Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015008.1 Kokia drynarioides strain JFW-HI SEQ_130052, 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: 119612
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 180 characters in sequence are not A, C, G, or T
Found at i:219 original size:20 final size:21
Alignment explanation
Indices: 194--236 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
184 TACTTACTAC
194 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
214 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
235 TA
1 TA
237 AAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:2325 original size:22 final size:24
Alignment explanation
Indices: 2282--2325 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
2272 TAGTTTTTAG
2282 TTTTTATTATTATTAACATAAATA
1 TTTTTATTATTATTAACATAAATA
*
2306 TTTTTATT-TT-TTAACGTAAA
1 TTTTTATTATTATTAACATAAA
2326 ATTATCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTTATTATTATTAACATAAATA
Found at i:2965 original size:19 final size:19
Alignment explanation
Indices: 2924--2965 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2914 TATATAAAAT
*
2924 AAAAGTTGTAACATATTTG
1 AAAAGTTGTAACATATTTA
2943 AAAAGTTAGTAA-ATATTTA
1 AAAAGTT-GTAACATATTTA
2962 AAAA
1 AAAA
2966 TTACTACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAAGTTGTAACATATTTA
Found at i:10388 original size:3 final size:3
Alignment explanation
Indices: 10382--10418 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
10372 TTTTATTTTT
*
10382 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
10419 TTGGTGGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:15789 original size:18 final size:18
Alignment explanation
Indices: 15768--15815 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
15758 ATAATTCATA
*
15768 TCACTTTTAATTCCACTT
1 TCACTTTCAATTCCACTT
* *
15786 TCACTTTCACTTTCACTT
1 TCACTTTCAATTCCACTT
15804 TCACTTTCAATT
1 TCACTTTCAATT
15816 TTGATCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (18 bp):
TCACTTTCAATTCCACTT
Found at i:15792 original size:6 final size:6
Alignment explanation
Indices: 15781--15812 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
15771 CTTTTAATTC
15781 CACTTT CACTTT CACTTT CACTTT CACTTT CA
1 CACTTT CACTTT CACTTT CACTTT CACTTT CA
15813 ATTTTGATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.34, G:0.00, T:0.47
Consensus pattern (6 bp):
CACTTT
Found at i:17071 original size:76 final size:66
Alignment explanation
Indices: 16964--17116 Score: 216
Period size: 76 Copynumber: 2.2 Consensus size: 66
16954 TATCTTAATC
16964 ACATGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGATGCATTTCTTTT
1 ACATGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGATGCATTTCTTTT
17029 A
66 A
17030 ACANNNNNNNNNNTGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGATG
1 ACA----------TGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGATG
17095 CATTTCTTTTA
56 CATTTCTTTTA
17106 ACATGTATTCA
1 ACATGTATTCA
17117 CATTAAAATC
Statistics
Matches: 77, Mismatches: 0, Indels: 20
0.79 0.00 0.21
Matches are distributed among these distances:
66 11 0.14
76 66 0.86
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.37
Consensus pattern (66 bp):
ACATGTATTCAACACTAATTCCCATTTTCTTTCTCCTCCAAGACAAGTATGGATGCATTTCTTTT
A
Found at i:19379 original size:24 final size:24
Alignment explanation
Indices: 19351--19413 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
19341 AGAAATAATC
* * *
19351 TTTCAGTTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
19375 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
* *
19399 TTTGAATCAAACTCT
1 TTTCAATTAAACTCT
19414 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:21578 original size:31 final size:32
Alignment explanation
Indices: 21511--21578 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 32
21501 TAAAAAATTC
* ***
21511 AATTTGACTCTATTTAAAAAAATTGATGGTTG
1 AATTTGACTCTATTTAAAAAAATTGAGGGCCA
**
21543 AATTTGACTCT-TTTAAAAAGTTTGAGGGCCA
1 AATTTGACTCTATTTAAAAAAATTGAGGGCCA
21574 AATTT
1 AATTT
21579 AGCTCAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (32 bp):
AATTTGACTCTATTTAAAAAAATTGAGGGCCA
Found at i:22465 original size:14 final size:13
Alignment explanation
Indices: 22440--22473 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
22430 AAATAGTTTG
22440 ATAAATTTAAAAA
1 ATAAATTTAAAAA
22453 ATAAATATTAAAAA
1 ATAAAT-TTAAAAA
*
22467 ATTAATT
1 ATAAATT
22474 ATTGAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATTTAAAAA
Found at i:22476 original size:15 final size:14
Alignment explanation
Indices: 22440--22468 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22430 AAATAGTTTG
22440 ATAAAT-TTAAAAA
1 ATAAATATTAAAAA
22453 ATAAATATTAAAAA
1 ATAAATATTAAAAA
22467 AT
1 AT
22469 TAATTATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAATATTAAAAA
Found at i:23322 original size:31 final size:31
Alignment explanation
Indices: 23297--23419 Score: 98
Period size: 31 Copynumber: 4.1 Consensus size: 31
23287 TTTGGTATTC
23297 AAACTTAACACTTTTTTCTAATTTGGTACCT
1 AAACTTAACACTTTTTTCTAATTTGGTACCT
* * * *
23328 AAACTTGACACTTTTTTTTAAGTTGGTACTT
1 AAACTTAACACTTTTTTCTAATTTGGTACCT
* *
23359 AAA-TT-----TTTTGGGGTCTAATTTGATACCT
1 AAACTTAACACTTTT---TTCTAATTTGGTACCT
*
23387 GAACTTAACTA-TTTTTTCTAATTTGGTACCT
1 AAACTTAAC-ACTTTTTTCTAATTTGGTACCT
23418 AA
1 AA
23420 TATTTTTTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
25 4 0.06
28 13 0.19
29 2 0.03
30 2 0.03
31 45 0.64
34 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (31 bp):
AAACTTAACACTTTTTTCTAATTTGGTACCT
Found at i:23331 original size:90 final size:89
Alignment explanation
Indices: 23227--23419 Score: 221
Period size: 90 Copynumber: 2.1 Consensus size: 89
23217 TTAATATTAC
* * *
23227 ATTTGGTACATAAACTTGATACTTTTTCTTAATTTAGTACCTAAACCTTTTTT-GATCAAATTTG
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTAGTACCTAAA--TTTTTTGGATCAAATTTG
* *
23291 GTA-TTCAAACTTAAC-ACTTTTTTCTA
64 ATACCT-AAACTTAACTA-TTTTTTCTA
* * * * *
23317 ATTTGGTACCTAAACTTGACACTTTTTTTTAAGTTGGTACTTAAATTTTTTGGGGTCTAATTTGA
1 ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTAGTACCTAAATTTTTT-GGATCAAATTTGA
*
23382 TACCTGAACTTAACTATTTTTTCTA
65 TACCTAAACTTAACTATTTTTTCTA
23407 ATTTGGTACCTAA
1 ATTTGGTACCTAA
23420 TATTTTTTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
88 6 0.07
90 80 0.91
91 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (89 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTAAGTTAGTACCTAAATTTTTTGGATCAAATTTGAT
ACCTAAACTTAACTATTTTTTCTA
Found at i:23376 original size:59 final size:60
Alignment explanation
Indices: 23313--23427 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 60
23303 AACACTTTTT
* *
23313 TCTAATTTGGTACCTAAACTTGACACT-TTTTTT-TAAGTTGGTACTTAA-ATTTTTTGGGG
1 TCTAATTTGATACCTAAACTT-A-ACTATTTTTTCTAAGTTGGTACCTAATATTTTTTGGGG
* *
23372 TCTAATTTGATACCTGAACTTAACTATTTTTTCTAATTTGGTACCTAATATTTTTT
1 TCTAATTTGATACCTAAACTTAACTATTTTTTCTAAGTTGGTACCTAATATTTTTT
23428 AATATTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 3 0.06
58 7 0.14
59 32 0.65
60 7 0.14
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (60 bp):
TCTAATTTGATACCTAAACTTAACTATTTTTTCTAAGTTGGTACCTAATATTTTTTGGGG
Found at i:23652 original size:33 final size:31
Alignment explanation
Indices: 23596--23700 Score: 94
Period size: 33 Copynumber: 3.4 Consensus size: 31
23586 AAAAAAAAGC
* *
23596 TTAGGTACCCAATTAGGAAAAAAAATGTCATGT
1 TTAGGTACCAAATT-GGATAAAAAATGTCA-GT
23629 TTAGGTACCAAATTGGATCAAAAAA----AGT
1 TTAGGTACCAAATTGGAT-AAAAAATGTCAGT
*
23657 TTAGGTACCAAATTAG-TAAAAAATGTCAAGT
1 TTAGGTACCAAATTGGATAAAAAATGTC-AGT
* *
23688 TCAAGTACCAAAT
1 TTAGGTACCAAAT
23701 GTTATATTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
26 6 0.10
27 1 0.02
28 17 0.28
29 1 0.02
31 14 0.23
32 3 0.05
33 19 0.31
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (31 bp):
TTAGGTACCAAATTGGATAAAAAATGTCAGT
Found at i:23679 original size:28 final size:28
Alignment explanation
Indices: 23586--23679 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
23576 ATTGAATCTT
* *
23586 AAAAAAAAGCTTAGGTACCCAATTAGGA
1 AAAAAAAAGTTTAGGTACCAAATTAGGA
23614 AAAAAAATGTCATGTTTAGGTACCAAATT-GGA
1 AAAAAAA----A-GTTTAGGTACCAAATTAGGA
* *
23646 TCAAAAAAAGTTTAGGTACCAAATTAGTA
1 -AAAAAAAAGTTTAGGTACCAAATTAGGA
23675 AAAAA
1 AAAAA
23680 TGTCAAGTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
28 27 0.50
29 3 0.06
32 4 0.07
33 20 0.37
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAAAAAAGTTTAGGTACCAAATTAGGA
Found at i:23696 original size:59 final size:62
Alignment explanation
Indices: 23569--23700 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 62
23559 ATAAATTTAG
* * * *
23569 GTACCAAATTGAATCTTAAAAAAAAGCTTAGGTACCCAATTAGGAAAAAAAATGTCATGTTTAG
1 GTACCAAATTGAATC-T-AAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAATGTCAAGTTCAA
* * *
23633 GTACCAAATTGGATC-AAAAAAAGTTTAGGTACCAAATTA-G-TAAAAAATGTCAAGTTCAA
1 GTACCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAATGTCAAGTTCAA
23692 GTACCAAAT
1 GTACCAAAT
23701 GTTATATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
59 24 0.39
60 1 0.02
61 22 0.36
64 14 0.23
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (62 bp):
GTACCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAATGTCAAGTTCAA
Found at i:33463 original size:33 final size:34
Alignment explanation
Indices: 33416--33480 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
33406 CACCAATAAT
*
33416 TAATTATTTTTTAATTTT-AAA-ACATATATTAA
1 TAATTATTTGTTAATTTTCAAATACATATATTAA
*
33448 TAATGTATTTGTTAATTTTCAAATAGATATATT
1 TAAT-TATTTGTTAATTTTCAAATACATATATT
33481 GTTAACGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.14
33 13 0.46
34 3 0.11
35 8 0.29
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (34 bp):
TAATTATTTGTTAATTTTCAAATACATATATTAA
Found at i:34718 original size:7 final size:7
Alignment explanation
Indices: 34706--34739 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
34696 TTATGTAAAT
34706 CAAAACC
1 CAAAACC
34713 CAAAACC
1 CAAAACC
34720 CAAAACC
1 CAAAACC
34727 CAAAACC
1 CAAAACC
34734 CAAAAC
1 CAAAAC
34740 AGTGAAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAACC
Found at i:48969 original size:60 final size:60
Alignment explanation
Indices: 48891--49007 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
48881 ATACAAGATC
* *
48891 TTCCTAGCCTCCACCATAGGTTTTCACTCAATACAATTCTCCAAACTAGCTTCCCAATCT
1 TTCCCAGCCTCCACCATAGGTTTCCACTCAATACAATTCTCCAAACTAGCTTCCCAATCT
* * *
48951 TTCCCAGCCTCCAGCATAGGTTTCCACTCAATATAATTCTCCAAACTATCTTCCCAA
1 TTCCCAGCCTCCACCATAGGTTTCCACTCAATACAATTCTCCAAACTAGCTTCCCAA
49008 CCTAAGTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.27, C:0.35, G:0.07, T:0.31
Consensus pattern (60 bp):
TTCCCAGCCTCCACCATAGGTTTCCACTCAATACAATTCTCCAAACTAGCTTCCCAATCT
Found at i:54063 original size:9 final size:9
Alignment explanation
Indices: 54049--54087 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
54039 TTTTTAAATA
54049 TAAAATTAT
1 TAAAATTAT
54058 TAAAATTATTT
1 TAAAATTA--T
54069 TAAAATTAT
1 TAAAATTAT
54078 TAAAATTAT
1 TAAAATTAT
54087 T
1 T
54088 TTTTTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 19 0.68
11 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TAAAATTAT
Found at i:54074 original size:20 final size:20
Alignment explanation
Indices: 54049--54089 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54039 TTTTTAAATA
54049 TAAAATTATTAAAATTATTT
1 TAAAATTATTAAAATTATTT
54069 TAAAATTATTAAAATTATTT
1 TAAAATTATTAAAATTATTT
54089 T
1 T
54090 TTTGAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATTATTAAAATTATTT
Found at i:60355 original size:25 final size:23
Alignment explanation
Indices: 60259--60367 Score: 114
Period size: 23 Copynumber: 4.7 Consensus size: 23
60249 GCCCAAATAA
* * *
60259 TGCTAAACAGAGAGTACACAAAG
1 TGCTAATCAGAGAGCACACACAG
* *
60282 TACTAATCAGAGAGCACACAAAG
1 TGCTAATCAGAGAGCACACACAG
60305 TGCTAATCAGAGAGCACACACAG
1 TGCTAATCAGAGAGCACACACAG
*
60328 TGCTAATAACAGAGAGCACGAGAC-G
1 TGCTAAT--CAGAGAGCAC-ACACAG
60353 TGCTAAAT-AGAGAGC
1 TGCT-AATCAGAGAGC
60368 GCGTTAGTGT
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
23 55 0.72
25 15 0.20
26 6 0.08
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (23 bp):
TGCTAATCAGAGAGCACACACAG
Found at i:68099 original size:27 final size:27
Alignment explanation
Indices: 68052--68108 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
68042 TTTTAACAAA
* *
68052 AAAAATAAAACACACTCTAAC-TTCAAT
1 AAAAATAAAACACAATATAACGTT-AAT
*
68079 AAAAATAAAATACAATATAACGTTAAT
1 AAAAATAAAACACAATATAACGTTAAT
68106 AAA
1 AAA
68109 GATCCTCACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.23
Consensus pattern (27 bp):
AAAAATAAAACACAATATAACGTTAAT
Found at i:69778 original size:3 final size:3
Alignment explanation
Indices: 69770--69799 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
69760 TGTAAACAGA
69770 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
69800 ACCTCCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:69862 original size:6 final size:6
Alignment explanation
Indices: 69851--69890 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
69841 CACTCCTTTG
69851 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT
69891 TAAAGTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCC
Found at i:70680 original size:35 final size:35
Alignment explanation
Indices: 70641--70709 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
70631 AGACAAACTG
70641 TGTTTTTTAAAATGGAATTATTGAATGTTCTATAT
1 TGTTTTTTAAAATGGAATTATTGAATGTTCTATAT
70676 TGTTTTTTAAAATGGAATTATTGAATGTTCTATA
1 TGTTTTTTAAAATGGAATTATTGAATGTTCTATA
70710 CGCATTCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (35 bp):
TGTTTTTTAAAATGGAATTATTGAATGTTCTATAT
Found at i:72717 original size:26 final size:26
Alignment explanation
Indices: 72683--72732 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
72673 TTGTGCTTTG
72683 TTTATTAATATGCTATTAGTATGGGT
1 TTTATTAATATGCTATTAGTATGGGT
72709 TTTATTAATATGCTATTAGTATGG
1 TTTATTAATATGCTATTAGTATGG
72733 CATAACTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.50
Consensus pattern (26 bp):
TTTATTAATATGCTATTAGTATGGGT
Found at i:78430 original size:17 final size:19
Alignment explanation
Indices: 78408--78476 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
78398 TAAAAATTAC
78408 AAAATTTAT-A-TTTTTAA
1 AAAATTTATAATTTTTTAA
78425 AAAA-TTATAATTTTTTAA
1 AAAATTTATAATTTTTTAA
* * * *
78443 AAAATTCTAAAAATATATAA
1 AAAATT-TATAATTTTTTAA
*
78463 AAAATTTAAAATTT
1 AAAATTTATAATTT
78477 AAAATAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.10
17 5 0.12
18 11 0.26
19 7 0.17
20 15 0.36
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTTATAATTTTTTAA
Found at i:79125 original size:20 final size:19
Alignment explanation
Indices: 79097--79150 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
79087 AATTTTAAAA
79097 ATTAAAAAAATATAAAAATT
1 ATTAAAAAAAT-TAAAAATT
* *
79117 ATTATAAAAATTAAAAATC
1 ATTAAAAAAATTAAAAATT
* *
79136 ACTAAAATAATTAAA
1 ATTAAAAAAATTAAA
79151 TACTAACATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTAAAAAAATTAAAAATT
Found at i:79408 original size:31 final size:28
Alignment explanation
Indices: 79370--79449 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 28
79360 ATACCAAAAC
* *
79370 TATACATGAATTATGGTTTAATGTGTAATTG
1 TATACATGAATT-TGATTT--TGTGCAATTG
*
79401 TATACATGAAATTTGATTTTGTGCAATTT
1 TATACATG-AATTTGATTTTGTGCAATTG
79430 TATACATGAAATTTTGATTT
1 TATACATG-AA-TTTGATTT
79450 GATCCAATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
29 19 0.43
30 8 0.18
31 13 0.30
32 4 0.09
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (28 bp):
TATACATGAATTTGATTTTGTGCAATTG
Found at i:79433 original size:29 final size:30
Alignment explanation
Indices: 79391--79449 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
79381 TATGGTTTAA
*
79391 TGTGTAATTGTATACATGAAA-TTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
*
79420 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
79450 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTGATTT
Found at i:79458 original size:30 final size:29
Alignment explanation
Indices: 79396--79458 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
79386 TTTAATGTGT
*
79396 AATTGTATACATGAAATTTGATTTTGTGC
1 AATTGTATACATGAAATTTGATTTTGTCC
*
79425 AATTTTATACATGAAATTTTGA-TTTGATCC
1 AATTGTATACATGAAA-TTTGATTTTG-TCC
79455 AATT
1 AATT
79459 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (29 bp):
AATTGTATACATGAAATTTGATTTTGTCC
Found at i:79641 original size:31 final size:30
Alignment explanation
Indices: 79591--79662 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
79581 GATTAAATCA
* *
79591 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAATTTCAAGTATACAATTGAACC
* * * *
79621 ACAATTAAAATTTTATGTATATAATTGGACC
1 A-AATTAAAATTTCAAGTATACAATTGAACC
79652 AAATTAAAATT
1 AAATTAAAATT
79663 CATATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (30 bp):
AAATTAAAATTTCAAGTATACAATTGAACC
Found at i:80396 original size:19 final size:22
Alignment explanation
Indices: 80360--80405 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
80350 TGGTACTTCA
80360 ATTTTTTTTACTCACAAG-TGGT
1 ATTTTTTTTACT-ACAAGTTGGT
80382 ATTTTTTTT-CT-CAAGTTGGT
1 ATTTTTTTTACTACAAGTTGGT
80402 ATTT
1 ATTT
80406 CCGTTAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 8 0.35
21 2 0.09
22 9 0.39
ACGTcount: A:0.20, C:0.11, G:0.13, T:0.57
Consensus pattern (22 bp):
ATTTTTTTTACTACAAGTTGGT
Found at i:83062 original size:26 final size:24
Alignment explanation
Indices: 83019--83066 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
83009 GTTTTTCAAC
*
83019 TTTTATTATTTTATTATTTTAAAT
1 TTTTATAATTTTATTATTTTAAAT
83043 TTTTATAATTATTAATTATTTTAA
1 TTTTATAATT-TT-ATTATTTTAA
83067 GTTATTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 2 0.10
26 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTATAATTTTATTATTTTAAAT
Found at i:83420 original size:22 final size:20
Alignment explanation
Indices: 83370--83425 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
83360 ATCTATCTTA
83370 TTTGTTTTATTT-TTTATTG
1 TTTGTTTTATTTATTTATTG
**
83389 TTT-TAATATTTAATTTATTG
1 TTTGTTTTATTT-ATTTATTG
83409 TTCTGTTTTATTTATTT
1 TT-TGTTTTATTTATTT
83426 TAGTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 6 0.21
19 3 0.10
20 9 0.31
21 5 0.17
22 6 0.21
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTGTTTTATTTATTTATTG
Found at i:83427 original size:22 final size:21
Alignment explanation
Indices: 83370--83427 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 21
83360 ATCTATCTTA
83370 TTTGTTTTA-TT-TTTTATTG
1 TTTGTTTTATTTATTTTATTG
** *
83389 TTT-TAATATTTAATTTATTG
1 TTTGTTTTATTTATTTTATTG
83409 TTCTGTTTTATTTATTTTA
1 TT-TGTTTTATTTATTTTA
83428 GTTATTTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 9 0.31
21 1 0.03
22 11 0.38
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTGTTTTATTTATTTTATTG
Found at i:83432 original size:13 final size:13
Alignment explanation
Indices: 83416--83440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83406 TTGTTCTGTT
83416 TTATTTATTTTAG
1 TTATTTATTTTAG
83429 TTATTTATTTTA
1 TTATTTATTTTA
83441 ATTGTATTCT
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:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTTATTTTAG
Found at i:83441 original size:40 final size:41
Alignment explanation
Indices: 83372--83448 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
83362 CTATCTTATT
*
83372 TGTTTTATTTTTTATTGTTTTAATATTTAATT-TATTGTTC
1 TGTTTTATTTTTTATAGTTTTAATATTTAATTGTATTGTTC
*
83412 TGTTTTATTTATTT-TAGTTATTTAT-TTTAATTGTATT
1 TGTTTTATTT-TTTATAGTT-TTAATATTTAATTGTATT
83449 CTTTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
40 21 0.66
41 11 0.34
ACGTcount: A:0.21, C:0.01, G:0.08, T:0.70
Consensus pattern (41 bp):
TGTTTTATTTTTTATAGTTTTAATATTTAATTGTATTGTTC
Found at i:91226 original size:30 final size:30
Alignment explanation
Indices: 91162--91228 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
91152 AATATAAATT
* * *
91162 TATTGTTATATATTTTTGGAAATATTTATT
1 TATTTTTATATATTTTTGAAAATATTTATA
91192 TATTTTTATATA-TTTT-AAAATATTATATAA
1 TATTTTTATATATTTTTGAAAATATT-TAT-A
91222 TATTTTT
1 TATTTTT
91229 TTGTCAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.22
29 7 0.22
30 18 0.56
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.61
Consensus pattern (30 bp):
TATTTTTATATATTTTTGAAAATATTTATA
Found at i:94652 original size:20 final size:20
Alignment explanation
Indices: 94615--94654 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
94605 ATGAAGAGAG
* *
94615 AATATTTATCTTAGATATTT
1 AATATCTATCTCAGATATTT
*
94635 AATATCTATCTCATATATTT
1 AATATCTATCTCAGATATTT
94655 TCATCTAGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (20 bp):
AATATCTATCTCAGATATTT
Found at i:105880 original size:18 final size:18
Alignment explanation
Indices: 105857--105893 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
105847 ACAATTCATA
105857 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
105875 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
105893 T
1 T
105894 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:108282 original size:3 final size:3
Alignment explanation
Indices: 108276--108312 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
108266 TGGCAACGAC
108276 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
108313 TTGGATTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:110456 original size:19 final size:20
Alignment explanation
Indices: 110425--110476 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
110415 AAAAATATAA
*
110425 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTAAAAATT
110445 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
*
110464 ATTTTAAATTTTT
1 ATTTTGAATTTTT
110477 GAAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 8 0.29
19 10 0.36
20 10 0.36
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:110481 original size:19 final size:18
Alignment explanation
Indices: 110425--110482 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
110415 AAAAATATAA
*
110425 ATTTTGAAATTTTTATAAAT
1 ATTTT-AAATTTTTA-AATT
* *
110445 ATTTTGAATTTTAAAAATT
1 ATTTTAAATTTT-TAAATT
110464 ATTTTAAATTTTTGAAATT
1 ATTTTAAATTTTT-AAATT
110483 TAATTATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTTTAAATTTTTAAATT
Found at i:110495 original size:27 final size:28
Alignment explanation
Indices: 110431--110495 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
110421 ATAAATTTTG
* *
110431 AAATTTTTATAAATATTTTGAATTTTAA
1 AAATTTTTTTAAATATTTTGAAATTTAA
*
110459 AAATTATTTTAAAT-TTTTGAAATTTAA
1 AAATTTTTTTAAATATTTTGAAATTTAA
**
110486 TTATTTTTTT
1 AAATTTTTTT
110496 TGTAATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
AAATTTTTTTAAATATTTTGAAATTTAA
Done.