Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000367.1 Kokia drynarioides strain JFW-HI SEQ_111158, 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: 79432
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:685 original size:29 final size:28
Alignment explanation
Indices: 652--853 Score: 215
Period size: 29 Copynumber: 6.9 Consensus size: 28
642 CCCTAAACCG
652 TCCAAAAATCCCATTTTTACCCTCGAACT
1 TCCAAAAATCCCATTTTTACCC-CGAACT
*
681 TCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTT-ACCCC-GAACT
* * **
711 TCTAAAAATCCCATTTTGACCCTAAAACT
1 TCCAAAAATCCCATTTTTACCC-CGAACT
* * *
740 TTCAAAAATTCCATTTTTACACCCGCACT
1 TCCAAAAATCCCATTTTTAC-CCCGAACT
*
769 TCCAAAAATCCCATTTTGACCCCGAAACT
1 TCCAAAAATCCCATTTTTACCCCG-AACT
*** *
798 TTTGAAAATTCCATTTTTACCCCCGAACT
1 TCCAAAAATCCCATTTTTA-CCCCGAACT
827 TCCAAAAATCCCATTTTTAACCCCGAA
1 TCCAAAAATCCCATTTTT-ACCCCGAA
854 TTTTCCCAAA
Statistics
Matches: 142, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 4 0.03
29 106 0.75
30 32 0.23
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (28 bp):
TCCAAAAATCCCATTTTTACCCCGAACT
Found at i:797 original size:58 final size:57
Alignment explanation
Indices: 652--853 Score: 244
Period size: 58 Copynumber: 3.5 Consensus size: 57
642 CCCTAAACCG
* * * *
652 TCCAAAAATCCCATTTTTACCCTCG-AACTTCCAAAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATCCCATTTTGACCC-CGAAACTTTCAAAAATTCCATTTTT-ACCCC-GAACT
* ** *
711 TCTAAAAATCCCATTTTGACCCTAAAACTTTCAAAAATTCCATTTTTACACCCGCACT
1 TCCAAAAATCCCATTTTGACCCCGAAACTTTCAAAAATTCCATTTTTAC-CCCGAACT
**
769 TCCAAAAATCCCATTTTGACCCCGAAACTTTTGAAAATTCCATTTTTACCCCCGAACT
1 TCCAAAAATCCCATTTTGACCCCGAAACTTTCAAAAATTCCATTTTTA-CCCCGAACT
*
827 TCCAAAAATCCCATTTTTAACCCCGAA
1 TCCAAAAATCCCA-TTTTGACCCCGAA
854 TTTTCCCAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
58 68 0.55
59 56 0.45
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (57 bp):
TCCAAAAATCCCATTTTGACCCCGAAACTTTCAAAAATTCCATTTTTACCCCGAACT
Found at i:2323 original size:12 final size:12
Alignment explanation
Indices: 2306--2348 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2296 ATGCTTAGGC
2306 TTAGAATTAATT
1 TTAGAATTAATT
*
2318 TTAGAATTAACCT
1 TTAGAATTAA-TT
* *
2331 TTAGAACTAGTT
1 TTAGAATTAATT
2343 TTAGAA
1 TTAGAA
2349 CTAGACTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (12 bp):
TTAGAATTAATT
Found at i:5237 original size:7 final size:7
Alignment explanation
Indices: 5218--5250 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
5208 AAGATTTATA
5218 ATTCAAG
1 ATTCAAG
5225 -TTCAAG
1 ATTCAAG
5231 ATTCAAG
1 ATTCAAG
*
5238 ATTCGAG
1 ATTCAAG
5245 ATTCAA
1 ATTCAA
5251 AGTTTAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (7 bp):
ATTCAAG
Found at i:9531 original size:19 final size:19
Alignment explanation
Indices: 9476--9532 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
9466 TTTTTAAAAA
*
9476 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
*
9494 TATAAATATTTTGACTTTT
1 TATAAATATTTTGAATTTT
9513 TGA-AAATTATTTT-AATTTT
1 T-ATAAA-TATTTTGAATTTT
9532 T
1 T
9533 TTATAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 7 0.21
19 19 0.58
20 7 0.21
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:9540 original size:20 final size:20
Alignment explanation
Indices: 9490--9540 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
9480 AATTTTGGAA
* *
9490 TTTTTATAAATATTTTGACT
1 TTTTTATAATTATTTTAACT
* * *
9510 TTTTGAAAATTATTTTAATT
1 TTTTTATAATTATTTTAACT
9530 TTTTTATAATT
1 TTTTTATAATT
9541 TTTGTTAAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATAATTATTTTAACT
Found at i:9720 original size:18 final size:20
Alignment explanation
Indices: 9697--9734 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
9687 TAACTCAACA
9697 TTTAAA-AAAATC-AATTTT
1 TTTAAATAAAATCGAATTTT
*
9715 TTTAAATCAAATCGAATTTT
1 TTTAAATAAAATCGAATTTT
9735 ACTCTCCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTAAATAAAATCGAATTTT
Found at i:11245 original size:15 final size:15
Alignment explanation
Indices: 11225--11261 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
11215 ATTGAGAATG
11225 TTTATTATTTTACTT
1 TTTATTATTTTACTT
* *
11240 TTTATTTTTTTATTT
1 TTTATTATTTTACTT
11255 TTTATTA
1 TTTATTA
11262 GTGGTTATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTATTATTTTACTT
Found at i:15573 original size:61 final size:62
Alignment explanation
Indices: 15477--15593 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 62
15467 CAGGTATTTT
* * *
15477 TTTATTCTACTTATGCTTCTATTTGAAGCAACTGGATTCTGTTATGTCTTTAATATATGCAA
1 TTTATTCTACTTATGCATCTAGTTAAAGCAACTGGATTCTGTTATGTCTTTAATATATGCAA
* * * *
15539 TTTATTCT-CTTATGCATCTGGTTAAAGTAACTGGATTCTGTTATTTCTTTGATAT
1 TTTATTCTACTTATGCATCTAGTTAAAGCAACTGGATTCTGTTATGTCTTTAATAT
15594 GGCTTTTCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 40 0.83
62 8 0.17
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (62 bp):
TTTATTCTACTTATGCATCTAGTTAAAGCAACTGGATTCTGTTATGTCTTTAATATATGCAA
Found at i:18355 original size:5 final size:6
Alignment explanation
Indices: 18339--18363 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18329 AAAACTGGCA
18339 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
18364 AATTTTCATA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:20729 original size:21 final size:21
Alignment explanation
Indices: 20685--20734 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
20675 ATTTAAGCTT
**
20685 TTTTTTTTTTAATTTCTCTCA
1 TTTTTTTTTTAATTTCTCGAA
* *
20706 TTTTTTTTTTATTTTTTCGAA
1 TTTTTTTTTTAATTTCTCGAA
*
20727 TTTGTTTT
1 TTTTTTTT
20735 ACACAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTTAATTTCTCGAA
Found at i:27942 original size:29 final size:29
Alignment explanation
Indices: 27867--27943 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
27857 TATGGATTTG
27867 AATTTTAAATTATGAAAAATTAAAAGATTA
1 AATTTTAAA-TATGAAAAATTAAAAGATTA
* *
27897 AATTTTTGAAA-AT-AAAAA-TATAATGATTC
1 AA-TTTT-AAATATGAAAAATTA-AAAGATTA
27926 AATTTTAAATATGAAAAA
1 AATTTTAAATATGAAAAA
27944 AGAATAAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
27 3 0.08
28 8 0.20
29 18 0.45
30 4 0.10
31 4 0.10
32 3 0.08
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.36
Consensus pattern (29 bp):
AATTTTAAATATGAAAAATTAAAAGATTA
Found at i:30462 original size:24 final size:24
Alignment explanation
Indices: 30431--30477 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
30421 CATAAATATA
*
30431 ATAAATATTTTATTATATTAAAAT
1 ATAAATATTTTAATATATTAAAAT
30455 ATAAATATTTTAATATATTAAAA
1 ATAAATATTTTAATATATTAAAA
30478 ACACAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAAATATTTTAATATATTAAAAT
Found at i:30485 original size:25 final size:24
Alignment explanation
Indices: 30433--30486 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
30423 TAAATATAAT
* * *
30433 AAATATTTTATTATATTAAAATAT
1 AAATATTTTAATATATTAAAACAC
30457 AAATATTTTAATATATTAAAAACAC
1 AAATATTTTAATATATT-AAAACAC
30482 AAATA
1 AAATA
30487 AATATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATATTTTAATATATTAAAACAC
Found at i:30498 original size:62 final size:61
Alignment explanation
Indices: 30404--30526 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 61
30394 TAAAAATATT
* *
30404 TATATTAAAAATACGACCATAAATATAATAAATATTTTATTATATTAAAATATAAATATTTTAA
1 TATATTAAAAACACGACAATAAATATAATAAATATTTTATTATATT-AAATA-AAAT-TTTTAA
30468 TATATTAAAAACAC-A-AATAAATATAATAAATATTTTATTATATTAAATAAAATTTTTAA
1 TATATTAAAAACACGACAATAAATATAATAAATATTTTATTATATTAAATAAAATTTTTAA
30527 GATTTTATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
59 6 0.11
60 4 0.07
61 5 0.09
62 28 0.49
63 1 0.02
64 13 0.23
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (61 bp):
TATATTAAAAACACGACAATAAATATAATAAATATTTTATTATATTAAATAAAATTTTTAA
Found at i:32485 original size:23 final size:23
Alignment explanation
Indices: 32455--32502 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
32445 TTACCGTACG
* *
32455 TGGTGGCAGATGACGATCGAGGA
1 TGGTGGCAGAGGACGATCGACGA
32478 TGGTGGCAGAGGACGATCGACGA
1 TGGTGGCAGAGGACGATCGACGA
32501 TG
1 TG
32503 AATAGGCGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.44, T:0.17
Consensus pattern (23 bp):
TGGTGGCAGAGGACGATCGACGA
Found at i:33195 original size:30 final size:29
Alignment explanation
Indices: 33159--33323 Score: 97
Period size: 30 Copynumber: 5.5 Consensus size: 29
33149 CTGAATTGTT
33159 CAAAAATCT-CATTTTAACCCCAAAACTTTC
1 CAAAAAT-TACATTTTAACCCC-AAACTTTC
* *
33189 CAAAAATTATATTTTAACCCCCTAAC-TTC
1 CAAAAATTACATTTTAA-CCCCAAACTTTC
* *
33218 ATAAAAATTACATTTTTACCCTCAAACTTTC
1 -CAAAAATTACATTTTAACCC-CAAACTTTC
* * * *
33249 CAAAAAAAATATATTTTGACCCTCGAAC-TTC
1 C--AAAAATTACATTTTAACCC-CAAACTTTC
* * *
33280 ATAAAAATTATATTTT-ACCCCTGAAC-TTC
1 -CAAAAATTACATTTTAACCCC-AAACTTTC
33309 CAAAAATTACCATTT
1 CAAAAATTA-CATTT
33324 ACCCTTGAAT
Statistics
Matches: 110, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
28 9 0.08
29 22 0.20
30 48 0.44
31 10 0.09
32 21 0.19
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTAACCCCAAACTTTC
Found at i:33253 original size:60 final size:60
Alignment explanation
Indices: 33160--33317 Score: 180
Period size: 62 Copynumber: 2.6 Consensus size: 60
33150 TGAATTGTTC
* *
33160 AAAAATCT-CATTTTAACCCCAAAACTTTCCAAAAATTATATTTTAACCCCCTAACTTCAT
1 AAAAAT-TACATTTTTACCCCAAAACTTTCCAAAAATTATATTTTAACCCCCGAACTTCAT
* * *
33220 AAAAATTACATTTTTACCCTC-AAACTTTCCAAAAAAAATATATTTTGACCCTCGAACTTCAT
1 AAAAATTACATTTTTACCC-CAAAACTTTCC--AAAAATTATATTTTAACCCCCGAACTTCAT
* **
33282 AAAAATTATA-TTTTACCCCTGAAC-TTCCAAAAATTA
1 AAAAATTACATTTTTACCCCAAAACTTTCCAAAAATTA
33318 CCATTTACCC
Statistics
Matches: 85, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
58 7 0.08
59 1 0.01
60 30 0.35
61 12 0.14
62 35 0.41
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (60 bp):
AAAAATTACATTTTTACCCCAAAACTTTCCAAAAATTATATTTTAACCCCCGAACTTCAT
Found at i:33265 original size:32 final size:30
Alignment explanation
Indices: 33190--33299 Score: 123
Period size: 30 Copynumber: 3.6 Consensus size: 30
33180 AAAACTTTCC
* * *
33190 AAAAATTATATTTTAACCCCCTAACTTCAT
1 AAAAATTATATTTTTACCCTCAAACTTCAT
* *
33220 AAAAATTACATTTTTACCCTCAAACTTTCCAA
1 AAAAATTATATTTTTACCCTCAAAC-TT-CAT
* * *
33252 AAAAAATATATTTTGACCCTCGAACTTCAT
1 AAAAATTATATTTTTACCCTCAAACTTCAT
33282 AAAAATTATA-TTTTACCC
1 AAAAATTATATTTTTACCC
33300 CTGAACTTCC
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
29 7 0.11
30 32 0.48
31 4 0.06
32 23 0.35
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAAATTATATTTTTACCCTCAAACTTCAT
Found at i:33323 original size:29 final size:28
Alignment explanation
Indices: 33268--33332 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
33258 TATATTTTGA
* *
33268 CCCTCGAACTTCATAAAAATTATATTTTAC
1 CCCT-GAACTTCACAAAAATTACA-TTTAC
33298 CCCTGAACTTC-CAAAAATTACCATTTAC
1 CCCTGAACTTCACAAAAATTA-CATTTAC
*
33326 CCTTGAA
1 CCCTGAA
33333 TTTTCTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 19 0.61
29 8 0.26
30 4 0.13
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (28 bp):
CCCTGAACTTCACAAAAATTACATTTAC
Found at i:37987 original size:28 final size:28
Alignment explanation
Indices: 37956--38016 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
37946 AAAATGTGAT
* *
37956 TTTTGGATACCCG-AGAGTAAAATAGTAA
1 TTTTGGACACCCGAAG-GCAAAATAGTAA
* *
37984 TTTTGGACACTCGAAGGCAAAATGGTAA
1 TTTTGGACACCCGAAGGCAAAATAGTAA
38012 TTTTG
1 TTTTG
38017 AGAATGTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (28 bp):
TTTTGGACACCCGAAGGCAAAATAGTAA
Found at i:38094 original size:58 final size:59
Alignment explanation
Indices: 38002--38485 Score: 555
Period size: 58 Copynumber: 8.3 Consensus size: 59
37992 ACTCGAAGGC
*** * * *
38002 AAAATGGTAA-TTTTGAGAATGTTCAGAGTTAAAAATGGAATTTTAGGCA-TTCGAGGGT
1 AAAATGGTAATTTTTG-GAAAAATCAGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
*
38060 AAAATGGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTA-GAAGTTT-AGGGT
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAA-TTTTAGGAAGTTTGAGGGT
* * *
38118 AAATTGGTAATTTTGGGGAAAATC-GAGGTTAAAAATGGAA-TTTAGGGAAGTTTG-GGGT
1 AAAATGGTAATTTTTGGAAAAATCAG-GGTTAAAAATGGAATTTTA-GGAAGTTTGAGGGT
* * *
38176 AAAATGGTAATTTTTGGAAAAATTAGGGTTAAAAATGGAATTTTTGGAAGTTTAAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
* * *
38235 AAAATGGTAATTTTTGGAAAAATAATGG-TAAAAATGGAATTTTGGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
*
38293 AAAATGGTAATTTTTGGAAAAATC-GAGGTTAAAAATGGAATTTTTA-GAAGTTTAAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAG-GGTTAAAAATGGAA-TTTTAGGAAGTTTGAGGGT
* *** ** * * *
38352 AAAATGGTATTTTTTGGAAGTTTTGGGGTCAAAAATAGAATTTT-GGAAG-TTCAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
*
38409 AAAAAT-GTAATTTTTGGAAAAATTAGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
1 -AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
38468 AAAAAT-GTAATTTTTGGA
1 -AAAATGGTAATTTTTGGA
38486 TTGTTTAGAG
Statistics
Matches: 367, Mismatches: 41, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
56 4 0.01
57 39 0.11
58 194 0.53
59 125 0.34
60 5 0.01
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
Found at i:38317 original size:175 final size:176
Alignment explanation
Indices: 38029--38485 Score: 606
Period size: 175 Copynumber: 2.6 Consensus size: 176
38019 AATGTTCAGA
* * ** *
38029 GTTAAAAATGGAATTTTAGGCA-TTCGAGGGTAAAATGGTAATTTTTGGAAAAATCAGGGTCAAA
1 GTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATAAGGGT-AAA
* * *
38093 AATGGAATTTTTA-GAAGTTT-AGGGTAAATTGGTAATTTTGGGGAAAATCGAGGTTAAAAATGG
65 AATGGAA-TTTTAGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGG
* *
38156 AATTTAGGGAAGTTT-GGGGTAAAATGGTAATTTTTGGAAAAATTAGG
129 AATTTAGAGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATTAGG
*
38203 GTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATAATGGTAAAA
1 GTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATAAGGGTAAAA
*
38268 ATGGAATTTTGGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAA
66 ATGGAATTTTAGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAA
** * *** *
38333 TTTTTAGAAGTTTAAGGGTAAAATGGTATTTTTTGGAAGTTTTGGG
131 TTTAGAGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATTAGG
* * * *
38379 GTCAAAAATAGAA-TTTTGGAAG-TTCAGGGTAAAAAT-GTAATTTTTGGAAAAATTAGGGTTAA
1 GTTAAAAATGGAATTTTTGGAAGTTTAAGGGT-AAAATGGTAATTTTTGGAAAAATAAGGG-TAA
38441 AAATGGAATTTTAGGAAGTTTGAGGGTAAAAAT-GTAATTTTTGGA
64 AAATGGAATTTTAGGAAGTTTGAGGGT-AAAATGGTAATTTTTGGA
38486 TTGTTTAGAG
Statistics
Matches: 251, Mismatches: 25, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
173 4 0.02
174 64 0.25
175 141 0.56
176 42 0.17
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (176 bp):
GTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATAAGGGTAAAA
ATGGAATTTTAGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAA
TTTAGAGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATTAGG
Found at i:39663 original size:13 final size:13
Alignment explanation
Indices: 39645--39674 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39635 ATTTATTTAT
39645 TTAATATTAAATA
1 TTAATATTAAATA
*
39658 TTAATATTAATTA
1 TTAATATTAAATA
39671 TTAA
1 TTAA
39675 AAGTTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAATATTAAATA
Found at i:39672 original size:20 final size:20
Alignment explanation
Indices: 39645--39690 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39635 ATTTATTTAT
39645 TTAA-TATTAAATA-TTAATA
1 TTAATTATTAAA-AGTTAATA
*
39664 TTAATTATTAAAAGTTATTA
1 TTAATTATTAAAAGTTAATA
39684 TTAATTA
1 TTAATTA
39691 CCGTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTAATTATTAAAAGTTAATA
Found at i:40375 original size:13 final size:13
Alignment explanation
Indices: 40357--40394 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
40347 TGGGTCTCAA
40357 TTGTAATTGGACT
1 TTGTAATTGGACT
*
40370 TTGTAATTGGATT
1 TTGTAATTGGACT
*
40383 TTTTAATTGGAC
1 TTGTAATTGGAC
40395 CTTTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (13 bp):
TTGTAATTGGACT
Found at i:40401 original size:12 final size:12
Alignment explanation
Indices: 40360--40402 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
40350 GTCTCAATTG
40360 TAATTGGACTTT
1 TAATTGGACTTT
*
40372 GTAATTGGATTTTT
1 -TAATTGGA-CTTT
*
40386 TAATTGGACCTT
1 TAATTGGACTTT
40398 TAATT
1 TAATT
40403 TAAAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 7 0.27
13 16 0.62
14 3 0.12
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (12 bp):
TAATTGGACTTT
Found at i:40419 original size:17 final size:17
Alignment explanation
Indices: 40399--40463 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
40389 TTGGACCTTT
40399 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* *
40416 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATTTA
* * *
40433 AATTAAAAATGAATTTG
1 AATTTAAAATAAATTTA
*
40450 AATTTAAAAAAAAT
1 AATTTAAAATAAAT
40464 CAATTATTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:46234 original size:1 final size:1
Alignment explanation
Indices: 46230--46258 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
46220 NNNNNNNNNN
46230 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46259 ATCTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46265 original size:11 final size:11
Alignment explanation
Indices: 46230--46274 Score: 58
Period size: 10 Copynumber: 4.3 Consensus size: 11
46220 NNNNNNNNNN
46230 TTTTTTTTT-T
1 TTTTTTTTTAT
46240 TTTTTTTTT-T
1 TTTTTTTTTAT
46250 TTTTTTTTTAT
1 TTTTTTTTTAT
* *
46261 CTTTTATTTAT
1 TTTTTTTTTAT
46272 TTT
1 TTT
46275 GCATGCATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 19 0.61
11 12 0.39
ACGTcount: A:0.07, C:0.02, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTAT
Found at i:49257 original size:21 final size:21
Alignment explanation
Indices: 49202--49289 Score: 74
Period size: 21 Copynumber: 4.2 Consensus size: 21
49192 AGGCTCGAGG
49202 TTTAATATTTAGGGTTTAAG--
1 TTTAA-ATTTAGGGTTTAAGAT
* *
49222 TTTAAGATTCAAGGGTTTAATAT
1 TTTAA-ATT-TAGGGTTTAAGAT
** **
49245 TTTAGGTTTAGGGTTCGAGAT
1 TTTAAATTTAGGGTTTAAGAT
49266 TTTAAATTTAGGGTTTAAG-T
1 TTTAAATTTAGGGTTTAAGAT
49286 TTTA
1 TTTA
49290 GAGTTAAAGA
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
20 13 0.25
21 33 0.63
22 2 0.04
23 4 0.08
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (21 bp):
TTTAAATTTAGGGTTTAAGAT
Found at i:50785 original size:16 final size:17
Alignment explanation
Indices: 50761--50804 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
50751 AATTTTTTAA
*
50761 AATTTTAAAATTAA-TT
1 AATTATAAAATTAATTT
*
50777 AATTATAAAAATAATTT
1 AATTATAAAATTAATTT
*
50794 AAATATAAAAT
1 AATTATAAAAT
50805 ATTATACGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTATAAAATTAATTT
Found at i:51434 original size:22 final size:21
Alignment explanation
Indices: 51395--51438 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
51385 AAGGATTATT
*
51395 TAAATTTAATTTCAAAATGAGA
1 TAAATTTAATATCAAAAT-AGA
**
51417 TAAATTTAATATGGAAATAGA
1 TAAATTTAATATCAAAATAGA
51438 T
1 T
51439 CAAAAGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (21 bp):
TAAATTTAATATCAAAATAGA
Found at i:77906 original size:9 final size:9
Alignment explanation
Indices: 77892--77934 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
77882 AAATTTAAAA
77892 ATTAAAATT
1 ATTAAAATT
77901 ATTAAAATT
1 ATTAAAATT
*
77910 ATTAAAAAGT
1 ATT-AAAATT
*
77920 ATGAAAATT
1 ATTAAAATT
77929 A-TAAAA
1 ATTAAAA
77935 AATACTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 4 0.14
9 18 0.62
10 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (9 bp):
ATTAAAATT
Found at i:77913 original size:18 final size:18
Alignment explanation
Indices: 77892--77934 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
77882 AAATTTAAAA
* *
77892 ATTAAAATTATTAAAATT
1 ATTAAAAGTATGAAAATT
77910 ATTAAAAAGTATGAAAATT
1 ATT-AAAAGTATGAAAATT
77929 A-TAAAA
1 ATTAAAA
77935 AATACTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 4 0.18
19 14 0.64
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
ATTAAAAGTATGAAAATT
Done.