Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 129 of 221
Found at i:39705892 original size:18 final size:19
Alignment explanation
Indices: 39705855--39705894 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
39705845 ATAAATACAA
*
39705855 ATATATAATTATTATTTAAC
1 ATATATAATTA-TATATAAC
39705875 ATATATAATTA-ATATAAC
1 ATATATAATTATATATAAC
39705893 AT
1 AT
39705895 TTTTTATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATATAATTATATATAAC
Found at i:39706141 original size:18 final size:18
Alignment explanation
Indices: 39706118--39706153 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39706108 ATAGTTTGAC
39706118 TAAAACCGAATTAACCAA
1 TAAAACCGAATTAACCAA
39706136 TAAAACCGAATTAACCAA
1 TAAAACCGAATTAACCAA
39706154 CCGAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.06, T:0.17
Consensus pattern (18 bp):
TAAAACCGAATTAACCAA
Found at i:39706468 original size:3 final size:3
Alignment explanation
Indices: 39706455--39706489 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
39706445 CGAAGCAAAT
39706455 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
39706490 GAACTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39707515 original size:12 final size:12
Alignment explanation
Indices: 39707498--39707522 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39707488 GCTACTCTGT
39707498 CATTATTTTCTA
1 CATTATTTTCTA
39707510 CATTATTTTCTA
1 CATTATTTTCTA
39707522 C
1 C
39707523 TAAATTTGTC
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:0.20, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTATTTTCTA
Found at i:39711644 original size:22 final size:22
Alignment explanation
Indices: 39711619--39711688 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
39711609 AAATTCAATA
39711619 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
39711641 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
39711663 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
39711685 TCAA
1 TCAA
39711689 ACTCTCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.31, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:39711694 original size:30 final size:30
Alignment explanation
Indices: 39711660--39711718 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
39711650 TTCAAAAATT
* *
39711660 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
39711690 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
39711719 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:39711695 original size:52 final size:51
Alignment explanation
Indices: 39711638--39711740 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
39711628 TTCAAAAATT
* * *
39711638 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
39711690 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
39711741 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:39711729 original size:21 final size:22
Alignment explanation
Indices: 39711690--39711731 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39711680 TTCTCTCAAA
39711690 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
39711712 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
39711732 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:39711830 original size:28 final size:29
Alignment explanation
Indices: 39711773--39711829 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
39711763 ATTAAATTTC
39711773 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
39711802 ATTTTTTTAA-AATAATTTTAAAATTTTT
1 ATTTTTTTAAGAA-AATTTTAAAATTTTT
39711830 AATATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:39711837 original size:29 final size:29
Alignment explanation
Indices: 39711776--39711837 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
39711766 AAATTTCATT
* *
39711776 TTTTTAAGAAAATTTTAAAATTTTTTATT
1 TTTTTAAGAAAATTTTAAAATTTTTAATA
39711805 TTTTTAA-AATAATTTTAAAATTTTTAATA
1 TTTTTAAGAA-AATTTTAAAATTTTTAATA
39711834 TTTT
1 TTTT
39711838 CAACAATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:39714142 original size:23 final size:23
Alignment explanation
Indices: 39714116--39714204 Score: 151
Period size: 23 Copynumber: 3.9 Consensus size: 23
39714106 TAAAAACCCT
*
39714116 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
*
39714139 AACCCTAACTTAACTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
*
39714162 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
39714185 AACCCTAACCTAACTTAATT
1 AACCCTAACCTAACTTAATT
39714205 TAATTTGATT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (23 bp):
AACCCTAACCTAACTTAATTAAA
Found at i:39714183 original size:46 final size:46
Alignment explanation
Indices: 39714116--39714204 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
39714106 TAAAAACCCT
*
39714116 AACCCTAACCTAATTTAATTAAAAACCCTAACTTAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTAATTAAA
39714162 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTAATT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTAATT
39714205 TAATTTGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (46 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTTAATTAAA
Found at i:39716627 original size:32 final size:32
Alignment explanation
Indices: 39716568--39716633 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
39716558 AAACCTGTTA
39716568 AACTTACTCCGAAAAATCATGCCACAAACAATT
1 AACTTACTCCGAAAAATCATGCCACAAA-AATT
* **
39716601 AACTTACTCC-TAAAATCATGTGACAAAAATT
1 AACTTACTCCGAAAAATCATGCCACAAAAATT
39716632 AA
1 AA
39716634 AATTCCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 6 0.20
32 14 0.47
33 10 0.33
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.24
Consensus pattern (32 bp):
AACTTACTCCGAAAAATCATGCCACAAAAATT
Found at i:39725667 original size:63 final size:64
Alignment explanation
Indices: 39725595--39725757 Score: 179
Period size: 63 Copynumber: 2.6 Consensus size: 64
39725585 GTATCTTTGT
*
39725595 CCCATGTGACTCTAATTTCAAAACAGTGAGTTACACAG-CCTAGACACACACTCGTGTCCCTAA
1 CCCATGTGACTCTAATTTCAAAACAGTGAGTTACACAGACCTAGACACACACTCATGTCCCTAA
* * * * * **
39725658 CCCGTGTGACTCTAA-TTCTAAAGCAGTGAGTTACGC-GACCTGGACGCACACTCATGTCCCTGG
1 CCCATGTGACTCTAATTTC-AAAACAGTGAGTTACACAGACCTAGACACACACTCATGTCCCTAA
* * * * *
39725721 TCCATGTGACTTTAATTTTAAAATAGTGTGTTACACA
1 CCCATGTGACTCTAATTTCAAAACAGTGAGTTACACA
39725758 ATCGTGTTGC
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
62 4 0.05
63 74 0.93
64 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (64 bp):
CCCATGTGACTCTAATTTCAAAACAGTGAGTTACACAGACCTAGACACACACTCATGTCCCTAA
Found at i:39739240 original size:34 final size:34
Alignment explanation
Indices: 39739163--39739242 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 34
39739153 ATATCATATT
* *
39739163 AGAATGTCACATTACCAAAAACATATATCAAATC
1 AGAATGTCATATTACCAAAAACATATACCAAATC
* * *
39739197 AAAATGTCATATTCCCAAAAACATATACCAGATC
1 AGAATGTCATATTACCAAAAACATATACCAAATC
39739231 AGAATGTCATAT
1 AGAATGTCATAT
39739243 CAAATTAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (34 bp):
AGAATGTCATATTACCAAAAACATATACCAAATC
Found at i:39748218 original size:22 final size:22
Alignment explanation
Indices: 39748193--39748237 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
39748183 TTGGCTGAGA
*
39748193 TAGGAGAAATGGTTGGAAAGGT
1 TAGGAGAAATGGTTAGAAAGGT
39748215 TAGGAGAAATGGTTAGAAAGGT
1 TAGGAGAAATGGTTAGAAAGGT
39748237 T
1 T
39748238 GTCAAGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (22 bp):
TAGGAGAAATGGTTAGAAAGGT
Found at i:39754099 original size:16 final size:16
Alignment explanation
Indices: 39754078--39754109 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39754068 TTTTTTGTAT
*
39754078 TTTTTAATATTAAATA
1 TTTTTAAAATTAAATA
39754094 TTTTTAAAATTAAATA
1 TTTTTAAAATTAAATA
39754110 ACATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTTAAAATTAAATA
Found at i:39757425 original size:4 final size:4
Alignment explanation
Indices: 39757416--39757440 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39757406 GATTTTTCAA
39757416 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
39757441 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:39757445 original size:2 final size:2
Alignment explanation
Indices: 39757438--39757464 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39757428 AAATAAATAA
39757438 AT 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 AT A
39757465 AATGAGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39764355 original size:28 final size:27
Alignment explanation
Indices: 39764304--39764378 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 27
39764294 TTAAGAAAAT
* *
39764304 AAATAAAAAAT-AAAAGCAACTAAAACA
1 AAATAAAAAATGAAAA-AAAATAAAACA
* *
39764331 AAATTTAAAAAA-GATAAAAAATAAAATA
1 AAA--TAAAAAATGAAAAAAAATAAAACA
39764359 AAATAAAAAATGAAAAAAAA
1 AAATAAAAAATGAAAAAAAA
39764379 ACTTAATGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
26 7 0.18
27 11 0.28
28 11 0.28
29 10 0.26
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (27 bp):
AAATAAAAAATGAAAAAAAATAAAACA
Found at i:39764364 original size:17 final size:17
Alignment explanation
Indices: 39764337--39764378 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
39764327 AACAAAATTT
*
39764337 AAAAAAGATAAAAAAT-
1 AAAAAAAATAAAAAATG
39764353 AAAATAAAATAAAAAATG
1 AAAA-AAAATAAAAAATG
39764371 AAAAAAAA
1 AAAAAAAA
39764379 ACTTAATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAAAAATAAAAAATG
Found at i:39764378 original size:12 final size:11
Alignment explanation
Indices: 39764337--39764379 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
39764327 AACAAAATTT
*
39764337 AAAAAAGATAA
1 AAAAAAAATAA
39764348 AAAATAAAATAA
1 AAAA-AAAATAA
39764360 AATAAAAAATGAA
1 AA-AAAAAAT-AA
39764373 AAAAAAA
1 AAAAAAA
39764380 CTTAATGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.14
12 18 0.64
13 6 0.21
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:39774280 original size:14 final size:14
Alignment explanation
Indices: 39774261--39774288 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39774251 TTCAAACACT
39774261 ACATGTTCGATAGA
1 ACATGTTCGATAGA
39774275 ACATGTTCGATAGA
1 ACATGTTCGATAGA
39774289 GGCTTGAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
ACATGTTCGATAGA
Found at i:39774949 original size:23 final size:24
Alignment explanation
Indices: 39774910--39774957 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
39774900 TTTATTTGAT
39774910 AATATGTTTTGATATAACAAATTAA
1 AATATGTTTTGATATAA-AAATTAA
*
39774935 AATAT-TTTTGA-ATAAAAGTTAA
1 AATATGTTTTGATATAAAAATTAA
39774957 A
1 A
39774958 GTTGAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 4 0.18
24 6 0.27
25 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
AATATGTTTTGATATAAAAATTAA
Found at i:39775085 original size:20 final size:18
Alignment explanation
Indices: 39775060--39775111 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
39775050 TCAACATTTA
39775060 AATCAAGTTAAAATGGTTTT
1 AATCAAGTTAAAAT--TTTT
*
39775080 AATCAAGTTAGAACTTTTT
1 AATCAAGTTA-AAATTTTT
39775099 AATCAAAGTTAAA
1 AATC-AAGTTAAA
39775112 TTGTCTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.34
20 16 0.55
21 3 0.10
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (18 bp):
AATCAAGTTAAAATTTTT
Found at i:39775120 original size:20 final size:18
Alignment explanation
Indices: 39775060--39775120 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 18
39775050 TCAACATTTA
*
39775060 AATCAAGTTAAAATGGTTTT
1 AATCAAGTT-AAATTG-TTT
39775080 AATCAAGTTAGAACTT-TTT
1 AATCAAGTTA-AA-TTGTTT
39775099 AATCAAAGTTAAATTGTCTT
1 AATC-AAGTTAAATTGT-TT
39775119 AA
1 AA
39775121 AACAAGTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
19 11 0.31
20 21 0.60
21 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.39
Consensus pattern (18 bp):
AATCAAGTTAAATTGTTT
Found at i:39777873 original size:77 final size:80
Alignment explanation
Indices: 39777769--39777950 Score: 192
Period size: 82 Copynumber: 2.3 Consensus size: 80
39777759 TATATACCAT
* ** * *
39777769 TAGTGGCGTTTTTCTTATAAACGCCGCAAAAGGTAAAGC-A-T-GCA-TTTCTCCTATAAACGCC
1 TAGTGGCGTTTTCCCCATAAATGCCGCAAAAGGTAAAGCAAGTGGCATTTTC-CCTATAAACACC
39777830 GCAAAAGATAAAGCAA
65 GCAAAAGATAAAGCAA
* * *
39777846 TAGTGGCGTTTTCCCCATAAATGCCGCAAAAGGTGAGGCAATAGTGGCATTTTCCCTATAAACAT
1 TAGTGGCGTTTTCCCCATAAATGCCGCAAAAGGTAAAGC-A-AGTGGCATTTTCCCTATAAACAC
** * *
39777911 CGTTAAAGGTAAGGCAA
64 CGCAAAAGATAAAGCAA
*
39777928 TAGCGGCGTTTTCCCCATAAATG
1 TAGTGGCGTTTTCCCCATAAATG
39777951 TCGCGAATTT
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
77 33 0.38
80 1 0.01
81 1 0.01
82 47 0.55
83 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (80 bp):
TAGTGGCGTTTTCCCCATAAATGCCGCAAAAGGTAAAGCAAGTGGCATTTTCCCTATAAACACCG
CAAAAGATAAAGCAA
Found at i:39777887 original size:41 final size:41
Alignment explanation
Indices: 39777821--39777948 Score: 157
Period size: 41 Copynumber: 3.1 Consensus size: 41
39777811 CATTTCTCCT
* *
39777821 ATAAACGCCGCAAAAGATAAAGCAATAGTGGCGTTTTCCCC
1 ATAAACGCCGCAAAAGGTAAGGCAATAGTGGCGTTTTCCCC
* * * *
39777862 ATAAATGCCGCAAAAGGTGAGGCAATAGTGGCATTTTCCCT
1 ATAAACGCCGCAAAAGGTAAGGCAATAGTGGCGTTTTCCCC
** ** *
39777903 ATAAACATCGTTAAAGGTAAGGCAATAGCGGCGTTTTCCCC
1 ATAAACGCCGCAAAAGGTAAGGCAATAGTGGCGTTTTCCCC
39777944 ATAAA
1 ATAAA
39777949 TGTCGCGAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (41 bp):
ATAAACGCCGCAAAAGGTAAGGCAATAGTGGCGTTTTCCCC
Found at i:39779084 original size:10 final size:10
Alignment explanation
Indices: 39779069--39779093 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
39779059 ACATACACTT
39779069 TAGCTAGAAG
1 TAGCTAGAAG
39779079 TAGCTAGAAG
1 TAGCTAGAAG
39779089 TAGCT
1 TAGCT
39779094 TACTCATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (10 bp):
TAGCTAGAAG
Found at i:39779798 original size:24 final size:24
Alignment explanation
Indices: 39779766--39779813 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39779756 TACAAATAAG
39779766 ATCATATGTTTGATTTAGGTTTAT
1 ATCATATGTTTGATTTAGGTTTAT
39779790 ATCATATGTTTGATTTAGGTTTAT
1 ATCATATGTTTGATTTAGGTTTAT
39779814 CTTATGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (24 bp):
ATCATATGTTTGATTTAGGTTTAT
Found at i:39789555 original size:18 final size:17
Alignment explanation
Indices: 39789532--39789572 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
39789522 AAAATTGTTA
39789532 AAAAAAAGAAGAAAAAAG
1 AAAAAAAGAAG-AAAAAG
*
39789550 AAAAAAAGAAGAATAAG
1 AAAAAAAGAAGAAAAAG
39789567 AAAAAA
1 AAAAAA
39789573 GAAAAGGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAGAAAAAG
Found at i:39789578 original size:21 final size:19
Alignment explanation
Indices: 39789531--39789572 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
39789521 AAAAATTGTT
39789531 AAAAAAAAGAAGAAAAAAG
1 AAAAAAAAGAAGAAAAAAG
*
39789550 -AAAAAAAGAAG-AATAAG
1 AAAAAAAAGAAGAAAAAAG
39789567 AAAAAA
1 AAAAAA
39789573 GAAAAGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGAAGAAAAAAG
Found at i:39790940 original size:45 final size:44
Alignment explanation
Indices: 39790809--39791031 Score: 200
Period size: 44 Copynumber: 5.0 Consensus size: 44
39790799 AACAGATCAG
* * *
39790809 TGAAGATAGCAGATCTTACCTTCCTGTACTAACGGTGAAGCAGA
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGA
* * * * * *
39790853 TCGAAGACATCAG-CCTTACCTTCCTGTATTGACAGCGAAGCAGA
1 T-GAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGA
* **
39790897 CTGAAGATAGCAGATCTTGCCTTTCTGTACTGATGGTGAAGCAGA
1 -TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGA
* * * * *
39790942 TCGAAGACACCAG-CCTTGCTTTCCTGTACTGACAG-CAGAGCAGA
1 T-GAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGA-AGCAGA
* * *
39790986 TTGAAGATAGCAGATCATGCCTTCCTGTACTGGCAGCGAAGCAGA
1 -TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGA
39791031 T
1 T
39791032 CGAAAAATAA
Statistics
Matches: 140, Mismatches: 31, Indels: 16
0.75 0.17 0.09
Matches are distributed among these distances:
43 1 0.01
44 70 0.50
45 68 0.49
46 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (44 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGA
Found at i:39790966 original size:89 final size:89
Alignment explanation
Indices: 39790809--39791035 Score: 321
Period size: 89 Copynumber: 2.6 Consensus size: 89
39790799 AACAGATCAG
* * *
39790809 TGAAGATAGCAGATCTTACCTTCCTGTACTAACGGTGAAGCAGATCGAAGACATCAGCCTTACCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTACCT
*
39790874 TCCTGTATTGACAGC-GAAGCAGAC
66 TCCTGTACTGACAGCAG-AGCAGAC
* * * *
39790898 TGAAGATAGCAGATCTTGCCTTTCTGTACTGATGGTGAAGCAGATCGAAGACACCAGCCTTGCTT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTACCT
*
39790963 TCCTGTACTGACAGCAGAGCAGAT
66 TCCTGTACTGACAGCAGAGCAGAC
* * * *
39790987 TGAAGATAGCAGATCATGCCTTCCTGTACTGGCAGCGAAGCAGATCGAA
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAA
39791036 AAATAACGAA
Statistics
Matches: 122, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
89 121 0.99
90 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (89 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACACCAGCCTTACCT
TCCTGTACTGACAGCAGAGCAGAC
Found at i:39790984 original size:44 final size:45
Alignment explanation
Indices: 39790810--39791035 Score: 208
Period size: 45 Copynumber: 5.1 Consensus size: 45
39790800 ACAGATCAGT
* * * * * *
39790810 GAAGATAGCAGATCTTACCTTCCTGTACTAACGGTGAAGCAGATC
1 GAAGACAGCAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
* * *
39790855 GAAGACATCAG-CCTTACCTTCCTGTATTGACAGCGAAGCAGA-C
1 GAAGACAGCAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
* * * ** *
39790898 TGAAGATAGCAGATCTTGCCTTTCTGTACTGATGGTGAAGCAGATC
1 -GAAGACAGCAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
* * *
39790944 GAAGACACCAG-CCTTGCTTTCCTGTACTGACAGC-AGAGCAGATT
1 GAAGACAGCAGACCTTGCCTTCCTGTACTGACAGCGA-AGCAGATC
* * * *
39790988 GAAGATAGCAGATCATGCCTTCCTGTACTGGCAGCGAAGCAGATC
1 GAAGACAGCAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
39791033 GAA
1 GAA
39791036 AAATAACGAA
Statistics
Matches: 143, Mismatches: 32, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
43 2 0.01
44 68 0.48
45 71 0.50
46 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.23
Consensus pattern (45 bp):
GAAGACAGCAGACCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
Found at i:39791414 original size:115 final size:115
Alignment explanation
Indices: 39791197--39791420 Score: 279
Period size: 115 Copynumber: 1.9 Consensus size: 115
39791187 AGTGGACCAA
* * * *
39791197 ACTAAAACCGCGAATCTCATCCCCCTGAAGTTGTCGCGAAGAAGATTGAAGTTACAAGTCGTATC
1 ACTAAAACCACGAATCTCATCCCCCTGAAGTTGTCGCGAAGAAGATTGAAGCTACAACTCATATC
* * * *
39791262 TCTCTGAAGTGCAATAGAGTGGATTGAAGCTAGAAGACACAGTGAAGCAG
66 TCTCTGAAGTGCAATAGAGTGGATCGAAACAACAAGACACAGTGAAGCAG
* ** * * *
39791312 ACTAAAACCATGAATCTTGTCCCTCTGAAGTTG-CTGTGAAGAAGATTGATGCTACAACTCATAT
1 ACTAAAACCACGAATCTCATCCCCCTGAAGTTGTC-GCGAAGAAGATTGAAGCTACAACTCATAT
* * *
39791376 CTCTCTGAAGTGCAGTAGAGTGTATCGAAACAACAAGACCCAGTG
65 CTCTCTGAAGTGCAATAGAGTGGATCGAAACAACAAGACACAGTG
39791421 GACTGGAATG
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
114 1 0.01
115 90 0.99
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (115 bp):
ACTAAAACCACGAATCTCATCCCCCTGAAGTTGTCGCGAAGAAGATTGAAGCTACAACTCATATC
TCTCTGAAGTGCAATAGAGTGGATCGAAACAACAAGACACAGTGAAGCAG
Found at i:39792901 original size:6 final size:6
Alignment explanation
Indices: 39792890--39792917 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39792880 CTTTTTATAT
39792890 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
39792918 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:39792932 original size:18 final size:17
Alignment explanation
Indices: 39792881--39792935 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
39792871 GTATCAACAC
39792881 TTTTTATATTTTTAATTT
1 TTTTTAT-TTTTTAATTT
*
39792899 TAATTTTA-ATTTTAATTT
1 T--TTTTATTTTTTAATTT
39792917 TTTTTATTTTTATAATTT
1 TTTTTATTTTT-TAATTT
39792935 T
1 T
39792936 AAATTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 5 0.16
17 3 0.10
18 18 0.58
20 5 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTTAATTT
Found at i:39792988 original size:8 final size:8
Alignment explanation
Indices: 39792975--39793020 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
39792965 CTATGTTAAA
39792975 TTATAATT
1 TTATAATT
39792983 TTATAATT
1 TTATAATT
39792991 TTAT--TT
1 TTATAATT
*
39792997 TTTTAATT
1 TTATAATT
*
39793005 TTTTAATT
1 TTATAATT
39793013 TTA-AATT
1 TTATAATT
39793020 T
1 T
39793021 AGCTAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 5 0.15
7 5 0.15
8 24 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTATAATT
Found at i:39793422 original size:13 final size:13
Alignment explanation
Indices: 39793406--39793447 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
39793396 AGCTTGAAAA
39793406 AATATTTGTAACT
1 AATATTTGTAACT
*
39793419 AATATTCGTAACT
1 AATATTTGTAACT
*
39793432 AACT-TTTGTAATT
1 AA-TATTTGTAACT
39793445 AAT
1 AAT
39793448 TAGGTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (13 bp):
AATATTTGTAACT
Found at i:39793813 original size:31 final size:32
Alignment explanation
Indices: 39793776--39793850 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 32
39793766 AAGAGTCAAT
39793776 ATTTAAAGATGATAATCATAACTTACATAAA-
1 ATTTAAAGATGATAATCATAACTTACATAAAC
* *
39793807 ATTTAAAGTTTATGATTATCATAACTTATATAAAC
1 ATTTAAAG---ATGATAATCATAACTTACATAAAC
39793842 ATTTAAAGA
1 ATTTAAAGA
39793851 ATATAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
31 8 0.21
32 1 0.03
34 21 0.55
35 8 0.21
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (32 bp):
ATTTAAAGATGATAATCATAACTTACATAAAC
Found at i:39793828 original size:34 final size:35
Alignment explanation
Indices: 39793784--39793849 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
39793774 ATATTTAAAG
39793784 ATGATAATCATAACTTACATAAA-ATTTAAAGTTT
1 ATGATAATCATAACTTACATAAACATTTAAAGTTT
* *
39793818 ATGATTATCATAACTTATATAAACATTTAAAG
1 ATGATAATCATAACTTACATAAACATTTAAAG
39793850 AATATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (35 bp):
ATGATAATCATAACTTACATAAACATTTAAAGTTT
Found at i:39800170 original size:43 final size:43
Alignment explanation
Indices: 39800092--39800199 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
39800082 CCGCAAAATA
* * * *
39800092 TCATGTTCTTTAGCGGCGTTTGTGTGAAAACCGCCGCTAAAGG
1 TCATGTTCTATAGCGGCATTTTTATGAAAACCGCCGCTAAAGG
* *
39800135 TCATGTTCTATAGCGGCATTTTTATGAGAAGCGCCGCTAAAGG
1 TCATGTTCTATAGCGGCATTTTTATGAAAACCGCCGCTAAAGG
**
39800178 TCATGTTCTATAGTAGCATTTT
1 TCATGTTCTATAGCGGCATTTT
39800200 CCCACATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (43 bp):
TCATGTTCTATAGCGGCATTTTTATGAAAACCGCCGCTAAAGG
Found at i:39812099 original size:30 final size:30
Alignment explanation
Indices: 39812027--39812091 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
39812017 ATAATAATGA
39812027 CACACG-ACTGTGTAGGGTGGCCATGTGTGG
1 CACACGAAC-GTGTAGGGTGGCCATGTGTGG
* *
39812057 CACACGAACGTGTAGGGTGGTCGTGTGTGG
1 CACACGAACGTGTAGGGTGGCCATGTGTGG
39812087 CACAC
1 CACAC
39812092 AGCCGTGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.18, C:0.22, G:0.38, T:0.22
Consensus pattern (30 bp):
CACACGAACGTGTAGGGTGGCCATGTGTGG
Found at i:39828088 original size:25 final size:24
Alignment explanation
Indices: 39828029--39828105 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 24
39828019 CTCACCACAA
*
39828029 CTCGTATGAGCTTACCTATTTCAG
1 CTCGTATGAGCTTACCAATTTCAG
*
39828053 CTCGTGA-GAGCTTACCAATTCTCCG
1 CTCGT-ATGAGCTTACCAATT-TCAG
*
39828078 CTCGTATGAGCTTACCGATTTCCAG
1 CTCGTATGAGCTTACCAATTT-CAG
39828103 CTC
1 CTC
39828106 ATGAGAGCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
24 19 0.42
25 26 0.58
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.32
Consensus pattern (24 bp):
CTCGTATGAGCTTACCAATTTCAG
Found at i:39828113 original size:25 final size:25
Alignment explanation
Indices: 39828036--39828122 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 25
39828026 CAACTCGTAT
*
39828036 GAGCTTACCTATTT-CAGCTCGTGA
1 GAGCTTACCGATTTCCAGCTCGTGA
*
39828060 GAGCTTACCAATTCTCC-GCTCGT-A
1 GAGCTTACCGATT-TCCAGCTCGTGA
*
39828084 TGAGCTTACCGATTTCCAGCTCATGA
1 -GAGCTTACCGATTTCCAGCTCGTGA
* *
39828110 GAGCATACTGATT
1 GAGCTTACCGATT
39828123 CATAGCTCGT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
24 16 0.30
25 35 0.66
26 2 0.04
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGATTTCCAGCTCGTGA
Found at i:39828131 original size:50 final size:49
Alignment explanation
Indices: 39828029--39828138 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 49
39828019 CTCACCACAA
* * * *
39828029 CTCGTATGAGCTTACCTATTTCAGCTCGTGAGAGCTTACCAATTCTCCG
1 CTCGTATGAGCTTACCGATTTCAGCTCATGAGAGCATACCAATTCTCAG
**
39828078 CTCGTATGAGCTTACCGATTTCCAGCTCATGAGAGCATACTGATTCAT-AG
1 CTCGTATGAGCTTACCGATTT-CAGCTCATGAGAGCATACCAATTC-TCAG
39828128 CTCGTATGAGC
1 CTCGTATGAGC
39828139 ATACATGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
49 20 0.38
50 32 0.60
51 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (49 bp):
CTCGTATGAGCTTACCGATTTCAGCTCATGAGAGCATACCAATTCTCAG
Found at i:39835345 original size:134 final size:134
Alignment explanation
Indices: 39835097--39835894 Score: 829
Period size: 134 Copynumber: 6.0 Consensus size: 134
39835087 GAACCTAAAC
* * * *
39835097 TGTGATCGTAAATTAGCTAACTGTTTCAATGGAGTTGTGATCGTAAATCAGCTAACTCAAAATAA
1 TGTGATCGTAAATCAACTAACTGTTTGAATGGAGTTGCGATCGTAAATCAGCTAACTCAAAATAA
* * * * *
39835162 ATTGTTCACGATTGTAAATCAGTGAACTTAGGTTGTGCTCGTAATTCAGCGAGCCTTAATAATAT
66 ATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAGCCTTAATAATAT
*
39835227 TAGT
131 CAGT
* * *
39835231 CGTGATCGTAAATCAACTAACTGTTTGAATGGAGTTGCGATCGTAAATTAGGTAACTCAAAATAA
1 TGTGATCGTAAATCAACTAACTGTTTGAATGGAGTTGCGATCGTAAATCAGCTAACTCAAAATAA
* * * * *
39835296 AATGTTCATGATCGTAAAGCAGTGAACTTAGGTTGTGATTGTAAATCAGCGAGCCTTAATATTAT
66 ATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAGCCTTAATAATAT
*
39835361 TAGT
131 CAGT
* * * *
39835365 TATGGTCGTAAATCAA-TGAACTGTTTGAATGGAGTTGCGATCGTAAATTAGCTAACTCAGAATA
1 TGTGATCGTAAATCAACT-AACTGTTTGAATGGAGTTGCGATCGTAAATCAGCTAACTCAAAATA
* * *
39835429 AATCT-TTTATGATCGTAAAGT-AGA-GAACTTAGGCTGTGATCATAAATCAGCGAGCCTTAATA
65 AAT-TGTTCATGATCGTAAA-TCA-ATGAACTTAGGTTGTGATCGTAAATCAGCGAGCCTTAATA
39835491 ATATCAGT
127 ATATCAGT
* * * * * *
39835499 TGTGATCATAAATC-ATTAAATTATTTGAATGGATTTGCGATCGTAAATCACCTAACTCAAAATA
1 TGTGATCGTAAATCAACT-AACTGTTTGAATGGAGTTGCGATCGTAAATCAGCTAACTCAAAATA
* * * * * * * *
39835563 AATTGTTCAAGATCATAAATCAATGGACTTAGGCTGTGATCGTAAATTAGTGAGGCTTAATAGTA
65 AATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAGCCTTAATAATA
39835628 TCAGT
130 TCAGT
* * * * * * ** * * * *
39835633 TGTGATCATAAATCATCGAACAGTTTCACTGGAGTTATGATTGTAAAACAACTAACTCATAAT-A
1 TGTGATCGTAAATCAACTAACTGTTTGAATGGAGTTGCGATCGTAAATCAGCTAACTCAAAATAA
* * * * * *
39835697 ATTATTCATGATCATAAATCAATGAACTTA-ATCTGTTATCGTAAATCAACGACCCTTAATAATA
66 ATTGTTCATGATCGTAAATCAATGAACTTAGGT-TGTGATCGTAAATCAGCGAGCCTTAATAATA
*
39835761 TAAGT
130 TCAGT
* * * * * * * * * *
39835766 CGTGATGGTAAACCATCAAACTGTTTGAATGGAGTTGCAACCGTTAATCGGCTAACTCAGAATAA
1 TGTGATCGTAAATCAACTAACTGTTTGAATGGAGTTGCGATCGTAAATCAGCTAACTCAAAATAA
* * *
39835831 ATTGTTCATG-TACGTAAATCAATGAACTTAGGTTGTGATCATAAATTAACGAGCCTTAATAATA
66 ATTGTTCATGAT-CGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAGCCTTAATAATA
39835895 ATGTAACACC
Statistics
Matches: 550, Mismatches: 101, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
133 107 0.19
134 441 0.80
135 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (134 bp):
TGTGATCGTAAATCAACTAACTGTTTGAATGGAGTTGCGATCGTAAATCAGCTAACTCAAAATAA
ATTGTTCATGATCGTAAATCAATGAACTTAGGTTGTGATCGTAAATCAGCGAGCCTTAATAATAT
CAGT
Found at i:39836157 original size:17 final size:17
Alignment explanation
Indices: 39836135--39836174 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
39836125 AGAACATGGG
* *
39836135 TCACACAGTCGTCTGAC
1 TCACACAGTCATATGAC
*
39836152 TCACACTGTCATATGAC
1 TCACACAGTCATATGAC
39836169 TCACAC
1 TCACAC
39836175 GGCTGAGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.25
Consensus pattern (17 bp):
TCACACAGTCATATGAC
Found at i:39848388 original size:222 final size:222
Alignment explanation
Indices: 39848002--39849333 Score: 2502
Period size: 222 Copynumber: 6.0 Consensus size: 222
39847992 TTAATAACAC
*
39848002 TCCGTAAATATTTAGTAAAATATTTATAACTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
1 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
39848067 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
66 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
39848132 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
131 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
39848197 CTTACTCGTTGGATTTGTGGCCACAAA
196 CTTACTCGTTGGATTTGTGGCCACAAA
*
39848224 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATATCTCATTT
1 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
39848289 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
66 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
* **
39848354 TTCCAATTCAAATTTATTTTAATATAATATTTGACTCATAAATATTAAATAATATCATTTACGAA
131 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
39848419 CTTACTCGTTGGATTTGTGGCCACAAA
196 CTTACTCGTTGGATTTGTGGCCACAAA
*
39848446 TCCGTAAATATTTAGTAAAATATTTATAGCTCGGTTTATAGAAACTAGATCTCGATACCTCATTT
1 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
39848511 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
66 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
* **
39848576 TTCCAATTCAAATTTATTTTAATATAATATTTGACTCATAAATATTAAATAATATCATTTACGAA
131 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
39848641 CTTACTCGTTGGATTTGTGGCCACAAA
196 CTTACTCGTTGGATTTGTGGCCACAAA
* *
39848668 TCCGTAAATATTTAGTAAAATATTTATAGCTCGGTTTATAGAAACTAGATCTCGATACCTCGTTT
1 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
39848733 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
66 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
*
39848798 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTGAATAATATCATTTACGAA
131 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
39848863 CTTACTCGTTGGATTTGTGGCCACAAA
196 CTTACTCGTTGGATTTGTGGCCACAAA
39848890 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
1 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
* * *
39848955 TCTAACACCATTTGACTTTAGGGTAAGACTACTTAACCCTAATTATTCATTCAAATGACATAAAT
66 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
*
39849020 TACCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
131 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
39849085 CTTACTCGTTGGATTTGTGGCCACAAA
196 CTTACTCGTTGGATTTGTGGCCACAAA
* *
39849112 TCTGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATATCGATACCTCATTT
1 TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
39849177 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
66 TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
39849242 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
131 TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
39849307 CTTACTCGTTGGATTTGTGGCCACAAA
196 CTTACTCGTTGGATTTGTGGCCACAAA
39849334 ACCACTATTT
Statistics
Matches: 1085, Mismatches: 25, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
222 1085 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (222 bp):
TCCGTAAATATTTAGTAAAATATTTATAGCTCAGTTTATAGAAACTAGATCTCGATACCTCATTT
TCTAACACCACTTGACTTTAGGGTAAGACTACTTAAACCTAATTATTCATTCAAATAACATAAAT
TGCCAATTCAAATTTATTTTAATACCATATTTGACTCATAAATATTAAATAATATCATTTACGAA
CTTACTCGTTGGATTTGTGGCCACAAA
Found at i:39850096 original size:13 final size:13
Alignment explanation
Indices: 39850078--39850106 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
39850068 ACTTTGGGAG
39850078 AGTGATATTTGTA
1 AGTGATATTTGTA
39850091 AGTGATATTTGTA
1 AGTGATATTTGTA
39850104 AGT
1 AGT
39850107 CTGTACAAAA
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:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (13 bp):
AGTGATATTTGTA
Found at i:39859700 original size:18 final size:18
Alignment explanation
Indices: 39859677--39859712 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39859667 TTAGGTTTCC
*
39859677 AAAAATGGAAATGGAAAT
1 AAAAATGAAAATGGAAAT
*
39859695 AAAAATGAAAATTGAAAT
1 AAAAATGAAAATGGAAAT
39859713 TATCTATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (18 bp):
AAAAATGAAAATGGAAAT
Found at i:39865426 original size:7 final size:7
Alignment explanation
Indices: 39865414--39865444 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
39865404 CCAATCAAAT
39865414 TTTATTC
1 TTTATTC
39865421 TTTATTC
1 TTTATTC
39865428 TTTATTC
1 TTTATTC
39865435 TTTATT-
1 TTTATTC
39865441 TTTA
1 TTTA
39865445 ATTAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTATTC
Found at i:39869503 original size:25 final size:25
Alignment explanation
Indices: 39869468--39869538 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
39869458 ACACACCACA
*
39869468 GCTCTCTTGAGCTTCCCGATACTTG
1 GCTCTCATGAGCTTCCCGATACTTG
* *
39869493 GCTCTCATGAGCTTCTCGATATTTG
1 GCTCTCATGAGCTTCCCGATACTTG
* *
39869518 GCTCACAAGAGCTTCCCGATA
1 GCTCTCATGAGCTTCCCGATA
39869539 TACAGCTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.32
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATACTTG
Found at i:39875863 original size:23 final size:23
Alignment explanation
Indices: 39875780--39875900 Score: 95
Period size: 23 Copynumber: 5.1 Consensus size: 23
39875770 CTCACCACAA
*
39875780 CTCGTATGAGCTTCCCGATATATCAG
1 CTCGTATGAGCTTACCG-T-T-TCAG
* * * *
39875806 CTCGTAAGAGGTTACTGTTTTCAA
1 CTCGTATGAGCTTACCG-TTTCAG
*
39875830 CTCAT-TGGAGCTTACCGTTTCAG
1 CTCGTAT-GAGCTTACCGTTTCAG
*
39875853 CTCGTATGAGCTTACTGTTT-AG
1 CTCGTATGAGCTTACCGTTTCAG
*
39875875 CTCGT-TAGAGCTTACCATTTCAG
1 CTCGTAT-GAGCTTACCGTTTCAG
39875898 CTC
1 CTC
39875901 AATAGAGCCT
Statistics
Matches: 76, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
21 1 0.01
22 18 0.24
23 26 0.34
24 16 0.21
25 1 0.01
26 14 0.18
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.36
Consensus pattern (23 bp):
CTCGTATGAGCTTACCGTTTCAG
Found at i:39875868 original size:47 final size:46
Alignment explanation
Indices: 39875802--39875917 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 46
39875792 TCCCGATATA
* * * *
39875802 TCAGCTCGTAAGAGGTTACTGTTTTCAACTCATTGGAGCTTACCGTT
1 TCAGCTCGTATGAGCTTACTGTTTT-AACTCATTAGAGCTTACCATT
* *
39875849 TCAGCTCGTATGAGCTTACTG-TTTAGCTCGTTAGAGCTTACCATT
1 TCAGCTCGTATGAGCTTACTGTTTTAACTCATTAGAGCTTACCATT
* *
39875894 TCAGCTC-AATAGAGCCTACTGTTT
1 TCAGCTCGTAT-GAGCTTACTGTTT
39875918 ATTAGCTCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
44 2 0.03
45 33 0.56
46 5 0.08
47 19 0.32
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (46 bp):
TCAGCTCGTATGAGCTTACTGTTTTAACTCATTAGAGCTTACCATT
Found at i:39875906 original size:23 final size:22
Alignment explanation
Indices: 39875837--39875917 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
39875827 CAACTCATTG
*
39875837 GAGCTTACCGTTTCAGCTCGTA
1 GAGCTTACCGTTTCAGCTCATA
* *
39875859 TGAGCTTACTGTTT-AGCTCGTTA
1 -GAGCTTACCGTTTCAGCTC-ATA
*
39875882 GAGCTTACCATTTCAGCTCAATA
1 GAGCTTACCGTTTCAGCTC-ATA
* *
39875905 GAGCCTACTGTTT
1 GAGCTTACCGTTT
39875918 ATTAGCTCAG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 16 0.34
23 31 0.66
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (22 bp):
GAGCTTACCGTTTCAGCTCATA
Found at i:39877084 original size:13 final size:13
Alignment explanation
Indices: 39877066--39877090 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39877056 CATATGTTGG
39877066 ATATGAAATTGAT
1 ATATGAAATTGAT
39877079 ATATGAAATTGA
1 ATATGAAATTGA
39877091 CATTGAATTT
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:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
ATATGAAATTGAT
Found at i:39877725 original size:7 final size:7
Alignment explanation
Indices: 39877705--39877778 Score: 132
Period size: 7 Copynumber: 10.6 Consensus size: 7
39877695 GTTTAACATT
39877705 TATT-TA
1 TATTATA
39877711 TATCTATA
1 TAT-TATA
39877719 TATTATA
1 TATTATA
39877726 TATTATA
1 TATTATA
39877733 TATTATA
1 TATTATA
39877740 TATTATA
1 TATTATA
39877747 TATTATA
1 TATTATA
39877754 TATTATA
1 TATTATA
39877761 TATTATA
1 TATTATA
39877768 TATTATA
1 TATTATA
39877775 TATT
1 TATT
39877779 TTCAATTGTT
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
6 3 0.05
7 58 0.88
8 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTATA
Found at i:39877997 original size:31 final size:31
Alignment explanation
Indices: 39877962--39878021 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
39877952 ACTAAGTACT
* * *
39877962 AATTTGGATCAAAAAGCCAATTTTAGGTATC
1 AATTTGAACCAAAAAGCCAAGTTTAGGTATC
*
39877993 AATTTGAACCAAGAAGCCAAGTTTAGGTA
1 AATTTGAACCAAAAAGCCAAGTTTAGGTA
39878022 CCTAATTAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (31 bp):
AATTTGAACCAAAAAGCCAAGTTTAGGTATC
Found at i:39878035 original size:31 final size:31
Alignment explanation
Indices: 39877975--39878035 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
39877965 TTGGATCAAA
* * *
39877975 AAGCCAATTTTAGGTATCAATTTGAACCAAG
1 AAGCCAAGTTTAGGTACCAATTAGAACCAAG
39878006 AAGCCAAGTTTAGGTACCTAATTAG-ACCAA
1 AAGCCAAGTTTAGGTACC-AATTAGAACCAA
39878036 AATAAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (31 bp):
AAGCCAAGTTTAGGTACCAATTAGAACCAAG
Found at i:39884198 original size:17 final size:17
Alignment explanation
Indices: 39884153--39884195 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
39884143 TTATTTAATC
*
39884153 AATTAATTTAATTAACTA
1 AATTAATTT-CTTAACTA
*
39884171 AATTAATTTCTTAATTA
1 AATTAATTTCTTAACTA
39884188 AA-TAATTT
1 AATTAATTT
39884196 TCTCAACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 8 0.35
18 9 0.39
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAATTTCTTAACTA
Found at i:39887580 original size:20 final size:20
Alignment explanation
Indices: 39887554--39887607 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
39887544 ACAAAAGCTT
*
39887554 TAGTAATTTTGTAAGAGAT-
1 TAGTAATTTTGTAAGAAATA
* *
39887573 TCAGTAATATTGTAATAAATA
1 T-AGTAATTTTGTAAGAAATA
39887594 TAGTAATTTTGTAA
1 TAGTAATTTTGTAA
39887608 AAAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.43
Consensus pattern (20 bp):
TAGTAATTTTGTAAGAAATA
Found at i:39892857 original size:19 final size:19
Alignment explanation
Indices: 39892833--39892871 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39892823 ACTCCATTTG
39892833 ATTTTTGAATTTTT-TTTTC
1 ATTTTT-AATTTTTATTTTC
*
39892852 ATTTTTCATTTTTATTTTC
1 ATTTTTAATTTTTATTTTC
39892871 A
1 A
39892872 GAAAGTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (19 bp):
ATTTTTAATTTTTATTTTC
Found at i:39906108 original size:26 final size:26
Alignment explanation
Indices: 39906079--39906215 Score: 71
Period size: 28 Copynumber: 5.0 Consensus size: 26
39906069 TATATTTTTA
39906079 TTAAATTATATTTAATAATTATTATT
1 TTAAATTATATTTAATAATTATTATT
* * *
39906105 TTAAATTATTTTTTATAGTATTA-TATA
1 TTAAATTATATTTAATA--ATTATTATT
* * * * *
39906132 TTATGATTTTAGTAAATTCATATATT-TT
1 TTA-AATTATATTTAA-TAAT-TATTATT
* *
39906160 ATTAAATTATATTTAATAATAATTATG
1 -TTAAATTATATTTAATAATTATTATT
* * *
39906187 TTAAAATATGATTAAATTATTTATTATT
1 TTAAATTAT-ATTTAA-TAATTATTATT
39906215 T
1 T
39906216 ATATTAATAA
Statistics
Matches: 78, Mismatches: 23, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
26 26 0.33
27 17 0.22
28 30 0.38
29 5 0.06
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (26 bp):
TTAAATTATATTTAATAATTATTATT
Found at i:39906111 original size:13 final size:13
Alignment explanation
Indices: 39906079--39906119 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
39906069 TATATTTTTA
39906079 TTAAATTA-TATT
1 TTAAATTATTATT
*
39906091 TAATAATTATTATT
1 TTA-AATTATTATT
39906105 TTAAATTATT-TT
1 TTAAATTATTATT
39906117 TTA
1 TTA
39906120 TAGTATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAAATTATTATT
Found at i:39906132 original size:61 final size:61
Alignment explanation
Indices: 39905960--39906154 Score: 158
Period size: 64 Copynumber: 3.2 Consensus size: 61
39905950 AAGTAGATTA
*
39905960 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAG
1 TAAATTATATTTAATAATTATTATTTTAAATTAT-TTTTATAGTATTATATA-TAT-ATTTTAG
* ** *
39906024 TAAATTCATA--TAAGAA-TATTTAATACTAAGA--A-TTTTATCA--AAT-TATATAT-TTTTA
1 TAAATT-ATATTTAATAATTA-TT-ATTTTAA-ATTATTTTTAT-AGTATTATATATATATTTTA
*
39906079 T
61 G
39906080 TAAATTATATTTAATAATTATTATTTTAAATTATTTTTTATAGTATTATATATTATGATTTTAG
1 TAAATTATATTTAATAATTATTATTTTAAATTA-TTTTTATAGTATTATATA-TAT-ATTTTAG
39906144 TAAATTCATAT
1 TAAATT-ATAT
39906155 ATTTTATTAA
Statistics
Matches: 101, Mismatches: 11, Indels: 37
0.68 0.07 0.25
Matches are distributed among these distances:
55 4 0.04
56 16 0.16
57 8 0.08
58 6 0.06
59 10 0.10
60 4 0.04
61 10 0.10
62 5 0.05
63 8 0.08
64 22 0.22
65 8 0.08
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (61 bp):
TAAATTATATTTAATAATTATTATTTTAAATTATTTTTATAGTATTATATATATATTTTAG
Found at i:39906160 original size:18 final size:17
Alignment explanation
Indices: 39906137--39906171 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39906127 ATATATTATG
39906137 ATTTTAGTAAATTCATAT
1 ATTTTAGTAAATT-ATAT
*
39906155 ATTTTATTAAATTATAT
1 ATTTTAGTAAATTATAT
39906172 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTAGTAAATTATAT
Found at i:39906381 original size:16 final size:16
Alignment explanation
Indices: 39906360--39906412 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
39906350 AGAATTACCT
39906360 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* *
39906376 ATTACGCATTTATTCC
1 ATTACGCCTCTATTCC
*
39906392 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
39906408 ATTAC
1 ATTAC
39906413 AGTGAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.25, C:0.32, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:39911440 original size:27 final size:26
Alignment explanation
Indices: 39911373--39911470 Score: 133
Period size: 28 Copynumber: 3.6 Consensus size: 26
39911363 TAATGAGATT
39911373 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATT-AA
*
39911400 ATGCACTAAGTGTGCGAGTATAATGTAA
1 A-GCACTAAGTGTGCGAGTTTAAT-TAA
*
39911428 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAATTA--A
39911456 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
39911471 TACTTATTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
26 2 0.03
27 21 0.33
28 40 0.62
29 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGAGTTTAATTAA
Found at i:39912505 original size:22 final size:22
Alignment explanation
Indices: 39912477--39912653 Score: 167
Period size: 22 Copynumber: 7.6 Consensus size: 22
39912467 GAGTATATTG
39912477 ATGCTGTCCATTTTAATGTATA
1 ATGCTGTCCATTTTAATGTATA
39912499 ATGCTGTCCAATTTTGAATGTACTA
1 ATGCTGTCC-ATTTT-AATGTA-TA
*
39912524 ATGCTGTCCATTTTAATGTATG
1 ATGCTGTCCATTTTAATGTATA
* *
39912546 ATGCTGTCCAATTTTGAGTGTATTG
1 ATGCTGTCC-ATTTT-AATGTA-TA
*
39912571 ATGCTGTCCATTTTAATTTATA
1 ATGCTGTCCATTTTAATGTATA
* *
39912593 ATGCTATCCGATTTTGA-GTATA
1 ATGCTGTCC-ATTTTAATGTATA
* * * *
39912615 TTTAAGCTGTCTAATTTGATGTATA
1 ---ATGCTGTCCATTTTAATGTATA
39912640 ATGCTGTCCATTTT
1 ATGCTGTCCATTTT
39912654 GAGCATATTA
Statistics
Matches: 129, Mismatches: 15, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
22 43 0.33
23 26 0.20
24 27 0.21
25 33 0.26
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (22 bp):
ATGCTGTCCATTTTAATGTATA
Found at i:39912528 original size:47 final size:47
Alignment explanation
Indices: 39912457--39912697 Score: 263
Period size: 47 Copynumber: 5.1 Consensus size: 47
39912447 CCAAATTTGA
* *
39912457 TGTCC-ATTTTGAGTATATTGATGCTGTCCATTTTAATGTATAATGC
1 TGTCCAATTTTGAGTGTATTAATGCTGTCCATTTTAATGTATAATGC
* * *
39912503 TGTCCAATTTTGAATGTACTAATGCTGTCCATTTTAATGTATGATGC
1 TGTCCAATTTTGAGTGTATTAATGCTGTCCATTTTAATGTATAATGC
* *
39912550 TGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATTTATAATGC
1 TGTCCAATTTTGAGTGTATTAATGCTGTCCATTTTAATGTATAATGC
* * * * * *
39912597 TATCCGATTTTGAGTATATTTAA-GCTGTCTAATTTGATGTATAATGC
1 TGTCCAATTTTGAGTGTA-TTAATGCTGTCCATTTTAATGTATAATGC
** * * ** *
39912644 TGTCC-ATTTTGAGCATATTATTGCTGTCCAATTTGTTGAATAATTGC
1 TGTCCAATTTTGAGTGTATTAATGCTGTCCATTTTAATGTATAA-TGC
39912691 TGTCCAA
1 TGTCCAA
39912698 AACAGGGTTG
Statistics
Matches: 166, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
45 3 0.02
46 34 0.20
47 125 0.75
48 4 0.02
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (47 bp):
TGTCCAATTTTGAGTGTATTAATGCTGTCCATTTTAATGTATAATGC
Found at i:39912693 original size:23 final size:22
Alignment explanation
Indices: 39912620--39912697 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
39912610 GTATATTTAA
* *
39912620 GCTGTCTAATTTGATGTATAA-T
1 GCTGTCCAATTTG-TGAATAATT
* * *
39912642 GCTGTCCATTTTGAGCATATTATT
1 GCTGTCCAATTTGTG-A-ATAATT
39912666 GCTGTCCAATTTGTTGAATAATT
1 GCTGTCCAATTTG-TGAATAATT
39912689 GCTGTCCAA
1 GCTGTCCAA
39912698 AACAGGGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
21 1 0.02
22 11 0.25
23 17 0.39
24 14 0.32
25 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (22 bp):
GCTGTCCAATTTGTGAATAATT
Found at i:39913807 original size:91 final size:91
Alignment explanation
Indices: 39913660--39913867 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
39913650 TTGATTTTAG
*
39913660 TAAATTCATATAAGAACATTTTATTATTAAAAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATTAAAAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
39913725 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* *
39913752 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAAAATTTTATGAAATTATATATCATTATTAAATTATA
39913817 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* * *
39913843 CAAATTCATATTAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
39913868 GTTATAATTA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 91 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAAAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:39913836 original size:26 final size:28
Alignment explanation
Indices: 39913771--39913842 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
39913761 ATAAGAAAAT
* *
39913771 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
*
39913801 TTATTATTAAATTATATGTAATAATA-A
1 TTATTATTAAATTATATGAAATAATATA
39913828 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
39913843 CAAATTCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 14 0.36
29 1 0.03
30 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:39914038 original size:16 final size:16
Alignment explanation
Indices: 39914017--39914059 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
39914007 TTATTAAATT
39914017 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
39914033 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
39914048 AT-TATGTTAATT
1 ATATATTTTAATT
39914060 TATATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:39914157 original size:239 final size:239
Alignment explanation
Indices: 39913883--39914418 Score: 941
Period size: 239 Copynumber: 2.2 Consensus size: 239
39913873 AATTATTTTA
* * * *
39913883 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
*
39913947 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTGTTAAGAATTTTATT
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATT
39914012 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCA
130 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCA
39914077 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
195 TATATTATGA-TTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
39914123 AA-TTTATTATATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
39914187 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTA
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
*
39914252 AATTATATATTTTAATTATAATATATTTAATAATTATTATGTTAATTTATATTTTATAGTATCAT
131 AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
*
39914317 ATATTATGATTGAGTAAATTCATATAAGAATATTGATTATTAAG
196 ATATTATGATTGAGTAAATTCATATAAGAATATTAATTATTAAG
39914361 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
39914419 ATGATTAAAT
Statistics
Matches: 281, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
238 36 0.13
239 236 0.84
240 9 0.03
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (239 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTA
AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
ATATTATGATTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:39914188 original size:119 final size:120
Alignment explanation
Indices: 39913883--39914413 Score: 942
Period size: 119 Copynumber: 4.4 Consensus size: 120
39913873 AATTATTTTA
* * * * *
39913883 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
*
39913947 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTGTTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
39914003 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
39914068 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
39914123 AA-TTTATTATATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
39914187 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
39914242 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
39914307 ATAGTATCATATATTATGA-TTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
39914361 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
39914414 TAAATATGAT
Statistics
Matches: 398, Mismatches: 11, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
119 204 0.51
120 192 0.48
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:39914396 original size:16 final size:16
Alignment explanation
Indices: 39914375--39914416 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39914365 TTATTAAATT
*
39914375 ATATATTTTAATTATA
1 ATATATTTTAATAATA
39914391 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
39914406 AT-TATGTTTAA
1 ATATAT-TTTAA
39914417 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:39914401 original size:15 final size:15
Alignment explanation
Indices: 39914366--39914407 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39914356 TTAAGAATTT
*
39914366 TATTAAATTAT-ATA
1 TATTTAATTATAATA
39914380 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
39914394 TATTTAATAATAAT
1 TATTTAATTATAAT
39914408 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:39914651 original size:16 final size:16
Alignment explanation
Indices: 39914630--39914683 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
39914620 TTGATTTGCT
*
39914630 ATTACACCTCTATTTC
1 ATTACACCTCTATTCC
39914646 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
39914662 GTTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
39914678 AATACA
1 ATTACA
39914684 GCGAACCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:39920083 original size:13 final size:13
Alignment explanation
Indices: 39920067--39920132 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
39920057 TTTAAACCAA
39920067 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
39920080 ACTTCTCAAAAAC
1 ACTTTTCAAAAGC
* *
39920093 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
39920106 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
39920119 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
39920132 A
1 A
39920133 ATAAAGAACT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39929618 original size:47 final size:47
Alignment explanation
Indices: 39929565--39929764 Score: 305
Period size: 47 Copynumber: 4.3 Consensus size: 47
39929555 ATGATTTTAG
* * * *
39929565 TAAATTCATATAAGAATATTTATTATTAAGAATT-TTATAAAATTATA
1 TAAATTCATATAAGAAAATTTATTAGTAATAATTATT-TTAAATTATA
39929612 TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
1 TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
*
39929659 CAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
1 TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
* *
39929706 CAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTTTA
1 TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
39929753 TTAAA-TCATATA
1 -TAAATTCATATA
39929765 CTTTAATTAA
Statistics
Matches: 144, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
47 139 0.97
48 5 0.03
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (47 bp):
TAAATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATTATA
Found at i:39929810 original size:59 final size:57
Alignment explanation
Indices: 39929732--39930030 Score: 206
Period size: 59 Copynumber: 5.2 Consensus size: 57
39929722 AATTTATTAG
39929732 TAATAATTATTT-TA--A-ATTTTATTAAATCATATACTTTAATTAAAATATATTTAA
1 TAATAATTATTTATATTATATTTTATTAAATCATATA-TTTAATTAAAATATATTTAA
** * ** * * *
39929786 TAATAATTATTTCATATTATATTTTATTGTATCATATATTATGATTTTAGTAAATTCATA
1 TAATAATTATTT-ATATTATATTTTATTAAATCATATATT-TAATTAAAATATATTTA-A
* *
39929846 TAAGAA-TATTTATTATTAAGAATTTTATTAAATCATATATTTTAATTAAAATATATTTAA
1 TAATAATTATTTA-TATT-A-TATTTTATTAAATCATATA-TTTAATTAAAATATATTTAA
* * * * *
39929906 TAATAATTATATTAAATTATATTTTA-TAGTATCATATATTATTATATGAAAT-TCATATAA
1 TAATAATTAT-TTATATTATATTTTATTA-AATCATATATT-TAAT-TAAAATAT-ATTTAA
* * * * *
39929966 GAAT-ATTGA-TTAT-TAAGAATTTTATTAAATTATAT-TTTAATTAAAATATATCTAA
1 TAATAATT-ATTTATATTA-TATTTTATTAAATCATATATTTAATTAAAATATATTTAA
39930021 TAATAATTAT
1 TAATAATTAT
39930031 GTTAAAATAT
Statistics
Matches: 187, Mismatches: 35, Indels: 44
0.70 0.13 0.17
Matches are distributed among these distances:
54 12 0.06
55 14 0.07
56 9 0.05
57 4 0.02
58 23 0.12
59 59 0.32
60 28 0.15
61 33 0.18
62 5 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (57 bp):
TAATAATTATTTATATTATATTTTATTAAATCATATATTTAATTAAAATATATTTAA
Found at i:39929874 original size:15 final size:16
Alignment explanation
Indices: 39929846--39929875 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39929836 TAAATTCATA
39929846 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
39929862 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
39929876 AATCATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:39929895 original size:18 final size:15
Alignment explanation
Indices: 39929867--39929932 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
39929857 ATTATTAAGA
39929867 ATTTTATTAAATCATAT
1 ATTTTATTAAA--ATAT
39929884 ATTTTAATTAAAATAT
1 ATTTT-ATTAAAATAT
*
39929900 A-TTTA--ATAATA-
1 ATTTTATTAAAATAT
* *
39929911 ATTATATTAAATTAT
1 ATTTTATTAAAATAT
39929926 ATTTTAT
1 ATTTTAT
39929933 AGTATCATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 1 0.03
12 8 0.21
14 5 0.13
15 9 0.23
16 5 0.13
17 5 0.13
18 6 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTATTAAAATAT
Found at i:39929994 original size:117 final size:119
Alignment explanation
Indices: 39929746--39930036 Score: 457
Period size: 120 Copynumber: 2.5 Consensus size: 119
39929736 AATTATTTTA
* *
39929746 AATTTTATTAAATCATATACTTTAATTAAAATATATTTAATAATAATTATTTCATATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTT-AAATTATATTTT
* * *
39929811 ATTGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
65 ATAGTATCATATATTATGATTATAGTAAATTCATATAAGAATATTGATTATTAAG
39929866 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATATTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTATATTTT
*
39929931 ATAGTATCATATATTATTA-TAT-G-AAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTATAGTAAATTCATATAAGAATATTGATTATTAAG
*
39929983 AATTTTATTAAAT--TATATTTTAATTAAAATATATCTAATAATAATTATGTTAAA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAA
39930037 ATATGATTAA
Statistics
Matches: 162, Mismatches: 8, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
115 39 0.24
117 41 0.25
118 1 0.01
119 2 0.01
120 77 0.48
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTAAATTATATTTTA
TAGTATCATATATTATGATTATAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:39930002 original size:15 final size:16
Alignment explanation
Indices: 39929984--39930016 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39929974 ATTATTAAGA
*
39929984 ATTTT-ATTAAATTAT
1 ATTTTAATTAAAATAT
39929999 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
39930015 AT
1 AT
39930017 CTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:39930066 original size:117 final size:114
Alignment explanation
Indices: 39929746--39930066 Score: 380
Period size: 117 Copynumber: 2.7 Consensus size: 114
39929736 AATTATTTTA
* *
39929746 AATTTTATTAAATCATATACTTTAATTAAAATATATTTAATAATAATTATTTCATATTATATTTT
1 AATTTTATTAAAT-ATATATTTTAATTAAAATATATTTAATAATAATTATTT-AAATTATA--TT
* * * *
39929811 ATTGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
62 ATTATATTAT-TATTAT-ATTATAGTAAATTCATATAAGAATATTGATTATTAAG
39929866 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATATTAAATTATATT-T
1 AATTTTATTAAAT-ATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTATATTAT
* *
39929930 TATAGTATCATATATTATTATA-TGAAATTCATATAAGAATATTGATTATTAAG
64 TATATTATTAT-TA-TATTATAGT-AAATTCATATAAGAATATTGATTATTAAG
* *
39929983 AATTTTATTAAAT-TATATTTTAATTAAAATATATCTAATAATAATTATGTTAAAATATGATTAA
1 AATTTTATTAAATATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTAT-ATT--
39930047 ATTAT-TTATTATTGATATTA
62 ATTATATTATTATT-ATATTA
39930067 ATAATCTTAT
Statistics
Matches: 179, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
115 42 0.23
116 6 0.03
117 60 0.34
118 9 0.05
119 4 0.02
120 56 0.31
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (114 bp):
AATTTTATTAAATATATATTTTAATTAAAATATATTTAATAATAATTATTTAAATTATATTATTA
TATTATTATTATATTATAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:39930270 original size:16 final size:16
Alignment explanation
Indices: 39930249--39930285 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
39930239 TTGATTTGCT
39930249 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
39930265 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
39930281 ATTAC
1 ATTAC
39930286 AGCGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.32, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:39930804 original size:18 final size:19
Alignment explanation
Indices: 39930745--39930809 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 19
39930735 TTCAAAGCTT
* *
39930745 AATTTTTTAAAAAAATTAA
1 AATTTTATAAAAAATTTAA
* *
39930764 AA--ATAT-AAATATTTAA
1 AATTTTATAAAAAATTTAA
39930780 AATTTTA-AAAAAATTTATA
1 AATTTTATAAAAAATTTA-A
39930799 AA-TTTATAAAA
1 AATTTTATAAAA
39930810 CATTATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
16 10 0.29
17 2 0.06
18 14 0.40
19 9 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTTTATAAAAAATTTAA
Found at i:39931200 original size:37 final size:37
Alignment explanation
Indices: 39931153--39931233 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
39931143 GTCCAATTAA
* *
39931153 AAAATGTGTATCAATTATCTTATTATATGTGTAGACT
1 AAAAGGTGTATCAATTATCTTATTACATGTGTAGACT
* * *
39931190 AAAAGGTGTATCAATTATTTTCTTACATGTGTAGCCT
1 AAAAGGTGTATCAATTATCTTATTACATGTGTAGACT
39931227 AAAAGGT
1 AAAAGGT
39931234 TTAAATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (37 bp):
AAAAGGTGTATCAATTATCTTATTACATGTGTAGACT
Found at i:39937001 original size:19 final size:19
Alignment explanation
Indices: 39936974--39937011 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
39936964 ATTCTAGACT
39936974 TTAACTTTTAACTTTTTTTA
1 TTAACTTTTAA-TTTTTTTA
*
39936994 TTAATTTTTAATTTTTTT
1 TTAACTTTTAATTTTTTT
39937012 TTATTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTAACTTTTAATTTTTTTA
Found at i:39937002 original size:20 final size:18
Alignment explanation
Indices: 39936973--39937028 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
39936963 TATTCTAGAC
*
39936973 TTTAACTTTTAACTTTTTT
1 TTTAATTTTTAA-TTTTTT
39936992 TATTAATTTTTAATTTTTT
1 T-TTAATTTTTAATTTTTT
*
39937011 TTTATTTTTTGAATTTTT
1 TTTAATTTTT-AATTTTT
39937029 AAAAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.24
19 15 0.45
20 10 0.30
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTAATTTTTAATTTTTT
Found at i:39937010 original size:18 final size:19
Alignment explanation
Indices: 39936987--39937028 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
39936977 ACTTTTAACT
39936987 TTTTTTATTAATTTTT-AA
1 TTTTTTATTAATTTTTGAA
* *
39937005 TTTTTTTTTATTTTTTGAA
1 TTTTTTATTAATTTTTGAA
39937024 TTTTT
1 TTTTT
39937029 AAAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTATTAATTTTTGAA
Found at i:39937081 original size:29 final size:29
Alignment explanation
Indices: 39937049--39937104 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
39937039 CTATAAATTT
39937049 TAATAATGTTTTACAATT-TTTTAAAAAGC
1 TAATAATGTTTTA-AATTATTTTAAAAAGC
* *
39937078 TAATATTTTTTTAAATTATTTTAAAAA
1 TAATAATGTTTTAAATTATTTTAAAAA
39937105 ATTAAGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (29 bp):
TAATAATGTTTTAAATTATTTTAAAAAGC
Found at i:39943042 original size:30 final size:29
Alignment explanation
Indices: 39942985--39943057 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 29
39942975 CAACCCAATC
* *
39942985 ATAAAAATTACAAATAATTTAATAAATAAAA
1 ATAAAAA-TA-AAAAAATTTAAAAAATAAAA
39943016 ATAAAAATAAAAAAATTTTAAAAAATAAAA
1 ATAAAAATAAAAAAA-TTTAAAAAATAAAA
39943046 ATAAAAATAAAA
1 ATAAAAATAAAA
39943058 TATAAATAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 5 0.13
30 27 0.69
31 7 0.18
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (29 bp):
ATAAAAATAAAAAAATTTAAAAAATAAAA
Found at i:39943065 original size:6 final size:6
Alignment explanation
Indices: 39943008--39943063 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
39942998 ATAATTTAAT
***
39943008 AAATAA AAATAA AAATAA AAA-AA TTTTAAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAAT-AA AAATAA AAATAA AAATAA
39943056 AATATAA A
1 AA-ATAA A
39943064 TAGGCACATG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
5 2 0.05
6 31 0.76
7 8 0.20
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:39943225 original size:9 final size:9
Alignment explanation
Indices: 39943211--39943241 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39943201 GTAGTGATTC
39943211 AATTCGGTT
1 AATTCGGTT
*
39943220 AATTCGGGT
1 AATTCGGTT
39943229 AATTCGGTT
1 AATTCGGTT
39943238 AATT
1 AATT
39943242 TTTAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:39947484 original size:104 final size:105
Alignment explanation
Indices: 39947357--39947569 Score: 383
Period size: 104 Copynumber: 2.0 Consensus size: 105
39947347 TTACTCTGGT
* * *
39947357 AAGATAAAGTCAGGAGTGGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACC-AAA
1 AAGATAAAATCAAGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
*
39947421 AAAATGCTTACACGTTTATATACATTTATGTACATTTATA
66 AAAATGCTTACACGTTTATATACATTTACGTACATTTATA
39947461 AAGATAAAATCAAGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
1 AAGATAAAATCAAGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
39947526 AAAATGCTTACACGTTTATATACATTTACGTACATTTATA
66 AAAATGCTTACACGTTTATATACATTTACGTACATTTATA
39947566 AAGA
1 AAGA
39947570 ATTGTGTTAA
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 58 0.56
105 46 0.44
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (105 bp):
AAGATAAAATCAAGAGTAGTTTTTGTTTTTTAACTTGATGTATTAGTTAGTCTTGTTCACCAAAA
AAAATGCTTACACGTTTATATACATTTACGTACATTTATA
Found at i:39947822 original size:23 final size:23
Alignment explanation
Indices: 39947796--39947849 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
39947786 TTTAAAAGTT
* *
39947796 AAATATTATTTTATCCTAATATC
1 AAATATTATGTAATCCTAATATC
* *
39947819 AAATATTATGTAATTCTAATATT
1 AAATATTATGTAATCCTAATATC
39947842 AAATATTA
1 AAATATTA
39947850 ATTACAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATATTATGTAATCCTAATATC
Found at i:39950861 original size:13 final size:14
Alignment explanation
Indices: 39950837--39950865 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39950827 CATGCTTTTG
39950837 AACACTTTGATCAT
1 AACACTTTGATCAT
39950851 AACAC-TTGATCAT
1 AACACTTTGATCAT
39950864 AA
1 AA
39950866 ATCAACATTT
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:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (14 bp):
AACACTTTGATCAT
Found at i:39952845 original size:15 final size:15
Alignment explanation
Indices: 39952825--39952856 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39952815 CATTTCACTA
*
39952825 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
39952840 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
39952855 TT
1 TT
39952857 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:39958943 original size:33 final size:33
Alignment explanation
Indices: 39958906--39958979 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
39958896 CCTTGCCATA
* * * * *
39958906 GTCTTACGCTTATAGTGCCATAACTTAGATATG
1 GTCTTACGATTAGAATGCCATAACCTAAATATG
*
39958939 GTCTTATC-ATTAGAATGCCATAGCCTAAATATG
1 GTCTTA-CGATTAGAATGCCATAACCTAAATATG
39958972 GTCTTACG
1 GTCTTACG
39958980 TAAAGATTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (33 bp):
GTCTTACGATTAGAATGCCATAACCTAAATATG
Found at i:39960906 original size:13 final size:13
Alignment explanation
Indices: 39960888--39960914 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39960878 ATTTGTCAGG
39960888 ACGGTGGAAAGAA
1 ACGGTGGAAAGAA
39960901 ACGGTGGAAAGAA
1 ACGGTGGAAAGAA
39960914 A
1 A
39960915 ACTGACTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.37, T:0.07
Consensus pattern (13 bp):
ACGGTGGAAAGAA
Found at i:39978263 original size:16 final size:16
Alignment explanation
Indices: 39978244--39978288 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
39978234 GGCTACAATT
*
39978244 GAATAGAGCTGTAATG
1 GAATAAAGCTGTAATG
*
39978260 GAATAAAGTTGTAATG
1 GAATAAAGCTGTAATG
39978276 GAATAAAGCTGTA
1 GAATAAAGCTGTA
39978289 GTTAGTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (16 bp):
GAATAAAGCTGTAATG
Found at i:39982229 original size:33 final size:33
Alignment explanation
Indices: 39982185--39982261 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
39982175 CTTTATTCTA
* * **
39982185 TGTTTACTGTCCCATCAGACTATTTCTATTTCG
1 TGTTTACTGTCCCAACAGAATAACTCTATTTCG
* * *
39982218 TGTTTATTGTCCTAACAGAATAACTCTATTTTG
1 TGTTTACTGTCCCAACAGAATAACTCTATTTCG
39982251 TGTTTACTGTC
1 TGTTTACTGTC
39982262 TCAATGGATT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (33 bp):
TGTTTACTGTCCCAACAGAATAACTCTATTTCG
Found at i:39982319 original size:33 final size:34
Alignment explanation
Indices: 39982282--39982360 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 34
39982272 ATTTCTTTTC
** *
39982282 CGTGTTTAATGTCT-AGACGGGCTATATTTGTTT
1 CGTGTTTAATGTCTCAGACGAACTATATATGTTT
* *
39982315 CGTGTTTACTGT-TCAGATGAACTATATATGTTT
1 CGTGTTTAATGTCTCAGACGAACTATATATGTTT
*
39982348 CGTGTTTATTGTC
1 CGTGTTTAATGTC
39982361 CCAACAGACT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.19, C:0.13, G:0.22, T:0.47
Consensus pattern (34 bp):
CGTGTTTAATGTCTCAGACGAACTATATATGTTT
Found at i:39982579 original size:51 final size:50
Alignment explanation
Indices: 39982484--39982579 Score: 111
Period size: 51 Copynumber: 1.9 Consensus size: 50
39982474 CTCATCATAC
* **
39982484 CTAGCTGTCATAACATCTTTTATCTATAGTTTTACACCGTATACCTTATA
1 CTAGCTGTCATAACATCTTTAATCTATAGTTTTACACCACATACCTTATA
* * * **
39982534 CTAGACTGTCATAGCCTCTTTAATCTATGGTTTTATGCCACATACC
1 CTAG-CTGTCATAACATCTTTAATCTATAGTTTTACACCACATACC
39982580 ATCATTACGG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
50 4 0.11
51 33 0.89
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (50 bp):
CTAGCTGTCATAACATCTTTAATCTATAGTTTTACACCACATACCTTATA
Found at i:39991563 original size:138 final size:138
Alignment explanation
Indices: 39991300--39991563 Score: 397
Period size: 138 Copynumber: 1.9 Consensus size: 138
39991290 AGAGAACATA
* * *
39991300 AATATAATTAATGTATGAATTTGATTCATACAAAATATTAATTGTATGTATTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAGTTAT
* * *
39991365 TAATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAGGCGTGGAAATTAATATTCTT
66 TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACGTGGAAATGAATATTCTT
39991430 TTGGAAAG
131 TTGGAAAG
39991438 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAGTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAGTTAT
* * * * *
39991503 TAATATTAACAATTATATTAGTTAATTT-TGATCAAAATATAAACGACATTGGAAA-GAATAT
66 TAATATAAACAATTATATTAATTAATTTCAG-TCAAAATATAAAAGAC-GTGGAAATGAATAT
39991564 AATTTTGTTT
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
137 1 0.01
138 106 0.94
139 6 0.05
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (138 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAGTTAT
TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAGACGTGGAAATGAATATTCTT
TTGGAAAG
Found at i:39991630 original size:75 final size:75
Alignment explanation
Indices: 39991551--39991689 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
39991541 ATAAACGACA
* *
39991551 TTGGAAAGAATATAATT-TTGTTTTCTAACTTTCCATTTGCCTTCTTTATTAATAA-AGAAATAA
1 TTGGAAAGAATATAATTCAT-TTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGAG-AATAA
39991614 TGATATATTCTT
64 TGATATATTCTT
* *
39991626 TTGGAAATAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGAGAATAAT
1 TTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGAGAATAAT
39991690 CCTAGTTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
75 55 0.95
76 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.46
Consensus pattern (75 bp):
TTGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGAGAATAATG
ATATATTCTT
Found at i:39991649 original size:22 final size:22
Alignment explanation
Indices: 39991607--39991648 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39991597 TATTAATAAA
39991607 GAAATAATGATATATTCTTTTG
1 GAAATAATGATATATTCTTTTG
39991629 GAAATAAT-ATA-ATTCATTTT
1 GAAATAATGATATATTC-TTTT
39991649 TCTAACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (22 bp):
GAAATAATGATATATTCTTTTG
Found at i:39992329 original size:27 final size:27
Alignment explanation
Indices: 39992299--39992391 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
39992289 ATTCCAAATT
*
39992299 GGGTTCGCCAGTTGATTTGGCGAGCTG
1 GGGTTCGCCAGTTGATTTGGCGAGTTG
* *
39992326 GGGTTCTCCAATTGATTTGGCGAGTTG
1 GGGTTCGCCAGTTGATTTGGCGAGTTG
* * *
39992353 GGGTTCGCCAGATGGTTTAGCGAGTTG
1 GGGTTCGCCAGTTGATTTGGCGAGTTG
* *
39992380 GTGTTCACCAGT
1 GGGTTCGCCAGT
39992392 CAAAGTCAAG
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.14, C:0.17, G:0.37, T:0.32
Consensus pattern (27 bp):
GGGTTCGCCAGTTGATTTGGCGAGTTG
Found at i:39996123 original size:17 final size:17
Alignment explanation
Indices: 39996101--39996137 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
39996091 AATTTTTGAA
39996101 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
39996118 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
39996135 TTA
1 TTA
39996138 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:39997415 original size:46 final size:46
Alignment explanation
Indices: 39997362--39997593 Score: 410
Period size: 46 Copynumber: 5.0 Consensus size: 46
39997352 CCATGGAAAA
*
39997362 TTGTGAAAAGTAGATATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
39997408 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
39997454 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
39997500 TTGTGAAAAGTAGGCATGGTGTTTCAGTGAAGAAAACCATACTGAT
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
39997546 TTGTGAAAAGTAGATATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
39997592 TT
1 TT
39997594 ATAGCATTGT
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 178 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:40001655 original size:20 final size:20
Alignment explanation
Indices: 40001626--40001670 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
40001616 CTATTTATGC
* *
40001626 ACATATTC-AAGAGACTTAA
1 ACATATTCAAACACACTTAA
40001645 ACATCATTCAAACACACTTAA
1 ACAT-ATTCAAACACACTTAA
40001666 ACATA
1 ACATA
40001671 CCATTTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 13 0.59
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.24
Consensus pattern (20 bp):
ACATATTCAAACACACTTAA
Found at i:40011448 original size:95 final size:95
Alignment explanation
Indices: 40011281--40011458 Score: 329
Period size: 95 Copynumber: 1.9 Consensus size: 95
40011271 TATTATTTAG
40011281 AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGGTACAATTATGATATTGCATGT
1 AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGGTACAATTATGATATTGCATGT
*
40011346 TTGTTTATGTTTCATGCATTATACGAATGC
66 TTCTTTATGTTTCATGCATTATACGAATGC
* *
40011376 AATATGCCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGGTGCAATTATGATATTGCATGT
1 AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGGTACAATTATGATATTGCATGT
40011441 TTCTTTATGTTTCATGCA
66 TTCTTTATGTTTCATGCA
40011459 CGAATGCATC
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (95 bp):
AATATACCTTTAGATGTTAATATATAAAACCAGTGTCAGTGGGGTACAATTATGATATTGCATGT
TTCTTTATGTTTCATGCATTATACGAATGC
Found at i:40016020 original size:13 final size:14
Alignment explanation
Indices: 40015990--40016022 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40015980 TTCAATAATC
40015990 AAAAATAGAAAATG
1 AAAAATAGAAAATG
*
40016004 AAAATTAGAAAAT-
1 AAAAATAGAAAATG
40016017 AAAAAT
1 AAAAAT
40016023 GAATATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (14 bp):
AAAAATAGAAAATG
Found at i:40018549 original size:18 final size:18
Alignment explanation
Indices: 40018521--40018564 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
40018511 GGTTAAAGAG
* *
40018521 TTATT-AAAATATTTTTC
1 TTATTCAAAATAGTTTTA
40018538 TTATTCAAAATAGTTTTA
1 TTATTCAAAATAGTTTTA
40018556 TTATTCAAA
1 TTATTCAAA
40018565 GTTATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATTCAAAATAGTTTTA
Found at i:40018839 original size:18 final size:19
Alignment explanation
Indices: 40018816--40018856 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
40018806 ATCAAAATTT
*
40018816 ATTTTAATTTTTTTAT-AC
1 ATTTTAATTTTATTATGAC
40018834 ATTTTAATTTTATTATGAC
1 ATTTTAATTTTATTATGAC
40018853 ATTT
1 ATTT
40018857 ATTACTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTAATTTTATTATGAC
Done.