Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 5 of 196
Found at i:1308331 original size:26 final size:26
Alignment explanation
Indices: 1308279--1308336 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
1308269 ATTTTTGTTT
* **
1308279 TTTTTATTGATTTTACATTCTTTAAA
1 TTTTTATTGATTTTAAATGATTTAAA
1308305 TTTTTATTGA-TTTAAATGATTTCAAA
1 TTTTTATTGATTTTAAATGATTT-AAA
1308331 TATTTT
1 T-TTTT
1308337 TAACTTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 9 0.33
26 14 0.52
27 4 0.15
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (26 bp):
TTTTTATTGATTTTAAATGATTTAAA
Found at i:1323772 original size:63 final size:63
Alignment explanation
Indices: 1323694--1323822 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
1323684 TCCAACTGAG
* * * *
1323694 TATGTTCCGCTAACTATTATGTAACTGCTGTAACTCTAATTAAGTTGCGTGCACATACACAGT
1 TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
* * ** *
1323757 TATGTTCCGTTAACTATTATGTAACCGCTGTAGCACAAATGAAGTTGTTTGCGCATACACAGT
1 TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
1323820 TAT
1 TAT
1323823 CAAGAAGACT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (63 bp):
TATGTTCCGCTAACTATTATGTAACCGCTGTAACACAAATGAAGTTGCGTGCACATACACAGT
Found at i:1324353 original size:16 final size:16
Alignment explanation
Indices: 1324332--1324364 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1324322 AGATCGGTCT
*
1324332 TTCTAGCACCATTCTC
1 TTCTAGCAACATTCTC
1324348 TTCTAGCAACATTCTC
1 TTCTAGCAACATTCTC
1324364 T
1 T
1324365 ATCGTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
TTCTAGCAACATTCTC
Found at i:1327558 original size:3 final size:3
Alignment explanation
Indices: 1327550--1327579 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1327540 ACGGATACCC
1327550 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1327580 ATGTGTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1332518 original size:41 final size:41
Alignment explanation
Indices: 1332461--1332562 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
1332451 GCATAGCGCT
*
1332461 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
* *
1332502 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
1332543 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
1332563 TACTGAATCA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.05
41 54 0.95
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTATATGTC
Found at i:1367071 original size:11 final size:11
Alignment explanation
Indices: 1367054--1367083 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1367044 TTTTATTTTT
1367054 TAATTTTAAAA
1 TAATTTTAAAA
*
1367065 TATTTTTAAAA
1 TAATTTTAAAA
1367076 TAATTTTA
1 TAATTTTA
1367084 TTTTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:1367085 original size:17 final size:17
Alignment explanation
Indices: 1367065--1367099 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1367055 AATTTTAAAA
1367065 TATTTTTAAAATAATTT
1 TATTTTTAAAATAATTT
*
1367082 TATTTTTAAAATTATTT
1 TATTTTTAAAATAATTT
1367099 T
1 T
1367100 TTGGTGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTAAAATAATTT
Found at i:1368941 original size:105 final size:103
Alignment explanation
Indices: 1368748--1368941 Score: 280
Period size: 105 Copynumber: 1.9 Consensus size: 103
1368738 TGCTATTGAC
* *
1368748 GAGGATGTAAGTGATGGTAATTTTTAAATCTCTAAAGAATTCAAGTGTTTACTTTGCTTGTGAGT
1 GAGGAGGTAAGTGATGGTAATTTCTAAATCTCTAAAGAATTCAAGTGTTTACTTTGCTTGTGAGT
*
1368813 AAAGATAAGCTAATTATTAATGAACATATGGAATTGGT
66 AAAGATAAACTAATTATTAATGAACATATGGAATTGGT
* ** * *
1368851 GAGGAGGTAAGTGATGGTAGTTTCTGGATCTTTAAAGAATTCAAGTGTGTTTATTTTGCTTGTGA
1 GAGGAGGTAAGTGATGGTAATTTCTAAATCTCTAAAGAATTCAA--GTGTTTACTTTGCTTGTGA
* *
1368916 GTAAATATAAACTACTTATTAATGAA
64 GTAAAGATAAACTAATTATTAATGAA
1368942 GAGCGCATCA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
103 38 0.48
105 41 0.52
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.38
Consensus pattern (103 bp):
GAGGAGGTAAGTGATGGTAATTTCTAAATCTCTAAAGAATTCAAGTGTTTACTTTGCTTGTGAGT
AAAGATAAACTAATTATTAATGAACATATGGAATTGGT
Found at i:1370251 original size:29 final size:28
Alignment explanation
Indices: 1370206--1370274 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
1370196 CATCCTTCCT
* *
1370206 TTTTTATTTTTTAATAAATGACCCAATA
1 TTTTTATTTTTGAATAAATAACCCAATA
*
1370234 TTTTTACTTTTTGCATAAATAACCCAATA
1 TTTTTA-TTTTTGAATAAATAACCCAATA
*
1370263 TGTTTATGTTTT
1 TTTTTAT-TTTT
1370275 TTCTTCTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.20
29 28 0.80
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTTTATTTTTGAATAAATAACCCAATA
Found at i:1380862 original size:40 final size:42
Alignment explanation
Indices: 1380788--1380907 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 42
1380778 ACACTGTTCA
1380788 TGCCACGTCAGCAAATCGCGTCCTAGA-G-GG-CGCGATTTCCT-
1 TGCCACGTCAGCAAATCGCG--CT-GACGTGGACGCGATTTCCTG
1380829 T-CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCTG
1 TGCCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCTG
* * * *
1380870 TGCGTAC-CCTG-ACATCGCGCTGACGTGGACGCGATTTC
1 TGC-CACGTCAGCAAATCGCGCTGACGTGGACGCGATTTC
1380908 GTGAAAAATG
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
37 2 0.03
38 3 0.04
39 2 0.03
40 29 0.42
41 28 0.41
42 3 0.04
43 2 0.03
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.23
Consensus pattern (42 bp):
TGCCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCTG
Found at i:1389378 original size:3 final size:3
Alignment explanation
Indices: 1389370--1389401 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1389360 ATCACATGTT
*
1389370 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1389402 TGGATGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1389521 original size:73 final size:73
Alignment explanation
Indices: 1389402--1389587 Score: 354
Period size: 73 Copynumber: 2.5 Consensus size: 73
1389392 TATTATTATT
**
1389402 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1389467 ATTTTAAG
66 ATTTTAAG
1389475 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1389540 ATTTTAAG
66 ATTTTAAG
1389548 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTT
1389588 GTCAAGTTGT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 111 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATAAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:1394935 original size:20 final size:20
Alignment explanation
Indices: 1394906--1394944 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1394896 ATTTAGCCAT
*
1394906 TTTTTATTTTTATTTTAATA
1 TTTTTATTTTTAATTTAATA
*
1394926 TTTTTGTTTTTAATTTAAT
1 TTTTTATTTTTAATTTAAT
1394945 TGTTACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTATTTTTAATTTAATA
Found at i:1397892 original size:44 final size:43
Alignment explanation
Indices: 1397815--1397898 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
1397805 TATGCCCTTG
* *
1397815 ATAAATTTTAAAATTAATTATTTAAACCATAATTATATTTTTCT
1 ATAAATTTTAAAATTAAATATTCAAACCATAATTA-ATTTTTCT
* *
1397859 ATAATTTTTAAAATTAAATATTCAAA-TAGTAATTAATTTT
1 ATAAATTTTAAAATTAAATATTCAAACCA-TAATTAATTTT
1397899 GTTCTTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 6 0.17
44 29 0.83
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (43 bp):
ATAAATTTTAAAATTAAATATTCAAACCATAATTAATTTTTCT
Found at i:1413435 original size:30 final size:30
Alignment explanation
Indices: 1413399--1413459 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1413389 ATCATGATCA
*
1413399 AAATTCACCAGTTGATATAGCACAGAACTT
1 AAATTCACCAGTTGATATAACACAGAACTT
* *
1413429 AAATTCACGAGTTGATATAACACGGAACTT
1 AAATTCACCAGTTGATATAACACAGAACTT
1413459 A
1 A
1413460 TTTGGAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (30 bp):
AAATTCACCAGTTGATATAACACAGAACTT
Found at i:1424693 original size:17 final size:17
Alignment explanation
Indices: 1424671--1424792 Score: 84
Period size: 17 Copynumber: 7.7 Consensus size: 17
1424661 AAAAAGTATT
1424671 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
1424688 TTAAAAAAAATTTAAAAA
1 TT-AAAAATATTTTAAAA
*
1424706 GTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
**
1424723 TTAAAAA-ATAATAAAA
1 TTAAAAATATTTTAAAA
*
1424739 --AAAAGTA--TT----
1 TTAAAAATATTTTAAAA
1424748 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
1424765 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTTAAAA
* *
1424781 ATAAATATATTT
1 TTAAAAATATTT
1424793 ATTATATCGG
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
11 6 0.08
13 3 0.04
14 4 0.05
15 1 0.01
16 20 0.25
17 32 0.40
18 14 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:1424700 original size:18 final size:18
Alignment explanation
Indices: 1424673--1424732 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
1424663 AAAGTATTTT
1424673 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTA
* * *
1424691 AAAAAAATTTAAAAAGT-
1 AAAAATATTTTAAAATTA
1424708 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTA
1424726 AAAAATA
1 AAAAATA
1424733 ATAAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 14 0.40
18 21 0.60
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAAATATTTTAAAATTA
Found at i:1424740 original size:18 final size:18
Alignment explanation
Indices: 1424673--1424739 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
1424663 AAAGTATTTT
* *
1424673 AAAAATATTTTAAAATTA
1 AAAAATAATTAAAAATTA
*
1424691 AAAAA-AATTTAAAAAGT-
1 AAAAATAA-TTAAAAATTA
* *
1424708 AAAAATATTTTAAAATTA
1 AAAAATAATTAAAAATTA
1424726 AAAAATAA-TAAAAA
1 AAAAATAATTAAAAA
1424740 AAAGTATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
17 18 0.47
18 20 0.53
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAAATAATTAAAAATTA
Found at i:1424793 original size:17 final size:16
Alignment explanation
Indices: 1424751--1424793 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1424741 AAGTATTTTA
* *
1424751 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
*
1424767 AAAAAATTTAAAAAAT
1 AAAATATTTAAAAAAT
1424783 AAATATATTTA
1 AAA-ATATTTA
1424794 TTATATCGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:1430358 original size:30 final size:29
Alignment explanation
Indices: 1430301--1430361 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
1430291 AATTTTAAAA
* **
1430301 TATTTTTAAAATACTTTTTTTTATTTTTT
1 TATTTTTAAAATAATTTTTGGTATTTTTT
*
1430330 TATTTTTAAAATAAATTTTTGGTGTTTTTT
1 TATTTTTAAAAT-AATTTTTGGTATTTTTT
1430360 TA
1 TA
1430362 AAAAATGGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (29 bp):
TATTTTTAAAATAATTTTTGGTATTTTTT
Found at i:1430692 original size:17 final size:18
Alignment explanation
Indices: 1430658--1430694 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1430648 AAATATTGTG
1430658 AAAAAAAATAAAACACGA
1 AAAAAAAATAAAACACGA
*
1430676 AAAAAAAATGAAA-ACGA
1 AAAAAAAATAAAACACGA
1430693 AA
1 AA
1430695 TTATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.05
Consensus pattern (18 bp):
AAAAAAAATAAAACACGA
Found at i:1431009 original size:17 final size:17
Alignment explanation
Indices: 1430977--1431010 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1430967 CGAAAATACT
1430977 AACTACAATAATAACAA
1 AACTACAATAATAACAA
1430994 AACTAACAATAA-AACAA
1 AACT-ACAATAATAACAA
1431011 GTGTTATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.15
Consensus pattern (17 bp):
AACTACAATAATAACAA
Found at i:1432044 original size:15 final size:15
Alignment explanation
Indices: 1432026--1432064 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1432016 TATTTCATTT
*
1432026 TTAAATATTGTATTA
1 TTAAATATTATATTA
*
1432041 TTAAACATTATATTA
1 TTAAATATTATATTA
*
1432056 TTAACTATT
1 TTAAATATT
1432065 TTATCATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAAATATTATATTA
Found at i:1437671 original size:39 final size:41
Alignment explanation
Indices: 1437613--1437696 Score: 120
Period size: 39 Copynumber: 2.1 Consensus size: 41
1437603 TTTAAAATTC
*
1437613 AAAA-ATATAAAAACTATTTTTA-AAAATT-AAAATTTTAA
1 AAAATATATAAAAAATATTTTTATAAAATTAAAAATTTTAA
**
1437651 AAAATATATAAAAAATATTTTTATAATTTTAAAAATTTTAA
1 AAAATATATAAAAAATATTTTTATAAAATTAAAAATTTTAA
1437692 AAAAT
1 AAAAT
1437697 TAATTAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 4 0.10
39 17 0.43
40 4 0.10
41 15 0.38
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (41 bp):
AAAATATATAAAAAATATTTTTATAAAATTAAAAATTTTAA
Found at i:1438061 original size:16 final size:15
Alignment explanation
Indices: 1438017--1438066 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1438007 TCATAATACA
*
1438017 TATTTTTTATACTACT
1 TATTTTTTATATTA-T
*
1438033 TA-TTTTAATATTAT
1 TATTTTTTATATTAT
1438047 TATTTTTTATA--AT
1 TATTTTTTATATTAT
1438060 TATTTTT
1 TATTTTT
1438067 GGGTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
15 16 0.53
16 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTATATTAT
Found at i:1444442 original size:15 final size:15
Alignment explanation
Indices: 1444422--1444452 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1444412 TTTGAAATTT
1444422 AAAATTAAAAATAAA
1 AAAATTAAAAATAAA
*
1444437 AAAATTAAAATTAAA
1 AAAATTAAAAATAAA
1444452 A
1 A
1444453 TTACCAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATTAAAAATAAA
Found at i:1444444 original size:21 final size:21
Alignment explanation
Indices: 1444420--1444478 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1444410 CTTTTGAAAT
1444420 TTAAAATTAAAAATAAAAAAA
1 TTAAAATTAAAAATAAAAAAA
* **
1444441 TTAAAATTAAAATTACCAAAA
1 TTAAAATTAAAAATAAAAAAA
*
1444462 -GAGAAATTAAAAATAAA
1 TTA-AAATTAAAAATAAA
1444479 GTTTGAGAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (21 bp):
TTAAAATTAAAAATAAAAAAA
Found at i:1445869 original size:23 final size:22
Alignment explanation
Indices: 1445835--1445882 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
1445825 TTAGCCATTC
*
1445835 TATTGTTTTTACTATTTTTTTAT
1 TATTGTTTTTACTA-TTTATTAT
1445858 TATT-TTTATTACTATTTATTAT
1 TATTGTTT-TTACTATTTATTAT
1445880 TAT
1 TAT
1445883 ACTGCTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTGTTTTTACTATTTATTAT
Found at i:1445923 original size:16 final size:15
Alignment explanation
Indices: 1445899--1445928 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1445889 ATGTACCTAT
1445899 TTATATATTATTTTA
1 TTATATATTATTTTA
1445914 TTATACTATTATTTT
1 TTATA-TATTATTTT
1445929 TTTTAACTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATATTATTTTA
Found at i:1453655 original size:46 final size:45
Alignment explanation
Indices: 1453556--1453734 Score: 331
Period size: 46 Copynumber: 3.9 Consensus size: 45
1453546 TTTGAGTACT
1453556 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1453601 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1453647 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
1453693 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACAC
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACAC
1453735 CTACACCTTT
Statistics
Matches: 132, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
45 41 0.31
46 91 0.69
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:1454351 original size:32 final size:32
Alignment explanation
Indices: 1454310--1454374 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1454300 ATAGGTGTTG
1454310 TATCTATGTTGACAATTTTAACTTGGTACTTA
1 TATCTATGTTGACAATTTTAACTTGGTACTTA
1454342 TATCTATGTTGACAATTTTAACTTGGTACTTA
1 TATCTATGTTGACAATTTTAACTTGGTACTTA
1454374 T
1 T
1454375 CTTGATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (32 bp):
TATCTATGTTGACAATTTTAACTTGGTACTTA
Found at i:1457369 original size:31 final size:31
Alignment explanation
Indices: 1457299--1457375 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
1457289 TTCTTTAATT
* *
1457299 TGATTAATTTTGGTCTTAGTATTTTTTGAAA
1 TGATAAATTTTAGTCTTAGTATTTTTTGAAA
*
1457330 TGATAAATTTTAGTCTTTGTACTTTTTT-AAA
1 TGATAAATTTTAGTCTTAGTA-TTTTTTGAAA
*
1457361 -GTTGAAATTTTAGTC
1 TGAT-AAATTTTAGTC
1457376 CCGATCCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 2 0.05
31 32 0.80
32 6 0.15
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.53
Consensus pattern (31 bp):
TGATAAATTTTAGTCTTAGTATTTTTTGAAA
Found at i:1458408 original size:10 final size:10
Alignment explanation
Indices: 1458388--1458425 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1458378 CAGAATAAGC
1458388 TATTT-TATA
1 TATTTATATA
1458397 TATTTATATA
1 TATTTATATA
1458407 TATTTATATA
1 TATTTATATA
*
1458417 TATATATAT
1 TATTTATAT
1458426 CTTGGCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 5 0.19
10 22 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTATATA
Found at i:1468281 original size:48 final size:47
Alignment explanation
Indices: 1468226--1468335 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 47
1468216 TGGTGTAATG
* * * *
1468226 CCTCGCAAGATTGCAAGGTGTTCTACCTCGCAAGGAGTTGATGTTCCA
1 CCTCGCAAGGTTGCAA-GCGTTCCACCTCGCAAGGAGTTGATATTCCA
* * * * *
1468274 CCTCGCAAGGTTGTGAAGCGTTCCATCTTGCGAGGTGTTGATATTCCA
1 CCTCGCAAGGTTG-CAAGCGTTCCACCTCGCAAGGAGTTGATATTCCA
1468322 CCTCGCAAGGTTGC
1 CCTCGCAAGGTTGC
1468336 GGGGGGTTCC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
48 49 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.28
Consensus pattern (47 bp):
CCTCGCAAGGTTGCAAGCGTTCCACCTCGCAAGGAGTTGATATTCCA
Found at i:1468332 original size:23 final size:23
Alignment explanation
Indices: 1468250--1468332 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 23
1468240 AAGGTGTTCT
* *
1468250 ACCTCGCAAGGAGTTGATGTTCC
1 ACCTCGCAAGGTGTTGATATTCC
1468273 ACCTCGCAAGGT-TGTGA-AGCGTTCC
1 ACCTCGCAAGGTGT-TGATA---TTCC
* * *
1468298 ATCTTGCGAGGTGTTGATATTCC
1 ACCTCGCAAGGTGTTGATATTCC
1468321 ACCTCGCAAGGT
1 ACCTCGCAAGGT
1468333 TGCGGGGGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
22 1 0.02
23 27 0.59
25 16 0.35
26 2 0.04
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (23 bp):
ACCTCGCAAGGTGTTGATATTCC
Found at i:1469061 original size:54 final size:54
Alignment explanation
Indices: 1469002--1469139 Score: 168
Period size: 54 Copynumber: 2.5 Consensus size: 54
1468992 GGCAAACCGA
* **
1469002 AAGATTTTGAAAATCTTATAAGTATATGGTTGCGATCTTAAATTGGCGAACTGT
1 AAGATTTTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAACTGT
* * * * * *
1469056 AAGATTCTGAAAATCTTATAAATAAAAGGTCGTGATCTTAAATCAGTGAACTGT
1 AAGATTTTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAACTGT
* *
1469110 AAGATTTCTAAAAATCGTATAAGTATATGG
1 AAGATTT-TGAAAATCTTATAAGTATATGG
1469140 CGGCTGTGAC
Statistics
Matches: 68, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
54 51 0.75
55 17 0.25
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (54 bp):
AAGATTTTGAAAATCTTATAAGTATATGGTCGCGATCTTAAATCAGCGAACTGT
Found at i:1470749 original size:7 final size:7
Alignment explanation
Indices: 1470737--1470788 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
1470727 AATGCCATCA
1470737 ATATGTG
1 ATATGTG
*
1470744 ATATGTA
1 ATATGTG
*
1470751 ATATATG
1 ATATGTG
1470758 ATATGTG
1 ATATGTG
*
1470765 ATTTGTG
1 ATATGTG
**
1470772 CGATGTG
1 ATATGTG
1470779 ATGATGTG
1 AT-ATGTG
1470787 AT
1 AT
1470789 GATGAAGAAG
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (7 bp):
ATATGTG
Found at i:1474083 original size:25 final size:25
Alignment explanation
Indices: 1474061--1474168 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 25
1474051 GAGTGCTCAT
1474061 TCGAGCACATA-AACGAGAAGCTCTG
1 TCGAGC-CATATAACGAGAAGCTCTG
*
1474086 TTGAGCCATATAACGAGAAGCTCCTG
1 TCGAGCCATATAACGAGAAGCT-CTG
* * *
1474112 T-GAGCTATGTAACGGGAAGCTCAT-
1 TCGAGCCATATAACGAGAAGCTC-TG
*
1474136 ACGAGCCA-ATATA-GAGAAGCTCTG
1 TCGAGCCATATA-ACGAGAAGCTCTG
**
1474160 GAGAGCCAT
1 TCGAGCCAT
1474169 TAATTGGGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 21 0.32
25 40 0.61
26 4 0.06
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
TCGAGCCATATAACGAGAAGCTCTG
Found at i:1474112 original size:26 final size:25
Alignment explanation
Indices: 1474063--1474133 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
1474053 GTGCTCATTC
1474063 GAGCACATA-AACGAGAAGCT-CTGTT
1 GAGC-CATATAACGAGAAGCTCCTG-T
1474088 GAGCCATATAACGAGAAGCTCCTGT
1 GAGCCATATAACGAGAAGCTCCTGT
* * *
1474113 GAGCTATGTAACGGGAAGCTC
1 GAGCCATATAACGAGAAGCTC
1474134 ATACGAGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
24 4 0.10
25 34 0.83
26 3 0.07
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGAGAAGCTCCTGT
Found at i:1480215 original size:17 final size:16
Alignment explanation
Indices: 1480193--1480222 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1480183 ATAATATATT
1480193 TTTA-AAATTTTTTAA
1 TTTATAAATTTTTTAA
1480208 TTTATAAATTTTTTA
1 TTTATAAATTTTTTA
1480223 CGAAAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTATAAATTTTTTAA
Found at i:1481754 original size:26 final size:26
Alignment explanation
Indices: 1481725--1481778 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1481715 AATCCGAAAG
1481725 TTTGCAACAAGTTAACAACTACAATC
1 TTTGCAACAAGTTAACAACTACAATC
*
1481751 TTTGCAGCAAGTTAACAACTACAATC
1 TTTGCAACAAGTTAACAACTACAATC
1481777 TT
1 TT
1481779 AAACTTGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (26 bp):
TTTGCAACAAGTTAACAACTACAATC
Found at i:1482456 original size:17 final size:17
Alignment explanation
Indices: 1482408--1482458 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1482398 TTAACAAAGT
*
1482408 TAGCACATTTGGTGA-C
1 TAGCACATTTGATGAGC
* *
1482424 TCGCAC-TTTTAGTGAGC
1 TAGCACATTTGA-TGAGC
1482441 TAGCACATTTGATGAGC
1 TAGCACATTTGATGAGC
1482458 T
1 T
1482459 CATAATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 3 0.11
16 8 0.30
17 12 0.44
18 4 0.15
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (17 bp):
TAGCACATTTGATGAGC
Found at i:1482474 original size:18 final size:18
Alignment explanation
Indices: 1482451--1482494 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1482441 TAGCACATTT
* *
1482451 GATGAGCTCATAATTTTG
1 GATGAGCTCACAATTTTA
* *
1482469 GATGAGTTCGCAATTTTA
1 GATGAGCTCACAATTTTA
1482487 GATGAGCT
1 GATGAGCT
1482495 TGCAGGTGCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.36
Consensus pattern (18 bp):
GATGAGCTCACAATTTTA
Found at i:1493096 original size:46 final size:46
Alignment explanation
Indices: 1493029--1493230 Score: 347
Period size: 46 Copynumber: 4.5 Consensus size: 46
1493019 TGATCAGTGA
1493029 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1493075 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1493121 CAAGTGACAAAGT-ATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
1493166 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
1493212 C-AGGGAC-TAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
1493231 ATCACATATA
Statistics
Matches: 150, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
44 11 0.07
45 49 0.33
46 90 0.60
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:1493149 original size:91 final size:92
Alignment explanation
Indices: 1493029--1493230 Score: 347
Period size: 91 Copynumber: 2.2 Consensus size: 92
1493019 TGATCAGTGA
1493029 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
* *
1493094 TGGTAGCTTTAGCTACAGTTATCTGAT
66 TGGTAGCCTTAGCTACACTTATCTGAT
1493121 CAAGTGACAAAGT-ATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
1493185 TGGTAGCCTTAGCTACACTTATCTGAT
66 TGGTAGCCTTAGCTACACTTATCTGAT
* *
1493212 C-AGGGAC-TAGTGATAAGTG
1 CAAGTGACAAAGTGATAAGTG
1493231 ATCACATATA
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
89 3 0.03
90 12 0.11
91 77 0.73
92 13 0.12
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (92 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
TGGTAGCCTTAGCTACACTTATCTGAT
Found at i:1494563 original size:49 final size:49
Alignment explanation
Indices: 1494491--1494627 Score: 175
Period size: 49 Copynumber: 2.8 Consensus size: 49
1494481 AAAATGTGAT
1494491 TATGTGATCTTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAAATGA
1 TATGTGAT-TTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAAATGA
* * * * **
1494541 TATGTGATTTTGTGTAAAACCATAGCTGGGTTATGGCATCGGTATGTGA
1 TATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAAATGA
* * * *
1494590 TATGTGATTACATGTAAGACCATAGTTGGACTATGGCA
1 TATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCA
1494628 ATGTGAAAAC
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 66 0.89
50 8 0.11
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (49 bp):
TATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGATAAATGA
Found at i:1499410 original size:45 final size:44
Alignment explanation
Indices: 1499341--1499493 Score: 236
Period size: 45 Copynumber: 3.4 Consensus size: 44
1499331 ATCAGTGACA
1499341 AGTGACAAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATC
1 AGTGAC-AAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATC
1499386 GAGTGACAAAGTG-TAAGTGGTAGCTTTAGCTACAGTTATCTGATC
1 -AGTGAC-AAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATC
* *
1499431 AAGTGACAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATC
1 -AGTGACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATC
*
1499476 AGGGACAAGTGATAAGTG
1 AGTGACAAGTGATAAGTG
1499494 ATCACATATA
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
44 22 0.22
45 68 0.67
46 12 0.12
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATCTGATC
Found at i:1503074 original size:18 final size:18
Alignment explanation
Indices: 1503051--1503086 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1503041 GTTTTATTCA
1503051 AAGATTTCTAGGTTTTCT
1 AAGATTTCTAGGTTTTCT
* *
1503069 AAGATTTTTGGGTTTTCT
1 AAGATTTCTAGGTTTTCT
1503087 CATTCAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.53
Consensus pattern (18 bp):
AAGATTTCTAGGTTTTCT
Found at i:1503425 original size:20 final size:19
Alignment explanation
Indices: 1503369--1503426 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1503359 TAATTATTTC
* *
1503369 TTATATATATATTTTAGAGT
1 TTATATATA-ATTTTATAAT
1503389 TTATATATAATTTTTATAAT
1 TTATATATAA-TTTTATAAT
*
1503409 TTATATTTAGATTTTATA
1 TTATATATA-ATTTTATA
1503427 TAGTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATATATAATTTTATAAT
Found at i:1503552 original size:20 final size:19
Alignment explanation
Indices: 1503527--1503587 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
1503517 ATTTATATAC
1503527 ATATTTTTTCGAAATTTTAT
1 ATATTTTTTC-AAATTTTAT
* *
1503547 ATATTTATTTCTATTTTTAT
1 ATATTT-TTTCAAATTTTAT
**
1503567 A-ATTTTTT-AAGGTTTAT
1 ATATTTTTTCAAATTTTAT
1503584 ATAT
1 ATAT
1503588 GTTTGGCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 4 0.12
20 14 0.41
21 4 0.12
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (19 bp):
ATATTTTTTCAAATTTTAT
Found at i:1504198 original size:21 final size:22
Alignment explanation
Indices: 1504148--1504202 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1504138 TAGTGAGATG
*
1504148 ACAACAAAACAATGGAAAAATA
1 ACAACAAAACAATGGAAAAACA
* * *
1504170 GCAGCAAAATAAT-GAAAAACA
1 ACAACAAAACAATGGAAAAACA
1504191 ACAACAAAACAA
1 ACAACAAAACAA
1504203 CAAGTTTTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.67, C:0.16, G:0.09, T:0.07
Consensus pattern (22 bp):
ACAACAAAACAATGGAAAAACA
Found at i:1504983 original size:29 final size:30
Alignment explanation
Indices: 1504951--1505007 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1504941 TTTGATATAA
1504951 TTTTTTTATA-ACTTTCCTATTTTCTAACT
1 TTTTTTTATATACTTTCCTATTTTCTAACT
** *
1504980 TTTTTTTATATTTTTTGCTATTTTCTAA
1 TTTTTTTATATACTTTCCTATTTTCTAA
1505008 TTAATTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTTTTTATATACTTTCCTATTTTCTAACT
Found at i:1518751 original size:16 final size:16
Alignment explanation
Indices: 1518714--1518752 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1518704 TTTGGTTCAG
*
1518714 TGTAATGGAATAGAGC
1 TGTAATTGAATAGAGC
* *
1518730 TATAATTGAATAGAGT
1 TGTAATTGAATAGAGC
1518746 TGTAATT
1 TGTAATT
1518753 AGTAATTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (16 bp):
TGTAATTGAATAGAGC
Found at i:1518993 original size:58 final size:58
Alignment explanation
Indices: 1518930--1519055 Score: 173
Period size: 58 Copynumber: 2.2 Consensus size: 58
1518920 TTTTAAAAAG
* * *
1518930 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAGTTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
1518988 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
1519046 ATTATTATTA
1 ATTATTATTA
1519056 TATGAATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 21 0.35
58 39 0.65
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:1519091 original size:58 final size:57
Alignment explanation
Indices: 1518930--1519092 Score: 145
Period size: 58 Copynumber: 2.8 Consensus size: 57
1518920 TTTTAAAAAG
* * * * ** *
1518930 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAGTTTAACCATATT-TTAACATA
1 ATTATTATT-AATATAATTTAA-AAAAATAATATATAATCTAATAAAATTCTTAACATA
* * *
1518988 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATT-AATATAATTTAAAAAAATAATATATAATCTAATAAAATTCTTAACATA
1519046 ATTATTATT-ATATGAA-TTAAAAAATCATAATATATAATACT-ATAAAA
1 ATTATTATTAATAT-AATTTAAAAAA--ATAATATATAAT-CTAATAAAA
1519093 ATAATATATA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
56 11 0.12
57 23 0.26
58 55 0.61
59 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (57 bp):
ATTATTATTAATATAATTTAAAAAAATAATATATAATCTAATAAAATTCTTAACATA
Found at i:1519929 original size:98 final size:98
Alignment explanation
Indices: 1519806--1519998 Score: 305
Period size: 98 Copynumber: 2.0 Consensus size: 98
1519796 ATATAAAAAT
* * * *
1519806 TTTAAAAGAACATCCACTCGTCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCC
1 TTTAAAAAAACATCCACTCATCCAAGATTTAAAAAACCACACCCAATACGTTAGGGCACAATCCC
1519871 TTTAGAATCCCAAACTCAGAATATTTCCTTTAA
66 TTTAGAATCCCAAACTCAGAATATTTCCTTTAA
* * *
1519904 TTTAAAAAAACATCCACTTATCCAAGATTTAAAAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAAAACATCCACTCATCCAAGATTTAAAAAACCACACCCAATACGTTAGGGCACAATCCC
* *
1519969 TTTAGAATCTCAAACTCGGAATATTTCCTT
66 TTTAGAATCCCAAACTCAGAATATTTCCTT
1519999 CATGATTTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 86 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (98 bp):
TTTAAAAAAACATCCACTCATCCAAGATTTAAAAAACCACACCCAATACGTTAGGGCACAATCCC
TTTAGAATCCCAAACTCAGAATATTTCCTTTAA
Found at i:1520279 original size:12 final size:12
Alignment explanation
Indices: 1520262--1520286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1520252 AACGAGCAAC
1520262 ATAATATAAATG
1 ATAATATAAATG
1520274 ATAATATAAATG
1 ATAATATAAATG
1520286 A
1 A
1520287 AAGCACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATATAAATG
Found at i:1520675 original size:25 final size:25
Alignment explanation
Indices: 1520631--1520679 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1520621 ATTATATATA
1520631 TTAAAACAAAATAAAAAAAACTAAAT
1 TTAAAACAAAATAAAAAAAA-TAAAT
**
1520657 TTAAAA-AAAATAAGGAAAATAAA
1 TTAAAACAAAATAAAAAAAATAAA
1520680 AAAAGGGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (25 bp):
TTAAAACAAAATAAAAAAAATAAAT
Found at i:1520803 original size:8 final size:8
Alignment explanation
Indices: 1520790--1520814 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1520780 AGAAAGGAAA
1520790 ATTTCCCT
1 ATTTCCCT
1520798 ATTTCCCT
1 ATTTCCCT
1520806 ATTTCCCT
1 ATTTCCCT
1520814 A
1 A
1520815 AACGGCGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTCCCT
Found at i:1521804 original size:14 final size:14
Alignment explanation
Indices: 1521785--1521817 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1521775 CACTATTTGG
*
1521785 TTTGGGCCTCTGAA
1 TTTGGGCCACTGAA
1521799 TTTGGGCCACTGAA
1 TTTGGGCCACTGAA
1521813 TTTGG
1 TTTGG
1521818 TTTTGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.36
Consensus pattern (14 bp):
TTTGGGCCACTGAA
Found at i:1524652 original size:41 final size:41
Alignment explanation
Indices: 1524607--1524875 Score: 412
Period size: 41 Copynumber: 6.6 Consensus size: 41
1524597 GGTTTTAAAA
*
1524607 CCTAGCAGGCTAAGTGTCGGTGATCTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
*
1524648 CCTAGCAGGCTAAGTGCCGGTGAACTAAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* *
1524689 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* *
1524730 TCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* ** *
1524771 CCTAGCAGGCTAAGTGCCGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
*
1524812 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
* * *
1524853 CCTAACAAGCTAAGTGCCAGTGA
1 CCTAGCAGGCTAAGTGCCGGTGA
1524876 ATCTGTTTAA
Statistics
Matches: 209, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 209 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAG
Found at i:1528478 original size:14 final size:14
Alignment explanation
Indices: 1528459--1528488 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1528449 ACCATTAGTA
1528459 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
*
1528473 AAAGAAAAGAAAAG
1 AAAGAAAAAAAAAG
1528487 AA
1 AA
1528489 TGTGTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:1528550 original size:16 final size:16
Alignment explanation
Indices: 1528531--1528564 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1528521 GACGTTTAAT
*
1528531 ATGATTTTTTTGTAGC
1 ATGATTTGTTTGTAGC
1528547 ATGATTTGTTTGTAGC
1 ATGATTTGTTTGTAGC
1528563 AT
1 AT
1528565 TTTACTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.53
Consensus pattern (16 bp):
ATGATTTGTTTGTAGC
Found at i:1528752 original size:28 final size:27
Alignment explanation
Indices: 1528691--1528752 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
1528681 ATAACATAAA
*
1528691 TTAAAGATATCAAAAATAAAAATAGTT
1 TTAAATATATCAAAAATAAAAATAGTT
* *
1528718 TTAAAATATATTAAAAGATTAAAATAGTT
1 TT-AAATATATCAAAA-ATAAAAATAGTT
1528747 TTAAAT
1 TTAAAT
1528753 GAAACATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.07
28 15 0.50
29 13 0.43
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (27 bp):
TTAAATATATCAAAAATAAAAATAGTT
Found at i:1529270 original size:42 final size:42
Alignment explanation
Indices: 1529212--1529506 Score: 299
Period size: 42 Copynumber: 7.0 Consensus size: 42
1529202 ACGTTTACAG
*
1529212 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCTGCGCTTTA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* *
1529254 AAAAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * * *
1529295 AAAAAAGACACCGCTAAAGGTCATGTTCTTTTGCAGCGC-TTA
1 AAAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * *
1529337 AAGAAAAAGGCCGCTAAAGATCATGTTCTTTAGAGGCTC-TTA
1 AA-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * * *
1529379 ACGAAAAATGCCGCTAAAGATCATGCTCTTTAGCGGCGCTTTG
1 A-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
* * * *
1529422 CATAAAACGCCGCGAAAGATCATGTTTTTTAGCGGCGCTTTTA
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTTA
** * * * * *
1529465 TCACAAACGCCGCAAAAAAGTAAAGTTCTTTAGCGGCGCTTT
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTT
1529507 CTTCACAATT
Statistics
Matches: 210, Mismatches: 37, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
41 9 0.04
42 160 0.76
43 25 0.12
44 16 0.08
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTA
Found at i:1529504 original size:44 final size:44
Alignment explanation
Indices: 1529405--1529514 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
1529395 AAGATCATGC
* * * *
1529405 TCTTTAGCGGCGCTTTGC-AT-A-AAACGCCGCGAAAGATCATGT
1 TCTTTAGCGGCGCTTT-CTATCACAAACGCCGCAAAAAATAAAGT
*
1529447 TTTTTAGCGGCGCTTT-TATCACAAACGCCGCAAAAAAGTAAAGT
1 TCTTTAGCGGCGCTTTCTATCACAAACGCCGCAAAAAA-TAAAGT
1529491 TCTTTAGCGGCGCTTTCT-TCACAA
1 TCTTTAGCGGCGCTTTCTATCACAA
1529515 TTGCCGCTAG
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
41 2 0.04
42 16 0.28
43 13 0.23
44 25 0.44
45 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (44 bp):
TCTTTAGCGGCGCTTTCTATCACAAACGCCGCAAAAAATAAAGT
Found at i:1529975 original size:21 final size:21
Alignment explanation
Indices: 1529951--1530019 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
1529941 ACTTCTCTCG
*
1529951 CTGCTTCTCTTGCTGCAGCTT
1 CTGCTTCTCTTGCTGCAGCCT
*
1529972 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTTGCTGCAGCCT
* *
1529993 CTGCTTCCCTTGCTGCCGCCT
1 CTGCTTCTCTTGCTGCAGCCT
1530014 CTGCTT
1 CTGCTT
1530020 TAATTTGTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.03, C:0.41, G:0.19, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTTGCTGCAGCCT
Found at i:1535560 original size:7 final size:7
Alignment explanation
Indices: 1535550--1535595 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
1535540 TGATATATTT
1535550 TTATGTA
1 TTATGTA
1535557 TTATGTAA
1 TTATGT-A
1535565 GTTATGTAA
1 -TTATGT-A
1535574 GTTATGTA
1 -TTATGTA
1535582 TTATGTA
1 TTATGTA
1535589 TTATGTA
1 TTATGTA
1535596 AGTACTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:1535834 original size:27 final size:27
Alignment explanation
Indices: 1535557--1535858 Score: 257
Period size: 25 Copynumber: 11.8 Consensus size: 27
1535547 TTTTTATGTA
1535557 TTATGTAAGTTATGTAAGTTATGT-A-
1 TTATGTAAGTTATGTAAGTTATGTAAG
1535582 TTATGT-A-TTATGTAAG-TACTGTAAG
1 TTATGTAAGTTATGTAAGTTA-TGTAAG
* *
1535607 TAATGTAAGTTATGTAAGTAATGT-A-
1 TTATGTAAGTTATGTAAGTTATGTAAG
* *
1535632 TTATGTAAGTTGTGTATA-ATAT-TAA-
1 TTATGTAAGTTATGTA-AGTTATGTAAG
* * *
1535657 TTATGTGAGTTGTGT-A-TAATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
* * *
1535682 TTAAG-AAGGTTATGT-A-TAATATAAG
1 TTATGTAA-GTTATGTAAGTTATGTAAG
*
1535707 TTATTTAAGTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
* *
1535734 TTGTGT-A-TAATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
* *
1535759 TTATTTAATTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
* *
1535786 TTATGTAAGTTATTTAATTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
*
1535813 TTATGTAAGTTATGTAGGTTATGT-A-
1 TTATGTAAGTTATGTAAGTTATGTAAG
* *
1535838 TTATGTTAGTTAT-TATGTTAT
1 TTATGTAAGTTATGTAAGTTAT
1535859 TATATAAGTT
Statistics
Matches: 229, Mismatches: 32, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.01
23 15 0.07
24 14 0.06
25 104 0.45
26 9 0.04
27 84 0.37
28 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (27 bp):
TTATGTAAGTTATGTAAGTTATGTAAG
Found at i:1535877 original size:29 final size:30
Alignment explanation
Indices: 1535845--1535949 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 30
1535835 GTATTATGTT
1535845 AGTTAT-TATGTTATTATATAAGTTATGCA
1 AGTTATATATGTTATTATATAAGTTATGCA
* **
1535874 AGTTTCTATATATG-T-TTATAT-ATTGTATGTT
1 AG--T-TATATATGTTATTATATAAGT-TATGCA
1535905 AGTTAT-TATGTTATTATATAAGTTATGCA
1 AGTTATATATGTTATTATATAAGTTATGCA
* *
1535934 AGATATATAAGTTATT
1 AGTTATATATGTTATT
1535950 TAAGTTATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
27 4 0.07
28 4 0.07
29 18 0.31
30 12 0.20
31 13 0.22
32 4 0.07
33 4 0.07
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (30 bp):
AGTTATATATGTTATTATATAAGTTATGCA
Found at i:1535979 original size:31 final size:31
Alignment explanation
Indices: 1535936--1536088 Score: 125
Period size: 31 Copynumber: 4.9 Consensus size: 31
1535926 GTTATGCAAG
*
1535936 ATATATAAGTTATTTAAGTTATTATGTTATT
1 ATATATAAGTTATGTAAGTTATTATGTTATT
* * *
1535967 ATATGTAAGTTATGTAAGTTATTATGTAAGT
1 ATATATAAGTTATGTAAGTTATTATGTTATT
** * *
1535998 -TATGCAAGCTTATATTTAAGTTATGTA--TTATA
1 ATATATAAG--T-TATGTAAGTTAT-TATGTTATT
* *
1536030 ACATA-AAGTACTATGTAATTTATTATGTTATT
1 ATATATAAGT--TATGTAAGTTATTATGTTATT
*
1536062 ATATATAAGTTATGCAAGTTATTATGT
1 ATATATAAGTTATGTAAGTTATTATGT
1536089 AAGTTATGCA
Statistics
Matches: 95, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
30 10 0.11
31 52 0.55
32 14 0.15
33 17 0.18
34 2 0.02
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48
Consensus pattern (31 bp):
ATATATAAGTTATGTAAGTTATTATGTTATT
Found at i:1535982 original size:9 final size:9
Alignment explanation
Indices: 1535918--1535988 Score: 53
Period size: 9 Copynumber: 8.4 Consensus size: 9
1535908 TATTATGTTA
*
1535918 TTATATAAG
1 TTATGTAAG
*
1535927 TTATGCAAG
1 TTATGTAAG
* *
1535936 ATATATAAG
1 TTATGTAAG
*
1535945 TTATTTAAG
1 TTATGTAAG
*
1535954 TTAT-TATG
1 TTATGTAAG
1535962 TTAT-T-A-
1 TTATGTAAG
1535968 -TATGTAAG
1 TTATGTAAG
1535976 TTATGTAAG
1 TTATGTAAG
1535985 TTAT
1 TTAT
1535989 TATGTAAGTT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
5 3 0.06
6 1 0.02
7 1 0.02
8 8 0.16
9 36 0.73
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1535993 original size:12 final size:12
Alignment explanation
Indices: 1535945--1536000 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
1535935 GATATATAAG
*
1535945 TTATTTAAGTTA
1 TTATGTAAGTTA
*
1535957 TTATGTTA-TTA
1 TTATGTAAGTTA
1535968 -TATGTAAG---
1 TTATGTAAGTTA
1535976 TTATGTAAGTTA
1 TTATGTAAGTTA
1535988 TTATGTAAGTTA
1 TTATGTAAGTTA
1536000 T
1 T
1536001 GCAAGCTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
9 8 0.22
10 6 0.17
11 3 0.08
12 19 0.53
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:1535994 original size:21 final size:21
Alignment explanation
Indices: 1535945--1536024 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
1535935 GATATATAAG
* *
1535945 TTATTTAAGTTAT-TATGTTA
1 TTATGTAAGTTATGTAAGTTA
1535965 TTATATGTAAGTTATGTAAGTTA
1 -T-TATGTAAGTTATGTAAGTTA
*
1535988 TTATGTAAGTTATGCAAGCTTA
1 TTATGTAAGTTATGTAAG-TTA
*
1536010 -TATTTAAGTTATGTA
1 TTATGTAAGTTATGTA
1536025 TTATAACATA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
21 30 0.59
22 15 0.29
23 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.50
Consensus pattern (21 bp):
TTATGTAAGTTATGTAAGTTA
Found at i:1536001 original size:9 final size:9
Alignment explanation
Indices: 1535557--1535850 Score: 257
Period size: 9 Copynumber: 34.4 Consensus size: 9
1535547 TTTTTATGTA
1535557 TTATGTAAG
1 TTATGTAAG
1535566 TTATGTAAG
1 TTATGTAAG
1535575 TTATGT-A-
1 TTATGTAAG
1535582 TTATGT-A-
1 TTATGTAAG
1535589 TTATGTAAG
1 TTATGTAAG
1535598 -TACTGTAAG
1 TTA-TGTAAG
*
1535607 TAATGTAAG
1 TTATGTAAG
1535616 TTATGTAAG
1 TTATGTAAG
*
1535625 TAATGT-A-
1 TTATGTAAG
1535632 TTATGTAAG
1 TTATGTAAG
*
1535641 TTGTGTATA-
1 TTATGTA-AG
*
1535650 ATAT-TAA-
1 TTATGTAAG
*
1535657 TTATGTGAG
1 TTATGTAAG
*
1535666 TTGTGT-A-
1 TTATGTAAG
*
1535673 TAATGTAAG
1 TTATGTAAG
*
1535682 TTAAG-AAGG
1 TTATGTAA-G
1535691 TTATGT-A-
1 TTATGTAAG
* *
1535698 TAATATAAG
1 TTATGTAAG
*
1535707 TTATTTAAG
1 TTATGTAAG
1535716 TTATGTAAG
1 TTATGTAAG
1535725 TTATGTAAG
1 TTATGTAAG
*
1535734 TTGTGT-A-
1 TTATGTAAG
*
1535741 TAATGTAAG
1 TTATGTAAG
1535750 TTATGTAAG
1 TTATGTAAG
* *
1535759 TTATTTAAT
1 TTATGTAAG
1535768 TTATGTAAG
1 TTATGTAAG
1535777 TTATGTAAG
1 TTATGTAAG
1535786 TTATGTAAG
1 TTATGTAAG
* *
1535795 TTATTTAAT
1 TTATGTAAG
1535804 TTATGTAAG
1 TTATGTAAG
1535813 TTATGTAAG
1 TTATGTAAG
*
1535822 TTATGTAGG
1 TTATGTAAG
1535831 TTATGT-A-
1 TTATGTAAG
*
1535838 TTATGTTAG
1 TTATGTAAG
1535847 TTAT
1 TTAT
1535851 TATGTTATTA
Statistics
Matches: 232, Mismatches: 34, Indels: 38
0.76 0.11 0.12
Matches are distributed among these distances:
7 40 0.17
8 18 0.08
9 172 0.74
10 2 0.01
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1536093 original size:21 final size:21
Alignment explanation
Indices: 1536064--1536117 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1536054 ATGTTATTAT
*
1536064 ATATAAGTTATGCAAG-TTATT
1 ATATAAGTTATGCAAGCTTA-A
*
1536085 ATGTAAGTTATGCAAGCTTAA
1 ATATAAGTTATGCAAGCTTAA
1536106 ATATAAGTTATG
1 ATATAAGTTATG
1536118 TATTATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (21 bp):
ATATAAGTTATGCAAGCTTAA
Found at i:1536266 original size:16 final size:16
Alignment explanation
Indices: 1536241--1536278 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1536231 GAAAACGAAG
*
1536241 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
*
1536256 TAAATTTTAATGCAAA
1 TAAATTTTAATACAAA
1536272 TAAATTT
1 TAAATTT
1536279 AGAAAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:1536293 original size:13 final size:13
Alignment explanation
Indices: 1536275--1536302 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1536265 ATGCAAATAA
1536275 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1536288 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1536301 AT
1 AT
1536303 AAAATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1536341 original size:61 final size:61
Alignment explanation
Indices: 1536160--1536428 Score: 358
Period size: 62 Copynumber: 4.4 Consensus size: 61
1536150 TGTATTATGT
* * *
1536160 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAA
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
* ** * * *
1536221 CACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
** *
1536283 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTGTTACTAACAAATTTAGAA
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
* ** * * *
1536344 CACTTATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
1 AACTTATTTAGAAAACTTA-TAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
1536406 AACTTATTTAGAAAACTTATAAA
1 AACTTATTTAGAAAACTTATAAA
1536429 TTTAGAAAAC
Statistics
Matches: 176, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
61 71 0.40
62 105 0.60
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (61 bp):
AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTAATACAAACAAATTTAGAA
Found at i:1536379 original size:123 final size:123
Alignment explanation
Indices: 1536160--1536428 Score: 520
Period size: 123 Copynumber: 2.2 Consensus size: 123
1536150 TGTATTATGT
*
1536160 AACTTATGTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
1536225 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
*
1536283 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTGTTACTAACAAATTTAGAACACT
1 AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
1536348 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
66 TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
1536406 AACTTATTTAGAAAACTTATAAA
1 AACTTATTTAGAAAACTTATAAA
1536429 TTTAGAAAAC
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 144 1.00
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (123 bp):
AACTTATTTAGAAAACTTATAAAATTAATACTAATAAATTTTATTACTAACAAATTTAGAACACT
TATTTAGAAAACGAAGTAAATTTAATACTAATAAATTTTAATGCAAATAAATTTAGAA
Found at i:1536389 original size:16 final size:16
Alignment explanation
Indices: 1536364--1536401 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1536354 GAAAACGAAG
*
1536364 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
*
1536379 TAAATTTTAATGCAAA
1 TAAATTTTAATACAAA
1536395 TAAATTT
1 TAAATTT
1536402 AGAAAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:1536416 original size:13 final size:13
Alignment explanation
Indices: 1536398--1536425 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1536388 ATGCAAATAA
1536398 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1536411 ATTTAGAAAACTT
1 ATTTAGAAAACTT
1536424 AT
1 AT
1536426 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:1536433 original size:17 final size:17
Alignment explanation
Indices: 1536394--1536443 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
1536384 TTTAATGCAA
1536394 ATAAATTTAGAAAAC-T
1 ATAAATTTAGAAAACTT
1536410 -T--ATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
1536424 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
1536441 ATA
1 ATA
1536444 TAGATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 2 0.07
17 16 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:1539726 original size:7 final size:7
Alignment explanation
Indices: 1539687--1539711 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1539677 TTAAACACTG
1539687 AAACCCT
1 AAACCCT
1539694 AAACCCT
1 AAACCCT
1539701 AAACCCT
1 AAACCCT
1539708 AAAC
1 AAAC
1539712 ATTATAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:1540715 original size:20 final size:20
Alignment explanation
Indices: 1540663--1540717 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
1540653 CGCTGAAATG
* *
1540663 TAAACTCTAAACCTTAAAAC
1 TAAACTCTAAGCCCTAAAAC
* * *
1540683 TCAATCTCCAAGCCCTAAACC
1 T-AAACTCTAAGCCCTAAAAC
1540704 TAAACTCTAAGCCC
1 TAAACTCTAAGCCC
1540718 AGAACACAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.40, C:0.35, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAACTCTAAGCCCTAAAAC
Found at i:1541399 original size:114 final size:114
Alignment explanation
Indices: 1541199--1541413 Score: 317
Period size: 114 Copynumber: 1.9 Consensus size: 114
1541189 TATCCCAATA
* * *
1541199 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAGCAATAAAACAGTAGCGTTTT
1 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAGTACCGTGTT
*
1541264 GTCCAAATTTTTTCCTTAAATTAGATATCTTTACCGCCCAATTCAATCT
66 GTCCAAATTTTTTCCTCAAATTAGATATCTTTACCGCCCAATTCAATCT
* *
1541313 TTTGCGGCGTTTTTTACAATGCGCTACTAAAGCAATAAAATGAAACAATAAAAC-GATACCGTGT
1 TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAG-TACCGTGT
* * *
1541377 TG-CTCACATTTTTTCCTCAAATTTGTTATCTTTACCG
65 TGTC-CAAATTTTTTCCTCAAATTAGATATCTTTACCG
1541414 GCGTTTCTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
113 2 0.02
114 88 0.98
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (114 bp):
TTTGCGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAATAAAACAGTACCGTGTT
GTCCAAATTTTTTCCTCAAATTAGATATCTTTACCGCCCAATTCAATCT
Found at i:1541996 original size:17 final size:18
Alignment explanation
Indices: 1541976--1542028 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
1541966 TTTGGTGACT
*
1541976 TCGCATTTTTAG-TGAGC
1 TCGCACTTTTAGATGAGC
* *
1541993 TCGCACATTT-GATAAGC
1 TCGCACTTTTAGATGAGC
*
1542010 TCGCAGTTTTAGATGAGC
1 TCGCACTTTTAGATGAGC
1542028 T
1 T
1542029 TGCAGGTGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 1 0.04
17 20 0.71
18 7 0.25
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (18 bp):
TCGCACTTTTAGATGAGC
Found at i:1544891 original size:68 final size:67
Alignment explanation
Indices: 1544812--1544947 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 67
1544802 TGATTAAACT
* *
1544812 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTATATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATAC-TATCAAGATAAATATTAAATTAAATTTAATATT
1544877 AAA
65 AAA
** *
1544880 TAATCACTTTAATATTAAATTAATAAAATACTATTTAGATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAATTTAATATTA
1544945 AA
66 AA
1544947 T
1 T
1544948 CTATTAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
67 33 0.52
68 30 0.48
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (67 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATCAAGATAAATATTAAATTAAATTTAATATTA
AA
Found at i:1544901 original size:24 final size:23
Alignment explanation
Indices: 1544812--1544911 Score: 59
Period size: 24 Copynumber: 4.3 Consensus size: 23
1544802 TGATTAAACT
1544812 TAATCACTTTAATATTAAATTAATA
1 TAAT-ACTTTAATATTAAATTAA-A
*
1544837 TAATACTTATCAAGA-TAAA-T--A
1 TAATACTT-T-AATATTAAATTAAA
* *
1544858 TTATA-TTAAAT-TTAATATTAAA
1 TAATACTTTAATATTAA-ATTAAA
1544880 TAATCACTTTAATATTAAATTAATA
1 TAAT-ACTTTAATATTAAATTAA-A
*
1544905 AAATACT
1 TAATACT
1544912 ATTTAGATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 23
0.66 0.08 0.26
Matches are distributed among these distances:
18 5 0.09
19 1 0.02
20 3 0.05
21 5 0.09
22 4 0.07
23 1 0.02
24 18 0.32
25 17 0.30
26 3 0.05
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATACTTTAATATTAAATTAAA
Found at i:1544961 original size:68 final size:68
Alignment explanation
Indices: 1544821--1544964 Score: 182
Period size: 67 Copynumber: 2.1 Consensus size: 68
1544811 TTAATCACTT
* *
1544821 TAATATTAAATTAATATAATACTTATCAAGATAAATATTATATTAAATTTAATATTAAATAATCA
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATAATCA
***
1544886 CTT
66 AAA
** * * *
1544889 TAATATTAAATTAATAAAATAC-TATTTAGATAAGTATTAAATTAAATTTAATATTAAATCTATT
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAT-AATC
1544953 AAAA
65 AAAA
1544957 TAATATTA
1 TAATATTA
1544965 TTTTTAGAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
67 33 0.51
68 32 0.49
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (68 bp):
TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATAATCA
AAA
Found at i:1545225 original size:11 final size:11
Alignment explanation
Indices: 1545211--1545270 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
1545201 ATTTTTTTTT
1545211 TATTTTTAAAA
1 TATTTTTAAAA
1545222 TA-TTTTAAAA
1 TATTTTTAAAA
*
1545232 TACTTTTT---T
1 TA-TTTTTAAAA
*
1545241 TATTTTTTAAA
1 TATTTTTAAAA
1545252 TATTTTTAAAA
1 TATTTTTAAAA
1545263 TACTTTTT
1 TA-TTTTT
1545271 TAATTTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
8 5 0.12
9 2 0.05
10 10 0.25
11 14 0.35
12 9 0.22
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:1545239 original size:31 final size:32
Alignment explanation
Indices: 1545204--1545271 Score: 113
Period size: 30 Copynumber: 2.2 Consensus size: 32
1545194 AATAAATATT
1545204 TTTTTTTTATTTTTAAAATA-TTTTAAAATAC
1 TTTTTTTTATTTTTAAAATATTTTTAAAATAC
*
1545235 -TTTTTTTATTTTTTAAATATTTTTAAAATAC
1 TTTTTTTTATTTTTAAAATATTTTTAAAATAC
1545266 TTTTTT
1 TTTTTT
1545272 AATTTTCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 18 0.53
31 11 0.32
32 5 0.15
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTTTTTTATTTTTAAAATATTTTTAAAATAC
Found at i:1545277 original size:31 final size:31
Alignment explanation
Indices: 1545205--1545289 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
1545195 ATAAATATTT
*
1545205 TTTTTTTATTTTTAAAATA-TTTTAAAATAC
1 TTTTTTTATTTTTTAAATATTTTTAAAATAC
1545235 TTTTTTTATTTTTTAAATATTTTTAAAATAC
1 TTTTTTTATTTTTTAAATATTTTTAAAATAC
* * *
1545266 TTTTTTAATTTTCTAAATTTTTTT
1 TTTTTTTATTTTTTAAATATTTTT
1545290 TGGTGTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 18 0.36
31 32 0.64
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.66
Consensus pattern (31 bp):
TTTTTTTATTTTTTAAATATTTTTAAAATAC
Found at i:1555177 original size:23 final size:24
Alignment explanation
Indices: 1555151--1555242 Score: 76
Period size: 23 Copynumber: 4.2 Consensus size: 24
1555141 TAATAAATAC
* *
1555151 AAAAAATTTGTTTTAAAAAT-TTT
1 AAAAAATGTATTTTAAAAATATTT
1555174 AAAAAATGTATTTTAAAAATATTT
1 AAAAAATGTATTTTAAAAATATTT
* *
1555198 -TAAAAT-TA----AAAAATA-AT
1 AAAAAATGTATTTTAAAAATATTT
1555215 AAAAAA-GTATTTTAAAAATATTT
1 AAAAAATGTATTTTAAAAATATTT
*
1555238 TAAAA
1 AAAAA
1555243 TTAAAAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
17 1 0.02
18 13 0.24
22 9 0.17
23 28 0.52
24 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (24 bp):
AAAAAATGTATTTTAAAAATATTT
Found at i:1555196 original size:11 final size:11
Alignment explanation
Indices: 1555161--1555242 Score: 59
Period size: 11 Copynumber: 7.7 Consensus size: 11
1555151 AAAAAATTTG
1555161 TTTTAAAAAT-
1 TTTTAAAAATA
*
1555171 TTTAAAAAATGTA
1 TTTTAAAAA--TA
1555184 TTTTAAAAATA
1 TTTTAAAAATA
1555195 TTTT--AAA-A
1 TTTTAAAAATA
*
1555203 -TTAAAAAATA
1 TTTTAAAAATA
* *
1555213 -ATAAAAAAGTA
1 TTTTAAAAA-TA
1555224 TTTTAAAAATA
1 TTTTAAAAATA
1555235 TTTTAAAA
1 TTTTAAAA
1555243 TTAAAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
7 2 0.03
8 1 0.02
9 6 0.10
10 16 0.28
11 18 0.31
12 7 0.12
13 8 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:1555208 original size:40 final size:39
Alignment explanation
Indices: 1555163--1555249 Score: 138
Period size: 40 Copynumber: 2.2 Consensus size: 39
1555153 AAAATTTGTT
**
1555163 TTAAAAATTTTAAAAAATGTATTTTAAAAATATTTTAAAA
1 TTAAAAATAATAAAAAA-GTATTTTAAAAATATTTTAAAA
1555203 TTAAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAA
1 TT-AAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAA
1555243 TTAAAAA
1 TTAAAAA
1555250 AAATTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 5 0.11
40 26 0.59
41 13 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (39 bp):
TTAAAAATAATAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:1555250 original size:40 final size:41
Alignment explanation
Indices: 1555173--1555250 Score: 149
Period size: 40 Copynumber: 1.9 Consensus size: 41
1555163 TTAAAAATTT
1555173 TAAAAAATGTATTTTAAAAATATTTTAAAATTAAAAAATAA
1 TAAAAAATGTATTTTAAAAATATTTTAAAATTAAAAAATAA
1555214 TAAAAAA-GTATTTTAAAAATATTTTAAAATTAAAAAA
1 TAAAAAATGTATTTTAAAAATATTTTAAAATTAAAAAA
1555251 AATTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 30 0.81
41 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (41 bp):
TAAAAAATGTATTTTAAAAATATTTTAAAATTAAAAAATAA
Found at i:1555940 original size:9 final size:9
Alignment explanation
Indices: 1555928--1555971 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
1555918 AATTTAACAT
1555928 ATTTTTATA
1 ATTTTTATA
1555937 ATTTTTATA
1 ATTTTTATA
1555946 A-TTTT-TA
1 ATTTTTATA
*
1555953 ATTTTTAAA
1 ATTTTTATA
*
1555962 ATTTTAATA
1 ATTTTTATA
1555971 A
1 A
1555972 CTTAATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 3 0.10
8 8 0.27
9 19 0.63
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:1555956 original size:16 final size:17
Alignment explanation
Indices: 1555930--1555967 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1555920 TTTAACATAT
*
1555930 TTTTATAATTTTTATAA
1 TTTTATAATTTTTAAAA
1555947 TTTT-TAATTTTTAAAA
1 TTTTATAATTTTTAAAA
1555963 TTTTA
1 TTTTA
1555968 ATAACTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATAATTTTTAAAA
Found at i:1557396 original size:13 final size:13
Alignment explanation
Indices: 1557367--1557407 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1557357 AAAAAATAAT
*
1557367 AAAATTTATAAAC
1 AAAATTTATAAAA
1557380 AAAATTTATAAAAA
1 AAAATTTAT-AAAA
*
1557394 AAAAGTTATAAAA
1 AAAATTTATAAAA
1557407 A
1 A
1557408 GTTTACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAATTTATAAAA
Found at i:1557402 original size:14 final size:14
Alignment explanation
Indices: 1557367--1557407 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1557357 AAAAAATAAT
*
1557367 AAAATTTAT-AAAC
1 AAAATTTATAAAAA
1557380 AAAATTTATAAAAA
1 AAAATTTATAAAAA
*
1557394 AAAAGTTATAAAAA
1 AAAATTTATAAAAA
1557408 GTTTACAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (14 bp):
AAAATTTATAAAAA
Found at i:1557407 original size:12 final size:12
Alignment explanation
Indices: 1557362--1557395 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1557352 TTATTAAAAA
*
1557362 ATAATAAAATTT
1 ATAAAAAAATTT
1557374 ATAAACAAAATTT
1 ATAAA-AAAATTT
1557387 ATAAAAAAA
1 ATAAAAAAA
1557396 AAGTTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAAAAAAATTT
Found at i:1557985 original size:22 final size:23
Alignment explanation
Indices: 1557949--1557992 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
1557939 AATTTTGTTT
1557949 ATAATTTTTATAATTTTAAAAAA
1 ATAATTTTTATAATTTTAAAAAA
1557972 ATAATTTTTA-AATTTTAAAAA
1 ATAATTTTTATAATTTTAAAAA
1557993 GGATTAATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAATTTTTATAATTTTAAAAAA
Found at i:1559398 original size:12 final size:13
Alignment explanation
Indices: 1559378--1559407 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1559368 AGCCAACAAA
1559378 TATTATTTATTTT
1 TATTATTTATTTT
1559391 TATT-TTTATTTT
1 TATTATTTATTTT
1559403 TATTA
1 TATTA
1559408 GTAGTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTATTTATTTT
Found at i:1565775 original size:5 final size:5
Alignment explanation
Indices: 1565731--1565757 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1565721 GATTCTTGTT
1565731 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1565758 GGTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1567982 original size:107 final size:110
Alignment explanation
Indices: 1567859--1568056 Score: 269
Period size: 107 Copynumber: 1.8 Consensus size: 110
1567849 GTAAAAATTT
* *
1567859 TTTCATTTTGAACAAAATGAC-TCCGTTTTGCTATTCTAAAAAAATTTTA-TT-TT-TTTTATAA
1 TTTCATCTTGAACAAAATGACGT-CGTTTTGCTATGCTAAAAAAATTTTATTTATTGTTTTATAA
1567920 ATTGATTTAAATTTTGCGGCGTTTTTATATAAAAAAAACGCCGCTA
65 ATTGATTTAAATTTTGCGGCGTTTTTATATAAAAAAAACGCCGCTA
*** *
1567966 TTTCATCTTGAACAAAATGACGTCGTTTTGCTATGCTAAAATTTTTTTATTTTATTGTTTTATAT
1 TTTCATCTTGAACAAAATGACGTCGTTTTGCTATGCTAAAAAAATTTTA-TTTATTGTTTTATAA
***
1568031 ATTGATTTGTTTTTTGCGGCGTTTTT
65 ATTGATTTAAATTTTGCGGCGTTTTT
1568057 TTCTATTTCA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
107 42 0.55
108 1 0.01
109 2 0.03
110 2 0.03
111 30 0.39
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (110 bp):
TTTCATCTTGAACAAAATGACGTCGTTTTGCTATGCTAAAAAAATTTTATTTATTGTTTTATAAA
TTGATTTAAATTTTGCGGCGTTTTTATATAAAAAAAACGCCGCTA
Found at i:1568081 original size:96 final size:95
Alignment explanation
Indices: 1567963--1568153 Score: 283
Period size: 96 Copynumber: 2.0 Consensus size: 95
1567953 AAAAACGCCG
* ** **
1567963 CTATTTCATCTTGAACAAAATGACGTCGTTTTGCTATGCTAAAATTTTTTTATTTTATTGTTTTA
1 CTATTTCATCTTCAACAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATT-TTTTA
* *
1568028 TATATTGATTTGTTTTTTGCGGCGTTTTTTT
65 TAAATTGATTTATTTTTTGCGGCGTTTTTTT
* * *
1568059 CTATTTCATTTTCAGCAGAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTAT
1 CTATTTCATCTTCAACAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTAT
1568124 AAATTGATTTATTTTTTGCGGCGTTTTTTT
66 AAATTGATTTATTTTTTGCGGCGTTTTTTT
1568154 TTTAAAACGC
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 34 0.40
96 51 0.60
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.54
Consensus pattern (95 bp):
CTATTTCATCTTCAACAAAATGACACCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTAT
AAATTGATTTATTTTTTGCGGCGTTTTTTT
Found at i:1568321 original size:114 final size:115
Alignment explanation
Indices: 1568178--1568514 Score: 410
Period size: 108 Copynumber: 3.0 Consensus size: 115
1568168 ATTGCTTACC
* *
1568178 TTTAGCGGCGTTTTTATGAGAAATGCCGCAAAAAATTTTTCATTTTGAACAAAATGACGCCATTT
1 TTTAGCGGCGTTTTTATGAGAAACGCCGCAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTT
1568243 TGCTATGCTAAAAATTTTTTATTTTATTTTTTATATATATTGATTTGTT-T
66 TGCTATGCTAAAAATTTTTTATTTTATTTTTTATATA-ATTGATTTGTTCT
* * *
1568293 TTT-GCGGCGTTTTTTAT-AAAAACGCCGC----AA--TTTCATTTTCAGCAAAATGACGCCGTT
1 TTTAGCGGCG-TTTTTATGAGAAACGCCGCAAAAAATTTTTCATTTTGAACAAAATGACGCCGTT
** * *
1568350 TTGCTATATTAAAAAATTTTTATTTTATTTTTT-TATAAATTGATGTATTTTTTGCT
65 TTGCTATGCTAAAAATTTTTTATTTTATTTTTTATAT-AA-T--TG-ATTTGTT-CT
* *
1568406 TTTAGCAGCGTTTTTATGAGAAACGCCGCAAAAATTTTTTCATTTTGAACAAAATGACGCCGTTT
1 TTTAGCGGCGTTTTTATGAGAAACGCCGCAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTT
1568471 TGCTATGCTAAAAATTTTTTATTTT-TATTTTTATA-AATTGATTT
66 TGCTATGCTAAAAATTTTTTATTTTAT-TTTTTATATAATTGATTT
1568515 CTTATAAAAT
Statistics
Matches: 187, Mismatches: 17, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
107 4 0.02
108 56 0.30
110 4 0.02
111 6 0.03
113 11 0.06
114 30 0.16
115 14 0.07
116 2 0.01
118 2 0.01
119 3 0.02
120 53 0.28
121 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.47
Consensus pattern (115 bp):
TTTAGCGGCGTTTTTATGAGAAACGCCGCAAAAAATTTTTCATTTTGAACAAAATGACGCCGTTT
TGCTATGCTAAAAATTTTTTATTTTATTTTTTATATAATTGATTTGTTCT
Found at i:1569088 original size:15 final size:14
Alignment explanation
Indices: 1569071--1569141 Score: 65
Period size: 14 Copynumber: 4.9 Consensus size: 14
1569061 ATCCCTGAAT
*
1569071 CCCTAAACCTTAAAT
1 CCCTAAACCTT-AAC
1569086 CCCT-AACTCTTAAC
1 CCCTAAAC-CTTAAC
*
1569100 CCCT-AACATCTAAC
1 CCCTAAACCT-TAAC
*
1569114 CCCTAAACTCCTAAC
1 CCCTAAAC-CTTAAC
1569129 CCCTAAACCTTAA
1 CCCTAAACCTTAA
1569142 ATCCCACCCC
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.02
14 24 0.51
15 22 0.47
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAACCTTAAC
Found at i:1569164 original size:20 final size:20
Alignment explanation
Indices: 1569127--1569166 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1569117 TAAACTCCTA
*
1569127 ACCCCTAAACCTTAAATCCC
1 ACCCCTAAACCATAAATCCC
1569147 ACCCCTTAAACCAT-AATCCC
1 ACCCC-TAAACCATAAATCCC
1569167 TAATTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.20
Consensus pattern (20 bp):
ACCCCTAAACCATAAATCCC
Found at i:1569175 original size:14 final size:14
Alignment explanation
Indices: 1569157--1569198 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1569147 ACCCCTTAAA
1569157 CCATAATCCCTAAT
1 CCATAATCCCTAAT
*
1569171 TCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
1569186 CCATACTCCCTAA
1 CCATAATCCCTAA
1569199 ACCTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:1569195 original size:15 final size:15
Alignment explanation
Indices: 1569153--1569199 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1569143 TCCCACCCCT
1569153 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
1569167 T-AATTCATAATCCC
1 TAAATCCATAATCCC
*
1569181 TAAATCCATACTCCC
1 TAAATCCATAATCCC
1569196 TAAA
1 TAAA
1569200 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:1569403 original size:15 final size:15
Alignment explanation
Indices: 1569385--1569435 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1569375 CCTAGCATGT
1569385 CTAACCCTTAAATCC
1 CTAACCCTTAAATCC
* *
1569400 CTAACCATCT-AACCC
1 CTAACCCT-TAAATCC
*
1569415 CTAAACCTTAAATCC
1 CTAACCCTTAAATCC
1569430 C-AACCC
1 CTAACCC
1569436 CTAATCCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
14 5 0.18
15 22 0.79
16 1 0.04
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (15 bp):
CTAACCCTTAAATCC
Found at i:1569991 original size:114 final size:113
Alignment explanation
Indices: 1569765--1570301 Score: 700
Period size: 114 Copynumber: 4.7 Consensus size: 113
1569755 AGCATTTTTG
** * *
1569765 GCCGCTAAATCCCTAAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGAATTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTA-AGTTTTTTGCGGCGCTTTC
* *
1569830 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTCTTAAAAAT
65 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * *
1569879 GCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTCAAGTTTTTTGCGGCGCTTTCT
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAGTTTTTTGCGGCGCTTTCT
*
1569944 CAAAAACGCCGCAAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAAC
66 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAAAAC
* * * * * * * *
1569993 GCCACTAAATCCCTGAAAGCTAACAAAACGGTGTCGTTGGGTTTAGGATTTCTTGCGGCG-TTTT
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAG-TTTTTTGCGGCGCTTTC
* * * *
1570057 TGAGGAAGCGCCGCTAAATCCCTGAGCATTAGCGGCGCTTTAC-TAAAAAC
65 TCA-AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTT-CTTAAAAAC
*
1570107 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAGTTTTTTTGCGGCACTTTT
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAG-TTTTTTGCGGCGC-TTT
* *
1570172 ATCAAAAACGCCGCTAAAGCCCTGAGCATTAGTGGCGCTTTCTTAAAAAC
64 CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * **** * *
1570222 GCCACTAAACCCCCGAAAGCTTGGGAAACGGTGTCGTTGGGCTTAGGTTTTTTGCGGCGCTTTCT
1 GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAGTTTTTTGCGGCGCTTTCT
1570287 CAAAAACGCCGCTAA
66 CAAAAACGCCGCTAA
1570302 TGCTTATTTT
Statistics
Matches: 368, Mismatches: 48, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
113 78 0.21
114 160 0.43
115 124 0.34
116 6 0.02
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (113 bp):
GCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAGTTTTTTGCGGCGCTTTCT
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
Found at i:1582947 original size:18 final size:17
Alignment explanation
Indices: 1582924--1582961 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
1582914 AAAAAAATGT
1582924 AATAATGTAATCTCATGC
1 AATAATGTAATCTCAT-C
1582942 AATAATGTAATCTCATC
1 AATAATGTAATCTCATC
1582959 AAT
1 AAT
1582962 TACACTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (17 bp):
AATAATGTAATCTCATC
Found at i:1592358 original size:18 final size:17
Alignment explanation
Indices: 1592325--1592363 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1592315 TTTTATAAAT
1592325 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1592343 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1592360 TGTG
1 TGTG
1592364 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1592608 original size:23 final size:23
Alignment explanation
Indices: 1592581--1592656 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
1592571 AGTGTTATTG
1592581 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1592604 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1592627 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1592650 ATCAGTG
1 ATCAGTG
1592657 TGGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1594755 original size:16 final size:16
Alignment explanation
Indices: 1594722--1594775 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1594712 AAAAGATCCA
**
1594722 AGCCCGAGAAAATTTG
1 AGCCCGAGAAAACCTG
*
1594738 AGCCCGACAAAACCTG
1 AGCCCGAGAAAACCTG
**
1594754 AGCTTGAGAAAACCTG
1 AGCCCGAGAAAACCTG
1594770 AGCCCG
1 AGCCCG
1594776 TAACAAACTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.35, C:0.28, G:0.24, T:0.13
Consensus pattern (16 bp):
AGCCCGAGAAAACCTG
Found at i:1595518 original size:22 final size:23
Alignment explanation
Indices: 1595490--1595536 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1595480 CATAGAATGT
1595490 ATTATTAT-TATATATAATAATA
1 ATTATTATATATATATAATAATA
*
1595512 ATTATTATAATATATATTATAATA
1 ATTATTAT-ATATATATAATAATA
1595536 A
1 A
1595537 AAGATATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
24 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTATTATATATATATAATAATA
Found at i:1595523 original size:12 final size:13
Alignment explanation
Indices: 1595489--1595536 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
1595479 ACATAGAATG
* *
1595489 TATTATTATTATA
1 TATTATAATAATA
*
1595502 TATAATAATAAT-
1 TATTATAATAATA
1595514 TATTATAAT-ATA
1 TATTATAATAATA
1595526 TATTATAATAA
1 TATTATAATAA
1595537 AAGATATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 2 0.07
12 17 0.59
13 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTATAATAATA
Done.