Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006177.1 Kokia drynarioides strain JFW-HI SEQ_120742, 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: 72873
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 155 characters in sequence are not A, C, G, or T
Found at i:225 original size:28 final size:27
Alignment explanation
Indices: 194--253 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
184 AAAATGAGAC
* *
194 TTTGGA-TACCCGAGGGTAAAATGGTAAT
1 TTTGGACT-CCCG-GGGCAAAATGATAAT
*
222 TTTGGACTCTCGGGGCAAAATGATAAT
1 TTTGGACTCCCGGGGCAAAATGATAAT
249 TTTGG
1 TTTGG
254 GAAAATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 18 0.64
28 9 0.32
29 1 0.04
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (27 bp):
TTTGGACTCCCGGGGCAAAATGATAAT
Found at i:494 original size:117 final size:116
Alignment explanation
Indices: 372--796 Score: 475
Period size: 117 Copynumber: 3.6 Consensus size: 116
362 AATGGGGATC
* * * * *
372 AAAAATAGAGTTTTTGGACGTTCGAGGGTAAAAATGTAATTTTCAAAAGTTTTGAGGTCAAAATG
1 AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAATG
* *
437 GAATTTTTTAAGGTTT-AGGGGTAAAAATGTAATTTTTGAAAGTTTTGAGGTT
66 GAATTTTTTAA-GTTTGA-GGGTAAAAATATAATTTTTGAAAGTTTCGAGGTT
* * * ** ** * *
489 TAAAATGGAATTTTTGGAAGTT-TAGGGGT-AAAATGGAATTTTTGGAAGTTTAGAGGTTAAAAA
1 AAAAATAGAATTTTTGGAAGTTCGA-GGGTAAAAATATAATTTTCAGAAGTTTCGAGG-TCAAAA
* *
552 TGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATATTTTGAAAGTTTCAAGG-T
64 TGGAATTTTT-TAAGTTTGAGGGTAAAAATATAAT-TTTTGAAAGTTTCGAGGTT
* * * *
606 CAAAAT-GAAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCATAAGTTTCGGGGTTAAAAT
1 AAAAATAG-AATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAAT
* *
670 GGAATTTTTAGAAGTTCGAGGGTAAAAATATAATTTTT-AGAAGTTTCGAGGTT
65 GGAATTTTT-TAAGTTTGAGGGTAAAAATATAATTTTTGA-AAGTTTCGAGGTT
* *
723 AAAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTCAAAATG
1 AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAATG
* *
788 AAATATTTT
66 GAATTTTTT
797 GACAGTTTAA
Statistics
Matches: 260, Mismatches: 37, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
115 1 0.00
116 38 0.15
117 181 0.70
118 40 0.15
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.36
Consensus pattern (116 bp):
AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCAGAAGTTTCGAGGTCAAAATG
GAATTTTTTAAGTTTGAGGGTAAAAATATAATTTTTGAAAGTTTCGAGGTT
Found at i:797 original size:59 final size:58
Alignment explanation
Indices: 373--797 Score: 448
Period size: 58 Copynumber: 7.3 Consensus size: 58
363 ATGGGGATCA
* * * * * * *
373 AAAATAGAGTTTTTGGACGTTCGAGGGTAAAAATGTAATTTTCAAAAGTTTTGAGGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
* * * * *
431 AAAATGGAATTTTT-TAAGGTT-TAGGGGTAAAAATGTAATTTTT-GAAAGTTTTGAGGTTT
1 AAAATGGAATTTTTGGAA-GTTCGA-GGGTAAAAATATAATTTTTAG-AAGTTTCGAGG-TC
* ** * * *
490 AAAATGGAATTTTTGGAAGTT-TAGGGGT-AAAATGGAATTTTTGGAAGTTTAGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATATAATTTTTAGAAGTTTCGAGG-TC
* *
548 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATATTTT-GAAAGTTTCAAGGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAAT-TTTTAG-AAGTTTCGAGGTC
* * * * *
607 AAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTCATAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
* *
665 AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGG-TC
* *
724 AAAATAGAATTTTTGGAAGTTCGGGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
*
782 AAAATGAAATATTTTG
1 AAAATGGAAT-TTTTG
798 ACAGTTTAAG
Statistics
Matches: 317, Mismatches: 37, Indels: 25
0.84 0.10 0.07
Matches are distributed among these distances:
57 2 0.01
58 167 0.53
59 133 0.42
60 15 0.05
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTAGAAGTTTCGAGGTC
Found at i:1682 original size:7 final size:7
Alignment explanation
Indices: 1670--1720 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
1660 CTTTTTTTGG
1670 TTATTAA
1 TTATTAA
1677 TTATTAA
1 TTATTAA
1684 TTATT-A
1 TTATTAA
1690 TTATTAA
1 TTATTAA
*
1697 TAATATTTTA
1 T--TA-TTAA
*
1707 TTAATAA
1 TTATTAA
1714 TTATTAA
1 TTATTAA
1721 GGTTATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 6 0.17
7 22 0.61
8 2 0.06
9 2 0.06
10 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATTAA
Found at i:1786 original size:21 final size:19
Alignment explanation
Indices: 1736--1787 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
1726 TTTATTACCG
*
1736 TTATTTATTATTAATATCA
1 TTATTTATTATTAATAACA
*
1755 TTATTAATATTATTAATAAAACC
1 TTATT--TATTATTAAT--AACA
1778 TTATTTATTA
1 TTATTTATTA
1788 CTCATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 5 0.19
21 15 0.56
23 7 0.26
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATTTATTATTAATAACA
Found at i:2497 original size:6 final size:6
Alignment explanation
Indices: 2486--2579 Score: 58
Period size: 6 Copynumber: 16.7 Consensus size: 6
2476 TTTGGACATT
* * * *
2486 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--CA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * * *
2532 AA-GTA AATTTA AACTTA AA--TA AATTTA ATTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
2576 AATT
1 AATT
2580 ATGTTGGGCC
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
4 6 0.09
5 11 0.17
6 46 0.71
7 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:2511 original size:17 final size:16
Alignment explanation
Indices: 2486--2579 Score: 89
Period size: 17 Copynumber: 5.6 Consensus size: 16
2476 TTTGGACATT
*
2486 AATTTAAATTTAAATTT
1 AATTTAAATTTAAA-TA
* * *
2503 AACTCAAATTTATAACA
1 AATTTAAATTTA-AATA
*
2520 AATTTAAATTTTAAGTA
1 AATTTAAA-TTTAAATA
*
2537 AATTTAAACTTAAATA
1 AATTTAAATTTAAATA
*
2553 AATTTAATTTTAAAATA
1 AATTTAAATTT-AAATA
2570 AATTTAAATT
1 AATTTAAATT
2580 ATGTTGGGCC
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
16 15 0.25
17 40 0.66
18 6 0.10
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:2720 original size:94 final size:94
Alignment explanation
Indices: 2613--3408 Score: 1187
Period size: 94 Copynumber: 8.7 Consensus size: 94
2603 CTTCAACAAT
*
2613 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
2678 TATCAAATAATGTGTTGATTTGACAATAC
66 TATCAAATAATGTGTTGATTTGACAATAC
* *
2707 ATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
*
2772 TATCAAATAATGTGTTGATTTGATAATAC
66 TATCAAATAATGTGTTGATTTGACAATAC
*
2801 ATTATTTACCAAATTTTAATATTT-AA---A--T--A-AAAAAA-TATTATAATATTACAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
* *
2856 TATCATATAA--TG-TG-TTTGACAATAA
66 TATCAAATAATGTGTTGATTTGACAATAC
*
2881 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
* *
2946 TATCAAATAATGTGTTGATTTAATAATAC
66 TATCAAATAATGTGTTGATTTGACAATAC
* *
2975 ATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
*
3040 TATCAAATAATATGTTGATTTGACAATAC
66 TATCAAATAATGTGTTGATTTGACAATAC
*
3069 ATTATTTACC--A----AAT-TTT-AA--TATTTAAATAAAAAA-TATTATCATATTACAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
* *
3123 TATTAAATAATGTGTTGATTTGACAATAA
66 TATCAAATAATGTGTTGATTTGACAATAC
*
3152 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
* * *
3217 TATCAAATAATGTATTGATTTAATAATAC
66 TATCAAATAATGTGTTGATTTGACAATAC
* *
3246 ATTATTTATCAAATTTTAATATTTAAATTTATTTAAATCAAAAACTATTATTATATTTA-AATTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATA-TTACAATTT
3310 TTATCAAATAATGTGTTGATTTGACAATAC
65 TTATCAAATAATGTGTTGATTTGACAATAC
*
3340 ATTATTTACCAAATTTTAAT-TTTAAATTTATTTAAATAAAAAGCTATTATTATATTACAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
3404 TATCA
66 TATCA
3409 TATTTTAAAT
Statistics
Matches: 635, Mismatches: 40, Indels: 55
0.87 0.05 0.08
Matches are distributed among these distances:
80 33 0.05
81 4 0.01
82 2 0.00
83 54 0.09
84 43 0.07
85 7 0.01
86 4 0.01
87 3 0.00
88 5 0.01
89 9 0.01
90 31 0.05
91 2 0.00
92 6 0.01
93 62 0.10
94 368 0.58
95 2 0.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (94 bp):
ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACAATTTT
TATCAAATAATGTGTTGATTTGACAATAC
Found at i:2760 original size:49 final size:48
Alignment explanation
Indices: 2612--2766 Score: 124
Period size: 47 Copynumber: 3.2 Consensus size: 48
2602 GCTTCAACAA
2612 TATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
1 TATTATTTA-CAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
* * * * * * ** *
2661 TATTATATTAC--ATTTT-TTA-TCAAATAATGTGTTGATTTGACAA-TA-
1 TATTAT-TTACAAATTTTAATATTTAAAT-TTAT-TTAAATAAAAAACTAT
*
2706 CATTATTTATCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
1 TATTATTTA-CAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
2755 TATTATATTACA
1 TATTAT-TTACA
2767 TTTTTTATCA
Statistics
Matches: 75, Mismatches: 20, Indels: 22
0.64 0.17 0.19
Matches are distributed among these distances:
44 3 0.04
45 11 0.15
46 6 0.08
47 24 0.32
48 6 0.08
49 19 0.25
50 6 0.08
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (48 bp):
TATTATTTACAAATTTTAATATTTAAATTTATTTAAATAAAAAACTAT
Found at i:2979 original size:48 final size:48
Alignment explanation
Indices: 2927--3074 Score: 139
Period size: 48 Copynumber: 3.1 Consensus size: 48
2917 ATAAAAAACT
*
2927 ATTATTATATTTCAATTTTTATCAAATAATGTGTTGATTTAATAATAC
1 ATTATTATATTTCAATTTTTATCAAATAATATGTTGATTTAATAATAC
* ** *
2975 ATTATT-TA--TCAAATTTTAAT-ATTTAA-AT-TT-ATTTAAATAAAAAAC
1 ATTATTATATTTC-AATTTTTATCAAATAATATGTTGATTT-AAT--AATAC
* *
3020 TATTATTATATTTCAATTTTTATCAAATAATATGTTGATTTGACAATAC
1 -ATTATTATATTTCAATTTTTATCAAATAATATGTTGATTTAATAATAC
3069 ATTATT
1 ATTATT
3075 TACCAAATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
42 4 0.05
43 5 0.06
44 1 0.01
45 10 0.13
46 14 0.18
47 4 0.05
48 20 0.26
49 10 0.13
50 2 0.03
51 3 0.04
52 4 0.05
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (48 bp):
ATTATTATATTTCAATTTTTATCAAATAATATGTTGATTTAATAATAC
Found at i:3250 original size:48 final size:48
Alignment explanation
Indices: 3198--3345 Score: 121
Period size: 48 Copynumber: 3.1 Consensus size: 48
3188 ATAAAAAACT
3198 ATTATTATATTTCAATTTTTATCAAATAATGTATTGATTTAATAATAC
1 ATTATTATATTTCAATTTTTATCAAATAATGTATTGATTTAATAATAC
* ** * *
3246 ATTATT-TA--TCAAATTTTAAT-ATTTAA---ATTTATTTAAATCAAAAAC
1 ATTATTATATTTC-AATTTTTATCAAATAATGTATTGATTT-AAT--AATAC
* * * *
3291 TATTATTATATTTAAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 -ATTATTATATTTCAATTTTTATCAAATAATGTATTGATTTAATAATAC
3340 ATTATT
1 ATTATT
3346 TACCAAATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 24
0.66 0.12 0.21
Matches are distributed among these distances:
42 7 0.09
43 3 0.04
45 10 0.14
46 14 0.19
47 4 0.05
48 20 0.27
49 9 0.12
51 1 0.01
52 6 0.08
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (48 bp):
ATTATTATATTTCAATTTTTATCAAATAATGTATTGATTTAATAATAC
Found at i:3268 original size:271 final size:268
Alignment explanation
Indices: 2613--3366 Score: 1332
Period size: 271 Copynumber: 2.8 Consensus size: 268
2603 CTTCAACAAT
* *
2613 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTACATTTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
* *
2678 TATCAAATAATGTGTTGATTTGACAATACATTATTTATCAAATTTTAATATTTAAATTTATTTAA
66 TATCAAATAATGTGTTGATTTAATAATACATTATTTATCAAATTTTAATATTTAAATTTATTTAA
* * *
2743 ATAAAAAACTATTATTATATTACATTTTTTATCAAATAATGTGTTGATTTGATAATACATTATTT
131 ATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
*
2808 ACCAAATTTTAATATTTAAATAAAAAAATATTATAATATTACAATTTTTATCATATAATGTGTTT
196 ACCAAATTTTAATATTTAAATAAAAAAATATTATAATATTACAATTTTTATCAAATAATGTGTTT
2873 GACAATAA
261 GACAATAA
2881 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
2946 TATCAAATAATGTGTTGATTTAATAATACATTATTTATCAAATTTTAATATTTAAATTTATTTAA
66 TATCAAATAATGTGTTGATTTAATAATACATTATTTATCAAATTTTAATATTTAAATTTATTTAA
*
3011 ATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATATGTTGATTTGACAATACATTATTT
131 ATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
* *
3076 ACCAAATTTTAATATTTAAAT-AAAAAATATTATCATATTACAATTTTTATTAAATAATGTGTTG
196 ACCAAATTTTAATATTTAAATAAAAAAATATTATAATATTACAATTTTTATCAAATAA--TG-TG
3140 ATTTGACAATAA
258 -TTTGACAATAA
3152 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
1 ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
*
3217 TATCAAATAATGTATTGATTTAATAATACATTATTTATCAAATTTTAATATTTAAATTTATTTAA
66 TATCAAATAATGTGTTGATTTAATAATACATTATTTATCAAATTTTAATATTTAAATTTATTTAA
* *
3282 ATCAAAAACTATTATTATATTTAAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
131 ATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
3347 ACCAAATTTTAAT-TTTAAAT
196 ACCAAATTTTAATATTTAAAT
3367 TTATTTAAAT
Statistics
Matches: 467, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
267 33 0.07
268 208 0.45
269 2 0.00
270 9 0.02
271 215 0.46
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (268 bp):
ATTATTTACCAAATTTTAATATTTAAATTTATTTAAATAAAAAACTATTATTATATTTCAATTTT
TATCAAATAATGTGTTGATTTAATAATACATTATTTATCAAATTTTAATATTTAAATTTATTTAA
ATAAAAAACTATTATTATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
ACCAAATTTTAATATTTAAATAAAAAAATATTATAATATTACAATTTTTATCAAATAATGTGTTT
GACAATAA
Found at i:3538 original size:22 final size:22
Alignment explanation
Indices: 3506--3561 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
3496 GACCACCCAT
*
3506 ATTCCAGCTCACCTAAACCGAA
1 ATTCCAGCTCACCAAAACCGAA
*
3528 ATTTCAGCTCACCAAAACCGAA
1 ATTCCAGCTCACCAAAACCGAA
3550 ATTCCAGCTCAC
1 ATTCCAGCTCAC
3562 TACCACCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.20
Consensus pattern (22 bp):
ATTCCAGCTCACCAAAACCGAA
Found at i:3573 original size:22 final size:22
Alignment explanation
Indices: 3506--3576 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
3496 GACCACCCAT
3506 ATTCCAGCTCACCTA-AACCGAA
1 ATTCCAGCTCA-CTACAACCGAA
* * *
3528 ATTTCAGCTCACCAAAACCGAA
1 ATTCCAGCTCACTACAACCGAA
* *
3550 ATTCCAGCTCACTACCACCTAA
1 ATTCCAGCTCACTACAACCGAA
3572 ATTCC
1 ATTCC
3577 GTCGTTAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 2 0.05
22 39 0.95
ACGTcount: A:0.35, C:0.37, G:0.07, T:0.21
Consensus pattern (22 bp):
ATTCCAGCTCACTACAACCGAA
Found at i:5242 original size:12 final size:12
Alignment explanation
Indices: 5227--5294 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
5217 GCTCGAGGAT
5227 GAGCCCAATGAC
1 GAGCCCAATGAC
5239 GAGCCCACA-GAC
1 GAGCCCA-ATGAC
* * *
5251 CAGCCCACTGAT
1 GAGCCCAATGAC
* *
5263 GAGCCCGATTAC
1 GAGCCCAATGAC
5275 GAGCCCGAA-GAC
1 GAGCCC-AATGAC
*
5287 TAGCCCAA
1 GAGCCCAA
5295 GTACCAACCG
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.31, C:0.37, G:0.24, T:0.09
Consensus pattern (12 bp):
GAGCCCAATGAC
Found at i:5277 original size:36 final size:36
Alignment explanation
Indices: 5224--5293 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
5214 CGAGCTCGAG
5224 GATGAGCCCAATGACGAGCCC-ACAGACCAGCCCACT
1 GATGAGCCCAATGACGAGCCCGA-AGACCAGCCCACT
* * *
5260 GATGAGCCCGATTACGAGCCCGAAGACTAGCCCA
1 GATGAGCCCAATGACGAGCCCGAAGACCAGCCCA
5294 AGTACCAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.30, C:0.36, G:0.24, T:0.10
Consensus pattern (36 bp):
GATGAGCCCAATGACGAGCCCGAAGACCAGCCCACT
Found at i:5791 original size:30 final size:30
Alignment explanation
Indices: 5746--5927 Score: 240
Period size: 30 Copynumber: 6.1 Consensus size: 30
5736 TTTGATTTTT
* *
5746 TTTCATTTATTTTTTAAATTTAATTTTTAA
1 TTTCGTTTATATTTTAAATTTAATTTTTAA
*
5776 TTTCGTTTATATTTTAAATTTAATTTATAA
1 TTTCGTTTATATTTTAAATTTAATTTTTAA
**
5806 TTTCGTACATATTTTAAATTTAAATTTTT-A
1 TTTCGTTTATATTTTAAATTT-AATTTTTAA
* *
5836 TTTCGTGTATATTTTAATTTTAATTTTTAA
1 TTTCGTTTATATTTTAAATTTAATTTTTAA
* * *
5866 TTTCGTGTATATTTTAATTTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTTTAA
* *
5896 TTTCGTTTATATTTTAAATTTCATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTTTAA
5926 TT
1 TT
5928 ATTATTTTTT
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
29 7 0.05
30 124 0.91
31 6 0.04
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTTTAA
Found at i:5802 original size:18 final size:18
Alignment explanation
Indices: 5762--5804 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5752 TTATTTTTTA
*
5762 AATTTA-ATTTTTAATTT
1 AATTTATATTTTAAATTT
**
5779 CGTTTATATTTTAAATTT
1 AATTTATATTTTAAATTT
5797 AATTTATA
1 AATTTATA
5805 ATTTCGTACA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTATATTTTAAATTT
Found at i:6859 original size:37 final size:37
Alignment explanation
Indices: 6795--6867 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
6785 AACATTAAAA
* *
6795 AAATTTGAATTTTTTGTCAGATAAAAAAGGTGGTGTT
1 AAATTTGAATTTTTTATCAGATAAAAAAGGTAGTGTT
* *
6832 AAATTTGATTTTTTTTATCGGAT-AAAAAGGTAGTGT
1 AAATTTGA-ATTTTTTATCAGATAAAAAAGGTAGTGT
6868 CGACCAATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 20 0.65
38 11 0.35
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (37 bp):
AAATTTGAATTTTTTATCAGATAAAAAAGGTAGTGTT
Found at i:6919 original size:60 final size:61
Alignment explanation
Indices: 6842--7291 Score: 447
Period size: 61 Copynumber: 7.4 Consensus size: 61
6832 AAATTTGATT
* * * *
6842 TTTTTTATCGGATAAAAAGGTAGTGTCGACCAATGC-ATGACCAACACAAAAAAATTTGAA
1 TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCAATGGCCAACACAAAAAAAATTGAA
* * * *
6902 TTTTTTGTCAGATAAAAAAGGTGATGTCGATC-ATGCAATGGCCAACACAAAAAAAATTGAT
1 TTTTTTATCAGAT-AAAAAGGTGGTGTCGACCAATGCAATGGCCAACACAAAAAAAATTGAA
* * * *
6963 TTTTTTATCAGATAAAAAGGTGGTGTCGACAAATGC-ACGGTCAATACAAAAAAAATTGAA
1 TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCAATGGCCAACACAAAAAAAATTGAA
* * * * * * * *
7023 TTTTTTGTCATATAAAAAAGATGGTGTCGA-TAATGCAATGTCCAATA-TAAAAAATTTG-A
1 TTTTTTATCAGAT-AAAAAGGTGGTGTCGACCAATGCAATGGCCAACACAAAAAAAATTGAA
* *
7082 TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGC-TTGGTCAACACAAAAAAAAAATTGAA
1 TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCAATGGCCAACAC--AAAAAAAATTGAA
* * *
7144 TTTTTTGTCAGATTAAAAAGGTGGTGTCGA-CAATGCAATTGCTAACACAAAAAAAAATTG-A
1 TTTTTTATCAGA-TAAAAAGGTGGTGTCGACCAATGCAATGGCCAACAC-AAAAAAAATTGAA
** * * * *
7205 TTTTTTATCAGATAAAAAAAATTGTGTCGACC-ATGCAATGGCCTACACCAAAAAAATT-AT
1 TTTTTTATCAGAT-AAAAAGGTGGTGTCGACCAATGCAATGGCCAACACAAAAAAAATTGAA
* *
7265 TTTTTTAT-ATTATAAAAAGGTGATGTC
1 TTTTTTATCA-GATAAAAAGGTGGTGTC
7292 AGCTAAGCAA
Statistics
Matches: 320, Mismatches: 54, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
58 21 0.07
59 28 0.09
60 95 0.30
61 121 0.38
62 31 0.10
63 24 0.08
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (61 bp):
TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCAATGGCCAACACAAAAAAAATTGAA
Found at i:7012 original size:121 final size:120
Alignment explanation
Indices: 6842--7270 Score: 524
Period size: 121 Copynumber: 3.5 Consensus size: 120
6832 AAATTTGATT
* * ** *
6842 TTTTTTATCGGATAAAAAGGTAGTGTCGACCAATGCATGACCAACACAAAAAAATTTGAATTTTT
1 TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGGTCAACACAAAAAAAATTGAATTTTT
*
6907 TGTCAGATAAAAAAGGTGATGTCGATCATGCAATGGCCAACACAAAAAAAATTGA
66 TGTCAGATAAAAAAGGTGGTGTCGATCATGCAATGGCCAACACAAAAAAAATTGA
* * *
6962 TTTTTTTATCAGATAAAAAGGTGGTGTCGACAAATGCACGGTCAATACAAAAAAAATTGAATTTT
1 -TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGGTCAACACAAAAAAAATTGAATTTT
* * * * * * *
7027 TTGTCATATAAAAAAGATGGTGTCGATAATGCAATGTCCAATA-TAAAAAATTTGA
65 TTGTCAGATAAAAAAGGTGGTGTCGATCATGCAATGGCCAACACAAAAAAAATTGA
*
7082 TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCTTGGTCAACACAAAAAAAAAATTGAATTT
1 TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGGTCAACAC--AAAAAAAATTGAATTT
* * *
7147 TTTGTCAGATTAAAAAGGTGGTGTCGA-CAATGCAATTGCTAACACAAAAAAAAATTGA
64 TTTGTCAGATAAAAAAGGTGGTGTCGATC-ATGCAATGGCCAACAC-AAAAAAAATTGA
** * * * * *
7205 TTTTTTATCAGATAAAAAAAATTGTGTCGACC-ATGCAATGGCCTACACCAAAAAAATT-ATTTT
1 TTTTTTATCAGAT-AAAAAGGTGGTGTCGACCAATGC-ATGGTCAACACAAAAAAAATTGAATTT
7268 TTT
64 TTT
7271 ATATTATAAA
Statistics
Matches: 263, Mismatches: 38, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
119 43 0.16
120 10 0.04
121 151 0.57
122 9 0.03
123 27 0.10
124 23 0.09
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (120 bp):
TTTTTTATCAGATAAAAAGGTGGTGTCGACCAATGCATGGTCAACACAAAAAAAATTGAATTTTT
TGTCAGATAAAAAAGGTGGTGTCGATCATGCAATGGCCAACACAAAAAAAATTGA
Found at i:7356 original size:54 final size:53
Alignment explanation
Indices: 7258--7430 Score: 153
Period size: 55 Copynumber: 3.3 Consensus size: 53
7248 TACACCAAAA
* * * *
7258 AAATTATTTTTTT-ATATTATAAAAAGGTGATGTCAG-CTAAGCAATAGTCAACACC
1 AAATTTTTTTTTTCATA-T-TAAAAAGGTGATGT-TGTC-ATGCAATAGCCAACACC
* *
7313 AAATTTTTTTTTTCATATTAAAAAGGTGATGTTGGTCATGCAATGGCCAACATCA
1 AAATTTTTTTTTTCATATTAAAAAGGTGATGTT-GTCATGCAATAGCCAACA-CC
* * *
7368 AAAATTTTTTTGTCAGATTAAAAAGGTG--G-TGT--TGCAATAGCCAACACC
1 AAATTTTTTTTTTCATATTAAAAAGGTGATGTTGTCATGCAATAGCCAACACC
*
7416 AATTTTTTTTTTTCA
1 AAATTTTTTTTTTCA
7431 AAATCTCGTT
Statistics
Matches: 100, Mismatches: 14, Indels: 15
0.78 0.11 0.12
Matches are distributed among these distances:
48 13 0.13
49 13 0.13
51 2 0.02
52 1 0.01
53 1 0.01
54 27 0.27
55 40 0.40
56 3 0.03
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (53 bp):
AAATTTTTTTTTTCATATTAAAAAGGTGATGTTGTCATGCAATAGCCAACACC
Found at i:18284 original size:3 final size:3
Alignment explanation
Indices: 18276--18302 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18266 AGATGACGAT
18276 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
18303 TTGACATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:34369 original size:20 final size:20
Alignment explanation
Indices: 34341--34379 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34331 AGATATGACC
34341 CATTAAAAACCTTCCAAATA
1 CATTAAAAACCTTCCAAATA
* * *
34361 CATTGAAAAGCTTCGAAAT
1 CATTAAAAACCTTCCAAAT
34380 TTCGAATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (20 bp):
CATTAAAAACCTTCCAAATA
Found at i:35777 original size:12 final size:13
Alignment explanation
Indices: 35756--35782 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35746 TTGATTGGAA
35756 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
35769 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
35782 T
1 T
35783 ATAAGGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:50169 original size:1 final size:1
Alignment explanation
Indices: 50165--50190 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
50155 NNNNNNNNNN
50165 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
50191 GGATATATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:60727 original size:2 final size:2
Alignment explanation
Indices: 60720--60751 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
60710 TCTATTTGAA
60720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60752 TGATGCCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62688 original size:337 final size:335
Alignment explanation
Indices: 62075--62744 Score: 1268
Period size: 337 Copynumber: 2.0 Consensus size: 335
62065 AAGCTCAACG
62075 TATAGGCAAACAACTAAACAAACAATTCTCGAAATCAAAAAGCTATTATTAAGATCCCATAATTA
1 TATAGGCAAACAACTAAACAAACAATTCTCGAAATCAAAAAGCTATTATTAAGATCCCATAATTA
*
62140 TGACTCAAAGCTTTCCTCAGTTCACAACAAAAAAAAAAGGAAAGGGGAGACCTATGATTCTGCTA
66 TGACTCAAAGCTTTCCTCAGTTCACAACAAAAAAAAAAGGAAAAGGGAGACCTATGATTCTGCTA
*
62205 TTGATCATCACTATCATCGGCGGACACCTTCAATAAGCCTAGCCCTAACTCTATCCAGCTTTTTA
131 TTGATCATCACTATCATCGGCGGACACCTTCAATAAGCCTAGCCCCAACTCTATCCAGCTTTTTA
62270 ACCATTGCTACCGATCTCAAATGCCCGTCTTCTAAAAACGCCTCCACCATTATTTGCCCAATCTG
196 ACCATTGCTACCGATCTCAAATGCCCGTCTTCTAAAAACGCCTCCACCATTATTTGCCCAATCTG
62335 CTTCCCTTTCTCTTCATTGTCTATCACAGCCACCGCCGTCGGCCCAGCACCACTAATAGTACACC
261 CTTCCCTTTCTCTTCATTGTCTATCACAGCCACCGCCGTCGGCCCAGCACCACTAATAGTACACC
62400 CGAAAGCTAT
326 CGAAAGCTAT
*
62410 TATAGGCAAACAACTAAACTAACAATTCTCGAAATCAAAAAGCTATTATTAAGATCCCATAATTA
1 TATAGGCAAACAACTAAACAAACAATTCTCGAAATCAAAAAGCTATTATTAAGATCCCATAATTA
62475 TGACTCAAAGCTTTCCTCAGTTCACAACAAAAAAAAAAAAGGAAAAGGGAGACCTATGATTCTGC
66 TGACTCAAAGCTTTCCTCAGTTCACAAC--AAAAAAAAAAGGAAAAGGGAGACCTATGATTCTGC
* *
62540 TATTGATCATCATTATCATCGGGGGACACCTTCAATAAGCCTAGCCCCAACTCTATCCAGCTTTT
129 TATTGATCATCACTATCATCGGCGGACACCTTCAATAAGCCTAGCCCCAACTCTATCCAGCTTTT
*
62605 TAACCATTGCTACCGATCTCAAATGCCCGTCTTCTAAAAACGCCTCCACCATTTTTTGCCCAATC
194 TAACCATTGCTACCGATCTCAAATGCCCGTCTTCTAAAAACGCCTCCACCATTATTTGCCCAATC
62670 TGCTTCCCTTTCTCTTCATTGTCTATCACAGCCACCGCCGTCGGCCCAGCACCACTAATAGTACA
259 TGCTTCCCTTTCTCTTCATTGTCTATCACAGCCACCGCCGTCGGCCCAGCACCACTAATAGTACA
62735 CCCGAAAGCT
324 CCCGAAAGCT
62745 CCGGACTTGA
Statistics
Matches: 327, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
335 92 0.28
337 235 0.72
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (335 bp):
TATAGGCAAACAACTAAACAAACAATTCTCGAAATCAAAAAGCTATTATTAAGATCCCATAATTA
TGACTCAAAGCTTTCCTCAGTTCACAACAAAAAAAAAAGGAAAAGGGAGACCTATGATTCTGCTA
TTGATCATCACTATCATCGGCGGACACCTTCAATAAGCCTAGCCCCAACTCTATCCAGCTTTTTA
ACCATTGCTACCGATCTCAAATGCCCGTCTTCTAAAAACGCCTCCACCATTATTTGCCCAATCTG
CTTCCCTTTCTCTTCATTGTCTATCACAGCCACCGCCGTCGGCCCAGCACCACTAATAGTACACC
CGAAAGCTAT
Found at i:71739 original size:20 final size:20
Alignment explanation
Indices: 71708--71748 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
71698 AAGCAATAAG
71708 AAGAAAAAGAAGCAGA-AAC
1 AAGAAAAAGAAGCAGAGAAC
71727 AAGAAACAAGAAGCAGAGAAC
1 AAGAAA-AAGAAGCAGAGAAC
71748 A
1 A
71749 CACCTTGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 10 0.50
21 4 0.20
ACGTcount: A:0.66, C:0.12, G:0.22, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAGCAGAGAAC
Done.