Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1966
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: 403291
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 3
Found at i:333532 original size:16 final size:17
Alignment explanation
Indices: 333503--333543 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
333493 TAGTGATTGT
333503 ACAAA-AAATAAAATAA
1 ACAAATAAATAAAATAA
333519 ACAAATAAAT-AAATAA
1 ACAAATAAATAAAATAA
*
333535 AAAAATAAA
1 ACAAATAAA
333544 CACCTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (17 bp):
ACAAATAAATAAAATAA
Found at i:335288 original size:21 final size:21
Alignment explanation
Indices: 335245--335288 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
335235 TAAATCAAAG
335245 AAAATAACAAACAAATTTATAC
1 AAAATAACAAACAAA-TTATAC
*
335267 AAAATAAACACACAAA-TATAC
1 AAAAT-AACAAACAAATTATAC
335288 A
1 A
335289 TGGAAAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 5 0.25
23 9 0.45
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAATAACAAACAAATTATAC
Found at i:335676 original size:51 final size:50
Alignment explanation
Indices: 335612--335777 Score: 210
Period size: 51 Copynumber: 3.3 Consensus size: 50
335602 AGAAATAACA
*
335612 GGGTTAGAA-TATCCCTGATTATAGAAAATCGGTATTTGAAAATTAAAATCG
1 GGGTT-GAAGTATCCCTGATTATAGAAAATTGGTATTTGAAAA-TAAAATCG
*
335663 GGGTTGAAGTATCCCTGATTATAGAAAATTGGTGTTTTGAAAATAAAATCG
1 GGGTTGAAGTATCCCTGATTATAGAAAATTGGT-ATTTGAAAATAAAATCG
* * * * *
335714 GAGTTGGAGTATCCCCGATTATAAAAAATTGGTATTTTAGAAATAAAATCG
1 GGGTTGAAGTATCCCTGATTATAGAAAATTGGTATTTGA-AAATAAAATCG
335765 GGGTT-AGAGTATC
1 GGGTTGA-AGTATC
335778 TCCTCGGAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
50 7 0.07
51 86 0.85
52 8 0.08
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (50 bp):
GGGTTGAAGTATCCCTGATTATAGAAAATTGGTATTTGAAAATAAAATCG
Found at i:335858 original size:108 final size:107
Alignment explanation
Indices: 335716--335944 Score: 298
Period size: 108 Copynumber: 2.1 Consensus size: 107
335706 TAAAATCGGA
* *** * *
335716 GTTGGAGTATCCCCGATTATAAAAAATTGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCTCC
1 GTTGGAGTACCCCCGATTATAAAAAATCAATATTTTAGAAATAAAACCAGGGTTAGAGTATCTCC
** *
335781 TCGGAAATAAC-AGGATTGGAGTATCCCTTATGACATAACGGG
66 TCGGAAATAACGAGG-TTGGAGTATCCCCAATGAAATAACGGG
* * * *
335823 GTTGGAGTAGCCCCCGATTATTAAAAATCAATATTTTAGATATAAAGCCAGGGTTGGAGTATCTC
1 GTTGGAGTA-CCCCCGATTATAAAAAATCAATATTTTAGAAATAAAACCAGGGTTAGAGTATCTC
335888 CTCGGAAATAACGAGGTTGGAGTATCCCCAATGAAATAACGGG
65 CTCGGAAATAACGAGGTTGGAGTATCCCCAATGAAATAACGGG
* *
335931 GTTTGAGTATCCCC
1 GTTGGAGTACCCCC
335945 AATTGTGAAA
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
107 13 0.12
108 89 0.85
109 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (107 bp):
GTTGGAGTACCCCCGATTATAAAAAATCAATATTTTAGAAATAAAACCAGGGTTAGAGTATCTCC
TCGGAAATAACGAGGTTGGAGTATCCCCAATGAAATAACGGG
Found at i:335923 original size:28 final size:28
Alignment explanation
Indices: 335874--335947 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
335864 ATAAAGCCAG
* ***
335874 GGTTGGAGTATCTCCTCGGAAATAACGA
1 GGTTGGAGTATCCCCAATGAAATAACGA
*
335902 GGTTGGAGTATCCCCAATGAAATAACGG
1 GGTTGGAGTATCCCCAATGAAATAACGA
*
335930 GGTTTGAGTATCCCCAAT
1 GGTTGGAGTATCCCCAAT
335948 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCAATGAAATAACGA
Found at i:335992 original size:51 final size:51
Alignment explanation
Indices: 335935--336072 Score: 145
Period size: 49 Copynumber: 2.7 Consensus size: 51
335925 AACGGGGTTT
* *
335935 GAGTATCCCCAATTGTGAAAAATTGATGTTTTGAAAATAAAATCGAAGTTG
1 GAGTATCCCCGATTGAGAAAAATTGATGTTTTGAAAATAAAATCGAAGTTG
* * ** ** * *
335986 GAGTATCCCTGATTGCGGTAAATCAATGCTTT-AAAA-AAAATCGGAGTTG
1 GAGTATCCCCGATTGAGAAAAATTGATGTTTTGAAAATAAAATCGAAGTTG
* * *
336035 AAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAAT
1 GAGTATCCCCGATTGAGAAAAATTGATGTTTTGAAAAT
336073 GGAACCGGGA
Statistics
Matches: 66, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
49 35 0.53
50 7 0.11
51 24 0.36
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCGATTGAGAAAAATTGATGTTTTGAAAATAAAATCGAAGTTG
Found at i:338453 original size:20 final size:20
Alignment explanation
Indices: 338430--338483 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
338420 ATATCGATAT
*
338430 AATGTATCGATACAATG-AGC
1 AATGTATCGATACAATGCA-A
338450 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
338470 AATGTATCGATACA
1 AATGTATCGATACA
338484 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:338458 original size:33 final size:33
Alignment explanation
Indices: 338397--338466 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
338387 AAAATGCATG
* *
338397 AATGTATCGATACATTGTAAAATATATCGATAT
1 AATGTATCGATACAATGTAAAATATATCGATAC
* *
338430 AATGTATCGATACAATG-AGCAATGTATCGATAC
1 AATGTATCGATACAATGTA-AAATATATCGATAC
338463 AATG
1 AATG
338467 CAAAATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.31
Consensus pattern (33 bp):
AATGTATCGATACAATGTAAAATATATCGATAC
Found at i:338546 original size:13 final size:13
Alignment explanation
Indices: 338499--338528 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
338489 GTAAACTTAG
*
338499 AATGTATTGATAC
1 AATGTATCGATAC
338512 AATGTATCGATAC
1 AATGTATCGATAC
338525 AATG
1 AATG
338529 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:344331 original size:16 final size:17
Alignment explanation
Indices: 344299--344331 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
344289 TCACATTGAG
344299 AACTTAAAGAAATTCTGC
1 AACTTAAAG-AATTCTGC
344317 AACTTAAAG-ATTCTG
1 AACTTAAAGAATTCTG
344332 TCATCAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (17 bp):
AACTTAAAGAATTCTGC
Found at i:344874 original size:2 final size:2
Alignment explanation
Indices: 344867--344891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
344857 AAATGAAATA
344867 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 A
344892 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:344896 original size:2 final size:2
Alignment explanation
Indices: 344891--344945 Score: 94
Period size: 2 Copynumber: 27.5 Consensus size: 2
344881 ATATATATAT
344891 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CA- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG
344933 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
344946 ATAGAGTACA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:347641 original size:6 final size:6
Alignment explanation
Indices: 347632--347657 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
347622 TAAAAATATT
347632 TTTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TT
347658 ATGCTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:348949 original size:3 final size:3
Alignment explanation
Indices: 348943--348968 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
348933 ATGTATTATT
348943 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
348969 GCATCCATTT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:350502 original size:20 final size:20
Alignment explanation
Indices: 350461--350507 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
350451 TTAATTTAAC
*
350461 TTATTTTTCTATTAAAATAT
1 TTATTTTTCTATTAAAAAAT
350481 TTATTTTT-TATTAAAGAAAT
1 TTATTTTTCTATTAAA-AAAT
*
350501 TTCTTTT
1 TTATTTT
350508 ACCTTATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATTTTTCTATTAAAAAAT
Found at i:350879 original size:22 final size:22
Alignment explanation
Indices: 350844--350885 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
350834 TATTTGTATT
350844 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
350866 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
350886 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:351388 original size:25 final size:24
Alignment explanation
Indices: 351321--351388 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
351311 ATGTATTTAT
* *
351321 TTCATGTTCATGTTA-TTTACATA
1 TTCATATTCATATTATTTTACATA
* *
351344 TTGCATTTTAATTATT-TTTTACATA
1 TT-CATATTCA-TATTATTTTACATA
351369 TGTCATATTCATATTATTTT
1 T-TCATATTCATATTATTTT
351389 GTTCATATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.06
24 10 0.29
25 22 0.63
26 1 0.03
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.57
Consensus pattern (24 bp):
TTCATATTCATATTATTTTACATA
Found at i:353268 original size:20 final size:20
Alignment explanation
Indices: 353240--353314 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
353230 TTTTACCCAG
*
353240 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
353260 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
353280 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
353300 ATGTATCGATACATT
1 ATGTATCGATACATT
353315 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:353307 original size:40 final size:39
Alignment explanation
Indices: 353240--353317 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
353230 TTTTACCCAG
* *
353240 ATGTATCGATACATTTTTTAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
353280 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
353318 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:354251 original size:22 final size:22
Alignment explanation
Indices: 354225--354275 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
354215 AGCCTTTGAC
354225 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
354247 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
354269 CATGCAT
1 CATGCAT
354276 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:355902 original size:13 final size:13
Alignment explanation
Indices: 355886--355912 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
355876 ATCTAATTCC
355886 AATATTATATAAT
1 AATATTATATAAT
355899 AATATTATATAAT
1 AATATTATATAAT
355912 A
1 A
355913 GAAAAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATTATATAAT
Found at i:363660 original size:20 final size:20
Alignment explanation
Indices: 363635--363675 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
363625 ATGTTATGAT
363635 AATGATTTTTATTAGTCTTG
1 AATGATTTTTATTAGTCTTG
363655 AATGATTTTTATTAGTCTTG
1 AATGATTTTTATTAGTCTTG
363675 A
1 A
363676 GTAATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.54
Consensus pattern (20 bp):
AATGATTTTTATTAGTCTTG
Found at i:363682 original size:20 final size:20
Alignment explanation
Indices: 363639--363683 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
363629 TATGATAATG
*
363639 ATTTTTATTAGTCTTGAATG
1 ATTTTTATTAGTCTTGAATA
*
363659 ATTTTTATTAGTCTTGAGTA
1 ATTTTTATTAGTCTTGAATA
363679 ATTTT
1 ATTTT
363684 ATTTTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.58
Consensus pattern (20 bp):
ATTTTTATTAGTCTTGAATA
Found at i:363685 original size:19 final size:20
Alignment explanation
Indices: 363635--363686 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
363625 ATGTTATGAT
*
363635 AATGATTTTTATTAGTCTTG
1 AATGAATTTTATTAGTCTTG
*
363655 AATGATTTTTATTAGTCTTG
1 AATGAATTTTATTAGTCTTG
*
363675 AGT-AATTTTATT
1 AATGAATTTTATT
363687 TTTTTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (20 bp):
AATGAATTTTATTAGTCTTG
Found at i:364638 original size:2 final size:2
Alignment explanation
Indices: 364631--364655 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
364621 TGATAAGATG
364631 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 A
364656 AAAGAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:365410 original size:22 final size:21
Alignment explanation
Indices: 365375--365415 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
365365 TTATTGTTAA
*
365375 AAATAGATATAAGATCAATAAT
1 AAATAGATAAAAGAT-AATAAT
*
365397 AAATATATAAAAGATAATA
1 AAATAGATAAAAGATAATA
365416 CTTTTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (21 bp):
AAATAGATAAAAGATAATAAT
Found at i:374922 original size:76 final size:76
Alignment explanation
Indices: 374829--374975 Score: 204
Period size: 76 Copynumber: 1.9 Consensus size: 76
374819 ACTTGTTTTT
* * * **
374829 ATGTATTAATTCAATCTTGGAGGCCGTTATGTAGCATGTATATGTGGCAACTTTGTTACTCGTTT
1 ATGTATTAATTCAATCTTGGAGACCGTTATATAGCATGTATATGTGGCAACGTTGTTACTCACTT
374894 ATATGCCTTTA
66 ATATGCCTTTA
* ** * *
374905 ATGTATTAATTCGATCTTGGAGATTGTTATATAGCATGTATGTGTGGTAACGTTGTTACTCACTT
1 ATGTATTAATTCAATCTTGGAGACCGTTATATAGCATGTATATGTGGCAACGTTGTTACTCACTT
374970 ATATGC
66 ATATGC
374976 TTGATTTGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.42
Consensus pattern (76 bp):
ATGTATTAATTCAATCTTGGAGACCGTTATATAGCATGTATATGTGGCAACGTTGTTACTCACTT
ATATGCCTTTA
Found at i:377333 original size:22 final size:22
Alignment explanation
Indices: 377308--377357 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
377298 GCTCTGCCAC
377308 TCTTTTCGTTAATATTTGGACT
1 TCTTTTCGTTAATATTTGGACT
*
377330 TCTTTTTGTTAATATTTGGACT
1 TCTTTTCGTTAATATTTGGACT
377352 TCTTTT
1 TCTTTT
377358 ATTGGTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.12, G:0.12, T:0.60
Consensus pattern (22 bp):
TCTTTTCGTTAATATTTGGACT
Found at i:380104 original size:2 final size:2
Alignment explanation
Indices: 380097--380126 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
380087 TCTTGTGTTG
380097 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
380127 TTGGCTCTTC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:382682 original size:32 final size:33
Alignment explanation
Indices: 382641--382704 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
382631 CTTTTTATGG
382641 TGTATCGATACAAAG-AACACGTATCGATACAA
1 TGTATCGATACAAAGCAACACGTATCGATACAA
* * *
382673 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACAAAGCAACACGTATCGATACA
382705 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACACGTATCGATACAA
Found at i:383955 original size:27 final size:27
Alignment explanation
Indices: 383904--383955 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
383894 AGACGAAGCT
*
383904 AAAGGAAAAGTATATGTGCCCCAAGAA
1 AAAGGAAAAGTATATGTGCACCAAGAA
*
383931 AAAGGAAAAGTATATGTGCATCAAG
1 AAAGGAAAAGTATATGTGCACCAAG
383956 GAAGGAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (27 bp):
AAAGGAAAAGTATATGTGCACCAAGAA
Found at i:384569 original size:107 final size:107
Alignment explanation
Indices: 384458--384706 Score: 302
Period size: 107 Copynumber: 2.3 Consensus size: 107
384448 GAAAAATTGG
* * * * *
384458 TATTTTAGAAATAAAATCAGCGTTGGAGTATTCCCTCGAAAATAACGGGATTTGAGTATCCCTGA
1 TATTTTAGAAATAAAATCGGAGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGA
* * *
384523 TGACATAACGGGGTTGGAGTACCCCCGATAATGAAAAATCAA
66 TGAAATAACGGGGTTCGAGTACCCCCAATAATGAAAAATCAA
* * * * *
384565 TATTTTAGATAT-AAAGCTGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCG
1 TATTTTAGAAATAAAATC-GGAGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCG
* ** * *
384629 ATGAAATAACGGGGTTCGAGTATCCCCAATTGTGAAAAATTAG
65 ATGAAATAACGGGGTTCGAGTACCCCCAATAATGAAAAATCAA
* *
384672 TGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 TATTTTAGAAATAAAATCGGAGTTGGAGTATCCCC
384707 GATTGCGGTA
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
106 4 0.03
107 110 0.93
108 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (107 bp):
TATTTTAGAAATAAAATCGGAGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGA
TGAAATAACGGGGTTCGAGTACCCCCAATAATGAAAAATCAA
Found at i:384623 original size:28 final size:28
Alignment explanation
Indices: 384583--384655 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
384573 ATATAAAGCT
**
384583 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
384611 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
384639 GGGGTTCGAGTATCCCC
1 GGGGTTGGAGTATCCCC
384656 AATTGTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:384706 original size:51 final size:51
Alignment explanation
Indices: 384646--384810 Score: 165
Period size: 51 Copynumber: 3.2 Consensus size: 51
384636 AACGGGGTTC
* *
384646 GAGTATCCCCAATTGTGAAAAATT-AGTGTTTTGGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGAGAAAAATTGA-TGTTTTGGAAATAAAATCGGAGTTG
* ** * * * *
384697 GAGTATCCCCGATTGCGGTAAATCGATGCTTTAGAAAAAAAATCGGAGTTG
1 GAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTG
* * *
384748 GAGTA-CTCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACTGGGA-TTG
1 GAGTATC-CCCGATTGAGAAAAATTGATGTTTTGGAAAT-AAAATCGGAGTTG
*
384799 GATTATCCCCGA
1 GAGTATCCCCGA
384811 GATGAAAAAT
Statistics
Matches: 91, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
50 1 0.01
51 81 0.89
52 9 0.10
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (51 bp):
GAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTG
Found at i:387162 original size:20 final size:20
Alignment explanation
Indices: 387139--387243 Score: 117
Period size: 20 Copynumber: 5.8 Consensus size: 20
387129 TACATTGTAA
387139 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGC
387159 AATGTATCGATAC--T-A-C
1 AATGTATCGATACAATGAGC
387175 AATGTAT-GATACAATGAGC
1 AATGTATCGATACAATGAGC
387194 AATGTATCGATACAAT----
1 AATGTATCGATACAATGAGC
*
387210 -A--TATCGATACAATGAGT
1 AATGTATCGATACAATGAGC
387227 AATGTATCGATACAATG
1 AATGTATCGATACAATG
387244 CAAAATGATC
Statistics
Matches: 73, Mismatches: 0, Indels: 24
0.75 0.00 0.25
Matches are distributed among these distances:
13 12 0.16
15 6 0.08
16 8 0.11
17 2 0.03
18 3 0.04
19 8 0.11
20 34 0.47
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGC
Found at i:387188 original size:35 final size:36
Alignment explanation
Indices: 387139--387239 Score: 156
Period size: 35 Copynumber: 2.9 Consensus size: 36
387129 TACATTGTAA
387139 AATGTATCGATACAATGAGCAATGTATCGATACTAC
1 AATGTATCGATACAATGAGCAATGTATCGATACTAC
387175 AATGTAT-GATACAATGAGCAATGTATCG--A-TAC
1 AATGTATCGATACAATGAGCAATGTATCGATACTAC
* *
387207 AATATATCGATACAATGAGTAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
387240 AATGCAAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
32 9 0.15
33 21 0.36
35 22 0.37
36 7 0.12
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (36 bp):
AATGTATCGATACAATGAGCAATGTATCGATACTAC
Found at i:387214 original size:13 final size:13
Alignment explanation
Indices: 387193--387222 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
387183 ATACAATGAG
*
387193 CAATGTATCGATA
1 CAATATATCGATA
387206 CAATATATCGATA
1 CAATATATCGATA
387219 CAAT
1 CAAT
387223 GAGTAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (13 bp):
CAATATATCGATA
Found at i:387224 original size:33 final size:33
Alignment explanation
Indices: 387143--387242 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
387133 TTGTAAAATG
*
387143 TATCGATACAATGAGCAATGTATCGATACTACAATG
1 TATCGATACAATGAGCAATGTATCG--A-TACAATA
387179 TAT-GATACAATGAGCAATGTATCGATACAATA
1 TATCGATACAATGAGCAATGTATCGATACAATA
*
387211 TATCGATACAATGAGTAATGTATCGATACAAT
1 TATCGATACAATGAGCAATGTATCGATACAAT
387243 GCAAAATGAT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
32 9 0.15
33 28 0.46
35 21 0.34
36 3 0.05
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (33 bp):
TATCGATACAATGAGCAATGTATCGATACAATA
Found at i:387250 original size:20 final size:19
Alignment explanation
Indices: 387119--387259 Score: 115
Period size: 20 Copynumber: 7.7 Consensus size: 19
387109 AAAATGCCTG
* * *
387119 AATGTATTGATACATTGTAA
1 AATGTATCGATACAATG-AC
387139 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
387159 AATGTATCGATAC--T-AC
1 AATGTATCGATACAATGAC
387175 AATGTAT-GATACAATGAGC
1 AATGTATCGATACAATGA-C
387194 AATGTATCGATACAAT---
1 AATGTATCGATACAATGAC
*
387210 -A--TATCGATACAATGAGT
1 AATGTATCGATACAATGA-C
*
387227 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
387247 AATG-ATCGATACA
1 AATGTATCGATACA
387260 TCTGGGTAAA
Statistics
Matches: 103, Mismatches: 4, Indels: 29
0.76 0.03 0.21
Matches are distributed among these distances:
13 12 0.12
15 6 0.06
16 8 0.08
17 2 0.02
18 3 0.03
19 18 0.17
20 53 0.51
21 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:387293 original size:13 final size:13
Alignment explanation
Indices: 387275--387304 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
387265 GTAAACCCAG
387275 AATGTATCGATAA
1 AATGTATCGATAA
*
387288 AATGTATCGATAC
1 AATGTATCGATAA
387301 AATG
1 AATG
387305 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAA
Found at i:387313 original size:20 final size:20
Alignment explanation
Indices: 387288--387342 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
387278 GTATCGATAA
*
387288 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATAAAC
*
387308 AATGTATCGATGCAATAAAC
1 AATGTATCGATACAATAAAC
387328 AATGTATCGATACAA
1 AATGTATCGATACAA
387343 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAATAAAC
Found at i:391229 original size:20 final size:20
Alignment explanation
Indices: 391204--391243 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
391194 ATTGGGCTTA
*
391204 ATGTATCGATATAATTTATT
1 ATGTATCGATACAATTTATT
391224 ATGTATCGATACAATTTATT
1 ATGTATCGATACAATTTATT
391244 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (20 bp):
ATGTATCGATACAATTTATT
Found at i:392606 original size:27 final size:27
Alignment explanation
Indices: 392568--392622 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
392558 AGACGAAGCT
**
392568 AAAGGAAAAGTATATGTGCCCCAAGGA
1 AAAGGAAAAGTATATGTGCAACAAGGA
392595 AAAGGAAAAGTATATGTGCAACAAGGA
1 AAAGGAAAAGTATATGTGCAACAAGGA
392622 A
1 A
392623 GGAACAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.25, T:0.15
Consensus pattern (27 bp):
AAAGGAAAAGTATATGTGCAACAAGGA
Found at i:393293 original size:16 final size:16
Alignment explanation
Indices: 393274--393332 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
393264 TATATATACT
393274 TTTTATAATATAAATA
1 TTTTATAATATAAATA
393290 TTTTAGTAAT-TAAATA
1 TTTTA-TAATATAAATA
*
393306 TATTA-AA-ATAAATTA
1 TTTTATAATATAAA-TA
*
393321 TTCTTGTAATAT
1 TT-TTATAATAT
393333 TATGTCAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 17 0.50
17 6 0.18
18 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (16 bp):
TTTTATAATATAAATA
Found at i:397891 original size:29 final size:29
Alignment explanation
Indices: 397830--397893 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
397820 CATATGCCAT
*** *
397830 TTTAAATTAAGTCATCAATTAGATGTCAT
1 TTTAAATTAAGTCATCAATTAGATCAAAA
* *
397859 TTTAAATTAAGTGATCAATTATATCAAAA
1 TTTAAATTAAGTCATCAATTAGATCAAAA
397888 TTTAAA
1 TTTAAA
397894 CTAATTAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTAAATTAAGTCATCAATTAGATCAAAA
Done.