Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 3 of 14
Found at i:339661 original size:49 final size:51
Alignment explanation
Indices: 339608--339721 Score: 196
Period size: 50 Copynumber: 2.3 Consensus size: 51
339598 TAAACAGTAC
339608 ATGTATCGATACATTCTA-TTTTTTACCCAAATGTATCGATACATT-TTCA
1 ATGTATCGATACATTCTATTTTTTTACCCAAATGTATCGATACATTATTCA
* *
339657 ATGTATCGATACATTCTATTTTTTTACCCAGATGTATCGATACATTATTTA
1 ATGTATCGATACATTCTATTTTTTTACCCAAATGTATCGATACATTATTCA
339708 ATGTATCGATACAT
1 ATGTATCGATACAT
339722 CTAGTTTGTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
49 18 0.30
50 26 0.43
51 17 0.28
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (51 bp):
ATGTATCGATACATTCTATTTTTTTACCCAAATGTATCGATACATTATTCA
Found at i:343689 original size:18 final size:18
Alignment explanation
Indices: 343666--343700 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
343656 TATATTGATA
* *
343666 TATTTAATTTTTTAAAAT
1 TATTTAAATATTTAAAAT
343684 TATTTAAATATTTAAAA
1 TATTTAAATATTTAAAA
343701 AATTATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTAAATATTTAAAAT
Found at i:343734 original size:14 final size:14
Alignment explanation
Indices: 343691--343735 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
343681 AATTATTTAA
*
343691 ATATTTAAAAAATT
1 ATATTTAAATAATT
**
343705 ATATTTTTATAATT
1 ATATTTAAATAATT
*
343719 ATATTTAAATATTT
1 ATATTTAAATAATT
343733 ATA
1 ATA
343736 CACAAATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATTTAAATAATT
Found at i:344898 original size:2 final size:2
Alignment explanation
Indices: 344891--344932 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
344881 GTTTTAGAAC
344891 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
344933 TAAATCCCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345699 original size:50 final size:50
Alignment explanation
Indices: 345657--345842 Score: 248
Period size: 50 Copynumber: 3.7 Consensus size: 50
345647 AATTATAGTT
* * * *
345657 ACCTTTCTCTATTGTCAAA-GATTGGTGAAGAATAGTCAACAATTACGACT
1 ACCTCTCTCGATTGTCAAATG-TTGGTGAAGAATAGTCAACAATTACGGCC
* * *
345707 ACCTCTCTCGATTGTCAAATGTTGGTGAATAATAGTCAGCAATTACGGTC
1 ACCTCTCTCGATTGTCAAATGTTGGTGAAGAATAGTCAACAATTACGGCC
* * * *
345757 ACCTCTCTCGATTGCCAAAGGTTGGTGAAGAATAATCAATAATTACGGCC
1 ACCTCTCTCGATTGTCAAATGTTGGTGAAGAATAGTCAACAATTACGGCC
*
345807 ACCTCTCTCGATTGTTAAATGTTGGTGAAGAATAGT
1 ACCTCTCTCGATTGTCAAATGTTGGTGAAGAATAGT
345843 TAAATCACTT
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
50 116 0.99
51 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (50 bp):
ACCTCTCTCGATTGTCAAATGTTGGTGAAGAATAGTCAACAATTACGGCC
Found at i:345813 original size:100 final size:100
Alignment explanation
Indices: 345657--345842 Score: 282
Period size: 100 Copynumber: 1.9 Consensus size: 100
345647 AATTATAGTT
* * * * *
345657 ACCTTTCTCTATTGTCAAAGATTGGTGAAGAATAGTCAACAATTACGACTACCTCTCTCGATTGT
1 ACCTCTCTCGATTGCCAAAGATTGGTGAAGAATAATCAACAATTACGACCACCTCTCTCGATTGT
*
345722 CAAATGTTGGTGAATAATAGTCAGCAATTACGGTC
66 CAAATGTTGGTGAAGAATAGTCAGCAATTACGGTC
* * *
345757 ACCTCTCTCGATTGCCAAAGGTTGGTGAAGAATAATCAATAATTACGGCCACCTCTCTCGATTGT
1 ACCTCTCTCGATTGCCAAAGATTGGTGAAGAATAATCAACAATTACGACCACCTCTCTCGATTGT
*
345822 TAAATGTTGGTGAAGAATAGT
66 CAAATGTTGGTGAAGAATAGT
345843 TAAATCACTT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 76 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (100 bp):
ACCTCTCTCGATTGCCAAAGATTGGTGAAGAATAATCAACAATTACGACCACCTCTCTCGATTGT
CAAATGTTGGTGAAGAATAGTCAGCAATTACGGTC
Found at i:350255 original size:50 final size:50
Alignment explanation
Indices: 350185--350387 Score: 273
Period size: 50 Copynumber: 4.1 Consensus size: 50
350175 ATATGCTTAG
* * *
350185 AGTCAACAATTACGATCACCTTTCTCTATTGTCAAAGGTTAGT-AAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTAGTGAAA-AAT
* * * * *
350235 AATTAACAATTACAACCACCTCTCTCGATTATCAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTAGTGAAAAAT
* * *
350285 AGTCAACAATTACGACTACCTCTCTCGATTGTCAAAGATTGGTGAAAAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTAGTGAAAAAT
* *
350335 AGTCAACAATTACGATCACCTCTCTCGATTGTCAAAAGTTAGTGAAAAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTAGTGAAAAAT
350385 AGT
1 AGT
350388 TAAATCATTT
Statistics
Matches: 133, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
50 130 0.98
51 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAGGTTAGTGAAAAAT
Found at i:351682 original size:2 final size:2
Alignment explanation
Indices: 351670--351700 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
351660 TTAAATTAGC
*
351670 TA TA CA 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 T
351701 TCACTTGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:352112 original size:20 final size:20
Alignment explanation
Indices: 352069--352112 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
352059 TACTACGTTA
*
352069 TTTAATTTCATTATTTTAAT
1 TTTAATTTCATTATATTAAT
*
352089 TTTAATTTTATTA-ATTAAT
1 TTTAATTTCATTATATTAAT
352108 CTTTA
1 -TTTA
352113 TCGCTGTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAATTTCATTATATTAAT
Found at i:353117 original size:2 final size:2
Alignment explanation
Indices: 353105--353148 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
353095 AATATTCATT
* *
353105 TA TA TA CA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
353147 TA
1 TA
353149 ATACATAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:355485 original size:29 final size:27
Alignment explanation
Indices: 355450--355513 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
355440 TTGTTATCTC
*
355450 AAAAAATAATAATAAAATTAATTTATTAT
1 AAAAAATAATAATAAAA-T-ATATATTAT
* * *
355479 ATAAAATAATTATTAAATATATATTAT
1 AAAAAATAATAATAAAATATATATTAT
355506 AAAAAATA
1 AAAAAATA
355514 TGATATATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 15 0.50
28 1 0.03
29 14 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAAAATAATAATAAAATATATATTAT
Found at i:355493 original size:16 final size:18
Alignment explanation
Indices: 355461--355493 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
355451 AAAAATAATA
355461 ATAAAATTAATTTATTAT
1 ATAAAATTAATTTATTAT
355479 ATAAAA-TAA-TTATTA
1 ATAAAATTAATTTATTA
355494 AATATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTATTAT
Found at i:356319 original size:3 final size:3
Alignment explanation
Indices: 356311--356354 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
356301 GATTAAAGTT
356311 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
356355 TTGGCAGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:357630 original size:11 final size:11
Alignment explanation
Indices: 357614--357660 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
357604 TGTTAGCATT
357614 TTATATTTATA
1 TTATATTTATA
*
357625 TTATATTTATG
1 TTATATTTATA
*
357636 TTATTTTTAATA
1 TTATATTT-ATA
357648 TTATTATTT-TA
1 TTA-TATTTATA
357659 TT
1 TT
357661 TAAATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 21 0.70
12 5 0.17
13 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
TTATATTTATA
Found at i:357668 original size:24 final size:27
Alignment explanation
Indices: 357623--357676 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
357613 TTTATATTTA
**
357623 TATTATATTTATGTTATTTTTAAT-AT
1 TATTATATTTATGTTAAATTTAATAAT
357649 TATTAT-TTTAT-TTAAATTTAATAAT
1 TATTATATTTATGTTAAATTTAATAAT
357674 TAT
1 TAT
357677 ATAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 10 0.40
26 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TATTATATTTATGTTAAATTTAATAAT
Found at i:357681 original size:17 final size:17
Alignment explanation
Indices: 357656--357719 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
357646 TATTATTATT
*
357656 TTATTTAAATTTAATAA
1 TTATATAAATTTAATAA
*
357673 TTATATAAATTTTAAAATA
1 TTATATAAA-TTTAATA-A
357692 TTA-AT-AATTT-AT-A
1 TTATATAAATTTAATAA
357705 TTATATAAATCTTAA
1 TTATATAAAT-TTAA
357720 CATAGGTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
13 4 0.11
14 2 0.05
15 4 0.11
16 5 0.13
17 11 0.29
18 8 0.21
19 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATATAAATTTAATAA
Found at i:359119 original size:2 final size:2
Alignment explanation
Indices: 359112--359140 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
359102 CACAAAGAGG
359112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
359141 ACATTAAAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:362204 original size:2 final size:2
Alignment explanation
Indices: 362197--362238 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
362187 ATTCATGTTT
*
362197 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
362239 AATAAAATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:362719 original size:25 final size:25
Alignment explanation
Indices: 362690--362761 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 25
362680 ATTATATTTA
*
362690 TATTATATTTATATATTT-TATTAAT
1 TATTATATTT-TATATTTATATAAAT
362715 TATTATATTTTATATTTATATAAAT
1 TATTATATTTTATATTTATATAAAT
*
362740 TTTGATATATTTTA-ATTTATAT
1 TAT--TATATTTTATATTTATAT
362762 TATATAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
24 7 0.17
25 18 0.43
26 8 0.19
27 9 0.21
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (25 bp):
TATTATATTTTATATTTATATAAAT
Found at i:362751 original size:10 final size:9
Alignment explanation
Indices: 362682--362767 Score: 54
Period size: 10 Copynumber: 9.4 Consensus size: 9
362672 CATAAACAAT
362682 TATA-TTTA
1 TATATTTTA
362690 TATTATATTTA
1 TA-TAT-TTTA
362701 TATATTTTA
1 TATATTTTA
*
362710 T-TA-ATTA
1 TATATTTTA
362717 TTATATTTTA
1 -TATATTTTA
*
362727 TAT-TTATA
1 TATATTTTA
*
362735 TAAATTTTGA
1 TATATTTT-A
362745 TATATTTTAA
1 TATATTTT-A
* *
362755 TTTATATTA
1 TATATTTTA
362764 TATA
1 TATA
362768 AATTAAAATA
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
7 3 0.05
8 11 0.18
9 19 0.32
10 21 0.35
11 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (9 bp):
TATATTTTA
Found at i:362759 original size:32 final size:32
Alignment explanation
Indices: 362692--362808 Score: 97
Period size: 32 Copynumber: 3.8 Consensus size: 32
362682 TATATTTATA
** *
362692 TTATATTTATATATTTTATTAATTATTATATT
1 TTATATTTATATAAATTATTAATTATTATAAT
* *
362724 TTATATTTATATAAATT-TTGATATATTTTAAT
1 TTATATTTATATAAATTATTAAT-TATTATAAT
*
362756 TTATA-TTATATAAATTA--AAATA-TAT-AT
1 TTATATTTATATAAATTATTAATTATTATAAT
*
362783 TTATA-TTATATTATATT-TTAATTATT
1 TTATATTTATA-TAAATTATTAATTATT
362809 TTATTTCATA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
27 12 0.17
28 7 0.10
29 6 0.09
30 2 0.03
31 15 0.22
32 27 0.39
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
TTATATTTATATAAATTATTAATTATTATAAT
Found at i:363789 original size:2 final size:2
Alignment explanation
Indices: 363782--363811 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
363772 AAGGAGGAAA
363782 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
363812 TTTCAGGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:364026 original size:29 final size:29
Alignment explanation
Indices: 363962--364031 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
363952 CTTAAAGTTT
*
363962 AATTTAATATTT-ATATAATTATTTTTAA
1 AATTTAATATTTAATATAATTAATTTTAA
**
363990 AAGATAATATTTAATA-AATTTAATTTTAA
1 AATTTAATATTTAATATAA-TTAATTTTAA
*
364019 ATTTTAATATTTA
1 AATTTAATATTTA
364032 TAATTTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 12 0.35
29 22 0.65
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
AATTTAATATTTAATATAATTAATTTTAA
Found at i:366126 original size:16 final size:17
Alignment explanation
Indices: 366097--366136 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
366087 TTTAAACATG
366097 TTATA-TAA-TGTTTTA
1 TTATATTAATTGTTTTA
*
366112 TTATATTAATTTTTTTA
1 TTATATTAATTGTTTTA
366129 TT-TATTAA
1 TTATATTAA
366137 ATATGTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 9 0.41
17 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTATATTAATTGTTTTA
Found at i:367181 original size:24 final size:24
Alignment explanation
Indices: 367153--367204 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
367143 TTTTATTTAA
367153 ATTTA-ATTATAAA-AATATATAAAT
1 ATTTATATTA-AAATAAT-TATAAAT
*
367177 ATTTATATTAAAATAATTTTAAAT
1 ATTTATATTAAAATAATTATAAAT
367201 ATTT
1 ATTT
367205 TAATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTATATTAAAATAATTATAAAT
Found at i:367228 original size:19 final size:19
Alignment explanation
Indices: 367187--367231 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
367177 ATTTATATTA
* *
367187 AAATA-ATTTTAAATATTT
1 AAATATATTTTAAAGAGTT
*
367205 TAATATATTTTAAAGAGTT
1 AAATATATTTTAAAGAGTT
367224 AAATATAT
1 AAATATAT
367232 ATTTTAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
AAATATATTTTAAAGAGTT
Found at i:368762 original size:22 final size:22
Alignment explanation
Indices: 368737--368787 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
368727 TTAATTTAAT
368737 AAAAATAACA-TATTAA-ATATAA
1 AAAAATAA-AGTATTAATA-ATAA
*
368759 AAAATTAAAGTATTAATAATAA
1 AAAAATAAAGTATTAATAATAA
*
368781 AATAATA
1 AAAAATA
368788 CTTGCACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATAAAGTATTAATAATAA
Found at i:369311 original size:12 final size:12
Alignment explanation
Indices: 369294--369329 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
369284 AAATATAAAT
369294 AATTAAATTTAA
1 AATTAAATTTAA
*
369306 AATTAAATATAAA
1 AATTAAAT-TTAA
369319 AATTAAATTTA
1 AATTAAATTTA
369330 CTTTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTAAATTTAA
Found at i:369408 original size:19 final size:19
Alignment explanation
Indices: 369370--369409 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
369360 AAACTCAAAC
*
369370 AATTAAAATTTTAAATTAA
1 AATTAAAATTTTAAAATAA
369389 AATTAAAA-TTTACAAATAA
1 AATTAAAATTTTA-AAATAA
369408 AA
1 AA
369410 CTCAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAAAATTTTAAAATAA
Found at i:378447 original size:21 final size:22
Alignment explanation
Indices: 378423--378475 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
378413 GTTAAGGTTC
378423 TATTTATTTTTTAAA-TAATTT
1 TATTTATTTTTTAAATTAATTT
378444 TATTT-TTTATTTAAATTAATTT
1 TATTTATTT-TTTAAATTAATTT
*
378466 T-TTTAATTTT
1 TATTTATTTTT
378476 AATTTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.11
21 16 0.57
22 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTATTTTTTAAATTAATTT
Found at i:378481 original size:14 final size:15
Alignment explanation
Indices: 378459--378498 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
378449 TTTATTTAAA
378459 TTAATTTTTTTAATT
1 TTAATTTTTTTAATT
378474 TTAATTTTTTTAATT
1 TTAATTTTTTTAATT
*
378489 TAAATTTTTT
1 TTAATTTTTT
378499 AAATATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTAATTTTTTTAATT
Found at i:378496 original size:29 final size:31
Alignment explanation
Indices: 378438--378500 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
378428 ATTTTTTAAA
* *
378438 TAATTTTATTTTTTATTTAAATTAATTTTTT
1 TAATTTTATATTTTATTTAAATTAAATTTTT
*
378469 TAATTTTA-ATTTT-TTTAATTTAAATTTTT
1 TAATTTTATATTTTATTTAAATTAAATTTTT
378498 TAA
1 TAA
378501 ATATCAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.59
30 4 0.14
31 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (31 bp):
TAATTTTATATTTTATTTAAATTAAATTTTT
Found at i:378499 original size:14 final size:14
Alignment explanation
Indices: 378448--378500 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
378438 TAATTTTATT
*
378448 TTTTATTTAAATTAA
1 TTTT-TTTAATTTAA
378463 TTTTTTTAATTTTAA
1 TTTTTTTAA-TTTAA
378478 TTTTTTTAATTTAA
1 TTTTTTTAATTTAA
*
378492 ATTTTTTAA
1 TTTTTTTAA
378501 ATATCAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
14 18 0.51
15 17 0.49
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTTTAATTTAA
Found at i:378736 original size:3 final size:3
Alignment explanation
Indices: 378728--378764 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
378718 TGACAAACTT
378728 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
378765 TACAGGTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:379211 original size:22 final size:21
Alignment explanation
Indices: 379167--379209 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
379157 ATACTTTTTT
*
379167 TAAAAAAATTATAATTTTAAA
1 TAAAAAAATTATAATATTAAA
379188 TAAAAAAATTTATAAATATTAA
1 TAAAAAAA-TTAT-AATATTAA
379210 TATTCGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAAAAATTATAATATTAAA
Found at i:380068 original size:17 final size:17
Alignment explanation
Indices: 380043--380076 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
380033 TATATTTTAC
*
380043 AAAATTAAAAATTAATT
1 AAAAATAAAAATTAATT
380060 AAAAATAAAAATTAATT
1 AAAAATAAAAATTAATT
380077 TAATTCAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATAAAAATTAATT
Found at i:384883 original size:30 final size:31
Alignment explanation
Indices: 384849--384940 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 31
384839 TAAAATAATT
384849 AAAATATAATTTAAAATTTAATAT-AATATA
1 AAAATATAATTTAAAATTTAATATGAATATA
* * **
384879 AAAATATAATAT-AAGTGAAATATGAATATA
1 AAAATATAATTTAAAATTTAATATGAATATA
*
384909 TAAATAT--TTTAAAATTTTAATATGAAT-TA
1 AAAATATAATTTAAAA-TTTAATATGAATATA
384938 AAA
1 AAA
384941 TTTTGATACA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
28 2 0.04
29 14 0.29
30 33 0.67
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (31 bp):
AAAATATAATTTAAAATTTAATATGAATATA
Found at i:384886 original size:13 final size:13
Alignment explanation
Indices: 384868--384915 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
384858 TTTAAAATTT
384868 AATATAATATAAA
1 AATATAATATAAA
384881 AATATAATATAAGTGA
1 AATATAATATAA---A
*
384897 AATATGAATATATA
1 AATAT-AATATAAA
384911 AATAT
1 AATAT
384916 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.40
14 6 0.20
16 6 0.20
17 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (13 bp):
AATATAATATAAA
Found at i:385894 original size:2 final size:2
Alignment explanation
Indices: 385887--385916 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
385877 ATATGTATGT
385887 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
385917 CTTGTGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:387708 original size:2 final size:2
Alignment explanation
Indices: 387701--387734 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
387691 ACAACTAACA
387701 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
387735 TCTTAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:394350 original size:19 final size:18
Alignment explanation
Indices: 394328--394371 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
394318 ATTTTGATAA
394328 AAATATTAAATTAAAAAAT
1 AAATATTAAA-TAAAAAAT
*
394347 AAAT-TTTAATAAAAAAT
1 AAATATTAAATAAAAAAT
*
394364 AAAAATTA
1 AAATATTA
394372 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 11 0.52
18 6 0.29
19 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATTAAATAAAAAAT
Found at i:394377 original size:18 final size:17
Alignment explanation
Indices: 394337--394380 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
394327 AAAATATTAA
**
394337 ATTAAAAAATAAATTTT
1 ATTAAAAAATAAAAATT
*
394354 AATAAAAAATAAAAATT
1 ATTAAAAAATAAAAATT
*
394371 ATTTAAAAAT
1 ATTAAAAAAT
394381 TAATCAAATC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAAAAATAAAAATT
Found at i:394469 original size:23 final size:22
Alignment explanation
Indices: 394434--394490 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 22
394424 ATTTTTTAAT
394434 TATATAATA-TATATTTTATAT
1 TATATAATATTATATTTTATAT
* *
394455 TTTATATATATTATAATTTATAT
1 TATATA-ATATTATATTTTATAT
394478 TATATAAATATTA
1 TATAT-AATATTA
394491 AATATACACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 3 0.10
23 21 0.70
24 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATAATATTATATTTTATAT
Found at i:394474 original size:16 final size:16
Alignment explanation
Indices: 394441--394482 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
394431 AATTATATAA
* *
394441 TATATATTTTATATTT
1 TATATATATTATAATT
394457 TATATATATTATAATT
1 TATATATATTATAATT
394473 TATATTATAT
1 TATA-TATAT
394483 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATATATTATAATT
Found at i:394528 original size:14 final size:14
Alignment explanation
Indices: 394479--394528 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
394469 AATTTATATT
394479 ATATAAATATTAAA
1 ATATAAATATTAAA
* *
394493 TATACACAATATTATA
1 -ATATA-AATATTAAA
394509 ATATAAATATTAAA
1 ATATAAATATTAAA
*
394523 AAATAA
1 ATATAA
394529 GTTAAATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 13 0.45
15 8 0.28
16 8 0.28
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATAAATATTAAA
Found at i:394670 original size:19 final size:21
Alignment explanation
Indices: 394631--394671 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
394621 TGAATTTTAA
*
394631 AATATTTTATATTTATAATTT
1 AATAATTTATATTTATAATTT
394652 AATAATTTAT-TTTAT-ATTT
1 AATAATTTATATTTATAATTT
394671 A
1 A
394672 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 5 0.26
21 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
AATAATTTATATTTATAATTT
Found at i:394677 original size:14 final size:14
Alignment explanation
Indices: 394633--394678 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
394623 AATTTTAAAA
394633 TATTTTATATTTAT
1 TATTTTATATTTAT
* * *
394647 AATTTAATA-AT-T
1 TATTTTATATTTAT
394659 TATTTTATATTTAT
1 TATTTTATATTTAT
394673 TATTTT
1 TATTTT
394679 TTAATTATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
12 8 0.33
13 2 0.08
14 14 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTATATTTAT
Found at i:394683 original size:26 final size:27
Alignment explanation
Indices: 394632--394690 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
394622 GAATTTTAAA
394632 ATATTTTATATTTATAATTTAATAATT
1 ATATTTTATATTTATAATTTAATAATT
* **
394659 -TATTTTATATTTATTATTTTTTAATT
1 ATATTTTATATTTATAATTTAATAATT
394685 ATATTT
1 ATATTT
394691 AAAAGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
ATATTTTATATTTATAATTTAATAATT
Found at i:394686 original size:14 final size:14
Alignment explanation
Indices: 394633--394690 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
394623 AATTTTAAAA
*
394633 TATTTTATATTTAT
1 TATTTTATAATTAT
* *
394647 AATTTAATAA-T-T
1 TATTTTATAATTAT
*
394659 TATTTTATATTTAT
1 TATTTTATAATTAT
*
394673 TATTTTTTAATTA-
1 TATTTTATAATTAT
394686 TATTT
1 TATTT
394691 AAAAGATTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
12 8 0.24
13 7 0.21
14 19 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTATAATTAT
Found at i:396807 original size:15 final size:14
Alignment explanation
Indices: 396788--396853 Score: 68
Period size: 12 Copynumber: 4.9 Consensus size: 14
396778 ATTTACTTAT
396788 ATTATATTTTTTTA
1 ATTATATTTTTTTA
396802 ATT-TA-TTTTTTA
1 ATTATATTTTTTTA
*
396814 AGGTATATTTTTTTA
1 A-TTATATTTTTTTA
396829 ATT-TA-TTTTTTA
1 ATTATATTTTTTTA
*
396841 AGGTATATTTTTT
1 A-TTATATTTTTT
396854 AAAATTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
12 16 0.37
13 6 0.14
14 8 0.19
15 13 0.30
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTATATTTTTTTA
Found at i:396810 original size:13 final size:13
Alignment explanation
Indices: 396792--396839 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
396782 ACTTATATTA
396792 TATTTTTTTAATT
1 TATTTTTTTAATT
*
396805 TA-TTTTTTAAGGTA
1 TATTTTTTTAA--TT
396819 TATTTTTTTAATT
1 TATTTTTTTAATT
396832 TATTTTTT
1 TATTTTTT
396840 AAGGTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 8 0.27
13 11 0.37
14 3 0.10
15 8 0.27
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (13 bp):
TATTTTTTTAATT
Found at i:396822 original size:14 final size:14
Alignment explanation
Indices: 396805--396855 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
396795 TTTTTTAATT
396805 TATTTTTTAAGGTA
1 TATTTTTTAAGGTA
*
396819 TATTTTTTTAA--TT
1 TA-TTTTTTAAGGTA
396832 TATTTTTTAAGGTA
1 TATTTTTTAAGGTA
396846 TATTTTTTAA
1 TATTTTTTAA
396856 AATTTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 13 0.41
15 8 0.25
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (14 bp):
TATTTTTTAAGGTA
Found at i:396822 original size:27 final size:27
Alignment explanation
Indices: 396790--396853 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
396780 TTACTTATAT
396790 TATATTTTTTTAATTTATTTTTTAAGG
1 TATATTTTTTTAATTTATTTTTTAAGG
396817 TATATTTTTTTAATTTATTTTTTAAGG
1 TATATTTTTTTAATTTATTTTTTAAGG
396844 TATATTTTTT
1 TATATTTTTT
396854 AAAATTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (27 bp):
TATATTTTTTTAATTTATTTTTTAAGG
Found at i:396999 original size:21 final size:21
Alignment explanation
Indices: 396975--397015 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
396965 AAAAATTGTA
396975 TAATATA-AATAAATATAAAAT
1 TAATATATAATAAAT-TAAAAT
*
396996 TAATATATTATAAATTAAAA
1 TAATATATAATAAATTAAAA
397016 AAATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATATATAATAAATTAAAAT
Found at i:397025 original size:20 final size:22
Alignment explanation
Indices: 396983--397025 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
396973 TATAATATAA
* *
396983 ATAAATATAAAATTAATATATT
1 ATAAATATAAAATAAATAAATT
397005 ATAAAT-TAAAA-AAATAAATT
1 ATAAATATAAAATAAATAAATT
397025 A
1 A
397026 ATTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAAATATAAAATAAATAAATT
Found at i:397092 original size:23 final size:23
Alignment explanation
Indices: 397039--397094 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
397029 TAAATTTTAA
*
397039 ATATTAAAACTAAAATTTAATTT
1 ATATTTAAACTAAAATTTAATTT
*
397062 ATATTTTAAAC-AAATTTTAATTTT
1 ATA-TTTAAACTAAAATTTAA-TTT
*
397086 TTATTTAAA
1 ATATTTAAA
397095 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTTAAACTAAAATTTAATTT
Found at i:397680 original size:3 final size:3
Alignment explanation
Indices: 397672--397698 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
397662 TGAGTCTCCC
397672 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
397699 ACTGGGTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:400922 original size:2 final size:2
Alignment explanation
Indices: 400915--400946 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
400905 GGAATTCCGT
400915 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
400947 GTTATATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:402348 original size:39 final size:42
Alignment explanation
Indices: 402261--402341 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
402251 TTAAAGAACC
* *
402261 AATATATATATATATATATGTATTAATCAATAATTAAAAAATA
1 AATAAATATATATATATATATATTAATCAATAATT-AAAAATA
* *
402304 AATAAATATATATATATATAT-TTAATGAATCATTAAAA
1 AATAAATATATATATATATATATTAATCAATAATTAAAA
402342 TGATAAAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.12
42 11 0.32
43 19 0.56
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (42 bp):
AATAAATATATATATATATATATTAATCAATAATTAAAAATA
Found at i:402572 original size:17 final size:18
Alignment explanation
Indices: 402544--402586 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
402534 TGAAATACAG
*
402544 TTTATATTATTTTAATTA
1 TTTATATTATTTTAAATA
402562 TTTAT-TTATTTTAAATA
1 TTTATATTATTTTAAATA
*
402579 TTCATATT
1 TTTATATT
402587 TTATATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATATTATTTTAAATA
Found at i:402883 original size:8 final size:8
Alignment explanation
Indices: 402848--402891 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
402838 TGAGGAGGGA
402848 ATATATAC
1 ATATATAC
*
402856 ATACATAC
1 ATATATAC
*
402864 ATACATAC
1 ATATATAC
*
402872 ATATATAT
1 ATATATAC
*
402880 ATATATAT
1 ATATATAC
402888 ATAT
1 ATAT
402892 TTGTAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:402891 original size:12 final size:12
Alignment explanation
Indices: 402848--402890 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
402838 TGAGGAGGGA
402848 ATATATACATAC
1 ATATATACATAC
*
402860 ATACATACATAC
1 ATATATACATAC
* *
402872 ATATATATATAT
1 ATATATACATAC
402884 ATATATA
1 ATATATA
402891 TTTGTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATATACATAC
Found at i:405002 original size:23 final size:23
Alignment explanation
Indices: 404946--405002 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
404936 ATTTTTATTT
404946 AATTTTATATAAAAATATATAAA
1 AATTTTATATAAAAATATATAAA
* * *
404969 TA-TTAATATAAAAATAATTTAAA
1 AATTTTATATAAAAAT-ATATAAA
404992 AATTTTA-ATAA
1 AATTTTATATAA
405003 TAATTTAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
22 12 0.44
23 12 0.44
24 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTTTATATAAAAATATATAAA
Found at i:406005 original size:21 final size:21
Alignment explanation
Indices: 405981--406023 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
405971 ATTTTAATTG
* *
405981 ATTAATATTTTATATTATATA
1 ATTAATAATATATATTATATA
* *
406002 ATTATTAATATATATTTTATA
1 ATTAATAATATATATTATATA
406023 A
1 A
406024 CATGTTTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATAATATATATTATATA
Found at i:408124 original size:18 final size:18
Alignment explanation
Indices: 408103--408137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
408093 TTAATTAAGA
* *
408103 AAATTTATCTAATAAAAC
1 AAATTAATCTAACAAAAC
408121 AAATTAATCTAACAAAA
1 AAATTAATCTAACAAAA
408138 AAACTTATTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATTAATCTAACAAAAC
Found at i:409395 original size:2 final size:2
Alignment explanation
Indices: 409388--409420 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
409378 GATGAACTGC
409388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
409421 AACATCAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:411536 original size:34 final size:34
Alignment explanation
Indices: 411472--411654 Score: 251
Period size: 34 Copynumber: 5.4 Consensus size: 34
411462 CGTCCCTGGC
* *
411472 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
411505 TGTTGACTAAATGGGAAATTTGATAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
411539 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
411573 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
411607 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
411641 TGTTGATTAAATGG
1 TGTTGATTAAATGG
411655 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
33 11 0.08
34 119 0.92
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:412015 original size:19 final size:19
Alignment explanation
Indices: 411959--412021 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
411949 TGGTTGTCGA
**
411959 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
411978 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
411997 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
412016 GTTACT
1 GGTACT
412022 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:416153 original size:34 final size:34
Alignment explanation
Indices: 416087--416271 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
416077 AAGTGGGAGA
* *
416087 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
416120 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
416154 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
416188 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
416222 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
416256 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
416272 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:417592 original size:22 final size:22
Alignment explanation
Indices: 417557--417611 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
417547 ATATTATTTT
*
417557 TATT-TAAAT-TTAATTTTAAAA
1 TATTATAAATATTAA-TATAAAA
417578 -ATTATAAATATTAATATAAAA
1 TATTATAAATATTAATATAAAA
*
417599 TATTAAAAATATT
1 TATTATAAATATT
417612 TTAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 3 0.10
21 11 0.38
22 15 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATTATAAATATTAATATAAAA
Found at i:417858 original size:16 final size:15
Alignment explanation
Indices: 417834--417863 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
417824 TTTTAGAACT
417834 TTTATTATTTATATG
1 TTTATTATTTATATG
417849 TTTATATATTTATAT
1 TTTAT-TATTTATAT
417864 TAAATAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTATTATTTATATG
Found at i:418397 original size:22 final size:24
Alignment explanation
Indices: 418349--418401 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
418339 TTAAAAAAAC
* *
418349 TAATGTTTTTATTATTAAATTTAAA
1 TAATTTTTTTATAATTAAA-TTAAA
418374 TAATTTTTTTATAATTAAA-T-AA
1 TAATTTTTTTATAATTAAATTAAA
418396 TAATTT
1 TAATTT
418402 AATTTGGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
23 1 0.04
25 17 0.65
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TAATTTTTTTATAATTAAATTAAA
Found at i:419012 original size:57 final size:58
Alignment explanation
Indices: 418909--419020 Score: 165
Period size: 57 Copynumber: 1.9 Consensus size: 58
418899 ATCACAACTT
418909 TAATCCTTTGCCTTTCTTTCTCACTTCTAAACTCTAGCCAAAAATCCATTTTTTTCTC
1 TAATCCTTTGCCTTTCTTTCTCACTTCTAAACTCTAGCCAAAAATCCATTTTTTTCTC
* * * *
418967 TAATCCTTT-CCTTTCTTTCTCATTTCTAAGCTTTAG-TAAATAATCCATTTTTTT
1 TAATCCTTTGCCTTTCTTTCTCACTTCTAAACTCTAGCCAAA-AATCCATTTTTTT
419021 TCATAAATGC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 3 0.06
57 37 0.76
58 9 0.18
ACGTcount: A:0.22, C:0.25, G:0.04, T:0.49
Consensus pattern (58 bp):
TAATCCTTTGCCTTTCTTTCTCACTTCTAAACTCTAGCCAAAAATCCATTTTTTTCTC
Found at i:419487 original size:16 final size:16
Alignment explanation
Indices: 419456--419485 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
419446 AAGTCTCATT
419456 ATTTTATCTGATTTTA
1 ATTTTATCTGATTTTA
419472 ATTTTATCT-ATTTT
1 ATTTTATCTGATTTT
419486 TACATCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTATCTGATTTTA
Found at i:421914 original size:2 final size:2
Alignment explanation
Indices: 421907--421934 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
421897 TTTGATCTGA
421907 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
421935 GTCTACCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:422837 original size:14 final size:15
Alignment explanation
Indices: 422818--422848 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
422808 TCGAAGTTTG
422818 TTATATTTAT-ATAT
1 TTATATTTATGATAT
422832 TTATATTTATGATAT
1 TTATATTTATGATAT
422847 TT
1 TT
422849 CAGAGTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTATATTTATGATAT
Found at i:429545 original size:22 final size:23
Alignment explanation
Indices: 429519--429574 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
429509 TAATACATTG
*
429519 CCTAACACACCTAATATGC-TCA
1 CCTAACACACCTAATATACTTCA
429541 CCTAACACACCTAATATACTTCA
1 CCTAACACACCTAATATACTTCA
*
429564 CCTAGCACACC
1 CCTAACACACC
429575 ACCTAACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.36, C:0.39, G:0.04, T:0.21
Consensus pattern (23 bp):
CCTAACACACCTAATATACTTCA
Found at i:429579 original size:35 final size:34
Alignment explanation
Indices: 429539--429606 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
429529 CTAATATGCT
*
429539 CACCTAACACACCTAATATACTTCACCTAGCACAC
1 CACCTAACACACCTAATATAC-TCACCTAACACAC
* * *
429574 CACCTAACATACTTAATATGCTCACCTAACACA
1 CACCTAACACACCTAATATACTCACCTAACACA
429607 TATAATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.38, C:0.37, G:0.03, T:0.22
Consensus pattern (34 bp):
CACCTAACACACCTAATATACTCACCTAACACAC
Found at i:429612 original size:22 final size:22
Alignment explanation
Indices: 429574--429633 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
429564 CCTAGCACAC
*
429574 CACCTAACATACTTAATATGCT
1 CACCTAACACACTTAATATGCT
*
429596 CACCTAACACA-TATAATATGTT
1 CACCTAACACACT-TAATATGCT
* * *
429618 TACTTAACACGCTTAA
1 CACCTAACACACTTAA
429634 CAAAGAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (22 bp):
CACCTAACACACTTAATATGCT
Found at i:440533 original size:1 final size:1
Alignment explanation
Indices: 440527--440606 Score: 97
Period size: 1 Copynumber: 80.0 Consensus size: 1
440517 TGGCAATTGG
* * * ** *
440527 AAAAAAAAAAAAAAAAAACAAAACAAAAAAAAAAAGAAAAAAACCAAAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
440592 AAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAA
440607 GTGAAGATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.91, C:0.07, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:440555 original size:25 final size:24
Alignment explanation
Indices: 440527--440606 Score: 124
Period size: 25 Copynumber: 3.2 Consensus size: 24
440517 TGGCAATTGG
440527 AAAAAAAAAAAAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAACAAAA-A
*
440552 AAAAAAAAAAGAAAAAAACCAAAAA
1 AAAAAAAAAA-AAAAAAAACAAAAA
*
440577 AAAAAAACAAAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAACAAAAA
440601 AAAAAA
1 AAAAAA
440607 GTGAAGATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
24 19 0.37
25 20 0.39
26 12 0.24
ACGTcount: A:0.91, C:0.07, G:0.01, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAAAAAAAACAAAAA
Found at i:440587 original size:39 final size:37
Alignment explanation
Indices: 440533--440606 Score: 121
Period size: 39 Copynumber: 1.9 Consensus size: 37
440523 TTGGAAAAAA
440533 AAAAAAAAAAAACAAAACAAAAAAAAAAAGAAAAAAACC
1 AAAAAAAAAAAACAAAA-AAAAAAAAAAA-AAAAAAACC
*
440572 AAAAAAAAAAAACAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA
440607 GTGAAGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 7 0.21
38 10 0.29
39 17 0.50
ACGTcount: A:0.91, C:0.08, G:0.01, T:0.00
Consensus pattern (37 bp):
AAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAACC
Found at i:443383 original size:17 final size:18
Alignment explanation
Indices: 443350--443383 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
443340 AAAAGATCTC
*
443350 AAGCTTGCTTTGGTGTGA
1 AAGCTTGCTTTGATGTGA
443368 AAGCTT-CTTTGATGTG
1 AAGCTTGCTTTGATGTG
443384 CTCCATCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41
Consensus pattern (18 bp):
AAGCTTGCTTTGATGTGA
Found at i:444178 original size:35 final size:34
Alignment explanation
Indices: 444136--444217 Score: 119
Period size: 35 Copynumber: 2.4 Consensus size: 34
444126 TAAAATATCT
*
444136 TGCTCACCTAACACATCACCTAACATACCTAATA
1 TGCTCACCTAACACACCACCTAACATACCTAATA
* *
444170 TGCTTCACCTAACACACCACCTAACATAGCTAATG
1 TGC-TCACCTAACACACCACCTAACATACCTAATA
*
444205 TGCTCACTTAACA
1 TGCTCACCTAACA
444218 AAGAAATTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 12 0.28
35 31 0.72
ACGTcount: A:0.35, C:0.34, G:0.06, T:0.24
Consensus pattern (34 bp):
TGCTCACCTAACACACCACCTAACATACCTAATA
Found at i:445843 original size:20 final size:20
Alignment explanation
Indices: 445818--445880 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
445808 TTATTTAAAA
445818 ATATTAAAAATATTATTTTT
1 ATATTAAAAATATTATTTTT
* * *
445838 ATATTAATATTTTTATATTTT
1 ATATTAAAAATATTAT-TTTT
* *
445859 ATAAATAAAAA-ATTACTTTT
1 AT-ATTAAAAATATTATTTTT
445879 AT
1 AT
445881 TAGTGAAAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 19 0.58
21 9 0.27
22 5 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTAAAAATATTATTTTT
Found at i:446080 original size:2 final size:2
Alignment explanation
Indices: 446073--446116 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
446063 ATCATAAAGA
446073 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
446115 AT
1 AT
446117 GGCCATGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:446730 original size:17 final size:18
Alignment explanation
Indices: 446692--446730 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
446682 TACGTATATC
* *
446692 ATATTCATATTATTTTTT
1 ATATTCATATTATATTTA
446710 ATATT-ATATTATATTTA
1 ATATTCATATTATATTTA
446727 ATAT
1 ATAT
446731 ATTAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTCATATTATATTTA
Found at i:446747 original size:17 final size:19
Alignment explanation
Indices: 446692--446755 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 19
446682 TACGTATATC
*
446692 ATATTCATATTAT-TTT-TT
1 ATATT-ATATTATATTTAAT
446710 ATATTATATTATATTTAAT
1 ATATTATATTATATTTAAT
446729 ATATTA-ATTA-A-TTATAT
1 ATATTATATTATATTTA-AT
446746 ATATTTATAT
1 ATA-TTATAT
446756 AAATTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
16 3 0.08
17 13 0.32
18 15 0.38
19 9 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTATATTATATTTAAT
Found at i:447061 original size:2 final size:2
Alignment explanation
Indices: 447054--447105 Score: 63
Period size: 2 Copynumber: 26.0 Consensus size: 2
447044 TGTAAAGCTA
*
447054 AT AT AT AT AT AT AT AT AT AT AT GT A- AGT GA- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT
447096 AT AT AT AT AT
1 AT AT AT AT AT
447106 GTAAGTGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 2 0.05
2 41 0.93
4 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:447087 original size:30 final size:30
Alignment explanation
Indices: 447053--447114 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
447043 TTGTAAAGCT
447053 AATATATATATATATATATATATGTAAGTG
1 AATATATATATATATATATATATGTAAGTG
447083 AATATATATATATATATATATATGTAAGTG
1 AATATATATATATATATATATATGTAAGTG
447113 AA
1 AA
447115 ACATCAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (30 bp):
AATATATATATATATATATATATGTAAGTG
Found at i:449068 original size:2 final size:2
Alignment explanation
Indices: 449063--449100 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
449053 TTCCATTTCC
449063 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
449101 TTTAAGACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:449296 original size:18 final size:20
Alignment explanation
Indices: 449273--449320 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 20
449263 TTAATAAAAG
449273 ATATTAAAA-AT-TATTTTT
1 ATATTAAAATATATATTTTT
449291 ATATTAAAATTATATATTTTT
1 ATATTAAAA-TATATATTTTT
449312 ATAATTAAA
1 AT-ATTAAA
449321 TTTAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.35
20 2 0.08
21 9 0.35
22 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATATTAAAATATATATTTTT
Found at i:449339 original size:21 final size:21
Alignment explanation
Indices: 449319--449357 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
449309 TTTATAATTA
449319 AATTTAA-TTAAAAATATATT
1 AATTTAATTTAAAAATATATT
*
449339 ATTTTAATTTAAAAATATA
1 AATTTAATTTAAAAATATA
449358 ATTTTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTAATTTAAAAATATATT
Found at i:449356 original size:19 final size:20
Alignment explanation
Indices: 449321--449364 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
449311 TATAATTAAA
*
449321 TTTAATTAAAAATATATTAT
1 TTTAATTAAAAATATATAAT
*
449341 TTTAATTTAAAA-ATATAAT
1 TTTAATTAAAAATATATAAT
449360 TTTAA
1 TTTAA
449365 ATCAGCTCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATTAAAAATATATAAT
Found at i:453055 original size:18 final size:19
Alignment explanation
Indices: 453028--453074 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
453018 TTATTAAAAT
453028 TTAAAAATAATTT-TAATA
1 TTAAAAATAATTTATAATA
*
453046 TTAAATATAATTTATAATTA
1 TTAAAAATAATTTATAA-TA
*
453066 TCAAAAATA
1 TTAAAAATA
453075 TATATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
19 3 0.12
20 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAAAATAATTTATAATA
Found at i:453972 original size:21 final size:21
Alignment explanation
Indices: 453947--453986 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
453937 AATTTTTATT
453947 TAAAT-TTAATTATAAAATACA
1 TAAATATTAA-TATAAAATACA
453968 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
453987 ATTAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATATAAAATACA
Found at i:455611 original size:14 final size:14
Alignment explanation
Indices: 455592--455621 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
455582 ATATTATCTC
*
455592 CTTAATTTCTTTGT
1 CTTAATTTCCTTGT
455606 CTTAATTTCCTTGT
1 CTTAATTTCCTTGT
455620 CT
1 CT
455622 AAATAATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (14 bp):
CTTAATTTCCTTGT
Found at i:459760 original size:16 final size:16
Alignment explanation
Indices: 459739--459770 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
459729 TAACTCTTTA
*
459739 ATATTATTTCGATTAG
1 ATATTATTTCAATTAG
459755 ATATTATTTCAATTAG
1 ATATTATTTCAATTAG
459771 TGAAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.50
Consensus pattern (16 bp):
ATATTATTTCAATTAG
Found at i:461410 original size:2 final size:2
Alignment explanation
Indices: 461388--461437 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
461378 CAACCACCCC
*
461388 AT AT AT TT AT AT -T AT AT -T AT AT AT AT -T 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
461427 AT AT AT AT AT A
1 AT AT AT AT AT A
461438 AAATCTCTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:462913 original size:30 final size:30
Alignment explanation
Indices: 462879--462952 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
462869 AAAGTTTGCT
*
462879 TAGATATAAATTAATGGTTAAAAACTTATA
1 TAGATATAAATTAAAGGTTAAAAACTTATA
* * * *
462909 TAGATATAAATTAAAGTTTAAGAATTTATT
1 TAGATATAAATTAAAGGTTAAAAACTTATA
462939 TAG-TATAAATTAAA
1 TAGATATAAATTAAA
462953 AATTGAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 11 0.28
30 28 0.72
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.39
Consensus pattern (30 bp):
TAGATATAAATTAAAGGTTAAAAACTTATA
Found at i:463052 original size:22 final size:22
Alignment explanation
Indices: 463025--463069 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
463015 AGGTTTTTTA
463025 TTATTATTTTAACCTTTAAAAT
1 TTATTATTTTAACCTTTAAAAT
463047 TTATTATTTTAACCTTTAAAAT
1 TTATTATTTTAACCTTTAAAAT
463069 T
1 T
463070 CAATTTCCAG
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:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTATTTTAACCTTTAAAAT
Found at i:468969 original size:52 final size:52
Alignment explanation
Indices: 468891--469091 Score: 341
Period size: 52 Copynumber: 3.9 Consensus size: 52
468881 CGAAATATGA
*
468891 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
468943 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
468995 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
469047 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
469092 ATGTATCGAT
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
51 2 0.01
52 141 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:469098 original size:13 final size:13
Alignment explanation
Indices: 469080--469104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
469070 CAAAGATCAG
469080 TGTATCGATACAA
1 TGTATCGATACAA
469093 TGTATCGATACA
1 TGTATCGATACA
469105 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:469185 original size:13 final size:13
Alignment explanation
Indices: 469167--469191 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
469157 CAAAAAAACA
469167 TGTATCGATACAT
1 TGTATCGATACAT
469180 TGTATCGATACA
1 TGTATCGATACA
469192 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:469290 original size:21 final size:21
Alignment explanation
Indices: 469249--469290 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
469239 GTTGGGACCT
*
469249 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
469270 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
469291 AAATGTAATT
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:470155 original size:52 final size:52
Alignment explanation
Indices: 470076--470234 Score: 192
Period size: 52 Copynumber: 3.2 Consensus size: 52
470066 AAAGCTGAGA
* *
470076 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
* *
470129 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T--
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
* *
470173 -AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
470224 AAAAGGTGCCA
1 AAAAGGTGCCA
470235 CCGATTTGTG
Statistics
Matches: 89, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
43 37 0.42
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.47
53 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
Found at i:470191 original size:43 final size:43
Alignment explanation
Indices: 470130--470219 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
470120 TAAAGATGGA
*
470130 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
470173 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
470216 AAAG
1 AAAG
470220 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:470421 original size:88 final size:87
Alignment explanation
Indices: 470225--470758 Score: 510
Period size: 88 Copynumber: 6.1 Consensus size: 87
470215 TAAAGATGGA
* * * * *
470225 AAAGG-TGCCACCGATTTGTGGGC-TTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTG--AAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAA-GATGCCACTGACTTGTGGGCTTTGAAAAGG
* *
470286 TTGCCACTGACTTGTGGGCTTTTT
65 GTGCCACTAACTTGTGGGC-TTTT
* *
470310 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAGATGCCACTGACTTGTGGGC-TTTGAAAAGG
470375 GTGCCACTAACTTGTGGGCTTTT
65 GTGCCACTAACTTGTGGGCTTTT
*
470398 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAGATGCCACTGACTTGTGGGC-TTTGAAAAGG
470463 GTGCCACTAACTTGTGGGCTTTT
65 GTGCCACTAACTTGTGGGCTTTT
** * * *
470486 GAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGC--TGAAAAG
1 -AAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAAG
* * * * **
470549 AGTGCTA-TAGAGTTGTGAGCTTACA
64 GGTGCCACTA-ACTTGTGGGCTT-TT
* * * * * * *
470574 AAAGAAAAAGAGTGCCACGGAGTTGTGGAC-TTTGGAAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAG-----G-TTGCCACTGACTTGTGGGCTTTTGAAAAAGATGCCACTGACTTGTGGGCTT-TG
* *
470638 AAAAGGGTGCCACTGATTTGTGGGC-TTT
59 AAAAGGGTGCCACTAACTTGTGGGCTTTT
* * * **
470666 GAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAA
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGG
* * *
470731 ATGCCACTGACTTGTGGACTTTT
65 GTGCCACTAACTTGTGGGCTTTT
*
470754 GAAGG
1 AAAGG
470759 GTGATGAATG
Statistics
Matches: 371, Mismatches: 56, Indels: 41
0.79 0.12 0.09
Matches are distributed among these distances:
85 5 0.01
86 50 0.13
87 62 0.17
88 123 0.33
89 24 0.06
90 44 0.12
91 24 0.06
92 18 0.05
93 1 0.00
94 19 0.05
95 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (87 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGG
TGCCACTAACTTGTGGGCTTTT
Found at i:470678 original size:27 final size:27
Alignment explanation
Indices: 470615--470761 Score: 105
Period size: 29 Copynumber: 5.1 Consensus size: 27
470605 TTGGAAAAGA
* *
470615 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGG
* *
470645 TGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGG
***
470672 TGCCACTGACTTGTGGGCTTTCGAAAAAAAA
1 TGCCACTGACTTGTGGGCTTT-G---AAGGG
***
470703 TGCCACTGACTTGTGGGCTTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTG--AAGGG
*
470732 TGCCACTGACTTGTGGACTTTTGAAGGG
1 TGCCACTGACTTGTGGGC-TTTGAAGGG
470760 TG
1 TG
470762 ATGAATGTCT
Statistics
Matches: 100, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
27 24 0.24
28 5 0.05
29 25 0.25
30 23 0.23
31 23 0.23
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGG
Found at i:470686 original size:121 final size:117
Alignment explanation
Indices: 470472--470747 Score: 304
Period size: 121 Copynumber: 2.3 Consensus size: 117
470462 GGTGCCACTA
* **
470472 ACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTG
1 ACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTG
* *
470537 TGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGG
65 TGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTAC-AAA-AAAAA-A-TGCCACGG
* * * * * * *
470594 AGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGT
1 ACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGT
*** * * * *
470659 GGGCTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTCGAAAAAAAATGCCACTG
66 GGGCTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACAAAAAAAAATGCCACGG
470711 ACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
1 ACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
470748 ACTTTTGAAG
Statistics
Matches: 129, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
117 39 0.30
118 1 0.01
119 5 0.04
120 3 0.02
121 72 0.56
122 9 0.07
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (117 bp):
ACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGT
GGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACAAAAAAAAATGCCACGG
Found at i:470755 original size:30 final size:30
Alignment explanation
Indices: 470223--470756 Score: 465
Period size: 30 Copynumber: 18.1 Consensus size: 30
470213 CTTAAAGATG
* * *
470223 GAAAAGG-TGCCACCGATTTGTGGGC-TTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
470251 GAAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
*
470281 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
470309 -TAAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
470338 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * *
470368 GAACAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
*
470398 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
470426 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
470456 GAAAAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
470486 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
470516 GAAAAGGGTGCCACTAACTTGTGGGC---T
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * * **
470543 GAAAA-GAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GAAAAGGA-TGCCACT-GACTTGTGGGCTT----TT
* * * * *
470577 GAAAAAGAGTGCCACGGAGTTGTGGACTTTG
1 GAAAAGGA-TGCCACTGACTTGTGGGCTTTT
* **
470608 GAAAA-GATGCCACCGACTTGTGGGCTTCG
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
470637 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
470666 G--AAGGTTGCCACTGACTTGTGGGCTTTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
470694 GAAAAAAAATGCCACTGACTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
** *
470724 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
470754 GAA
1 GAA
470757 GGGTGATGAA
Statistics
Matches: 421, Mismatches: 60, Indels: 48
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.00
27 60 0.14
28 32 0.08
29 82 0.19
30 197 0.47
31 25 0.06
34 5 0.01
35 18 0.04
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGATGCCACTGACTTGTGGGCTTTT
Found at i:472199 original size:1 final size:1
Alignment explanation
Indices: 472195--472343 Score: 109
Period size: 1 Copynumber: 149.0 Consensus size: 1
472185 CCGGACCCCC
* * * * * * **
472195 TTTTTTTTTGTTTGTTTTTTTATTGTTTTTTGTTTTTTTTTTGTTTTTTTTTTTTTTTTGCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * ** ** **
472260 TTTTTGTTTTTTTTTTTTTTTTGGTTTTTCTTTTTTCATTTTTTTTTTTGGTTTTTCATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** *
472325 TCGTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTT
472344 GGAGGACGCC
Statistics
Matches: 114, Mismatches: 34, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 114 1.00
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (1 bp):
T
Found at i:472228 original size:18 final size:17
Alignment explanation
Indices: 472195--472344 Score: 137
Period size: 17 Copynumber: 8.6 Consensus size: 17
472185 CCGGACCCCC
*
472195 TTTTTTTTTG--TTTGT
1 TTTTTTTTTGTTTTTTT
*
472210 TTTTTTATTGTTTTTTGT
1 TTTTTTTTTGTTTTTT-T
472228 TTTTTTTTTGTTTTTTT
1 TTTTTTTTTGTTTTTTT
472245 TTTTTTTTTGCTTTTTTT
1 TTTTTTTTTG-TTTTTTT
472263 TTGTTTTTTT-TTTTTTT
1 TT-TTTTTTTGTTTTTTT
472280 TTGGTTTTTCTT-TTTTCATTT
1 TT--TTTTT-TTGTTTT--TTT
* **
472301 TTTTTTTTGGTTTTTCA
1 TTTTTTTTTGTTTTTTT
*
472318 TTTTTTTTCGTTTTTTT
1 TTTTTTTTTGTTTTTTT
*
472335 TTTTGTTTTG
1 TTTTTTTTTG
472345 GAGGACGCCG
Statistics
Matches: 114, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
15 9 0.08
17 46 0.40
18 32 0.28
19 22 0.19
21 5 0.04
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTGTTTTTTT
Found at i:472301 original size:28 final size:29
Alignment explanation
Indices: 472205--472338 Score: 134
Period size: 28 Copynumber: 4.7 Consensus size: 29
472195 TTTTTTTTTG
*
472205 TTTGTT-TTTTTATTGTTTTTT-GTTTTTTT
1 TTTGTTCTTTTT-TT-TTTTTTGGTTTTTCT
* *
472234 TTTGTTTTTTTTTTTTTTTTGCTTTTT-T
1 TTTGTTCTTTTTTTTTTTTTGGTTTTTCT
*
472262 TTTGTTTTTTTTTTTTTTTTGGTTTTTCT
1 TTTGTTCTTTTTTTTTTTTTGGTTTTTCT
*
472291 TTT-TTC-ATTTTTTTTTTTGGTTTTTCATT
1 TTTGTTCTTTTTTTTTTTTTGGTTTTTC--T
* *
472320 TTTTTTCGTTTTTTTTTTT
1 TTTGTTCTTTTTTTTTTTT
472339 GTTTTGGAGG
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
27 19 0.20
28 35 0.38
29 21 0.23
30 8 0.09
31 10 0.11
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (29 bp):
TTTGTTCTTTTTTTTTTTTTGGTTTTTCT
Found at i:482048 original size:10 final size:10
Alignment explanation
Indices: 482033--482059 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
482023 ATGTATCAAG
482033 CAAAAACAAA
1 CAAAAACAAA
482043 CAAAAACAAA
1 CAAAAACAAA
482053 CAAAAAC
1 CAAAAAC
482060 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:486266 original size:52 final size:52
Alignment explanation
Indices: 486188--486388 Score: 341
Period size: 52 Copynumber: 3.9 Consensus size: 52
486178 CGAAATATGA
*
486188 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
486240 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
486292 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
486344 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
486389 ATGTATCGAT
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
51 2 0.01
52 141 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:486395 original size:13 final size:13
Alignment explanation
Indices: 486377--486401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486367 CAAAGATCAG
486377 TGTATCGATACAA
1 TGTATCGATACAA
486390 TGTATCGATACA
1 TGTATCGATACA
486402 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:486482 original size:13 final size:13
Alignment explanation
Indices: 486464--486488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
486454 CAAAAAAACA
486464 TGTATCGATACAT
1 TGTATCGATACAT
486477 TGTATCGATACA
1 TGTATCGATACA
486489 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:486587 original size:21 final size:21
Alignment explanation
Indices: 486546--486587 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
486536 GTTGGGACCT
*
486546 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
486567 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
486588 AAATGTAATT
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:487642 original size:20 final size:21
Alignment explanation
Indices: 487602--487647 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
487592 AAATATGATT
*
487602 ATAATATATAAAAATATATAA
1 ATAATATATAAAAATACATAA
*
487623 ATAATA-ATACAAATACATAA
1 ATAATATATAAAAATACATAA
487643 ATAAT
1 ATAAT
487648 TAAATCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATATATAAAAATACATAA
Done.