Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 7 of 85
Found at i:2502782 original size:19 final size:19
Alignment explanation
Indices: 2502754--2502793 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
2502744 ATAGGGAAAG
2502754 AAAAAAAAATTAAA-AGAA
1 AAAAAAAAATTAAAGAGAA
2502772 AAAACAAAAATTAAAGAGAA
1 AAAA-AAAAATTAAAGAGAA
2502792 AA
1 AA
2502794 TATGGTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAAATTAAAGAGAA
Found at i:2511555 original size:105 final size:105
Alignment explanation
Indices: 2511320--2511633 Score: 344
Period size: 105 Copynumber: 3.0 Consensus size: 105
2511310 TGTGATATTG
* * * * * *
2511320 TCACATATAATATATTGATCGATGCACATTGTAAGGAGGGGATGATTTATAAAGCTGTAGATATC
1 TCACGTATAATATATTTATTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATATC
* * * * *
2511385 GTTGATACAATG-GTGAAGCAAGGCATTGAACCTAATATTG
66 GTTGACACAATGAG-AAAGCAAGGCATTGAGCCTAATGTTA
* * *
2511425 TCACGTATAATATATTTATTGATGCATATTGCAAGGAGGGGATGGTTTCTAAAGCTGTAGAAACC
1 TCACGTATAATATATTTATTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATATC
*
2511490 ATTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
66 GTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
* * ** ** * *
2511530 TCACGTATAATATA-TTAGTTTATGCATATTTTAACAAGGCAATGGTTTCTGAAGCTGAAGATAT
1 TCACGTATAATATATTTA-TTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATAT
* * * * *
2511594 TGTTGACACAATGATAAAGCAGGGTATTGAGCCTGATGTT
65 CGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTT
2511634 GTTACCTATA
Statistics
Matches: 175, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
104 3 0.02
105 171 0.98
106 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (105 bp):
TCACGTATAATATATTTATTGATGCATATTGTAAGGAGGGGATGGTTTCTAAAGCTGTAGATATC
GTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
Found at i:2525239 original size:14 final size:14
Alignment explanation
Indices: 2525220--2525253 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2525210 TCATCATTTG
2525220 CCTATAACCAAAAC
1 CCTATAACCAAAAC
*
2525234 CCTATAACTAAAAC
1 CCTATAACCAAAAC
2525248 CC-ATAA
1 CCTATAA
2525254 ACCCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:2525516 original size:141 final size:142
Alignment explanation
Indices: 2525346--2525629 Score: 498
Period size: 141 Copynumber: 2.0 Consensus size: 142
2525336 AGAAGTAGAA
2525346 GAGAATGGAAAATAAAGAAAAAAGAAAGAAAGAAAGTTAAAAGAACATAAAAGAATTAAATTGCT
1 GAGAATGGAAAATAAAG-AAAAAGAAAGAAAGAAAGTTAAAAGAACATAAAAGAATTAAATTGCT
*
2525411 CAAAACGAAAAATTATGGGGACCAATTGTATAATTTAACCTAAAATTTTTATTTGAAATGATAAT
65 CAAAACGAAAAATTATGGGGACCAATTGTACAATTTAACCTAAAATTTTTATTTGAAATGATAAT
2525476 TTAACGTGCCACG
130 TTAACGTGCCACG
*
2525489 GAGAATGGAAAATAAAG-AAAAGAAAGAAAGAAAGTTAAAATAACATAAAAGAATTAAATTGCTC
1 GAGAATGGAAAATAAAGAAAAAGAAAGAAAGAAAGTTAAAAGAACATAAAAGAATTAAATTGCTC
* * *
2525553 AAAATGAAAAATTATGGGGACCAATTGTACAATTTAACCTAAAGTTTTTGTTTGAAATGATAATT
66 AAAACGAAAAATTATGGGGACCAATTGTACAATTTAACCTAAAATTTTTATTTGAAATGATAATT
*
2525618 TAACGTGTCACG
131 TAACGTGCCACG
2525630 TCAGCTTACC
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
141 118 0.87
143 17 0.13
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (142 bp):
GAGAATGGAAAATAAAGAAAAAGAAAGAAAGAAAGTTAAAAGAACATAAAAGAATTAAATTGCTC
AAAACGAAAAATTATGGGGACCAATTGTACAATTTAACCTAAAATTTTTATTTGAAATGATAATT
TAACGTGCCACG
Found at i:2525892 original size:23 final size:22
Alignment explanation
Indices: 2525849--2525892 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2525839 TACAAAATAG
* *
2525849 TCATTGAATTATTGAATTGTTT
1 TCATTGAATTATTCAACTGTTT
*
2525871 TCATTTAAGTTATTCAACTGTT
1 TCATTGAA-TTATTCAACTGTT
2525893 AAATTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.52
Consensus pattern (22 bp):
TCATTGAATTATTCAACTGTTT
Found at i:2529856 original size:5 final size:5
Alignment explanation
Indices: 2529833--2529890 Score: 66
Period size: 5 Copynumber: 11.4 Consensus size: 5
2529823 TTATGTTATG
*
2529833 TATAT TATTT TAT-T ATATAT TATAT TA-AT TATAT TATAT TATAT TATTAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT
2529883 ATATAT TA
1 -TATAT TA
2529891 AATAAAGTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
4 5 0.11
5 33 0.70
6 7 0.15
7 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:2529864 original size:19 final size:17
Alignment explanation
Indices: 2529828--2529890 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 17
2529818 GATTTTTATG
* *
2529828 TTATGTATATTATTTTA
1 TTATATATATTATATTA
2529845 -T-TATATATTATATTAA
1 TTATATATATTATATT-A
2529861 TTATATTATATTATATTA
1 TTATA-TATATTATATTA
2529879 TTATATATATTA
1 TTATATATATTA
2529891 AATAAAGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 11 0.28
16 2 0.05
17 8 0.20
18 8 0.20
19 11 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATATATATTATATTA
Found at i:2529888 original size:31 final size:29
Alignment explanation
Indices: 2529833--2529891 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
2529823 TTATGTTATG
2529833 TATATTATTTTATTATATATTATATTAAT
1 TATATTATTTTATTATATATTATATTAAT
2529862 TATATTATATTATATTAT-TATATATATTAA
1 TATATTAT-TT-TATTATATAT-TATATTAA
2529892 ATAAAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.30
30 5 0.19
31 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TATATTATTTTATTATATATTATATTAAT
Found at i:2538079 original size:25 final size:24
Alignment explanation
Indices: 2538051--2538106 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
2538041 TATTTGGGCT
2538051 ATATAACGGAAAGCTCATAAGAGCC
1 ATATAACGG-AAGCTCATAAGAGCC
* *
2538076 ATAT-TCAGGAAGCTCATACGAGCC
1 ATATAAC-GGAAGCTCATAAGAGCC
2538100 A-ATAACG
1 ATATAACG
2538107 AGTAACTCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
23 3 0.12
24 17 0.65
25 6 0.23
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (24 bp):
ATATAACGGAAGCTCATAAGAGCC
Found at i:2539767 original size:31 final size:29
Alignment explanation
Indices: 2539732--2539802 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 29
2539722 ACAATATCAT
2539732 ATTTAATACTTATATTTTGATGAAATATTTA
1 ATTTAATACTTATATTTTGA--AAATATTTA
* *
2539763 ATTTAATATTTTTATTTTGAAAATATTTA
1 ATTTAATACTTATATTTTGAAAATATTTA
* *
2539792 ATGTGATACTT
1 ATTTAATACTT
2539803 GAACTACCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 17 0.49
31 18 0.51
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTAATACTTATATTTTGAAAATATTTA
Found at i:2540016 original size:12 final size:12
Alignment explanation
Indices: 2539999--2540023 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2539989 AAGGCACATT
2539999 GTATTCTCAAAG
1 GTATTCTCAAAG
2540011 GTATTCTCAAAG
1 GTATTCTCAAAG
2540023 G
1 G
2540024 GAGATACAGA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (12 bp):
GTATTCTCAAAG
Found at i:2555362 original size:21 final size:21
Alignment explanation
Indices: 2555338--2555379 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2555328 CTCCACGACC
*
2555338 GCCTCCTCTACCACCACCTCT
1 GCCTCCTCCACCACCACCTCT
*
2555359 GCCTCCTCCACGACCACCTCT
1 GCCTCCTCCACCACCACCTCT
2555380 TCCACCACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.57, G:0.07, T:0.21
Consensus pattern (21 bp):
GCCTCCTCCACCACCACCTCT
Found at i:2557138 original size:20 final size:20
Alignment explanation
Indices: 2557071--2557138 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2557061 TCAAAATATA
* *
2557071 AATTCATATATTTATATTTT
1 AATTTATATAATTATATTTT
2557091 AATTTAT-TAATGGT-TATTTT
1 AATTTATATAAT--TATATTTT
* *
2557111 TATATTATATAATTAAATTTT
1 AAT-TTATATAATTATATTTT
2557132 AATTTAT
1 AATTTAT
2557139 TTTAAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.08
20 19 0.50
21 12 0.32
22 4 0.11
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (20 bp):
AATTTATATAATTATATTTT
Found at i:2563077 original size:13 final size:14
Alignment explanation
Indices: 2563059--2563087 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2563049 GTACTACAAG
2563059 ATTATTTT-TTTAA
1 ATTATTTTATTTAA
2563072 ATTATTTTATTTAA
1 ATTATTTTATTTAA
2563086 AT
1 AT
2563088 GTCTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTATTTAA
Found at i:2563503 original size:25 final size:25
Alignment explanation
Indices: 2563433--2563492 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
2563423 ACTTTAGCGC
2563433 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
2563458 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
*
2563483 GCTCTTTGAT
1 GCTCTCTGAT
2563493 ATTTAGTACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:2563553 original size:22 final size:21
Alignment explanation
Indices: 2563505--2563560 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2563495 TTAGTACGTC
* *
2563505 AGTGCTATCTGTTTAGCACAT
1 AGTGCTCTCTGTATAGCACAT
*
2563526 ATGTGCTCTCTGTATAGCACTTT
1 A-GTGCTCTCTGTATAGCAC-AT
2563549 AGTGCTCTCTGT
1 AGTGCTCTCTGT
2563561 TCATTAGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 27 0.90
23 2 0.07
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (21 bp):
AGTGCTCTCTGTATAGCACAT
Found at i:2568309 original size:67 final size:67
Alignment explanation
Indices: 2568201--2568332 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 67
2568191 TTTTCAATTC
*
2568201 AGAGAGCACACTCCCGTGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
2568266 CA
66 CA
2568268 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
2568333 TAATATAAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGAGATTACCAGTCCAGGCTAAATCCCCTG
CA
Found at i:2569473 original size:46 final size:46
Alignment explanation
Indices: 2569406--2569497 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
2569396 AACTCATAAT
2569406 AAATTTTTTTTTTACAATTTTTAATGATTTTCCAAAGTCAGAATAG
1 AAATTTTTTTTTTACAATTTTTAATGATTTTCCAAAGTCAGAATAG
2569452 AAATTTTTTTTTTACAATTTTTAATGATTTTCCAAAGTCAGAATAG
1 AAATTTTTTTTTTACAATTTTTAATGATTTTCCAAAGTCAGAATAG
2569498 GGGAAACCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (46 bp):
AAATTTTTTTTTTACAATTTTTAATGATTTTCCAAAGTCAGAATAG
Found at i:2570817 original size:19 final size:17
Alignment explanation
Indices: 2570772--2570820 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
2570762 TGATGAACTC
*
2570772 TTTTATAATTTTCTTGAA
1 TTTTGTAATTTT-TTGAA
2570790 TTTTG-AATTTTTTGAA
1 TTTTGTAATTTTTTGAA
2570806 TATCTTGTAATTTTT
1 T-T-TTGTAATTTTT
2570821 AAACTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.22
17 7 0.26
18 7 0.26
19 7 0.26
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.63
Consensus pattern (17 bp):
TTTTGTAATTTTTTGAA
Found at i:2580120 original size:7 final size:7
Alignment explanation
Indices: 2580108--2580133 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2580098 ATCATGAGTT
2580108 ACATGTG
1 ACATGTG
2580115 ACATGTG
1 ACATGTG
2580122 ACATGTG
1 ACATGTG
2580129 ACATG
1 ACATG
2580134 CCACATGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (7 bp):
ACATGTG
Found at i:2580139 original size:14 final size:14
Alignment explanation
Indices: 2580108--2580141 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2580098 ATCATGAGTT
**
2580108 ACATGTGACATGTG
1 ACATGTGACATGCC
2580122 ACATGTGACATGCC
1 ACATGTGACATGCC
2580136 ACATGT
1 ACATGT
2580142 CACTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (14 bp):
ACATGTGACATGCC
Found at i:2580218 original size:25 final size:25
Alignment explanation
Indices: 2580171--2580218 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2580161 TAGTCATACC
* * * *
2580171 AGTTTTTAATAATAGAAATAGATGA
1 AGTTTTTAACAAAAAAAAAAGATGA
2580196 AGTTTTTAACAAAAAAAAAAGAT
1 AGTTTTTAACAAAAAAAAAAGAT
2580219 TAATTTCCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (25 bp):
AGTTTTTAACAAAAAAAAAAGATGA
Found at i:2582026 original size:124 final size:124
Alignment explanation
Indices: 2581843--2582079 Score: 370
Period size: 124 Copynumber: 1.9 Consensus size: 124
2581833 CATGTACAAT
* * * * *
2581843 GTATTAATTATGTCATTTTAAGTTTTAGTTTAATGTATTGTAATAACGAGGATAACATAAGTTTA
1 GTATTAATTATGTCATTTTAAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
* *
2581908 AACGTGCTTAATCGTGTATTTCTCTTT-GATTTAAGAGTTTGAGAGGATTATAAGTAAAAC
66 AACGTGCTTAATCATGTATTT-T-TTTCAATTTAAGAGTTTGAGAGGATTATAAGTAAAAC
*
2581968 GTATTAATTATGTCA-TTTGAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
1 GTATTAATTATGTCATTTTAAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
2582032 AACGTGCTTAATCATGTATTTTTTTCAATTTAAGAGTTTGAGAGGATT
66 AACGTGCTTAATCATGTATTTTTTTCAATTTAAGAGTTTGAGAGGATT
2582080 TTAAACAAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
122 3 0.03
123 22 0.21
124 63 0.61
125 15 0.15
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.41
Consensus pattern (124 bp):
GTATTAATTATGTCATTTTAAGTTTCAGTTTAATCTATTGTAATAACCAGGAGAACATAAGTTCA
AACGTGCTTAATCATGTATTTTTTTCAATTTAAGAGTTTGAGAGGATTATAAGTAAAAC
Found at i:2593796 original size:22 final size:22
Alignment explanation
Indices: 2593734--2593798 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
2593724 CTCTAATTAT
* *
2593734 TAGCACATTAAG-GCTCTCCGTT
1 TAGCACATT-AGTGCTCTCTGTA
*
2593756 TAGCACATTCGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTA
*
2593778 TAGCACTTTAGTGCTCTCTGT
1 TAGCACATTAGTGCTCTCTGT
2593799 TCAATAATGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTA
Found at i:2598825 original size:11 final size:11
Alignment explanation
Indices: 2598803--2598854 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
2598793 AACTAATACT
2598803 CTCTCAAATTTC
1 CTCTC-AATTTC
2598815 CTCTCAATTTC
1 CTCTCAATTTC
*
2598826 CTCTAAATTTC
1 CTCTCAATTTC
*
2598837 CTCTCAATTTG
1 CTCTCAATTTC
2598848 CTCTCAA
1 CTCTCAA
2598855 ATTACTTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
11 32 0.86
12 5 0.14
ACGTcount: A:0.23, C:0.33, G:0.02, T:0.42
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:2598836 original size:22 final size:23
Alignment explanation
Indices: 2598803--2598857 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
2598793 AACTAATACT
2598803 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
2598826 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
2598848 CTCTCAAATT
1 CTCTCAAATT
2598858 ACTTCCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.44
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:2598868 original size:34 final size:34
Alignment explanation
Indices: 2598803--2598878 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
2598793 AACTAATACT
* *
2598803 CTCTCAAATTTCCTCTCAATTTCCTCTAAATTTC
1 CTCTCAAATTTCCTCTCAATTACCTCCAAATTTC
* *
2598837 CTCTC-AATTTGCTCTCAAATTACTTCCAAATTT-
1 CTCTCAAATTTCCTCTC-AATTACCTCCAAATTTC
*
2598870 CTCTAAAAT
1 CTCTCAAAT
2598879 CCATATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 14 0.40
34 21 0.60
ACGTcount: A:0.28, C:0.29, G:0.01, T:0.42
Consensus pattern (34 bp):
CTCTCAAATTTCCTCTCAATTACCTCCAAATTTC
Found at i:2598896 original size:51 final size:51
Alignment explanation
Indices: 2598838--2598937 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
2598828 CTAAATTTCC
*
2598838 TCTCAATTTGCTCTCAAATTACTTC-CAAATTTCTCTAAAATCCATATTTAA
1 TCTCAATTTGCTCTC-AATTACCTCTCAAATTTCTCTAAAATCCATATTTAA
* * * * *
2598889 TCTCAATTTTCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTACCTCTCAAATTTCTCTAAAATCCATATTT
2598938 TTAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 7 0.17
51 35 0.83
ACGTcount: A:0.28, C:0.25, G:0.01, T:0.46
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTACCTCTCAAATTTCTCTAAAATCCATATTTAA
Found at i:2599506 original size:30 final size:30
Alignment explanation
Indices: 2599472--2599529 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2599462 ACCGAAGTAA
2599472 AAAGAATCTGATATGCTCGGGCATACATAG
1 AAAGAATCTGATATGCTCGGGCATACATAG
2599502 AAAGAATCTGATATGCTCGGGCATACAT
1 AAAGAATCTGATATGCTCGGGCATACAT
2599530 TCTTCAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (30 bp):
AAAGAATCTGATATGCTCGGGCATACATAG
Found at i:2603598 original size:127 final size:126
Alignment explanation
Indices: 2603327--2603769 Score: 658
Period size: 125 Copynumber: 3.5 Consensus size: 126
2603317 CCAAACATGC
*
2603327 TACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTGC
1 TACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGC
*
2603391 TAGAAGCA-TTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACA
65 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACA
*
2603452 TACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTTTTCTCATAAAGCATCCTGCT
1 TACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
* *
2603517 TGAAGCATTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACT
66 TGAAGCA-TTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACA
** * * *
2603579 TACTGTAGCAAAAGCGCGTCCGTGAGGGCGTGATTTCACAAATTCTTTTCATATAGCATCCTGCT
1 TACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
* * *
2603644 TGAAGCGTTTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTT-TTCCAGGACC
66 TGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACA
* * * * * * * *
2603704 TACTGTAGCAAAAGCGCGTACAAGTGGGCGCGACTTCAGAAATCCTTCTGATAAAGCATTCTGCT
1 TACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
2603769 T
66 T
2603770 TGATTTTATC
Statistics
Matches: 288, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
125 129 0.45
126 43 0.15
127 116 0.40
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (126 bp):
TACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
TGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACA
Found at i:2603931 original size:15 final size:15
Alignment explanation
Indices: 2603894--2603941 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2603884 TAAAACTCTA
*
2603894 AAAATCCTAAAAACAT
1 AAAATCC-AAAAACCT
* * *
2603910 TAAATCCTAAACCCT
1 AAAATCCAAAAACCT
2603925 AAAATCCAAAAACCT
1 AAAATCCAAAAACCT
2603940 AA
1 AA
2603942 CGTGGGAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATCCAAAAACCT
Found at i:2613038 original size:93 final size:93
Alignment explanation
Indices: 2612879--2613050 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
2612869 CAGGGGCAGA
* *
2612879 AAATATCAACCTGCATAGTCTCAAATGAAGACAAATCGAAGAAATGATGCAACTTAAACAGTTTT
1 AAATATCAACCTGCAGAGTCTCAAATGAAGACAAATCGAAGAAATGATGCAACTTAAACAGGTTT
2612944 CTCATAAATATATATGTGTGTGAGAGAG
66 CTCATAAATATATATGTGTGTGAGAGAG
* * * ** *
2612972 AAATATCAGCTTGCAGAGTCTCAAATGAAGAGAAATCGGTGAAATGATGCAACTTCAACAGGTTT
1 AAATATCAACCTGCAGAGTCTCAAATGAAGACAAATCGAAGAAATGATGCAACTTAAACAGGTTT
*
2613037 CTCATATATATATA
66 CTCATAAATATATA
2613051 CATGTGTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (93 bp):
AAATATCAACCTGCAGAGTCTCAAATGAAGACAAATCGAAGAAATGATGCAACTTAAACAGGTTT
CTCATAAATATATATGTGTGTGAGAGAG
Found at i:2619692 original size:11 final size:12
Alignment explanation
Indices: 2619678--2619707 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2619668 ATTTTTTATA
2619678 TTTAAAATA-TT
1 TTTAAAATACTT
2619689 TTTAAAATACTT
1 TTTAAAATACTT
2619701 TTTAAAA
1 TTTAAAA
2619708 AAATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAAAATACTT
Found at i:2619717 original size:15 final size:16
Alignment explanation
Indices: 2619699--2619728 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2619689 TTTAAAATAC
2619699 TTTTTAAAA-AAATTA
1 TTTTTAAAATAAATTA
2619714 TTTTTAAAATAAATT
1 TTTTTAAAATAAATT
2619729 TGAAGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTAAAATAAATTA
Found at i:2634247 original size:19 final size:21
Alignment explanation
Indices: 2634225--2634302 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 21
2634215 TTATTAAATT
*
2634225 TTAGTAAAAATA-T-TAAAAA
1 TTAGTAAAAAAATTATAAAAA
2634244 TTAG-AAAAAAATTATAAAAA
1 TTAGTAAAAAAATTATAAAAA
*
2634264 TTA-T-AAAAAATTGT-AAAA
1 TTAGTAAAAAAATTATAAAAA
** *
2634282 TTTTTATAAAAATTATAAAAA
1 TTAGTAAAAAAATTATAAAAA
2634303 ATTCGAGTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 12 0.25
19 15 0.31
20 17 0.35
21 4 0.08
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
TTAGTAAAAAAATTATAAAAA
Found at i:2634273 original size:30 final size:30
Alignment explanation
Indices: 2634229--2634305 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
2634219 TAAATTTTAG
*
2634229 TAAAAA-TATTAAAAATTAG-AAAAAAATTA
1 TAAAAATTATAAAAAATT-GTAAAAAAATTA
***
2634258 TAAAAATTATAAAAAATTGTAAAATTTTTA
1 TAAAAATTATAAAAAATTGTAAAAAAATTA
2634288 TAAAAATTATAAAAAATT
1 TAAAAATTATAAAAAATT
2634306 CGAGTGTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 7 0.17
30 35 0.83
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (30 bp):
TAAAAATTATAAAAAATTGTAAAAAAATTA
Found at i:2634302 original size:9 final size:9
Alignment explanation
Indices: 2634189--2634302 Score: 68
Period size: 9 Copynumber: 11.8 Consensus size: 9
2634179 AATAATGAAA
*
2634189 ATAAAAATAA
1 ATAAAAAT-T
*
2634199 ATAAAAGTT
1 ATAAAAATT
*
2634208 ATAAAATTT
1 ATAAAAATT
**
2634217 ATTAAATTTT
1 A-TAAAAATT
2634227 AGTAAAAA-T
1 A-TAAAAATT
2634236 ATTAAAAATT
1 A-TAAAAATT
*
2634246 AGAAAAAAATT
1 --ATAAAAATT
2634257 ATAAAAATT
1 ATAAAAATT
2634266 ATAAAAAATT
1 AT-AAAAATT
* *
2634276 GTAAAATTTTT
1 ATAAAA--ATT
2634287 ATAAAAATT
1 ATAAAAATT
2634296 ATAAAAA
1 ATAAAAA
2634303 ATTCGAGTGT
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
9 40 0.48
10 28 0.34
11 14 0.17
12 1 0.01
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2635007 original size:32 final size:33
Alignment explanation
Indices: 2634948--2635014 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
2634938 AAAAATTGCA
*
2634948 ACATAAGCCCCTCTACTTTTTTTTATATAAATTT
1 ACATAAACCCCTCTAC-TTTTTTTATATAAATTT
2634982 ACATAAACCCCTCTAC-TTTTTTATATAAATTT
1 ACATAAACCCCTCTACTTTTTTTATATAAATTT
2635014 A
1 A
2635015 ATTGGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 17 0.53
34 15 0.47
ACGTcount: A:0.33, C:0.21, G:0.01, T:0.45
Consensus pattern (33 bp):
ACATAAACCCCTCTACTTTTTTTATATAAATTT
Found at i:2636400 original size:24 final size:24
Alignment explanation
Indices: 2636352--2636400 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2636342 AAATGTTCAT
* *
2636352 GGATTGATCAATCCTAGAATAAAG
1 GGATTGAGCAATCCTAGAACAAAG
*
2636376 GGATTGAGCAATCCTAGAACGAAG
1 GGATTGAGCAATCCTAGAACAAAG
2636400 G
1 G
2636401 AGGAAGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (24 bp):
GGATTGAGCAATCCTAGAACAAAG
Found at i:2639160 original size:87 final size:87
Alignment explanation
Indices: 2639030--2639205 Score: 271
Period size: 87 Copynumber: 2.0 Consensus size: 87
2639020 CCAACTGATT
* * *
2639030 AGGGGTCACTCTATTAGATAATCCAGAGGAACTAACACCAGAATCAGCACTTGGACCTGATAATG
1 AGGGATCACTCTATTAGATAATCCAGAAGAACTAACACCAGAATCACCACTTGGACCTGATAATG
*
2639095 AAGGTAACACTTCTGCAGTTCC
66 AAGGCAACACTTCTGCAGTTCC
* * ** *
2639117 AGGGATCACTCTATTAGATGATCCGGAAGAACTAACAGTAGAATCACCAGTTGGACCTGATAATG
1 AGGGATCACTCTATTAGATAATCCAGAAGAACTAACACCAGAATCACCACTTGGACCTGATAATG
2639182 AAGGCAACACTTCTGCAGTTCC
66 AAGGCAACACTTCTGCAGTTCC
2639204 AG
1 AG
2639206 TACTTGACCC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (87 bp):
AGGGATCACTCTATTAGATAATCCAGAAGAACTAACACCAGAATCACCACTTGGACCTGATAATG
AAGGCAACACTTCTGCAGTTCC
Found at i:2647046 original size:31 final size:31
Alignment explanation
Indices: 2647010--2647068 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2647000 AAATGGTCAT
*
2647010 TGAACTATTT-GAAAGTTTTTATTTAAATCAC
1 TGAACTATTTGGAAA-TTTTCATTTAAATCAC
2647041 TGAACTATTTGGAAATTTTCATTTAAAT
1 TGAACTATTTGGAAATTTTCATTTAAAT
2647069 TAATGAGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (31 bp):
TGAACTATTTGGAAATTTTCATTTAAATCAC
Found at i:2647080 original size:31 final size:31
Alignment explanation
Indices: 2647010--2647080 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
2647000 AAATGGTCAT
* *
2647010 TGAACTATTTGAAAGTTTTTATTTAAATCAC
1 TGAACTATTTGAAAGTTTTCATTTAAATCAA
*
2647041 TGAACTATTTGGAAA-TTTTCATTTAAATTAA
1 TGAACTATTT-GAAAGTTTTCATTTAAATCAA
*
2647072 TGAGCTATT
1 TGAACTATT
2647081 AATTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTCATTTAAATCAA
Found at i:2652062 original size:18 final size:18
Alignment explanation
Indices: 2652036--2652078 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2652026 TAATAAATAA
*
2652036 ATATTTTTTTAAT-TTTT
1 ATATTTTTTGAATGTTTT
2652053 ATACTTTTTTGAATGTTTT
1 ATA-TTTTTTGAATGTTTT
2652072 ATATTTT
1 ATATTTT
2652079 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
ATATTTTTTGAATGTTTT
Found at i:2652235 original size:23 final size:24
Alignment explanation
Indices: 2652199--2652247 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
2652189 TTATGCCTTA
* *
2652199 TTTTTTTATCAATGGAAGTAATTC
1 TTTTTATATCAATGCAAGTAATTC
*
2652223 TTTTTATAT-AATGCAAGTGATTC
1 TTTTTATATCAATGCAAGTAATTC
2652246 TT
1 TT
2652248 AAACAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (24 bp):
TTTTTATATCAATGCAAGTAATTC
Found at i:2660626 original size:22 final size:21
Alignment explanation
Indices: 2660574--2660637 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
2660564 TAAATATCCC
2660574 ATAAAAATATTTTAAAATATAT
1 ATAAAAA-ATTTTAAAATATAT
** *
2660596 ATGTCAAAATTTTAAAATTATTT
1 AT-AAAAAATTTTAAAA-TATAT
*
2660619 ATAAAAAATTAGTAAAATA
1 ATAAAAAATT-TTAAAATA
2660638 GTTAATTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (21 bp):
ATAAAAAATTTTAAAATATAT
Found at i:2661007 original size:24 final size:25
Alignment explanation
Indices: 2660971--2661027 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
2660961 AAAAGAGAAT
2660971 GAAAAAAAGTTAAAAGAA-CATAAAA
1 GAAAAAAAGTTAAAAGAATCA-AAAA
* *
2660996 GAAAAAAA-TTAAAATAATCAAAAT
1 GAAAAAAAGTTAAAAGAATCAAAAA
2661020 GAAAAAAA
1 GAAAAAAA
2661028 ATATAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 19 0.66
25 10 0.34
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.14
Consensus pattern (25 bp):
GAAAAAAAGTTAAAAGAATCAAAAA
Found at i:2661035 original size:24 final size:23
Alignment explanation
Indices: 2660992--2661036 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2660982 AAAAGAACAT
*
2660992 AAAAGAAAAAAATTAAAATAATC
1 AAAAGAAAAAAAATAAAATAATC
*
2661015 AAAATGAAAAAAAATATAATAA
1 AAAA-GAAAAAAAATAAAATAA
2661037 CTAATTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAAGAAAAAAAATAAAATAATC
Found at i:2661260 original size:16 final size:16
Alignment explanation
Indices: 2661239--2661308 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
2661229 TTTGGTTCGC
* *
2661239 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
2661255 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
2661271 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
2661287 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
2661303 TGTAAT
1 TGTAAT
2661309 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:2661341 original size:45 final size:44
Alignment explanation
Indices: 2661287--2661381 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 44
2661277 GGAATAGAGG
*
2661287 TGTAATGGAATAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGC-AATC-ATGTGTTTGGTTGAA
*
2661332 TGTAATGGAATAGAGGCGTAATAGCAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAA
2661376 TGTAAT
1 TGTAAT
2661382 AGAGGTGTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.47
45 24 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAATCATGTGTTTGGTTGAA
Found at i:2661562 original size:18 final size:17
Alignment explanation
Indices: 2661541--2661575 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2661531 TTATTATTAA
*
2661541 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2661559 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2661576 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2663424 original size:11 final size:11
Alignment explanation
Indices: 2663410--2663436 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2663400 AAAAATCAAT
2663410 ACAAAAGTTTC
1 ACAAAAGTTTC
2663421 ACAAAAGTTTC
1 ACAAAAGTTTC
2663432 ACAAA
1 ACAAA
2663437 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:2663799 original size:14 final size:14
Alignment explanation
Indices: 2663780--2663810 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2663770 AAAATATTAA
2663780 CAACAAATAGTTCC
1 CAACAAATAGTTCC
2663794 CAACAAATAGTTCC
1 CAACAAATAGTTCC
2663808 CAA
1 CAA
2663811 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (14 bp):
CAACAAATAGTTCC
Found at i:2669307 original size:51 final size:51
Alignment explanation
Indices: 2669231--2669332 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
2669221 TATTCAACAC
*
2669231 TAGTTCGAGTCTGGATAATGATTCAAGATAGAAGAAGAAACCTACAAAGGG
1 TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTACAAAGGG
*
2669282 TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTGCAAAGGG
1 TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTACAAAGGG
2669333 GAACTACTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (51 bp):
TAGTTCGAGTCTGGATAATAATTCAAGATAGAAGAAGAAACCTACAAAGGG
Found at i:2671770 original size:150 final size:147
Alignment explanation
Indices: 2671591--2671992 Score: 436
Period size: 149 Copynumber: 2.7 Consensus size: 147
2671581 GGACTCAGTC
* * * *
2671591 TGAAAATGTTATGTTATATGCAATTTGGTTCATATGGCTGCCTTCTGAGTTCAACGTTTCATTAC
1 TGAAAATGTT-TGTTATATGCTATATGGTTCATATGGCTGCTTTC-AAGTTCAACGTTTCATTAC
* * * *
2671656 TTGTATTTCAGTTCTAGAAT-CTCAATGACTAATGGAAAAGCAGGC-CAAACGAAGAAATCTCAA
64 TTCTATTTCAGTTCTACAATGCTCAATGACTAATGGAAAAGCAGGCAC-AACCAACAAATCTCAA
*
2671719 GCATGATGCTAACAGATTAACTT
128 GC-T--TGATAACAGATTAACTT
* * * *
2671742 T-AAAATGTATTGTTATATGCTATATGGTTCATGTAGCTGCTTTCAAGTTC-ACTCTTTCATTTC
1 TGAAAATGT-TTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAAC-GTTTCATTAC
* * * *
2671805 TTCTATTTCAGTTCTACAATGCTCAATGGCTAATGGAAAGGCAGGCACTACCAACAAATCTCAGG
64 TTCTATTTCAGTTCTACAATGCTCAATGACTAATGGAAAAGCAGGCACAACCAACAAATCTCAAG
*
2671870 CTTGATAACAGATTCACTT
129 CTTGATAACAGATTAACTT
* * * * *
2671889 TGAAAATGTCTTGTTATAATGCTA-ATGGCTTCATATGGATGCTTTCAAGCTCAATGCTTCATTG
1 TGAAAATGT-TTGTTAT-ATGCTATATGG-TTCATATGGCTGCTTTCAAGTTCAACGTTTCATTA
* * *
2671953 CTTCTATTTCAGCTCTACAATGTTCGATGACTAATGGAAA
63 CTTCTATTTCAGTTCTACAATGCTCAATGACTAATGGAAA
2671993 CCAAAAAGCA
Statistics
Matches: 212, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
147 16 0.08
148 20 0.09
149 99 0.47
150 74 0.35
151 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (147 bp):
TGAAAATGTTTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAACGTTTCATTACTT
CTATTTCAGTTCTACAATGCTCAATGACTAATGGAAAAGCAGGCACAACCAACAAATCTCAAGCT
TGATAACAGATTAACTT
Found at i:2680274 original size:44 final size:43
Alignment explanation
Indices: 2680226--2680351 Score: 139
Period size: 44 Copynumber: 2.9 Consensus size: 43
2680216 TGGGGCCACT
* *
2680226 ATAGGTTAACGTTTTATTTTTCTCATTTATATTTTAGGATTCAA
1 ATAGGTTAACGTTTT-TTTTTCTAATTTAAATTTTAGGATTCAA
* * *
2680270 ATAGGTT-ACATTTTTTTTTCTAATTTAGATCTTAAGG-TTCAA
1 ATAGGTTAACGTTTTTTTTTCTAATTTAAAT-TTTAGGATTCAA
* * *
2680312 ATAGGTTAGAAGTTTGTTTTTCTAATTTAAATCTTAGGAT
1 ATAGGTTA-ACGTTTTTTTTTCTAATTTAAATTTTAGGAT
2680352 AAAATTTTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 26 0.38
43 15 0.22
44 27 0.40
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (43 bp):
ATAGGTTAACGTTTTTTTTTCTAATTTAAATTTTAGGATTCAA
Found at i:2680296 original size:42 final size:42
Alignment explanation
Indices: 2680226--2680351 Score: 128
Period size: 42 Copynumber: 2.9 Consensus size: 42
2680216 TGGGGCCACT
* * *
2680226 ATAGGTTAACGTTTTATTTTTCTCATTTATATTTTAGGATTCAA
1 ATAGGTT-ACATTTT-TTTTTCTAATTTAAATTTTAGGATTCAA
* *
2680270 ATAGGTTACATTTTTTTTTCTAATTTAGATCTTAAGG-TTCAA
1 ATAGGTTACATTTTTTTTTCTAATTTAAAT-TTTAGGATTCAA
* * *
2680312 ATAGGTTAGAAGTTTGTTTTTCTAATTTAAATCTTAGGAT
1 ATAGGTTA-CA-TTTTTTTTTCTAATTTAAATTTTAGGAT
2680352 AAAATTTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
42 27 0.39
43 16 0.23
44 26 0.38
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (42 bp):
ATAGGTTACATTTTTTTTTCTAATTTAAATTTTAGGATTCAA
Found at i:2682695 original size:44 final size:43
Alignment explanation
Indices: 2682639--2682774 Score: 150
Period size: 44 Copynumber: 3.1 Consensus size: 43
2682629 ATTTAGGTCC
* * *
2682639 TAGGATTTAAATAGGTTAACGTTTTATTTTTCTCATTTATATTT
1 TAGGATTCAAATAGGTTAACGTTTT-TTTTTCTAATTTAAATTT
* *
2682683 TAGGATTCAAATAGGTT-ACATTTTTTTTTCTAATTTAGATCTT
1 TAGGATTCAAATAGGTTAACGTTTTTTTTTCTAATTTAAAT-TT
* * * *
2682726 AAGG-TTCAAATAGGTTAGAAGTTTGTTTTTCTAATTTAAATCT
1 TAGGATTCAAATAGGTTA-ACGTTTTTTTTTCTAATTTAAATTT
2682769 TAGGAT
1 TAGGAT
2682775 AAAATTTTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
42 26 0.34
43 15 0.19
44 36 0.47
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.49
Consensus pattern (43 bp):
TAGGATTCAAATAGGTTAACGTTTTTTTTTCTAATTTAAATTT
Found at i:2684610 original size:14 final size:14
Alignment explanation
Indices: 2684591--2684630 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2684581 TTGTTTACCA
*
2684591 GTAAAATGTTTTCC
1 GTAAAATGATTTCC
*
2684605 GTAAAATGATTTCT
1 GTAAAATGATTTCC
*
2684619 GAAAAATGATTT
1 GTAAAATGATTT
2684631 ATTTTTATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (14 bp):
GTAAAATGATTTCC
Found at i:2684729 original size:32 final size:32
Alignment explanation
Indices: 2684644--2684729 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
2684634 TTTATGGAAA
*
2684644 ATGATTTACTGAAAATATTTTCTGGTGTTTGG
1 ATGATTTACTGAAAATATTTTCTGCTGTTTGG
* ** *
2684676 ATGAATCTGTTTAAAATATTTTCTGCTGTTTGG
1 ATG-ATTTACTGAAAATATTTTCTGCTGTTTGG
*
2684709 -TAGATTTCCTGAAAATATTTT
1 AT-GATTTACTGAAAATATTTT
2684730 TCGGAAAAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
32 18 0.42
33 25 0.58
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (32 bp):
ATGATTTACTGAAAATATTTTCTGCTGTTTGG
Found at i:2699273 original size:18 final size:17
Alignment explanation
Indices: 2699250--2699284 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
2699240 TTTGCAACCC
2699250 AAGGGGAAGGAGAAAAGG
1 AAGGGGAAGG-GAAAAGG
2699268 AAGGGGAAGGGAAAAGG
1 AAGGGGAAGGGAAAAGG
2699285 GGAGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (17 bp):
AAGGGGAAGGGAAAAGG
Found at i:2699452 original size:14 final size:14
Alignment explanation
Indices: 2699433--2699460 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2699423 AGAAAAGCCT
2699433 GAAAAGCTTTTACA
1 GAAAAGCTTTTACA
2699447 GAAAAGCTTTTACA
1 GAAAAGCTTTTACA
2699461 AGTTATCAAA
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
GAAAAGCTTTTACA
Found at i:2701972 original size:3 final size:3
Alignment explanation
Indices: 2701964--2701989 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2701954 TGTTTCCTTT
2701964 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
2701990 TGTGTACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2703794 original size:22 final size:20
Alignment explanation
Indices: 2703752--2703795 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
2703742 CAACAAATAT
*
2703752 ATTTATTAAAATATAACTTA
1 ATTTATTAAAATAAAACTTA
*
2703772 ATTTATATATAAATAAAATTTA
1 ATTTAT-TA-AAATAAAACTTA
2703794 AT
1 AT
2703796 AATTTTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 2 0.10
22 12 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATTAAAATAAAACTTA
Found at i:2706805 original size:24 final size:24
Alignment explanation
Indices: 2706777--2706822 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2706767 TATATGAAAT
* *
2706777 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
2706801 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
2706823 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:2710042 original size:17 final size:16
Alignment explanation
Indices: 2710002--2710052 Score: 68
Period size: 17 Copynumber: 3.2 Consensus size: 16
2709992 AAAAATATAT
2710002 AAAAAAA-AGAAAGAA
1 AAAAAAAGAGAAAGAA
*
2710017 AAATAAAGAGAAAGAA
1 AAAAAAAGAGAAAGAA
*
2710033 AAAAAGAAGAAAAAGAA
1 AAAAA-AAGAGAAAGAA
2710050 AAA
1 AAA
2710053 GGAGAGGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 6 0.19
16 12 0.39
17 13 0.42
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAGAAAGAA
Found at i:2710556 original size:107 final size:106
Alignment explanation
Indices: 2710371--2710681 Score: 441
Period size: 107 Copynumber: 2.9 Consensus size: 106
2710361 TAATTTATTC
2710371 TCATTTCGTATCTTAGC-AAATTTGCTATCTTG--A-TTATTTATTTCGAGCTTTGTTCTCAATA
1 TCATTTCGTATCTTAGCAAAATTTGCTATCTTGTTATTTATTTATTTCGAGCTTTGTTCTCAATA
* *
2710432 AAATTCCATATTGTCCATTGTGATAATCCTTTTCATTTTAT
66 AAATTCCATCTTGTCCATTGTGATAATCCTTTTCATCTTAT
* *
2710473 TCATTTCGTATCTTAGCAAAATTTGCTATCTTGATTATTTATTTATTTCGAGCATTGCTCTCAAT
1 TCATTTCGTATCTTAGCAAAATTTGCTATCTTG-TTATTTATTTATTTCGAGCTTTGTTCTCAAT
* *
2710538 AAAATCCCATCTTATCCATTGTGATAATCCTTTTCATCTTAT
65 AAAATTCCATCTTGTCCATTGTGATAATCCTTTTCATCTTAT
* * * *
2710580 TCAGTTCGTATCTTAGCAAAAGTTGCTATCTTGGTTAATTTATTCATCTCGAGCTTTGTTCTCAA
1 TCATTTCGTATCTTAGCAAAATTTGCTATCTT-GTT-ATTTATTTATTTCGAGCTTTGTTCTCAA
* * * *
2710645 TAAAATTTCATCTTGTCCATTGTAAGAATCTTTTTCA
64 TAAAATTCCATCTTGTCCATTGTGATAATCCTTTTCA
2710682 AGCATTTTTC
Statistics
Matches: 184, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
102 17 0.09
103 15 0.08
106 1 0.01
107 95 0.52
108 56 0.30
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (106 bp):
TCATTTCGTATCTTAGCAAAATTTGCTATCTTGTTATTTATTTATTTCGAGCTTTGTTCTCAATA
AAATTCCATCTTGTCCATTGTGATAATCCTTTTCATCTTAT
Found at i:2711392 original size:8 final size:8
Alignment explanation
Indices: 2711379--2711409 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2711369 AAAACAGTTT
2711379 ATATATAC
1 ATATATAC
2711387 ATATATAC
1 ATATATAC
*
2711395 ATATATAT
1 ATATATAC
2711403 ATATATA
1 ATATATA
2711410 AGAAAACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATATAC
Found at i:2717713 original size:13 final size:14
Alignment explanation
Indices: 2717694--2717751 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 14
2717684 TAAAGTTAAA
2717694 ATATATATTATAAT
1 ATATATATTATAAT
2717708 ATTATAATATTAT-AT
1 A-TAT-ATATTATAAT
*
2717723 CT-TA-ATTATTAAGT
1 ATATATATTA-TAA-T
2717737 ATATATATTATAAT
1 ATATATATTATAAT
2717751 A
1 A
2717752 AGTAAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
11 4 0.11
12 2 0.06
13 2 0.06
14 6 0.17
15 10 0.29
16 11 0.31
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
ATATATATTATAAT
Found at i:2717761 original size:22 final size:21
Alignment explanation
Indices: 2717689--2717761 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
2717679 AAACTTAAAG
2717689 TTAAA-ATATATATTATAATA
1 TTAAATATATATATTATAATA
2717709 TTATAATAT-TATATCT-TAATTA
1 TTA-AATATATATAT-TATAA-TA
*
2717731 TTAAGTATATATATTATAATAA
1 TTAAATATATATATTATAAT-A
*
2717753 GTAAATATA
1 TTAAATATA
2717762 AATAAAAGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 3 0.07
21 16 0.37
22 24 0.56
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (21 bp):
TTAAATATATATATTATAATA
Found at i:2718817 original size:37 final size:40
Alignment explanation
Indices: 2718727--2718834 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 40
2718717 CTTCGAGTCA
* *
2718727 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCG
1 ATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAACTCG
* * *
2718768 ATGAGGCACTGGGTGTCAA-TT-TACTTCGGTTTAGCT-G
1 ATGAGACACTGGGTGTCAATTTATACTTCGGATTAACTCG
* *
2718805 ATGAGACACTGGGTGTTAAATTATTACTTC
1 ATGAGACACTGGGTGTCAATTTA-TACTTC
2718835 AAATTATCTG
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
37 18 0.32
38 13 0.23
40 8 0.14
41 18 0.32
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAATTTATACTTCGGATTAACTCG
Found at i:2720191 original size:31 final size:31
Alignment explanation
Indices: 2720156--2720216 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2720146 AAAAAAGATA
* *
2720156 CATGTGGCAAAGGGAATAATTTTTTAGCAAG
1 CATGTAGCAAAGGGAATAATTTTTGAGCAAG
2720187 CATGTAGCAAAGGGAATAATTTTTGAGCAA
1 CATGTAGCAAAGGGAATAATTTTTGAGCAA
2720217 ATATGGTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (31 bp):
CATGTAGCAAAGGGAATAATTTTTGAGCAAG
Found at i:2723361 original size:24 final size:25
Alignment explanation
Indices: 2723334--2723380 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2723324 CTGTTAATTT
2723334 CTCTTCG-GAGCTACCCGTTATAGG
1 CTCTTCGTGAGCTACCCGTTATAGG
* *
2723358 CTCTTTGTGAGCTTCCCGTTATA
1 CTCTTCGTGAGCTACCCGTTATA
2723381 TTGCCCAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.15, C:0.28, G:0.21, T:0.36
Consensus pattern (25 bp):
CTCTTCGTGAGCTACCCGTTATAGG
Found at i:2729909 original size:242 final size:242
Alignment explanation
Indices: 2729448--2729932 Score: 891
Period size: 242 Copynumber: 2.0 Consensus size: 242
2729438 AACAATCAGA
* *
2729448 CCATAACATTCCATATTTGACCCGTAAGCATTCGATTCTAATTTTTAGCTACTTCGATTTAATTA
1 CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAATTA
*
2729513 AATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCATTACACCAAATGTAGCAAGG
66 AATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAGG
*
2729578 CAAAGAGAGCTAGAAACATTGCTCTTCCGATAAATGAGAAATTGCCAACTCCCCAGAATGTTACC
131 CAAAGAGAGC-AGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACC
*
2729643 ATTGAAGATCTTTAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
195 ATTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
2729691 CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAATTT
1 CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAA-TT
2729756 AAATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAG
65 AAATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAG
*
2729821 GCAAAGAGAG-AGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACT
130 GCAAAGAGAGCAGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACC
2729885 ATTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
195 ATTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
2729933 AAGACTTTTA
Statistics
Matches: 235, Mismatches: 6, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
242 99 0.42
243 60 0.26
244 76 0.32
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (242 bp):
CCATAACATTCCATATTTGACCCGTAAGCATTCCATTCTAATTTTCAGCTACTTCGATTTAATTA
AATCAACTTTGAACCAATTTTTCAACACGAACGAAAATCAGGTCAATACACCAAATGTAGCAAGG
CAAAGAGAGCAGAAACATTGCTCTTCCGATAAATGAGAAATTCCCAACTCCCCAGAATGTTACCA
TTGAAGATCTTCAGGAGTAAATTGCCTTGCTTACTCAGAATTTTAGT
Found at i:2735969 original size:18 final size:18
Alignment explanation
Indices: 2735919--2736004 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 18
2735909 TTTATATATG
*
2735919 ATTTAGAATTTTTTTAAAA
1 ATTT-GAATTTTTTAAAAA
*
2735938 ATTATTATACTTTTTTAAAAA
1 ATT-TGA-A-TTTTTTAAAAA
*
2735959 ATTTGAA-TTTTT-AGAA
1 ATTTGAATTTTTTAAAAA
*
2735975 ATATT-ATACTTTTTAAAAA
1 AT-TTGA-ATTTTTTAAAAA
2735994 ATTTGAATTTT
1 ATTTGAATTTT
2736005 GAGAAATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
16 6 0.11
17 8 0.15
18 11 0.21
19 11 0.21
20 4 0.08
21 13 0.25
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTTGAATTTTTTAAAAA
Found at i:2735971 original size:17 final size:17
Alignment explanation
Indices: 2735949--2736004 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
2735939 TTATTATACT
2735949 TTTTTAAAAAATTTGAA
1 TTTTTAAAAAATTTGAA
* *
2735966 TTTTTAGAAATATTAT-AC
1 TTTTTA-AAAAATT-TGAA
2735984 TTTTTAAAAAATTTGAA
1 TTTTTAAAAAATTTGAA
2736001 TTTT
1 TTTT
2736005 GAGAAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.53
18 13 0.41
19 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
TTTTTAAAAAATTTGAA
Found at i:2735995 original size:35 final size:36
Alignment explanation
Indices: 2735929--2736011 Score: 132
Period size: 35 Copynumber: 2.3 Consensus size: 36
2735919 ATTTAGAATT
*
2735929 TTTTTAAAAATTATTATACTTTTTTAAAAAATTTGAA
1 TTTTTAGAAA-TATTATACTTTTTTAAAAAATTTGAA
2735966 TTTTTAGAAATATTATAC-TTTTTAAAAAATTTGAA
1 TTTTTAGAAATATTATACTTTTTTAAAAAATTTGAA
*
2736001 TTTTGAGAAAT
1 TTTTTAGAAAT
2736012 TATGTTGATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 27 0.61
36 8 0.18
37 9 0.20
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (36 bp):
TTTTTAGAAATATTATACTTTTTTAAAAAATTTGAA
Found at i:2736954 original size:23 final size:23
Alignment explanation
Indices: 2736921--2736970 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2736911 AATTATTTTT
2736921 TTTAATAATTTTAAATAAATAAAA
1 TTTAATAATTTTAAATAAA-AAAA
* *
2736945 TTTAA-AATTTTAAGTATAAAAA
1 TTTAATAATTTTAAATAAAAAAA
2736967 TTTA
1 TTTA
2736971 CCATCAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 11 0.46
24 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTTAATAATTTTAAATAAAAAAA
Found at i:2737005 original size:21 final size:21
Alignment explanation
Indices: 2736955--2737011 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2736945 TTTAAAATTT
2736955 TAAGTATAAA-AAT-TTACCA
1 TAAGTATAAATAATATTACCA
2736974 TCAA--AGTAAATAATATTACCA
1 T-AAGTA-TAAATAATATTACCA
*
2736995 TAAGTATAAATATTATT
1 TAAGTATAAATAATATT
2737012 TATCTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 7 0.23
21 17 0.55
22 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (21 bp):
TAAGTATAAATAATATTACCA
Found at i:2738474 original size:3 final size:3
Alignment explanation
Indices: 2738468--2738495 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2738458 TGAAATATTG
2738468 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2738496 TACTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2767830 original size:2 final size:2
Alignment explanation
Indices: 2767787--2767815 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2767777 ACTTTAACCT
2767787 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
2767816 CAATCTCTCA
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:2776231 original size:24 final size:23
Alignment explanation
Indices: 2776164--2776233 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
2776154 CGTATGTAAG
*
2776164 TTTTTATTTAATTTCTAATTAATATA
1 TTTTTAATT-ATTT-TAATT-ATATA
2776190 TTTTTAATTATTTTAATTATATA
1 TTTTTAATTATTTTAATTATATA
* *
2776213 TTTTTATTTTTTTTGAATTAT
1 TTTTTAATTATTTT-AATTAT
2776234 TGAACCTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 17 0.43
24 11 0.28
25 4 0.10
26 8 0.20
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (23 bp):
TTTTTAATTATTTTAATTATATA
Found at i:2779250 original size:3 final size:3
Alignment explanation
Indices: 2779242--2779271 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2779232 CATCACTAGT
2779242 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2779272 ACATAGGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:2781713 original size:409 final size:409
Alignment explanation
Indices: 2780954--2781771 Score: 1636
Period size: 409 Copynumber: 2.0 Consensus size: 409
2780944 ACATGCTCCA
2780954 TCACTTTGTAAATAGTCTGCAATCTACATCATTAAATCCACAACATTTCTTCATTAATCTCTATG
1 TCACTTTGTAAATAGTCTGCAATCTACATCATTAAATCCACAACATTTCTTCATTAATCTCTATG
2781019 TCAAAAGCAAAGGATTCATGAAGGAAACCAAACAGCAAGGAAAAATAAATAAATATATTTATAGA
66 TCAAAAGCAAAGGATTCATGAAGGAAACCAAACAGCAAGGAAAAATAAATAAATATATTTATAGA
2781084 CATACAAATAGATGTTACATCTATATATATGCACTTTTAAGCAACATATTTGTTTTGGTCAGATA
131 CATACAAATAGATGTTACATCTATATATATGCACTTTTAAGCAACATATTTGTTTTGGTCAGATA
2781149 GCCTCAGCTAGTGCAGTCTGGTATAACCCGAATCAGAACTTAGGTTAGATGAAAGCTTTTTTGAG
196 GCCTCAGCTAGTGCAGTCTGGTATAACCCGAATCAGAACTTAGGTTAGATGAAAGCTTTTTTGAG
2781214 TTTGCTATCAAAAAACAGAAATAAACAAACATCACAATTGGCACTTACATGATTGGCAAGAGCCA
261 TTTGCTATCAAAAAACAGAAATAAACAAACATCACAATTGGCACTTACATGATTGGCAAGAGCCA
2781279 TGCCACTTAAAGCAGCCGACTCTAAATTCGATCCCAATAACCAATCGCCGCAGATACCGGCCCTT
326 TGCCACTTAAAGCAGCCGACTCTAAATTCGATCCCAATAACCAATCGCCGCAGATACCGGCCCTT
2781344 CCATGAGGATCGAAAATAC
391 CCATGAGGATCGAAAATAC
2781363 TCACTTTGTAAATAGTCTGCAATCTACATCATTAAATCCACAACATTTCTTCATTAATCTCTATG
1 TCACTTTGTAAATAGTCTGCAATCTACATCATTAAATCCACAACATTTCTTCATTAATCTCTATG
2781428 TCAAAAGCAAAGGATTCATGAAGGAAACCAAACAGCAAGGAAAAATAAATAAATATATTTATAGA
66 TCAAAAGCAAAGGATTCATGAAGGAAACCAAACAGCAAGGAAAAATAAATAAATATATTTATAGA
2781493 CATACAAATAGATGTTACATCTATATATATGCACTTTTAAGCAACATATTTGTTTTGGTCAGATA
131 CATACAAATAGATGTTACATCTATATATATGCACTTTTAAGCAACATATTTGTTTTGGTCAGATA
2781558 GCCTCAGCTAGTGCAGTCTGGTATAACCCGAATCAGAACTTAGGTTAGATGAAAGCTTTTTTGAG
196 GCCTCAGCTAGTGCAGTCTGGTATAACCCGAATCAGAACTTAGGTTAGATGAAAGCTTTTTTGAG
2781623 TTTGCTATCAAAAAACAGAAATAAACAAACATCACAATTGGCACTTACATGATTGGCAAGAGCCA
261 TTTGCTATCAAAAAACAGAAATAAACAAACATCACAATTGGCACTTACATGATTGGCAAGAGCCA
2781688 TGCCACTTAAAGCAGCCGACTCTAAATTCGATCCCAATAACCAATCGCCGCAGATACCGGCCCTT
326 TGCCACTTAAAGCAGCCGACTCTAAATTCGATCCCAATAACCAATCGCCGCAGATACCGGCCCTT
2781753 CCATGAGGATCGAAAATAC
391 CCATGAGGATCGAAAATAC
2781772 ATGGGATACC
Statistics
Matches: 409, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
409 409 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (409 bp):
TCACTTTGTAAATAGTCTGCAATCTACATCATTAAATCCACAACATTTCTTCATTAATCTCTATG
TCAAAAGCAAAGGATTCATGAAGGAAACCAAACAGCAAGGAAAAATAAATAAATATATTTATAGA
CATACAAATAGATGTTACATCTATATATATGCACTTTTAAGCAACATATTTGTTTTGGTCAGATA
GCCTCAGCTAGTGCAGTCTGGTATAACCCGAATCAGAACTTAGGTTAGATGAAAGCTTTTTTGAG
TTTGCTATCAAAAAACAGAAATAAACAAACATCACAATTGGCACTTACATGATTGGCAAGAGCCA
TGCCACTTAAAGCAGCCGACTCTAAATTCGATCCCAATAACCAATCGCCGCAGATACCGGCCCTT
CCATGAGGATCGAAAATAC
Found at i:2789227 original size:39 final size:40
Alignment explanation
Indices: 2789184--2789359 Score: 178
Period size: 40 Copynumber: 4.4 Consensus size: 40
2789174 CGTTTGGATA
2789184 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCG-CTTTAG
1 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
* ** *
2789223 AAAAAACGCCGCTAAAGATTTAGTATTAGCGGCGTTTTTAG
1 -AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
* * * * *
2789264 GAAAACGCTGCTAAAGATCCAGTATTAGCGGCGTTTTTAG
1 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
* * * **
2789304 GAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-CTTTCC
1 AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
*
2789342 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
2789360 CCTAAGCACA
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
38 7 0.06
39 23 0.20
40 82 0.70
41 5 0.04
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG
Found at i:2789278 original size:80 final size:79
Alignment explanation
Indices: 2789185--2789335 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 79
2789175 GTTTGGATAA
* * *
2789185 AAAACGCCGCTAAAAATCAAGTATTAGCGGCG-CTTTAGAAAAAACGCCGCTAAAGATTTAGTAT
1 AAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAG-AAAAACGCCGCTAAA-AATGAGCAT
2789249 TAGCGGCGTTTTTAGG
64 TAGCGGCGTTTTTAGG
* * * * *
2789265 AAAACGCTGCTAAAGATCCAGTATTAGCGGCGTTTTTAGGAAAACGCCGCTAAAAATGAGCATTA
1 AAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAGAAAAACGCCGCTAAAAATGAGCATTA
2789330 GCGGCG
66 GCGGCG
2789336 CTTTCCAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
79 14 0.23
80 43 0.69
81 5 0.08
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (79 bp):
AAAACGCCGCTAAAAATCAAGTATTAGCGGCGTCTTTAGAAAAACGCCGCTAAAAATGAGCATTA
GCGGCGTTTTTAGG
Found at i:2789461 original size:41 final size:41
Alignment explanation
Indices: 2789399--2789671 Score: 397
Period size: 41 Copynumber: 6.7 Consensus size: 41
2789389 TTTCGGGGTG
2789399 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
* *
2789440 TTAGCGGCGTTTTTTAGGAAGCGCCGCTAATGCTGC-GGGCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCT-CTGGTCT
* * * *
2789481 TTAGTGGCGTTTTTGAAGAAACGCTGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
*
2789522 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
*
2789563 TTAGCGGCGTTTTTTGAA-AAGCGCCGCTAATGCTCGGGTCT
1 TTAGCGGCGTTTTTT-AAGAAGCGCCGCTAATGCTCTGGTCT
* * *
2789604 TTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGGGCT
1 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
* *
2789645 TTAGCGGCGTTTTTGAAAAAGCGCCGC
1 TTAGCGGCGTTTTTTAAGAAGCGCCGC
2789672 AAAATTTTTT
Statistics
Matches: 212, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
40 3 0.01
41 206 0.97
42 3 0.01
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTGGTCT
Found at i:2790111 original size:15 final size:15
Alignment explanation
Indices: 2790031--2790098 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
2790021 ATTGTTTATG
*
2790031 TTATGATTT-GCGGT
1 TTATGATTTAGGGGT
* *
2790045 TTAAGAGTT-GGGGT
1 TTATGATTTAGGGGT
*
2790059 TTA-AAGTTTAGGGGT
1 TTATGA-TTTAGGGGT
2790074 TTATGATTTAGGGGT
1 TTATGATTTAGGGGT
*
2790089 TTATGTTTTA
1 TTATGATTTA
2790099 TGATTTAGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
13 1 0.02
14 16 0.36
15 26 0.59
16 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (15 bp):
TTATGATTTAGGGGT
Found at i:2790228 original size:35 final size:36
Alignment explanation
Indices: 2790189--2790274 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 36
2790179 TTAGGGGTTA
2790189 GGGTTTAAGGTTTAGGTG-GTAGGGGTTAAGGGATG
1 GGGTTTAAGGTTTAGGTGTGTAGGGGTTAAGGGATG
* * * * * *
2790224 GGGTTTAGGGGTTA-TTGTTTAGGGTTTAAGGGTTG
1 GGGTTTAAGGTTTAGGTGTGTAGGGGTTAAGGGATG
*
2790259 GTGTTTAAGGTTTAGG
1 GGGTTTAAGGTTTAGG
2790275 GTCTTGGGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
34 2 0.05
35 37 0.95
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.38
Consensus pattern (36 bp):
GGGTTTAAGGTTTAGGTGTGTAGGGGTTAAGGGATG
Found at i:2790248 original size:21 final size:21
Alignment explanation
Indices: 2790224--2790275 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2790214 TTAAGGGATG
*
2790224 GGGTTTAGGGGTTATTGTTTA
1 GGGTTTAGGGGTTAGTGTTTA
* *
2790245 GGGTTTAAGGGTTGGTGTTTA
1 GGGTTTAGGGGTTAGTGTTTA
*
2790266 AGGTTTAGGG
1 GGGTTTAGGG
2790276 TCTTGGGTTT
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:0.15, C:0.00, G:0.42, T:0.42
Consensus pattern (21 bp):
GGGTTTAGGGGTTAGTGTTTA
Found at i:2790255 original size:8 final size:7
Alignment explanation
Indices: 2790172--2790285 Score: 58
Period size: 7 Copynumber: 16.3 Consensus size: 7
2790162 TTTTAATTTA
2790172 TTAGGGT
1 TTAGGGT
*
2790179 TTAGGGG
1 TTAGGGT
2790186 TTAGGGT
1 TTAGGGT
*
2790193 TTAAGGT
1 TTAGGGT
2790200 TTA-GGT
1 TTAGGGT
*
2790206 GGTAGGGGT
1 -TTA-GGGT
*
2790215 TAAGGG-
1 TTAGGGT
* *
2790221 ATGGGGT
1 TTAGGGT
*
2790228 TTAGGGG
1 TTAGGGT
**
2790235 TTATTGT
1 TTAGGGT
2790242 TTAGGGT
1 TTAGGGT
2790249 TTAAGGG-
1 TT-AGGGT
2790256 TT-GGTGT
1 TTAGG-GT
*
2790263 TTAAGGT
1 TTAGGGT
2790270 TTAGGGT
1 TTAGGGT
2790277 CTT-GGGT
1 -TTAGGGT
2790284 TT
1 TT
2790286 TTAAGATAGG
Statistics
Matches: 79, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
5 2 0.03
6 9 0.11
7 57 0.72
8 8 0.10
9 3 0.04
ACGTcount: A:0.16, C:0.01, G:0.43, T:0.40
Consensus pattern (7 bp):
TTAGGGT
Found at i:2790284 original size:35 final size:32
Alignment explanation
Indices: 2790175--2790285 Score: 78
Period size: 35 Copynumber: 3.2 Consensus size: 32
2790165 TAATTTATTA
* *
2790175 GGGTTTAGGGGTTAGGGTTTAAGGTTTAGGTGGTA
1 GGGTTTAAGGGTT-GGGTTTAAGGTTTAGGT--TT
* * * * *
2790210 GGGGTTAAGGGATGGGGTTTAGGGGTTATTGTTT
1 GGGTTTAAGGG-TTGGGTTTAAGGTTTA-GGTTT
2790244 AGGGTTTAAGGGTTGGTGTTTAAGGTTTAGGGTCTT
1 -GGGTTTAAGGGTTGG-GTTTAAGGTTTA-GGT-TT
2790280 GGGTTT
1 GGGTTT
2790286 TTAAGATAGG
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
34 4 0.07
35 49 0.84
36 5 0.09
ACGTcount: A:0.15, C:0.01, G:0.44, T:0.40
Consensus pattern (32 bp):
GGGTTTAAGGGTTGGGTTTAAGGTTTAGGTTT
Found at i:2794277 original size:43 final size:43
Alignment explanation
Indices: 2794201--2794411 Score: 239
Period size: 43 Copynumber: 4.9 Consensus size: 43
2794191 GTTTTTCAAA
* * * * *
2794201 AAAAGCGCTGCTAAAAGTCATGATCTATT-GCGGCATTTGT-GG
1 AAAAGCGCCGCTAAAGGTCATGGTCT-TTAGCGGCGTTTATGGG
*
2794243 AAGAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGGG
1 AA-AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGGG
* * * *
2794287 AAAAGCGCCGTTAAAGATCATAGTTTTTAGCGGCGTTTATGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGGG
* * * *
2794330 AAAAGCGCCGCTAAAGATAATGGTCTTTAGCGGCGTTTGT-GA
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGGG
**
2794372 AAAAGCGCCGCTAAAGGTCATGACCTTTAGCGGCGTTTAT
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTAT
2794412 TTCTAAAAAC
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
42 40 0.28
43 100 0.69
44 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGGG
Found at i:2794425 original size:86 final size:86
Alignment explanation
Indices: 2794252--2794429 Score: 209
Period size: 86 Copynumber: 2.1 Consensus size: 86
2794242 GAAGAAGCGT
* * * * **
2794252 CGCTAAAGGTCATGGTCTTTAGCGGCGTTTATGGGAAAAGCGCCGTTAAAGATCATAGTTTTTAG
1 CGCTAAAGATAATGGTCTTTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAGATCATAGCCTTTAG
* *
2794317 CGGCGTTTATGGGAAAAGCGC
66 CGGCGTTTATGCGAAAAACGC
* *
2794338 CGCTAAAGATAATGGTCTTTAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCAT-GACCTTTA
1 CGCTAAAGATAATGGTCTTTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAGATCATAG-CCTTTA
* *
2794401 GCGGCGTTTATTTCTAAAAACGC
65 GCGGCGTTTA-TGCGAAAAACGC
2794424 CG-TAAA
1 CGCTAAA
2794430 AGTTAGCGAC
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
84 1 0.01
85 38 0.49
86 39 0.50
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (86 bp):
CGCTAAAGATAATGGTCTTTAGCGGCGTTTATGGAAAAAGCGCCGCTAAAGATCATAGCCTTTAG
CGGCGTTTATGCGAAAAACGC
Found at i:2807056 original size:13 final size:13
Alignment explanation
Indices: 2807040--2807073 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2807030 ATTTTTTATG
2807040 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
2807053 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
2807066 CTTGGGTT
1 ATTGGGTT
2807074 TATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.03, G:0.44, T:0.41
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:2810768 original size:19 final size:19
Alignment explanation
Indices: 2810742--2810794 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2810732 TTTTAAAATA
2810742 ATTTTAACTTGATTGAAA-
1 ATTTTAACTTGATTGAAAC
**
2810760 ATGTTTAACTCAATTGAAACC
1 AT-TTTAACTTGATTGAAA-C
2810781 ATTTTAACTTGATT
1 ATTTTAACTTGATT
2810795 TTATCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 10 0.36
21 2 0.07
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (19 bp):
ATTTTAACTTGATTGAAAC
Found at i:2820267 original size:18 final size:16
Alignment explanation
Indices: 2820234--2820267 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2820224 TAATTATAAT
2820234 TTAATATTTTTTATTA
1 TTAATATTTTTTATTA
*
2820250 TTAATA-TGTTTATTA
1 TTAATATTTTTTATTA
2820265 TTA
1 TTA
2820268 CAAAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATATTTTTTATTA
Found at i:2820328 original size:108 final size:109
Alignment explanation
Indices: 2820201--2820417 Score: 427
Period size: 108 Copynumber: 2.0 Consensus size: 109
2820191 TTTTAATTAT
2820201 TAGAATGCGCTTTAGGAATTATTTAATTATAATTTAATATTTTTTATTATTAATATGTTTATTAT
1 TAGAATGCGCTTTAGGAATTATTTAATTATAATTTAATATTTTTTATTATTAATATGTTTATTAT
2820266 TACAAAGAATTGTATATTATTAATATTGTGGTTTTTGAAATCGA
66 TACAAAGAATTGTATATTATTAATATTGTGGTTTTTGAAATCGA
2820310 TAGAATGCGC-TTAGGAATTATTTAATTATAATTTAATATTTTTTATTATTAATATGTTTATTAT
1 TAGAATGCGCTTTAGGAATTATTTAATTATAATTTAATATTTTTTATTATTAATATGTTTATTAT
2820374 TACAAAGAATTGTATATTATTAATATTGTGGTTTTTGAAATCGA
66 TACAAAGAATTGTATATTATTAATATTGTGGTTTTTGAAATCGA
2820418 ATCAACCAAT
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 98 0.91
109 10 0.09
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (109 bp):
TAGAATGCGCTTTAGGAATTATTTAATTATAATTTAATATTTTTTATTATTAATATGTTTATTAT
TACAAAGAATTGTATATTATTAATATTGTGGTTTTTGAAATCGA
Found at i:2820375 original size:18 final size:16
Alignment explanation
Indices: 2820342--2820375 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2820332 TAATTATAAT
2820342 TTAATATTTTTTATTA
1 TTAATATTTTTTATTA
*
2820358 TTAATA-TGTTTATTA
1 TTAATATTTTTTATTA
2820373 TTA
1 TTA
2820376 CAAAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATATTTTTTATTA
Found at i:2823183 original size:6 final size:6
Alignment explanation
Indices: 2823172--2823196 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2823162 AATCCATCAG
2823172 ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
2823197 AAATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:2827385 original size:50 final size:50
Alignment explanation
Indices: 2827310--2827409 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
2827300 TCTATCAGAG
* * * * *
2827310 AGTTTACTTTTAAATTGAGTTTTCCAATTGCTCTTTAGAGACTCAAATTT
1 AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
2827360 AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
1 AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
2827410 GGGTGGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (50 bp):
AGTTTACCTTTAAATCGAGTCTTCCAACTGCTCTTTAGAGACCCAAATTT
Found at i:2828323 original size:18 final size:18
Alignment explanation
Indices: 2828286--2828341 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
2828276 AATTTGAAAG
**
2828286 AAATA-TTAAAATTATAA
1 AAATAGTTAAAAAAATAA
*
2828303 AAATA-TTAAATAAATTAA
1 AAATAGTTAAA-AAAATAA
2828321 AAA-AGTTAAAAAAATAA
1 AAATAGTTAAAAAAATAA
2828338 AAAT
1 AAAT
2828342 CATTTAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 20 0.62
18 12 0.38
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATAGTTAAAAAAATAA
Found at i:2828983 original size:19 final size:19
Alignment explanation
Indices: 2828959--2828997 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2828949 TTTGAATTTT
*
2828959 ATTTATTTAT-TTTTATAAA
1 ATTTATTAATGTTTT-TAAA
2828978 ATTTATTAATGTTTTTAAA
1 ATTTATTAATGTTTTTAAA
2828997 A
1 A
2828998 AATTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTATTAATGTTTTTAAA
Found at i:2829037 original size:16 final size:15
Alignment explanation
Indices: 2828965--2829039 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 15
2828955 TTTTATTTAT
2828965 TTATTTTTATAAAATTTA
1 TTATTTTT-TAAAA--TA
*
2828983 TTAATGTTTTTAAAAAA
1 TT-AT-TTTTTAAAATA
2829000 TTATATTTTATAAAAT-
1 TTAT-TTTT-TAAAATA
*
2829016 TAATTTTTTAAAATA
1 TTATTTTTTAAAATA
2829031 TGTATTTTT
1 T-TATTTTT
2829040 AATTAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.13
15 5 0.11
16 15 0.32
17 8 0.17
18 2 0.04
19 7 0.15
20 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TTATTTTTTAAAATA
Found at i:2833598 original size:21 final size:21
Alignment explanation
Indices: 2833569--2833608 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2833559 TAATGTTACC
2833569 GCTCACAAATTAAATCATACT
1 GCTCACAAATTAAATCATACT
*
2833590 GCTCTCAAATTAAATCATA
1 GCTCACAAATTAAATCATA
2833609 ACGTTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (21 bp):
GCTCACAAATTAAATCATACT
Found at i:2837397 original size:20 final size:19
Alignment explanation
Indices: 2837374--2837412 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2837364 AAAAAATAAA
2837374 ATAATAAAATTTAAAAATTT
1 ATAATAAAA-TTAAAAATTT
* *
2837394 ATAATTATATTAAAAATTT
1 ATAATAAAATTAAAAATTT
2837413 TATCACATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAAAATTAAAAATTT
Found at i:2856760 original size:31 final size:29
Alignment explanation
Indices: 2856722--2856783 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 29
2856712 ATCTCAAAAT
2856722 TATATATGAACTTTAACTTAATGTGTAATTA
1 TATATATGAACTTTAA-TTAA-GTGTAATTA
*
2856753 TATATATGAACTTTAATTTAGTGTAATTA
1 TATATATGAACTTTAATTAAGTGTAATTA
2856782 TA
1 TA
2856784 CACGTGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 11 0.37
30 3 0.10
31 16 0.53
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.47
Consensus pattern (29 bp):
TATATATGAACTTTAATTAAGTGTAATTA
Found at i:2856791 original size:29 final size:31
Alignment explanation
Indices: 2856727--2856791 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
2856717 AAAATTATAT
* *
2856727 ATGAACTTTAACTTAATGTGTAATTATATAT
1 ATGAACTTTAACTTAATGTGTAATTATACAC
*
2856758 ATGAACTTTAA-TTTA-GTGTAATTATACAC
1 ATGAACTTTAACTTAATGTGTAATTATACAC
*
2856787 GTGAA
1 ATGAA
2856792 ATTCTGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 3 0.10
31 11 0.37
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (31 bp):
ATGAACTTTAACTTAATGTGTAATTATACAC
Found at i:2859688 original size:18 final size:16
Alignment explanation
Indices: 2859672--2859719 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2859662 AAAACAATAA
2859672 ATTTTATTATAAGAAT
1 ATTTTATTATAAGAAT
2859688 ATTTTATTAT---AA-
1 ATTTTATTATAAGAAT
*
2859700 ATTTTATTATAAAAAT
1 ATTTTATTATAAGAAT
2859716 ATTT
1 ATTT
2859720 ACGAGAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 10 0.36
13 2 0.07
15 2 0.07
16 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTTATTATAAGAAT
Found at i:2859705 original size:12 final size:12
Alignment explanation
Indices: 2859668--2859712 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 12
2859658 TTTAAAAACA
2859668 ATAAATTTTATT
1 ATAAATTTTATT
2859680 ATAAGAATATTTTATT
1 AT---AA-ATTTTATT
2859696 ATAAATTTTATT
1 ATAAATTTTATT
2859708 ATAAA
1 ATAAA
2859713 AATATTTACG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 15 0.52
13 2 0.07
15 2 0.07
16 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
ATAAATTTTATT
Found at i:2862725 original size:29 final size:30
Alignment explanation
Indices: 2862681--2862777 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
2862671 ATACAAAAAA
* *
2862681 AAAATTTATATTTTGATTCC-TTAACTTTTTT
1 AAAA-TTATATTTTGA-CCCTTTAACTTTTTC
*
2862712 AAAATTAT-TTTTGACCCTTTACCTTTTTC
1 AAAATTATATTTTGACCCTTTAACTTTTTC
* * * *
2862741 AAAATTATATTTTGACCCCTAAAGTTTCTC
1 AAAATTATATTTTGACCCTTTAACTTTTTC
2862771 AAAATTA
1 AAAATTA
2862778 CACTTGGCCT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 23 0.41
30 27 0.48
31 4 0.07
ACGTcount: A:0.32, C:0.15, G:0.04, T:0.48
Consensus pattern (30 bp):
AAAATTATATTTTGACCCTTTAACTTTTTC
Found at i:2863346 original size:11 final size:11
Alignment explanation
Indices: 2863322--2863394 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
2863312 AAGAGGGAAG
2863322 GAAG-AAGAAGA
1 GAAGAAAGAA-A
2863333 GAAGAAAGAAA
1 GAAGAAAGAAA
*
2863344 GAA-AAAAAAA
1 GAAGAAAGAAA
*
2863354 GAAAAAAAGAAA
1 G-AAGAAAGAAA
2863366 GGAA-AAAGAAA
1 -GAAGAAAGAAA
* *
2863377 AAAAAAAGAAA
1 GAAGAAAGAAA
*
2863388 AAAGAAA
1 GAAGAAA
2863395 AAAATTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.17
11 30 0.57
12 13 0.25
13 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAGAAAGAAA
Found at i:2863363 original size:22 final size:21
Alignment explanation
Indices: 2863337--2863398 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
2863327 AGAAGAGAAG
2863337 AAAGAAAGAAAAAAAAAGAAAA
1 AAAGAAAGAAAAAAAAA-AAAA
*
2863359 AAAGAAAGGAAAAAGAAAAAAA
1 AAAGAAA-GAAAAAAAAAAAAA
*
2863381 AAAGAAA-AAAGAAAAAAA
1 AAAGAAAGAAAAAAAAAAA
2863399 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 9 0.25
22 18 0.50
23 9 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAAAAAAAAAAA
Found at i:2863396 original size:8 final size:8
Alignment explanation
Indices: 2863347--2863417 Score: 58
Period size: 8 Copynumber: 9.0 Consensus size: 8
2863337 AAAGAAAGAA
2863347 AAAAAAAG
1 AAAAAAAG
2863355 AAAAAAAG
1 AAAAAAAG
**
2863363 AAAGGAA-
1 AAAAAAAG
*
2863370 AAAGAAA-
1 AAAAAAAG
2863377 AAAAAAAG
1 AAAAAAAG
2863385 -AAAAAAG
1 AAAAAAAG
*
2863392 AAAAAAATT
1 AAAAAAA-G
*
2863401 AAAAAAAT
1 AAAAAAAG
2863409 AATAAAAAG
1 AA-AAAAAG
2863418 TCGGGTCGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
7 19 0.36
8 22 0.42
9 12 0.23
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2863398 original size:18 final size:18
Alignment explanation
Indices: 2863334--2863398 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
2863324 AGAAGAAGAG
*
2863334 AAGAAAGAAAGAAA-AAAA
1 AAGAAA-AAAAAAAGAAAA
*
2863352 AAGAAAAAAAGAAAGGAAA
1 AAGAAAAAAA-AAAGAAAA
2863371 AAGAAAAAAAAAAGAAAA
1 AAGAAAAAAAAAAGAAAA
2863389 AAGAAAAAAA
1 AAGAAAAAAA
2863399 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 3 0.07
18 26 0.62
19 13 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAAGAAAA
Found at i:2863761 original size:15 final size:16
Alignment explanation
Indices: 2863741--2863783 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2863731 CAGGCCAGCC
2863741 AAAAAAGGAAAAAAG-
1 AAAAAAGGAAAAAAGA
*
2863756 AAAAAA-GAGAAGAAGA
1 AAAAAAGGA-AAAAAGA
2863772 AAAAAAGGAAAA
1 AAAAAAGGAAAA
2863784 GACCCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 8 0.35
17 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAGGAAAAAAGA
Found at i:2864286 original size:18 final size:18
Alignment explanation
Indices: 2864236--2864286 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2864226 AAAAAGAAAG
*
2864236 ATCGTGTTTTCAAAAGTTT
1 ATCGTG-TTTCAAAAATTT
* *
2864255 -TCATGTTTCCAAAATTT
1 ATCGTGTTTCAAAAATTT
2864272 ATCGTGTTTCAAAAA
1 ATCGTGTTTCAAAAA
2864287 ATAATAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (18 bp):
ATCGTGTTTCAAAAATTT
Found at i:2864434 original size:18 final size:18
Alignment explanation
Indices: 2864413--2864545 Score: 68
Period size: 17 Copynumber: 7.6 Consensus size: 18
2864403 ACTTTTCGCT
2864413 TTTTCAAAAATTTTCCTG
1 TTTTCAAAAATTTTCCTG
*
2864431 TTTTC-AAAATTTCTCGTG
1 TTTTCAAAAATTT-TCCTG
* *
2864449 TTTTTC--GACTTTT-CTCG
1 -TTTTCAAAAATTTTCCT-G
*
2864466 TTTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCCTG
*
2864484 TTTT-AGAAATTTT-CT-
1 TTTTCAAAAATTTTCCTG
* *
2864499 TATTTCTAAAATTCT-C-G
1 T-TTTCAAAAATTTTCCTG
*
2864516 TATTTCAAAAAATTTCCGTG
1 T-TTTCAAAAATTTTCC-TG
*
2864536 TTCTCAAAAA
1 TTTTCAAAAA
2864546 AATTATTATC
Statistics
Matches: 87, Mismatches: 16, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
15 1 0.01
16 10 0.11
17 36 0.41
18 24 0.28
19 14 0.16
20 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTTCAAAAATTTTCCTG
Found at i:2864497 original size:35 final size:37
Alignment explanation
Indices: 2864420--2864498 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 37
2864410 GCTTTTTCAA
*
2864420 AAATTTTC-CTGTTTTCAAAATTTCTCGTGTTTTTCG
1 AAATTTTCTCTGTTTTCAAAATTTCTCGTGTTTTTAG
*
2864456 -ACTTTTCTC-GTTTTCAAAAATTT-TCGTG-TTTTAG
1 AAATTTTCTCTGTTTTC-AAAATTTCTCGTGTTTTTAG
2864490 AAATTTTCT
1 AAATTTTCT
2864499 TATTTCTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
34 5 0.14
35 24 0.65
36 8 0.22
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (37 bp):
AAATTTTCTCTGTTTTCAAAATTTCTCGTGTTTTTAG
Found at i:2864510 original size:17 final size:17
Alignment explanation
Indices: 2864463--2864545 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
2864453 TCGACTTTTC
2864463 TCGT-TTTCAAAAATTT
1 TCGTATTTCAAAAATTT
* * *
2864479 TCGTGTTTTAGAAATTT
1 TCGTATTTCAAAAATTT
* * *
2864496 TCTTATTTCTAAAATTC
1 TCGTATTTCAAAAATTT
2864513 TCGTATTTCAAAAAATTT
1 TCGTATTTC-AAAAATTT
* *
2864531 CCGTGTTCTCAAAAA
1 TCGTATT-TCAAAAA
2864546 AATTATTATC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
16 4 0.08
17 29 0.57
18 16 0.31
19 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.46
Consensus pattern (17 bp):
TCGTATTTCAAAAATTT
Found at i:2871135 original size:78 final size:76
Alignment explanation
Indices: 2870775--2872146 Score: 1601
Period size: 78 Copynumber: 17.8 Consensus size: 76
2870765 AGAATTATAG
* * *
2870775 TTTTCAATTTCTATTTTTC--AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTTAGGCCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGG--G
*
2870838 -CACGCCGAGGTA-
63 TCACGCTGAGGTAT
** * * **
2870850 TTTTCAATTTCAATTTTTCAAAAAAATCAACTCAGAATGCGAGAAATGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
2870915 CGCTGAGATAT
66 CGCTGAGGTAT
* * * * * *
2870926 TTTT-AGTTTCTATTTTTCAAAAAAATCAGCTCATAATGCGAGAAGTGGGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
2870990 CGCTGATGTAT
66 CGCTGAGGTAT
* * *
2871001 TTTT-AATTTCTATTTTTC-AAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
2871064 CGCTGAGGTA-
66 CGCTGAGGTAT
*** *
2871074 TTTTCAATTTCTGTTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTTCAATTTCTG---TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
2871139 TCACGCTGAGGTA-
63 TCACGCTGAGGTAT
* *** * **
2871152 TTTTCAATTTCTTTTTTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGACA
1 TTTTCAATTTC-TGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-GT
* *
2871217 CACGCCGATGTAT
64 CACGCTGAGGTAT
** * *
2871230 TTTTCAATTTAAGTTTTTC-GAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
2871294 CATCCTGAGGTAT
66 C--GCTGAGGTAT
* *
2871307 TTTTCAATTTATGTTTTTC-AAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
2871371 CATCTTTAGGTAT
66 C-GC-TGAGGTAT
2871384 TTTTCAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
2871449 ACATCTTGAGGTAT
65 AC-GC-TGAGGTAT
* * * *
2871463 TTTTCAATTTTTTGCTTTTCAAAAAAATGAATTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTCAA-TTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
2871528 ACATCCTGAGGTAT
65 AC--GCTGAGGTAT
* *
2871542 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTTA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
2871607 CATCATGAGGTAT
66 C-GC-TGAGGTAT
* *
2871620 TTTTCAATTTCTGTTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
*
2871685 CACGTTGAGGTAT
64 CACGCTGAGGTAT
* * *
2871698 TTTTCAATTTTTGCTTTTCGAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
*
2871763 CACCCTGAGGTAT
64 CACGCTGAGGTAT
* * * *
2871776 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCAAGATGTGGGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
2871841 CACGCTGAGGTAT
64 CACGCTGAGGTAT
* *
2871854 TTTTCAATTTTTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
2871919 CACGCTGAGGTAT
64 CACGCTGAGGTAT
* *
2871932 TTTTCAATTTCTGTTTTT--AAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGTCG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--
*
2871995 CATGCTGAGGTAT
64 CACGCTGAGGTAT
* *
2872008 TTTTCAATTTCTGTTGTTCAAAAAAAATCAACTCATATTGCGATG-GGTGAGTTGAGCCTCAGG-
1 TTTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGA-GAGGTGAGTTGAGCCTCGGGT
**
2872071 CACATGCCAAGGTA-
64 CAC--GCTGAGGTAT
* * * * * * *
2872085 TTTTCGATTTTTGTTTTTC--GAAGATCAACTCATAATCCGAGAGGTGAGTTGAGCTTCGGGTC
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
2872147 GCATGCTCGG
Statistics
Matches: 1152, Mismatches: 115, Indels: 60
0.87 0.09 0.05
Matches are distributed among these distances:
73 5 0.00
74 93 0.08
75 112 0.10
76 165 0.14
77 163 0.14
78 437 0.38
79 163 0.14
80 14 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (76 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
CGCTGAGGTAT
Done.