Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold73
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: 1308442
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.31
Warning! 157727 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:305562 original size:63 final size:62
Alignment explanation
Indices: 305432--305555 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 62
305422 GATCGAGTTA
* ** * * *
305432 TAAT-ATTATTTTTTTAAATAAAATTTATTTAAAATTTATTTTAATTTAATTTAAAATTTTAT
1 TAATAATTATATTTTTAAATAAAATTTAAATAAAATATATTTTAAATT-ATTTAAAAATTTAT
*
305494 TAATAATTATATTTTTATAATTAAATTTAAATAAAA-ATATTTTAAATT-TTTAAAAATTTAT
1 TAATAATTATATTTTTA-AATAAAATTTAAATAAAATATATTTTAAATTATTTAAAAATTTAT
305555 T
1 T
305556 TAAATAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
61 13 0.25
62 4 0.08
63 21 0.40
64 15 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (62 bp):
TAATAATTATATTTTTAAATAAAATTTAAATAAAATATATTTTAAATTATTTAAAAATTTAT
Found at i:305715 original size:21 final size:22
Alignment explanation
Indices: 305689--305729 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
305679 TATTAAATAT
*
305689 TATTTTAT-ATTAATTTTTATA
1 TATTTTATAATTAAATTTTATA
305710 TATTTTATAATTAAATTTTA
1 TATTTTATAATTAAATTTTA
305730 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTATAATTAAATTTTATA
Found at i:305764 original size:18 final size:19
Alignment explanation
Indices: 305741--305778 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
305731 AAAATTAATT
* *
305741 AATAAATAATTTA-ATTTA
1 AATAAAAAATATATATTTA
305759 AATAAAAAATATATATTTA
1 AATAAAAAATATATATTTA
305778 A
1 A
305779 TTTTAATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAAAATATATATTTA
Found at i:312861 original size:2 final size:2
Alignment explanation
Indices: 312854--312889 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
312844 AGGAAATAAC
312854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
312890 GAACTACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:315422 original size:2 final size:2
Alignment explanation
Indices: 315415--315439 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
315405 CAGCAGCAAC
315415 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
315440 AAGAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:317802 original size:35 final size:35
Alignment explanation
Indices: 317709--317802 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
317699 TTTTCAAGAT
* * *
317709 ATTATTTTAATATT-ATTTTATTTAATATAGTAAAA
1 ATTA-TTTAATATTAAATTAATTTAATATAATAAAA
* *
317744 A--ATATATTATTAATATTATATTTAATATAATAAAA
1 ATTATTTAATATTAA-ATTA-ATTTAATATAATAAAA
317779 ATTATTTAATATTAAATTAATTTA
1 ATTATTTAATATTAAATTAATTTA
317803 TAAATTAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
32 7 0.15
33 2 0.04
34 2 0.04
35 22 0.47
36 4 0.09
37 10 0.21
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
ATTATTTAATATTAAATTAATTTAATATAATAAAA
Found at i:323101 original size:20 final size:20
Alignment explanation
Indices: 323078--323119 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
323068 TTAAAAATTA
* * *
323078 AAAATTTGTTTGATTAAAAT
1 AAAATTTATTTAAATAAAAT
323098 AAAATTTATTTAAATAAAAT
1 AAAATTTATTTAAATAAAAT
323118 AA
1 AA
323120 TAAAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
AAAATTTATTTAAATAAAAT
Found at i:323770 original size:31 final size:29
Alignment explanation
Indices: 323735--323802 Score: 68
Period size: 28 Copynumber: 2.3 Consensus size: 29
323725 ATAAAGTCAA
323735 TAAATTTTTATATTCGATAAAAATAATATAT
1 TAAATTTTTATATTC-ATAAAAATAATA-AT
* * *
323766 TAAA--TATATATTCTTTAAAATAATAAT
1 TAAATTTTTATATTCATAAAAATAATAAT
323793 TAAATATTTT
1 TAAAT-TTTT
323803 TAACTAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
27 6 0.20
28 10 0.33
29 8 0.27
30 2 0.07
31 4 0.13
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
TAAATTTTTATATTCATAAAAATAATAAT
Found at i:323784 original size:29 final size:27
Alignment explanation
Indices: 323743--323799 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
323733 AATAAATTTT
323743 TATATTCGATAAAAATAATATATTAAATA
1 TATATTCGAT-AAAATAATA-ATTAAATA
**
323772 TATATTCTTTAAAATAATAATTAAATA
1 TATATTCGATAAAATAATAATTAAATA
323799 T
1 T
323800 TTTTAACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 9 0.35
28 9 0.35
29 8 0.31
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
TATATTCGATAAAATAATAATTAAATA
Found at i:324835 original size:3 final size:3
Alignment explanation
Indices: 324827--324864 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
324817 TTACCAAGTT
324827 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
324865 GTTATGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:325242 original size:18 final size:16
Alignment explanation
Indices: 325202--325246 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
325192 TAAGAATTAT
*
325202 TTATTTTGTATTTTAA
1 TTATTTTATATTTTAA
*
325218 TTTTTTTATATTTAATAA
1 TTATTTTATATTT--TAA
325236 TTATTTTATAT
1 TTATTTTATAT
325247 ATCATTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTTTATATTTTAA
Found at i:326959 original size:27 final size:27
Alignment explanation
Indices: 326929--327013 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 27
326919 ATATAATATA
326929 TTATATAATATATAATTATATTAAATT
1 TTATATAATATATAATTATATTAAATT
* * *
326956 TTATATAAAATAAAATTTTAATATATTAAAAT
1 TTATATAATATATAA---T--TATATTAAATT
*
326988 TTATATAAATATATAA-TATTTTAAAT
1 TTATAT-AATATATAATTATATTAAAT
327014 ATAATTATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
27 21 0.47
30 1 0.02
32 16 0.36
33 7 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTATATAATATATAATTATATTAAATT
Found at i:326960 original size:20 final size:19
Alignment explanation
Indices: 326919--327010 Score: 63
Period size: 20 Copynumber: 5.1 Consensus size: 19
326909 AATAATTAAA
* **
326919 ATATAATATATTATATAAT
1 ATATAATATATTAAATTTT
326938 ATATAATTATATTAAATTTT
1 ATATAA-TATATTAAATTTT
*
326958 ATATAA-A-A-TAAA-ATT
1 ATATAATATATTAAATTTT
*
326973 -T-TAATATATTAAAATTT
1 ATATAATATATTAAATTTT
326990 ATATAA-ATATATAATATTTT
1 ATATAATATAT-TAA-ATTTT
327010 A
1 A
327011 AATATAATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
13 3 0.05
14 2 0.03
15 3 0.05
16 8 0.14
17 3 0.05
18 6 0.10
19 12 0.21
20 21 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATAATATATTAAATTTT
Found at i:326981 original size:32 final size:36
Alignment explanation
Indices: 326908--327016 Score: 115
Period size: 32 Copynumber: 3.2 Consensus size: 36
326898 ATACGAAAAA
* * *
326908 AAATA-ATTAAAATATA-ATATATTATATAATA-TAT
1 AAATATATTAAAATTTATATA-AATATATAATATTTT
* *
326942 AATTATATTAAATTTTATATAAA-ATA-AA-ATTTT
1 AAATATATTAAAATTTATATAAATATATAATATTTT
326975 -AATATATTAAAATTTATATAAATATATAATATTTT
1 AAATATATTAAAATTTATATAAATATATAATATTTT
327010 AAATATA
1 AAATATA
327017 ATTATAATAC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
32 21 0.34
33 7 0.11
34 9 0.15
35 15 0.25
36 9 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
AAATATATTAAAATTTATATAAATATATAATATTTT
Found at i:327874 original size:20 final size:20
Alignment explanation
Indices: 327810--327874 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
327800 AAGTTGAATA
*
327810 TATATATTT-TTATTAATTATT
1 TATATATTTAATATTAA--ATT
*
327831 TATTATATTTAATATTAAAAT
1 TA-TATATTTAATATTAAATT
*
327852 TATATATTTAATATTTAATT
1 TATATATTTAATATTAAATT
327872 TAT
1 TAT
327875 TTTTTAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 19 0.50
21 6 0.16
22 7 0.18
23 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATATTTAATATTAAATT
Found at i:331123 original size:13 final size:14
Alignment explanation
Indices: 331099--331127 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
331089 TAGTTTGAAA
331099 ATAATCTTATTTTG
1 ATAATCTTATTTTG
331113 ATAAT-TTATTTTG
1 ATAATCTTATTTTG
331126 AT
1 AT
331128 TTCAAGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (14 bp):
ATAATCTTATTTTG
Found at i:332024 original size:34 final size:34
Alignment explanation
Indices: 331981--332055 Score: 150
Period size: 34 Copynumber: 2.2 Consensus size: 34
331971 TAATGCTTAA
331981 CCTTTTGTTTATTTCTTCGTCGATAAGTTCATAT
1 CCTTTTGTTTATTTCTTCGTCGATAAGTTCATAT
332015 CCTTTTGTTTATTTCTTCGTCGATAAGTTCATAT
1 CCTTTTGTTTATTTCTTCGTCGATAAGTTCATAT
332049 CCTTTTG
1 CCTTTTG
332056 ATTTTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.53
Consensus pattern (34 bp):
CCTTTTGTTTATTTCTTCGTCGATAAGTTCATAT
Found at i:335686 original size:22 final size:22
Alignment explanation
Indices: 335669--335719 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
335659 GATGAAACTT
*
335669 AGAGAAAAGCTACTTGAAGCCA
1 AGAGAAAAGCTACTTGAAGCTA
*
335691 AGAGCGAAAAGCTACTTGAAGCTG
1 AGA--GAAAAGCTACTTGAAGCTA
335715 AGAGA
1 AGAGA
335720 CAAACAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.20
24 20 0.80
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.14
Consensus pattern (22 bp):
AGAGAAAAGCTACTTGAAGCTA
Found at i:336718 original size:2 final size:2
Alignment explanation
Indices: 336711--336742 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
336701 TCATATAACA
336711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
336743 GAATATTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339142 original size:20 final size:20
Alignment explanation
Indices: 339113--339166 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
339103 AAGATTACTC
*
339113 AATATGATTACATTT-ACCTT
1 AATATAATTACATTTAACC-T
339133 AATATAATTACATTTAACCT
1 AATATAATTACATTTAACCT
339153 AATATAATTACATT
1 AATATAATTACATT
339167 CAATTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (20 bp):
AATATAATTACATTTAACCT
Found at i:339175 original size:20 final size:20
Alignment explanation
Indices: 339113--339189 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
339103 AAGATTACTC
* * *
339113 AATATGATTACATTTACCTT
1 AATATAATTACATTCAACTT
* *
339133 AATATAATTACATTTAACCT
1 AATATAATTACATTCAACTT
*
339153 AATATAATTACATTCAATTT
1 AATATAATTACATTCAACTT
* *
339173 AATATGATTATATTCAA
1 AATATAATTACATTCAA
339190 ATCATACGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.43
Consensus pattern (20 bp):
AATATAATTACATTCAACTT
Found at i:340308 original size:19 final size:20
Alignment explanation
Indices: 340270--340329 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 20
340260 TTTAAAAAAT
* * *
340270 ATTATATTTAACTTAATATA
1 ATTATATTCAAATCAATATA
340290 ATTATATTCAAA-CAATATA
1 ATTATATTCAAATCAATATA
*
340309 ATTATATTTAAATC-ATATA
1 ATTATATTCAAATCAATATA
340328 AT
1 AT
340330 ACTGTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 24 0.69
20 11 0.31
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATATTCAAATCAATATA
Found at i:341006 original size:18 final size:17
Alignment explanation
Indices: 340957--341011 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
340947 TTGGGTCAAG
340957 TATTATTATAATTATAGA
1 TATTATTATAATTATA-A
* *
340975 TA-TAATAAATATTATAA
1 TATTATTATA-ATTATAA
340992 TATTATTATTAATTATAA
1 TATTATTA-TAATTATAA
341010 TA
1 TA
341012 AATACAAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 8 0.27
18 21 0.70
19 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATTATTATAATTATAA
Found at i:342380 original size:22 final size:23
Alignment explanation
Indices: 342337--342380 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
342327 TTTTAATTTT
*
342337 TTTAATAATTTATGAATAATAAA
1 TTTAAAAATTTATGAATAATAAA
*
342360 TTTAAAAATTT-TGAATTATAA
1 TTTAAAAATTTATGAATAATAA
342381 CTTAGTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTAAAAATTTATGAATAATAAA
Found at i:342915 original size:2 final size:2
Alignment explanation
Indices: 342908--342944 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
342898 TGAATCATAC
*
342908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
342945 TTGGTACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:345840 original size:8 final size:8
Alignment explanation
Indices: 345827--345858 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
345817 TCTAGATAAC
345827 TGCAAGCA
1 TGCAAGCA
345835 TGCAAGCA
1 TGCAAGCA
345843 TGCAAGCA
1 TGCAAGCA
*
345851 AGCAAGCA
1 TGCAAGCA
345859 ACATAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.41, C:0.25, G:0.25, T:0.09
Consensus pattern (8 bp):
TGCAAGCA
Found at i:346425 original size:22 final size:21
Alignment explanation
Indices: 346400--346440 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
346390 ATTAAAAAGT
* *
346400 TATATTTTAAAATTTAAATAAA
1 TATATATT-AAATATAAATAAA
346422 TATATATTAAATATAAATA
1 TATATATTAAATATAAATA
346441 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATATTAAATATAAATAAA
Found at i:346433 original size:15 final size:14
Alignment explanation
Indices: 346411--346451 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
346401 ATATTTTAAA
346411 ATTTAAATAAATAT
1 ATTTAAATAAATAT
346425 ATATTAAATATAA-AT
1 AT-TTAAATA-AATAT
346440 ATTTAAA-AAATA
1 ATTTAAATAAATA
346452 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.08
13 2 0.08
14 7 0.29
15 11 0.46
16 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTTAAATAAATAT
Found at i:347814 original size:35 final size:37
Alignment explanation
Indices: 347775--347845 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
347765 ATATATTAAT
*
347775 AATAAATC-ATAAT-ATATTATTTTATTAAAA-AATAA
1 AATAAATCTA-AATAATATTATTTTAATAAAATAATAA
*
347810 AATAAATCTAAATAATTTTATTTTAATAAAATAATA
1 AATAAATCTAAATAATATTATTTTAATAAAATAATA
347846 TTATTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 11 0.35
36 16 0.52
37 4 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (37 bp):
AATAAATCTAAATAATATTATTTTAATAAAATAATAA
Found at i:347865 original size:29 final size:29
Alignment explanation
Indices: 347770--347866 Score: 69
Period size: 29 Copynumber: 3.4 Consensus size: 29
347760 AACAAATATA
* *
347770 TTAATAATAAATCATAAT-ATATTATTTTA-
1 TTAATAAT-AAT-AAAATAATATTATTTAAT
**
347799 TTAA-AA-AATAAAATAA-ATCTAAATAAT
1 TTAATAATAATAAAATAATAT-TATTTAAT
* **
347826 TTTATTTTAATAAAATAATATTATTTAAT
1 TTAATAATAATAAAATAATATTATTTAAT
347855 TTAATAATAATA
1 TTAATAATAATA
347867 CATCGTATTA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
25 6 0.12
26 8 0.16
27 3 0.06
28 2 0.04
29 29 0.58
30 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAATAATAATAAAATAATATTATTTAAT
Found at i:348883 original size:21 final size:21
Alignment explanation
Indices: 348849--348908 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 21
348839 TATTTTAAAG
*
348849 AAAACTTATATTTTTTAAATTA
1 AAAAATTAT-TTTTTTAAATTA
348871 AAAAATTA-TTTTTT--ATTA
1 AAAAATTATTTTTTTAAATTA
** *
348889 TTAAATTATTATTTTAAATT
1 AAAAATTATTTTTTTAAATT
348909 TTTTTAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
20 6 0.19
21 3 0.10
22 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAAATTATTTTTTTAAATTA
Found at i:349062 original size:2 final size:2
Alignment explanation
Indices: 349055--349091 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
349045 ATTGAGCTAT
349055 TA TA TA 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 TA TA TA T
349092 GGAGAGAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:349098 original size:2 final size:2
Alignment explanation
Indices: 349093--349141 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
349083 TATATATATG
349093 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
349135 GA GA GA G
1 GA GA GA G
349142 GAATATATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:350778 original size:21 final size:22
Alignment explanation
Indices: 350733--350778 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
350723 CGGTTACATA
* * *
350733 AAATTTAAAAAAATTTTAATTT
1 AAATTTAAAAAAATATCAATCT
350755 AAATTT-AAAAAATATCAATCT
1 AAATTTAAAAAAATATCAATCT
350776 AAA
1 AAA
350779 AATTTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATTTAAAAAAATATCAATCT
Found at i:350821 original size:26 final size:25
Alignment explanation
Indices: 350734--350827 Score: 79
Period size: 25 Copynumber: 3.7 Consensus size: 25
350724 GGTTACATAA
350734 AATTTAAAAAA-A-T-TT-TAATTT
1 AATTTAAAAAATATTATTATAATTT
* *
350755 AAATTTAAAAAATATCAATCTAAAAATTT
1 -AATTTAAAAAATAT-TAT-T-ATAATTT
* *
350784 ATTTTATAAAATATTATTATAATTT
1 AATTTAAAAAATATTATTATAATTT
350809 AATTTAAATAAATATTATT
1 AATTTAAA-AAATATTATT
350828 TATATTATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
22 11 0.20
23 1 0.02
25 12 0.21
26 12 0.21
27 3 0.05
28 12 0.21
29 5 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTAAAAAATATTATTATAATTT
Found at i:350828 original size:20 final size:20
Alignment explanation
Indices: 350805--350899 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
350795 TATTATTATA
350805 ATTTAAT-TTAAATAAATATT
1 ATTTAATATTAAAT-AATATT
350825 ATTTATATTATTAAATAATA--
1 ATTTA-A-TATTAAATAATATT
*
350845 ATTTAA-ATTAAATTATATT
1 ATTTAATATTAAATAATATT
* *
350864 AATTAATATT-TATAAATATT
1 ATTTAATATTAAAT-AATATT
* *
350884 ATTTAAAATTTAATAA
1 ATTTAATATTAAATAA
350900 ATTTTAACTC
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
17 10 0.17
19 8 0.13
20 28 0.47
21 3 0.05
22 5 0.08
23 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAATATTAAATAATATT
Found at i:350873 original size:40 final size:39
Alignment explanation
Indices: 350801--350901 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 39
350791 AAAATATTAT
* *
350801 TATAATTTAATTTAAATAAATATTATTTATA-TTATTAAA
1 TATAATTTAAATTAAATAAATATTATTAATATTTA-TAAA
*
350840 TAATAATTTAAATTAAAT-TATATTAATTAATATTTATAAA
1 T-ATAATTTAAATTAAATAAATATT-ATTAATATTTATAAA
* *
350880 TATTATTTAAAATTTAATAAAT
1 TATAATTT-AAATTAAATAAAT
350902 TTTAACTCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
39 12 0.24
40 34 0.67
41 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
TATAATTTAAATTAAATAAATATTATTAATATTTATAAA
Found at i:352397 original size:10 final size:10
Alignment explanation
Indices: 352382--352413 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
352372 ATTAATTTTA
352382 TAATTTAAAT
1 TAATTTAAAT
*
352392 TAATTTAATT
1 TAATTTAAAT
352402 TAATTTAAAT
1 TAATTTAAAT
352412 TA
1 TA
352414 TTATTCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:352506 original size:18 final size:19
Alignment explanation
Indices: 352485--352520 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
352475 AAATTACAAT
352485 TTAA-TTTAAAAAATAATA
1 TTAATTTTAAAAAATAATA
*
352503 TTAATTTTTAAAAATAAT
1 TTAATTTTAAAAAATAAT
352521 CATATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATTTTAAAAAATAATA
Found at i:355240 original size:12 final size:13
Alignment explanation
Indices: 355213--355237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
355203 ACATTAATAA
355213 AAAATATAATTTT
1 AAAATATAATTTT
355226 AAAATATAATTT
1 AAAATATAATTT
355238 AAATAATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATATAATTTT
Found at i:357255 original size:14 final size:15
Alignment explanation
Indices: 357230--357261 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
357220 TTTAATTTTA
357230 ATTTTATTAAAAATT
1 ATTTTATTAAAAATT
357245 ATTTT-TTAAAAATT
1 ATTTTATTAAAAATT
357259 ATT
1 ATT
357262 ACATAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTATTAAAAATT
Found at i:358420 original size:4 final size:4
Alignment explanation
Indices: 358413--358473 Score: 54
Period size: 4 Copynumber: 14.8 Consensus size: 4
358403 AGGTTTTATT
* *
358413 TTTA TTTA TTTA TTTA TTTA TTTAAA TTTA -TTA ATT- TTTA TTTGTG
1 TTTA TTTA TTTA TTTA TTTA TTT--A TTTA TTTA TTTA TTTA -TT-TA
358459 TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
358474 GAGTAATTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
3 5 0.10
4 34 0.71
5 4 0.08
6 5 0.10
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:358599 original size:13 final size:13
Alignment explanation
Indices: 358581--358617 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
358571 TTTTTAATAA
358581 ATTTAAATATTAT
1 ATTTAAATATTAT
358594 ATTT-AATATTTAT
1 ATTTAAATA-TTAT
358607 ATTTAAATATT
1 ATTTAAATATT
358618 TATCACTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAAATATTAT
Found at i:360724 original size:3 final size:3
Alignment explanation
Indices: 360718--360751 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
360708 TAATAAGAGT
360718 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
360752 AATAAAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:361041 original size:24 final size:25
Alignment explanation
Indices: 361009--361073 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
360999 GTTAATGATG
* *
361009 AATAAAATTATTAATTTTTA-AATT
1 AATATAATTATTAATTTTTATAAAT
361033 AATATAATT-TT-ATTTTTATAAAT
1 AATATAATTATTAATTTTTATAAAT
*
361056 AATAT-GTTAATTAATTTT
1 AATATAATT-ATTAATTTT
361074 AAAGAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 9 0.26
23 10 0.29
24 10 0.29
25 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
AATATAATTATTAATTTTTATAAAT
Found at i:361308 original size:44 final size:44
Alignment explanation
Indices: 361260--361344 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
361250 TATATCAATA
* *
361260 ATAAAA-AAA-TTTATAAATAAAATTAATAAAATAATATATACCTC
1 ATAAAATAAATTTTAAAAAT-AAATAAATAAAAT-ATATATACCTC
*
361304 ATAAAATATATTTTAAAAATAAATAAATAAAATATATATAC
1 ATAAAATAAATTTTAAAAATAAATAAATAAAATATATATAC
361345 TTCGTTAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 14 0.39
45 14 0.39
46 8 0.22
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (44 bp):
ATAAAATAAATTTTAAAAATAAATAAATAAAATATATATACCTC
Found at i:362363 original size:17 final size:17
Alignment explanation
Indices: 362331--362374 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
362321 AATTTTGAAC
* *
362331 ATAATATAATTATATAAT
1 ATAATATGA-TATATAAA
*
362349 ATGATATGATATATAAA
1 ATAATATGATATATAAA
362366 ATAATATGA
1 ATAATATGA
362375 GTAAATACGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
ATAATATGATATATAAA
Found at i:362420 original size:15 final size:15
Alignment explanation
Indices: 362400--362440 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
362390 CGAAAATGAT
*
362400 AAATTTATATAACTC
1 AAATTTATATAACTA
*
362415 AAATTTATAT-ATTA
1 AAATTTATATAACTA
362429 AAATTTATATAA
1 AAATTTATATAA
362441 ATTAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTTATATAACTA
Found at i:362451 original size:29 final size:27
Alignment explanation
Indices: 362400--362458 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
362390 CGAAAATGAT
*
362400 AAATTTATATAACTCAAATTTATATATTA
1 AAATTTATATAAATCAAATTTAT-T-TTA
*
362429 AAATTTATATAAAT-TAATATTATTTTA
1 AAATTTATATAAATCAAAT-TTATTTTA
362456 AAA
1 AAA
362459 ATAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.22
28 4 0.15
29 17 0.63
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTTATATAAATCAAATTTATTTTA
Found at i:363682 original size:29 final size:29
Alignment explanation
Indices: 363589--363726 Score: 88
Period size: 29 Copynumber: 4.8 Consensus size: 29
363579 ACTTGTACTA
* * **
363589 AAAGTATTTATGTCAAAAGTA-CACGTACC
1 AAAGTATTTGTGTCAAAAGTATCTC-TATT
* * *
363618 AAAGTACTTGTATCAAAA-TATCTAT-TT
1 AAAGTATTTGTGTCAAAAGTATCTCTATT
*
363645 AAAAATATTTGTGTCAAAAGTATCTCTATT
1 -AAAGTATTTGTGTCAAAAGTATCTCTATT
* * *
363675 AAAGTATTTATATCAAAAGT-TCTTGTATT
1 AAAGTATTTGTGTCAAAAGTATC-TCTATT
* **
363704 AAAATATCCGTGTC-AAAGTATCT
1 AAAGTATTTGTGTCAAAAGTATCT
363727 ATGTCAAAGA
Statistics
Matches: 83, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
28 26 0.31
29 55 0.66
30 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (29 bp):
AAAGTATTTGTGTCAAAAGTATCTCTATT
Found at i:364718 original size:49 final size:47
Alignment explanation
Indices: 364640--364734 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 47
364630 AAATTTAATG
*
364640 TTATTTTTATATAAATTATAAATATTTAATTTTATTAAATTAAATTATT
1 TTATTTTTATAT-AATTATAAATATTTAATTATATT-AATTAAATTATT
*
364689 TTATTTTTAT-T-ATTAATAAATATAATTAATTATATTAATTATATTA
1 TTATTTTTATATAATT-ATAAATAT--TTAATTATATTAATTAAATTA
364735 AATAATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
46 3 0.07
47 8 0.20
48 10 0.24
49 20 0.49
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (47 bp):
TTATTTTTATATAATTATAAATATTTAATTATATTAATTAAATTATT
Found at i:364872 original size:21 final size:21
Alignment explanation
Indices: 364842--364881 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
364832 TAAATAAATT
*
364842 TTTTATTTAT-TAATATTAAAA
1 TTTTAATTATATAAT-TTAAAA
364863 TTTTAATTATATAATTTAA
1 TTTTAATTATATAATTTAA
364882 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAATTATATAATTTAAAA
Found at i:369018 original size:9 final size:9
Alignment explanation
Indices: 369004--369038 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
368994 GTATATATTT
369004 AATTTTTAA
1 AATTTTTAA
*
369013 AATTTTTTA
1 AATTTTTAA
*
369022 TATTTTTAA
1 AATTTTTAA
369031 AATTTTTA
1 AATTTTTA
369039 TGAAAGTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATTTTTAA
Found at i:369039 original size:17 final size:18
Alignment explanation
Indices: 369001--369037 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
368991 TTTGTATATA
369001 TTTA-ATTTTTAAAATTT
1 TTTATATTTTTAAAATTT
369018 TTTATATTTTTAAAATTT
1 TTTATATTTTTAAAATTT
369036 TT
1 TT
369038 ATGAAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATTTTTAAAATTT
Found at i:369720 original size:23 final size:25
Alignment explanation
Indices: 369694--369752 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 25
369684 ATGATTTAAA
369694 TTATATAAATATAAATT--ATA-AT
1 TTATATAAATATAAATTAAATATAT
*
369716 TT-TATAAAAAT-AATTAAATATAT
1 TTATATAAATATAAATTAAATATAT
369739 TTATAATAAATATA
1 TTAT-ATAAATATA
369753 TTATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 4 0.14
21 8 0.28
22 5 0.17
23 4 0.14
24 1 0.03
25 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATATAAATATAAATTAAATATAT
Found at i:369728 original size:27 final size:27
Alignment explanation
Indices: 369698--369773 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
369688 TTTAAATTAT
369698 ATAAATATAAATTATAATTTTATAA-AA
1 ATAAAT-TAAATTATAATTTTATAATAA
369725 AT-AATTAAA-TAT-A-TTTATAATAA
1 ATAAATTAAATTATAATTTTATAATAA
* *
369748 ATATATTATATT-TAATATTTATAATA
1 ATAAATTAAATTATAAT-TTTATAATA
369774 TTTAATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
22 7 0.17
23 5 0.12
24 9 0.22
25 6 0.15
26 3 0.07
27 11 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAATTAAATTATAATTTTATAATAA
Found at i:369750 original size:15 final size:16
Alignment explanation
Indices: 369725--369754 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
369715 TTTTATAAAA
369725 ATAATTAAATATATTT
1 ATAATTAAATATATTT
369741 ATAA-TAAATATATT
1 ATAATTAAATATATT
369755 ATATTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATTAAATATATTT
Found at i:369758 original size:22 final size:23
Alignment explanation
Indices: 369694--369758 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
369684 ATGATTTAAA
369694 TTAT-ATAAATATAAATTATA-ATT
1 TTATAATAAATAT--ATTATATATT
*
369717 TTATAA-AAATA-ATTAAATATAT
1 TTATAATAAATATATTATATAT-T
369739 TTATAATAAATATATTATAT
1 TTATAATAAATATATTATAT
369759 TTAATATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 5 0.14
21 2 0.06
22 7 0.20
23 14 0.40
24 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATAATAAATATATTATATATT
Found at i:370154 original size:32 final size:28
Alignment explanation
Indices: 370118--370178 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 28
370108 TTAAATTATA
370118 ATGTAATAAGATATAACAATAAAAATATTTTT
1 ATGTAAT-AG-TATAA-AATAAAAA-ATTTTT
*
370150 ATGTAATAGTATAAAATTAAAAATTTTT
1 ATGTAATAGTATAAAATAAAAAATTTTT
370178 A
1 A
370179 ATTAAGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.25
29 7 0.25
30 5 0.18
31 2 0.07
32 7 0.25
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (28 bp):
ATGTAATAGTATAAAATAAAAAATTTTT
Found at i:370830 original size:17 final size:17
Alignment explanation
Indices: 370810--370859 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
370800 GTCAATTTAA
370810 ATTTAATTTAAATTATT
1 ATTTAATTTAAATTATT
*
370827 ATTTAATAATAAATT-TT
1 ATTTAAT-TTAAATTATT
370844 ATTTATATTT-AATTAT
1 ATTTA-ATTTAAATTAT
370860 AAAAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAATTTAAATTATT
Found at i:370866 original size:29 final size:28
Alignment explanation
Indices: 370807--370884 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 28
370797 CAAGTCAATT
* * *
370807 TAAATTTAATTTAAATTATTATTTAATAA
1 TAAATTTAATTTATATT-TAATTTAAAAA
*
370836 TAAATTTTATTTATATTTAATTATAAAAA
1 TAAATTTAATTTATATTTAATT-TAAAAA
*
370865 TATAATATTAATATATATTT
1 TA-AAT-TTAATTTATATTT
370885 TTAATATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 4 0.10
29 22 0.55
30 3 0.08
31 11 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAAATTTAATTTATATTTAATTTAAAAA
Found at i:372624 original size:14 final size:15
Alignment explanation
Indices: 372595--372625 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
372585 AAAAATATTT
372595 TAAATTTATATTATA
1 TAAATTTATATTATA
372610 TAAATTTAT-TTATA
1 TAAATTTATATTATA
372624 TA
1 TA
372626 TTCATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATTTATATTATA
Found at i:375396 original size:6 final size:6
Alignment explanation
Indices: 375387--375439 Score: 51
Period size: 7 Copynumber: 9.0 Consensus size: 6
375377 AATAAATAAG
375387 AAATTT AAATTT -AATTT AAAATTT AAAATTT AAAATTT -AATTT -AA-TT
1 AAATTT AAATTT AAATTT -AAATTT -AAATTT -AAATTT AAATTT AAATTT
375434 AAATTT
1 AAATTT
375440 TATTTTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
4 2 0.05
5 14 0.33
6 8 0.19
7 19 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:375409 original size:7 final size:7
Alignment explanation
Indices: 375387--375426 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
375377 AATAAATAAG
375387 AAATTT-
1 AAATTTA
375393 AAATTT-
1 AAATTTA
375399 -AATTTA
1 AAATTTA
375405 AAATTTA
1 AAATTTA
375412 AAATTTA
1 AAATTTA
375419 AAATTTA
1 AAATTTA
375426 A
1 A
375427 TTTAATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 6 0.19
7 21 0.66
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AAATTTA
Found at i:375935 original size:20 final size:19
Alignment explanation
Indices: 375905--375958 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
375895 AAAATTATAG
*
375905 TTTAAAGATAAAATAAAAA
1 TTTAAATATAAAATAAAAA
* *
375924 TTATAAATATAAATATTAATA
1 TT-TAAATATAAA-ATAAAAA
*
375945 TTTAAATTTAAAAT
1 TTTAAATATAAAAT
375959 TTATTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 18 0.62
21 7 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TTTAAATATAAAATAAAAA
Found at i:384150 original size:2 final size:2
Alignment explanation
Indices: 384143--384172 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
384133 CTGCCTTGAT
384143 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
384173 ATGTACAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:386467 original size:15 final size:15
Alignment explanation
Indices: 386449--386490 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
386439 ATGTAAATAA
*
386449 ATTAAATTATTAATT
1 ATTAAATTATTAAAT
386464 ATTAAATTTATATAAAT
1 ATTAAA-TTAT-TAAAT
386481 A-TAAATTATT
1 ATTAAATTATT
386491 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.42
16 8 0.33
17 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAAATTATTAAAT
Found at i:394511 original size:16 final size:15
Alignment explanation
Indices: 394488--394566 Score: 72
Period size: 16 Copynumber: 5.1 Consensus size: 15
394478 TAATACAATA
394488 TTAAATTTAATTAAT
1 TTAAATTTAATTAAT
394503 TTAAAATTTAATT-AT
1 TT-AAATTTAATTAAT
* *
394518 ATAAATTATAAATAAT
1 TTAAATT-TAATTAAT
*
394534 TTAAATTTAAAATAA-
1 TTAAATTT-AATTAAT
*
394549 TTATAATTTAATAAAT
1 TTA-AATTTAATTAAT
394565 TT
1 TT
394567 TAATGTTATA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
14 5 0.09
15 17 0.32
16 31 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAATTTAATTAAT
Found at i:394570 original size:15 final size:16
Alignment explanation
Indices: 394498--394640 Score: 72
Period size: 16 Copynumber: 8.2 Consensus size: 16
394488 TTAAATTTAA
394498 TTAATTTAAAATTTAATT
1 TTAATTTAAAA--TAATT
*
394516 ATATAAATTATAAATAATT
1 -T-TAATTTA-AAATAATT
*
394535 TAAATTTAAAATAATT
1 TTAATTTAAAATAATT
* *
394551 ATAATTTAATA-AATT
1 TTAATTTAAAATAATT
**
394566 TTAATGTTATATTTAATT
1 TTAAT-TTA-AAATAATT
394584 AGTCTAAATTTAAAATAATT
1 --T-T-AATTTAAAATAATT
** *
394604 TTAATAAAAAATTATT
1 TTAATTTAAAATAATT
* *
394620 TAAAATTAAAATAACTT
1 TTAATTTAAAATAA-TT
394637 TTAA
1 TTAA
394641 AAAATAATTA
Statistics
Matches: 95, Mismatches: 19, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
15 8 0.08
16 39 0.41
17 13 0.14
18 6 0.06
19 6 0.06
20 13 0.14
21 7 0.07
22 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (16 bp):
TTAATTTAAAATAATT
Found at i:394626 original size:33 final size:34
Alignment explanation
Indices: 394579--394666 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 34
394569 ATGTTATATT
**
394579 TAATTAGTCTAAATTTAAAATAA-TTTTAATAAAA
1 TAATTAGTAAAAATTTAAAATAACTTTTAA-AAAA
* *
394613 -AATTATTTAAAA-TTAAAATAACTTTTAAAAAA
1 TAATTAGTAAAAATTTAAAATAACTTTTAAAAAA
*
394645 TAATTAGTAAAAATATAAAATA
1 TAATTAGTAAAAATTTAAAATA
394667 GTTCAACTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
32 13 0.29
33 25 0.56
34 7 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (34 bp):
TAATTAGTAAAAATTTAAAATAACTTTTAAAAAA
Found at i:402933 original size:19 final size:19
Alignment explanation
Indices: 402906--402973 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
402896 TAATTTGATA
402906 TAAATATAATATAAAAATAT
1 TAAA-ATAATATAAAAATAT
*
402926 TAAAATAAAATATAAAATA-
1 TAAAATAATATA-AAAATAT
* *
402945 TAATATAATACAAAAATAT
1 TAAAATAATATAAAAATAT
*
402964 TAACATAATA
1 TAAAATAATA
402974 AATATATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.15
19 25 0.61
20 10 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATAATATAAAAATAT
Found at i:402977 original size:33 final size:36
Alignment explanation
Indices: 402903--402987 Score: 100
Period size: 38 Copynumber: 2.3 Consensus size: 36
402893 TTTTAATTTG
*
402903 ATATAAATATAATATAAAAATATTAAAATAAAATATAAA
1 ATAT-AATATAATACAAAAATATTAAAAT--AATATAAA
* *
402942 ATATAATATAATACAAAAATATTAACATAATA-AAT
1 ATATAATATAATACAAAAATATTAAAATAATATAAA
*
402977 ATATTATATAA
1 ATATAATATAA
402988 AAATTTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 12 0.29
36 4 0.10
38 22 0.52
39 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (36 bp):
ATATAATATAATACAAAAATATTAAAATAATATAAA
Found at i:402990 original size:30 final size:28
Alignment explanation
Indices: 402947--403028 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
402937 ATAAAATATA
* *
402947 ATATAATACAAAAATATTAACATAATAAAT
1 ATATTATATAAAAAT-TT-ACATAATAAAT
*
402977 ATATTATATAAAAATTTATATAATAAAT
1 ATATTATATAAAAATTTACATAATAAAT
* *
403005 -TATTAATATATCAAATTTATATAA
1 ATATT-ATATA-AAAATTTACATAA
403029 ATATTAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 4 0.09
28 15 0.33
29 14 0.30
30 13 0.28
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATTATATAAAAATTTACATAATAAAT
Found at i:402997 original size:12 final size:12
Alignment explanation
Indices: 402980--403041 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
402970 AATAAATATA
402980 TTATATAAAAAT
1 TTATATAAAAAT
402992 TTATATAATAAATT
1 TTATATAA-AAA-T
*
403006 ATTAATATATCAAAT
1 -TT-ATATA-AAAAT
*
403021 TTATATAAATAT
1 TTATATAAAAAT
*
403033 TAATATAAA
1 TTATATAAA
403042 TATAAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 19 0.46
13 8 0.20
14 3 0.07
15 3 0.07
16 8 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATATAAAAAT
Found at i:403020 original size:16 final size:14
Alignment explanation
Indices: 402999--403076 Score: 61
Period size: 17 Copynumber: 5.1 Consensus size: 14
402989 AATTTATATA
402999 ATAAATTATTAATAT
1 ATAAATTATTAA-AT
403014 ATCAAATTTATATAAAT
1 AT-AAA-TTAT-TAAAT
*
403031 ATTAA-TA-TAAAT
1 ATAAATTATTAAAT
403043 ATAAATTATTAATAT
1 ATAAATTATTAA-AT
403058 ATTAAATTTATTTAAAT
1 A-TAAA-TTA-TTAAAT
403075 AT
1 AT
403077 TATTATAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
12 9 0.17
13 2 0.04
14 5 0.10
15 5 0.10
16 10 0.19
17 14 0.27
18 7 0.13
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (14 bp):
ATAAATTATTAAAT
Found at i:403038 original size:25 final size:24
Alignment explanation
Indices: 402971--403088 Score: 84
Period size: 25 Copynumber: 4.8 Consensus size: 24
402961 TATTAACATA
* *
402971 ATAAATATATTATATAAAAATTTATAT
1 ATAAATAT-TAATATATAAA-TT-TAT
402998 AATAAATTATTAATATATCAAATTTAT
1 -ATAAA-TATTAATATAT-AAATTTAT
403025 ATAAATATT-A-ATATAAA--TAT
1 ATAAATATTAATATATAAATTTAT
*
403045 A-AATTATTAATATATTAAATTTAT
1 ATAAATATTAATATA-TAAATTTAT
* *
403069 TTAAATATTATTATAATAAA
1 ATAAATATTAATAT-ATAAA
403089 AAAATATATA
Statistics
Matches: 75, Mismatches: 6, Indels: 21
0.74 0.06 0.21
Matches are distributed among these distances:
19 6 0.08
20 5 0.07
21 3 0.04
22 7 0.09
23 4 0.05
24 4 0.05
25 18 0.24
26 6 0.08
27 3 0.04
28 13 0.17
29 6 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAAATATTAATATATAAATTTAT
Found at i:403042 original size:12 final size:12
Alignment explanation
Indices: 402903--403044 Score: 58
Period size: 13 Copynumber: 10.8 Consensus size: 12
402893 TTTTAATTTG
402903 ATATAAATA-TA
1 ATATAAATATTA
402914 ATATAAAAATATTA
1 ATAT--AAATATTA
*
402928 AAATAAA-ATATA
1 ATATAAATAT-TA
*
402940 AAATATAATA-TA
1 ATATA-AATATTA
*
402952 ATACAAAAATATTAA
1 AT--ATAAATATT-A
*
402967 CATAATAAATATATT
1 -AT-ATAAATAT-TA
*
402982 ATATAAAAATTTA
1 ATATAAATA-TTA
402995 TATAATAAATTATTA
1 -AT-ATAAA-TATTA
*
403010 ATATATCAA-ATTT
1 ATATA--AATATTA
403023 ATATAAATATTA
1 ATATAAATATTA
403035 ATATAAATAT
1 ATATAAATAT
403045 AAATTATTAA
Statistics
Matches: 101, Mismatches: 11, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
11 8 0.08
12 26 0.26
13 29 0.29
14 16 0.16
15 18 0.18
16 4 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATAAATATTA
Found at i:403044 original size:29 final size:29
Alignment explanation
Indices: 402982--403062 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
402972 TAAATATATT
* *
402982 ATATAAAAATTTATATAATAAATT-ATTA
1 ATATATAAATTTATATAATATATTAATTA
403010 ATATATCAAATTTATATAA-ATATTAATATA
1 ATATAT-AAATTTATATAATATATTAAT-TA
403040 A-ATATAAA-TTAT-TAATATATTAA
1 ATATATAAATTTATATAATATATTAA
403063 ATTTATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
26 3 0.06
27 11 0.23
28 12 0.26
29 18 0.38
30 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATATAAATTTATATAATATATTAATTA
Found at i:403048 original size:44 final size:44
Alignment explanation
Indices: 402999--403084 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
402989 AATTTATATA
402999 ATAAATTATTAATATATCAAATTTATATAAATATTAATATAAAT
1 ATAAATTATTAATATATCAAATTTATATAAATATTAATATAAAT
* * *
403043 ATAAATTATTAATATATTAAATTTATTTAAATATTATTATAA
1 ATAAATTATTAATATATCAAATTTATATAAATATTAATATAA
403085 TAAAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (44 bp):
ATAAATTATTAATATATCAAATTTATATAAATATTAATATAAAT
Found at i:403054 original size:19 final size:18
Alignment explanation
Indices: 402903--403058 Score: 74
Period size: 19 Copynumber: 8.6 Consensus size: 18
402893 TTTTAATTTG
* *
402903 ATATAAATATAATATAAAA
1 ATATTAATATAA-ATATAA
*
402922 ATATTAAAATAAAATATAA
1 ATATTAATAT-AAATATAA
* *
402941 A-ATATAATATAATACAAAA
1 ATAT-TAATATAA-ATATAA
*
402960 ATATTAACAT-AATA-AA
1 ATATTAATATAAATATAA
* **
402976 TATATT-ATATAAAAATTT
1 -ATATTAATATAAATATAA
*
402994 ATA-TAATA-AATTATTAA
1 ATATTAATATAAATA-TAA
* **
403011 TATATCAA-ATTTATATAA
1 -ATATTAATATAAATATAA
403029 ATATTAATATAAATATAA
1 ATATTAATATAAATATAA
403047 ATTATTAATATA
1 A-TATTAATATA
403059 TTAAATTTAT
Statistics
Matches: 100, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
16 9 0.09
17 23 0.23
18 21 0.21
19 43 0.43
20 4 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATTAATATAAATATAA
Found at i:408469 original size:13 final size:13
Alignment explanation
Indices: 408451--408476 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
408441 TTCATTTTTA
408451 AAATAATTATATT
1 AAATAATTATATT
408464 AAATAATTATATT
1 AAATAATTATATT
408477 TAATTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATAATTATATT
Found at i:411574 original size:14 final size:14
Alignment explanation
Indices: 411555--411592 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
411545 AAAATTAAAA
*
411555 AATATTTTTATATT
1 AATATTTATATATT
411569 AATATTTATA-ATT
1 AATATTTATATATT
411582 AA-ATTTATATA
1 AATATTTATATA
411593 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 6 0.27
14 9 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATATTTATATATT
Found at i:416877 original size:21 final size:21
Alignment explanation
Indices: 416844--416894 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
416834 AAAGGAATTA
416844 ATTTTAAATAAATAAAAAATAAT
1 ATTTT-AA-AAATAAAAAATAAT
* * *
416867 TTTTTAAAAATATATAATAAT
1 ATTTTAAAAATAAAAAATAAT
416888 ATTTTAA
1 ATTTTAA
416895 TTTTTTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 2 0.08
23 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTTTAAAAATAAAAAATAAT
Found at i:416995 original size:14 final size:14
Alignment explanation
Indices: 416978--417008 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
416968 CATAGTCCGT
416978 TTTTTGAATTACTG
1 TTTTTGAATTACTG
*
416992 TTTTTGAATTATTG
1 TTTTTGAATTACTG
417006 TTT
1 TTT
417009 AAGAAGGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTTTGAATTACTG
Found at i:417228 original size:15 final size:16
Alignment explanation
Indices: 417204--417251 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
417194 AATATATAAA
417204 TATATTAAATTTATAT
1 TATATTAAATTTATAT
*
417220 TAT-TTAAA-TTATTAA
1 TATATTAAATTTA-TAT
417235 TATATTAAATTTTATAT
1 TATATTAAA-TTTATAT
417252 AAACATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 8 0.31
17 2 0.08
18 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTAAATTTATAT
Found at i:420522 original size:74 final size:75
Alignment explanation
Indices: 420401--420546 Score: 240
Period size: 74 Copynumber: 2.0 Consensus size: 75
420391 AATTGCAGAA
* * *
420401 GAGCTTAAAGCATGGCTAATTGTTCTGATAGCTTGTTCACCATTGCGGTGTAATTGGA-TCATCC
1 GAGCTTAAAGCATGGCTAATCGTTCTGATAGCTTGTTCACCATTGCGGTGCAATTGGACCCATCC
420465 TTTTGATATG
66 TTTTGATATG
**
420475 GAGCTTAAAGCATGGCTGGTCGTTCTGATAGCTTGTTCACCATTGCGGTGCAATTGGACCCATCC
1 GAGCTTAAAGCATGGCTAATCGTTCTGATAGCTTGTTCACCATTGCGGTGCAATTGGACCCATCC
420540 TTTTGAT
66 TTTTGAT
420547 GCTAATCATT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 54 0.82
75 12 0.18
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (75 bp):
GAGCTTAAAGCATGGCTAATCGTTCTGATAGCTTGTTCACCATTGCGGTGCAATTGGACCCATCC
TTTTGATATG
Found at i:422992 original size:11 final size:11
Alignment explanation
Indices: 422972--423024 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
422962 ATTAGATGTA
422972 ATATTTATATC
1 ATATTTATATC
* *
422983 ATATTCATATA
1 ATATTTATATC
*
422994 ATATTTTTATC
1 ATATTTATATC
* *
423005 ATATTTTATTTT
1 ATA-TTTATATC
423017 ATATTTAT
1 ATATTTAT
423025 TTTAATTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTATATC
Found at i:423070 original size:2 final size:2
Alignment explanation
Indices: 423065--423104 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
423055 GTTCAAAATT
423065 TA TA TA T- TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
423105 GTAAAGTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:425258 original size:2 final size:2
Alignment explanation
Indices: 425251--425283 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
425241 ATTTTGATAA
425251 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
425284 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:425289 original size:2 final size:2
Alignment explanation
Indices: 425284--425312 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
425274 CTCTCTCTCT
425284 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
425313 GAGGAATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:430430 original size:27 final size:25
Alignment explanation
Indices: 430385--430437 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
430375 ATTTATAGAA
430385 TATAAAATATAAATATTAAATTATAAT
1 TATAAAATATAAATATT-AATTA-AAT
* * *
430412 TATAATATATAATTTTTAATTAAAT
1 TATAAAATATAAATATTAATTAAAT
430437 T
1 T
430438 TATTTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATAAAATATAAATATTAATTAAAT
Found at i:430541 original size:24 final size:23
Alignment explanation
Indices: 430513--430592 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 23
430503 TATAATATTT
430513 TAAATTTTTTTATTAATTTAAAAA
1 TAAA-TTTTTTATTAATTTAAAAA
* **
430537 TAAATTATTTATT-ATAAAAAAA
1 TAAATTTTTTATTAATTTAAAAA
**
430559 TAAATTTAAT-TTAATTTAAATAA
1 TAAATTTTTTATTAATTTAAA-AA
*
430582 CTACATTTTTT
1 -TAAATTTTTT
430593 TATTTATAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
21 2 0.05
22 19 0.45
23 10 0.24
24 11 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATTTTTTATTAATTTAAAAA
Found at i:431287 original size:2 final size:2
Alignment explanation
Indices: 431280--431312 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
431270 AAATATTCAC
431280 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
431313 AGAAACTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:433183 original size:28 final size:27
Alignment explanation
Indices: 433152--433223 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 27
433142 AAAATTAAAT
*
433152 AATATTTTTATATTATTATTTAAAATTA
1 AATATATTTATATTATTATTT-AAATTA
* * * *
433180 AATAAAAATAATTTTATTATTTAAATTA
1 AAT-ATATTTATATTATTATTTAAATTA
*
433208 AATATATTTAAATTAT
1 AATATATTTATATTAT
433224 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
27 8 0.24
28 12 0.36
29 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATATATTTATATTATTATTTAAATTA
Found at i:433198 original size:32 final size:31
Alignment explanation
Indices: 433137--433200 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
433127 TTTTAAATAA
* *
433137 TATTAAAAATTAAATAATATTTTTATATTAT
1 TATTAAAAATTAAATAAAATATTTATATTAT
*
433168 TATTTAAAATTAAATAAAAATAATTT-TATTAT
1 TATTAAAAATTAAAT-AAAAT-ATTTATATTAT
433200 T
1 T
433201 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 14 0.50
32 11 0.39
33 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
TATTAAAAATTAAATAAAATATTTATATTAT
Found at i:433881 original size:17 final size:15
Alignment explanation
Indices: 433850--433900 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
433840 TTTTTATTAT
433850 ATTTTATATTTATAA
1 ATTTTATATTTATAA
433865 ATTTTAATATATTAT-A
1 ATTTT-ATAT-TTATAA
*
433881 A-TTTATATTAAATAA
1 ATTTTATATT-TATAA
433896 ATTTT
1 ATTTT
433901 TAAATATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 1 0.03
14 6 0.20
15 10 0.33
16 9 0.30
17 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTATATTTATAA
Found at i:433899 original size:31 final size:31
Alignment explanation
Indices: 433844--433950 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 31
433834 TAATTGTTTT
* *
433844 TATTATATTTTATATT-TATAAATTTTAATA
1 TATTATAATTTATATTAAATAAATTTTAATA
433874 TATTATAATTTATATTAAATAAATTTTTAA-A
1 TATTATAATTTATATTAAATAAA-TTTTAATA
* *
433905 TATT-TATATTTTTATTTAATATCATATTTTAATA
1 TATTATA-ATTTATA-TTAA-AT-AAATTTTAATA
*
433939 -ATTATATTTTAT
1 TATTATAATTTAT
433951 TATTTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
30 17 0.27
31 16 0.25
32 10 0.16
33 15 0.24
34 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TATTATAATTTATATTAAATAAATTTTAATA
Found at i:433912 original size:32 final size:30
Alignment explanation
Indices: 433844--433950 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 30
433834 TAATTGTTTT
* *
433844 TATTATATTTTATATTTATAAATTTTAATA
1 TATTATAATTTATATTAATAAATTTTAATA
433874 TATTATAATTTATATTAAATAAATTTTTAA-A
1 TATTATAATTTATATT-AATAAA-TTTTAATA
*
433905 TATT-TATATTTTTATTTAATATCATATTTTAATA
1 TATTATA-ATTTATA-TTAATA--A-ATTTTAATA
*
433939 -ATTATATTTTAT
1 TATTATAATTTAT
433951 TATTTTAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
30 17 0.27
31 20 0.32
32 8 0.13
33 14 0.22
34 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
TATTATAATTTATATTAATAAATTTTAATA
Found at i:434399 original size:29 final size:30
Alignment explanation
Indices: 434347--434409 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
434337 ACTGTTAATT
* * *
434347 ATAATCATTTTAATTTTTTTATAAAATAAA
1 ATAATCATTTTAATATGTTAATAAAATAAA
**
434377 ATAAT-ATTTTAATATGTTAATAATTTAAA
1 ATAATCATTTTAATATGTTAATAAAATAAA
434406 ATAA
1 ATAA
434410 AAATATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
ATAATCATTTTAATATGTTAATAAAATAAA
Found at i:435725 original size:20 final size:20
Alignment explanation
Indices: 435688--435726 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
435678 TTTATATGTA
*
435688 TAAAATATATTTATATAATT
1 TAAAATATATATATATAATT
435708 TAAAAT-TATATATTATAAT
1 TAAAATATATATA-TATAAT
435727 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATATATATATATAATT
Found at i:435755 original size:36 final size:36
Alignment explanation
Indices: 435680--435756 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
435670 AATACTTTTT
*
435680 TATATGTATAAAATATATTTATATAATTTAAAATTA
1 TATATGTATAAAATATATTTATATAATTTAAAATAA
* **
435716 TATAT-TATAATAT-TATTTATATTATATTTGTAATAA
1 TATATGTATAAAATATATTTATA-TA-ATTTAAAATAA
435752 TATAT
1 TATAT
435757 AATTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 8 0.23
35 9 0.26
36 18 0.51
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (36 bp):
TATATGTATAAAATATATTTATATAATTTAAAATAA
Found at i:435761 original size:22 final size:22
Alignment explanation
Indices: 435693--435790 Score: 83
Period size: 22 Copynumber: 4.4 Consensus size: 22
435683 ATGTATAAAA
* *
435693 TATATTTAT-ATAATTTAAAAT
1 TATATTTATAATAATATATAAT
* *
435714 TATATATTATAATATTATTTATAT
1 TATAT-TTATAATAATATATA-AT
*
435738 TATATTTGTAATAATATATAAT
1 TATATTTATAATAATATATAAT
* *
435760 TATTTTTAT-ATAATAATATAAA
1 TATATTTATAATAAT-ATATAAT
*
435782 TAAATTTAT
1 TATATTTAT
435791 TTTTAAAATT
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
21 10 0.16
22 26 0.43
23 18 0.30
24 7 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (22 bp):
TATATTTATAATAATATATAAT
Found at i:436674 original size:17 final size:17
Alignment explanation
Indices: 436640--436673 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
436630 CTTGACGGAG
*
436640 TAATAAATTTTTAATTT
1 TAATAAATTTTAAATTT
436657 TAAT-AATTTTAAATTT
1 TAATAAATTTTAAATTT
436673 T
1 T
436674 TTTAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATAAATTTTAAATTT
Found at i:437256 original size:23 final size:21
Alignment explanation
Indices: 437215--437257 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
437205 TTATCTATTT
437215 TATTATTTATTTTTAATTTAA
1 TATTATTTATTTTTAATTTAA
*
437236 TATTAATTTAATTTTTTATTTA
1 TATT-ATTT-ATTTTTAATTTA
437258 TTTTACGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 4 0.21
23 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATTTATTTTTAATTTAA
Found at i:437260 original size:11 final size:11
Alignment explanation
Indices: 437204--437261 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
437194 ATACATATAA
*
437204 TTTATCTATTT
1 TTTATTTATTT
437215 TATTATTTATTT
1 T-TTATTTATTT
* * *
437227 TTAATTTAATA
1 TTTATTTATTT
*
437238 TTAATTTAATTT
1 TTTATTT-ATTT
437250 TTTATTTATTT
1 TTTATTTATTT
437261 T
1 T
437262 ACGATAAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 20 0.53
12 18 0.47
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:437758 original size:21 final size:22
Alignment explanation
Indices: 437721--437766 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
437711 TATTTATTTA
437721 AATTTTATTCAATTTAAAAAATT
1 AATTTTATT-AATTTAAAAAATT
*
437744 AATTTTATT-ATTTAAAATATT
1 AATTTTATTAATTTAAAAAATT
437765 AA
1 AA
437767 AATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
23 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTTATTAATTTAAAAAATT
Found at i:438376 original size:16 final size:17
Alignment explanation
Indices: 438353--438390 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
438343 TATTTTAATT
438353 ATTT-TATCATAT-TAA
1 ATTTATATCATATCTAA
*
438368 ATTTATATCATATCTCA
1 ATTTATATCATATCTAA
438385 ATTTAT
1 ATTTAT
438391 TTTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 8 0.40
17 8 0.40
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATATCATATCTAA
Found at i:439642 original size:20 final size:22
Alignment explanation
Indices: 439609--439657 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
439599 TATATAAAAG
439609 TATTTAAAATTATTTA-AATTAA
1 TATTT-AAATTATTTATAATTAA
*
439631 TATTTAAA-TATTTATGATTAA
1 TATTTAAATTATTTATAATTAA
439652 -ATTTAA
1 TATTTAA
439658 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 12 0.48
21 8 0.32
22 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTAAATTATTTATAATTAA
Found at i:440048 original size:2 final size:2
Alignment explanation
Indices: 440041--440068 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
440031 GTAAACTATG
440041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
440069 TAACTTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:440432 original size:4 final size:4
Alignment explanation
Indices: 440423--440455 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
440413 TTGGCATGAC
*
440423 AAAT AAAT AAAT AAAT AAGT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
440456 GTTTTAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:441937 original size:15 final size:16
Alignment explanation
Indices: 441912--441944 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
441902 TTTATTAGTT
*
441912 TTAATTATAAAATATA
1 TTAATTATAAAAAATA
441928 TTAA-TATAAAAAATA
1 TTAATTATAAAAAATA
441943 TT
1 TT
441945 TTAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAATTATAAAAAATA
Found at i:442935 original size:17 final size:17
Alignment explanation
Indices: 442884--442940 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
442874 TTTAAATTAA
442884 TTTAAATAAATATTTTTAT
1 TTTAAATAAA-A-TTTTAT
*
442903 TTT-TATAAAATATTTAT
1 TTTAAATAAAAT-TTTAT
* *
442920 TTTAAATTAAATTTTAA
1 TTTAAATAAAATTTTAT
442937 TTTA
1 TTTA
442941 TACTGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.53
18 11 0.34
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAATAAAATTTTAT
Found at i:442939 original size:18 final size:18
Alignment explanation
Indices: 442880--442939 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
442870 ATCCTTTAAA
442880 TTAA-TTTAAATAAATATT
1 TTAATTTTAAATAAA-ATT
* *
442898 TTTATTTT-TATAAAATAT
1 TTAATTTTAAATAAAAT-T
*
442916 TT-ATTTTAAATTAAATT
1 TTAATTTTAAATAAAATT
442933 TTAATTT
1 TTAATTT
442940 ATACTGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 10 0.29
18 21 0.62
19 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATTTTAAATAAAATT
Found at i:443177 original size:20 final size:19
Alignment explanation
Indices: 443147--443192 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
443137 ATTAAATGAA
*
443147 TATTT-ATATTTTTATAAAT
1 TATTTAATATTTATA-AAAT
443166 TATTTAATATTTATAAAAT
1 TATTTAATATTTATAAAAT
443185 TAATTTAA
1 T-ATTTAA
443193 ATTATGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTAATATTTATAAAAT
Found at i:443197 original size:18 final size:18
Alignment explanation
Indices: 443147--443192 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
443137 ATTAAATGAA
*
443147 TATTTATATTTTTATAAAT
1 TATTTA-ATATTTATAAAT
443166 TATTTAATATTTATAAAAT
1 TATTTAATATTTAT-AAAT
443185 TAATTTAA
1 T-ATTTAA
443193 ATTATGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 11 0.46
20 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTAATATTTATAAAT
Found at i:443315 original size:15 final size:15
Alignment explanation
Indices: 443276--443314 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
443266 AGAAACAAAA
443276 AAATAAAAATTAATTT
1 AAAT-AAAATTAATTT
*
443292 ATATAAAATTAATTTT
1 AAATAAAATTAA-TTT
443308 AAATAAA
1 AAATAAA
443315 TACTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAAAATTAATTT
Found at i:445549 original size:20 final size:19
Alignment explanation
Indices: 445518--445568 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
445508 ATCGATTTAA
445518 TTAAAAAT-ATTTTAAATAT
1 TTAAAAATAATTTT-AATAT
445537 TTAAAAATAATTTTAATAT
1 TTAAAAATAATTTTAATAT
*
445556 TAAATAAATAATT
1 TTAA-AAATAATT
445569 AATAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAAAATAATTTTAATAT
Found at i:450085 original size:2 final size:2
Alignment explanation
Indices: 450024--450072 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
450014 TTACATTTTC
*
450024 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
450066 AA AT AT A
1 AT AT AT A
450073 CACACATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:452871 original size:20 final size:21
Alignment explanation
Indices: 452843--452889 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
452833 ATAATAAAAT
* *
452843 TTAAATAAA-AATATTTTTAA
1 TTAAATAAATAATAATTTAAA
*
452863 TTAATTAAATAATAATTTAAA
1 TTAAATAAATAATAATTTAAA
452884 TTAAAT
1 TTAAAT
452890 CAATTAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAATAAATAATAATTTAAA
Found at i:452922 original size:34 final size:30
Alignment explanation
Indices: 452861--452923 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
452851 AAATATTTTT
* *
452861 AATTAATTAAATAATAATTTAAATTAAATC
1 AATTAATTAAAAAATAATTCAAATTAAATC
452891 AATTAATTAAAAAAATTATATTCAAACTTAAAT
1 AATTAATT-AAAAAA-TA-ATTCAAA-TTAAAT
452924 TCGTCTGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.30
31 5 0.19
32 2 0.07
33 6 0.22
34 6 0.22
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTAATTAAAAAATAATTCAAATTAAATC
Done.