Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000816.1 Kokia drynarioides strain JFW-HI SEQ_111903, 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: 253564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:167805 original size:145 final size:145
Alignment explanation
Indices: 167544--168238 Score: 907
Period size: 145 Copynumber: 4.8 Consensus size: 145
167534 TTGAGCTCTA
* * * * *
167544 CTTCATTGTTTTGATCCATTTCTTTATATCTCATC-AGAA-ATATGGGGTTTGAAGTTTCACTCT
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAAGAAGATA-GGGGTTTGAAGTTTCACTTT
* * * *
167607 ACTCCATT-TAACGTCAGGGATGTTGAGCTTTGCTTCATTGTTTTGGTCCACTTCTCTCTATCTC
65 ACTCCATTATAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTCTCTGTATCTC
167671 ATCAAGAAGATGACCG
130 ATCAAGAAGATGACCG
*
167687 CTTCATCGTTTTGATCCACTTCTCTATATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTTTA
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTTTA
* * * * * *
167752 CTCCACTATAACCTTAGGGATGTTGAGCTCTGCTTCACTATTTAGGTCCACTTCTTTGTATCTTA
66 CTCCATTATAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCA
*
167817 TCAGGAAGATGACCG
131 TCAAGAAGATGACCG
* * * *
167832 CTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTTAAGTTTCACTTTA
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTTTA
* * *
167897 CTCCATTATAACCTTACGGATGTTGAGCTCTGCTTCATTATTTTGGTCTACTTCAT-TGTATCTC
66 CTCCATTATAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTC-TCTGTATCTC
* *
167961 AT-TAGAAAGATGATCG
130 ATCAAG-AAGATGACCG
* * * * *
167977 CTTCATCGTTTTGATCCACTTATCTGTATCTAATCAGGGAGCTA-GGGTTTGAAGTTTCACTTTA
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTTTA
* * * *
168041 CTCCATTGTAATCTTAAGGATGTTGAGCTCTACTTCATTGTTTTGGTCCACTTCTCTGTATCTCA
66 CTCCATTATAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCA
**
168106 TCAAGAAGATGTTCG
131 TCAAGAAGATGACCG
* * * * * * *
168121 CTTCATCGTTTTAAACCACTTCTCTGTATCTAATCGAGGAGATAGGGGTTTGAAGTTTTACTCTA
1 CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTTTA
* *
168186 CTCCATTGTAACCTTAGGGATGTTTAGCTCTGCTTCATTGTTTTGGTCCACTT
66 CTCCATTATAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTT
168239 TGGTTAAAAT
Statistics
Matches: 488, Mismatches: 56, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
143 33 0.07
144 155 0.32
145 299 0.61
146 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (145 bp):
CTTCATCGTTTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGGGGTTTGAAGTTTCACTTTA
CTCCATTATAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCA
TCAAGAAGATGACCG
Found at i:168091 original size:289 final size:288
Alignment explanation
Indices: 167544--168238 Score: 930
Period size: 289 Copynumber: 2.4 Consensus size: 288
167534 TTGAGCTCTA
* * * * *
167544 CTTCATTGTTTTGATCCATTTCTTTATATCTCATCAGAAATATGGGGTTTGAAGTTTCACTCTAC
1 CTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCTAC
* * *
167609 TCCATTTAACGTCAGGGATGTTGAGCTTTGCTTCATTGTTTTGGTCCACTTCTCTCTATCTCATC
66 TCCATTTAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTCTCTCTATCTCATC
* *
167674 AAGAAGATGACCGCTTCATCGTTTTGATCCACTTCTCTATATCTCATCAAGAAGATAGGGGTTTG
131 AAGAAGATGACCGCTTCATCGTTTTGATCCACTTATCTATATCTAATCAAGAAGATAGGGGTTTG
* *
167739 AAGTTTCACTTTACTCCACTATAACCTTAGGGATGTTGAGCTCTGCTTCACTATTTAGGTCCACT
196 AAGTTTCACTTTACTCCACTATAACCTTAAGGATGTTGAGCTCTACTTCACTATTTAGGTCCACT
* * *
167804 TCTTTGTATCTTATCAGGAAGATGACCG
261 TCTCTGTATCTCATCAAGAAGATGACCG
* *
167832 CTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGGTTTTAAGTTTCACTTTA
1 CTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCTA
* * * *
167897 CTCCATTATAACCTTACGGATGTTGAGCTCTGCTTCATTATTTTGGTCTACTTCAT-TGTATCTC
65 CTCCATT-TAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTC-TCTCTATCTC
* * * * * *
167961 AT-TAGAAAGATGATCGCTTCATCGTTTTGATCCACTTATCTGTATCTAATCAGGGAGCTA-GGG
128 ATCAAG-AAGATGACCGCTTCATCGTTTTGATCCACTTATCTATATCTAATCAAGAAGATAGGGG
* * * * * *
168024 TTTGAAGTTTCACTTTACTCCATTGTAATCTTAAGGATGTTGAGCTCTACTTCATTGTTTTGGTC
192 TTTGAAGTTTCACTTTACTCCACTATAACCTTAAGGATGTTGAGCTCTACTTCACTATTTAGGTC
**
168089 CACTTCTCTGTATCTCATCAAGAAGATGTTCG
257 CACTTCTCTGTATCTCATCAAGAAGATGACCG
* * * * *
168121 CTTCATCGTTTTAAACCACTTCTCTGTATCTAATCGAGG-AGATAGGGGTTTGAAGTTTTACTCT
1 CTTCATTGTTTTGATCCACTTCTCTGTATCTCATC-AGGAAGAT-GGGGTTTGAAGTTTCACTCT
*
168185 ACTCCATTGTAACCTTAGGGATGTTTAGCTCTGCTTCATTGTTTTGGTCCACTT
64 ACTCCATT-TAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTT
168239 TGGTTAAAAT
Statistics
Matches: 354, Mismatches: 48, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
288 38 0.11
289 216 0.61
290 99 0.28
291 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (288 bp):
CTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCTAC
TCCATTTAACCTTAGGGATGTTGAGCTCTGCTTCATTGTTTTGGTCCACTTCTCTCTATCTCATC
AAGAAGATGACCGCTTCATCGTTTTGATCCACTTATCTATATCTAATCAAGAAGATAGGGGTTTG
AAGTTTCACTTTACTCCACTATAACCTTAAGGATGTTGAGCTCTACTTCACTATTTAGGTCCACT
TCTCTGTATCTCATCAAGAAGATGACCG
Found at i:172396 original size:59 final size:57
Alignment explanation
Indices: 172296--172618 Score: 270
Period size: 59 Copynumber: 5.5 Consensus size: 57
172286 GGAGAATTTG
* * * * * ** *
172296 GGGTCAAAATGTAATCTTGGAAAAATTTAAGGCTTAAAATGTAATTTTTTAAAGTCTA
1 GGGTTAAAATGTAAT-TTTGAAAAGTTTAAGGGTCAAAATGTAATTTTGAAAAGTTTA
* * * * * ** *
172354 GGGGTTAAAATGTGATTTTAGTAAAGTTCAAGGGTCAAAATGTGATTTTAGGAGGGTTCA
1 -GGGTTAAAATGTAATTTT-GAAAAGTTTAAGGGTCAAAATGTAATTTT-GAAAAGTTTA
* *
172414 GGGTCAAAATGTAATTTTGAAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTA
1 GGGTTAAAATGTAATTTTG-AAAAGTTTAAGGGTCAAAATGTAATTTT-GAAAAGTTTA
* * * * *
172473 GGGTTAAAATATGATTTTGGAAGAGTTT-GGGGTCAAAATGTAATATTAGAAAAGTTTA
1 GGGTTAAAATGTAATTTT-GAAAAGTTTAAGGGTCAAAATGTAAT-TTTGAAAAGTTTA
* * * **
172531 GGGGTAAAATGCAATTTTAGAAAAGTTTAAGGGTTAAAATGGATTTTTTTGAAAAGTTTA
1 GGGTTAAAATGTAATTTT-GAAAAGTTTAAGGGTCAAAAT-G-TAATTTTGAAAAGTTTA
*
172591 TGGTTAAAATGTAATTTTGGAAAAGTTT
1 GGGTTAAAATGTAATTTT-GAAAAGTTT
172619 GAGGTTAAAT
Statistics
Matches: 210, Mismatches: 46, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
58 51 0.24
59 115 0.55
60 42 0.20
61 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (57 bp):
GGGTTAAAATGTAATTTTGAAAAGTTTAAGGGTCAAAATGTAATTTTGAAAAGTTTA
Found at i:172490 original size:88 final size:86
Alignment explanation
Indices: 172331--172570 Score: 284
Period size: 88 Copynumber: 2.7 Consensus size: 86
172321 TTTAAGGCTT
** * * * * * *
172331 AAAATGTAATTTTTTAAAGTCTAGGGGTTAAAATGTGATTTTAGTAAAGTTCAAGGGTCAAAATG
1 AAAATGTAATTTTAAAAAGTTTAGGGG-TAAAATGTAATTTTAGAAAAGTT-TAGGGTTAAAATA
*
172396 TGATTTTAGG-AGGGTTCAGGGTC
64 TGATTTT-GGAAGAGTTCAGGGTC
*
172419 AAAATGTAATTTTGAAAAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATA
1 AAAATGTAATTTT-AAAAAGTTTAGGGGT-AAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATA
**
172484 TGATTTTGGAAGAGTTTGGGGTC
64 TGATTTTGGAAGAGTTCAGGGTC
* *
172507 AAAATGTAATATTAGAAAAGTTTAGGGGTAAAATGCAATTTTAGAAAAGTTTAAGGGTTAAAAT
1 AAAATGTAATTTTA-AAAAGTTTAGGGGTAAAATGTAATTTTAGAAAAGTTT-AGGGTTAAAAT
172571 GGATTTTTTT
Statistics
Matches: 132, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
87 24 0.18
88 78 0.59
89 30 0.23
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (86 bp):
AAAATGTAATTTTAAAAAGTTTAGGGGTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATATG
ATTTTGGAAGAGTTCAGGGTC
Found at i:172618 original size:29 final size:29
Alignment explanation
Indices: 172296--172627 Score: 274
Period size: 29 Copynumber: 11.3 Consensus size: 29
172286 GGAGAATTTG
* * *
172296 GGGTCAAAATGTAATCTTGGAAAAATTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTT-A
* ** *
172326 GGCTTAAAATGTAATTTT-TTAAAGTCTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* * * *
172354 GGGGTTAAAATGTGATTTTAGTAAAGTTCAA
1 -GGGTTAAAATGTAATTTTGGAAAAGTT-TA
* * ** *
172385 GGGTCAAAATGTGATTTTAGG-AGGGTTCA
1 GGGTTAAAATGTAATTTT-GGAAAAGTTTA
* *
172414 GGGTCAAAATGTAATTTTGAAAAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
*
172443 GGGGTCAAAATGTAATTTTGGAAAAGTTTA
1 -GGGTTAAAATGTAATTTTGGAAAAGTTTA
* * * *
172473 GGGTTAAAATATGATTTTGGAAGAGTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* * *
172502 GGGTCAAAATGTAATATTAGAAAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* * *
172531 GGGGTAAAATGCAATTTTAGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTT-A
* * *
172561 GGGTTAAAATGGATTTTTTTGAAAAGTTTA
1 GGGTTAAAATGTA-ATTTTGGAAAAGTTTA
*
172591 TGGTTAAAATGTAATTTTGGAAAAGTTT-
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
172619 GAGGTTAAA
1 G-GGTTAAA
172628 TTTTTTTTTA
Statistics
Matches: 245, Mismatches: 48, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
28 2 0.01
29 134 0.55
30 94 0.38
31 15 0.06
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:172636 original size:28 final size:28
Alignment explanation
Indices: 172419--172664 Score: 99
Period size: 29 Copynumber: 8.6 Consensus size: 28
172409 GTTCAGGGTC
** * *
172419 AAAATGTAATTTTGAAAAAGTTTAGGGGTC
1 AAAATGTTTTTTTG-AAAAGTTTA-TGGTT
* * *
172449 AAAATGTAATTTTGGAAAAGTTTAGGGTT
1 AAAATGT-TTTTTTGAAAAGTTTATGGTT
* * * * ** *
172478 AAAATATGATTTTGGAAGAGTTTGGGGTC
1 AAAATGT-TTTTTTGAAAAGTTTATGGTT
* * * * *
172507 AAAATGTAATATTAGAAAAGTTTAGGGGT
1 AAAATGT-TTTTTTGAAAAGTTTATGGTT
** * *
172536 AAAATGCAATTTTAGAAAAGTTTAAGGGTT
1 AAAATG-TTTTTTTGAAAAGTTT-ATGGTT
172566 AAAATGGATTTTTTTGAAAAGTTTATGGTT
1 AAAAT-G-TTTTTTTGAAAAGTTTATGGTT
* *
172596 AAAATGTAATTTTGGAAAAGTTTGA-GGTT
1 AAAATGT-TTTTTTGAAAAGTTT-ATGGTT
*
172625 -AAAT-TTTTTTT--TAAGTTT-TGGGTT
1 AAAATGTTTTTTTGAAAAGTTTAT-GGTT
*
172649 AAAATGTATTTTTGAA
1 AAAATGTTTTTTTGAA
172665 TAAAACAGGG
Statistics
Matches: 173, Mismatches: 31, Indels: 26
0.75 0.13 0.11
Matches are distributed among these distances:
24 10 0.06
25 4 0.02
26 10 0.06
27 1 0.01
28 5 0.03
29 87 0.50
30 37 0.21
31 19 0.11
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (28 bp):
AAAATGTTTTTTTGAAAAGTTTATGGTT
Found at i:173341 original size:3 final size:3
Alignment explanation
Indices: 173333--173382 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
173323 TTGATTTGTT
173333 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
173381 TT
1 TT
173383 TTAAAACAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:175040 original size:209 final size:210
Alignment explanation
Indices: 174607--175421 Score: 1038
Period size: 209 Copynumber: 3.9 Consensus size: 210
174597 CTGTATCTCA
* * ** * *
174607 TCAGGACGATGATCGCTTTATTGCTTCGACCTTC-TTTCTGTATCTCATCAGGAAGATAGAGTTT
1 TCAGGAAGATGATCACTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAAGAAGATAGGGTTT
* * ** *
174671 TGAAGTTTCACTTACACTGAGCTTTTGCTTCATTGAATTGGTCTACTTCTCTGTATCTTATCAGG
66 GGAAGTTTCACTTACATTGAGCTTTCACTTCATTGAATTGGTCTACTTCTCTGTATCTCATCAGG
**
174736 AAGATGAGAGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCA-GAAGAC-G-TATTTGGTT
131 AAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGAT-TTTGGTT
174798 CACTTCTCTGCATCTTG
195 CACTTCTCTGCAT-TTG
* *
174815 TCAGGAAGATGATCACTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAAAAAGATGGGGTTT
1 TCAGGAAGATGATCACTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAAGAAGATAGGGTTT
* * * * * *
174880 GGAAGTTTTACTCATATTAATC-TTCACTTCATTGAATTGGTCTACTTCTC-GATATCTCATCCG
66 GGAAGTTTCACTTACATTGAGCTTTCACTTCATTGAATTGGTCTACTTCTCTG-TATCTCATCAG
* * * *
174943 GAAAATGACCGCTTCATTGTTTTAATTCACTTCTTTGTATCTCATCAGGAAGAC-GATTTTGGTT
130 GAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTTGGTT
*
175007 CACTTCACTGCATTTCG
195 CACTTCTCTGCATTT-G
* * * *
175024 TCAGGAAGATGATCACTTTATTGCTTCAACTCACTTCTT-TGTATGTCCTCAAGAAGATAGGGTT
1 TCAGGAAGATGATCACTTTATTGCTTCGACCCACTT-TTCTGTATCTCATCAAGAAGATAGGGTT
* * * * * *
175088 TAGAAGTTTCACTAATATTGATC-TTCACTTCATTAAATTGGTCTACTTCTCTATATCTCATCAG
65 TGGAAGTTTCACTTACATTGAGCTTTCACTTCATTGAATTGGTCTACTTCTCTGTATCTCATCAG
* * *
175152 GAAGACGACCGCTTCATTGTTTTAATCCACTTCTCTGTATCTTATCAGGAAGACAGATTTTGGTT
130 GAAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTTGGTT
175217 CACTTCTCTGCATTTTG
195 CACTTCTCTGCA-TTTG
** * * * * * *
175234 TTTGGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGTATCTTATCAAGAAGGTGGGGTTT
1 TCAGGAAGATGATCACTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAAGAAGATAGGGTTT
* * *
175299 GGAAGTTTCACTTACATTGAGCTTTGA-TTCATTGAATTGGTCTACTTCTCTGTATATCATCAAG
66 GGAAGTTTCACTTACATTGAGCTTTCACTTCATTGAATTGGTCTACTTCTCTGTATCTCATCAGG
* *
175363 AAGATGACCGCTTCATTATTTTAATTCACTTCTCTGTATCTCATCAGGAAGACGGATTT
131 AAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTT
175422 GATATACTTC
Statistics
Matches: 525, Mismatches: 71, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
207 1 0.00
208 108 0.21
209 229 0.44
210 181 0.34
211 6 0.01
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (210 bp):
TCAGGAAGATGATCACTTTATTGCTTCGACCCACTTTTCTGTATCTCATCAAGAAGATAGGGTTT
GGAAGTTTCACTTACATTGAGCTTTCACTTCATTGAATTGGTCTACTTCTCTGTATCTCATCAGG
AAGATGACCGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTTGGTTC
ACTTCTCTGCATTTG
Found at i:175453 original size:419 final size:417
Alignment explanation
Indices: 174593--175454 Score: 1137
Period size: 419 Copynumber: 2.1 Consensus size: 417
174583 CTTGGTCTAT
* * * *
174593 TTCTCTGTATCTCATCAGGACGATGATCGCTTTATTGCTTCGACCTTCTTTCTGTATCTCATCAG
1 TTCTCTGTATCTCATCAGGAAGATGATCACTTTATTGCTTCAACCTTCTTTCTGTATCTCATCAA
* * ** *
174658 GAAGATAGAGTTTTGAAGTTTCACTTACACTGAGCTTTTGCTTCATTGAATTGGTCTACTTCTCT
66 GAAGATAGAGTTTAGAAGTTTCACTAACACTGAGCTTTCACTTCATTAAATTGGTCTACTTCTCT
* * * *
174723 GTATCTTATCAGGAAGATGAGAGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGAAGAC
131 ATATCTCATCAGGAAGACGACAGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGAAGAC
* * *
174788 GTATTTGGTTCACTTCTCTGCATCTTGTCAGGAAGATGATCACTTTATTGCTTCGACCCACTTTT
196 GTATTTGGTTCACTTCTCTGCATCTTGTCAGGAAGATGACCACTTTATTACTTCGACCCACTTCT
* * *
174853 CTGTATCTCATCAAAAAGATGGGGTTTGGAAGTTTTACTCATATTAATCTTCACTTCATTGAATT
261 CTGTATCTCATCAAAAAGATGGGGTTTGGAAGTTTCACTCACATTAAGCTTCACTTCATTGAATT
* ** * *
174918 GGTCTACTTCTCGATATCTCATCCGGAAAATGACCGCTTCATTGTTTTAATTCACTTCTTTGTAT
326 GGTCTACTTCTCGATATATCATCAAGAAAATGACCGCTTCATTATTTTAATTCACTTCTCTGTAT
*
174983 CTCATCAGGAAGACGATTTTGGTTCAC
391 CTCATCAGGAAGACGATTTTGATTCAC
* * * * * *
175010 TTCACTGCATTTCGTCAGGAAGATGATCACTTTATTGCTTCAACTCACTTC-TT-TGTATGTCCT
1 TTCTCTGTATCTCATCAGGAAGATGATCACTTTATTGCTTCAA--C-CTTCTTTCTGTATCTCAT
* * * *
175073 CAAGAAGATAGGGTTTAGAAGTTTCACTAATATTGATC-TTCACTTCATTAAATTGGTCTACTTC
63 CAAGAAGATAGAGTTTAGAAGTTTCACTAACACTGAGCTTTCACTTCATTAAATTGGTCTACTTC
* * *
175137 TCTATATCTCATCAGGAAGACGACCGCTTCATTGTTTTAATCCACTTCTCTGTATCTTATCAGGA
128 TCTATATCTCATCAGGAAGACGACAGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCA-GA
* **
175202 AGACAG-ATTTTGGTTCACTTCTCTGCATTTTGTTTGGAAGATGACCACTTTATTACTTCGACCC
192 AGAC-GTA-TTTGGTTCACTTCTCTGCATCTTGTCAGGAAGATGACCACTTTATTACTTCGACCC
* * * * * *
175266 ACTTCTCTGTATCTTATCAAGAAGGTGGGGTTTGGAAGTTTCACTTACATTGAGCTTTGA-TTCA
255 ACTTCTCTGTATCTCATCAAAAAGATGGGGTTTGGAAGTTTCACTCACATTAAGC-TTCACTTCA
*
175330 TTGAATTGGTCTACTTCTCTG-TATATCATCAAGAAGATGACCGCTTCATTATTTTAATTCACTT
319 TTGAATTGGTCTACTTCTC-GATATATCATCAAGAAAATGACCGCTTCATTATTTTAATTCACTT
175394 CTCTGTATCTCATCAGGAAGACGGA-TTTGATAT-AC
383 CTCTGTATCTCATCAGGAAGAC-GATTTTGAT-TCAC
*
175429 TTCTCTGTATCTCATCAAGAAGATGA
1 TTCTCTGTATCTCATCAGGAAGATGA
175455 GGTTTGAAGT
Statistics
Matches: 382, Mismatches: 53, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
417 114 0.30
418 46 0.12
419 211 0.55
420 11 0.03
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (417 bp):
TTCTCTGTATCTCATCAGGAAGATGATCACTTTATTGCTTCAACCTTCTTTCTGTATCTCATCAA
GAAGATAGAGTTTAGAAGTTTCACTAACACTGAGCTTTCACTTCATTAAATTGGTCTACTTCTCT
ATATCTCATCAGGAAGACGACAGCTTCATTATTTTAATCCACTTCTCTGTATCTCATCAGAAGAC
GTATTTGGTTCACTTCTCTGCATCTTGTCAGGAAGATGACCACTTTATTACTTCGACCCACTTCT
CTGTATCTCATCAAAAAGATGGGGTTTGGAAGTTTCACTCACATTAAGCTTCACTTCATTGAATT
GGTCTACTTCTCGATATATCATCAAGAAAATGACCGCTTCATTATTTTAATTCACTTCTCTGTAT
CTCATCAGGAAGACGATTTTGATTCAC
Found at i:175501 original size:160 final size:161
Alignment explanation
Indices: 175265--175614 Score: 467
Period size: 160 Copynumber: 2.2 Consensus size: 161
175255 TACTTCGACC
* * * * * *
175265 CACTTCTCTGTATCTTATCAAGAAGGTGGGGTTTGGAAGTTTCACTTACATTGAGCTTTGATTCA
1 CACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGGAAGTATCACTTAAATTGAGCTTTCATTCA
* *
175330 TTGAATTGGTCTACTTCTCTGTATATCATCAAGAAGATGACCGCTTCATT-ATTTTAATTCACTT
66 TTGAATTGGTCTACCTCTCTGTATATCATCAAGAAGATGACCGCTTCATTGA-TTTAATCCACTT
*
175394 CTCTGTATCTCATCAGGAAGACGGATTTGATA
130 CTCTGTATCTCATCAGGAAGACGAATTTGATA
*
175426 TACTTCTCTGTATCTCATCAAGAAGATGAGGTTT-GAAGTATCA-TTCAAATTGAGC-TTCACTT
1 CACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGGAAGTATCACTT-AAATTGAGCTTTCA-TT
* * * *
175488 CATTGATTTGGTCTACCTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGATTTAATCCACT
64 CATTGAATTGGTCTACCTCTCTGTATATCATCAAGAAGATGACCGCTTCATTGATTTAATCCACT
* * *
175553 TCTCTGTATCTCATCAGGAAGGCGAATTTGGTC
129 TCTCTGTATCTCATCAGGAAGACGAATTTGATA
*
175586 CACTTCTCTATATCTCATC-AGAAAGATGA
1 CACTTCTCTGTATCTCATCAAG-AAGATGA
175615 TCGCTTTATT
Statistics
Matches: 166, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
159 7 0.04
160 128 0.77
161 31 0.19
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (161 bp):
CACTTCTCTGTATCTCATCAAGAAGATGAGGTTTGGAAGTATCACTTAAATTGAGCTTTCATTCA
TTGAATTGGTCTACCTCTCTGTATATCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTC
TCTGTATCTCATCAGGAAGACGAATTTGATA
Found at i:175637 original size:85 final size:84
Alignment explanation
Indices: 175493--175818 Score: 253
Period size: 85 Copynumber: 4.0 Consensus size: 84
175483 CACTTCATTG
* * * * * * *
175493 ATTTGGTCTACCTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGATTTGACCCACTTCTCT
175558 GTATCTCATCAGGAAGGCGA
66 GTATCTCATCAGGAAGG-GA
* * *
175578 ATTTGGTCCACTTCTCTATATCTCATCAGAAAGATGATCGCTTTATTGCTTTGACCCACTTCTCT
1 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGATTTGACCCACTTCTCT
*
175643 ATATCTCATCAGGAAGAGGA
66 GTATCTCATCAGGAAG-GGA
* ** * * * * ** *
175663 GGTTT-G---AAGTCTC-AT-TCGT-AT---TAAGCT--TCGCTTAATTGATTTGGTCTACTTCT
1 -ATTTGGTCCACTTCTCTATATC-TCATCAGGAAGATGACCGCTTTATTGATTTGACCCACTTCT
* *
175716 TTGTATCTCATCAGGAAGGTGG
64 CTGTATCTCATCAGGAAGG-GA
* * ** * * *
175738 ATTTGGTCCACTTCTCTATATCTTATCAGGAGGATGACCTTTTTATTGCTTTGACTCACTTCTTT
1 ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGATTTGACCCACTTCTCT
175803 GTATCTCATCAGGAAG
66 GTATCTCATCAGGAAG
175819 ATAAAGTTTT
Statistics
Matches: 186, Mismatches: 39, Indels: 32
0.72 0.15 0.12
Matches are distributed among these distances:
74 4 0.02
75 39 0.21
77 4 0.02
78 5 0.03
79 3 0.02
80 8 0.04
81 3 0.02
82 5 0.03
83 3 0.02
85 108 0.58
86 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (84 bp):
ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGATTTGACCCACTTCTCT
GTATCTCATCAGGAAGGGA
Found at i:175703 original size:160 final size:160
Alignment explanation
Indices: 175531--175819 Score: 434
Period size: 160 Copynumber: 1.8 Consensus size: 160
175521 GGAAGATGAC
*
175531 CGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTCTCTA
1 CGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTCTCTA
*
175596 TATCTCATCAGAAAGATGATCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGAG
66 TATCTCATCAGAAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGAG
175661 GAGGTTTGAAGTCTCATTCGTATTAAGCTT
131 GAGGTTTGAAGTCTCATTCGTATTAAGCTT
** * * * *
175691 CGCTTAATTGATTTGGTCTACTTCTTTGTATCTCATCAGGAAGGTGGATTTGGTCCACTTCTCTA
1 CGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTCTCTA
* * * ** * * *
175756 TATCTTATCAGGAGGATGACCTTTTTATTGCTTTGACTCACTTCTTTGTATCTCATCAGGAAGA
66 TATCTCATCAGAAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGA
175820 TAAAGTTTTG
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
160 113 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (160 bp):
CGCTTAATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTCTCTA
TATCTCATCAGAAAGATGACCGCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGAG
GAGGTTTGAAGTCTCATTCGTATTAAGCTT
Found at i:183708 original size:30 final size:29
Alignment explanation
Indices: 183659--183732 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
183649 TTTGAGTGTC
* * *
183659 AAATGTAATTTTTGGAAAGTTTAAGGGTTA
1 AAATGTGA-TTTTGGAAAGTTCAAGGGTCA
*
183689 AAATTTGATTTTGGCAAAGTTCAAGGGTCA
1 AAATGTGATTTTGG-AAAGTTCAAGGGTCA
183719 AAATGTGATTTTGG
1 AAATGTGATTTTGG
183733 GAGAGTTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 6 0.16
30 32 0.84
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
AAATGTGATTTTGGAAAGTTCAAGGGTCA
Found at i:183846 original size:29 final size:29
Alignment explanation
Indices: 183601--183993 Score: 184
Period size: 29 Copynumber: 13.4 Consensus size: 29
183591 AAGGGGTCGA
*
183601 AAAATG-AAGTTTTGGAGAA-TTTAGGGTC
1 AAAATGTAA-TTTTGGAAAATTTTAGGGTC
*** * * *
183629 AAAATGTAATCCCGAATAAATTTGAGTGTC
1 AAAATGTAATTTTGGA-AAATTTTAGGGTC
* * *
183659 -AAATGTAATTTTTGGAAAGTTTAAGGGTT
1 AAAATGTAA-TTTTGGAAAATTTTAGGGTC
* * * **
183688 AAAATTTGATTTTGGCAAAGTTCAAGGGTC
1 AAAATGTAATTTTGG-AAAATTTTAGGGTC
* * * **
183718 AAAATGTGATTTTGGGAGAGTTTGGGGGTC
1 AAAATGTAATTTT-GGAAAATTTTAGGGTC
** * * * *
183748 AAAATACAATATTGAAAAAGTTTAGGCTC
1 AAAATGTAATTTTGGAAAATTTTAGGGTC
* * * * *
183777 AAAATGGAATTTAGGAAAAGTTTATGCTC
1 AAAATGTAATTTTGGAAAATTTTAGGGTC
* *
183806 AAAATGAAATTTTGGAAAATTTTGGGGTC
1 AAAATGTAATTTTGGAAAATTTTAGGGTC
* * * * *
183835 AAAATGTGATTTT-GAGAGAGTTTGGGGTT
1 AAAATGTAATTTTGGA-AAATTTTAGGGTC
* ** *
183864 AAAATGTAATATTAAAAAAGTTTAAGGGT-
1 AAAATGTAATTTTGGAAAA-TTTTAGGGTC
* * *
183893 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAATTTTA-GGGTC
* * ** * * *
183923 AAAATGGAGTTTTTAAAAAGTTTAAGGTT
1 AAAATGTAATTTTGGAAAATTTTAGGGTC
* *
183952 AAAATGTAATTTTGGAAAAATTTAGGGCC
1 AAAATGTAATTTTGGAAAATTTTAGGGTC
*
183981 AAAATTTAATTTT
1 AAAATGTAATTTT
183994 TTAAAGTTTG
Statistics
Matches: 276, Mismatches: 77, Indels: 23
0.73 0.20 0.06
Matches are distributed among these distances:
28 14 0.05
29 174 0.63
30 86 0.31
31 2 0.01
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAATTTTAGGGTC
Found at i:183941 original size:59 final size:60
Alignment explanation
Indices: 183659--183978 Score: 235
Period size: 59 Copynumber: 5.4 Consensus size: 60
183649 TTTGAGTGTC
* * * * ** *
183659 AAATGTAATTTTTGGAAAGTTTAAGGGTTAAAATTTG-ATTTTGGCAAAGTTCAAGGGTCA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTTAAAA-TGGAATTTTGAAAAAGTTTAAGGGTCA
* * * * * * ** * *
183719 AAATGTGATTTTGGGAGAGTTTGGGGGTCAAAATACAATATTGAAAAAGTTT-AGGCTCA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGGAATTTTGAAAAAGTTTAAGGGTCA
* * * * * * **
183778 AAATGGAA-TTTAGGAAAAGTTTA-TGCTCAAAATGAAATTTTGGAAAA-TTTTGGGGTCA
1 AAATGTAATTTTA-GAAAAGTTTAGGGGTTAAAATGGAATTTTGAAAAAGTTTAAGGGTCA
* * * * *
183836 AAATGTGATTTT-GAGAGAGTTT-GGGGTTAAAATGTAATATTAAAAAAGTTTAAGGGT-A
1 AAATGTAATTTTAGA-AAAGTTTAGGGGTTAAAATGGAATTTTGAAAAAGTTTAAGGGTCA
* * *
183894 AAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGGAGTTTTTAAAAAGTTTAA-GGTTA
1 AAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGGAATTTTGAAAAAGTTTAAGGGTCA
* *
183953 AAATGTAATTTTGGAAAAATTTAGGG
1 AAATGTAATTTTAGAAAAGTTTAGGG
183979 CCAAAATTTA
Statistics
Matches: 203, Mismatches: 47, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
57 5 0.02
58 76 0.37
59 84 0.41
60 38 0.19
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (60 bp):
AAATGTAATTTTAGAAAAGTTTAGGGGTTAAAATGGAATTTTGAAAAAGTTTAAGGGTCA
Found at i:184013 original size:58 final size:59
Alignment explanation
Indices: 183864--184022 Score: 178
Period size: 59 Copynumber: 2.7 Consensus size: 59
183854 GTTTGGGGTT
* * * * * **
183864 AAAATGTAATATTAAAAAAGTTTAAGGGTAAAATGTAATTTTAGAAAAGTTTAGGGGTT
1 AAAATGGAATTTTTAAAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAATTTAGGGGCC
* *
183923 AAAATGGAGTTTTTAAAAAGTTTAAGGTTAAAATGTAATTTTGGAAAAATTTA-GGGCC
1 AAAATGGAATTTTTAAAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAATTTAGGGGCC
** * *
183981 AAAATTTAATTTTT-TAAAGTTTGAAGGTTAAAATGTGATTTT
1 AAAATGGAATTTTTAAAAAGTTT-AAGGTTAAAATGTAATTTT
184023 TTTAATAAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
57 7 0.08
58 32 0.38
59 46 0.54
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38
Consensus pattern (59 bp):
AAAATGGAATTTTTAAAAAGTTTAAGGTTAAAATGTAATTTTAGAAAAATTTAGGGGCC
Found at i:185066 original size:2 final size:2
Alignment explanation
Indices: 185053--185086 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
185043 TAATTAACAA
*
185053 AT AT AA AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
185087 CCTTGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:187367 original size:30 final size:30
Alignment explanation
Indices: 187207--187367 Score: 121
Period size: 30 Copynumber: 5.4 Consensus size: 30
187197 AAGGAAAAAT
*
187207 GGGTCAAAA-ATAAAATTTTGGAAAGTTTGA
1 GGGTCAAAACAT-AATTTTTGGAAAGTTTGA
* ** * * *
187237 GGGCCAAATTAAAATTTTTTTGAACGTTTG-
1 GGGTCAAAACATAA-TTTTTGGAAAGTTTGA
* * * * *
187267 CGATC-AAACTATAATTTTTTGAAAATTTAA
1 GGGTCAAAAC-ATAATTTTTGGAAAGTTTGA
* * * *
187297 GGGTCAAAACGTATTTTTTAGAAAGTTTTA
1 GGGTCAAAACATAATTTTTGGAAAGTTTGA
187327 GGGTCAAAACATAATTTTTGGAAAGTTTGA
1 GGGTCAAAACATAATTTTTGGAAAGTTTGA
*
187357 GGATCAAAACA
1 GGGTCAAAACA
187368 CCATTTTTTA
Statistics
Matches: 99, Mismatches: 27, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
29 14 0.14
30 68 0.69
31 17 0.17
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.35
Consensus pattern (30 bp):
GGGTCAAAACATAATTTTTGGAAAGTTTGA
Found at i:190110 original size:30 final size:30
Alignment explanation
Indices: 189993--190111 Score: 148
Period size: 30 Copynumber: 4.0 Consensus size: 30
189983 GCTAATTTCA
* * *
189993 AATTTTTGGAAAGTTTAGGGGTTAAAATAT
1 AATTTTTAGAAAGTTTAAGGGTTAAAACAT
* * *
190023 AATTTTTTGAAAATTTAAGGGTTAAAACTT
1 AATTTTTAGAAAGTTTAAGGGTTAAAACAT
* *
190053 ATTTTTTAGAAAGCTTAAGGGTTAAAACAT
1 AATTTTTAGAAAGTTTAAGGGTTAAAACAT
* *
190083 AATTTTTAGAAAGTTCAAGGGTCAAAACA
1 AATTTTTAGAAAGTTTAAGGGTTAAAACA
190112 CCATTTTAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTAAGGGTTAAAACAT
Found at i:190272 original size:35 final size:35
Alignment explanation
Indices: 190231--190305 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
190221 TTATTAGGAA
* *
190231 AAATTGAAATAAATTAAAAATAGCACAAAATGATT
1 AAATTGAAACAAATAAAAAATAGCACAAAATGATT
190266 AAATTGAAACAAATAAAAAATAGCACAAAATGATT
1 AAATTGAAACAAATAAAAAATAGCACAAAATGATT
190301 AAATT
1 AAATT
190306 ATCAGGTGTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.24
Consensus pattern (35 bp):
AAATTGAAACAAATAAAAAATAGCACAAAATGATT
Found at i:192682 original size:4 final size:4
Alignment explanation
Indices: 192667--192700 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
192657 AAAAAAAGGA
*
192667 AAAG AGAG AAAG AAAG AAAG AAAG AAA- AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
192701 AAGAAAAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:192682 original size:18 final size:17
Alignment explanation
Indices: 192658--192704 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
192648 AAAAGAGGTA
192658 AAAAAAGGAAAAGAGAG
1 AAAAAAGGAAAAGAGAG
*
192675 AAAGAAA-G-AAAGAAAG
1 AAA-AAAGGAAAAGAGAG
*
192691 AAAAAAGAAAAAGA
1 AAAAAAGGAAAAGA
192705 AAAGGGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 10 0.40
17 9 0.36
18 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAAAAGAGAG
Found at i:193650 original size:6 final size:6
Alignment explanation
Indices: 193636--193698 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
193626 AGAGAGAGAG
* *
193636 AAAAG- AAAAGAA AAAAGG AAAAGA AAAAGA AAAA-A GAAA-A AAAAGA
1 AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
193682 AGAAGA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAG
193699 GATAGGTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
5 13 0.27
6 31 0.63
7 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:193656 original size:13 final size:13
Alignment explanation
Indices: 193636--193691 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
193626 AGAGAGAGAG
193636 AAAA-GAAAAGAA
1 AAAAGGAAAAGAA
193648 AAAAGGAAAAG-A
1 AAAAGGAAAAGAA
*
193660 AAAAGAAAAAAGAAA
1 AAAAG-GAAAAG-AA
*
193675 AAAAAGAAGAAGAA
1 AAAAGGAA-AAGAA
193689 AAA
1 AAA
193692 GAAAAAGGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 10 0.28
13 11 0.31
14 7 0.19
15 8 0.22
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAGGAAAAGAA
Found at i:194801 original size:15 final size:16
Alignment explanation
Indices: 194773--194802 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
194763 TTATTTCGAA
194773 ATATAAATAAAATAAG
1 ATATAAATAAAATAAG
194789 ATATAAA-AAAATAA
1 ATATAAATAAAATAA
194803 TACAAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
ATATAAATAAAATAAG
Found at i:197305 original size:21 final size:21
Alignment explanation
Indices: 197281--197322 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
197271 TTACGGTCAT
197281 AAATAA-ATAATTAAAGTATTA
1 AAATAATATAA-TAAAGTATTA
*
197302 AAATAATATAATAATGTATTA
1 AAATAATATAATAAAGTATTA
197323 TTATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
AAATAATATAATAAAGTATTA
Found at i:197701 original size:12 final size:13
Alignment explanation
Indices: 197678--197704 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
197668 AAGTCACCTA
197678 TTTCCTTTTTTTT
1 TTTCCTTTTTTTT
197691 TTTCCTTTTTTTT
1 TTTCCTTTTTTTT
197704 T
1 T
197705 CAGCAACCTA
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:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCCTTTTTTTT
Found at i:199489 original size:30 final size:30
Alignment explanation
Indices: 199455--199570 Score: 146
Period size: 30 Copynumber: 3.9 Consensus size: 30
199445 TTAAAAATGG
199455 TGTTTTGACCCTCAAACTTTCCAAAAATTA
1 TGTTTTGACCCTCAAACTTTCCAAAAATTA
** *
199485 TGTTTTGACCCTTGAACTTTCTAAAAATTA
1 TGTTTTGACCCTCAAACTTTCCAAAAATTA
* * *
199515 TGTTTTGACCCTTAAATTTTTCAAAAATTA
1 TGTTTTGACCCTCAAACTTTCCAAAAATTA
*
199545 TATTTTGACCC-CTAAAC-TTCCAAAAA
1 TGTTTTGACCCTC-AAACTTTCCAAAAA
199571 ATTGAATTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
29 8 0.11
30 66 0.89
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.40
Consensus pattern (30 bp):
TGTTTTGACCCTCAAACTTTCCAAAAATTA
Found at i:199521 original size:60 final size:60
Alignment explanation
Indices: 199446--199573 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
199436 CTATTTCATT
** * * * *
199446 TAAAAATGGTGTTTTGACCCTCAAACTTTCCAAAAATTATGTTTTGACCCTTGAACTTTC
1 TAAAAATTATGTTTTGACCCTCAAACTTTCCAAAAATTATATTTTGACCCCTAAACTTCC
* * *
199506 TAAAAATTATGTTTTGACCCTTAAATTTTTCAAAAATTATATTTTGACCCCTAAACTTCC
1 TAAAAATTATGTTTTGACCCTCAAACTTTCCAAAAATTATATTTTGACCCCTAAACTTCC
*
199566 AAAAAATT
1 TAAAAATT
199574 GAATTTGGCT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (60 bp):
TAAAAATTATGTTTTGACCCTCAAACTTTCCAAAAATTATATTTTGACCCCTAAACTTCC
Found at i:217062 original size:23 final size:22
Alignment explanation
Indices: 217030--217091 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 22
217020 GAACAAAACA
*
217030 AAATACCTAAATCCTAAGAAAAG
1 AAATAACTAAA-CCTAAGAAAAG
217053 AAATAACTAAACCCTAAGAAAAG
1 AAATAACTAAA-CCTAAGAAAAG
*
217076 AAATAATTAAACCTAA
1 AAATAACTAAACCTAA
217092 ATTTATTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.60, C:0.16, G:0.06, T:0.18
Consensus pattern (22 bp):
AAATAACTAAACCTAAGAAAAG
Found at i:230309 original size:23 final size:23
Alignment explanation
Indices: 230279--230335 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
230269 CTAGAGACAT
230279 GGTCGTGTGATCTTGCAACACAC
1 GGTCGTGTGATCTTGCAACACAC
230302 GGTCGTGTGATCTTGCAACACAC
1 GGTCGTGTGATCTTGCAACACAC
230325 GGTCGTGTGAT
1 GGTCGTGTGAT
230336 GCGACACACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (23 bp):
GGTCGTGTGATCTTGCAACACAC
Found at i:230344 original size:20 final size:21
Alignment explanation
Indices: 230279--230345 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 21
230269 CTAGAGACAT
230279 GGTCGTGTGATCTTGCAACACAC
1 GGTCGTGTGA--TTGCAACACAC
230302 GGTCGTGTGATCTTGCAACACAC
1 GGTCGTGTGA--TTGCAACACAC
*
230325 GGTCGTGTGA-TGCGACACAC
1 GGTCGTGTGATTGCAACACAC
230345 G
1 G
230346 AGCTGGCCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
20 10 0.23
23 33 0.77
ACGTcount: A:0.21, C:0.25, G:0.30, T:0.24
Consensus pattern (21 bp):
GGTCGTGTGATTGCAACACAC
Found at i:232231 original size:3 final size:3
Alignment explanation
Indices: 232223--232263 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
232213 GAAGTTGACT
232223 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
232264 TGTTTGATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:232612 original size:20 final size:21
Alignment explanation
Indices: 232576--232614 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
232566 GTAATTCATT
232576 AAAAAATTAATTATTAAAATA
1 AAAAAATTAATTATTAAAATA
232597 AAAATAATT-ATT-TTAAAA
1 AAAA-AATTAATTATTAAAA
232615 ATCAAATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAATTAATTATTAAAATA
Found at i:241678 original size:70 final size:70
Alignment explanation
Indices: 241595--241737 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
241585 CTTAATCTAT
241595 AAATAAGATGATAATACACTTCAGCGCACTTATGAATAAATTACGATTACTTTATTTTAGTTTTT
1 AAATAAGATGATAATACACTTCAGCGCACTTATGAATAAATTACGATTACTTTATTTTAGTTTTT
241660 GTAGG
66 GTAGG
*
241665 AAATAAGATGATAATGCACTTCAGCGCACTTATGAATAAATTACGATTACTTTATTTTAGTTTTT
1 AAATAAGATGATAATACACTTCAGCGCACTTATGAATAAATTACGATTACTTTATTTTAGTTTTT
241730 GTAGG
66 GTAGG
241735 AAA
1 AAA
241738 AAATTATATT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (70 bp):
AAATAAGATGATAATACACTTCAGCGCACTTATGAATAAATTACGATTACTTTATTTTAGTTTTT
GTAGG
Done.