Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002153.1 Kokia drynarioides strain JFW-HI SEQ_114102, 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: 47927
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6138 original size:24 final size:24
Alignment explanation
Indices: 6110--6168 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
6100 TAGACTAATA
*
6110 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * * *
6134 AGAGTTTAATTGAAATAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
6158 AGAGTTTAACT
1 AGAGTTTAACT
6169 AAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:17070 original size:19 final size:18
Alignment explanation
Indices: 17041--17095 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
17031 TAATTTAACC
*
17041 ATTTTTATTTTTATTTTA
1 ATTTTTATTTTTAATTTA
*
17059 ATATTTTGTTTTTAATTTA
1 AT-TTTTATTTTTAATTTA
*
17078 ATTTTTACATTTTAATTT
1 ATTTTTA-TTTTTAATTT
17096 TTTTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTATTTTTAATTTA
Found at i:17089 original size:25 final size:25
Alignment explanation
Indices: 17042--17090 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
17032 AATTTAACCA
* * *
17042 TTTTTATTTTTATTTTAATATTTTG
1 TTTTTAATTTAATTTTAACATTTTG
*
17067 TTTTTAATTTAATTTTTACATTTT
1 TTTTTAATTTAATTTTAACATTTT
17091 AATTTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (25 bp):
TTTTTAATTTAATTTTAACATTTTG
Found at i:17121 original size:14 final size:14
Alignment explanation
Indices: 17048--17124 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
17038 ACCATTTTTA
* *
17048 TTTTTATTTTAATA
1 TTTTTTTTTTAATT
*
17062 TTTTGTTTTTAATT
1 TTTTTTTTTTAATT
17076 TAATTTTTACATTTTAA-T
1 T--TTTTT---TTTTAATT
*
17094 TTTTTTTTCT--TT
1 TTTTTTTTTTAATT
17106 TTTTTTTTTTAATT
1 TTTTTTTTTTAATT
17120 TTTTT
1 TTTTT
17125 AGGTTCTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
12 10 0.20
13 3 0.06
14 19 0.39
16 9 0.18
18 2 0.04
19 6 0.12
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTTTTTTTTAATT
Found at i:17134 original size:25 final size:25
Alignment explanation
Indices: 17087--17134 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17077 AATTTTTACA
** *
17087 TTTTAATTTTTTTTTCTTTTTTTTT
1 TTTTAATTTTTTTAGCTTCTTTTTT
*
17112 TTTTAATTTTTTTAGGTTCTTTT
1 TTTTAATTTTTTTAGCTTCTTTT
17135 AGTAGCAACC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTAATTTTTTTAGCTTCTTTTTT
Found at i:18363 original size:25 final size:25
Alignment explanation
Indices: 18335--18382 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
18325 AATGAATCAT
18335 ATAAATAAATAA-TAAATAGAAAACA
1 ATAAATAAA-AATTAAATAGAAAACA
18360 ATAAATAAAAATTAAATAGAAAA
1 ATAAATAAAAATTAAATAGAAAA
18383 TAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (25 bp):
ATAAATAAAAATTAAATAGAAAACA
Found at i:22474 original size:18 final size:17
Alignment explanation
Indices: 22451--22486 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
22441 TTATTTTGTT
22451 AAAAAAATCGAAAAGAAA
1 AAAAAAATCGAAAA-AAA
*
22469 AAAAAAATTGAAAAAAA
1 AAAAAAATCGAAAAAAA
22486 A
1 A
22487 TTGAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAAAATCGAAAAAAA
Found at i:26386 original size:29 final size:28
Alignment explanation
Indices: 26354--26544 Score: 108
Period size: 29 Copynumber: 6.6 Consensus size: 28
26344 GGTTCGAGGT
*
26354 TAAAAACGGAATTTTTAGATATTCGGGGG
1 TAAAAATGGAATTTTTAGA-ATTCGGGGG
*
26383 T-AAAATGGTAATTTTTGGAAGGTTC-GGGG
1 TAAAAATGG-AATTTTTAGAA--TTCGGGGG
* *
26412 TAAAAATGGCATTTTTAGACATTCGAGGG
1 TAAAAATGGAATTTTTAGA-ATTCGGGGG
* *
26441 T-AAAATGGTAATTTTT-GAAAGGTT-TGAGG
1 TAAAAATGG-AATTTTTAG-AA--TTCGGGGG
*
26470 TCAAAAAT-GATATTTTTAGACATTCGAGGG
1 T-AAAAATGGA-ATTTTTAGA-ATTCGGGGG
* * *
26500 TAAAATTGTAA-TTTTGGAAAGTTCGGGGG
1 TAAAAATGGAATTTTTAG-AA-TTCGGGGG
*
26529 TAAAAATGTAATTTTT
1 TAAAAATGGAATTTTT
26545 GGAACATTCG
Statistics
Matches: 125, Mismatches: 17, Indels: 39
0.69 0.09 0.22
Matches are distributed among these distances:
28 25 0.20
29 64 0.51
30 29 0.23
31 7 0.06
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
TAAAAATGGAATTTTTAGAATTCGGGGG
Found at i:26394 original size:59 final size:59
Alignment explanation
Indices: 26325--26556 Score: 292
Period size: 59 Copynumber: 3.9 Consensus size: 59
26315 GCTTGGGAAC
* * * * *
26325 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAACGGAATTTTTAGATATTCGGGGGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGGTAAAAATGGAATTTTTAGACATTCGAGGGT
* *
26384 AAAATGGTAATTTTTGGAAGGTTCG-GGGTAAAAATGGCATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGGTAAAAATGGAATTTTTAGACATTCGAGGGT
*
26442 AAAATGGTAATTTTTGAAAGGTTTGA-GGTCAAAAAT-GATATTTTTAGACATTCGAGGGT
1 AAAATGGTAATTTTTGAAAGGTTCGAGGGT-AAAAATGGA-ATTTTTAGACATTCGAGGGT
* * * * *
26501 AAAATTGTAATTTTGGAAA-GTTCGGGGGTAAAAATGTAATTTTTGGAACATTCGAG
1 AAAATGGTAATTTTTGAAAGGTTCGAGGGTAAAAATGGAATTTTTAG-ACATTCGAG
26557 ATAAAAAATG
Statistics
Matches: 151, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
58 72 0.48
59 79 0.52
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGAAAGGTTCGAGGGTAAAAATGGAATTTTTAGACATTCGAGGGT
Found at i:26562 original size:117 final size:116
Alignment explanation
Indices: 26325--26762 Score: 360
Period size: 117 Copynumber: 3.7 Consensus size: 116
26315 GCTTGGGAAC
* * * * * *
26325 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAACG-GAATTTTTAGATATTCGGGGGT-AAAA
1 AAAATGG-AATTTTTGAAA-GTTTGAGGGTAAAAATGATAATTTTTAGA-ATTC-GAGGTCAAAA
* * ** * *
26388 TGGTAATTTTTGGAAGGTTC-GGGGTAAAAATGGCATTTTTAG-ACATTCGAGGGT
62 TTGTAA-TTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAACATTCGAGGAT
26442 AAAATGGTAATTTTTGAAAGGTTTGA-GGTCAAAAATGAT-ATTTTTAGACATTCGAGGGT-AAA
1 AAAATGG-AATTTTTGAAA-GTTTGAGGGT-AAAAATGATAATTTTTAGA-ATTCGA-GGTCAAA
26504 ATTGTAATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAACATTCGA-GAT
61 ATTGTAATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAACATTCGAGGAT
* * * * *
26559 AAAAAATGGAATTTTGGAAAATTTAAGGGTAAAAAT-ATAATTTTTGGAAAATTCGAAGTCAAAA
1 --AAAATGGAATTTTTGAAAGTTTGAGGGTAAAAATGATAATTTTT--AGAATTCGAGGTCAAAA
* * ** * * * ** *
26623 TTGGAATTTTGGAAATTTTTGGAGTACAAATGTAATTTTTGGAAAATTTAAGGTT
62 TTGTAATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAACATTCGAGGAT
*
26678 AAAATTGGAATTTTTGAAAGTTT-AGGGTAAAAATG-TAAGTTTTGGAGAATTCGAGGTCAAAAA
1 AAAA-TGGAATTTTTGAAAGTTTGAGGGTAAAAATGATAA-TTTT-TAGAATTCGAGGTC-AAAA
* *
26741 TAG-AATTTTGGAAAGTTTGGGG
62 TTGTAATTTTGGAAAGTTCGGGG
26763 ATCTCTAGGG
Statistics
Matches: 266, Mismatches: 37, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
116 17 0.06
117 139 0.52
118 99 0.37
119 11 0.04
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (116 bp):
AAAATGGAATTTTTGAAAGTTTGAGGGTAAAAATGATAATTTTTAGAATTCGAGGTCAAAATTGT
AATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAACATTCGAGGAT
Found at i:26564 original size:30 final size:30
Alignment explanation
Indices: 26384--26754 Score: 166
Period size: 29 Copynumber: 12.6 Consensus size: 30
26374 ATTCGGGGGT
** *
26384 AAAATGGTAATTTTTGGAAGGTTCG-GGGTA
1 AAAAT-GTAATTTTTGGAAAATTCGAGGATA
** * * *
26414 AAAATGGCATTTTTAG-ACATTCGAGGGT-
1 AAAATGTAATTTTTGGAAAATTCGAGGATA
* *
26442 AAAATGGTAATTTTT-GAAAGGTTTGAGG-TCA
1 AAAAT-GTAATTTTTGGAAA-ATTCGAGGAT-A
* * *
26473 AAAATG-ATATTTTTAG-ACATTCGAGGGTA
1 AAAATGTA-ATTTTTGGAAAATTCGAGGATA
* * * *
26502 AAATTGTAA-TTTTGGAAAGTTCGGGGGTA
1 AAAATGTAATTTTTGGAAAATTCGAGGATA
*
26531 AAAATGTAATTTTTGGAACATTCGA-GATAA
1 AAAATGTAATTTTTGGAAAATTCGAGGAT-A
* ** *
26561 AAAATGGAA-TTTTGGAAAATTTAAGGGTA
1 AAAATGTAATTTTTGGAAAATTCGAGGATA
* *
26590 AAAATATAATTTTTGGAAAATTCGAAG-TCA
1 AAAATGTAATTTTTGGAAAATTCGAGGAT-A
* * ***
26620 AAATTGGAA-TTTTGG-AAATTTTTGGAGTA
1 AAAATGTAATTTTTGGAAAATTCGAGGA-TA
* ** *
26649 CAAATGTAATTTTTGGAAAATTTAAGGTTA
1 AAAATGTAATTTTTGGAAAATTCGAGGATA
* * * * *
26679 AAATTGGAATTTTT-GAAAGTT-TAGGGTA
1 AAAATGTAATTTTTGGAAAATTCGAGGATA
* *
26707 AAAATGTAAGTTTTGGAGAATTCGAGG-TCA
1 AAAATGTAATTTTTGGAAAATTCGAGGAT-A
26737 AAAATAG-AA-TTTTGGAAA
1 AAAAT-GTAATTTTTGGAAA
26755 GTTTGGGGAT
Statistics
Matches: 258, Mismatches: 59, Indels: 49
0.70 0.16 0.13
Matches are distributed among these distances:
28 38 0.15
29 109 0.42
30 96 0.37
31 15 0.06
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAATTCGAGGATA
Found at i:26572 original size:59 final size:58
Alignment explanation
Indices: 26384--26762 Score: 306
Period size: 59 Copynumber: 6.5 Consensus size: 58
26374 ATTCGGGGGT
* * ** *
26384 AAAATGGTAATTTTTGG-AAGGTTCGGGGTAAAAATGGCATTTTTAG-ACATTCGAGGGT-
1 AAAATGG-AA-TTTTGGAAAGTTTTGGGGTAAAAATGTAATTTTTGGAACATTCGA-GGTA
* * * *
26442 AAAATGGTAATTTTTGAAAGGTTTGAGGTCAAAAATG-ATATTTTTAG-ACATTCGAGGGTA
1 AAAATGG-AATTTTGGAAAGTTTTGGGGT-AAAAATGTA-ATTTTTGGAACATTCGA-GGTA
* * ** *
26502 AAATTGTAATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAACATTCGAGATAA
1 AAAATGGAATTTTGGAAAGTTTTGGGGTAAAAATGTAATTTTTGGAACATTCGAGGT-A
* ** * * *
26561 AAAATGGAATTTTGGAAAATTTAAGGGTAAAAATATAATTTTTGGAAAATTCGAAGTCA
1 AAAATGGAATTTTGGAAAGTTTTGGGGTAAAAATGTAATTTTTGGAACATTCGAGGT-A
* * * * * **
26620 AAATTGGAATTTTGGAAATTTTTGGAGTACAAATGTAATTTTTGGAAAATTTAAGGTTA
1 AAAATGGAATTTTGGAAAGTTTTGGGGTAAAAATGTAATTTTTGGAACATTCGAGG-TA
* * * *
26679 AAATTGGAATTTTTGAAAG-TTTAGGGTAAAAATGTAAGTTTTGGAGA-ATTCGAGGTCA
1 AAAATGGAATTTTGGAAAGTTTTGGGGTAAAAATGTAATTTTTGGA-ACATTCGAGGT-A
*
26737 AAAATAGAATTTTGGAAAG-TTTGGGG
1 AAAATGGAATTTTGGAAAGTTTTGGGG
26763 ATCTCTAGGG
Statistics
Matches: 265, Mismatches: 46, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
57 6 0.02
58 87 0.33
59 166 0.63
60 6 0.02
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTGGAAAGTTTTGGGGTAAAAATGTAATTTTTGGAACATTCGAGGTA
Found at i:27768 original size:3 final size:3
Alignment explanation
Indices: 27760--27833 Score: 64
Period size: 3 Copynumber: 24.7 Consensus size: 3
27750 CTCTTTTTAT
* * * *
27760 TTA TTA TTA ATA TTTA TTA ATA TCT- TTA ATA TTA TTA -AA TCTA TT-
1 TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA T-TA TTA
27805 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27834 TTGAAAAACC
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
2 4 0.07
3 48 0.84
4 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28279 original size:12 final size:12
Alignment explanation
Indices: 28262--28286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28252 GATGCAAAAT
28262 TGGCAGTCCAAG
1 TGGCAGTCCAAG
28274 TGGCAGTCCAAG
1 TGGCAGTCCAAG
28286 T
1 T
28287 TGGTGGTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (12 bp):
TGGCAGTCCAAG
Found at i:28516 original size:11 final size:11
Alignment explanation
Indices: 28502--28572 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
28492 ATTAAATTTC
28502 AATTTAAAATA
1 AATTTAAAATA
28513 AATTT-AAAT-
1 AATTTAAAATA
28522 --TTTAAAATA
1 AATTTAAAATA
*
28531 AATTTAAACTCA
1 AATTTAAAAT-A
* **
28543 AA-GTAAGTTTA
1 AATTTAA-AATA
28554 AATTTAAAATA
1 AATTTAAAATA
28565 AATTTAAA
1 AATTTAAA
28573 CTTAAAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
10 4 0.09
11 28 0.61
12 7 0.15
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:28516 original size:17 final size:17
Alignment explanation
Indices: 28494--28585 Score: 121
Period size: 17 Copynumber: 5.4 Consensus size: 17
28484 CACTTTTAAT
*
28494 TAAATTTCAATTTAAAA
1 TAAATTTAAATTTAAAA
28511 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
* * *
28529 TAAATTTAAACTCAAAG
1 TAAATTTAAATTTAAAA
*
28546 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
28563 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
28580 TAAATT
1 TAAATT
28586 GAAGTTTTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 47 0.73
18 17 0.27
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28527 original size:7 final size:6
Alignment explanation
Indices: 28493--28578 Score: 54
Period size: 6 Copynumber: 14.8 Consensus size: 6
28483 ACACTTTTAA
* * * *
28493 TTAAAT TTCAAT TTAAA- ATAAAT TTAAATT TTAAA- ATAAAT TTAAAC
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT
* * * * *
28540 TCAAA- GTAAGT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
28579 ATAAATTGAA
Statistics
Matches: 59, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
5 14 0.24
6 39 0.66
7 6 0.10
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:28534 original size:35 final size:35
Alignment explanation
Indices: 28494--28597 Score: 138
Period size: 34 Copynumber: 3.0 Consensus size: 35
28484 CACTTTTAAT
* *
28494 TAAATTTCAATTTAAAATAAATTTAAATTTTAAAA
1 TAAATTTAAACTTAAAATAAATTTAAATTTTAAAA
* * *
28529 TAAATTTAAACTCAAAGTAAGTTTAAA-TTTAAAA
1 TAAATTTAAACTTAAAATAAATTTAAATTTTAAAA
* *
28563 TAAATTTAAACTTAAAATAAATTGAAGTTTTAAAA
1 TAAATTTAAACTTAAAATAAATTTAAATTTTAAAA
28598 ACAATCCAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 29 0.50
35 29 0.50
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (35 bp):
TAAATTTAAACTTAAAATAAATTTAAATTTTAAAA
Found at i:29476 original size:49 final size:50
Alignment explanation
Indices: 29423--29968 Score: 224
Period size: 49 Copynumber: 11.2 Consensus size: 50
29413 TCTTTCTTGT
*
29423 CATGTTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCATTT-CCTC
1 CATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCATTTCCCTC
* * * * * *
29472 CATGTCCTTGT--GGTAC-TGGATTCGCTGTTGCGGCTTAAATC-TTTCCCTT
1 CATGT--TTCTAAGGTACAAGG-TTCGCCGTTGCGACTTAAACCATTTCCCTC
* * * * *
29521 CATTTTTCTTAGGTACAATGTTCACTGTTGCGACTTAAACCA-TTCCCTC
1 CATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCATTTCCCTC
* * * * * ** * * *
29570 TATATCTCCATGGTA-TTGGATTCGCCGTTGCGGCTTAAATC-TTTCCCTT
1 CATGTTTCTAAGGTACAAGG-TTCGCCGTTGCGACTTAAACCATTTCCCTC
* * * * *
29619 CATTTTTCTGAGGTACAAGGTTCACCATTGCGACTTAAACCA-TTCACT-
1 CATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCATTTCCCTC
* * * * * *
29667 CGTGTCTTCGT--GGTAC-TGGATTCGCCGTTAC-AGCTTAAA-TATTTTCCTT
1 CATGT-TTC-TAAGGTACAAGG-TTCGCCGTTGCGA-CTTAAACCATTTCCCTC
* * * * *
29716 CATGCTTCTGAGGCACAAGGTTCACCGTTGCGACTTAAACC-TTTCCCCC
1 CATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCATTTCCCTC
* ** * * * *
29765 CATATCTT-TGTGGTAC-TGGATTCGTCGTTGC-AGCTTAAATC-TTTCCCTT
1 CATGT-TTCTAAGGTACAAGG-TTCGCCGTTGCGA-CTTAAACCATTTCCCTC
* * * ** *
29814 TATGCTTCTGAGACACAAGGTTCGCCGTTGCGACTTAAATC-TTTCCCTC
1 CATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCATTTCCCTC
* * * * * * *
29863 CATATCTTC-ATGGTAC-TGGATTCGCCGTTGTGGCTTAAATC-TTTCCCTT
1 CATGT-TTCTAAGGTACAAGG-TTCGCCGTTGCGACTTAAACCATTTCCCTC
* * * ** *
29912 TATGCTTCTGAGGTACAAGGTTCGCAATTGCGACTTTAACC-TTTCCCTC
1 CATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCATTTCCCTC
29961 CATGTTTC
1 CATGTTTC
29969 GCGGTATTGA
Statistics
Matches: 358, Mismatches: 106, Indels: 66
0.68 0.20 0.12
Matches are distributed among these distances:
47 8 0.02
48 45 0.13
49 285 0.80
50 17 0.05
51 3 0.01
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (50 bp):
CATGTTTCTAAGGTACAAGGTTCGCCGTTGCGACTTAAACCATTTCCCTC
Found at i:29584 original size:98 final size:98
Alignment explanation
Indices: 29422--29963 Score: 647
Period size: 98 Copynumber: 5.5 Consensus size: 98
29412 ATCTTTCTTG
* * ** * *
29422 TCATGTTTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCATTTCCTCCATGTCCTT-GTGGT
1 TCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCATTCCCTCCATAT-CTTCGTGGT
*
29486 ACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCT
65 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
** * * * * * *
29520 TCATTTTTCTTAGGTACAATGTTCACTGTTGCGACTTAAACCATTCCCTCTATATCTCCATGGTA
1 TCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCATTCCCTCCATATCTTCGTGGTA
*
29585 TTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
** * * * *
29618 TCATTTTTCTGAGGTACAAGGTTCACCATTGCGACTTAAACCATTCACT-CGTGTCTTCGTGGTA
1 TCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCATTCCCTCCATATCTTCGTGGTA
* * * *
29682 CTGGATTCGCCGTTACAGCTTAAATATTTTCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * * *
29715 TCATGCTTCTGAGGCACAAGGTTCACCGTTGCGACTTAAACCTTTCCCCCCATATCTTTGTGGTA
1 TCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCATTCCCTCCATATCTTCGTGGTA
* *
29780 CTGGATTCGTCGTTGCAGCTTAAATCTTTCCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* ** * * * *
29813 TTATGCTTCTGAGACACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTCCATATCTTCATGGTA
1 TCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCATTCCCTCCATATCTTCGTGGTA
*
29878 CTGGATTCGCCGTTGTGGCTTAAATCTTTCCCT
66 CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
* * ** * *
29911 TTATGCTTCTGAGGTACAAGGTTCGCAATTGCGACTTTAACCTTTCCCTCCAT
1 TCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCATTCCCTCCAT
29964 GTTTCGCGGT
Statistics
Matches: 384, Mismatches: 58, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
97 82 0.21
98 302 0.79
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (98 bp):
TCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAACCATTCCCTCCATATCTTCGTGGTA
CTGGATTCGCCGTTGCGGCTTAAATCTTTCCCT
Found at i:30422 original size:18 final size:18
Alignment explanation
Indices: 30396--30430 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30386 AAAATTGCCG
*
30396 AATATTTACAAGGAACAA
1 AATAATTACAAGGAACAA
30414 AATAATTACAAGGAACA
1 AATAATTACAAGGAACA
30431 GCATTAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (18 bp):
AATAATTACAAGGAACAA
Found at i:41895 original size:29 final size:30
Alignment explanation
Indices: 41825--42044 Score: 133
Period size: 29 Copynumber: 7.5 Consensus size: 30
41815 CTTTGGGAAC
* *
41825 AAAATGGTAATTTTT-GAAAACTTCGAGGTTA
1 AAAATGGTAATTTTTAG-ACA-TTCGAGGGTA
** *
41856 AAAAAAG-AATTTTTAGACATTCGAGAGT-
1 AAAATGGTAATTTTTAGACATTCGAGGGTA
* *
41884 AAAATGGTAATTTTTGGA-AGGTTCG-GAGTCA
1 AAAATGGTAATTTTTAGACA--TTCGAGGGT-A
* *
41915 AAAATGG-CATTTTTAAACATTCGAGGGT-
1 AAAATGGTAATTTTTAGACATTCGAGGGTA
*
41943 AAAATGGTAATTTTGTA-AGATTCGA-GGTCA
1 AAAATGGTAATTTT-TAGACATTCGAGGGT-A
* * *
41973 AAAATGG-CATTTTTAGATATTCAAGGGT-
1 AAAATGGTAATTTTTAGACATTCGAGGGTA
* * *
42001 AAAATGGTAA-ATTTGGAAAGTTCGAGGGTA
1 AAAATGGTAATTTTTAGACA-TTCGAGGGTA
42031 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
42045 GAAAAATTTG
Statistics
Matches: 148, Mismatches: 23, Indels: 37
0.71 0.11 0.18
Matches are distributed among these distances:
28 31 0.21
29 60 0.41
30 43 0.29
31 14 0.09
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTAGACATTCGAGGGTA
Found at i:42043 original size:58 final size:59
Alignment explanation
Indices: 41825--42094 Score: 250
Period size: 58 Copynumber: 4.6 Consensus size: 59
41815 CTTTGGGAAC
* * * ** * *
41825 AAAATGGTAATTTTTGAAAACTTCGA-GGTTAAAAAAAGAATTTTTAGACATTCGAGAGT
1 AAAATGGTAA-TTTTGGAAAGTTCGAGGGTCAAAAATGGAATTTTTAAACATTCGAGGGT
* * *
41884 AAAATGGTAATTTTTGGAAGGTTCG-GAGTCAAAAATGGCATTTTTAAACATTCGAGGGT
1 AAAATGGTAA-TTTTGGAAAGTTCGAGGGTCAAAAATGGAATTTTTAAACATTCGAGGGT
* * * * *
41943 AAAATGGTAATTTT-GTAAGATTCGA-GGTCAAAAATGGCATTTTTAGATATTCAAGGGT
1 AAAATGGTAATTTTGGAAAG-TTCGAGGGTCAAAAATGGAATTTTTAAACATTCGAGGGT
* * * * *
42001 AAAATGGTAAATTTGGAAAGTTCGAGGGT-AAAAATGTAATTTTTGAAAAATTTG-GGAT
1 AAAATGGTAATTTTGGAAAGTTCGAGGGTCAAAAATGGAATTTTT-AAACATTCGAGGGT
*
42059 CAAAATGG-AATTTTGGAAAGTTCCAGGGT-AAAAATG
1 -AAAATGGTAATTTTGGAAAGTTCGAGGGTCAAAAATG
42095 TAAATTTAGG
Statistics
Matches: 177, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
57 3 0.02
58 97 0.55
59 77 0.44
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTGGAAAGTTCGAGGGTCAAAAATGGAATTTTTAAACATTCGAGGGT
Found at i:42048 original size:29 final size:29
Alignment explanation
Indices: 41825--42097 Score: 127
Period size: 29 Copynumber: 9.3 Consensus size: 29
41815 CTTTGGGAAC
* *
41825 AAAATGGTAATTTTTGAAAACTTCGAGGTTAA
1 AAAAT-GTAATTTTTG-AAAGTTCGAGGGT-A
* * *
41857 AAAAAG-AATTTTTAGACA-TTCGAGAGT-
1 AAAATGTAATTTTT-GAAAGTTCGAGGGTA
* *
41884 AAAATGGTAATTTTTGGAAGGTTCG-GAGTCA
1 AAAAT-GTAATTTTT-GAAAGTTCGAGGGT-A
** *
41915 AAAATGGCATTTTT-AAACATTCGAGGGT-
1 AAAATGTAATTTTTGAAA-GTTCGAGGGTA
*
41943 AAAATGGTAA-TTTTGTAAGATTCGA-GGTCA
1 AAAAT-GTAATTTTTGAAAG-TTCGAGGGT-A
** * *
41973 AAAATGGCATTTTTAGATA-TTCAAGGGT-
1 AAAATGTAATTTTT-GAAAGTTCGAGGGTA
* *
42001 AAAATGGTAAATTTGGAAAGTTCGAGGGTA
1 AAAAT-GTAATTTTTGAAAGTTCGAGGGTA
* * * *
42031 AAAATGTAATTTTTGAAAAATTTG-GGATC
1 AAAATGTAATTTTTG-AAAGTTCGAGGGTA
* * *
42060 AAAATGGAATTTTGGAAAGTTCCAGGGTA
1 AAAATGTAATTTTTGAAAGTTCGAGGGTA
42089 AAAATGTAA
1 AAAATGTAA
42098 ATTTAGGGTC
Statistics
Matches: 178, Mismatches: 42, Indels: 45
0.67 0.16 0.17
Matches are distributed among these distances:
27 4 0.02
28 28 0.16
29 87 0.49
30 46 0.26
31 9 0.05
32 4 0.02
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTCGAGGGTA
Found at i:42110 original size:48 final size:49
Alignment explanation
Indices: 42048--42142 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
42038 AATTTTTGAA
42048 AAATTTGGGATC-AAAATGGAATTTTGGAAAGTTCCA-GGGTAAAAATGT
1 AAATTTGGGATCAAAAATGGAATTTTGGAAAGTT-CAGGGGTAAAAATGT
*
42096 AAATTTAGGG-TCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAAT
1 AAATTT-GGGATCAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAAT
42143 ATCATTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
48 9 0.21
49 34 0.79
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.29
Consensus pattern (49 bp):
AAATTTGGGATCAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAAATGT
Found at i:42141 original size:29 final size:28
Alignment explanation
Indices: 42099--42247 Score: 106
Period size: 29 Copynumber: 5.1 Consensus size: 28
42089 AAAATGTAAA
*
42099 TTTAGGGTCAAAAATGGAATTTTGGAAAG
1 TTTAGGGT-AAAAATAGAATTTTGGAAAG
* * * *
42128 TTTAGGGGTAAAAATATCATTTTTTGAAAA
1 TTTA-GGGTAAAAATA-GAATTTTGGAAAG
* *
42158 TTCTA-GGTTAAAATTGAAATTTTGGAAAG
1 TT-TAGGGTAAAAATAG-AATTTTGGAAAG
*
42187 TTTGAGGGTAAAAATATAATTTGTGAAGAAA-
1 TTT-AGGGTAAAAATAGAATTT-TG--GAAAG
* *
42218 TTTAGGGT-CAACTAGAATTTTGGAAAG
1 TTTAGGGTAAAAATAGAATTTTGGAAAG
42245 TTT
1 TTT
42248 GGGGACCTCC
Statistics
Matches: 93, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
26 4 0.04
27 3 0.03
28 3 0.03
29 44 0.47
30 30 0.32
31 5 0.05
32 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.36
Consensus pattern (28 bp):
TTTAGGGTAAAAATAGAATTTTGGAAAG
Found at i:42159 original size:59 final size:59
Alignment explanation
Indices: 42096--42251 Score: 178
Period size: 59 Copynumber: 2.7 Consensus size: 59
42086 GTAAAAATGT
* *
42096 AAATTTAGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAAATATCATTTTTTG-A-
1 AAATTTAGGGTCAAAAATGGAATTTTGGAAAGTTT-GGGGTAAAAATAT-AATTTGTGAAG
* * *
42155 AAATTCTA-GGTTAAAATTGAAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTGTGAAG
1 AAATT-TAGGGTCAAAAATGGAATTTTGGAAAGTTTG-GGGTAAAAATATAATTTGTGAAG
* *
42215 AAATTTAGGGTC--AACTAGAATTTTGGAAAGTTTGGGG
1 AAATTTAGGGTCAAAAATGGAATTTTGGAAAGTTTGGGG
42252 ACCTCCAGGG
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
57 3 0.04
58 26 0.31
59 44 0.53
60 10 0.12
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
AAATTTAGGGTCAAAAATGGAATTTTGGAAAGTTTGGGGTAAAAATATAATTTGTGAAG
Found at i:42197 original size:108 final size:108
Alignment explanation
Indices: 42001--42201 Score: 257
Period size: 108 Copynumber: 1.9 Consensus size: 108
41991 ATTCAAGGGT
* * *
42001 AAAATGGTAAATTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGAAAAATTTGGGATCAAAATG
1 AAAATGGTAAATTTGGAAAGTTAGAGGGTAAAAATATAATTTTTGAAAAATTTAGGATCAAAATG
*
42066 GAATTTTGGAAAGTTCCAGGGTAAAAATGTAAATTTAGGGTCA
66 AAATTTTGGAAAGTTCCAGGGTAAAAATGTAAATTTAGGGTCA
* * *
42109 AAAATGG-AATTTTGGAAAGTTTAG-GGGTAAAAATATCATTTTTTG-AAAATTCTAGG-TTAAA
1 AAAATGGTAAATTTGGAAAG-TTAGAGGGTAAAAATAT-AATTTTTGAAAAATT-TAGGATCAAA
**
42170 ATTGAAATTTTGGAAAGTTTGAGGGTAAAAAT
63 A-TGAAATTTTGGAAAGTTCCAGGGTAAAAAT
42202 ATAATTTGTG
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
107 33 0.41
108 47 0.59
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (108 bp):
AAAATGGTAAATTTGGAAAGTTAGAGGGTAAAAATATAATTTTTGAAAAATTTAGGATCAAAATG
AAATTTTGGAAAGTTCCAGGGTAAAAATGTAAATTTAGGGTCA
Found at i:43327 original size:3 final size:3
Alignment explanation
Indices: 43319--43415 Score: 108
Period size: 3 Copynumber: 31.7 Consensus size: 3
43309 CTCTTTTTAT
* * * *
43319 TTA TTA TTA ATA TTTA TTA ATA TGT- TTA TTA TTA TTA -AA CCTA TTTA
1 TTA TTA TTA TTA -TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA -TTA
43366 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43414 TT
1 TT
43416 CATTTAATGC
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.02
3 73 0.90
4 6 0.07
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:44889 original size:43 final size:43
Alignment explanation
Indices: 44743--44952 Score: 147
Period size: 43 Copynumber: 4.9 Consensus size: 43
44733 GAAAACGTCG
* * * * * * **
44743 CTAAAGAACATGGTCTTTAGCGGCGC-TATCCCAAAAACGCTG
1 CTAAAGAACATGATCTTTAGCAGCACTTTTCTCACAAACGCCA
* * *
44785 CTAAAGAACATGATTTTTA-AAGACGCTTTTTCTCACAAACGCCA
1 CTAAAGAACATGATCTTTAGCAG-CAC-TTTTCTCACAAACGCCA
* * ** *
44829 CTAAAGAATATGGTCTTTAGTGGCACTTTTCTCACAAACGTCA
1 CTAAAGAACATGATCTTTAGCAGCACTTTTCTCACAAACGCCA
* * **
44872 TTACAGAACATGATCTTTAGCAGCACTTTTCTCACAAACGCTG
1 CTAAAGAACATGATCTTTAGCAGCACTTTTCTCACAAACGCCA
* * ** *
44915 CTAATGAACAT-AGTCTTTAGTAGCGTTTTTCCCACAAA
1 CTAAAGAACATGA-TCTTTAGCAGCACTTTTCTCACAAA
44953 AGCTTCTAAA
Statistics
Matches: 131, Mismatches: 32, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
41 1 0.01
42 21 0.16
43 79 0.60
44 29 0.22
45 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (43 bp):
CTAAAGAACATGATCTTTAGCAGCACTTTTCTCACAAACGCCA
Found at i:45517 original size:2 final size:2
Alignment explanation
Indices: 45510--45535 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45500 CAATGTAAAC
45510 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
45536 GTTTATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.