Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 5 of 120
Found at i:1564872 original size:15 final size:16
Alignment explanation
Indices: 1564842--1564890 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1564832 AAAATAATAG
*
1564842 TAATAATATTTAAAAA
1 TAATAATATGTAAAAA
1564858 TAATAATA-GTAAAAA
1 TAATAATATGTAAAAA
* *
1564873 TAATGATAATGTTAAAA
1 TAATAAT-ATGTAAAAA
1564890 T
1 T
1564891 TAATTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.43
16 9 0.32
17 7 0.25
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAATAATATGTAAAAA
Found at i:1568883 original size:7 final size:7
Alignment explanation
Indices: 1568862--1568915 Score: 81
Period size: 7 Copynumber: 7.7 Consensus size: 7
1568852 TTAGTACTTC
*
1568862 TGATCAG
1 TGATAAG
*
1568869 TGACAAG
1 TGATAAG
1568876 TGATAAG
1 TGATAAG
1568883 TGATAAG
1 TGATAAG
*
1568890 TGATAAT
1 TGATAAG
1568897 TGATAAG
1 TGATAAG
1568904 TGATAAG
1 TGATAAG
1568911 TGATA
1 TGATA
1568916 GCTTCAGCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.30
Consensus pattern (7 bp):
TGATAAG
Found at i:1568964 original size:51 final size:51
Alignment explanation
Indices: 1568901--1569229 Score: 356
Period size: 51 Copynumber: 6.1 Consensus size: 51
1568891 GATAATTGAT
* *
1568901 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTTATCAGTGACAAGTGGC
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGC
1568952 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGC
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGC
*
1569003 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGT-ACACTTATCTGATCAGTAAC
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA---A---G-T--G--GC
** * *
1569064 AAGTGGCAAGTGATAAGTGATGGCTTTAGTTACACTTATCTGATCAGCGACAAGTGGC
1 AAGTGATAAGTG---A-T-A--GCTTTAGCTACACTTATCTGATCAGTGACAAGTGGC
* *
1569122 AAGTGATAAGTGATAGCTTTAGTTACACTTATCTGATCAGCGACAAGTGGC
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGC
* * * **
1569173 AAGTGATAAGTGGTAAC-TTAGCTACACTTATCTGATCAGAGACAAGTGAT
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGC
1569223 AAGTGAT
1 AAGTGAT
1569230 CATATGTAAG
Statistics
Matches: 243, Mismatches: 16, Indels: 39
0.82 0.05 0.13
Matches are distributed among these distances:
50 39 0.16
51 141 0.58
53 2 0.01
54 1 0.00
55 1 0.00
56 1 0.00
57 1 0.00
58 11 0.05
59 1 0.00
60 1 0.00
61 11 0.05
62 1 0.00
63 1 0.00
64 1 0.00
65 1 0.00
66 2 0.01
68 24 0.10
69 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (51 bp):
AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGC
Found at i:1569048 original size:17 final size:17
Alignment explanation
Indices: 1569026--1569061 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1569016 TAGCTTTAGC
1569026 TACACTTATCTGATCAG
1 TACACTTATCTGATCAG
1569043 TACACTTATCTGATCAG
1 TACACTTATCTGATCAG
1569060 TA
1 TA
1569062 ACAAGTGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (17 bp):
TACACTTATCTGATCAG
Found at i:1569055 original size:68 final size:68
Alignment explanation
Indices: 1568975--1569110 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
1568965 TAGCTTTAGC
*
1568975 TACACTTATCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 TACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1569040 CAG
66 CAG
* *
1569043 TACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATGGCTTTAGTTACACTTATCTGAT
1 TACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1569108 CAG
66 CAG
1569111 CGACAAGTGG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (68 bp):
TACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
CAG
Found at i:1569077 original size:119 final size:120
Alignment explanation
Indices: 1568919--1569162 Score: 427
Period size: 119 Copynumber: 2.0 Consensus size: 120
1568909 AGTGATAGCT
* *
1568919 TCAGCTACACTTATCTTATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTAT
1 TCAGCTACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTAT
*
1568984 CTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGA
66 CTGATCAGCGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGA
* *
1569039 TCAG-TACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATGGCTTTAGTTACACTTAT
1 TCAGCTACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTAT
*
1569103 CTGATCAGCGACAAGTGGCAAGTGATAAGTGATAGCTTTAGTTACACTTATCTGA
66 CTGATCAGCGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGA
1569158 TCAGC
1 TCAGC
1569163 GACAAGTGGC
Statistics
Matches: 117, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
119 113 0.97
120 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (120 bp):
TCAGCTACACTTATCTGATCAGTAACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTAT
CTGATCAGCGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGA
Found at i:1569183 original size:170 final size:169
Alignment explanation
Indices: 1568901--1569211 Score: 532
Period size: 170 Copynumber: 1.8 Consensus size: 169
1568891 GATAATTGAT
* *
1568901 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTTATCAGTGACAAGTGGCAAGTGATAAGTGAT
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGAT
* *
1568966 AGCTTTAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACAC
66 AGCTTTAGCTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGATAAC-TTAGCTACAC
1569031 TTATCTGATCAGTACACTTATCTGATCAGTAACAAGTGGC
130 TTATCTGATCAGTACACTTATCTGATCAGTAACAAGTGGC
* * *
1569071 AAGTGATAAGTGATGGCTTTAGTTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGAT
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGAT
* *
1569136 AGCTTTAGTTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGGTAACTTAGCTACACT
66 AGCTTTAGCTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGATAACTTAGCTACACT
1569201 TATCTGATCAG
131 TATCTGATCAG
1569212 AGACAAGTGA
Statistics
Matches: 132, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
169 22 0.17
170 110 0.83
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (169 bp):
AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGAT
AGCTTTAGCTACACTTATCTGATCAGCGACAAGTGGCAAGTGATAAGTGATAACTTAGCTACACT
TATCTGATCAGTACACTTATCTGATCAGTAACAAGTGGC
Found at i:1576314 original size:18 final size:18
Alignment explanation
Indices: 1576291--1576327 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1576281 TAAATAATTT
1576291 TTTTATTAAGTAATAATA
1 TTTTATTAAGTAATAATA
*
1576309 TTTTATTAATTAATAATA
1 TTTTATTAAGTAATAATA
1576327 T
1 T
1576328 AATATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTATTAAGTAATAATA
Found at i:1576320 original size:22 final size:18
Alignment explanation
Indices: 1576283--1576325 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1576273 ACGGCTTTTA
1576283 AATAATTTTTTTATTAAGT
1 AATAATTTTTTTATTAA-T
*
1576302 AATAA-TATTTTATTAATT
1 AATAATTTTTTTATTAA-T
1576320 AATAAT
1 AATAAT
1576326 ATAATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AATAATTTTTTTATTAAT
Found at i:1590693 original size:7 final size:7
Alignment explanation
Indices: 1590681--1590723 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
1590671 TAAAAATAGT
1590681 TTTTTTC
1 TTTTTTC
1590688 TTTTTTC
1 TTTTTTC
1590695 TTTTTTC
1 TTTTTTC
1590702 -TTTTTC
1 TTTTTTC
1590708 -TTTTTC
1 TTTTTTC
1590714 TTTTTT-
1 TTTTTTC
1590720 TTTT
1 TTTT
1590724 CTGGTTGACG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 16 0.46
7 19 0.54
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:1590698 original size:6 final size:6
Alignment explanation
Indices: 1590682--1590725 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
1590672 AAAAATAGTT
1590682 TTTTTC TTTTTTC TTTTTTC TTTTTC TTTTTC TTTTT- TTTTTC T
1 TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
1590726 GGTTGACGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.14
6 18 0.50
7 13 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:1590705 original size:19 final size:19
Alignment explanation
Indices: 1590680--1590725 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1590670 ATAAAAATAG
1590680 TTTTTTTCT-TTTTTCTTT
1 TTTTTTTCTCTTTTTCTTT
1590698 TTTCTTTT-TCTTTTTCTTT
1 TTT-TTTTCTCTTTTTCTTT
1590717 TTTTTTTCT
1 TTTTTTTCT
1590726 GGTTGACGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTTTTTCTCTTTTTCTTT
Found at i:1594421 original size:2 final size:2
Alignment explanation
Indices: 1594416--1594455 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1594406 AACACACAAG
1594416 TA TA 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
1594456 ATGTATTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1599650 original size:22 final size:22
Alignment explanation
Indices: 1599600--1599652 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1599590 TCAGGCCAAT
* *
1599600 AACAACAAAATAGTAACAATAT
1 AACAACAAAATAGTAACAAAAC
* * *
1599622 AATAACAAAATGGTAGCAAAAC
1 AACAACAAAATAGTAACAAAAC
1599644 AACAACAAA
1 AACAACAAA
1599653 TTAACTTATG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.64, C:0.15, G:0.08, T:0.13
Consensus pattern (22 bp):
AACAACAAAATAGTAACAAAAC
Found at i:1601394 original size:31 final size:29
Alignment explanation
Indices: 1601359--1601435 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
1601349 TTAATAGCTC
*
1601359 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* ***
1601390 AGTGACAAAAATGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
1601419 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
1601436 CTAAAGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:1604114 original size:12 final size:13
Alignment explanation
Indices: 1604097--1604125 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1604087 ATCATGAATA
1604097 AATTTTAAAAAT-
1 AATTTTAAAAATC
1604109 AATTTTAAAAATC
1 AATTTTAAAAATC
1604122 AATT
1 AATT
1604126 AAATTATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTTTAAAAATC
Found at i:1618677 original size:20 final size:20
Alignment explanation
Indices: 1618654--1618707 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1618644 TAAAGTTTAG
1618654 AAAAAGATTATAAAAATTGT
1 AAAAAGATTATAAAAATTGT
*
1618674 -AAAAGATTAT-AAAATTTT
1 AAAAAGATTATAAAAATTGT
*
1618692 ATAAAATATTATAAAA
1 A-AAAAGATTATAAAA
1618708 TATATAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 7 0.24
19 10 0.34
20 9 0.31
21 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
AAAAAGATTATAAAAATTGT
Found at i:1618708 original size:10 final size:10
Alignment explanation
Indices: 1618655--1618720 Score: 73
Period size: 10 Copynumber: 6.7 Consensus size: 10
1618645 AAAGTTTAGA
*
1618655 AAAAGATTAT
1 AAAATATTAT
*
1618665 AAAA-ATTGT
1 AAAATATTAT
*
1618674 AAAAGATTAT
1 AAAATATTAT
*
1618684 AAAATTTTAT
1 AAAATATTAT
1618694 AAAATATTAT
1 AAAATATTAT
1618704 AAAATA-TAT
1 AAAATATTAT
1618713 AGAAATAT
1 A-AAATAT
1618721 ATTTTTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
9 12 0.25
10 36 0.75
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (10 bp):
AAAATATTAT
Found at i:1618769 original size:10 final size:9
Alignment explanation
Indices: 1618741--1618793 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
1618731 AAGTTGTAAG
*
1618741 AAAATGATA
1 AAAATTATA
1618750 AAAA-TATA
1 AAAATTATA
1618758 AAGAATTAT-
1 AA-AATTATA
1618767 AAAATTCATA
1 AAAATT-ATA
1618777 AAAATTATA
1 AAAATTATA
1618786 AAAATTAT
1 AAAATTAT
1618794 CGTACCAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 9 0.23
9 21 0.54
10 9 0.23
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:1618975 original size:10 final size:10
Alignment explanation
Indices: 1618962--1619035 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 10
1618952 TTTTTATGCA
*
1618962 TTTTATAATT
1 TTTTATAAAT
*
1618972 TTTTAT-GAT
1 TTTTATAAAT
*
1618981 TTTTATAAAA
1 TTTTATAAAT
*
1618991 TTTTATAAAA
1 TTTTATAAAT
*
1619001 TTTTAT-ATT
1 TTTTATAAAT
*
1619010 TTTTATTAAAG
1 TTTTA-TAAAT
*
1619021 TTTAAT-AAT
1 TTTTATAAAT
1619030 TTTTAT
1 TTTTAT
1619036 TGATTTTGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 20 0.40
10 25 0.50
11 5 0.10
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:1618975 original size:19 final size:18
Alignment explanation
Indices: 1618951--1619015 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
1618941 TTAAAAGATG
1618951 TTTTTTATGCATTTTATAA
1 TTTTTTATG-ATTTTATAA
1618970 TTTTTTATGATTTTTATAAAA
1 TTTTTTATGA-TTTTAT--AA
* **
1618991 TTTTATAAAATTTTAT-A
1 TTTTTTATGATTTTATAA
1619008 TTTTTTAT
1 TTTTTTAT
1619016 TAAAGTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 7 0.18
18 1 0.03
19 15 0.39
20 6 0.16
21 9 0.24
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTTTTATGATTTTATAA
Found at i:1618993 original size:29 final size:29
Alignment explanation
Indices: 1618961--1619042 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
1618951 TTTTTTATGC
1618961 ATTTTATAATTTTTTATGATTTTTA-TAAA
1 ATTTTATAA-TTTTTATGATTTTTATTAAA
*
1618990 ATTTTATAAAATTTTAT-ATTTTTTATTAAA
1 ATTTTAT-AATTTTTATGA-TTTTTATTAAA
* *
1619020 GTTTAATAATTTTTATTGATTTT
1 ATTTTATAATTTTTA-TGATTTT
1619043 GTTTTTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 1 0.02
29 26 0.59
30 16 0.36
31 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (29 bp):
ATTTTATAATTTTTATGATTTTTATTAAA
Found at i:1619359 original size:89 final size:88
Alignment explanation
Indices: 1619197--1619408 Score: 266
Period size: 89 Copynumber: 2.4 Consensus size: 88
1619187 GAATGCAAAA
* *
1619197 AAAAAAAAAAGCAAGGGCTTAATTGCTTTTTTTAAAAAATTCTGAGGGTCTTTTTATGCATTTTG
1 AAAAAAAAAAGCAGGGGCTTAATT--TTTTTTTAAAAAATTCTGAGGGCCTTTTTATGCATTTTG
*
1619262 ACAATTTAAGTACTCAATTGAGTGC
64 ACAATTTAAGTACCCAATTGAGTGC
** *
1619287 AAAAAAAAAAGCAGGGGCTTAAATTTTTTTTTTTAAAGTT-TGAGGGCCTTTTTGATGCATTTTG
1 AAAAAAAAAAGCAGGGGCTT-AATTTTTTTTTAAAAAATTCTGAGGGCCTTTTT-ATGCATTTTG
*
1619351 A-AAGTTTAAGTGCCCAATTGAGTGC
64 ACAA-TTTAAGTACCCAATTGAGTGC
* * * *
1619376 AAAACAAAGAGCAGAGTCTTAATTTTTTTTTAA
1 AAAAAAAAAAGCAGGGGCTTAATTTTTTTTTAA
1619409 TTTGAGGGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
88 25 0.24
89 58 0.55
90 19 0.18
91 4 0.04
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (88 bp):
AAAAAAAAAAGCAGGGGCTTAATTTTTTTTTAAAAAATTCTGAGGGCCTTTTTATGCATTTTGAC
AATTTAAGTACCCAATTGAGTGC
Found at i:1623259 original size:49 final size:49
Alignment explanation
Indices: 1623187--1623286 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
1623177 GTCTTAGCTA
*
1623187 AATAGTTGTAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1623236 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1 AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
1623285 AA
1 AA
1623287 GTGAACCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (49 bp):
AATAGTTGCAATAGTCTAATCCAAAGAAGAAAAGAAAGAGCTATTATGT
Found at i:1627658 original size:56 final size:59
Alignment explanation
Indices: 1627598--1627724 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 59
1627588 ATGTGAGAAT
* * *
1627598 AATTGTCAAGTTCATG-GAGTAACTT-GA-AAAAAAAA-TTCA-AGCTCCAATATGGGAAC
1 AATTGTCAAGTTCA-GAGACTAACTTAGACAAAAAAAAGTTCAGATCT-CAATATGCGAAC
*
1627654 AATTGTCGAA-TTCAGAGACTAACTTAGACAAAAAAAAGTTCAGATCTCAATGTGCGAAC
1 AATTGTC-AAGTTCAGAGACTAACTTAGACAAAAAAAAGTTCAGATCTCAATATGCGAAC
*
1627713 AATTGCCAAGTT
1 AATTGTCAAGTT
1627725 TAGGTCTCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
55 1 0.02
56 19 0.32
57 4 0.07
58 10 0.17
59 22 0.37
60 3 0.05
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (59 bp):
AATTGTCAAGTTCAGAGACTAACTTAGACAAAAAAAAGTTCAGATCTCAATATGCGAAC
Found at i:1627716 original size:59 final size:56
Alignment explanation
Indices: 1627569--1627724 Score: 147
Period size: 56 Copynumber: 2.7 Consensus size: 56
1627559 AACGTGGGCC
* * *
1627569 AAAAAAAGTTCAAACACTAATGTGAGAATAATTGTCAAGTTCATGGAGTAACTTGAA
1 AAAAAAAGTTCAAACTC-AATGTGAGAACAATTGTCAAGTTCATGGACTAACTTGAA
* * *
1627626 AAAAAAA-TTCAAGCTCCAATATGGGAACAATTGTCGAA-TTCA-GAGACTAACTTAGACA
1 AAAAAAAGTTCAAACT-CAATGTGAGAACAATTGTC-AAGTTCATG-GACTAACTT-GA-A
* * *
1627684 AAAAAAAGTTCAGATCTCAATGTGCGAACAATTGCCAAGTT
1 AAAAAAAGTTCA-AACTCAATGTGAGAACAATTGTCAAGTT
1627725 TAGGTCTCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
55 1 0.01
56 33 0.41
57 12 0.15
58 10 0.12
59 22 0.27
60 3 0.04
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (56 bp):
AAAAAAAGTTCAAACTCAATGTGAGAACAATTGTCAAGTTCATGGACTAACTTGAA
Found at i:1630201 original size:40 final size:40
Alignment explanation
Indices: 1630156--1630233 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
1630146 ATTTCAAATT
* *
1630156 CACTTTCGATTCAAT-CACAATTCAATTCAATTTCACTTTC
1 CACTTTCGAATCAATACACAATTCAAAT-AATTTCACTTTC
** *
1630196 CACTTTTTAATCAATACACAGTTCAAATAATTTCACTT
1 CACTTTCGAATCAATACACAATTCAAATAATTTCACTT
1630234 CGATTCAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 22 0.69
41 10 0.31
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (40 bp):
CACTTTCGAATCAATACACAATTCAAATAATTTCACTTTC
Found at i:1631139 original size:20 final size:21
Alignment explanation
Indices: 1631114--1631155 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1631104 ATTTGGCACC
* *
1631114 ATTTAATTTATTTAT-TTTAT
1 ATTTAATTAATTAATATTTAT
1631134 ATTTAATTAATTAATATTTAT
1 ATTTAATTAATTAATATTTAT
1631155 A
1 A
1631156 AATATCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAATTAATTAATATTTAT
Found at i:1631319 original size:13 final size:13
Alignment explanation
Indices: 1631301--1631332 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1631291 AATAATTACA
1631301 ATAATAATTTAAT
1 ATAATAATTTAAT
1631314 ATAATAATTTAAT
1 ATAATAATTTAAT
*
1631327 AAAATA
1 ATAATA
1631333 TCTATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAATAATTTAAT
Found at i:1633505 original size:2 final size:2
Alignment explanation
Indices: 1633498--1633537 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
1633488 CAACTTACTG
1633498 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1633538 TCATAAATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1634693 original size:45 final size:44
Alignment explanation
Indices: 1634583--1634784 Score: 142
Period size: 44 Copynumber: 4.6 Consensus size: 44
1634573 ATCTGATGCG
* *
1634583 ATCCGCTCTACTGCAACTTCAGAGAGATGAGATCTGCGATTTTA
1 ATCCGCTCCACTGCAACTTCAGGGAGATGAGATCTGCGATTTTA
* * * * *
1634627 ATCCACTCCACAGTAACTTCAGGGAGATGAGATCTGC-TTTCTTCT
1 ATCCGCTCCACTGCAACTTCAGGGAGATGAGATCTGCGATT-TT-A
* * * ***
1634672 GTCCGCTCCACTGCAACTTCAGGGAGATAAGA-CTG-G-GTGCG
1 ATCCGCTCCACTGCAACTTCAGGGAGATGAGATCTGCGATTTTA
* * * * * * *
1634713 ATCTGCTCTACTGCAACTTCAGAGATATAAGATCTGTGGTTTTA
1 ATCCGCTCCACTGCAACTTCAGGGAGATGAGATCTGCGATTTTA
* * * *
1634757 ATCCACTCCATTGCAGCTTCAAGGAGAT
1 ATCCGCTCCACTGCAACTTCAGGGAGAT
1634785 AGGATTGGTA
Statistics
Matches: 119, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
41 27 0.23
42 3 0.03
43 4 0.03
44 58 0.49
45 27 0.23
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
ATCCGCTCCACTGCAACTTCAGGGAGATGAGATCTGCGATTTTA
Found at i:1634974 original size:132 final size:132
Alignment explanation
Indices: 1634828--1635726 Score: 1379
Period size: 132 Copynumber: 6.8 Consensus size: 132
1634818 ACATGAAGAC
* ** * *
1634828 AAGATCTGCT-ATCTTCGATCTATTCCACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATAT
1 AAGATCTG-TAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGT
* * * *
1634892 ACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTGCCTAGGAA
65 ACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGA
1634957 GAT
130 GAT
* * * *
1634960 AAGACCTGTAATCTTCAATCTATTTCACTGCTGCCCAAGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
*
1635025 CTCCACTGTAACCTCAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1635090 AT
131 AT
*
1635092 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCATGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
* *
1635157 CTCCACTGTAACCTTAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGAAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1635222 AT
131 AT
* * * **
1635224 AAAATCTGTAATCTTCAATCTATTCAACTGCTGCCCAGGGAGATAGAATTACCAGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
*
1635289 CTCCACTGTAACTTCAGGGAGGTAAAATCCACATCCGCCATCTTCGATCTGCTCCACTACTGCTT
66 CTCCACTGTAACCTCAGGGAGGT--AA---A-ATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1635354 AGGGAGAT
125 AGGGAGAT
1635362 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
* * * * *
1635427 CTCCACTGTAACCTCAAGGAGGTAAAATCCACCATCTTTGATCTTCTCCATTACTGCTTAGGGAG
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1635492 AT
131 AT
*
1635494 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAAAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
* * * * * *
1635559 CTCCACTGTAACCTTAGGGAGGTAAAATCTGCCATATTTGATCTACTCCACTATTG-TCTAGGGA
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCT-TAGGGA
1635623 GAT
130 GAT
*
1635626 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCTCAGGGAGATAGAATTACTGGCTTCAATGTA
1 AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
*
1635691 CTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATC
66 CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATC
1635727 CTTGCTCCAC
Statistics
Matches: 705, Mismatches: 54, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
131 2 0.00
132 576 0.82
133 1 0.00
134 2 0.00
136 2 0.00
137 1 0.00
138 121 0.17
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
AAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTA
CTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
AT
Found at i:1635268 original size:44 final size:44
Alignment explanation
Indices: 1634831--1635670 Score: 291
Period size: 44 Copynumber: 19.0 Consensus size: 44
1634821 TGAAGACAAG
* * * * * *
1634831 ATCTGCTATCTTCGATCTATTCCACTGCCGACCAGGGAGATAGA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* *** * * *
1634875 AT-TACTGGCTTCAATATACTCCACTG-TAACCTCAGGGAGGTAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCT-GCC-CAGGGAGATAAA
* * * * * *
1634919 ATCTGCCATCTTCGATCTACTCCACTACTGCCTAGGAAGATAAG
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* * * * * *
1634963 ACCTGTAATCTTCAATCTATTTCACTGCTGCCCAAGGAGATAGA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* *** * * * *
1635007 AT-TACTGGCTTCAATGTACTCCACTG-TAACCTCAGAGAGGTAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCT-GCC-CAGGGAGATAAA
* * * * * ** *
1635051 ATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* * * * *
1635095 ATCTGTAATCTTCAATCTATTCCACTGTTGCCCATGGAGATAGA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* *** * * * *
1635139 AT-TACTGGCTTCAATGTACTCCACTG-TAACCTTAGGGAGGTAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCT-GCC-CAGGGAGATAAA
* * * * * ** *
1635183 ATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* * * *
1635227 ATCTGTAATCTTCAATCTATTCAACTGCTGCCCAGGGAGATAGA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* * * * * * *
1635271 AT-TACCAGCTTCAATGTACTCCACTG-TAACTTCAGGGAGGTAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCT-GC-CCAGGGAGATAAA
* * * * ** *
1635315 ATCCACATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
1 AT---C-T--GCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* * * *
1635365 ATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* *** * * * *
1635409 AT-TACTGGCTTCAATGTACTCCACTG-TAACCTCAAGGAGGTAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCT-GCC-CAGGGAGATAAA
** * ** * * * ** *
1635453 ATCCACCATCTTTGATCTTCTCCATTACTGCTTAGGGAGATAAG
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* * *
1635497 ATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* *** * * * *
1635541 AT-TACTGGCTTCAATGTACTCCACTG-TAACCTTAGGGAGGTAAA
1 ATCTGCAATCTTCAATCTACTCCACTGCT-GCC-CAGGGAGATAAA
* * ** ** * * *
1635585 ATCTGCCATATTTGATCTACTCCACTATTGTCTAGGGAGATAAG
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
* * * *
1635629 ATCTGTAATCTTCAATCTATTCCACTGTTGCTCAGGGAGATA
1 ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATA
1635671 GAATTACTGG
Statistics
Matches: 546, Mismatches: 220, Indels: 60
0.66 0.27 0.07
Matches are distributed among these distances:
42 5 0.01
43 112 0.21
44 308 0.56
45 82 0.15
46 6 0.01
47 1 0.00
49 1 0.00
50 12 0.02
51 18 0.03
52 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCAATCTTCAATCTACTCCACTGCTGCCCAGGGAGATAAA
Found at i:1635538 original size:402 final size:398
Alignment explanation
Indices: 1634838--1635720 Score: 1405
Period size: 402 Copynumber: 2.2 Consensus size: 398
1634828 AAGATCTGCT
* * * *
1634838 ATCTTCGATCTATTCCACTGCCGACCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
1634903 ACCTCAGGGAGGTAAAAT--CTGCCATCTTCGATCTACTCCACTACTGCCTAGGAAGATAAGACC
66 ACCTCAGGGAGGTAAAATCCCTGCCATCTTCGATCTACTCCACTACTGCCTAGGAAGATAAGACC
*
1634966 TGTAATCTTCAATCTATTTCACTGCTGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCAC
131 TGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCAC
*
1635031 TGTAACCTCAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
196 TGTAACCTCAGAGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
* *
1635096 TCTGTAATCTTCAATCTATTCCACTGTTGCCCATGGAGATAGAATTACTGGCTTCAATGTACTCC
261 TCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAAAATTACTGGCTTCAATGTACTCC
* *
1635161 ACTGTAACCTTAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG-CTTAGGAAGATA
326 ACTGTAACCTTAGGGAGGTAAAATCCGCCATATTCGATCTACTCCACTACTGTC-TAGGAAGATA
1635225 AAATCTGTA
390 AAATCTGTA
* **
1635234 ATCTTCAATCTATTCAACTGCTGCCCAGGGAGATAGAATTACCAGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
* * * *
1635299 ACTTCAGGGAGGTAAAATCCACATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAA
66 ACCTCAGGGAGGTAAAATCC-C-T--GCCATCTTCGATCTACTCCACTACTGCCTAGGAAGATAA
* * *
1635364 GATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACT
127 GACCTGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAATTACTGGCTTCAATGTACT
* * *
1635429 CCACTGTAACCTCA-AGGAGGTAAAATCCACCATCTTTGATCTTCTCCATTACTGCTTAGGGAGA
192 CCACTGTAACCTCAGA-GAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1635493 TAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAAAATTACTGGCTTCAATGT
256 TAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAAAATTACTGGCTTCAATGT
* * * *
1635558 ACTCCACTGTAACCTTAGGGAGGTAAAATCTGCCATATTTGATCTACTCCACTATTGTCTAGGGA
321 ACTCCACTGTAACCTTAGGGAGGTAAAATCCGCCATATTCGATCTACTCCACTACTGTCTAGGAA
*
1635623 GATAAGATCTGTA
386 GATAAAATCTGTA
* *
1635636 ATCTTCAATCTATTCCACTGTTGCTCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
*
1635701 ACCTCAAGGAGGTAAAATCC
66 ACCTCAGGGAGGTAAAATCC
1635721 GCCATCCTTG
Statistics
Matches: 444, Mismatches: 35, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
396 75 0.17
399 1 0.00
400 1 0.00
401 1 0.00
402 365 0.82
403 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (398 bp):
ATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
ACCTCAGGGAGGTAAAATCCCTGCCATCTTCGATCTACTCCACTACTGCCTAGGAAGATAAGACC
TGTAATCTTCAATCTATTCCACTGCTGCCCAAGGAGATAGAATTACTGGCTTCAATGTACTCCAC
TGTAACCTCAGAGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
TCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAAAATTACTGGCTTCAATGTACTCC
ACTGTAACCTTAGGGAGGTAAAATCCGCCATATTCGATCTACTCCACTACTGTCTAGGAAGATAA
AATCTGTA
Found at i:1635842 original size:44 final size:44
Alignment explanation
Indices: 1635793--1635930 Score: 133
Period size: 44 Copynumber: 3.2 Consensus size: 44
1635783 CAATGTAGGA
1635793 AGGCAAGATTTGCTATCTTTAACTTGCTCCACTGCAACTGAGGG
1 AGGCAAGATTTGCTATCTTTAACTTGCTCCACTGCAACTGAGGG
** * * * * *
1635837 AGGCAAGGCTT--TAT-TTTCGA-TCTGCTTCACTGTCGA-TGCAAGA
1 AGGCAAGATTTGCTATCTTT-AACT-TGCTCCACTG-CAACTG-AGGG
*
1635880 AGGCAAGATTTGCTATCTTTAACTTGCTCCACTACAACTGAGGG
1 AGGCAAGATTTGCTATCTTTAACTTGCTCCACTGCAACTGAGGG
1635924 AGGCAAG
1 AGGCAAG
1635931 GCTTTATAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
41 4 0.06
42 15 0.21
43 13 0.19
44 20 0.29
45 14 0.20
46 4 0.06
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (44 bp):
AGGCAAGATTTGCTATCTTTAACTTGCTCCACTGCAACTGAGGG
Found at i:1635888 original size:87 final size:87
Alignment explanation
Indices: 1635727--1635937 Score: 314
Period size: 87 Copynumber: 2.4 Consensus size: 87
1635717 ATCCGCCATC
* * * * * * *
1635727 CTTGCTCCACTACCACCGAGGGAGGTAAGGCTGGTATCTTCAATCTGCTTCGCTGTCAATGTAGG
1 CTTGCTCCACTACAACTGAGGGAGGCAAGGCT-TTATCTTCAATCTGCTTCACTGTCAATGCAAG
1635792 AAGGCAAGATTTGCTATCTTTAA
65 AAGGCAAGATTTGCTATCTTTAA
* * * *
1635815 CTTGCTCCACTGCAACTGAGGGAGGCAAGGCTTTATTTTCGATCTGCTTCACTGTCGATGCAAGA
1 CTTGCTCCACTACAACTGAGGGAGGCAAGGCTTTATCTTCAATCTGCTTCACTGTCAATGCAAGA
1635880 AGGCAAGATTTGCTATCTTTAA
66 AGGCAAGATTTGCTATCTTTAA
1635902 CTTGCTCCACTACAACTGAGGGAGGCAAGGCTTTAT
1 CTTGCTCCACTACAACTGAGGGAGGCAAGGCTTTAT
1635938 AATTTCACTG
Statistics
Matches: 111, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
87 83 0.75
88 28 0.25
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (87 bp):
CTTGCTCCACTACAACTGAGGGAGGCAAGGCTTTATCTTCAATCTGCTTCACTGTCAATGCAAGA
AGGCAAGATTTGCTATCTTTAA
Found at i:1637215 original size:8 final size:7
Alignment explanation
Indices: 1637171--1637212 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1637161 TTAGCCTCTC
1637171 CATTTTT
1 CATTTTT
1637178 -ACTTTTT
1 CA-TTTTT
1637185 CATTTTT
1 CATTTTT
1637192 CA-TTTT
1 CATTTTT
1637198 CATCTTTT
1 CAT-TTTT
1637206 CATTTTT
1 CATTTTT
1637213 TCACATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 16 0.52
8 8 0.26
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:1638165 original size:21 final size:21
Alignment explanation
Indices: 1638141--1638188 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1638131 ATAATTTGGC
1638141 AGAAAAAAATCTG-AAAGAATG
1 AGAAAAAAAT-TGTAAAGAATG
1638162 AGAAAAAAATTGTAAAGAATG
1 AGAAAAAAATTGTAAAGAATG
1638183 A-AAAAA
1 AGAAAAA
1638189 CATTTGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.15
Consensus pattern (21 bp):
AGAAAAAAATTGTAAAGAATG
Found at i:1638488 original size:63 final size:63
Alignment explanation
Indices: 1638415--1638541 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
1638405 ATTATTCACC
1638415 ACTTCTTCATTCATTGCATTCCCTCCATCATCAATCATGTTTGGGTAGCGGATTTCCTGCACT
1 ACTTCTTCATTCATTGCATTCCCTCCATCATCAATCATGTTTGGGTAGCGGATTTCCTGCACT
1638478 ACTTCTTCATTCATTGCATTCCCTCCATCATCAATCATGTTTGGGTAGCGGATTTCCTGCACT
1 ACTTCTTCATTCATTGCATTCCCTCCATCATCAATCATGTTTGGGTAGCGGATTTCCTGCACT
1638541 A
1 A
1638542 GACGAGTTAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (63 bp):
ACTTCTTCATTCATTGCATTCCCTCCATCATCAATCATGTTTGGGTAGCGGATTTCCTGCACT
Found at i:1640194 original size:13 final size:13
Alignment explanation
Indices: 1640176--1640201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1640166 GTTCAATTTT
1640176 TTTACTAGAAAAC
1 TTTACTAGAAAAC
1640189 TTTACTAGAAAAC
1 TTTACTAGAAAAC
1640202 AAATCTCTTT
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:1641912 original size:2 final size:2
Alignment explanation
Indices: 1641905--1641949 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1641895 ACATTTACGA
1641905 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
1641947 AT A
1 AT A
1641950 ACTATAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1642134 original size:25 final size:26
Alignment explanation
Indices: 1642085--1642140 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1642075 ACCCATAAAA
*
1642085 GTATATATTAAAATATACACATATAT
1 GTATATATAAAAATATACACATATAT
* **
1642111 -TATATATAAAAATATGCATGTATAT
1 GTATATATAAAAATATACACATATAT
1642136 GTATA
1 GTATA
1642141 GCAAATACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.39
Consensus pattern (26 bp):
GTATATATAAAAATATACACATATAT
Found at i:1644218 original size:31 final size:29
Alignment explanation
Indices: 1644180--1644256 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
1644170 CTAACGGCTC
*
1644180 AGTGACTAAAATGTTACAACGCGATAACATA
1 AGTGACTAAAATGTAACAACGC-A-AACATA
* ***
1644211 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACGCAAACATA
1644240 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
1644257 CTGAGCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACGCAAACATA
Found at i:1644367 original size:20 final size:18
Alignment explanation
Indices: 1644342--1644397 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
1644332 TTACAAAAAA
1644342 AAAATAATTTTCAAAAATTC
1 AAAATAATTTT--AAAATTC
*
1644362 AAAATAAATTTTAAAATTT
1 AAAAT-AATTTTAAAATTC
1644381 AAAAT-ATTTATAAAATT
1 AAAATAATTT-TAAAATT
1644398 TATATATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.12
18 7 0.21
19 11 0.33
20 5 0.15
21 6 0.18
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATAATTTTAAAATTC
Found at i:1644398 original size:9 final size:9
Alignment explanation
Indices: 1644367--1644430 Score: 51
Period size: 9 Copynumber: 6.7 Consensus size: 9
1644357 AATTCAAAAT
1644367 AAATTT-TA
1 AAATTTATA
1644375 AAATTTA-A
1 AAATTTATA
1644383 AATATTTATA
1 AA-ATTTATA
1644393 AAATTTATA
1 AAATTTATA
1644402 TATATATTTTATA
1 -A-A-A-TTTATA
*
1644415 AAAATTATA
1 AAATTTATA
1644424 GAAATTT
1 -AAATTT
1644431 TACAAAATTC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
8 9 0.20
9 17 0.37
10 10 0.22
11 2 0.04
12 2 0.04
13 6 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (9 bp):
AAATTTATA
Found at i:1644415 original size:22 final size:20
Alignment explanation
Indices: 1644373--1644439 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 20
1644363 AAATAAATTT
1644373 TAAAATTTA-AAATA-TTTA
1 TAAAATTTATAAATATTTTA
1644391 TAAAATTTATATATATATTTTA
1 TAAAATTTATA-A-ATATTTTA
*
1644413 TAAAAATTATAGAA-ATTTTA
1 TAAAATTTATA-AATATTTTA
*
1644433 CAAAATT
1 TAAAATT
1644440 CTAAAGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.22
19 1 0.02
20 12 0.29
21 4 0.10
22 15 0.37
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (20 bp):
TAAAATTTATAAATATTTTA
Found at i:1645152 original size:17 final size:17
Alignment explanation
Indices: 1645115--1645153 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1645105 CTGAGTTTCT
* *
1645115 ATTTTTTAATTTTTTGT
1 ATTTTTTAATTTTATGA
1645132 ATTTTTTAATTTTATGA
1 ATTTTTTAATTTTATGA
1645149 ATTTT
1 ATTTT
1645154 CTTCTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (17 bp):
ATTTTTTAATTTTATGA
Found at i:1649324 original size:23 final size:23
Alignment explanation
Indices: 1649297--1649341 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1649287 CAAAAATATT
1649297 AAATATATATA-TTTTTATTTTTA
1 AAATATA-ATAGTTTTTATTTTTA
1649320 AAATATAATAGTTTTTTATTTT
1 AAATATAATAG-TTTTTATTTT
1649342 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 7 0.35
24 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AAATATAATAGTTTTTATTTTTA
Found at i:1649452 original size:9 final size:9
Alignment explanation
Indices: 1649438--1649465 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1649428 TTTTGTTACA
1649438 ACAATTAAT
1 ACAATTAAT
1649447 ACAATTAAT
1 ACAATTAAT
1649456 ACAATTAAT
1 ACAATTAAT
1649465 A
1 A
1649466 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:1649487 original size:68 final size:66
Alignment explanation
Indices: 1649408--1649549 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
1649398 TCAAGTTTGT
*
1649408 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1649473 AAA
64 AAA
1649476 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
1649541 T
66 A
1649542 TTTACTAA
1 TTTACTAA
1649550 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:1649559 original size:16 final size:16
Alignment explanation
Indices: 1649538--1649579 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1649528 AATAATTTGA
*
1649538 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
1649554 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
1649570 TAGTTTTAAT
1 TAATTTTAAT
1649580 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:1649563 original size:22 final size:22
Alignment explanation
Indices: 1649553--1649602 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1649543 TTACTAACAA
* * *
1649553 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
1649575 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
1649597 TTAATT
1 TTAATT
1649603 AAAAACGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:1649568 original size:59 final size:66
Alignment explanation
Indices: 1649408--1649571 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
1649398 TCAAGTTTGT
*
1649408 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
1649473 AAA
64 AAA
1649476 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
1649539 AAT
64 AAA
*
1649542 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
1649572 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:1649595 original size:16 final size:17
Alignment explanation
Indices: 1649576--1649607 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1649566 CAATTAGTTT
1649576 TAATTTT-ATTAAAAAA
1 TAATTTTAATTAAAAAA
1649592 TAATTTTAATTAAAAA
1 TAATTTTAATTAAAAA
1649608 CGGGCCGGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTTAATTAAAAAA
Found at i:1651319 original size:26 final size:28
Alignment explanation
Indices: 1651289--1651344 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
1651279 GTGTTTAAAA
*
1651289 ATAATATGAAAAT-AATAATGAAA-CAT
1 ATAATATGAAAATAAATAATAAAAGCAT
* *
1651315 ATAATTTGAAACTAAATAATAAAAGCAT
1 ATAATATGAAAATAAATAATAAAAGCAT
1651343 AT
1 AT
1651345 GAAATATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 11 0.44
27 9 0.36
28 5 0.20
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (28 bp):
ATAATATGAAAATAAATAATAAAAGCAT
Found at i:1652099 original size:31 final size:31
Alignment explanation
Indices: 1652041--1652099 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1652031 AATGTGTAAA
**
1652041 TTGAATCAAAATAAAAGTTTAGTGTATACAT
1 TTGAATCAAAATAAAAGTTTAACGTATACAT
* *
1652072 TTGAATCACAATCAAAGTTTAACGTATA
1 TTGAATCAAAATAAAAGTTTAACGTATA
1652100 TAATTGCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (31 bp):
TTGAATCAAAATAAAAGTTTAACGTATACAT
Found at i:1657356 original size:110 final size:110
Alignment explanation
Indices: 1657163--1657385 Score: 437
Period size: 110 Copynumber: 2.0 Consensus size: 110
1657153 GCTGCAATCA
1657163 TTGCAGTTTATCTTATTACATAAATTTGTCGACAACCACTTGATTTTAACTCTTAGAGCATAAAA
1 TTGCAGTTTATCTTATTACATAAATTTGTCGACAACCACTTGATTTTAACTCTTAGAGCATAAAA
*
1657228 TTTTCGGTGAAGAAGACATACCTGGATCCTCTATTGAATCCTCTT
66 TTTTCGGTGAAGAAGACATACCTGGACCCTCTATTGAATCCTCTT
1657273 TTGCAGTTTATCTTATTACATAAATTTGTCGACAACCACTTGATTTTAACTCTTAGAGCATAAAA
1 TTGCAGTTTATCTTATTACATAAATTTGTCGACAACCACTTGATTTTAACTCTTAGAGCATAAAA
1657338 TTTTCGGTGAAGAAGACATACCTGGACCCTCTATTGAATCCTCTT
66 TTTTCGGTGAAGAAGACATACCTGGACCCTCTATTGAATCCTCTT
1657383 TTG
1 TTG
1657386 TTTTCGTAGG
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (110 bp):
TTGCAGTTTATCTTATTACATAAATTTGTCGACAACCACTTGATTTTAACTCTTAGAGCATAAAA
TTTTCGGTGAAGAAGACATACCTGGACCCTCTATTGAATCCTCTT
Found at i:1660792 original size:11 final size:11
Alignment explanation
Indices: 1660776--1660808 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1660766 TTAAAAGAAA
1660776 AAAAATATAAT
1 AAAAATATAAT
1660787 AAAAATATAAT
1 AAAAATATAAT
1660798 AAAAATTATAA
1 AAAAA-TATAA
1660809 ATTATAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAATATAAT
Found at i:1661024 original size:13 final size:13
Alignment explanation
Indices: 1661006--1661031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1660996 TATTCTATTT
1661006 TTTCAACGAAAAA
1 TTTCAACGAAAAA
1661019 TTTCAACGAAAAA
1 TTTCAACGAAAAA
1661032 GTGTAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
TTTCAACGAAAAA
Found at i:1665226 original size:7 final size:7
Alignment explanation
Indices: 1665216--1665240 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1665206 CTTGTCAAGT
1665216 TTTGAAA
1 TTTGAAA
1665223 TTTGAAA
1 TTTGAAA
1665230 TTTGAAA
1 TTTGAAA
1665237 TTTG
1 TTTG
1665241 GGTTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (7 bp):
TTTGAAA
Found at i:1676896 original size:16 final size:18
Alignment explanation
Indices: 1676864--1676896 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1676854 TGTTATAGAA
1676864 TAAATTTAGTGTTAATTG
1 TAAATTTAGTGTTAATTG
1676882 TAAATTT-GT-TTAATT
1 TAAATTTAGTGTTAATT
1676897 TTGTGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TAAATTTAGTGTTAATTG
Found at i:1680090 original size:15 final size:17
Alignment explanation
Indices: 1680064--1680095 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1680054 CAACTAAAAA
1680064 AAAAATTGAAT-ATTAT
1 AAAAATTGAATAATTAT
1680080 AAAAATT-AATAATTAT
1 AAAAATTGAATAATTAT
1680096 TGAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAAATTGAATAATTAT
Found at i:1681250 original size:27 final size:26
Alignment explanation
Indices: 1681218--1681275 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1681208 ACATTTTTAA
*
1681218 AAAAATTACAAGAA-ATTGTAAAAATAT
1 AAAAATTA-AAAAATATTGTAAAAAT-T
*
1681245 AAAAATTAAAAAATATTTTAAAAATT
1 AAAAATTAAAAAATATTGTAAAAATT
1681271 AAAAA
1 AAAAA
1681276 AATTGGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (26 bp):
AAAAATTAAAAAATATTGTAAAAATT
Found at i:1681276 original size:9 final size:9
Alignment explanation
Indices: 1681214--1681279 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
1681204 GGTTACATTT
1681214 TTAAAAAAA
1 TTAAAAAAA
*
1681223 TTACAAGAAA
1 TTA-AAAAAA
**
1681233 TTGTAAAAA
1 TTAAAAAAA
*
1681242 -TATAAAAA
1 TTAAAAAAA
1681250 TTAAAAAATA
1 TTAAAAAA-A
**
1681260 TTTTAAAAA
1 TTAAAAAAA
1681269 TTAAAAAAA
1 TTAAAAAAA
1681278 TT
1 TT
1681280 GGTGTTGATC
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
8 7 0.16
9 23 0.52
10 14 0.32
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1681829 original size:22 final size:22
Alignment explanation
Indices: 1681793--1681852 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1681783 GGCCCGGCCC
1681793 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATACCAAAA
***
1681815 ATTTATTTTAAAAATTTTAAAA
1 ATTTATTTTAAAAATACCAAAA
**
1681837 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
1681853 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTATTTTAAAAATACCAAAA
Found at i:1681849 original size:11 final size:11
Alignment explanation
Indices: 1681818--1681888 Score: 82
Period size: 11 Copynumber: 6.9 Consensus size: 11
1681808 ACCAAAAATT
1681818 TATTTTAAAAA
1 TATTTTAAAAA
*
1681829 T-TTTAAAAAA
1 TATTTTAAAAA
1681839 GTATTTTAAAAA
1 -TATTTTAAAAA
1681851 TATTTT--AAA
1 TATTTTAAAAA
1681860 -A--TTAAAAA
1 TATTTTAAAAA
1681868 TATTTTAAAAA
1 TATTTTAAAAA
1681879 TATTTTAAAA
1 TATTTTAAAA
1681889 TTAAAAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
6 2 0.04
8 4 0.08
9 4 0.08
10 8 0.16
11 25 0.49
12 8 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:1681871 original size:28 final size:28
Alignment explanation
Indices: 1681834--1681933 Score: 132
Period size: 28 Copynumber: 3.6 Consensus size: 28
1681824 AAAAATTTTA
1681834 AAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAAA-TATTTTAAAAATATTTTAAAATT
1681863 AAAAATATTTTAAAAATATTTTAAAATT
1 AAAAATATTTTAAAAATATTTTAAAATT
**
1681891 AAAAA-A-TAAAAAAAGTATTTTAAAATT
1 AAAAATATTTTAAAAA-TATTTTAAAATT
* *
1681918 AAAAAAAATTTAAAAA
1 AAAAATATTTTAAAAA
1681934 ATAAATGTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
26 6 0.09
27 18 0.28
28 29 0.45
29 11 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAAATATTTTAAAAATATTTTAAAATT
Found at i:1681895 original size:17 final size:17
Alignment explanation
Indices: 1681844--1681877 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1681834 AAAAAGTATT
1681844 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
1681861 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
1681878 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:1682934 original size:13 final size:13
Alignment explanation
Indices: 1682918--1682944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1682908 GACTAAAATA
1682918 AATGTGTAAACAT
1 AATGTGTAAACAT
1682931 AATGTGTAAACAT
1 AATGTGTAAACAT
1682944 A
1 A
1682945 TTGTTAGAGA
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:0.15, T:0.30
Consensus pattern (13 bp):
AATGTGTAAACAT
Found at i:1683807 original size:31 final size:31
Alignment explanation
Indices: 1683769--1683831 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1683759 ATTCGATAAC
1683769 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1683800 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1 TTAGAATATTTGTTTTGTTAGTTAGAATAGT
1683831 T
1 T
1683832 AAATTTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (31 bp):
TTAGAATATTTGTTTTGTTAGTTAGAATAGT
Found at i:1686404 original size:20 final size:19
Alignment explanation
Indices: 1686342--1686397 Score: 96
Period size: 18 Copynumber: 2.9 Consensus size: 19
1686332 TTTAAAATAC
1686342 TTTTAAAATAATTTTTTTAT
1 TTTTAAAATAA-TTTTTTAT
1686362 TTTTAAAAT-ATTTTTTAT
1 TTTTAAAATAATTTTTTAT
1686380 TTTTAAAATAATTTTTTA
1 TTTTAAAATAATTTTTTA
1686398 ATGTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 17 0.49
19 9 0.26
20 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAAAATAATTTTTTAT
Found at i:1686715 original size:15 final size:17
Alignment explanation
Indices: 1686695--1686727 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1686685 TTGGAGTTTG
1686695 AAAAATA-A-TTTTAAA
1 AAAAATATATTTTTAAA
1686710 AAAAATATATTTTTAAA
1 AAAAATATATTTTTAAA
1686727 A
1 A
1686728 GTAATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATATATTTTTAAA
Found at i:1690375 original size:97 final size:97
Alignment explanation
Indices: 1690209--1690410 Score: 404
Period size: 97 Copynumber: 2.1 Consensus size: 97
1690199 GAAGATAGTG
1690209 AGGTAGGTAAACAAGTGTCTGATGACAAGAAGAAAAGATAAAGCCCAGCGCCATGGATGACAGAG
1 AGGTAGGTAAACAAGTGTCTGATGACAAGAAGAAAAGATAAAGCCCAGCGCCATGGATGACAGAG
1690274 CTTAGTATGCGAGGAAGTTGTTGCTTCTACTC
66 CTTAGTATGCGAGGAAGTTGTTGCTTCTACTC
1690306 AGGTAGGTAAACAAGTGTCTGATGACAAGAAGAAAAGATAAAGCCCAGCGCCATGGATGACAGAG
1 AGGTAGGTAAACAAGTGTCTGATGACAAGAAGAAAAGATAAAGCCCAGCGCCATGGATGACAGAG
1690371 CTTAGTATGCGAGGAAGTTGTTGCTTCTACTC
66 CTTAGTATGCGAGGAAGTTGTTGCTTCTACTC
1690403 AGGTAGGT
1 AGGTAGGT
1690411 TGTCCACAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 105 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (97 bp):
AGGTAGGTAAACAAGTGTCTGATGACAAGAAGAAAAGATAAAGCCCAGCGCCATGGATGACAGAG
CTTAGTATGCGAGGAAGTTGTTGCTTCTACTC
Found at i:1692708 original size:14 final size:14
Alignment explanation
Indices: 1692691--1692735 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1692681 GTGGAATATT
*
1692691 TTATTATTATCATA
1 TTATTATTATAATA
1692705 TTATTATTAATAATTA
1 TTATTATT-ATAA-TA
1692721 TT-TTATTATAATA
1 TTATTATTATAATA
1692734 TT
1 TT
1692736 TTAATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 8 0.29
16 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATTATAATA
Found at i:1695676 original size:21 final size:20
Alignment explanation
Indices: 1695629--1695674 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1695619 AATAAACACC
*
1695629 AAAAATTTATTTTAAAAATA
1 AAAAAATTATTTTAAAAATA
*
1695649 AAAAAATTATTTTAAAATTA
1 AAAAAATTATTTTAAAAATA
1695669 AAAAAA
1 AAAAAA
1695675 ATAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTATTTTAAAAATA
Found at i:1714003 original size:29 final size:30
Alignment explanation
Indices: 1713947--1714041 Score: 140
Period size: 29 Copynumber: 3.2 Consensus size: 30
1713937 ACAAAAATAA
*
1713947 AAAATTACATTTTGACCCCTAAAATTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTTC
1713977 AAAATTACATTTT-ACCCCTAAACTTTTT-
1 AAAATTACATTTTGACCCCTAAACTTTTTC
* **
1714005 TAAATTACATTTTGACCCCTAAACTTTCCC
1 AAAATTACATTTTGACCCCTAAACTTTTTC
1714035 AAAATTA
1 AAAATTA
1714042 TGTTTCGGCC
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
28 12 0.21
29 27 0.47
30 19 0.33
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAACTTTTTC
Found at i:1714401 original size:3 final size:3
Alignment explanation
Indices: 1714395--1714426 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1714385 AAGCTAAAGA
1714395 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1714427 AGAAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1714562 original size:14 final size:13
Alignment explanation
Indices: 1714543--1714577 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1714533 CCAAAGCAAA
1714543 AAAAAAAAAACCAG
1 AAAAAAAAAA-CAG
*
1714557 AAAAAAGAAACAG
1 AAAAAAAAAACAG
1714570 AAAAAAAA
1 AAAAAAAA
1714578 TCATAATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAG
Found at i:1714625 original size:19 final size:19
Alignment explanation
Indices: 1714601--1714640 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1714591 CCATTTTCAG
1714601 CAGGCCCAA-CGCAGCAGGC
1 CAGGCCCAAGC-CAGCAGGC
1714620 CAGGCCCAAGCCAGCAGGC
1 CAGGCCCAAGCCAGCAGGC
1714639 CA
1 CA
1714641 CCAGCAGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.42, G:0.30, T:0.00
Consensus pattern (19 bp):
CAGGCCCAAGCCAGCAGGC
Found at i:1714723 original size:10 final size:10
Alignment explanation
Indices: 1714708--1714788 Score: 91
Period size: 10 Copynumber: 8.5 Consensus size: 10
1714698 TTAGCCCAGC
1714708 AGAAAAAAAA
1 AGAAAAAAAA
* *
1714718 AGAAAAGAGA
1 AGAAAAAAAA
*
1714728 AGGAAAAAAA
1 AGAAAAAAAA
1714738 AG-AAAAAAA
1 AGAAAAAAAA
1714747 AG-AAAAAAA
1 AGAAAAAAAA
1714756 AGAAAGAAAAA
1 AGAAA-AAAAA
1714767 AG---AAAAA
1 AGAAAAAAAA
1714774 AGAAAAAAAA
1 AGAAAAAAAA
1714784 AGAAA
1 AGAAA
1714789 TGGTTCAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
7 7 0.11
9 18 0.30
10 29 0.48
11 7 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:1714728 original size:7 final size:7
Alignment explanation
Indices: 1714713--1714781 Score: 72
Period size: 7 Copynumber: 9.9 Consensus size: 7
1714703 CCAGCAGAAA
1714713 AAAAAAG
1 AAAAAAG
*
1714720 AAAAGAG
1 AAAAAAG
1714727 AAGGAAAA-
1 AA--AAAAG
1714735 AAAAGAA-
1 AAAA-AAG
1714742 AAAAAAG
1 AAAAAAG
1714749 AAAAAA-
1 AAAAAAG
*
1714755 AAGAAAG
1 AAAAAAG
1714762 AAAAAAG
1 AAAAAAG
1714769 AAAAAAG
1 AAAAAAG
1714776 AAAAAA
1 AAAAAA
1714782 AAAGAAATGG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
6 9 0.17
7 39 0.74
8 2 0.04
9 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1714735 original size:1 final size:1
Alignment explanation
Indices: 1714731--1714784 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
1714721 AAAGAGAAGG
* * * * * *
1714731 AAAAAAAAGAAAAAAAAGAAAAAAAAGAAAGAAAAAAGAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1714785 GAAATGGTTC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:1714736 original size:18 final size:16
Alignment explanation
Indices: 1714708--1714788 Score: 62
Period size: 17 Copynumber: 4.9 Consensus size: 16
1714698 TTAGCCCAGC
*
1714708 AGAAAAAAAAAGAAAA
1 AGAAGAAAAAAGAAAA
1714724 GAGAAGGAAAAAA-AAGAA
1 -AGAA-GAAAAAAGAA-AA
1714742 A-AA-AAAGAAA-AAAA
1 AGAAGAAA-AAAGAAAA
1714756 AGAAAGAAAAAAGAAAAA
1 AG-AAGAAAAAAG-AAAA
*
1714774 AGAAAAAAAAAGAAA
1 AGAAGAAAAAAGAAA
1714789 TGGTTCAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
14 6 0.11
15 5 0.09
16 10 0.19
17 19 0.35
18 14 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAGAAAAAAGAAAA
Found at i:1714751 original size:29 final size:29
Alignment explanation
Indices: 1714711--1714788 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1714701 GCCCAGCAGA
* *
1714711 AAAAAAAAGAAAAGAGAAGGAA-AAAAAAG
1 AAAAAAAAGAAAA-AAAAGAAAGAAAAAAG
1714740 AAAAAAAAGAAAAAAAAGAAAGAAAAAAG
1 AAAAAAAAGAAAAAAAAGAAAGAAAAAAG
*
1714769 AAAAAAGA-AAAAAAAAGAAA
1 AAAAAAAAGAAAAAAAAGAAA
1714789 TGGTTCAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 18 0.40
29 27 0.60
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (29 bp):
AAAAAAAAGAAAAAAAAGAAAGAAAAAAG
Found at i:1714762 original size:37 final size:38
Alignment explanation
Indices: 1714711--1714788 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
1714701 GCCCAGCAGA
*
1714711 AAAAAAAAGAAAAGAGAAGGAA-AAAAAAG-AAAAAAAAG
1 AAAAAAAAGAAAAGA-AA-AAAGAAAAAAGAAAAAAAAAG
1714749 AAAAAAAAG-AAAGAAAAAAGAAAAAAGAAAAAAAAAG
1 AAAAAAAAGAAAAGAAAAAAGAAAAAAGAAAAAAAAAG
1714786 AAA
1 AAA
1714789 TGGTTCAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 2 0.05
36 9 0.24
37 17 0.46
38 9 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (38 bp):
AAAAAAAAGAAAAGAAAAAAGAAAAAAGAAAAAAAAAG
Found at i:1714765 original size:28 final size:26
Alignment explanation
Indices: 1714710--1714788 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 26
1714700 AGCCCAGCAG
*
1714710 AAAAAAAAAGAAAAGAGAAGGAAAAAAA
1 AAAAAAAAAGAAAA-A-AAAGAAAAAAA
1714738 AGAAAAAAAAGAAAAAAAAGAAAGAAAA
1 A-AAAAAAAAGAAAAAAAAGAAA-AAAA
*
1714766 AAGAAAAAAGAAAAAAAAAGAAA
1 AAAAAAAAAG-AAAAAAAAGAAA
1714789 TGGTTCAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.30
28 19 0.41
29 13 0.28
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAAAGAAAAAAA
Found at i:1715130 original size:20 final size:22
Alignment explanation
Indices: 1715100--1715139 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1715090 TGTAAATATT
1715100 CAAACAAATTT-CGTGTTTTCA
1 CAAACAAATTTCCGTGTTTTCA
1715121 CAAA-AAATTTCCGTGTTTT
1 CAAACAAATTTCCGTGTTTT
1715140 GAAATTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
CAAACAAATTTCCGTGTTTTCA
Found at i:1715316 original size:37 final size:37
Alignment explanation
Indices: 1715170--1715360 Score: 123
Period size: 37 Copynumber: 5.2 Consensus size: 37
1715160 ATAATTTTTC
* * * *
1715170 TCGTG-TTTC-AAAAAATTCTCGTGTTTTAAAAAAATT
1 TCGTGTTTTCTAAAAACTTC-CGTGTATCAAAAAATTT
* * * **
1715206 CCGTGTTTTC--AAAACTTTTCGTGTTTC-AAAAATAC
1 TCGTGTTTTCTAAAAAC-TTCCGTGTATCAAAAAATTT
* * *
1715241 TCGTGTTTT-TTAAAACTTTCGTGTTTCAAAAAAATTT
1 TCGTGTTTTCTAAAAACTTCCGTGTATC-AAAAAATTT
*
1715278 TCGTGTTTTC-AAAAA-TTCTGAT-TATCAAAGAAATTTT
1 TCGTGTTTTCTAAAAACTTCCG-TGTATCAAA-AAA-TTT
*
1715315 TCGTTTTTTTCTAAAAACTTCCGTGTATC-AAAAATTT
1 TCG-TGTTTTCTAAAAACTTCCGTGTATCAAAAAATTT
1715352 TCGTGTTTT
1 TCGTGTTTT
1715361 TTTTTTAAAT
Statistics
Matches: 124, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
35 27 0.22
36 34 0.27
37 38 0.31
38 9 0.07
39 8 0.06
40 8 0.06
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (37 bp):
TCGTGTTTTCTAAAAACTTCCGTGTATCAAAAAATTT
Found at i:1715394 original size:21 final size:20
Alignment explanation
Indices: 1715370--1715411 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1715360 TTTTTTTAAA
1715370 TTCCGGTTTTTTAAAAAAATT
1 TTCC-GTTTTTTAAAAAAATT
* *
1715391 TTCCGTGTTTTCAAAAAATT
1 TTCCGTTTTTTAAAAAAATT
1715411 T
1 T
1715412 CTCCTGTTTC
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:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (20 bp):
TTCCGTTTTTTAAAAAAATT
Found at i:1715505 original size:18 final size:18
Alignment explanation
Indices: 1715108--1715514 Score: 154
Period size: 18 Copynumber: 21.9 Consensus size: 18
1715098 TTCAAACAAA
1715108 TTTCGTGTTTTCACAAAAAAT
1 TTTCGTGTTTT---AAAAAAT
* *
1715129 TTCCGTGTTTT--GAAAT
1 TTTCGTGTTTTAAAAAAT
* *
1715145 TTTCGTGGCTTCAAAATAATTT
1 TTTCGT-GTTTTAAAA-AA--T
*
1715167 TTCTCGTGTTTCAAAAAAT
1 TT-TCGTGTTTTAAAAAAT
* *
1715186 TCTCGTGTTTTAAAAAAA
1 TTTCGTGTTTTAAAAAAT
* * *
1715204 TTCCGTGTTTTCAAAACT
1 TTTCGTGTTTTAAAAAAT
*
1715222 TTTCGTG-TTTCAAAAAT
1 TTTCGTGTTTTAAAAAAT
** ** *
1715239 ACTCGTGTTTTTTAAAAC
1 TTTCGTGTTTTAAAAAAT
*
1715257 TTTCGTGTTTCAAAAAAAT
1 TTTCGTGTTT-TAAAAAAT
*
1715276 TTTCGTGTTTTCAAAAA-
1 TTTCGTGTTTTAAAAAAT
*
1715293 -TTC-TGATTATCAAAGAAATT
1 TTTCGTG-TT-TTAAA-AAA-T
* * *
1715313 TTTCGTTTTTTTCTAAAAAC
1 TTTCG-TGTTTT-AAAAAAT
* * *
1715333 TTCCGTG-TATCAAAAAT
1 TTTCGTGTTTTAAAAAAT
***
1715350 TTTCGTGTTTTTTTTTTAAA-
1 TTTCGTG---TTTTAAAAAAT
* *
1715370 TTCCGGTTTTTTAAAAAAAT
1 TTTC-GTGTTTT-AAAAAAT
1715390 TTTCCGTGTTTTCAAAAAAT
1 TTT-CGTGTTTT-AAAAAAT
* *
1715410 TTCTCCTG-TTT-CAAAAT
1 TT-TCGTGTTTTAAAAAAT
* *
1715427 TGTCGTGTTTTCAAAAAT
1 TTTCGTGTTTTAAAAAAT
* *
1715445 TTTCGTGTTTTTAAGAAT
1 TTTCGTGTTTTAAAAAAT
*
1715463 TTTCGTGTCTCT--AAAAT
1 TTTCGTGT-TTTAAAAAAT
*
1715480 TCTCGTGTTTTAAAAAAT
1 TTTCGTGTTTTAAAAAAT
* *
1715498 TTTAGTGTGTTAAAAAA
1 TTTCGTGTTTTAAAAAA
1715515 AAAGTTTCAA
Statistics
Matches: 285, Mismatches: 69, Indels: 67
0.68 0.16 0.16
Matches are distributed among these distances:
15 2 0.01
16 20 0.07
17 51 0.18
18 109 0.38
19 26 0.09
20 29 0.10
21 28 0.10
22 15 0.05
23 5 0.02
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTCGTGTTTTAAAAAAT
Found at i:1719055 original size:11 final size:11
Alignment explanation
Indices: 1719015--1719047 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1719005 CTGTTTACCG
1719015 TTGTTTTGCTA
1 TTGTTTTGCTA
1719026 TTGTTTTGCTA
1 TTGTTTTGCTA
1719037 TTGTTTTGCTA
1 TTGTTTTGCTA
1719048 CTATTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (11 bp):
TTGTTTTGCTA
Found at i:1719062 original size:22 final size:22
Alignment explanation
Indices: 1719014--1719063 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1719004 GCTGTTTACC
* *
1719014 GTTGTTTTGCTATTGTTTTGCT
1 GTTGTTTTGCTACTATTTTGCT
* *
1719036 ATTGTTTTGCTACTATTTTGTT
1 GTTGTTTTGCTACTATTTTGCT
1719058 GTTGTT
1 GTTGTT
1719064 ATTTGAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (22 bp):
GTTGTTTTGCTACTATTTTGCT
Found at i:1725885 original size:19 final size:20
Alignment explanation
Indices: 1725856--1725905 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1725846 AATATATAAG
1725856 TTTTGGAATTTTTATAAA-TA
1 TTTT-GAATTTTTATAAATTA
1725876 TTTTGAA-TTTTATAAATTA
1 TTTTGAATTTTTATAAATTA
1725895 TTTTG-ATTTTT
1 TTTTGAATTTTT
1725906 TTTTGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.36
19 14 0.50
20 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTTTATAAATTA
Found at i:1725886 original size:18 final size:18
Alignment explanation
Indices: 1725830--1725904 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 18
1725820 CTTTTTAAAC
*
1725830 TTTTATAAA-ATTTTAAA
1 TTTTATAAATATTTTGAA
* * * *
1725847 ATATATAAGT-TTTGGAA
1 TTTTATAAATATTTTGAA
1725864 TTTTTATAAATATTTTGAA
1 -TTTTATAAATATTTTGAA
1725883 TTTTATAAATTATTTTG-A
1 TTTTATAAA-TATTTTGAA
1725901 TTTT
1 TTTT
1725905 TTTTTGTAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
17 11 0.24
18 21 0.47
19 13 0.29
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTTATAAATATTTTGAA
Found at i:1734924 original size:2 final size:2
Alignment explanation
Indices: 1734917--1734945 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1734907 TTAAAAAGAC
1734917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1734946 TAAATTGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1739775 original size:6 final size:6
Alignment explanation
Indices: 1739764--1739816 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
1739754 ATCGCAAAGA
1739764 AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG
1 AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG AAATAG
1739812 AAATA
1 AAATA
1739817 AAGAACACAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (6 bp):
AAATAG
Found at i:1741128 original size:67 final size:67
Alignment explanation
Indices: 1741045--1741178 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
1741035 ACTTAGGTAC
1741045 AATTTACTTATTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTCTTTGCTGGTCCCAAATC
1 AATTTACTTATTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTCTTTGCTGGTCCCAAATC
1741110 TT
66 TT
*
1741112 AATTTACTTATTTTTCTATCTTTGAGAATCTCCATACCAAGTATCTTCTTTGCTGGTCCCAAATC
1 AATTTACTTATTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTCTTTGCTGGTCCCAAATC
1741177 TT
66 TT
1741179 TCATCTCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (67 bp):
AATTTACTTATTTTTCTATCTCTGAGAATCTCCATACCAAGTATCTTCTTTGCTGGTCCCAAATC
TT
Found at i:1746666 original size:19 final size:18
Alignment explanation
Indices: 1746631--1746668 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1746621 TGGTTTTCTC
*
1746631 AAAATGGAAATAGAAATG
1 AAAATGAAAATAGAAATG
1746649 AAAATGAAAATCAGAAATG
1 AAAATGAAAAT-AGAAATG
1746668 A
1 A
1746669 TTCATTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.63, C:0.03, G:0.18, T:0.16
Consensus pattern (18 bp):
AAAATGAAAATAGAAATG
Found at i:1748161 original size:37 final size:37
Alignment explanation
Indices: 1748108--1748181 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
1748098 TCAGTTTTTC
* **
1748108 GTGACGTTTTAGAAATGCCACGGGCTAGAAAATATTT
1 GTGACATTTTAGAAATGCCACGAACTAGAAAATATTT
* * *
1748145 GTGACATTTTATAAATGTCATGAACTAGAAAATATTT
1 GTGACATTTTAGAAATGCCACGAACTAGAAAATATTT
1748182 CTTTTCAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (37 bp):
GTGACATTTTAGAAATGCCACGAACTAGAAAATATTT
Found at i:1760812 original size:20 final size:19
Alignment explanation
Indices: 1760778--1760815 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1760768 CCCTAAACTT
*
1760778 TAAAACTCAAACCTTAAAC
1 TAAAACACAAACCTTAAAC
1760797 TAAAACACATAACCTTAAA
1 TAAAACACA-AACCTTAAA
1760816 TCTTAACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAACACAAACCTTAAAC
Found at i:1760896 original size:14 final size:14
Alignment explanation
Indices: 1760856--1760930 Score: 57
Period size: 14 Copynumber: 5.2 Consensus size: 14
1760846 TAATAATCAT
1760856 AATCCATAAACACTA
1 AATCC-TAAACACTA
* *
1760871 GAA-CATATAACATTA
1 -AATCCTA-AACACTA
1760886 AATCCTAAACACTA
1 AATCCTAAACACTA
1760900 AATCCTAAAC-CTA
1 AATCCTAAACACTA
*
1760913 GAAT-CTCAAACCCTA
1 -AATCCT-AAACACTA
1760928 AAT
1 AAT
1760931 AAAAATATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
13 5 0.10
14 30 0.60
15 13 0.26
16 2 0.04
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.23
Consensus pattern (14 bp):
AATCCTAAACACTA
Found at i:1761368 original size:21 final size:21
Alignment explanation
Indices: 1761331--1761371 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1761321 CTCAAACACA
*
1761331 TTAAACCCATATATCTTAAAC
1 TTAAACCCATACATCTTAAAC
1761352 TTAAACCC-TACACTCTTAAA
1 TTAAACCCATACA-TCTTAAA
1761372 TATATAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAACCCATACATCTTAAAC
Found at i:1761646 original size:16 final size:16
Alignment explanation
Indices: 1761622--1761670 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
1761612 TTCGCTGTAT
1761622 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
1761638 TGGATTAGAGGCGTAA
1 TGGAATAGAGGCGTAA
1761654 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
1761670 T
1 T
1761671 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:1761701 original size:45 final size:44
Alignment explanation
Indices: 1761650--1761739 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
1761640 GATTAGAGGC
1761650 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
1761695 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
1761739 G
1 G
1761740 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 23 0.55
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:1761921 original size:16 final size:16
Alignment explanation
Indices: 1761884--1761925 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1761874 TTAATCATAT
*
1761884 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
1761900 TT-AAATATATTATAA
1 TTAAAATATATTATAA
1761915 TTAAAATATAT
1 TTAAAATATAT
1761926 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:1761932 original size:14 final size:15
Alignment explanation
Indices: 1761893--1761934 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1761883 TTTAAACATA
*
1761893 ATTATTATTAAATAT
1 ATTATAATTAAATAT
1761908 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
1761922 A-TATAATTTAATA
1 ATTATAATTAAATA
1761935 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:1761984 original size:61 final size:61
Alignment explanation
Indices: 1761919--1762106 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
1761909 TTATAATTAA
1761919 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
* * * * * * * * *
1761980 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATAAATTTACTCA-AATCAT
* *
1762039 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
1762100 AATATAT
1 AATATAT
1762107 GATACTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 31 0.32
60 23 0.24
61 37 0.38
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATAAATTTACTCAAATCAT
Found at i:1762030 original size:120 final size:121
Alignment explanation
Indices: 1761887--1762179 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 121
1761877 ATCATATTTA
1761887 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
1761952 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
*
1762007 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
1762072 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* * *
1762128 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
1762180 TAAAATAATT
Statistics
Matches: 165, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 163 0.99
121 2 0.01
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:1762043 original size:59 final size:59
Alignment explanation
Indices: 1761887--1762183 Score: 184
Period size: 59 Copynumber: 5.0 Consensus size: 59
1761877 ATCATATTTA
* * * *
1761887 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAAT
* * * * *
1761946 AATCA-ATATTCTTATATAAATTTACTCA-AATCATAATATATGATACT-ATAAAA-TATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATGAT-CTAATAAAATTATAAA-T
* * * *
1762007 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAAT
* * * * * * *
1762066 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAA-GATAATT
1 AACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATGAT-CTAATAAAATTATAA-A
1762126 T
59 T
* * *
1762127 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT-TAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAA
1762184 ATAATTATAA
Statistics
Matches: 177, Mismatches: 39, Indels: 45
0.68 0.15 0.17
Matches are distributed among these distances:
57 10 0.06
58 11 0.06
59 56 0.32
60 28 0.16
61 51 0.29
62 12 0.07
63 9 0.05
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (59 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATCTAATAAAATTATAAAT
Found at i:1762052 original size:14 final size:15
Alignment explanation
Indices: 1762003--1762054 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1761993 ATAAAATATA
1762003 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
1762018 TATTAAATATATTAT
1 AATTAAATATATTAT
1762033 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
1762046 AATTTAATA
1 AATTAAATA
1762055 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:1762279 original size:27 final size:27
Alignment explanation
Indices: 1762226--1762296 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 27
1762216 TTTGTATAAT
* * *
1762226 TTAA-AATAAT-TATTATTACATATAA
1 TTAATAATAATATATAATTTCATAAAA
1762251 TTAATAATAATATATAATTTCATAAAA
1 TTAATAATAATATATAATTTCATAAAA
**
1762278 TTCTTAATAATA-A-AATTTC
1 TTAATAATAATATATAATTTC
1762297 TTATATGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 10 0.26
26 7 0.18
27 22 0.56
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAATAATAATATATAATTTCATAAAA
Found at i:1762483 original size:22 final size:22
Alignment explanation
Indices: 1762458--1762502 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1762448 ACTTAGCTTG
1762458 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
1762480 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
1762502 A
1 A
1762503 GTTAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTCATTAAATTACTTTCAA
Found at i:1765230 original size:20 final size:19
Alignment explanation
Indices: 1765207--1765265 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1765197 ACTCAAACAT
1765207 ATAACTTTAAACCCTAAACC
1 ATAA-TTTAAACCCTAAACC
1765227 ATAATCTTAAACCCTAAACC
1 ATAAT-TTAAACCCTAAACC
* **
1765247 TTAAGTACAAACCCTAAAC
1 ATAA-TTTAAACCCTAAAC
1765266 TCAAACCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAATTTAAACCCTAAACC
Found at i:1765422 original size:21 final size:21
Alignment explanation
Indices: 1765398--1765471 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
1765388 CATAACCTTG
1765398 AATCTTAAACCACAAACCCTA
1 AATCTTAAACCACAAACCCTA
* * *
1765419 AATCTAAAAACATAAACCCTA
1 AATCTTAAACCACAAACCCTA
* *
1765440 AA-CTCAAA-CACATAACACTA
1 AATCTTAAACCACA-AACCCTA
*
1765460 AACCCTTAAACC
1 AA-TCTTAAACC
1765472 TTATACCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 13 0.31
21 20 0.48
22 5 0.12
23 1 0.02
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (21 bp):
AATCTTAAACCACAAACCCTA
Found at i:1766006 original size:35 final size:34
Alignment explanation
Indices: 1765906--1766028 Score: 117
Period size: 35 Copynumber: 3.5 Consensus size: 34
1765896 GAACACATTC
* *
1765906 AACCATAAACCCAAACCTTGAATCCTAAACTCAT
1 AACCATAAACCCAAACCTTTAAACCTAAACTCAT
* *
1765940 AACTCAT-AACCCTAAACCATTACACCTTAAACTCA-
1 AAC-CATAAACCC-AAACCTTTAAACC-TAAACTCAT
*
1765975 AACCATAAATCCCAAACCTTTAAACCATAAAC-CTT
1 AACCATAAA-CCCAAACCTTTAAACC-TAAACTCAT
*
1766010 AACCTTAAACCACAAACCT
1 AACCATAAACC-CAAACCT
1766029 AAACCCTAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
34 14 0.19
35 48 0.66
36 11 0.15
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (34 bp):
AACCATAAACCCAAACCTTTAAACCTAAACTCAT
Found at i:1766019 original size:20 final size:20
Alignment explanation
Indices: 1765946--1766038 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
1765936 TCATAACTCA
* *
1765946 TAACCCTAAACCATTACACCT
1 TAACCTTAAACCA-TAAACCT
* * *
1765967 TAAACTCAAACCATAAATCCC
1 TAACCTTAAACCATAAA-CCT
*
1765988 AAACCTTTAAACCATAAACCT
1 TAACC-TTAAACCATAAACCT
*
1766009 TAACCTTAAACCACAAACCT
1 TAACCTTAAACCATAAACCT
* *
1766029 AAACCCTAAA
1 TAACCTTAAA
1766039 TCTAAAATCT
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
20 25 0.44
21 21 0.37
22 11 0.19
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.20
Consensus pattern (20 bp):
TAACCTTAAACCATAAACCT
Found at i:1766183 original size:25 final size:22
Alignment explanation
Indices: 1766140--1766184 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
1766130 TTACTATTTT
*
1766140 TAAAAAAAAAATTAGTTGCATA
1 TAAAAAAAAAATTACTTGCATA
1766162 TAAATAAAAAACATTAACTTGCA
1 TAAA-AAAAAA-ATT-ACTTGCA
1766185 CAAAATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 3 0.16
25 6 0.32
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.27
Consensus pattern (22 bp):
TAAAAAAAAAATTACTTGCATA
Found at i:1767264 original size:21 final size:22
Alignment explanation
Indices: 1767223--1767265 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1767213 TTAACTATTC
*
1767223 AAATATGATTTATGAGTATTTT
1 AAATATGATTTATGAGAATTTT
1767245 AAATATG-TTTATTGA-AATTTT
1 AAATATGATTTA-TGAGAATTTT
1767266 GTGTATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
AAATATGATTTATGAGAATTTT
Found at i:1767585 original size:33 final size:31
Alignment explanation
Indices: 1767543--1767621 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
1767533 TAAATTGTTT
1767543 TTGTATTGGTTATTGTCTATCATGTTGTATTAAA
1 TTGT-TTGGTTATTGTC-AT-ATGTTGTATTAAA
* *
1767577 TTGTTTGGTCATTG-CCTATGTTGTATTAAA
1 TTGTTTGGTTATTGTCATATGTTGTATTAAA
*
1767607 TTGTTTGGTTGTTGT
1 TTGTTTGGTTATTGT
1767622 TTGCCTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 25 0.62
31 1 0.03
32 1 0.03
33 9 0.22
34 4 0.10
ACGTcount: A:0.18, C:0.06, G:0.22, T:0.54
Consensus pattern (31 bp):
TTGTTTGGTTATTGTCATATGTTGTATTAAA
Found at i:1770088 original size:21 final size:21
Alignment explanation
Indices: 1770062--1770113 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1770052 CAAGTGGTTG
1770062 CCCCAACTCAGCAACAGACTA
1 CCCCAACTCAGCAACAGACTA
* * * *
1770083 CCCCAAATCAGTAAGAGACTG
1 CCCCAACTCAGCAACAGACTA
1770104 CCCCAACTCA
1 CCCCAACTCA
1770114 ATAGGAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.40, G:0.12, T:0.12
Consensus pattern (21 bp):
CCCCAACTCAGCAACAGACTA
Done.