Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014802.1 Kokia drynarioides strain JFW-HI SEQ_129844, 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: 52095
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Warning! 237 characters in sequence are not A, C, G, or T
Found at i:2369 original size:22 final size:22
Alignment explanation
Indices: 2343--2386 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2333 AGTTTATGAT
2343 TTTAAAATTAGGTTTAAATTTA
1 TTTAAAATTAGGTTTAAATTTA
* **
2365 TTTAAATTTATTTTTAAATTTA
1 TTTAAAATTAGGTTTAAATTTA
2387 AATTTATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTAAAATTAGGTTTAAATTTA
Found at i:2373 original size:6 final size:6
Alignment explanation
Indices: 2355--2447 Score: 61
Period size: 6 Copynumber: 15.8 Consensus size: 6
2345 TAAAATTAGG
**
2355 TTTAAA TTT--A TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
** * **
2400 TTTAAA TTTATCTT TTTAAA TTTAAA ATT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
2448 TCAAATTTGA
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
4 6 0.09
5 4 0.06
6 49 0.75
7 2 0.03
8 4 0.06
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:2400 original size:17 final size:18
Alignment explanation
Indices: 2364--2446 Score: 107
Period size: 17 Copynumber: 4.6 Consensus size: 18
2354 GTTTAAATTT
*
2364 ATTTAAATTTATTTTTAA
1 ATTTAAATTTATCTTTAA
2382 ATTTAAATTTATC-TTAA
1 ATTTAAATTTATCTTTAA
2399 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC--TTTAA
* *
2419 ATTTAAAATT-GCTTTAA
1 ATTTAAATTTATCTTTAA
2436 ATTTAAATTTA
1 ATTTAAATTTA
2447 ATCAAATTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
17 31 0.54
18 12 0.21
19 1 0.02
20 13 0.23
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (18 bp):
ATTTAAATTTATCTTTAA
Found at i:2409 original size:29 final size:28
Alignment explanation
Indices: 2355--2409 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
2345 TAAAATTAGG
**
2355 TTTAAATTTATTTAAATTTATTTTTAAA
1 TTTAAATTTATTTAAATTTAAATTTAAA
2383 TTTAAATTTATCTTAAATTTAAATTTA
1 TTTAAATTTAT-TTAAATTTAAATTTA
2410 TCTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTAAATTTATTTAAATTTAAATTTAAA
Found at i:2425 original size:37 final size:35
Alignment explanation
Indices: 2364--2446 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 35
2354 GTTTAAATTT
**
2364 ATTTAAATTTATTTTTAAATTT-AAATTTATCTTAA
1 ATTTAAATTTATTTTTAAATTTAAAATTGCT-TTAA
2399 ATTTAAATTTATCTTTTTAAATTTAAAATTGCTTTAA
1 ATTTAAATTTA--TTTTTAAATTTAAAATTGCTTTAA
2436 ATTTAAATTTA
1 ATTTAAATTTA
2447 ATCAAATTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 11 0.26
37 26 0.60
38 6 0.14
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (35 bp):
ATTTAAATTTATTTTTAAATTTAAAATTGCTTTAA
Found at i:2529 original size:14 final size:15
Alignment explanation
Indices: 2510--2539 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2500 AAATTAAATT
2510 AAAGTCC-AATTACA
1 AAAGTCCAAATTACA
2524 AAAGTCCAAATTACA
1 AAAGTCCAAATTACA
2539 A
1 A
2540 TGACCCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (15 bp):
AAAGTCCAAATTACA
Found at i:5705 original size:30 final size:29
Alignment explanation
Indices: 5662--5919 Score: 245
Period size: 30 Copynumber: 8.8 Consensus size: 29
5652 GAGGTCTTTA
*
5662 AACTTCCAAAATTTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
*
5691 AACTTCCAAAAATTTCATTTTTGA-CCCCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
* **
5720 AAACTTCCAAAAATTCCATTTTTGACCTCAA
1 -AACTTCCAAAAATTCCATTTTT-ACCCCCG
* **
5751 AACTTCCAAAAAATCCA-TTTTACCATCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* * *
5779 AAGTTCCAAAAATTCTATTTTTACCCCTG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
*
5808 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
*
5838 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
** *
5867 AAACTTCCAAAAACTAT-TTTTTTTACCCTCG
1 -AACTTCCAAAAA-T-TCCATTTTTACCCCCG
** *
5898 AACCACCAAAATTTCCATTTTT
1 AACTTCCAAAAATTCCATTTTT
5920 GATCCCGAAA
Statistics
Matches: 190, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
28 18 0.09
29 70 0.37
30 88 0.46
31 13 0.07
32 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:5858 original size:59 final size:59
Alignment explanation
Indices: 5662--5950 Score: 311
Period size: 59 Copynumber: 4.9 Consensus size: 59
5652 GAGGTCTTTA
* *
5662 AACTTCCAAAATTTCCATTTTT-ACCCCCG-AACTTCCAAAAATTTCATTTTTGACCC-CG
1 AACTTCCAAAAATTCCATTTTTGA-CCCCGAAACTTCCAAAAATTCCATTTTT-ACCCTCG
* * * *
5720 AAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAAATCCA-TTTTACCATCG
1 -AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* *
5779 AAGTTCCAAAAATTCTATTTTT-ACCCCTGAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCC-GAAACTTCCAAAAATTCCATTTTTACCCTCG
* **
5838 AACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAACTAT-TTTTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAA-T-TCCATTTTTACCCTCG
** * * ** *
5898 AACCACCAAAATTTCCATTTTTGATCCCGAAACTTTAAAAAATTAACATTTTT
1 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTT
5951 CCCCCGGATG
Statistics
Matches: 194, Mismatches: 26, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
57 4 0.02
58 41 0.21
59 75 0.39
60 73 0.38
61 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:5988 original size:59 final size:58
Alignment explanation
Indices: 5911--6021 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
5901 CACCAAAATT
* * * *
5911 TCCATTTTTGATCCCGAAACTTTAAAAAATTAACATTTTTCCCCCGGATGTCTTAAACC
1 TCCATTTTCGATCCCGAAACTCT-AAAAATTAACATTTTACCCCCGAATGTCTTAAACC
* * *
5970 TCCATTTTCGA-CCTCGAAACTCTCAAAATTACCCTTTTACCCCCGAATGTCT
1 TCCATTTTCGATCC-CGAAACTCTAAAAATTAACATTTTACCCCCGAATGTCT
6022 AAAAATTCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
58 26 0.59
59 18 0.41
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (58 bp):
TCCATTTTCGATCCCGAAACTCTAAAAATTAACATTTTACCCCCGAATGTCTTAAACC
Found at i:6035 original size:58 final size:58
Alignment explanation
Indices: 5936--6045 Score: 130
Period size: 58 Copynumber: 1.9 Consensus size: 58
5926 GAAACTTTAA
* * * * *
5936 AAAATTAACATTTTTCCCCCGGATGTCTTAAACCTCCATTTTCGACCTCGAAACTCTC
1 AAAATTAACATTTTACCCCCGAATGTCTAAAAACTCCATTTTCAACCTCGAAACTCTC
* * * * *
5994 AAAATTACCCTTTTACCCCCGAATGTCTAAAAATTCTATTTTTAACCTCGAA
1 AAAATTAACATTTTACCCCCGAATGTCTAAAAACTCCATTTTCAACCTCGAA
6046 CTTTCCCAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 42 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (58 bp):
AAAATTAACATTTTACCCCCGAATGTCTAAAAACTCCATTTTCAACCTCGAAACTCTC
Found at i:10373 original size:22 final size:21
Alignment explanation
Indices: 10332--10374 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
10322 CCTAGACAAA
*
10332 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
10353 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
10375 GCAGGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:19569 original size:22 final size:21
Alignment explanation
Indices: 19528--19570 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
19518 CCTAGACAAA
*
19528 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
19549 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
19571 GCAGGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:27376 original size:47 final size:47
Alignment explanation
Indices: 27322--27437 Score: 223
Period size: 47 Copynumber: 2.5 Consensus size: 47
27312 GAACCCCAGG
27322 TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
1 TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
27369 TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
1 TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
*
27416 TTCCTGATGAGATACTGAGAAG
1 TTCCTGATGAGACACTGAGAAG
27438 TGGACCAAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.22
Consensus pattern (47 bp):
TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
Found at i:27570 original size:252 final size:252
Alignment explanation
Indices: 27117--27632 Score: 915
Period size: 252 Copynumber: 2.0 Consensus size: 252
27107 GAACCCCAGG
* * * * *
27117 TTCCTAATGAGACATTGAGAAGCAGGTCGAAGTAATAAAAGGTTAGCTTTCTGATGAGATGCTAA
1 TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTAA
27182 GAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTC
66 GAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTC
* *
27247 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTT
131 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCTTC
*
27312 GAACCCCAGGTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
196 GAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
* *
27369 TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGCTTCCTGATGAGATACTGA
1 TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTAA
* *
27434 GAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAAACAAACGACGCGGTC
66 GAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTC
27499 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCTTC
131 ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCTTC
*
27564 GAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
196 GAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
27621 TTCCTGATGAGA
1 TTCCTGATGAGA
27633 TACAAAGAAG
Statistics
Matches: 251, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
252 251 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (252 bp):
TTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTAA
GAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTC
ATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCTTC
GAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGTTAGC
Found at i:27736 original size:168 final size:169
Alignment explanation
Indices: 27452--27804 Score: 555
Period size: 168 Copynumber: 2.1 Consensus size: 169
27442 CCAAATTCGT
* * * * *
27452 CTTCCTGATGAGATATAGAGAAGCGAATTGAAACAAACGACGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAAAGAAGCAAATTGAAACAAACGACGCGATCATCTTCCTGATGAGAGAC
* *
27517 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCTTCGAACCCCAGCTTCCTGAT
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCCTCGAACCCCAGCTTCCTAAT
*
27582 GAGACATTGAGAAGCAGGTCGAAGCAATAAAAT-GTTAG
131 GAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
* *
27620 CTTCCTGATGAGATACAAAGAAGCAAATTGAAACAAATGACTCGATCATCTTCCTGATGAGAGAC
1 CTTCCTGATGAGATACAAAGAAGCAAATTGAAACAAACGACGCGATCATCTTCCTGATGAGAGAC
* *
27685 TGAGAAGAAGACCAAATCAAATCCACGCTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTAAT
66 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCCTCGAACCCCAGCTTCCTAAT
* * * *
27750 GAGATACTGAGAAGTAGGTTGAAGTAATAAAATGGTTAG
131 GAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
27789 CTTCCTGATGAGATAC
1 CTTCCTGATGAGATAC
27805 TGAGAATTGA
Statistics
Matches: 168, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
168 147 0.88
169 21 0.12
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (169 bp):
CTTCCTGATGAGATACAAAGAAGCAAATTGAAACAAACGACGCGATCATCTTCCTGATGAGAGAC
TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAACAAATCCTCGAACCCCAGCTTCCTAAT
GAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAG
Found at i:27983 original size:206 final size:206
Alignment explanation
Indices: 27620--28052 Score: 645
Period size: 206 Copynumber: 2.1 Consensus size: 206
27610 AAAATGTTAG
* * *
27620 CTTCCTGATGAGATACAAAGAAGCAAATTGAAACAAATGACTCGATCATCTTCCTGATGAGAGAC
1 CTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAATGACGCGATCATCTTCCTGATGAGACAC
* *
27685 TGAGAAGAAGACCAAATCAAATCCACGCTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTAAT
66 AGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTAAT
* ** * * *
27750 GAGATACTGAGAAGTAGGTTGAAGTAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAATTGA
131 GAGATACTGAGAAGCAGGTCAAAGTAATAAAATGGTTAGCTTCCTGATGAAATACGGAGAAGTGA
* *
27815 ACCAAATTCGT
196 ACCAAAATCAT
* ** *
27826 CTTCCTGTTGAGATACAGAGAAGCGGATTGAAACAAATGACGCGGTCATCTTCCTGATGAGACAC
1 CTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAATGACGCGATCATCTTCCTGATGAGACAC
* * *
27891 AGA-AGAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTTGA
66 AGAGA-AGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTAA
*
27955 TGAGATACTGAGAAGCAGGTCAAAGTAATAAAATGGTTAGCTTCCTGATGAAATACGGGGAAGTG
130 TGAGATACTGAGAAGCAGGTCAAAGTAATAAAATGGTTAGCTTCCTGATGAAATACGGAGAAGTG
28020 AACCAAAATCAT
195 AACCAAAATCAT
*
28032 CTTCCTGATGA-AAACAGAGAA
1 CTTCCTGATGAGATACAGAGAA
28053 ATGGATCAAA
Statistics
Matches: 203, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
205 10 0.05
206 193 0.95
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (206 bp):
CTTCCTGATGAGATACAGAGAAGCAAATTGAAACAAATGACGCGATCATCTTCCTGATGAGACAC
AGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCCTCGAACCCCAGCTTCCTAAT
GAGATACTGAGAAGCAGGTCAAAGTAATAAAATGGTTAGCTTCCTGATGAAATACGGAGAAGTGA
ACCAAAATCAT
Found at i:28489 original size:6 final size:6
Alignment explanation
Indices: 28468--28530 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
28458 TTTAAATTGG
** **
28468 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTT-GC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
28514 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
28531 TCAAATTTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
4 2 0.04
5 5 0.11
6 36 0.80
7 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:28503 original size:17 final size:17
Alignment explanation
Indices: 28468--28529 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
28458 TTTAAATTGG
*
28468 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TCTTAAA
28486 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
28503 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATC-TTAAA
28520 TTTAAATTTA
1 TTTAAATTTA
28530 ATCAAATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.03
17 29 0.73
18 10 0.25
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:29297 original size:10 final size:10
Alignment explanation
Indices: 29282--29383 Score: 50
Period size: 10 Copynumber: 10.4 Consensus size: 10
29272 ATAATTTCAT
29282 TAATAATTAA
1 TAATAATTAA
29292 TAATAA-TAA
1 TAATAATTAA
*
29301 TAATAATAAA
1 TAATAATTAA
* *
29311 TAACAAATTTA
1 TAA-TAATTAA
* *
29322 TGATAA-TGA
1 TAATAATTAA
*
29331 TAGTAA-TAA
1 TAATAATTAA
*
29340 GTATTAA-TAA
1 -TAATAATTAA
* *
29350 CAGTAATTAA
1 TAATAATTAA
** *
29360 TAATACCTAC
1 TAATAATTAA
29370 TAATAATTAA
1 TAATAATTAA
29380 TAAT
1 TAAT
29384 TAATATTTAG
Statistics
Matches: 67, Mismatches: 21, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
9 21 0.31
10 40 0.60
11 6 0.09
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (10 bp):
TAATAATTAA
Found at i:30505 original size:30 final size:29
Alignment explanation
Indices: 30437--30662 Score: 229
Period size: 30 Copynumber: 7.7 Consensus size: 29
30427 CCCTGGAGGT
* *
30437 CCCGAAACTTCAAAAAATTCCAGTTTTAC
1 CCCGAAACTTCCAAAAATTCCATTTTTAC
*
30466 CCTCG-AACTTCCAAAAATTCTATTTTTGAC
1 CC-CGAAACTTCCAAAAATTCCATTTTT-AC
**
30496 ATCGAAACTTCCAAAAATTCCATTTTTGAC
1 CCCGAAACTTCCAAAAATTCCATTTTT-AC
* *
30526 CCCGTAACTTCCAAAAATTCCCTTTTTACC
1 CCCGAAACTTCCAAAAATTCCATTTTTA-C
* * ** *
30556 CCCAAAACTTCTAAAAATAACTTTTTTAC
1 CCCGAAACTTCCAAAAATTCCATTTTTAC
*
30585 CCCCAAACTTCCAAAAATTCCATTTTTAC
1 CCCGAAACTTCCAAAAATTCCATTTTTAC
** *
30614 CCTTAAACTTCCAAAAATTTCATTTTTGAC
1 CCCGAAACTTCCAAAAATTCCATTTTT-AC
* * *
30644 CTCAAAACTTTCAAAAATT
1 CCCGAAACTTCCAAAAATT
30663 ACAATTTTGC
Statistics
Matches: 164, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
29 73 0.45
30 91 0.55
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCGAAACTTCCAAAAATTCCATTTTTAC
Found at i:30640 original size:59 final size:59
Alignment explanation
Indices: 30441--30662 Score: 216
Period size: 59 Copynumber: 3.8 Consensus size: 59
30431 GGAGGTCCCG
* * * * * * *
30441 AAACTTCAAAAAATTCCAGTTTT-ACCCTCGAACTTCCAAAAATTCTATTTTTGA-CATCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATTCCATTTTT-ACCCT-A
** * *
30500 AAACTTCCAAAAATTCCATTTTTGACCCCGTAACTTCCAAAAATTCCCTTTTTACCCCCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATTCCATTTTTA-CCCTA
* ** * *
30560 AAACTTCTAAAAATAAC-TTTTTTACCCCCAAACTTCCAAAAATTCCATTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATTCCATTTTTACCCTA
* * * *
30618 AAACTTCCAAAAATTTCATTTTTGACCTCAAAACTTTCAAAAATT
1 AAACTTCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATT
30663 ACAATTTTGC
Statistics
Matches: 133, Mismatches: 26, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
58 17 0.13
59 77 0.58
60 38 0.29
61 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATTCCATTTTTACCCTA
Found at i:30697 original size:59 final size:58
Alignment explanation
Indices: 30634--30794 Score: 153
Period size: 59 Copynumber: 2.7 Consensus size: 58
30624 CCAAAAATTT
* * *
30634 CATTTTTGACCTCAAAACTTTCAAAAATTACAATTTTGCCCTCGGATGTCTGAAAACTC
1 CATTTTTGACCTCAAAACTTTC-AAAATTACCATTTTGCCCCCGGATGTCTAAAAACTC
* * ** * * * * *
30693 CATTTTCGATCTTGAAACTCTCAAAATTACCCTTTTACCCCCGTATGTCTAAAAATTC
1 CATTTTTGACCTCAAAACTTTCAAAATTACCATTTTGCCCCCGGATGTCTAAAAACTC
* * *
30751 TATTTTTAACC-CCAAACTTTCTCAAAATTACCATTTTGCCCCCG
1 CATTTTTGACCTCAAAAC-TT-TCAAAATTACCATTTTGCCCCCG
30795 AGAATCCAAA
Statistics
Matches: 79, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
57 4 0.05
58 37 0.47
59 38 0.48
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.35
Consensus pattern (58 bp):
CATTTTTGACCTCAAAACTTTCAAAATTACCATTTTGCCCCCGGATGTCTAAAAACTC
Found at i:45833 original size:175 final size:168
Alignment explanation
Indices: 45521--45866 Score: 469
Period size: 175 Copynumber: 2.0 Consensus size: 168
45511 ATTTATACCT
* * * * * * *
45521 AAAATGTAATGAGAAAAAAATGCCAATAGTACATTTTCACAATCTTAAGTCAATATGTAAGTTGT
1 AAAATGTAAAGAGAAAAAAATGCAAATAATAAATTTTCACAATCTTAAGTCAATATGCAAATTAT
* * * *
45586 TTTTCAAATGAGTTCATATAACATATTTAATCAAAACGTGAGAAAATTGTATCTTTTGAGTTAAT
66 TTTTCAAATGAATTCATATAACATATTTAATCAAAACCTAAGAAAATCGTATCTTTTGAGTTAAT
45651 CCAAACATTTTTTTTAGTAAAAAAATATTATTAAAATATTAAA
131 CCAAACA--TTTTTTA--AAAAAAATATTATT-AAATATTAAA
* * *
45694 AAAATTGTAAAGAGAAAAAAAATTCAAATAATAAATTTTCACAATCTTGAGTTAATATGCAAATT
1 AAAA-TGTAAAGAG-AAAAAAATGCAAATAATAAATTTTCACAATCTTAAGTCAATATGCAAATT
*
45759 ATTTTTCAAATGAATTCGTATAACATATTTAATCAAAACCTAAGAAAATCGTATCTTTTGAGTTA
64 ATTTTTCAAATGAATTCATATAACATATTTAATCAAAACCTAAGAAAATCGTATCTTTTGAGTTA
*
45824 A-CTCAAACATTTTTTAATAAAAATATTATTAAATATTAAA
129 ATC-CAAACATTTTTTAAAAAAAATATTATTAAATATTAAA
45864 AAA
1 AAA
45867 TATTTATTTT
Statistics
Matches: 154, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
170 13 0.08
171 13 0.08
173 11 0.07
174 9 0.06
175 108 0.70
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (168 bp):
AAAATGTAAAGAGAAAAAAATGCAAATAATAAATTTTCACAATCTTAAGTCAATATGCAAATTAT
TTTTCAAATGAATTCATATAACATATTTAATCAAAACCTAAGAAAATCGTATCTTTTGAGTTAAT
CCAAACATTTTTTAAAAAAAATATTATTAAATATTAAA
Found at i:45957 original size:2 final size:2
Alignment explanation
Indices: 45950--45975 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45940 TATCAAAATC
45950 TA 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
45976 GTTCAATCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.