Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012637.1 Kokia drynarioides strain JFW-HI SEQ_127647, 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: 30154
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:12 original size:3 final size:3
Alignment explanation
Indices: 5--34 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1 TTCT
5 TAA TAA TAA TAA TAA TAA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
35 TGATTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:40 original size:12 final size:13
Alignment explanation
Indices: 5--44 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
1 TTCT
5 TAATAATAA-TAA
1 TAATAATAATTAA
17 TAATAATAATTAA
1 TAATAATAATTAA
*
30 TAAT-ATGATTAA
1 TAATAATAATTAA
42 TAA
1 TAA
45 AAGAAAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
TAATAATAATTAA
Found at i:1175 original size:29 final size:28
Alignment explanation
Indices: 1131--1382 Score: 233
Period size: 29 Copynumber: 8.6 Consensus size: 28
1121 CCCTAAGTTG
* *
1131 TCCAAAAATTCTATTTTTACCTTCGAACT
1 TCCAAAAATTCCATTTTTACC-CCGAACT
1160 TCCAAAAATTCCATTTTTAGCCCCGAACT
1 TCCAAAAATTCCATTTTTA-CCCCGAACT
*
1189 TCCAAAAA-TCTCGTTTTTGACCCCGAAACT
1 TCCAAAAATTC-CATTTTT-ACCCCG-AACT
1219 TCCAAAAATTCCATTTTTAGCCCCGAACT
1 TCCAAAAATTCCATTTTTA-CCCCGAACT
*
1248 TCCAAAAATTCCATTTTTGACGCCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCG-AACT
* *
1278 TCCTAAAATTACCA-TTTTACCCTCGGA-T
1 TCCAAAAATT-CCATTTTTACCC-CGAACT
* * *
1306 GTCCAAAAACTCCATTTTCGACCTCGTAACT
1 -TCCAAAAATTCCATTTT-TACCCCG-AACT
* * *
1337 TCCTAAAATTACCA-TTTTACCCCCAAAT
1 TCCAAAAATT-CCATTTTTACCCCGAACT
1365 ATCCAAAAATTCCATTTT
1 -TCCAAAAATTCCATTTT
1383 CGTCCTCGAA
Statistics
Matches: 185, Mismatches: 20, Indels: 36
0.77 0.08 0.15
Matches are distributed among these distances:
28 12 0.06
29 103 0.56
30 61 0.33
31 9 0.05
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (28 bp):
TCCAAAAATTCCATTTTTACCCCGAACT
Found at i:1228 original size:59 final size:61
Alignment explanation
Indices: 1131--1468 Score: 268
Period size: 59 Copynumber: 5.8 Consensus size: 61
1121 CCCTAAGTTG
* *
1131 TCCAAAAAT-TCTATTTTT-ACCTTCG-AACTTCCAAAAATT-CCATTTTTAGCCCCGAACT
1 TCCAAAAATCTCCATTTTTGACC-CCGAAACTTCCAAAAATTACCATTTTTAGCCCCGAACT
*
1189 TCCAAAAATCT-CGTTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTTAGCCCCGAACT
1 TCCAAAAATCTCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTTAGCCCCGAACT
* * *
1248 TCCAAAAAT-TCCATTTTTGACGCCGAAACTTCCTAAAATTACCA-TTTTA-CCCTCGGA-T
1 TCCAAAAATCTCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTTAGCCC-CGAACT
* * * * * *
1306 GTCCAAAAA-CTCCATTTTCGACCTCGTAACTTCCTAAAATTACCA-TTTTA-CCCCCAAAT
1 -TCCAAAAATCTCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTTAGCCCCGAACT
* * * * * *
1365 ATCCAAAAAT-TCCATTTTCGTCCTCGAAAC-TCTC-AAAATTACC-CTTTTA-CCCCTAA-G
1 -TCCAAAAATCTCCATTTTTGACCCCGAAACTTC-CAAAAATTACCATTTTTAGCCCCGAACT
* * * **
1422 TCTAAAAAT-TCCATTTTTAACCCTGAATTTTCTC-AAAATTACCATTT
1 TCCAAAAATCTCCATTTTTGACCCCGAAACTTC-CAAAAATTACCATTT
1469 CACCCCCGAG
Statistics
Matches: 239, Mismatches: 27, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
56 21 0.09
57 13 0.05
58 47 0.20
59 155 0.65
60 3 0.01
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.34
Consensus pattern (61 bp):
TCCAAAAATCTCCATTTTTGACCCCGAAACTTCCAAAAATTACCATTTTTAGCCCCGAACT
Found at i:1311 original size:88 final size:89
Alignment explanation
Indices: 1129--1382 Score: 242
Period size: 88 Copynumber: 2.9 Consensus size: 89
1119 GTCCCTAAGT
*
1129 TGTCCAAAAATTCTATTTTTA-CCTTCGAACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCCA
1 TGTCCAAAAATTCCATTTTTAGCC-TCGAACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCCA
**
1193 AAAATCTCGTTTTTGACCCCGAAAC
65 AAAATCTCCATTTTGACCCCGAAAC
* *
1218 T-TCCAAAAATTCCATTTTTAGCCCCGAACTTCCAAAAATTCCATTTTT-GACGCCGAAACTTCC
1 TGTCCAAAAATTCCATTTTTAGCCTCGAACTTCCAAAAATTCCATTTTTAG-CCCCG-AACTTCC
* *
1281 TAAAAT-TACCATTTT-ACCCTCG-GA-
64 AAAAATCT-CCATTTTGACCC-CGAAAC
* * * * *
1305 TGTCCAAAAACTCCA-TTTTCGACCTCGTAACTTCCTAAAATTACCA-TTTTA-CCCCCAAATAT
1 TGTCCAAAAATTCCATTTTTAG-CCTCG-AACTTCCAAAAATT-CCATTTTTAGCCCCGAACT-T
1367 CCAAAAAT-TCCATTTT
62 CCAAAAATCTCCATTTT
1383 CGTCCTCGAA
Statistics
Matches: 139, Mismatches: 15, Indels: 24
0.78 0.08 0.13
Matches are distributed among these distances:
87 17 0.12
88 80 0.58
89 39 0.28
90 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.33
Consensus pattern (89 bp):
TGTCCAAAAATTCCATTTTTAGCCTCGAACTTCCAAAAATTCCATTTTTAGCCCCGAACTTCCAA
AAATCTCCATTTTGACCCCGAAAC
Found at i:13247 original size:6 final size:6
Alignment explanation
Indices: 13238--13335 Score: 69
Period size: 6 Copynumber: 16.5 Consensus size: 6
13228 GTTTAAGTTT
* * *
13238 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTA--A
* * * **
13287 TTTTAA ATTTAA ATTT-G CTTTAA ATTTAA ATTT-A ATCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
13333 ATT
1 ATT
13336 GATATTAAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
4 2 0.03
5 8 0.12
6 53 0.77
7 2 0.03
8 4 0.06
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:13274 original size:17 final size:17
Alignment explanation
Indices: 13238--13346 Score: 105
Period size: 17 Copynumber: 6.2 Consensus size: 17
13228 GTTTAAGTTT
*
13238 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
13256 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
13273 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTATC---TTAA
*
13293 ATTTAAATTT-GCTTTAA
1 ATTTAAATTTATC-TTAA
*
13310 ATTTAAATTTAATC-AAA
1 ATTTAAATTT-ATCTTAA
* *
13327 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
13344 ATT
1 ATT
13347 AAAAACCCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.03
17 49 0.63
18 11 0.14
19 2 0.03
20 14 0.18
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:13283 original size:29 final size:28
Alignment explanation
Indices: 13229--13283 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
13219 TTAAGTTGGG
* **
13229 TTTAAGTTTATTTAAATTTATTTTTAAA
1 TTTAAATTTATTTAAATTTAAATTTAAA
13257 TTTAAATTTATCTTAAATTTAAATTTA
1 TTTAAATTTAT-TTAAATTTAAATTTA
13284 TCTTTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTAAATTTATTTAAATTTAAATTTAAA
Found at i:13297 original size:37 final size:35
Alignment explanation
Indices: 13238--13320 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 35
13228 GTTTAAGTTT
*
13238 ATTTAAATTTATTTTTAAATTTAAATTT-ATCTTAA
1 ATTTAAATTTATTTTTAAATTTAAATTTGCT-TTAA
13273 ATTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAA
1 ATTTAAATTTA--TTTTTAAATTTAAATTTGCTTTAA
13310 ATTTAAATTTA
1 ATTTAAATTTA
13321 ATCAAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 11 0.25
37 32 0.73
38 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
ATTTAAATTTATTTTTAAATTTAAATTTGCTTTAA
Found at i:13350 original size:23 final size:23
Alignment explanation
Indices: 13305--13350 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
13295 TTAAATTTGC
* *
13305 TTTAAATTTAAATTTAATCAAAA
1 TTTAAATTGAAATTAAATCAAAA
* *
13328 TTTAAATTGATATTAAATTAAAA
1 TTTAAATTGAAATTAAATCAAAA
13351 ACCCAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAATTGAAATTAAATCAAAA
Found at i:14084 original size:10 final size:10
Alignment explanation
Indices: 14055--14112 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
14045 ATAAATAAGC
14055 AATAAATATGT
1 AATAAATAT-T
14066 AATAAATATT
1 AATAAATATT
*
14076 AAAAAATATT
1 AATAAATATT
*
14086 AATAAATAAT
1 AATAAATATT
* *
14096 -ATTAATAAT
1 AATAAATATT
14105 AATAAATA
1 AATAAATA
14113 AATAAAGGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
9 8 0.20
10 24 0.59
11 9 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
AATAAATATT
Found at i:14096 original size:13 final size:13
Alignment explanation
Indices: 14075--14117 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
14065 TAATAAATAT
*
14075 TAAAAAATATTAA
1 TAAATAATATTAA
14088 TAAATAATATTAA
1 TAAATAATATTAA
14101 T-AATAATA--AA
1 TAAATAATATTAA
14111 TAAATAA
1 TAAATAA
14118 AGGGAGTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 3 0.11
11 5 0.18
12 7 0.25
13 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAATATTAA
Found at i:14100 original size:23 final size:23
Alignment explanation
Indices: 14070--14117 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
14060 ATATGTAATA
14070 AATATTAA-AA-AATATTAATAAAT
1 AATATTAATAATAATA--AATAAAT
14093 AATATTAATAATAATAAATAAAT
1 AATATTAATAATAATAAATAAAT
14116 AA
1 AA
14118 AGGGAGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 17 0.74
24 2 0.09
25 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATATTAATAATAATAAATAAAT
Found at i:14730 original size:53 final size:53
Alignment explanation
Indices: 14672--14777 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 53
14662 AAAAGAAAAG
14672 AGAAAATG-AAAAAAAAGCTTAAAGCATGTCTTATATAGGCTTCCAAAACGGC
1 AGAAAATGAAAAAAAAAGCTTAAAGCATGTCTTATATAGGCTTCCAAAACGGC
14724 NAGAAAATGAAAAAAAAAGCTTAAAGCATGTCTTATATAGGCTTCCAAAACGGC
1 -AGAAAATGAAAAAAAAAGCTTAAAGCATGTCTTATATAGGCTTCCAAAACGGC
14778 GTCGTTTTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 8 0.15
54 44 0.85
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.21
Consensus pattern (53 bp):
AGAAAATGAAAAAAAAAGCTTAAAGCATGTCTTATATAGGCTTCCAAAACGGC
Found at i:15275 original size:29 final size:29
Alignment explanation
Indices: 15224--15509 Score: 328
Period size: 29 Copynumber: 9.8 Consensus size: 29
15214 GAAAGTATCT
*
15224 AAACTGTCCGAAAATTCCATTTTTACCCTC
1 AAACT-TCCAAAAATTCCATTTTTACCCTC
* *
15254 GAACTTCCAAAAATTACATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
**
15283 AAACTTCCAAAAATTATATTTTTA-CCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
15311 AAAACTTCCAAAAATTCCATTTTTACCC-C
1 -AAACTTCCAAAAATTCCATTTTTACCCTC
* *
15340 TGAACTTCCAAAAATTCCATTTTTGACTCC-A
1 -AAACTTCCAAAAATTCCATTTTT-AC-CCTC
* * *
15371 AAACTTTCAAAAATT-CATTTTTGACCTTA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTC
*
15400 AAACTTCCAAAAATTCCATTTTTACACTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* **
15429 GAACTTCCAAAAATTCCATTTTTTACCCAA
1 AAACTTCCAAAAATTCCA-TTTTTACCCTC
*
15459 AAACTTCCAAAAATTACATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCTC
* *
15488 GAACCTCCAAAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
15510 CGACCCCAAA
Statistics
Matches: 221, Mismatches: 28, Indels: 15
0.84 0.11 0.06
Matches are distributed among these distances:
28 5 0.02
29 162 0.73
30 52 0.24
31 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCTC
Found at i:15433 original size:88 final size:85
Alignment explanation
Indices: 15224--15509 Score: 367
Period size: 88 Copynumber: 3.3 Consensus size: 85
15214 GAAAGTATCT
* * **
15224 AAACTGTCCGAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCTCAAACTT
1 AAACT-TCCAAAAATTCCATTTTTA-CCTCGAACTTCCAAAAATTCCATTTTTACCCAAAAACTT
* *
15289 CCAAAAATTATATTTTTACCTCA
64 CCAAAAATT-CATTTTTACCTTA
*
15312 AAACTTCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACTCC-AAAACT
1 AAACTTCCAAAAATTCCATTTTTACCTC-GAACTTCCAAAAATTCCATTTTT-AC-CCAAAAACT
*
15376 TTCAAAAATTCATTTTTGACCTTA
63 TCCAAAAATTCATTTTT-ACCTTA
15400 AAACTTCCAAAAATTCCATTTTTACACTCGAACTTCCAAAAATTCCATTTTTTACCCAAAAACTT
1 AAACTTCCAAAAATTCCATTTTTAC-CTCGAACTTCCAAAAATTCCA-TTTTTACCCAAAAACTT
* *
15465 CCAAAAATTACATTTTTACCCTC
64 CCAAAAATT-CATTTTTACCTTA
* *
15488 GAACCTCCAAAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
15510 CGACCCCAAA
Statistics
Matches: 177, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
86 3 0.02
87 48 0.27
88 110 0.62
89 16 0.09
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (85 bp):
AAACTTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTCCATTTTTACCCAAAAACTTCC
AAAAATTCATTTTTACCTTA
Found at i:15521 original size:59 final size:58
Alignment explanation
Indices: 15224--15522 Score: 345
Period size: 59 Copynumber: 5.1 Consensus size: 58
15214 GAAAGTATCT
* *
15224 AAACTGTCCGAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCTC-
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCC-CA
** * *
15283 AAACTTCCAAAAATTATATTTTTA-CCTCAAAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATTCCATTTTTACCCCA
* ** * **
15341 GAACTTCCAAAAATTCCATTTTTGACTCC-AAAACTTTCAAAAATT-CATTTTTGACCTTA
1 AAACTTCCAAAAATTCCATTTTT-AC-CCTCGAACTTCCAAAAATTCCATTTTT-ACCCCA
* *
15400 AAACTTCCAAAAATTCCATTTTTACACTCGAACTTCCAAAAATTCCATTTTTTACCCAA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTTACCCCA
* * *
15459 AAACTTCCAAAAATTACATTTTTACCCTCGAACCTCCAAAAATTCCATTTTCGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTT-TACCCCA
15518 AAACT
1 AAACT
15523 CTCAATATTA
Statistics
Matches: 205, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
57 6 0.03
58 87 0.42
59 105 0.51
60 5 0.02
61 2 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTACCCCA
Found at i:15561 original size:58 final size:59
Alignment explanation
Indices: 15224--15568 Score: 223
Period size: 59 Copynumber: 5.9 Consensus size: 59
15214 GAAAGTATCT
* * * * * * * **
15224 AAACTGTCCGAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTACATTTT-TACCCTC
1 AAACT-TCCAAAAATTACACTTTTACCCCCGAACCTCCAAAAATTCCATTTTCGACCCAA
* * * ** * * **
15283 AAACTTCCAAAAATTATATTTTTACCTCAAAACTTCCAAAAATTCCATTTT-TACCCCT
1 AAACTTCCAAAAATTACACTTTTACCCCCGAACCTCCAAAAATTCCATTTTCGACCCAA
* * * * ** * * * **
15341 GAACTTCCAAAAATTCCATTTTTGACTCCAAAACTTTCAAAAATT-CATTTTTGACCTTA
1 AAACTTCCAAAAATTACACTTTT-ACCCCCGAACCTCCAAAAATTCCATTTTCGACCCAA
* * * * * **
15400 AAACTTCCAAAAATTCCATTTTTACACTCGAACTTCCAAAAATTCCATTTTTTACCCAA
1 AAACTTCCAAAAATTACACTTTTACCCCCGAACCTCCAAAAATTCCATTTTCGACCCAA
* * *
15459 AAACTTCCAAAAATTACATTTTTACCCTCGAACCTCCAAAAATTCCATTTTCGACCCCA
1 AAACTTCCAAAAATTACACTTTTACCCCCGAACCTCCAAAAATTCCATTTTCGACCCAA
* * ** *
15518 AAAC-TCTC-AATATTACCCTTTTACCCCCGAATGTCTAAAAATTCCAATTTT
1 AAACTTC-CAAAAATTACACTTTTACCCCCGAACCTCCAAAAATTCC-ATTTT
15569 AACCCTAAAC
Statistics
Matches: 239, Mismatches: 42, Indels: 10
0.82 0.14 0.03
Matches are distributed among these distances:
58 117 0.49
59 122 0.51
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTACACTTTTACCCCCGAACCTCCAAAAATTCCATTTTCGACCCAA
Found at i:15620 original size:28 final size:28
Alignment explanation
Indices: 15582--15644 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
15572 CCTAAACTTT
* *
15582 TCCAAAATTACTATTTTGCCCTCGAGAA
1 TCCAAAATTACCATTTTGCCCCCGAGAA
*
15610 TCCAAAATTACCATTTTGCCCCCGAGTA
1 TCCAAAATTACCATTTTGCCCCCGAGAA
15638 TCCAAAA
1 TCCAAAA
15645 AGTCTCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCCCGAGAA
Found at i:21133 original size:256 final size:252
Alignment explanation
Indices: 20620--21110 Score: 567
Period size: 256 Copynumber: 1.9 Consensus size: 252
20610 TCATTTCTAG
*
20620 TTTAAATCGGACTTTTTATAAAAATACTTTTTGGACTAATTAGTAAGAGGCCTCTCTATTTTTAG
1 TTTAAATCGGACTTTTTATAAAAATACTTTTTGGACTAATTAGTAAGAGACCTCTCTATTTTTAG
**** *
20685 TGTTAAAGGAGAATAAAAGAAAATAATAAACAAGGGGGGCTATAAAGGAATTTACCCTTCTTAAT
66 TGTTAAAGGAGAATAAAAGAAAATAATAAACAAAAAAGGCTATAAAGCAATTTACCCTTCTTAAT
** ** *
20750 GTTTGGGGCCGCCACTGTTTTAGCTGCACCTTAATCACTTTTCTAAGCTTCTTAAAACGGTATAT
131 GTTTGGAACCGCCACTGTTCAAGCTGCACATTAATCACTTTTCTAAGCTTCTTAAAACGGTATAT
* * * **
20815 TTCATATTAGGTACTTAGATATTTTAAGTCATTACAAAAATAAATAAAATTTATTTCTAA
196 TTCATATTAGGTACTGAGATATTTTAAATCATTAC---AATAAATAAAATGTATCGCTAA
*
20875 TTTAAATCGGACTTTTTTATAAAAATACTTTTTGGATTAATT-GATAAGAGACCTCTCTATTTTT
1 TTTAAATCGGAC-TTTTTATAAAAATACTTTTTGGACTAATTAG-TAAGAGACCTCTCTATTTTT
* * ** * *
20939 AGTGTTAAAGGTGAATAAAATAATAATAATAAACAAAAAAAGTTTATAAAGCAATTTACCTTTTT
64 AGTGTTAAAGGAGAATAAAAGAA-AATAATAAAC-AAAAAAGGCTATAAAGCAATTTACCCTTCT
* * * *
21004 TAATGTTTGGAATCGTCACAT-TGTCAAG-TCGCACATTAATCTCTTTTCTAAGCTTCTTAAAAT
127 TAATGTTTGGAACCGCCAC-TGT-TCAAGCT-GCACATTAATCACTTTTCTAAGCTTCTTAAAAC
* * * *
21067 GGTATATTTACTTATTAGATTCCTGA-ATATTTTAAATTATTACA
189 GGTATATTT-CATATTAG-GTACTGAGATATTTTAAATCATTACA
21111 TTTTAATCTG
Statistics
Matches: 199, Mismatches: 28, Indels: 16
0.82 0.12 0.07
Matches are distributed among these distances:
255 13 0.07
256 68 0.34
257 11 0.06
258 38 0.19
259 43 0.22
260 22 0.11
261 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (252 bp):
TTTAAATCGGACTTTTTATAAAAATACTTTTTGGACTAATTAGTAAGAGACCTCTCTATTTTTAG
TGTTAAAGGAGAATAAAAGAAAATAATAAACAAAAAAGGCTATAAAGCAATTTACCCTTCTTAAT
GTTTGGAACCGCCACTGTTCAAGCTGCACATTAATCACTTTTCTAAGCTTCTTAAAACGGTATAT
TTCATATTAGGTACTGAGATATTTTAAATCATTACAATAAATAAAATGTATCGCTAA
Found at i:21561 original size:60 final size:59
Alignment explanation
Indices: 21465--21618 Score: 164
Period size: 60 Copynumber: 2.6 Consensus size: 59
21455 TGCTTTTTAT
* * * * * **
21465 TAATTTGGTACCTAAACTTTTTGGGACCCAATTTGGTACTTGATTTTGACATATTTTTC
1 TAATTTGGTATCTAAATTTTTTTGGACTCAATTTGGTACCTGAACTTGACATATTTTTC
* * *
21524 TAATTTGGAATCTAAATTTTTTTTGGACTCAATTTGGTACCTGAACTTGATATTTTTTTC
1 TAATTTGGTATCTAAA-TTTTTTTGGACTCAATTTGGTACCTGAACTTGACATATTTTTC
* * * *
21584 TAATTTGGTATATAAGCTTTTTTTAGATTCAATTT
1 TAATTTGGTATCTAA-ATTTTTTTGGACTCAATTT
21619 AGCACTTAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
59 14 0.18
60 64 0.82
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (59 bp):
TAATTTGGTATCTAAATTTTTTTGGACTCAATTTGGTACCTGAACTTGACATATTTTTC
Found at i:21915 original size:31 final size:31
Alignment explanation
Indices: 21857--21915 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
21847 ACTTAAAAAA
*
21857 AAAAAGTGTCAAGTTTAGGTACTAAATTAGG
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
21888 AAAAAGTGTCAAGTTT-GAGTACCAAATT
1 AAAAAGTGTCAAGTTTAG-GTACCAAATT
21916 GAACCCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.29
Consensus pattern (31 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTAGG
Found at i:26049 original size:18 final size:19
Alignment explanation
Indices: 26003--26053 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
25993 TAAAAAAATT
26003 TAAT-AAATAAAATATATA
1 TAATAAAATAAAATATATA
*
26021 TAA-AATTATAAAATAT-TA
1 TAATAA-AATAAAATATATA
26039 TAATAAAATAAAATA
1 TAATAAAATAAAATA
26054 AAATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAAATAAAATATATA
Done.