCCCTAAATTTC
3786166 ATTTAAATCCCTAAATTTC
1 ATTTAAATCCCTAAATTTC
3786185 A
1 A
3786186 AATTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTAAATCCCTAAATTTC
Found at i:3787094 original size:24 final size:24
Alignment explanation
Indices: 3787067--3787153 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
3787057 TAGCTCTTCG
*
3787067 GAGCTACCCGTTATTGGCTCGTAT
1 GAGCTTCCCGTTATTGGCTCGTAT
* *
3787091 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGTAT
* * *
3787115 GAGCTTCCCGTTATATAGCCCGGAT
1 GAGCTTCCCGTTAT-TGGCTCGTAT
*
3787140 AAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
3787154 ATGACTCGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.06
24 26 0.51
25 22 0.43
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.34
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGTAT
Found at i:3787145 original size:49 final size:49
Alignment explanation
Indices: 3787042--3787147 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 49
3787032 TGACAATCCA
* * * *
3787042 AAGCTTCCTGAATAATAGCTCTTCGGAGCTACCCGTTATTGGCTCGTAT
1 AAGCTTCCTGAATAATAGCTCTTAGGAGCTACCCGTTATTAGCCCGGAT
* * * * *
3787091 GAGCTTCCTG-ATTATGGCTCTTATGAGCTTCCCGTTATATAGCCCGGAT
1 AAGCTTCCTGAATAATAGCTCTTAGGAGCTACCCGTTAT-TAGCCCGGAT
3787140 AAGCTTCC
1 AAGCTTCC
3787148 CGTTATATGA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
48 23 0.50
49 23 0.50
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (49 bp):
AAGCTTCCTGAATAATAGCTCTTAGGAGCTACCCGTTATTAGCCCGGAT
Found at i:3789701 original size:50 final size:50
Alignment explanation
Indices: 3789621--3789945 Score: 519
Period size: 50 Copynumber: 6.5 Consensus size: 50
3789611 CCATGGCAAC
* * *
3789621 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTAA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
3789671 AAGTAATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
3789721 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
3789771 AAGTGATAAGTGATAGCTTCGGCTACACTTATTTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
3789821 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
3789871 AAGTGATAAGTGATAGCTTCAGCTACA-TTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
3789921 AAGTAAAAAGTGGTAGCTTC-GCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
3789946 CTGATCAATG
Statistics
Matches: 258, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
49 25 0.10
50 233 0.90
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:3789962 original size:30 final size:31
Alignment explanation
Indices: 3789926--3789983 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
3789916 ATGGCAAGTA
3789926 AAAAGTGGTAGCTTC-GCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
3789956 AAAAGTGGTAGCTTCGGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
3789984 TCGGCTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:3790033 original size:31 final size:31
Alignment explanation
Indices: 3789985--3790053 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3789975 ACCTGATCAT
* * *
3789985 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
3790016 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
3790047 CGGCTAC
1 CGGCTAC
3790054 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:3794928 original size:50 final size:50
Alignment explanation
Indices: 3794853--3795128 Score: 455
Period size: 50 Copynumber: 5.5 Consensus size: 50
3794843 CCATGGCAAC
* *
3794853 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
3794903 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
3794953 AAGTGATAAGTGATAGCTTCGGCTACACTTAT-TGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
3795002 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
3795052 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
3795103 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
3795129 CTGATCAATG
Statistics
Matches: 212, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
49 47 0.22
50 142 0.67
51 23 0.11
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:3795020 original size:99 final size:100
Alignment explanation
Indices: 3794853--3795128 Score: 464
Period size: 99 Copynumber: 2.8 Consensus size: 100
3794843 CCATGGCAAC
*
3794853 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGAAAGTGATAAGTGATA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAAAGTGATAAGTGATA
3794918 GCTTCGGCTACACTTATCTGATCAAGGACAAATGA
66 GCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
3794953 AAGTGATAAGTGATAGCTTCGGCTACACTTAT-TGATCAAGGATAAGTGAAAGTGATAAGTGATA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAAAGTGATAAGTGATA
3795017 GCTTCGGCTACACTTATCTGATCAAGGACAAATGA
66 GCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * * * *
3795052 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGCAAGTAAAAAGTGGT
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGT-GAAAGTGATAAGTGAT
3795117 AGCTTCGGCTAC
65 AGCTTCGGCTAC
3795129 CTGATCAATG
Statistics
Matches: 165, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
99 96 0.58
100 45 0.27
101 24 0.15
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (100 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGAAAGTGATAAGTGATA
GCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:3795077 original size:149 final size:150
Alignment explanation
Indices: 3794853--3795128 Score: 482
Period size: 149 Copynumber: 1.8 Consensus size: 150
3794843 CCATGGCAAC
* *
3794853 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGAAAGTGATAAGTGATA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATA
* * *
3794918 GCTTCGGCTACACTTATCTGATCAAGGACAAAT-GAAAGTGATAAGTGATAGCTTCGGCTACACT
66 GCTTCAGCTACACTTATCTGATCAAGGACAAATGGAAAGTAAAAAGTGATAGCTTCGGCTACACT
3794982 TATTGATCAAGGATAAGTGA
131 TATTGATCAAGGATAAGTGA
3795002 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATA
* *
3795067 GCTTCAGCTACACTTATCTGATCAAGGACAAATGGCAAGTAAAAAGTGGTAGCTTCGGCTAC
66 GCTTCAGCTACACTTATCTGATCAAGGACAAATGGAAAGTAAAAAGTGATAGCTTCGGCTAC
3795129 CTGATCAATG
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
149 95 0.80
150 24 0.20
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (150 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAAAGTGATAAGTGATA
GCTTCAGCTACACTTATCTGATCAAGGACAAATGGAAAGTAAAAAGTGATAGCTTCGGCTACACT
TATTGATCAAGGATAAGTGA
Found at i:3795159 original size:30 final size:31
Alignment explanation
Indices: 3795108--3795165 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3795098 ATGGCAAGTA
3795108 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAATG
3795139 AAAAGTGGTAGCTT-GGCTACCTGATCA
1 AAAAGTGGTAGCTTCGGCTACCTGATCA
3795166 TCGGCTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAATG
Found at i:3795170 original size:45 final size:45
Alignment explanation
Indices: 3795121--3795210 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
3795111 AGTGGTAGCT
*
3795121 TCGGCTACCTGATCAATGAAAAGTGGTAGCT-TGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAA-TGGTAGCTCCGGCTACCTGATCA
* * *
3795166 TCGGCTACTTGATTAGTGAAAATGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAATGGTAGCTCCGGCTACCTGATCA
3795211 GTGAATAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 8 0.20
45 32 0.80
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (45 bp):
TCGGCTACCTGATCAATGAAAATGGTAGCTCCGGCTACCTGATCA
Found at i:3795203 original size:30 final size:31
Alignment explanation
Indices: 3795167--3795234 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
3795157 ACCTGATCAT
* * *
3795167 CGGCTACTTGATTAGTGAA-AATGGTAGCTC
1 CGGCTACCTGATCAGTGAATAATGATAGCTC
* *
3795197 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAATAATGATAGCTC
3795228 CGGCTAC
1 CGGCTAC
3795235 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAATAATGATAGCTC
Found at i:3802449 original size:55 final size:53
Alignment explanation
Indices: 3802259--3802513 Score: 227
Period size: 55 Copynumber: 4.8 Consensus size: 53
3802249 ACGCGGGTAC
* * * * *
3802259 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGT-A---T-CCTTTTGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG-AA
* *
3802308 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATGAA
* * * *
3802361 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGG-AACATTTGCCTTATAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAAC-CTTGCCTTAT-G-AA
* * **
3802416 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATG-AA
* * * *
3802469 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGTAACCTT
3802514 AAACCCTAAT
Statistics
Matches: 169, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
49 34 0.20
52 2 0.01
53 47 0.28
54 14 0.08
55 71 0.42
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTAACCTTGCCTTATGAA
Found at i:3802450 original size:108 final size:110
Alignment explanation
Indices: 3802306--3802506 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
3802296 ATCCTTTTGA
* *
3802306 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
3802369 -TGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
* * *
3802414 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
3802479 TTCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
3802507 TATCCTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 27 0.32
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGAACATTTGCCTTATAGT
Found at i:3805426 original size:30 final size:31
Alignment explanation
Indices: 3805392--3805460 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 31
3805382 TGGCCCAAGA
* * *
3805392 GTAAATATTCAAAATTTGAAGGATTAA-AGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
3805422 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
1 GTAAATATTAAAAAGTTGAAGGACTAATAGT
*
3805452 GCAAATATT
1 GTAAATATT
3805461 TTAAGGGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.48
30 16 0.48
31 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (31 bp):
GTAAATATTAAAAAGTTGAAGGACTAATAGT
Found at i:3805439 original size:29 final size:30
Alignment explanation
Indices: 3805392--3805459 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3805382 TGGCCCAAGA
* * *
3805392 GTAAATATTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TAAAAAGTTGAAGGACTAATAGT
3805422 GTAAATATAAAAAGTTGAAGGACTAATAGT
1 GTAAATATAAAAAGTTGAAGGACTAATAGT
*
3805452 GCAAATAT
1 GTAAATAT
3805460 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.29
Consensus pattern (30 bp):
GTAAATATAAAAAGTTGAAGGACTAATAGT
Found at i:3807663 original size:46 final size:46
Alignment explanation
Indices: 3807611--3807838 Score: 314
Period size: 46 Copynumber: 5.0 Consensus size: 46
3807601 AGTGTGCTCT
* *
3807611 CTGATATGAAATGTGTAAGACCATGGTTAAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
3807657 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAT
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3807703 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
3807749 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
3807795 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
3807839 TCATGTCAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 166 0.99
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3808145 original size:16 final size:17
Alignment explanation
Indices: 3808124--3808156 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3808114 ATGATGGAGC
3808124 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
3808140 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
3808157 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:3809259 original size:25 final size:25
Alignment explanation
Indices: 3809231--3809278 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3809221 GACCTCAGCA
3809231 TGCTCTCTGATTACTAGCACATTAG
1 TGCTCTCTGATTACTAGCACATTAG
*
3809256 TGCTCTCTGATTATTAGCACATT
1 TGCTCTCTGATTACTAGCACATT
3809279 CAGCACATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (25 bp):
TGCTCTCTGATTACTAGCACATTAG
Found at i:3810631 original size:30 final size:31
Alignment explanation
Indices: 3810597--3810663 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
3810587 TGGCCCAAGA
* *
3810597 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATACTCAAAAGTTGAAGGACTAATAGT
* *
3810627 GTAAAT-GTGAAAAGTTGAAGGACTAATAGT
1 GTAAATACTCAAAAGTTGAAGGACTAATAGT
*
3810657 GCAAATA
1 GTAAATA
3810664 TTTTAAGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAAATACTCAAAAGTTGAAGGACTAATAGT
Found at i:3815692 original size:28 final size:28
Alignment explanation
Indices: 3815639--3815722 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
3815629 CACTTTGTGC
3815639 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
3815668 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
3815696 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
3815723 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:3815734 original size:23 final size:24
Alignment explanation
Indices: 3815643--3815736 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 24
3815633 TTGTGCTATT
3815643 CTGGTGTGTTTTGGATGGATTATATTA
1 CTGGTGTGTTTTGGA-GGA-TATA-TA
*
3815670 TTCTGGTGTGTTTGGGAGGATTATATGATA
1 --CTGGTGTGTTTTGGAGG---ATAT-ATA
3815700 CTGGTGTGTTTTGGAGGAT-TATA
1 CTGGTGTGTTTTGGAGGATATATA
3815723 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
3815737 TTGGACATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 2 0.03
28 18 0.31
29 14 0.24
30 5 0.08
31 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46
Consensus pattern (24 bp):
CTGGTGTGTTTTGGAGGATATATA
Found at i:3815964 original size:22 final size:23
Alignment explanation
Indices: 3815927--3815971 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
3815917 GCTTTACTGA
3815927 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
3815950 TCAGGCAC-TTATGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
3815972 CTGATCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:3820501 original size:46 final size:46
Alignment explanation
Indices: 3820434--3820706 Score: 386
Period size: 46 Copynumber: 5.9 Consensus size: 46
3820424 GTGTGCTCTC
**
3820434 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
** *
3820480 TGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* *
3820526 TTATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* * *
3820572 TGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAATG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
*
3820618 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
* * * * *
3820664 TGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
3820707 TCATGTCAAA
Statistics
Matches: 206, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.00
46 205 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
Found at i:3820593 original size:92 final size:92
Alignment explanation
Indices: 3820434--3820706 Score: 429
Period size: 92 Copynumber: 3.0 Consensus size: 92
3820424 GTGTGCTCTC
** * * * *
3820434 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGTGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
3820499 CCATAGTTGAAAGATACCATGGCAACG
66 CCATAGTTGAAAGATACCATGGCAACG
* *
3820526 TTATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAATAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
* *
3820591 CCATGGTTGAAAGATACCATGGCAATG
66 CCATAGTTGAAAGATACCATGGCAACG
*
3820618 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
* *
3820683 CCATAGTTGAAAGACACTATGGCA
66 CCATAGTTGAAAGATACCATGGCA
3820707 TCATGTCAAA
Statistics
Matches: 165, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 165 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (92 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
CCATAGTTGAAAGATACCATGGCAACG
Found at i:3825023 original size:4 final size:4
Alignment explanation
Indices: 3825014--3825092 Score: 52
Period size: 4 Copynumber: 19.2 Consensus size: 4
3825004 CCCTTTTTTA
* ** * **
3825014 TTTC TTTC TTTC TTTC CTTC TTTC TTTC TCAC GTTTGC TCTC TGTT- AGTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC T-TTC TTTC
* *
3825064 TTTC TATA TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
3825093 CACGTTTGCT
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
3 1 0.02
4 49 0.89
5 4 0.07
6 1 0.02
ACGTcount: A:0.05, C:0.25, G:0.05, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:3825136 original size:14 final size:14
Alignment explanation
Indices: 3825117--3825147 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3825107 GTAACTTTTC
3825117 TATTCTTTACTCAT
1 TATTCTTTACTCAT
*
3825131 TATTCTTTATTCAT
1 TATTCTTTACTCAT
3825145 TAT
1 TAT
3825148 ACTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTCTTTACTCAT
Found at i:3826557 original size:162 final size:162
Alignment explanation
Indices: 3826364--3826839 Score: 871
Period size: 162 Copynumber: 2.9 Consensus size: 162
3826354 TTAAATTTAA
3826364 ATTATATATTTTTAAAAATATTTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAGAATCA
1 ATTATATATTTTTAAAAATATTTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAGAATCA
* *
3826429 AATTGAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTTT
66 AATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTAT
3826494 ATAAAAGTTGAATTTAAATTTAAATTTAAATT
131 ATAAAAGTTGAATTTAAATTTAAATTTAAATT
3826526 ATTATATATTTTTAAAAATATTTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAGAATCA
1 ATTATATATTTTTAAAAATATTTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAGAATCA
*
3826591 AATTAAGAGCATTTGTAAATTTTAAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTAT
66 AATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTAT
*
3826656 ATAAAATTTGAATTTAAATTTAAATTTAAATT
131 ATAAAAGTTGAATTTAAATTTAAATTTAAATT
*
3826688 ATTATATATTTTTAAAAATATTTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAAAATCA
1 ATTATATATTTTTAAAAATATTTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAGAATCA
*
3826753 AATTAAGAGTATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTAT
66 AATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTAT
* *
3826818 ATAAAAGGTGAAGGTTAAATTT
131 ATAAAAGTTGAA-TTTAAATTT
3826840 GTTATTATAC
Statistics
Matches: 303, Mismatches: 10, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
162 295 0.97
163 8 0.03
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.50
Consensus pattern (162 bp):
ATTATATATTTTTAAAAATATTTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAGAATCA
AATTAAGAGCATTTGTAAATTTTGAAAGTTATTTTTTAAAACTTATGACTAAATTGATATATTAT
ATAAAAGTTGAATTTAAATTTAAATTTAAATT
Found at i:3826637 original size:86 final size:85
Alignment explanation
Indices: 3826547--3826799 Score: 194
Period size: 87 Copynumber: 3.1 Consensus size: 85
3826537 TTAAAAATAT
*
3826547 TTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAGAATCAAATTAAGAGCATTTGTAAATT
1 TTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTA-AATCAAATTAAGAGTATTTGTAAATT
3826612 TTAAAAGTTATTTTTTAAAAC
65 TTAAAAGTTATTTTTTAAAAC
** * * * ** * * * *
3826633 TTATGACTAAATTGATATATTATAT-AAAATTTGA-ATTTAAATTTAAATTTAA-ATTA-TTATA
1 TTATG--TATTTTTATAT-TTTTTTGAATTTTTTAGATTTAAA-TCAAA-TTAAGAGTATTTGTA
* *
3826694 TATTTTTAAAA---A-TATTT-A---
61 -AATTTTAAAAGTTATTTTTTAAAAC
3826712 ---TGTATTTTTATATTTTTTTGAATTTTTTAGATTTAAAATCAAATTAAGAGTATTTGTAAATT
1 TTATGTATTTTTATATTTTTTTGAATTTTTTAGATTT-AAATCAAATTAAGAGTATTTGTAAATT
*
3826774 TTGAAAGTTATTTTTTAAAAC
65 TTAAAAGTTATTTTTTAAAAC
3826795 TTATG
1 TTATG
3826800 ACTAAATTGA
Statistics
Matches: 117, Mismatches: 28, Indels: 44
0.62 0.15 0.23
Matches are distributed among these distances:
73 4 0.03
74 18 0.15
75 19 0.16
76 9 0.08
78 1 0.01
79 4 0.03
80 1 0.01
82 1 0.01
83 4 0.03
84 1 0.01
86 13 0.11
87 20 0.17
88 18 0.15
89 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (85 bp):
TTATGTATTTTTATATTTTTTTGAATTTTTTAGATTTAAATCAAATTAAGAGTATTTGTAAATTT
TAAAAGTTATTTTTTAAAAC
Found at i:3840387 original size:17 final size:19
Alignment explanation
Indices: 3840351--3840388 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
3840341 TCTTAACAAT
*
3840351 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTCTAA
3840370 AATTC-AAAT-ATTTCTAA
1 AATTCAAAATAATTTCTAA
3840387 AA
1 AA
3840389 ATTCCATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATAATTTCTAA
Found at i:3840469 original size:40 final size:41
Alignment explanation
Indices: 3840411--3840489 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
3840401 ATATTTTTAA
*
3840411 AATATATATAAAAATTAAATATTCTAAAA-AAAATCTAATG
1 AATATATATAAAAATTAAAAATTCTAAAAGAAAATCTAATG
* *
3840451 AATATATA-AAAAAGTTAAAAATTTTAAAAGAAATTCTAA
1 AATATATATAAAAA-TTAAAAATTCTAAAAGAAAATCTAA
3840490 AGTAATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 5 0.15
40 21 0.62
41 8 0.24
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (41 bp):
AATATATATAAAAATTAAAAATTCTAAAAGAAAATCTAATG
Found at i:3844424 original size:3 final size:3
Alignment explanation
Indices: 3844418--3844452 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3844408 AAAAAGGAAA
3844418 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3844453 GAAGGAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3848206 original size:129 final size:129
Alignment explanation
Indices: 3847976--3848236 Score: 522
Period size: 129 Copynumber: 2.0 Consensus size: 129
3847966 TGTTCACTTT
3847976 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
1 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
3848041 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
66 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
3848105 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
1 AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
3848170 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
66 CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
3848234 AAT
1 AAT
3848237 GGTAAAATAC
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 132 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (129 bp):
AATTACTACATGATTACTATGTATAGATCATACTACAAAGAAATCAGATAATTCTTCTACAGTGC
CAATAATATGAAGAATTCAAGTGATAAGTTAGGGAGCCAATGCTGAAATGAGAAGCCATCATCC
Found at i:3850761 original size:15 final size:15
Alignment explanation
Indices: 3850741--3850770 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3850731 ATGGATTCAT
*
3850741 TAAAAAGTAAATAAA
1 TAAAAAATAAATAAA
3850756 TAAAAAATAAATAAA
1 TAAAAAATAAATAAA
3850771 AGAGGGGGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (15 bp):
TAAAAAATAAATAAA
Found at i:3851149 original size:64 final size:66
Alignment explanation
Indices: 3851045--3851176 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 66
3851035 TCCACGATGG
*
3851045 AACAGGAAAAAAATGGATGACACCCATTCTTGATTACAATGTTC-TTTAAGGATAATTCGACAAA
1 AACAGGAAAAAAATGGATGACACCCATTCTAGATTACAATGTTCTTTTAAGGATAATTCGACAAA
3851109 C
66 C
* *
3851110 AACAGG-AAAAAAT-TATTGACACCCATTCTAGATTGCAATGTTCTTTTAAGGATAATTCGACAA
1 AACAGGAAAAAAATGGA-TGACACCCATTCTAGATTACAATGTTCTTTTAAGGATAATTCGACAA
3851173 AC
65 AC
3851175 AA
1 AA
3851177 GGAGGAAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
63 1 0.02
64 32 0.52
65 29 0.47
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (66 bp):
AACAGGAAAAAAATGGATGACACCCATTCTAGATTACAATGTTCTTTTAAGGATAATTCGACAAA
C
Found at i:3852799 original size:46 final size:46
Alignment explanation
Indices: 3852725--3852860 Score: 177
Period size: 46 Copynumber: 3.0 Consensus size: 46
3852715 TTATCTATAT
* *
3852725 TCTATAAACTT--GCCGGTTTGGCTCGAATTATTTATTTAAATTAA
1 TCTATAAACTTAATCCGGTTTGACTCGAATTATTTATTTAAATTAA
* * * *
3852769 TCTATAAATTTAATCCGGATTGACTCGAATTATTTACTTAAACTAA
1 TCTATAAACTTAATCCGGTTTGACTCGAATTATTTATTTAAATTAA
* * *
3852815 TCTATAAACTTAATTCAGTTTGACTCGAATTGTTTATTTAAATTAA
1 TCTATAAACTTAATCCGGTTTGACTCGAATTATTTATTTAAATTAA
3852861 CCGTTGAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
44 10 0.13
46 67 0.87
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (46 bp):
TCTATAAACTTAATCCGGTTTGACTCGAATTATTTATTTAAATTAA
Found at i:3856428 original size:16 final size:16
Alignment explanation
Indices: 3856409--3856453 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
3856399 CAAGAGTTTG
*
3856409 AAATAACTCAAAATCA
1 AAATAATTCAAAATCA
* *
3856425 AAATTATTCAAATTCA
1 AAATAATTCAAAATCA
3856441 AAATAATTCAAAA
1 AAATAATTCAAAA
3856454 AATTTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAATTCAAAATCA
Found at i:3860593 original size:20 final size:20
Alignment explanation
Indices: 3860565--3860602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3860555 TTTAATTAAT
*
3860565 TTAGCTTAATTAACTTAAAC
1 TTAGCTTAATTAAATTAAAC
*
3860585 TTAGTTTAATTAAATTAA
1 TTAGCTTAATTAAATTAA
3860603 GCTAACCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAGCTTAATTAAATTAAAC
Found at i:3867386 original size:32 final size:32
Alignment explanation
Indices: 3867350--3867413 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3867340 TGCTTATATT
3867350 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
1 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
3867382 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
1 CTAAAGCTCCAAACAATTCTTAAATTATTCCA
3867414 ATAGTGGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.25, G:0.03, T:0.31
Consensus pattern (32 bp):
CTAAAGCTCCAAACAATTCTTAAATTATTCCA
Found at i:3867581 original size:25 final size:25
Alignment explanation
Indices: 3867531--3867582 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
3867521 TTATGTAAAG
* * **
3867531 AAATATTTCATAAATAATGATGAAT
1 AAATAATTCATAAATAATAACAAAT
3867556 AAATAATTCATAAATAATAACAAAT
1 AAATAATTCATAAATAATAACAAAT
3867581 AA
1 AA
3867583 CTCGAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATAATTCATAAATAATAACAAAT
Found at i:3868786 original size:29 final size:29
Alignment explanation
Indices: 3868750--3868821 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
3868740 AACTCAAAAA
3868750 TAGTCACTTATGTTTTAAATGTTACATTT
1 TAGTCACTTATGTTTTAAATGTTACATTT
*
3868779 TAGTCACTTATGTTTTAAATGTTACGTTT
1 TAGTCACTTATGTTTTAAATGTTACATTT
3868808 TAGTCACTTATGTT
1 TAGTCACTTATGTT
3868822 ATTATTTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.51
Consensus pattern (29 bp):
TAGTCACTTATGTTTTAAATGTTACATTT
Found at i:3869326 original size:31 final size:30
Alignment explanation
Indices: 3869259--3869327 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
3869249 ATAATAATAT
*
3869259 AAGTGACTAAAACGTAACATTTCAAACATA
1 AAGTGACTAAAACGTAACATGTCAAACATA
*
3869289 AA-TGACTAAAATGTAACATGAGTCAAACA-A
1 AAGTGACTAAAACGTAACAT--GTCAAACATA
3869319 AAGTGACTA
1 AAGTGACTA
3869328 TTTTTGAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 16 0.47
30 5 0.15
31 13 0.38
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (30 bp):
AAGTGACTAAAACGTAACATGTCAAACATA
Found at i:3879701 original size:15 final size:14
Alignment explanation
Indices: 3879675--3879720 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
3879665 GAAAATTAAT
3879675 ATAAAATCTAAAATA
1 ATAAAAT-TAAAATA
*
3879690 ATAATAATTAAAAAAA
1 ATAA-AATT-AAAATA
3879706 ATAAAATTAAAATA
1 ATAAAATTAAAATA
3879720 A
1 A
3879721 ACTTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.22
15 9 0.33
16 12 0.44
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAAATTAAAATA
Done.