Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013135.1 Kokia drynarioides strain JFW-HI SEQ_128154, 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: 22501
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Warning! 119 characters in sequence are not A, C, G, or T
Found at i:492 original size:19 final size:19
Alignment explanation
Indices: 465--521 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 19
455 CCATGTCAGC
*
465 AAATGATTTTAAAAATATT
1 AAATTATTTTAAAAATATT
484 AAATTATTTTTTAAAAATA-T
1 AAATTA--TTTTAAAAATATT
* *
504 AAAAT-TTTTAAAATTATT
1 AAATTATTTTAAAAATATT
522 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 10 0.31
18 1 0.03
19 5 0.16
20 5 0.16
21 11 0.34
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATTATTTTAAAAATATT
Found at i:520 original size:30 final size:29
Alignment explanation
Indices: 474--552 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 29
464 CAAATGATTT
*
474 TAAAAATATT-AAATTATTTTTTAAAAATA
1 TAAAATTATTAAAATTATTTTTT-AAAATA
*
503 TAAAATTTTTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
532 TAAAATTATTAAAATTATTTT
1 TAAAATTATTAAAATTATTTT
553 AAAATTATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 34 0.74
30 12 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:523 original size:29 final size:29
Alignment explanation
Indices: 474--562 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
464 CAAATGATTT
*
474 TAAAAATATT-AAATTATTTTTTAAAAATA
1 TAAAATTATTAAAATTA-TTTTTAAAAATA
* *
503 TAAAATTTTTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAAATA
*
532 TAAAATTATTAAAATTA-TTTTAAAATTA
1 TAAAATTATTAAAATTATTTTTAAAAATA
560 TAA
1 TAA
563 TCATCATCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
28 12 0.23
29 35 0.66
30 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTAAAAATA
Found at i:1928 original size:27 final size:28
Alignment explanation
Indices: 1867--1932 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
1857 CAACACTATC
1867 CCAAAATCTCCAAAATCAAAAACCGTAAA
1 CCAAAATC-CCAAAATCAAAAACCGTAAA
* * *
1896 CAAAAATCCCCAAATC-AAAACTC-TTAA
1 CCAAAATCCCAAAATCAAAAAC-CGTAAA
1923 CCAAAATCCC
1 CCAAAATCCC
1933 TTAATTCGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 17 0.53
28 8 0.25
29 7 0.22
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.15
Consensus pattern (28 bp):
CCAAAATCCCAAAATCAAAAACCGTAAA
Found at i:2184 original size:6 final size:6
Alignment explanation
Indices: 2153--2257 Score: 94
Period size: 6 Copynumber: 18.2 Consensus size: 6
2143 TTTTATTGGG
* ** *
2153 TTTAAA TTT--A TTCAAA TTTATT TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
2198 TTTAAA TTTATAT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
2245 TTAAAA TTTAAA T
1 TTTAAA TTTAAA T
2258 GGATTTAAAA
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
4 3 0.04
5 11 0.14
6 58 0.75
7 5 0.06
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:2196 original size:17 final size:17
Alignment explanation
Indices: 2166--2257 Score: 121
Period size: 17 Copynumber: 5.2 Consensus size: 17
2156 AAATTTATTC
2166 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAATTT
2184 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
2201 AAATTTATATTTTAAATTT
1 AAA-TT-TATTTTAAATTT
**
2220 AAATTTGCTTTAAATTT
1 AAATTTATTTTAAATTT
* *
2237 AAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
2254 AAAT
1 AAAT
2258 GGATTTAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
17 41 0.61
18 11 0.16
19 15 0.22
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:2212 original size:29 final size:29
Alignment explanation
Indices: 2153--2220 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2143 TTTTATTGGG
**
2153 TTTAAATTTATTCAAATTTATTTTTAAA-
1 TTTAAATTTATTCAAATTTAAATTTAAAT
* *
2181 TTTAAATTTATTTTAAATTTAAATTTATAT
1 TTTAAATTTA-TTCAAATTTAAATTTAAAT
2211 TTTAAATTTA
1 TTTAAATTTA
2221 AATTTGCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 10 0.29
29 14 0.41
30 10 0.29
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTAAATTTATTCAAATTTAAATTTAAAT
Found at i:2219 original size:36 final size:36
Alignment explanation
Indices: 2166--2257 Score: 136
Period size: 36 Copynumber: 2.6 Consensus size: 36
2156 AAATTTATTC
*
2166 AAATTTAT-TTTTAAATTTAAATTTATTTTAAATTT
1 AAATTTATATTTTAAATTTAAATTTACTTTAAATTT
*
2201 AAATTTATATTTTAAATTTAAATTTGCTTTAAATTT
1 AAATTTATATTTTAAATTTAAATTTACTTTAAATTT
*
2237 AAATTTA-A-TTAAAATTTAAAT
1 AAATTTATATTTTAAATTTAAAT
2258 GGATTTAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 12 0.23
35 9 0.17
36 32 0.60
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (36 bp):
AAATTTATATTTTAAATTTAAATTTACTTTAAATTT
Found at i:2246 original size:11 final size:12
Alignment explanation
Indices: 2153--2257 Score: 94
Period size: 11 Copynumber: 9.1 Consensus size: 12
2143 TTTTATTGGG
2153 TTTAAATTT--A
1 TTTAAATTTAAA
* **
2163 TTCAAATTTATT
1 TTTAAATTTAAA
2175 TTTAAATTTAAA
1 TTTAAATTTAAA
*
2187 TTT-ATTTTAAA
1 TTTAAATTTAAA
*
2198 TTTAAATTTATAT
1 TTTAAATTTA-AA
2211 TTTAAATTTAAA
1 TTTAAATTTAAA
**
2223 TTT-GCTTTAAA
1 TTTAAATTTAAA
2234 TTTAAATTT-AA
1 TTTAAATTTAAA
*
2245 TTAAAATTTAAA
1 TTTAAATTTAAA
2257 T
1 T
2258 GGATTTAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
10 8 0.11
11 29 0.39
12 27 0.36
13 11 0.15
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:2265 original size:17 final size:17
Alignment explanation
Indices: 2178--2272 Score: 75
Period size: 17 Copynumber: 5.5 Consensus size: 17
2168 ATTTATTTTT
* *
2178 AAATTTAAATTTATTTT
1 AAATTTAAATTGATTTA
* *
2195 AAATTTAAATTTATATTTT
1 AAATTTAAA-TT-GATTTA
*
2214 AAATTTAAATTTGCTTT-
1 AAATTTAAA-TTGATTTA
* *
2231 AAATTTAAATTTAATTA
1 AAATTTAAATTGATTTA
*
2248 AAATTTAAATGGATTTA
1 AAATTTAAATTGATTTA
*
2265 AAACTTAA
1 AAATTTAA
2273 TTAAAGTCCA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
16 4 0.06
17 39 0.59
18 5 0.08
19 18 0.27
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTGATTTA
Found at i:2984 original size:3 final size:3
Alignment explanation
Indices: 2976--3021 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
2966 AGTTATTAAT
* * *
2976 TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAG CAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
3022 AAAAAGGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3000 original size:22 final size:24
Alignment explanation
Indices: 2972--3021 Score: 77
Period size: 22 Copynumber: 2.1 Consensus size: 24
2962 TTAAAGTTAT
2972 TAATTAATAATA-A-TAATAATAA
1 TAATTAATAATACATTAATAATAA
2994 TAATTAATAATAGCATTAATAATAA
1 TAATTAATAATA-CATTAATAATAA
3019 TAA
1 TAA
3022 AAAAAGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 12 0.48
24 1 0.04
25 12 0.48
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
TAATTAATAATACATTAATAATAA
Found at i:4083 original size:29 final size:29
Alignment explanation
Indices: 4007--4289 Score: 189
Period size: 29 Copynumber: 9.6 Consensus size: 29
3997 CTCGAACCTG
* *
4007 TCAAAAAATTCCATTTTCACCCTCG-AACT
1 TCAAAAAATTCCATTTTTA-CCTTGAAACT
* *
4036 ACCAAAAAATTTCATTTTTGACCTTGAAACT
1 -TCAAAAAATTCCATTTTT-ACCTTGAAACT
* * *
4067 TCAAAAAATTTCATTTTTACCCTCAAACT
1 TCAAAAAATTCCATTTTTACCTTGAAACT
* * *
4096 TCTAAAAATCCCATTTTTACCCCT-AAACT
1 TCAAAAAATTCCATTTTTA-CCTTGAAACT
**
4125 TTTAAAAA-TCCAATTTTTGACCTTGAAACT
1 TCAAAAAATTCC-ATTTTT-ACCTTGAAACT
* * **
4155 TCCAAAAATTCCATTTTCACCCCCG-AACT
1 TCAAAAAATTCCATTTTTA-CCTTGAAACT
* * **
4184 TCCAAAAATTTCATTTTTACCTCAAAACT
1 TCAAAAAATTCCATTTTTACCTTGAAACT
* *
4213 TCCAAAAATTCCATTTTTACCCCTG-AACT
1 TCAAAAAATTCCATTTTTA-CCTTGAAACT
* * ***
4242 TCCAAAAATCCCATTTTTTACCACAAAACT
1 TCAAAAAATTCCA-TTTTTACCTTGAAACT
*
4272 TCCAAAAATTACCATTTT
1 TCAAAAAATT-CCATTTT
4290 GCCCCCGAAT
Statistics
Matches: 209, Mismatches: 31, Indels: 26
0.79 0.12 0.10
Matches are distributed among these distances:
28 5 0.02
29 108 0.52
30 85 0.41
31 11 0.05
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
TCAAAAAATTCCATTTTTACCTTGAAACT
Found at i:4154 original size:59 final size:57
Alignment explanation
Indices: 4040--4317 Score: 267
Period size: 59 Copynumber: 4.7 Consensus size: 57
4030 CGAACTACCA
* * * * *
4040 AAAAATTTCATTTTTGA-CCTTGAAACTTCAAAAAATTTCATTTTTACCCTC-AAACTTCT
1 AAAAATTCCATTTTT-ACCCCTG-AACTTCCAAAAA-TCCATTTTTA-CCTCAAAACTTCC
* * ** **
4099 AAAAATCCCATTTTTACCCCTAAACTTTTAAAAATCCAATTTTTGACCTTGAAACTTCC
1 AAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCC-ATTTTT-ACCTCAAAACTTCC
* * *
4158 AAAAATTCCATTTTCACCCCCGAACTTCCAAAAATTTCATTTTTACCTCAAAACTTCC
1 AAAAATTCCATTTTTACCCCTGAACTTCCAAAAA-TCCATTTTTACCTCAAAACTTCC
*
4216 AAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCCATTTTTTACCACAAAACTTCC
1 AAAAATTCCATTTTTACCCCTGAACTTCCAAAAAT-CCA-TTTTTACCTCAAAACTTCC
* *
4275 AAAAATTACCA-TTTTGCCCCCGAA-TGTCCAAAAACTCCATTTT
1 AAAAATT-CCATTTTTACCCCTGAACT-TCCAAAAA-TCCATTTT
4318 CGACCTTGAA
Statistics
Matches: 185, Mismatches: 24, Indels: 21
0.80 0.10 0.09
Matches are distributed among these distances:
57 3 0.02
58 71 0.38
59 105 0.57
60 6 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCATTTTTACCTCAAAACTTCC
Found at i:4162 original size:88 final size:88
Alignment explanation
Indices: 4040--4329 Score: 293
Period size: 88 Copynumber: 3.3 Consensus size: 88
4030 CGAACTACCA
* * * * *
4040 AAAAATTTCATTTTTGACCTTGAAACTTCAAAAAATTTCATTTTTACCCTCAAACTTCTAAAAAT
1 AAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAT
* **
4105 CCCATTTTTACCCCTAAACTTTT
66 CCCATTTTTACCCCAAAACTTCC
* *
4128 AAAAA-TCCAATTTTTGACCTTGAAACTTCCAAAAATTCCATTTTCACCCCCGAACTTCCAAAAA
1 AAAAATTCC-ATTTTTGACCTTGAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAA
** *
4192 TTTCATTTTTACCTCAAAACTTCC
65 TCCCATTTTTACCCCAAAACTTCC
* * * *
4216 AAAAATTCCATTTTT-ACCCCTG-AACTTCCAAAAATCCCATTTTTTACCACAAAACTTCCAAAA
1 AAAAATTCCATTTTTGA-CCTTGAAACTTCCAAAAATTCCA-TTTTTACCCCCAAACTTCCAAAA
* * **
4279 ATTACCA-TTTTGCCCCCGAA-TGTCC
64 A-TCCCATTTTTACCCCAAAACT-TCC
* *
4304 AAAAACTCCATTTTCGACCTTGAAAC
1 AAAAATTCCATTTTTGACCTTGAAAC
4330 GCTCAAAATT
Statistics
Matches: 166, Mismatches: 28, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
87 20 0.12
88 136 0.82
89 10 0.06
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (88 bp):
AAAAATTCCATTTTTGACCTTGAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAAT
CCCATTTTTACCCCAAAACTTCC
Found at i:4220 original size:117 final size:117
Alignment explanation
Indices: 4063--4317 Score: 336
Period size: 117 Copynumber: 2.2 Consensus size: 117
4053 TTGACCTTGA
* * **
4063 AACTTCAAAAAATTTCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTACCCCTAAACTTTT
1 AACTTCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCC
***
4128 AAAAATCCAATTTTTGACCTTGAAACTTCCAAAAATT-CCATTTTCACCCCCG
66 AAAAATCCAATTTTTGACCACAAAACTTCCAAAAATTACCATTTT-ACCCCCG
* *
4180 AACTTCCAAAAATTTCATTTTTA-CCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACTTC
1 AACTTCCAAAAATTTCATTTTTACCCTC-AAACTTCCAAAAATCCCATTTTTACCCCTAAACTTC
* * *
4244 CAAAAATCCCATTTTTTACCACAAAACTTCCAAAAATTACCATTTTGCCCCCG
65 CAAAAATCCAATTTTTGACCACAAAACTTCCAAAAATTACCATTTTACCCCCG
* *
4297 AA-TGTCCAAAAACTCCATTTT
1 AACT-TCCAAAAATTTCATTTT
4318 CGACCTTGAA
Statistics
Matches: 121, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
116 5 0.04
117 109 0.90
118 7 0.06
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (117 bp):
AACTTCCAAAAATTTCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCC
AAAAATCCAATTTTTGACCACAAAACTTCCAAAAATTACCATTTTACCCCCG
Found at i:15317 original size:160 final size:160
Alignment explanation
Indices: 15132--15474 Score: 533
Period size: 160 Copynumber: 2.1 Consensus size: 160
15122 ATGCGGTCAC
15132 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCAAATCTT
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCAAATCTT
** * * *
15197 TGAACCCCAACTTCCTAACGAGATACTGAGAGGTAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
66 CAAACCCCAACTTCCTAACGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCTG
*
15262 ATGAGATACTAAGAAGTGTACCAAATTCAT
131 ATGAGATACTAAGAAGTGAACCAAATTCAT
* *
15292 CTTCCTGATGAGATACTGTGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGTGAGCAAATCTT
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCAAATCTT
* * * * *
15357 CAAATCTCAGCTTCCTGACGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGGTTCCTG
66 CAAACCCCAACTTCCTAACGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCTG
* *
15422 ATGAGATACTGAGAAGTGAACCAAATTCGT
131 ATGAGATACTAAGAAGTGAACCAAATTCAT
* *
15452 CTTTCTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
15475 CGAATTGAAA
Statistics
Matches: 165, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
160 165 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (160 bp):
CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAACGAGGCTCAAAGCGAGCAAATCTT
CAAACCCCAACTTCCTAACGAGATACTGAGAAGCAGGTCGAAGCAATAAAACGGTTAGCTTCCTG
ATGAGATACTAAGAAGTGAACCAAATTCAT
Found at i:16886 original size:96 final size:96
Alignment explanation
Indices: 16702--16893 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
16692 TTTTTGGGAA
** * * *
16702 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTCGCGCCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAATATTTCA
16767 GAATCGAAGATAAGAAAACATTGCCTCGATT
66 GAATCGAAGATAAGAAAACATTGCCTCGATT
* * * * *
16798 AAGGGTATTCGATTATTTCGATTTGAGGAAAAATTGCACCTAGTGAGTTAAGACACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAATA-TTTC
*
16862 -GAAACTCGAA-ATAA-AAGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAGAA-AACATTGCCTCGATT
16894 TTAAAGTTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 4 0.05
96 72 0.89
97 5 0.06
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAATATTTCA
GAATCGAAGATAAGAAAACATTGCCTCGATT
Found at i:17235 original size:29 final size:29
Alignment explanation
Indices: 17201--17295 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 29
17191 GTAAAATAGA
17201 ATTTTTAGAAATTTCGGGATCAAAAATGG
1 ATTTTTAGAAATTTCGGGATCAAAAATGG
* * *
17230 -TGTTTTTGGAAGTTCGGGGA-CAAAAATGG
1 AT-TTTTAGAAATTTC-GGGATCAAAAATGG
* *
17259 AATTTTTGGAAGTTTCGTGG-TCAAAAATGGG
1 -ATTTTTAGAAATTTCG-GGATCAAAAAT-GG
17290 ATTTTT
1 ATTTTT
17296 GGAAGTTCGG
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
28 1 0.02
29 20 0.38
30 28 0.54
31 3 0.06
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (29 bp):
ATTTTTAGAAATTTCGGGATCAAAAATGG
Found at i:17264 original size:59 final size:58
Alignment explanation
Indices: 17193--17683 Score: 339
Period size: 59 Copynumber: 8.4 Consensus size: 58
17183 ATTCGAGGGT
* * *
17193 AAAATAGAATTTTTAGAAATTTCGGGATCAAAAATGGTG-TTTTTGGAAGTTCGGGGACA
1 AAAATGGAATTTTTGGAAGTTTCGGG-TCAAAAATGG-GATTTTTGGAAGTTCGGGGACA
**
17252 AAAATGGAATTTTTGGAAGTTTCGTGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGTCAAAAATGGGATTTTTGGAAGTTCGGGGACA
* * ** * *
17311 AAATTGAAATTTTTGGAAGTTTCGGGTCAAAAATAAGATTTTTGGAAGTTAGAGGG--G
1 AAAATGGAATTTTTGGAAGTTTCGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGACA
** * * * ** **
17368 AAAATGGGTTTTTTGAAAG-TTCGGGGGT-AAAAATTGAATTTTTGGAAGTTTCAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTC--GGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGACA
* * ** **
17427 AAAATGGGA-TTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTC--GGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGACA
* * *
17485 AAAATGGGATTTTTGGAAG-TTCAAGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTC--GGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGACA
* * * * *
17544 AAATTGGGATTTTTGGAAG-TTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTTGAGGG--T
1 AAAATGGAATTTTTGGAAGTTTC--GGGTCAAAAATGGGATTTTTGGAAG-TTCG-GGGACA
* * * *
17602 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAAT-TGATTTTTTGGAAGTTTAGGGG-TA
1 AAAATGGAATTTTTGGAAG-TTTCGGGTCAAAAATGGGA-TTTTTGGAAG-TTCGGGGACA
17661 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
17684 AGGAACCTTC
Statistics
Matches: 373, Mismatches: 43, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
56 3 0.01
57 33 0.09
58 112 0.30
59 216 0.58
60 9 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGACA
Found at i:17304 original size:29 final size:29
Alignment explanation
Indices: 17165--17683 Score: 465
Period size: 29 Copynumber: 17.8 Consensus size: 29
17155 TTTTTTTTTT
*
17165 AAAATGGAATTTTTAGACA--TTCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTTCG-GGGTA
* * * *
17193 AAAATAGAATTTTTAGAAATTTCGGGATCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
** *
17223 AAAATGGTGTTTTTGGAAG-TTCGGGGACA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
*
17252 AAAATGGAATTTTTGGAAGTTTCGTGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
*
17282 AAAATGGGATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* *
17311 AAATTGAAATTTTTGGAAGTTTC-GGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* * *
17340 AAAAT-AAGATTTTTGGAAG-TTAGAGGG-G
1 AAAATGGA-ATTTTTGGAAGTTTCG-GGGTA
** *
17368 AAAATGGGTTTTTTGAAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* * *
17397 AAAATTGAATTTTTGGAAGTTTCAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
*
17427 AAAATGGGA-TTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* *
17455 AAAATGGAATTTTTGGAAGTTTCAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* *
17485 AAAATGGGATTTTTGGAAG-TTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
17514 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* *
17544 AAATTGGGATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
*
17573 AAAATGGAATTTTTGGAAGTTTTGAGGGT-
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
17602 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* * *
17632 AAAATTGATTTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
17661 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
17684 AGGAACCTTC
Statistics
Matches: 407, Mismatches: 55, Indels: 56
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.00
28 65 0.16
29 191 0.47
30 150 0.37
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:17342 original size:88 final size:88
Alignment explanation
Indices: 17222--17683 Score: 507
Period size: 88 Copynumber: 5.3 Consensus size: 88
17212 TTTCGGGATC
** * * *
17222 AAAAATGGTGTTTTTGGAAG-TTCGGGGACAAAAATGGAATTTTTGGAAGTTTCGTGGTCAAAAA
1 AAAAATGGAATTTTTGGAAGTTTCAGGG-TAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAA
17286 TGGGATTTTTGGAAGTTCGGGGGT
65 TGGGATTTTTGGAAGTTCGGGGGT
* * * * *
17310 AAAATTGAAATTTTTGGAAGTTTC-GGGTCAAAAAT-AAGATTTTTGGAAG-TTAGAGGG--GAA
1 AAAAATGGAATTTTTGGAAGTTTCAGGGT-AAAAATGGA-ATTTTTGGAAGTTTCG-GGGTCAAA
* *
17370 AATGGGTTTTTTGAAAGTTCGGGGGT
63 AATGGGATTTTTGGAAGTTCGGGGGT
* * *
17396 AAAAATTGAATTTTTGGAAGTTTCAAGGTTAAAAATGGGA-TTTTGGAAG-TTCGAGGGT-AAAA
1 AAAAATGGAATTTTTGGAAGTTTC-AGGGTAAAAATGGAATTTTTGGAAGTTTCG-GGGTCAAAA
* ** *
17458 ATGGAATTTTTGGAAGTTTCAAGGTT
64 ATGGGATTTTTGGAAG-TTCGGGGGT
* *
17484 AAAAATGGGATTTTTGGAAG-TTCAAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAT
1 AAAAATGGAATTTTTGGAAGTTTC-AGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAA
17548 TGGGATTTTTGGAAGTTCGGGGGT
65 TGGGATTTTTGGAAGTTCGGGGGT
* *
17572 AAAAATGGAATTTTTGGAAGTTTTGAGGGT-AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAA
1 AAAAATGGAATTTTTGGAAG-TTTCAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAA
* **
17636 T-TGATTTTTTGGAAGTTTAGGGGT
65 TGGGA-TTTTTGGAAGTTCGGGGGT
17660 AAAAATGGAATTTTTGGACAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
17684 AGGAACCTTC
Statistics
Matches: 317, Mismatches: 41, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
86 63 0.20
87 46 0.15
88 174 0.55
89 32 0.10
90 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.35
Consensus pattern (88 bp):
AAAAATGGAATTTTTGGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAAT
GGGATTTTTGGAAGTTCGGGGGT
Found at i:18856 original size:3 final size:3
Alignment explanation
Indices: 18771--18845 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
18761 AATGTTACAT
18771 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18819 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
18846 AATTTATTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19604 original size:17 final size:16
Alignment explanation
Indices: 19582--19660 Score: 77
Period size: 17 Copynumber: 4.8 Consensus size: 16
19572 TTGGACTTTC
19582 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
19599 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
*
19616 TAAATTTAAATTTAAAA
1 TAAATTT-AATTTTAAA
* * *
19633 TGAACTTAAATTTAAA
1 TAAATTTAATTTTAAA
*
19649 TAAATTCAATTT
1 TAAATTTAATTT
19661 CCAATAGGCT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
16 15 0.29
17 30 0.59
18 6 0.12
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:19620 original size:34 final size:33
Alignment explanation
Indices: 19582--19660 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
19572 TTGGACTTTC
* *
19582 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTT-AAA
* *
19616 TAAATTTAAATTTAAAATGAACTTAAATTTAAA
1 TAAATTTAATTTTAAAATAAACTTAAATTTAAA
*
19649 TAAATTCAATTT
1 TAAATTTAATTT
19661 CCAATAGGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 13 0.33
34 26 0.67
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (33 bp):
TAAATTTAATTTTAAAATAAACTTAAATTTAAA
Found at i:21329 original size:182 final size:182
Alignment explanation
Indices: 21022--21394 Score: 611
Period size: 182 Copynumber: 2.0 Consensus size: 182
21012 ACCTTGTTTG
*
21022 GATTAAATAATTAGTTCATAAGCTTCTCAACATTGTTTATGCATGAACAAATGTCATGGGCAGCA
1 GATTAAATAATTAGTTCATAAGCTTCTCAACATTGTTTACGCATGAACAAATGTCATGGGCAGCA
21087 GTTCAAAGCCCATGACAATAGCACAAAATGTGTCCCAAGAAGGTCTATCAATTAGATGGGGCTCA
66 GTTCAAAGCCCATGACAATAGCACAAAATGTGTCCCAAGAAGGTCTATCAATTAGATGGGGCTCA
* * * *
21152 TTTGACCGACGAGAGCTAACCTGATTCAAAGTGTTGTTGAAGAAGGTTGTTA
131 TTTGACCCACGAGAGCTAACCCGATTCAAAGAGTTGTTGAAGAAGGATGTTA
*
21204 GATTAAATAATTAGTTCATAAGCTTCTCAACATTGTTTACGCATGAACAAATGTCATGGGCCGCA
1 GATTAAATAATTAGTTCATAAGCTTCTCAACATTGTTTACGCATGAACAAATGTCATGGGCAGCA
* * * * * * *
21269 GTTTAAAGCCCGTGACCATTGCATAAAATGTGTCCCAATAAGGTCTATCAGTTAGATGGGGCTCA
66 GTTCAAAGCCCATGACAATAGCACAAAATGTGTCCCAAGAAGGTCTATCAATTAGATGGGGCTCA
*
21334 TTTGACCCACGAGAGCTAACCCGATTCAAAGAGTTGTTGGAGAAGGATGTTA
131 TTTGACCCACGAGAGCTAACCCGATTCAAAGAGTTGTTGAAGAAGGATGTTA
21386 GATTGAAAT
1 GATT-AAAT
21395 CTGGATGGTC
Statistics
Matches: 176, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
182 172 0.98
183 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (182 bp):
GATTAAATAATTAGTTCATAAGCTTCTCAACATTGTTTACGCATGAACAAATGTCATGGGCAGCA
GTTCAAAGCCCATGACAATAGCACAAAATGTGTCCCAAGAAGGTCTATCAATTAGATGGGGCTCA
TTTGACCCACGAGAGCTAACCCGATTCAAAGAGTTGTTGAAGAAGGATGTTA
Found at i:22059 original size:13 final size:14
Alignment explanation
Indices: 22041--22070 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22031 TTGATTTGAT
22041 TTGATTATGTAA-A
1 TTGATTATGTAATA
22054 TTGATTATGTAATA
1 TTGATTATGTAATA
22068 TTG
1 TTG
22071 TAAATCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TTGATTATGTAATA
Done.