Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_pilon, whole genome shotgun sequence
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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 22
Found at i:1573423 original size:39 final size:43
Alignment explanation
Indices: 1573338--1573445 Score: 127
Period size: 39 Copynumber: 2.6 Consensus size: 43
1573328 TTAACTAACT
*
1573338 ACAAACTAATTAACTATTTTTTATATATAACTAACGACTAACAA
1 ACAAACTAATTAAATATTTTTTATATATAACTAAC-ACTAACAA
* *
1573382 ACAAACTAATTAATTATTTTTT-TA-AT-A-TATA-ACTATCAA
1 ACAAACTAATTAAATATTTTTTATATATAACTA-ACACTAACAA
1573421 ACAAACTAATTAAATAATTTTTTAT
1 ACAAACTAATTAAAT-ATTTTTTAT
1573446 TTATGTATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
39 21 0.36
40 9 0.16
41 3 0.05
42 2 0.03
43 2 0.03
44 21 0.36
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (43 bp):
ACAAACTAATTAAATATTTTTTATATATAACTAACACTAACAA
Found at i:1574051 original size:26 final size:26
Alignment explanation
Indices: 1574015--1574064 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1574005 CCTCGCATAG
* *
1574015 CTCGCTCGGATGCCCTGGCGACCTAC
1 CTCGCACGGATGCCATGGCGACCTAC
*
1574041 CTCGCACGGATGCCATGGTGACCT
1 CTCGCACGGATGCCATGGCGACCT
1574065 TCAACAGCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.38, G:0.28, T:0.20
Consensus pattern (26 bp):
CTCGCACGGATGCCATGGCGACCTAC
Found at i:1574540 original size:37 final size:36
Alignment explanation
Indices: 1574481--1574551 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
1574471 TTATAAATAT
* * *
1574481 AAAAATATAATATCAAACAAATTTATTATTTTAAGA
1 AAAAATATAATATAAAACAAATTAATTATATTAAGA
* *
1574517 AAAATATATAATTTAAAATAAATTAATTATATTAA
1 AAAA-ATATAATATAAAACAAATTAATTATATTAA
1574552 TATATTATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 4 0.14
37 25 0.86
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (36 bp):
AAAAATATAATATAAAACAAATTAATTATATTAAGA
Found at i:1575496 original size:23 final size:22
Alignment explanation
Indices: 1575470--1575519 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1575460 TATCAAACAA
*
1575470 TTTAATTATATTTAATAATGAAT
1 TTTAATTATATTTAA-AATAAAT
*
1575493 TTTAAATTATTTTTAAAATAAAT
1 TTT-AATTATATTTAAAATAAAT
1575516 TTTA
1 TTTA
1575520 TAATAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 12 0.50
24 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAATTATATTTAAAATAAAT
Found at i:1575507 original size:24 final size:23
Alignment explanation
Indices: 1575473--1575519 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1575463 CAAACAATTT
*
1575473 AATTATATTTAATAATGAATTTTA
1 AATTATATTTAA-AATAAATTTTA
*
1575497 AATTATTTTTAAAATAAATTTTA
1 AATTATATTTAAAATAAATTTTA
1575520 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTATATTTAAAATAAATTTTA
Found at i:1577278 original size:17 final size:17
Alignment explanation
Indices: 1577253--1577286 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1577243 TACGACTGTA
*
1577253 CCTTTTTTGATTTCCTT
1 CCTTATTTGATTTCCTT
1577270 CCTTATTTGATTTCCTT
1 CCTTATTTGATTTCCTT
1577287 TTCTACTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.06, T:0.62
Consensus pattern (17 bp):
CCTTATTTGATTTCCTT
Found at i:1581036 original size:31 final size:31
Alignment explanation
Indices: 1580994--1581077 Score: 127
Period size: 31 Copynumber: 2.7 Consensus size: 31
1580984 GACTATTAAA
*
1580994 AATATACAAGGTTTGTTACATTTTAGGGTA-
1 AATATACAAGGTTTATTACATTTTAGGGTAC
*
1581024 AAGTATATAAGGTTTATTACATTTTAGGGTAC
1 AA-TATACAAGGTTTATTACATTTTAGGGTAC
1581056 AATATACAAGGTTTATTA-ATTT
1 AATATACAAGGTTTATTACATTT
1581078 AAGATGATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 6 0.12
31 41 0.84
32 2 0.04
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (31 bp):
AATATACAAGGTTTATTACATTTTAGGGTAC
Found at i:1586818 original size:35 final size:35
Alignment explanation
Indices: 1586767--1586834 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1586757 AATACAGTCC
* *
1586767 TCAATTTCATTCTAAACCCCAAATTTTAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCTAAAATAAT
* *
1586802 TCAATTACATTTTAAACCCTAAATTCTAAAATA
1 TCAATTACATTCTAAACCCCAAATTCTAAAATA
1586835 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1586870 original size:33 final size:34
Alignment explanation
Indices: 1586828--1586898 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
1586818 CCCTAAATTC
*
1586828 TAAAATATTTT-AATTTAGGGTTTATAATATAAT
1 TAAAATATTTTGAATTTAGGGTTTAAAATATAAT
* *
1586861 TAAAGTATTTTGGAATTTGGGGTTTAAAATATAAT
1 TAAAATATTTT-GAATTTAGGGTTTAAAATATAAT
1586896 TAA
1 TAA
1586899 GTGTTTTGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 10 0.30
35 23 0.70
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (34 bp):
TAAAATATTTTGAATTTAGGGTTTAAAATATAAT
Found at i:1586911 original size:34 final size:35
Alignment explanation
Indices: 1586839--1586912 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1586829 AAAATATTTT
*
1586839 AATTTAGGGTTTATAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAAAATATAATTAAAGTATTTTGG
* *
1586874 AATTTGGGGTTTAAAATATAATT-AAGTGTTTTGG
1 AATTTAGGGTTTAAAATATAATTAAAGTATTTTGG
1586908 AATTT
1 AATTT
1586913 TGAACATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 15 0.42
35 21 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (35 bp):
AATTTAGGGTTTAAAATATAATTAAAGTATTTTGG
Found at i:1595814 original size:44 final size:44
Alignment explanation
Indices: 1595765--1595891 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
1595755 TTAAGCATTA
1595765 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
**
1595809 TATTTTAAT-TAAGTTTTAGG-A---TA--TT--AT---TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
*
1595841 TATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1595885 TATTTTA
1 TATTTTA
1595892 ATTAGGATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
31 2 0.03
32 14 0.22
33 6 0.09
36 4 0.06
38 4 0.06
40 4 0.06
43 6 0.09
44 22 0.34
45 2 0.03
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.60
Consensus pattern (44 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
Found at i:1595838 original size:82 final size:78
Alignment explanation
Indices: 1595737--1595968 Score: 286
Period size: 76 Copynumber: 3.0 Consensus size: 78
1595727 GATTAAACTC
*
1595737 AAGTTTTAGGATAATATTTTAAGCATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG
1 AAGTTTTAGGATATTATTTT-A--ATTATATTTTATCTTT-TTTTAGGTATTTTAGTTTAAATAG
1595802 GTTTTAGTATTTTAATT
62 GTTTTAGTATTTTAATT
1595819 AAGTTTTAGGATATTA-TTT--TTATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTT
1 AAGTTTTAGGATATTATTTTAATTATATTTTATCTTT-TTTTAGGTATTTTAGTTTAAATAGGTT
1595881 TTAGTATTTTAATT
65 TTAGTATTTTAATT
* * *
1595895 AGGATTTT-GAATATTATTTTAA--ATA--TTAT-TATTTTTAGGTATTTTAGTTTAAATA-GTT
1 AAG-TTTTAGGATATTATTTTAATTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGGTT
*
1595953 TTAAGTGTTTTAATT
65 TT-AGTATTTTAATT
1595968 A
1 A
1595969 GGATTTAAGA
Statistics
Matches: 139, Mismatches: 6, Indels: 19
0.85 0.04 0.12
Matches are distributed among these distances:
72 5 0.04
73 35 0.25
74 2 0.01
75 4 0.03
76 65 0.47
77 10 0.07
81 3 0.02
82 15 0.11
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.56
Consensus pattern (78 bp):
AAGTTTTAGGATATTATTTTAATTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGGTTT
TAGTATTTTAATT
Found at i:1595869 original size:76 final size:74
Alignment explanation
Indices: 1595762--1595974 Score: 297
Period size: 76 Copynumber: 2.9 Consensus size: 74
1595752 ATTTTAAGCA
1595762 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAG-TTTT
1 TTATATTTTATCTTT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTT
*
1595826 AGGATATTATTT
65 -GAATATTA-TT
*
1595838 TTATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTT
1 TTATATTTTATCTTT-TTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTT
1595903 GAATATTATT
65 GAATATTATT
* * * * *
1595913 TTAAATATTAT-TATTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTT
1 TTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAAGATTT
1595975 AAGATGTTTT
Statistics
Matches: 128, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
72 5 0.04
73 41 0.32
74 2 0.02
75 11 0.09
76 65 0.51
77 4 0.03
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (74 bp):
TTATATTTTATCTTTTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTTG
AATATTATT
Found at i:1595996 original size:21 final size:20
Alignment explanation
Indices: 1595950--1595990 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1595940 AGTTTAAATA
1595950 GTTTTAAGTGTTTTAATTAG
1 GTTTTAAGTGTTTTAATTAG
*
1595970 GATTTAAGATGTTTTAGATTA
1 GTTTTAAG-TGTTTTA-ATTA
1595991 TTTTTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTTTAAGTGTTTTAATTAG
Found at i:1596108 original size:12 final size:12
Alignment explanation
Indices: 1596070--1596113 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
1596060 AATAAAATCT
1596070 TATTTTTCTCTC
1 TATTTTTCTCTC
**
1596082 TAGCTTTCTCTC
1 TATTTTTCTCTC
1596094 TATTTTTCTCTC
1 TATTTTTCTCTC
1596106 TATTTTTC
1 TATTTTTC
1596114 GCATACTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.09, C:0.25, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTTTTCTCTC
Found at i:1596591 original size:17 final size:17
Alignment explanation
Indices: 1596566--1596599 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1596556 CTTTATCCCA
*
1596566 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
1596583 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
1596600 TTATCTCATT
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:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:1602177 original size:5 final size:5
Alignment explanation
Indices: 1602154--1602256 Score: 75
Period size: 5 Copynumber: 20.2 Consensus size: 5
1602144 CATTTCGTTC
* *
1602154 TATTT T-TTT TATTT CATTT TATTT TCGTTT TATTTT TATTT TATTTT
1 TATTT TATTT TATTT TATTT TATTT T-ATTT TA-TTT TATTT TA-TTT
*** * * * *
1602201 TAGCA AACTT TATTT TCATTA TA-TT TATTT TAATT TATTT TATTT TATTT
1 TATTT TATTT TATTT T-ATTT TATTT TATTT TATTT TATTT TATTT TATTT
1602251 TATTT T
1 TATTT T
1602257 TCTTTGAACA
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
4 7 0.09
5 50 0.67
6 18 0.24
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:1602194 original size:22 final size:21
Alignment explanation
Indices: 1602160--1602200 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1602150 GTTCTATTTT
1602160 TTTTATTTCATTTTATTTTCG
1 TTTTATTTCATTTTATTTTCG
*
1602181 TTTTATTTTTATTTTATTTT
1 TTTTA-TTTCATTTTATTTT
1602201 TAGCAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTATTTCATTTTATTTTCG
Found at i:1604166 original size:44 final size:44
Alignment explanation
Indices: 1604117--1604243 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
1604107 TTAAACATTA
1604117 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
**
1604161 TATTTTAAT-TAAGTTTTAGG-A---TA---T---TAT-TTTTA-
1 TATTTT-ATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
*
1604193 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAG
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
1604237 TATTTTA
1 TATTTTA
1604244 ATTAGGATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 28
0.66 0.05 0.29
Matches are distributed among these distances:
31 2 0.03
32 15 0.23
33 6 0.09
34 3 0.05
36 2 0.03
37 1 0.02
39 1 0.02
40 2 0.03
42 2 0.03
43 6 0.09
44 22 0.34
45 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.61
Consensus pattern (44 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAG
Found at i:1604221 original size:76 final size:75
Alignment explanation
Indices: 1604114--1604329 Score: 312
Period size: 76 Copynumber: 2.9 Consensus size: 75
1604104 ATTTTAAACA
*
1604114 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTA
*
1604179 GGATATTATTT
65 GAATATTATTT
*
1604190 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGATTTA
1604255 GAATATTATTT
65 GAATATTATTT
* * *
1604266 TAAATATTATTA--TTT-TTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTATGATT
1 T-TATATT-TTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAAGATT
1604328 TA
63 TA
1604330 AGATGTTTTT
Statistics
Matches: 130, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
74 5 0.04
75 41 0.32
76 76 0.58
77 5 0.04
78 3 0.02
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (75 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGATTTAG
AATATTATTT
Found at i:1610882 original size:55 final size:55
Alignment explanation
Indices: 1610822--1611063 Score: 261
Period size: 55 Copynumber: 4.4 Consensus size: 55
1610812 TTGAATTAAC
* * *
1610822 GATTGAGCACCTTTGTGCTTCAATCAAGAGCTGACACCTCTATGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCAAGAGCTGACACCTCTATGCAGCCAAAAAT
* * * **
1610877 GATTGAGCACCTCTATGCTTCAATCGAGAACTGACACCTCTATGCAGTTAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCAAGAGCTGACACCTCTATGCAGCCAAAAAT
* ** * * * * * * *
1610932 GACTGAGCACCTCTGTGCTTCAGCCAGGAGCTGACACCTTTGTGTAGCTAAGACT
1 GATTGAGCACCTCTGTGCTTCAATCAAGAGCTGACACCTCTATGCAGCCAAAAAT
* * *
1610987 GATTGAGCACCTCTGTGCTTCAATCGAAGA-CTAACACCTCTGTGCAGTCAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATC-AAGAGCTGACACCTCTATGCAGCCAAAAAT
* *
1611042 GACTGAGCACCTCTGCGCTTCA
1 GATTGAGCACCTCTGTGCTTCA
1611064 GTATAAAATC
Statistics
Matches: 152, Mismatches: 34, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
55 149 0.98
56 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (55 bp):
GATTGAGCACCTCTGTGCTTCAATCAAGAGCTGACACCTCTATGCAGCCAAAAAT
Found at i:1610994 original size:110 final size:110
Alignment explanation
Indices: 1610825--1611064 Score: 338
Period size: 110 Copynumber: 2.2 Consensus size: 110
1610815 AATTAACGAT
* ** *
1610825 TGAGCACCTTTGTGCTTCAATCAAGAGCTGACACCTCTATGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAGCCAAGAGCTGACACCTCTATGTAGCCAAAACTGATTGAGCACCTC
* *
1610890 TATGCTTCAATCG-AGAACTGACACCTCTATGCAGTTAAAAATGAC
66 TATGCTTCAATCGAAG-ACTAACACCTCTATGCAGTCAAAAATGAC
* * * * *
1610935 TGAGCACCTCTGTGCTTCAGCCAGGAGCTGACACCTTTGTGTAGCTAAGACTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAGCCAAGAGCTGACACCTCTATGTAGCCAAAACTGATTGAGCACCTC
* *
1611000 TGTGCTTCAATCGAAGACTAACACCTCTGTGCAGTCAAAAATGAC
66 TATGCTTCAATCGAAGACTAACACCTCTATGCAGTCAAAAATGAC
*
1611045 TGAGCACCTCTGCGCTTCAG
1 TGAGCACCTCTGTGCTTCAG
1611065 TATAAAATCT
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
110 113 0.98
111 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAGCCAAGAGCTGACACCTCTATGTAGCCAAAACTGATTGAGCACCTC
TATGCTTCAATCGAAGACTAACACCTCTATGCAGTCAAAAATGAC
Found at i:1611053 original size:28 final size:28
Alignment explanation
Indices: 1610906--1611056 Score: 82
Period size: 28 Copynumber: 5.5 Consensus size: 28
1610896 TCAATCGAGA
* *
1610906 ACTGA-CACCTCTATGCAGTTAAAAATG
1 ACTGAGCACCTCTGTGCAGTCAAAAATG
* *** *
1610933 ACTGAGCACCTCTGTGC-TTCAGCCAGG
1 ACTGAGCACCTCTGTGCAGTCAAAAATG
* * * *
1610960 AGCTGA-CACCTTTGTGTAG-CTAAGACTG
1 A-CTGAGCACCTCTGTGCAGTC-AAAAATG
* * *
1610988 ATTGAGCACCTCTGTGC-TTCAATCGAA-G
1 ACTGAGCACCTCTGTGCAGTCAA--AAATG
*
1611016 ACT-AACACCTCTGTGCAGTCAAAAATG
1 ACTGAGCACCTCTGTGCAGTCAAAAATG
1611043 ACTGAGCACCTCTG
1 ACTGAGCACCTCTG
1611057 CGCTTCAGTA
Statistics
Matches: 88, Mismatches: 25, Indels: 21
0.66 0.19 0.16
Matches are distributed among these distances:
26 2 0.02
27 41 0.47
28 43 0.49
29 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (28 bp):
ACTGAGCACCTCTGTGCAGTCAAAAATG
Found at i:1611125 original size:54 final size:56
Alignment explanation
Indices: 1610822--1611141 Score: 210
Period size: 55 Copynumber: 5.8 Consensus size: 56
1610812 TTGAATTAAC
* * * * * * *
1610822 GATTGAGCACCTTTGTGCTTCAATC-AAGAGCT-GACACCTCTATGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAATCTAG-CACCTCTGTGCAGTCAAAAAT
* * * * *
1610877 GATTGAGCACCTCTATGCTTCAATCGAGAA-CT-GACACCTCTATGCAGTTAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAATCTAG-CACCTCTGTGCAGTCAAAAAT
* * * ** * * * * *
1610932 GACTGAGCACCTCTGTGCTTC-AGCCAGGAGCT-GACACCTTTGTGTAG-CTAAGACT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAATCTAG-CACCTCTGTGCAGTC-AAAAAT
* * *
1610987 GATTGAGCACCTCTGTGCTTCAATCGAAGA-CTAACACCTCTGTGCAGTCAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAATCTAGCACCTCTGTGCAGTCAAAAAT
* * * * * * *
1611042 GACTGAGCACCTCTGCGCTTCAGTATAAAATCTGGCACCTCTGTGCA-T-TAGAAT
1 GATTGAGCACCTCTGTGCTTCAATCTAAAATCTAGCACCTCTGTGCAGTCAAAAAT
* * * *
1611096 GATTGAGCACCTCTTTGCTACAATCTAAAATCAAGCACCTCCGTGC
1 GATTGAGCACCTCTGTGCTTCAATCTAAAATCTAGCACCTCTGTGC
1611142 TTTTACAAAC
Statistics
Matches: 211, Mismatches: 47, Indels: 15
0.77 0.17 0.05
Matches are distributed among these distances:
54 46 0.22
55 143 0.68
56 22 0.10
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (56 bp):
GATTGAGCACCTCTGTGCTTCAATCTAAAATCTAGCACCTCTGTGCAGTCAAAAAT
Found at i:1611135 original size:110 final size:109
Alignment explanation
Indices: 1610825--1611141 Score: 284
Period size: 110 Copynumber: 2.9 Consensus size: 109
1610815 AATTAACGAT
* * * * * *
1610825 TGAGCACCTTTGTGCTTCA-ATCAAGAGCTGACACCTCTATGTAGCCAA-AAGTGATTGAGCACC
1 TGAGCACCTCTGCGCTTCAGA-CAAAAGCTGACACCTCTGTGCA-CTAAGAA-TGATTGAGCACC
* * * *
1610888 TCTATGCTTCAATCGAGAAC-TGACACCTCTATGCAGTTAAAAATGAC
63 TCTATGCTTCAATCGAAAACAAG-CACCTCTGTGCAGTCAAAAATGAC
* * ** * * *
1610935 TGAGCACCTCTGTGCTTCAGCCAGGAGCTGACACCTTTGTGTAGCTAAGACTGATTGAGCACCTC
1 TGAGCACCTCTGCGCTTCAGACAAAAGCTGACACCTCTGTGCA-CTAAGAATGATTGAGCACCTC
* *
1611000 TGTGCTTCAATCGAAGACTAA-CACCTCTGTGCAGTCAAAAATGAC
65 TATGCTTCAATCGAAAAC-AAGCACCTCTGTGCAGTCAAAAATGAC
* * * *
1611045 TGAGCACCTCTGCGCTTCAGTATAAAATCTGGCACCTCTGTGCA-TTAGAATGATTGAGCACCTC
1 TGAGCACCTCTGCGCTTCAG-ACAAAAGCTGACACCTCTGTGCACTAAGAATGATTGAGCACCTC
* * * *
1611109 TTTGCTACAATCTAAAATCAAGCACCTCCGTGC
65 TATGCTTCAATCGAAAA-CAAGCACCTCTGTGC
1611142 TTTTACAAAC
Statistics
Matches: 171, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
109 33 0.19
110 122 0.71
111 16 0.09
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (109 bp):
TGAGCACCTCTGCGCTTCAGACAAAAGCTGACACCTCTGTGCACTAAGAATGATTGAGCACCTCT
ATGCTTCAATCGAAAACAAGCACCTCTGTGCAGTCAAAAATGAC
Found at i:1618581 original size:115 final size:115
Alignment explanation
Indices: 1618377--1618593 Score: 303
Period size: 115 Copynumber: 1.9 Consensus size: 115
1618367 GATTGCATTG
* * *
1618377 TTGAGTGGTTGGAGACAAGACATTTATGTCCGTTGTCACTATCAAATGCCAAGTTAATGAAGTTT
1 TTGAGTGGTTGGAGACAAGACATTTATATCCGTTGTCAATATCAAATACCAAGTTAATGAAGTTT
* * *
1618442 ATTCCAATCTTCTTTTATTGCATTGTTAGTTGATGTACATTGTTTGTATT
66 ATTCCAATCTTCTTCTATTACATTGTTAATTGATGTACATTGTTTGTATT
* * * *
1618492 TTGAGTGGTTGGAGACAAGTCATTTATATCCGTTGTCTCAATATCAAGTATCAATTTAATGAAGT
1 TTGAGTGGTTGGAGACAAGACATTTATATCCGTTG--TCAATATCAAATACCAAGTTAATGAAGT
*
1618557 TTATTCTAATCTT-TTCT-TTACATTGTTAATTGATGTA
64 TTATTCCAATCTTCTTCTATTACATTGTTAATTGATGTA
1618594 TTTTGATAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
115 51 0.57
116 3 0.03
117 35 0.39
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (115 bp):
TTGAGTGGTTGGAGACAAGACATTTATATCCGTTGTCAATATCAAATACCAAGTTAATGAAGTTT
ATTCCAATCTTCTTCTATTACATTGTTAATTGATGTACATTGTTTGTATT
Found at i:1619415 original size:23 final size:22
Alignment explanation
Indices: 1619389--1619455 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 22
1619379 TCTTTCATTT
1619389 TAAAAAAATGAAAATAACATAA-A
1 TAAAAAAAT-AAAATAA-ATAATA
*
1619412 TAAATAAATAAAATGAAATAATA
1 TAAAAAAATAAAAT-AAATAATA
*
1619435 TAAAATAATAATAATAAATAA
1 TAAAAAAATAA-AATAAATAA
1619456 GGCGAAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
22 9 0.24
23 26 0.68
24 3 0.08
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (22 bp):
TAAAAAAATAAAATAAATAATA
Found at i:1619444 original size:13 final size:14
Alignment explanation
Indices: 1619400--1619452 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
1619390 AAAAAAATGA
*
1619400 AAATAACAT-AAAT
1 AAATAATATAAAAT
1619413 AAATAA-ATAAAAT
1 AAATAATATAAAAT
1619426 GAAATAATATAAAAT
1 -AAATAATATAAAAT
1619441 -AATAATAATAAA
1 AAATAAT-ATAAA
1619453 TAAGGCGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.06
13 16 0.44
14 11 0.31
15 7 0.19
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (14 bp):
AAATAATATAAAAT
Found at i:1620436 original size:34 final size:34
Alignment explanation
Indices: 1620379--1620455 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
1620369 GTTCGAATAG
* * **
1620379 TAAAAATAAAATGTTAAACAGTTAATTTGAGCAA
1 TAAAAATAAAATGCTAAACAGTTAACTCCAGCAA
* *
1620413 TAAAAATAAAATGCTAGAGAGTTAACTCCAGCAA
1 TAAAAATAAAATGCTAAACAGTTAACTCCAGCAA
1620447 T-AAAATAAA
1 TAAAAATAAA
1620456 GGGTTAGTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 8 0.22
34 29 0.78
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.25
Consensus pattern (34 bp):
TAAAAATAAAATGCTAAACAGTTAACTCCAGCAA
Found at i:1620736 original size:2 final size:2
Alignment explanation
Indices: 1620731--1620761 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1620721 ATTTTTTCAT
1620731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1620762 TTTAAGCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1622741 original size:38 final size:37
Alignment explanation
Indices: 1622699--1622815 Score: 119
Period size: 38 Copynumber: 3.1 Consensus size: 37
1622689 CCAAATATGT
**
1622699 TATTTAATTGAAATATGAATATATTATTTA-TAATTTTA
1 TATTTAATT-AAATAAAAATATATTATTTATTAA-TTTA
* * *
1622737 TATTTTATTAAATAAAAATTTAATATTTATTAATTTA
1 TATTTAATTAAATAAAAATATATTATTTATTAATTTA
* * **
1622774 TATTCAATAAAAATAAAAATATATTATTTAAGAATTTA
1 TATTTAAT-TAAATAAAAATATATTATTTATTAATTTA
1622812 TATT
1 TATT
1622816 CGATTAAAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
37 26 0.40
38 39 0.60
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (37 bp):
TATTTAATTAAATAAAAATATATTATTTATTAATTTA
Found at i:1624221 original size:23 final size:23
Alignment explanation
Indices: 1624195--1624404 Score: 257
Period size: 23 Copynumber: 9.2 Consensus size: 23
1624185 TTGAAGACTG
1624195 AGAAATGGGTTTATGGAAGAAGA
1 AGAAATGGGTTTATGGAAGAAGA
*
1624218 AGAAATGGGTTTATGGAAGAAAA
1 AGAAATGGGTTTATGGAAGAAGA
* *
1624241 AGAAATGGGTTTATAGAGGAAGA
1 AGAAATGGGTTTATGGAAGAAGA
** *
1624264 AGAAATGCTTTTATGGAAGAAAA
1 AGAAATGGGTTTATGGAAGAAGA
*
1624287 AGAAATGTGTTTATGGAAGAAGA
1 AGAAATGGGTTTATGGAAGAAGA
*
1624310 A-AAAGGGGTTTATGGAAGGAA-A
1 AGAAATGGGTTTATGGAA-GAAGA
* *
1624332 AGAAACGAGTTTATGGAAGAAGA
1 AGAAATGGGTTTATGGAAGAAGA
* *
1624355 AGAAATGGGTTTATGGACGAAAA
1 AGAAATGGGTTTATGGAAGAAGA
*
1624378 ATAAAAT--GTTTATGGAAGAAGA
1 A-GAAATGGGTTTATGGAAGAAGA
1624400 AGAAA
1 AGAAA
1624405 CATATTTATG
Statistics
Matches: 159, Mismatches: 24, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
21 3 0.02
22 33 0.21
23 119 0.75
24 4 0.03
ACGTcount: A:0.47, C:0.01, G:0.30, T:0.22
Consensus pattern (23 bp):
AGAAATGGGTTTATGGAAGAAGA
Found at i:1624245 original size:46 final size:46
Alignment explanation
Indices: 1624195--1624404 Score: 291
Period size: 46 Copynumber: 4.6 Consensus size: 46
1624185 TTGAAGACTG
1624195 AGAAATGGGTTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAA
1 AGAAATGGGTTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAA
* * **
1624241 AGAAATGGGTTTATAGAGGAAGAAGAAATGCTTTTATGGAAGAAAA
1 AGAAATGGGTTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAA
* * *
1624287 AGAAATGTGTTTATGGAAGAAGAA-AAAGGGGTTTATGGAAGGAAA
1 AGAAATGGGTTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAA
* * *
1624332 AGAAACGAGTTTATGGAAGAAGAAGAAATGGGTTTATGGACGAAAA
1 AGAAATGGGTTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAA
*
1624378 ATAAAAT--GTTTATGGAAGAAGAAGAAA
1 A-GAAATGGGTTTATGGAAGAAGAAGAAA
1624405 CATATTTATG
Statistics
Matches: 144, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
45 59 0.41
46 82 0.57
47 3 0.02
ACGTcount: A:0.47, C:0.01, G:0.30, T:0.22
Consensus pattern (46 bp):
AGAAATGGGTTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAA
Found at i:1624413 original size:68 final size:66
Alignment explanation
Indices: 1624204--1624426 Score: 243
Period size: 68 Copynumber: 3.3 Consensus size: 66
1624194 GAGAAATGGG
* * *
1624204 TTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAAAGAAATGGGTTTATAGAGGAAGAAGAAA
1 TTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAAAAAAAT--GTTTATGGAAGAAGAAGAAA
1624269 TGC-T
64 --CAT
* * ***
1624273 TTTATGGAAGAAAAAGAAATGTGTTTATGGAAGAAGAAAAAGGGGTTTATGGAAGGAA-AAGAAA
1 TTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAA-AAAAAAATGTTTATGGAA-GAAGAAGAAA
*
1624337 CGAG
64 C-AT
*
1624341 TTTATGGAAGAAGAAGAAATGGGTTTATGGACGAAAAATAAAATGTTTATGGAAGAAGAAGAAAC
1 TTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAAA-AAAATGTTTATGGAAGAAGAAGAAAC
1624406 AT
65 AT
* *
1624408 ATTTATGAAAGAACAAGAA
1 -TTTATGGAAGAAGAAGAA
1624427 TGGTTCAGAA
Statistics
Matches: 129, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
66 1 0.01
67 7 0.05
68 81 0.63
69 36 0.28
70 4 0.03
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (66 bp):
TTTATGGAAGAAGAAGAAATGGGTTTATGGAAGAAAAAAAAATGTTTATGGAAGAAGAAGAAACA
T
Found at i:1625306 original size:2 final size:2
Alignment explanation
Indices: 1625299--1625352 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
1625289 ATCCTTATTT
* * * * * *
1625299 TA TA TA TA TT TA TA TA TA TT TA TA TA TA TA CA TA CA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1625341 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1625353 CACACACACA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1625312 original size:10 final size:10
Alignment explanation
Indices: 1625297--1625327 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1625287 TTATCCTTAT
1625297 TTTATATATA
1 TTTATATATA
1625307 TTTATATATA
1 TTTATATATA
1625317 TTTATATATA
1 TTTATATATA
1625327 T
1 T
1625328 ACATACACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTATATATA
Found at i:1625341 original size:24 final size:24
Alignment explanation
Indices: 1625314--1625362 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
1625304 ATATTTATAT
* *
1625314 ATATTTATATATATACATACACAC
1 ATATATATATATATACACACACAC
1625338 ATATATATATATATACACACACAC
1 ATATATATATATATACACACACAC
1625362 A
1 A
1625363 CTAAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATATATATATATACACACACAC
Found at i:1625342 original size:20 final size:20
Alignment explanation
Indices: 1625319--1625358 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1625309 TATATATATT
1625319 TATATATATACATACACACA
1 TATATATATACATACACACA
*
1625339 TATATATATATATACACACA
1 TATATATATACATACACACA
1625359 CACACTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (20 bp):
TATATATATACATACACACA
Found at i:1626589 original size:21 final size:22
Alignment explanation
Indices: 1626565--1626605 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1626555 ACAAGAGGCA
*
1626565 TAATTGTCAA-ATAAATAAACC
1 TAATTCTCAATATAAATAAACC
*
1626586 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
1626606 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACC
Found at i:1629858 original size:21 final size:21
Alignment explanation
Indices: 1629834--1629880 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1629824 AATTTCAAAA
* *
1629834 GAAAAGTTGGTTACGTCCCAG
1 GAAAAGTTAGTTACATCCCAG
* *
1629855 GAAAAGTTAGTTGCATCCTAG
1 GAAAAGTTAGTTACATCCCAG
1629876 GAAAA
1 GAAAA
1629881 ATTCCAAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (21 bp):
GAAAAGTTAGTTACATCCCAG
Found at i:1634017 original size:14 final size:14
Alignment explanation
Indices: 1633987--1634031 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1633977 TTTAGCAAAC
**
1633987 TTTATTTCATTCCA
1 TTTATTTCATTTTA
1634001 TTTATTTCATTTTA
1 TTTATTTCATTTTA
*
1634015 TTTTATTTTATTTTA
1 -TTTATTTCATTTTA
1634030 TT
1 TT
1634032 AGATGTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTCATTTTA
Found at i:1634021 original size:15 final size:15
Alignment explanation
Indices: 1633987--1634054 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
1633977 TTTAGCAAAC
**
1633987 TTTATTTCATTCCA-
1 TTTATTTCATTTTAT
1634001 TTTATTTCATTTTAT
1 TTTATTTCATTTTAT
*
1634016 TTTATTTTATTTTAT
1 TTTATTTCATTTTAT
* * *
1634031 TAGATGTTTAATTTTAT
1 T--TTATTTCATTTTAT
1634048 TTTATTT
1 TTTATTT
1634055 TTCTCTGAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
14 12 0.28
15 19 0.44
17 12 0.28
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTATTTCATTTTAT
Found at i:1634056 original size:6 final size:5
Alignment explanation
Indices: 1634001--1634055 Score: 65
Period size: 5 Copynumber: 10.6 Consensus size: 5
1633991 TTTCATTCCA
* **
1634001 TTTAT TTCAT TTTAT TTTAT TTTAT TTTAT TAGAT GTTTAAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT -TTT-AT TTTAT TTTAT
1634053 TTT
1 TTT
1634056 TCTCTGAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
5 36 0.86
6 4 0.10
7 2 0.05
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:1638734 original size:14 final size:14
Alignment explanation
Indices: 1638715--1638741 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1638705 GCTATCGGTT
1638715 AAAAGAAAATATTG
1 AAAAGAAAATATTG
1638729 AAAAGAAAATATT
1 AAAAGAAAATATT
1638742 AAGTTTGTTC
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:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (14 bp):
AAAAGAAAATATTG
Found at i:1640077 original size:43 final size:41
Alignment explanation
Indices: 1640004--1640120 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 41
1639994 ACCAAACGTT
* *
1640004 GCTAAAGGTTATG-TTTTTCAGCAGCATTTTTTTTACAAAAGCC
1 GCTAAAGGTTATGATATTT-AGCGGC--TTTTTTTACAAAAGCC
* * *
1640047 GCTAAAGGTAATGATATTTAGCGGC-TTTTTTACAAACGTC
1 GCTAAAGGTTATGATATTTAGCGGCTTTTTTTACAAAAGCC
*
1640087 GCTAGAGGTTATGATATTTTAGCGG-TGTTTTTTA
1 GCTAAAGGTTATGATA-TTTAGCGGCT-TTTTTTA
1640121 TCCAAATGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
40 27 0.43
41 8 0.13
42 7 0.11
43 17 0.27
44 4 0.06
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (41 bp):
GCTAAAGGTTATGATATTTAGCGGCTTTTTTTACAAAAGCC
Found at i:1640090 original size:40 final size:42
Alignment explanation
Indices: 1640032--1640120 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 42
1640022 CAGCAGCATT
1640032 TTTTTTACAAAAGCCGCTAAAGGTAATGATA-TTTAGCGG-C
1 TTTTTTACAAAAGCCGCTAAAGGTAATGATATTTTAGCGGTC
* * * * *
1640072 TTTTTTACAAACGTCGCTAGAGGTTATGATATTTTAGCGGTG
1 TTTTTTACAAAAGCCGCTAAAGGTAATGATATTTTAGCGGTC
1640114 TTTTTTA
1 TTTTTTA
1640121 TCCAAATGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 27 0.64
41 8 0.19
42 7 0.17
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.40
Consensus pattern (42 bp):
TTTTTTACAAAAGCCGCTAAAGGTAATGATATTTTAGCGGTC
Found at i:1640213 original size:44 final size:44
Alignment explanation
Indices: 1640164--1640248 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
1640154 CGTTTTGTAT
* * *
1640164 CAAAAACATCACTAAATGTTATGACATATAGTGGCGTTTGTTCC
1 CAAAAACACCACTAAATGGTATGACATATAGTGGCGCTTGTTCC
** * *
1640208 CAAAAATGCCGCTAAATGGTATGTCATATAGTGGCGCTTGT
1 CAAAAACACCACTAAATGGTATGACATATAGTGGCGCTTGT
1640249 GAATGTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
CAAAAACACCACTAAATGGTATGACATATAGTGGCGCTTGTTCC
Found at i:1640440 original size:21 final size:21
Alignment explanation
Indices: 1640414--1640471 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1640404 ATTATCTAAT
*
1640414 AAACTTGACATCCATAGCAAC
1 AAACTTGAAATCCATAGCAAC
* *
1640435 AAACTTGAAATCTATAGCAAG
1 AAACTTGAAATCCATAGCAAC
1640456 AAACTTGAAATCCATA
1 AAACTTGAAATCCATA
1640472 ATAATAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAGCAAC
Found at i:1643179 original size:41 final size:42
Alignment explanation
Indices: 1643111--1643192 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
1643101 GATAAATTGC
* *
1643111 GGTGTTTATTAAAAAAATGTAATTAAAGTACGAGTTTTTAGA
1 GGTGTTTATTAAAAAAATGTAACTAAAGTACGAGTCTTTAGA
* * *
1643153 GGTGTTTATT-TAGAAATGTCACTAAAGTACGAGTCTTTAG
1 GGTGTTTATTAAAAAAATGTAACTAAAGTACGAGTCTTTAG
1643193 CGGTATTTGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 25 0.71
42 10 0.29
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (42 bp):
GGTGTTTATTAAAAAAATGTAACTAAAGTACGAGTCTTTAGA
Found at i:1643217 original size:41 final size:41
Alignment explanation
Indices: 1643134--1643507 Score: 299
Period size: 41 Copynumber: 9.2 Consensus size: 41
1643124 AAAATGTAAT
* * * * * * * *
1643134 TAAAGTACGAGTTTTTAGAGGTGTTTATTTAGAAATGTCAC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCAC
* ** *
1643175 TAAAGTACGAGTCTTTAGCGGTATTTGTATAAAAATACCAC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCAC
* * * *
1643216 T-AAGTACGAGTCTATAACAGCGTTTGTATAAAAAGGCCGC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCAC
* ***
1643256 TAAAGTAC-AGATCTATAGCGGCGTTTATATAAATGCGCCAC
1 TAAAGTACGAG-TCTATAGCGGCGTTTGTATAAAAATGCCAC
* * * * **
1643297 TAAAATATGAGTCTATAACGACGTTTGTATAAAAACACCAC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCAC
* * * * * **
1643338 TAATGTACAAGTCTATAGCAGCATTTGTACAAAAACACCAC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCAC
* * **
1643379 TAATGTACGAGTCTATAGCAGTATTTGTATAAAAACT-CCAC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAA-TGCCAC
* *
1643420 TAAAGTACGAGTCTTTAGCGGCGTTTGTATAGAAATGCCAC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCAC
* * * *
1643461 TAAAGTAC-AGTATTTAGCGGTGTTTCTATAAAAACT-CCAC
1 TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAA-TGCCAC
1643501 TAAAGTA
1 TAAAGTA
1643508 TGAATATTTA
Statistics
Matches: 273, Mismatches: 54, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
40 68 0.25
41 203 0.74
42 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (41 bp):
TAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAATGCCAC
Found at i:1650170 original size:19 final size:20
Alignment explanation
Indices: 1650148--1650190 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
1650138 CTTTTATTCC
1650148 TTTTATTTAATTTT-TTTAA
1 TTTTATTTAATTTTATTTAA
1650167 TTTTATTTAATTTTATTTAA
1 TTTTATTTAATTTTATTTAA
1650187 TTTT
1 TTTT
1650191 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTAATTTTATTTAA
Found at i:1650175 original size:10 final size:10
Alignment explanation
Indices: 1650148--1650190 Score: 79
Period size: 10 Copynumber: 4.4 Consensus size: 10
1650138 CTTTTATTCC
1650148 TTTTATTTAA
1 TTTTATTTAA
1650158 TTTT-TTTAA
1 TTTTATTTAA
1650167 TTTTATTTAA
1 TTTTATTTAA
1650177 TTTTATTTAA
1 TTTTATTTAA
1650187 TTTT
1 TTTT
1650191 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 9 0.28
10 23 0.72
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:1650199 original size:29 final size:28
Alignment explanation
Indices: 1650148--1650206 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1650138 CTTTTATTCC
1650148 TTTTATTTAATTTTTTTAATTTTATTTAA
1 TTTTATTTAATTTTTTTAATTTT-TTTAA
* *
1650177 TTTTATTTAA-TTTTTTATTTTTTTTTA
1 TTTTATTTAATTTTTTTAATTTTTTTAA
1650204 TTT
1 TTT
1650207 ATAGAGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.25
28 11 0.39
29 10 0.36
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTATTTAATTTTTTTAATTTTTTTAA
Found at i:1651152 original size:3 final size:3
Alignment explanation
Indices: 1651130--1651182 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
1651120 TGACCTGAAA
1651130 AAT AA- AAT AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1651175 AAT AAT AA
1 AAT AAT AA
1651183 CAGGTGGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.13
3 41 0.87
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1651639 original size:135 final size:135
Alignment explanation
Indices: 1651371--1651797 Score: 398
Period size: 135 Copynumber: 3.2 Consensus size: 135
1651361 CATTCCATTA
* ** * * * * *
1651371 TTCTTCAGGGAATATTGAATCGAGGCAGACTTGTTCCACTACTACTCAAGGAAGGTCAAATCTTG
1 TTCTTCAGGGAAGATTGAATCGAGATAGACATGTTCCACTATTCCTCAGGGAAGATCAAAT-TTG
* ** * * * * *
1651436 --AAAGAGATTGATCTGTTCCGC-AGCTCCTTGAGAGAAAATCAGATCTGGAAATGTTGATTCAT
65 AAAAAAAGAGGGATATATTCCACTA-CTTCTTGAGGGAAAATCAGATCTGGAAATGTTGATTCAT
*
1651498 TCCACTG
129 TTCACTG
* * * *
1651505 TTCTTCAGGGCAGATTGAATCGAGATAGACTTGTTCCATTATTCCTCAGGGATGATCAAATCTAT
1 TTCTTCAGGGAAGATTGAATCGAGATAGACATGTTCCACTATTCCTCAGGGAAGATCAAAT-T-T
* * * *
1651570 -AAAAAAA-ATGGATATGTTCCACTATTTCTTGAGGGAAAATCAGATCTGGAAATGTTGGTTCAT
64 GAAAAAAAGAGGGATATATTCCACTACTTCTTGAGGGAAAATCAGATCTGGAAATGTTGATTCAT
1651633 TTCACTG
129 TTCACTG
* * * **
1651640 TTCTTCAGGGAAGATTGAATTGAGGTAGACATGTTCCACTATTCTTTTGGGAAGATCAAATTTGA
1 TTCTTCAGGGAAGATTGAATCGAGATAGACATGTTCCACTATTCCTCAGGGAAGATCAAATTTGA
* ** * * * * *
1651705 AAAAAAGAGGGATCTATTCTGCTGCTTCTTGAGGGAAAGTCAGATATAGAAATTTTGACTT-ATT
66 AAAAAAGAGGGATATATTCCACTACTTCTTGAGGGAAAATCAGATCTGGAAATGTTGA-TTCATT
**
1651769 TCGTTG
130 TCACTG
*
1651775 TTCTTCAGGGAAAATTGAATCGA
1 TTCTTCAGGGAAGATTGAATCGA
1651798 TTTCGCTTCT
Statistics
Matches: 242, Mismatches: 44, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
133 1 0.00
134 61 0.25
135 173 0.71
136 7 0.03
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (135 bp):
TTCTTCAGGGAAGATTGAATCGAGATAGACATGTTCCACTATTCCTCAGGGAAGATCAAATTTGA
AAAAAAGAGGGATATATTCCACTACTTCTTGAGGGAAAATCAGATCTGGAAATGTTGATTCATTT
CACTG
Found at i:1651950 original size:27 final size:27
Alignment explanation
Indices: 1651888--1651943 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1651878 TTGAAAAATC
*
1651888 ATACTTGAATATTAGGATTTCAAGATA
1 ATACTTGAAGATTAGGATTTCAAGATA
1651915 ATACTTGAAGATTAGGATTTCAAGATA
1 ATACTTGAAGATTAGGATTTCAAGATA
1651942 AT
1 AT
1651944 CTTTGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (27 bp):
ATACTTGAAGATTAGGATTTCAAGATA
Found at i:1658158 original size:34 final size:34
Alignment explanation
Indices: 1658120--1658251 Score: 129
Period size: 34 Copynumber: 3.6 Consensus size: 34
1658110 CCATAGCAGA
*
1658120 AATGCATATGGGTACATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
1658154 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTT
1 AATGCATATGGGTGCATTATCGGCAT--AA-AA-G--A-A--T
* *
1658197 GAAATGCGTATGGGTGCATTATCGGCATAAAATAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
1658233 AATGCATATGGGTGCATTA
1 AATGCATATGGGTGCATTA
1658252 CTGGCATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
34 42 0.52
36 3 0.04
37 2 0.02
38 2 0.02
39 1 0.01
40 1 0.01
41 1 0.01
42 2 0.02
43 3 0.04
45 24 0.30
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:1658201 original size:79 final size:79
Alignment explanation
Indices: 1658065--1658308 Score: 407
Period size: 79 Copynumber: 3.1 Consensus size: 79
1658055 GAATGAATGA
*
1658065 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCAGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
1658130 GGTACATTATCGGC
66 GGTGCATTATCGGC
* * *
1658144 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGCGTATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1658209 GGTGCATTATCGGC
66 GGTGCATTATCGGC
* *
1658223 ATAAAATAATAATGCATATGGGTGCATTACTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
1658288 GGTGCATTATTGGC
66 GGTGCATTATCGGC
*
1658302 ATGAAAG
1 ATAAAAG
1658309 GATGTCATAG
Statistics
Matches: 152, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 152 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
GGTGCATTATCGGC
Found at i:1658295 original size:124 final size:124
Alignment explanation
Indices: 1658154--1658421 Score: 437
Period size: 124 Copynumber: 2.2 Consensus size: 124
1658144 ATAAAAGAAT
*** * *
1658154 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGCGTATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCACAAATGCATATGGCTGCATTAT
*
1658219 CGGCATAAAATAATAATGCATATGGGTGCATTACTGGCATGAAAGGATGCCATAGCTGA
66 CGGCATAAAAGAATAATGCATATGGGTGCATTACTGGCATGAAAGGATGCCATAGCTGA
* *
1658278 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCACAAATGCATATGGCTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCACAAATGCATATGGCTGCATTAT
* * *
1658343 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGTTGA
66 CGGCATAAAAGAATAATGCATATGGGTGCATTACTGGCATGAAAGGATGCCATAGCTGA
1658402 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
1658422 CGATATAAAA
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
124 133 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (124 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCACAAATGCATATGGCTGCATTAT
CGGCATAAAAGAATAATGCATATGGGTGCATTACTGGCATGAAAGGATGCCATAGCTGA
Found at i:1658361 original size:34 final size:34
Alignment explanation
Indices: 1658323--1658470 Score: 127
Period size: 34 Copynumber: 4.0 Consensus size: 34
1658313 TCATAGCACA
*
1658323 AATGCATATGGCTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
1658357 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGTT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
**
1658400 GAAATGCATATGGGTGCATTATCGATATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
1658436 AATGCACATGGGTGCATTATTGGCATTAAAA-AAT
1 AATGCATATGGGTGCATTATCGGCA-TAAAAGAAT
1658470 A
1 A
1658471 CCATAAATAA
Statistics
Matches: 93, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
34 49 0.53
35 8 0.09
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.03
45 23 0.25
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:1658361 original size:79 final size:79
Alignment explanation
Indices: 1658278--1658461 Score: 289
Period size: 79 Copynumber: 2.3 Consensus size: 79
1658268 CCATAGCTGA
1658278 AATGCATATGGGTGCATTATTGGCATGAAAGGATG-TCATAGCACAAATGCATATGGCTGCATTA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCT-ATAGCACAAATGCATATGGCTGCATTA
*
1658342 TCGGCATAAAAGAAT
65 TCGACATAAAAGAAT
*** *
1658357 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGCACAAATGCATATGGCTGCATTAT
*
1658422 CGATATAAAAGAAT
66 CGACATAAAAGAAT
*
1658436 AATGCACATGGGTGCATTATTGGCAT
1 AATGCATATGGGTGCATTATTGGCAT
1658462 TAAAAAATAC
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
79 96 0.99
80 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGCACAAATGCATATGGCTGCATTAT
CGACATAAAAGAAT
Found at i:1658439 original size:203 final size:203
Alignment explanation
Indices: 1658075--1658461 Score: 666
Period size: 203 Copynumber: 1.9 Consensus size: 203
1658065 ATAAAAGAAT
* *
1658075 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCAGAAATGCATATGGGTACATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCACAAATGCATATGGCTACATTAT
*
1658140 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGCG
66 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGCA
* * *
1658205 TATGGGTGCATTATCGGCATAAAATAATAATGCATATGGGTGCATTACTGGCATGAAAGGATGCC
131 TATGGGTGCATTATCGACATAAAAGAATAATGCACATGGGTGCATTACTGGCATGAAAGGATGCC
1658270 ATAGCTGA
196 ATAGCTGA
* *
1658278 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCACAAATGCATATGGCTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCACAAATGCATATGGCTACATTAT
* *
1658343 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGTTGAAATGCA
66 CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGCA
* *
1658408 TATGGGTGCATTATCGATATAAAAGAATAATGCACATGGGTGCATTATTGGCAT
131 TATGGGTGCATTATCGACATAAAAGAATAATGCACATGGGTGCATTACTGGCAT
1658462 TAAAAAATAC
Statistics
Matches: 172, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
203 172 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (203 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCACAAATGCATATGGCTACATTAT
CGGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATGCA
TATGGGTGCATTATCGACATAAAAGAATAATGCACATGGGTGCATTACTGGCATGAAAGGATGCC
ATAGCTGA
Found at i:1658484 original size:79 final size:79
Alignment explanation
Indices: 1658278--1658487 Score: 269
Period size: 79 Copynumber: 2.7 Consensus size: 79
1658268 CCATAGCTGA
* * *
1658278 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCA-CAAATGCATATGGCTGCATTA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA-AATAAAATGCATATGGCTGCATTA
*
1658342 TCGGCATAAAAGAAT
65 TCGACATAAAAGAAT
* ** * *
1658357 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAGTTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAAATAAAATGCATATGGCTGCATTAT
*
1658422 CGATATAAAAGAAT
66 CGACATAAAAGAAT
* * ** *
1658436 AATGCACATGGGTGCATTATTGGCATTAAAAAATACCATAAATAAAATGCAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAAATAAAATGCAT
1658488 GAAATAATGC
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
79 113 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAAATAAAATGCATATGGCTGCATTAT
CGACATAAAAGAAT
Found at i:1658508 original size:46 final size:46
Alignment explanation
Indices: 1658472--1658590 Score: 184
Period size: 46 Copynumber: 2.6 Consensus size: 46
1658462 TAAAAAATAC
* *
1658472 CATAAATAAAATGCATGAAATAATGCACTAAGGCATTGAAGGATGT
1 CATAAATAAAATGCATGAAATGATGCACTAAGGCATTAAAGGATGT
* * * *
1658518 CATAAATAAAATGCATGAAATGATACATTAAGGCATGAAAGGACGT
1 CATAAATAAAATGCATGAAATGATGCACTAAGGCATTAAAGGATGT
1658564 CATAAATAAAATGCATGAAATGATGCA
1 CATAAATAAAATGCATGAAATGATGCA
1658591 TGAAAGGATG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (46 bp):
CATAAATAAAATGCATGAAATGATGCACTAAGGCATTAAAGGATGT
Found at i:1664506 original size:26 final size:26
Alignment explanation
Indices: 1664445--1664497 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1664435 ACCAAATAGA
1664445 AAACTCAAAATATTGAAAATTTATTT
1 AAACTCAAAATATTGAAAATTTATTT
1664471 AAACTCAAAATATTGAAAATTTATTT
1 AAACTCAAAATATTGAAAATTTATTT
1664497 A
1 A
1664498 CTCTGAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.38
Consensus pattern (26 bp):
AAACTCAAAATATTGAAAATTTATTT
Found at i:1667489 original size:3 final size:3
Alignment explanation
Indices: 1667461--1667512 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
1667451 TGACCTAAAA
* * *
1667461 AAT AA- AAT AAT AA- AAT ATT AGT -AT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1667506 AAT AAT A
1 AAT AAT A
1667513 GCGGGACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 5 0.12
3 36 0.88
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1668141 original size:82 final size:83
Alignment explanation
Indices: 1667991--1668150 Score: 187
Period size: 82 Copynumber: 1.9 Consensus size: 83
1667981 GTCGCAACAT
* *
1667991 TTGTTGAAAAAACGCCACTGCGGATGAACCCTATTACGATATTTATGTAAAAACACCGCTAAAAT
1 TTGTTGAAAAAACGCCACTGCGGATGAACCCTATTACGACATTTATATAAAAACACCGCTAAAAT
1668056 ACTAATCTGTCACGGTGC
66 ACTAATCTGTCACGGTGC
* * * * * * * * * *
1668074 TTGTTGAAAAAATGCCATTGTGGATGAA-CCTATTGCGGCGTTTGTATAAAAACTCCTCTAAAGT
1 TTGTTGAAAAAACGCCACTGCGGATGAACCCTATTACGACATTTATATAAAAACACCGCTAAAAT
* *
1668138 ACTACTTTGTCAC
66 ACTAATCTGTCAC
1668151 AGCGTTTTGT
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
82 38 0.60
83 25 0.40
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (83 bp):
TTGTTGAAAAAACGCCACTGCGGATGAACCCTATTACGACATTTATATAAAAACACCGCTAAAAT
ACTAATCTGTCACGGTGC
Found at i:1668167 original size:82 final size:82
Alignment explanation
Indices: 1667934--1668171 Score: 200
Period size: 83 Copynumber: 2.9 Consensus size: 82
1667924 CTTAAAGCAT
* * * *
1667934 TGAA-CTATTGCGGTGTTTGTACAAAAACAT-CGCTAAAGTACTACTTTGTCGCAAC-ATTTGT-
1 TGAACCTATTGCGGTGTTTGTATAAAAAC-TCCGCTAAAGTACTACTTTGTCACAGCGTTTTGTA
*
1667995 TGAAAAAACGCCACTGCGGA
65 T--AAAAATGCCACTGCGGA
* * * * * * * * * * *
1668015 TGAACCCTATTACGATATTTATGTAAAAACACCGCTAAAATACTAATCTGTCACGGTGCTTGTTG
1 TGAA-CCTATTGCGGTGTTTGTATAAAAACTCCGCTAAAGTACTACTTTGTCACAGCG-TT-TTG
* *
1668080 -A-AAAAATGCCATTGTGGA
63 TATAAAAATGCCACTGCGGA
* *
1668098 TGAACCTATTGCGGCGTTTGTATAAAAACTCCTCTAAAGTACTACTTTGTCACAGCGTTTTGTAT
1 TGAACCTATTGCGGTGTTTGTATAAAAACTCCGCTAAAGTACTACTTTGTCACAGCGTTTTGTAT
1668163 AAAAATGCC
66 AAAAATGCC
1668172 GCTAAAGTTA
Statistics
Matches: 117, Mismatches: 31, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
80 3 0.03
81 7 0.06
82 49 0.42
83 54 0.46
85 1 0.01
86 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (82 bp):
TGAACCTATTGCGGTGTTTGTATAAAAACTCCGCTAAAGTACTACTTTGTCACAGCGTTTTGTAT
AAAAATGCCACTGCGGA
Found at i:1679161 original size:2 final size:2
Alignment explanation
Indices: 1679154--1679189 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1679144 CATCTACAAT
1679154 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1679190 AAATAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1679259 original size:41 final size:43
Alignment explanation
Indices: 1679179--1679260 Score: 98
Period size: 45 Copynumber: 1.9 Consensus size: 43
1679169 ATATATATAT
*
1679179 ATATATATATAAAATAAATTAATTAATAAAGTATTAATAAAATCA
1 ATATATATATAAAATAAATTAA-TAATAAAG-ATAAATAAAATCA
*
1679224 ATATATATATATAATAAA-TAA-AATCAAA-ATAAATAAA
1 ATATATATATAAAATAAATTAATAAT-AAAGATAAATAAA
1679261 TTAATAAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
41 8 0.24
42 3 0.09
43 3 0.09
44 3 0.09
45 17 0.50
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (43 bp):
ATATATATATAAAATAAATTAATAATAAAGATAAATAAAATCA
Found at i:1679264 original size:49 final size:51
Alignment explanation
Indices: 1679171--1679268 Score: 121
Period size: 53 Copynumber: 1.9 Consensus size: 51
1679161 ATATATATAT
* *
1679171 ATATATATATATATATATAAAATAAATTAATTAATAAAGTATTAATAAAATCA
1 ATATATATATATATAAATAAAATAAA-TAATAAATAAAG-ATTAATAAAATCA
*
1679224 ATATATATATATAATAAATAAAATCAA-AATAAAT-AA-ATTAATAAA
1 ATATATATATAT-ATAAATAAAATAAATAATAAATAAAGATTAATAAA
1679269 GTATTAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 9 0.22
51 2 0.05
52 6 0.15
53 12 0.29
54 12 0.29
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (51 bp):
ATATATATATATATAAATAAAATAAATAATAAATAAAGATTAATAAAATCA
Found at i:1679267 original size:60 final size:61
Alignment explanation
Indices: 1679163--1679281 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 61
1679153 TTATATATAT
* * *
1679163 ATATATATATATATATATATATATATAAAATAAATTAATTAATAAAGTATTAATAAAATCA
1 ATATATATATATATATAAATATAAATAAAATAAATAAATTAATAAAGTATTAATAAAATCA
1679224 ATATATATATATA-ATAAATA-AAATCAAAATAAATAAATTAATAAAGTATTAATAAAAT
1 ATATATATATATATATAAATATAAAT-AAAATAAATAAATTAATAAAGTATTAATAAAAT
1679282 AAAAACCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 3 0.06
60 38 0.70
61 13 0.24
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (61 bp):
ATATATATATATATATAAATATAAATAAAATAAATAAATTAATAAAGTATTAATAAAATCA
Found at i:1679280 original size:28 final size:28
Alignment explanation
Indices: 1679187--1679284 Score: 110
Period size: 28 Copynumber: 3.4 Consensus size: 28
1679177 ATATATATAT
*
1679187 ATAAAATAAATTAATTAATAAAGTATTA
1 ATAAAATAAATAAATTAATAAAGTATTA
*
1679215 ATAAAATCAATATATATATATAATAAA-TA-AA
1 ATAAAAT-AA-ATA-A-AT-TAATAAAGTATTA
1679246 ATCAAAATAAATAAATTAATAAAGTATTA
1 AT-AAAATAAATAAATTAATAAAGTATTA
1679275 ATAAAATAAA
1 ATAAAATAAA
1679285 AACCAAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
27 7 0.12
28 19 0.32
29 6 0.10
30 5 0.08
31 6 0.10
32 9 0.15
33 7 0.12
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAAAATAAATAAATTAATAAAGTATTA
Found at i:1681218 original size:28 final size:28
Alignment explanation
Indices: 1681166--1681232 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
1681156 GGTCAACAGT
* * *
1681166 TGTTGCTCTTTGTTGTCATACCTTTCGA
1 TGTTGCTCTTTGTCGTCACAACTTTCGA
* * *
1681194 TGTTTCTCTTTGTCGTCACAACTTTTGG
1 TGTTGCTCTTTGTCGTCACAACTTTCGA
1681222 TGTTGCTCTTT
1 TGTTGCTCTTT
1681233 ATTACTTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.09, C:0.21, G:0.18, T:0.52
Consensus pattern (28 bp):
TGTTGCTCTTTGTCGTCACAACTTTCGA
Found at i:1694302 original size:20 final size:20
Alignment explanation
Indices: 1694277--1694314 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1694267 TTTGGTTAAC
1694277 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1694297 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1694315 AGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1696672 original size:44 final size:41
Alignment explanation
Indices: 1696610--1696692 Score: 105
Period size: 44 Copynumber: 2.0 Consensus size: 41
1696600 AAAATATGTC
*
1696610 TAAATAACAATTATTAATTTGT-TAACAAATAATAATAAATGA
1 TAAATAACAATAATTAATTT-TCTAACAAATAATAA-AAATGA
*
1696652 TAAATTAACAATAAATTAATTTTCTAATAAATAATAAAAAT
1 TAAA-TAACAAT-AATTAATTTTCTAACAAATAATAAAAAT
1696693 ATTATTAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
42 4 0.11
43 12 0.33
44 20 0.56
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (41 bp):
TAAATAACAATAATTAATTTTCTAACAAATAATAAAAATGA
Found at i:1702245 original size:18 final size:18
Alignment explanation
Indices: 1702219--1702253 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1702209 TTTATATCAA
1702219 TTTTCAAAATGTTTTGAT
1 TTTTCAAAATGTTTTGAT
* *
1702237 TTTTTAAAATTTTTTGA
1 TTTTCAAAATGTTTTGA
1702254 CCTAAATTTA
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:0.29, C:0.03, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTTCAAAATGTTTTGAT
Found at i:1705094 original size:31 final size:29
Alignment explanation
Indices: 1705056--1705115 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
1705046 TTTGACGAGC
* *
1705056 TTAACGAGCATGAGTTGAGCAACAATTTTTA
1 TTAACGAGCACGAGTCGAGC-AC-ATTTTTA
1705087 TTAACGAGCACGAGTCGAGCACATTTTTA
1 TTAACGAGCACGAGTCGAGCACATTTTTA
1705116 ACGAGCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 2 0.07
31 18 0.67
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (29 bp):
TTAACGAGCACGAGTCGAGCACATTTTTA
Found at i:1707923 original size:2 final size:2
Alignment explanation
Indices: 1707916--1707942 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1707906 CCATGGCAGT
1707916 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1707943 GACATGCGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1709006 original size:17 final size:17
Alignment explanation
Indices: 1708984--1709026 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
1708974 TAGTTATCTT
1708984 AAAAAATTGTTTCATTA
1 AAAAAATTGTTTCATTA
1709001 AAAAAATTGTTTCATTA
1 AAAAAATTGTTTCATTA
1709018 AAAAAATTG
1 AAAAAATTG
1709027 CTAATTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (17 bp):
AAAAAATTGTTTCATTA
Found at i:1712198 original size:11 final size:11
Alignment explanation
Indices: 1712184--1712209 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1712174 CAATTAGAAC
1712184 GCAACTGTAAT
1 GCAACTGTAAT
1712195 GCAACTGTAAT
1 GCAACTGTAAT
1712206 GCAA
1 GCAA
1712210 TTGGATTGGG
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:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (11 bp):
GCAACTGTAAT
Found at i:1713837 original size:3 final size:3
Alignment explanation
Indices: 1713829--1713893 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1713819 TAATTTTCTG
1713829 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1713877 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
1713894 TGTGCACTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1716450 original size:53 final size:53
Alignment explanation
Indices: 1716370--1716491 Score: 208
Period size: 53 Copynumber: 2.3 Consensus size: 53
1716360 AACGATATAA
* ** *
1716370 AATTTCAGGGTGGATATAATCAATAAAATAAGTAAATAATTGGAGAAAATTTG
1 AATTTCATGGTGGGCATAATCAATAAAATAAGTAAATAATTAGAGAAAATTTG
1716423 AATTTCATGGTGGGCATAATCAATAAAATAAGTAAATAATTAGAGAAAATTTG
1 AATTTCATGGTGGGCATAATCAATAAAATAAGTAAATAATTAGAGAAAATTTG
1716476 AATTTCATGGTGGGCA
1 AATTTCATGGTGGGCA
1716492 CATGCCCACC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (53 bp):
AATTTCATGGTGGGCATAATCAATAAAATAAGTAAATAATTAGAGAAAATTTG
Found at i:1717718 original size:19 final size:20
Alignment explanation
Indices: 1717684--1717721 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1717674 ATTAAAAATA
1717684 AAAATAAAAAAAAAACTTTG
1 AAAATAAAAAAAAAACTTTG
*
1717704 AAAAT-AAAGAAAAACTTT
1 AAAATAAAAAAAAAACTTT
1717722 TATAAAGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATAAAAAAAAAACTTTG
Found at i:1720824 original size:124 final size:124
Alignment explanation
Indices: 1720648--1720916 Score: 396
Period size: 124 Copynumber: 2.2 Consensus size: 124
1720638 TAATGTACTT
* *
1720648 TAGTGGCATTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGCACAAACGCC
1 TAGTGGCATTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGAAAAAACGCC
* *
1720713 GCTAATTACACATAT-TTTAGTGGTATTTTACATACAAACGCCGCTAATTACACGCACTA
66 GCTAATTACACAT-TCTTTAGTGGCATTTTACACACAAACGCCGCTAATTACACGCACTA
*
1720772 TAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGAAAAAACGCC
1 TAGTGGCATTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGAAAAAACGCC
** * * * *
1720837 GCTAATTACATGTTCTTTAGTGGCGTTTTATACACAAACGCCGCTAATTACACGTACTC
66 GCTAATTACACATTCTTTAGTGGCATTTTACACACAAACGCCGCTAATTACACGCACTA
* * *
1720896 TAGTTGCATTTCTATATAAAC
1 TAGTGGCATTTTTATACAAAC
1720917 ACCAAGAAAT
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
123 1 0.01
124 128 0.99
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (124 bp):
TAGTGGCATTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGAAAAAACGCC
GCTAATTACACATTCTTTAGTGGCATTTTACACACAAACGCCGCTAATTACACGCACTA
Found at i:1720862 original size:42 final size:41
Alignment explanation
Indices: 1720642--1721087 Score: 318
Period size: 42 Copynumber: 10.9 Consensus size: 41
1720632 GGAATATAAT
* * * **
1720642 GTACTTTAGTGGCATTTTTATACAAACGCCGCTAA--AGGTC
1 GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTA-CAC
1720682 GTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACAC
* * ** *
1720724 ATATTTTAGTGGTATTTTACATACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
* * * * **
1720766 GCACTATAGTGGCGTTTTTATACAAACGCCGCTAA--AGGTC
1 GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTA-CAC
* * *
1720806 GTACTTTAGTGGCGTTTTAAGAAAAAACGCCGCTAATTACAT
1 GTACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACAC
*
1720848 GTTCTTTAGTGGCGTTTTATACACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
* * * * * * *** *
1720890 GTACTCTAGTTGCATTTCT-ATATAAACACCAAGAAATACTA-
1 GTACTTTAGTGGCGTTT-TAACACAAACGCCGCTAATTAC-AC
* * * * **
1720931 -TACTTTAGTGGTGTTTTTATATAAACGCCGCTAA-TAGTC
1 GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACAC
** * *
1720970 GTACTTTAGTGGCGTTGCAAGCACAAATGCCACTAATTACAC
1 GTACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACAC
* * *
1721012 GTACTTTTGTGGCATTTTATGCACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
* *
1721054 GTACTTTAGTGGCATTTTTAA-A-AAACGCCACTAA
1 GTACTTTAGTGGC-GTTTTAACACAAACGCCGCTAA
1721088 AGGTTGTCTT
Statistics
Matches: 315, Mismatches: 73, Indels: 36
0.74 0.17 0.08
Matches are distributed among these distances:
39 4 0.01
40 86 0.27
41 68 0.22
42 147 0.47
43 10 0.03
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (41 bp):
GTACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACAC
Found at i:1720935 original size:124 final size:122
Alignment explanation
Indices: 1720642--1721028 Score: 325
Period size: 124 Copynumber: 3.1 Consensus size: 122
1720632 GGAATATAAT
* * * *** * * *
1720642 GTACTTTAGTGGCATTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGCACA
1 GTACTATAGTGGCATTTCTATACAAACACCAAGAAA-GTCATACTTTAGTGGCGTTTTAAGAAAA
** ** *
1720707 AACGCCGCTAATTACACATAT-TTTAGTGGTATTTTACATACAAACGCCGCTAATTACAC
65 AACGCCGCTAATTACATGT-TCTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
* * * * *** *
1720766 GCACTATAGTGGCGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGAAAA
1 GTACTATAGTGGCATTTCTATACAAACACCAAGAAA-GTCATACTTTAGTGGCGTTTTAAGAAAA
1720831 AACGCCGCTAATTACATGTTCTTTAGTGGCGTTTTATACACAAACGCCGCTAATTACAC
65 AACGCCGCTAATTACATGTTCTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACAC
* * * * * * *
1720890 GTACTCTAGTTGCATTTCTATATAAACACCAAGAAA-TACTATACTTTAGTGGTGTTTTTA-TAT
1 GTACTATAGTGGCATTTCTATACAAACACCAAGAAAGT-C-ATACTTTAGTGGCGTTTTAAGAAA
* * ** * *
1720953 AAACGCCGCTAA-TA-GTCGTACTTTAGTGGCGTTGCAAGCACAAATGCCACTAATTACAC
64 AAACGCCGCTAATTACAT-GTTCTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACAC
* *
1721012 GTACTTTTGTGGCATTT
1 GTACTATAGTGGCATTT
1721029 TATGCACAAA
Statistics
Matches: 223, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
121 2 0.01
122 52 0.23
123 15 0.07
124 154 0.69
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (122 bp):
GTACTATAGTGGCATTTCTATACAAACACCAAGAAAGTCATACTTTAGTGGCGTTTTAAGAAAAA
ACGCCGCTAATTACATGTTCTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACAC
Found at i:1720959 original size:164 final size:164
Alignment explanation
Indices: 1720772--1721070 Score: 447
Period size: 164 Copynumber: 1.8 Consensus size: 164
1720762 ACACGCACTA
**
1720772 TAGTGGCGTTTTTATACAAACGCCGCTAA-AGGTCGTACTTTAGTGGCGTTTTAAGAAAAAACGC
1 TAGTGGCGTTTTTATACAAACGCCGCTAATA-GTCGTACTTTAGTGGCGTTGCAAGAAAAAACGC
* * * * *
1720836 CGCTAATTACATGTTCTTTAGTGGCGTTTTATACACAAACGCCGCTAATTACACGTACTCTAGTT
65 CACTAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGCTAATTACACGTACTCTAGTG
1720901 GCATTTCTATATAAACACCAAGAAATACTATACTT
130 GCATTTCTATATAAACACCAAGAAATACTATACTT
* * * * *
1720936 TAGTGGTGTTTTTATATAAACGCCGCTAATAGTCGTACTTTAGTGGCGTTGCAAGCACAAATGCC
1 TAGTGGCGTTTTTATACAAACGCCGCTAATAGTCGTACTTTAGTGGCGTTGCAAGAAAAAACGCC
* * *
1721001 ACTAATTACACGTACTTTTGTGGCATTTTATGCACAAACGCCGCTAATTACACGTACTTTAGTGG
66 ACTAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGCTAATTACACGTACTCTAGTGG
1721066 CATTT
131 CATTT
1721071 TTAAAAAACG
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
164 118 0.99
165 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (164 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAATAGTCGTACTTTAGTGGCGTTGCAAGAAAAAACGCC
ACTAATTACACGTACTTTAGTGGCATTTTATACACAAACGCCGCTAATTACACGTACTCTAGTGG
CATTTCTATATAAACACCAAGAAATACTATACTT
Found at i:1722578 original size:27 final size:29
Alignment explanation
Indices: 1722512--1722578 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
1722502 TAACATTAGT
* *
1722512 TATAAAGGAGTTAACACTGGTACTTTCAAAA
1 TATAAAGGAGTTAACACTAGTA-TAT-AAAA
1722543 TATAAAGGAGTTAACACTAGT-TAT-AAA
1 TATAAAGGAGTTAACACTAGTATATAAAA
1722570 TATAAAGGA
1 TATAAAGGA
1722579 CTTCCATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 12 0.35
29 2 0.06
31 20 0.59
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.28
Consensus pattern (29 bp):
TATAAAGGAGTTAACACTAGTATATAAAA
Found at i:1725164 original size:21 final size:20
Alignment explanation
Indices: 1725123--1725165 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
1725113 TCATTAGTCT
1725123 ATTTATGTTTCTTAACATCA
1 ATTTATGTTTCTTAACATCA
*
1725143 ATTT-TGTTTTTTATACTATCA
1 ATTTATGTTTCTTA-AC-ATCA
1725164 AT
1 AT
1725166 ATTACTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTATGTTTCTTAACATCA
Found at i:1726340 original size:43 final size:43
Alignment explanation
Indices: 1726290--1726427 Score: 197
Period size: 43 Copynumber: 3.2 Consensus size: 43
1726280 ACGGTCATTA
* *
1726290 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCAACCTATT
* * *
1726333 GTGGCGTTTGTTCCAAAAACGCCGCTACAAATCTCAACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTATT
* *
1726376 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTATT
1726419 GCGGCGTTT
1 GCGGCGTTT
1726428 TTTGTTCACA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 20 0.24
43 64 0.76
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCAACCTATT
Found at i:1733309 original size:20 final size:20
Alignment explanation
Indices: 1733282--1733335 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1733272 CTTATTTAAT
* *
1733282 AGGTATCGATATCGAATGGGG
1 AGGTATCGATATC-AAAGGGA
*
1733303 A-GTATCGATAGCAAAGGGA
1 AGGTATCGATATCAAAGGGA
1733322 AGGTATCGATATCA
1 AGGTATCGATATCA
1733336 TTCAAAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 21 0.75
21 1 0.04
ACGTcount: A:0.35, C:0.11, G:0.31, T:0.22
Consensus pattern (20 bp):
AGGTATCGATATCAAAGGGA
Found at i:1739428 original size:20 final size:19
Alignment explanation
Indices: 1739384--1739428 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1739374 TTATTTAATA
* *
1739384 GGTATCGATACCAAAGGGG
1 GGTATCAATACCAAAGGGC
1739403 GAGTATCAATACCAAAGGGAC
1 G-GTATCAATACCAAAGGG-C
1739424 GGTAT
1 GGTAT
1739429 AGATACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.18
Consensus pattern (19 bp):
GGTATCAATACCAAAGGGC
Found at i:1739434 original size:20 final size:19
Alignment explanation
Indices: 1739384--1739434 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1739374 TTATTTAATA
* *
1739384 GGTATCGATACCAAAGGGG
1 GGTATAGATACCAAAGGGC
1739403 GAGTATCA-ATACCAAAGGGAC
1 G-GTAT-AGATACCAAAGGG-C
1739424 GGTATAGATAC
1 GGTATAGATAC
1739435 TATTGAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (19 bp):
GGTATAGATACCAAAGGGC
Found at i:1739510 original size:22 final size:22
Alignment explanation
Indices: 1739459--1739529 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 22
1739449 TACAAAACTG
*
1739459 GTATCGATACCATAG-A--ATA
1 GTATCGATACCATAGTATGGTA
* * *
1739478 GTGTCGGTACCATAGTGTGGTA
1 GTATCGATACCATAGTATGGTA
*
1739500 GTATCGATACCATGGTATGG--
1 GTATCGATACCATAGTATGGTA
1739520 GTATCGATAC
1 GTATCGATAC
1739530 TGAGAAGCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 13 0.32
20 10 0.24
22 18 0.44
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (22 bp):
GTATCGATACCATAGTATGGTA
Found at i:1740405 original size:54 final size:54
Alignment explanation
Indices: 1739854--1740390 Score: 729
Period size: 54 Copynumber: 9.9 Consensus size: 54
1739844 GTGTACAAAC
* *
1739854 CACGGAATTCATCATATGTTGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
1 CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
* *
1739908 CACGGAATTCATCCTAGGTGGATGAAAAATCGTTTCGGCACTAAGTGTGCATTT
1 CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
** *
1739962 CTTGGAATTCATCCTATTTGGATGAATAA-CTGTTTCGGCACTAAGTGTGCATTT
1 CACGGAATTCATCCTATGTGGATGAATAATC-GTTTCGGCACTAAGTGTGCATTT
** * *
1740016 CACATAATTCATCCTACGTGGATGAATAA-CAGTTTTGGCACTAAGTGTGCATTT
1 CACGGAATTCATCCTATGTGGATGAATAATC-GTTTCGGCACTAAGTGTGCATTT
* * *
1740070 CACGGAATTCATCCTAGGTGGATGAATAACCGTTTCGGCACTAAGTGTGCACTT
1 CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
* * * * *
1740124 CACGGAATTCATCTTATGTGGATGAATAATCGTTTCGGTATTAACTATGCATTT
1 CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
* * *
1740178 CA-GGAAATTCATCCTAGGTGGATGAATAACCGTTTCGGTACTAAGTGTGCATTT
1 CACGG-AATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
* * *
1740232 CACGGAATTCATCTTATGTGGATGAATAATTGTTTCGACACTAAGTGTGCATTT
1 CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
* * *
1740286 CACGGAATTCATCCTAAGTGGATGAATAATCGTTTTGGCACTAAGTGTTCATTT
1 CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
* * * * *
1740340 CACGGAGTTCATCCTATGCGGATGAATAATCATTTTGGCACTATGTGTGCA
1 CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCA
1740391 AACCACGAAA
Statistics
Matches: 425, Mismatches: 54, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
53 3 0.01
54 419 0.99
55 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
CACGGAATTCATCCTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
Found at i:1745160 original size:31 final size:31
Alignment explanation
Indices: 1745125--1745205 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 31
1745115 TATGCACCCG
1745125 ACCTGAACCCGAATTGAACCGAA-AATATGA
1 ACCTGAACCCGAATTGAACCGAATAATATGA
* * *
1745155 TACCTGAACCCGAAGTGCATCCGAATGATATGA
1 -ACCTGAACCCGAATTG-AACCGAATAATATGA
*
1745188 ACCAGAACCCGATATTGA
1 ACCTGAACCCGA-ATTGA
1745206 CCTGGTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
31 15 0.36
32 18 0.43
33 9 0.21
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (31 bp):
ACCTGAACCCGAATTGAACCGAATAATATGA
Found at i:1745319 original size:16 final size:16
Alignment explanation
Indices: 1745298--1745330 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1745288 TGATTTGATC
1745298 TGACATTTACCTGACT
1 TGACATTTACCTGACT
1745314 TGACATTTACCTGACT
1 TGACATTTACCTGACT
1745330 T
1 T
1745331 ATATTACCAT
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:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (16 bp):
TGACATTTACCTGACT
Found at i:1745440 original size:40 final size:40
Alignment explanation
Indices: 1745376--1745454 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 40
1745366 AATTGTGAGA
*
1745376 TTTTAAGTTTATAATAAATCATACTAATTA-ATATAATTAAT
1 TTTTAAATTTATAATAAA-CATACTAATTATA-ATAATTAAT
1745417 TTTTAAATGTTATAATAAA-ATACTAATTATAATAATTA
1 TTTTAAAT-TTATAATAAACATACTAATTATAATAATTA
1745455 TATTATCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
40 17 0.49
41 8 0.23
42 10 0.29
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (40 bp):
TTTTAAATTTATAATAAACATACTAATTATAATAATTAAT
Found at i:1746010 original size:17 final size:17
Alignment explanation
Indices: 1745988--1746035 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
1745978 TCCATATTAA
1745988 TTCATGTTGAATTGCAT
1 TTCATGTTGAATTGCAT
*
1746005 TTCATGTTAAATTGCAT
1 TTCATGTTGAATTGCAT
*
1746022 TTCATGTTGCATTG
1 TTCATGTTGAATTG
1746036 TATGTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (17 bp):
TTCATGTTGAATTGCAT
Found at i:1746679 original size:30 final size:30
Alignment explanation
Indices: 1746618--1746680 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1746608 CTACGAATTT
* *
1746618 TATAATTTAATATATATAATTCTATATTTA
1 TATAATTTAATACATATAATTCTATACTTA
* *
1746648 TATACTTTAATACAT-TACATTTTATACTTA
1 TATAATTTAATACATATA-ATTCTATACTTA
1746678 TAT
1 TAT
1746681 TAAATAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (30 bp):
TATAATTTAATACATATAATTCTATACTTA
Found at i:1746727 original size:57 final size:57
Alignment explanation
Indices: 1746657--1746841 Score: 187
Period size: 57 Copynumber: 3.2 Consensus size: 57
1746647 ATATACTTTA
* * * *
1746657 ATACATTACATTTTATACTTATATTAAATAGTTTAATACTTTGTATTATACACTTAT
1 ATACTTTATATTTTATACTTATATTATATAGTTTAATACTTTGTAGTATACACTTAT
* * * *
1746714 ATACTTTATATTTTATATTTAATATTTATATACTTTAATACTTTATGTGGTATAC-TTTA-
1 ATACTTTATATTTTATACTT-ATA-TTATATAGTTTAATAC-TT-TGTAGTATACACTTAT
* * * *
1746773 ATACTATATATTTAATACTTATATTATATAGTTTAATACTTTATAGTATATACTT-T
1 ATACTTTATATTTTATACTTATATTATATAGTTTAATACTTTGTAGTATACACTTAT
1746829 AATACTTATATAT
1 -ATACTT-TATAT
1746842 ACTATATAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
55 7 0.07
56 4 0.04
57 37 0.36
58 11 0.11
59 31 0.30
60 5 0.05
61 8 0.08
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (57 bp):
ATACTTTATATTTTATACTTATATTATATAGTTTAATACTTTGTAGTATACACTTAT
Found at i:1746790 original size:22 final size:22
Alignment explanation
Indices: 1746735--1746854 Score: 104
Period size: 22 Copynumber: 5.3 Consensus size: 22
1746725 TTTATATTTA
*
1746735 ATATTTATATACTTTAATACTTT
1 ATATTTA-ATACTTTAATACTAT
* *
1746758 ATGTGGT-ATACTTTAATACTAT
1 ATAT-TTAATACTTTAATACTAT
*
1746780 ATATTTAATAC-TT-ATATTAT
1 ATATTTAATACTTTAATACTAT
*
1746800 ATAGTTTAATACTTT-ATAGTAT
1 ATA-TTTAATACTTTAATACTAT
1746822 ATACTTTAATACTTATATATACTAT
1 ATA-TTTAATACTT-TA-ATACTAT
1746847 ATAATTTA
1 AT-ATTTA
1746855 TATATATACT
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
20 9 0.11
21 11 0.14
22 42 0.52
23 4 0.05
24 1 0.01
25 12 0.15
26 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (22 bp):
ATATTTAATACTTTAATACTAT
Found at i:1746795 original size:13 final size:14
Alignment explanation
Indices: 1746764--1746841 Score: 54
Period size: 14 Copynumber: 5.4 Consensus size: 14
1746754 CTTTATGTGG
1746764 TATACTTTAATACTA
1 TATA-TTTAATACTA
1746779 TATATTTAATACT-
1 TATATTTAATACTA
* *
1746792 TATA-TTATATAGTT
1 TATATTTA-ATACTA
*
1746806 TAATACTTT-ATAGTA
1 T-ATA-TTTAATACTA
1746821 TATACTTTAATACTTA
1 TATA-TTTAATAC-TA
1746837 TATAT
1 TATAT
1746842 ACTATATAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
12 3 0.06
13 8 0.15
14 17 0.32
15 17 0.32
16 6 0.11
17 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (14 bp):
TATATTTAATACTA
Found at i:1746840 original size:2 final size:2
Alignment explanation
Indices: 1746835--1747935 Score: 170
Period size: 2 Copynumber: 553.0 Consensus size: 2
1746825 CTTTAATACT
* * *
1746835 TA TA TA TA CTA TA TA -A TT TA TA TA TA TA CT- TA TG T- TG TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
1746876 GTG TA TA TA CT- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** * * *
1746919 TA CG T- TA TA GTT TA TA TA TA TA TA TA TA CT- TA TA T- TT TT TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
1746960 TG TA TA TA TA CT- TA TA TA CTT TA TA T- TA TA TA CTT TA -A TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
1747000 CTT TA TA T- TA TA TA CTA -A AA CTT TA TA TA TA TA TA CTC TT TA
1 -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* *
1747042 TA GTT TA TA TA TA TA CT- TA TA TA CTT TA TA T- TA TA TA CT- TA
1 TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
1747083 TA CTT TA TA CA TA TA TA TA CT- TG TA TA CTA TA TA GTT TA TA TA
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA
* * * * *
1747126 TT TA TA TA TT TA TA TA CT- TA TA TA CTT TA GTC TT TA TA -A T-
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA -TA TA TA TA TA TA
* ** *
1747166 TA TA CTT TA TA TA TA TA TA TA TA -A TA TA CG TA TA CTT TA TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
1747208 TA T- TA TA TA TG TA TA TA CA -A TT TA TA CTA -A AA CTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * ** * * * * *
1747249 TA TA TA TA TA TA TA TA TA AA CA CG CA CA CTT TG TA GTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
1747293 TA TA CT- TA TA TT TA -A TA CT- TA TA TA T- TT TA TA T- TA TA AA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
1747332 CT- TG TA TA CTT TA TA T- TA TA TGC T- TA TA TA CTT TA GTC TT TA
1 -TA TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA -TA TA -TA TA TA
*
1747374 TA -A T- TA TA CTT TA TA T- TA TA TA TA -A TA TA TA -A TA TA CT-
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
1747412 TA TA CTT TA TA T- TA T- TA TA TA TG TA TA TA TA CTT TA TA TA CT-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
* * * *
1747454 TA TA TA GTT TA T- TC TT TA TA -A T- TA TA CTT TA TA TA TA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
1747494 TA TA TA CT- TA TA CTT TA TA T- TA T- TA TA TA TG TA TA TA TGA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * * *
1747534 TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TT TG TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
1747576 TA TA TA TA TA CT- TA TA TA CTT TA TA TT TA AA CTA TA TA -A TT
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA
* *
1747617 TA TA CA TA GTA TA TA TA -A TT TA TA -A T- TA TA TA T- TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1747656 TA AA TA TA -A GT- TG TA TA TA TT TA AA TA TA -A T- TCA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* * * *
1747696 -A TT TA TA TA TA AA CTA TA TA -A TT TA TA T- TA -A TA AA CTA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
1747736 TA -A TT TA TA TA TA GT- TCA -A TA GT- TCA TA TA TA AA CTC TA TT
1 TA TA TA TA TA TA TA -TA T-A TA TA -TA T-A TA TA TA TA -TA TA TA
* ** * *
1747777 TA TA CA -A GG TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1747818 TA TA CA TA CA TA CA TA TA TA TA GTA TA TA -A TA -A TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
1747859 TA AA CTA TA TA GTT TA TA TA TA TA -A TA TA TA TA TA TA TA TA CTT
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
1747903 TA TA TA TA CA CTA TA TA GTT TA TA TA TA T- TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
1747936 ATTGTTGAAC
Statistics
Matches: 786, Mismatches: 172, Indels: 282
0.63 0.14 0.23
Matches are distributed among these distances:
1 73 0.09
2 645 0.82
3 68 0.09
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1746904 original size:22 final size:22
Alignment explanation
Indices: 1746835--1747931 Score: 248
Period size: 22 Copynumber: 51.2 Consensus size: 22
1746825 CTTTAATACT
*
1746835 TATATATAC-TATATA-ATTTA
1 TATATATACTTATATATATATA
* *
1746855 TATATATACTTATGT-TGTATA
1 TATATATACTTATATATATATA
*
1746876 GTGTATATACTTATATATATATA
1 -TATATATACTTATATATATATA
1746899 TATATATA--TATATATATATA
1 TATATATACTTATATATATATA
*
1746919 TACGT-TATA-GT-T-TATATATA
1 TA--TATATACTTATATATATATA
* * *
1746939 TATATATACTTATATTTTTTATG
1 TATATATACTTATA-TATATATA
*
1746962 TATATATACTTATATACTTTATA
1 TATATATACTTATATA-TATATA
*
1746985 T-TATATACTT-TA-ATACTTTA
1 TATATATACTTATATATA-TATA
* *
1747005 TATTATATAC-TA-AAACTTTATA
1 TA-TATATACTTATATA-TATATA
*
1747027 TATATATACTCT-T-TATAGTTTA
1 TATATATACT-TATATATA-TATA
*
1747049 TATATATACTTATATACTTTATA
1 TATATATACTTATATA-TATATA
* *
1747072 T-TATATACTTATACTTTATACA
1 TATATATACTTATA-TATATATA
*
1747094 TATATATACTTGTATACTATATA
1 TATATATACTTATATA-TATATA
* * *
1747117 GTTTATATATTTATATATTTATA
1 -TATATATACTTATATATATATA
* *
1747140 TACTTATATACTT-TAGTCTTTATA
1 TA--TATATACTTATA-TATATATA
1747164 -AT-TATACTTTATATATATATA
1 TATATATAC-TTATATATATATA
* *
1747185 TATAATATACGTATACTTTATAT-
1 TAT-ATATACTTATA-TATATATA
* *
1747208 TAT-TATA--TATGTATATACA
1 TATATATACTTATATATATATA
* * * *
1747227 -ATTTATACTAAAACTTTATATA
1 TATATATACTTATA-TATATATA
*
1747249 TATATATA--TATATATATAAA
1 TATATATACTTATATATATATA
* *** * * *
1747269 CACGCACACTT-TGTAGTTTATA
1 TATATATACTTATATA-TATATA
*
1747291 T--ATATACTTATATTTA-ATA
1 TATATATACTTATATATATATA
*
1747310 CT-TATATA-TTTTATAT-TATA
1 -TATATATACTTATATATATATA
* *
1747330 AACTTGTATACTT-TATAT-TATA
1 TA--TATATACTTATATATATATA
* * *
1747352 TGCTTATATACTT-TAGTCTTTATA
1 T--ATATATACTTATA-TATATATA
1747376 -AT-TATACTT-TATAT-TATA
1 TATATATACTTATATATATATA
1747394 TATA-ATA--TATA-ATATACTTA
1 TATATATACTTATATATATA--TA
* *
1747414 TACTTTATA-TTAT-TATATATG
1 TA-TATATACTTATATATATATA
1747435 TATATATACTT-TATATACTTATA
1 TATATATACTTATATATA--TATA
* *
1747458 TAGTTTATTCTT-TATA-AT-TA
1 TA-TATATACTTATATATATATA
*
1747478 TACTTTATA--TATATA-ATATA
1 TA-TATATACTTATATATATATA
1747498 TACT-TATACTTTATATTATTATATA
1 TA-TATATAC-TTATA-TA-TATATA
* * *
1747523 TGTATATA-TGATTTATATATA
1 TATATATACTTATATATATATA
1747544 TATATATA--TATATATATATA
1 TATATATACTTATATATATATA
* * *
1747564 TAATTTGTAGTT-TATATATATA
1 T-ATATATACTTATATATATATA
1747586 CT-TATATACTT-TATAT-T-TA
1 -TATATATACTTATATATATATA
* * *
1747605 AACTATATAATT-TATACATAGTA
1 TA-TATATACTTATATATATA-TA
*
1747628 TATATA-ATTTATA-AT-TATA
1 TATATATACTTATATATATATA
*
1747647 TAT-TATA--TATAAATATA-A
1 TATATATACTTATATATATATA
* * *
1747665 GTTGTATATATTTAAATATA-AT-
1 --TATATATACTTATATATATATA
* *
1747687 TCATATATAATT-TATATATAAA
1 T-ATATATACTTATATATATATA
*
1747709 CTATATA-ATTTATAT-TA-ATA
1 -TATATATACTTATATATATATA
* *
1747729 AACTATATAATT-TATATATAGT-
1 TA-TATATACTTATATATATA-TA
* * * *
1747751 T-CA-ATAGTTCATATATAAACTC
1 TATATATACTT-ATATATATA-TA
* **
1747773 TATTTATAC--A-AGGTATATA
1 TATATATACTTATATATATATA
* *
1747792 TAGTTTATACATA-ATATATATA
1 TA-TATATACTTATATATATATA
* *
1747814 TATATATACATACATACATATATA
1 TATATATAC-T-TATATATATATA
* * *
1747838 TAGTATATAATAATATAAATATA
1 TA-TATATACTTATATATATATA
* *
1747861 AACTATATAGTT-TATATATATA
1 TA-TATATACTTATATATATATA
*
1747883 -ATATATA--TATATATATACTT
1 TATATATACTTATATATATA-TA
* *
1747903 TATATATACACTATATAGTTTATA
1 TATATATAC-TTATATA-TATATA
1747927 TATAT
1 TATAT
1747932 TATAATTGTT
Statistics
Matches: 802, Mismatches: 143, Indels: 260
0.67 0.12 0.22
Matches are distributed among these distances:
17 7 0.01
18 23 0.03
19 59 0.07
20 165 0.21
21 144 0.18
22 173 0.22
23 130 0.16
24 82 0.10
25 19 0.02
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (22 bp):
TATATATACTTATATATATATA
Found at i:1747031 original size:65 final size:65
Alignment explanation
Indices: 1746835--1747516 Score: 241
Period size: 65 Copynumber: 10.8 Consensus size: 65
1746825 CTTTAATACT
* * * *
1746835 TATATATAC-TATATAATTTATA-TATATACTTATGT--TGTATAGTGTATATACTT--A-TATA
1 TATATATACTTATATACTTTATATTATATACTTATATACTTTATA-T-TATATACTTAAACTTTA
1746893 TA
64 TA
* * *
1746895 TATATATA--TATATA-TATATA-TATATACGTTATAGTTTA-TATATATATATATACTTATATT
1 TATATATACTTATATACTTTATATTATATAC-TTATA---TACTTTATAT-TATATACTTA-A-A
* *
1746955 TTTTATG
59 CTTTATA
*
1746962 TATATATACTTATATACTTTATATTATATACTT-TAATACTTTATATTATATACTAAAACTTTAT
1 TATATATACTTATATACTTTATATTATATACTTAT-ATACTTTATATTATATACTTAAACTTTAT
1747026 A
65 A
* * *
1747027 TATATATACTCTTTATAGTTTATA-TATATACTTATATACTTTATATTATATACTTATACTTTAT
1 TATATATACT-TATATACTTTATATTATATACTTATATACTTTATATTATATACTTAAACTTTAT
1747091 ACA
65 --A
* * * * **
1747094 TATATATACTTGTATACTATATAGTTTATATATTTATATATTTATATACTTATATACTTTAGTCT
1 TATATATACTTATATACTTTATA--TTATATACTTATATACTT-TATA-TTATATAC-TTAAACT
1747159 TTATA
61 TTATA
* * *
1747164 -AT-TATACTTTATATA-TATATATATAATATAC--GTATACTTTATATTAT-TA--TATA-TGT
1 TATATATAC-TTATATACT-T-TATATTATATACTTATATACTTTATATTATATACTTAAACT-T
1747220 ATATA
62 -TATA
* * * * * * ** * *
1747225 CAATTTATAC-TA-AAACTTTATA-TATATA--TATATA-TATATA-TAAACACGCACACTTTGT
1 -TATATATACTTATATACTTTATATTATATACTTATATACTTTATATTATATACTTAAACTTTAT
1747283 A
65 A
* * *
1747284 GT-T-TATA--TATATAC-TTATATT-TAATACTTATATATTTTATATTATAAACTTGTATACTT
1 -TATATATACTTATATACTTTATATTAT-ATACTTATATACTTTATATTATATAC-T-TAAACTT
1747343 TATA
62 TATA
* * *
1747347 T-TATATGCTTATATACTTTAGTCTT-TATA-AT-TATACTTTATATTATATA--T-AA---TAT
1 TATATATACTTATATACTTTA-TATTATATACTTATATACTTTATATTATATACTTAAACTTTAT
1747402 A
65 A
* *
1747403 TA-ATATAC-T-TATACTTTATATTATTATATATGTATATATACTTTATATACTTATATAGTTTA
1 TATATATACTTATATAC-TT-TA-TATTATATA-CT-TATATAC-TT-TATA-TTATATA-CTTA
**
1747465 TTCTTTATA
57 AACTTTATA
* *
1747474 -AT-TATACTT-TATA-TATATAATATATAC-T-TATACTTTATATTAT
1 TATATATACTTATATACTTTATATTATATACTTATATACTTTATATTAT
1747517 TATATATGTA
Statistics
Matches: 482, Mismatches: 66, Indels: 148
0.69 0.09 0.21
Matches are distributed among these distances:
54 5 0.01
55 3 0.01
56 23 0.05
57 17 0.04
58 19 0.04
59 30 0.06
60 29 0.06
61 22 0.05
62 20 0.04
63 29 0.06
64 33 0.07
65 63 0.13
66 35 0.07
67 47 0.10
68 20 0.04
69 31 0.06
70 23 0.05
71 24 0.05
72 9 0.02
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (65 bp):
TATATATACTTATATACTTTATATTATATACTTATATACTTTATATTATATACTTAAACTTTATA
Found at i:1747169 original size:85 final size:83
Alignment explanation
Indices: 1747051--1747225 Score: 228
Period size: 85 Copynumber: 2.1 Consensus size: 83
1747041 ATAGTTTATA
* **
1747051 TATATACTTATATACTTTATATTATATACTTATACTTTATACATATATATACTTGTATACTATAT
1 TATATACTTATATACTTTATATTATATAATTATACTTTATACATATATATA-TAATATAC-ATAT
* *
1747116 AGTTTATA-TATTTATATATT
64 ACTTTATATTA-TTATATATG
* * *
1747136 TATATACTTATATACTTTAGTCTT-TATAATTATACTTTATATATATATATATAATATACGTATA
1 TATATACTTATATACTTTA-TATTATATAATTATACTTTATACATATATATATAATATACATATA
1747200 CTTTATATTATTATATATG
65 CTTTATATTATTATATATG
1747219 TATATAC
1 TATATAC
1747226 AATTTATACT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
83 25 0.31
84 8 0.10
85 44 0.55
86 3 0.04
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (83 bp):
TATATACTTATATACTTTATATTATATAATTATACTTTATACATATATATATAATATACATATAC
TTTATATTATTATATATG
Found at i:1747265 original size:297 final size:295
Alignment explanation
Indices: 1746962--1747614 Score: 684
Period size: 306 Copynumber: 2.2 Consensus size: 295
1746952 ATTTTTTATG
1746962 TATATATACTTATATACTTTATATTATATACTTTAATACTTTATA-TTATATAC-TA-AAACTTT
1 TATATATACTT-TATACTTTATATTATATACTTTAATACTTTATATTTA-ATACTTATAAACTTT
* * * *
1747024 ATATATATATACTCTTTATAGTTTATA-TATATACTTATATACTTTA-TATTA-TATAC-TTATA
64 ATAT-TATAAACT-TGTATACTTTATATTATATACTTATATACTTTATTATAATTATACTTTATA
1747085 CT-T-TAT-ACATAT-ATATACTTGTATACTATATAGT-TTATATAT-T-TATATA-TTTATATA
127 CTATATATAACATATAATATAC-T-TATACTATATAGTATTATATATGTATATATACTTTATATA
1747142 CTTATATACTTTAGTCTTTATAATTATACTTTATATATATATATATAATATACGTATACTTTATA
190 CTTATATACTTTAGTCTTTATAATTATAC-TT-TATATATATA-AT-ATATACGTATACTTTATA
1747207 TTATTATATATGTATATACAATTTATACTAAAACTTTATATATATATATATA
251 TTATTATATATGTATATACAATTTATA-T---A---TATATATATATATATA
*** * * * * *
1747259 TATATATAAACACGCACACTTTGTAGTT-TATA-TAT-ATAC-TTATATTTAATACTTATATATT
1 TATATAT--AC-TTTATACTTTATA-TTATATACTTTAATACTTTATATTTAATACTTATAAACT
*
1747320 TTATATTATAAACTTGTATACTTTATATTATATGCTTATATACTTTAGTCTTTATAATTATACTT
62 TTATATTATAAACTTGTATACTTTATATTATATACTTATATACTTTA----TTATAATTATACTT
* * * *
1747385 TATATTATATATAATATATAATATACTTATACTTTATATTATTATATATGTATATATACTTTATA
123 TATACTATATATAACATATAATATACTTATACTATATAGTATTATATATGTATATATACTTTATA
* * *
1747450 TACTTATATAGTTTATTCTTTATAATTATACTTTATATATATAATATATACTTATACTTTATATT
188 TACTTATATACTTTAGTCTTTATAATTATACTTTATATATATAATATATACGTATACTTTATATT
**
1747515 ATTATATATGTATATATGATTTATATATATATATATATATATA
253 ATTATATATGTATATACAATTTATATATATATATATATATATA
* * *
1747558 TATATATAATTTGTAGTTTATA-TATATAC-TTATATACTTTATATTTAA-ACTATATAA
1 TATATATACTTTATACTTTATATTATATACTTTA-ATACTTTATATTTAATACT-TATAA
1747615 TTTATACATA
Statistics
Matches: 295, Mismatches: 32, Indels: 57
0.77 0.08 0.15
Matches are distributed among these distances:
294 1 0.00
295 5 0.02
296 26 0.09
297 49 0.17
298 25 0.08
299 37 0.13
300 2 0.01
302 5 0.02
303 5 0.02
304 6 0.02
305 2 0.01
306 56 0.19
307 16 0.05
308 17 0.06
309 8 0.03
310 35 0.12
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.51
Consensus pattern (295 bp):
TATATATACTTTATACTTTATATTATATACTTTAATACTTTATATTTAATACTTATAAACTTTAT
ATTATAAACTTGTATACTTTATATTATATACTTATATACTTTATTATAATTATACTTTATACTAT
ATATAACATATAATATACTTATACTATATAGTATTATATATGTATATATACTTTATATACTTATA
TACTTTAGTCTTTATAATTATACTTTATATATATAATATATACGTATACTTTATATTATTATATA
TGTATATACAATTTATATATATATATATATATATA
Found at i:1747557 original size:98 final size:98
Alignment explanation
Indices: 1747348--1747531 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 98
1747338 TACTTTATAT
*
1747348 TATATGCTTATATACTTTAGTCTTTATAATTATACTTTATATTATATATAATATATAATATACTT
1 TATATACTTATATACTTTAGTCTTTATAATTATACTTTATATTATATATAATATATAATATACTT
*
1747413 ATACTTTATATTATTATATATGTATATATACTT
66 ATACTTTATATTATTATATATGTATATATACTA
* *
1747446 TATATACTTATATAGTTTATTCTTTATAATTATAC----T-TTATATAT-ATA-AT-ATATACTT
1 TATATACTTATATACTTTAGTCTTTATAATTATACTTTATATTATATATAATATATAATATACTT
1747503 ATACTTTATATTATTATATATGTATATAT
66 ATACTTTATATTATTATATATGTATATAT
1747532 GATTTATATA
Statistics
Matches: 83, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
90 37 0.45
91 2 0.02
92 3 0.04
93 8 0.10
94 1 0.01
98 32 0.39
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.54
Consensus pattern (98 bp):
TATATACTTATATACTTTAGTCTTTATAATTATACTTTATATTATATATAATATATAATATACTT
ATACTTTATATTATTATATATGTATATATACTA
Found at i:1747600 original size:88 final size:89
Alignment explanation
Indices: 1747384--1747602 Score: 254
Period size: 90 Copynumber: 2.4 Consensus size: 89
1747374 TAATTATACT
1747384 TTAT-ATTATATATAATATATAATATACTTATACTTTATATTATTATATATGTATATATACTTTA
1 TTATAATT-TATAT-ATATAT-ATATACTTATACTTTATATTATTATATATGTATATATACTTTA
* * *
1747448 TATACTTATATAGTTTATTCTTTATAA
63 TATACTTATATAGTATATTATATATAA
*
1747475 TTATACTTTATATATATAATATATACTTATACTTTATATTATTATATATGTATATATGA-TTTAT
1 TTATAATTTATATATAT-ATATATACTTATACTTTATATTATTATATATGTATATAT-ACTTTAT
1747539 ATA--TATATA-TATA-TATATAT-A
64 ATACTTATATAGTATATTATATATAA
* *
1747560 TATATAATTTGTAGTTTATATATATACTTATATACTTTATATT
1 T-TATAATTTATA-TATATATATATAC-T-TATACTTTATATT
1747603 TAAACTATAT
Statistics
Matches: 114, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
85 2 0.02
86 22 0.19
87 8 0.07
88 19 0.17
90 49 0.43
91 12 0.11
92 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.54
Consensus pattern (89 bp):
TTATAATTTATATATATATATATACTTATACTTTATATTATTATATATGTATATATACTTTATAT
ACTTATATAGTATATTATATATAA
Found at i:1747663 original size:141 final size:143
Alignment explanation
Indices: 1747435--1747707 Score: 321
Period size: 141 Copynumber: 1.9 Consensus size: 143
1747425 ATTATATATG
** * *
1747435 TATATATACTTTATATACTTATATAGTTTATTCTTTATAATTATACTTTATATATATAATATATA
1 TATATATACTTTATATACTTATATAGTTTAAACTATATAATTATACTATATATATATAATATATA
* * * *
1747500 CTTATACTTTATATTATTATATATG-TATATATGATTTATATAT-ATAT-ATATATATATATATA
66 ATTATACTTTATATTATAATATAAGTTATATAT-ATTTAAATATAAT-TCATATATA-ATATATA
1747562 TATAATTTGTAGTTTA
128 TATAATTTGTAGTTTA
*
1747578 TATATATAC-TTATATACTT-TATA-TTTAAACTATATAATTTATAC-ATAGTATATATAATTTA
1 TATATATACTTTATATACTTATATAGTTTAAACTATATAA-TTATACTATA-TATATATAATATA
* *
1747639 TAATTATA-TATTATA-TATAAATATAAGTTGTATATATTTAAATATAATTCATATATAATTTAT
64 TAATTATACT-TTATATTAT-AATATAAGTTATATATATTTAAATATAATTCATATATAATATAT
1747702 ATATAA
127 ATATAA
1747708 ACTATATAAT
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
140 17 0.15
141 61 0.54
142 25 0.22
143 9 0.08
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (143 bp):
TATATATACTTTATATACTTATATAGTTTAAACTATATAATTATACTATATATATATAATATATA
ATTATACTTTATATTATAATATAAGTTATATATATTTAAATATAATTCATATATAATATATATAT
AATTTGTAGTTTA
Found at i:1747680 original size:21 final size:21
Alignment explanation
Indices: 1747637--1747707 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 21
1747627 ATATATAATT
1747637 TATAATT-ATATATTATATATAAA
1 TATAATTCATATA-TAT-T-TAAA
*
1747660 TATAAGTT-GTATATATTTAAA
1 TATAA-TTCATATATATTTAAA
*
1747681 TATAATTCATATATAATTTATA
1 TATAATTCATATAT-ATTTAAA
1747703 TATAA
1 TATAA
1747708 ACTATATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.05
21 14 0.33
22 12 0.29
23 8 0.19
24 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (21 bp):
TATAATTCATATATATTTAAA
Found at i:1747709 original size:102 final size:100
Alignment explanation
Indices: 1747516--1747722 Score: 258
Period size: 102 Copynumber: 2.0 Consensus size: 100
1747506 CTTTATATTA
* * * * * *
1747516 TTATATATGTATATATGATTTATATATATATATATATATATATATATATAATTTGTAGTTTATAT
1 TTATACATGTATATATAATTTATATATATATATATATATATATAAATATAATTTATAATTTAAAT
* * *
1747581 ATATACTTATATACTTTATATTTAAACTATATAAT
66 ATATACATATATAATTTATATATAAACTATATAAT
1747616 TTATACATAGTATATATAATTTATA-AT-TATATAT-TATATATAAATATAAGTTGTATATATTT
1 TTATACAT-GTATATATAATTTATATATATATATATATATATATAAATATAA-TT-TATA-ATTT
*
1747678 AAATATAATTCATATATAATTTATATATAAACTATATAAT
62 AAATAT-ATACATATATAATTTATATATAAACTATATAAT
1747718 TTATA
1 TTATA
1747723 TTAATAAACT
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
98 14 0.15
99 9 0.10
100 12 0.13
101 23 0.25
102 34 0.37
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (100 bp):
TTATACATGTATATATAATTTATATATATATATATATATATATAAATATAATTTATAATTTAAAT
ATATACATATATAATTTATATATAAACTATATAAT
Found at i:1747906 original size:11 final size:10
Alignment explanation
Indices: 1747864--1747932 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 10
1747854 AAATATAAAC
1747864 TATATAGTTTA
1 TATATA-TTTA
*
1747875 TATATA-TAA
1 TATATATTTA
*
1747884 TATATATATA
1 TATATATTTA
1747894 TATATACTTTA
1 TATATA-TTTA
*
1747905 TATATA--CA
1 TATATATTTA
1747913 CTATATAGTTTA
1 -TATATA-TTTA
1747925 TATATATT
1 TATATATT
1747933 ATAATTGTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
8 1 0.02
9 14 0.30
10 9 0.20
11 21 0.46
12 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (10 bp):
TATATATTTA
Found at i:1747918 original size:39 final size:36
Alignment explanation
Indices: 1747797--1747935 Score: 108
Period size: 37 Copynumber: 3.9 Consensus size: 36
1747787 ATATATAGTT
* *
1747797 TATACATA-ATAT-ATATATATATATACATACATACA
1 TATACATATATATAATATATATATATATATAC-TATA
* * *
1747832 TATATATAGTATATAATA-ATATAAATATAAACTATA
1 TATACATA-TATATAATATATATATATATATACTATA
**
1747868 TAGTTTATATATATAATATATATATATATATACTTTATA
1 TA-TACATATATATAATATATATATATATATAC--TATA
* * *
1747907 TATACA-CTATATAGTTTATATATAT-TATA
1 TATACATATATATAATATATATATATATATA
1747936 ATTGTTGAAC
Statistics
Matches: 84, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
35 7 0.08
36 18 0.21
37 48 0.57
38 5 0.06
39 6 0.07
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (36 bp):
TATACATATATATAATATATATATATATATACTATA
Found at i:1747931 original size:13 final size:13
Alignment explanation
Indices: 1747483--1747910 Score: 109
Period size: 13 Copynumber: 31.8 Consensus size: 13
1747473 AATTATACTT
1747483 TATATATATAATA
1 TATATATATAATA
* *
1747496 TATACT-TATACTT
1 TATA-TATATAATA
*
1747509 TATAT-TATTATA
1 TATATATATAATA
*
1747521 TATGTATAT-ATGA
1 TATATATATAAT-A
*
1747534 TTTATATATATATA
1 TATATATATA-ATA
1747548 TATATATATATATA
1 TATATATATA-ATA
* * * *
1747562 TATAATTTGTAGTT
1 TAT-ATATATAATA
*
1747576 TATATATATACT-
1 TATATATATAATA
* *
1747588 TATATACTTTATATT
1 TATATA-TATA-ATA
* *
1747603 TAAACTATATAATT
1 TATA-TATATAATA
*
1747617 TATACATAGT-ATA
1 TATATATA-TAATA
*
1747630 TATAATTTATAAT-
1 TAT-ATATATAATA
1747643 TATATAT-T-ATA
1 TATATATATAATA
* *
1747654 TATAAATATAAGTTG
1 TATATATATAA--TA
*
1747669 TATATATTTAAATA
1 TATATATAT-AATA
*
1747683 TAATTCATATATAATT
1 T-A-T-ATATATAATA
1747699 TATATATA-AACTA
1 TATATATATAA-TA
* *
1747712 TATAATTTATATTAA
1 TAT-ATATATAAT-A
* *
1747727 TAAACTATATAATT
1 TATA-TATATAATA
1747741 TATATATAGTTCAATA
1 TATATATA--T-AATA
1747757 GT-TCATATATAA-A
1 -TAT-ATATATAATA
* *
1747770 CTCTATTTATACA-A
1 -TATATATATA-ATA
** *
1747784 GGTATATATAGT-
1 TATATATATAATA
*
1747796 T-TATACATAATA
1 TATATATATAATA
1747808 TATATATAT-ATA
1 TATATATATAATA
* *
1747820 TACATACATACATA
1 TATATATATA-ATA
1747834 TATATAGTAT-ATA
1 TATATA-TATAATA
1747847 -ATA-ATATAAATA
1 TATATATAT-AATA
* * *
1747859 TAAACTATATAGTT
1 TATA-TATATAATA
1747873 TATATATATAATA
1 TATATATATAATA
1747886 TATATATATATATA
1 TATATATATA-ATA
*
1747900 CTTTATATATA
1 -TATATATATA
1747911 CACTATATAG
Statistics
Matches: 305, Mismatches: 63, Indels: 92
0.66 0.14 0.20
Matches are distributed among these distances:
10 5 0.02
11 16 0.05
12 40 0.13
13 102 0.33
14 68 0.22
15 50 0.16
16 13 0.04
17 11 0.04
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (13 bp):
TATATATATAATA
Found at i:1757141 original size:74 final size:74
Alignment explanation
Indices: 1757045--1757475 Score: 562
Period size: 74 Copynumber: 5.9 Consensus size: 74
1757035 GCAAAGATAA
* * * * *
1757045 AAAAATTTATCTCACTCGAGATAATTTTTCTTAAAATAAACTTCATATCGCTTGAGACAGTTTTC
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
1757110 ACTCGAAAC
66 ACTCGAAAC
* * * *
1757119 AAAATTTTATCTCATTCAAGATAGTTTTTCTTAAAACGAACTTCGTCTCGCTTTAGACAGTTTTC
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
*
1757184 ACTAGAAAC
66 ACTCGAAAC
* *
1757193 AAAACTTTATCTCACTCGAGATAGCTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
1757258 ACTCGAAAC
66 ACTCGAAAC
** * *
1757267 AAAATTTTATCTTTCTTGAGATTGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
1757332 ACTCGAAAC
66 ACTCGAAAC
* * * * * * * *
1757341 CAAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTCTCG---AAGGCAATTTTT
1 AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
1757403 ACTCGAAAC
66 ACTCGAAAC
* * * * * *
1757412 AAGAATTTTATCTCACTCGAGATTGTATTTCTTAAAACAAATTTCATCTCGCATGAGAAAGTTT
1 AA-AATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTT
1757476 CGCTTGAAAT
Statistics
Matches: 312, Mismatches: 41, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
71 18 0.06
72 43 0.14
74 245 0.79
75 6 0.02
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (74 bp):
AAAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAGTTTTC
ACTCGAAAC
Found at i:1757182 original size:36 final size:36
Alignment explanation
Indices: 1757069--1757390 Score: 171
Period size: 38 Copynumber: 8.7 Consensus size: 36
1757059 CTCGAGATAA
* * *
1757069 TTTTTCTTAAAATAAACTTCATATCGCTTGAGACAG
1 TTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
* ** * ** * * *
1757105 TTTTCACTCGAAACAAAATTTTATCTC-ATTCAAGATAG
1 TTTT-TCTTAAAAC-AAACTTCGTCTCGCTT-GAGACAG
* *
1757143 TTTTTCTTAAAACGAACTTCGTCTCGCTTTAGACAG
1 TTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
* ** * * *
1757179 -TTTTCACTAGAAACAAAACTTTATCTCACTCGAGATAG
1 TTTTTC-TTA-AAAC-AAACTTCGTCTCGCTTGAGACAG
*
1757217 CTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
1 TTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
* ** * ** ** **
1757253 TTTTCACTCGAAACAAAATTTTATCTTTCTTGAGATTG
1 TTTT-TCTTAAAAC-AAACTTCGTCTCGCTTGAGACAG
1757291 TTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
1 TTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
* * * * ** * **
1757327 TTTTCACTCGAAACCAAATTTTATCTCACTTGAGATTG
1 TTTT-TCT-TAAAACAAACTTCGTCTCGCTTGAGACAG
*
1757365 TTTTTCTTAAAACAAACTTTGTCTCG
1 TTTTTCTTAAAACAAACTTCGTCTCG
1757391 AAGGCAATTT
Statistics
Matches: 204, Mismatches: 70, Indels: 24
0.68 0.23 0.08
Matches are distributed among these distances:
35 5 0.02
36 74 0.36
37 39 0.19
38 81 0.40
39 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
TTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
Found at i:1757535 original size:23 final size:23
Alignment explanation
Indices: 1757504--1757553 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1757494 TCAAACTGTT
*
1757504 TCACTTGAAACAATAAGTTTATC
1 TCACCTGAAACAATAAGTTTATC
1757527 TCACCTGAAACAATAAGTTTATC
1 TCACCTGAAACAATAAGTTTATC
1757550 TCAC
1 TCAC
1757554 TTGAGATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (23 bp):
TCACCTGAAACAATAAGTTTATC
Done.