Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014031.1 Kokia drynarioides strain JFW-HI SEQ_129062, whole genome shotgun sequence
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: 261919
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 146 characters in sequence are not A, C, G, or T
Found at i:2466 original size:23 final size:23
Alignment explanation
Indices: 2440--2503 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2430 CTATCGTGCT
* *
2440 ATAAAAATAGATAAAACCATGTC
1 ATAAAAGTAGACAAAACCATGTC
* *
2463 ATAAAAGTAAACAAAATCATGTC
1 ATAAAAGTAGACAAAACCATGTC
2486 ATAAAAGTAGACAAAACC
1 ATAAAAGTAGACAAAACC
2504 GTTGTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.58, C:0.14, G:0.09, T:0.19
Consensus pattern (23 bp):
ATAAAAGTAGACAAAACCATGTC
Found at i:12181 original size:11 final size:11
Alignment explanation
Indices: 12165--12200 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12155 TCCCCCCTCA
* *
12165 TTCTTTTTCTC
1 TTCTTTCTCCC
12176 TTCTTTCTCCC
1 TTCTTTCTCCC
12187 TTCTTTCTCCC
1 TTCTTTCTCCC
12198 TTC
1 TTC
12201 CCCTCTCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (11 bp):
TTCTTTCTCCC
Found at i:13114 original size:20 final size:19
Alignment explanation
Indices: 13089--13136 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
13079 CTGACCAAAG
13089 TAAAAAATAT-ATCAAAAAA
1 TAAAAAATATAAT-AAAAAA
*
13108 CTAAAAAGTATAATAAAAAA
1 -TAAAAAATATAATAAAAAA
*
13128 TAATAAATA
1 TAAAAAATA
13137 AAAAATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 7 0.29
20 15 0.62
21 2 0.08
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAAAATATAATAAAAAA
Found at i:26399 original size:45 final size:45
Alignment explanation
Indices: 26350--26436 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
26340 GTGCTGGTGG
* * * *
26350 TGGTGGTGATTTTGGCAGGGGGAGAGGTGTAGGCAATGGTGGTCT
1 TGGTGGAGATTTCGGCAGAGGGAGAGGTATAGGCAATGGTGGTCT
* *
26395 TGGTGGAGGTTTCGGCAGAGGGCGAGGTATAGGCAATGGTGG
1 TGGTGGAGATTTCGGCAGAGGGAGAGGTATAGGCAATGGTGG
26437 AGCCGGGGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.17, C:0.08, G:0.49, T:0.25
Consensus pattern (45 bp):
TGGTGGAGATTTCGGCAGAGGGAGAGGTATAGGCAATGGTGGTCT
Found at i:26686 original size:15 final size:15
Alignment explanation
Indices: 26666--26697 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
26656 TGGTTACCCA
26666 GGTGGAGGAAAAGGT
1 GGTGGAGGAAAAGGT
26681 GGTGGAGGAAAAGGT
1 GGTGGAGGAAAAGGT
26696 GG
1 GG
26698 CAGATATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.56, T:0.12
Consensus pattern (15 bp):
GGTGGAGGAAAAGGT
Found at i:36152 original size:20 final size:20
Alignment explanation
Indices: 36127--36164 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
36117 TGCCTTCTTT
36127 TATTATTTCACTTACCCCTG
1 TATTATTTCACTTACCCCTG
36147 TATTATTTCACTTACCCC
1 TATTATTTCACTTACCCC
36165 ACCATTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.45
Consensus pattern (20 bp):
TATTATTTCACTTACCCCTG
Found at i:36171 original size:20 final size:20
Alignment explanation
Indices: 36128--36171 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
36118 GCCTTCTTTT
***
36128 ATTATTTCACTTACCCCTGT
1 ATTATTTCACTTACCCCACC
36148 ATTATTTCACTTACCCCACC
1 ATTATTTCACTTACCCCACC
36168 ATTA
1 ATTA
36172 AAGTTCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTATTTCACTTACCCCACC
Found at i:37623 original size:28 final size:27
Alignment explanation
Indices: 37575--37631 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
37565 TTATATAATT
* *
37575 TTTAGAGGATTAAATTAAATTTTTATTA
1 TTTAGAGGAGTAAAGTAAA-TTTTATTA
37603 TTTAG-GGAGTAAAGTACAATTTTATTA
1 TTTAGAGGAGTAAAGTA-AATTTTATTA
37630 TT
1 TT
37632 ATTAATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (27 bp):
TTTAGAGGAGTAAAGTAAATTTTATTA
Found at i:39970 original size:20 final size:20
Alignment explanation
Indices: 39924--39970 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
39914 GTTTTACTAT
* *
39924 TGTTTTTCTATTTTTTATGC
1 TGTTTTTCTACTTTTTATAC
39944 TGTTTTTCTACTTTTTATTAC
1 TGTTTTTCTACTTTTTA-TAC
39965 TGTTTT
1 TGTTTT
39971 GTAACCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.70
Consensus pattern (20 bp):
TGTTTTTCTACTTTTTATAC
Found at i:55452 original size:17 final size:18
Alignment explanation
Indices: 55416--55453 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
55406 CAATTGAAAA
* *
55416 TTAATATTTTTAATTGAT
1 TTAAAATTTTTAACTGAT
55434 TTAAAATTTTTAACT-AT
1 TTAAAATTTTTAACTGAT
55451 TTA
1 TTA
55454 TCAAACAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
TTAAAATTTTTAACTGAT
Found at i:56554 original size:27 final size:27
Alignment explanation
Indices: 56522--56585 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
56512 GAAGTGGTAC
56522 GACTCGTCGCCACAGAAACGATCAGCT
1 GACTCGTCGCCACAGAAACGATCAGCT
56549 GACTCGTCGCCACAGAAACGATCAGCT
1 GACTCGTCGCCACAGAAACGATCAGCT
56576 GACTCGTCGC
1 GACTCGTCGC
56586 AACTCGGCCT
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:0.27, C:0.34, G:0.23, T:0.16
Consensus pattern (27 bp):
GACTCGTCGCCACAGAAACGATCAGCT
Found at i:96176 original size:16 final size:16
Alignment explanation
Indices: 96130--96176 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
96120 AAAATATATT
96130 TATATTGTTTTATTTTA
1 TATATT-TTTTATTTTA
* *
96147 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
96163 TATATTTTTTATTT
1 TATATTTTTTATTT
96177 ATTGAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:111340 original size:19 final size:21
Alignment explanation
Indices: 111313--111352 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
111303 ACTTAAAAAT
111313 AATATTATATA-TTTAATATA
1 AATATTATATATTTTAATATA
111333 AATA-TATATATTTTAATATA
1 AATATTATATATTTTAATATA
111353 TTCTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTATATATTTTAATATA
Found at i:117972 original size:60 final size:60
Alignment explanation
Indices: 117796--118130 Score: 254
Period size: 60 Copynumber: 5.5 Consensus size: 60
117786 AAAAATTTAG
* * * *
117796 TGTTGGTCATGCCATGACCGACA-CCCCTTTTTATTAGATAAAAAATTTAAATTTTTAGA
1 TGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGA
* * * ** *
117855 TATTGGCCATTG-CATGGCCGACATCTTCTTTTTATCTAAATAAAAAA-TCAAATTTTTTGA
1 TGTTGGTCA-TGCCATGGCCGACACCCCCTTTTTATC-AGATAAAAAATTCAAATTTTTTGA
*
117915 TGTTGATCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTCAAATTTTTT--
1 TGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGA
* ** * ** * * *
117973 TTTTGTGTTAGCTATAACATGGTCGACACCATCTTTTTATCTGGTAAAAAATTAAAATTTTTTTG
1 TGTTG-G-T--C-ATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTCAAA-TTTTTTG
118038 -
60 A
* * ** * * * * *
118038 TGTTGGTCATACAATGATCGACACTCCCTTTTTGTCAGATAAAAAATTCGAA-TTTCTGG
1 TGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGA
*
118097 TGTTGGCCATTG-CATGGCCGACACCCCCGTTTTT
1 TGTTGGTCA-TGCCATGGCCGACACCCCC-TTTTT
118131 TATTTGGTAA
Statistics
Matches: 216, Mismatches: 45, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
58 9 0.04
59 48 0.22
60 100 0.46
61 10 0.05
62 1 0.00
63 37 0.17
64 7 0.03
65 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (60 bp):
TGTTGGTCATGCCATGGCCGACACCCCCTTTTTATCAGATAAAAAATTCAAATTTTTTGA
Found at i:118023 original size:123 final size:123
Alignment explanation
Indices: 117768--118092 Score: 323
Period size: 123 Copynumber: 2.7 Consensus size: 123
117758 TCGGCCACCT
*
117768 TTTTTATCTAACA-AAAAAA-AAAA---TTTAGTGTTGGTCATGCCATGACCGACA-CCCCTTTT
1 TTTTTATCTAA-ATAAAAAATAAAATTTTTTTGTGTTGGTCATGCCATGACCGACACCCCCTTTT
* * * ** * *
117827 TATTAGATAAAAAATTTAAA---TTTTTAGATATTGGCCATTGCATGGCCGACATCTTC
65 TATCAGATAAAAAATTCAAATTTTTTTTAGATATTAGCCATAACATGGCCGACACCATC
* * *
117883 TTTTTATCTAAATAAAAAATCAAA-TTTTTTGATGTTGATCATGCCATGGCCGACACCCCCTTTT
1 TTTTTATCTAAATAAAAAATAAAATTTTTTTG-TGTTGGTCATGCCATGACCGACACCCCCTTTT
* * * *
117947 TATCAGATAAAAAATTCAAATTTTTTTTTTG-TGTTAGCTATAACATGGTCGACACCATC
65 TATCAGATAAAAAATTCAAA-TTTTTTTTAGATATTAGCCATAACATGGCCGACACCATC
** * * * *
118006 TTTTTATCT-GGTAAAAAATTAAAATTTTTTTGTGTTGGTCATACAATGATCGACACTCCCTTTT
1 TTTTTATCTAAATAAAAAA-TAAAATTTTTTTGTGTTGGTCATGCCATGACCGACACCCCCTTTT
* *
118070 TGTCAGATAAAAAATTCGAATTT
65 TATCAGATAAAAAATTCAAATTT
118093 CTGGTGTTGG
Statistics
Matches: 172, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
114 1 0.01
115 17 0.10
116 3 0.02
118 4 0.02
119 21 0.12
120 26 0.15
122 10 0.06
123 77 0.45
124 13 0.08
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (123 bp):
TTTTTATCTAAATAAAAAATAAAATTTTTTTGTGTTGGTCATGCCATGACCGACACCCCCTTTTT
ATCAGATAAAAAATTCAAATTTTTTTTAGATATTAGCCATAACATGGCCGACACCATC
Found at i:121860 original size:12 final size:12
Alignment explanation
Indices: 121843--121890 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
121833 TATTTGTGTA
121843 AAAATTAATTTG
1 AAAATTAATTTG
121855 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
121869 TTGAAATTAATTTG
1 --AAAATTAATTTG
121883 AAAATTAA
1 AAAATTAA
121891 GGTTCATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 18 0.60
14 2 0.07
16 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:122244 original size:86 final size:86
Alignment explanation
Indices: 122005--122309 Score: 454
Period size: 86 Copynumber: 3.5 Consensus size: 86
121995 AATTTAACAT
* * *
122005 TATTTAAAT-AAAAATGATTGTTATTATATTTCAATTTATATCAAATAATATGTTGATTTAACAA
1 TATTTAAATAAAAAAT-ATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAACAA
*
122069 TACATTATTTATCAAAATTTAA
65 TACATTATTTATCAAATTTTAA
* *
122091 TATTTAAATAAAAAAGATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGAC
1 TATTTAAAT-AAAAA-A-TATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAAC
*
122156 AATACATTATTTATTAAATTTTAA
63 AATACATTATTTATCAAATTTTAA
*
122180 TATTTAAATAAAAAATAGTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAACAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAACAAT
*
122245 ACATTATTTACCAAATTTTAA
66 ACATTATTTATCAAATTTTAA
* *
122266 TATTTAAAT-TAAAA-ATTATTATTATATTTCAATTTTTATCAAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAAT
122310 TTTAAATTTA
Statistics
Matches: 200, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
84 28 0.14
85 4 0.02
86 84 0.42
87 1 0.00
88 9 0.05
89 73 0.37
90 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (86 bp):
TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTTAACAAT
ACATTATTTATCAAATTTTAA
Found at i:123501 original size:30 final size:30
Alignment explanation
Indices: 123465--123521 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
123455 ATGTAAGATA
123465 TATTTTTG-AAT-TTTTTATAATATTTTTTTC
1 TATTTTTGAAATGTTTTT-T-ATATTTTTTTC
123495 TATTTTTGAAATGTTTTTTATATTTTT
1 TATTTTTGAAATGTTTTTTATATTTTT
123522 GAATTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
30 16 0.64
31 4 0.16
32 5 0.20
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (30 bp):
TATTTTTGAAATGTTTTTTATATTTTTTTC
Found at i:124764 original size:9 final size:9
Alignment explanation
Indices: 124733--124775 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
124723 ATATATATAT
*
124733 AAGAAATAA
1 AAGAAAAAA
124742 AAGAATAAAGA
1 AAGAA-AAA-A
124753 AAGAAAAAA
1 AAGAAAAAA
*
124762 AAGAAACAA
1 AAGAAAAAA
124771 AAGAA
1 AAGAA
124776 GAAAGAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 19 0.63
10 5 0.17
11 6 0.20
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:127086 original size:30 final size:30
Alignment explanation
Indices: 127045--127135 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
127035 CCCGTTTACT
* * *
127045 TTTTAATTTTAATTTGTAATTTCATTTTTA
1 TTTTAATTTTAATTTCTAATTTCATGTATA
* *
127075 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAATTTTAATTTCTAATTTCATGTATA
*
127105 TTTTAATTTTAATTTCTAATTTCCTGTATA
1 TTTTAATTTTAATTTCTAATTTCATGTATA
127135 T
1 T
127136 ATTATTATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAATTTTAATTTCTAATTTCATGTATA
Found at i:127127 original size:7 final size:6
Alignment explanation
Indices: 127045--127126 Score: 58
Period size: 6 Copynumber: 12.5 Consensus size: 6
127035 CCCGTTTACT
* * *
127045 TTTTAA TTTTAA TTTGTAA -TTTCA TTTTTA TTTTAA ATTTAA TTTCTAA
1 TTTTAA TTTTAA TTT-TAA TTTTAA TTTTAA TTTTAA TTTTAA TTT-TAA
127094 TTTCCTGTATA TTTTAA TTTTAA TTTCTAA TTT
1 -TT--T-TA-A TTTTAA TTTTAA TTT-TAA TTT
127127 CCTGTATATA
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
5 2 0.03
6 37 0.60
7 14 0.23
8 3 0.05
10 5 0.08
11 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.63
Consensus pattern (6 bp):
TTTTAA
Found at i:127737 original size:58 final size:58
Alignment explanation
Indices: 127675--127815 Score: 135
Period size: 59 Copynumber: 2.4 Consensus size: 58
127665 TTGGTGTCGA
* * * *
127675 CCAACACAAAAAAATTGATTTTTTACTA-GAGAAAAAAATGGTGTCGGTCATGCA-ATAG
1 CCAACACAAAAAAATTGATTTTTTA-TATGACAAAAAAAGGGTATCGATCAT-CACATAG
* ** * *
127733 CCAACAC-CAAAAATTCGAATTTTTTATATGACAAAAAGGGGGTATCGATCATTACATGG
1 CCAACACAAAAAAATT-G-ATTTTTTATATGACAAAAAAAGGGTATCGATCATCACATAG
*
127792 ACAACACAAAAAAATTGATTTTTT
1 CCAACACAAAAAAATTGATTTTTT
127816 TCCAGATAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
57 7 0.10
58 18 0.27
59 35 0.52
60 7 0.10
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (58 bp):
CCAACACAAAAAAATTGATTTTTTATATGACAAAAAAAGGGTATCGATCATCACATAG
Found at i:127874 original size:59 final size:57
Alignment explanation
Indices: 127811--127952 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 57
127801 AAAAATTGAT
* *
127811 TTTTTTCCAGATAAAAAATTCAAATTTTTGGATATTAGACATTGCATGATCGACACCCC
1 TTTTTT-CTGATAAAAAATTCAAAATTTTGGATATTAGACATTGCATGATCGACA-CCC
* * * ** * *
127870 TTTTTATCTTATAAAAAATTCAAAATTTTGGGTATTGGTTATTGTATGGTCGACACCC
1 TTTTT-TCTGATAAAAAATTCAAAATTTTGGATATTAGACATTGCATGATCGACACCC
127928 TTTTTTGTCTGATAAAAAATTCAAA
1 -TTTTT-TCTGATAAAAAATTCAAA
127953 GCGTAGCAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 3 0.04
59 66 0.94
60 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (57 bp):
TTTTTTCTGATAAAAAATTCAAAATTTTGGATATTAGACATTGCATGATCGACACCC
Found at i:151703 original size:24 final size:23
Alignment explanation
Indices: 151662--151707 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
151652 CGGTAAGATA
*
151662 TTTTCCTTTTCTTATTCACAGAG
1 TTTTCCTTCTCTTATTCACAGAG
*
151685 TTTTCCATTCTCTTCTTCACAGA
1 TTTTCC-TTCTCTTATTCACAGA
151708 ATCTTCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTTCCTTCTCTTATTCACAGAG
Found at i:154345 original size:17 final size:17
Alignment explanation
Indices: 154323--154357 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
154313 TTATAATTAT
154323 TAATATATTTAATTTGA
1 TAATATATTTAATTTGA
154340 TAATATATTTAATTTGA
1 TAATATATTTAATTTGA
154357 T
1 T
154358 GTATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TAATATATTTAATTTGA
Found at i:154587 original size:19 final size:20
Alignment explanation
Indices: 154563--154608 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
154553 CATCCAAACA
154563 CCAGAAAA-T-ATTAACTTTT
1 CCAGAAAAGTAATTAA-TTTT
*
154582 CCAGAAAAGTAATTCATTTT
1 CCAGAAAAGTAATTAATTTT
154602 CCAGAAA
1 CCAGAAA
154609 TCATTTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (20 bp):
CCAGAAAAGTAATTAATTTT
Found at i:157806 original size:139 final size:139
Alignment explanation
Indices: 157556--157883 Score: 647
Period size: 139 Copynumber: 2.4 Consensus size: 139
157546 CAATTGTATG
157556 AGATAGTGTGATGCATACTAATCTGAATTGATTTTGTTTTTCAATATAGATAATCATATCGGTTG
1 AGATAGTGTGATGCATACTAATCTGAATTGATTTTGTTTTTCAATATAGATAATCATATCGGTTG
157621 ATTCTAATCGAATTGTAAGTGATGAAATTGAAAGTAACACTCCCACCTGTAATAAGAGAGCTACT
66 ATTCTAATCGAATTGTAAGTGATGAAATTGAAAGTAACACTCCCACCTGTAATAAGAGAGCTACT
157686 AATCAATAT
131 AATCAATAT
*
157695 AGATAGTGTGATGCATATTAATCTGAATTGATTTTGTTTTTCAATATAGATAATCATATCGGTTG
1 AGATAGTGTGATGCATACTAATCTGAATTGATTTTGTTTTTCAATATAGATAATCATATCGGTTG
157760 ATTCTAATCGAATTGTAAGTGATGAAATTGAAAGTAACACTCCCACCTGTAATAAGAGAGCTACT
66 ATTCTAATCGAATTGTAAGTGATGAAATTGAAAGTAACACTCCCACCTGTAATAAGAGAGCTACT
157825 AATCAATAT
131 AATCAATAT
157834 AGATAGTGTGATGCATACTAATCTGAATTGATTTTGTTTTTCAATATAGA
1 AGATAGTGTGATGCATACTAATCTGAATTGATTTTGTTTTTCAATATAGA
157884 AATGCCTTTA
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 187 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (139 bp):
AGATAGTGTGATGCATACTAATCTGAATTGATTTTGTTTTTCAATATAGATAATCATATCGGTTG
ATTCTAATCGAATTGTAAGTGATGAAATTGAAAGTAACACTCCCACCTGTAATAAGAGAGCTACT
AATCAATAT
Found at i:169599 original size:49 final size:49
Alignment explanation
Indices: 169538--169690 Score: 186
Period size: 49 Copynumber: 3.1 Consensus size: 49
169528 GAAATTAATT
* * *
169538 AAATTAAGTTAGAAACAAATTGATA-TTGTTCTTAATTTAATCAAAACCA
1 AAATTAATTTAGAAACAAATT-AAAGTTGATCTTAATTTAATCAAAACCA
*
169587 AAATTAATTTAGAAACAAATTAAAGTTGATCTTAATTTAATTAAAACCA
1 AAATTAATTTAGAAACAAATTAAAGTTGATCTTAATTTAATCAAAACCA
* * * * *
169636 AAATTAATCTAGAAACAAATTAAAATT-AACTTTAATTTAATTAAAA-AA
1 AAATTAATTTAGAAACAAATTAAAGTTGATC-TTAATTTAATCAAAACCA
169684 AAATTAA
1 AAATTAA
169691 ATCGAAATCC
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
48 12 0.13
49 82 0.87
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (49 bp):
AAATTAATTTAGAAACAAATTAAAGTTGATCTTAATTTAATCAAAACCA
Found at i:179726 original size:22 final size:22
Alignment explanation
Indices: 179698--179742 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
179688 CATCAGATAC
179698 CACTAGCATTAGCCATTAGGGA
1 CACTAGCATTAGCCATTAGGGA
179720 CACTAGCATTAGCCATTAGGGA
1 CACTAGCATTAGCCATTAGGGA
179742 C
1 C
179743 TTACTCATAA
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:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (22 bp):
CACTAGCATTAGCCATTAGGGA
Found at i:179972 original size:22 final size:22
Alignment explanation
Indices: 179944--179988 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
179934 CATCAGATAC
179944 CACTAGCATTAGCCATTAGGGA
1 CACTAGCATTAGCCATTAGGGA
179966 CACTAGCATTAGCCATTAGGGA
1 CACTAGCATTAGCCATTAGGGA
179988 C
1 C
179989 TTACTCATAA
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:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (22 bp):
CACTAGCATTAGCCATTAGGGA
Found at i:180090 original size:246 final size:246
Alignment explanation
Indices: 179656--180148 Score: 986
Period size: 246 Copynumber: 2.0 Consensus size: 246
179646 TTTATGCCCT
179656 TCCCACTTTCCGGTTATTCTTAATTTACTATGCATCAGATACCACTAGCATTAGCCATTAGGGAC
1 TCCCACTTTCCGGTTATTCTTAATTTACTATGCATCAGATACCACTAGCATTAGCCATTAGGGAC
179721 ACTAGCATTAGCCATTAGGGACTTACTCATAAAGTTGAAAGAGAGGAGTATGGAGGTGCCTGACA
66 ACTAGCATTAGCCATTAGGGACTTACTCATAAAGTTGAAAGAGAGGAGTATGGAGGTGCCTGACA
179786 AAATCTGAGATTCCTGTGATAAAATTTTTTTGACTGTTGTCTGCAGTTTAATGCAATGTGAATAT
131 AAATCTGAGATTCCTGTGATAAAATTTTTTTGACTGTTGTCTGCAGTTTAATGCAATGTGAATAT
179851 CTGAATGTGACTGTGGTGCACATTGACATTTCTAGTCCAAAATGTGGGATA
196 CTGAATGTGACTGTGGTGCACATTGACATTTCTAGTCCAAAATGTGGGATA
179902 TCCCACTTTCCGGTTATTCTTAATTTACTATGCATCAGATACCACTAGCATTAGCCATTAGGGAC
1 TCCCACTTTCCGGTTATTCTTAATTTACTATGCATCAGATACCACTAGCATTAGCCATTAGGGAC
179967 ACTAGCATTAGCCATTAGGGACTTACTCATAAAGTTGAAAGAGAGGAGTATGGAGGTGCCTGACA
66 ACTAGCATTAGCCATTAGGGACTTACTCATAAAGTTGAAAGAGAGGAGTATGGAGGTGCCTGACA
180032 AAATCTGAGATTCCTGTGATAAAATTTTTTTGACTGTTGTCTGCAGTTTAATGCAATGTGAATAT
131 AAATCTGAGATTCCTGTGATAAAATTTTTTTGACTGTTGTCTGCAGTTTAATGCAATGTGAATAT
180097 CTGAATGTGACTGTGGTGCACATTGACATTTCTAGTCCAAAATGTGGGATA
196 CTGAATGTGACTGTGGTGCACATTGACATTTCTAGTCCAAAATGTGGGATA
180148 T
1 T
180149 GAAGAAAGCA
Statistics
Matches: 247, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 247 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (246 bp):
TCCCACTTTCCGGTTATTCTTAATTTACTATGCATCAGATACCACTAGCATTAGCCATTAGGGAC
ACTAGCATTAGCCATTAGGGACTTACTCATAAAGTTGAAAGAGAGGAGTATGGAGGTGCCTGACA
AAATCTGAGATTCCTGTGATAAAATTTTTTTGACTGTTGTCTGCAGTTTAATGCAATGTGAATAT
CTGAATGTGACTGTGGTGCACATTGACATTTCTAGTCCAAAATGTGGGATA
Found at i:185912 original size:3 final size:3
Alignment explanation
Indices: 185904--185930 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
185894 CATCTCTATT
185904 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
185931 GTGTTCTCGA
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:187643 original size:3 final size:3
Alignment explanation
Indices: 187635--187659 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
187625 AACAGTTGTT
187635 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
187660 ATAAAGCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:189017 original size:20 final size:22
Alignment explanation
Indices: 188989--189031 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
188979 TTTTAAAAAA
188989 ATTATAAATTTAT-AAAATATT
1 ATTATAAATTTATAAAAATATT
189010 ATTA-AAATTTATAAAAATATT
1 ATTATAAATTTATAAAAATATT
189031 A
1 A
189032 AATAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTATAAATTTATAAAAATATT
Found at i:189032 original size:18 final size:18
Alignment explanation
Indices: 188982--189033 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 18
188972 AAATATTTTT
*
188982 TAAAAAAATTATAAATTTA
1 TAAAAATATTA-AAATTTA
189001 TAAAATATTATTAAAATTTA
1 TAAAA-A-TATTAAAATTTA
189021 TAAAAATATTAAA
1 TAAAAATATTAAA
189034 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.23
19 6 0.20
20 13 0.43
21 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATATTAAAATTTA
Found at i:189876 original size:2 final size:2
Alignment explanation
Indices: 189869--189895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
189859 AATTAAAATT
189869 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
189896 TATTTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:199800 original size:14 final size:15
Alignment explanation
Indices: 199776--199813 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
199766 TTTTTAATTT
* *
199776 TTATATATTTTTTAA
1 TTATTTATTTTTGAA
199791 TT-TTTATTTTTGAA
1 TTATTTATTTTTGAA
199805 TTATTTATT
1 TTATTTATT
199814 GACATGACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTATTTATTTTTGAA
Found at i:213738 original size:18 final size:18
Alignment explanation
Indices: 213715--213751 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
213705 TTTGTGATCA
213715 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
213733 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
213751 A
1 A
213752 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:216253 original size:37 final size:38
Alignment explanation
Indices: 216191--216269 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
216181 TTTGAAGCAA
** *
216191 TAAAGTGACACCCAGTGTCTCATCG-ACCTAGCCGAAG
1 TAAAGTGACACCCAGTACCTAATCGAACCTAGCCGAAG
* * *
216228 TAAAGTGGCACCCAGTACCTAATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTACCTAATCGAACCTAGCCGAAG
216266 TAAA
1 TAAA
216270 ATAATGACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 21 0.60
38 14 0.40
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (38 bp):
TAAAGTGACACCCAGTACCTAATCGAACCTAGCCGAAG
Found at i:219380 original size:14 final size:15
Alignment explanation
Indices: 219354--219393 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
219344 ATATGTTTTT
219354 CTTTTCTTCTTTGTC
1 CTTTTCTTCTTTGTC
*
219369 CTTTTC-TCTTTGTT
1 CTTTTCTTCTTTGTC
*
219383 TTTTTCTTCTT
1 CTTTTCTTCTT
219394 ATCTTTGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (15 bp):
CTTTTCTTCTTTGTC
Found at i:221804 original size:38 final size:38
Alignment explanation
Indices: 221733--221810 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 38
221723 AGATGAGATT
* *
221733 AAAATTATTTAATAATTTTAAATAAATTTATATTTCAAA
1 AAAATAATATAATAATTTTAAATAAATTTATATTT-AAA
*
221772 AAAATAATATAATAATTTT-AATAATTTTATATTTAAA
1 AAAATAATATAATAATTTTAAATAAATTTATATTTAAA
221809 AA
1 AA
221811 TTAATTTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 5 0.14
38 14 0.39
39 17 0.47
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (38 bp):
AAAATAATATAATAATTTTAAATAAATTTATATTTAAA
Found at i:222393 original size:60 final size:61
Alignment explanation
Indices: 222297--222412 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 61
222287 CATAATTTTT
*
222297 TTCTTTCAAAGTGAAAAGATTAAAATACACTCGAATCAAATTATGTATTTTAATTATTTGA
1 TTCTTTCAAAGTGAAAAGACTAAAATACACTCGAATCAAATTATGTATTTTAATTATTTGA
* * *
222358 TTCTTTTAAAGTGAAAA-ACTAAAATACACTTGAATCAAGTTATGTATTTTAATTA
1 TTCTTTCAAAGTGAAAAGACTAAAATACACTCGAATCAAATTATGTATTTTAATTA
222413 CAAAAGAGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 35 0.69
61 16 0.31
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (61 bp):
TTCTTTCAAAGTGAAAAGACTAAAATACACTCGAATCAAATTATGTATTTTAATTATTTGA
Found at i:243718 original size:24 final size:24
Alignment explanation
Indices: 243686--243735 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
243676 CCCCTTTCCA
243686 TGGCGGAAATCAAAATGAAAAAGT
1 TGGCGGAAATCAAAATGAAAAAGT
243710 TGGCGGAAATCAAAATGAAAAAGT
1 TGGCGGAAATCAAAATGAAAAAGT
243734 TG
1 TG
243736 ACATATCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.08, G:0.26, T:0.18
Consensus pattern (24 bp):
TGGCGGAAATCAAAATGAAAAAGT
Found at i:248078 original size:24 final size:24
Alignment explanation
Indices: 248023--248085 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
248013 AAGAGGTCCA
248023 ATTTTTTTTATTTTATTATTGGTAT
1 ATTTTTTTTATTTTATTATT-GTAT
*
248048 A-TGTTTTTATTTTATTATAT-TAT
1 ATTTTTTTTATTTTATTAT-TGTAT
248071 ATTTTTTTTAATTTT
1 ATTTTTTTT-ATTTT
248086 TTAAAAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (24 bp):
ATTTTTTTTATTTTATTATTGTAT
Found at i:249761 original size:61 final size:60
Alignment explanation
Indices: 249619--249761 Score: 137
Period size: 60 Copynumber: 2.4 Consensus size: 60
249609 AACATGACCA
* * * * * *
249619 ACACCCCTTTTTTGTAAGAT-AAAATATTCAATTTTTTTCGTGTTGGCCATGCATGGCCG
1 ACACCCCTTTTTTATATGATAAAAAAAATCAAATTTTTTCGTGTTAGCCATGCATGGCCG
** * * **
249678 GTACCCC-TTTTTATTTGAATAAAAAAAATCAAATTTTTTGGTGTTAGCCATTGCATGGGTG
1 ACACCCCTTTTTTATATG-ATAAAAAAAATCAAATTTTTTCGTGTTAGCCA-TGCATGGCCG
*
249739 ACACCCCTTTTTTATCTGATAAA
1 ACACCCCTTTTTTATATGATAAA
249762 TTTTTTTTAA
Statistics
Matches: 65, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
58 7 0.11
59 7 0.11
60 24 0.37
61 18 0.28
62 9 0.14
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (60 bp):
ACACCCCTTTTTTATATGATAAAAAAAATCAAATTTTTTCGTGTTAGCCATGCATGGCCG
Found at i:249865 original size:60 final size:58
Alignment explanation
Indices: 249773--249924 Score: 166
Period size: 58 Copynumber: 2.6 Consensus size: 58
249763 TTTTTTTAAT
* * *
249773 TTTTTTTTGTGTTGGTCATGTATTGACCGACACTACCT-TTTTATCAAATAAAAAAA-TCAA
1 TTTTTTTAGTGTGGGTCATGCATTGACCGACAC--CCTCTTTT-T-AAATAAAAAAATTCAA
* *
249833 TTTTTTTGGTGTGGGTCATTGCA-TGACCGACACCCTCTTTTTAGATAAAAAAATTCAA
1 TTTTTTTAGTGTGGGTCA-TGCATTGACCGACACCCTCTTTTTAAATAAAAAAATTCAA
* * *
249891 TTTTTTTAGTGTTGGCCATGCATTGGCCGACACC
1 TTTTTTTAGTGTGGGTCATGCATTGACCGACACC
249925 AATATTGGTT
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
57 14 0.17
58 33 0.41
59 4 0.05
60 26 0.32
61 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (58 bp):
TTTTTTTAGTGTGGGTCATGCATTGACCGACACCCTCTTTTTAAATAAAAAAATTCAA
Found at i:250686 original size:22 final size:23
Alignment explanation
Indices: 250652--250707 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
250642 AAGTACTTAA
* *
250652 CAGTAAGCACACACAGTGC-AAT
1 CAGTAGGCACACACAGCGCAAAT
* *
250674 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGCGCAAAT
*
250697 CAATAGGCACA
1 CAGTAGGCACA
250708 TGAGGTGCGA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.39, C:0.27, G:0.21, T:0.12
Consensus pattern (23 bp):
CAGTAGGCACACACAGCGCAAAT
Found at i:250749 original size:23 final size:23
Alignment explanation
Indices: 250652--250749 Score: 72
Period size: 23 Copynumber: 4.3 Consensus size: 23
250642 AAGTACTTAA
*
250652 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACAAAGTGCGAAT
* * * * *
250674 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACAAAGTGCGAAT
* * ** * *
250697 CAATAGGCACATGAGGTGCGAAA
1 CAGTAAGCACACAAAGTGCGAAT
*
250720 CAATAAGCACACAAAGTGCGAAT
1 CAGTAAGCACACAAAGTGCGAAT
250743 CAGTAAG
1 CAGTAAG
250750 AGCGCTAGCA
Statistics
Matches: 56, Mismatches: 19, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
22 15 0.27
23 41 0.73
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACAAAGTGCGAAT
Found at i:252706 original size:68 final size:68
Alignment explanation
Indices: 252597--252724 Score: 256
Period size: 68 Copynumber: 1.9 Consensus size: 68
252587 AGATGAACAT
252597 TATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAT
1 TATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAT
252662 GTA
66 GTA
252665 TATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACAGTTGTACTGTTGAGTTATTGAT
1 TATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACAGTTGTACTGTTGAGTTATTGAT
252725 AAATGTCCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (68 bp):
TATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAT
GTA
Found at i:252847 original size:151 final size:151
Alignment explanation
Indices: 252573--252875 Score: 588
Period size: 151 Copynumber: 2.0 Consensus size: 151
252563 AAGACTATCC
*
252573 TAAATGTCCAAAGAAGATGAACATTATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACAGTT
1 TAAATGTCCAAAGAAGATGAACATTATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTT
*
252638 GTACTGTTGAGTTATTGATTCAATGTATATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACA
66 GTACTGTTGAGTTATTGATTCAACGTATATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACA
252703 GTTGTACTGTTGAGTTATTGA
131 GTTGTACTGTTGAGTTATTGA
252724 TAAATGTCCAAAGAAGATGAACATTATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTT
1 TAAATGTCCAAAGAAGATGAACATTATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTT
252789 GTACTGTTGAGTTATTGATTCAACGTATATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACA
66 GTACTGTTGAGTTATTGATTCAACGTATATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACA
252854 GTTGTACTGTTGAGTTATTGA
131 GTTGTACTGTTGAGTTATTGA
252875 T
1 T
252876 TCAACGTAGA
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (151 bp):
TAAATGTCCAAAGAAGATGAACATTATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTT
GTACTGTTGAGTTATTGATTCAACGTATATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACA
GTTGTACTGTTGAGTTATTGA
Found at i:252857 original size:68 final size:68
Alignment explanation
Indices: 252748--252883 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
252738 AGATGAACAT
252748 TATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAC
1 TATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAC
252813 GTA
66 GTA
*
252816 TATCTGCGTTGGAAGAATTGTTATCCTGCAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAC
1 TATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAC
252881 GTA
66 GTA
252884 GATGATATAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (68 bp):
TATCTGCGTTGGAAGAATTGTTATCCTACAATTCAACAGTTGTACTGTTGAGTTATTGATTCAAC
GTA
Found at i:253085 original size:59 final size:60
Alignment explanation
Indices: 252954--253093 Score: 151
Period size: 59 Copynumber: 2.4 Consensus size: 60
252944 GGTCGATGAC
* * * * *
252954 TGCAATGATCAACACAAAAAAATTTGATTTTTTTATTCAGATAAAAAGGGGTATCGGTCA
1 TGCAATGACCAACACAAAAAAATTTAAATTTTTTATTCAGACAAAAAGAGGTATCGGTCA
* * *
253014 TGGC-ATGACCAACACCAAAAAATTTAAATTTTTTA-TCTGACAAAAAGAGGTGTCGG-CTA
1 T-GCAATGACCAACACAAAAAAATTTAAATTTTTTATTCAGACAAAAAGAGGTATCGGTC-A
* *
253073 TGCAATGGCCAACATAAAAAA
1 TGCAATGACCAACACAAAAAA
253094 GGCATGCAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
58 3 0.05
59 33 0.50
60 28 0.42
61 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.27
Consensus pattern (60 bp):
TGCAATGACCAACACAAAAAAATTTAAATTTTTTATTCAGACAAAAAGAGGTATCGGTCA
Found at i:258090 original size:60 final size:58
Alignment explanation
Indices: 257975--258147 Score: 168
Period size: 60 Copynumber: 2.9 Consensus size: 58
257965 TAACGTTTAC
* ** * * * *
257975 TTTTTCTTAATTTGGTACCTAAATTTTTTTTTTGACCTAATTTGTTACTTGAACTTGATATT
1 TTTTTCTTAATTTGGTACCTAACTTTTTTTAAT--CC-AATTTGGTACCTAAACTTGACA-T
*
258037 TTTTTCTTAATTTGGTACCTAAGCTTTTTTTAATCCAATTTGGTACCTAAACTTGGCAT
1 TTTTTCTTAATTTGGTACCTAA-CTTTTTTTAATCCAATTTGGTACCTAAACTTGACAT
* * *
258096 TTTTTCTCTAATTTGATACCTAAAC-TTTTTTATATTCAATTTTGTACCTAAA
1 TTTTTCT-TAATTTGGTACCT-AACTTTTTTTA-ATCCAATTTGGTACCTAAA
258148 TTTATTAAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
59 15 0.16
60 47 0.49
61 4 0.04
62 22 0.23
63 8 0.08
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (58 bp):
TTTTTCTTAATTTGGTACCTAACTTTTTTTAATCCAATTTGGTACCTAAACTTGACAT
Found at i:258109 original size:32 final size:28
Alignment explanation
Indices: 257975--258147 Score: 102
Period size: 32 Copynumber: 5.9 Consensus size: 28
257965 TAACGTTTAC
257975 TTTTTCT-TAATTTGGTACCTAAA-TTT
1 TTTTTCTCTAATTTGGTACCTAAACTTT
* * * *
258001 TTTTTTTGACCTAATTTGTTACTTGAACTTGAT
1 TTTTTCT---CTAATTTGGTACCTAAACTT--T
* *
258034 ATTTTTTTCTTAATTTGGTACCTAAGCTTT
1 -TTTTTCTC-TAATTTGGTACCTAAACTTT
** *
258064 TTTTAATCCAATTTGGTACCTAAACTTGGCAT
1 TTTTTCTCTAATTTGGTACCTAAACTT----T
*
258096 TTTTTCTCTAATTTGATACCTAAACTTT
1 TTTTTCTCTAATTTGGTACCTAAACTTT
*
258124 TTTATAT-TC-AATTTTGTACCTAAA
1 TTT-T-TCTCTAATTTGGTACCTAAA
258148 TTTATTAAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 28
0.71 0.11 0.17
Matches are distributed among these distances:
26 6 0.05
28 34 0.30
29 9 0.08
30 15 0.13
31 3 0.03
32 39 0.34
33 1 0.01
34 7 0.06
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (28 bp):
TTTTTCTCTAATTTGGTACCTAAACTTT
Found at i:258136 original size:28 final size:27
Alignment explanation
Indices: 258035--258147 Score: 95
Period size: 28 Copynumber: 4.0 Consensus size: 27
258025 GAACTTGATA
* *
258035 TTTTTTTCTT-AATTTGGTACCTAAGC
1 TTTTTTTATTCAATTTGGTACCTAAAC
*
258061 TTTTTTTAATCCAATTTGGTACCTAAAC
1 TTTTTTT-ATTCAATTTGGTACCTAAAC
*
258089 TTGGCATTTTT-TCTCTAATTTGATACCTAAAC
1 TT----TTTTTAT-TC-AATTTGGTACCTAAAC
*
258121 TTTTTTATATTCAATTTTGTACCTAAA
1 TTTTTT-TATTCAATTTGGTACCTAAA
258148 TTTATTAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
26 7 0.10
27 1 0.01
28 34 0.49
29 3 0.04
30 2 0.03
31 1 0.01
32 22 0.31
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (27 bp):
TTTTTTTATTCAATTTGGTACCTAAAC
Found at i:258366 original size:31 final size:31
Alignment explanation
Indices: 258296--258366 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
258286 AAAGATTAGG
** **
258296 TACTAAATTAGGAAAAAGAGTCAAGTTCATG
1 TACTAAATTAAAAAAAAGAGTCAAGTTCAAA
* *
258327 TA-TCAAATTAAAAAAAAGTGTCAAGTTTAAA
1 TACT-AAATTAAAAAAAAGAGTCAAGTTCAAA
258358 TACTAAATT
1 TACTAAATT
258367 GGACCAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
30 1 0.03
31 30 0.94
32 1 0.03
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (31 bp):
TACTAAATTAAAAAAAAGAGTCAAGTTCAAA
Found at i:261482 original size:2 final size:2
Alignment explanation
Indices: 261475--261503 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
261465 TGTTTCTTTA
261475 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
261504 ATGCTAACGT
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
Done.