Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009581.1 Kokia drynarioides strain JFW-HI SEQ_124295, 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: 34201
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3447 original size:29 final size:29
Alignment explanation
Indices: 3348--3593 Score: 98
Period size: 29 Copynumber: 8.4 Consensus size: 29
3338 GCACAGGGGC
* * * **
3348 AAAATGGTAGTTTTGGAAGGTTCTGAATCA
1 AAAATGGGA-TTTTAGAAGGTTCGGGGTCA
* * *
3378 AAAATGAGATTTTTGAAAGTTCGGGGGT--
1 AAAATGGGATTTTAGAAGGTTC-GGGGTCA
* *
3406 AAGATGGTAATTTTAGAAGGTTCGGGGTCA
1 AAAATGG-GATTTTAGAAGGTTCGGGGTCA
* * ** * *
3436 AAAATGGGATTTTTGGACATTCAGGGTTA
1 AAAATGGGATTTTAGAAGGTTCGGGGTCA
* *
3465 AAATTGGGATTTTTG--GGAATTCAGGGGT--
1 AAAATGGGATTTTAGAAGG--TTC-GGGGTCA
** **
3493 AAAATGATTATTTTTAGAAGGTTCAAGGTCA
1 AAAATG-GGA-TTTTAGAAGGTTCGGGGTCA
*
3524 AAAA-GAGATTTTTAGAA-GTTCAGGGGT--
1 AAAATGGGA-TTTTAGAAGGTTC-GGGGTCA
* *
3551 AAGATGGTAATTTTAGAAGGTTCGGGGTCA
1 AAAATGG-GATTTTAGAAGGTTCGGGGTCA
3581 AAAATGGGATTTT
1 AAAATGGGATTTT
3594 TGGACATTCA
Statistics
Matches: 158, Mismatches: 39, Indels: 39
0.67 0.17 0.17
Matches are distributed among these distances:
27 3 0.02
28 33 0.21
29 82 0.52
30 34 0.22
31 4 0.03
32 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGGATTTTAGAAGGTTCGGGGTCA
Found at i:3534 original size:58 final size:57
Alignment explanation
Indices: 3472--3604 Score: 160
Period size: 58 Copynumber: 2.3 Consensus size: 57
3462 TTAAAATTGG
* *
3472 GATTTTTGGGAATTCAGGGGTAAAATGATTATTTTTAGAAGGTTCAAGGTCAAAAA-GA
1 GATTTTT-GGAATTCAGGGGTAAAATG-GTAATTTTAGAAGGTTCAAGGTCAAAAATGA
* * ** *
3530 GATTTTTAGAAGTTCAGGGGTAAGATGGTAATTTTAGAAGGTTCGGGGTCAAAAATGG
1 GATTTTTGGAA-TTCAGGGGTAAAATGGTAATTTTAGAAGGTTCAAGGTCAAAAATGA
3588 GATTTTTGGACATTCAG
1 GATTTTTGGA-ATTCAG
3605 ATTTAAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 27 0.42
58 36 0.56
59 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (57 bp):
GATTTTTGGAATTCAGGGGTAAAATGGTAATTTTAGAAGGTTCAAGGTCAAAAATGA
Found at i:3642 original size:29 final size:28
Alignment explanation
Indices: 3610--3899 Score: 140
Period size: 30 Copynumber: 9.8 Consensus size: 28
3600 TTCAGATTTA
3610 AAAATTGGGATTTTTGGGAA-TTTGAGGGT
1 AAAA-TGGGATTTTT-GGAAGTTTGAGGGT
* * * * *
3639 AAAATGGTAATTTTTAGAAGGTTCAAGGT
1 AAAATGG-GATTTTTGGAAGTTTGAGGGT
* *
3668 AAAAAATGGGATTTTTGGGAA-TTTGGGGGC
1 --AAAATGGGATTTTT-GGAAGTTTGAGGGT
* * * *
3698 AAAATGGTAATTTTTAGAAGGTTTAAGGTT
1 AAAATGG-GATTTTTGGAA-GTTTGAGGGT
*
3728 AAAAATGGGATTTTTGGAAGTTTTAGGGTT
1 -AAAATGGGATTTTTGGAAGTTTGAGGG-T
* *
3758 AAAATTGGGATTTTTAGAGGGTTTG-GGGTT
1 AAAA-TGGGATTTTTGGA-AGTTTGAGGG-T
*
3788 AAAAT-GGAGTTGTTGGAAGTTTCG-GGGTT
1 AAAATGGGA-TTTTTGGAAGTTT-GAGGG-T
* * *
3817 AAAATGGTGATTTTCGAAAGTTTTGAGGTT
1 AAAATGG-GATTTTTGGAAG-TTTGAGGGT
* * *
3847 AAAAATGTGATTTTTTGAAAGTTTGGGGGT
1 -AAAATGGGA-TTTTTGGAAGTTTGAGGGT
** *
3877 AAAATAGTAATTTTTAGAAGTTT
1 AAAAT-GGGATTTTTGGAAGTTT
3900 CGGGGTTAAA
Statistics
Matches: 201, Mismatches: 39, Indels: 42
0.71 0.14 0.15
Matches are distributed among these distances:
28 23 0.11
29 67 0.33
30 68 0.34
31 43 0.21
ACGTcount: A:0.31, C:0.01, G:0.30, T:0.38
Consensus pattern (28 bp):
AAAATGGGATTTTTGGAAGTTTGAGGGT
Found at i:3642 original size:30 final size:29
Alignment explanation
Indices: 3608--3924 Score: 157
Period size: 29 Copynumber: 10.7 Consensus size: 29
3598 CATTCAGATT
3608 TAAAAATTGGGATTTTTGGGAA-TTTGAGGG
1 TAAAAA-TGGGATTTTT-GGAAGTTTGAGGG
* * * * *
3638 T-AAAATGGTAATTTTTAGAAGGTTCAAGG
1 TAAAAATGG-GATTTTTGGAAGTTTGAGGG
3667 TAAAAAATGGGATTTTTGGGAA-TTTG-GGG
1 T-AAAAATGGGATTTTT-GGAAGTTTGAGGG
** * * * *
3696 GCAAAATGGTAATTTTTAGAAGGTTTAAGGT
1 TAAAAATGG-GATTTTTGGAA-GTTTGAGGG
*
3727 TAAAAATGGGATTTTTGGAAGTTTTAGGG
1 TAAAAATGGGATTTTTGGAAGTTTGAGGG
* * *
3756 TTAAAATTGGGATTTTTAGAGGGTTTG-GGG
1 -TAAAAATGGGATTTTTGGA-AGTTTGAGGG
* *
3786 TTAAAAT-GGAGTTGTTGGAAGTTTCG-GGG
1 TAAAAATGGGA-TTTTTGGAAGTTT-GAGGG
* * * *
3815 TTAAAATGGTGATTTTCGAAAGTTTTGAGGT
1 TAAAAATGG-GATTTTTGGAAG-TTTGAGGG
* * *
3846 TAAAAATGTGATTTTTTGAAAGTTTGGGGG
1 TAAAAATGGGA-TTTTTGGAAGTTTGAGGG
** *
3876 T-AAAATAGTAATTTTTAGAAGTTTCG-GGG
1 TAAAAAT-GGGATTTTTGGAAGTTT-GAGGG
**
3905 TTAAAAACAGGATTTTTGGA
1 -TAAAAATGGGATTTTTGGA
3925 CAATCTAAGG
Statistics
Matches: 217, Mismatches: 48, Indels: 44
0.70 0.16 0.14
Matches are distributed among these distances:
28 23 0.11
29 72 0.33
30 72 0.33
31 50 0.23
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTGAGGG
Found at i:3671 original size:59 final size:59
Alignment explanation
Indices: 3607--3923 Score: 261
Period size: 59 Copynumber: 5.3 Consensus size: 59
3597 ACATTCAGAT
3607 TTAAAAATTGGGATTTTTGGGAATTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCAAGG
1 TTAAAAA-TGGGATTTTTGGGAATTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCAAGG
* * * *
3667 TAAAAAATGGGATTTTTGGGAATTTGGGGGCAAAATGGTAATTTTTAGAAGGTTTAAGG
1 TTAAAAATGGGATTTTTGGGAATTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCAAGG
* * * ***
3726 TTAAAAATGGGATTTTT-GGAAGTTTTAGGGTTAAAATTGG-GATTTTTAGAGGGTTTGGGG
1 TTAAAAATGGGATTTTTGGGAA-TTTGAGGG-TAAAA-TGGTAATTTTTAGAAGGTTCAAGG
* * * * **
3786 TT-AAAAT-GGAGTTGTT-GGAAGTTTCG-GGGTTAAAATGGTGA-TTTTCGAAAGTTTTGAGG
1 TTAAAAATGGGA-TTTTTGGGAA-TTT-GAGGG-TAAAATGGTAATTTTTAG-AAGGTTCAAGG
* * * * * * **
3845 TTAAAAATGTGATTTTTTGAAAGTTTGGGGGTAAAATAGTAATTTTTAGAAGTTTCGGGG
1 TTAAAAATGGGATTTTTGGGAA-TTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCAAGG
**
3905 TTAAAAACAGGATTTTTGG
1 TTAAAAATGGGATTTTTGG
3924 ACAATCTAAG
Statistics
Matches: 215, Mismatches: 30, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
58 15 0.07
59 109 0.51
60 71 0.33
61 20 0.09
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.38
Consensus pattern (59 bp):
TTAAAAATGGGATTTTTGGGAATTTGAGGGTAAAATGGTAATTTTTAGAAGGTTCAAGG
Found at i:3731 original size:89 final size:90
Alignment explanation
Indices: 3638--3910 Score: 245
Period size: 89 Copynumber: 3.1 Consensus size: 90
3628 AATTTGAGGG
* * * * *
3638 TAAAATGGTAATTTTTAGAAGGTTCAAGGTAAAAAATGGGATTTTTGGGAATTTGGGGGCAAAAT
1 TAAAATGGTGATTTTTAGAAGTTTTAAGGTTAAAAATGGGATTTTTGGGAATTTGGGGGTAAAAT
3703 GGTAATTTTTAGAAGGTTT-AAGGT
66 GGTAATTTTTAGAAGGTTTCAAGGT
* * * * *
3727 TAAAAATGG-GATTTTTGGAAGTTTTAGGGTTAAAATTGGGATTTTTAGAGG-GTTTGGGGTTAA
1 T-AAAATGGTGATTTTTAGAAGTTTTAAGGTTAAAAATGGGATTTTT-G-GGAATTTGGGGGTAA
* * * **
3790 AATGG-AGTTGTTGGAA-GTTTCGGGGT
63 AATGGTAATTTTTAGAAGGTTTCAAGGT
* * * * *
3816 TAAAATGGTGA-TTTTCGAAAGTTTTGAGGTTAAAAATGTGATTTTTTGAAAGTTTGGGGGTAAA
1 TAAAATGGTGATTTTTAG-AAGTTTTAAGGTTAAAAATGGGATTTTTGGGAA-TTTGGGGGTAAA
* **
3880 ATAGTAATTTTTAGAA-GTTTCGGGGT
64 ATGGTAATTTTTAGAAGGTTTCAAGGT
3906 TAAAA
1 TAAAA
3911 ACAGGATTTT
Statistics
Matches: 147, Mismatches: 28, Indels: 17
0.77 0.15 0.09
Matches are distributed among these distances:
87 1 0.01
88 16 0.11
89 83 0.56
90 45 0.31
91 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (90 bp):
TAAAATGGTGATTTTTAGAAGTTTTAAGGTTAAAAATGGGATTTTTGGGAATTTGGGGGTAAAAT
GGTAATTTTTAGAAGGTTTCAAGGT
Found at i:5893 original size:17 final size:18
Alignment explanation
Indices: 5857--5949 Score: 111
Period size: 17 Copynumber: 5.3 Consensus size: 18
5847 TTATAGTAAT
*
5857 TTTAAATTTGAAAATAAA
1 TTTAAATTTCAAAATAAA
* *
5875 TTTAAACTT-AAATTAAA
1 TTTAAATTTCAAAATAAA
5892 TTTAAA-TTCAAAATAAA
1 TTTAAATTTCAAAATAAA
5909 TTTAAATTT-AAAATAAA
1 TTTAAATTTCAAAATAAA
** *
5926 TTTAAATTTTTAAACAAA
1 TTTAAATTTCAAAATAAA
5944 TTTAAA
1 TTTAAA
5950 GGGAGTTTGG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
16 2 0.03
17 43 0.64
18 22 0.33
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (18 bp):
TTTAAATTTCAAAATAAA
Found at i:5922 original size:7 final size:6
Alignment explanation
Indices: 5857--5934 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
5847 TTATAGTAAT
* * *
5857 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
5904 -ATAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
5935 TTAAACAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 15 0.26
6 40 0.69
7 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:5932 original size:23 final size:23
Alignment explanation
Indices: 5871--5920 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5861 AATTTGAAAA
* *
5871 TAAATTTAAACTTAAATTAAATT
1 TAAATTCAAACATAAATTAAATT
5894 TAAATTCAAA-ATAAATTTAAATT
1 TAAATTCAAACATAAA-TTAAATT
5917 TAAA
1 TAAA
5921 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTCAAACATAAATTAAATT
Found at i:8539 original size:24 final size:24
Alignment explanation
Indices: 8511--8561 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
8501 GTGATAATGC
8511 TTAAATATAACATACTTTTAGA-TA
1 TTAAATAT-ACATACTTTTAGAGTA
* *
8535 TTAAATATATATATTTTTAGAGTA
1 TTAAATATACATACTTTTAGAGTA
8559 TTA
1 TTA
8562 TCATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
TTAAATATACATACTTTTAGAGTA
Found at i:9533 original size:15 final size:16
Alignment explanation
Indices: 9513--9542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9503 CTTCCCTATT
9513 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
9528 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
9543 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:9535 original size:22 final size:22
Alignment explanation
Indices: 9508--9568 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
9498 TTCGACTTCC
9508 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
9530 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
9552 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
9569 CTTTAGTTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:9558 original size:21 final size:22
Alignment explanation
Indices: 9522--9568 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
9512 TTTCTATTTC
*
9522 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
9544 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
9565 TTTT
1 TTTT
9569 CTTTAGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:21766 original size:29 final size:28
Alignment explanation
Indices: 21708--21774 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
21698 ATTAGAATCA
21708 AATAACAATAAAACTATCAAATATCAAAT
1 AATAACAATAAAACTATCAAATAT-AAAT
* *
21737 AATAATAATTAAACTTATCAAATA-ATAAT
1 AATAACAATAAAAC-TATCAAATATA-AAT
*
21766 AAAAACAAT
1 AATAACAAT
21775 GTTGGACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.03
29 22 0.69
30 9 0.28
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (28 bp):
AATAACAATAAAACTATCAAATATAAAT
Found at i:21861 original size:44 final size:43
Alignment explanation
Indices: 21804--21912 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 43
21794 CGAACAATAT
* * *
21804 AAATA-AAAAAAATATTTATATAAAATA-CAATATTTGA-ACAAA
1 AAATATAAATAAATATTTATATAAAACATC-ATATCT-ATACAAA
*
21846 ACAATATAAATAAATATTTATGTAAAACATCATATCTATACAAA
1 A-AATATAAATAAATATTTATATAAAACATCATATCTATACAAA
*
21890 AAAAATTAAATAAATATTTATAT
1 AAATA-TAAATAAATATTTATAT
21913 TTATCTAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
42 1 0.02
43 8 0.14
44 46 0.82
45 1 0.02
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (43 bp):
AAATATAAATAAATATTTATATAAAACATCATATCTATACAAA
Found at i:23962 original size:82 final size:80
Alignment explanation
Indices: 23888--24129 Score: 340
Period size: 81 Copynumber: 3.0 Consensus size: 80
23878 ATTTAATCAT
* * * *
23888 TTCTTGTTTGGAAACAAAATCAAAATGGAATAAAATCTGTTGAACGATAAGAATAAATTCCAAAA
1 TTCTTGTTTGAAAAC-AAATCAAAATAGAATAAAATCTGTTGAA-GATAAGAATAAATCCCGAAA
*
23953 CAAATTTATTCAGTTAA
64 CAAATTTATTCAATTAA
* *
23970 TTCTTGTTTGAAAACAAATCAAAATAGAATAAAATCAGTTGAAGGACAAGAATAAATCCCGAAAC
1 TTCTTGTTTGAAAACAAATCAAAATAGAATAAAATCTGTTGAA-GATAAGAATAAATCCCGAAAC
*
24035 AGATTTATTCAATTAA
65 AAATTTATTCAATTAA
* * *
24051 TTCTTGTTTGAAAACAAATCAAAATAGAATAAAATTTGTTGAATAGTAGGAATAAATCCCGAAAC
1 TTCTTGTTTGAAAACAAATCAAAATAGAATAAAATCTGTTGAAGA-TAAGAATAAATCCCGAAAC
*
24116 ATATTTATTCAATT
65 AAATTTATTCAATT
24130 TTATTTTTTA
Statistics
Matches: 144, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 1 0.01
81 129 0.90
82 14 0.10
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (80 bp):
TTCTTGTTTGAAAACAAATCAAAATAGAATAAAATCTGTTGAAGATAAGAATAAATCCCGAAACA
AATTTATTCAATTAA
Found at i:24324 original size:50 final size:50
Alignment explanation
Indices: 24264--24373 Score: 168
Period size: 50 Copynumber: 2.2 Consensus size: 50
24254 TAAATATAAA
* *
24264 ATATTTATATAAAATATAATATCTGAACAAAAC-AATATAAATAAATATTT
1 ATATTTATATAAAACATAATATCTAAACAAAACAAAT-TAAATAAATATTT
* *
24314 ATGTTTATATAAAACATCATATCTAAACAAAACAAATTAAATAAATATTT
1 ATATTTATATAAAACATAATATCTAAACAAAACAAATTAAATAAATATTT
24364 ATATTTATAT
1 ATATTTATAT
24374 TTATTTAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 51 0.94
51 3 0.06
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (50 bp):
ATATTTATATAAAACATAATATCTAAACAAAACAAATTAAATAAATATTT
Found at i:24383 original size:56 final size:54
Alignment explanation
Indices: 24264--24393 Score: 144
Period size: 50 Copynumber: 2.4 Consensus size: 54
24254 TAAATATAAA
* * *
24264 ATATTTATATAAAATATAATATCTGAACAAAACAATATAAATAAATATTTATGTT
1 ATATTTAT-TAAAAAATCATATCTAAACAAAACAATATAAATAAATATTTATGTT
* *
24319 -TA--TA-TAAAACATCATATCTAAACAAAACAA-ATTAAATAAATATTTATATTT
1 ATATTTATTAAAAAATCATATCTAAACAAAACAATA-TAAATAAATATTTAT-GTT
24370 ATATTTATTTAAAAAATCATATCT
1 ATATTTA-TTAAAAAATCATATCT
24394 TAAAACAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
49 1 0.02
50 38 0.60
51 2 0.03
52 4 0.06
54 4 0.06
56 14 0.22
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (54 bp):
ATATTTATTAAAAAATCATATCTAAACAAAACAATATAAATAAATATTTATGTT
Found at i:26018 original size:47 final size:47
Alignment explanation
Indices: 25958--26054 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 47
25948 ATAAAACACG
* * *
25958 ATTTGAAAGTAAAAATAAAAATAAAAGATGATTAAATTTTTAAAAAA
1 ATTTAAAAATAAAAATAAAAATAAAAGATGATTAAATTTTAAAAAAA
26005 ATTTAAAAATAAAAATAAAAATAAAAGATGATTAAATTTTAAAAAAA
1 ATTTAAAAATAAAAATAAAAATAAAAGATGATTAAATTTTAAAAAAA
26052 ATT
1 ATT
26055 AATTAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (47 bp):
ATTTAAAAATAAAAATAAAAATAAAAGATGATTAAATTTTAAAAAAA
Found at i:26069 original size:46 final size:45
Alignment explanation
Indices: 25968--26070 Score: 145
Period size: 47 Copynumber: 2.2 Consensus size: 45
25958 ATTTGAAAGT
*
25968 AAAAATAAAAATAAAAGATGATTAAATTTTTAAAAAAATTTAAAAA
1 AAAAATAAAAATAAAAGATGATTAAATTTTTAAAAAAAATT-AAAA
**
26014 TAAAAATAAAAATAAAAGATGATTAAA-TTTTAAAAAAAATTAATT
1 -AAAAATAAAAATAAAAGATGATTAAATTTTTAAAAAAAATTAAAA
26059 AAAAATATAAAA
1 AAAAATA-AAAA
26071 GGAGAAAACA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 7 0.13
45 6 0.12
46 13 0.25
47 26 0.50
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (45 bp):
AAAAATAAAAATAAAAGATGATTAAATTTTTAAAAAAAATTAAAA
Found at i:27218 original size:21 final size:21
Alignment explanation
Indices: 27167--27211 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27157 GATGTAAATT
* *
27167 TCATTATTATAATATCTAATC
1 TCATTGTTATAATATCTAATA
27188 TCATTGTTATAATAAT-TAATA
1 TCATTGTTATAAT-ATCTAATA
27209 TCA
1 TCA
27212 CTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (21 bp):
TCATTGTTATAATATCTAATA
Found at i:32982 original size:6 final size:6
Alignment explanation
Indices: 32957--32995 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
32947 TCAATTCATA
* * *
32957 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
32996 GTTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:32995 original size:18 final size:18
Alignment explanation
Indices: 32945--32983 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
32935 GATTTTCAAT
*
32945 TTTCAATT-C-ATATCAC
1 TTTCAATTCCAATTTCAC
32961 TTTCAATTCCAATTTCAC
1 TTTCAATTCCAATTTCAC
32979 TTTCA
1 TTTCA
32984 CTTTCACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTCAATTCCAATTTCAC
Done.