Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011902.1 Kokia drynarioides strain JFW-HI SEQ_126900, 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: 107104
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:7051 original size:27 final size:27
Alignment explanation
Indices: 6990--7053 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
6980 TACATTTTAA
* *
6990 ATAAAAAATATTAAAATTATAATTTCT
1 ATAAAAAATATTAAAACTATAAATTCT
7017 ATACAAAAAT-TTAAAACTATGAAAATT-T
1 ATA-AAAAATATTAAAACTAT--AAATTCT
7045 ATAAAAAAT
1 ATAAAAAAT
7054 GCTATTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 18 0.56
28 10 0.31
29 4 0.12
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAAAAAATATTAAAACTATAAATTCT
Found at i:7626 original size:25 final size:26
Alignment explanation
Indices: 7575--7628 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
7565 GTTTTGAATT
* * *
7575 TTTTATTTACTGTATTTTGAATAAAA
1 TTTTATATAATGTATTTTAAATAAAA
*
7601 TTTTATATAATGT-TTTTAAATTAAA
1 TTTTATATAATGTATTTTAAATAAAA
7626 TTT
1 TTT
7629 GGAATAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (26 bp):
TTTTATATAATGTATTTTAAATAAAA
Found at i:10628 original size:72 final size:72
Alignment explanation
Indices: 10524--10677 Score: 229
Period size: 72 Copynumber: 2.1 Consensus size: 72
10514 CTATAGGGTG
* *
10524 CACATAGGCAAGACACACGAGAGTGTGCCAGACTATGTGTGCATACTGTTTTGAGAATTAAGGTA
1 CACACAGGCAAGACACACGAGAGTGTGCCAGACCATGTGTGCATACTGTTTTGAGAATTAAGGTA
*
10589 CAGGAGA
66 CAAGAGA
* * *
10596 CACACAGGCCAAG-CACACGGGCGTGTTCCAGACCATGTGTGCATACTGTTTTGAGAATTAAGGT
1 CACACAGG-CAAGACACACGAGAGTGTGCCAGACCATGTGTGCATACTGTTTTGAGAATTAAGGT
10660 ACAAGAGA
65 ACAAGAGA
*
10668 CACACTGGCA
1 CACACAGGCA
10678 TGTGTCAGAC
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
71 2 0.03
72 68 0.92
73 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.21
Consensus pattern (72 bp):
CACACAGGCAAGACACACGAGAGTGTGCCAGACCATGTGTGCATACTGTTTTGAGAATTAAGGTA
CAAGAGA
Found at i:13736 original size:52 final size:52
Alignment explanation
Indices: 13678--13781 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
13668 GTGTCTACCT
* *
13678 GTGTGATTACTGCACCTAGTTTTTAAAATGGCACACGTCCATGTGATAGCCC
1 GTGTGATTACTGCACCTAGTTTTTAAAATGGCACACGGCCATGTGACAGCCC
*
13730 GTGTGATTACTGCACCTAGTTTTTAAAATGGCACACGGCCGTGTGACAGCCC
1 GTGTGATTACTGCACCTAGTTTTTAAAATGGCACACGGCCATGTGACAGCCC
13782 ATATCACAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (52 bp):
GTGTGATTACTGCACCTAGTTTTTAAAATGGCACACGGCCATGTGACAGCCC
Found at i:14455 original size:35 final size:35
Alignment explanation
Indices: 14366--14472 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 35
14356 TATACCAACA
** *
14366 ATGATTTGCGCCCAGCGTTAGTCAGAT-AACCGATG
1 ATGA-TTGCGCCCAGCACTAGTCAGATAAACCGACG
* * * *
14401 AT-ATATGTGCCCAACACTAGTTAGATAAACTGACG
1 ATGAT-TGCGCCCAGCACTAGTCAGATAAACCGACG
*
14436 ATGATTGCGCCCAGCACTAGTCGGATAAACCGACG
1 ATGATTGCGCCCAGCACTAGTCAGATAAACCGACG
14471 AT
1 AT
14473 TGGTATAATG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
33 1 0.02
34 17 0.30
35 37 0.65
36 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (35 bp):
ATGATTGCGCCCAGCACTAGTCAGATAAACCGACG
Found at i:14502 original size:40 final size:39
Alignment explanation
Indices: 14402--14588 Score: 111
Period size: 40 Copynumber: 4.9 Consensus size: 39
14392 TAACCGATGA
* * * **
14402 TATATGTGCCCAACACTAGTTAGATAAACTGACGA-T-G
1 TATATGAGCCCAACTCTAGTTGGATAAACCAACGATTGG
* * * * *
14439 -AT-TGCGCCCAGCACTAGTCGGATAAACCGACGATTGG
1 TATATGAGCCCAACTCTAGTTGGATAAACCAACGATTGG
* * *
14476 TATAATGAGCCCAACTCTAATTGGATATACCAAC-AATGG
1 TAT-ATGAGCCCAACTCTAGTTGGATAAACCAACGATTGG
* * * * *
14515 T-T-TGCGCCCAACGCTAGTTGGATAAACCGACAATAT-A
1 TATATGAGCCCAACTCTAGTTGGATAAACCAACGAT-TGG
* *
14552 AATAGTGAGCCCAGCTCTAGTTGGATAAACCAACGAT
1 TATA-TGAGCCCAACTCTAGTTGGATAAACCAACGAT
14589 GTTTTACGTC
Statistics
Matches: 114, Mismatches: 26, Indels: 17
0.73 0.17 0.11
Matches are distributed among these distances:
35 26 0.23
36 27 0.24
37 2 0.02
38 5 0.04
39 5 0.04
40 49 0.43
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (39 bp):
TATATGAGCCCAACTCTAGTTGGATAAACCAACGATTGG
Found at i:14532 original size:76 final size:76
Alignment explanation
Indices: 14336--14625 Score: 227
Period size: 76 Copynumber: 3.9 Consensus size: 76
14326 TATAAAAGGG
* * * * * **
14336 TGAGCCAAACTCTAGTTGAATATACCAACAATGATTTGCGCCCAGCGTTAGTCAGAT-AA-C--C
1 TGAGCCCAACTCTAGTTGGATAAACCAACAATGGTTTGCGCCCAACACTAGTCAGATAAACCGAC
14397 GA-TGATAT-A
66 GATTGATATAA
* * * ** * * * *
14406 TGTGCCCAACACTAGTTAGATAAACTGACGAT-GATTGCGCCCAGCACTAGTCGGATAAACCGAC
1 TGAGCCCAACTCTAGTTGGATAAACCAACAATGGTTTGCGCCCAACACTAGTCAGATAAACCGAC
*
14470 GATTGGTATAA
66 GATTGATATAA
* * * **
14481 TGAGCCCAACTCTAATTGGATATACCAACAATGGTTTGCGCCCAACGCTAGTTGGATAAACCGAC
1 TGAGCCCAACTCTAGTTGGATAAACCAACAATGGTTTGCGCCCAACACTAGTCAGATAAACCGAC
* * *
14546 AATAT-AAATAG
66 GAT-TGATATAA
* * * * * * *
14557 TGAGCCCAGCTCTAGTTGGATAAACCAACGATGTTTTACGTCCAACATTAGTCAAATAAACCGAC
1 TGAGCCCAACTCTAGTTGGATAAACCAACAATGGTTTGCGCCCAACACTAGTCAGATAAACCGAC
14622 GATT
66 GATT
14626 TGTTTATTAA
Statistics
Matches: 168, Mismatches: 44, Indels: 11
0.75 0.20 0.05
Matches are distributed among these distances:
69 19 0.11
70 25 0.15
71 1 0.01
73 3 0.02
74 5 0.03
75 26 0.15
76 88 0.52
77 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
TGAGCCCAACTCTAGTTGGATAAACCAACAATGGTTTGCGCCCAACACTAGTCAGATAAACCGAC
GATTGATATAA
Found at i:21831 original size:14 final size:15
Alignment explanation
Indices: 21812--21840 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21802 AAGCGCAGGA
21812 AGGAGGAA-AAGAAG
1 AGGAGGAAGAAGAAG
21826 AGGAGGAAGAAGAAG
1 AGGAGGAAGAAGAAG
21841 CATCGTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (15 bp):
AGGAGGAAGAAGAAG
Found at i:34246 original size:15 final size:15
Alignment explanation
Indices: 34226--34255 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34216 ATTTGGACAG
34226 AAAGACAAGTTTAGC
1 AAAGACAAGTTTAGC
34241 AAAGACAAGTTTAGC
1 AAAGACAAGTTTAGC
34256 CCTATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
AAAGACAAGTTTAGC
Found at i:35573 original size:20 final size:20
Alignment explanation
Indices: 35544--35581 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35534 ACTGCTGATC
35544 GTTGACCGTTGACTTTTTGG
1 GTTGACCGTTGACTTTTTGG
*
35564 GTTGATCGTTGACTTTTT
1 GTTGACCGTTGACTTTTT
35582 TCAAAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.13, G:0.26, T:0.50
Consensus pattern (20 bp):
GTTGACCGTTGACTTTTTGG
Found at i:38082 original size:14 final size:14
Alignment explanation
Indices: 38062--38100 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
38052 TAAATTCATT
38062 CAAAAATTAAAT-A
1 CAAAAATTAAATAA
*
38075 CTAAAAATAAAATAA
1 C-AAAAATTAAATAA
38090 CAAAAATTAAA
1 CAAAAATTAAA
38101 GAAAAGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 1 0.05
14 19 0.86
15 2 0.09
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (14 bp):
CAAAAATTAAATAA
Found at i:38543 original size:18 final size:18
Alignment explanation
Indices: 38522--38560 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
38512 CTCCATAGGA
* *
38522 TCTTCCTCATGATCTTCT
1 TCTTCCTCAGGATCCTCT
38540 TCTTCCTCAGGATCCTCT
1 TCTTCCTCAGGATCCTCT
38558 TCT
1 TCT
38561 GGATCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.36, G:0.08, T:0.46
Consensus pattern (18 bp):
TCTTCCTCAGGATCCTCT
Found at i:39261 original size:82 final size:82
Alignment explanation
Indices: 39124--39288 Score: 303
Period size: 82 Copynumber: 2.0 Consensus size: 82
39114 TTATGTGTCT
*
39124 TTGCAGTACTACGAGTCTAGAAACAATGATGGCCACATGTGGATACTGTATTGGTGCGAGGGATA
1 TTGCAGTACTACGAGTCTAAAAACAATGATGGCCACATGTGGATACTGTATTGGTGCGAGGGATA
39189 AATGTTAAAGTAACCCC
66 AATGTTAAAGTAACCCC
* *
39206 TTGCAGTACTACGAGTCTAAAAACAATGATGGCCATATGTGGATACTGTATTGGTGTGAGGGATA
1 TTGCAGTACTACGAGTCTAAAAACAATGATGGCCACATGTGGATACTGTATTGGTGCGAGGGATA
39271 AATGTTAAAGTAACCCC
66 AATGTTAAAGTAACCCC
39288 T
1 T
39289 CGAATTATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (82 bp):
TTGCAGTACTACGAGTCTAAAAACAATGATGGCCACATGTGGATACTGTATTGGTGCGAGGGATA
AATGTTAAAGTAACCCC
Found at i:47160 original size:36 final size:37
Alignment explanation
Indices: 47106--47249 Score: 174
Period size: 36 Copynumber: 4.0 Consensus size: 37
47096 TGGTAACAGG
* *
47106 CATGACCTT-C-GAGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTGCAG-GTCAACAAGAAGTAAAATGAGCAT
*
47142 CATGA-CTTGCAGGCCAACAAGAAGTAAAATGAGCAT
1 CATGACCTTGCAGGTCAACAAGAAGTAAAATGAGCAT
*
47178 CATGACCTTTG-A-GTCAACAAAAAGTAAAATGAGCAT
1 CATGACC-TTGCAGGTCAACAAGAAGTAAAATGAGCAT
* *
47214 CATGACCTT-CGGGTCAACAAGGAGTAAAATGAGCAT
1 CATGACCTTGCAGGTCAACAAGAAGTAAAATGAGCAT
47250 TATAACCTCA
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
35 5 0.05
36 83 0.88
37 3 0.03
38 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (37 bp):
CATGACCTTGCAGGTCAACAAGAAGTAAAATGAGCAT
Found at i:47232 original size:72 final size:72
Alignment explanation
Indices: 47106--47268 Score: 213
Period size: 72 Copynumber: 2.3 Consensus size: 72
47096 TGGTAACAGG
***
47106 CATGACCTTCGAGTCAACAGGGAGTAAAATGAGCATCATGACTTGCAGGCCAACAAGAAGTAAAA
1 CATGACCTTCGAGTCAACAAAAAGTAAAATGAGCATCATGACTTGCAGGCCAACAAGAAGTAAAA
47171 TGAGCAT
66 TGAGCAT
* * * *
47178 CATGACCTTTGAGTCAACAAAAAGTAAAATGAGCATCATGACCTT-CGGGTCAACAAGGAGTAAA
1 CATGACCTTCGAGTCAACAAAAAGTAAAATGAGCATCATGA-CTTGCAGGCCAACAAGAAGTAAA
47242 ATGAGCAT
65 ATGAGCAT
* * *
47250 TATAACC-TCAAGTCAACAA
1 CATGACCTTCGAGTCAACAA
47269 GGAATAAAAC
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
71 10 0.13
72 66 0.84
73 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (72 bp):
CATGACCTTCGAGTCAACAAAAAGTAAAATGAGCATCATGACTTGCAGGCCAACAAGAAGTAAAA
TGAGCAT
Found at i:55480 original size:26 final size:26
Alignment explanation
Indices: 55442--55530 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 26
55432 TCTTTGACTA
* *
55442 GCGAACCCCAATTCGCAACTTAATTG
1 GCGAACCCCAATTCACAACTTAACTG
* *
55468 GTGAACCCCAATTCACAACTTACCTG
1 GCGAACCCCAATTCACAACTTAACTG
* * *
55494 GCGAACCCCTATTCTCCAA-TTATACTA
1 GCGAACCCCAATTC-ACAACTTA-ACTG
55521 GCGAACCCCA
1 GCGAACCCCA
55531 TCTCGCCAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
26 37 0.73
27 14 0.27
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.22
Consensus pattern (26 bp):
GCGAACCCCAATTCACAACTTAACTG
Found at i:55528 original size:27 final size:26
Alignment explanation
Indices: 55494--55552 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
55484 AACTTACCTG
* *
55494 GCGAACCCCTAT-TCTCCAATTATACTA
1 GCGAACCCC-ATCTCGCCAA-TACACTA
55521 GCGAACCCCATCTCGCCAATACACTA
1 GCGAACCCCATCTCGCCAATACACTA
55547 GCGAAC
1 GCGAAC
55553 TTGCCTCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.31, C:0.37, G:0.12, T:0.20
Consensus pattern (26 bp):
GCGAACCCCATCTCGCCAATACACTA
Found at i:62910 original size:3 final size:3
Alignment explanation
Indices: 62902--62987 Score: 118
Period size: 3 Copynumber: 28.7 Consensus size: 3
62892 ACCAAATGGA
* * * * * *
62902 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AAC CAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62950 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
62988 CCTAAATATA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:66783 original size:17 final size:17
Alignment explanation
Indices: 66761--66837 Score: 102
Period size: 17 Copynumber: 4.6 Consensus size: 17
66751 AATTTTAAAT
66761 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
* *
66778 TTTAAACTTATTTTGAG
1 TTTAAATTTATTTTAAG
* *
66795 TTTGAATTTATTTTAAT
1 TTTAAATTTATTTTAAG
66812 TTTAAATTTATTTTAA-
1 TTTAAATTTATTTTAAG
*
66828 ATTAAATTTA
1 TTTAAATTTA
66838 AATTTTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
16 9 0.17
17 43 0.83
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:67493 original size:13 final size:13
Alignment explanation
Indices: 67475--67499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67465 TACTAAGCGT
67475 TATAATAAATAAA
1 TATAATAAATAAA
67488 TATAATAAATAA
1 TATAATAAATAA
67500 TAAAAAGTCA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAATAAATAAA
Found at i:68310 original size:30 final size:29
Alignment explanation
Indices: 68274--68428 Score: 152
Period size: 30 Copynumber: 5.2 Consensus size: 29
68264 CTATTTTATT
* * *
68274 TAAAAATTACATTTTGACCCTCGAACTGTA
1 TAAAAATTACATTTTTACCCTCAAACT-TC
*
68304 TAAAAATTAAATTTTTAGCCCT-AAACTTC
1 TAAAAATTACATTTTTA-CCCTCAAACTTC
*
68333 TCAAAAATTACATTTTTACCCTTAAACTTC
1 T-AAAAATTACATTTTTACCCTCAAACTTC
* *
68363 TCAAAAATTACATTTTTTCCCTCGAACTTC
1 T-AAAAATTACATTTTTACCCTCAAACTTC
* * * *
68393 CAAAAATCACATTTTT-GCCTCGAACTTC
1 TAAAAATTACATTTTTACCCTCAAACTTC
68421 TCAAAAAT
1 T-AAAAAT
68429 CATATCTTTA
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
28 11 0.10
29 26 0.24
30 68 0.62
31 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.36
Consensus pattern (29 bp):
TAAAAATTACATTTTTACCCTCAAACTTC
Found at i:68369 original size:60 final size:59
Alignment explanation
Indices: 68275--68428 Score: 179
Period size: 60 Copynumber: 2.6 Consensus size: 59
68265 TATTTTATTT
* *
68275 AAAAATTACATTTTGACCCTCGAACTGTAT-AAAAATTAAATTTTTAGCCCT-AAACTTCTC
1 AAAAATTACATTTTTACCCTCGAACT-TCTCAAAAATTAAATTTTT-GCCCTCAAACTTC-C
** * * *
68335 AAAAATTACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTTTCCCTCGAACTTCC
1 AAAAATTACATTTTTACCCTCGAACTTCTCAAAAATTAAATTTTTGCCCTCAAACTTCC
* *
68394 AAAAATCACATTTTT-GCCTCGAACTTCTCAAAAAT
1 AAAAATTACATTTTTACCCTCGAACTTCTCAAAAAT
68429 CATATCTTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 17 0.21
59 21 0.26
60 43 0.53
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.36
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCTCGAACTTCTCAAAAATTAAATTTTTGCCCTCAAACTTCC
Found at i:69577 original size:36 final size:36
Alignment explanation
Indices: 69537--69677 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
69527 CTGTTGTGAA
* * *
69537 AATAAAAATGTGGGTATTTTATTCATGCCATAAGAC
1 AATAAATATGTGGGTATGTTATTCATGCCATGAGAC
* *
69573 AATAAATATGTGGGTATGTCATTCATGCCATGTGAC
1 AATAAATATGTGGGTATGTTATTCATGCCATGAGAC
* *
69609 AGTAAATATGTGAGTATGTTATTCATGCCATGAGAC
1 AATAAATATGTGGGTATGTTATTCATGCCATGAGAC
* *
69645 AGTAAATATGTGGGTATGTTATTCATGTCATGA
1 AATAAATATGTGGGTATGTTATTCATGCCATGA
69678 CAGTGAATAT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (36 bp):
AATAAATATGTGGGTATGTTATTCATGCCATGAGAC
Found at i:70014 original size:64 final size:65
Alignment explanation
Indices: 69912--70046 Score: 182
Period size: 64 Copynumber: 2.1 Consensus size: 65
69902 GGGGAAATAA
** * *
69912 GGAGAGTGTTAGCTTTACACTTCACTTTTGGGACATGTTTGAC-TCTGAGTCTTTTGGTGTGTTT
1 GGAGAGTGTTAGCTTTACACTTCACTTTTGGGACATGTTCCACTTATGAGTCATTTGGTGTGTTT
** *
69976 GGAGAGTGTTAGCTTTATGCTTCACTTTTGGGATATGTTCCACTTTATGAGTCATTTGGTGTGTT
1 GGAGAGTGTTAGCTTTACACTTCACTTTTGGGACATGTTCCAC-TTATGAGTCATTTGGTGTGTT
70041 T
65 T
*
70042 CGAGA
1 GGAGA
70047 TCCGTGTATC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 38 0.62
66 23 0.38
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (65 bp):
GGAGAGTGTTAGCTTTACACTTCACTTTTGGGACATGTTCCACTTATGAGTCATTTGGTGTGTTT
Found at i:70182 original size:39 final size:39
Alignment explanation
Indices: 70134--70227 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
70124 ACTGAATGCA
*
70134 ATTATATGTGATTAATATGTGATGTGATAAATGCTGAAAT
1 ATTA-ATGTGATTAATATGTGATGTGATAAACGCTGAAAT
* *
70174 ATTAATGTGATTAATTTGTGATGTGATAAACGTTGAAAT
1 ATTAATGTGATTAATATGTGATGTGATAAACGCTGAAAT
* *
70213 ATTCATGTGACTAAT
1 ATTAATGTGATTAAT
70228 GTGATTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 45 0.92
40 4 0.08
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.40
Consensus pattern (39 bp):
ATTAATGTGATTAATATGTGATGTGATAAACGCTGAAAT
Found at i:70256 original size:68 final size:68
Alignment explanation
Indices: 70177--70306 Score: 224
Period size: 68 Copynumber: 1.9 Consensus size: 68
70167 CTGAAATATT
* * *
70177 AATGTGATTAATTTGTGATGTGATAAACGTTGAAATATTCATGTGACTAATGTGATTAAATGAGA
1 AATGTGATTAATATGTGATGTGATAAACGCTGAAATATTCATATGACTAATGTGATTAAATGAGA
70242 CTA
66 CTA
*
70245 AATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATATGACTAATGTGATTAAATG
1 AATGTGATTAATATGTGATGTGATAAACGCTGAAATATTCATATGACTAATGTGATTAAATG
70307 TGATTAATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (68 bp):
AATGTGATTAATATGTGATGTGATAAACGCTGAAATATTCATATGACTAATGTGATTAAATGAGA
CTA
Found at i:70300 original size:32 final size:33
Alignment explanation
Indices: 70194--70306 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 33
70184 TTAATTTGTG
* * *
70194 ATGTGA-TAAACGTTGAAATATTCATGTGACTA
1 ATGTGATTAAATGCTGAAATATTCATATGACTA
* *
70226 ATGTGATTAAATGAGACT-AAATGTGATTAATATG--TG
1 ATGTGATTAAAT--G-CTGAAA--T-ATTCATATGACTA
70262 ATGTGA-TAAATGCTGAAATATTCATATGACTA
1 ATGTGATTAAATGCTGAAATATTCATATGACTA
70294 ATGTGATTAAATG
1 ATGTGATTAAATG
70307 TGATTAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
30 8 0.13
31 1 0.02
32 15 0.24
33 14 0.22
35 9 0.14
36 8 0.13
37 1 0.02
38 7 0.11
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (33 bp):
ATGTGATTAAATGCTGAAATATTCATATGACTA
Found at i:70354 original size:58 final size:58
Alignment explanation
Indices: 70226--70354 Score: 159
Period size: 58 Copynumber: 2.2 Consensus size: 58
70216 CATGTGACTA
*
70226 ATGTGATTAAATGAGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGATT-AATGAGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATACTC
* * * * * * * * *
70285 ATATGACTAATGTGATTAAATGTGATTAATATGTGTTGTGTTAAATGTTTAAGTACTC
1 ATGTGATTAATGAGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATACTC
70343 ATGTGATTAATG
1 ATGTGATTAATG
70355 CAATTAATTT
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
58 52 0.90
59 6 0.10
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.40
Consensus pattern (58 bp):
ATGTGATTAATGAGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATACTC
Found at i:79983 original size:22 final size:21
Alignment explanation
Indices: 79956--79996 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
79946 TTGAGGCAGA
79956 AGAAGGAAGAAGAAAGAAGAAG
1 AGAAGGAAGAA-AAAGAAGAAG
79978 AGAAGGAAGAAAAAGAAGA
1 AGAAGGAAGAAAAAGAAGA
79997 TGTTGCCCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AGAAGGAAGAAAAAGAAGAAG
Found at i:80420 original size:17 final size:18
Alignment explanation
Indices: 80382--80439 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 18
80372 TTAGTTGCAT
*
80382 GCATTTTT-TTTG-TCATT
1 GCATTTTTATTTGCTC-TA
80399 GCATTTTTATTAT-CTCTA
1 GCATTTTTATT-TGCTCTA
80417 -CA-TTTTATTTGCTCTA
1 GCATTTTTATTTGCTCTA
80433 GCATTTT
1 GCATTTT
80440 GCATTGTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
15 1 0.03
16 12 0.35
17 12 0.35
18 6 0.18
19 3 0.09
ACGTcount: A:0.17, C:0.16, G:0.09, T:0.59
Consensus pattern (18 bp):
GCATTTTTATTTGCTCTA
Found at i:81081 original size:2 final size:2
Alignment explanation
Indices: 81074--81115 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
81064 AAGAAGAAGA
*
81074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81116 TATTATACAA
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:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85248 original size:25 final size:24
Alignment explanation
Indices: 85217--85266 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
85207 TCAAGTTTTT
85217 TTATTTC-ATTAATTCAATTTTATGA
1 TTATTTCTATT-ATT-AATTTTATGA
*
85242 TTATTTCTATTATTATTTTTATGA
1 TTATTTCTATTATTAATTTTATGA
85266 T
1 T
85267 GTTTAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
25 10 0.43
26 3 0.13
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (24 bp):
TTATTTCTATTATTAATTTTATGA
Found at i:86964 original size:100 final size:101
Alignment explanation
Indices: 86794--87029 Score: 323
Period size: 100 Copynumber: 2.3 Consensus size: 101
86784 TATACCGCGG
* * * *
86794 TATGTGAGCCCAGCTCTAGTTGAATTATCTAACGGTTTGCGCCCAGCACTAGTCGGATAAACCGA
1 TATGTGAGCCCAGCTCTGGTTGGATTAACCAACGGTTT-CGCCCAGCACTAGTCGGATAAACCGA
**
86859 CGGTTATGGAACTTAGTGCCTAGCAGATAAACCACGA
65 CGGTTATGGAACCCAGTGCCTAGCAGATAAACCACGA
* *
86896 TATGTGAGCCTAGCTCTGGTTGGATTAACCAATGGTTT-GCCCAGCACTAGTCGGATAAACCGAC
1 TATGTGAGCCCAGCTCTGGTTGGATTAACCAACGGTTTCGCCCAGCACTAGTCGGATAAACCGAC
* * * *
86960 GGTTATGGCACCCAGTGCCTAGCGGATAAATCGCGA
66 GGTTATGGAACCCAGTGCCTAGCAGATAAACCACGA
*
86996 TATGTGAGCCCAGCTC-GAGTTGGATCAACCAACG
1 TATGTGAGCCCAGCTCTG-GTTGGATTAACCAACG
87030 AATAATCCCT
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
99 1 0.01
100 85 0.72
102 32 0.27
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (101 bp):
TATGTGAGCCCAGCTCTGGTTGGATTAACCAACGGTTTCGCCCAGCACTAGTCGGATAAACCGAC
GGTTATGGAACCCAGTGCCTAGCAGATAAACCACGA
Found at i:87603 original size:14 final size:14
Alignment explanation
Indices: 87584--87612 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
87574 CTTTGTATTC
87584 AACTCATTTCAACA
1 AACTCATTTCAACA
87598 AACTCATTTCAACA
1 AACTCATTTCAACA
87612 A
1 A
87613 TCCAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AACTCATTTCAACA
Found at i:87705 original size:142 final size:144
Alignment explanation
Indices: 87452--87740 Score: 433
Period size: 142 Copynumber: 2.0 Consensus size: 144
87442 CTTTGTATTC
* **
87452 AACTCGTTTCAACAATCCAAAATGTTCAATATAATTCACATGGCAAAAACCATTTATTTATTTAT
1 AACTCATTTCAACAATCCAAAATGTTCAATATAATTCACA-GGCAAAAA-CATGCATTTATTTAT
* ** * *
87517 TTCCAGCCACCAAATATGCATATCAATATATATAATGATTCAAATCTTTCATTAATCCTTTGTAT
64 TTCCAACCACCAAATATGCATATCAATATATATAACAAATCAAATCTTTCATTAATCCATTGTAT
87582 TCAACTCATTTCAACA
129 TCAACTCATTTCAACA
87598 AACTCATTTCAACAATCCAAAATGTTCAATATAACTTCCACA-G-AAAAA-A-GCATTTATTTAT
1 AACTCATTTCAACAATCCAAAATGTTCAATATAA-TT-CACAGGCAAAAACATGCATTTATTTAT
*
87659 TTCCAACCACCAAATATGCATATCAATATATATAACAAATCAAATCTTTCATTAATTCATTGTAT
64 TTCCAACCACCAAATATGCATATCAATATATATAACAAATCAAATCTTTCATTAATCCATTGTAT
87724 TCAACTCATTTCAACA
129 TCAACTCATTTCAACA
87740 A
1 A
87741 TCCAAAATGT
Statistics
Matches: 132, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
142 86 0.65
143 1 0.01
145 5 0.04
146 34 0.26
147 2 0.02
148 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (144 bp):
AACTCATTTCAACAATCCAAAATGTTCAATATAATTCACAGGCAAAAACATGCATTTATTTATTT
CCAACCACCAAATATGCATATCAATATATATAACAAATCAAATCTTTCATTAATCCATTGTATTC
AACTCATTTCAACA
Found at i:87823 original size:2 final size:2
Alignment explanation
Indices: 87816--87847 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
87806 ATGCATATGA
87816 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
87848 TCATATTTAA
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):
AT
Found at i:87830 original size:142 final size:139
Alignment explanation
Indices: 87411--87834 Score: 454
Period size: 128 Copynumber: 3.1 Consensus size: 139
87401 TTCTTGCTCT
* * * *
87411 ATATATATGACAATTCAAATATTTCATTAATCTTTGTATTCAACTCGTTTCAACAATCCAAAATG
1 ATATATATAACAATTCAAATCTTTCATTAATCATTGTATTCAACTCATTTCAACAATCCAAAATG
* *
87476 TTCAATATAATTCACATGGCAAAAACCATTTATTTATTTATTTCCAGCCACCAAATATGCATATC
66 TTCAATATAATTCACATGGAAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT-
87541 AATATATATA
130 AATATATATA
* * *
87551 ATGAT-TCA-AATC-TTTCATTAATCCTTTGTATTCAACTCATT-TCA-ACAAACTCATTTCAAC
1 AT-ATAT-ATAA-CAATTCA--AAT-CTTT-CATT-AA-TCATTGT-ATTC-AACTCATTTCAAC
*
87611 AATCCAAAATGTTCAATATAACTTCCACA--GAAAAAAGC----ATTTATTTATTTCCAACCACC
55 AATCCAAAATGTTCAATATAA-TT-CACATGGAAAAAAGCATTTATTTATTTATTTCCAGCCACC
*
87670 AAATATGC-------ATAT-CA
118 AAATATGCATATAATATATATA
*
87684 ATATATATAACAAATCAAATCTTTCATTAATTCATTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATCTTTCATTAA-TCATTGTATTCAACTCATTTCAACAATCCAAAAT
87749 GTTCAATATAATTCACATGGAAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
65 GTTCAATATAATTCACATGGAAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATAT
87814 GAATATATATA
130 -AATATATATA
87825 TATATATATA
1 -ATATATATA
87835 TATATATATA
Statistics
Matches: 232, Mismatches: 18, Indels: 66
0.73 0.06 0.21
Matches are distributed among these distances:
126 4 0.02
127 2 0.01
128 51 0.22
129 5 0.02
130 4 0.02
131 3 0.01
132 32 0.14
133 9 0.04
134 4 0.02
140 12 0.05
141 5 0.02
142 40 0.17
143 3 0.01
144 3 0.01
145 4 0.02
146 45 0.19
147 2 0.01
148 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (139 bp):
ATATATATAACAATTCAAATCTTTCATTAATCATTGTATTCAACTCATTTCAACAATCCAAAATG
TTCAATATAATTCACATGGAAAAAAGCATTTATTTATTTATTTCCAGCCACCAAATATGCATATA
ATATATATA
Found at i:90367 original size:43 final size:43
Alignment explanation
Indices: 90289--90389 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 43
90279 ATAGACCATA
* * **
90289 TGCTAGACCGTGTATCTATACTGACTTGGGCCACACGGTCGTG
1 TGCTAGACCGTGTGTCTATACTGACTTGGACCACACAATCGTG
*
90332 TGCTAGACCGTGTGTCTATACTGACTTGGATCACACAATCGTG
1 TGCTAGACCGTGTGTCTATACTGACTTGGACCACACAATCGTG
*
90375 T-CTCAGCCCGTGTGT
1 TGCT-AGACCGTGTGT
90390 ATGCCCATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 2 0.04
43 49 0.96
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (43 bp):
TGCTAGACCGTGTGTCTATACTGACTTGGACCACACAATCGTG
Found at i:91128 original size:20 final size:20
Alignment explanation
Indices: 91105--91151 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
91095 AGTAAATGAT
91105 TTTAAAATTATTAAAATTAA
1 TTTAAAATTATTAAAATTAA
*
91125 TTTAAAATTATTAAAATTAT
1 TTTAAAATTATTAAAATTAA
91145 TTTAAAA
1 TTTAAAA
91152 ATATAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAATTATTAAAATTAA
Found at i:91129 original size:11 final size:10
Alignment explanation
Indices: 91105--91151 Score: 62
Period size: 9 Copynumber: 4.7 Consensus size: 10
91095 AGTAAATGAT
91105 TTTAAAATTA
1 TTTAAAATTA
91115 -TTAAAATTAA
1 TTTAAAATT-A
91125 TTTAAAATTA
1 TTTAAAATTA
91135 -TTAAAATTA
1 TTTAAAATTA
91144 TTTTAAAA
1 -TTTAAAA
91152 ATATAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 17 0.52
10 2 0.06
11 14 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:92136 original size:20 final size:20
Alignment explanation
Indices: 92111--92183 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
92101 GATGATGATT
*
92111 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAAATTTA
* * *
92131 ATAATTTTATATTAAAAAAGTAA
1 ATAATTTTA-A--AATAAATTTA
92154 ATTAATTTTAAAATAAATTTA
1 A-TAATTTTAAAATAAATTTA
92175 ATAATTTTA
1 ATAATTTTA
92184 TATTTTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 17 0.40
21 9 0.21
23 8 0.19
24 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
ATAATTTTAAAATAAATTTA
Found at i:94688 original size:36 final size:36
Alignment explanation
Indices: 94607--94719 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
94597 TGATGACTGT
*
94607 TGTGAAAGTAAATATGTGGGTAT-TTATTCATGTCA
1 TGTGAAAGTAAATATGTGGGTATGTTATTCATGCCA
* *
94642 TGAGACAGTAAATATGTGGGTATGTTATTCATGCCA
1 TGTGAAAGTAAATATGTGGGTATGTTATTCATGCCA
* * *
94678 TGTGATAGTAAATATGTGAGCATGTTATTCATGCCA
1 TGTGAAAGTAAATATGTGGGTATGTTATTCATGCCA
94714 TGTGAA
1 TGTGAA
94720 TATGTAGTGA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 21 0.30
36 48 0.70
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (36 bp):
TGTGAAAGTAAATATGTGGGTATGTTATTCATGCCA
Found at i:95059 original size:66 final size:66
Alignment explanation
Indices: 94948--95083 Score: 184
Period size: 66 Copynumber: 2.1 Consensus size: 66
94938 GTGAAATAAG
* * * *
94948 GAGAGTGTTAGTTTTATGCTTCACTTTTGGGACATGTTCGGCTCTATGA-GTCTTTTGGTGTGTT
1 GAGAGTGTTAGCTTTATGCTTCACTTTTGGGACATGTTCGACTCTA-AATGTCATTTGGTGTGTT
95012 TA
65 TA
* * *
95014 GAGAGTTTTAGCTTTATGTTTCACTTTTGGGATATGTTCGACTCTAAATGTCATTTGGTGTGTTT
1 GAGAGTGTTAGCTTTATGCTTCACTTTTGGGACATGTTCGACTCTAAATGTCATTTGGTGTGTTT
*
95079 G
66 A
95080 GAGA
1 GAGA
95084 TCCGTGTATT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.02
66 60 0.98
ACGTcount: A:0.18, C:0.11, G:0.26, T:0.45
Consensus pattern (66 bp):
GAGAGTGTTAGCTTTATGCTTCACTTTTGGGACATGTTCGACTCTAAATGTCATTTGGTGTGTTT
A
Found at i:95229 original size:49 final size:49
Alignment explanation
Indices: 95169--95280 Score: 163
Period size: 49 Copynumber: 2.3 Consensus size: 49
95159 ACTGAATGTA
* *
95169 ATTATATGTGATTAATATGTGATGTGATAAATGCTAAAATATTCATATG
1 ATTAAATGTGATTAATATGTGATGTGATAAACGCTAAAATATTCATATG
* * *
95218 ATTAAATGTGATTAATATGTGATGTGATAAACGTTGAAATATTCATGTG
1 ATTAAATGTGATTAATATGTGATGTGATAAACGCTAAAATATTCATATG
*
95267 ACT-AATGTGATTAA
1 ATTAAATGTGATTAA
95281 ATGAGACTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 11 0.19
49 46 0.81
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.39
Consensus pattern (49 bp):
ATTAAATGTGATTAATATGTGATGTGATAAACGCTAAAATATTCATATG
Found at i:95282 original size:58 final size:58
Alignment explanation
Indices: 95216--95410 Score: 214
Period size: 68 Copynumber: 3.2 Consensus size: 58
95206 AATATTCATA
*
95216 TGATTAAATGTGATTAATATGTGATGTGATAAACGTTGAAATATTCATGTGACTAATG
1 TGATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATG
*
95274 TGATTAAATGAGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACTA
1 TG-----AT-----TAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTA
95339 ATG
56 ATG
* * * * *
95342 TGATTAAATGTGATTAATATGTGTTGTGTTAAATGCTT-AAGTACTCATGTGATTAATG
1 TGATTAAATGTGATTAATATGTGATGTGATAAATG-TTGAAATATTCATGTGACTAATG
95400 TGATT-AATGTG
1 TGATTAAATGTG
95411 TAAAATAATG
Statistics
Matches: 118, Mismatches: 8, Indels: 23
0.79 0.05 0.15
Matches are distributed among these distances:
57 6 0.05
58 53 0.45
59 1 0.01
63 4 0.03
68 54 0.46
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (58 bp):
TGATTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATG
Found at i:95299 original size:68 final size:68
Alignment explanation
Indices: 95220--95351 Score: 246
Period size: 68 Copynumber: 1.9 Consensus size: 68
95210 TTCATATGAT
*
95220 TAAATGTGATTAATATGTGATGTGATAAACGTTGAAATATTCATGTGACTAATGTGATTAAATGA
1 TAAATGTGATTAATATGTGATGTGATAAACGCTGAAATATTCATGTGACTAATGTGATTAAATGA
95285 GAC
66 GAC
*
95288 TAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACTAATGTGATTAAATG
1 TAAATGTGATTAATATGTGATGTGATAAACGCTGAAATATTCATGTGACTAATGTGATTAAATG
95352 TGATTAATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.36
Consensus pattern (68 bp):
TAAATGTGATTAATATGTGATGTGATAAACGCTGAAATATTCATGTGACTAATGTGATTAAATGA
GAC
Found at i:96345 original size:26 final size:26
Alignment explanation
Indices: 96297--96346 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
96287 GGGTGTTACA
*
96297 GAACACCAACTCACACAACTCTTGGC
1 GAACACCAACTCACACAAATCTTGGC
* * *
96323 GAACACCAATTCTCATAAATCTTG
1 GAACACCAACTCACACAAATCTTG
96347 ATGAACCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.32, G:0.10, T:0.22
Consensus pattern (26 bp):
GAACACCAACTCACACAAATCTTGGC
Found at i:99913 original size:17 final size:17
Alignment explanation
Indices: 99891--99949 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
99881 AAGAATATGA
99891 AAGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
99908 AAGGTTAAAGGTCAAG--GG
1 AAGGTT-AAGG--AAGATGG
99926 -AGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
99942 AAGGTTAA
1 AAGGTTAA
99950 AAGTTAAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.08
16 6 0.17
17 18 0.50
18 6 0.17
20 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.39, T:0.19
Consensus pattern (17 bp):
AAGGTTAAGGAAGATGG
Found at i:99935 original size:34 final size:34
Alignment explanation
Indices: 99892--99961 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
99882 AGAATATGAA
*
99892 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
*
99926 AGGTTAAGGAAGATGGAAGGTTAAAAGTTAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
99960 AG
1 AG
99962 ATGAAAGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.40, C:0.01, G:0.40, T:0.19
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
Found at i:105390 original size:17 final size:17
Alignment explanation
Indices: 105368--105426 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
105358 AAGAATATGA
105368 AAGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
105385 AAGGTTAAAGGTCAAG--GG
1 AAGGTT-AAGG--AAGATGG
105403 -AGGTTAAGGAAGATGG
1 AAGGTTAAGGAAGATGG
105419 AAGGTTAA
1 AAGGTTAA
105427 AAGTCAAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.08
16 6 0.17
17 18 0.50
18 6 0.17
20 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.39, T:0.19
Consensus pattern (17 bp):
AAGGTTAAGGAAGATGG
Found at i:105412 original size:34 final size:34
Alignment explanation
Indices: 105369--105438 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
105359 AGAATATGAA
*
105369 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
105403 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
105437 AG
1 AG
105439 ATGAAAGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.03, G:0.40, T:0.17
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAAGTCAAGGG
Done.