Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold206
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: 2736418
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 22040 characters in sequence are not A, C, G, or T
File 12 of 20
Found at i:1458883 original size:20 final size:20
Alignment explanation
Indices: 1458841--1458884 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1458831 AATAATTTTT
* * *
1458841 AATATTAAATAAATATTATA
1 AATAATAAATAAATAATAAA
*
1458861 AATAATAAATAATTAATAAA
1 AATAATAAATAAATAATAAA
1458881 AATA
1 AATA
1458885 TACATTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AATAATAAATAAATAATAAA
Found at i:1459094 original size:23 final size:23
Alignment explanation
Indices: 1459066--1459109 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1459056 ATTCGATTCA
*
1459066 ATTTTTTTTCATCATATTATTTT
1 ATTTTTTTACATCATATTATTTT
*
1459089 ATTTTTTTACATCATTTTATT
1 ATTTTTTTACATCATATTATT
1459110 AATTTATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTTTTTACATCATATTATTTT
Found at i:1460549 original size:20 final size:21
Alignment explanation
Indices: 1460497--1460548 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1460487 CATGCCACCT
*
1460497 TGACCTTTTTTCCAACAAAAA
1 TGACCATTTTTCCAACAAAAA
1460518 TGACCATTTTTCCAACAAAAA
1 TGACCATTTTTCCAACAAAAA
1460539 TGACCATTTT
1 TGACCATTTT
1460549 CTGCCATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (21 bp):
TGACCATTTTTCCAACAAAAA
Found at i:1467536 original size:3 final size:3
Alignment explanation
Indices: 1467521--1467560 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
1467511 TAGTTTTTTG
*
1467521 ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
1467561 TTAGTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1467816 original size:17 final size:17
Alignment explanation
Indices: 1467789--1467831 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1467779 TTTATAATTA
* *
1467789 ATTTAATTTAATTTAA-
1 ATTTTATTTAAATTAAG
1467805 ATTATTATTTAAATTAAG
1 ATT-TTATTTAAATTAAG
1467823 ATTTTATTT
1 ATTTTATTT
1467832 TTAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTTATTTAAATTAAG
Found at i:1467837 original size:18 final size:19
Alignment explanation
Indices: 1467794--1467849 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 19
1467784 AATTAATTTA
*
1467794 ATTTAATTTAAA--TTATT
1 ATTTAAATTAAATTTTATT
1467811 ATTTAAATTAAGATTTTATT
1 ATTTAAATTAA-ATTTTATT
*
1467831 -TTT-AATTAAATTTAATT
1 ATTTAAATTAAATTTTATT
1467848 AT
1 AT
1467850 AAAAATTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
17 17 0.52
18 8 0.24
19 3 0.09
20 5 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTTAAATTAAATTTTATT
Found at i:1467843 original size:17 final size:16
Alignment explanation
Indices: 1467778--1467843 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 16
1467768 TTTTTTTATA
1467778 ATTTATAATT-AA-TTT
1 ATTT-TAATTAAATTTT
*
1467793 AATTTAATTTAAATTATT
1 ATTTTAA-TTAAATT-TT
*
1467811 ATTTAAATTAAGATTTT
1 ATTTTAATTAA-ATTTT
1467828 ATTTTTAATTAAATTT
1 A-TTTTAATTAAATTT
1467844 AATTATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
14 3 0.07
15 5 0.12
16 2 0.05
17 12 0.29
18 19 0.46
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTTAATTAAATTTT
Found at i:1468396 original size:20 final size:20
Alignment explanation
Indices: 1468359--1468410 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1468349 TTGGTTAATT
1468359 ATATTAAAATAAAAAATTTAA
1 ATATT-AAATAAAAAATTTAA
* * *
1468380 ATATTAAATATATAATTTCA
1 ATATTAAATAAAAAATTTAA
*
1468400 ATAATAAATAA
1 ATATTAAATAA
1468411 GTATTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
ATATTAAATAAAAAATTTAA
Found at i:1468439 original size:18 final size:17
Alignment explanation
Indices: 1468418--1468461 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1468408 TAAGTATTAA
1468418 ATATAATTTAATAAGAAT
1 ATATAATTTAATAA-AAT
* *
1468436 ATATATTTTAATTAAAT
1 ATATAATTTAATAAAAT
1468453 AGTATAATT
1 A-TATAATT
1468462 GTTTAATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1468566 original size:19 final size:19
Alignment explanation
Indices: 1468544--1468586 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1468534 TTTTTAAAAT
1468544 TTTAAT-AATGTTTTATCTA
1 TTTAATCAAT-TTTTATCTA
* *
1468563 TTTAATCGATTTTTATTTA
1 TTTAATCAATTTTTATCTA
1468582 TTTAA
1 TTTAA
1468587 AAATATGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTAATCAATTTTTATCTA
Found at i:1468618 original size:15 final size:15
Alignment explanation
Indices: 1468581--1468618 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1468571 ATTTTTATTT
* *
1468581 ATTTAAAAATATGTA
1 ATTTAAATATATATA
1468596 ATTT-AATATATATA
1 ATTTAAATATATATA
1468610 ATTTAAATA
1 ATTTAAATA
1468619 AATTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTTAAATATATATA
Found at i:1469761 original size:28 final size:29
Alignment explanation
Indices: 1469721--1469792 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
1469711 TACGATTCAG
1469721 AATGTATCGATACATGAACAATGACG-AA
1 AATGTATCGATACATGAACAATGACGAAA
* * *
1469749 AATGTATCGATACATGAATAGTGATGAAA
1 AATGTATCGATACATGAACAATGACGAAA
1469778 AATGTATCGATACAT
1 AATGTATCGATACAT
1469793 CTGGGTATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 23 0.57
29 17 0.43
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.26
Consensus pattern (29 bp):
AATGTATCGATACATGAACAATGACGAAA
Found at i:1470777 original size:24 final size:25
Alignment explanation
Indices: 1470749--1470813 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
1470739 TTTTTTATAT
*
1470749 AAAATTAAAATAATAAAAAAAT-TA
1 AAAATTAAAATAATAAAAAAATAAA
*
1470773 AAAATT-AAA-AATTAAAAAATCAAA
1 AAAATTAAAATAATAAAAAAAT-AAA
1470797 AAAATTAAAAATAATAA
1 AAAATT-AAAATAATAA
1470814 TATTCAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 10 0.30
23 3 0.09
24 13 0.39
26 3 0.09
27 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAATTAAAATAATAAAAAAATAAA
Found at i:1470797 original size:14 final size:14
Alignment explanation
Indices: 1470749--1470798 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
1470739 TTTTTTATAT
1470749 AAAATTAAAATAATAAA
1 AAAATTAAAA-AAT--A
*
1470766 AAAATTAAAAATTA
1 AAAATTAAAAAATA
1470780 AAAATTAAAAAATCA
1 AAAATTAAAAAAT-A
1470795 AAAA
1 AAAA
1470799 AATTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 13 0.43
15 5 0.17
16 2 0.07
17 10 0.33
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAAAATA
Found at i:1470808 original size:7 final size:7
Alignment explanation
Indices: 1470765--1470790 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1470755 AAAATAATAA
1470765 AAAAATT
1 AAAAATT
1470772 AAAAATT
1 AAAAATT
1470779 AAAAATT
1 AAAAATT
1470786 AAAAA
1 AAAAA
1470791 ATCAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:1470876 original size:8 final size:9
Alignment explanation
Indices: 1470755--1470876 Score: 52
Period size: 9 Copynumber: 14.4 Consensus size: 9
1470745 ATATAAAATT
1470755 AAAATAATA
1 AAAATAATA
1470764 AAAA-AATTA
1 AAAATAA-TA
1470773 AAAAT--TA
1 AAAATAATA
*
1470780 AAAATTA-A
1 AAAATAATA
1470788 AAAATCAA-A
1 AAAAT-AATA
1470797 AAAAT--TA
1 AAAATAATA
1470804 AAAATAATA
1 AAAATAATA
* *
1470813 ATATTCAAT-
1 AAAAT-AATA
*
1470822 ATAATAATA
1 AAAATAATA
*
1470831 AAAATCA-A
1 AAAATAATA
*
1470839 GAAATAA-A
1 AAAATAATA
*
1470847 AAATTCAA-A
1 AAAAT-AATA
*
1470856 AAAATAATC
1 AAAATAATA
1470865 AAAAT-ATA
1 AAAATAATA
1470873 AAAA
1 AAAA
1470877 AATGCCAATT
Statistics
Matches: 88, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
7 13 0.15
8 29 0.33
9 43 0.49
10 3 0.03
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (9 bp):
AAAATAATA
Found at i:1471048 original size:5 final size:5
Alignment explanation
Indices: 1471038--1471062 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1471028 AATGACATCT
1471038 CATTG CATTG CATTG CATTG CATTG
1 CATTG CATTG CATTG CATTG CATTG
1471063 GATTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
CATTG
Found at i:1471071 original size:15 final size:15
Alignment explanation
Indices: 1471037--1471071 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1471027 AAATGACATC
1471037 TCATTGCATTGCATT
1 TCATTGCATTGCATT
* *
1471052 GCATTGCATTGGATT
1 TCATTGCATTGCATT
1471067 TCATT
1 TCATT
1471072 TGCTGCCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (15 bp):
TCATTGCATTGCATT
Found at i:1473904 original size:69 final size:69
Alignment explanation
Indices: 1473787--1473933 Score: 215
Period size: 69 Copynumber: 2.1 Consensus size: 69
1473777 ATTCCTTCAA
*
1473787 GGGGATACTCCAACTCTGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCTAAATTATCAT
1 GGGGATACTCCAACTCTGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCCAAATTATCAT
1473852 TGTC
66 TGTC
* * * * *
1473856 GGGTATACTCCAGC-CTCGTTTTTAAACTCATCGAAATTTAAGTCTTATTTTGTCCAAATTATCA
1 GGGGATACTCCAACTCT-GTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCCAAATTATCA
*
1473920 TTTTC
65 TTGTC
1473925 GGGGATACT
1 GGGGATACT
1473934 TTAACCTCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 2 0.03
69 67 0.97
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.41
Consensus pattern (69 bp):
GGGGATACTCCAACTCTGTTTTTAAACTCATCAAAATTTAAATATTATTTTGTCCAAATTATCAT
TGTC
Found at i:1480087 original size:28 final size:28
Alignment explanation
Indices: 1480053--1480201 Score: 158
Period size: 28 Copynumber: 5.3 Consensus size: 28
1480043 AACTTTTTCA
1480053 AAGTCCACGATTCAGGGCATTCCTTTTT
1 AAGTCCACGATTCAGGGCATTCCTTTTT
*
1480081 AAGTCCACGATTCAGGGCATTCCCTTTT
1 AAGTCCACGATTCAGGGCATTCCTTTTT
* *
1480109 AAGTTCACGATTCAGGGGCATTCCCTTTT
1 AAGTCCACGATTCA-GGGCATTCCTTTTT
* * * *
1480138 AAGTCCACAACTCCGTGGCA-CCCTTTTT
1 AAGTCCACGATTCAG-GGCATTCCTTTTT
* * * *
1480166 AAGTCCACAACTCCGTGGCA-CCCTTTTT
1 AAGTCCACGATTCAG-GGCATTCCTTTTT
1480194 AAGTCCAC
1 AAGTCCAC
1480202 AACTCTGTGG
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
28 83 0.75
29 28 0.25
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (28 bp):
AAGTCCACGATTCAGGGCATTCCTTTTT
Found at i:1480202 original size:28 final size:28
Alignment explanation
Indices: 1480134--1480641 Score: 688
Period size: 28 Copynumber: 18.3 Consensus size: 28
1480124 GGGCATTCCC
1480134 TTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
1480162 TTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
*
1480190 TTTTAAGTCCACAACTCTGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
* *
1480218 TTTAAAATCCACAACTCCGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
* * *
1480246 TTTAAAATCCACAAATCCGTGGCA-CCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
* * *
1480273 TTTTAAAGTCCACAACTCGGCGACACCCT
1 TTTT-AAGTCCACAACTCCGTGGCACCCT
* *
1480302 TTTAAAGTCCACAACTCCGTGGTA-CCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
*
1480329 TTTTAAGTCCATAACTCCGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
* *
1480357 TTTTAAGTCCACAACTCTGTGGCATCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
* **
1480385 TTTAAAGTCCACAACTCTATGGCACCC-
1 TTTTAAGTCCACAACTCCGTGGCACCCT
*
1480412 TTTTAAGTCCACAACTCCGTGGCACCAT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
*
1480440 TTTAAAGTCCACAACTCCGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
* * *
1480468 TTTAAAGTCCACAACTCTGTGGCATCC-
1 TTTTAAGTCCACAACTCCGTGGCACCCT
1480495 TTTTAAGGTCCACAACTCCGTGGCACCC-
1 TTTTAA-GTCCACAACTCCGTGGCACCCT
* * * *
1480523 TTTTAAGACCACAACTCTGCGGTACCC-
1 TTTTAAGTCCACAACTCCGTGGCACCCT
1480550 TTTTAAGTCCACAACTCCGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
* *
1480578 TTTAAAGTCCACAACTCCATGGCACCC-
1 TTTTAAGTCCACAACTCCGTGGCACCCT
*
1480605 TTTTAAGTTCACAACTCCGTGGCACCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCT
1480633 TTTTAAGTC
1 TTTTAAGTC
1480642 TAAGTCGATG
Statistics
Matches: 423, Mismatches: 50, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
27 122 0.29
28 295 0.70
29 6 0.01
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.29
Consensus pattern (28 bp):
TTTTAAGTCCACAACTCCGTGGCACCCT
Found at i:1480679 original size:32 final size:32
Alignment explanation
Indices: 1480643--1481207 Score: 586
Period size: 32 Copynumber: 17.6 Consensus size: 32
1480633 TTTTAAGTCT
* * *
1480643 AAGTCGATGGCAAACCTTCTTAAGGCCCACAC
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
* * *
1480675 AAGTCGGTGGTAACCCTT-TTCAAAGCCTACAA
1 AAGTCGGTGGCAACCCTTCTT-AAAGCCCACAC
* * * *
1480707 AAATCAGTGGCAACCCTTCTCAAAGCCTACAC
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
*
1480739 AAATCGGTGGCAACCCTT-TTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCTTCTT-AAAGCCCACAC
* * *
1480771 AAGTAGGTGGCAACCCTTCTCAAAGTCCACAC
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
1480803 AAGTCGGTGGCAACCCTT-TTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCTTCTT-AAAGCCCACAC
*
1480835 AAGTCGGTGGCAACCCTTCTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
*
1480867 AAGTCAGTGGCAACCCTTCTTAAAGCCCACAC
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
* *
1480899 AAGTCGGTGGCAACCCTTCTCAAAGCTCACAC
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
*
1480931 AAGTCAGTGGCAACCCTTCTTAAAGCCCACAC
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
* *
1480963 AAGTCGGTGACAA-CCTTTTTCAAAGCCCACAC
1 AAGTCGGTGGCAACCCTTCTT-AAAGCCCACAC
* * * *
1480995 AAGTTGGTGGCAACCCTTTTTAAAGCCTACAT
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
* * * * *
1481027 AAGTCGATGGTAACCCTTTTTAAAACCCACAT
1 AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
* * * * *
1481059 AAGTCGGTGGTAA-CTTTTTTCAAAGCTCACAT
1 AAGTCGGTGGCAACCCTTCTT-AAAGCCCACAC
* * * *
1481091 AAGTCGATGGCAACCATT-TTCAAAACCCATAC
1 AAGTCGGTGGCAACCCTTCTT-AAAGCCCACAC
* * *
1481123 AAGTCGATGGCAACCCTTTTTTAAAGCCCACAT
1 AAGTCGGTGGCAACCC-TTCTTAAAGCCCACAC
* * *
1481156 AAGTTGGTGGCAA-CCTACTTTAAAGCCCGCAC
1 AAGTCGGTGGCAACCCTTC-TTAAAGCCCACAC
* *
1481188 AAATCGATGGCAACCCTTCT
1 AAGTCGGTGGCAACCCTTCT
1481208 AAGCTCAATG
Statistics
Matches: 452, Mismatches: 67, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
31 17 0.04
32 395 0.87
33 38 0.08
34 2 0.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (32 bp):
AAGTCGGTGGCAACCCTTCTTAAAGCCCACAC
Found at i:1481940 original size:8 final size:8
Alignment explanation
Indices: 1481918--1481968 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
1481908 TTTTTTATAT
*
1481918 AAAATTAA
1 AAAAATAA
*
1481926 AACAATAA
1 AAAAATAA
1481934 AAAAAT--
1 AAAAATAA
*
1481940 AAAAATTA
1 AAAAATAA
1481948 AAAAATCAA
1 AAAAAT-AA
1481957 AAAAATAA
1 AAAAATAA
1481965 AAAA
1 AAAA
1481969 TAATAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 6 0.17
8 23 0.64
9 7 0.19
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:1481946 original size:23 final size:23
Alignment explanation
Indices: 1481918--1481967 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
1481908 TTTTTTATAT
1481918 AAAATTAAAACAAT-AAAAAAATA
1 AAAATTAAAA-AATCAAAAAAATA
1481941 AAAATTAAAAAATCAAAAAAATA
1 AAAATTAAAAAATCAAAAAAATA
1481964 AAAA
1 AAAA
1481968 ATAATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAATTAAAAAATCAAAAAAATA
Found at i:1481966 original size:7 final size:7
Alignment explanation
Indices: 1481918--1481971 Score: 54
Period size: 7 Copynumber: 7.1 Consensus size: 7
1481908 TTTTTTATAT
*
1481918 AAAATTA
1 AAAAATA
1481925 AAACAATAA
1 AAA-AAT-A
1481934 AAAAATA
1 AAAAATA
*
1481941 AAAATTA
1 AAAAATA
1481948 AAAAATCAA
1 AAAAAT--A
1481957 AAAAATA
1 AAAAATA
1481964 AAAAATA
1 AAAAATA
1481971 A
1 A
1481972 TAATATTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 24 0.60
8 5 0.12
9 11 0.28
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAATA
Found at i:1481969 original size:16 final size:15
Alignment explanation
Indices: 1481918--1481971 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1481908 TTTTTTATAT
* *
1481918 AAAATTAAAACAATA
1 AAAAATAAAAAAATA
*
1481933 AAAAA-ATAAAAATTA
1 AAAAATA-AAAAAATA
1481948 AAAAATCAAAAAAATA
1 AAAAAT-AAAAAAATA
1481964 AAAAATAA
1 AAAAATAA
1481972 TAATATTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.03
15 17 0.53
16 13 0.41
17 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:1485056 original size:69 final size:69
Alignment explanation
Indices: 1484942--1485096 Score: 195
Period size: 69 Copynumber: 2.2 Consensus size: 69
1484932 CCTTCGAGGG
* *
1484942 GATACTCTAA-CTCCGTTTTTAAACTCATCAAAATTTAAATATTATTTGGGCTAAATTATAATTG
1 GATACTCTAACCT-CATTTTTAAACTCATCAAAATTTAAATATTATTTGGGCCAAATTATAATTG
1485006 TCGAA
65 TCGAA
** * * * * *
1485011 GATACTCTAACCTCATTTTTAAACTCATTGAAATTTAATTCTTATTTTGTCCAAATTATTATTGT
1 GATACTCTAACCTCATTTTTAAACTCATCAAAATTTAAATATTATTTGGGCCAAATTATAATTGT
*
1485076 CGGA
66 CGAA
*
1485080 GATACTCTAACCCCATT
1 GATACTCTAACCTCATT
1485097 CCTTTGAGGA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
69 72 0.97
70 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (69 bp):
GATACTCTAACCTCATTTTTAAACTCATCAAAATTTAAATATTATTTGGGCCAAATTATAATTGT
CGAA
Found at i:1493823 original size:13 final size:13
Alignment explanation
Indices: 1493805--1493829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1493795 TTATGATTTG
1493805 TTAAATATTAACT
1 TTAAATATTAACT
1493818 TTAAATATTAAC
1 TTAAATATTAAC
1493830 GATGAAAAAA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATATTAACT
Found at i:1494026 original size:21 final size:20
Alignment explanation
Indices: 1493995--1494037 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
1493985 TGTGATTTTG
1493995 CTTTTTAATTTAATTTTGTAAT
1 CTTTTTAATTT-ATTTT-TAAT
1494017 CTTTTT-ATTTATTTTTAAT
1 CTTTTTAATTTATTTTTAAT
1494036 CT
1 CT
1494038 GTTCTTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 5 0.24
21 4 0.19
22 6 0.29
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (20 bp):
CTTTTTAATTTATTTTTAAT
Found at i:1494857 original size:22 final size:22
Alignment explanation
Indices: 1494831--1494904 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 22
1494821 TTCAGATTAA
1494831 TTATTTAATAATAAAAATAATT
1 TTATTTAATAATAAAAATAATT
1494853 TTATTTAAATTTAATTAAAAA-ATATAT
1 TTATTT-AA--TAA-TAAAAATA-AT-T
*
1494880 TAATATTAAT-ATAAAAATAATT
1 TTAT-TTAATAATAAAAATAATT
1494902 TTA
1 TTA
1494905 AATTTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
22 9 0.21
23 10 0.24
24 2 0.05
25 5 0.12
26 8 0.19
27 6 0.14
28 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTATTTAATAATAAAAATAATT
Found at i:1494944 original size:30 final size:30
Alignment explanation
Indices: 1494883--1494944 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1494873 AATATATTAA
* *
1494883 TATTAATATAAAAATAATTTTAAATTTTTT
1 TATTAATATAAAAATAATATTAAATATTTT
* *
1494913 TATTAATTTATAAATAATAATTAAA-ATTTT
1 TATTAATATAAAAATAAT-ATTAAATATTTT
1494943 TA
1 TA
1494945 AATTAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTAATATAAAAATAATATTAAATATTTT
Found at i:1494950 original size:32 final size:32
Alignment explanation
Indices: 1494889--1494950 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1494879 TTAATATTAA
* **
1494889 TATAAAAATAATTTTAAATTTTTTTATTAATT
1 TATAAAAATAATTTAAAATTTTTAAATTAATT
1494921 TATAAATAATAA-TTAAAATTTTTAAATTAA
1 TATAAA-AATAATTTAAAATTTTTAAATTAA
1494951 ATTAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TATAAAAATAATTTAAAATTTTTAAATTAATT
Found at i:1494955 original size:19 final size:20
Alignment explanation
Indices: 1494917--1494960 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1494907 TTTTTTTATT
1494917 AATTTATAAATAATAATTAA
1 AATTTATAAATAATAATTAA
* *
1494937 AATTTTTAAATTA-AATT-A
1 AATTTATAAATAATAATTAA
1494955 AATTTA
1 AATTTA
1494961 ACTTAAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTATAAATAATAATTAA
Found at i:1495812 original size:26 final size:26
Alignment explanation
Indices: 1495783--1495835 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
1495773 ATAAATATTT
1495783 TAAAATATTT-TTTATTA-ATTTAAAAA
1 TAAAATATTTATTT-TTATA-TTAAAAA
1495809 TAAAATATTTATTTTTATATTAAAAA
1 TAAAATATTTATTTTTATATTAAAAA
1495835 T
1 T
1495836 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TAAAATATTTATTTTTATATTAAAAA
Found at i:1496682 original size:7 final size:7
Alignment explanation
Indices: 1496664--1496697 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
1496654 AATAAATTAT
1496664 TTATACTA
1 TTATA-TA
1496672 TTATATA
1 TTATATA
1496679 TTATATA
1 TTATATA
1496686 TTATATA
1 TTATATA
1496693 TTATA
1 TTATA
1496698 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATATA
Found at i:1501097 original size:2 final size:2
Alignment explanation
Indices: 1501090--1501136 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1501080 CTTAATTTAA
1501090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1501132 AT AT A
1 AT AT A
1501137 AAAGACTATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1502845 original size:15 final size:16
Alignment explanation
Indices: 1502815--1502849 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1502805 ATGAATATCA
1502815 AATATGAATTTATATTT
1 AATATGAA-TTATATTT
1502832 AATATGAA-TATATTT
1 AATATGAATTATATTT
1502847 AAT
1 AAT
1502850 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
17 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (16 bp):
AATATGAATTATATTT
Found at i:1504020 original size:16 final size:16
Alignment explanation
Indices: 1503982--1504021 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
1503972 TTATAATTAA
1503982 ATTTAAA-T-AAAAAT
1 ATTTAAATTAAAAAAT
1503996 A-TT-AATTAAAAAAT
1 ATTTAAATTAAAAAAT
1504010 ATTTAAATTAAA
1 ATTTAAATTAAA
1504022 CTACAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.09
13 3 0.14
14 8 0.36
15 2 0.09
16 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAATTAAAAAAT
Found at i:1505750 original size:19 final size:19
Alignment explanation
Indices: 1505728--1505764 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1505718 AAAAATAACT
1505728 AATTAAATTAATTAATTTC
1 AATTAAATTAATTAATTTC
*
1505747 AATTTAATTAATTAATTT
1 AATTAAATTAATTAATTT
1505765 TTTACTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTAAATTAATTAATTTC
Found at i:1510564 original size:26 final size:25
Alignment explanation
Indices: 1510535--1510596 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
1510525 CTATTTTTTT
*
1510535 AAATATTTATTTTTAAT-ATAAATATA
1 AAATATTTATTTTAAATAAT-AAT-TA
**
1510561 AAATATAAATTTTAAATAATAATTA
1 AAATATTTATTTTAAATAATAATTA
1510586 AATATATTTAT
1 AA-ATATTTAT
1510597 ATTCAGTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 4 0.14
26 23 0.79
27 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATATTTATTTTAAATAATAATTA
Found at i:1510577 original size:13 final size:13
Alignment explanation
Indices: 1510531--1510578 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
1510521 CTTTCTATTT
**
1510531 TTTTAAATATTTA
1 TTTTAAATATAAA
*
1510544 TTTTTAATATAAA
1 TTTTAAATATAAA
* *
1510557 TATAAAATATAAA
1 TTTTAAATATAAA
1510570 TTTTAAATA
1 TTTTAAATA
1510579 ATAATTAAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAATATAAA
Found at i:1510814 original size:24 final size:25
Alignment explanation
Indices: 1510782--1510838 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
1510772 GTAAGTTAAA
1510782 AAATATAATTATTTAAAT-TAAAAT
1 AAATATAATTATTTAAATATAAAAT
* * *
1510806 AAATTTAATTTTTTTAATATAAAAAAT
1 AAATATAA-TTATTTAA-ATATAAAAT
1510833 AAATAT
1 AAATAT
1510839 TTTATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.27
25 7 0.27
26 2 0.08
27 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATATAATTATTTAAATATAAAAT
Found at i:1511907 original size:19 final size:18
Alignment explanation
Indices: 1511883--1511928 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1511873 ATTAATAACT
1511883 TATATTATATAGATTTTAA
1 TATATTATATA-ATTTTAA
* *
1511902 TATATTCATATATTTTTAT
1 TATATT-ATATAATTTTAA
1511921 TATATTAT
1 TATATTAT
1511929 TATTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.71
20 5 0.21
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TATATTATATAATTTTAA
Found at i:1512084 original size:23 final size:23
Alignment explanation
Indices: 1512058--1512102 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1512048 TTGTGTATTA
1512058 ATGTCATATTTAAATTATTTTTT
1 ATGTCATATTTAAATTATTTTTT
* *
1512081 ATGTCATATTTTAGTTATTTTT
1 ATGTCATATTTAAATTATTTTT
1512103 CTGGGTTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (23 bp):
ATGTCATATTTAAATTATTTTTT
Found at i:1513157 original size:23 final size:22
Alignment explanation
Indices: 1513131--1513179 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1513121 CATATTAGTA
1513131 TATATATATAT-ATATGTAATTTT
1 TATATA-ATATGATAT-TAATTTT
*
1513154 TATATAATATGATATTTATTTT
1 TATATAATATGATATTAATTTT
1513176 TATA
1 TATA
1513180 ATTTTTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TATATAATATGATATTAATTTT
Found at i:1513242 original size:73 final size:72
Alignment explanation
Indices: 1513159--1513302 Score: 207
Period size: 73 Copynumber: 2.0 Consensus size: 72
1513149 ATTTTTATAT
* * *
1513159 AATATGATATTTATTTTTATAATTTTTTAGTATTAACGTAAATTTTTTTATAAATATAATATAAT
1 AATACGATATTTATTTTTATAATTTTTTAGTATTAACATAAAATTTTTTA-AAATATAATATAAT
1513224 TAACATGC
65 TAACATGC
* * * * *
1513232 AATACGATATTTATTTTTATGATTTTTTATTATTAATATAAAATTTTTTAAAATGTAATGTAATT
1 AATACGATATTTATTTTTATAATTTTTTAGTATTAACATAAAATTTTTTAAAATATAATATAATT
1513297 AACATG
66 AACATG
1513303 TAAAATCACT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 19 0.30
73 44 0.70
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (72 bp):
AATACGATATTTATTTTTATAATTTTTTAGTATTAACATAAAATTTTTTAAAATATAATATAATT
AACATGC
Found at i:1513981 original size:19 final size:19
Alignment explanation
Indices: 1513959--1514009 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1513949 ATATTCGATA
* * *
1513959 TAAATATATTTTATTTTTT
1 TAAATATTTTTTATATATT
*
1513978 TAAATTTTTTTTATATATT
1 TAAATATTTTTTATATATT
1513997 TAAATATTTTTTA
1 TAAATATTTTTTA
1514010 AATAAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TAAATATTTTTTATATATT
Found at i:1514031 original size:20 final size:21
Alignment explanation
Indices: 1514006--1514047 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1513996 TTAAATATTT
1514006 TTTAAATAAAAATATTT-ATA
1 TTTAAATAAAAATATTTGATA
* *
1514026 TTTAAATATATATATTTGATA
1 TTTAAATAAAAATATTTGATA
1514047 T
1 T
1514048 AAATATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAAATAAAAATATTTGATA
Found at i:1514032 original size:14 final size:14
Alignment explanation
Indices: 1514015--1514060 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1514005 TTTTAAATAA
*
1514015 AAATATTTATATTT
1 AAATATATATATTT
1514029 AAATATATATATTT
1 AAATATATATATTT
* *
1514043 -GATATAAATA-TT
1 AAATATATATATTT
1514055 AAATAT
1 AAATAT
1514061 GATAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 2 0.07
13 12 0.44
14 13 0.48
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AAATATATATATTT
Found at i:1515918 original size:52 final size:52
Alignment explanation
Indices: 1515840--1515944 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
1515830 AATTATTTCT
1515840 ACGTTTTTTCATGTCTTTTGAGTATTTGTGTAGAATCATATCCTCACACCCC
1 ACGTTTTTTCATGTCTTTTGAGTATTTGTGTAGAATCATATCCTCACACCCC
*
1515892 ACGTTTTTTCATGTCTTTTGAGTATTTGTGTAGAATCATATCCTCATACCCC
1 ACGTTTTTTCATGTCTTTTGAGTATTTGTGTAGAATCATATCCTCACACCCC
1515944 A
1 A
1515945 TATTCGGATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (52 bp):
ACGTTTTTTCATGTCTTTTGAGTATTTGTGTAGAATCATATCCTCACACCCC
Found at i:1518310 original size:23 final size:23
Alignment explanation
Indices: 1518279--1518356 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
1518269 TAGAATTCGG
* *
1518279 TTCGGTTTTTTTATGGTATCAAA
1 TTCGATTTTTATATGGTATCAAA
* * * **
1518302 TTCGATTTTAAAAT-TTAAGAATA
1 TTCGATTTTTATATGGTATCAA-A
* *
1518325 TTCGGTTTTTGTATGGTATCAAA
1 TTCGATTTTTATATGGTATCAAA
1518348 TTCGATTTT
1 TTCGATTTT
1518357 AAAATTTAAG
Statistics
Matches: 38, Mismatches: 15, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
22 4 0.11
23 30 0.79
24 4 0.11
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (23 bp):
TTCGATTTTTATATGGTATCAAA
Found at i:1518330 original size:46 final size:46
Alignment explanation
Indices: 1518279--1518372 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
1518269 TAGAATTCGG
*
1518279 TTCGGTTTTTTTATGGTATCAAATTCGATTTTAAAATTTAAGAATA
1 TTCGGTTTTTGTATGGTATCAAATTCGATTTTAAAATTTAAGAATA
1518325 TTCGGTTTTTGTATGGTATCAAATTCGATTTTAAAATTTAAGAATA
1 TTCGGTTTTTGTATGGTATCAAATTCGATTTTAAAATTTAAGAATA
1518371 TT
1 TT
1518373 GCATATTAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (46 bp):
TTCGGTTTTTGTATGGTATCAAATTCGATTTTAAAATTTAAGAATA
Found at i:1518786 original size:8 final size:8
Alignment explanation
Indices: 1518761--1518800 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1518751 GTTTTTGAAA
*
1518761 AAAAGTTT
1 AAAATTTT
**
1518769 AAAAAATT
1 AAAATTTT
1518777 AAAATTTT
1 AAAATTTT
1518785 AAAATTTT
1 AAAATTTT
1518793 AAAATTTT
1 AAAATTTT
1518801 TTATGCTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (8 bp):
AAAATTTT
Found at i:1519365 original size:21 final size:21
Alignment explanation
Indices: 1519310--1519374 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1519300 TTAATTTATT
*
1519310 ATTAAATAAATTTATTTAATGAA
1 ATTAAATAAATTTA-TTCAT-AA
**
1519333 ATT-AAT-TTTTTATTCATAA
1 ATTAAATAAATTTATTCATAA
*
1519352 ATTAAATAAATTTACTCATAA
1 ATTAAATAAATTTATTCATAA
1519373 AT
1 AT
1519375 CTATTTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 16 0.47
22 3 0.09
23 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTAAATAAATTTATTCATAA
Found at i:1519536 original size:15 final size:16
Alignment explanation
Indices: 1519505--1519538 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1519495 TTTTAAACCT
1519505 TTTATATTTTATCTAA
1 TTTATATTTTATCTAA
*
1519521 TTTATA-TTTATTTAA
1 TTTATATTTTATCTAA
1519536 TTT
1 TTT
1519539 TGATATAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATATTTTATCTAA
Found at i:1521538 original size:65 final size:65
Alignment explanation
Indices: 1521424--1521548 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 65
1521414 GATACAAGGT
* *
1521424 ACTCTCAACTCGACGATAAACATTCTTACTCAAAAGAATGATGCTCTCGAAGTCATGATGAAAGA
1 ACTCTCAACTCGACGATAAACATTCTTACTCAAAAGAATAATGCCCTCGAAGTCATGATGAAAGA
** * *
1521489 ACTCTCAACTCGGTGATAAACATTTTTACTCAGAAGAATAATGCCCTCGAAGTCATGATG
1 ACTCTCAACTCGACGATAAACATTCTTACTCAAAAGAATAATGCCCTCGAAGTCATGATG
1521549 GAGGCCATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (65 bp):
ACTCTCAACTCGACGATAAACATTCTTACTCAAAAGAATAATGCCCTCGAAGTCATGATGAAAGA
Found at i:1522199 original size:12 final size:12
Alignment explanation
Indices: 1522182--1522206 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1522172 CCAAATCCAG
1522182 TAGCTTTCAAGT
1 TAGCTTTCAAGT
1522194 TAGCTTTCAAGT
1 TAGCTTTCAAGT
1522206 T
1 T
1522207 CACTAAGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TAGCTTTCAAGT
Found at i:1523810 original size:19 final size:17
Alignment explanation
Indices: 1523786--1523821 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
1523776 TACCATTTAA
1523786 ATTAAAATTCTAAAAAATT
1 ATTAAAA-T-TAAAAAATT
1523805 ATTAAAATTAAAAAATT
1 ATTAAAATTAAAAAATT
1523822 GAGAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTAAAATTAAAAAATT
Found at i:1524543 original size:23 final size:22
Alignment explanation
Indices: 1524516--1524558 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1524506 TAGCTAGCCC
1524516 ATATTATTATTTAAATATTAAAA
1 ATATTATTATTTAAAT-TTAAAA
*
1524539 ATATTTTTATTTAAATTTAA
1 ATATTATTATTTAAATTTAA
1524559 TTATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTATTATTTAAATTTAAAA
Found at i:1525945 original size:25 final size:25
Alignment explanation
Indices: 1525893--1525947 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1525883 ACCAGTGTGA
* *
1525893 TATAAATAGTAAAATATATTTATATT
1 TATAAATAG-AAAATAAATTTAAATT
1525919 TATAAATA-AAAATAAATTTTAAATT
1 TATAAATAGAAAATAAA-TTTAAATT
1525944 TATA
1 TATA
1525948 TAAATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 7 0.27
25 11 0.42
26 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TATAAATAGAAAATAAATTTAAATT
Found at i:1526176 original size:19 final size:18
Alignment explanation
Indices: 1526118--1526183 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 18
1526108 AGAAAAGAAA
*
1526118 ATATAATAAAAAATATAAT
1 ATATAA-AAATAATATAAT
* *
1526137 ATGTTGAAAA-AATATAAT
1 AT-ATAAAAATAATATAAT
1526155 ATATAAAAATAATATAAAT
1 ATATAAAAATAATAT-AAT
*
1526174 ATATCAAAAT
1 ATATAAAAAT
1526184 TTATTAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 5 0.13
18 15 0.38
19 17 0.44
20 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATAAAAATAATATAAT
Found at i:1526194 original size:18 final size:19
Alignment explanation
Indices: 1526143--1526194 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
1526133 TAATATGTTG
1526143 AAAA-AATA-TAATATATA
1 AAAATAATATTAATATATA
* *
1526160 AAAATAATATAAATATATC
1 AAAATAATATTAATATATA
*
1526179 AAAAT-TTATTAATATA
1 AAAATAATATTAATATA
1526195 AATTATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.14
18 13 0.45
19 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAATATTAATATATA
Found at i:1526231 original size:27 final size:26
Alignment explanation
Indices: 1526186--1526243 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1526176 ATCAAAATTT
* *
1526186 ATTAATATAAATTATTAAT-TTATTAAA
1 ATTAATATAAATAAATAATATT-TT-AA
1526213 ATTAATATAAATAAATAATATTTTAA
1 ATTAATATAAATAAATAATATTTTAA
1526239 ATTAA
1 ATTAA
1526244 ATTATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.25
27 19 0.68
28 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTAATATAAATAAATAATATTTTAA
Found at i:1527572 original size:29 final size:29
Alignment explanation
Indices: 1527515--1527572 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1527505 TCAAATCATT
* *
1527515 ATTTAATAATTAAAAATATTTTTATTTAA
1 ATTTAATAATTAAAAATATATTAATTTAA
*
1527544 ATTTAATTA-TAAAAATATATTAATATTAA
1 ATTTAATAATTAAAAATATATTAAT-TTAA
1527573 TATCAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTTAATAATTAAAAATATATTAATTTAA
Found at i:1528806 original size:20 final size:20
Alignment explanation
Indices: 1528781--1528820 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1528771 TCGAATATGC
1528781 GTCAAACAATGAAAAAGTGT
1 GTCAAACAATGAAAAAGTGT
*
1528801 GTCAAACAATTAAAAAGTGT
1 GTCAAACAATGAAAAAGTGT
1528821 TGGAGATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (20 bp):
GTCAAACAATGAAAAAGTGT
Found at i:1530361 original size:52 final size:53
Alignment explanation
Indices: 1530270--1530376 Score: 137
Period size: 52 Copynumber: 2.0 Consensus size: 53
1530260 CCCAATTTTG
* *
1530270 GGTCATAACGCTCATACTTGCACCTTTAAACCTGCAAACTCGAGCCA-TAAAA
1 GGTCATAACGCCCATACTTGCACCTTTAAAACTGCAAACTCGAGCCATTAAAA
* * * *
1530322 GGTCGTAACGCCCATACTTGTACCTTTAAAGAC-GGAAACTTGAGCCATTAAAA
1 GGTCATAACGCCCATACTTGCACCTTTAAA-ACTGCAAACTCGAGCCATTAAAA
1530375 GG
1 GG
1530377 CTGATTATAG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 39 0.83
53 8 0.17
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (53 bp):
GGTCATAACGCCCATACTTGCACCTTTAAAACTGCAAACTCGAGCCATTAAAA
Found at i:1531261 original size:33 final size:31
Alignment explanation
Indices: 1531219--1531284 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1531209 ATGAATCGAA
1531219 AATTGGACCCAATGGAACAATATATATATATAT
1 AATTGGACCCAAT-GAA-AATATATATATATAT
* *
1531252 AATTGGACCCAATGTATATATATATATATAT
1 AATTGGACCCAATGAAAATATATATATATAT
1531283 AA
1 AA
1531285 AATTAAGGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 16 0.52
32 2 0.06
33 13 0.42
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (31 bp):
AATTGGACCCAATGAAAATATATATATATAT
Found at i:1531384 original size:12 final size:12
Alignment explanation
Indices: 1531359--1531414 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
1531349 AAGATTGAAA
* *
1531359 AAATATTATCAT
1 AAATAATATAAT
1531371 AAATAATATAAT
1 AAATAATATAAT
*
1531383 -AATACTAATAAT
1 AAATAAT-ATAAT
*
1531395 AAATAAAATAGAT
1 AAATAATATA-AT
1531408 AAATAAT
1 AAATAAT
1531415 GGTTTCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 5 0.14
12 18 0.51
13 12 0.34
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (12 bp):
AAATAATATAAT
Found at i:1532067 original size:22 final size:22
Alignment explanation
Indices: 1532042--1532091 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1532032 CTAAAGTTAT
1532042 TTTATTATT-TAAATAAATTTTA
1 TTTATTATTGTAAA-AAATTTTA
* * *
1532064 TTTAATATTGTTAAAAATTTTC
1 TTTATTATTGTAAAAAATTTTA
1532086 TTTATT
1 TTTATT
1532092 TGTTCTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTATTATTGTAAAAAATTTTA
Found at i:1532720 original size:28 final size:29
Alignment explanation
Indices: 1532681--1532739 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 29
1532671 AATACTTATA
1532681 AATTATATATAAT-GTTAATATCTGAATC
1 AATTATATATAATAGTTAATATCTGAATC
*
1532709 AATTATGA-ATAATAAATTTAATATCTGAATC
1 AATTAT-ATATAAT--AGTTAATATCTGAATC
1532740 TATAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 11 0.42
29 1 0.04
31 14 0.54
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (29 bp):
AATTATATATAATAGTTAATATCTGAATC
Found at i:1534258 original size:13 final size:13
Alignment explanation
Indices: 1534242--1534267 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1534232 TGATTAACAT
1534242 AAAAAATTAAATA
1 AAAAAATTAAATA
1534255 AAAAAATTAAATA
1 AAAAAATTAAATA
1534268 CGATGCTTAT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAATTAAATA
Found at i:1536401 original size:11 final size:11
Alignment explanation
Indices: 1536387--1536471 Score: 65
Period size: 11 Copynumber: 8.1 Consensus size: 11
1536377 ATTTATAAAT
*
1536387 TTTTTATGTTA
1 TTTTTATATTA
1536398 TTTTTATATTA
1 TTTTTATATTA
*
1536409 TATTTATA-TA
1 TTTTTATATTA
**
1536419 AATTT-TATTA
1 TTTTTATATTA
*
1536429 TTTTATAAATT-
1 TTTT-TATATTA
1536440 TTTGTTATA-TA
1 TTT-TTATATTA
1536451 -TTTTA-ATTA
1 TTTTTATATTA
1536460 TTTTTATATTA
1 TTTTTATATTA
1536471 T
1 T
1536472 ATAATTATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
8 1 0.02
9 7 0.12
10 18 0.31
11 29 0.49
12 4 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTTTATATTA
Found at i:1536435 original size:30 final size:33
Alignment explanation
Indices: 1536395--1536473 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 33
1536385 ATTTTTTATG
1536395 TTATTTTTATATTATATTT-ATATAAATTTT-A
1 TTATTTTTATATTATATTTGATATAAATTTTAA
* * * *
1536426 TTA-TTTTATA-AATTTTTGTTATATATTTTAA
1 TTATTTTTATATTATATTTGATATAAATTTTAA
1536457 TTATTTTTATATTATAT
1 TTATTTTTATATTATAT
1536474 AATTATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 5 0.13
30 16 0.42
31 7 0.18
32 7 0.18
33 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (33 bp):
TTATTTTTATATTATATTTGATATAAATTTTAA
Found at i:1536612 original size:8 final size:8
Alignment explanation
Indices: 1536599--1536652 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
1536589 ATTATAAATT
1536599 TTAATATA
1 TTAATATA
1536607 TTAATA-A
1 TTAATATA
1536614 TT-ATATGA
1 TTAATAT-A
*
1536622 TATAA-ATT
1 T-TAATATA
1536630 TTAATATA
1 TTAATATA
*
1536638 TTTATATA
1 TTAATATA
1536646 TTAATAT
1 TTAATAT
1536653 TATATTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
6 3 0.08
7 6 0.16
8 24 0.65
9 3 0.08
10 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (8 bp):
TTAATATA
Found at i:1536628 original size:31 final size:33
Alignment explanation
Indices: 1536591--1536657 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 33
1536581 CATGTTTAAT
1536591 TATAAATTTTAATATATTAATA-ATT-ATATGA
1 TATAAATTTTAATATATTAATATATTAATATGA
* *
1536622 TATAAATTTTAATATATTTATATATTAATATTA
1 TATAAATTTTAATATATTAATATATTAATATGA
1536655 TAT
1 TAT
1536658 TTTATTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 21 0.66
32 3 0.09
33 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (33 bp):
TATAAATTTTAATATATTAATATATTAATATGA
Found at i:1536638 original size:14 final size:14
Alignment explanation
Indices: 1536585--1536638 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
1536575 AATAATCATG
1536585 TTTAAT-TATAAAT
1 TTTAATATATAAAT
*
1536598 TTTAATATATTAAT
1 TTTAATATATAAAT
*
1536612 AATTATATGATATAAAT
1 -TTTA-AT-ATATAAAT
1536629 TTTAATATAT
1 TTTAATATAT
1536639 TTATATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
13 6 0.18
14 10 0.30
15 5 0.15
16 5 0.15
17 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TTTAATATATAAAT
Found at i:1536652 original size:6 final size:5
Alignment explanation
Indices: 1536603--1536711 Score: 52
Period size: 5 Copynumber: 22.2 Consensus size: 5
1536593 TAAATTTTAA
* * * *
1536603 TATAT TAATAAT TATAT GATA- TAAAT TTTAA TATAT T-TA- TATAT TAATAT
1 TATAT T-AT-AT TATAT TATAT TATAT TATAT TATAT TATAT TATAT T-ATAT
* * * *
1536653 TATAT TTTAT TAT-T TATTT TATAT TATAT TTTAAT TA-AT T-TTT TA-AT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT
1536700 TATAT TCATAT T
1 TATAT T-ATAT T
1536712 TTATAATTGT
Statistics
Matches: 77, Mismatches: 15, Indels: 23
0.67 0.13 0.20
Matches are distributed among these distances:
3 1 0.01
4 18 0.23
5 38 0.49
6 17 0.22
7 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1536656 original size:19 final size:19
Alignment explanation
Indices: 1536602--1536687 Score: 61
Period size: 19 Copynumber: 4.5 Consensus size: 19
1536592 ATAAATTTTA
*
1536602 ATATATTAATAATTATATGAT
1 ATATATTAAT-ATTATAT-TT
* * *
1536623 ATAAATT-TTAATATATTT
1 ATATATTAATATTATATTT
1536641 ATATATTAATATTATATTT
1 ATATATTAATATTATATTT
* *
1536660 -TATTATTTATTTTATA-TT
1 ATA-TATTAATATTATATTT
*
1536678 ATATTTTAAT
1 ATATATTAAT
1536688 TAATTTTTTA
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
18 16 0.31
19 28 0.55
20 1 0.02
21 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (19 bp):
ATATATTAATATTATATTT
Found at i:1536676 original size:24 final size:24
Alignment explanation
Indices: 1536649--1536705 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
1536639 TTATATATTA
*
1536649 ATATTATATTTT-ATTATTTATTTT
1 ATATTATATTTTAATTAATT-TTTT
1536673 ATATTATATTTTAATTAATTTTTT
1 ATATTATATTTTAATTAATTTTTT
1536697 A-ATTATATT
1 ATATTATATT
1536706 CATATTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 8 0.26
24 17 0.55
25 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATATTATATTTTAATTAATTTTTT
Found at i:1536685 original size:17 final size:18
Alignment explanation
Indices: 1536634--1536716 Score: 73
Period size: 19 Copynumber: 4.6 Consensus size: 18
1536624 TAAATTTTAA
*
1536634 TATATTTATATATTAATAT
1 TATATTT-TATATTTATAT
*
1536653 TATATTTTATTATTTATTT
1 TATATTTTA-TATTTATAT
*
1536672 TATATTATAT-TTTA-AT
1 TATATTTTATATTTATAT
* *
1536688 TA-ATTTTTTAATTATAT
1 TATATTTTATATTTATAT
1536705 TCATATTTTATA
1 T-ATATTTTATA
1536717 ATTGTAATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.10
16 6 0.12
17 7 0.14
18 4 0.08
19 29 0.57
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (18 bp):
TATATTTTATATTTATAT
Found at i:1536995 original size:33 final size:33
Alignment explanation
Indices: 1536958--1537044 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 33
1536948 TATGTTTAAT
*
1536958 TTATTAAAATAAAATAAAATTATAATAACATAA
1 TTATTAAAATAAAATAAAATAATAATAACATAA
**
1536991 TTATTTTTAAAAATTAAAATAAAATAATTTTAACATAA
1 TTA---TT-AAAA-TAAAATAAAATAATAATAACATAA
*
1537029 TTAATAAAATAAAATA
1 TTATTAAAATAAAATA
1537045 TTATAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
33 10 0.22
34 4 0.09
35 1 0.02
36 2 0.04
37 4 0.09
38 24 0.53
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (33 bp):
TTATTAAAATAAAATAAAATAATAATAACATAA
Found at i:1537884 original size:24 final size:24
Alignment explanation
Indices: 1537857--1537904 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1537847 ATTAATTTGA
** *
1537857 ATTTGAATTTTGATAATAATAAAT
1 ATTTGAATTTAAATAATAAAAAAT
1537881 ATTTGAATTTAAATAATAAAAAAT
1 ATTTGAATTTAAATAATAAAAAAT
1537905 TTAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
ATTTGAATTTAAATAATAAAAAAT
Found at i:1538603 original size:13 final size:13
Alignment explanation
Indices: 1538585--1538613 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1538575 TTCAAATATT
1538585 TATCAAATATAAA
1 TATCAAATATAAA
1538598 TATCAAATATAAA
1 TATCAAATATAAA
1538611 TAT
1 TAT
1538614 TTAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
TATCAAATATAAA
Found at i:1538970 original size:16 final size:17
Alignment explanation
Indices: 1538949--1538991 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1538939 TTTATTTTTT
1538949 TAATTAATCATAT-TTA
1 TAATTAATCATATATTA
*
1538965 TAATTAAT-ATTTATTA
1 TAATTAATCATATATTA
1538981 TAATT-ATCATA
1 TAATTAATCATA
1538992 ATAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTAATCATATATTA
Found at i:1540976 original size:15 final size:15
Alignment explanation
Indices: 1540926--1540976 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1540916 ATGTTTGTAT
*
1540926 TATTAGTTA-GATTA
1 TATTAGATATGATTA
*
1540940 GTATTAGATATAAATATA
1 -TATTAGATAT-GAT-TA
1540958 TATTAGATATGATTA
1 TATTAGATATGATTA
1540973 TATT
1 TATT
1540977 TAATTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 14 0.47
16 2 0.07
17 12 0.40
18 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (15 bp):
TATTAGATATGATTA
Found at i:1542124 original size:5 final size:5
Alignment explanation
Indices: 1542105--1542157 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
1542095 AAGGGAGAGG
* *
1542105 AAAGG AAAGA AAAGA AAAGA AAA-A AAAGA AATGTA AAAGA AAA-A AATAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAG-A AAAGA AAAGA AA-AGA
1542155 AAA
1 AAA
1542158 TTGTGATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 7 0.17
5 27 0.66
6 7 0.17
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (5 bp):
AAAGA
Found at i:1544152 original size:14 final size:14
Alignment explanation
Indices: 1544133--1544163 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1544123 ATAGGATTAT
1544133 TTAAATTATTTTTA
1 TTAAATTATTTTTA
1544147 TTAAATTATTTTTA
1 TTAAATTATTTTTA
1544161 TTA
1 TTA
1544164 TAAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTAAATTATTTTTA
Found at i:1544176 original size:32 final size:33
Alignment explanation
Indices: 1544129--1544208 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
1544119 CACTATAGGA
*
1544129 TTATT-TAAAT-T-ATTTTTATTAAATT-ATTT
1 TTATTATAAATATAATTTTTAATAAATTAATTT
*
1544158 TTATTATAAATATAATTTTTAATAATTTAATTT
1 TTATTATAAATATAATTTTTAATAAATTAATTT
* *
1544191 TTAATATAATTATAATTT
1 TTATTATAAATATAATTT
1544209 AGTAATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.12
30 5 0.12
31 1 0.02
32 12 0.28
33 20 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TTATTATAAATATAATTTTTAATAAATTAATTT
Found at i:1544199 original size:33 final size:33
Alignment explanation
Indices: 1544140--1544290 Score: 121
Period size: 33 Copynumber: 4.5 Consensus size: 33
1544130 TATTTAAATT
* * *
1544140 ATTTTTATTAAATTATT-TTTATTATAAATATA
1 ATTTTTAATAATTTATTATTTAATATAAATATA
*
1544172 ATTTTTAATAATTTAATT-TTTAATATAATTATA
1 ATTTTTAATAATTT-ATTATTTAATATAAATATA
* * * *
1544205 ATTTAGTAATTAA-TTATTATTTAACATTAATA-C
1 ATTT-TTAA-TAATTTATTATTTAATATAAATATA
*
1544238 ATTTTTAATTTATATTTTATTATTTAATATAAATTTA
1 ATTTTTAA--TA-A-TTTATTATTTAATATAAATATA
*
1544275 ATTTTTAATTATTTAT
1 ATTTTTAATAATTTAT
1544291 CCTTATATAC
Statistics
Matches: 95, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
32 15 0.16
33 35 0.37
34 17 0.18
35 4 0.04
36 16 0.17
37 8 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (33 bp):
ATTTTTAATAATTTATTATTTAATATAAATATA
Found at i:1544218 original size:18 final size:17
Alignment explanation
Indices: 1544154--1544290 Score: 72
Period size: 18 Copynumber: 7.9 Consensus size: 17
1544144 TTATTAAATT
* *
1544154 ATTTTTATTATAAATATA
1 ATTTTTAAT-TAATTATA
1544172 ATTTTTAA-TAATT-TA
1 ATTTTTAATTAATTATA
1544187 ATTTTTAATATAATTATA
1 ATTTTTAAT-TAATTATA
* *
1544205 ATTTAGTAATTAATTATT
1 ATTT-TTAATTAATTATA
* *
1544223 A-TTTAACATTAA-TA-C
1 ATTTTTA-ATTAATTATA
*
1544238 ATTTTTAATTTATATT-TT
1 ATTTTTAA-TTA-ATTATA
1544256 ATTATTTAATATAAATT-TA
1 ATT-TTTAAT-T-AATTATA
*
1544275 ATTTTTAATTATTTAT
1 ATTTTTAATTAATTAT
1544291 CCTTATATAC
Statistics
Matches: 94, Mismatches: 11, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
15 12 0.13
16 17 0.18
17 15 0.16
18 32 0.34
19 17 0.18
20 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
ATTTTTAATTAATTATA
Found at i:1544265 original size:19 final size:18
Alignment explanation
Indices: 1544238--1544284 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
1544228 ACATTAATAC
* *
1544238 ATTTTTAATTTATATTTT
1 ATTTTTAATTTAAATTTA
*
1544256 ATTATTTAATATAAATTTA
1 ATT-TTTAATTTAAATTTA
1544275 ATTTTTAATT
1 ATTTTTAATT
1544285 ATTTATCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAATTTAAATTTA
Found at i:1546876 original size:18 final size:18
Alignment explanation
Indices: 1546847--1546881 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1546837 TAATTAGATA
1546847 AATTTATATATATATTTTT
1 AATTTATATATAT-TTTTT
1546866 AATTT-TATATATTTTT
1 AATTTATATATATTTTT
1546882 ATTATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTATATATATTTTTT
Found at i:1547773 original size:22 final size:22
Alignment explanation
Indices: 1547748--1547809 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
1547738 TTGAATTATT
*
1547748 ATTTAATAATAAAAATATTTAA
1 ATTTAATAATAAAAATATATAA
*
1547770 ATTTAATTATAAAAATATATAA
1 ATTTAATAATAAAAATATATAA
*
1547792 ATATTAATATATTAAAAT
1 AT-TTAATA-ATAAAAAT
1547810 TTTTTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 22 0.65
23 5 0.15
24 7 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTAATAATAAAAATATATAA
Found at i:1550345 original size:2 final size:2
Alignment explanation
Indices: 1550333--1550375 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1550323 TATTTTCATC
*
1550333 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1550375 T
1 T
1550376 GCATGGAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1552885 original size:17 final size:17
Alignment explanation
Indices: 1552863--1552905 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1552853 AAATCCGTTG
1552863 AATTTATATAATATTTA
1 AATTTATATAATATTTA
* *
1552880 AATTTATTTATTATTTA
1 AATTTATATAATATTTA
1552897 AATTTATAT
1 AATTTATAT
1552906 TTGATTTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTATATAATATTTA
Found at i:1552912 original size:17 final size:17
Alignment explanation
Indices: 1552875--1552913 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1552865 TTTATATAAT
*
1552875 ATTTAAATTTATTTATT
1 ATTTAAATTTATTTATG
1552892 ATTTAAATTTATATT-TG
1 ATTTAAATTTAT-TTATG
1552909 ATTTA
1 ATTTA
1552914 GATAGTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTAAATTTATTTATG
Found at i:1553199 original size:15 final size:14
Alignment explanation
Indices: 1553177--1553233 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
1553167 TAAAATTTAT
1553177 TCAAATATATAATA
1 TCAAATATATAATA
*
1553191 TCTAAATATATAAAAA
1 TC-AAATATAT-AATA
*
1553207 TCAAATTAGATAATA
1 TCAAA-TATATAATA
1553222 TCAAATAT-TAAT
1 TCAAATATATAAT
1553234 TTTTTTTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
13 4 0.11
14 4 0.11
15 19 0.53
16 9 0.25
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (14 bp):
TCAAATATATAATA
Found at i:1553848 original size:27 final size:27
Alignment explanation
Indices: 1553778--1553853 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
1553768 AAAACCACCA
* *
1553778 TTTATTTGTAAAAAATAGTGATTACTT
1 TTTATTTGTAAAAAATGGTGGTTACTT
* * * *
1553805 TATGTTTGTTAAAAATGGTGGTTTCTT
1 TTTATTTGTAAAAAATGGTGGTTACTT
*
1553832 TTTATTTGTCAAAAATGGTGGT
1 TTTATTTGTAAAAAATGGTGGT
1553854 ATGTTGTTTG
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (27 bp):
TTTATTTGTAAAAAATGGTGGTTACTT
Found at i:1554595 original size:30 final size:30
Alignment explanation
Indices: 1554559--1554651 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
1554549 GAAAAATTCT
1554559 TGAAGAAGAGCAATCAGAATAAACTCCCTA
1 TGAAGAAGAGCAATCAGAATAAACTCCCTA
* ** * * *
1554589 TGAAGAAGTG-AATTTGAACGAAAAAT-TCT-
1 TGAAGAAGAGCAATCAGAA--TAAACTCCCTA
1554618 TGAAGAAGAGCAATCAGAATAAACTCCCTA
1 TGAAGAAGAGCAATCAGAATAAACTCCCTA
1554648 TGAA
1 TGAA
1554652 AAAGTGAATT
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
28 4 0.09
29 17 0.37
30 21 0.46
31 4 0.09
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.20
Consensus pattern (30 bp):
TGAAGAAGAGCAATCAGAATAAACTCCCTA
Found at i:1554634 original size:59 final size:59
Alignment explanation
Indices: 1554542--1554661 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
1554532 TATGGACAGC
*
1554542 TTTGAACGAAAAATTCTTGAAGAAGAGCAATCAGAATAAACTCCCTATGAAGAAGTGAA
1 TTTGAACGAAAAATTCTTGAAGAAGAGCAATCAGAATAAACTCCCTATGAAAAAGTGAA
1554601 TTTGAACGAAAAATTCTTGAAGAAGAGCAATCAGAATAAACTCCCTATGAAAAAGTGAA
1 TTTGAACGAAAAATTCTTGAAGAAGAGCAATCAGAATAAACTCCCTATGAAAAAGTGAA
1554660 TT
1 TT
1554662 GTTTCGCTTC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.23
Consensus pattern (59 bp):
TTTGAACGAAAAATTCTTGAAGAAGAGCAATCAGAATAAACTCCCTATGAAAAAGTGAA
Found at i:1557603 original size:32 final size:34
Alignment explanation
Indices: 1557547--1557623 Score: 113
Period size: 32 Copynumber: 2.3 Consensus size: 34
1557537 TAATATTATT
1557547 ATATAAATATATAAATATATTAAATTTTATAT-A
1 ATATAAATATATAAATATATTAAATTTTATATAA
* *
1557580 ATATAAAT-TATTAATTTATTAAATTTTATATAA
1 ATATAAATATATAAATATATTAAATTTTATATAA
1557613 ATATATAATAT
1 ATATA-AATAT
1557624 TTTTTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 21 0.54
33 14 0.36
34 3 0.08
35 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
ATATAAATATATAAATATATTAAATTTTATATAA
Found at i:1559361 original size:19 final size:21
Alignment explanation
Indices: 1559337--1559381 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1559327 TACTCATTAT
*
1559337 AAAAT-AAAAAAT-TTTAAAA
1 AAAATAAAAAAATAATTAAAA
1559356 AAAATAAAAAAATAATTAAAA
1 AAAATAAAAAAATAATTAAAA
1559377 AAAAT
1 AAAAT
1559382 CTTCTCTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 7 0.30
21 11 0.48
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAATAAAAAAATAATTAAAA
Found at i:1560028 original size:17 final size:18
Alignment explanation
Indices: 1559984--1560028 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1559974 TTTAATTTAA
* *
1559984 TTAATTTATATAATAATTT
1 TTAATTTA-AAAATAATAT
1560003 TTAATTTAAAAATAATAT
1 TTAATTTAAAAATAATAT
1560021 TT-ATTTAA
1 TTAATTTAA
1560029 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTTAAAAATAATAT
Found at i:1560035 original size:21 final size:21
Alignment explanation
Indices: 1559978--1560036 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1559968 AATTAATTTA
* *
1559978 ATTTAATTAATTT-ATATAAT
1 ATTTATTTAATTTAAAATAAT
*
1559998 AATT-TTTAATTTAAAAATAAT
1 ATTTATTTAATTT-AAAATAAT
1560019 ATTTATTTAATTTAAAAT
1 ATTTATTTAATTTAAAAT
1560037 TTTAATTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 7 0.22
20 3 0.09
21 14 0.44
22 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTATTTAATTTAAAATAAT
Found at i:1560044 original size:22 final size:22
Alignment explanation
Indices: 1559993--1560035 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1559983 ATTAATTTAT
*
1559993 ATAATAATT-TTTAATTTAAAA
1 ATAATATTTATTTAATTTAAAA
1560014 ATAATATTTATTTAATTTAAAA
1 ATAATATTTATTTAATTTAAAA
1560036 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATATTTATTTAATTTAAAA
Found at i:1560184 original size:23 final size:22
Alignment explanation
Indices: 1560152--1560199 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1560142 TATAATTATA
*
1560152 TAATTTAAATATAAAAATAAAAT
1 TAATTAAAATATAAAAA-AAAAT
* *
1560175 TAATTAAAATATTATAAAAAAT
1 TAATTAAAATATAAAAAAAAAT
1560197 TAA
1 TAA
1560200 AATTTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TAATTAAAATATAAAAAAAAAT
Found at i:1560199 original size:18 final size:19
Alignment explanation
Indices: 1560176--1560212 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1560166 AAATAAAATT
1560176 AATTAAAA-TATTATAAAA
1 AATTAAAATTATTATAAAA
1560194 AATTAAAATTTATTATAAA
1 AATTAAAA-TTATTATAAA
1560213 TATATGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAAAATTATTATAAAA
Found at i:1560203 original size:28 final size:27
Alignment explanation
Indices: 1560164--1560258 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 27
1560154 ATTTAAATAT
1560164 AAAAA-TAAAATTAATTAAAATATTATA
1 AAAAATTAAAATT-ATTAAAATATTATA
1560191 AAAAATTAAAATTTATTATAAATA-TATGA
1 AAAAATTAAAA-TTATTA-AAATATTAT-A
* *
1560220 ATATATTAAAATTATATAAAATAATTAT-
1 AAAAATTAAAATTAT-TAAAAT-ATTATA
*
1560248 ATAAATTAAAA
1 AAAAATTAAAA
1560259 AAATTTAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
27 5 0.09
28 30 0.52
29 20 0.34
30 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
AAAAATTAAAATTATTAAAATATTATA
Found at i:1560529 original size:22 final size:21
Alignment explanation
Indices: 1560496--1560538 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1560486 TATTATATTT
*
1560496 AATTTAAATTTAATATTTAAA
1 AATTTAAATTTAATATATAAA
1560517 AATTTATAATTTAATATATAAA
1 AATTTA-AATTTAATATATAAA
1560539 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTAAATTTAATATATAAA
Found at i:1560744 original size:24 final size:24
Alignment explanation
Indices: 1560712--1560757 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1560702 GGATATAAAA
* *
1560712 TTTAAGTATTAAATTATTAATTTT
1 TTTAAGTATAAAATTATAAATTTT
1560736 TTTAAGTATAAAATTATAAATT
1 TTTAAGTATAAAATTATAAATT
1560758 AAATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TTTAAGTATAAAATTATAAATTTT
Found at i:1562243 original size:16 final size:16
Alignment explanation
Indices: 1562200--1562249 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1562190 AAAATAATCT
*
1562200 ATAAAT-TAATTTAAA
1 ATAAATATAATTTATA
1562215 ATAAATA-ATATTTATA
1 ATAAATATA-ATTTATA
1562231 ATAAATATAATTTAATA
1 ATAAATATAATTT-ATA
1562248 AT
1 AT
1562250 TTTTATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 7 0.23
16 17 0.57
17 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAATATAATTTATA
Found at i:1562746 original size:25 final size:23
Alignment explanation
Indices: 1562694--1562758 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 23
1562684 AATATTTTTA
1562694 TTTAAAT-TTAATTATAAAAATT
1 TTTAAATATTAATTATAAAAATT
*
1562716 TATAAATATTAATTA-ACAAATTATT
1 TTTAAATATTAATTATA-AAA--ATT
*
1562741 TTTAAATAATAATT-TAAA
1 TTTAAATATTAATTATAAA
1562759 TCATCCGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 7 0.20
23 10 0.29
24 2 0.06
25 16 0.46
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAATATTAATTATAAAAATT
Found at i:1564105 original size:27 final size:27
Alignment explanation
Indices: 1564060--1564111 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1564050 ATACGAGAAT
* * *
1564060 AATAAAAATATATTTATTTTTAATAAA
1 AATAAAAATATAATAATTTTAAATAAA
*
1564087 AATAAAAATTTAATAATTTTAAATA
1 AATAAAAATATAATAATTTTAAATA
1564112 TGATTATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAAAAATATAATAATTTTAAATAAA
Found at i:1577699 original size:24 final size:24
Alignment explanation
Indices: 1577672--1577719 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1577662 TTGCCTTTGA
*
1577672 CAGCTAACCTTGTTTTTTAAGTAT
1 CAGCTAACCTTGCTTTTTAAGTAT
*
1577696 CAGCTAGCCTTGCTTTTTAAGTAT
1 CAGCTAACCTTGCTTTTTAAGTAT
1577720 ATGTGATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.44
Consensus pattern (24 bp):
CAGCTAACCTTGCTTTTTAAGTAT
Found at i:1578846 original size:21 final size:20
Alignment explanation
Indices: 1578818--1578856 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1578808 ATATTATTTT
*
1578818 AATTAATAAACTTATTAAAA
1 AATTAATAAAATTATTAAAA
1578838 AATTAAATAAAATTATTAA
1 AATT-AATAAAATTATTAA
1578857 TAATAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTAATAAAATTATTAAAA
Found at i:1578858 original size:12 final size:12
Alignment explanation
Indices: 1578819--1578859 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1578809 TATTATTTTA
*
1578819 ATTAATAAACTT
1 ATTAATAAAATT
1578831 ATTAA-AAAATT
1 ATTAATAAAATT
1578842 A--AATAAAATT
1 ATTAATAAAATT
1578852 ATTAATAA
1 ATTAATAA
1578860 TAGATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
9 2 0.08
10 7 0.28
11 6 0.24
12 10 0.40
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
ATTAATAAAATT
Found at i:1579435 original size:18 final size:18
Alignment explanation
Indices: 1579399--1579434 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
1579389 TTTGTTAGAG
1579399 ATAATTATAAAAAATAAA
1 ATAATTATAAAAAATAAA
1579417 ATAATTAT-AAAAATAAA
1 ATAATTATAAAAAATAAA
1579434 A
1 A
1579435 AAATAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAATTATAAAAAATAAA
Found at i:1579608 original size:3 final size:3
Alignment explanation
Indices: 1579600--1579632 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1579590 TTAAAGGGTG
*
1579600 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1579633 CTAAATTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1590720 original size:3 final size:3
Alignment explanation
Indices: 1590707--1590750 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
1590697 GTTAAAATAG
* * *
1590707 TTA TAA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1590751 TTGAATTAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1591240 original size:20 final size:21
Alignment explanation
Indices: 1591201--1591240 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1591191 AAAAACTAAA
* *
1591201 ATTTTAAATATATTTTATATT
1 ATTTTAAAAATATATTATATT
1591222 ATTTTAAAAATA-ATTATAT
1 ATTTTAAAAATATATTATAT
1591241 AAATTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTAAAAATATATTATATT
Done.