Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009562.1 Kokia drynarioides strain JFW-HI SEQ_124274, 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: 109450
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 327 characters in sequence are not A, C, G, or T
Found at i:150 original size:13 final size:12
Alignment explanation
Indices: 132--169 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
122 CTCACCAACT
132 ATAACAACATTAA
1 ATAACAA-ATTAA
*
145 ATAACAAATCAA
1 ATAACAAATTAA
157 ATAA-AAATTAA
1 ATAACAAATTAA
168 AT
1 AT
170 TAAAGAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 8 0.35
12 8 0.35
13 7 0.30
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACAAATTAA
Found at i:433 original size:18 final size:16
Alignment explanation
Indices: 410--448 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 16
400 ATTTTTTTTC
410 CTTCTCCTTCTTTCCCTT
1 CTTCTCCTTC-TT-CCTT
428 CTTCTCCTTCTTCCTT
1 CTTCTCCTTCTTCCTT
444 CTTCT
1 CTTCT
449 TTTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 10 0.48
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (16 bp):
CTTCTCCTTCTTCCTT
Found at i:456 original size:24 final size:24
Alignment explanation
Indices: 401--477 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
391 ACACATAACA
401 TTTTTTT-TCCTTCTCCTTCTTTC
1 TTTTTTTCTCCTTCTCCTTCTTTC
** *
424 CCTTCTTCTCCTTCTTCCTTC-TTC
1 TTTTTTTCTCCTTC-TCCTTCTTTC
448 TTTTTTTCT--TTCT--TTCTTTC
1 TTTTTTTCTCCTTCTCCTTCTTTC
468 TCTTTTTTCT
1 T-TTTTTTCT
478 TTCTTTTTTC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 3 0.07
20 4 0.09
21 9 0.20
22 3 0.07
23 4 0.09
24 15 0.34
25 6 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTTTTCTCCTTCTCCTTCTTTC
Found at i:459 original size:4 final size:4
Alignment explanation
Indices: 445--487 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
435 TTCTTCCTTC
* *
445 TTCT TTTT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
488 CTTCAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:475 original size:21 final size:19
Alignment explanation
Indices: 445--487 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 19
435 TTCTTCCTTC
445 TTCTTTTTTTCTTTCTTTCT
1 TTCTTTTTTTCTTTCTTT-T
465 TTCTCTTTTTTCTTTCTTTT
1 TTCT-TTTTTTCTTTCTTTT
485 TTC
1 TTC
488 CTTCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTTTTTCTTTCTTTT
Found at i:478 original size:13 final size:13
Alignment explanation
Indices: 454--486 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
444 CTTCTTTTTT
454 TCTTTCTTTCTTTC
1 TCTTT-TTTCTTTC
468 TCTTTTTTCTTTC
1 TCTTTTTTCTTTC
481 T-TTTTT
1 TCTTTTT
487 CCTTCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 9 0.47
14 5 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:832 original size:5 final size:6
Alignment explanation
Indices: 821--845 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
811 TTTTAAATAT
821 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
846 CAAGTGTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:8593 original size:82 final size:80
Alignment explanation
Indices: 8447--8602 Score: 249
Period size: 82 Copynumber: 1.9 Consensus size: 80
8437 CCTCAAGAAT
* * *
8447 AAAGACATGTGGCAGGTCGAAAGGCCACCCGAGAGTTAAACTCCACCGGAAGGACACCATAAGTT
1 AAAGACATGTGGCAGGTCGAAAGGCCACCCGAAAGATAAACTCCACCGGAAGGACACCAAAAGTT
8512 TCACCTCCCCATGAAC
66 TCACC-CCCCATGAAC
* *
8528 AAAGACATGTGGCAGGTCGGAAGGCCACCCCGAAAGATAAACTCCATCGGAAGGACACCAAAAGT
1 AAAGACATGTGGCAGGTCGAAAGGCCA-CCCGAAAGATAAACTCCACCGGAAGGACACCAAAAGT
8593 TTCACCCCCC
65 TTCACCCCCC
8603 GTCTTTGACA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
81 30 0.43
82 39 0.57
ACGTcount: A:0.34, C:0.30, G:0.22, T:0.13
Consensus pattern (80 bp):
AAAGACATGTGGCAGGTCGAAAGGCCACCCGAAAGATAAACTCCACCGGAAGGACACCAAAAGTT
TCACCCCCCATGAAC
Found at i:9046 original size:22 final size:22
Alignment explanation
Indices: 9021--9066 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
9011 GTGTTTTTAG
9021 TAAAAATAGAA-AAATCAAATTA
1 TAAAAATA-AAGAAATCAAATTA
*
9043 TAAAATTAAAGAAATCAAATTA
1 TAAAAATAAAGAAATCAAATTA
9065 TA
1 TA
9067 TCATGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (22 bp):
TAAAAATAAAGAAATCAAATTA
Found at i:9850 original size:82 final size:83
Alignment explanation
Indices: 9639--9855 Score: 318
Period size: 81 Copynumber: 2.7 Consensus size: 83
9629 GATTTGGGGC
* * *
9639 AGAAGTTGAGATTTCTTTG-TTTCATTGGTTTTCTATGCTTTCTTGCATTTG-TTCTGAAATGAG
1 AGAAGTTGAAATTTTTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTGTTTCTAAAATGAG
*
9702 TTTTTTGGTTCATCGAGT
66 TTTTTTAGTTCATCGAGT
*
9720 AGAAGTTGAAATTTTTTTGTTTTCATTGG-TTTCTATGCTTTTTTGCATTTGTTTC-AAAATG-G
1 AGAAGTTGAAATTTTTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTGTTTCTAAAATGAG
** *
9782 ATTTTTTAGTTTTTGGAGT
66 -TTTTTTAGTTCATCGAGT
9801 AGAAGTTGAAATTTTTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTGTTT
1 AGAAGTTGAAATTTTTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTGTTT
9856 TGAAACTAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
80 1 0.01
81 86 0.70
82 36 0.29
ACGTcount: A:0.18, C:0.09, G:0.19, T:0.54
Consensus pattern (83 bp):
AGAAGTTGAAATTTTTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTGTTTCTAAAATGAG
TTTTTTAGTTCATCGAGT
Found at i:12135 original size:29 final size:29
Alignment explanation
Indices: 12100--12184 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 29
12090 AATTAGTAAA
12100 GATAAAATTATATTTTAATCCCTAAAAAT
1 GATAAAATTATATTTTAATCCCTAAAAAT
* *
12129 GATAAAAATT-TAATTTAATCCTTTAAAAAT
1 GAT-AAAATTATATTTTAATCC-CTAAAAAT
* * *
12159 TAT-AATTTA-ATTTCAATCCCCTAAAA
1 GATAAAATTATATTTTAAT-CCCTAAAA
12185 TAATTTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 15 0.33
29 15 0.33
30 15 0.33
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (29 bp):
GATAAAATTATATTTTAATCCCTAAAAAT
Found at i:12156 original size:30 final size:30
Alignment explanation
Indices: 12103--12163 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
12093 TAGTAAAGAT
*
12103 AAAATTATATTTTAATCCCTAAAAATGATA
1 AAAATTATAATTTAATCCCTAAAAATGATA
* *
12133 AAAATT-TAATTTAATCCTTTAAAAATTATA
1 AAAATTATAATTTAATCC-CTAAAAATGATA
12163 A
1 A
12164 TTTAATTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTATAATTTAATCCCTAAAAATGATA
Found at i:12184 original size:27 final size:28
Alignment explanation
Indices: 12130--12204 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 28
12120 CCTAAAAATG
* **
12130 ATAAAAATTTAATTT-AATCCTTTAAAA
1 ATAATAATTTAATTTCAATCCCCTAAAA
*
12157 ATTATAATTTAATTTCAATCCCCT-AAA
1 ATAATAATTTAATTTCAATCCCCTAAAA
** *
12184 ATAATTTTTTAACTTCAATCC
1 ATAATAATTTAATTTCAATCC
12205 TGACAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 33 0.85
28 6 0.15
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAATAATTTAATTTCAATCCCCTAAAA
Found at i:13450 original size:30 final size:30
Alignment explanation
Indices: 13388--13451 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
13378 ATGTTGCATT
* * * *
13388 AAAATTTTGGGGTTTAATTAAAATTTTTAA
1 AAAAATTTGGAGTTTAATGAAAATTTTCAA
13418 AAAAATTTGGAGTTTAATGACAAA-TTTCAA
1 AAAAATTTGGAGTTTAATGA-AAATTTTCAA
13448 AAAA
1 AAAA
13452 GGGGTCTAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (30 bp):
AAAAATTTGGAGTTTAATGAAAATTTTCAA
Found at i:18174 original size:10 final size:9
Alignment explanation
Indices: 18149--18176 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
18139 TATATATTTA
18149 TTTAAAAAT
1 TTTAAAAAT
18158 TTTAAAAAT
1 TTTAAAAAT
18167 TTTAAAAAT
1 TTTAAAAAT
18176 T
1 T
18177 AAAACCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:20122 original size:30 final size:32
Alignment explanation
Indices: 20081--20139 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
20071 GAATTATAAT
*
20081 TTTTTTGAA-GGGTTAAAATATAATTTTATCA
1 TTTTTTGAAGGGGTCAAAATATAATTTTATCA
*
20112 TTTTTT-AAGGGGTCAAAGTATAATTTTA
1 TTTTTTGAAGGGGTCAAAATATAATTTTA
20140 CTATATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.47
Consensus pattern (32 bp):
TTTTTTGAAGGGGTCAAAATATAATTTTATCA
Found at i:25334 original size:24 final size:24
Alignment explanation
Indices: 25288--25334 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
25278 TTATAATAAA
*
25288 AAAATCGAATAAATTAATCAAATC
1 AAAATCGAATAAATCAATCAAATC
* * *
25312 AAAATCGATTCAATCAATTAAAT
1 AAAATCGAATAAATCAATCAAAT
25335 TGATTTAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAATCGAATAAATCAATCAAATC
Found at i:32461 original size:2 final size:2
Alignment explanation
Indices: 32417--32441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32407 CTGATGTCTT
32417 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 T
32442 TCTGATGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33722 original size:23 final size:22
Alignment explanation
Indices: 33685--33727 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
33675 TTAAATAATT
**
33685 TATATGATACTTTTTATACAAAA
1 TATATGATAAATTTTA-ACAAAA
33708 TATATGATAAATTTTAACAA
1 TATATGATAAATTTTAACAA
33728 TCCTTGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (22 bp):
TATATGATAAATTTTAACAAAA
Found at i:35087 original size:5 final size:5
Alignment explanation
Indices: 35079--35109 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
35069 ATATAATCTT
*
35079 AAATA AAATG AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
35110 CAATTGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:35354 original size:3 final size:3
Alignment explanation
Indices: 35346--35389 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
35336 ACATACATAA
35346 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
35390 CAAACTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:35440 original size:18 final size:19
Alignment explanation
Indices: 35393--35446 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
35383 TTATTATCAA
*
35393 ACTTAATATAATATTTGAT
1 ACTTAATTTAATATTTGAT
*
35412 ACTTAAATTTAATATTT-TT
1 ACTT-AATTTAATATTTGAT
*
35431 TCTTAATTTAATATTT
1 ACTTAATTTAATATTT
35447 AAATATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.39
19 8 0.26
20 11 0.35
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (19 bp):
ACTTAATTTAATATTTGAT
Found at i:35829 original size:26 final size:24
Alignment explanation
Indices: 35793--35844 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
35783 AAAAAATATT
* *
35793 AAATTTGAATATCAAATTGAACAAAA
1 AAATTTAAATACCAAATT-AA-AAAA
35819 AAATTTAAATACCAAATTAAAAAA
1 AAATTTAAATACCAAATTAAAAAA
35843 AA
1 AA
35845 TGTCAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 2 0.08
26 16 0.67
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.25
Consensus pattern (24 bp):
AAATTTAAATACCAAATTAAAAAA
Found at i:40371 original size:9 final size:9
Alignment explanation
Indices: 40359--40394 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
40349 GGATGATGGG
*
40359 TTAACCGGC
1 TTAACCGGT
40368 TTAACCGGT
1 TTAACCGGT
40377 TTAACCGGT
1 TTAACCGGT
40386 TTAACCGGT
1 TTAACCGGT
40395 AAACCTCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (9 bp):
TTAACCGGT
Found at i:42287 original size:60 final size:60
Alignment explanation
Indices: 42211--42407 Score: 208
Period size: 57 Copynumber: 3.4 Consensus size: 60
42201 GTTGACCATG
* * *
42211 CCTTTTTGGA-AAAAAAAATTCAAAAATTTTTGGTGTTTGGTCATGCAATGGTCGACGCC
1 CCTTTTTTGAGAAAAAAAATTCAAAAATTTTTGGTGTTTGGTCATGCAATGGACGACACC
* * **
42270 CTTTTTTTGAGAAAAAAAATT---ACATTTTTGG-GTGTTGACCATGCAATGGACGACACC
1 CCTTTTTTGAGAAAAAAAATTCAAAAATTTTTGGTGT-TTGGTCATGCAATGGACGACACC
* * * * *
42327 CCTGTTTTGAGAAAAAAAATTTCAAAATTTTTTGGT-ATTAGTCATGCAATGGCCGACACC
1 CCTTTTTTGAGAAAAAAAA-TTCAAAAATTTTTGGTGTTTGGTCATGCAATGGACGACACC
* *
42387 CCCTTTTTGATAAAAAAAATT
1 CCTTTTTTGAGAAAAAAAATT
42408 GTATTTTTGA
Statistics
Matches: 112, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
56 2 0.02
57 45 0.40
58 2 0.02
59 10 0.09
60 45 0.40
61 8 0.07
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (60 bp):
CCTTTTTTGAGAAAAAAAATTCAAAAATTTTTGGTGTTTGGTCATGCAATGGACGACACC
Found at i:42308 original size:102 final size:100
Alignment explanation
Indices: 42120--42313 Score: 293
Period size: 102 Copynumber: 1.9 Consensus size: 100
42110 TTTTGTCAAA
42120 AAAAAAAAATTCAAAAATTTTTGGTGTCGGCTATGCAATGGCCGAAACTCCTTTTTTGAGAAAAA
1 AAAAAAAAATTCAAAAATTTTTGGTGTCGGCTATGCAATGGCCGAAACTCCTTTTTTGAGAAAAA
*
42185 AATTGCATTTTTGGGTGTTGACCATGCCTTTTTGG
66 AATTACATTTTTGGGTGTTGACCATGCCTTTTTGG
* * **
42220 AAAAAAAAATTCAAAAATTTTTGGTGTTTGG-TCATGCAATGGTCGACGC-CCTTTTTTTGAGAA
1 AAAAAAAAATTCAAAAATTTTTGGTG-TCGGCT-ATGCAATGGCCGAAACTCC-TTTTTTGAG-A
42283 AAAAAATTACATTTTTGGGTGTTGACCATGC
62 AAAAAATTACATTTTTGGGTGTTGACCATGC
42314 AATGGACGAC
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
100 29 0.34
101 25 0.29
102 31 0.36
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (100 bp):
AAAAAAAAATTCAAAAATTTTTGGTGTCGGCTATGCAATGGCCGAAACTCCTTTTTTGAGAAAAA
AATTACATTTTTGGGTGTTGACCATGCCTTTTTGG
Found at i:42874 original size:60 final size:58
Alignment explanation
Indices: 42770--42884 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 58
42760 AAAATGTAAT
** *
42770 TTTTTTTTCTCAAAAAGGGGTGTCGACCATTGCATGACCTACACCAAAAAATTTTGAA
1 TTTTTTTTCTCAAAAAACGGTGTCGACCATTGCATGACCAACACCAAAAAATTTTGAA
* * * *
42828 TTTTTTTTCTGACAAAAAACGGTGTCGACTA-TGCAATGATCAACACCCAAAATTTTT
1 TTTTTTTTCT--CAAAAAACGGTGTCGACCATTGC-ATGACCAACACCAAAAAATTTT
42885 TTTAAAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 10 0.21
59 3 0.06
60 34 0.72
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (58 bp):
TTTTTTTTCTCAAAAAACGGTGTCGACCATTGCATGACCAACACCAAAAAATTTTGAA
Found at i:45905 original size:19 final size:19
Alignment explanation
Indices: 45881--45919 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
45871 TATGTCAGAA
45881 TGAGGTACTGTCTAGTTAT
1 TGAGGTACTGTCTAGTTAT
45900 TGAGGTACTGTCTAGTTAT
1 TGAGGTACTGTCTAGTTAT
45919 T
1 T
45920 CTTTCAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.44
Consensus pattern (19 bp):
TGAGGTACTGTCTAGTTAT
Found at i:59526 original size:17 final size:16
Alignment explanation
Indices: 59502--59543 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
59492 TTAAAATTAA
59502 TTATAATTTTAT-TAT
1 TTATAATTTTATATAT
59517 TT-TAATAATTTATATAT
1 TTATAAT--TTTATATAT
59534 TTATAATTTT
1 TTATAATTTT
59544 TAAAAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.17
15 2 0.09
16 8 0.35
17 5 0.22
18 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATAATTTTATATAT
Found at i:59566 original size:30 final size:31
Alignment explanation
Indices: 59530--59595 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
59520 AATAATTTAT
*
59530 ATATTTATAATTTTTAAAA-AGT-AAAATAAA
1 ATATTTAT-ATTTTAAAAAGAGTCAAAATAAA
*
59560 ATATTTATATTTTAAAAAGAGTCAAAATATA
1 ATATTTATATTTTAAAAAGAGTCAAAATAAA
59591 ATATT
1 ATATT
59596 ACGGTTACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 9 0.28
30 11 0.34
31 12 0.38
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (31 bp):
ATATTTATATTTTAAAAAGAGTCAAAATAAA
Found at i:68696 original size:17 final size:17
Alignment explanation
Indices: 68644--68699 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
68634 ACAGGCTTAA
68644 TTTTTTTTGTCCAAATT
1 TTTTTTTTGTCCAAATT
* * *
68661 TACTTTTTAGTCC-TATT
1 T-TTTTTTTGTCCAAATT
68678 TTTTTTTTGTCCAAATT
1 TTTTTTTTGTCCAAATT
68695 TTTTT
1 TTTTT
68700 ATATTTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 9 0.29
17 13 0.42
18 9 0.29
ACGTcount: A:0.16, C:0.12, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTTTTGTCCAAATT
Found at i:73731 original size:15 final size:16
Alignment explanation
Indices: 73702--73732 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
73692 AATATATTTT
73702 TTCAATTATATTAATA
1 TTCAATTATATTAATA
73718 TTCAATTA-ATTAATA
1 TTCAATTATATTAATA
73733 ACAATAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
TTCAATTATATTAATA
Found at i:74316 original size:24 final size:26
Alignment explanation
Indices: 74284--74332 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
74274 TCAAAAAAAA
74284 AAAAGGTAAAAATTAA-A-TTAAATG
1 AAAAGGTAAAAATTAAGAGTTAAATG
* *
74308 AAAATGTAAAAGTTAAGAGTTAAAT
1 AAAAGGTAAAAATTAAGAGTTAAAT
74333 TTATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 1 0.05
26 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (26 bp):
AAAAGGTAAAAATTAAGAGTTAAATG
Found at i:86461 original size:17 final size:17
Alignment explanation
Indices: 86431--86464 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
86421 ACAAATGCTT
86431 TTAAAATAATAACAAAA
1 TTAAAATAATAACAAAA
86448 TTAACAATAA-AACAAAA
1 TTAA-AATAATAACAAAA
86465 GTTGTACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
TTAAAATAATAACAAAA
Found at i:90644 original size:6 final size:6
Alignment explanation
Indices: 90633--90658 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
90623 TTGGGAAGGT
90633 GGTTGG GGTTGG GGTTGG GGTTGG GG
1 GGTTGG GGTTGG GGTTGG GGTTGG GG
90659 ATAATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (6 bp):
GGTTGG
Found at i:96731 original size:2 final size:2
Alignment explanation
Indices: 96718--96747 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
96708 ATAGAAGTGG
*
96718 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96748 CAAGACATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:101673 original size:2 final size:2
Alignment explanation
Indices: 101666--101696 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
101656 AAATATAGTG
101666 TA TA 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 TA TA T
101697 TTACAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:102401 original size:24 final size:23
Alignment explanation
Indices: 102374--102419 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
102364 TCAGCACGAC
102374 TAATTAATAGAGACTTTCAATTTA
1 TAATTAATAGA-ACTTTCAATTTA
* *
102398 TAATTCATATAACTTTCAATTT
1 TAATTAATAGAACTTTCAATTT
102420 CAATTTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (23 bp):
TAATTAATAGAACTTTCAATTTA
Found at i:103081 original size:15 final size:15
Alignment explanation
Indices: 103040--103082 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
103030 AATTCTAGTT
*
103040 TCTCCTTTTTCTTTT
1 TCTCCTTTTTCTTTC
*
103055 TCCTTCCATTTTCTTTC
1 T-C-TCCTTTTTCTTTC
103072 TCTCCTTTTTC
1 TCTCCTTTTTC
103083 GTTTGAGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 9 0.39
16 2 0.09
17 12 0.52
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTCCTTTTTCTTTC
Found at i:103122 original size:23 final size:23
Alignment explanation
Indices: 103096--103141 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
103086 TGAGCTTCTG
103096 TTCTTCCTTCTTTTGT-TTCTTTT
1 TTCTT-CTTCTTTTGTATTCTTTT
* *
103119 TTCTTTTTCTTTTTTATTCTTTT
1 TTCTTCTTCTTTTGTATTCTTTT
103142 ATATTCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (23 bp):
TTCTTCTTCTTTTGTATTCTTTT
Done.